Chem & BioDraw 10 User's Manual

Chem & BioDraw 10 User's Manual
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User’s Guide
CS Chem & Bio Draw 10.0
for Windows and Macintosh
Chem & Bio Draw is a standalone application within
Chem & Bio Office, an integrated suite including
Chem & Bio 3D for molecular modeling and analysis,
BioAssay for biological data retrieval and visualization,
Inventory for managing and searching reagents,
E-Notebook for electronic journal and information,
Chem & Bio Finder for searching and information integration, and
ChemInfo for chemical and reference databases.
Chem & Bio Draw
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Chem & Bio Drawing Standard
License Information
ChemOffice, BioOffice ChemDraw, Chem3D, ChemINDEX, ChemFinder, and ChemInfo programs, all resources
in the ChemOffice, ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are
Copyright © 1986-2006 by CambridgeSoft Corporation (CS) with all rights reserved worldwide. MOPAC 2002 is
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change without notice and does not represent a commitment on the part of CS. Both these materials and the right
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agreement; they may be used only as provided for in said agreement.
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are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for your personal
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ChemOffice, BioOffice, ChemDraw, Chem3D, ChemINDEX, ChemFinder, ChemInfo and ChemACX are
registered trademarks of CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
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MOPAC 2002 is a trademark of Fujitsu Limited.
Microsoft Windows, Windows 2000, Windows XP, and Microsoft Word are registered trademarks of Microsoft Corp.
Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered trademarks of Apple
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The ChemSelect Reaction Database is copyrighted © by InfoChem GmbH 1997.
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InChI™ is a trademark of the International Union of Pure and Applied Chemistry. InChI™ Material in ChemDraw
is © IUPAC 2005.
SCHRÖDINGER® Jaguar
GAMESS is copyrighted © by Ames Laboratory
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Documentation, or (f ) modify or adapt the Software or merge it into another program. The Software may be placed
on a file or disk server connected to a network, provided that a license has been purchased for every computer with
access to that server. You may make only those copies of the Software which are necessary to install and use it as permitted by this agreement, or are for purposes of backup and archival records; all copies shall bear CambridgeSoft’s
copyright and proprietary notices. You may not make copies of any accompanying written materials.
4. Assignment Restrictions for CD/DVD databases. You may not rent, lease, or otherwise sublet the Software or
any part thereof. You may transfer on a permanent basis the rights granted under this license provided you transfer
this Agreement and all copies of the Software, including prior versions, and all accompanying materials. The recipient must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft.
5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly prohibited, and
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other applicable civil or criminal penalties. Similarly, sharing a Subscriber password with a non-Subscriber or otherwise making this Paid Subscription Service available to third parties other than the Authorized User as defined above
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Subscription Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties under
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conditions of this Agreement. In all other cases, only the Subscriber is permitted to access the Paid Subscription
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8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or other Supplier
harmless from any damages, expenses and costs (including reasonable attorneys’ fees) arising out of any breach or
alleged breach of these Terms and Conditions, representations and/or warranties herein, by the User or any third party
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In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such
as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use
of the software by you or the services provided for in this agreement, even if CS, Merck, and/or other Supplier has
been advised of the possibility of such damages. CS and/or Merck’s entire liability and your exclusive remedy shall be,
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The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term
or condition by the other party.
This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts, United States of
America.
: IS IT OK TO COPY MY COLLEAGUE’S
SOFTWARE?
NO, it’s not okay to copy your colleague’s
software. Software is protected by federal copyright law,
which says that you can't make such additional copies
without the permission of the copyright holder. By
protecting the investment of computer software
companies in software development, the copyright law
serves the cause of promoting broad public availability of
new, creative, and innovative products. These companies
devote large portions of their earnings to the creation of
new software products and they deserve a fair return on
their investment. The creative teams who develop the
software–programmers, writers, graphic artists and
others–also deserve fair compensation for their efforts.
Without the protection given by our copyright laws, they
would be unable to produce the valuable programs that
have become so important to our daily lives: educational
software that teaches us much needed skills; business
software that allows us to save time, effort and money;
and entertainment and personal productivity software
that enhances leisure time.
Q
Q: That makes sense, but what do I get out of
purchasing my own software?
A: When you purchase authorized copies of software
programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase
upgrades, and technical support from the software
publishers. For most software programs, you can read
about user benefits in the registration brochure or
upgrade flyer in the product box.
Q: What exactly does the law say about copying
software?
A: The law says that anyone who purchases a copy of
software has the right to load that copy onto a single
computer and to make another copy “for archival
purposes only” or, in limited circumstances, for
“purposes only of maintenance or repair.” It is illegal
to use that software on more than one computer or to
make or distribute copies of that software for any
other purpose unless specific permission has been
obtained from the copyright owner. If you pirate
software, you may face not only a civil suit for
damages and other relief, but criminal liability as well,
including fines and jail terms of up to one year
Q: So I'm never allowed to copy software for any other
reason?
A: That’s correct. Other than copying the software you
purchase onto a single computer and making another
copy “for archival purposes only” or “purposes only of
maintenance or repair,” the copyright law prohibits
you from making additional copies of the software for
any other reason unless you obtain the permission of
the software company.
Q: At my company, we pass disks around all the time.
We all assume that this must be okay since it was
the company that purchased the software in the
first place.
A: Many employees don’t realize that corporations are
bound by the copyright laws, just like everyone else.
Such conduct exposes the company (and possibly the
persons involved) to liability for copyright
infringement. Consequently, more and more
corporations concerned about their liability have
written policies against such “softlifting”. Employees
may face disciplinary action if they make extra copies
of the company’s software for use at home or on
additional computers within the office. A good rule to
remember is that there must be one authorized copy
of a software product for every computer upon which
it is run
Q: Can I take a piece of software owned by my
company and install it on my personal computer at
home if instructed by my supervisor?
A: A good rule of thumb to follow is one software
package per computer, unless the terms of the license
agreement allow for multiple use of the program. But
some software publishers’ licenses allow for “remote”
or “home” use of their software. If you travel or
telecommute, you may be permitted to copy your
software onto a second machine for use when you are
not at your office computer. Check the license carefully to see if you are allowed to do this.
Q: What should I do if become aware of a company
that is not compliant with the copyright law or its
software licenses?
A: Cases of retail, corporate and Internet piracy or noncompliance with software licenses can be reported on
the Internet at http://www.siia.net/piracy/report.asp
or by calling the Anti-Piracy Hotline:
(800) 388-7478.
Q: Do the same rules apply to bulletin boards and user
groups? I always thought that the reason they got
together was to share software.
A: Yes. Bulletin boards and user groups are bound by the
copyright law just as individuals and corporations.
However, to the extent they offer shareware or public
domain software, this is a perfectly acceptable
practice. Similarly, some software companies offer
bulletin boards and user groups special demonstration
versions of their products, which in some instances
may be copied. In any event, it is the responsibility of
the bulletin board operator or user group to respect
copyright law and to ensure that it is not used as a
vehicle for unauthorized copying or distribution.
Q: I'll bet most of the people who copy software don't
even know that they're breaking the law.
A: Because the software industry is relatively new, and
because copying software is so easy, many people are
either unaware of the laws governing software use or
choose to ignore them. It is the responsibility of each
and every software user to understand and adhere to
copyright law. Ignorance of the law is no excuse. If
you are part of an organization, see what you an do to
initiate a policy statement that everyone respects.
Also, suggest that your management consider
conducting a software audit. Finally, as an individual,
help spread the word that users should be “software
legal.”
Q: What are the penalties for copyright infringement?
A: The Copyright Act allows a copyright owner to
recover monetary damages measured either by: (1) its
actual damages plus any additional profits of the
infringer attributable to the infringement, or (2)
statutory damages, of up to $150,000 for each copyrighted work infringed. The copyright owner also has
the right to permanently enjoin an infringer from
engaging in further infringing activities and may be
awarded costs and attorneys’ fees. The law also
permits destruction or other reasonable disposition of
all infringing copies and devices by which infringing
copies have been made or used in violation of the
copyright owner’s exclusive rights. In cases of willful
infringement, criminal penalties may also be assessed
against the infringer.
SIIA also offers a number of other materials designed to
help you comply with the Federal Copyright Law. These
materials include:
"It's Just Not Worth the Risk" video.
This 12–minute video, available $10, has helped over
20,000 organizations dramatize to their employees the
implications and consequences of software piracy.
“Don’t Copy that Floppy” video
This 9 minute rap video, available for $10, is designed
to educate students on the ethical use of software.
Other education materials including, “Software Use
and the Law”, a brochure detailing the copyright law
and how software should be used by educational
institutions, corporations and individuals; and several
posters to help emphasize the message that unauthorized
copying of software is illegal.
To order any of these materials, please send your request to:
“SIIA Anti-Piracy Materials”
Software & Information Industry Association
1090 Vermont Ave, Sixth Floor,
Washington, D.C. 20005
(202) 289-7442
We urge you to make as many copies as you would like
in order to help us spread the word that unauthorized
copying of software is illegal.
A Guide to CambridgeSoft Manuals
Includes
M
an
ua
ls
Chem & Bio Draw
Software
Chem & Bio 3D
Chem & Bio Finder
BioAssay Desktop
BioViz Desktop
Inventory Desktop
E-Notebook Desktop
Desktop Applications
ChemDraw/Excel
Struct <=> Name
CombiChem/Excel
ChemNMR
ChemFinder/Office
MOPAC, GAMESS, MM2
CS Gaussian, Jaguar Interface
Chem & Bio Office Enterprise
Enterprise Solutions
E-Notebook Enterprise, Workgroup
Document Enterprise
BioAssay Enterprise, Workgroup
BioSAR Enterprise
Inventory Enterprise, Workgroup
Registration Enterprise
Formulations & Mixtures
Oracle Cartridge
The Merck Index
Databases
ChemACX, ChemMSDX
Sigma Aldrich MSDS
ChemINDEX, NCI & AIDS, ChemRXN
Ashgate Drugs, Traditional Chinese Medicines
ChemSynth, ChemReact68
Medicinal Chemistry
Tips
Structure Drawing Tips
Searching Tips
Importing SD Files
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Contents
Introduction
About ChemDraw . . . . . . . . . . . . . . . . . . . . . . . 9
About BioDraw . . . . . . . . . . . . . . . . . . . . . . . . . 9
About ChemDraw/Excel. . . . . . . . . . . . . . . . . . 9
About This Manual . . . . . . . . . . . . . . . . . . . . . . 9
What’s New in ChemDraw 10.0 . . . . . . . . . . . 10
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Additional Information . . . . . . . . . . . . . . . . . . 11
Quick Reference Card . . . . . . . . . . . . . . . . . .11
Help System . . . . . . . . . . . . . . . . . . . . . . . . . .11
CambridgeSoft Web Pages. . . . . . . . . . . . . . .11
Installation and System Requirements. . . . . . . 11
Microsoft Windows Requirements . . . . . . . .11
Macintosh Requirements . . . . . . . . . . . . . . . .12
Site License Network Installation
Instructions . . . . . . . . . . . . . . . . . . . . . . . . . .12
Chapter 1: Introducing Chem & Bio Draw
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
The ChemDraw Graphical User Interface . . . 13
The Main Tools Palette . . . . . . . . . . . . . . . . . . 14
Tearing Off Palettes . . . . . . . . . . . . . . . . . . . .17
Optional Toolbars . . . . . . . . . . . . . . . . . . . . . . 17
Showing and Hiding Toolbars . . . . . . . . . . . .17
Docking and Undocking Toolbars . . . . . . . . 17
The Status Bar or Message Area (Windows) 18
The Analysis Window . . . . . . . . . . . . . . . . . . 18
The Chemical Properties Window . . . . . . . 18
The Info Window. . . . . . . . . . . . . . . . . . . . . .18
Periodic Table . . . . . . . . . . . . . . . . . . . . . . . . .19
Character Map . . . . . . . . . . . . . . . . . . . . . . . .19
BioDraw . . . . . . . . . . . . . . . . . . . . . . . . . . . . .20
Customizable Objects . . . . . . . . . . . . . . . . 21
Other Toolbars . . . . . . . . . . . . . . . . . . . . . . . .21
Using Documents. . . . . . . . . . . . . . . . . . . . . . . 21
Creating a Document . . . . . . . . . . . . . . . . . . 21
Creating a New Document . . . . . . . . . . . . 21
Creating a Document Using a Style Sheet
or Stationery Pad . . . . . . . . . . . . . . . . . . . 21
ChemDraw 10
Opening a Document. . . . . . . . . . . . . . . . . . .22
Discarding Recent Changes to a Document 22
Saving Documents. . . . . . . . . . . . . . . . . . . . . 22
Saving a Document in a Different File
Format . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Reversing and Repeating Actions . . . . . . . . . . 23
Repeating Actions . . . . . . . . . . . . . . . . . . . . . 23
The Window Menu . . . . . . . . . . . . . . . . . . . . 23
Chapter 2: Tutorials
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Tutorial 1: Reaction Schemes . . . . . . . . . . . . . . 25
Tutorial 2: Drawing an Intermediate . . . . . . . . 31
Tutorial 3: Using Rings. . . . . . . . . . . . . . . . . . . 34
Tutorial 4: Fischer Projections . . . . . . . . . . . . . 36
Tutorial 5: Perspective Drawings . . . . . . . . . . . 38
Tutorial 6: Newman Projections . . . . . . . . . . . 41
Tutorial 7: Showing Stereochemistry . . . . . . . . 43
Chapter 3: Drawing Chemical Structures
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Drawing Bonds. . . . . . . . . . . . . . . . . . . . . . . . . 47
Drawing Constrained Bonds . . . . . . . . . . . . .47
Drawing with Fixed Lengths . . . . . . . . . . . 47
Drawing with Fixed Angles . . . . . . . . . . . . 48
Toggling Fixed Lengths and Fixed Angles 48
Multiple Bonds . . . . . . . . . . . . . . . . . . . . . . .48
Double Bonds . . . . . . . . . . . . . . . . . . . . . . 48
Double Either Bonds . . . . . . . . . . . . . . . . 49
Triple Bonds . . . . . . . . . . . . . . . . . . . . . . . 49
Quadruple Bonds . . . . . . . . . . . . . . . . . . . 49
Dative Bonds and Wedged Bonds . . . . . . . . .49
Adding a Bond by Clicking . . . . . . . . . . . . . .49
Adding Bonds by Dragging . . . . . . . . . . . . . .50
Drawing Rings . . . . . . . . . . . . . . . . . . . . . . . . . 50
Drawing a Ring . . . . . . . . . . . . . . . . . . . . . . .50
Drawing Cyclohexane Chair Rings . . . . . . . .51
Drawing Resonance Delocalized Rings . . . . .51
•
Administrator
Drawing Cyclopentadiene and Benzene
Rings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Drawing Acyclic Chains . . . . . . . . . . . . . . . . . . 52
Adding Chains. . . . . . . . . . . . . . . . . . . . . . . . 52
Changing Chain Direction . . . . . . . . . . . . . . 53
Editing Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Changing Bond Types . . . . . . . . . . . . . . . . . 53
Changing Double Bonds . . . . . . . . . . . . . . . 53
Editing Bonds With the Context Menu. . . . 54
Changing Orientation of Wedged and
Dative Bonds . . . . . . . . . . . . . . . . . . . . . . . . 54
Changing Alignment of Double Bonds . . . . 54
Moving Atoms With a Bond Tool . . . . . . . . 54
Changing Bond Crossings . . . . . . . . . . . . . . 55
Changing the Bond Order . . . . . . . . . . . . . . 55
Automatic Warnings . . . . . . . . . . . . . . . . . . . . . 55
Warning Preferences. . . . . . . . . . . . . . . . . . . 56
Creating Text. . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Coloring Text . . . . . . . . . . . . . . . . . . . . . . . . 57
Creating Captions . . . . . . . . . . . . . . . . . . . . . 57
Entering Non-Roman Text . . . . . . . . . . . . 57
Chemical Significance . . . . . . . . . . . . . . . . 57
Editing a Caption . . . . . . . . . . . . . . . . . . . . 58
Changing the Caption Width . . . . . . . . . . . 58
Adding Analysis Data to a Caption . . . . . . 58
Creating Atom Labels. . . . . . . . . . . . . . . . . . . . 58
Labeling Atoms With the Text Tool . . . . . . 59
Editing Atom Labels . . . . . . . . . . . . . . . . . 59
Deleting an Atom Label . . . . . . . . . . . . . . 59
Labeling Atoms With a Bond or Ring
Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Automatic Labeling of Terminal Carbons 59
Hiding Implicit Hydrogens . . . . . . . . . . . . 60
Repeating an Atom Label . . . . . . . . . . . . . 60
Using the Text Tool With a Selection
Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Labeling Atoms with HotKeys . . . . . . . . . . 60
Labeling multiple atoms . . . . . . . . . . . . . . 61
Using a Selection Tool . . . . . . . . . . . . . . . . . . . 61
Toggling Between Selection Tools . . . . . . . . 61
Toggling Between Other Tools . . . . . . . . . . 61
New Selection Box . . . . . . . . . . . . . . . . . . . . 61
Selecting Objects with the Lasso Tool. . . . . 62
•
Selecting Objects with the Marquee Tool . . 63
Selecting Entire Structures . . . . . . . . . . . . . 63
Selecting Objects by Clicking . . . . . . . . . . 63
Removing Objects from the Selection . . . 63
Making Multiple Selections . . . . . . . . . . . . 64
Selecting and Deselecting All Objects . . . . 64
Moving Objects. . . . . . . . . . . . . . . . . . . . . . . 64
Moving Atoms With a Selection Tool . . . 64
Duplicating Objects . . . . . . . . . . . . . . . . . . . 65
Deleting Objects . . . . . . . . . . . . . . . . . . . . . . 65
Rotating Objects . . . . . . . . . . . . . . . . . . . . . . 65
Chapter 4: Advanced Drawing Techniques
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Joining Objects . . . . . . . . . . . . . . . . . . . . . . . . . 67
Grouping Objects . . . . . . . . . . . . . . . . . . . . . . . 68
Ungrouping Objects . . . . . . . . . . . . . . . . . . . 68
Creating Integral Groups . . . . . . . . . . . . . . . 69
Scaling Objects . . . . . . . . . . . . . . . . . . . . . . . . . 69
Reflecting Objects Through Planes . . . . . . . . . 69
Flipping Objects . . . . . . . . . . . . . . . . . . . . . . 70
Creating Mirror Images . . . . . . . . . . . . . . . . 70
Expanding and Contracting Labels . . . . . . . . . 70
Contracting Labels . . . . . . . . . . . . . . . . . . . . 71
Multi-Attached Labels . . . . . . . . . . . . . . . . . 71
Adding Bonds to an Atom Label . . . . . . . 72
Structure CleanUp . . . . . . . . . . . . . . . . . . . . . . 72
Multi-Center and Variable Attachments . . . . . 73
Creating a Multi-Center Bond . . . . . . . . . . . 73
Creating a Variable Attachment Point . . . . . 74
Viewing Attachment Points . . . . . . . . . . . . . 74
Atom Numbering . . . . . . . . . . . . . . . . . . . . . . . 75
Showing and Hiding Atom Numbers . . . . . 75
Editing Atom Numbers . . . . . . . . . . . . . . . . 75
Positioning Atom Number Indicators . . . . . 75
Structure Perspective . . . . . . . . . . . . . . . . . . . . 76
Flatten Command . . . . . . . . . . . . . . . . . . . . . 76
Mass Fragmentation Tool . . . . . . . . . . . . . . . . 76
Drawing Reactions . . . . . . . . . . . . . . . . . . . . . . 78
Drawing with Templates. . . . . . . . . . . . . . . . . . 78
The Templates Tool . . . . . . . . . . . . . . . . . . . 78
Choosing a Template . . . . . . . . . . . . . . . . . . 78
Using Templates . . . . . . . . . . . . . . . . . . . . . . 79
Drawing a Template . . . . . . . . . . . . . . . . . . 79
CambridgeSoft
Fusing a Template With an Existing
Structure . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Drawing with the Same Template . . . . . . 79
Creating Templates and Template
Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Creating Templates . . . . . . . . . . . . . . . . . . . .80
Orientation of Templates . . . . . . . . . . . . . 80
Resizing Template Panes . . . . . . . . . . . . . 81
Template Panels . . . . . . . . . . . . . . . . . . . . 81
Saving Template Documents . . . . . . . . . . 81
Using Nicknames . . . . . . . . . . . . . . . . . . . . . . . 81
Applying Nicknames . . . . . . . . . . . . . . . . . . .82
Defining Nicknames . . . . . . . . . . . . . . . . . . .82
Deleting Nicknames . . . . . . . . . . . . . . . . . . . .83
Defining Peptides with Nicknames . . . . . . . .83
Troubleshooting Nicknames . . . . . . . . . . . . .83
Chapter 5: Query Structures
What Are Query Structures? . . . . . . . . . . . . . . 85
Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . 85
Viewing Atom Property Values . . . . . . . . . . .86
Removing Atom Properties . . . . . . . . . . . . . .86
Atom Property Options. . . . . . . . . . . . . . . . . . 87
Substituents. . . . . . . . . . . . . . . . . . . . . . . . . . .87
Implicit Hydrogens. . . . . . . . . . . . . . . . . . . . .87
Ring Bond Count . . . . . . . . . . . . . . . . . . . . . .88
Unsaturation . . . . . . . . . . . . . . . . . . . . . . . . . .88
Reaction Change. . . . . . . . . . . . . . . . . . . . . . .89
Reaction Stereo. . . . . . . . . . . . . . . . . . . . . . . .89
Translation . . . . . . . . . . . . . . . . . . . . . . . . . . .89
Isotopic Abundance . . . . . . . . . . . . . . . . . . . .90
Abnormal Valence . . . . . . . . . . . . . . . . . . . . .90
Bond Properties . . . . . . . . . . . . . . . . . . . . . . . . 90
Viewing Bond Property Values . . . . . . . . . . .91
Removing Bond Properties . . . . . . . . . . . . . .91
Bond Property Options . . . . . . . . . . . . . . . . .92
Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . 92
Topology . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Reaction Center . . . . . . . . . . . . . . . . . . . . . 94
3D Properties . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Query Tools Palette . . . . . . . . . . . . . . . . . . . . . 95
Query Indicators . . . . . . . . . . . . . . . . . . . . . .96
Viewing Query Indicators . . . . . . . . . . . . . 96
Hiding Query Indicators . . . . . . . . . . . . . . 96
ChemDraw 10
Removing Query Indicators . . . . . . . . . . . 96
Positioning Query Indicators . . . . . . . . . . 96
Drawing Stereochemical Symbols . . . . . . . . .96
Drawing Free Sites . . . . . . . . . . . . . . . . . . . . .97
Generic Nicknames . . . . . . . . . . . . . . . . . . . . . 97
Element Lists . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Element Not-Lists . . . . . . . . . . . . . . . . . . . . .98
Link Nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Representing Polymers and Other
Repeating Units . . . . . . . . . . . . . . . . . . . . . . . . 99
Setting Bracket Properties . . . . . . . . . . . . . . .99
Bracket Usage . . . . . . . . . . . . . . . . . . . . . . . .100
Structure-based Polymer Representations 100
Source-based Polymer Representations . 100
Repeat Pattern. . . . . . . . . . . . . . . . . . . . . . . .101
Flip Type . . . . . . . . . . . . . . . . . . . . . . . . . . . .102
Alternative Groups . . . . . . . . . . . . . . . . . . . . . 102
Defining an Alternative Group . . . . . . . . . .102
Multiple Attachment Points . . . . . . . . . . . . .103
Showing Attachment Rank Indicators. . . . .104
Attachment Point Numbering . . . . . . . . . . .104
Anonymous Alternative Groups . . . . . . . . . . 104
Atom-to-Atom Mapping . . . . . . . . . . . . . . . . 105
Always Display and Print Atom Mapping . .105
Automatic Mapping . . . . . . . . . . . . . . . . . . .105
Manual Mapping . . . . . . . . . . . . . . . . . . . . . .106
Clearing Reaction Mapping . . . . . . . . . . . . .106
Exporting Reaction Mapping. . . . . . . . . . . .107
Export Compatibility . . . . . . . . . . . . . . . . . . . 107
Chapter 6: Chemistry Features
Checking Chemistry . . . . . . . . . . . . . . . . . . . . 111
Check Structure . . . . . . . . . . . . . . . . . . . . . . 111
Check Structure when Copying to
Clipboard or Exporting . . . . . . . . . . . . . . .111
Viewing Analysis Information . . . . . . . . . . . . 111
Showing Stereochemistry . . . . . . . . . . . . . . . . 113
Stereochemistry Indicators. . . . . . . . . . . . . .113
Hiding Indicators . . . . . . . . . . . . . . . . . . . 113
Removing Indicators . . . . . . . . . . . . . . . . 113
Positioning Indicators . . . . . . . . . . . . . . . 113
Relative Stereochemistry . . . . . . . . . . . . . . .114
Converting Structures to 3D . . . . . . . . . . . . . 115
Viewing Chemical Properties . . . . . . . . . . . . 115
•
Stoichiometry Grid . . . . . . . . . . . . . . . . . . . . . 118
Expand Generic Structures . . . . . . . . . . . . . . 119
Administrator
Chapter 7: Struct<=>Name
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Improvements to Struct=Name . . . . . . . . 121
Struct=Name . . . . . . . . . . . . . . . . . . . . . . . . 121
Auto Update. . . . . . . . . . . . . . . . . . . . . . . . 122
Name=Struct . . . . . . . . . . . . . . . . . . . . . . . . . 122
Converting Names to Structures . . . . . . . 123
Insert Structure . . . . . . . . . . . . . . . . . . . . 123
Paste Special . . . . . . . . . . . . . . . . . . . . . . . 123
Converting Captions to Structures . . . . . . 123
Types of Structures Supported by
Struct=Name. . . . . . . . . . . . . . . . . . . . . . . 124
Chapter 8: ChemNMR
Spectrum-Structure Assignments . . . . . . . . . 127
Assigning Structures to Spectra . . . . . . . . . 127
Viewing Spectral Assignments . . . . . . . . . . 127
Removing Spectral Assignments . . . . . . . . 128
NMR Shift Information—ChemNMR . . . . 128
Chapter 9: Drawing Objects
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Selecting Tools From a Palette . . . . . . . . . . . . 131
The Orbital Tools Palette . . . . . . . . . . . . . . . . 131
s-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Sigma Orbitals. . . . . . . . . . . . . . . . . . . . . . . 132
Single Lobe Orbitals . . . . . . . . . . . . . . . . . . 132
p-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Hybrid Orbitals. . . . . . . . . . . . . . . . . . . . . . 133
d-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
dz2-orbitals . . . . . . . . . . . . . . . . . . . . . . . . . 133
The Chemical Symbols Tools Palette. . . . . . . 134
H-dot and H-dash. . . . . . . . . . . . . . . . . . . . 134
Lone Pair . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Radical Cation and Radical Anion . . . . . . . 135
Charge Symbols . . . . . . . . . . . . . . . . . . . . . 135
Attachment Points . . . . . . . . . . . . . . . . . . . 135
Rotating a Symbol. . . . . . . . . . . . . . . . . . . . 136
The Arrow Tools Palette . . . . . . . . . . . . . . . . 136
The Drawing Elements Tools Palette . . . . . . 138
•
Drawing Boxes . . . . . . . . . . . . . . . . . . . . . . 139
Drawing Circles and Ovals . . . . . . . . . . . . . 139
Resizing or Rotating Drawing Elements . . 139
Drawing Lines . . . . . . . . . . . . . . . . . . . . . . . 140
The Brackets Tools Palette . . . . . . . . . . . . . . . 140
Drawing Single Brackets . . . . . . . . . . . . . . . 140
Drawing Paired Brackets. . . . . . . . . . . . . . . . . 140
Drawing Daggers . . . . . . . . . . . . . . . . . . . . 140
Framing Objects . . . . . . . . . . . . . . . . . . . . . 140
The Arc Tools Palette . . . . . . . . . . . . . . . . . . . 141
Drawing Arcs . . . . . . . . . . . . . . . . . . . . . . . 141
Editing Arcs . . . . . . . . . . . . . . . . . . . . . . . . 141
The Pen Tool. . . . . . . . . . . . . . . . . . . . . . . . . . 141
Drawing Bézier Curves by Dragging . . . . . 142
Drawing Segments by Clicking. . . . . . . . . . 142
Editing a Curve . . . . . . . . . . . . . . . . . . . . . . 143
Changing the Shape of a Curve . . . . . . . . 143
Adding a Segment . . . . . . . . . . . . . . . . . . 143
Deleting a Segment . . . . . . . . . . . . . . . . . 143
Applying a Style to a Shape . . . . . . . . . . . . 144
Filled and Closed Styles . . . . . . . . . . . . . . 144
Shaded Style . . . . . . . . . . . . . . . . . . . . . . . 144
Plain Style . . . . . . . . . . . . . . . . . . . . . . . . . 144
The TLC Tool . . . . . . . . . . . . . . . . . . . . . . . . 144
Rf Display. . . . . . . . . . . . . . . . . . . . . . . . . . 146
Resizing Spots . . . . . . . . . . . . . . . . . . . . . . 146
Custom Spots. . . . . . . . . . . . . . . . . . . . . . . 146
Chapter 10: Page Layout
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Controlling the Drawing Area . . . . . . . . . . . . 149
Setting up Pages . . . . . . . . . . . . . . . . . . . . . . . 149
Paged Document Setup . . . . . . . . . . . . . . . 149
Poster Documents Setup . . . . . . . . . . . . . . 150
Creating Headers and Footers . . . . . . . . . . 150
Page Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Page Orientation . . . . . . . . . . . . . . . . . . . . . 152
Reduce or Enlarge. . . . . . . . . . . . . . . . . . . . 152
Saving Page Setup Settings . . . . . . . . . . . . . 152
35mm Slide Boundary Guides . . . . . . . . . . . . 152
Changing Perspectives . . . . . . . . . . . . . . . . . . 153
Magnifying with the View Menu . . . . . . . . 153
Magnify . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Actual Size . . . . . . . . . . . . . . . . . . . . . . . . 153
CambridgeSoft
Reduce . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Fit to Window . . . . . . . . . . . . . . . . . . . . . 153
Using the Magnification Control . . . . . . . . .153
Arranging Objects . . . . . . . . . . . . . . . . . . . . . 154
Using Rulers . . . . . . . . . . . . . . . . . . . . . . . . .154
Showing Rulers . . . . . . . . . . . . . . . . . . . . . . .154
Hiding Rulers . . . . . . . . . . . . . . . . . . . . . . . .155
Using the Crosshair . . . . . . . . . . . . . . . . . . .155
Displaying the Crosshair . . . . . . . . . . . . . . .155
Moving the Crosshair . . . . . . . . . . . . . . . . . .155
Aligning Objects using the Crosshair . . . . .155
Hiding the Crosshair . . . . . . . . . . . . . . . . . .155
Centering on a Page . . . . . . . . . . . . . . . . . . .156
Aligning Objects. . . . . . . . . . . . . . . . . . . . . .156
Distributing Objects. . . . . . . . . . . . . . . . . . .156
Front to Back Ordering . . . . . . . . . . . . . . . .156
Send to Back . . . . . . . . . . . . . . . . . . . . . . 157
Bring to Front . . . . . . . . . . . . . . . . . . . . . 157
Creating Tables . . . . . . . . . . . . . . . . . . . . . . . . 157
Creating Tables with the Table Tool . . . . . .157
Creating Tables with the Text Tool . . . . . . .160
Creating the First Row
(column headings) . . . . . . . . . . . . . . . . . 160
Creating a New Row . . . . . . . . . . . . . . . . 161
Adjusting Row or Column Spacing . . . . 161
Moving Around In Tables . . . . . . . . . . . 161
Inserting a New Row . . . . . . . . . . . . . . . . 162
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Chapter 11: Sharing Information
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Using the Clipboard . . . . . . . . . . . . . . . . . . . . 163
SMILES and SMIRKS Strings. . . . . . . . . . .163
Creating SMILES Strings . . . . . . . . . . . . 164
Pasting SMILES from Clipboard . . . . . 164
Creating SLN Strings . . . . . . . . . . . . . . . . .164
Creating InChI™ Strings . . . . . . . . . . . . . .165
Using Drag-and-Drop . . . . . . . . . . . . . . . . . . 165
Transferring Between ChemDraw
Documents . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Autoscaling . . . . . . . . . . . . . . . . . . . . . . . . . .165
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .166
Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . .166
Captions . . . . . . . . . . . . . . . . . . . . . . . . . . . .166
ChemDraw 10
Non-bond Objects and Color . . . . . . . . . . .166
Pasting to an Empty Document Window . .166
Embedding Objects (Windows). . . . . . . . . . . 167
Edit Graphic Object (Macintosh) . . . . . . . . . 167
Transferring PostScript (Macintosh) . . . . . . . 167
Importing and Exporting. . . . . . . . . . . . . . . . 168
Improved ISIS compatibility . . . . . . . . . . . .169
Attached Data . . . . . . . . . . . . . . . . . . . . . 169
Modifying Attached Data . . . . . . . . . . . . 170
Graphics export border preference . . . . . . .170
File Formats . . . . . . . . . . . . . . . . . . . . . . . . .170
Bitmap BMP) . . . . . . . . . . . . . . . . . . . . . . 171
ChemDraw Template (CTP, CTR) . . . . . 171
ChemDraw (CDX) . . . . . . . . . . . . . . . . . 171
ChemDraw XML (XML) . . . . . . . . . . . . 172
ChemDraw 3.5 (CHM) . . . . . . . . . . . . . . 172
ChemDraw 2.0 and ChemDraw 2.1
(CHM) Import Only . . . . . . . . . . . . . . . 172
ChemDraw Stationery/Style Sheet
(CDS) . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Connection Table (CT) . . . . . . . . . . . . . 172
Chemical Markup Language (CML) . . . 172
Encapsulated PostScript (Macintosh)
PostScript, EPS (Windows) . . . . . . . . . . 172
GIF Image (GIF) . . . . . . . . . . . . . . . . . . . 173
ISIS/SKC and ISIS/TGF . . . . . . . . . . . 173
ISIS/Reactions (RXN) . . . . . . . . . . . . . . 174
JDX (JDX, DX) Import Only . . . . . . . . 174
JPEG (JPG, JPEG) Import Only . . . . . . 174
MDL MolFile (MOL) . . . . . . . . . . . . . . . 174
Molecular Simulations MolFile (MSM) . 175
PICT (Macintosh) . . . . . . . . . . . . . . . . . . 175
PICT scaled 4X (Macintosh) . . . . . . . . . . 175
PNG file (PNG) . . . . . . . . . . . . . . . . . . . 175
SMD (SMD) . . . . . . . . . . . . . . . . . . . . . . 175
SPC (SPC) Import Only . . . . . . . . . . . . . 175
Template Style Sheet (CTS) . . . . . . . . . . 176
Windows Metafile (WMF) . . . . . . . . . . . . 176
TIFF file (TIF) . . . . . . . . . . . . . . . . . . . . 176
Inserting Objects from Other
Applications . . . . . . . . . . . . . . . . . . . . . . . .177
Transferring ChemDraw Documents
Across Platforms. . . . . . . . . . . . . . . . . . . . . . 178
•
Administrator
Transferring from Macintosh to
Windows . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Transferring from Windows to
Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . 178
Transferring Files to
ChemDraw/Plus 3.1 for the Macintosh 179
Chapter 12: ChemDraw/Excel
Setting Up ChemDraw/Excel . . . . . . . . . . . . 181
Importing Tables . . . . . . . . . . . . . . . . . . . . . . 181
Converting and Upgrading. . . . . . . . . . . . . . . 182
Upgrading Workbooks . . . . . . . . . . . . . . . . 182
Importing Hit Lists. . . . . . . . . . . . . . . . . . . . . 183
Importing a Hit list . . . . . . . . . . . . . . . . . . . 183
Error Messages . . . . . . . . . . . . . . . . . . . . . . 183
Exporting Tables . . . . . . . . . . . . . . . . . . . . . . 183
Adding Structures . . . . . . . . . . . . . . . . . . . . . . 184
Adding Structures with ChemDraw . . . . . 184
Adding a Structure From a File . . . . . . . . . 184
Adding a Structure with a SMILES String 185
Adding Structures by Name. . . . . . . . . . . . 185
Saving Structures . . . . . . . . . . . . . . . . . . . . . . 185
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Filter Tables. . . . . . . . . . . . . . . . . . . . . . . . . 186
Similarity Searches . . . . . . . . . . . . . . . . . . . 187
Working with Structures. . . . . . . . . . . . . . . . . 187
Naming Structures . . . . . . . . . . . . . . . . . . . 187
Using the Clipboard . . . . . . . . . . . . . . . . . . 187
Viewing Structures . . . . . . . . . . . . . . . . . . . 188
Showing and Hiding Structures . . . . . . . . 188
Aligning Structures . . . . . . . . . . . . . . . . . 188
Resizing Structures . . . . . . . . . . . . . . . . . . 188
Resizing Structures With a Macro . . . . . . 188
Using ChemDraw/Excel Functions . . . . . . . 189
Using ChemProp Functions. . . . . . . . . . . . 191
ChemProp Properties . . . . . . . . . . . . . . . 191
Inserting Functions. . . . . . . . . . . . . . . . . . . 191
Chapter 13: BioDraw
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
The BioDraw Tools Palette . . . . . . . . . . . . 193
Customizable Objects. . . . . . . . . . . . . . . . . 194
Drawing a Membrane Line . . . . . . . . . . . 195
Drawing a Membrane Arc . . . . . . . . . . . . 195
•
Drawing a Helix Protein . . . . . . . . . . . . . 196
Drawing a DNA Molecule . . . . . . . . . . . . 196
Appendix A: Customizing ChemDraw
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Setting Preferences . . . . . . . . . . . . . . . . . . . . . 197
Setting the Default Document Location . . 197
Setting the Default Open File Format . . 197
Setting the Default Tool . . . . . . . . . . . . . . . 198
Saving Changes Automatically . . . . . . . . . 198
Undoing Actions . . . . . . . . . . . . . . . . . . . 198
Redoing Actions . . . . . . . . . . . . . . . . . . . . 199
Setting the Default Save File Format . . . 199
Creating a New Line and Closing Text
Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Using Bitmap Fonts When Available
(Macintosh) . . . . . . . . . . . . . . . . . . . . . . . . 199
Setting the Highlight Box Tolerance . . . . . 200
The ChemDraw Items Folder . . . . . . . . . . 200
Accessing Documents Quickly . . . . . . . . 200
The Open Special Submenu . . . . . . . . . . 200
Document and Object Settings . . . . . . . . . . . 200
Default Style Sheet or Stationery Pad . . . . 201
Saving Customized Settings as Style
Sheets or Stationery Pads . . . . . . . . . . . . . 201
Applying Document Settings From
Other Documents . . . . . . . . . . . . . . . . . . 202
Applying Object Settings from
Other Documents . . . . . . . . . . . . . . . . . . 202
Drawing Settings . . . . . . . . . . . . . . . . . . . . . 202
Configuring Settings for Documents . . . 204
Configuring Settings for Objects . . . . . . . 205
Formatting Text . . . . . . . . . . . . . . . . . . . . . . . 206
Setting Font parameters . . . . . . . . . . . . . . . 206
Setting the Baseline Style . . . . . . . . . . . . . . 206
Specifying Line Spacing . . . . . . . . . . . . . . . 207
Aligning Text. . . . . . . . . . . . . . . . . . . . . . . . 207
Captions . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Atom Labels . . . . . . . . . . . . . . . . . . . . . . . 207
Automatic Alignment . . . . . . . . . . . . . . . . 208
Changing the Default Caption or Atom
Label Text Format . . . . . . . . . . . . . . . . . . . 208
Specifying Document Settings for
CambridgeSoft
New Text . . . . . . . . . . . . . . . . . . . . . . . . 208
Setting an Individual Text Format
Before Typing . . . . . . . . . . . . . . . . . . . . 209
Changing the Spacing of Individual
Text Objects . . . . . . . . . . . . . . . . . . . . . . 209
Fractional Character Widths
(Macintosh) . . . . . . . . . . . . . . . . . . . . . . 209
Specifying the Margin Width . . . . . . . . . . . .209
Creating HotKeys. . . . . . . . . . . . . . . . . . . . . . 210
Hard-Coded HotKeys . . . . . . . . . . . . . . . . .210
Working with Color . . . . . . . . . . . . . . . . . . . . 210
Coloring Objects . . . . . . . . . . . . . . . . . . . . .211
Displaying the Color Palette . . . . . . . . . . . .211
Customizing the Color Palette . . . . . . . . . .212
Windows Color Settings. . . . . . . . . . . . . . . .212
Adding or Customizing Windows
Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Macintosh Color Settings. . . . . . . . . . . . . . .213
Adding or Customizing Macintosh
Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Removing Colors . . . . . . . . . . . . . . . . . . . . .213
Templates and Color . . . . . . . . . . . . . . . . . .214
Saving Color Palette Settings . . . . . . . . . . . .214
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Printing Background Color . . . . . . . . . . . . .214
Macintosh Print Preferences . . . . . . . . . . . .214
Optimize Pictures for High-Resolution
Non-PostScript Printing . . . . . . . . . . . . 214
Include PostScript . . . . . . . . . . . . . . . . . . 215
Include ChemDraw Laser Prep . . . . . . . 215
Appendix B: Document Settings
Creating Style Sheets or
Stationery Pads . . . . . . . . . . . . . . . . . . . . . . . 217
ChemDraw Style Sheets or Stationery
Pads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217
ACS 1996 . . . . . . . . . . . . . . . . . . . . . . . . . 217
Adv.Synth Catal. . . . . . . . . . . . . . . . . . . . 218
J.Chin. Chem. Soc. . . . . . . . . . . . . . . . . . . 218
J. Mol. Mod. . . . . . . . . . . . . . . . . . . . . . . . 219
New Document . . . . . . . . . . . . . . . . . . . . 220
New Slide . . . . . . . . . . . . . . . . . . . . . . . . . 221
Phytomedicine . . . . . . . . . . . . . . . . . . . . . 222
ChemDraw 10
RSC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Science of Synthesis . . . . . . . . . . . . . . . . . 223
Synthesis, Synlett . . . . . . . . . . . . . . . . . . . 223
Verlag Helvetica Chimica Acta . . . . . . . . 224
Wiley Document . . . . . . . . . . . . . . . . . . . 224
Appendix C: Chemistry File Formats
Connection Table File Format . . . . . . . . . . . 225
Appendix D: ChemDraw Chemistry
Chemical Intelligence in ChemDraw. . . . . . . 229
Database Conventions . . . . . . . . . . . . . . . . .229
Chemical Conventions . . . . . . . . . . . . . . . . . . 230
Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . .230
Chemically Significant Text . . . . . . . . . . . . .231
Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . .232
Isotopes and Elements . . . . . . . . . . . . . . . . .232
Radicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . .233
H-Dot/H-Dash . . . . . . . . . . . . . . . . . . . . . .233
Complexes. . . . . . . . . . . . . . . . . . . . . . . . . . .233
Multi-center Attachments . . . . . . . . . . . . . .234
Stereochemistry . . . . . . . . . . . . . . . . . . . . . .234
Stereochemical Indicators . . . . . . . . . . . . 235
Stereochemical Flags . . . . . . . . . . . . . . . . . .235
Polymer Representations . . . . . . . . . . . . . . .235
References . . . . . . . . . . . . . . . . . . . . . . . . 235
Query Properties . . . . . . . . . . . . . . . . . . . . .236
Analysis Messages. . . . . . . . . . . . . . . . . . . . .236
Appendix E: How ChemProp Works
ChemProp Values . . . . . . . . . . . . . . . . . . . . . . 239
LogP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .239
Henry’s Law . . . . . . . . . . . . . . . . . . . . . . . . .239
Molar Refractivity . . . . . . . . . . . . . . . . . . . . .239
ClogP and CMR . . . . . . . . . . . . . . . . . . . . . .240
Topological Polar Surface Area . . . . . . . . . .240
Other Properties. . . . . . . . . . . . . . . . . . . . . .240
Appendix F: How ChemNMR Works
ChemNMR Limitations. . . . . . . . . . . . . . . .241
Appendix CS-1: Technical Support
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Serial Numbers . . . . . . . . . . . . . . . . . . . . . . . . 243
•
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . 243
Performance. . . . . . . . . . . . . . . . . . . . . . . . . 244
System Crashes . . . . . . . . . . . . . . . . . . . . . . 244
Administrator
Appendix CS-2: Accessing the
CambridgeSoft Web Site
Online Menu Overview . . . . . . . . . . . . . . . . . 245
Registering Online . . . . . . . . . . . . . . . . . . . . . 245
Accessing the Online ChemDraw User’s
Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
•
Accessing CambridgeSoft Technical Support 246
Finding Information on ChemFinder.com . . 246
Finding Chemical Suppliers on ACX.com. . . 247
Finding ACX Structures and Numbers . . . . . 247
ACX Structures . . . . . . . . . . . . . . . . . . . . . . 247
ACX Numbers . . . . . . . . . . . . . . . . . . . . . . 248
Browsing ChemStore.com . . . . . . . . . . . . . . . 248
Browsing CambridgeSoft.com . . . . . . . . . . . . 248
Using the ChemOffice SDK . . . . . . . . . . . . . 249
CambridgeSoft
Introduction
This User’s Manual provides information on three
CambridgeSoft products: ChemDraw, BioDraw,
and ChemDraw/Excel.
About ChemDraw
ChemDraw® is a desktop application that enables
professional scientists, science students, and scientific authors to communicate chemical structures.
It is designed to work according to conventions
that we have found to be most intuitive for such
users. Our goal has been to make ChemDraw as
easy to use as possible while providing superior
drawing quality.
ChemDraw is integrated with the following
CambridgeSoft products:
•
•
•
•
ChemFinder
Chem3D
ChemDraw/Excel
ChemOffice 2006
About BioDraw
BioDraw® is a desktop application for drawing and
presenting biological pathways. Common pathway
elements (membranes, DNA, enzymes, receptors,
etc.) are built in, and other elements may be
imported. The pathways you create with BioDraw
can be exported for use in presentations, grant proposals, and publications.
About ChemDraw/Excel
The ChemDraw/Excel® add-in is an extension of
Microsoft© Excel© for Windows.
ChemDraw/Excel enables you to:
ChemDraw 10
• Add chemical structures and other data from
ChemDraw or a ChemFinder database to an
Excel spreadsheet.
• Search using the same search features as ChemFinder.
• Perform calculations on chemical structures.
See the ChemOffice manual for information on
other CambridgeSoft add-ins for Excel.
About This Manual
This User’s Manual contains information for the
ChemDraw application for Windows and Macintosh. It assumes that you are familiar with the
basics of your Windows operating system. If you
are not, please refer to your system manual before
using the applications. Some of the material
describes tasks that must be performed in conjunction with other integrated CambridgeSoft products. The material on the Addins describes tasks
that must be performed in conjunction with
Microsoft Excel. If you are not familiar with this
product, please consult the relevant User’s Manual
for more detailed information.
The chapters in this guide are organized by task.
They are intended to help you familiarize yourself
with the ChemDraw applications and start using
them as quickly and efficiently as possible.
New users should read the Introducing ChemDraw chapter to get an overview of the product
GUI and how to use it. They may then continue
with Chapter 2 Tutorials, which demonstrate
most of the features of the application. Perform
the tutorials in the order they are presented.
Chapter 3 covers the basic structure drawing techniques: bonds, atom labels, selecting and moving
objects.
Introduction
About ChemDraw
•
9
Administrator
Chapter 4 continues the discussion of structures
with more advanced techniques: drawing reactions,
joining and grouping structures, formatting and
repeating labels, constrained bonds, and more.
Chapter 5 discusses the special ChemDraw features that allow you to create query structures for
searching databases.
Chapter 6 discusses ChemDraw’s chemistry features: chemical analysis and properties, stereochemistry, and the new Stoichiometry Grid.
Chapter 7 discusses ChemDraw’s naming algorithms, Struct=Name and Name=Struct.
Chapter 8 discusses ChemNMR.
Chapter 9 describes the Drawing Objects you can
add to your ChemDraw structures to produce
drawings for publication or presentations.
Chapter 10 continues the topic of publication/
presentation with a detailed discussion of page layout.
Chapter 11 discusses sharing information, both
importing other chemical and graphical formats
and exporting to chemical software, spreadsheet,
or publication software.
Chapter 12 discusses BioDraw.
Chapter 13 discusses ChemDraw/Excel.
The appendices discuss using the CambridgeSoft
website, ChemDraw customization, details of
ChemDraw’s chemistry features, file formats, document setting, and troubleshooting.
What’s New in ChemDraw
10.0
Enhancements to ChemDraw 10.0 include:
• New Lasso
• New Arrows (see also “Tutorial 2: Drawing an
Intermediate” on page 31)
• Adjustable Drawing Objects
• Terminal Carbon Labels
10 •
Introduction
•
Pro Relative Stereochemistry
•
Ultra
Improvements to Struct=Name
•
Ultra
BioDraw
•
Ultra
Stoichiometry Grid
•
Pro Improved ISIS compatibility
• Improved Table tool behavior
• InChI™ support
Enhancements to PlugIns and ActiveX include:
• More Browser Support
Conventions
The following notations are used throughout this
user’s guide:
Ultra The Ultra symbol indicates that a feature
is available in the Ultra version only.
Pro
The Pro symbol indicates that a feature
is available in both the Pro and Ultra versions.
Features that are available in the Standard version
are not indicated by a symbol.
NOTE: Notes such as this are used to highlight important
information.
TIP: Tips supply useful, “nice to know”, information supplemental to the main text.
CAUTION
Indicates important information that, if ignored, might
lead to data loss or other serious problems.
When a shortcut key sequence is given, the Windows OS sequence is listed first, with the Macintosh OS sequence following, for example: “Use the
command: Shift+Control+G or Shift+Command+G
to ungroup objects.”
CambridgeSoft
About ChemDraw
A special font is used to indicate labels or commands in the GUI, for example: “Click the Help
Contents. command on the Help menu.” The exact
text you will see in the GUI is used in these references.
Additional Information
Additional sources of ChemDraw information are:
• The Quick Reference Cards.
• The Help system
• CambridgeSoft Web Pages.
http://www.cambridgesoft.com/
Quick Reference Card
The ChemDraw Quick Reference Cards are
located in the back of the manual. The cards provide summaries of ChemDraw Desktop Application commands and features. Because many of the
instructions require knowledge of the interface elements, use the Quick Reference card as you perform the tutorials in Chapter 2: “Tutorials”.
Help System
ChemDraw provides the following types of Help:
• ChemDraw Help. An HTML reference
guide.
• Context-sensitive Help (Windows). Help
topics related to user interface objects. To
access Context sensitive Help type Shift+F1.
• ToolTips. Short descriptions of user interface
objects displayed by pointing.
• Status Bar. The lower left corner of the GUI
displays useful information as you work.
CambridgeSoft Web Pages
The following table contains the addresses of
ChemDraw-related web pages.
Table 1: ChemDraw-related web pages
For
information
about …
Access …
Technical
Support
http://www.cambridgesoft.com/services
ChemDraw
Plugin
http://www.cambridgesoft.com/services/documentation/chemdrawplugin/
Chem3D
http://www.cambridgeActiveX control soft.com/services/documentation/chem3dcontrol/
Software Devel- http://sdk.cambridgeoper’s kit
soft.com/
Purchasing
CambridgeSoft
products and
chemicals
http://chemstore.cambridgesoft.com/
Installation and System
Requirements
Before installation, see the “ReadMeFirst” and any
other ReadMe documents on the installation CDROM.
Microsoft®Windows®
Requirements
• Windows 2000 or XP.
• Microsoft®Office add-ins require Office 2000,
2003, or XP.
ChemDraw 10
Introduction
About ChemDraw
•
11
• Screen resolution must be 800 x 600 or higher.
Administrator
ChemDraw plugins/ActiveX® controls support
Microsoft IE 6.x, Netscape® 7.x and 8.x, Mozilla
1.x, and Firefox 1.x.
The Chem3D ActiveX control supports Microsoft
IE 6.x, Netscape® 7.x and 8.0, Mozilla 1.x, and
Firefox 1.x.
NOTE: Windows XP Service Pack 2 includes security
features that automatically block active content. This means
that by default, Internet Explorer blocks ChemDraw and
Chem3D ActiveX controls. To activate them, you must
choose the option to “allow blocked content” from the bar
appearing under the address bar notifying you that the security settings have blocked some of the content of the page. IE
does not remember this information, so you must repeat the
activation each time you access the page.
If you visit a site frequently, you can add it to the list of
trusted sites in IE’s security settings.
Macintosh® Requirements
• Mac®OS X 10.2.2-10.2.8, 10.3.x, or 10.4
• Screen resolution must be 800 x 600 or higher.
ChemDraw Plugin supports Safari 1.4 or higher,
Mozilla 1.7.5 or higher, Firefox 1.x, and Netscape
7.0.x
Site License Network Installation
Instructions
If you have purchased a site license, please see the
following web site for network installation instructions:
http://www.cambridgesoft.com/services/sl/
12 •
Introduction
CambridgeSoft
About ChemDraw
Chapter 1: Introducing Chem & Bio Draw
Overview
This section introduces the new user to the
ChemDraw GUI. It covers the following topics:
• Identifying the parts of the ChemDraw interface.
• Creating, opening, and saving documents.
Figure 1.1: ChemDraw Windows Ultra GUI
Title bar
The ChemDraw Graphical
User Interface
Although the Macintosh and Windows versions of
the ChemDraw graphical user interface (GUI) differ slightly, the essential GUI consists of the same
elements. The Windows version of ChemDraw is
shown in Figure 1.1.
Magnification controls Object toolbar
Menu bar
General
toolbar
Text style
toolbar
Main tools
palette
Rotation handle
Resize handles
Selection box
BioDraw
Toolbar
Resize
Status bar
The Mac GUI is shown in Figure 1.2.
ChemDraw 10
Figure 1.2: ChemDraw Mac Ultra GUI
Introducing Chem & Bio Draw
Overview
•
13
Magnification control
Administrator
Menu bar
General
toolbar
Object toolbar
Title bar
Text style toolbar
Rotation handle
Main tool
palette
Resize handles
Scroll bar
Selection box
BioDraw
toolbar
Resize
The Main Tools Palette
different for the different versions of ChemDraw.
Use the main tools palette to create and manipulate
drawings. The appearance of the toolbar is slightly
14 •
Introducing Chem & Bio Draw
CambridgeSoft
Overview
The toolbar for ChemDraw Ultra is shown in
Figure 1.3.
Figure 1.3: Main Tools Palette
Table 2 describes the functions of the tools for all
versions. Some of the tools have multiple options
that can be selected from a tool palette.
Table 2: Main Tools Palette
Lasso
Structure Perspective
Solid Bond
Marquee
Eraser
Text
Dashed Bond
Pen
Hashed Bond
Arrows
Bold Bond
Bold Wedged Bond
Hollow Wedged Bond
Wavy bond
Brackets
Chemical Symbols
Query tools
Acyclic Chain
Templates
Cyclopropane Ring
Cyclobutane Ring
Cyclopentane Ring
Cyclohexane Ring
Cycloheptane Ring
Cyclooctane Ring
ChemDraw 10
Lasso. Select objects by dragging
around them.
Marquee. Select objects by dragging
diagonally across them.
Selected objects can be further
manipulated using menu commands.
Drawing Elements
TLC plate
Cyclopentadiene Ring
Selection
Orbitals
Table
Cyclohexane chair 1
Use to…
Fragmentation tools
Multiple Bonds
Hashed Wedged Bond
Tool
Cyclohexane chair 2
Benzene Ring
Structure
Rotate a selected object in three
Perspective dimensions.
Fragmenta- Fragmentation tool. Splits moletion toolbar cules across specific bonds.
Dissociation tool. Breaks bonds and
draws a reaction.
Retrosynthesis tool. Breaks bonds
and draws a reaction.
Bond
Draw bonds and set bond properties.
Eraser
Delete objects. Click on an object to
delete; drag to delete multiple objects.
If you click a multiple bond, it will
reduce the bond order. If you doubleclick any part of a structure, it deletes
the entire structure
Multiple
Bond
toolbar
Draw multiple bonds and set bond
properties. Bonds of different types
can be selected from the Multiple
Bonds tool palette.
Introducing Chem & Bio Draw
Overview
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15
Table 2: Main Tools Palette
Table 2: Main Tools Palette
Administrator
Tool
Use to…
Tool
Use to…
Text
Create atom labels and captions.
Arcs
toolbar
Pen
Draw freehand shapes such as
custom arrows and orbitals.
Draw arcs. Arcs of different degrees
can be selected from the Arcs tool
palette.
Arrows
toolbar
Draw arrows. Arrows of different
types can be selected from the Arrows
toolbar.
Orbitals
toolbar
Draw orbitals. Orbitals of different
types can be selected from the
Orbitals toolbar.
Drawing
Elements
toolbar
Draw annotations that lack chemical
significance, such as boxes and lines.
Drawing Elements of different types
can be selected from the Drawing
Elements toolbar.
The Arcs tool is a separate tool only
on ChemDraw Standard.
Acyclic
Chain
Draw chains of any length.
Query
Tools
toolbar
Draw stereochemical flags, indicate
free sites, alternative groups and
correspondences between atoms in
query structures. Various options can
be selected from the Query tool
palette.
Templates
toolbars
Draw structures with templates
stored in template documents.
Templates can be selected from the
Templates toolbars.
Rings
Draw common structural components.
Table
Draw tables with multiple rows and
columns.
TLC Plate
Pro
Draw TLC plates with multiple lanes
and adjustable solvent front and
spots.
Includes the Arc tools.
Pro
Brackets
toolbar
Chemical
Symbols
toolbar
16 •
Draw brackets, parentheses, and
braces. Brackets of different types can
be selected from the Brackets tool
palette.
Draw chemically significant symbols
such as charges, radicals, and lone
pairs. Symbols of different types can
be selected from the Symbols tool
palette.
Introducing Chem & Bio Draw
CambridgeSoft
Overview
Tearing Off Palettes
Figure 1.6: Optional toolbars on the View menu
Some tools have toolbars extending from them,
indicated by an arrow at the bottom right of the
tool button.
standard
toolbars
Figure 1.4: Tearing off the symbols palette
information
windows
You can “tear off ” these toolbars and place them
anywhere in the ChemDraw screen. You cannot
dock torn off toolbars.
To tear off a toolbar:
tool
palettes
• Click the arrow on the lower right of the tool.
• Holding the mouse button down, point to the
title bar and release the mouse button.
Figure 1.5: Symbols as a floating toolbar
templates
You can drag the toolbar by its title bar to reposition it.
You can also show or hide a toolbar by selecting it
from the Other Toolbars submenu on the View
menu.
Optional Toolbars
ChemDraw provides a number of optional toolbars and information windows to facilitate production of ChemDraw documents. These toolbars are
accessed from the View menu. They are divided
into three basic groups: Standard Toolbars and
Show Windows, Tool Palettes, and Templates
ChemDraw 10
Showing and Hiding Toolbars
To show or hide a toolbar:
• select a toolbar from the View menu.
A check mark appears next to the item when
the toolbar is displayed.
Docking and Undocking Toolbars
The standard toolbars, can be docked or
undocked. Docked toolbars can attach to any edge
of the ChemDraw window. Undocked toolbars
can float anywhere in the on your monitor screen.
To dock a toolbar do one of the following
Introducing Chem & Bio Draw
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17
Administrator
• Drag the toolbar to the edge of the ChemDraw
screen where you want it to dock.
• Double-click the toolbar background. This will
dock the toolbar in the default position. (All
toolbars default to the top of the ChemDraw
window, except for the Tools toolbar which
defaults to the left side.)
To undock a toolbar do one of the following:
Pro The Chemical Properties
Window
The Chemical Properties window displays properties of the selected structure. When no structure is
selected, properties will be displayed only if there is
one (and only one) structure in the document.
Figure 1.9: Chemical Properties window
• Drag the toolbar into the position you want
• Double-click the toolbar.
The Status Bar or Message Area
(Windows)
The status bar or message area displays information about the menu or toolbar you are using.
Figure 1.7: Status bar
The Paste button inserts all selected items into the
document. The button
The Analysis Window
The Analysis window displays the chemical analysis of the selected structure. If nothing is selected,
the values shown are for the entire document.
Figure 1.8: Analysis window
shrinks the window to
just the title bar, while leaving it active.
NOTE: CLogP and CMR values are displayed only in
ChemDraw Ultra.
The Info Window
The Info window shows size/positioning information about what's going on in ChemDraw.
Figure 1.10: Info window
See “Viewing Analysis Information” on page 111
for information on the Analysis window.
The Paste button inserts all selected items into
the document. The button shrinks the window to just the title bar.
18 •
Introducing Chem & Bio Draw
CambridgeSoft
Overview
The fields are shown in Table 3.
Table 3: Info window fields
Field
Shows…
Pointer:
X/Y
current mouse coordinates
Pointer:
dX/dY
change in X and Y coordinates
of a moved selection
Click an element symbol to highlight the element
and activate the Text tool. Drag across the table to
highlight each element in turn. Click the
button to show or hide the detailed information.
After selecting an element, click in the document
to add an atom label consisting of that element and
the appropriate number of hydrogens. Labeling
behavior is shown in Table 4.
Table 4: Labeling with the Periodic Table
click on… to…
Selection:
X/Y
W/H
Angle:
Dist:
%
position of a selection
width/height of a selection
angle of a bond; rotation of a
selection
length of a bond; distance a
selection has been moved
% of original size when resizing
a selection
Periodic Table
The Periodic Table window displays a floating
periodic table. It can be used both for reference
and to insert elements into structures. To show or
hide the Periodic Table, select/deselect it in the
View menu.
Figure 1.11: Periodic Table:
ChemDraw 10
an existing
unlabeled
atom
label the atom
an existing
labeled
atom
cycle the hydrogen count (if it
matches the selected element)
or change the label
an empty
space
create a new atom
Double-clicking on an existing atom will open it
for editing without changing the label.
NOTE: Some element names conflict with ChemDraw
Hotkeys, and may not be interpreted correctly by Chemical
Warnings or Check Structure. For more information and
troubleshooting see “Defining Nicknames” on page 82.
Character Map
The floating Character Map window displays the
256 ASCII characters in any font. The default font
is Symbol. Use it to add symbols or styled fonts to
labels.‘
Introducing Chem & Bio Draw
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19
Figure 1.12: Character map
BioDraw
Administrator
ChemDraw Ultra now incorporates BioDraw
tools, allowing you to include drawings of metabolic pathways in ChemDraw files.
Figure 1.13: Partial depiction of the mechanism of
action of glyceraldehyde 3-phosphate dehydrogenase1
Enzyme
R
H
SH
R
C
S
O
N
R1
The character map is active only when a text box is
open for editing. It will appear grayed-out at all
other times With a text box open, mouse over the
character map to view a larger version of the characters in the top right corner of the window. Click
any character in the table to enter that character in
the text box. The selected font (shown in the character map window) is applied to that character
only. It does not change the active font in the text
box.
NOTE: You can cancel a selection by dragging to some
other character before releasing.
The 8 most recently used characters are displayed
at the top of the window. These characters retain
their font and are not affected by changes to the
window. A single character may appear more than
once in this section if the versions use different
fonts.
Click the back button to toggle between the 8
most recently used characters and the entire
character map.
C
H
OH
N
CONH2
R1
The BioDraw tools palette is activated from the
View menu. The toolbar contains special drawing
tools such as enzymes and receptors. Standard
shapes, such as circles or ellipses, can be added
from the Drawing Elements tool palette. You can
also use the Pen tool to create custom shapes.
Figure 1.14: BioDraw Toolbar
1-substrate enzyme
2-substrate enzyme
Receptor
Ion Channel
Helix Protein
Membrane (line)
Membrane (arc)
Golgi Body
Cloud
G-protein (alpha subunit)
G-protein (beta subunit)
G-protein (gamma subunit)
Immunoglobulin
DNA
Micelle
Membrane (ellipse)
Endoplasmic Reticulum
Mitochondrion
As with the Drawing Elements, you can change the
color of an object with the Color menu, and the
line and fill properties with the Curves menu. You
can also rotate, or change the size, after selecting it.
You create a BioDraw object by either clicking or
dragging on the page where you want it to appear.
Clicking gives you the default size and shape, dragging allows you not only to enlarge the object, but
to distort it as well by dragging differently on the x
1. H. Lodish, et. al., Molecular Cell Biology,
Scientific American Books, New York, NY,
1995, p. 743.
20 •
Introducing Chem & Bio Draw
CONH2
CambridgeSoft
Overview
and y axes. Linear objects elongate in the direction
they are dragged. The membrane and protein tools
(DNA and Helix) add more subunits as they are
dragged; proteins display the subunit count.
main Tools Palette and a list of structure and clip
art templates that users may find useful.
Customizable Objects
BioArt
Some of the BioDraw objects can be customized
after being created. The table below describes the
customization options.
Amino Acids Aromatics
Bicyclics
Table 5: Customizable BioDraw Objects
Conformers
Cp Rings
Nanotubes
Amino Acid
side chains
DNA
templates
RNA
templates
Functional
groups
Hexoses
Supramolecules
Ph Rings
Polyhedra
Stereocenters
Tool
Customization
Options
1-Substrate Enzyme size of the enzyme opening
Receptor
width
Helix Protein
height, width of the strands,
width of the cylinders,
spacing
Table 6: Structure and Clipart Templates
Clipware 1
Clipware 2
Using Documents
Documents are the ChemDraw workspace where
you create and manipulate structures. You can create a new document or open an existing document
and edit it.
DNA
height, width of the strands,
offset of the second strand,
spacing
Membrane (line)
size of subunit
Membrane (arc)
length, arc, size of subunit
You can create a new, blank document using the
ChemDraw default settings, or use a Style Sheet or
Stationery Pad with customized settings.
Membrane (ellipse)
size of subunit
Creating a New Document
Creating a Document
To create a document:
Micelle
size of subunit
Golgi part (long)
length, width, curvature
Other Toolbars
The Other Toolbars command on the View menu
gives a list of toolbars that can be opened from the
ChemDraw 10
Click the New Document command on the File
menu.
Creating a Document Using a Style
Sheet or Stationery Pad
To create a new document using a different Style
Sheet or Stationery Pad:
Introducing Chem & Bio Draw
Overview
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21
Administrator
1. Click the Open Special command on the File
menu.
2. Choose a Style Sheet or Stationery Pad from
the list.
A new document is created with the settings
(and objects) stored in the Style Sheet or Stationery Pad.
ChemDraw provides pre-defined Style Sheets or
Stationery Pads located in the ChemDraw Items
folder. For example, the ACS Document 1996 is
configured to create documents that are set with
the bond lengths, bond width, spacing, and fonts
used in the 2-column format of all American
Chemical Society journals. For a list of the settings
stored in these documents, see Appendix B: “Document Settings”. For more information on publication guidelines, see
http://www.cambridgesoft.com/services/downloads/stylesheets.cfm
NOTE: Predefined Style Sheets or Stationery Pads may
restrict your options in unexpected ways. For example, not all
Save As... format options are available in all Style Sheets or
Stationery Pads. For general use, you should stay with the
default Style Sheet or Stationery Pad.
Opening a Document
To open a document:
From the File menu, do one of the following:
• Choose Open, and in the Open dialog box,
select the name and location of the file and
click Open or OK.
• Choose the document from the list of previously opened documents at the bottom of
the menu.
Discarding Recent Changes to a
Document
To retrieve the last saved version of a file, click the
Revert command on the File menu.
22 •
Introducing Chem & Bio Draw
All changes made to the file since it was
saved last are discarded and the previous
version of the file appears.
NOTE: You can use the Undo command in the Edit menu
to remove each individual action since the last save.
Saving Documents
To save a ChemDraw document in the default
ChemDraw CDX file format:
1. Click the Save command on the File menu.
The Save dialog box appears. The appearance
of the dialog box depends on the platform you
are using.
2. Choose a folder in which to store the file.
3. Type a file name in the File name (Windows) or
Save As (Macintosh) text box. You may type
up to 255 characters for a file name, including
spaces. For example: “my first structure in
ChemDraw”.
4. Click Save or OK to create the file.
The title of the document window changes to
the name of the saved file. The file name is
added to the bottom of the File menu.
CAUTION
ChemDraw uses the CDX file format to store chemical
information accurately with a structure drawing. Other file
formats may be capable of storing a picture of your
drawing, but they might lose chemically relevant
information about the structure. For example, if you save
a ChemDraw drawing in the EPS file format, you will
store only a picture of the structure without storing the
chemical significance of the connections between atoms and
bonds.
Saving a Document in a Different File
Format
To save a ChemDraw document in another file
format:
CambridgeSoft
Overview
1. Click the Save As command on the File menu.
The Save As dialog box appears.
2. Select a folder in which to save the document.
3. Type a file name in the in the File name or Save
As box.
4. Select a file format from the File Format or
Save as Format list.
NOTE: When you select some formats, the Options button
becomes active. Click it to open a dialog box for setting
options specific to these formats. For more information about
these options, see Chapter 11: “Sharing Information”.
5. Click Save or OK.
If you type a name that already exists in the same
directory, the existing document is replaced. If you
do not want to replace the original ChemDraw
document, use a different name. For information
about other file formats, see Chapter 11: “Sharing
Information”.
Reversing and Repeating
Actions
choosing the Undo command then restore them
with the Redo command. The number of actions
that can be undone or redone is limited only by the
amount of memory (RAM and virtual memory)
available for use by ChemDraw. When you save
your document the Undo queue is reset and starts
over.
Repeating Actions
If an action is repeatable, the name of the action
appears next to the Repeat command on the Edit
Menu.
To repeat an action:
Click the Repeat command on the Edit menu.
The last action performed is repeated.
The Window Menu
The Window menu lists all open ChemDraw and
Template documents. The document you choose
from the Window menu becomes the active window.
ChemDraw keeps track of the actions you perform. You can reverse actions one at a time by
ChemDraw 10
Introducing Chem & Bio Draw
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23
Administrator
24 •
Introducing Chem & Bio Draw
CambridgeSoft
Overview
Chapter 2: Tutorials
Overview
The tutorials are designed to teach you the fundamental drawing techniques available in ChemDraw. In addition to the major theme (“Reaction
Schemes”, “Perspective Drawings”) each tutorial
introduces new techniques, or variations of techniques learned in previous tutorials. We therefore
suggest that you do the tutorials in order.
Before you begin, you may want to review “Conventions” on page 10 to familiarize yourself with
the terminology used in the tutorials. You may also
want to use your Quick Reference Card while you
perform the tutorials.
ChemDraw automatically checks for correct chemical syntax as you draw. If ChemDraw finds a
potential problem, a red box is displayed around
the erroneous object. The red box is displayed on
screen only and does not print.
To disable the automatic warning on a specific
object:
• Right-click the object and deselect the Display
Warnings command on the context menu.
NOTE: Some of the following tutorials make use of HotKeys. They assume the default configuration, i.e. that none of
the HotKey assignments have been changed.
Figure 2.15: Tutorial 1: Drawing a reaction scheme
O
O
OH
OH
2-propanone
2 moles
4-hydroxy-4-methyl-2-pentanone
1 mole
Create a ChemDraw Document:
1. Start ChemDraw.
2. Click the Save As command on the File menu.
3. Type tut1.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
6. Click the Show General Toolbar command on
the View menu.
7. Click the Show Info Window command on the
View menu.
The Info window appears and displays drawing
parameters as you draw.
Figure 2.16: The Info window
Tutorial 1: Reaction
Schemes
In this tutorial, you will draw the following (simplified) reaction scheme:
8. Click the Object menu and make sure there is
a check mark next to the Fixed Lengths and
Fixed Angles commands. If either command is
not checked, select it.
ChemDraw 10
Tutorials
Overview
•
25
Figure 2.17: Checking fixed lengths and angles
Figure 2.20: Adding a third bond.
A
Administrator
NOTE: Applying fixed lengths and fixed angles enables
you to create structures with consistent bond lengths and
angles. The fixed length dimension is set in the Drawing Settings tab of the Document settings dialog box. The fixed
angle dimension increments angles by 15 degrees.
Create a bond:
1. Select the Solid Bond tool
.
2. Position the pointer (+) anywhere in the document window and click.
The bond is extended to its fixed length at a
30-degree angle.
Figure 2.18: Adding the first bond
Add a second bond:
1. Point to the right atom of the bond.
2. Click the atom to add a bond.
Figure 2.19: Attaching a bond to an existing bond
A
B
B
Change the single bond into a double bond:
1. Point to the atom shown in Figure 2.21 A and
hold the mouse button down.
2. Drag as shown below over the existing single
bond. Release the mouse button.
Figure 2.21: Adding a double bond
A
B
Add labels to the structure:
1. Point to the atom shown in Figure 2.22 A, and
double-click.
A text box appears on the atom position to
allow you to create an atom label. See “Creating
Text” on page 56 for an explanation of the difference between atom labels and captions.
2. Type an uppercase O in the text box that
appears.
Figure 2.22: Adding an atom label
A
B
C
O
A second bond is drawn, forming a 120-degree
angle between the bonds.
NOTE: The angle used when clicking to add bonds is
controlled by the Chain Angle setting in the Drawing
Settings tab of the Document settings dialog box. If this
bond angle cannot be established, the next smaller and
logical bond angle is used.
Add a third bond to the same atom:
1. Continue pointing to the atom shown in Figure
2.20 A.
2. Click the atom to add a bond.
26 •
Tutorials
3. Close the text box by doing one of the following:
• Use the Esc key.
• Click another tool.
Next, you duplicate a structure and create another
structure from the duplicate.
Duplicate the structure:
CambridgeSoft
Overview
1. Click the Lasso tool
.
The last structure drawn is automatically
selected.
2. Point over the Selection Rectangle.
Figure 2.25: Duplicating a structure
A
B
O
O
O
O
Figure 2.23: Selecting a structure
O
3. Press and hold the Ctrl or option key.
TIP: Just a reminder that instructions of this type give
the PC function first, followed by the equivalent Mac
function.
NOTE: When you create a copy as shown above you can
drag it anywhere in the document window. If you want the
copy to remain aligned with the original, hold Shift while
dragging.
Modify the duplicated structure:
.
1. Click the Solid Bond tool
2. Point, in the copied structure, to the atom
shown in Figure 2.26 A and click.
Figure 2.26: Adding more bonds
A
O
B
O
The hand pointer with a plus sign indicates that
you are in the duplication mode of a selection
tool.
Figure 2.24: The duplication hand icon
O
4. Drag the Selection Rectangle to the right.
As you begin drag, a copy of the structure
appears and the selection box is not visible.
The original structure remains in its position.
Release the mouse button when the copy is
clear of the original.
Add several bonds to a single atom:
1. Point to the atom shown in Figure 2.27 A.
2. Click the atom three times, allowing a pause
between each click.
NOTE: If you click too fast, the click is interpreted
either as a double-click, which opens a text box or a
triple-click, which duplicates your last atom label.
Figure 2.27: Adding multiple bonds to an atom
A O
B O
Create another atom label, this time using HotKeys. HotKeys are keys on your keyboard that are
linked to specific atom labels. For more information about HotKeys, see “Labeling Atoms with
HotKeys” on page 60.
1. Point to the atom shown in Figure 2.28 A.
ChemDraw 10
Tutorials
Overview
•
27
2. Type O or o.
Figure 2.30: Moving a structure
Figure 2.28: Adding an atom label with a HotKey
O
A
B
O
O
O
Administrator
OH
When you use HotKeys that represent a single element, the correct number of hydrogen atoms is
added to the label.
Align the structures:
1. Select both structures with the Lasso or Marquee.
2. Point to Align on the Object menu, and click
the T/B centers command.
You structures should appear as shown in Figure
2.29.
OH
Add arrows to the reaction scheme.
to display the Arrow
1. Click the Arrow tool
palette.
NOTE: The triangle in the lower right corner of the
Arrow icon indicates it contains a palette.
2. Holding the mouse button down, move the
mouse to the palette title bar, then release the
mouse button.
Figure 2.31: Dragging a palette
Figure 2.29: Tutorial intermediate status: two structures
O
O
correct cursor
position for
dragging a palette
OH
In the following steps, you use a different method
for selecting structures and separate the structures
to make room for an arrow.
.
1. Click the Marquee tool
NOTE: Alternatively, you can select the Lasso tool
and hold Alt or option to use the Marquee tool.
The palette becomes a floating tool bar. Drag
the palette to the location you want.
3. Click the third arrow from the left in the top
row.
Figure 2.32: Selecting an arrow
The last object drawn is selected.
Drag the selection to make room for an arrow:
• Press Shift to maintain the alignment of the
structure and drag the Selection Rectangle to
the right.
28 •
Tutorials
CambridgeSoft
Overview
4. After the arrow is selected, close the Arrows
palette.
NOTE: The arrow you choose from the palette
becomes the default arrow type. To change the arrow
type, display the arrow palette and select the arrow type
you want.
Draw the arrow you selected:
1. Point after the first structure and drag the
arrow toward the second structure.
O
OH
Use the Text tool to add line formula or other captions for representing reagents and reactions.
Insert text in the drawing:
.
1. Click the Text tool
2. Point above the arrow. A text insertion point
appears. When you have positioned the text
pointer where you want it, click to create a text
box.
3. Type OH.
Figure 2.34: Adding a caption
O
OH
O
OH
TIP: If you want to realign the caption, use a selection
tool to drag the caption.
If Show Chemical Warnings is turned on
OH
(the default) a red box will appear around
the OH label as soon as you change tools or open
another text box indicating an error. Ignore this for
now.
Add a charge symbol using the specialized symbols
available in the Chemical Symbols tool palette:
1. Click the Chemical Symbol tool
.
ChemDraw 10
Figure 2.35: Selecting a symbol
3. Point to the center of the OH label. Moving the
cursor slightly right or left will cause either the
O or the H to be selected.
4. With the O selected, drag the charge symbol
around the atom to the desired position.
Figure 2.33: Adding an arrow to a drawing
O
2. Holding the mouse button down, select the circled negative charge symbol, as shown in
Figure 2.35.
Figure 2.36: Adding a symbol
A
OH
B
OH
Objects added from the Chemical Symbols palette
are associated chemically with the structure they
are closest to. Note that the red valence error
warning disappeared when you added the minus
charge. To show this, try dragging the minus sign
around to the other oxygen atoms in the drawing.
What happens? Don’t forget to put it back when
you’ve finished experimenting.
Some objects, such as arrows, are not associated
automatically. You can manually group objects
using the Group command. You can then select
the grouped objects to manipulate or move them
together.
To group objects:
1. Click the Marquee tool.
2. Do one of the following:
• Draw a box around the arrow, caption and
symbol to select them.
• Click the arrow, then hold the shift key
down while you click the OH caption and
the charge symbol.
Tutorials
Overview
•
29
2. Press the Enter or Return key to insert a new
line.
3. Type 2 moles.
Figure 2.37: Selecting multiple objects
Administrator
OH
Figure 2.40: Adding a caption with two lines
O
O
2-propanone
2-propanone
2 moles
The Shift key allows you to add objects to a
selection without deselecting other objects.
NOTE: If you click a selected object while holding
Shift, that object is deselected.
3. Click the Group command on the Object
menu.
Figure 2.38: Grouped objects
Create an aligned caption for the other structure.
1. Press the Tab key to create another Text box
that is aligned adjacent to the first.
Figure 2.41: Aligning a second textbox
O
OH
NOTE: You can still select individual objects within
a group by clicking them.
Use the Text tool to create a caption containing the
name and amount of reactant, and center the caption under the structure.
1. Click the Text tool
.
2. Point below the first structure.
3. Click to create a text box. The default cursor is
flush left.
4. Click the Centered command on the Text
menu.
The cursor moves to the center of the text box.
Figure 2.39: Centering text in the textbox
A
O
B
Type the caption:
1. Type 2-propanone.
30 •
Tutorials
O
C
O
2-propanone
2 moles
NOTE: You can use the Tab key in the caption mode
of the text tool to create multiple aligned captions with
the same font, font size, style, and justification as the
previous caption.
2. Type 4-hydroxy-4-methyl-2-pentanone, press
the Enter or Return key, and type 1 mole.
If your captions are not aligned properly beneath
the structures you can move them using a selection
tool.
1. Click a Selection tool (Lasso or Marquee).
The text box is automatically selected because
it is the last object drawn.
NOTE: The object that is automatically selected is set in
the Preferences dialog box.
2. Press the Left or Right Arrow key to center the
caption beneath its structure. This method
maintains the alignment created by the Tab
key.
CambridgeSoft
Overview
To complete the drawing, add a shadowed box
around the scheme:
1. Click the Drawing Elements tool
.
2. Select the shadowed box from the palette of
drawing elements.
Figure 2.44: Tutorial 2: Intermediate structure with
arrows
OOH
Figure 2.42: Shadowed box drawing element
Select Rectangle 150 dpi
3. Point to the upper left corner of the reaction
scheme. Hold the down the mouse button and
drag diagonally downward to the right to draw
the box.
Figure 2.43: Adding a drawing element
O
OH
O
OH
2-propanone
2 moles
4-hydroxy-4-methyl-2-pentanone
1 mole
Save and close the document:
1. Click the Save command on the File menu.
Your document is saved.
2. Click the Close command on the File menu.
Tutorial 2: Drawing an
Intermediate
In this tutorial you will draw the following intermediate structure starting from a ring and add arrows
with customized shapes using the Pen tool.
Create a new ChemDraw Document:
1. Click the New Document command on the File
menu.
2. Click the Save As command on the File menu.
3. Type tut2.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Draw a ring:
1. Click the Cyclohexane Ring tool
.
2. Point in the document window. The Cyclohexane cursor
appears.
3. Click to add a ring.
Figure 2.45: Using the cyclohexane ring tool
Delete an atom and its bonds from the ring:
1. Click the Eraser tool
.
2. Point to the atom shown in Figure 2.46 A.
3. Click the atom.
Figure 2.46: Erasing an atom
A
B
NOTE: You can delete a bond individually by pointing at
the center of the bond and clicking.
You can also drag the eraser to make multiple deletions.
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31
Administrator
Add a bond:
1. Click the Solid Bond tool
.
2. Point to the atom shown in Figure 2.47.
3. Click to add a bond.
The OH label changes to O–.
Figure 2.51: Changing OH to O – with a HotKey
O-
Figure 2.47: Adding a bond
Add second and third bonds:
1. Point to the atom shown in Figure 2.48, and
click twice (slowly) to add two more bonds.
Figure 2.48: Adding two bonds to an atom
Complete the intermediate structure by adding
another OH:
1. Point to the atom shown inFigure 2.52 A.
2. Do one of the following:
• Type the letter o.
• Double-click the atom to open a text box,
and type OH.
Figure 2.52: Completing the intermediate structure
A OB OOH
Create a double bond. This is a different method
than the one used in the first tutorial:
1. Point to the bond shown in Figure 2.49and
click.
The double bond will initially form to the
inside. Click twice more to move it to the outside, as shown in Figure 2.49 B.
Figure 2.49: Creating a double bond.
A
B
Next you will add arrows to indicate electron flow.
The first arrow will demonstrate the new adjustable Arrows tool. The others will be created with
the Pen tool.
Add an arrow with the arrows tool:
1. Choose an upward curved arrow from the
Arrows palette.
Figure 2.53: Selecting an arrow
Add an atom label. This step will expand on your
HotKeys knowledge from Tutorial 1.
1. Point to the atom to label shown in Figure 2.50
and type the letter o.
Figure 2.50: Adding an atom label with a HotKey:
A
B OH
2. Without moving the cursor, type a “-” (minus).
32 •
Tutorials
2. Point near the double bond where you want to
indicate the start of electron flow.
CambridgeSoft
Overview
3. Drag to the right. Don’t worry about the size of
the arrow right now, just make it approximate.
Figure 2.56: Drawing custom arrows
O-
O-
Figure 2.54: Dragging an arrow
OH
OH
O-
O-
OH
OH
4. Point to the arrow.
Adjustment handles appear at the ends and in
the middle.
5. Drag the center up to decrease the curve. You
may also drag the ends or the point-width
adjustment handles to adjust the arrow as necessary.
Refine the shape of the arrow:
1. Point to the handle at the lower end. You
should see a plain hand without the plus sign.
2. Drag up to the right, as shown in Figure 2.57 A.
This creates a tangent line that adjusts the curvature.
3. Point to the end and drag it to the correct location.
Figure 2.57: Adjusting a curve
A
B
Figure 2.55: Adjusting an arrow
OOH
O-
OOH
OH
4. Add an arrow head. Click the Full Arrow at End
command on the Curves menu.
Figure 2.58: The Curves menu
The remaining arrows are created with the Pen
tool.
To create a customized arrow using the Pen tool.
.
1. Select the Pen tool
2. Starting just to the right of the O – atom label,
drag upward and to the right. Release the
mouse button.
The hand with a “+” cursor indicates that you
are in the editing mode of the Pen tool.
3. Position the cursor where you want the arrowhead to appear, and click.
ChemDraw 10
TIP: You may select more than one option, as long as
they do not conflict. For example, you may specify
arrows at both start and end.
Tutorials
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33
5. Press Esc when you are finished.
TIP: To edit a curve you have finished drawing, select
it with a selection tool first, then click the Pen tool.
Administrator
6. Create the remaining arrow as described above
to complete the intermediate as shown below.
Figure 2.59: Tutorial 2: final drawing
5. Click Save.
Create a ring:
1. Click the Cyclohexane Ring tool
.
2. Point in an empty area of a document window.
3. Click to add a ring.
Figure 2.61: Drawing with the ring tool
OOH
NOTE: If you want to magnify the entire document so you
can see arrows or other objects that are in small places, choose
Magnify from the View menu.
Save and close the document:
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
Fuse a second ring to the first:
1. Point to the center of lower right bond in the
ring.
2. Click to fuse another ring.
Figure 2.62: Fusing rings
Tutorial 3: Using Rings
In this tutorial you will draw more complex structures by using rings.
Figure 2.60: Tutorial 3: Using ring structures
O
CH
Fuse a third ring:
1. Point to the bond shown in Figure 2.63.
2. Click to fuse another ring. Your document
should contain the structure shown in Figure
2.63 B.
Figure 2.63: Fusing a third ring
A
Create a ChemDraw Document:
1. Click the New Document command on the File
menu.
2. Click the Save As command on the File menu.
3. Type tut3.cdx in the appropriate text box.
4. Select a folder in which to save the file.
34 •
Tutorials
B
Fuse a fourth ring:
1. Point to the bond shown below.
2. Click to fuse another ring.
CambridgeSoft
Overview
Figure 2.64: Adding a fourth ring
Remove atoms and their bonds from the ring using
the Eraser tool:
1. Click the Eraser tool
.
2. Point to the atom shown in Figure 2.65.
A highlight box appears on the atom to be
removed.
3. Click to delete the atom and its bonds.
Add double bonds to the structure. In Tutorial 1
you turned a single bond into a double bond by
dragging over the bond. In Tutorial 2, the method
of clicking on the single bond was introduced.
Here, you will learn two more methods.
1. Click the Solid Bond tool
. (Actually, any
bond tool will do.)
2. Point to the bond indicated in Figure 2.67.
3. Type the number 2 to change the single bond
to a double bond.
TIP: The numbers 1-4 are bond order HotKeys.
Figure 2.67: Creating a double bond with a HotKey
Figure 2.65: Removing atoms and bonds with the
eraser tool
Add another double bond:
1. Point to the bond shown below.
2. Right-click, point to Double on the Bond Context menu, and choose Plain.
4. Click each of the atoms shown below to delete
the bonds.
The resulting structure is shown in Figure 2.66.
Figure 2.68: Creating a double bond from the context
menu
Figure 2.66: Creating the final skeleton structure
Realign the double bond so it is centered:
1. Point to the center of the upper double bond.
2. Right-click, point to Bond position, and choose
Centered.
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35
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
Figure 2.69: Centering a double bond
Administrator
Tutorial 4: Fischer
Projections
Add a carbon atom label:
1. Point to the atom shown in Figure 2.70.
Figure 2.70: Adding an atom label with a HotKey
This tutorial demonstrates creating a Fischer projection of glucose (shown below) by drawing a linear series of bonds. You can also create the same
drawing using a template. It also demonstrates the
use of standard document Style sheets (Windows)
or Sationery Pads (Mac).
Figure 2.72: Tutorial 4: Fischer projections
CH
CHO
HFischer
Glucose
HO70%
2. Type the c key on your keyboard. Note that the
Hotkey assigned to the atom label C is the
lower case letter. Typing an uppercase C will
create the atom label Cl.
The CH atom label appears with the correct
number of hydrogen atoms.
Add an oxygen atom label to complete the structure:
1. Point to the atom shown in Figure 2.71.
2. Type the o key on your keyboard. By default,
both upper and lower case O Hotkeys are
assigned to the atom label O.
Figure 2.71: Completing the drawing
O
CH
Save and close the document:
36 •
Tutorials
CH
OH
H
H
OH
H
OH
CH 2 OH
1. Point to Open Special on the File menu, and
choose ACS Document 1996.
Special Documents are Style sheets or Sationery Pads. They allow you to have pre-configured settings for different tasks.
NOTE: In this example, the ACS template provides the
required settings for structures to be published in all ACS
journals:
• One-column layout (Page Setting)
• Bonds with a Fixed length of 0.2 inches
(Drawing Setting)
• Atom Labels in 10 point Arial or Helvetica font (Text
Setting)
2. Click the Save As command on the File menu.
3. Type tut4.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Draw the first bond:
CambridgeSoft
Overview
1. Click the Solid Bond tool
.
2. Point in the document window. Drag downward vertically to draw the first bond.
3. Point to the lower atom, and drag downward
again to draw the second bond.
The red wavy box appears because Show
Chemical Warnings flags colinear bonds. You
can ignore it, or turn off warnings from the
View menu.
4. Repeat step 3 three more times to draw a total
of five bonds.
Figure 2.73: Drawing the backbone
A
B
C
D
Figure 2.74: Adding horizontal bonds to the backbone
A
B
C
D
E
Add labels to C1 and C6:
1. Select the Text tool.
2. Click the C1 atom to create a text box, and type
CHO.
3. Click the C6 atom, and type CH2OH.
Figure 2.75: Adding atom labels
CHO
NOTE: When you drag the pointer along the length of the
bonds, the pointer alternates between an arrow and a cross.
The arrow indicates you are pointing over the center of a bond,
and the cross indicates you are pointing to an atom.
Add horizontal bonds to the second atom in the
string of bonds you created:
1. Point to C2 and click the atom to add a perpendicular bond.
Note that the red wavy box disappears as soon
as you add a bond.
2. Click again to add a horizontal bond in the
opposite direction.
3. Repeat steps 1 and 2 with each successive backbone carbon until all horizontal bonds are
added.
CHO
CH2OH
Add the repeating labels for the hydrogens and
hydroxyls:
1. Click the atom shown in Figure 2.76 A and type
the letter H.
2. Double-click each of the other atoms labeled as
hydrogen in Figure 2.76 B.
TIP: Double clicking with the text tool repeats the last
label.
Figure 2.76: Adding repeating atom labels
B
CHO
CHO
A
H
H
H
H
H
CH2OH
ChemDraw 10
CH2OH
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37
Administrator
3. Click one of the remaining atoms and type
OH.
4. Double-click the remaining atoms to repeat the
label.
Figure 2.79: Fischer projection with analysis
CHO
H
HO
OH
H
Figure 2.77: Completing the drawing
CHO
H
OH
H
H
H
CHO
H
OH
HO
H
H
CH2OH
H
OH
OH
CH2OH
View the basic properties of the structure you drew
and paste the information into your document:
1. Click a selection tool to automatically select the
last structure drawn. If the structure is not
selected, double-click the structure.
2. Click the Analysis Window command on the
View menu.
The Analysis window appears. You can drag
the window to any position.
Figure 2.78: The Analysis window
3. Click Paste to paste the information as a caption below the structure.
H
OH
H
OH
CH2OH
C6H12O6
Exact Mass: 180.06
Mol. Wt.: 180.16
m/e: 180.06 (100.0%), 181.07 (7.1%), 182.07 (1.4%)
C, 40.00; H, 6.71; O, 53.29
Save and close the document:
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
Tutorial 5: Perspective
Drawings
In this tutorial you will learn how to create a perspective drawing by creating a model of α -D-glucose as a Haworth projection.
NOTE: This tutorial was written before the Structure Perspective tool was added to the ChemDraw toolbar, to demonstrate how to create perspective drawings without such a tool.
If you want to use the Structure Perspective tool for this tutorial, distort the ring before adding any bonds. Otherwise, the
tutorial is the same.
Figure 2.80: Tutorial 5: Perspective drawings
CH2OH
O
OH
OH
OH
OH
Create a new document using the ChemDraw
default style:
38 •
Tutorials
CambridgeSoft
Overview
1. Point to Open Special on the File menu, and
choose the New Document command.
NOTE: If you are doing the tutorials in order,
ChemDraw will remember that your last drawing used
the ACS style sheet, and open that as the default.
Step 1 resets the default to New Document.
2. Click the Save As command on the File menu.
3. Type tut5.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Draw a ring:
1. Click the Cyclohexane Ring tool
.
2. Point in an empty area of a document window.
3. Click to add a ring.
Rotate the ring:
1. Click the Select All command on the Edit menu
(or type Ctrl+A).
2. Drag the Rotation handle to the right about 30
degrees. The amount of rotation is displayed
on the screen and in the Info window.
Figure 2.81: Rotating the structure
NOTE: The cursor changes to a curved double-sided arrow
to indicate the rotation mode of a selection tool is activated.
Even though Fixed Angles is on, the angle is not
constrained. The Fixed Angles feature constrains
angles only when they are being drawn. For example, if you created this ring by dragging instead of
clicking, the angle would be constrained when
Fixed Angles is on.
Change cyclohexane to tetrahydropyran:
1. Click outside the structure to deselect it.
ChemDraw 10
2. Point to the atom indicated in Figure 2.82, and
type the lower case letter o.
Figure 2.82: Adding an atom label with a HotKey
O
Add vertical bonds:
.
1. Click the Solid Bond tool
2. Point to the atom shown in Figure 2.83 and drag
upward to create a bond.
3. Point to the same atom, and drag downward to
create another bond.
Figure 2.83: Adding a pair of vertical bonds
O
O
O
4. Repeat this procedure three more times, adding
the pairs of vertical bonds shown in Figure 2.84.
Figure 2.84: Repeating the procedure
O
The final pair of vertical bonds has to be drawn
slightly differently:
1. Drag up from the last remaining carbon atom
to form a bond.
2. Point to the atom shown below.
For the final downward bond, you must turn
Fixed Lengths off. Otherwise, the bond will be
joined to the upward bond of C3.
3. Hold down the mouse button, press the Alt or
option key, and drag downward from C5. Stop
dragging about half the distance to the upward
bond on C3.
Tutorials
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39
Figure 2.85: Adding the final pair of bonds
O
Administrator
O
1. Select the Solid Bond tool, point to the atom
shown in Figure 2.87 A and double-click to
open a text box.
2. Type OH, move the pointer to the next atom as
shown, and triple-click to repeat the atom label.
Figure 2.87: Adding the OH labels
O
O
OH
Distort the structure to change its aspect ratio to
give the perspective of viewing the structure along
the Z-axis.
1. Click a selection tool, and select the entire
structure.
2. Drag the bottom center resize handle upwards
until you have distorted the structure to about
50%, as shown on the screen or in the Info
window.
Figure 2.86: Distorting the structure
O
OH
OH
OH
OH
TIP: If you find it difficult to place the labels because
of the size of the drawing, choose Magnify from the
View menu.
NOTE: The third OH from the right is on the bond
extending up from C3, not the bond extending down
from C5.
Add the CH2OH label:
O
1. Triple-click the upper atom of C5.
2. Press the Enter or Return key to open the
atom label text box. Type CH2 before the OH.
Figure 2.88: Adding the CH2OH label
CH2OH
OH
O
O
OH
OH
OH
OH
OH
OH
NOTE: Even though you took precautions to make one of
the bonds shorter than the others, you might still have a problem with proximity after distorting the structure. If this happens, delete the upward bond on C3 and redraw it, holding
the Alt or option key to cancel fixed bond length.
Next, you create OH labels. You can use the
repeating bond label technique in Tutorial 4, or use
HotKeys. For the HotKey method, just point and
type “o”. The Text tool method is repeated here,
with a slight variation.
40 •
Tutorials
OH
OH
OH
NOTE: When used with a bond tool active, Enter or
Return is a Hotkey that opens a text box for the last
atom labeled.
Change the type of the front bonds:
.
1. Click the Bold Bond tool
2. Point to the center of the bond shown below.
3. Click to change to the new bond type.
The cursor changes to a bold arrow as you
point at the bond.
CambridgeSoft
Overview
Figure 2.89: Adding a bold bond
CH2OH
Figure 2.91: Tutorial 7 Newman projection
CH2OH
O
O
OH
OH
OH
OH
OH
OH
OH
OH
4. Click the Bold Wedge bond tool
.
5. Click each of the ring bonds adjacent to the
bold bond.
For each bond, point slightly off center in the
direction that you want the wide end of the
wedge to be oriented and click.
TIP: If you move the pointer too far, the highlight box
disappears. Choose Magnify from the View menu if you
find it difficult to place the pointer.
NOTE: If the wedge is pointed in the wrong direction,
click the bond again to flip its orientation.
The resulting structure is shown in Figure 2.90.
Figure 2.90: a-D--glucose, Haworth projection
CH2OH
O
OH
OH
OH
Create a ChemDraw Document:
1. Click the New Document command on the File
menu.
2. Click the Save As command on the File menu.
3. Type tut6.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Create the first structure:
1. Click the Solid Bond tool
.
2. In the document window, drag downward to
create the first bond.
3. Point at the lower atom and click to add a second bond.
4. Continue pointing at the same atom and click
again to add a third bond.
Figure 2.92: Creating the initial structure
OH
Save and close the document:
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
Tutorial 6: Newman
Projections
This tutorial demonstrates how to draw a Newman
projection. You can also create the same drawing
using a template.
ChemDraw 10
Duplicate the structure:
1. Click a selection tool.
The last structure you drew is automatically
selected.
2. Create a duplicate by holding the Ctrl or
option key while dragging the Selection rectangle upward to the right of the original.
The selection box disappears while you are
dragging.
Tutorials
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•
41
Figure 2.93: Creating a duplicate structure
Administrator
The size of the orbital is constrained just like
bonds are. The constraint is based on a percentage of the Fixed Length setting in the on
the Drawing Settings tab of the Document settings dialog box.
Figure 2.96: Adding an orbital
Add a bond between the duplicated structures:
.
1. Click the Solid Bond tool
2. Point to the central atom of the lower fragment.
3. Drag to the central atom of the upper fragment.
NOTE: When connecting existing atoms, the Fixed
Length and Fixed Angles commands are ignored.
4. Release the mouse button when the highlight
box over the central atom appears.
Figure 2.94: Connecting the structures
In this step, you will use the Orbital tool to draw
the hollow circle that is particular to Newman Projections, rather than an orbital.
1. Click the Orbital tool, and select the
unfilled s orbital.
NOTE: Orbitals are not automatically grouped with
the closest structure. If you want to group the orbital
with the existing structure so you can move them as a
unit, choose Group from the Object menu.
Move part of the structure to the front to overlap
the orbital:
1. Click the Marquee tool
.
The orbital is selected. Click in the worksheet
to deselect it.
2. Point above the structure and drag around the
upper fragment to select the three bonds. Do
not select the bond connecting the two fragments. You can Shift+click on each bond separately, if that is easier.
TIP: The new selection box makes it easy to tell which
bonds are selected – selected bonds have a dot on them.‘
Figure 2.97: Selecting the fragment to overlay
Figure 2.95: The Orbitals tool palette
2. Point to the left center carbon and drag outward.
42 •
Tutorials
Rotate the selection:
CambridgeSoft
Overview
1. Double-click the rotation handle to open the
Rotate dialog box.
2. Type 180 in the text box, select degrees CW,
and click the Rotate button.
Figure 2.100: Overlaying the structure
Figure 2.98: The Rotation dialog box
RotateObjectsDB 150 dpi
Figure 2.99: After rotation
NOTE: If chemical warnings are turned on, you will
see a red warning box when you overlay the structure,
because the center atoms are “on top of ” each other.
3. Release the mouse button and click outside the
Selection Rectangle to deselect the structure.
Figure 2.101: Completed Newman projection
3. With the rotated bonds still selected, change
the layering of the structure so that the selection is in front by clicking the Bring to Front
command on the Object menu.
There is no visible change when you do this.
Orient the front part of the structure to create a
Newman projection.
1. Point within the Selection Rectangle until the
pointer changes to a hand.
2. Drag the selection until the central atom of the
selection is centered within the orbital.
ChemDraw 10
Save and close the document:
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
Tutorial 7: Showing
Stereochemistry
This tutorial demonstrates using Stereochemistry
markers and the flip command.
Create a new document.
1. Click the New Document command on the File
menu.
2. Click the Save As command on the File menu.
3. Type tut7.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
Draw the following structure:
Tutorials
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43
Figure 2.102: S-(2,3)-dimethylbutanoic acid
Figure 2.106: adding a double bond
O
Administrator
OH
1. Click the Solid Bond tool
.
2. The first three steps are identical to the previous tutorial: create an isobutane structure.
Figure 2.103: Beginning the structure
3. Point to the atom shown in Figure 2.104 and
type the number 9.
When used with a bond tool, the number 9 is a
HotKey for sprouting two bonds. The number
8 sprouts three bonds.
Figure 2.104: Sprouting bonds with a HotKey
4. Point to the bond shown in Figure 2.105, and
type 9 again to sprout two more bonds.
Now, the lower bond has to be changed to a solid
wedge bond. In tutorial 5 you were introduced to
the wedge bond tool. You can also use a HotKey.
6. Point to the bond shown in Figure 2.107 and do
one of the following:
• Select the Wedge Bond tool, and click the
bond.
• Point to the bond and type the letter w.
Figure 2.107: Adding a wedge bond
Add atom labels.
1. Double-click the atom shown below, and type
NH2 in the text box that appears. Press the Esc
key when you finish.
2. Add the O and OH with the text box or the
HotKey o.
Figure 2.108: Adding the atom labels
O
Figure 2.105: Repeating the bond sprouting
OH
NH 2
5. The upper bond on the right has to be made
into a double bond. If you’ve gone through all
the tutorials, you’ve learned four different ways
of doing that. Use your preferred method.
44 •
Tutorials
Display the stereochemical markers.
1. Select the entire structure with the Lasso or
Marquee.
2. Click the Show Stereochemistry command on
the Object menu.
The S marker appears.
CambridgeSoft
Overview
Figure 2.109: Showing stereochemistry
O
4. With the structure selected, click the Rotate
180° Vertical command on the Object menu.
Figure 2.111: Vertical rotation
(S)
NH 2
3. Select the structure and click the Flip Horizontal command on the Object menu.
The R marker appears.
Figure 2.110: Flipping stereochemistry
O
HO
NH2
OH
(R)
HO
(R)
O
The Wedged bond becomes hashed and the
(R) stereochemistry is preserved.
Save and close the document:
1. Click the Save command on the File menu.
2. Click the Close command on the File menu.
NH2
ChemDraw 10
Tutorials
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45
Administrator
46 •
Tutorials
CambridgeSoft
Overview
Chapter 3: Drawing Chemical Structures
Overview
This section describes the use of bond and ring
tools used to create chemical structures.
ChemDraw provides the following tools for drawing chemical structures:
• Bond tools
• Ring tools
• An acyclic chain tool
• Text tool
These are the basic building tools for creating and
labeling structures. In addition to these basic building tools, ChemDraw gives you two selection
tools, a Marquee to select large contiguous areas
and a Lasso for difficult shapes, and an Eraser tool.
The remaining tools are for more advanced features, described in other sections of this manual.
Especially useful when making multiple changes to
structures, ChemDraw’s automatic error detection
flags errors that you might otherwise overlook. See
“Automatic Warnings” on page 55 for more information.
Drawing Bonds
The Main Tools palette contains the bond tools
shown below:
ChemDraw 10
Figure 3.112: Multiple bond tools
Solid Bond
Multiple Bonds
Dashed Bond
Hashed Bond
Hashed Wedged Bond
Bold Bond
Bold Wedged Bond
Hollow Wedged Bond
Wavy Bond
Drawing Constrained Bonds
You can draw any bond length or create any angle
relative to the X-axis. Use the Info Window to
display the bond length and angle as you drag the
bond.
However, it is generally more useful to draw bonds
that are constrained to a fixed length and a fixed
angle relative to the X-axis. This is the default
setting.
Drawing with Fixed Lengths
To draw bonds that are constrained to a fixed
length:
1. Click the Fixed Lengths command on the
Object menu.
Drawing Chemical Structures
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47
Administrator
A check mark appears next to the Fixed
Lengths command indicating that it is selected.
All bonds are constrained to the fixed length
specified on the Drawing Settings tab of the
dialog box.
2. Click a bond tool.
3. Drag from one end of the bond to the other.
The Info Window displays the bond length.
You can use the tools on the Multiple Bond palette
to create the following multiple bonds:
Table 7: Multiple bond types
Double
Bold Double
Tautomeric
Drawing with Fixed Angles
To draw bonds with constrained angles that are
multiples of 15 degrees relative to the X-axis:
1. Click the Fixed Angles command on the Object
menu.
A check mark appears next to the Fixed Angles
command indicating that it is on.
2. Click a bond tool.
3. Click in a document window.
The bond appears at a standard 120° bond
angle (relative to the x-axis).
4. Using a selection tool, move the end of the
bond to other angles.
The Info Window shows that the bond angle is
constrained to 15-degree increments.
Toggling Fixed Lengths and Fixed
Angles
If fixed lengths or fixed angles are selected, you
can temporarily deselect them. To suppress fixed
lengths and fixed angles, press the Alt or option
key as you drag the bond.
Multiple Bonds
The Multiple Bond tool on the Main toolbar
includes the palette shown in Figure 3.113.
Figure 3.113: Multiple bond palette
48 •
Drawing Chemical Structures
Aromatic
Double Either
Dative
Triple
Quadruple
TIP: You can also draw multiple bonds by right-clicking
over a bond and selecting the bond type from the shortcut
menu or by using the bond properties dialog box, or by using
HotKeys. For more information on the Bond Properties dialog box, see “Bond Properties” on page 90. For more information on HotKeys, see “Labeling Atoms with HotKeys” on
page 60.
Double Bonds
There are three ways to draw a double bond:
• Use the Double bond tool.
• Using the Solid, Dashed, or Bold bond tool,
click an existing single bond.
• Using any bond or selection tool, point to an
existing bond and type the HotKey ‘2’.
CambridgeSoft
Overview
Double Either Bonds
Dative Bonds and Wedged Bonds
To draw a double either bond select the double
either bond tool from the Multiple Bonds palette,
or:
1. Draw a bond using the Wavy Bond tool.
2. Point to the center of the bond and click to create a double bond
3. Click again to create a double either bond.
Dative bonds and wedged bonds are drawn with a
fixed orientation in a document window.
To draw a dative bond:
1. Click the Dative Bond tool.
Figure 3.114: Dative bond tool
Triple Bonds
You can draw a triple bond by drawing another
single bond on top of a double bond. All bonds in
a triple bond are solid bonds.
To draw a triple bond select the triple bond tool
from the Multiple Bonds palette, or:
1. Click any bond tool.
2. Drag from one end of an existing double bond
to the other.
Quadruple Bonds
To draw a quadruple bond select the quadruple
bond tool from the Multiple Bonds palette, or:
1. Click any bond tool.
2. Drag from one end of an existing triple bond to
the other.
The triple bond changes to a quadruple bond.
To change a quadruple bond into a single bond:
1. Click any bond tool.
2. Drag from one end of an existing quadruple
bond to the other.
The quadruple bond changes into a single bond
corresponding to the tool used to draw over
the bond.
NOTE: You can also use the Eraser tool to reduce the bond
order. For more information, see “Changing the Bond
Order” on page 29.
ChemDraw 10
2. Drag from the positive to the negative end
(arrow head) of the dative bond.
Figure 3.115: Drawing a dative bond
drag direction
To draw a wedged bond:
1. Click one of the wedged bond tools.
2. Drag from the narrow end of the wedged bond
to the wide end of the wedged bond.
Figure 3.116: Drawing a wedged bond
drag direction
To change the orientation of the dative or wedged
bond, click the center of the bond using the matching bond tool.
Adding a Bond by Clicking
To add a fixed length bond:
1. Select a bond tool.
2. Click an atom.
A new bond is drawn and joined to the atom
you clicked.
Drawing Chemical Structures
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49
Figure 3.117: Adding a bond to an atom
Administrator
Bonds drawn by this method are always drawn
using the fixed length specified on the Drawing
Settings tab of the Document settings dialog box.
The angle that the deposited bond makes with its
nearest neighbor is equal to the Chain Angle set on
the Drawing Settings tab of the Document settings
dialog box. If this angle cannot be established, a
smaller angle is used.
Adding Bonds by Dragging
To control the orientation of bonds that you draw,
you can add bonds by dragging.
By using this dragging method for drawing the
bond, you can control the orientation of the other
end of the bond.
To add a bond by dragging:
1. Click a bond tool.
2. Point to an atom.
A highlight box appears over the atom indicating where the bond will be joined.
3. Drag from the atom at which you are pointing
in the direction you want the new bond to
extend.
A new bond is drawn, joined to the atom where
the highlight box appeared.
Figure 3.118: Adding a bond by dragging
Drawing Rings
Figure 3.119: Ring tools
Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Cycloheptane
Cyclooctane
Cyclohexane Chair (1)
Cyclohexane Chair (2)
Benzene
Cyclopentadiene
Drawing a Ring
To draw a ring, select a ring tool. When you point
in the document window, the pointer changes to a
ring tool pointer. The highlight box on the ring
tool pointer indicates the atom that is drawn first.
The bond directly below the highlight box is the
bond that is drawn first.
Figure 3.120: Ring tool pointer
First atom drawn
First bond drawn
Click in the document window. A ring appears,
centered around the pointer, and in the orientation
shown on the ring tool icon. To draw a ring in a
different orientation, drag the tool instead of clicking.
TIP: If Fixed Lengths is on when you draw a ring, the
length of each bond in the ring is automatically set to the fixed
length. If Fixed Angles is on, the angle the first bond in the
ring makes with the X-axis is restricted to 15-degree increments. For more information, see “Drawing Constrained
Bonds” on page 20.
If you click an atom, the ring is fused to that atom.
The Main Tools palette contains the following ring
tools that enable you to draw ring sizes and types:
50 •
Drawing Chemical Structures
CambridgeSoft
Overview
Figure 3.121: Adding a ring to an atom
Figure 3.124: Sprouting rings instead of spiro linkage
If you click a bond, the ring is fused to that bond.
Figure 3.122: Adding a ring to a bond
Drawing Cyclohexane Chair
Rings
If you click an atom in a ring, a spiro linkage is
formed.
Figure 3.123: Adding a spiro linkage
You can draw Cyclohexane chair rings in two
orientations: horizontal and vertical.When you
draw a cyclohexane chair ring by clicking, the chair
is drawn in a horizontal orientation.
To draw a cyclohexane chair ring in some other
orientation, drag with the chair tool to the orientation you want.
Figure 3.125: Drawing a cyclohexane ring – dragging and clicking
NOTE: This behavior is controlled on the Building/ Display tab of the Preferences dialog box. See “Setting Preferences” on page 197 for more information.
You may change this default behavior to sprout a
bond instead.
1. Select Preferences on the File (Mac: ChemDraw) Menu.
2. On the Building/Display tab, check the box
next to Sprout Rings Instead of Spiro When
Clicking.
ChemDraw 10
Horizontal Orientation
Vertical Orientation
Drawing Resonance Delocalized
Rings
With the exception of the cyclohexane chairs, any
of the ring tools can be used to draw a resonance
delocalized form.
To draw a resonance delocalized ring:
1. Click a ring tool.
2. Press the Ctrl or command key and drag or
click to draw the ring.
A circle appears inside the ring.
Drawing Chemical Structures
Overview
•
51
Figure 3.126: Drawing a resonance delocalized ring
and fixed angles switches on the Object menu, and
by the chain angle setting on the Object Settings
dialog box.
Administrator
NOTE: Modifying the Chain Angle value for an existing
object will have no effect on that object, but new bonds/chains
sprouted from it will sprout at the specified angle.
NOTE: The circle is automatically grouped with the ring
when drawn. For more information on grouping objects, see
“Grouping Objects” on page 112.
Drawing Cyclopentadiene and
Benzene Rings
The double bonds in the cyclopentadiene or
benzene ring tools can be drawn in either of two
forms.
When you draw a cyclopentadiene or benzene ring
a double bond is drawn first (see Figure 22). The
Cyclopentadiene and Benzene Ring tool pointers
indicate this orientation. To shift the orientation so
the first bond drawn is a single bond, hold down
the shift key as you click or drag in the structure
window.
Figure 3.127: Changing orientation with the shift key
First
bond
First
bond
To draw an acyclic chain:
1. Click the Acyclic Chain tool.
2. Drag in the direction you want the chain to
grow in a document window.
A number appears at the end of the chain indicating how many atoms you have drawn.
Figure 3.128: Drawing with the acyclic chain tool
When Fixed Lengths is on, the pointer on the
acyclic chain tool can be dragged to make any angle
relative to the X-axis. At a constant chain length,
the positions of the first bond and all subsequent
odd-numbered atoms depend on the direction you
drag. Before releasing the mouse button, this position can be changed by dragging in the opposite
direction. When Fixed Angles is on, the angle the
acyclic chain makes relative to the X-axis is
constrained to 15-degree increments.
Adding Chains
Orientation without
shift key
Orientation with
shift key
Drawing Acyclic Chains
Use the Acyclic Chain tool to draw long
hydrocarbon chains. The behavior of the
Acyclic Chain tool is affected by the fixed lengths
52 •
Drawing Chemical Structures
To add an acyclic chain to an existing atom:
1. Click the Acyclic Chain tool.
2. Point to the atom to which you want to attach
the chain.
3. Drag in the direction you want the chain to
grow.
CambridgeSoft
Overview
Figure 3.129: Adding a chain to a bond
Figure 3.131: Reversing chain direction
NOTE: If Fixed Lengths is off, use Ctrl+Alt or command+option to reverse chain direction. Fixed Angles
must be on to reverse direction.
Editing Bonds
To specify a chain length:
1. Click the Acyclic Chain tool.
2. Click an existing atom or an empty area in a
document window.
The Add Chain dialog box appears.
Figure 3.130: The Add Chain dialog box
You can modify the appearance of chemical
structures by:
•
•
•
•
•
Changing Bond Types
Changing bond alignment and orientation
Moving Atoms
Layering bonds
Changing the bond order
Changing Bond Types
To change a single bond from one type to another:
3. Type the number of bonds in the chain.
4. Click Add.
To add another chain of the same length anywhere
in a document window, Alt+click or
option+click an existing atom or an empty area
within the document window.
1. Click a bond tool.
2. Point at the center of an existing bond and
click.
Figure 3.132: Changing a bond type
Changing Chain Direction
To change the direction of the chain as you draw,
press the Ctrl or command key while drawing the
chain in the direction you want.
TIP: Make sure to release the mouse button before you
release the Ctrl or command key.
The bond that you click changes to the new
bond type.
You can also change the bond type using HotKeys,
see “Labeling Atoms with HotKeys” on page 60
Changing Double Bonds
To change one type of double bond to another:
1. Click the Bold, Dashed, or Solid Bond tool.
2. Point to one of the bonds in the double bond.
ChemDraw 10
Drawing Chemical Structures
Overview
•
53
Figure 3.133: Changing double bonds
• Above
• Below
Administrator
• Centered
3. Click the bond.
The double bond changes to the new bond
type. One of the bonds in the double bond is
always a solid or dashed bond.
NOTE: If you click a tautomeric bond (solid/dashed) a
second time with the dashed bond tool, you create an aromatic
double bond (dashed/dashed).
Editing Bonds With the Context
Menu
You can change an existing bond by right-clicking
or Control-clicking on it and selecting a different
bond type from the context menu.
Changing Orientation of Wedged
and Dative Bonds
When you draw or change a bond to a wedged or
dative bond, the orientation of the bond is chosen
appropriately.
To change the orientation, click the dative or
wedged bond with the tool used to create it.
The dative or wedged bond is changed to the
opposite orientation.
To change the alignment of a double bond:
1. Click the bond tool used to create the existing
double bond.
2. Do one of the following:
• Click the center of the double bond.
The alignment changes. Click the center of
the double bond again to change to the next
alignment.
• Right-click or Control-click, point to Bond
Position on the context menu, and choose
the alignment.
Moving Atoms With a Bond Tool
You can use any of the bond tools to move an
atom within acyclic or cyclic structures. You
cannot use a ring tool.
To move an atom in a chemical structure:
1. Click a bond tool.
2. Point at the atom to move.
A highlight box appears over the atom.
3. Shift+drag the atom.
Figure 3.135: Moving atoms
Figure 3.134: Changing bond orientation
COOH
COOH
H
HO
CH 3
H
HO
CH 3
Changing Alignment of Double
Bonds
The bonds in a double bond can have one of three
alignments relative to other bonds:
54 •
Drawing Chemical Structures
You can convert ring types by dragging one atom
on top of an adjacent atom. For example, you can
use this method if you want to convert a
6-membered ring into a 5-membered ring.
To convert ring types:
1. With a bond tool selected, point to an atom
and Shift+Drag.
CambridgeSoft
Overview
2. Release when one atom is on top of the other.
The bond between the atoms disappears.
Figure 3.136: Changing a ring type
NOTE: You can also move atoms using a selection tool.
For more information see “Moving Objects” on page 107.
Changing Bond Crossings
When one bond crosses another, white space is
used to indicate which bond is in front of the
other.
To change which bond is in front:
1. Click any bond tool.
2. Double-click the bond to bring it to the front.
Figure 3.137: Changing the bond layering
You can layer bonds using the Bring to Front and
Send to Back commands. For more information,
see “Front to Back Ordering” on page 193. You
can also change the bond crossing using HotKeys,
see “Labeling Atoms with HotKeys” on page 60.
TIP: To make changing the bond layering easier, magnify
the view. See “Changing Perspectives” on page 190.
Changing the Bond Order
You can reduce or increase the order of bonds in a
structure by using the Bond Properties dialog box
or with the shortcut menus as follows.
To reduce the bond order:
1. Point to the bond to change and Right-click or
Control-click.
ChemDraw 10
2. Choose the appropriate bond type from the
context menu that appears.
To use the eraser tool to reduce the bond order:
1. Select the Eraser tool.
2. Click a single, double, or triple bond.
The bond order is reduced by one.
To change the bond order using HotKeys, see
“Tutorial 3: Using Rings” on page 34.
Automatic Warnings
ChemDraw automatically checks for correct chemical syntax as you draw. If ChemDraw finds a
potential problem, a wavy red box is displayed
around the questionable object. The red box is displayed on screen only and does not print.
Displaying warnings is the default setting. You have
two options for not displaying them:
• Turn off the automatic warnings option.
NOTE: This setting applies to all open documents.
• Suppress warnings for a specific object.
To disable the automatic display of chemical
warnings, deselect the Show Chemical Warnings
command on the View menu.
To disable the automatic error checking on a specific object, right-click the object and deselect the
Display Warnings command on the context menu.
When Display Warnings is deselected for an object:
• Red boxes are not displayed for questionable
objects.
• Problems are reported by the Check Structure
command.
To view a description of the problem, do one of the
following:
• Point at the warning with the mouse to display
a tool tip that describes the error.
Drawing Chemical Structures
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•
55
Administrator
• Right-click on the warning and choose Explain
This Warning.
• Select the structure, and choose Check Structure from the Structure menu.
For more information, see “Checking Chemistry” on page 129.
and Object Settings” on page 200 for more
information. You may set different defaults for
captions and labels.
Figure 3.138: Caption text
OH
Warning Preferences
You can choose what Chemical Warnings will flag
in the Preferences dialog box. The option list
includes:
Table 4: Chemical Warnings
Valence and Charge errors
Isolated bonds
Unbalanced parentheses
Invalid isotopes
Unspecified stereochemistry Linear atoms
Caption Text
phenol
• Atom label text—Identify atoms and substructures by their chemical symbols and formulas.
Figure 3.139: Atom label text
Atom Label
Text
OH
Ambiguous stereochemistry Atoms near other
bonds
Stereobond between chiral
atoms
Miscellaneous
warnings
To select which types of chemical warnings to display:
1. Click the Preferences command on the File
menu.
2. Click the Display Warnings tab.
3. In the Chemical Warnings section, click the
types of warnings you want to display.
Creating Text
Use the Text tool to create captions and atom
labels.
• Caption text—Create annotations, chemical
names, chemical formulas, page titles, and
information in tables. Default text formats are
set in the Document Settings. See “Document
56 •
Drawing Chemical Structures
phenol
To change formatting for an individual caption or
label:
1. Select the text object with a selection tool.
2. Click the Object Settings command on the
Object menu.
The Object Settings dialog box opens.
3. Click the Captions or Atom Labels tab, as
appropriate, and change the setting.
The change affects on the selected caption or
atom label only.
The behavior of atom labels is controlled by the
Automatic Atom Label Alignment and Automatically Rectify Hydrogens in Atom Labels checkboxes
on the Building/Display tab of the Preferences dialog box. The default is to have both of these preferences selected.
CambridgeSoft
Overview
When Automatic Atom Labels is selected, the
alignment of atom labels will adjust according to
the positions of any bonds attached to the atom
label.
For example, a CH3 atom label entered at the left
end of a horizontal bond would reverse itself to
H3C.
When Automatically Rectify Hydrogens in Atom
Labels is selected, hydrogens will be added to or
removed from atom labels as necessary to preserve
standard valences when bonds are added or
changed.
You can use HotKeys to label atoms. For more
information see “Labeling Atoms with HotKeys”
on page 60.
NOTE: ChemDraw does not install its own fonts. If you
open a ChemDraw document containing fonts that are not
available on your computer, they are substituted with available fonts.
Coloring Text
You can color captions and atom labels before or
after they are typed, and as a whole or in part.
To color a caption or atom label:
1. Select the Text tool.
2. Click in the position where you want to place
the text.
3. Choose a color from the Color menu.
4. Type the caption or atom label.
To color individual characters:
1. Select part of an existing caption or atom label
using the Text tool.
2. Choose a color from the Color menu.
NOTE: Macintosh: Captions that contain multiple colors
change to the foreground color when rotated. However, all colors contained in the caption are printed.
To color several captions or atom labels at once:
1. Select the captions or labels using a selection
tool.
ChemDraw 10
2. Choose a color from the Color menu.
Creating Captions
To create a caption:
1. Click the Text tool
.
2. Point in an empty space in a document window.
A caption text box with a flashing insertion
point appears.
Figure 3.140: Caption text box
3. Type a caption.
The text box widens as you type to accommodate the caption.
4. To create a new line, press the Enter or return
key.
5. To close the text box, click outside the text box
or select another tool.
Entering Non-Roman Text
Use the Character Map for entering non-Roman
text. (See “Character Map” on page 19 for details.)
Any font available on the computer can be entered
into a label using the Character Map.
NOTE: Two-byte fonts such as Chinese may not work reliably with the Character Map.
Chemical Significance
By default, captions are considered to be chemically significant if possible. For example, if you create a caption like CH3OH, you will be able to attach
bonds to it (and it will be modified appropriately)
even though you intended it to be a label, not a
molecule. Moreover, its values are included in the
Analysis Window, which could be confusing. If
you try to label structures “A”, “B”, and “C”, the
“B” and “C” labels will be marked with a red box
because they have “incorrect valences”. You can
Drawing Chemical Structures
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•
57
Administrator
change this behavior for the entire document, or
for an individual label.
To change a single label:
1. Select the label with the Lasso or Marquee tool.
2. Right+click or Control+click in the selection.
3. Deselect the Interpret Chemically command
on the context menu.
To change the behavior of labels in the entire document, deselect the Interpret Chemically When
Possible option on the Captions tab of the Document Settings dialog box.
NOTE: You can verify the chemical significance of a caption using the Check Structure command after selecting it
with the Lasso or Marquee tool.
Editing a Caption
To open a caption for editing:
1. Click the Text tool
.
2. Point to a caption and click to open the text
box.
The caption text is highlighted.
3. To change all of the highlighted
text within an open text box, type the
new caption text over the highlighted
text.
• If not all the text is highlighted and you want
to select all of the caption text, click the
Select All command on the Edit menu.
• To change part of the caption
text, drag the insertion point
over a part of the caption, then type in the
new text.
The Caption text box appears around the
caption. The right side of the text box contains
a Resize handle.
Figure 3.141: Caption box resize handle
Resize handle
2. Drag the Resize handle.
The point at which the text wraps is adjusted as
you drag the Resize handle.
Ultra
Adding Analysis Data to a
Caption
You can add properties from the Analysis Window
to a caption created by Struct=Name. If autoupdate is on (see “Auto Update” on page 122), the
values will update as you modify the structure.
To add values to a label:
1. Point to the label.
2. Right-click, point to Analysis on the context
menu, and choose a property from the list.
The property appears in the label displaying the
current value.
TIP: You may need to update the window before you can see
the new value. If you don’t see it immediately, it will appear
with the next modification to the structure.
Figure 3.142: Displaying analysis data
o-xylene
Chemical Formula: C 8H10
Molecular Weight: 106.16
Changing the Caption Width
To edit the width of a caption:
1. Select a caption using the Text tool.
58 •
Drawing Chemical Structures
Creating Atom Labels
The default format options of any new atom labels
you create are specified in the Atom Labels tab of
the Document Settings dialog box. You may edit
CambridgeSoft
Overview
these options at any time. The settings affect the
current document only.
Figure 3.144: Editing an atom label
CH 2OH
Labeling Atoms With the Text
Tool
To place an atom label on an atom:
.
1. Click the Text tool
2. Point to an atom.
The pointer changes when it is positioned
correctly over an atom to indicate that you will
create an atom label rather than a caption.
3. Click the atom.
An Atom Label text box appears over the
atom.
Figure 3.143: Opening an atom label text box
2. Type the new atom label text over the highlighted text.
Deleting an Atom Label
To delete an atom label, leaving the underlying
bonds unchanged, do one of the following:
• Select the Eraser tool and click the atom label.
• With a selection, bond, or ring tool selected,
point to the atom label and press the spacebar,
Backspace, or Delete Key.
Labeling Atoms With a Bond or Ring
Tool
4. Type an atom label.
Numbers are automatically subscripted.
5. To close the text box, click outside the text box
or select another tool.
NOTE: You can use HotKeys to label an atom instead of
using the Text tool. You can also label atoms using Nicknames that are text representations of substructures. For
more information, see “Labeling Atoms with HotKeys” on
page 60 and “Using Nicknames” on page 81.
To avoid switching back and forth between tools,
you can label atoms with a bond or ring tool.
To label an atom using a bond or ring tool:
1. Select a bond or ring tool.
2. Point to an atom and double-click.
An atom text label appears over the atom.
Figure 3.145: Labeling an atom with a ring tool
Editing Atom Labels
To edit an atom label:
1. Click an existing label using the Text tool.
The highlighted atom label text appears within
the Atom Label text box.
ChemDraw 10
3. Type the text.
Automatic Labeling of Terminal
Carbons
You can set the default for document, or for a
structure or group of structures, to insert terminal
carbon labels.
To set the default for a document:
1. Click Document Settings on the File menu.
Drawing Chemical Structures
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59
Administrator
2. On the Atom Labels tab, check the box for
Show Labels On Terminal Carbons.
To set the default for a structure:
1. Create a structure, or several structures.
2. Select the structure(s). Right-click, and click
Object Settings from the context menu.
The Object Settings dialog box appears.
3. On the Atom Labels tab, check the box next to
Show Labels On Terminal Carbons.
To add or remove a single terminal carbon label,
point to the label and select or deselect the Show
Terminal Carbons command on the atom context
menu.
Hiding Implicit Hydrogens
By default, implicit hydrogen atoms are displayed.
To hide implicit hydrogens:
1. Click Document Settings on the File menu.
2. On the Atom Labels tab, check the box next to
Hide Implicit Hydrogens.
CAUTION
This feature is provided solely for those who need to produce
ISIS-compatible documents. Documents produced with
this setting will likely be unacceptable for publication.
To label several atoms with the same text using a
bond, ring, or Acyclic Chain tool:
1. Click the tool.
2. Triple-click an atom to repeat the previous
label.
Using the Text Tool With a Selection
Tool
The Text tool used in conjunction with a selection
tool enables you to perform additional edits, such
as simultaneously changing several captions or
atom labels. For more information about selection
tools, see “New Selection Box” on page 61.
You can toggle between the Text tool and a selection tool as follows:
• After using the Text tool, press Ctrl+Alt+Tab
or command+option+tab.
The last-used selection tool is selected.
To switch from a selection tool to the Text tool
when a caption or atom label is selected, press
Ctrl+Alt+Tab or command+option+tab.
The Text tool is selected and the text box is
opened for editing.
NOTE: Ctrl+Alt+Tab and command+option+tab will always toggle between the last
selection tool used and last other tool used.
Repeating an Atom Label
Labeling Atoms with HotKeys
You can repeat an atom label using the text, bond,
or ring tools.
To label several atoms with the same text using the
Text tool:
1. Click the Text tool.
2. Label a single atom.
3. Double-click another atom to repeat the previous label.
HotKeys™ is a major ChemDraw feature for rapid
labeling of atoms.
TIP: You can access HotKey Help directly from the Help
menu in ChemDraw for Windows.
60 •
Drawing Chemical Structures
There are two basic methods for using HotKeys.
To label the last atom drawn:
1. Draw a bond.
2. Immediately type a HotKey.
CambridgeSoft
Overview
The last atom drawn is labeled. Each time you
draw a bond, the last atom drawn is the
HotKey atom.
NOTE: HotKeys are case-sensitive. For example, the
default for a carbon label is lower case ‘c’. Typing an upper
case ‘C’ will create a ‘Cl’ label. For information on changing
the defaults, see “Creating HotKeys” on page 223.
To label an atom by pointing:
1. Using a bond, ring, or Text tool, position the
pointer over an atom.
A highlight box appears over the atom.
TIP: You may also use a selection tool, but you have to
click the atom, not just point to it. You may use the
Text tool for HotKey labeling only if there is no open
text box.
2. Type a HotKey.
The label is added to the atom highlighted. If
the label is a single element, such as C, then the
appropriate number of hydrogen atoms are
added to the label. Repeatedly typing the
hotkey will cycle the number of hydrogens.
NOTE: HotKeys are “sticky”, that is, typing a HotKey
will always label the last atom highlighted, even if you are no
longer pointing to it. This is true if even you switch tools or
switch documents. You can even open another application,
type in it, and return to ChemDraw. If you then type a HotKey, it will label the last atom highlighted. Only when you
open a textbox is the behavior cancelled.
Labeling multiple atoms
To label several atoms with the same label:
1. Select several atoms using a selection tool.
2. Type a HotKey.
The selected atoms are labeled.
ChemDraw 10
Figure 3.146: Labeling several atoms at once
H 3C
C
H2
Using a Selection Tool
Use the Lasso or the Marquee selection tool to
select any object. You use the Lasso for freehand
selection and the Marquee to select rectangular
regions.
Toggling Between Selection Tools
You can set one selection tool to behave like the
other by clicking the Lasso or Marquee tool while
holding the Alt or option key down.
Toggling Between Other Tools
To toggle a selection tool and the last drawing tool
used, press Ctrl+Alt+Tab or command+option+tab.
This command will toggle the last selection tool
you have used with the last drawing tool you have
used. If you haven’t used either selection tool, it
defaults to the Lasso tool.
New Selection Box
ChemDraw 10 has a very obvious change in the
selection tools, improving the visualization and
behavior of the Lasso and Marquee. When you
select a structure or object, the selection is displayed as a solid box in highlight color (blue
against white background; white against blue background), with resize handles in the eight cardinal
locations.
Drawing Chemical Structures
Overview
•
61
Figure 3.147: The selection rectangle
Figure 3.149: Moving Objects
Rotation handle
Cursor correctly
positioned to drag
Administrator
Resize
handles
SH
O
S
SH
Resize w/
distortion
O
You have the following options while resizing:
• resize proportionately by dragging any corner
• resize with either X-axis or Y-axis distortion by
dragging any side
• resize freely (X and Y axis distortion) by holding the Shift key down while dragging
The rotation handle is at the top. See “Rotating
Objects” on page 65 for more information.
When you select multiple objects, each object displays a selection box, so that you can see exactly
what is selected. For example, in Figure 3.148 you
see clearly that the lower benzene ring was only
partially selected. Note that in the partially selected
ring, each selected atom and bond is marked.
Figure 3.148: Partial selection
Cursor between
objects
Attempting to drag the selection when the cursor is
placed between objects will result in the objects
being deselected.
The new Lasso tool also gives you more control
over objects. Most drawing objects can now be
rotated as well as resized.
Selecting Objects with the Lasso
Tool
Use the Lasso tool to make freehand selection of
irregular areas.
To select objects using the Lasso tool:
.
1. Select the Lasso tool
2. Press the mouse button while the pointer is not
over any object.
3. Drag around a portion of a chemical structure
or other object.
Figure 3.150: Selection with the lasso
Dragging any adjustment handle changes all of the
selected objects in unison. To move the selected
items, position the cursor inside a selection box to
display a hand, then drag. Note that spaces
between objects are “dead space” where you cannot grab the selection to drag it.
62 •
Drawing Chemical Structures
As you drag, a line appears which defines the
Selection area. Bonds, structures, or other
objects are selected only if they are entirely
CambridgeSoft
Overview
within this area. The end points of the Lasso
are automatically connected when you release
the mouse button.
Figure 3.152: Selecting an entire structure
Selecting Objects with the
Marquee Tool
Use the Marquee tool to select objects and structures within a rectangular area.
To select objects using the Marquee tool:
1. Select the Marquee tool
.
The pointer becomes a Marquee.
2. Drag diagonally across the chemical structures
or other objects.
Figure 3.151: Selecting with the marquee
If the chemical structure or other object is part of a
group, the entire group is selected. For more information, see “Grouping Objects” on page 68.
Selecting Objects by Clicking
To select an object by clicking:
1. Select the Lasso or the Marquee tool.
2. Point to an object in a document window.
A highlight box appears over the selected
object. If you point at a bond, the highlight box
appears over the length of the bond.
3. Click the object.
Figure 3.153: Selecting by clicking
As you drag, a rectangle appears which defines
the Selection area. Bonds and other objects are
selected only if they are entirely within the rectangle.
You can use the Marquee to select several objects
at once if they can be surrounded by a rectangle.
Selecting Entire Structures
To select an entire chemical structure, using a
selection tool, double-click a bond or atom within
the structure.
The entire chemical structure is selected.
The selected objects appear within the Selection Rectangle and the cursor changes to a
hand.
NOTE: If the bond or other object is part of a group you
can select it as an individual object. For more information, see
“Grouping Objects” on page 68.
Removing Objects from the Selection
To remove an object from the selection, press
Shift and select an object contained within the
Selection rectangle by clicking, double-clicking, or
with a selection tool.
The object is removed from the selection.
ChemDraw 10
Drawing Chemical Structures
Overview
•
63
Figure 3.154: Removing selected objects
3. Drag the object to a new location.
Figure 3.155: Moving an object
Administrator
The lack of a blue square on this
bond shows that it has been deselected
NOTE: Objects may appear within the borders of the Selection rectangle but not be selected. See the comment in Figure
3.154, above.
To constrain the movement to the horizontal or
vertical direction, Shift+drag the selected objects.
Making Multiple Selections
Figure 3.156: Constraining movement to the axes
To make multiple selections or add more objects
to the selection:
• Press Shift and select the other objects.
You can add objects to the Selection by clicking,
double-clicking, or by using the selection tools.
Selecting and Deselecting All Objects
To select all objects within a document window,
click the Select All command on the Edit menu.
To deselect all selected objects, do one of the
following:
• Click in any empty area in a document window
that is outside the Selection rectangle.
• Press Esc.
• Select a different tool.
• Select another object without holding down
Shift.
The selected objects are deselected.
Moving Objects
To move an object:
1. Select the object using a selection tool.
2. Point within the border of the Selection rectangle.
64 •
Drawing Chemical Structures
Small incremental movements are often useful for
aligning objects.To move an object a small distance:
1. Select the object.
2. Press an arrow key.
The selected object moves 1 point in the direction of the arrow.
To move in a larger increment, press Alt or option
plus an arrow key.
The selected objects move 10 points in the
direction of the arrow.
For more information about aligning objects, see
Chapter 10: “Page Layout”.
Moving Atoms With a Selection Tool
You can move the atoms within a chemical structure using a selection tool.
CambridgeSoft
Overview
To move a single atom:
1. Point to an atom using a selection tool.
2. Drag the atom.
The bonds connected to the atom stretch.
Figure 3.157: Moving an atom with a selection tool
To duplicate the selected objects and constrain the
alignment of the copy:
1. Select the objects.
2. Ctrl+Shift+drag or option+shift+drag to
create a copy and position it.
Movement is restricted to the vertical or horizontal axis.
Deleting Objects
To delete selected objects, do one of the following:
To move multiple atoms, select only the bonds
that have atoms on both ends that you want to
move.
The unselected bonds that are attached to the
selected atoms are stretched.
NOTE: You can also move atoms using the bond tool that
was used to draw the atom. For more information, see “Moving Atoms With a Bond Tool” on page 54.
Duplicating Objects
To duplicate objects with a selection tool:
1. Click a selection tool.
2. Select the objects.
3. Ctrl+drag or option+drag to create a copy
and position it.
A “+” appears in the hand to indicate duplication, and a copy of the selected object is moved
to the new position.
Figure 3.158: Duplicating objects
• Press the Delete key.
• Press the Backspace key.
• Click the Clear command on the Edit menu,.
Rotating Objects
To rotate objects:
1. Select the objects to rotate using a selection
tool.
The Rotation handle is located on the upper
right corner of the selection rectangle
2. Drag the Rotation handle clockwise or counterclockwise.
The screen and Info window indicate the
magnitude of the rotation around the center
of the Selection rectangle.
Figure 3.159: Rotating an object
NH
NH
By default, atom labels do not rotate with the
structure.
ChemDraw 10
Drawing Chemical Structures
Overview
•
65
To rotate an atom label with a structure, press Ctrl
or command while dragging the structure.
Administrator
If a single atom is unselected when a structure is
rotated, the structure rotates around the unselected
atom.
To rotate the selected objects a specified number
of degrees:
1. Do one of the following:
• Click the Rotate command on the Object
menu.
• Double-click the rotation handle.
The Rotate Objects dialog box appears.
Figure 3.160: Rotate objects dialog box
66 •
Drawing Chemical Structures
2. Enter a number and click either degrees CW
for a clockwise rotation or degrees CCW for
counterclockwise rotation.
3. If you want to rotate the atom label text, click
the Rotate Atom Labels checkbox.
4. Click the Rotate button.
Objects are rotated around the center of the
Selection rectangle.
To repeat the same rotation on any object in the
document window:
1. Immediately after performing a rotation, select
the other objects to rotate.
2. Click the Repeat Rotate command on the Edit
menu.
CambridgeSoft
Overview
Chapter 4: Advanced Drawing Techniques
Overview
ChemDraw provides advanced drawing features
that allow you to:
•
•
•
•
Join objects
Group objects
Scale objects
Create mirror images
•
Pro Contract and expand sections of
structures
•
Pro
Pro
Create Templates
• Label functional groups with Nicknames.
Joining Objects
Use the Join command in the Object menu to fuse
two chemical structures together. Once structures
are joined they can be easily selected by double-clicking.
ChemDraw 10
Figure 4.161: Selecting bonds for joining structures
Clean up structures
• Add bonds to specific characters in atom labels
• Create bonds whose attachment is not explicitly defined
• Add atom numbers
• View structure perspective
• Create Mass Fragmentation, Retrosynthesis,
and Dissociation drawings
• Draw with Templates
•
To join chemical structures along the length of a
bond:
1. Select a bond or atom in one of the molecules
2. Shift+click to select the corresponding bond
or atom on the second molecule that you wish
to fuse.
3. Click the Join command on the Object menu.
The structures are joined.
NOTE: In some earlier versions of ChemDraw, structures
had to be in close proximity before they could be joined. This
is not longer the case.
To join chemical structures at one atom to create a
spiro linkage:
1. Position the two chemical structures so that the
atoms you wish to fuse are more or less opposite each other.
2. Select the two atoms to be fused.
3. Click the Join command on the Object menu,.
Advanced Drawing Techniques
Overview
•
67
Figure 4.162: Creating a spiro linkage
Administrator
TIP: While you no longer have to position the chemical
structures exactly, attempts to fuse atoms that are not
approximately lined up will lead to incorrect results.
NOTE: When you join two differently colored bonds or
atom labels, the color of the front object becomes the color of
the resulting joined object. When you join two atoms that are
labeled, the front atom label becomes the atom label of the
resulting atom. For more information about front to back
ordering of objects, see Chapter 10: “Page Layout”.
Grouping Objects
You can group a number of objects drawn separately. Grouping creates an association between
objects so they can be easily selected. You can
select all grouped objects by double-clicking with a
selection tool. Objects within a group can be
selected individually and manipulated while still
remaining part of the group.
If you want to group objects so that the individual
objects in the group cannot be accessed, you can
create an Integral group. When you select any
object in an Integral group, the entire group is
selected.
Grouping does not lock the position or orientation
of objects. Grouped objects maintain their relative
68 •
Advanced Drawing Techniques
positions when they are centered on the page,
aligned or distributed.
Atoms and bonds making up a single chemical
structure are always grouped. If you group part of a
structure with other objects, the resulting group
contains the entire structure. If you add atoms or
bonds to a grouped structure, the new atoms and
bonds are part of the group.
To group several objects:
1. Select the objects to group using a selection
tool.
2. Click the Group command on the Object
menu.
To select an individual object within a group, move
the selection tool over an object until it is highlighted and click once.
The object is selected, not the group.
Figure 4.163: Selecting part of a group
O
H 3C
C
O
Na
To select grouped objects, move the selection tool
over an object until it is highlighted and double
click
The entire group is selected.
Figure 4.164: Selecting a group
O
H 3C
C
O
Na
Ungrouping Objects
To ungroup objects that are grouped:
1. Select a group, as above.
CambridgeSoft
Overview
2. Click the Ungroup command on the Object
menu.
All the objects previously grouped become
individual objects.
Creating Integral Groups
To create a group in which individual objects cannot be accessed:
1. Select the objects to group using a selection
tool.
2. Click the Group command on the Object
menu.
3. With the group selected, right-click, point to
Group in the context menu, and click Integral.
To restore an Integral group to a regular group:
1. Select the Integral group.
2. Right-click, point to Group in the context
menu, and deselect Integral.
Scaling Objects
To resize objects with the Scale command:
1. Select the objects to scale.
2. Do one of the following:
• Click the Scale command on the Object
menu.
• Double-click one of the Resize handles.
The Scale Objects dialog box appears.
Figure 4.165: Scale objects dialog box
median selected bond has a specified length based
on the following scale factor:
scale factor =
new median bond length
current median bond length
To scale bonds so that the Fixed Length becomes
the new median bond length:
1. Select the top option.
The fixed length presently on the Drawing Settings tab of the Document settings dialog box
is shown in parentheses at the end of the line
for this button.
2. Click the Scale button.
To scale the bonds to a new fixed length that you
specify:
1. Select the middle option.
2. Type the new median bond length in the box to
the right of the button.
3. The current median bond length for the selection is shown in the highlighted text box when
the dialog box initially appears.
4. Click the Scale button.
To scale objects by a percentage:
1. Select the Scale by radio button.
2. Type the percentage in the box to the right of
the button.
3. Click the Scale button.
This is the only available option when the selection
does not contain any atoms or bonds.
Reflecting Objects Through
Planes
Use the first two options in the Scale Objects dialog box to scale all selected objects so that the
ChemDraw 10
You can reflect structures through planes perpendicular to the X-axis or Y-axis using a selection
tool. Used with duplicating, you can create mirror
images of chemical structures for representing
racemic mixtures and other stereoisomers.
Advanced Drawing Techniques
Overview
•
69
Flipping Objects
Administrator
To reflect an object through a plane perpendicular
to the X-axis:
1. Select the objects to reflect.
2. Click the Flip Horizontal command on the
Object menu.
3. While the copy of the structure is still selected,
choose Flip Horizontal or Flip Vertical from the
Object menu.
Figure 4.168: Flip
Flip Horizontal
OH
HO
Figure 4.166: Horizontal flip
CH 3
H3C
Flip Vertical
OH
H3C
H3C
Atom labels and captions do not flip along with
the object.
To reflect an object through a plane perpendicular
to the Y-axis:
1. Select the objects to reflect.
2. Click the Flip Vertical command on the Object
menu.
OH
You can also preserve the absolute stereochemistry
while flipping by using the Rotate 180º commands
on the Object menu.
Figure 4.169: Rotate 180º
Rotate 180° Horizontal
OH
HO
Figure 4.167: Flip vertical
H 3C
CH 3
Rotate 180° Vertical
OH
Creating Mirror Images
You can create mirror images from structures with
defined stereochemistry by duplicating the structure and rotating it.
To create a mirror image:
1. Draw a structure with defined stereochemistry,
for example, wedged bonds.
2. Select the structure and make a copy with
Ctrl+Drag or option+drag.
70 •
Advanced Drawing Techniques
H 3C
H 3C
Pro
OH
Expanding and
Contracting Labels
If your structures contain defined nicknames, long
atom labels, or contracted labels, ChemDraw can
restore your structures to the fully expanded form.
CambridgeSoft
Overview
To create a contracted label:
1. Select the area of the structure to contract.
Figure 4.170: Expanded and contracted forms
Contracted Form
Ph
CH2CH2CHCH3
Figure 4.172: Selecting a structure to contract
CH 3
Expanded Form
2. Click the Contract Label command on the
Structure menu.
The Contract Label dialog box appears.
When you expand a label containing a divalent
nickname, for example H-Ala-OH, the first attachment is to the character to the left of the nickname
(H). The second attachment is to the character to
the right of the nickname (OH).
To expand atom labels:
1. Select a selection tool.
2. Select the label to expand or double-click the
structure to expand all possible labels.
3. Click the Expand Label command on the Structure menu.
Your structure is redrawn in its expanded form.
Figure 4.171: Expanding labels
Figure 4.173: Contract label dialog box
ContractLabel 150 dpi
3. Type a label for the contracted structure and
click the OK button.
The label replaces the selected portion of the
structure.
Figure 4.174: Contracted label
Hexylbenzene
Ph
CH2CH2CHCH3
or
Ph
CH2CH2CHCH3
CH 3
CH 3
CH2CH2CHCH3
CH 3
Pro
Contracting Labels
You can compress an area of a structure and
replace it with a text label by using the Contract
Label command. Contracted labels are similar to
Nicknames, but they are for one-time use only, in
the current document.
ChemDraw 10
NOTE: If the area of the structure you contract contains
errors, an error dialog box appears. Click Ignore to view any
other errors. Click Ignore All to ignore all errors or Stop to
end the contract process.
Multi-Attached Labels
Multi-attached atom labels enable you to draw
chemical structures more efficiently by allowing
you to attach bonds anywhere along an atom label.
Advanced Drawing Techniques
Overview
•
71
Figure 4.175: Multi-attached labels
H2
C
Administrator
CH2
NH
O
CH 3
Expanded structure
O
CH 2CH2NHCH2CH3
Compact structure with multi-attached atom labels
Adding Bonds to an Atom Label
To add bonds to an atom labels:
1. Draw the structure and attach any necessary
atom label.
2. Select a Bond tool.
3. Position the cursor where you want to attach
additional bonds.
The selected part of the atom label is highlighted.
4. Click or drag from the atom label to draw your
bonds.
Figure 4.176: Adding bonds to a label
Ph
CH 2CH2CH2CH 3
are several preferential orientations for the resulting bond:
• Adding from the end of an atom label creates
bonds that are preferentially horizontal.
• Adding from the middle of an atom label creates bonds that are preferentially vertical.
• Adding from the start of an atom label creates
bonds that try to attain the chain angle setting
on the Drawing Settings tab of the Document
Settings dialog box. If that angle cannot be
attained, the next best angle is used.
Pro
Structure CleanUp
The Structure CleanUp command is used to neaten
the appearance of molecules by regularizing bond
lengths and angles. Graphic objects such as arrows
and aromatic circles are not affected. Use Structure
CleanUp to redraw structures that you may have
drawn freehand or to neaten structures that you
may have imported from another application.
Structure CleanUp may not create the best structure. Most structures have many “clean” forms, a
problem that is particularly noticeable with
straight-chain alkanes.
If you select only part of a structure when you
choose Structure CleanUp, the other atoms and
bonds are not be affected.
NOTE: For some compounds, the Structure CleanUp
command produces a structure that extends beyond the
bounds of the page. To view the entire structure, scale the
structure or increase the size of the printed page. For more
information, see “Scaling Objects” on page 69 and “Page
Setup” on page 151.
General Rules for Structure CleanUp are:
Ph
CH 2CH2CHCH3
You can determine the orientation of the resulting
bond by dragging. If you click to add a bond, there
72 •
Advanced Drawing Techniques
• The Fixed Length setting on the Drawing Settings tab of the Document Settings dialog box
determines optimum bond lengths.
• A given ring is redrawn only if all of its bonds
are selected.
CambridgeSoft
Overview
• Multi-attached atom labels and variable attachment points cannot be cleaned.
• Multi-center bonds cannot be cleaned.
• Structures are rotated so that as many bonds as
possible are directed at a multiple of 15
degrees.
• Structure CleanUp preserves stereochemical
meaning rather than the precise identity of any
wedged or hashed bonds, as shown below.
Figure 4.177: Preservation of stereochemical
meaning
OH
Cl
O
Before
HO
Cl
attachment centers. The procedure is similar, and
in both cases, the structure retains chemical significance.
Figure 4.179: Drawing a polyhapto structure
Fe
Figure 4.180: Isomers of dibromobenzene
Br
O
Br
abbreviated
notation for:
After
Using Structure CleanUp:
1. Select the structure or part of the structure you
want to clean up with a selection tool.
Br
Br
Br
Br
Figure 4.178: Cleaning up a structure
Br
1,2-dibromobenzene
1,3-dibromobenzene
Br
1,4-dibromobenzene
Creating a Multi-Center Bond
2. Click the Structure CleanUp command on the
Structure menu.
NOTE: Structure CleanUp does not position molecules relative to other objects. Overlap may occur.
Multi-Center and Variable
Attachments
To create a multi-center attachment point:
1. Select the structure whose center you want
defined as a multi-center attachment point.
2. Click the Add Multi-Center Attachment command on the Structure menu.
An asterisk is displayed with the fragment to
show that it contains a multi-center node.
Figure 4.181: Adding the multi-center attachment
point
You can draw polyhapto structures such as ferrocene ((Cp)2Fe), or an abbreviated notation for
different positional isomers of a compound, using
ChemDraw 10
Advanced Drawing Techniques
Overview
•
73
Administrator
The asterisk is not visible once a bond is drawn to
it. You can view the attachment point with a bond
or selection tool. For more information, see
“Viewing Attachment Points” on page 74.
To draw a bond to a multi-center attachment
point:
1. Click the Bond tool.
2. Point to the asterisk and either click or drag to
create a bond.
Figure 4.182: Adding a bond to the multi-center point
2
1
Fe
TIP: Either disable or toggle Fixed Lengths to draw
the bond so that it extends from the ring.
Creating a Variable Attachment
Point
To create a variable attachment point:
1. Draw the structural fragment to which you
want to assign a variable attachment node.
2. Select the fragment using a selection tool.
3. Click the Add Variable Attachment command
on the Structure menu.
An asterisk appears in the center of your fragment.
4. Point to the asterisk and drag to draw a bond.
TIP: Either disable or toggle Fixed Lengths to draw
the bond so that it extends from the ring.
You can treat this attachment node as you
would treat the end of a normal bond.
5. Click a Bond tool.
After you draw a bond from the attachment
node, the asterisk disappears.
74 •
Advanced Drawing Techniques
Figure 4.183: Using a variable attachment point
Br
2
1
Br
Br
Viewing Attachment Points
After you draw a bond from a variable or multicenter attachment point, the asterisk disappears.
You can verify the node is present with a bond or a
selection tool. This provides a way to check the
definition of pre-existing attachment points.
To view a node with a selection tool, select the
selection tool and position the cursor over to
attachment point.
The attachment node is highlighted.
Figure 4.184: Highlighting with a selection tool
Fe
To view a node with a bond tool, select the bond
tool and position the cursor over the attachment
point.
The attachment node and all the atoms it represents are highlighted.
Figure 4.185: Highlighting with a bond tool
Fe
CambridgeSoft
Overview
Atom Numbering
You can add sequential numbering indicators to the
atoms in a structure. ChemDraw recognizes the
following types of indicators:
• Numbers (1, 2, 3, and so on)
• Text ending with a number (atom1)
• Greek letters in the Symbol font
• Letters (a, b, c, and so on)
The default indicator is numbers.
TIP: To use text instead of numbers, number an atom then
edit the number. See “Editing Atom Numbers” on page 75.
Showing and Hiding Atom
Numbers
To add Atom Numbering to an entire structure:
1. Select the structure.
2. While pointing to the selected structure, do one
of the following:
• Right-click or control+click, point to Atom
on the context menu, and click the Show
Atom Number command.
• Type the HotKey ‘ (single quote).
To number individual atoms
1. Select the atom.
2. Do one of the following:
• Right-click (Mac: control+click), and click
the Show Atom Number command.
• Type the HotKey ‘ (single quote).
To hide Atom Numbering in a structure:
1. Select the structure.
2. Right-click or control+click, point to Atom,
and deselect Show Atom Number.
To hide an individual atom number, do one of the
following:
ChemDraw 10
1. Point to or select the atom, right-click or control+click, and deselect the Show Atom Number.
2. Point to or select the atom number, right-click,
and select Hide Indicator.
To remove an atom number indicator, do one of
the following:
• Click the indicator with the Eraser tool.
• Point to the indicator with a Bond tool and
type Backspace or Delete.
Editing Atom Numbers
You can edit the text and style of atom number
indicators.
To edit atom number text:
1. Select the Text tool.
2. Select the atom number indicator and type the
changes.
NOTE: When you type in a new indicator, you reset the
counter for that structure to a new style. You may then continue numbering in that style with the standard means. For
example, if you type α in a text box, then point to another
atom and use the context menu or HotKey, the atom will be
labeled β. Switching to another structure resets the counter.
To edit the atom number style, select the atom
number indicator with the Text tool and use the
Text menu or Text formatting toolbar.
Positioning Atom Number
Indicators
Atom number indicators are positioned automatically and move appropriately if a structure is modified. You can reposition them by dragging them to
the desired position or use the Position Indicators
dialog box.
To reposition an indicator:
1. Right-click the indicator to move and click the
Position command on the context menu.
The Position Indicators dialog box appears.
Advanced Drawing Techniques
Overview
•
75
Figure 4.186: Position Indicators dialog box
Administrator
2. Click the appropriate position option, and
enter a value.
Table 8: Positioning atom number indicators
To position …
Type a value
for Position …
from the atom or bond by angle or by clock
center to the indicator
center
from the atom or bond by offset—horicenter to bottom left of zontal and vertical
indicator baseline
at specified coordinates absolute—horizontal and vertical
2. Place the cursor inside the marked rectangle
and drag in any direction.
The structure will rotate on the X or Y axis, or
a combination of X and Y.
3. Use Shift+drag to limit the rotation to the X or
Y axes only.
You can also select part of a complex molecule and
rotate it around a particular bond.
NOTE: Do not try to use the Trackball to rotate objects
such as orbitals or boxes. It was designed to manipulate
chemical structures only.
Flatten Command
Although the Structure Perspective tool is not
intended to be a 3D modeling tool, it does introduce z-coordinate information that is saved in
CDX files. This pseudo-3D structure can be confusing when opening files that have been saved
after perspective manipulation.
To remove perspective information:
1. Select a structure with the Marquee or Lasso
Tool.
2. Click the Flatten command on the Object
menu.
All z-coordinate information is removed from
the structure.
Pro
Structure Perspective
You can rotate molecules or portions of molecules
through three dimensions with the Trackball tool
. The Structure Perspective tool behaves similarly to the Marquee tool.
To rotate a structure:
1. Select the structure by dragging over it with the
Trackball tool.
76 •
Advanced Drawing Techniques
Mass Fragmentation
Tool
The Mass Fragmentation tool
allows you to
break existing structures across one or more
bonds. This mimics the molecular fragmentation in
a mass spectrometer, but does not have any predictive qualities: you must specify what bonds are to
be broken.
To fragment a structure, drag the mouse across
one or more bonds.
CambridgeSoft
Overview
A line is drawn across the bonds that disappears when you release the mouse button. The
operation is not final until the mouse is
released. This means you can drag the line
around holding the mouse button down to see
different possibilities, and still back out without breaking any bonds. When the mouse button is released, any bonds crossed by the line
are broken
Figure 4.187: Using the mass fragmentation tool
Chemical Formula: C3H7•
Exact Mass: 43.05
Chemical Formula: C3H7•
Exact Mass: 43.05
Chemical Formula:
C6H12••
Exact Mass: 84.09
When the line crosses a bond, the formula and
exact mass for the fragments on either side of the
bond are displayed as if the bond were homolytically broken. That is, a single bond turns into a
monoradical on each fragment; a double bonds
turns into a pair of diradicals. If more than one
bond is crossed, all fragments on each side of the
line are considered together. If the only bond
crossed is a ring bond, a single formula/mass pair
is displayed.
NOTE: It is possible to draw lines that tie themselves in
knots. Use this tool with caution to avoid unrealistic fragmentation.
You can reposition the formula and mass displays
(they are text objects), or delete them altogether.
Table 9: Mass Fragmentation tool procedures
If you want the line to remain on display, hold
down the Alt or option key after drawing the line.
operation
behavior
Figure 4.188: Mass fragmentation tool: displaying
the line
drag
Breaks bond(s). The action
does not take place until you
release the mouse button, so
you can “test alternatives”.
Chemical Formula: C3H6••
Exact Mass: 42.05
Chemical Formula: C3H 6••
Exact Mass: 42.05
NOTE: The order in which you release the mouse button
and the Alt or option key determines whether the line
remains displayed or not. Releasing the mouse button first
leaves the line displayed.
The Alt or option key also allows you to “turn corners” and cut more than one bond.
Figure 4.189: Mass fragmentation tool: turning
corners
Chemical Formula: C2H 4••
Exact Mass: 28.03
drag, holding
Draws a freehand line. If you
down the Alt or release the mouse button
option key
before releasing the Alt or
option key, the dashed line
display remains.
drag across a
bond, then
press the Alt or
option key.
Allows you to change direction
and draw a polyline. If you
release the mouse button
before releasing the Alt or
option key, the dashed line
display remains.
Chemical Formula: C4H8••
Exact Mass: 56.06
ChemDraw 10
Advanced Drawing Techniques
Overview
•
77
Pro
Drawing Reactions
Administrator
Two new tools speed the drawing of synthesis
reactions. Both tools are used in a similar manner
to the Mass Fragmentation tool: they are used to
cut a bond or bonds in a product. The Synthesis
tool
draws the resulting fragments as a stan-
dard reaction. The Retrosynthesis tool
draws
the reaction with the product on the left and a
broad arrow pointing to the reactants, as is customary in retrosynthetic analyses. In most cases,
you will have to clean up the reaction by adding or
deleting atoms or bonds.
Figure 4.190 shows how to use the tools for a demonstration of the Beyer Method for quinolines,
with the simple clean up.
Figure 4.190: Using the reaction drawing tools
N
R
cut these bonds
R
Rxn NH 2
The Templates Tool
The Templates tool contains a palette from which
you can select different types of structures or
objects. The Templates tool has two levels:
• The first level displays the available Template
documents.
• The second level displays the templates within
each Template document.
Figure 4.191: Using the template tool
1. Reaction created with the Retrosynthesis tool
Rxn N Rxn
structure in a Template document is named a template. Use an existing template instead of drawing
the structure to shorten the time required to create
documents.
The Template documents distributed with ChemDraw are stored in the ChemDraw Items folder in
the same folder as the ChemDraw application.
NOTE: Pro In ChemDraw Pro, you can define your
own commonly used structures as templates. Any Template
documents in the ChemDraw Folder are listed in the Windows menu (Macintosh) or Open Special on the File menu
(Windows).
R
+
Rxn
2. Reaction created with the Synthesis tool
Rxn NH2
Rxn N Rxn
R
+
Rxn
R
Rxn
Rxn
Rxn
TemplateExample 150 dpi
Rxn
3. After clean-up
R
Rxn N Rxn
Rxn NH2
Rxn
+
H
Rxn
Rxn
Rxn
O
These tools are found in the Fragmentation tools
section of the Main tools palette.
Drawing with Templates
Template documents are collections of structures
organized by structural type or functionality. A
78 •
Advanced Drawing Techniques
NOTE: Pro In ChemDraw Pro the pop-up menu is
segmented if any Template documents are open for editing.
The upper segment contains Template documents that are
currently open for editing.
Choosing a Template
To choose a template from the Template palette:
CambridgeSoft
Overview
1. Hold down the mouse button over the Tem.
plates tool
A menu listing the Template documents
appears.
2. Point to a Template document name.
A palette containing the available templates
appears.
3. Choose a template from the palette.
Using Templates
When you draw with templates, the first bond
drawn determines the position of the template in a
document window. All remaining bonds are drawn
counterclockwise. The most nearly vertical bond
on the far-left atom is drawn first, from top to bottom. If there are two equivalent bonds, the atoms
that are at a lower position are used to draw the
first bond.
Figure 4.192: Drawing direction of template structures
Fusing a Template With an Existing
Structure
To draw a template and fuse it with an existing
structure, click an existing bond in a document
window.
To deposit a template and create a spiro-linkage
with an existing structure, click an existing atom in
a document window.
To draw a template in a document window and
control the size and orientation, drag from the
beginning of the first bond in the template to the
end of the first bond.
When you drag upwards the bulk of the template is drawn to the left, and when you drag
downwards the bulk of the template is drawn
to the right. Templates must contain at least
one bond in order to be drawn by the dragging
method.
Drawing with the Same Template
To draw another template of the same type:
1. Click the Templates tool
.
2. Draw the template in a document window.
Templates are automatically scaled to the document settings of the current document in the active
window. For more information, see “Autoscaling”
on page 165.
After a template is drawn in a document window,
the structures or objects can be manipulated by
standard drawing and editing methods.
Drawing a Template
To draw a template, click in a document window.
The template is drawn centered around the
pointer in the orientation that it appears in the
Templates palette.
ChemDraw 10
Pro
Creating Templates
and Template Documents
In ChemDraw Pro you can create new templates
and add them to existing Template documents or
create new Template documents.
To create a new Template document, open the File
menu, point to Open Special, and choose New
Templates.
A new and untitled Template window appears. The
Template window is similar to a document window, but is divided in half by a moveable, horizontal line.
Advanced Drawing Techniques
Overview
•
79
Administrator
• Template panel—Top half of the window
consists of individual panes where newly created templates appear.
• Drawing area—Bottom half of the window
where you can draw new templates.
Figure 4.193: Template panel and drawing areas
the Template window exactly as they are used
to draw structures in the drawing area of a document window.
To select a different Template pane, click another
Template pane.
When you select a Template pane, the contents
of the pane appear in the drawing area.
Figure 4.194: Adding a drawing to a panel
Template Panel
Pane
Resize
Handle
Drawing Area
The templates you define are not limited to atoms
and bonds. Templates can contain any ChemDraw
objects such as captions, boxes, arcs, orbitals,
arrows, reaction mechanism symbols, and curves.
The ChemDraw objects in Template documents
can be colored. However, the colors do not appear
in the Templates tool palette. You can paste pictures from other applications into a Template
pane. Pasted objects are scaled to the current Template document settings. For more information,
see “Autoscaling” on page 165.
Pro
Creating Templates
To create a new template:
1. Point to Open Special on the File menu, and
choose the New Templates command.
2. Select a Template pane by clicking it.
3. Draw a structure or object in the drawing area
of the Template window.
The structure appears in the Template pane as
you draw. The tools in the Tools palette are
used to draw a template in the drawing area of
80 •
Advanced Drawing Techniques
Templates2 250 dpi
As you define templates they become available for
use in your document without having to save the
Template document.
To view the newly-defined Template, point at the
Templates tool
and hold down the mouse
button.
The name of the new Template document
appears in the menu.
TIP: If you haven’t saved it yet, the name will be
“Untitled Template”.
Orientation of Templates
To make the templates that you create as easy to
draw with as possible, it is recommended that you
orient your structures so that the bond that establishes the position of the template, for example, the
bond used for fusing is left and vertical. The most
CambridgeSoft
Overview
vertical left bond is drawn first. For examples, see
“Using Templates” on page 79.
Resizing Template Panes
To resize the Template panes in the Template
panel, drag the lower right corner of the Template
panel.
Figure 4.195: Resizing a template
2. Click the Delete Row command on the Edit
menu.
To delete a column of Template panes from the
Template panel:
1. Select a Template pane in the column you want
to delete.
2. Click the Delete Column command on the Edit
menu.
The column is removed and all other columns
are moved to the left.
Saving Template Documents
Grab this corner and drag
TIP: If you have the Info window open, the height and width
are displayed.
Template Panels
To increase the size of the Template panel, drag
the Template dividing line.
To add a row of panes to the Template panel:
1. Select a Template pane.
2. Click either the Add Row Before or the Add
Row After command on the Edit menu.
The new row is added before or after the Template pane you selected.
To add a column to the Template panel:
1. Select a Template pane.
2. Click either the Add Column Before or the Add
Column After command on the Edit menu.
The new column is added to the right or left of
the Template pane you selected.
To delete a row of Template panes from the Template panel:
1. Select a Template pane in the row you want to
delete.
ChemDraw 10
To save a Template document and have it available
in the Template pop-up menu and the Window
menu:
1. Click the Save As command on the File menu.
The Save As dialog box appears.
TIP: Saving a Template document in the ChemDraw
Items folder makes it accessible in the Open Special
submenu and in the Templates tools palette.
2. Type a name for the Template document and
click the OK or Save button.
Using Nicknames
Nicknames allow you to create short names for
functional groups to use as an atom label or part of
a label. When an atom is labeled with a Nickname,
the chemical significance of the expanded structure
is retained.
Commonly used Nicknames, such as Me, Et, and
Ph are provided with ChemDraw in the ChemDraw Nicknames file located in your ChemDraw
Items folder. You can edit this list using tools in
ChemDraw. You should not attempt to edit this
file directly.
You can assign HotKeys to Nicknames. For example, in the Nicknames and HotKeys provided with
ChemDraw, the Hotkey, “4” labels an atom with
Advanced Drawing Techniques
Overview
•
81
Administrator
“Ph” which is a Nickname representing a phenyl
group. For more information, see “Labeling
Atoms with HotKeys” on page 60.
You can use Generic Nicknames when drawing
query structures. For more information, see
“Generic Nicknames” on page 97.
Nickname, the label “OTHP” appears as “PHTO” when
applied to the left side of a structure. However, since the
Nickname “THP” is defined, the label appears as
“THPO”. For more information, see “Aligning Text” on
page 207.
Applying Nicknames
You may select a Nickname from the Nicknames
dialog box or type it in manually. In either case,
ChemDraw recognizes it as being chemically significant.
To select a Nickname to apply to an atom using a
Hotkey:
1. Point to an atom.
2. Press the Hotkey “=” (equal sign).
The Choose Nickname dialog box appears.
You can define Nicknames with one or two attachment points. The attachment points must be single
bonds.
To define a new Nickname:
1. Create a structure containing the functional
group you want to define as a Nickname.
2. Select the functional group.
You must indicate the connection point for the
functional group by selecting the new fragment
without the bond connected to the attachment point.
Figure 4.196: Nickname dialog box
Figure 4.197: Adding a nickname
Pro
OH
HO
ChooseNickname 150 dpi
3. Select a Nickname from the list.
TIP: You can jump to the approximately correct place
in the Nickname list by typing the first letter of the
Nickname.
4. Click the OK button.
To enter a Nickname as an atom label:
1. Double-click an atom with a bond tool or click
an atom with the Text tool.
An atom label text box appears.
2. Type a Nickname label such as Et or Tos.
NOTE: Nicknames are tokens and do not flip orientation
when applied to the left side of a structure when using Automatic Justification. For example, in the absence of a defined
82 •
Advanced Drawing Techniques
Defining Nicknames
P
O
N
O
O
OH
pyridoxal 5-phosphate
don’t include this bond
NOTE: If stereochemistry is indicated in a structure that
you are defining as a Nickname, the stereochemistry is
retained.
3. Click the Define Nickname command on the
Structure menu.
The number of connection points is shown by
radicals in the Formula. You can have only one
or two connection points in a nickname.
CambridgeSoft
Overview
Figure 4.198: Define nickname dialog box
DefineNickname 150 dpi
4. Type a short name for the Nickname.
5. Click the OK button.
The Nickname is defined.
Figure 4.199: Viewing the new nickname
1. Click the List Nicknames command on the File
menu.
2. Select the Nickname that you want to delete
from the list.
3. Click the Delete button.
The Nickname is removed from the list.
Defining Peptides with
Nicknames
The definition in the figure below was used for the
amino acid alanine. The unselected bond at each
end of the structure indicates the connection
points—Nitrogen on the left and Carbon on the
right.
Figure 4.200: Creating an amino acid nickname
If you use a Nickname that is the same as an element name, a message indicates that the element is
replaced with the Nickname. For example, using
Ac for an acetyl group replaces the element Actinium. The Check Structure command recognizes
the label as an acetyl group rather than Actinium.
ChemDraw provides the following default Nickname/Element conflicts:
Table 10: Nickname-element conflicts
Symbol
Nickname
Element
Ac
Acetyl
Actinium
Am
Amyl
Americium
Np
para-Nitrophenyl
Neptunium
Pr
Propyl
Praeseodymium
To remove the overriding Nicknames, choose List
Nicknames from the File menu and delete the
overriding Nickname definition.
Deleting Nicknames
To delete a Nickname:
ChemDraw 10
H
N
CH3
O
C
H
C
You can draw a peptide chain by:
• Stringing Nicknames together,
• Stringing Nicknames together in an atom
label as long as there is a bond attached. or
• Stringing Nicknames together and not
including bonds.
Figure 4.201: Creating peptides with nicknames
a.
H
Gly
Ala
OH
b.
H
c.
HGlyAlaOH
GlyAlaOH
Troubleshooting Nicknames
If the Define Nicknames command is disabled,
check for the following:
• A connection point is not present
• More than 2 connection points are defined
Advanced Drawing Techniques
Overview
•
83
Administrator
• The connection point is not a single bond
In Figure 4.202a, the entire functional group was
selected. Because there is no atom that indicates a
connection point, you cannot define a Nickname.
When the sulfonamide group is attached to an
unselected bond, you can define a Nickname.
In Figure 4.202b, there is more than one attachment
point on a single atom in a nickname.
Figure 4.202c attempts to define more than two
selection points.
Figure 4.202: Troubleshooting nicknames
Incorrect
Correct
a. No connection point
O
S
O
NH2
S
O
O
b. Double bond as connection point
c. Too many connection points
84 •
Advanced Drawing Techniques
CambridgeSoft
Overview
NH2
Chapter 5: Query Structures
What Are Query Structures?
Atom Properties
Using a query structure to specify properties for
atoms and bonds provides an efficient way to
search chemical databases such as ChemFinder,
DARC, RS3, or ISIS/Base. You can use a query
structure to narrow or broaden your search.
For example, creating a query structure indicating a
bond as either double or single might broaden your
search. Indicating atom properties where a particular atom must have a charge of +3 might narrow
your search.
To assign properties to selected atoms in a structure:
1. Do one of the following:
Select a single atom by clicking it with a selection
tool.
• Select multiple atoms by Shift+clicking the
Because ChemDraw is not a chemical database
application, the interpretation of query structures
involves other programs. Not all databases support
the same query properties. If you use a query structure containing properties not understood by a
given database, one of the following may happen:
• An error message appears
• The unsupported properties are ignored
To use query structures for searching you may do
either of the following:
• Paste the query structure into a database search
window and initiate a search.
• Save the structure in an appropriate file format
and open the file in the database application.
For more information on query properties see
“Query Properties” on page 236, or consult the
documentation for your chemical database.
NOTE: ChemOffice 2006 does not prevent or warn you if
you try to assign conflicting or nonsensical properties. For
example, you can require that one of the atoms in benzene is
not part of any ring, which is inherently impossible. The
results of such a search depend on the query system used, but
usually no matches are found.
ChemDraw 10
atoms.
2. Then do one of the following:
• Right-click, select the property you want,
and click the appropriate option.
• Click the Atom Properties command on the
Structure menu. The Atom Properties dialog
box appears.
• Press the Hotkey “/ ”. The Atom Properties
dialog box appears.
Figure 5.203: Atom Properties dialog box
In the Atom Properties dialog box, select the
properties to associate with the selected
atom(s). Click the OK button.
Query indicators appear next to atoms that
have associated atom properties.
Query Structures
What Are Query Structures?
•
85
Figure 5.204: Displaying query indicators
Table 11: Atom properties indicators
X3
Administrator
T
∗2HS
Indicator
Query Property
C
R
I
Isotopic Abundance
(none)
Abnormal Valence
S
The character that appears depends on which
query properties have been assigned. If more than
one property is assigned, more than one character
appears adjacent to the atom. For more information, see “Query Indicators” on page 96.
Table 11: Atom properties indicators
Indicator
Query Property
*
Substituents: Free Sites (followed
by the number of free sites)
U
Substituents: Up to (followed by
the maximum number of substituents)
X
Substituents: Exactly (followed by
the number of substituents)
H
Implicit Hydrogens
R
Ring Bond Count
S
Unsaturation
C
Reaction Change
T
Reaction Stereo
L
Translation
86 •
Query Structures
Viewing Atom Property Values
Except for the three Substituents query properties,
the characters indicate that a given property is
applied, but not the value of that property.
To find the value of a query property setting:
1. Select the atom.
2. Do one of the following:
• Right-click, point to an atom, and point to
the appropriate property.
• Click the Properties command on the Structure menu and view the settings on the Atom
Properties tab.
Removing Atom Properties
To remove all atom properties from an atom:
1. Select the atom.
2. Click the Properties command on the Structure
menu.
3. Click Use Defaults.
The atom properties are removed and the characters no longer appear.
To remove specific atom properties:
1. Select the atom.
2. Do one of the following:
• Right-click, point to an atom, point to the
property you want, and choose the appropriate option.
3. Click the Properties command on the Structure
menu and click the atom property to remove.
CambridgeSoft
What Are Query Structures?
Atom Property Options
Table 12: Substituent options
The following topics describe the atom properties
you can associate with an atom.
Option
Search Result
Substituents
Free Sites
Finds compounds in which the
selected atoms may contain a
range of substituents up to the
number specified plus the
number of bonds as drawn. A
value of zero finds a substituent
count as drawn. You can also use
the Free Sites symbol in the
Chemical Symbols palette to
apply free sites. For more information, see “The Chemical
Symbols Tools Palette” on page
134.
Up to
Finds compounds in which the
selected atoms may contain a
range of substituents up to the
number specified.
Exactly
Finds compounds in which the
selected atoms contain the exact
number of substituents as specified, up to 15 substituents.
The three Substituents properties specify the number of substituents that may be bonded to the
selected atoms. In ChemDraw, a substituent is
defined as a non-hydrogen atom connected by a
bond of any order.
For example, in the figure below, the carbonyl carbon, indicated by the arrow, has a substituent
count of two: the alpha carbon and the aldehyde
oxygen. The double bond to the aldehyde oxygen
counts as only one substituent and hydrogen atoms
never count as substituents.
Figure 5.205: Substituent count
O
α carbon
H
The substituent count atom property allows you to
specify the number of bonds to an atom in the target structure. This includes bonds already drawn in
the query structure.
Table 12: Substituent options
Option
Search Result
Unspecified
Default. Search is determined by
the target database. Some databases (including ISIS) find
compounds with any substitution at this atom and some databases (including DARC) find
only compounds with substitution exactly as drawn.
ChemDraw 10
Implicit Hydrogens
The Implicit Hydrogens property specifies whether
additional, implicit hydrogen atoms may be
attached to the selected atoms. If implicit hydrogen
Query Structures
What Are Query Structures?
•
87
atoms are not allowed, all valences to that atom
must be filled by bonds to non-hydrogen atoms.
Table 13: Implicit hydrogen options
Table 14: Ring bond count options
Option
Search Result
Administrator
Option
Search Result
Simple ring
Allowed
Default. Finds compounds
regardless of whether hydrogen
atoms are attached to the
selected atoms.
Finds compounds in which the
selected atoms is a member of only
one ring (the atom has two ring
bonds).
Fusion
Finds compounds in which the
selected atoms lies at ring fusions
(the atom has three ring bonds).
Spiro or
higher
Finds compounds in which the
selected atoms is a member of a
spiro or higher linkage (the atom
has four or more ring bonds).
Not allowed Finds compounds with no
additional hydrogen atoms
attached to the selected atoms.
Ring Bond Count
The Ring Bond Count specifies the number of
bonds attached to an atom that are part of rings of
any size. For simple cases, this also specifies the
maximum number of rings in which an atom can
reside.
Table 14: Ring bond count options
Option
Search Result
Any
Default. Finds compounds in
which the selected atoms can be a
member of any type of ring, or a
member of no ring at all.
No ring
bonds
As drawn
88 •
Finds compounds in which the
selected atoms are acyclic.
Finds compounds in which the
selected atoms reside in the same
type and number of rings as
drawn.
Query Structures
Unsaturation
The Unsaturation property specifies whether a
multiple bond is attached to the selected atoms.
Table 15: Unsaturation options
Option
Search Result
Unspecified
Default. Finds compounds
regardless of whether a multiple
bond is attached to the selected
atoms.
Must be absent Finds compounds that do not
have a multiple bond attached to
the selected atoms.
Must be
present
Finds compounds that have at
least one multiple bond (double,
triple or aromatic) attached to
the selected atoms.
CambridgeSoft
What Are Query Structures?
Reaction Change
The Reaction Change property specifies whether a
change occurs at selected atoms after a reaction.
This property is only meaningful when searching a
database containing chemical reactions. In ChemFinder, only the product atom is checked. The stereo designation is ignored on reactants.
Table 17: Reaction stereo options
Option
Search Result
Any
Default. Finds all compounds
regardless of the stereochemistry
at the selected atoms.
Inversion
Finds compounds in which the
selected atoms have an inverted
stereo configuration after a reaction.
Retention
Finds compounds whose selected
atoms have an unchanged stereo
configuration after a reaction.
Table 16: Reaction change options
Option
Search Result
May be
anything
Default. Finds all reactions regardless of any change to selected
atoms after a reaction.
Must be as
specified
Finds all reactions that are
changed at the selected atoms
exactly as specified by the reaction
center property in the Atom
Properties dialog box.
Figure 5.206: Indicating reaction change
Reaction change indicator
NH2
R2
Rxn
Cl
Br
Rxn
R1
R2
C
N
H
The Reaction Stereo property specifies that the
selected atoms are stereo-centers in a reaction.
This property is only meaningful when searching a
database containing chemical reactions.
Figure 5.207: Indicating reaction stereo
Reaction stereo indicator
Br
R2
NH2
Rxn
Cl
ChemDraw 10
Br
Rxn
R1
N
H
Option
Definition
Equal
Default. Matches specific to specific
or generic to generic terms.
Broad
Translates specific query atoms to
corresponding superatoms in the
database.
Narrow
Translates query superatoms to
corresponding specific atoms or
groups in the database.
Any
Translates generic or specific terms
to any term.
R1
Reaction Stereo
+
The Translation property specifies what is required
to match in the structure query and possible database hits in a Markush DARC query.
Table 18: Translation options
Br
+
Translation
R2
T
R1
Query Structures
What Are Query Structures?
•
89
For more information, refer to the Markush
DARC User Manual.
Isotopic Abundance
Administrator
The Isotopic Abundance property gives you the
ability to distinguish between different isotopic
compounds—for example between mono- and
hexa-deuterobenzene—by specifying a nuclide at
any location.
Table 19: Isotopic abundance options
Option
Search results
Unspecified Default
Any
For ChemFinder, the same as
default. Included for compatibility with other systems where
the default may be different.
Natural
Indicates an isotopically
unmodified nuclide.
Enriched
Deficient
Indicates a mixture of isotopically substituted and isotopically unmodified nuclides.
Indicates a depleted label, that
is, the nuclide is present in less
than the natural ratio.
Nonnatural Indicates an isotopically substituted nuclide, that is, essentially
all the molecules of the
compound have only the indicated nuclide.
Abnormal Valence
The Abnormal Valence property specifies whether
selected atoms can have a valence other than nor-
90 •
Query Structures
mal. “Normal” valences for each element are
defined in the Isotopes Table file in the ChemDraw Items folder.
NOTE: The Abnormal Valence atom property does not
provide a visual indicator.
Table 20: Abnormal valence options
Option
Search Result
Not allowed Default. Finds compounds where
the selected atoms only have
valences that are normal for that
element. If necessary, hydrogen
atoms are automatically added to or
removed from the atom before
transferring it to the chemical database. If the Check Structure When
Copying to Clipboard or Exporting
preference is turned on, an error
message warns of abnormal
valences.
Allowed
Finds compounds with the specific
valence drawn.
NOTE: If Abnormal Valence is Allowed, any Invalid
Valence messages for those atoms are ignored automatically
by the Check Structure command.
Bond Properties
To define bond properties of selected bonds in a
structure:
1. Do one of the following:
• Select a bond using a selection tool.
• Shift+click to select multiple bonds.
2. Then do one of the following:
• Right-click, point to Bond on the context
menu, point to the property you want, and
choose the appropriate option.
CambridgeSoft
What Are Query Structures?
• Click the Properties command on the Structure menu. On the Bond Properties tab,
select the bond properties to associate with
the selected bonds from the drop-down
lists. Click OK.
• Point to an bond and press the Hotkey “/ ”.
The Bond Properties dialog box appears.
Table 21: Bond property descriptors
Indicator
Bond Query Property
S/D
Bond Type: Single/Double
D/A
Bond Type: Double/Aromatic
S/A
Bond Type: Single/Aromatic
Rng
Topology: Ring
Chn
Topology: Chain
R/C
Topology: Ring or Chain
Rxn
Reaction Center
Figure 5.208: Bond property dialog box
In the Bond Properties dialog box, select the
properties to associate with the selected atoms.
Click OK.
Query indicators appear next to bonds that
have associated bond properties.
Figure 5.209: Displaying bond properties
Viewing Bond Property Values
The characters that appears depends on which
query properties have been assigned. If more than
one property is assigned, more than one descriptor
appears adjacent to the atoms. For more information, see “Query Indicators” on page 96.
The descriptor for the Reaction Center query
property indicates that the property is applied, but
not the value of the property.
To find the value of a query bond property setting:
1. Select the bond.
2. Do one of the following:
• Right-click, point to Bond, and point to the
appropriate property.
• Click the Bond Properties command on the
Structure menu, and view the settings of the
drop-down list boxes.
The indicators are described in the following table.
Removing Bond Properties
Table 21: Bond property descriptors
To remove all bond properties from selected
bonds:
1. Select the bonds.
2. Click the Properties command on the Structure
menu.
3. Click Use Defaults.
one bond
many bonds
Indicator
Bond Query Property
Any
Bond Type: Any
ChemDraw 10
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91
Administrator
The bond properties are removed and the indicators are no longer adjacent to the selected
bonds.
To remove specific bond properties:
1. Select the bond.
2. Do one of the following:
• Right-click, point to the appropriate property, and click the property to remove.
• Click the Properties command on the Structure menu, and click the bond property to
remove.
Bond Property Options
The following are the atom properties that you can
associate with an atom:
Bond Type
This property specifies the bond type of the
selected bonds. The default bond type corresponds
92 •
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What Are Query Structures?
to the current type of the bond (single, double,
etc.) as drawn.
Table 22: Bond type options
Option
Search Result
Search Result
D/A
Single (all) and Finds compounds with the bond
Dative
type you select for the selected
bonds.
Finds compounds whose
selected bonds are double or
aromatic.
S/A
Finds compounds whose
selected bonds are single or
aromatic.
Table 22: Bond type options
Option
Double or
Double Bold
Finds compounds whose
selected bonds are double.
Double Either Finds compounds whose
selected bonds are double bonds
and have either cis/trans stereochemical configuration.
Aromatic
Finds compounds whose
selected bonds are aromatic.
Tautomeric
Finds compounds whose
selected bonds are tautomeric.
Triple
Finds compounds whose
selected bonds are triple.
Quadruple
Finds compounds whose
selected bonds are quadruple.
Any
Finds compounds regardless of
the bond type of the selected
bonds.
S/D
Finds compounds whose
selected bonds are single or
double.
ChemDraw 10
NOTE: Not all bond types are supported in all file formats. When an unsupported bond type is saved to a given file
format, it is converted to the closest equivalent that is supported.
Topology
The Topology property specifies the ring environment of the selected bonds.
Table 23: Topology options
Option
Search Result
Unspecified
Default. Finds compounds
regardless of environment.
Ring
Finds compounds where the
selected bonds are part of a
ring.
Chain
Finds compounds where the
selected bonds are part of a
chain (and are specifically not
part of a ring).
Ring or Chain
Finds compounds where the
selected bonds are part of
either a ring or a chain.
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93
Reaction Center
Administrator
The Reaction Center property specifies how the
selected bonds are affected in a reaction. This
property is only meaningful when searching a database containing chemical reactions.
Table 24: Reaction center options
Option
Search Result
Unspecified
Default. Finds compounds regardless of whether the selected bonds
are affected by the reaction.
Center
Finds compounds where the
selected bonds are affected by a
reaction, but the type of change is
unspecified.
Make/Break
Finds compounds where the
selected bonds are either broken
or created in a reaction.
Change
Finds compounds where the bond
order of the selected bonds
changes in a reaction.
Make&
Change
Not Center
Finds compounds where the
selected bonds are formed,
broken, or undergo a change in
bond order.
Finds compounds where the
selected bonds are not part of the
reaction center.
Table 24: Reaction center options
Option
Search Result
Unmapped
Finds all compounds.
3D Properties
3D queries are particularly useful in pharmacophore searching where the user is looking for a particular 3D relationship among atoms and bonds, for
example in a series of potential receptor ligands.
To create a 3D query, you add geometries (lines,
planes, etc.) and constraints (specified as ranges) to
a query structure. For example, you might specify
that two atoms must be between 4 and 5 Å apart,
or that two planes must be separated by 80-100
degrees.
To assign 3D properties to a structure, select the
structure or sub-structure and select one of the following options from the Add 3D Property command on the Structure menu.
NOTE: Because some 3D properties specify an order, you
should use Shift+Click to select them in the proper order
rather than using the Marquee or Lasso tool to select them
all at once.
In the table below, points are may be atoms, centroids or points. Lines may be lines or Normals.
Table 25: 3D property options
Option
Search Result
Angle
Defines an angle constraint
between three points (in order).
Indicated as a range.
Not Modified Finds compounds where the
selected bond’s orders do not
change, but which may or may not
be part of the reaction center.
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Table 25: 3D property options
Table 25: 3D property options
Option
Search Result
Option
Search Result
Dihedral
Defines a dihedral (torsional)
angle constraint among four
points (in order), between two
lines, or two planes. Indicated as a
range.
Centroid
Defines a point positioned at the
average position of all other points
selected.
Distance
Defines a distance constraint
between two points, a point and a
line, or a point and a plane. Indicated as a range, in Angstroms.
Line
Defines the best-fit line for the
selected points.
Plane
Defines the best-fit plane for the
selected points, or for a point and
a line.
Exclusion
Sphere
Defines an exclusion sphere
around a point. If more than one
point is selected, the exclusion
sphere is around the first selected
point, and the subsequent points
are allowed within the exclusion
sphere when the query is evaluated. Indicated as a range, in Å,
beginning at 0.
Normal
Defines the normal from a defined
plane in the direction of a point.
Point
Defines a point positioned at a
specified distance from a first
point in the direction of a second
point (in order), or in the direction
of the normal.
ChemDraw 10
All constraint values can be edited with the text
tool. Only exclusion spheres show the change visually.
When you create a point, a dialog box is displayed.
Specify the distance from the first selected point to
the calculated point. The distance may be specified
as an absolute value in Å or as a percentage of the
distance between the selected points. Negative values indicate that the calculated point is further
from the second point than the first point is, rather
than being between them.
Geometry and constraint objects update dynamically when you change the structure; they cannot
be moved independently. They may be used with
CDX, MOL, SKC, and TGF files (full read-write
compatibility); they are not compatible with other
formats. They can, however, be saved in print-only
formats such as TIFF.
Query Tools Palette
ChemDraw provides Query tools to enable you to
draw query structures.
To display the Query tools, select Show Query
Tools from the Other Tools command on the View
menu, or click the Query Tools icon on the Main
Tool Palette:
• Click
.
The Query tools palette appears.
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95
Figure 5.210: Query tools palette
Free Site
Administrator
Reaction
Atom-Atom
Map
Racemic
Stereochemistry
Alternative
Group
Absolute
Stereochemistry
Relative
Stereochemistry
To reposition an indicator numerically:
1. With a selection tool, click the indicator to
move.
2. Right-click and choose Position.
The Position Indicator dialog box appears.
Figure 5.211: Position Indicators dialog box
Query Indicators
You can display small characters to indicate query
properties you assign to atoms and bonds.
Viewing Query Indicators
To display query indicators for a structure, select a
structure to which query indicators are assigned,
right-click, point to Atom or Bond on the context
menu, and click the Show Query Indicator command.
To display query indicators for individual atoms or
bonds, select the atom or bond, right-click, and
choose the Show Query Indicator command on the
context menu.
Hiding Query Indicators
To hide an individual indicator:
1. Select the indicator to hide.
2. Right-click and select Hide Indicator.
Removing Query Indicators
To delete a query indicator:
1. Click the indictor.
2. Click the eraser tool and click the indicator.
3. Click the appropriate Position option, and type
a value:
Table 26: Position options
To Position …
Type a value
for…
from the atom or bond angle, degrees or
center to indicator
clock, o’clock
center
from the atom or bond offset, horizontal and
center to bottom left of vertical
indicator baseline
at specified coordinates absolute, horizontal
and vertical
Positioning Query Indicators
Query indicators are positioned automatically and
move appropriately if a structure is modified. You
can reposition them by dragging them to the
desired position or with the Indicator Position dialog box.
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Query Structures
Drawing Stereochemical
Symbols
ChemDraw provides three types of stereochemical
flags that indicate that the molecule with which they
are associated represents one of the following:
CambridgeSoft
What Are Query Structures?
• Racemic—A racemic mixture.
• Absolute—A pure enantiomer of known configuration.
• Relative—A pure enantiomer of unknown
configuration.
See “Relative Stereochemistry” on page 114 for
changes in ChemDraw 10.
The font and size for stereochemical flags is determined by the default Atom Label size for the document.
To draw a stereochemical flag:
1. Click the tool for the flag you want to use on
the Query tools palette.
2. Position the pointer next to the structure to
which you want to assign the flag.
3. Click to deposit the symbol.
Drawing Free Sites
Use the Free Sites tool to increment or decrement
the number of free sites in a query structure.
To increment the number of Free Sites:
1. Click the Free Site tool on the Query tools palette.
Figure 5.212: Free site tool
Free Site tool
2. Position the pointer over the atom to which
you want to apply free sites.
3. Click to add the symbol.
4. Continue to click the atom to increment the
free site number.
To decrement the number of free sites, hold the
Alt or option key while clicking the atom.
You can also change the free sites by using the
Atom Properties dialog box or the shortcut menu.
For more information see “Atom Properties” on
page 85.
ChemDraw 10
Generic Nicknames
Generic nicknames represent a class of elements or
structural moieties. The generic nicknames recognized as chemically significant by ChemDraw are:
• A: used to represent any moiety
• M: used to represent metal
• Q: used to represent a non-hydrogen heteroatom
• X: used to represent any halide
• R: undefined; used in the usual way
If you are using a query system that recognizes
generic nicknames, you can use these nicknames in
your ChemDraw query structure.
To label an atomic position with a generic
nickname, do one of the following:
• Double-click on the atom to open a text box,
and type in the nickname.
• Right-click on the atom, point to Insert
Generic Label on the context menu, and click
the label you wish to insert on the sub-menu.
You can assign Generic nicknames, like other nicknames, to HotKeys. For information on assigning
a Hotkey to a nickname, see “Creating HotKeys”
on page 210.
You cannot define the meaning of a generic nickname in ChemDraw because generic nicknames
represent multiple (and perhaps an infinite number
of) substituents. Generic nicknames have meaning
only in the context of the search system you are
using.
The generic nicknames recognized as chemically
meaningful to ChemDraw are listed in Generic
Nicknames file in the ChemDraw Items folder.
To edit the generic nickname files, open the
Generic Nicknames file in a text editor and make
your changes. Follow examples in the file for the
correct format.
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97
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NOTE: If you perform Check Structure on a structure with
a generic nickname, a message is displayed because the structure contains variable substituents. If you ignore this message,
the generic nicknames are ignored and ChemDraw reports
the chemical formula, mass, and so on as if the atom label
containing the generic nickname were not selected.
• The bond type between the chalcogenide
and the other atom to be a single or double
bond.
Figure 5.215: Query example
(b)
(c)
(a)
Element Lists
You can define your search query more concisely
with the element list. By labeling an atom position
as a list of elements you specify that one of these
elements must match in the structure for which
you are searching. The elements in the element list
must be separated by commas. A space after each
comma and brackets are optional. An example of
an element list is shown below.
Figure 5.213: Element list
[S,Se,Te]
Element Not-Lists
NOTE: An element list may contain only atomic symbols,
plus D (deuterium) and T (tritium).
To create an element list:
1. Open an atom label text box.
2. Type an open bracket (“[“) followed by a list of
elements separated by commas (“Cl, Br, I”),
followed by a close bracket (“]”).
3. Close the text box.
Figure 5.214: Adding an element list to an atom label
[Br, I, Cl]
The “A” label indicates that the atom may match
any atom except hydrogen. The mark near the
bond indicates that the bond has special properties.
The bond type specified in the Bond Properties
dialog box must be single or double, S/D. The
“[S,Se,Te]” specifies that one of these elements
must match in the target structures.
[Br, I, Cl]
The element not-list specifies that the elements in
the list match must not match in the structure for
which you are searching. Commas must separate
the elements in the element not-list. A space after
each comma and brackets are optional.
The word NOT must be in all-caps and must be
followed by a space. Alternatively, the word NOT
may be replaced with a minus sign.
For example:
Figure 5.216: Element NOT lists
NOTE: An element not-list may contain only atomic elements, plus D (deuterium) and T (tritium).
Figure 5.215 shows a query structure created to find
compounds matching the following criteria:
• Non-oxygen chalcogenide bonded to
another atom.
• Not necessarily carbon (a generic nickname).
98 •
Query Structures
To create an element not-list:
1. Open an atom label text box.
2. Type an open bracket, the word NOT, and a
space (“[NOT”) followed by a list of elements
separated by commas (“Cl, Br, I”), followed by
a close bracket (“]”).
CambridgeSoft
What Are Query Structures?
Link Nodes
You can specify a variable-length chain or ring by
indicating that one of the atoms can be repeated
some number of times using link nodes.
Link nodes must have exactly two connecting
bonds. The atom label must conform to the
following conditions:
• No more than a single element symbol or a
generic nickname
• The last part of the label in the form: number
hyphen number, with the number and hyphen
subscripted
• Parentheses or braces may be used instead of
brackets
• Brackets can be omitted if not needed for clarity, for example with O1-3
The bracket properties are described in the following sections.
NOTE: This method will give a default value for component order, multiple group repeat count, or SRU label. To
change a default value, use the Bracket Properties dialog box.
Setting Bracket Properties
You can change the properties of brackets by the
context menus or Bracket Properties dialog box.
To use the Bracket Properties dialog box:
1. Select the right bracket with a selection tool.
2. Click Bracket Properties on the Structure
menu.
The Bracket Properties dialog box appears.
Figure 5.218: Bracket properties dialog box
To create a link node:
1. Open an atom label text box.
2. Type in the following format:
Figure 5.217: Link node
Representing Polymers and
Other Repeating Units
Brackets, parentheses, and braces enclose structures or structural fragments that are to be
repeated a number of times. The bracket properties in ChemDraw allow you to specify the context
and orientation of the repeating units.
To enclose structures with brackets:
1. Click the Bracket tool
and select one of
the double bracket tools.
2. Drag across the structure to draw the brackets.
3. Right-click or control-click and select the
appropriate bracket properties from the menu
that appears.
ChemDraw 10
The Flip Type option appears only for brackets
with exactly two crossing bonds, and is disabled in
other cases.
You can customize the text that appears to the bottom right of the bracket for the following bracket
types.
• Component (c#)—the Component Order
must be a non-negative integer, and is displayed as the letter “c” followed by that integer
(or “c” alone if an order of zero is specified).
• Multiple Group (#)—the Repeat Count must
be a positive integer.
• SRU (n)—the SRU label can be any text.
You can also edit the text for these Bracket Usage
types directly in the document using the Text tool.
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99
You cannot edit the text displayed for the other
Bracket Usage types.
Bracket Usage
Administrator
Representations of polymers are either structure-based or source-based. The type of bracket
you use depends on which type of representation
you need. For references, see “Polymer Representations” on page 235.
Structure-based Polymer
Representations
mode of polymerization may be obvious from context, or it might be unknown. Source-based representations are useful when describing processes
where the starting materials are known, but the
exact structure of the reaction product is not.
You can create a source-based representation by
enclosing a structure in “Monomer (mon)” brackets.
A source-based representation of poly(vinyl chloride) is shown in Figure 5.220.
Figure 5.220: Source-based polymer representation
Structure-based polymer representations enclose
only a portion of a structure within brackets. One
or more bonds cross each of the enclosing brackets. The crossing bonds “match up”, making the
polymer structure more explicit.
You create a structure-based polymer representation by enclosing a portion of a structure in brackets with a bracket type of SRU (n). The subscript
“n” is recommended by IUPAC to notate structure-based representations of unknown size, but
you can edit the text using the text tool.
A structure-based representation of
poly(vinyl chloride) is shown in Figure 5.219.
Cl
mon
You can use “Mer (mer)” brackets for components
of a copolymer where those individual components are known not to repeat themselves or alternate with the other components. An example is
shown in Figure 5.221.
Figure 5.221: Copolymer representation
Figure 5.219: Structure-based polymer representation
O
Cl
OH
*
n
*
You can also use the Bracket Usage types
“Crosslink (xl)”, “Graft (grf)”, and “Modification
(mod)” to represent specific types of repeating
units in a structure-based representation, but they
are rarely encountered and using them is discouraged.
Source-based Polymer Representations
Source-based polymer representations enclose an
entire discrete chemical substance in brackets. The
100•
Query Structures
OH
HO
HO
mer
O
mer
co
Copolymers represent substances with more than
one repeating unit. In general, you can use bracket
type “Component (co)”. You can also use “Copolymer, alternating (alt)”, “Copolymer, random
(ran)”, and “Copolymer, block (blk)” to represent
different specific types of copolymers in a sourcebased representation, but they are rarely used and
their use is discouraged.
CambridgeSoft
What Are Query Structures?
The bracket type, “Mixture, unordered (mix)” is
not for polymers, but to represent a collection of
substances that may all be present, but not necessarily in known amounts. Bracket type “Component (c)” indicates individual mixture elements. An
example is shown in Figure 5.222.
Figure 5.223: Brackets used to indicate multiple
groups
O
O
OH
HO
O
Na+
Na+
O-
-O
Figure 5.222: Brackets used to indicate mixtures
2
O
COOH
O
H
O
H
3
COOH
c1
c2
COOH
O
O
c3
O
COOH
c4
mix
Bracket type “Mixture, ordered (f)” is primarily
used to describe manufacturing processes, where
the ordering of components is a critical part of the
process (and where a different ordering might produce a different final product. As with Unordered
Mixtures, individual elements of an ordered mixture should be surrounded by brackets with a
bracket usage of “Component (c)”. Unlike with
Unordered Mixtures, however, components of
Ordered Mixtures must represent their ordering.
You can do this by editing the “c” label with the
text tool to include a number (“c1”, “c2”, and so
on.)
You use the bracket type, “Multiple Group (#)” to
indicate that the enclosed items are repeated a specific known number of times. Multiple Group
brackets may enclose entire structures, or may
enclose a portion of the structures only. You can
edit the numeric repeat count with the text tool.
Examples are shown in Figure 5.223.
ChemDraw 10
14
O
13
Because Multiple Group brackets represent a specific repeat count (unlike the unknown repeat
count of the other bracket types), it is possible to
calculate accurate molecular weights (and related
data) for such structures. That data is displayed in
the Analysis window as with any other structure.
Figure 5.224: Analysis with multiple groups.
O
14
O
13
Repeat Pattern
For simple linear polymers, the repeating units may
connect head-to-tail or head-to-head (or their
repeat pattern might be a mixture or unknown).
You can also assign this property to brackets.
Because of its prevalence, the Head-to-Tail type is
assumed to be the default Repeat Pattern, and does
not receive any special annotation on the brackets,
as shown in Figure 5.225.
Query Structures
What Are Query Structures?
• 101
Figure 5.225: Head-to-tail repeat pattern
Figure 5.227: Alternative groups
Administrator
Flip Type
For ladder-type polymers (those polymers with
two connecting bonds on each side), there is a
potential ambiguity in the order of the connections. You can assign the Flip Type property to
resolve that ambiguity. This property is appropriate
only for brackets with exactly two crossing bonds,
and is disabled in other cases.
Because of its prevalence the No Flip type does
not receive any special annotation.
Figure 5.226: Indicating flip type in ladder-type polymers
*
H
N
*
*
H
N
H
N
H
N
H
N
*
=
*
*
*
*
H
N
flip
*
*
H
N
H
N
*
*
=
*
*
*
N
H
N
H
*
Alternative Groups
You can create a search query that contains variable functional groups or substructures. Instead of
submitting multiple queries on structures that
share a common substructure, you can submit a
single query with the parent structure. The parent
structure can have attachment points to a list of
alternative groups that you can define.
Alternative groups, sometimes called R-Groups or
G-Groups (Generic Groups), are shown below.
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Defining an Alternative Group
In ChemDraw Pro, you can create alternative
group definitions (R, G, etc.) that represent a set of
substituents, any one of which will match the
query.
To define an alternative group:
1. Click the Alternative Group query tool
and drag with the tool to create an area large
enough to draw the alternative groups.
2. Type a title, such as R1, in the Alternative
Group Title box, then draw the substructure
fragments in the Alternative Group box.
Figure 5.228: Defining an alternative group
1
2
Specify where the fragments should bond to the
parent structure on the alternative group label by
defining Attachment Points
CambridgeSoft
What Are Query Structures?
3. Do one of the following:
• Select the diamond shaped Attachment
Point tool
on the Chemical Symbols
palette, and click a substructure fragment
where you want to place the attachment
point.
• Point to a substructure fragment where you
want to place the attachment point and press
the Hotkey “.” (period).
An attachment point symbol appears.
4. Repeat for all fragments.
Multiple Attachment Points
If you have well-defined multiple attachment
points on your structure fragments, you can perform searches for specific materials. This type of
search is especially useful for searching for conformationally similar structures.
For example, you want to find the two compounds
in Figure 5.231A. However, you are not interested
in the two compounds in Figure 5.231B.
Figure 5.231: Multiple attachment points
A
Figure 5.229: Adding attachment points
NH2
Attachment
point symbol
NH2
O
B
NH2
When you create a parent compound that contains
an alternative group you defined, an attachment
point symbol appears next to the label. The attachment point number matches that found in the definition.
Figure 5.230: Structure with R-group table
R1
1
R1
1
NH2
1
OH
1
F
The number displayed in the attachment point
symbol is the attachment rank order. See the example in “Multiple Attachment Points” on page 103.
ChemDraw 10
NH2
O
By specifying the attachment point order, you can
exclude the unwanted compounds. The parent
structure in Figure 5.232 satisfies the necessary
requirements.
To specify the attachment points order:
1. Draw the parent structure shown below.
Figure 5.232: Specifying the attachment point order
2. Create an Alternative Group Box labeled “R1”.
3. Draw the structure fragments and label them
with attachment points.
Query Structures
What Are Query Structures?
• 103
When the alternative group definition is
complete, the attachment point symbols
appear in the parent compound.
Figure 5.234: Hidden attachment rank indicators
R1
R1
NH2
Administrator
Figure 5.233: R-groups with multi-attachment points
R1
O
1
2
This change affects all documents.
Attachment Point Numbering
1
O
2
By numbering your attachment points, you have
unambiguously specified that the methyl group
must be adjacent to the amine group. The conformations that are not of interest are excluded.
Showing Attachment Rank
Indicators
You can hide the attachment rank indicators if
required. For example, sometimes—particularly in
publication-quality drawings—the numbering of
attachment points is implicit and the numbered
attachment rank indicators are superfluous.
To hide the attachment rank indicators and
remove the numbers from the attachment points:
1. Click the Preferences command on the File
menu.
2. In the Preferences dialog box, click Display.
3. Deselect Show Attachment Rank Indicators.
Figure 5.234 shows an alternative group definition
and a parent structure with the attachment rank
indicators hidden.
104•
Query Structures
Numbered attachment points allow you to specify
precisely how the structure fragments are connected to your parent structure.
The numbering of the attachment points is related
to the front to back order of the attachment points.
To set the order of the attachment points, click the
ends of the bonds in order.
The last point clicked has the highest number.
To change the ordering of the attachment points do
one of the following:
• Click the attachment points with the Attachment Point tool.
• Select an attachment point with a selection
tool, and click either the Bring to Front or the
Send To Back command on the Object menu.
The attachment point numbers are highest in
the front.
Anonymous Alternative
Groups
An anonymous alternative group is a cross
between an element list and an alternative group.
Element lists are restricted to single elements, but
anonymous alternative groups can contain any
structure that can be represented by text. Nicknames and generic nicknames are allowed in anon-
CambridgeSoft
What Are Query Structures?
ymous alternative groups. Anonymous alternative
groups are shortcut notation for regular alternative
groups, eliminating the need to specify a name
such as “R1”.
You can define your search query more concisely
with the anonymous alternative group. By labeling
an atom position as a list of substructures you
specify that one of these substructures must match
in the structure for which you are searching. Commas must separate the items in the anonymous
alternative group. A space after each comma and
the brackets are optional. Examples of anonymous
alternative groups are shown in Figure 5.235.
Figure 5.235: Anonymous alternative groups
To create anonymous alternative groups:
1. Open an atom label text box.
2. Type an open bracket “[”followed by a list of
elements, fragments, nicknames, or generic
nicknames separated by commas, followed by a
close bracket “]”.
Atom-to-Atom Mapping
You can create correspondences between atoms in
different structures for use in creating queries for
searching a reaction database. The reactions
mapped can be single or multi-step. You can assign
atom-to-atom mapping for creating records for a
reaction database and for creating queries for
searching a reaction database. You can assign atom
mapping in two ways:
• Automatic mapping, using the Map Reaction
Atoms command from the Structure menu.
• Manual mapping, using the Reaction
Atom-Atom Map tool
on the main tools
During either type of mapping process, the mapping algorithm perceives and assigns a reaction
center for the reactants and products.
When a reaction map is established, you can point
to an atom in one structure with the Reaction
Atom-Atom Map tool selected to highlight the
mapped atom in the other structure.
Always Display and Print Atom
Mapping
To make the symbols always appear and print on
the atoms when reaction mapping has been performed:
1. Click the Preferences command on the File
menu.
2. In the Preferences dialog box, click Display.
3. Select Always Display and Print Reaction Mapping.
4. Click OK.
Deselect Always Display and Print Atom Mapping
to show the symbols only when you select the
Reaction Atom-Atom Map tool. When this option
is deselected, atom mapping symbols do not print,
even though a reaction map has been created.
Automatic Mapping
To automatically create a reaction map:
1. Draw the reaction you want to map and select
the reactants and products.
TIP: Double-click the arrow with a selection tool to
select the entire reaction.
2. Click the Map Reaction Atoms command on
the Structure menu.
The symbol Rxn appears next to the bonds in
the reactant and product that are perceived by
the algorithm as being modified by the reaction. These symbols are bond properties that
palette.
ChemDraw 10
Query Structures
What Are Query Structures?
• 105
are automatically applied. For more information about the Reaction Center bond property,
see “Bond Properties” on page 90.
Administrator
Figure 5.236: Automatic reaction mapping
OSiMe3
Rxn
Rxn
Rxn
Ph
O
O
O
Rxn
Rxn
Ph
Rxn
Rxn
Figure 5.238: Finalized mapping
Manual Mapping
Rxn
In situations that require manual mapping of
atoms, you can use the Reaction Atom-Atom Map
tool. This might be necessary when the automatic
mapping is applied to complicated reactions, and
gives incorrect results. In these cases you can manually readjust the reaction mapping.
Figure 5.237 shows the initial mapping being
ammended by using the Reaction Atom-Atom
Map tool.
Figure 5.237: Automatic mapping to be ammended
Rxn
7
1
Rxn
Rxn
8
9
O
OH
Rxn
7
2
6
3
7
10
5
6
3
5
4
4
Rxn 1
8
Rxn
2
11
1
Rxn
Rxn
8
9
O
9
OH
Rxn
7
6
Rxn
7
10
Rxn
10
2
11
6
5
6
5
1
4
2
3
Rxn
Query Structures
3
4
5
4
5
4
3
When you perform manual mapping with the
Reaction Atom-Atom Map tool, you can suppress
automatic re-mapping of atoms other than your
target atom.
To suppress automatic re-mapping:
1. Click the Preferences command on the File
menu.
2. Select Automatic Reaction Mapping on the
General tab.
106•
1
OH
6
2
8
7
O
1
3. Click OK.
To use the Reaction Atom-Atom Map tool to supplement the automatic mapping:
.
1. Click the Reaction Atom-Atom Map tool
2. Point to the atom in the reactant whose mapping you want to establish. For example, in the
following drawing you would point to the acyclic carbon adjacent to the ether oxygen.
3. Drag from the reactant atom to the corresponding product atom.
The remaining atoms are automatically
mapped based on the manual mapping you
performed.
You can continue to set or change the mapping for
other atoms in the reaction if necessary until you
get exactly the mapping you want. For this example
additional manual mapping is not necessary.
Clearing Reaction Mapping
To clear all reaction mapping:
1. Select the structures whose mapping you want
to remove.
2. Click the Clear Reaction Map command on the
Structure menu.
CambridgeSoft
What Are Query Structures?
Exporting Reaction Mapping
Table 27: Query properties by export format
Reaction mapping and reaction center perception
information are stored in the native ChemDraw
file format (*.cdx) for reopening in ChemDraw
and the ISIS Reaction file format for transfer to
other applications that read atom mapping, such as
ChemFinder and ISIS/Base. You can also copy
mapped reactions to these same applications using
the Clipboard.
Export Compatibility
Because query properties are only useful in a chemical database, you must transfer your structures
from ChemDraw into your search system. Not all
file formats support the same query properties and
not all chemical databases support the same file
formats. Consult the documentation for your database to see which file formats are supported.
The following table lists the query properties that
ChemDraw writes to ISIS (SKC, TGF, and Clipboard) file formats. All query properties are written
to the ChemDraw (CDX) file format. CDX is the
preferred format to use to retain all query properties in a drawing.
Table 27: Query properties by export format
Exported
Query
Properties
ISIS
Mol
ISIS
Mol
Rxn
Xc
Xc
Xc
Not allowed
X
X
X
Allowed
X
X
X
Any
X
X
X
No ring bonds
X
X
X
As drawn
X
X
X
Simple ring
X
X
X
Fusion
X
X
X
Spiro or higher
X
X
X
X
X
X
X
X
X
Exactly
Implicit Hydrogens
Ring Bond Count
Rxn
Unsaturation
Atom Properties
Unspecified
Substituents
Unspecified
Exported
Query
Properties
Must be absent
X
X
X
Free Sites
b
b
b
Must be
present
Up to
a
a
a
Reaction Change
ChemDraw 10
Query Structures
What Are Query Structures?
• 107
Table 27: Query properties by export format
Mol
Table 27: Query properties by export format
Administrator
Exported
Query
Properties
ISIS
Rxn
May be
anything
X
X
Must be as
specified
X
X
ISIS
Mol
Rxn
Single
X
X
X
Dashed
X
X
X
Hashed
d
d
d
Wedged
Hashed
X
X
X
Bold
X
e
e
Wedged
X
X
X
Wavy
X
X
X
e
e
e
Broad
Hollow
Wedged
Any
Dative
f
f
f
Narrow
Double
Xg
Xg
Xg
Double Either
X
X
X
Reaction Stereo
Any
X
X
Inversion
X
X
Retention
X
X
Exported
Query
Properties
Bond Type
Translation
Equal
Abnormal Valence
Not Allowed
X
X
X
Double Bold
h
h
h
Allowed
X
X
X
Aromatic
X
X
X
Tautomeric
i
i
i
Bond Properties
108•
Query Structures
CambridgeSoft
What Are Query Structures?
Table 27: Query properties by export format
Exported
Query
Properties
Table 27: Query properties by export format
ISIS
Mol
Rxn
Triple
X
X
X
Quadruple
l
l
l
Any
X
X
X
S/D
X
X
X
D/A
S/A
X
X
X
X
ISIS
Not Center
Mol
Rxn
X
X
Other Query Attributes
Xj
Xj
Xj
Element Lists
Xko
Xko
Xko
Element NotLists
Xk
Xk
Xk
Alternative
Groups
X
Xm
Anonymous
Alternative
Groups
n
n
Link Nodes
p
p
p
Bracket
properties
X
X
X
Atom-Atom
mapping
X
Generic
Nicknames
X
X
Topology
Unspecified
X
X
X
Ring
X
X
X
Chain
X
X
X
Reaction Center
Unspecified
X
X
Center
X
X
Make/Break
X
X
Change
X
X
Make&Change
X
X
ChemDraw 10
Exported
Query
Properties
X
Variable
Attachment
Positions
3D query properties
Query Structures
What Are Query Structures?
• 109
aConverted
to the appropriate number of exact
gInterpreted
Administrator
substituents
ochemistry
b
Free Sites counts of zero translated to “Substitution as drawn”; all other Free Sites values written
as substitution counts equal to the total current
valence plus the free sites value.
h
c
k
Substituent counts of greater than 5 are translated
to “6 or more”
Converted to Double
i
Converted to S/D
jOnly
M, X, Q, A; others written as aliases
Truncated to the first 5 elements
lConverted
dConverted
to Wedged Hashed
eConverted
mAn
to Wedged
nConverted
f Converted
to a Single, with a positive charge
applied to that atom at the base of the dative bond
and a negative charge applied to the atom at the
point of the dative bond
110•
Query Structures
by ISIS as unspecified cis/trans stere-
to single.
RGFile will be created automatically.
to non-anonymous alternative groups.
oLists
of greater than 5 elements converted to
alternative groups.
pThe
low end of the repeat range is always treated
as 1.
CambridgeSoft
What Are Query Structures?
Chapter 6: Chemistry Features
Checking Chemistry
Check Structure
You can check the chemistry of a selected structure, part of a structure, or caption (in Formula
style). The Check Structure command identifies
errors in valences, labels and defined Nicknames.
To check the valences of all selected atoms in a
structure:
1. Select a structure, part of a structure, or caption
with a selection tool.
2. Click the Check Structure command on the
Structure menu.
Each label in the structure is checked. sequentially. When a label is incorrect, a message window appears.
Figure 6.239: Check structure information window
Check Structure when Copying to
Clipboard or Exporting
To have ChemDraw perform a check structure
analysis on any structure copied to the Clipboard:
1. Click the Preferences command on the File
menu.
2. Click the Check Structure When Copying to
Clipboard or Exporting check box.
This change affects all documents.
Viewing Analysis
Information
The Analysis window displays the chemical formula, exact mass, molecular weight, m/z, and elemental analysis for the entire document, a
structure, part of a structure, or a caption in Formula style.
To view analysis information, click the Show Analysis Window command on the View menu.
The Analysis window appears.
Figure 6.240: Analysis window
Analysis Toolbar 150 dpi
To continue checking the structure when a message appears, click Ignore.
To ignore all subsequent errors in a structure, click
Ignore All.
To stop checking a structure when a message
appears, click Stop.
ChemDraw 10
Values for selected objects in the document window are shown. If no structure is selected in your
document, values for the entire document are
shown.
You can have this window open as you draw in the
document. It shows the current values as you draw.
Chemistry Features
Checking Chemistry
• 111
The Decimals setting applies to Exact Mass,
Molecular Weight, and m/z only.
Table 28: Analysis properties
Administrator
Property Description
Formula
The molecular formula showing the
exact number of atoms of each
element in the molecule and charges,
radicals, and isotopes.
Exact Mass The exact molecular mass of the
structure, where atomic masses of
each atom are based on the most
common isotope for the element.
Molecular
Weight
m/z
The average molecular mass of the
structure, where atomic masses are
based on the natural abundance of all
isotopes of the element.
Mass/charge, where charge =1. The
weights of the most common
isotopes and a graphical representation of the isotopic abundance is
shown.
The molecular weight shown takes
the isotopes for each atom and their
natural abundance into account.
Where there is more than one abundant isotope, ChemDraw computes
multiple molecular weights. Low
abundance combinations (whether
because the isotope is in low abundance or because it includes many
moderate-abundance contributions)
are not taken into account.
Table 28: Analysis properties
Property Description
Elemental
Analysis
The percent by weight of each
element in the structure.
To paste information about a structure as a caption:
1. Click the check boxes for the information that
you want to paste.
2. Click Paste.
The information appears as a multiline caption
below the structure. You can edit this information
with the text tool.
Figure 6.241: Adding analysis information to a structure
HO
OH HO
O
HO
OH
glucose
Chemical Formula: C6H12O6
Exact Mass: 180.06
Molecular Weight: 180.16
m/z: 180.06 (100.0%), 181.07 (6.9%), 182.07 (1.4%)
Elemental Analysis: C, 40.00; H, 6.71; O, 53.29
The information in the label updates automatically
as you edit the structure. You can show or hide the
information as follows:
1. Right-click in the label. It does not matter
which tool you are using.
2. Point to Analysis, and select or deselect the
item you want to show/hide.
You cannot paste the graph in a
document.
112•
Chemistry Features
CambridgeSoft
Checking Chemistry
Figure 6.242: Analysis context menu
1. Select the entire structure.
2. Right-click and click Object Settings.
3. Check the appropriate boxes for atom and
bond stereochemistry.
The stereo-centers are marked as shown in the
following example.
Figure 6.243: Stereochemistry indicators
Showing Stereochemistry
When the Show Stereochemistry option is selected,
ChemDraw calculates the absolute stereochemistry
for tetrahedral atoms and double bonds according
to the Cahn-Ingold-Prelog (CIP) priority rules. For
more information about the CIP rules, see “Stereochemistry” on page 234.
Only tetrahedral and double-bond stereochemistry
are supported, and only non-racemic stereochemistry is interpreted. Stereochemical indicators for
aromatic bonds are not shown.
ChemDraw calculates and displays the following
stereochemical terms:
• (R), (S)—Standard tetrahedral stereochemistry
• (r), (s)—Tetrahedral stereochemistry determined by other stereochemical centers. For
example: cis-decalin and myo-inositol.
• (E), (Z)—Standard double-bond stereochemistry
The atom label settings determine the font style
and size of the terms. A setting on the Building/Display tab of the Preferences dialog box
determines whether or not the term will be displayed in parentheses. (The default is to display
parentheses.)
Stereochemistry Indicators
To show the stereochemistry of a structure:
ChemDraw 10
Cholesterol 60%
(R)
(R)
(R)
H
(S)
(S)
(R)
(S)
H
H
(S)
HO
(Z)
cholesterol
If you make changes to the drawing that affect the
stereochemistry, the stereochemistry is recalculated.
Hiding Indicators
To hide an individual indicator:
1. Select the indicator to hide.
2. Right-click and choose Hide Indicator.
Removing Indicators
To delete an indicator:
1. Click the indicator.
2. Click the eraser tool and click the indicator.
Positioning Indicators
Stereochemistry indicators are positioned automatically and move appropriately if a structure is modified. You can reposition them by dragging them to
the desired position or with the Indicator Position
dialog box.
To reposition an indicator numerically:
Chemistry Features
Checking Chemistry
• 113
Administrator
1. With a selection tool, click the indicator to
move.
2. Right-click and choose Position.
The Position Indicator dialog box appears.
Figure 6.244: Position Indicators dialog box
new notation gives you the ability to describe complex enantiomers in a compact form.
Table 30: Stereochemical Notation
New Notation
OH
Old Notation
OH
Abs
abs
Position Indicators 150 dpi
OH
OH
Rac
OH
Rel
&1
3. Click the appropriate Position option, and type
a value:
Table 29: Indicator positioning options
To Position …
Type a value for
the position
by…
from the atom or bond
center to indicator
center
angle, in degrees
or
clock, in clock time
OH
or1
The new notation is added to a structure by selecting an atom and choosing Enhanced Stereochemistry from the Structure menu.
Figure 6.245: Adding Stereochemistry
from the atom or bond offset, horizontal
center to bottom left of and vertical
indicator baseline
at specified coordinates
absolute, horizontal
and vertical
Relative Stereochemistry
Pro
Stereochemical representation has been enhanced
to allow specification of relationships between
groups of stereo-centers within a molecule. The
114•
Chemistry Features
See “Stereochemistry Indicators” on page 113 for
information on showing and hiding indicators.
The power of this new notation becomes clear
when you draw complex enantiomers. For example, beta-Cypermethrin is a mixture of four distinct
stereo isomers consisting of two enantiomeric
CambridgeSoft
Checking Chemistry
pairs. Drawing this with the old notation requires
two structures.
Figure 6.246: beta-Cypermethrin
New notation
O
&1
&2
(S)
O
(S)
&1
(R)
O
Cl
Cl
N
Old notation
Rac
O
(S)
(S)
O
(R)
O
and
Cl
Cl
N
Rac
O
(S)
(R)
O
(R)
O
Cl
Cl
N
Both stereo-centers marked with arrows in Figure
6.246 have the &1 designation because of their
fixed relative configuration: when one is (R) the
other must be (S). In other words, they form a
group.
To indicate stereochemistry for a group:
1. Select all atoms in the group using Shift + click.
2. Select the appropriate Enhanced Stereochemistry from the Structure menu.
The third stereo center varies independently, and
thus gets the &2 designation. Group numbers are
incremented automatically, but can be edited manually.
ChemDraw Enhanced Stereochemistry can be
saved in the following formats:
• CDX
• CDXML
ChemDraw 10
• MOL V3000
• RXN V3000
• SKC
• TGF
When saving to SKC or TGF format, the indicators are converted into corresponding Data
SGroups. When ChemDraw opens SKC or TGF
files containing such Data SGroups, they are converted into true Enhanced Stereochemistry values.
Converting Structures to 3D
You can convert a two-dimensional structure
drawn in ChemDraw to a three-dimensional structure. To use this feature, you must have CambridgeSoft Chem3D installed on your computer.
To convert a structure to 3D:
1. Select the structure to convert.
2. Click the Get 3D Model command on the Edit
menu.
The 3D structure appears in the document
window.
NOTE: 3D Objects inserted in this way cannot be transferred between platforms. For more information see “File
Formats” on page 170.
To edit the 3D structure:
1. Double-click the 3D structure.
Chem3D opens.
2. Edit the structure and close Chem3D when
you are finished.
The edited structure appears in the ChemDraw
document window.
Pro
Viewing Chemical
Properties
ChemDraw Pro and Ultra, using an add-on,
ChemProp, calculate predicted values for the physical and thermodynamic properties of a selected
Chemistry Features
Checking Chemistry
• 115
Administrator
structure of up to 100 atoms. You can view the values in the Chemical Properties window.
The properties are calculated using the most reliable methods for calculation for the given structure. Log P and MR values based on literature
values rather than a calculation are included in the
report file.
Viewing the Chemical Properties Window
2. Click the Show Chemical Properties Window
command on the View menu.
The Chemical Properties window appears.
Figure 6.247: Chemical properties window
ChemProperties
150 dpi
To view predicted properties for a selected structure:
1. Select the structure to analyze.
116•
Chemistry Features
CambridgeSoft
Checking Chemistry
The following basic values are displayed.
Table 31: ChemDraw chemical properties
Property
Description
Boiling Point
The boiling point for the
structure. Reported in Kelvin
at 1 atm.
Melting Point
The melting point for the
structure. Reported in Kelvin
at 1 atm.
Critical Tempera- The temperature above
ture
which the gas form of the
structure cannot be liquefied,
no matter the applied pressure (Tc). Reported in Kelvin.
Table 31: ChemDraw chemical properties
Property
Description
Heat of Formation
The heat of formation, ΔHf,
for the structure. Reported in
kJ/mol at 1 atm and 298.15K.
tPSA
Calculation of polar surface
area based on fragment
contributions.
CLogP
The calculated
n-octanol/water partition
coefficient (log Pow).
Ultra
CMR
Ultra
Critical Pressure
The minimum pressure that
must be applied to liquefy the
structure at the critical
temperature (Pc). Reported in
bars.
Critical Volume
The volume occupied at the
compound’s critical temperature and pressure (Vc).
Reported in cm3/mol.
Gibbs Energy
The Gibbs free energy, ΔG,
for the structure. Reported in
kJ/mol at 1 atm and 298.15K.
Henry’s Law
The inverse of the logarithm
of Henry’s law constant
[-log (H)] (no units).
ChemDraw 10
The calculated Molar Refractivity
NOTE: The CLogP and CMR algorithms incorporated in
ChemDraw are licensed from BioByte Corp, and have been
extensively tested and peer-reviewed as providing highly accurate results. The values produced by these algorithms in
ChemDraw should be exactly the same as values produced by
the standalone CLogP and CMR applications from BioByte.
For further information about CLogP and CMR, please
refer to the BioByte web site at:
http://www.biobyte.com
To paste the basic properties into your document:
• Click Paste.
To create a report and view results for other fragmentation methods including the Broto, Crippen,
Viswanadhan, Joback, and Joback/Stein methods:
• Click Report.
When you create a report, a detailed list of information used for performing the calculation is
shown in a text file. The list includes additional
Chemistry Features
Checking Chemistry
• 117
properties and literature references used to perform the calculation.
Figure 6.248: Fragmentation tools palette
Figure 6.249: Stoichiometry Grid
OH
O
catalyst
CN
H 3C
Administrator
Reactants
CN
H3C
H
Pr oducts
Formula
C3H3N
C2H4O
Formula
C5H 7NO
MW
53.06
44.05
MW
97.12
Limiting?
Yes
No
Equivalents
Equivalents
Expected Mass
Sample Mass
Expected Moles
%Weight
Measured Mass
Molarity
Purity
Density
Product Mass
Volume
Product Moles
Reactant Moles
Reactant Mass
%Yield
TIP: If you have a chemical label on the arrow that does not
enter in the reaction, but rather indicates a catalyst or condition, right+click on the label and deselect Interpret Chemically in the context menu before creating the grid.
To enter data in the grid:
1. Select the Text tool, and click in the empty column to enter a value.
Ultra
Stoichiometry Grid
Figure 6.250: Entering data in the Grid
The Stoichiometry Grid is a tool that calculates
stoichiometric data for a reaction. It is filled in
automatically as you modify a reaction drawing.
To create a Stoichiometry Grid:
1. Draw a reaction, or open a file containing a
reaction, and select the entire reaction.
2. Click the Analyze Stoichiometry command on
the Structure menu.
The Grid appears under the reaction.
2. Set the limiting compound. If the default setting is incorrect, point to the word “No” in the
correct column, right-click or control-click,
and select Set Limiting from the context menu.
118•
Chemistry Features
CambridgeSoft
Checking Chemistry
3. Enter values for all reactants, as applicable. If
you are using units other than the defaults, type
in the units along with the values (no space
required).
Table 32: Stoichiometry Input Values
Value
Pro
Expand Generic
Structures
Comments
Limiting reac- Only one reactant may be specified
tant
as limiting.
Sample Mass
Weight of reactant. Default units:
g.
%Weight
Reactant purity. Defaults to 100%.
Volume
Default units: ml Requires either a
Molarity or a Density value to also
be entered.
Molarity
Default units: M
Density
Default units: g/ml
Figure 6.251: Calculated stoichiometric values
Products
Formula
MW
C3H 6O2S
106.14
C2H4O
44.05
Formula
MW
Limiting?
Equivalents
Yes
No
Equivalents
Expected Mass
114.26g
Expected Moles
760.76mmol
Sample Mass
Entered values
%Weight
Molarity
Table 33: Combinatorial definition types
definition example
Anonymous Alternative
Groups
R1
1
R1
1
F
1
Cl
1
Br
1
NH2
[OMe, OH, NH2]
C5H 10O3S
150.20
Measured Mass
Purity
Density
807.50g/l
788.00g/l
Product Mass
Volume
Reactant Moles
100.00ml
760.76mmol
760.76mmol
Product Moles
%Yield
Reactant Mass
80.75g
33.51g
ChemDraw 10
You can generate multiple structures from an
abbreviated combinatorial structure with ChemDraw’s Expand Labels tool. The tool is designed
for “small” expansions, and is limited to a maximum of 500 generated structures. For large combinatorial expansions, use CambridgeSoft’s
CombiChem for Excel. Four kinds of abbreviated
combinatorial definitions may be used:
Alternative
Groups and
R-tables
As soon as you have entered the minimum amount
of information required, ChemDraw will calculate
values. As you continue entering information, or
edit inputs, the values are re-calculated. Entered
values are in bold-face; calculated values are in normal font.
Reactants
You can edit the grid for presentation with the
context menu, showing or hiding either rows or
columns. You can also change the color of the text.
Chemistry Features
Checking Chemistry
• 119
Table 33: Combinatorial definition types
Figure 6.252: Selecting a generic structure
definition example
Administrator
Element
Lists
CH3
[I, Br, Cl, F]
1
Variable
Attachment
NOTE: For alternative group/R-tables, both the
alternative group label and the table must be selected. If
the label is selected but not the table, the label will not
be modified by the expansion, and will appear as a label
in all generated structures.
CH3
1
Definitions are expanded into multiple complete
molecules. If more than one site is present in the
selection, the expansion will include all permutations of substitutions. Expansions are generated
into a new document.
To generate a combinatorial library:
1. Select at least one combinatorial substitution
definition.
2. Choose Expand Generic Structure from the
Structure menu.
The structures are generated to a new document.
Figure 6.253: Expanded generic structure
CH3
CH3
CH3
1
1
1
120•
Chemistry Features
CambridgeSoft
Checking Chemistry
Chapter 7: Struct<=>Name
Overview
Struct<=>Name is CambridgeSoft’s package of
structure-to-name and name-to-structure algorithms included with ChemDraw Ultra. Together,
they give you unprecedented power and convenience in creating and naming structures.
Struct=Name generates systematic names for
chemical structures with support for the CahnIngold-Prelog rules for stereochemistry. It is under
continuing development to improve the range of
compounds covered.
Name=Struct is a comprehensive algorithm for
converting English chemical names into chemical
structure diagrams. It is designed to interpret
chemical names as they are actually used by chemists. In other words, it recognizes the shorthand
and slang of everyday usage, in addition to recognizing most of the official IUPAC, IUBMB, and
CAS rules and recommendations. In addition, it
has an extensive algorithm for the identification of
common “typos” (typing errors, such as “mehtyl”)
to increase the odds of generating structures for
the names it is given.
Improvements to Struct=Name
In ChemDraw 10, Struct=Name has added support
for the following nomenclature types:
• Ring assemblies of two ring systems of any
type, such as binaphthyl. (added in 9.0.1)
• Spiro fusions between two ring systems of any
type. (added in 9.0.1)
• Ring fusions involving multiple rings attached
to a single core, such as dibenzo[b,d]furan.
ChemDraw 10
Struct=Name
You can insert the name of a selected structure as a
caption using the Convert Structure to Name command from the Structure menu.
The Struct=Name algorithm in use since ChemDraw 8.0 is a new proprietary naming algorithm
developed by CambridgeSoft. It replaces Beilstein’s AutoNom algorithm used in earlier versions
of ChemDraw. In ChemDraw 10.0, an auto-update
feature has been added that renames the structure
as you modify it.
The conversion of a structure to a name is limited
by many factors. Specifically, Struct=Name makes
little or no attempt to name the following:
• Bridged ring systems with more than one
bridge (for example, tricycles.)
• Radicals.
• Compounds with non-standard valence states.
• Spiro ring systems.
• Isotopically modified compounds.
• Polymers.
• Biochemicals. including specialized nomenclature for amino acids, carbohydrates, and steroids. For such compounds, only the fully
systematic organic name is produced.
Nomenclature types added in ChemDraw 10.0
include:
• Most of the most-common fused ring systems,
both those with trivial names (naphthalene,
indole) and those with systematic names
(benzo[e][1,4]diazepine, thieno[3,2b]thiophene).
• Most salts.
• Structures with a net charge.
Struct<=>Name
Overview
• 121
Administrator
• Simple mixtures and multicomponent systems.
• Heterochains.
• Multiplicative nomenclature.
• Ring assemblies.
• Bicyclics.
• Basic inorganics.
Nomenclature types added in ChemDraw 10.0
include:
• Ring assemblies of two ring systems of any
type, such as binaphthyl. (added in 9.0.1)
• Spiro fusions between two ring systems of any
type. (added in 9.0.1)
• Ring fusions involving multiple rings attached
to a single core, such as dibenzo[b,d]furan.
Struct=Name generates names with proper CIP
stereochemistry descriptors. It has no theoretical
limits to the size of the structures that can be
named.
To insert the name of a structure into your drawing:
1. Select the drawing for which you want to insert
a name.
Figure 7.254: Selecting the drawing
2. Click the Convert Structure to Name command
on the Structure menu.
Figure 7.255: Adding a name
cyclohexane
122•
Struct<=>Name
The name of the structure appears as a caption
under your drawing.
Auto Update
ChemDraw 10.0 captions include a “hot-link” feature. Chemical properties, including the chemical
name and analysis, can be included in a caption,
and will update automatically when you modify the
structure. For more information on adding data to
captions, see “Adding Analysis Data to a Caption”
on page 58.
To toggle the hot-link feature:
1. Point to the label.
2. Right-click and select Auto-update.
A check mark appears next to the command
when it is selected. Successive clicks toggle the
command on and off.
When auto-update is on (default) the label updates
each time you modify the structure.
NOTE: For large complex structures, it may take the new
label a few seconds to appear on the screen, depending on the
speed of your processor. You do not have to wait for the new
label to appear before continuing to modify your structure.
Name=Struct
You can draw a structure automatically from a
chemical name using Name=Struct.
Name=Struct recognizes most organic nomenclature. Inorganic chemistry is also usually recognized, especially when the rules closely match
those for organic chemistry.
The following are not supported:
•
•
•
•
Coordination complexes
Polyboranes
Polymers
Some highly-bridged ring systems, including
fullerenes and porphyrins/porphines
• Some stereochemistry designators: +, -, +/-,
+-, D, L, DL, endo, exo, syn, anti, r, t, c
CambridgeSoft
Overview
Although some trade names are supported,
Name=Struct is not intended to interpret trade or
common names. A chemical database, such as
chemfinder.com, is more appropriate for obtaining
structures for trade or common names. See “Finding Information on ChemFinder.com” on page
272 for more information.
NOTE: Because the syntax of German is very similar to
that of English, Name=Struct can also interpret many German names. Chemical names in other languages, however,
will generally not be recognized.
Converting Names to Structures
Figure 7.257: Inserting a named structure
Br
O
OH
2-bromobenzoic acid
If you should happen to type the name incorrectly,
Insert Structure will try to correct the error.
Figure 7.258: Typographical error warning
There are two ways to insert a name into the
document window as a structure:
• Insert Structure dialog box
• Paste Special command
Insert Structure
Insert Structure is designed for typed-in entries.
For example, to insert 2-bromobenzoic acid:
1. Choose Convert Name to Structure from the
Structure menu.
The Insert Structure dialog box appears.
2. Type 2-bromobenzoic acid.
Figure 7.256: Insert Structure dialog box
Click OK to accept the suggested spelling, or click
Cancel and start again to make a manual correction.
Paste Special
The Paste Special command allows you to paste a
name, copied to the clipboard from another application, as a structure in ChemDraw.
To paste a name from the clipboard:
1. Click in the document window.
2. Point to Paste Special on the Edit menu, and
choose Name as Structure.
The structure appears in your document.
Converting Captions to Structures
NOTE: You can also copy a name to the clipboard
and type Crtl+V or Command+V to paste the name
into the dialog box.
3. Click OK.
The molecular structure and name (if “Paste
name below structure” is selected) appear in
the drawing area.
ChemDraw 10
If a caption is already present in the drawing area
you can convert it to a structure as follows:
1. Select the caption.
Figure 7.259: Selecting a caption
2-bromobenzoic acid
Struct<=>Name
Overview
• 123
Administrator
2. Choose Convert Name to Structure from the
Structure menu.
The molecular structure and name appear in
the drawing area.
Types of Structures Supported by
Struct=Name
Struct=Name can name compounds in the following classes of structures:
Table 34: Struct=Name supported structure types
category
ChemDraw 8 supports...
ChemDraw 9 adds...
principal groups in both rings
and chains
Acid Halides
Amide derivatives of acids
Alcohols and chalcogen analogs
Anhydrides
Aldehydes and chalcogen analogs Carbonic acids
Amides
Imides
Amines and Imines
Nitric acids
Carboxylic Acids
Peroxy acids
Carboxylic Esters
Salts
Heteroatomic acid halides
Sulfides and chalcogen analogs
Heteroatomic acids (P, B, As)
Sulfoxides and chalcogen analogs
Heteroatomic esters
Hydrazides
Hydrazines
Hydroperoxides
Ketones and chalcogen analogs
Nitriles
Peroxides
S, Se and Te Amides
S, Se, and Te Acid Halides
S, Se, and Te Acids
S, Se, and Te Esters
Ringed structures
Carbomonocyclic structures
Bridged monocyclic structures
Heteromonocyclic structures
124•
Struct<=>Name
CambridgeSoft
Overview
Table 34: Struct=Name supported structure types
category
ChemDraw 8 supports...
ChemDraw 9 adds...
Fused polycyclic trivially-named
structures
Ring fusions of only two rings
Ring fusions of two multiple ring
systems
Other compounds
Phosphorous and Arsenic
compounds
Si, Ge, Sn, and Pb compounds
Boron compounds
Organometallic compounds
ChemDraw 10
Struct<=>Name
Overview
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126•
Struct<=>Name
CambridgeSoft
Overview
Chapter 8: ChemNMR
Spectrum-Structure
Assignments
Ultra
Figure 8.260: Selecting the structure and related spectrum
O
ChemDraw Ultra enables you to assign structures
to spectra.You can then display the structure associated with a specific peak by placing the pointer
on that peak.
Assigning Structures to Spectra
To assign structures to a spectrum:
1. Open a spectral file.
2. Draw the structure or structures you want to
assign to the spectrum.
3. Select specific atoms and bonds in the structure.
4. Shift-click the peak or peaks to which you want
the structure assigned.
The selection rectangle surrounds the selected
objects.
10
8
6
PPM
4
2
0
5. Click the Make Spectrum-Structure Assignment command on the Structure menu.
The selected atoms and bonds in the structure
are associated with the selected spectral peaks.
Viewing Spectral Assignments
To view the spectral assignments:
1. Click the Lasso or Marquee tool.
2. Place the pointer over a peak.
The assigned atoms or bonds are highlighted.
ChemDraw 10
ChemNMR
Spectrum-Structure Assignments
• 127
Figure 8.261: Viewing spectrum-structure assignments
NMR Shift Information—ChemNMR
Ultra
Administrator
ChemNMR is a feature of ChemDraw Ultra only.
ChemNMR estimates and displays proton and carbon-13 chemical shifts in ppm for a selected molecule.
To view 1H or 13C NMR information:
1. Select the target chemical structure.
Figure 8.262: Selecting a target
Removing Spectral Assignments
To remove spectrum to structure assignments:
1. Click the Lasso or Marquee tool.
2. Select the objects from which to remove the
assignment.
3. Click the Clear Spectrum-Structure Assignment command on the Structure menu.
128•
ChemNMR
2. Click the 1H-NMR Shifts or 13C-NMR Shifts
command on the Structure menu.
ChemNMR redraws the molecule with the estimated shifts and displays the information and
line spectrum in a new window as shown
below.
CambridgeSoft
NMR Shift Information—ChemNMR
Figure 8.263: Displaying the NMR spectrum
ChemNMR H-1 Estimation
7.01
3.22
7.02
H6.39
7.02
7.18
H
6.58
Estimation Quality: blue = good, magenta = medium, red = rough
7
6
5
4
PPM
3
2
1
0
Protocol of the H-1 NMR Prediction:
Node
Shift
CH
7.02
CH
7.02
CH
7.18
CH
7.01
CH2
3.22
H
6.58
H
6.39
ChemDraw 10
Base + Inc.
7.26
-0.12
-0.12
7.26
-0.05
-0.19
7.26
0.04
-0.12
7.26
-0.05
-0.20
1.37
1.22
0.63
5.25
1.65
-0.32
5.25
0.09
1.05
Comment (ppm rel. to TMS)
1-benzene
1 -C=C
1 -C
1-benzene
1 -C=C
1 -C
1-benzene
1 -C=C
1 -C
1-benzene
1 -C=C
1 -C
methylene
1 alpha -1:C*C*C*C*C*C*1
1 alpha -C=C
1-ethylene
1 -1:C*C(R)*C*C*C*C*1 gem
1 -C-1:C*C*C*C*C*C*1 trans
1-ethylene
1 -1:C*C(R)*C*C*C*C*1 trans
1 -C-1:C*C*C*C*C*C*1 gem
ChemNMR
NMR Shift Information—ChemNMR
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130•
ChemNMR
CambridgeSoft
NMR Shift Information—ChemNMR
Chapter 9: Drawing Objects
Overview
ChemDraw provides the following tools and tool
palettes that enable you to add chemical symbols
and shapes to your documents (A tool palette is
indicated by a
in the lower right corner of the
tool.):
• Orbital tools palette
—to draw orbitals.
• Chemical Symbols tools palette
—to
draw charges, radicals, and other symbols.
• Arrow tools palette
—to draw arrows.
• Drawing Elements tools palette
draw boxes, circles, and lines.
—to
• Brackets tools palette
—to draw brackets, braces, parentheses, and daggers.
• Arc tools palette
• Pen tool
—to draw arcs.
—to draw freehand shapes.
• TLC tool
. to reproduce TLC experiments.
You can use the tool palettes as extensions of the
Main Tool Palette, or you can tear them off and
place them anywhere on your screen.
Object behavior has improved in ChemDraw 10.0.
Most objects, with the exception of daggers and
some symbols, can be now be rotated as well as
scaled. Arrows have been completely revamped.
ChemDraw 10
Selecting Tools From a
Palette
Some tools have a palette containing different
types of that tool. When you choose a tool type
from the palette, it becomes the default tool. To
use a different tool type, select it.
To select a tool and use its default tool type, click
the tool’s icon to select it.
To choose a different tool type from the palette:
1. Click the tool’s icon and hold down the mouse
button.
The palette appears.
2. Drag to select a tool type from the palette.
3. Release the mouse button over the tool you
want to select.
The selected tool is now displayed on the Main
Tools Palette.
To display a tools palette, do one of the following:
• Select the Other Toolbars command on the
View menu, then select one of the palettes.
• Click the tool’s icon and drag to the palette’s
title bar. Release the mouse button over the
title bar.
The selected palette is displayed, and can be
dragged anywhere on the screen.
The Orbital Tools Palette
Use the Orbital tools to add orbitals to your chemical structures.
Drawing Objects
Overview
• 131
Figure 9.264: Orbital tools palette
Administrator
You draw orbitals so that the node appears first.
Depending on the orbital type, available fill patterns are:
• Background color
• Shaded
• Solid color
You can modify the fill colors with the Color
menu.
Display the Info window to view the orbital’s
length and angle relative to the X-axis while you
draw it. You can constrain the length and angle of
an orbital by selecting Fixed Lengths and Fixed
Angles on the Object menu.
NOTE: Orbitals are not normally part of the structure they
are drawn near and are not selected when you double-click a
bond, atom, or atom label with a selection tool. To group the
orbitals with the structure, use the Group command from the
Object menu. For more information, see “Grouping Objects”
on page 68.
Figure 9.266: Adding an s-orbital to an atom
Sigma Orbitals
The σ-orbital tools are shown in Figure 9.267:
Figure 9.267: Sigma orbital tools
To draw a σ-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the σ-orbital tool
from the palette.
2. Point where the orbital will be centered.
3. Drag outward along the long axis of the orbital.
Figure 9.268: Adding a sigma orbital to an atom
s-orbitals
Single Lobe Orbitals
The s-orbital tools are shown in Figure 9.265:
Single lobe orbitals are commonly used for indicating a lone pair. The single lobe orbital tools are
shown in Figure 9.269:
Figure 9.265: s-orbital tools
Figure 9.269: Single lobe orbital tools
To draw an s-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the s-orbital tool
from the palette.
2. Point to an atom where the orbital will be centered.
3. Drag outward.
132•
Drawing Objects
To draw a single lobe orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the single lobe
orbital tool from the palette.
2. Point to an atom where the narrow end of the
orbital is to be attached.
CambridgeSoft
Overview
3. Drag from the narrow end of the lobe to its
wide end.
Figure 9.270: Adding a single lobe orbital
2. Point to an atom where the node of the orbital
is to be attached.
3. Drag from the orbital node to the wide end of
the major lobe of the orbital.
Figure 9.274: Adding a hybrid orbital to an atom
p-orbitals
The p-orbital tools are shown in Figure 9.271:
d-orbitals
Figure 9.271: p-orbital tools
The d-orbital tools are shown in Figure 9.275:
Figure 9.275: d-orbital tools
To draw a p-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the p-orbital tool
from the palette.
2. Point to an atom where the node of the orbital
is to be attached.
3. Drag from the orbital node to the wide end of
the filled lobe.
Figure 9.272: Adding a p-orbital to an atom
To draw a d-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the d-orbital tool
from the palette.
2. Point to an atom where the node of the orbital
is to be attached.
3. Drag from the center of the orbital to the wide
end of a filled lobe.
Figure 9.276: Adding a d-orbital to an atom
Hybrid Orbitals
The hybrid-orbital tools are shown in Figure 9.273:
Figure 9.273: Hybrid orbital tools
dz2-orbitals
The dz orbital tools are shown in Figure 9.277:
2-
Figure 9.277: dz2-orbital tools
To draw a hybrid orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the hybrid-orbital
tool from the palette.
ChemDraw 10
To draw a dz orbital:
2-
Drawing Objects
Overview
• 133
Administrator
1. Hold down the mouse button over the Orbital
tool
and drag to select the dz2-orbital tool
from the palette.
2. Point to an atom where the node of the orbital
will be attached.
3. Drag from the center of the orbital to the wide
end of a lobe.
Figure 9.278: Adding a dz2-orbital
To represent a hydrogen atom that is directed
backwards into the plane away from you along the
Z-axis, use the H-dash symbol
. You can draw
H-dots and H-dashes only by clicking atoms.
To draw an H-dot or an H-dash:
1. Hold down the mouse button over the Chemical Symbols tool
and drag to select the
symbol from the palette.
2. Click an atom.
Figure 9.280: Adding an H-dot symbol to an atom
O
O
The Chemical Symbols Tools
Palette
Use the Chemical Symbols tools
to add
chemical symbols to your structure. When you
click the Chemical Symbols tool, the palette shown
in Figure 9.279 appears:
Figure 9.279: Chemical symbols palette
Symbols 94 dpi
When you attach a symbol (other than H-dot or Hdash) to an atom, it remains at a fixed distance
from the central character of the atom label. If you
drag the symbol, it will maintain that fixed distance
as it moves around the atom.
You can, however, use a symbol without attaching
it to an atom, place or move it anywhere, and resize
it.
H-dot symbol
O
Lone Pair
Use the lone pair symbol
to indicate a lone
pair of electrons common in Lewis structure representations.
To draw a lone pair:
1. Hold down the mouse button over the Chemical Symbols tool
and drag to select the
lone pair from the palette.
2. Click the atom where you want the lone pair
located, or drag in the appropriate direction to
position it.
The lone pair is offset from the atom at a fixed
position.
Figure 9.281: Adding a lone pair to an atom
OH
H-dot and H-dash
To represent a hydrogen atom that is coming out
of the plane toward you along the Z-axis, use the
H-dot symbol
.
134•
Drawing Objects
CambridgeSoft
Overview
Radical
Figure 9.282: Adding a charge symbol
Use the radical symbol
to indicate a single
non-bonded electron.
To draw a radical symbol:
1. Hold down the mouse button over the Chemical Symbols tool
and drag to select the
radical from the palette.
2. Point to the atom where you want the radical
symbol to appear.
3. Click to draw the symbol.
Radical Cation and Radical Anion
Use the charge radical symbols
NH3
O
H 2N
H
NH3
O
H 3N
to repre-
sent radicals that are charged.
To draw a radical cation or radical anion symbol:
1. Hold down the mouse button over the Chemical Symbols tool
and drag to select the
symbol from the palette.
2. Point to the atom where you want the symbol
to appear.
3. Drag from the charge portion of the symbol to
the radical portion of the symbol.
To add a radical cation or radical anion symbol in a
horizontal orientation, click an atom.
Charge Symbols
OH
H
OH
Attachment Points
The ability to indicate an attachment point is useful
in polymer-bound combinatorial synthesis, protein chemistry, and other situations. ChemDraw
has four standard attachment point drawing tools
that allow you to indicate a point of attachment
while maintaining chemical meaning.
Figure 9.283: Attachment point symbols
1
∗
Use the charge symbols to represent charges on
structures.
To draw a charge and associate it with a structure:
1. Hold down the mouse button over the Chemical Symbols tool
and drag to select the
charge symbol from the palette.
2. Click to the atom to which you want the charge
to correspond.
The number of hydrogen atoms increases or
decreases as appropriate for the addition of the
charge.
ChemDraw 10
The bead tool is specifically intended to indicate
attachment to a resin, but the tools are interchangeable. Any if these tools may be used for
variable attachments in queries (see “Multi-Center
and Variable Attachments” on page 73), but only
the diamond tool will show rank numbers. That is,
if you add more than one diamond to a structure,
the points will automatically number sequentially.
Drawing Objects
Overview
• 135
Administrator
Rotating a Symbol
other for arrow length or arrowhead length and
You can rotate the radical anion, cation, and lone
pair symbols by dragging the rotation handle on
the selection Rectangle. All symbols are rotated
around the same end from which they were originally drawn. For example, the radical cation symbol is rotated and resized from the charge. The
Info window shows the angle that one of the ends
of a symbol makes with the X-axis as you rotate
symbols.
To rotate a chemical symbol:
1. Select the chemical symbol with a selection
tool.
2. Drag the rotation handle on the chemical symbol.
For more information about rotating and resizing,
see “Rotating Objects” on page 65.
width.
When changing the angle of an arrow,
you are restricted to multiples of 15° if the Fixed
Angles option in the Object menu is selected. Hold
down the Alt or option key to drag to any angle.
Figure 9.285: Arrow Cursors
There are three basic arrowhead shapes, solid, hollow, and angled. Change the arrowhead type from
the context menu (see Figure 9.292) after creating
an arrow .
Figure 9.286: Arrow head types
The Arrow Tools Palette
Arrows are now customizable not only for length
and angle, but for arrowhead width and shape. You
can drag an arrow from the middle to create an arc,
allowing you to create arcs of any length.
When you mouse-over an arrow with the Lasso,
Marquee, or an Arrow tool selected, ChemDraw
switches into edit mode and adjustment handles
appear on the arrow.
Angled-head, or “line segments”, was a userrequested feature. Another user-requested feature
is “square” heads.
Figure 9.287: Square arrow head
Figure 9.284: Arrow adjustment handles
length adjustment
arc
adjustment
arrowhead shape
arrowhead length and width
Drag the adjustment handles to change the arrow
length, angle, or shape. Two different cursors
appear, one for arcs and arrowhead shape
136•
Drawing Objects
, the
ChemDraw 10.0 introduces four new arrow types:
two types of crossed (no-go) arrows, equilibrium
arrows of unequal lengths, and elliptical arcs. In
addition, you can create several new arc types (see
Figure 9.290).
For equilibrium arrows, changing the length
changes both arrows proportionately; changing the
shape of the arrowhead changes both arrowheads
identically. To change the length of only one
arrow, hold down the Alt or option key. Two new
CambridgeSoft
Overview
adjustment handles appear. When you have created
a disequilibrium arrow, only the shorter side can be
adjusted further.
Figure 9.289: Arc Variations from a Single Arrow
Figure 9.288: New Arrow Types
drag here to increase the diameter of an arc
drag here to lengthen an existing arc
Dragging the adjustment handle on the line segment creates an arc of increasing radius. After
choosing a radius, you can then adjust the arc from
1° to 359° by dragging the length. (At 360°, the line
becomes a point, and the arc starts over again.)
The assortment of pre-drawn arcs on the Arrows
Palette are for your convenience, and are customizable like other arrows. Figure 9.289shows an arrow
and two arcs created from it.
All arrows, except hollow or equilibrium arrows,
can be made into arcs. This means that dashed,
thick, double-headed, and crossed (no-go) arrows
can all be arcs.
Figure 9.290: Arc Variations
Click a modified arrow (with the same arrow tool)
to undo all changes to the shape, but not length, of
the arrow. Use Undo (Ctrl+Z) to step back
through multiple changes, or to undo changed
length. Click an unmodified arrow, or one that has
had only its length changed, to reverse its direction.
Hollow arrows have only two types of adjustment
handle—length and width. Changing the arrow-
ChemDraw 10
Drawing Objects
Overview
• 137
head width also changes the width of the line segment.
Figure 9.291: Hollow Arrow adjustment handles
Figure 9.293: Snapping arrows
1. Hold the Shift key down. This disables the adjust
handle and displays the snap point.
Administrator
2. Continue to hold the Shift key down as you drag
arrow up.
You can modify arrows with a Context menu.
Some of the context menu commands are also
available on the Curves menu. Use the Context
menu to create arrows for which there are no tools,
such as bold-dashed or dipole.
Figure 9.292: Arrows Context Menu
You can also drag existing arrows and snap them.
This method allows you to connect two arrows at
their midpoints.
Figure 9.294: Arrow Combinations
Arrows “snap” together at their end or midpoints.
To snap an arrow to an existing arrow, hold the
Shift key down to disable the adjustment handles
on the original arrow.
NOTE: The terms “left” and “right” in the context menu
are relative, and refer to the direction the arrowhead is pointing.
Finally, arrows can be rotated with the Structure
Perspective tool as well as the Lasso or Marquee.
Combining these methods allows you to draw an
unlimited number of arrows that are otherwise difficult to create.
The Drawing Elements Tools
Palette
The Drawing Elements tools provides shapes you
can add to your drawing.
Drawing elements are not a part of the structure
they are drawn near. If you double-click on a bond,
atom, or atom label with a drawing tool, they are
not selected. To group drawing elements with a
138•
Drawing Objects
CambridgeSoft
Overview
structure, use the Group command in the Object
menu. For more information, see “Grouping
Objects” on page 68.
Some drawing element types are available with fill
patterns: hollow (no fill pattern), gray, and black.
You can change the type of box, circle, or oval
using the Curves menu.
The Info window indicates the length and angle
relative to the X-axis while you use any of the
drawing element types.
Figure 9.295: Drawing elements palette
2. Point where you want the center of the circle to
be located.
3. Drag outward from the center.
Resizing or Rotating Drawing
Elements
Rectangles, circles, and ovals can now be adjusted
in a similar manner to the new arrows. You no
longer need to delete them and redraw from
scratch.
Pointing to a rectangle, circle, or oval with the
same tool or a selection tool displays adjustment
handles that can be dragged to reshape the object.
Figure 9.298: Object adjustment handles
Drawing Boxes
To draw a box:
1. Select one of the box tools.
Figure 9.296: Box tools
Circles have only a radius adjustment, but ovals
and rectangles can be resized for both length and
width. Rectangles also have corner handles that
adjust length and width proportionately.
Rectangles, circles, and ellipses can now be freely
rotated in three dimensions using the Structure
Perspective tool.
Figure 9.299: Perspective rotation of an objects
2. Point where you want a corner of the box to be
located.
3. Drag from one corner of the box diagonally to
the opposite corner.
Drawing Circles and Ovals
To draw a circle or oval:
1. Select one of the circle or oval tools.
When an object has been distorted by such rotation, dragging an adjustment point will modify the
shape while preserving the perspective.
Figure 9.297; Circle and oval tools
ChemDraw 10
Drawing Objects
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• 139
Figure 9.300: Dragging a distorted drawing object
2. Point where you want the bracket to start.
3. Drag from one end of the bracket to the other
end.
Administrator
Drawing Paired Brackets
Drawing Lines
Lines drawn with the line tool differ in two
significant ways from bonds drawn with the bond
tools:
• They are not included in chemical interpretation of the drawing
• Lines that cross appear solid
To draw using a line tool:
1. Select a line tool.
Figure 9.301: Line tools
Paired brackets can only be placed in a vertical orientation. A rectangle or box defines their position.
To draw a paired brackets:
1. Select a paired bracket tool.
Figure 9.303: Paired bracketed tools
2. Point where you want a corner of the bracket
to be located.
3. Drag from one corner of the box diagonally to
the opposite corner.
Drawing Daggers
To draw a dagger:
1. Select a dagger tool.
Figure 9.304: Dagger tools
2. Point where you want the line to start.
3. Drag from one end of the line to the other end.
Brackets includes braces { }, brackets [ ], and
parentheses ( ).
2. Point where you want the symbol to be located.
3. Click to deposit the dagger.
NOTE: The size of the dagger symbol is proportional to the
Atom Label font size specified in the Text Settings dialog
box.
Drawing Single Brackets
Framing Objects
A single bracket can be drawn in any orientation.
You can enclose your drawings or group structures
with a rectangle, brackets, parentheses, or braces.
To enclose your object:
1. Select the drawing to enclose.
2. Point to the Add Frame command on the
Object menu, and choose the type of frame to
add.
The Brackets Tools Palette
To draw a single bracket:
1. Select a single bracket tool.
Figure 9.302: Single bracket tools
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CambridgeSoft
Overview
The frame you selected is inserted in your
drawing.
The Arc Tools Palette
Use the Arc tools to draw solid or dashed arcs of
different angles: 90°, 120°, 180°, and 270°.
Figure 9.305: Arc tools palette
Arcs 94 dpi
Drawing Arcs
Where you access the arc tools depends on which
version of ChemDraw you are using.
To draw an arc:
1. Do one of the following:
• In ChemDraw Std, point to the Arc tool
and drag in the palette to select the
angle.
• In ChemDraw Pro or Ultra, point to the
Drawing Elements tool
and drag in the
tool palette to select the angle.
2. Dragging from left to right creates a convex
arc; from right to left a concave one.
The Info window shows the length between
the ends, and the angle the clockwise end
makes with the X-axis while you draw an arc.
Editing Arcs
To resize or rotate an arc using the Arc tool:
1. Select the Arc tool, and position it over the arc.
Three drag point appear – one on each end and
one in the middle.
ChemDraw 10
2. Drag either end of the arc to lengthen it.
3. Drag the center point to change the radius.
The arc is resized and rotated. The Info window
indicates the distance between the ends of the arc
and the angle the clockwise end makes with the
X-axis.
You can resize and rotate an arc by dragging the
Resize or Rotation handle on the Selection rectangle. The resize or rotation occurs around the center
defined by the Selection rectangle. When you drag
the Resize handle, the Info window indicates the
percentage enlarged or reduced. When you drag
the Rotation handle, the Info window indicates the
degree rotated. For more information, see “Rotating Objects” on page 65 and “New Selection Box”
on page 61.
The Pen Tool
Use the Pen tool to draw shapes that are not provided in the Arrow, Orbital, or Drawing Elements
palettes. For example, you can draw irregularly
shaped arrows, curves depicting graphs or reaction
coordinate diagrams, and other irregularly shaped
solids.
The Pen tool has two modes:
• Drawing—Used to create shapes. The hand
cursor appears with a “+” sign inside.
• Edit—Used to edit shapes. The hand cursor
appears without a “+” sign inside.
NOTE: To enter edit mode directly from drawing
mode, press the Esc key.
Some examples of shapes that you can draw using
the Pen tool are shown below.
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Figure 9.306: Drawing shapes with the pen tool
Administrator
Customized orbitals
Figure 9.307: Drawing Bézier curves with the pen
tool
Unique arrows
Anchor Point
Curves and axes
Geometric shapes
To toggle between a selection tool and the Pen
tool do one of the following:
• Press Ctrl+Alt+Tab or command+option+tab
• Click a selection tool.
The last drawn curve and a selection tool are
selected.
Drawing Bézier Curves by
Dragging
A Bézier curve is a curve that is calculated to connect separate points into a smooth line.You can
draw Bézier curves with the Pen tool by clicking
and dragging repeatedly to create curved segments.
To draw a Bézier Curve:
tool.
1. Select the Pen
2. Point to where you want the beginning of the
curve to appear and click.
An anchor point appears, and the cursor
changes from a “+” to a hand.
3. Move the cursor to another position and click.
A line connects the two points.
4. Position the cursor on one of the points (the
“+” in the hand will disappear when you are
correctly positioned) and drag to create an arc.
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Drawing Objects
A direction line appears tangentially to the curve.
Use the direction line to control the “curviness” of
the segment. The slope of the direction line determines the slope of the curve. The length of the
direction line determines the height of the curve.
Direction points appear at the ends of the direction
line. Use the direction points to adjust the curve by
dragging a point. You can further adjust the shape
by dragging an endpoint of the curve.
Figure 9.308: Adjusting a curve with the pen tool
Direction Point
Direction Line
Drawing Segments by Clicking
You can draw shapes with corners by clicking
repeatedly in an outline of the shape you want.
To draw segments:
tool.
1. Select the Pen
2. Point to where you want the beginning of the
curve to appear.
3. Click to deposit an anchor point.
4. Move the cursor and click again to add a second point.
5. Continue until you have the curve you want.
CambridgeSoft
Overview
Figure 9.309: Drawing line segments with the pen
tool
step 3
1. Select the Pen tool and click the existing curve
you want to edit.
2. Drag the direction lines to create the shape you
want.
Figure 9.311: Changing the shape of a curve
step 4
6. Press the Esc key or click another tool.
NOTE: To place the fewest strategically placed control
points for obtaining the smoothest curve, work in a magnified
view.
Editing a Curve
You can edit a curve by selecting it and manipulating it with the direction lines.
To select an existing curve:
1. Select the Pen
tool.
2. Point at the curve.
The cursor will change from a “+” to an arrow
when you are positioned correctly.
3. Click to select the curve.
The direction lines appear.
Figure 9.310: Editing curves with the pen tool
Adding a Segment
To extend an existing curve by adding a segment:
1. Select the Pen tool and click the existing curve
you want to edit.
2. Point to the endpoint of a curve until the cursor appears as a hand.
Figure 9.312: Adding a segment to a curve
3. Alt+click or option+click the endpoint.
The cursor appears as a hand with a “+” sign
inside.
Figure 9.313: Adding a segment; continued
Changing the Shape of a Curve
Use the endpoints of the direction lines to increase
or decrease the breadth of the curve or change its
direction.
To change the shape of a curve:
ChemDraw 10
4. Drag to connect more segments to your curve.
Deleting a Segment
To delete a curve segment, in the edit mode of the
Pen tool, Alt+Shift+click or option+shift+click
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the control point where you want to delete a curve
segment.
The cursor appears as the Eraser tool before
you click.
You can also delete entire curves using a selection
tool or the Eraser tool.
Applying a Style to a Shape
All curves are drawn with the last curve style chosen until you change the selections. Certain styles
are mutually exclusive. For example, if you choose
Closed, you cannot also choose Arrow at Start.
You can use the Doubled style to represent cell
membranes. The lines are separated by twice the
Bold Width setting for the drawing. Doubled lines
cannot be dashed or include arrows.
To apply a style to a curve:
1. Select a curve using either the Pen tool or a
selection tool.
2. Choose a style from the Curves menu.
Shaded Style
You can apply shading to any curve, however the
shaded style works best with convex or slightly
concave shapes. Shading may not appear as desired
in extremely concaved shapes.
Figure 9.316 below shows shapes with the Plain
style applied. Figure 9.317 shows the same shapes
with the Shaded style applied.
Figure 9.316: Plain closed curves
Figure 9.317: Shaded closed curves
Filled and Closed Styles
Figure 9.314 shows a shape with the Plain style
applied. Figure 9.315 shows the same shape with
the Filled and Closed styles applied. If you do not
want to fill the shape with a solid color, choose
Faded rather than Filled.
Figure 9.314: Plain style curve
Figure 9.315: Filled and closed style curve
Plain Style
To remove all styles from a curve, with a curve
selected, choose Plain from the Curves menu.
Pro
The TLC Tool
The TLC Tool is a drawing tool that allows you to
easily depict Thin Layer Chromatography plates
within a ChemDraw document. The tool creates a
rectangular plate with origin line, solvent front, and
one or more lanes. The lanes can be populated
with spots of different Rf, size, shape, or color.
To create a TLC plate:
1. Select the TLC tool
.
2. Drag in any direction from the point of origin.
The number of lanes is a function of the width
of the plate you create.
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Overview
Figure 9.318: Drawing TLC plates
Table 35: TLC plate tool options
If you want
to...
then...
Add, delete, or
duplicate a lane.
1. Position the cursor on
the lane you want to
delete or duplicate (or
between lanes to add).
2. Right-click or control-click in the plate.
3. Select the appropriate
action.
NOTE: You can also delete
lanes with the Eraser tool.
Move a spot.
Drag the spot. The Rf
displays as you drag.
You can manipulate parts of the plate as follows:
Table 35: TLC plate tool options
If you want
to...
then...
Change the height
or width of the
plate.
Drag a border or corner.
The number of lanes will
not change.
Duplicate a spot.
Ctrl+drag or option+drag
the spot.
Move the origin or
solvent front.
Drag the origin or solvent
front line.
Delete a spot.
Click on the spot with the
Eraser tool.
Show or hide the
origin, solvent
front, borders, or
side ticks.
1. Right-click or control-click in the plate.
2. Select the appropriate
action.
NOTE: Use the Transparent
option if you want to overlay the
TLC plate on a scanned plate.
Change the order of Drag the origin tick to the
lanes.
new location.
ChemDraw 10
NOTE: If you erase all spots in
a lane, the lane will be deleted.
Display or set the
Rf for a spot; add a
custom spot
1. Right-click or control-click on a spot.
2. Point to TLC Spots, and
take the appropriate
action.
NOTE: To display Rf for all
spots, Right-click or control-click in the plate and select
Show Rf from the TLC Spots
submenu.
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Table 35: TLC plate tool options
Administrator
If you want
to...
then...
Change the style or
color of a spot.
1. Right-click or control-click on a spot.
2. Choose the style or
color.
NOTE: To change the style for
all spots, Right-click or
control-click in the plate and
choose the style from the TLC
Spots submenu.
Enlarge or “smear” Shift+drag the spot. When
you position the cursor on a
a spot.
spot and press “Shift”, the
cursor assumes one of three
shapes, depending on how
it is positioned:
1. Cross arrows
.
used to enlarge a spot.
2. Horizontal arrow
.
used to widen a spot.
3. Vertical arrow
.
used to elongate a spot
or create a crescent.
NOTE: You may want to
zoom in to make positioning easier.
Rf Display
When you select Show Rf, a text label appears near
the spot showing the spot's retention factor value.
By default, the tag will show the Rf to two decimal
places. You can change the tag as follows:
• Select the tag with the Lasso or Marquee tool
and drag it to a new location, or Right-click or
control-click on the tag and choose Position...
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Drawing Objects
• Select the tag with the Text tool and edit the Rf
value.
If you change the Rf the spot will move to the
new position indicated.
If you edit the Rf to have different precision,
that precision will be preserved.
Resizing Spots
You can resize spots by holding down the Shift key
while pointing at an edge of the spot. Dragging the
left or right sides of the spot will adjust the spot’s
width only. Dragging from the top will adjust its
height only. Dragging from the bottom will adjust
the tail only. Dragging from any of the other four
corners will scale all three values. By using combinations of these dragging motions, you can reproduce any sized or shape spot you want.
Figure 9.319: Editing TLC spots
Solvent front
Crescent-shaped spo
Default spot
Enlarged spot
Elongated spot
Widened spot
Origin
Lanes
Custom Spots
The TLC tool can create the most common spot
shapes. Other types of spots, such as smears, can
be reproduced as custom spots. The Add Custom
Spot command allows you to insert a graphic file
for a spot. Typically, these files would be produced
by scanning a TLC plate and saving the spots in a
library of spot shapes.
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Overview
Chapter 10: Page Layout
Overview
The presentation quality of your ChemDraw document is determined by how well the chemical
structures and other objects are placed on the page
(layout). Effective layout of a drawing includes
proper alignment of chemical structures and other
objects, appropriate page size, and page orientation. The page layout tools include: setup of the
page and the use of the ruler, and the grouping, layering, aligning, and distributing commands. You
can also organize information on the page using
tables.
Controlling the Drawing
Area
The size of a document window is not necessarily
the same as the size of the drawing area of the
page. A document window, in most cases, actually
covers only a portion of the drawing area.
The following options allow you to set the drawing
area displayed on your screen.
• Document Settings and Page Setup from the
File menu allow you to set the size and orientation of the page, margins, headers, footers, and
the document type and size.
• View menu options: Actual Size, Fit to Window, Magnify, and Reduce.
• Magnification Controls: enlarge and reduce
• Dragging to enlarge the drawing area.
• Windows: Point to a border or corner of a
document window and drag to resize.
• Macintosh: Drag the Size box in the lower
right corner of the document window.
The size of drawing area displayed depends on the
size and resolution of your monitor. In some cases
you can see the entire document.
If you magnify a document, the drawing area size
and drawing objects become bigger. If you increase
the magnification so that the page size becomes
bigger than the screen, scroll bars become available.
Setting up Pages
You can create two types of documents:
Pages—A single document containing one or
more sheets, each of which is printed on a single
piece of paper.
Posters—A single large document, composed of
as many pieces of paper as necessary.
Paged Document Setup
To create a document with one or more page:
1. Click the Document Settings command on the
File menu.
The Document Settings dialog box appears.
Figure 10.320: Document Settings dialog box
2. On the Layout tab, check that Pages is selected.
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Page Layout
Overview
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Administrator
3. Specify the number of pages in the Document
Size section.
The size of the pages is determined by the Page
Setup settings. For more information, see
“Page Setup” on page 151.
4. Type the Margin settings.
The units of the margins are set in the Preferences dialog box. The paper size minus the
margins determines the drawing area.
5. Create Headers and Footers as described in
“Creating Headers and Footers” on page 150.
6. Click OK.
A document is created using your settings.
Poster Documents Setup
You can create a poster by creating a single large
drawing area, which will be printed on as many
separate pages as necessary. When you set the document size and how much each page overlaps,
ChemDraw calculates the number of pages needed
and the margin sizes. You can set registration
marks, which mark the overlap setting on each
page, to use as a guide when assembling the poster
from the separate pages.
To create a poster document:
1. Click the Document Settings command on the
File menu.
2. On the Layout tab, click Poster.
3. Type the Height, Width, and Page Overlap.
The number of pages and the margin dimensions are calculated.
4. Select whether to Print Registration Marks.
5. Create Headers and Footers as described in
“Creating Headers and Footers” on page 150.
6. Click OK.
An example of a 19-inch by 14-inch poster, consisting of six 8.5-inch by 11-inch pieces of paper
with a 1-inch overlap is shown below.
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Page Layout
Figure 10.321: Designing a poster document
8.5"
1"
1"
11"
1"
19" X 14" Poster
Creating Headers and Footers
You create headers and footers in the Document
Settings dialog box. In poster documents, only one
header and footer appear for the entire document.
To create headers and footers:
1. Click the Document Settings command on the
File menu.
2. Click the Footer tab.
Figure 10.322: The Footer tab of Document Settings
3. Type the value of the position from the edge of
the page that you want the header or footer to
appear.
4. Type the text to appear in the header or footer.
CambridgeSoft
Overview
5. Type additional information in the Text box
from the following table:
Table 36: Footer additional text codes
To include the…
Type …
file name
&f
page number
&p
date printed
&d
time printed
&t
of the printer driver for that printer is installed in
your System Folder.
To set the paper size, orientation, and margins:
1. Click the Page Setup command on the File
menu.
The Page Setup dialog box appears. The dialog
box appears slightly different depending on the
printer and platform you have.
A Windows dialog box for a typical postscript
printer is shown below.
Figure 10.323: Postscript printer print dialog
6. Position the text horizontally by typing the
characters in the table below. Any text following these characters is appropriately aligned.
Table 37: Footer formatting codes
To align the text …
Type …
centered
&c
right
&r
left (default)
&l
Page Setup
The Macintosh Page Setup dialog box with
common settings for a LaserWriter is shown
below.
Figure 10.324: Macintosh print page setup
The Page Setup parameters that affect the size of
the drawing area are:
• Page size
• Orientation
These parameters are specified in the Page Setup
dialog box. The Page Setup dialog box and the
options available vary depending on the printer
you have chosen. For the Macintosh, the version
ChemDraw 10
2. Select a paper size from the drop-down list.
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Administrator
The available page sizes vary depending on the
type of printer. Listed below are common sizes
available. The page orientation you choose
determines which of the measurements is
height and which is width:
Table 38: Standard paper sizes
Paper Type
Dimensions
US Letter
8.5 x 11 inches
US Legal
8.5 x 14 inches
A4 Letter
21 x 29.7 cm
B5 Letter
17.6 x 25 cm
Tabloid
11 x 17 inches
International
8.5 x 12 inches
Computer
14 x 11 inches
Page Orientation
To choose the orientation of the page, click the
vertical (portrait) or horizontal (landscape) orientation button.
The orientation of a document window
changes to the orientation you have chosen.
This is evident when the rulers are visible.
Reduce or Enlarge
Some printers include an option to reduce or
enlarge your drawings by a variable percentage (25400%). This option scales all objects and text in the
document window by the percentage specified.
This is not a change in magnification. The size of
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Page Layout
objects is changed relative to the paper size, margins, and orientation you have specified.
The enlarge or reduce option is useful for changing
the size of the available drawing area, while keeping the images on the screen at the normal size
when you are drawing. If your document is set so
that the drawing fills the page on one printer and
you use another printer that requires larger margins, the drawing my disappear off the edge of the
document window. You can reduce the size of the
drawing with the reduce option so that it fits in the
document window.
Saving Page Setup Settings
You can save Page Setup settings in a Style Sheet
or Stationery Pad. Whenever you open a Style
Sheet or Stationery Pad, these settings are automatically used. The Page Setup settings are saved in
addition to the Text settings, Drawing Settings,
and the Color Palette.
35mm Slide Boundary
Guides
If you make 35mm slides from a hard copy of a
ChemDraw document or from a screen shot, you
can display boundary lines that appear on your
screen positioned at 7 inches and 10.5 inches to
match the 2:3 ratio for the 35 mm slide format.
These guides help you keep your drawing within
this region to maintain the proper ratio, but are not
printed. The drawing area of the page must be at
least 7 x 10.5 inches for these boundary lines to be
visible.
To display the 35mm slide boundary lines:
1. Click the Preferences command on the File
menu.
2. Select the Show 35mm Slide Boundary Guides
check box.
3. Click the OK button.
CambridgeSoft
Overview
Two 35mm Slide Boundary Guides appear in
the same orientation you have chosen in the
Page Setup dialog box. These guides appear in
every document.
This preference affects all documents.
Actual Size
Changing Perspectives
Reduce
You can use a close-up view of objects in your
reaction scheme to make sure they are properly
positioned. At times, you may want to reduce your
view so that you can move groups of objects
around the page. You can change the magnification to perform these functions by using the Magnify and Reduce commands in the View menu, the
Zoom tool, or the magnification controls.
To reduce the magnification:
Magnifying with the View Menu
When you use the View menu to magnify or
reduce, the magnification is set to the next higher
or lower value. You can magnify up to 400% or
reduce to 25%.
Magnify
To magnify using the View menu:
1. Select the object around which you want to
magnify your view.
NOTE: If you do not select an object, the last object
drawn is the center point of the magnification.
2. Click the Magnify command on the View
menu.
The magnification occurs around the center of
the selected object. The magnification percentage appears in the Magnification drop-down
list.
Figure 10.325: Magnification display
Windows
Macintosh
You can continue to magnify your view to a maximum of 400%.
ChemDraw 10
To return to the actual size from any other magnification, click the Actual Size command on the
View menu.
The view is returned to the original size.
1. Select an object around which you want to
reduce the magnification.
NOTE: If you do not select an object, the last object
drawn is the center point of the magnification.
2. Click Reduce on the View menu.
The reduction in magnification appears in the
Magnification drop-down list.
Figure 10.326: Viewing reduced magnification
Windows
Macintosh
You can reduce the magnification until the entire
page fits on the screen. In the reduced view, you
can continue to use all of the drawing tools. In particular, you can use a selection tool to rearrange the
drawing in order to take better advantage of the
space available.
Fit to Window
Fit to Window reduces the magnification until the
entire page is visible in the document window.
To view the entire drawing area in a document
window at once, click the Fit to Window command
on the View menu.
The Magnification control shows the reduction
in magnification that was required to have the
entire page appear on the screen.
Using the Magnification Control
When you use the Magnification control, you can
display magnifications from 10% to 999% of the
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Overview
• 153
normal size of your page. The magnification control allows you to select a specific value.
To use the Magnification controls:
Figure 10.327: Displaying rulers
Administrator
Windows:
• Select a value from the drop-down list
or type a value.
Macintosh:
Do one of the following:
• Select a value from the drop-down list
.
• Select Other from the drop-down list. In the
dialog box that appears, type a value and click
OK.
As you move the pointer, Ruler Guides appear
on each ruler, indicating the position of the
pointer.
Figure 10.328: How rulers indicate position
Arranging Objects
This section describes methods for positioning,
aligning, and layering objects in a document window.
Ruler Guides
Using Rulers
You can use the rulers to position objects a measured distance away from some reference point or
create objects of an approximate size. The units
used for the ruler are set in the Preferences dialog
box, where you have the choice of inches, centimeters or points.
Showing Rulers
To display the rulers, click the Show Rulers command on the View menu.
A check mark appears next to the Show Rulers
command, and the rulers appear along the top
and left edges of a document window.
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Page Layout
Ruler guides also appear when you drag selected
objects. In this case, however, there are two Ruler
guides that bracket the object. With this bracketing
you can quickly establish the height and width of
the selected objects.
Figure 10.329: Using ruler guides to show height and
width
Ruler Guides
CambridgeSoft
Overview
Hiding Rulers
To Hide the rulers, deselect Show Rulers on the
View menu.
The check mark disappears.
Using the Crosshair
Use the Crosshair to align objects relative to each
other, and to space objects a consistent distance
apart. The axes of the Crosshair can be moved
within a document window.
Displaying the Crosshair
To show the Crosshair, click the Show Crosshair
command on the View menu.
A check mark appears next to the Show
Crosshair command and the Crosshair appear
within a document window.
To assist you in aligning objects, the Crosshair
includes grid lines that extend from the major division marks on each axis.
Figure 10.330: Displaying the crosshair grid
You can also show the Rulers while the Crosshairs
are displayed so that you can see the unit measurement associated with each of the divisions on the
Crosshair axes.
Moving the Crosshair
To move the Crosshair:
ChemDraw 10
1. Position the pointer where the Crosshair axes
intersect.
When the pointer is near to the center of the
Crosshair, it changes to an arrow.
2. Drag the Crosshair.
To constrain the movement of the Crosshair to the
X- or Y-direction, shift+drag the crosshair.
Aligning Objects using the
Crosshair
To use the Crosshair to align objects do one of the
following:
• Move the Crosshair axes and align it with the
object.
• Select an object and drag it until it is aligned
with either axis of the Crosshair, or a grid line.
In either case, if a bond or side of the object is parallel to one of the axis, it disappears when it is
exactly positioned over a Crosshair axis.
To align another object on the Crosshair:
1. Select a second object.
2. Drag the second object to the Crosshair axis or
grid line and align it to the first.
You can also move selected objects in small increments to align them with the Crosshair using the
Arrow keys available on some keyboards:
To move 1 point in the direction of an Arrow key,
select the objects and press an Arrow key.
NOTE: 1 point equals 1/72 inch or 0.035 cm.
To move 10 points using the Arrow key, for example, to the right, press Alt+Right Arrow or
option+right arrow.
Hiding the Crosshair
To hide the Crosshair, click the Show Crosshair
command on the View menu.
The check mark next to the Show Crosshair
command disappears.
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Centering on a Page
Administrator
To center an object (or group of objects) at the
center of the page:
1. Select the object you want to center using a
selection tool.
2. Click the Center on Page command on the
Object menu.
The selected objects move so that the center of
the Selection rectangle is positioned at the center of the page.
Aligning Objects
Use the Align commands to align objects relative
to each other. Examples of the types of alignments
are shown on the menu.
Figure 10.331: The Align submenu
Figure 10.332: Aligning structures
CH3
CH3
HO
HO
CH3
CH3
MeO
MeO
NOTE: If you look closely, you can see that the structures
in Figure 10.332 were aligned on left edges, not centers.
If you select only part of a structure or group with
a selection tool, only that part is used for the alignment operation, but the entire structure or group is
moved.
Distributing Objects
Use the distribute commands to distribute objects
horizontally or vertically and at an equal distance
apart. For reactants and products with different
shapes, select the parts of the objects to distribute.
To distribute 3 or more objects:
1. Select the 3 or more objects to distribute.
2. Point to the Distribute command on the Object
menu, and choose Vertically or Horizontally.
Figure 10.333: Distributing objects
H
OH
CH2Br
To align two or more objects:
1. Select the objects with a selection tool.
2. Choose one of the Align commands from the
Align submenu of the Object menu.
H
OH
CH2Br
The space between the objects is equalized.
The upper, lower, right, and left positions of
objects in your selection remain unchanged.
Front to Back Ordering
The front to back ordering is a useful method for
changing the orientation of one object relative to
another object within the same picture layer. For
156•
Page Layout
CambridgeSoft
Overview
additional information specific to the layering of
bonds, see “Changing Bond Crossings” on page
55.
table, you can draw it directly in the table, or copy
or drag it into the table.
The Table tool enables you to do the following:
Send to Back
• Create and modify tables
• Customize the borders
• Add or delete rows and columns
• Resize the table and its cells manually
• Fit a cell around its contents automatically
• Align cell contents
To create a table with the Table tool:
1. Select the Table tool on the Main Tools
palette.
2. Do one of the following:
• Click and drag in the document window to
create the table.
The default table has two rows and two
columns.
• Click in the document window. Type the
numbers of rows and columns in the Insert
Table dialog box, and click OK.
To place one object behind another within a layer:
1. Select the object that you want to send to the
back, in this example, the two upper orbitals.
2. Click the Send to Back command on the
Object menu.
Figure 10.334: Moving objects to the back
The selected object appears behind all other
objects in the same layer.
Bring to Front
To place one object in front of another within a
layer:
1. Select the object that you want to move forward.
2. Click the Bring to Front command on the
Object menu.
The selected object now appears in front of all
other objects.
NOTE: When bonds have 3D coordinates, those coordinates always determine the visible bond crossings. Bring To
Front and Send To Back have no visible effect in this case.
Figure 10.335: The Table tool dialog box
The table appears in the document window.
Figure 10.336: Adding a table to a document
Creating Tables
You can create tables of ChemDraw objects with
the Table tool or tables of text with the Text tool.
Creating Tables with the Table
Tool
Tables created with the Table tool are containers
for drawings and data. To place a structure in a
ChemDraw 10
Page Layout
Overview
• 157
To resize the rows or columns:
1. Place your pointer on the border to resize.
The pointer changes to a double-headed arrow.
Administrator
2. Drag the border to the desired size.
Changed Table tool behavior
Table 39: Table tool behavior in ChemDraw 10
when
you...
ChemDraw 9
ChemDraw
10
change the
width of a
column
with the
shift key:
Table width stays
the same; only the
column you are
adjusting changes.
Table width
resizes; other
columns stay
the same.
change the
height of a
row with
the shift
key:
Table height stays
the same; only the
row you are
adjusting changes.
Table height
stays the
same; only the
row you are
adjusting
changes.
Table 39: Table tool behavior in ChemDraw 10
when
you...
ChemDraw 9
ChemDraw
10
change the Table width stays
width of a the same; columns
column:
to the right move.
The result is that the
right-most column
also changes width.
Table width
stays the
same; only the
column you
are adjusting
changes.
change the Table height stays
height of a the same; rows
row:
below move. The
result is that the
bottom-most
column also
changes height.
Table height
changes with
the change in
the row. All
other rows
stay the same.
158•
Page Layout
change the Table resizes
table height proportionately.
(drag the
top or
bottom
border)
Top: table
resizes
proportionately.
change the Table resizes
table width proportionately.
(drag the
left or right
border)
Left: table
resizes
proportionately.
Bottom:
bottom row
resizes.
Right: right
column
resizes.
CambridgeSoft
Overview
Table 39: Table tool behavior in ChemDraw 10
when
you...
ChemDraw 9
change the Top: table resizes
table height proportionately.
with the
Bottom: bottom
shift key
row resizes.
ChemDraw
10
Top: table
resizes
proportionately.
Bottom:
bottom row
resizes.
change the Left: table resizes
table width proportionately.
with the
Right: right column
shift key
resizes.
Left: table
resizes
proportionately.
3. In the Setting section, click the borders to
which you want to apply the settings.
4. In the Style section, select the style, color and
width of the border to apply.
5. In the table diagram, click the borders to customize.
6. Click OK.
The table tool includes commands for alignment
of cell contents, fit, adding or deleting cells, and
clearing cells. In general, to change the whole table,
work with the right or bottom borders. To change
only a single row or column, work with the left or
top borders.
To make a cell fit around its contents, such as in
the table shown below:
Figure 10.338: Fitting a table cell around the contents
O
Right: right
column
resizes.
To customize the borders of the table:
1. With the Table tool selected, point to a border
and right-click (Mac: option-click).
2. Click Borders on the context menu.
The Table Borders dialog box appears.
Figure 10.337: The Table Borders dialog box
OH
1. Point to a border and right-click.
2. Choose Size To Fit Contents.
The cells resize to fit around the contents.
Figure 10.339: Resizing a table cell
O
OH
To add rows or columns to the table:
ChemDraw 10
Page Layout
Overview
• 159
1. Point to the top or left border where you want
to add the row or column.
The cursor changes as shown below.
Administrator
Figure 10.340: Table cursor when dragging
Table 40: Adding rows and columns to tables
If you want to …
Then choose …
delete the indicated
column and its
contents
Delete Column.
To align all of the objects in a column or row, point
to a top or left border, right-click, point to the Align
command on the context menu, and choose the
alignment you want.
2. Right-click or Option-click, and from the
menu that appears, choose the appropriate
option:
Table 40: Adding rows and columns to tables
If you want to …
Then choose …
add an empty row
above the indicated
row
Add Row Before.
add an empty row
below the indicated
row
Add Row After.
add an empty column
to the left of the indicated column
Add Column Before.
delete the indicated row Delete Row.
and its contents
Page Layout
Creating Tables with the Text
Tool
ChemDraw allows you to create tables of text
using the Tab key with the Text tool.
add an empty column Add Column After.
to the right of the indicated column
160•
The cell contents shift and stay in a fixed position relative to the cell. The default alignment
is unaligned.
To align all of the objects in a table, point to a bottom or right border, right-click, point to Align, and
choose the alignment you want.
Creating the First Row (column
headings)
To create the first row and establish the columns
of a table:
1. Click the Text tool.
2. Click in a document window where you want
the table to start.
3. Type a caption.
4. Press Tab.
A second caption box appears.
5. Type a second caption.
The second column is placed 20 points
(20/72 inch, 0.71 cm) to the right of the first.
CambridgeSoft
Overview
6. Press Tab again to create a third column, and
so on.
NOTE: The style, font, and size that you set in each column are maintained in all the rows that follow.
Figure 10.341 shows the creation of new columns
using the Tab key.
Figure 10.341: Using the Tab key in text tables
Compound
MW
LogP
LD50
To change the spacing between columns one point
at a time while editing a caption:
1. Select the caption.
2. Move the caption with the arrow keys.
For more information on moving objects, see
“Moving Objects” on page 64.
To create another column with this same spacing
as the previous, press Tab.
A third caption text box appears.
Creating a New Row
To start a new row that is exactly aligned with the
first, press Tab twice at the end of a row.
A caption text box appears exactly aligned
under the first caption positioned exactly 20
points below the first caption in the first row.
The Figure 10.342 illustrates the creation of a new
row.
To continue and fill in the row with captions, press
Tab to create another caption in the row, and then
press Tab twice to begin a new row.
The spacing between the newest row and the
row directly before it have the same spacing
that you specified between the previous two
rows.
Adjusting Row or Column Spacing
To use a selection tool to adjust the spacing in a
table:
1. Select all of the captions with a selection tool.
2. Shift+drag the caption.
The movement is constrained to the X-axis or
Y-axis so that you can maintain the row or column alignment.
Moving Around In Tables
To move within an existing table, click the Text
tool and select a caption.
Press Ctrl+arrow or command+arrow to
move to the next caption in the direction of the
arrow.
Alternatively, you can use the key combinations
shown in Table 41.:
Table 41: Moving around in a text table
Use …
To move …
Tab
right
Shift+Tab
left
Ctrl+Enter or
command+return
down
Ctrl+Shift+Enter or
command+shift+return
up
Figure 10.342: Creating a new row in a text table
To change the spacing between rows as you create
the table:
1. Select the captions in a row.
2. Move the captions using the arrow keys.
For more information on moving objects, see
“Moving Objects” on page 64.
ChemDraw 10
Page Layout
Overview
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Administrator
Inserting a New Row
Printing
To insert a row:
ChemDraw uses the standard system commands to
print ChemDraw documents. The options that you
have available to you depend on the printer that
you are using. Refer to your printer’s documentation for more information.
In general, to print a ChemDraw document:
1. Click Page Setup on the File menu.
2. Make all appropriate selections for the printer
you are using and click OK.
3. Click the Print command on the File menu.
4. Make your selections in the Print dialog box
and click OK.
To print a document from Windows Explorer or
from the Finder:
1. Select the document you want to print.
2. Click Print on the File menu.
The ChemDraw application is opened and the
Print dialog box appears.
3. Make your selections in the Print dialog box
and click OK.
1. Select a selection tool and select a row of captions.
2. Shift+drag the selected row.
Shift constrains the movement to the Y-axis to
maintain the column alignment.
3. Select the first caption in the row above or
below the space you created.
4. Ctrl+Shift+drag or command+shift+drag
to create a copy of the caption and position it
in the empty space you created.
The placement of this copied caption sets the
position of the inserted row.
To fill in the inserted row with caption text:
1. Click the Text tool and select the first caption
in the inserted row.
2. Type new text.
Press Tab to move to the second caption in the
inserted row, and so on.
162•
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CambridgeSoft
Overview
Chapter 11: Sharing Information
Overview
Figure 11.343: Copy As submenu
ChemDraw includes many of the standard system
commands for transferring information within and
between ChemDraw documents, and between
ChemDraw and documents created using other
applications.
You can transfer information using:
• the Clipboard
• drag and drop
• file formats
When you drag-and-drop ChemDraw information,
or use the clipboard, the object you are copying
can be edited.
Using the Clipboard
You can use the clipboard to transfer part or all of
the information within an active document window between applications on the same computer
or a networked computer. Use the standard
“Copy-and-Paste” or “Cut-and-Paste” tools to
transfer information to any application that supports these tools. The information is transferred as
a ChemDraw drawing object. Double-clicking on it
will open ChemDraw and allow you to edit the
object. See “Embedding Objects (Windows)” on
page 167 and “Edit Graphic Object (Macintosh)”
on page 167 for more information on editing
ChemDraw objects embedded in other documents.
You may also use the Copy As tool to translate a
selected structure to a SMILES, SLN, or InChI™
string.
ChemDraw 10
If the Clipboard contains ChemDraw structures
and you are pasting into another ChemDraw document, the pasted information is scaled to the settings in the current document. For more
information, see “Autoscaling” on page 165.
If you are pasting the ChemDraw drawing into a
document from which you are planning to print to
a PostScript printer, see“Transferring PostScript
(Macintosh)” on page 167.
SMILES and SMIRKS Strings
A SMILES string is a way to describe a chemical
structure in a line of text. Several software packages use SMILES strings as a way to enter and
store chemical structure information.
A SMIRKS string is a way to describe chemical
reactions in text. If you select a reaction and use
the Copy As SMILES command, a SMIRKS string
is copied to the clipboard. If you use the Paste Special SMILES command when a SMIRKS string is
on the clipboard, a reaction is pasted into your
document.
Sharing Information
Overview
• 163
Creating SMILES Strings
Administrator
To create the SMILES string for the following
structure:
1. Select the structure using a selection tool.
2. Point to the Copy As, command on the Edit
menu, and choose SMILES.
The SMILES string is transferred to the Clipboard.
Figure 11 - 1: Using SMILES strings
NH2
OH
N[[email protected]@H]1[[email protected]](O)CCCC1
To display the SMILES string, paste the string in a
document window.
When the SMILES string is on the Clipboard, you
can transfer it to another application that can interpret and manipulate SMILES strings.
If you select more than one structure in ChemDraw, and choose Copy SMILES from the Edit
menu, the SMILES string for each structure is copied to the Clipboard and separated from the previous SMILES string by a period.
SMILES supports an alternate notation for aromatic structures using lowercase letters. ChemDraw generates this type of SMILES string for any
structure drawn with explicit aromatic bonds,
either by using the Aromatic bond type in the
Atom Properties dialog box, or by placing a circle
within any ring structure.
164•
Sharing Information
Figure 11.2: Aromatic SMILES notation
C1=CC=CC=C1
Pro
c1ccccc1
Pasting SMILES from Clipboard
If you have a SMILES string, then you can automatically convert that text string into a ChemDraw
structure.
To paste a SMILES string as a ChemDraw structure:
1. Select the SMILES string using the Text tool.
2. Click the Copy command on the Edit menu.
3. Point to Paste Special on the Edit menu, and
choose SMILES.
The SMILES string is drawn as a structure.
NOTE: Pasting SMILES uses the same routines as the
Structure CleanUp command. For more information, see
“Multi-Center and Variable Attachments” on page 73.
Pro
Creating SLN Strings
You can copy a ChemDraw structure to the Clipboard as an SLN string for export to a Tripos
application.
To copy a ChemDraw structure as an SLN string:
1. Select a structure.
2. Point to Copy As on the Edit menu, and
choose SLN.
The Structure is copied to the clipboard as an
SLN String.
CambridgeSoft
Overview
Figure 11.3: SLN strings
C[1][email protected]
Pro
Creating InChI™1 Strings
ChemDraw 10 supports the IUPAC International
Chemical Identifier (InChI™) protocol. A new
addition to the Copy As submenu allows structures
to be copied to other documents as InChI™
strings. It is used the same way as the SLN command.
NOTE: InChI™ is not supported in either BioDraw Pro
or Ultra.
You may only copy legitimate InChI™ structures.
If you attempt to copy a structure not supported
by the InChI™ protocol, a warning appears
informing you that the structure is not supported.
For more information on InChI™, and on using
InChI™ strings in publications, see the InChI™
project page, http://www.iupac.org/inchi/, or the
informal FAQ at:
http://wwmm.ch.cam.ac.uk/inchifaq/.
Using Drag-and-Drop
You can use the drag-and-drop feature to copy
objects to place in other documents. To use this
feature in other applications, they must support
drag-and-drop. As when using the clipboard, the
information is transferred as a ChemDraw object
and can be edited.
You can also use the drag-and-drop feature to create clipping files (Macintosh) or scrap files (Windows).
1. InChI™ is a trademark of the International Union of Pure and Applied Chemistry. InChI™ Material in ChemDraw is ©
IUPAC 2005.
ChemDraw 10
To create a clipping file or a scrap file:
1. Select an object in a ChemDraw document.
2. Drag the selection out of the ChemDraw document window onto the desktop.
A clipping file or a scrap file is created on your
desktop.
To view the information within a clipping file or a
scrap file, double-click the file’s icon.
A window appears showing the ChemDraw
drawing. Click the close box to close the clipping file’s window.
To use the contents of a clipping or scrap file in a
document, drag the clipping or scrap file into an
open window of an application that supports the
drag-and-drop feature.
The contents of the clipping or scrap file are
copied to the open window. The clipping or
scrap file is unchanged.
Transferring Between
ChemDraw Documents
Whether you use the clipboard or drag-and-drop,
when you move objects into another ChemDraw
document they will behave in a well-defined way. In
particular, you should be aware of the behavior of:
•
•
•
•
•
•
Autoscaling
Bonds
Atom Labels
Captions
Non-bond Objects and Color
Pasting to an Empty Document Window
Autoscaling
When you transfer ChemDraw objects using the
Clipboard or drag and drop from one ChemDraw
document (the source document) to another
ChemDraw document (the destination document), the objects are automatically scaled to
Sharing Information
Overview
• 165
Administrator
match the document settings of the destination
document. Automatic scaling assures that the
objects being transferred match the settings of the
current document.
Bonds
All bonds drawn in the source document using the
values specified on the Drawing Settings tab of the
Document settings dialog box can be changed to
use the Drawing Settings in the destination document.
Any resized bond in the source document is scaled
in the destination document. The scale factor is
based on the ratio of the bond’s length after resizing (source) to the Fixed Length on the Drawing
Settings tab (source). This scaling process maintains the source document proportions in the destination document. All values on the Drawing
Settings tab are scaled using this method.
For example, the Fixed Length is set to 1.0 cm in a
source document. A benzene ring is resized in to
200%. The bond length is then 2.0 cm: a ratio of
2.0 cm:1.0 cm or a scale factor of 2. In the destination document, the Fixed Length set to 1.7 cm.
When the benzene ring is pasted into the destination document, the bonds are scaled by a factor of
2 to a final bond length of 3.4 cm.
Atom Labels
Atom labels are scaled the same way as bonds.
For example, in the source document, the atom
label font size is set to 16 points. One or two atom
labels in the source document are resized to 8
points, a ratio of 8:16 or a scale factor of 0.5. The
destination document has an atom label font size is
set to 14 points. When the atom label is pasted into
the destination document, the font size is scaled by
a factor of 0.5 to give a final atom label font size of
7 points.
166•
Sharing Information
Captions
ChemDraw autoscales captions are autoscaled
using the ratio of the fixed length in the destination
document to the fixed length in the source document times the caption font size. The font size of
the caption can be any size and is not related to the
setting in the Settings dialog box. This assures that
captions are always in proportion to the bonds
with which they are pasted.
For example, If the source document has a fixed
length of 1.0 cm and the destination document has
a fixed length of 2.0 cm, and the caption you are
pasting is 12 points, then the resulting caption size
after autoscaling is (2.0 cm /1.0 cm) x 12 points =
24 points.
Non-bond Objects and Color
All objects that are not affected by settings in the
Document Settings dialog boxes, such as arrows
and boxes, are scaled to maintain the same proportions to bonds that were present in the source document.
With the exception of the foreground and background color, the other colors present in the selection to be pasted are added to the destination
document’s Color Palette if they are not already
present (up to a maximum of 20 total colors). The
background color in the destination document is
unchanged, and all objects colored using the foreground color are changed to match the foreground
color in the destination document.
Pasting to an Empty Document
Window
If you paste a ChemDraw drawing into an empty
ChemDraw document and the settings between
the documents are different, the Change Settings
dialog box appears:
CambridgeSoft
Overview
Figure 11.4: Change Settings dialog box
To change the settings in the destination document
to match the settings in the source document, click
Change Settings.
All of the settings in the destination document
are changed to match those of the source document. All of the colors in the Color Palette of
the destination document are changed to those
specified in the source document.
To scale the objects from the source document to
the settings in the destination document, click
Don’t Change Settings.
The settings from the source document are
scaled to those in the destination document
using the ratios given above.
NOTE: If the source document was created in a ChemDraw version earlier than 3.0, the name of the document
appears as “Unknown” in the dialog box.
Embedding Objects
(Windows)
ChemDraw supports the Object Linking and
Embedding (OLE) protocol on Windows. This
allows you to edit ChemDraw structures that are
pasted in other types of documents. ChemDraw is
an OLE server, which means it can create OLE
objects that can be copied and pasted into other
OLE client applications.
When a drawing is transferred from ChemDraw
into another document type that supports OLE,
you can open the drawing and edit it from within
the client application.
ChemDraw 10
For example, to edit a ChemDraw drawing inserted
into Microsoft Word for Windows version 6.0 or
later, do one of the following:
• Select a ChemDraw drawing in a Word document and from the Edit menu, point to
CS ChemDraw Drawing Object, and choose
Edit.
• Double-click a ChemDraw drawing in a Word
document.
The ChemDraw tools and menus replace those
of Word. Use the ChemDraw tools to edit the
drawing.
When you have finished making changes, click in
another area of the document.
The Word tools and menus are restored.
Edit Graphic Object
(Macintosh)
ChemDraw supports the Edit Graphic Object
(EGO) protocol for editing ChemDraw structures
pasted into other types of documents. When you
drag an object from ChemDraw into another type
of document that supports the EGO protocol, or
copy it with the clipboard, you can double-click on
the object and it appears in a ChemDraw document window. When you close the ChemDraw
document window, any changes you made are
reflected in the other document.
NOTE: As of this writing, versions of Microsoft Word
after 5.0 do not support EGO.
Transferring PostScript
(Macintosh)
To obtain the highest quality drawings possible on
a PostScript printer, ChemDraw creates both a
screen representation and a PostScript representation of your drawing. PostScript is a page-definition language used to describe drawings. Many
Sharing Information
Overview
• 167
Administrator
printers, including most Apple LaserWriter printers, use PostScript to create high quality output.
For best print quality under all circumstances, we
recommend that you leave the Include PostScript
and Include ChemDraw Laser Prep preferences
selected (default) when you copy and paste from
ChemDraw to other applications. The ChemDraw
Laser Prep option adds approximately 11K to 12K
to each drawing, but these options give you the
greatest flexibility if you give your document to
someone else or later want to print it on a PostScript printer.
If you never plan to print to a PostScript printer or
never plan to give your document to someone who
uses a PostScript printer, you can turn the preferences off.
Importing and Exporting
Many applications can use the information contained within a ChemDraw document and saved to
another file format. Similarly, ChemDraw can
import and work with information in a number of
file formats. Not all formats are supported for
both import and export. See the individual format
descriptions for details. File formats are available in
a pop-up menu at the bottom of the “Open” and
“Save As” dialog boxes.
To export a file:
1. Click the Save As command on the File menu.
Figure 11.5: Save As dialog box
To deselect the PostScript preferences:
1. Click the Preferences on the File menu.
2. Deselect Include PostScript and Include ChemDraw LaserPrep.
To transfer only a few drawings to another document, select Include PostScript and Include ChemDraw Laser Prep in the Preferences dialog box.
The PostScript commands and the
ChemDraw Laser Prep are transferred with
each drawing. The transferred drawings can
be printed independently of ChemDraw.
If you do not check the Include PostScript check
box when printing to a PostScript printer ChemDraw sends QuickDraw commands to the printer.
For more information, see “Printing Background
Color” on page 214.
NOTE: You can also transfer drawings to a document in a
remote location whose printer cannot be initialized by ChemDraw.
To print to a non-PostScript printer, deselect both
Include PostScript and Include ChemDraw Laser
Prep on the General tab of the Preferences dialog
box.
168•
Sharing Information
2. In the Save As dialog box, do the following:
a. Type a name for the file and choose a location in which to save it. Use the “Go To
ChemDraw Items” button to quickly locate
the ChemDraw Items folder.
b. Select a file format from the bottom of the
dialog box.
c. Click OK or Save.
A copy of the current document is saved in the
format you specified. The current document
remains unchanged.
Some file formats do not support atom labels that
contain nicknames or structural fragments. When
you save in these formats, ChemDraw automatically expands all atom labels and saves the file
using the expanded form. For more information,
CambridgeSoft
Overview
see “Expanding and Contracting Labels” on page
70.
The following formats do not support nicknames
or structural fragments:
As drop down menu: ISIS Reaction V3000 (RXN)
and MDL Molfile V3000 (MOL). If you have used
features that require the V3000 format, you must
select it manually; there is no auto-detect on save.
• Connection Table
• MSI MolFile
• SMD
Some formats can be saved with different options.
If a format has no save options, the “Options”
button is grayed out. The following text-based formats can use the Text Options:
• ChemDraw XML
• CML
• Connection Table
• ISIS/TGF
• ISIS/Reactions
• MDL MolFile
• Molecular Simulations MolFile
• SMD
Attached Data
Figure 11.6: Text File options
ChemDraw 10 supports associating text fields with
objects such as atoms and bonds by defining a
“field name”. The feature is compatible with the
“Data SGroup” in MDL formats, and will be converted to Data SGroups when saved in MDL formats if:
• a field name is specified and
it is attached to:
• a collection of atoms and bonds, or
• a single set of brackets
If it is attached to both a collection of atoms and
bonds and a set of brackets, it will be converted to
two different Data SGroups.
To attach data to objects:
1. Select an object.
2. Click the Attach Data command on the Object
menu.
Figure 11.7: Attach Data command
Other format options are noted in format descriptions.
Improved ISIS compatibility
ChemDraw 10 has improved support for the
ISIS/Sketch (SKC), ISIS/TGF (TGF) and
ISIS/Reaction (RXN) formats. Support for both
import and export of the V3000 format has been
added.
ChemDraw auto-detects V3000 files on import.
For export, there are two new entries in the Save
ChemDraw 10
The Attach Data dialog box appears.
Figure 11.8: Attach Data dialog box
Sharing Information
Overview
• 169
3. Enter the field name and click OK.
Administrator
NOTE: Field names cannot be edited in ChemDraw
after they are created. While ChemDraw will allow any
field name length, MDL formats have restrictions that
users should be aware of before creating names.
Likewise, ChemDraw will allow data to be attached to
any object. When saving to MDL formats, this data
will be lost unless the object meets the rules noted above.
4. Enter the data in the text box under the object.
Modifying Attached Data
ChemDraw treats attached data as normal text for
most purposes. However, two additional commands appear on the context menu when attached
data is selected.
Figure 11.9: Attached data context menu
limited to: WMF, PICT, EPS, TIFF, GIF, BMP,
and PNG. It applies to both the clipboard and
saved files.
The default value is 2 points (0.278 in; 0.071 cm).
The value can be zero, meaning that the exported
image is exactly snug against the objects in the
graphic. However, this is not recommended
because a bug in Windows causes clipping at the
edges of metafiles when they are reduced in size.
The default value should prevent clipping with
reductions to about 20% of original size.
File Formats
ChemDraw supports both import and export
(except as noted below) of the following file formats. To export a ChemDraw file to one of these
formats, use the Save As... option when saving.
Not all formats are supported in all versions of
ChemDraw, as noted in the table below. For additional information on importing files, see “Inserting Objects from Other Applications” on page
177.
Table 42: Import and export of different file formats
• Select Linked Objects changes the selection to
include all of the objects associated with the
data.
• Position opens up the same dialog that is used
to position ObjectTags, allowing you to position the data relative to the associated structure.
NOTE: Positioning information is lost when saving to
MDL formats.
Graphics export border
preference
An explicit preference option allows the user to
specify the size of the border when exporting pictures. This preference affects the output of all
graphical formats, including but not necessarily
170•
Sharing Information
Format
Import Export
ChemDraw (CDX)
YES
YES
ChemDraw XML (CDXML) YES
YES
ChemDraw 3.5 (CHM)
YES
YES
ChemDraw 2.0 and ChemDraw 2.1 (CHM)
YES
NO
Pro ChemDraw
Template (CTP)
YES
YES
Pro ChemDraw
Template Style Sheet (CTS)
YES
YES
CambridgeSoft
Overview
Table 42: Import and export of different file formats
Table 42: Import and export of different file formats
Format
Import Export
Format
Import Export
ChemDraw Stationery/Style
Sheet (CDS)
YES
YES
PICT (Macintosh)
YES
YES
YES
YES
YES
Portable Network Graphics
(PNG)
YES
YES
Pro Standard Molecular YES
Data (SMD)
Pro
(SPC)
NO
Pro
(CT)
Connection Table
Pro Chemical Markup
Language (CML)
YES
YES
Bitmap (BMP)
YES
YES
Encapsulated PostScript
(Macintosh)
NO
YES
PostScript (EPS) (Windows)
Galactic Industries YES
Windows Metafile
(EMF, WMF)
YES
YES
TIFF file (TIF)
YES
YES
a. May have limitations. See the appropriate section
in the text.
Graphic Image Format (GIF) YES
YES
Pro
RXN)
YESa
Pro
ISIS (SKC, TGF,
YES
JCAMP (JDX, DX) YES
NO
JPEG (JPG, JPEG)
YES
NO
Pro
(MOL)
YES
YES
MDL MolFile
Bitmap BMP)
Bitmap (BMP) files store raster graphics in an array
of individual bits. Bitmap images are the most
common format for continuous-tone images.
Because they represent a fixed number of pixels,
bitmaps are resolution dependent and may appear
jagged and lose detail if they are scaled on-screen
or printed on a higher resolution printer than they
were created for.
ChemDraw Template (CTP, CTR)
YES
YES
Use the ChemDraw Template file format to save
template documents that appear in the template
pop-up menu.
(Macintosh) Pro Molec- YES
ular Simulations MolFile
(MSM)
YES
ChemDraw (CDX)
MDL RGFile (RGF)
ChemDraw 10
The ChemDraw file format is the native format for
ChemDraw version 4.0 and later. This is a public
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tagged file format that stores information about a
ChemDraw structure in a series of data blocks.
This format is designed to be easily generated and
interpreted by other programs. This format accurately stores anything that can be drawn in ChemDraw.
NOTE: Imported drawings saved within a ChemDraw file
created using ChemDraw for Macintosh are lost when the file
is opened using ChemDraw for Windows. The same applies
for objects saved in ChemDraw for Windows and opened on
a Macintosh. However, all ChemDraw specific information
is preserved.
Imported drawings include any graphics pasted into a ChemDraw document from another Macintosh application. They
also include Chem3D drawings imported using the Insert
Object dialog box or the “Get 3D Model” Edit menu command in ChemDraw for Windows.
version 2.x file format of ChemDraw for Macintosh. You cannot save files in these formats.
ChemDraw XML (XML)
(CML)
The CDXML file format is an interpreted version
of cdx that conforms to the XML specification
unlike binary cdx format. CDXML is text-based
but contains some data. For information about
XML in general, see http://www.xml.org.
CML is an extensible, chemically-aware markup
language based on XML. ChemDraw supports
both import and export of the format. More information can be found at http://www.xml-cml.org/
and http://cml.sourceforge.net.
ChemDraw 3.5 (CHM)
Encapsulated PostScript (Macintosh)
PostScript, EPS (Windows)
ChemDraw 3.5 file formats are used for saving or
opening ChemDraw documents using the version
3.5.x of ChemDraw. These documents can also be
opened in versions 3.0, 3.0.1, 3.0.2, and 3.1 of
ChemDraw as long as atom properties are not used
in the files.
NOTE: When you save a ChemDraw file in one of these
formats, all features specific to later versions are lost. For
example, multi-attached atom labels, variable attachment
points, and multicenter bonds are not be saved.
ChemDraw 2.0 and ChemDraw 2.1
(CHM) Import Only
ChemDraw 2.0 and ChemDraw 2.1 file formats are
used for opening ChemDraw documents using the
172•
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ChemDraw Stationery/Style Sheet
(CDS)
Use ChemDraw Stationery file format to save document settings and other objects.
Pro
Connection Table (CT)
The Connection Table file format is a simple format that saves a list of atom connectivities in terms
of an element, serial number, X and Y coordinates,
bond order, and bond type. For more information,
see , “Chemistry File Formats” on page 225
Pro
Chemical Markup Language
Encapsulated PostScript (EPS) files are ASCII text
files containing the scalable PostScript representation of a ChemDraw drawing that can be opened
using other applications and platforms. There are
two types: one containing text only, and one containing a graphic representation of the drawing.
The latter are known as Postscript with Preview or
Postscript Mac. For text only files, programs that
do not support the display of raw PostScript can
only print, not view an image on screen.
Use EPS files to share ChemDraw drawings with
desktop publishing applications such as Adobe
PageMaker and QuarkXPress.
CambridgeSoft
Overview
The Options dialog box allows you to select the
resolution (in dpi) and color depth of the saved file
The defaults are 300 dpi and Monochrome. For
Windows EPS with Preview, there is also a Preview option (default: WMF).
Figure 11.10: EPS Options dialog box.
If you select a color option, all colors are saved in
the EPS file except for the Background color. To
save an EPS file with a colored background, create
a large colored rectangular box using the Drawing
Elements tool and choose Send to Back before
saving the file. For more information, see “Drawing Boxes” on page 139 and “Multi-Center and
Variable Attachments” on page 73. These options
only affect embedded images. Objects created in
ChemDraw always output at maximum resolution
and in full color.
To include correct PostScript font names in Windows EPS files, you must have Adobe Type Manager (ATM) installed. Only ATM fonts are saved in
the EPS file.
Resolution
Available resolutions range from 72 (computer
monitor) to 1440 dpi (high resolution output).
When choosing a resolution, keep in mind that the
size of the file increases as the square of the resolution.
Color
You can select from the following color options:
• Monochrome—Forces all objects to black
and white.
• Grayscale—Translates colors to shades of
gray.
• 24-bit RGB —Stores colors using computer
monitor style of color encoding.
ChemDraw 10
• 32-bit CMYK—Uses printing press style of
color encoding. Groups each color type
sequentially. This provides better compression.
GIF Image (GIF)
Graphics interface format (GIF) is useful for
working with the hypertext markup language
(HTML) used in displaying information on the
World Wide Web. A GIF image can be displayed
directly on a Web page rather than having to
download the drawing for viewing in a Helper
application.
The default GIF format conforms to the GIF 89a
specifications with transparent backgrounds. You
can change this from the options menu.
Figure 11.11: GIF Options dialog box
Pro
ISIS/SKC and ISIS/TGF
You can save a ChemDraw document in an ISIS
file format for export to an ISIS application, or
import a file created by an ISIS application into
ChemDraw.
ChemDraw Pro provides two ISIS file formats:
• ISIS/Sketch (SKC)—For saving files as a
binary sketch file for transfer to another ISIS
application running on the same operating system (this format is used on the Clipboard).
• ISIS/TGF (*.tgf)—For saving as an ASCII
text file (a Transportable Graphics File) for
transfer to ISIS applications on different platforms.
NOTE: When transferring between ChemDraw and
ISIS/Draw, if information in a file or on the Clipboard contains only non-bond, unsupported objects, the information is
Sharing Information
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imported as a WMF (metafile) or PICT graphic. However,
if a supported object, such as a bond, is also in the file or on
the Clipboard, then only the supported object appears.
Administrator
NOTE: Object types in ISIS not supported in ChemDraw,
such as polymers, are not transferred. Object types in ChemDraw not supported in ISIS are not transferred. However,
in some cases, such as different arrow types, the arrow is converted to the most similar form.
Pro
ISIS/Reactions (RXN)
The ISIS/Reactions format is an MDL-developed
format for storing chemical reaction information
used by the ISIS family of products and others.
For single step single or multi-line reactions,
ChemDraw uses the point of the reaction arrow as
the dividing line to determine which molecules in a
reaction are reactants and which are products.
NOTE: You cannot save a reaction with an intermediate
step accurately in the RXN file format.
Molecules whose centers are behind or above the
tip of the arrow are considered reactants, and all
remaining molecules are products. The reaction
arrow can be at any orientation; it does not have to
be parallel to the x-axis. If a reaction contains multiple arrows, then the largest arrow is used as the
reaction arrow.
Reaction mapping and reaction center information
is stored in the RXN output file.
Pro
JDX (JDX, DX) Import Only
The Joint Commission on Atomic and Molecular
Properties (JCAMP) developed the JDX file format for spectral data. JDX is a public, but not well
defined format that has numerous variations.
ChemDraw supports many of the more common
spectral variations with uniform x-axis spacing.
174•
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ChemDraw also supports Bruker NMR JCAMP
data, which is saved with a DX file extension
When you import JDX files, they appear in the
window with a spectrum of a standard size that can
be re-sized by dragging.
You can export spectral data as part of a CDX file
only.
JPEG (JPG, JPEG) Import Only
ChemDraw supports import of digital images compressed with the widely used JPEG (Joint Photographic Experts Group) algorithm. JPEG images
are imported as objects, and can be scaled after
importing.
Pro
MDL MolFile (MOL)
MDL Information Systems, Inc. MolFile (MDL
MolFile) file format is used by several other Windows, Macintosh, and UNIX chemical databases
and drawing applications such as ISIS/Draw™,
ISIS/Base™, MACCS™, and REACCS™.
ChemDraw Pro provides two MDL MolFile
formats:
• MDL MolFile (Text)
• MDL MolFile (Mac) for Macintosh only. This
file type is saved with an mMol file type and can
be saved and opened with ISIS.
MDL MolFile files are ASCII text files that can be
created or edited in common word processing
applications or text editors. Atom and bond property information is stored in the MolFile.
MDL RGFile (RGF) file format is used by several
other chemical databases and drawing applications.
The MDL File RGFile supports alternate groups
whereas an MDL Molfile cannot. When you save a
ChemDraw file that contains alternate groups as an
MDL MolFile, it is automatically saved as an MDL
RGFile.
CambridgeSoft
Overview
Pro
Molecular Simulations MolFile
may provide higher quality output than regular
PICT files.
(MSM)
PNG file (PNG)
Molecular Simulations MolFile format is an ASCII
text file used by applications such as ChemNote™.
You can save a ChemDraw Pro document in
Molecular Simulations MolFile format for export
to one of these applications.
NOTE: ChemDraw uses the file extension “MSM” for
Molecular Simulations MolFiles rather than the standard
“MOL”, used by Molecular Simulation, Inc. ChemDraw
recognizes files with the “MOL” file extension as MDL
MolFiles. In addition, the extension “MSI” used in earlier
versions of ChemDraw is no longer recognized in ChemDraw. To open Molecular Simulations MolFiles that have
a “MOL” or “MSI” extension you must first change the
extension to “MSM”.
PNG (Portable Network Graphics) format is an
alternative to the GIF format for adding graphics
to web pages. You can save, but not open, files in
PNG format. The PNG format is fairly new and
was designed to address many of the shortcomings
of the GIF format. In particular, the PNG file format offers true color images, is less prone to transmission errors and offers a full alpha channel for
specifying background or transparency options.
For additional information about PNG visit:
http://www.boutell.com/boutell/png
PICT (Macintosh)
Standard Molecular Data (SMD) file format, version 4.3, is an ASCII text file commonly used by
programs that search Chemical Abstracts Databases such as STN Express™. You can save your
ChemDraw document in SMD format and use the
file for searching in a Chemical Abstracts database.
PICT files contain a QuickDraw representation of
a ChemDraw drawing that can be used by various
drawing applications. You can save a ChemDraw
document in the PICT format so it can be opened
by one of these other applications. The PICT file
format contains ChemDraw structural information. PICT files created by earlier versions of
ChemDraw can be reopened and edited by ChemDraw version 8.0. However, the pictures contained
in PICT files created by versions of CS ChemDraw
earlier than version 3.5, or by other applications,
are treated as a single, non-editable, imported picture.
All colors are saved in the PICT file except for the
Background color.
PICT scaled 4X (Macintosh)
PICT scaled 4X files are the same as PICT files,
except that the drawing is four times larger. When
these larger files are placed into certain other applications and shrunk back down to 1/4 size, they
ChemDraw 10
Pro
Pro
SMD (SMD)
SPC (SPC) Import Only
The SPC file format was developed by Galactic
Industries as part of the GRAMS software, which
reads spectral data from every type of spectrometer
and converts them to SPC format. SPC is a
well-defined, proprietary, but open standard format for spectral data.
ChemDraw imports most one-dimensional spectral SPC formats. When you import an SPC file, it
appears in the window with a spectrum of a standard size that can be re-sized by dragging.
You can export spectral data as part of a CDX file
only.
Sharing Information
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Pro
Template Style Sheet (CTS)
Administrator
The Template Style Sheet file format is used for
saving document settings and row and column
characteristics for creating ChemDraw Template
documents.
Windows Metafile (WMF)
The Windows Metafile file format saves the
Graphic Device Interface (GDI) representation of
a ChemDraw drawing. Using the WMF file format
you can transfer ChemDraw drawings to other
applications, such as Microsoft® Word, that support that WMF file format on the same or different
computers rather than using the Clipboard. The
WMF file format contains ChemDraw structural
information.
TIFF file (TIF)
TIFF format (Tagged Image File Format) is a high
resolution format commonly used for saving
graphics for importing into desktop publishing
applications on the same or on different computer
platforms. TIFF images can be saved using a variety of resolution, color, and compression options.
As TIFF images can get rather large, choosing
appropriate options is important. The TIFF format
is for export only.
Resolution
Available resolutions range from 72 (computer
monitor) to 1440 dpi (high resolution output).
When choosing a resolution, keep in mind that the
size of the file increases as the square of the resolution.
Color
You can select from the following color options:
• Monochrome—Forces all objects to black
and white.
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Sharing Information
• RGB Indexed—Stores colors using computer
monitor style of color encoding.
• CMYK Planar—Uses printing press style of
color encoding. Groups each color type
sequentially. This provides better compression.
For example: CCCCCCMMMMMMYYYYYYKKKKK rather than
CMYKCMYKCMYKCMYK. This option
produces far better compression than using the
PackBits compression method. However,
many desktop publishing packages do not support CMYK Planar files.
• CMYK Contiguous—Uses printing press
style of color encoding. Stores colors nonsequentially. For example: CMYKCMYK. The
PackBits compression type provides no compression for this type of file.
NOTE: If objects in your document are black and white
they are saved black and white regardless of which Color
options you set. If you import drawings from other applications and want them to print Black and White you must set
the Color option to Monochrome.
Compression
You can select from the following compression
options:
• PackBits—Used to reduce files size by encoding repeating bytes of information as output
when using the CMYK Planar color option.
Below is a highly simplified representation of
this compression scheme. For a line of color
information such as: CCCCCMMMMMYYYYYKKKKK, the compression
yields a smaller file by representing the information as C46M5Y5K.
• CCITT Group 3—Used for fax transmissions
of images.
• CCITT Group 4—Used for fax transmissions
of images.
CambridgeSoft
Overview
• Deflate—Similar to LZW compression.
Works well with all Color and Resolution
options.
Figure 11.13: Inserting a file into ChemDraw
Setting TIFF options
To set these options:
1. click the Options button in the Save dialog box
to display the TIFF options dialog box.
Figure 11.12: TIFF Options dialog box
3. Select the graphic and click Open.
The file is embedded into the ChemDraw file.
2. Select the options you want and click OK.
NOTE: In the Macintosh version you may want to increase
the memory allocated to ChemDraw if you are saving large
TIFF files.
Inserting Objects from Other
Applications
You can insert graphics or documents created in
other applications into ChemDraw. You can edit
inserted objects using the ChemDraw Edit menu.
Inserted objects can be resized or rotated using the
resize and rotate handles of a selected object. You
cannot flip inserted objects.
To insert a graphic from another application into
ChemDraw:
1. Click Insert File the Edit menu.
2. In the Open dialog box, select the file type
from the drop down menu.
ChemDraw 10
NOTE: If you select file type “All files” and choose a
file type that ChemDraw does not support (such as
TXT) you will get an error message, and the file will not
be embedded.
(Windows only)
To insert an object from another application into
ChemDraw:
1. Click the Insert Object command on the Edit
menu.
The Insert Object dialog box appears.
Figure 11.14: Insert Object dialog box
InsertObject 155 dpi
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2. Take the appropriate action:
Table 43: Insert object options
Administrator
If you want to … Then …
create a new object
Click Create New.
Select the Object Type.
for the appropriate versions shown in the table
below.
Table 44: Transferring from Mac to Windows
From
Mac
Version
To
Window
s
Version
Instructions
≥ 4.0
≥ 4.0
Save as ChemDraw
and add .cdx to the file
name.
≥ 4.0
3.x
Save as ChemDraw 3.x
and add .chm to the file
name.
≤ 3.5.x
= 3.x
Save as ChemDraw
and add .chm to the file
name.
Click OK.
insert an existing
graphic
Click Create from File.
Type the path or browse to
the object to insert.
Click OK.
Transferring ChemDraw
Documents Across Platforms
Use the following procedures to transfer ChemDraw documents across platforms. From the following table, determine the versions of the
ChemDraw software between which you want to
transfer documents and follow the appropriate
instructions.
When you transfer ChemDraw files across platforms, fonts are not transferred. If a font in the
transferred document is not available, ChemDraw
substitutes fonts for those that are available on the
new platform.
Transferring from Macintosh to
Windows
Transferring from Windows to
Macintosh
To be able to open a ChemDraw file created in
Windows on the Macintosh, follow the instructions for the appropriate versions shown in the
table below.
Table 45: Transferring from Window to Mac
From
Windows
Version
To Mac
Version
Instructions
≥ 4.0
≥ 4.0
Save as the default
ChemDraw (.cdx).
≤ 3.5.x
≥ 4.0
Save as ChemDraw
3.x (.chm).
To be able to open a ChemDraw file created on
the Macintosh in Windows, follow the instructions
178•
Sharing Information
CambridgeSoft
Overview
Table 45: Transferring from Window to Mac
≤ 3.5x
≤ 3.x
Save as ChemDraw
3.x (.chm) and
follow the instructions in “Transferring files to ChemDraw/Plus 3.1 for
the Macintosh”
below.
Transferring Files to ChemDraw/Plus
3.1 for the Macintosh
Use the following procedure to transfer a ChemDraw for Windows file to ChemDraw/Plus 3.1 for
the Macintosh. A file translator such as
PC Exchange or Apple File Exchange must be
running on your Macintosh.
To transfer from Windows to ChemDraw/Plus 3.1
for the Macintosh:
ChemDraw 10
1. In ChemDraw for Windows, save the file in the
ChemDraw (CHM) format.
2. Insert the disk with the ChemDraw for Windows files into the Mac floppy drive.
3. If you are using PC Exchange, double click the
floppy disk icon to display the files.
4. Select PC Exchange from the Control Panels.
5. Select Add.
6. Change the DOS suffix to CHM.
7. In the application selection, find CSC ChemDraw on your Mac and click once to highlight
the selection.
8. Change the document type to CHMS.
If you are using a translator other than
PC Exchange, you need to use an editor such as
ResEdit or Desktop to change the type and creator
of the files being transferred. The type should be
“CHMS” and the creator should be “CHMD.”
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CambridgeSoft
Overview
Chapter 12: ChemDraw/Excel
The ChemDraw/Excel add-in is an extension of
Microsoft© Excel© for Windows.
ChemDraw/Excel enables you to:
• Add chemical structures and other data from
ChemDraw or a ChemFinder database to an
Excel spreadsheet.
• Search using the same search features as ChemFinder.
• Perform calculations on chemical structures.
See the ChemOffice manual for information on
other CambridgeSoft add-ins for Excel.
NOTE: Any commands you use operate on the cells, not
the pictures in the cells.
Setting Up ChemDraw/Excel
When you install ChemFinder, ChemDraw/Excel is
automatically installed. Before you use ChemDraw/Excel for the first time, do the following:
1. Select Add-Ins on the Tools menu.
The Add-Ins dialog box appears.
2. In the Add-Ins dialog box check the ChemDraw for Excel checkbox and click OK.
A ChemOffice menu is added to the Excel
menu bar and a ChemOffice tool bar appears.
3. Point to Macro on the Tools menu, and select
Security.
The Macro Security dialog box appears.
4. In the Macro Security dialog box click the
Security Level tab and set the security level to
Medium.
NOTE: ChemDraw/Excel no longer requires this
step. You must set security to Medium only if you will
be using ChemDraw/Excel worksheets from version 8
or earlier without conversion.
5. Click OK to save and exit.
To create a ChemOffice worksheet:
• Select New ChemOffice Worksheet on the
ChemOffice menu, or click
.
A ChemOffice worksheet appears. When a
ChemOffice worksheet is active, ChemDraw/Excel appears in the title bar and the
ChemDraw tool bar is active.
Figure 12.16; A ChemOffice worksheet
Figure 12.15: ChemOffice menu item and toolbar
New
Import ChemFinder list
SMILES=Struct
worksheet Normal & Similarity search
Name=Struct
Import
Structure controls:
table Export Load; Save; Cut;
table
Copy; Paste; Name
ChemDraw 10
R-Group analysis
Structure controls:
Show; Hide;Resize;
Align
Importing Tables
ChemDraw/Excel allows you to import from the
following sources:
• MDL SDFiles—Imports all records in the
file. Each structure is given the name stored in
the SDFile.
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Administrator
• ChemDraw databases —Imports all fields
stored in the main form. Molecular weight and
formula fields are not imported because ChemDraw/Excel calculates them. Each structure is
named Structure <n>, where n is a unique
number.
NOTE: In order to import CFW files into Excel, make
sure you save them with the “allow CAL/OLE Automation access” security setting checked. See “Setting Security
Options” in Chapter 3 of the ChemFinder manual for
details.
When you import a table, structure data are transformed into structure drawings in the first column,
and all other fields are imported in separate columns.
To import a table:
1. Select the cell where you want the import to
start. The upper left corner of the import is at
this cell. Data is filled down and to the right.
2. Select Import Table on the ChemOffice menu,
or click
.
The Import Table dialog box appears.
Converting and Upgrading
Instead of copying and pasting information from a
non-ChemDraw/Excel worksheet, you can convert the existing worksheet into a ChemDraw/Excel worksheet.
To convert a worksheet:
Select Convert Worksheet from the ChemOffice menu.
The work sheet is converted to a ChemDraw/Excel worksheet.
Upgrading Workbooks
ChemDraw/Excel 9.0 improvements made workbooks created with older versions incompatible.
You can open and maintain old workbook formats,
but you may get error messages (depending on
your Excel security settings) and will be asked if
you want to upgrade each time you open them.
Figure 12.18: Version and macro warnings
Figure 12.17: Import Table dialog box
To upgrade a workbook:
1. Point to Macro on the Tools menu, and select
Security.
3. Type or select the file name to import and click
Open.
All records are added to your spreadsheet.
182•
ChemDraw/Excel
2. Click the Trusted Sources tab and make sure
that CambridgeSoft Corporation is listed as a
trusted source. Make sure the Trust access to
Visual Basic Project checkbox is selected.
3. Select Upgrade Workbook from the ChemOffice menu.
4. To maintain tight security, go back to the
Macro Security dialog box and deselect the
Trust access to Visual Basic Project checkbox.
CambridgeSoft
Importing Hit Lists
You can perform a search in ChemFinder and then
import the hit list structures with data into Excel
using the Import ChemFinder List command.
To use the Import ChemFinder List command,
ChemFinder must be open with a hit list present.
Importing a Hit list
To import a hit list:
1. Select Import ChemFinder List on the
ChemOffice menu, or click the
icon.
A message box similar to the one in Figure
12.19 appears:
Figure 12.19: Importing a ChemFinder hit list
2. Click Yes to import the hit list.
The records are imported into Excel, starting
with the currently selected cell and moving
down and to the right.
Error Messages
If all conditions required to use the Import ChemFinder List command are not met, one of the following error messages may appear.
ChemFinder is not running, would you like to
start it up?
ChemFinder is not running. Do the following:
1. Click Yes.
The message “After loading your desired database and performing your search, return to
Excel and redo the operation.” appears.
2. Click OK.
ChemFinder opens.
ChemDraw 10
3. Open a database and perform a search.
4. Return to Excel and from the ChemOffice
menu, select Import ChemFinder List,
or click
.
No database loaded in ChemFinder. Load a
database and perform your search. Then
return to Excel and redo the operation.
ChemFinder is running, but no database is loaded.
Do the following:
1. Click OK.
ChemFinder moves to the front.
2. Open a database and perform a search.
3. Return to Excel and from the ChemOffice
menu, select Import ChemFinder List,
or click
.
Form has no database or hit list has no
records. Load a database and perform your
search. Then return to Excel and redo the
operation.
4. Click OK.
ChemFinder moves to the front.
5. Open a database and perform a search.
6. Return to Excel and from the ChemOffice
menu, select Import ChemFinder List,
or click
.
Exporting Tables
ChemDraw/Excel allows you to export tables to
MDL SDFiles.
Selected cells are exported to a specified file. If no
cells are selected, the entire spreadsheet is
exported. The first column of the area to export
must have the word “Structure” in its top cell.
Structures outside the first column will be discarded.
ChemDraw/Excel
• 183
Figure 12.20: Selecting cells for export
Administrator
To export data:
1. Select the information to export:
Table 12 - 1: Selecting the area to export
If you want to
export
Then
a specified area of your
spreadsheet
Select the area to
export.
the entire spreadsheet
Do not make any
selection.
2. Select Export Table on the ChemOffice menu,
or click
.
The Save Table To dialog box appears.
Figure 12.21: Save Table dialog box
Adding Structures
You can add chemical structures from any file format supported by ChemDraw to a spreadsheet.
The names of added structures are retained. If the
structure does not have a name, ChemDraw
assigns the name: Structure <n>, where n is a number unique to the worksheet.
Adding Structures with
ChemDraw
The most direct way to insert a new structure into
a cell is by using ChemDraw.
To add a structure with ChemDraw:
1. Double-click in a cell.
The ChemDraw/Excel dialog box appears:
Figure 12.22: ChemDraw/Excel dialog box
2. Click Yes.
ChemDraw opens.
3. Draw the structure in ChemDraw.
4. Click Close and Return to New Molecule on
the ChemDraw File menu.
The new structure appears in the cell.
Adding a Structure From a File
To add a structure from a file:
3. Type the file name and click Save.
The table is saved to the specified file.
184•
ChemDraw/Excel
1. Select the cell into which you want to add the
structure.
2. Select Load Molecule on the ChemOffice
menu, or click
.
The Choose Molecule to Load dialog box
appears.
CambridgeSoft
Figure 12.23: Choose Molecule dialog box
If the cell contains a valid SMILES string, it is
replaced by a structure. The cell will display a
text string starting with “Structure” and
followed by a number. To display the structure,
click the Show Picture
icon.
If the cell did not contain a valid SMILES
string, the string remains.
Adding Structures by Name
NOTE: You can use the sample molecule file,
“SAMPLE.cdx” contained in the ChemDraw system
directory, or any CDX file to load.
3. Type the file name of the structure to add and
click Open.
The information is stored in the selected cell.
Adding a Structure with a SMILES
String
You can insert SMILES strings into cells and convert them to structures.
To insert SMILES strings:
1. Type or paste SMILES strings into cells.
2. Select the range of cells or single cell to convert.
NOTE: If you want to keep the original text, copy it
and paste it elsewhere.
3. Select Convert SMILES To Molecule on the
ChemOffice menu, or click
.
ChemDraw 10
You can type or paste the names of chemicals into
cells and convert them into structures as follows:
1. Enter the names into cells.
2. Select the range of cells to convert.
NOTE: If you want to keep the original text, copy it
and paste it elsewhere. Note that this command can also
convert names generated from Excel formulas.
3. Select Convert Name To Molecule on the
.
ChemOffice menu, or click
If the cell contains a name supported by ChemDraw Name=Struct, the structure corresponding to that name is added to the cell, with
the given name as the name of the cell. To
show the structure, select the cell and choose
Show Picture from the ChemOffice menu. For
more information about Name=Struct, see the
ChemDraw User’s Guide.
Saving Structures
You can save a chemical structure to a separate file.
1. In the spreadsheet, select the cell containing
the structure.
2. Select Save Molecule on the ChemOffice
menu, or click
.
The Save to File dialog box appears.
ChemDraw/Excel
• 185
Figure 12.24: Save to File dialog box
3. Select the search options:
Table 13: Search options
Administrator
If you want Then
to
3. Select an existing file or enter a new file name,
and click Save.
The structure is saved with the name and in the
location you selected.
search for a
structure
1. To load a structure,
right-click and select
Read Structure.
2. To edit the structure,
double-click it.
3. Select the Search
Type.
4. Select the Filter Type.
search for a
formula
1. Type the molecular
formula or formula
query in the And/Or
Formula Query box.
2. select Clear.
search for a
structure and a
formula
1. To edit the structure,
double-click it.
2. Select the Search
Type.
3. Select the Filter Type.
4. Type the molecular
formula in the
And/Or Formula
Query box.
Searching
You can perform the same types of searches in
ChemDraw/Excel as you can in ChemFinder:
• Exact structure searching
• Substructure searching
• Similarity searching
Filter Tables
Filter tables allows you to search for exact structures and substructures.
To perform a structure search:
1. Select a cell in the data table.
2. Select Filter Table on the ChemOffice menu, or
click
.
The Search Query dialog box appears.
see the RGroup Analysis
click the Show R-Group
Analysis box.
see the
click Restore Previous
previous query Query.
5. Click Search.
186•
ChemDraw/Excel
CambridgeSoft
The hit list is displayed in a column named
Match. Items matching the search criteria are
labeled as TRUE.
Similarity Searches
You can perform similarity searches to find structures with features corresponding to your search
structure. For more information about similarity
searching, see the ChemFinder User’s Guide.
To search for similarity:
1. Select a cell containing the label Structure.
2. Select Similarity Table on the ChemOffice
menu, or click
.
The Similarity Query dialog box appears.
Naming Structures
Excel recognizes certain characters as formulas. To
prevent the system from interpreting a chemical
structure name as an Excel formula, you can
rename a structure.
To name a structure:
1. Select the structure.
2. Select Name Molecule on the ChemOffice
menu, or click
.
The Name Molecule dialog box appears.
Figure 12.26: Name Molecule dialog box
Figure 12.25: Similarity Query dialog box
3. Type the name and click OK.
Using the Clipboard
3.
4.
5.
6.
Select the Search Type.
Select the Similarity Is value.
Select the Sort order.
Click Search.
The hit list is displayed in a column named
Match. Items matching the search criteria are
labeled as TRUE.
Working with Structures
ChemDraw/Excel allows you to rename structures
and use the clipboard to cut, copy, and paste structures.
ChemDraw 10
You can cut, copy, and paste structures using the
clipboard. After you cut or copy a structure, it is
placed on the clipboard. You can then paste it into
another cell or another application.
To cut a structure from a cell:
1. Select the structure.
2. Select Cut Molecule on the ChemOffice menu,
or click
.
The structure is removed from the cell and is
placed on the clipboard.
To copy a structure from a cell:
1. Select the structure.
2. Select Copy Molecule on the ChemOffice
menu, or click
.
The structure remains in the cell and a copy is
placed on the clipboard.
To paste a structure:
1. Select the area into which you want to paste the
structure.
ChemDraw/Excel
• 187
2. Select Paste Molecule on the ChemOffice
menu, or click
.
The structure is pasted from the clipboard.
Administrator
Viewing Structures
ChemDraw/Excel allows you to select whether or
not to display structures in a cell. You can also
adjust the height and width of cells to display their
entire contents.
Showing and Hiding Structures
To show structures:
1. Select the cells in which you want to display
pictures.
2. Select Show Picture on the ChemOffice menu,
or click
.
The structures are displayed in the selected
cells.
To hide structures:
1. Select the cells in which you do not want to display pictures.
2. Select Hide Picture on the ChemOffice menu,
or click
.
The structures are hidden and the cells resize.
Aligning Structures
A structure may fall outside the boundaries of its
cell because it is too big or because it is improperly
positioned within the cell. Use the Align All Pictures command to enlarge the cell or reposition the
structure. If the entire structure is within the cell,
regardless of its position, it is not affected by the
Align All Pictures.
To align structures:
Select Align Pictures on the ChemOffice menu,
or click
.
The cells adjust to display their entire contents.
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ChemDraw/Excel
Resizing Structures
To resize pictures use the Resize Picture command.
NOTE: When pictures are resized larger than their cells,
use Align Pictures to enlarge the cells. Align Pictures does not
make cells smaller.
To resize pictures:
1. Select the chemistry cells whose pictures you
want to resize.
It is not necessary to only select chemistry cells.
Non-chemical cells or chemical cells without
pictures will be ignored.
2. Select Resize Picture on the ChemOffice menu,
or click
.
Resize handles appear on the selected structures.
3. Click-drag the resize handles to resize a picture.
Any changes you make to a picture is proportionately reflected in the other pictures.
4. To end resizing, click a cell and the pictures are
deselected.
Resizing Structures With a Macro
To resize a large number of structures simultaneously, create the following macro:
CFXL.xla!CFxlDoSelectPicture
and assign it to an Excel button or menu item.
Then do the following:
1. Select the cells to be resized.
2. Run the macro.
3. Resize one structure.
All of the selected structures resize by the same
amount.
4. Select the Structure column and align (see
“Aligning Structures” on page 188).
For more information on creating and storing macros, see Excel Help.
CambridgeSoft
Using ChemDraw/Excel
Functions
ChemDraw/Excel supplies nine functions that
return information about chemistry objects in a
specified cell. Seven of these functions take only
one argument—the cell to which the function
refers. The remaining two functions may also take
a string as an optional second argument.
The function ISSTRUCTURE is an example of a
function that takes only one argument. To determine whether the content of cell A1 in an Excel
spreadsheet is a ChemDraw/Excel chemistry
object, you type =ISSTRUCTURE(A1) into a second cell. The second cell then displays TRUE or
FALSE depending on whether A1 contains a chemistry object.
The function CHEM.COMPOSITION is one of
the functions that may take an optional second
argument. It works in one of two ways:
With First Argument Only—
Without the second argument, it displays elemental
composition by weight percent of the entire chemical structure in cell A1 when you type
=CHEM.COMPOSITION(A1) into a second cell. For
benzene, it displays C, 92.26; H, 7.74.
With Both Arguments—The second argument
lets you find the percent composition of a single
element in the structure. Typing =CHEM.COMPOSITION(A1, “C”) returns the weight percent of carbon in the structure. For benzene it would display
0.922582. Notice that the display format for a single element is different from that of the whole
structure.
Table 14 outlines the ChemDraw/Excel functions.
Only CHEM.COMPOSITION and
CHEM.NUM.ATOMS take an optional second
ChemDraw 10
argument. The others only take the reference cell
argument.
Table 14: ChemDraw/Excel functions
Function
Action
ISSTRUCTURE
Returns TRUE if cell
referred to is any
ChemDraw/Excel
chemistry object
including reactions;
otherwise it returns
FALSE.
ISREACCTION
Returns TRUE if cell
reference is any ChemDraw/Excel chemistry
object and reaction;
otherwise it returns
FALSE.
CHEM.FORMULA
Returns formula for
structure in cell reference; it returns #N/A
error if cell doesn’t
contain a ChemDraw
structure.
CHEM.MOLWEIGHT
Returns molecular
weight for structure in
cell reference. Returns
#N/A error if cell
doesn’t contain ChemDraw structure.
ChemDraw/Excel
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Table 14: ChemDraw/Excel functions
Table 14: ChemDraw/Excel functions
Administrator
Function
Action
Function
CHEM.NUM.
HBACCEPTORS
Returns number of
hydrogen bond acceptors based on
topology. Returns
#N/A error if cell
doesn’t contain ChemDraw structure.
CHEM.NUM.
HBDONORS
Returns number of
hydrogen bond donors
based on topology.
Returns #N/A error if
cell doesn’t contain a
structure.
CHEM.SMILES
Returns SMILES
string for structure.
Returns #N/A error if
cell doesn’t contain
ChemDraw structure.
CHEM.COMPOSITION Returns elemental
percent by weight for
all elements in structure unless optional
second argument specifies a single element
symbol as a string. In
this case the elemental
percent is expressed as
a decimal number
between 0 and 1.
(75.1% would be
0.751) Returns #N/A
error if the cell referenced in first argument
doesn’t contain a
ChemDraw structure,
or if second argument
is not a valid element
symbol.
CHEM.NUM.ATOMS
190•
ChemDraw/Excel
Action
Returns total number
of atoms in the structure unless optional
second argument specifies a single element
symbol as a string. In
this case, it returns the
number of atoms of
that element only.
Returns #N/A error if
the cell referenced in
first argument doesn’t
contain a ChemDraw
structure or if second
argument is not a valid
element symbol.
CambridgeSoft
Using ChemProp Functions
If you are using ChemDraw Pro or Ultra with the
ChemProp add-on installed, you can calculate
physical and thermodynamic properties in ChemDraw/Excel. For detailed information on the
properties calculated and how ChemProp calculates them, see “Viewing Chemical Properties” on
page 115 and Appendix E “How ChemProp
Works.”
ChemProp Properties
In ChemDraw/Excel, you can use the ChemProp
functions to calculate the following properties:
Table 15: ChemProp functions
Property
Function
LogP (Ultra only)
CHEMPROP.LOGP
Molar Refractivity
(Ultra only)
CHEMPROP.MR
Henry’s Law
Constant
CHEMPROP.HENRY.
LAW.CONSTANT
Boiling Point
CHEMPROP.BOILING
Freezing Temperature
CHEMPROP.FREEZING
Critical Temperature
CHEMPROP.CRITICAL.
TEMP
Critical Pressure
CHEMPROP.CRITICAL.
PRESSURE
Critical Volume
ChemDraw 10
CHEMPROP.CRITICAL.
VOLUME
Table 15: ChemProp functions
Property
Function
Heat of Formation
CHEMPROP.HOF
Gibbs Free Energy
CHEMPROP.GIBBS
Ideal Gas Thermal
Capacity
CHEMPROP.IDEAL.GA
S
tPSA
CHEMPROP.TPSA
NOTE: Using ChemProp requires that you have a version
of ChemDraw that includes ChemProp installed.
Inserting Functions
To insert a ChemDraw/Excel function into your
worksheet:
1. Select an empty cell.
2. Select Function on the Insert menu.
The Paste Functions dialog box appears.
3. Select ChemDraw Functions.
Figure 12.27: Paste Functions dialog box
4. Select the function to insert from the list and
click OK.
A dialog box appears.
ChemDraw/Excel
• 191
Figure 12.28: Function arguments dialog box
Administrator
5. Enter the structure cell reference for which you
want to calculate properties in the Structure
box.
192•
ChemDraw/Excel
6. If the function takes a second argument, enter
it in the Element type box. Element type arguments are optional.
7. Click OK.
Each property is calculated using the “best available” method. For more information about calculation methods, see the ChemDraw manual. If the
cell reference argument does not point to a valid
structure cell, #N/A appears in the cell.
CambridgeSoft
Chapter 13: BioDraw
Overview
BioDraw tools are drawing objects. Before reading
this section, users should familiarize themselves
with the general behavior of ChemDraw drawing
tools by reading Chapter 9, “Drawing Objects” on
General toolbar
ChemDraw
main tools palette
The BioDraw Tools Palette
The BioDraw tools palette contains tools to draw
metabolic pathways, such as enzymes and receptors. Standard shapes, such as circles, ellipses, and
arrows, can be added from the Drawing Elements
tool palette or the Arrows tool palette. You can
also use the Pen tool to create custom shapes.
ChemDraw 10
page 131. Pay particular attention to “The Arrow
Tools Palette” on page 136, and “The Drawing
Elements Tools Palette” on page 138, as you will
want to use those tools in your BioDraw pathways.
Figure 13.29: The BioDraw Ultra GUI
Text toolbar
BioDraw
tools palette
As with ChemDraw Drawing Elements, you can
change the color of an object with the Color menu,
and the line and fill properties with the Curves
menu. You can also rotate, or change the size, after
selecting it. In general, anything you can do with a
ChemDraw drawing object you can do with a BioDraw object as well. We would, however caution
care in the use of shading (“Shaded Style” on page
BioDraw
Overview
• 193
Administrator
144). The effect of shading applied to irregularly
shaped objects such as receptors is unpredictable,
and generally quite unaesthetic.
You create a BioDraw object by either clicking or
dragging on the page where you want it to appear.
Clicking gives you the default size and shape, dragging allows you not only to enlarge the object, but
to distort it as well by dragging differently on the x
and y axes. Linear objects elongate in the direction
they are dragged. The membrane and protein tools
(DNA and Helix) add more subunits as they are
dragged and display the subunit count.
Figure 13.30: BioDraw Toolbar
1-substrate enzyme
2-substrate enzyme
Receptor
Ion Channel
Helix Protein
Membrane (line)
Membrane (arc)
Golgi Body
Cloud
Table 16: Customizable BioDraw Objects
Tool
Customization
Options
G-protein,
gamma subunit
shape
Helix Protein
height, width of the strands,
width of the cylinders,
spacing
DNA
height, width of the strands,
offset of the second strand,
spacing
Membrane
(line)
size of subunit
(The overall length remains
constant, and the number of
subunits changes in inverse
proportion to the size.)
Membrane
(arc)
length, arc, size of subunit
Membrane
size of subunit
Micelle
(ellipse)
size of subunit
G-protein (alpha subunit)
G-protein (beta subunit)
G-protein (gamma subunit)
Immunoglobulin
DNA
Micelle
Membrane (ellipse)
Endoplasmic Reticulum
Mitochondrion
Customizable Objects
Some of the BioDraw objects can be customized
after being created. Table 16 describes the customization options. When customizing a BioDraw
object, you must use the same tool used to create
it, or a selection tool.
Table 16: Customizable BioDraw Objects
Tool
Customization
Options
1-Substrate
Enzyme
size of the enzyme “mouth”
Receptor
width
194•
BioDraw
Table 17: Tools that are not customizable
2-Substrate
Enzyme
G-protein,
alpha subunit
Ion channel
G-protein,
beta subunit
Immunoglobulin
Golgi body
CambridgeSoft
Overview
Table 17: Tools that are not customizable
Endoplasmic
reticulum
Mitochondrion
Figure 13.32: Changing the membrane size
Drag to the right
Cloud
Drawing a Membrane Line
To create a membrane line:
1. Select the membrane line tool.
2. Drag in the work space.
Drag to the left
TIP: You may also click to draw the default size.
When orienting the membrane, note that if the
Fixed Angles option on the Object menu is
selected, you are constrained to 15 degree
increments. You can override the default by
holding down the Alt or option key as you
drag.
The membrane line has a single adjustment handle.
When you place the cursor over the handle, it turns
into a double-sided arrow. Dragging the handle to
the right increases the size of each subunit of the
membrane; dragging to the left decreases the size
of each subunit. When you change the subunit size,
the length of the membrane stays constant.
TIP: To change the length of the membrane, select it and
drag the left or right handle of the selection box. You may
then deselect it and readjust the subunit size.
Drawing a Membrane Arc
Creating a membrane arc is similar to creating a
membrane line. Begin by dragging in a straight line,
then drag in a curve.
Figure 13.33: Creating a membrane arc
Figure 13.31: Adjustment cursor
Regular cursor
Drag cursor
The membrane arc tool has three adjustment
handles:
• the handle at the starting point controls the
length
• the center handle controls the subunit size
• the handle at the leading edge controls the arc
ChemDraw 10
BioDraw
Overview
• 195
Drawing a Helix Protein
Drawing a DNA Molecule
To create a helix protein:
To create a DNA molecule:
Administrator
1. Select the Helix Protein tool.
2. Drag in the work space.
1. Select the DNA tool.
2. Drag in the work space.
TIP: You may also click to draw the default size.
TIP: You may also click to draw the default size.
When orienting the protein, note that if the
Fixed Angles option on the Object menu is
selected, you are constrained to 15 degree
increments. You can override the default by
holding down the Alt or option key as you
drag.
The helix protein has four adjustment handles:
height, width of the strands, width of the cylinders,
and spacing.
When orienting the DNA, note that if the Fixed
Angles option on the Object menu is selected,
you are constrained to 15 degree increments.
You can override the default by holding down
the Alt or option key as you drag.
DNA has four adjustment handles: height, width
of the strands, offset of the second strand, and
spacing
Figure 13.34: Helix protein adjustment handles
Figure 13.35: DNA adjustment handles
height
height
spacing
width
offset
spacing
width of cylinders
width of strands
196•
BioDraw
CambridgeSoft
Overview
Appendix A: Customizing ChemDraw
Overview
You can customize ChemDraw by configuring
Preferences and Document Settings.
Preferences allow you to change the default behavior of certain options that apply to every open document. Document Settings allow you to change the
default behavior of options that will affect only the
active document.
Setting Preferences
Preferences affect the way the ChemDraw application works, regardless of the document with which
you are working.
To open the Preferences dialog box click Preferences on the File menu.
The Preferences dialog box appears:
Setting the Default Document
Location
You can set what file location is shown in the
Open dialog box by using the Preferences dialog
box.
To set the default location:
1. Click Preferences on the File menu.
The Preferences dialog box appears.
2. Click the Directories tab.
3. Click the checkbox next to Use Documents
Location and type in or browse to the location
to use.
Figure A.37: Setting the default document location
Figure A.36: The Preferences dialog box
Default document location
If Use Documents Location is not selected, the first
time you use the Open dialog box your
My Documents folder is shown. Subsequent uses
show the last directory used.
Preferences-Gen 150dpi
To restore the CambridgeSoft default settings,
click the Use Defaults button.
ChemDraw 10
Setting the Default Open File Format
You can set what file format is selected by default
in the Open dialog box.
To set the default file format:
1. Click Preferences on the File menu.
Customizing ChemDraw
Overview
• 197
Administrator
The Preferences dialog box appears.
2. Click Open/Save.
3. Click Use Default File Format in the Opening
Files section, and choose the format you want
from the list
Figure A.38: Using default file format.
1. Click Preferences on the File menu.
The Preferences dialog box appears.
2. Click Open/Save.
3. Click the checkbox next to Autosave Every and
type or select the minutes to use.
Figure A.39: Setting Autosave
Autosave
Use Default File Format
If Use Default File Format is not selected, the first
time you use the Open dialog box the ChemDraw
format is shown. Subsequent uses show the last
format used.
The time starts counting down after the first
change is made.
Setting the Default Tool
To undo the last action performed, click the Undo
command on the Edit menu,
The last action performed is reversed. The
Redo command changes to reflect the undone
action. The Undo command changes to reflect
the next action you can undo.
For example, if you draw cyclohexane, create an
atom label text box, type a label, and select and
rotate the structure, you will be able to remove the
actions as follows:
1. Remove the rotation.
2. Remove atom label.
3. Remove the ring.
At each step, the text of the Undo command indicates the action being removed.
Use the Preferences dialog box to set which tool is
automatically selected when you open documents.
To set the default tool:
1. Click Preferences on the File menu.
The Preferences dialog box appears.
2. Click the Open/Save tab.
3. In the section labeled Opening Files, click the
Default Tool to be automatically selected when
you open a document.
Saving Changes Automatically
You can configure ChemDraw to save changes to a
document automatically at the time interval you
set.
To set the frequency at which ChemDraw automatically saves your changes:
198•
Customizing ChemDraw
Undoing Actions
CambridgeSoft
Overview
Redoing Actions
When you undo an action, the Redo command
becomes active so you can reverse the effect of the
Undo command.
To redo the last action undone, click the Redo
command on the Edit menu,.
The last action undone is reinstated. The Undo
command changes to reflect that action. The
Redo command changes to reflect the next
action that can be redone.
Setting the Default Save File Format
You can set what file format is selected by default
in the Save As dialog box.
To set the default file format:
1. Click Preferences on the File menu.
The Preferences dialog box appears.
2. Click Open/Save.
3. Click the checkbox next to Use Default File
Format in the Saving Files section, and choose
the format you want from the list.
Creating a New Line and Closing
Text Boxes
The default way to create a new line in a caption
text box is with the Enter or return key. The
default way to create a new line in an atom label is
with Alt+Enter or option+return. To close the
text box, click outside the text box or select
another tool.
To change the default do the following:
1. Click Preferences on the File menu.
TIP: In Mac OS X, the Preferences dialog box is
found on the ChemDraw menu.
2. Choose the appropriate option on the General
tab:
Table 18: Setting new line options
To change the
default for …
Select …
Atom Label text
Require Alt+Enter or
Option+Return to Create
New Line in Atom Labels.
Caption text
Require Alt+Enter or
Option+Return to Create
New Line in Captions.
Figure A.40: Setting the default save file
3. Click OK.
SaveFileFormats 150 dpi
If Use Default File Format is not selected, the first
time you use the Save dialog box, the ChemDraw
format is shown.
ChemDraw 10
Using Bitmap Fonts When
Available (Macintosh)
When text appears in a document on the screen, it
can appear using either a bitmap or a TrueType
font.
To use bitmap fonts if they are available:
1. Click Preferences on the File menu.
2. Select Use Bitmap Fonts When Available.
Customizing ChemDraw
Overview
• 199
Administrator
Text drawn using Bitmap fonts looks better and
appears more quickly than text drawn using TrueType fonts. However, the size and position of text
drawn using Bitmap fonts change somewhat when
printed.
For accurate correspondence between what you
see on the screen and what is printed, deselect Use
Bitmap Fonts When Available.
This change affects all documents.
A new path is added to the list.
Figure A.41: Adding a path to ChemDraw Items
Setting the Highlight Box
Tolerance
You determine the size of the highlight box and
how close you must get to activate an object by setting the Tolerance. The standard setting for the
Tolerance is 5 pixels. At this setting, the highlight
box appears on bonds if the pointer is located 5
pixels or less from any point on the bond.
To set the Tolerance:
1. Click Preferences on the File menu.
2. Select or type the tolerance.
This change affects all documents.
The ChemDraw Items Folder
The ChemDraw Items Folder is located by default
in the same folder as your ChemDraw application.
It contains the ChemDraw preferences, hotkeys,
nicknames, and isotopes files; scripts, and the
generic nicknames file. It also contains template
documents and template Stationery Pads. You can
have multiple ChemDraw Items folders. This is
useful in corporate installations for maintaining
personal files such as nicknames as well as standard
templates.
To add a path to a ChemDraw Items folder:
1. Click Preferences on the File menu.
The Preferences dialog box appears.
2. Click the Directories tab.
3. Click the Add New button, browse to a location, and click OK.
200•
Customizing ChemDraw
4. To rearrange the search order, use the Move Up
and Move Down buttons.
5. To delete a path, click the Remove button. To
delete all added paths, click the Default Paths
button.
Accessing Documents Quickly
You can access ChemDraw documents quickly by
placing them in the ChemDraw Items folder and
then selecting them from the Open Special menu.
You can access open documents quickly by using
the Window menu.
The Open Special Submenu
To select documents from the ChemDraw Items
folder, point to Open Special on the File menu and
select the file to open.
The Open Special submenu, listing documents
stored in the ChemDraw Items folder, appears.
Document and Object
Settings
Document and object settings are user-definable
settings that are applied to the current document.
Settings include:
CambridgeSoft
Overview
• Drawing settings—set drawing options such as
the fixed length used to draw bonds
• Caption and label text settings—set text
options such as the font used for atom labels
and captions
• Color settings—set available colors for objects
and the document background
• Print/Page Setup—set options such as the
page size used and text displayed in footers
You can apply document settings in the following
ways:
• Customize settings for the entire document
using the Document Settings dialog box
• Apply settings to the entire current document
from an existing document
• Apply settings to selected objects in the current
document from an existing document
Default Style Sheet or Stationery
Pad
When you open ChemDraw, the last Style Sheet or
Stationery Pad used opens as the default. If you
choose another Style Sheet or Stationery Pad, that
file becomes the default.
You can set a default that is not changed:
1. Click Preferences on the File (Mac: ChemDraw) menu.
2. Browse to the default Style Sheet (Stationery
Pad).
3. On the Open/Save tab, deselect the Opening
Any Style Sheet (Stationery Pad) Changes
Default checkbox.
To view the default Style Sheet or Stationery Pad,
click the File menu.
The New menu item displays the name of the
Style Sheet or Stationery Pad.
ChemDraw 10
Saving Customized Settings as
Style Sheets or Stationery Pads
Every new document created with ChemDraw
uses a Style Sheet or Stationery Pad to obtain its
document settings. Style Sheets or Stationery Pads
can also contain predefined objects. When you create a new document, you actually create an untitled
copy of the Style Sheet or Stationery Pad. Any
changes you make to the copy of the Style Sheet or
Stationery Pad do not affect the Style Sheet or Stationery Pad itself.
You can create a Style Sheet or Stationery Pad with
your own customized setting by saving it as a CDS
file. If you store the CDS file in the ChemDraw
Items folder, it appears in the Open Special menu
so you can access it from the File menu.
To save a document’s setting as a Style Sheet or
Stationery Pad:
1. Click the Save As command from the File
menu.
The Save As dialog box appears.
Figure A.42: The Save As dialog box
SaveAs 200 dpi
2. Name the file and change the type (in OS X:
format) to CD Style Sheet (cds) or ChemDraw
Stationery.
3. To save the file in the ChemDraw items folder,
click the Go To ChemDraw Items button.
Customizing ChemDraw
Overview
• 201
4. Click Save.
Applying Document Settings
From Other Documents
Administrator
To apply document settings to the active window
that are contained in a different document, point to
Apply Document Settings from...on the File menu,
and choose the document from which to apply the
settings.
The settings in the active document window
change to those found in the Style Sheet or Stationery Pad that you choose.
NOTE: When you apply settings, they apply to the current
document only are not saved as the default for the next document. Use Open Special from the File menu if you want to
change the default document settings.
To apply the document settings from a document
or style sheet not listed in the menu:
1. Click Other on the Apply Document Settings
from submenu of the File menu.
The Select document dialog box appears.
Figure A.43: The Select Document dialog box
SelectSettings 200 dpi
Applying Object Settings from Other
Documents
You can apply settings from another document to
selected objects in the current document. You can
apply the chosen settings to the selected objects
only, or to all new objects drawn in the current
document.
To apply object settings:
1. Select the object.
2. Point to Apply Object Settings from... on the
Object menu, and choose the document from
which to apply the settings.
A dialog box appears:
Figure A.44: Apply object settings dialog box
SetDefaults 150 dpi
3. Take the appropriate action:
Table 19: Applying object settings from other
documents
If you want to apply
the settings to the …
Then click …
selected object only
No
selected object and any new Yes
objects you draw
The settings are applied.
2. Open the appropriate folder and select a
ChemDraw document or Style Sheet / Stationery Pad.
3. Click Open.
202•
Customizing ChemDraw
Drawing Settings
Drawing settings are document settings that affect
how bonds and other objects are drawn. You can
configure the drawing settings for an entire document or for a particular object as follows:
• For the entire document, use the Document
Settings dialog box.
CambridgeSoft
Overview
• For an object, use the Object Settings dialog
box.
Changes made to the drawing settings affect the
active document window only. Drawing settings
can be saved in Style Sheets or Stationery Pads.
To apply settings from other documents to your
document, select “Apply Document Settings
from...” from the File menu.
The drawing settings are described in the following
table:
Table 20: Drawing settings
Adjust
this…
If you want to …
Bond
Spacing
Set the distance between the
lines in double or triple bonds.
The distance is set either as:
• The percent of the length
of the bond (between 1
and 100). This allows for
proportional spacing to be
used if different bond
lengths are used in the
drawing.
Table 20: Drawing settings
Adjust
this…
If you want to …
Chain Angle Set the angle (from 1 to 179
degrees) between bonds
created by the Acyclic chain
tool or modified by the Structure CleanUp command.
For more information see,
“Drawing Acyclic Chains” on
page 52 and “Structure CleanUp”
on page 72.
10%
14%
18%
An absolute value you choose
in the units specified for your
document.
Fixed
Length
Constrain the length of the
bonds drawn to the length you
specify when the Fixed Lengths
command in the Object menu
is selected (a check mark is next
to it). This also adjusts the
preferred bond length for
structures modified by the
Structure CleanUp command.
For more information see
“Drawing with Fixed Lengths”
on page 47 and “Structure
CleanUp” on page 72.
ChemDraw 10
Customizing ChemDraw
Overview
• 203
Table 20: Drawing settings
Adjust
this…
Table 20: Drawing settings
If you want to …
Administrator
Bold Width Set the width of the line used
when bold and wedge bonds
are drawn. The Bold Width
setting must be greater than the
Line Width setting. The end of
a wedge is 1.5 times the bold
width.
Adjust
this…
If you want to …
Hash
Spacing
Set the spacing between the
hashed lines used when wedged
hashed bonds, hashed bonds,
dashed bonds, dashed arrows,
or dashed curves are drawn.
2 Point
2 Point
4 Point
8 Point
Margin
Width
1 Point
1.5 Point
Change the amount of space
surrounding all atom labels that
will erase portions of the bonds
to which they are attached. The
margin width also determines
the amount of white space
surrounding the front bonds in
a bond crossing.
For more information, see
“Editing Atom Labels” on
page 59 and “Changing Bond
Crossings” on page 55.
204•
Customizing ChemDraw
8 Point
Color
Change the color in of selected
objects. For more information,
see “Customizing the Color
Palette” on page 212.
Units
Set the units used in the Object
Settings dialog box to centimeters, inches, points, or picas.
Atom and
Bond Indicators
Set which indicators you want
to display in your drawings. For
more information about using
indicators, see “Atom
Numbering” on page 75 and
“Showing Stereochemistry” on
page 113.
Line Width Set the width of all bonds, lines,
and arrowheads in the drawing.
0.5 Point
4 Point
Configuring Settings for Documents
To configure the drawing settings for an entire
document:
1. Click Document Settings on the File menu.
CambridgeSoft
Overview
Figure A.45: The Document Settings dialog box
3. Click OK when you are finished.
The settings you chose are applied to the entire
document.
Terminal Carbon Labels
There is a new Document Setting to automatically
display terminal carbon labels. The default on
installation is to not display terminal carbons.
If you prefer structures to display terminal carbons:
1. Click Document Settings on the File menu.
2. Select the Atom Labels tab.
3. Check the box next to Show Labels On Terminal Carbons.
Figure A.47: Setting automatic terminal carbons
2. Click the Drawing tab and configure the settings.
Figure A.46: Configuring settings on the Drawing tab
Show labels
on Terminal
Carbons
Configuring Settings for Objects
To configure the drawing settings for a selected
object:
1. Select the object.
2. Click Object Settings on the Object menu.
The Object Settings dialog box appears with
the Drawing tab displayed.
ChemDraw 10
Customizing ChemDraw
Overview
• 205
Figure A.48: The Object Settings dialog box
Administrator
To edit the document text settings for captions and
atom labels:
1. Click Document Settings on the File menu.
2. In the Document Settings dialog box, click
Captions or Atom Labels.
Figure A.49: Captions tab
3. Configure the settings and click OK.
The settings you chose are applied to the
selected object only.
Formatting Text
Text settings affect how captions and atom labels
for the current document are drawn and formatted.
Formatting options include:
• Font (font type)
• Size (font size)
• Style (font and baseline style)
• Line spacing
• Alignment
These options are described in the following sections.
Setting Font parameters
Changing text formats in the Document Settings
dialog box affects the current document only. You
can also change settings for individual objects by
using the Object Settings dialog box, the Text
menu, or the Style toolbar.
206•
Customizing ChemDraw
3. Change the settings if desired. The options are
described in the following sections.
4. Click OK.
The formatting is applied to the current document.
Setting the Baseline Style
You can specify the following baseline styles:
• Normal—Use this for standard text.
• Superscript—Reduces the text size by about
25 percent and raises its baseline.
• Subscript—Reduces the text by about
25 percent and lowers the baseline.
• Formula—Formats in a way that is appropriate for most chemical formulas, that is, numbers are automatically subscripted. You must,
however, capitalize manually.
You can apply several styles to the same selected
caption. You can also apply multiple styles to different portions of a single caption.
CambridgeSoft
Overview
If the captions you select have more than one style,
when you select the text with the Lasso or Marquee tool and select Style from the Text menu, a
hyphen appears next to each style (other than
Plain) that is applied to a portion of the selection.
A check mark appears next to each style that
applies to all of the selected text. Choosing a style
other than “Plain” adds the new style to all of the
selected captions. Previously applied styles are not
affected—that is, for example, if you select Italic
for a section that is Bold, it will be Bold Italic.
log box. All text in a single caption must have the
same Justification and Line Spacing.
There are four available justifications:
• Flush Left—creates left-justified caption text.
• Centered—creates centered caption text.
Specifying Line Spacing
You can specify the three types of line spacing:
• Automatic—Consistently spaced lines of text
based on the height of the tallest character in
the entire caption. This is the default line spacing.
• Variable—Lines of text with different spacing
based on the tallest character and the lowest
descender in each line.
• Fixed—Consistently spaced lines using a spacing that you specify.
• Flush Right—creates right-justified caption
text.
• Justified—creates right-left justified caption
text.
Aligning Text
Atom Labels
You can set the alignment of captions and atom
labels to justify text to suit your needs. The options
available depend on whether you are aligning captions or atom labels. Settings are made in the
Object Settings dialog box.
To open the object settings dialog box, do the following:
1. Select a caption or atom label with the Lasso or
Marquee tool.
2. Click Object Settings on the Object menu.
The Object Settings dialog box appears.
Use the Centered, Flush Left, Flush Right, Stacked
Above, or Automatic justifications to create labels
that identify atoms and functional groups in your
chemical structure without obscuring any bonds or
other atom labels.
NOTE: When using Stacked Above justification, enter the
tokens from top to bottom using Alt+Enter or
Option+Return to go to a new line. For instance, in the
example below, enter “OMe Alt+Enter [Option+Return]
CH2 Alt+Enter [Option+Return] N“.
Captions
You specify the caption justification and line spacing on the Captions tab of the Object Settings dia-
ChemDraw 10
If you change the justification after the label is entered, it will
in most cases generate a warning.
Examples of the atom label justifications are
shown below.
Customizing ChemDraw
Overview
• 207
Figure A.50: Atom label justification
OMe
CH2
N
RNH
Administrator
Stacked Above
Centered
N
CH2
OMe
N
CH2
OMe
Flush Left
Flush Right
When you justify Atom labels automatically,
ChemDraw breaks the label into tokens. A token
consists of an uppercase letter followed by any
numbers or lowercase letters. The first token is
attached to the atom and the rest of the label
appears without obscuring other parts of the
chemical structure.
For example, to create N-methylpiperidine, label
an atom in cyclohexane with the atom label NCH3,
which contains the three tokens, N and C and H3.
If you label C3, the tokens are placed from left to
right because there are bonds to the left of the
atom.
If you label C5, the tokens are placed from right to
left because there are bonds to the right of the
atom:
Figure A.51: Automatic alignment of atom labels
H3CN
Pro In ChemDraw Pro, you can force an
entire multi-atom label to be a token by defining it
208•
Customizing ChemDraw
Figure A.52: Using a Nickname as a token
CH 3
N
Automatic Alignment
NCH3
as a Nickname. This prevents the label from flipping when applied to the left side of a structure.
For example, if you define the Nickname CH3, and
label C5 with the combined label and nickname
NCH3, the final orientation is CH3N instead of
H3CN. In this case, the Nickname, CH3, is a token.
For more examples, see “Using Nicknames” on
page 81.
If you label C1, the second and third tokens are
placed above the first token since there are bonds
below the atom.
If you label C4, the second and third tokens are
placed below the first token.
N
CH 3
Changing the Default Caption or
Atom Label Text Format
Each new caption or atom label uses default document settings for the font, size, and style of captions and atom labels.
You can change the format by:
• Changing the document settings for subsequent drawings in the current document.
• Choosing a new format for an individual caption or label from the Text menu or toolbar
before you type.
• Selecting text and applying a new format to an
individual label after you type.
Specifying Document Settings for New
Text
To specify the text settings for new captions and
atom labels in the current document:
1. Click Document Settings on the File menu.
CambridgeSoft
Overview
2. Click Captions or Atom Labels in the Document Settings dialog box.
3. Click the appropriate options.
4. Click OK.
These settings affect all new captions or atom
labels in the current document. To use these settings in new documents save them in a Style Sheet
or Stationery Pad. For more information, see “Saving Customized Settings as Style Sheets or Stationery Pads” on page 201.
Setting an Individual Text Format Before
Typing
You can set the text format for an individual caption or atom label before you type. The format
change is applied to the current text only.
To set the text format before you type:
1. Click the Text tool and click in the document
window.
A text box appears.
2. Set the text format in one of the following
ways:
• Set Font, Style and Size options on the Text
menu.
• Set the format options from the Style toolbar.
3. Type the text in the text box.
The format is applied to the typed text. Any
subsequent text you type is formatted according to the default document settings for the
current document.
Changing the Spacing of Individual
Text Objects
You can change the text settings for a specific caption or atom. The setting change is applied to the
selected object only. You can also choose whether
to have the settings applied to the selected text and
to all subsequent text you type.
ChemDraw 10
To change the text settings for a specific caption or
atom label:
1. Select the text to change with a selection tool.
2. Set the appropriate options on the Text menu.
To change only a part of a single caption, select
part of the caption with the Text tool.
To specify a font and size for selected text, do one
of the following:
• Choose the font and size from the Text menu.
• Right-click and choose the font and size from
the right-click menu.
• Select the font and size from the drop-down
menus on the Style Toolbar.
Fractional Character Widths (Macintosh)
On the Macintosh, you can choose to have the
spacing between characters as close to proportional as possible. If you are printing to a PostScript printer, this option improves the font
appearance.
To set fractional widths:
1. Click Document Settings on the File menu.
2. Click the Footer tab in the Document Settings
dialog box.
3. Click Fractional Widths.
Specifying the Margin Width
You can adjust the white space surrounding the
atom label so that some of the attached bond is
hidden.
Figure A.53: Adjusting white space in atom labels
Cl
0.278 pt
Cl
0.6 pt
To adjust the white space:
1. Click Document Settings on the File menu.
The Document Settings dialog box appears.
Customizing ChemDraw
Overview
• 209
Administrator
2. Click the Drawing tab.
3. Type a new Margin Width value.
4. Click OK.
The margin width is applied to all subsequent
drawings in the current document.
Creating HotKeys
To add or edit ChemDraw HotKeys, use a text editor (Notepad etc.) to open the CS ChemDraw Hotkeys file in the ChemDraw Items folder.
You can use any uppercase or lowercase alphanumeric key as a Hotkey with the exception of the
hard coded HotKeys listed previously. If a capital
and lowercase Hotkey do not exist, the Hotkey is
assigned to both. If a key is used more than once in
the file, the one closer to the end of the file takes
precedence.
To add a Hotkey:
1. Add a new line and type the key you want to
use.
2. Type a space.
3. Type the letters to associate with the Hotkey.
HotKeys defined for single elements always
result in the adding of the appropriate number
of hydrogen atoms.
4. Save and close the HotKeys file.
To create a new HotKeys file:
1. Create a text file named CS ChemDraw Hotkeys.
2. Save the file in the ChemDraw Items folder.
3. Click OK or Save.
210•
Customizing ChemDraw
Hard-Coded HotKeys
You cannot edit hard-coded HotKeys. Table 21
contains a list of hard-coded HotKeys:
Table 21: Hard-coded HotKeys
Hotkey
Function
Enter or
return
Opens the atom label text box.
space
Removes an atom label.
Delete or
Backspace
Deletes objects.
NOTE: In earlier versions of ChemDraw, quite a few more
keys were hard-coded. In ChemDraw 10.0 any key not listed
above can be customized.
Working with Color
With the color capabilities of ChemDraw, you can
create full color presentations of your chemical
drawings to appear on your monitor, print on a
color printer, or create 35mm slides using a film
printer.
Most computers can display any of 16 million colors, but the number of colors that can appear at
any one time may be limited by the particular monitor and display card installed in your computer.
In ChemDraw, you can choose from a palette consisting of a Background Color, a Foreground
Color, and up to twenty additional colors for any
given drawing. A palette is stored in every document and Style Sheet or Stationery Pad. You can
use Style Sheets or Stationery Pads to create a
series of documents with the same color scheme.
Using color you can:
CambridgeSoft
Overview
• Color atoms and bonds in a mostly
black-on-white drawing to highlight areas of
interest.
• Color parts of a structure in a reaction scheme
to indicate where starting materials end up in
the products of a complicated mechanism.
• Use colored boxes and circles to highlight
atoms or molecules.
• Create slides that are easier to view by using
light objects on a dark background.
To view the Color palette:
1. Click Document Settings on the File menu.
2. Click the Colors tab.
Figure A.54: The Document settings colors tab
Coloring Objects
Any object that you can select with a selection tool
can be colored. You can color individual bonds,
part or all of a chemical structure, or objects such
as boxes, curves, arrows, orbitals and reaction
mechanism symbols.
The border of objects that are shaded or filled,
such as white filled s-orbitals in the Orbitals palette, are the same color as the shading or fill. The
border of objects that are hollow, such as circles
and hollow boxes in the Drawing Elements palette
can be colored, but the inside of the object cannot.
To color an object:
1. Select the object in a document window with a
selection tool.
2. Do one of the following:
• Click the Color button on the Style toolbar,
and select the color from the menu that
appears.
• Choose a color from the Color menu.
• Click the Color button on the Drawing
tab of the Object Settings dialog box,
and select the color from the menu that
appears.
Displaying the Color Palette
You can use the color palette to specify the color
of objects and text in the document within the
active window.
ChemDraw 10
Use the Color tab to specify the following colors:
• Background Color—Fills the background of
the current document in the active window.
• Foreground Color—Default color used when
you draw a new object.
• Other Colors—Colors available in the Color
Menu for changing the color of individual
objects. The colors are represented in the same
order that they appear in the Color menu.
You can customize the Color menu. Colors can be
added, or existing colors can be changed. Changing
a color, for example Other #2, changes all objects
that are using the color.
NOTE: If you select an individual or grouped object that
contains multiple colors, there is a check mark next to each
of the colors in the Color menu. The purpose of the check
marks is to alert you that a change would affect more than
one color.
Customizing ChemDraw
Overview
• 211
Customizing the Color Palette
Administrator
You can add, remove, or change the default foreground and background color and specify the
other colors available for coloring objects.
Changes made to the color palette affect the current document only. You can save Color Palette
settings (foreground, background, and up to 20
other colors) in a Style Sheet or Stationery Pad. For
more information, see “Saving Customized Settings as Style Sheets or Stationery Pads” on page
201.
A summary of each of the options is described in
the following table.
2. Click the Colors tab.
Figure A.55: Document settings Colors tab
Table 22: Color palette options
Option
Description
New Color
Add a new color box and set its
color using the Color Picker or
Color Wheel dialog box.
Remove Color
Set Color
Delete a color box that you have
selected in the left side of the
dialog box. Any objects using
the removed color are changed
to the Foreground color.
Change the color associated
with a color box that you have
selected in the left side of the
dialog box. Any objects using
the old color are changed to the
new color.
Windows Color Settings
To change the palette of colors used in the current
document:
1. Click Document Settings on the File menu.
The Document Settings dialog box appears.
212•
Customizing ChemDraw
3. Double-click the color to change.
Figure A.56: The Color dialog box
ColorPalette 150 dpi
4. Click a color box in the Basic Colors or the
Custom Colors section.
A highlighted border appears around the color
you select.
5. Click OK.
The color is changed to the new color and
added to the Color menu.
CambridgeSoft
Overview
Adding or Customizing Windows
Colors
Figure A.58: The Color Picker dialog box
To add colors or create customized colors:
1. Click Define Custom Colors in the Color dialog
box.
Figure A.57: Setting custom colors
Color Refiner box
Luminosity box
2. Click a color in the Color Refiner box to set the
hue and saturation.
The pointer turns into a Crosshair when you
click. You can drag to a different region to
change the hue and saturation.
3. Click in the Luminosity box to set the brightness of the color.
4. If necessary, change the hue, saturation, luminosity, and RGB components by typing the
values in the text boxes.
5. Click the Add to Custom Colors button.
Macintosh Color Settings
To change the palette of colors used in the current
document:
1. Click Document Settings on the File menu.
The Document Settings dialog box appears.
2. Click the Colors tab.
3. Click New Color.
4. Use one of the icons on the left to select a
method of defining your color, then select a
color.
For more information about the Macintosh
color options, refer to your System documentation.
5. Click OK.
The new color appears in the Colors tab in
place of the original color and is added to the
color menu.
Adding or Customizing Macintosh
Colors
To add a new color to the Color menu:
1. Click New Color or Set Other Color on the
Color tab.
The Color Picker dialog box appears.
2. Click a color in the Color Wheel.
3. If necessary, adjust the hue, saturation, brightness, and RGB components by typing in the
values.
4. Click OK.
The new color is added to the list of Other Colors.
Removing Colors
To remove a color from the Color menu:
ChemDraw 10
Customizing ChemDraw
Overview
• 213
Administrator
1. Click the color you want to remove.
A highlight box appears around the color.
2. Click Remove Color.
The color disappears from the list of other colors. Objects that were drawn in the removed
color are changed to the Foreground color
Templates and Color
The background and foreground colors used in a
template from the template pop-up palette are not
used when the template is drawn in a document
window. However, any other colors used in the
template are added to the color palette of the current document if they are not already present. This
is part of the autoscale feature. For more information, see “Autoscaling” on page 165.
Saving Color Palette Settings
You can save the Color Palette in a Style Sheet or
Stationery Pad. The Color Palette is saved in addition to other document settings such as Page Setup
settings, Text settings, and Drawing settings.
Printing
ChemDraw uses the standard system commands to
print ChemDraw documents. The options that you
have available to you depend on the printer that
you are using. Refer to your printer’s documentation for more information.
In general, to print a ChemDraw document:
1. Click Page Setup on the File menu.
2. Make all appropriate selections for the printer
you are using and click OK.
3. Click the Print command on the File menu.
4. Make your selections in the Print dialog box
and click OK.
To print a document:
1. Select the document you want to print.
2. Click Print on the File menu.
214•
Customizing ChemDraw
The ChemDraw application is opened and the
Print dialog box appears.
3. Make your selections in the Print dialog box
and click OK.
Printing Background Color
Print Background Color controls whether the
Background Color contained in your ChemDraw
document is printed.
To change whether the Background color is
printed:
1. Click Preferences on the File menu.
2. Click Print Background Color.
3. Click OK.
Macintosh Print Preferences
When you print a document, ChemDraw creates
both a QuickDraw representation and a PostScript
representation of the document’s contents.
QuickDraw is the graphical format that is supported by the Macintosh Operating System. Every
printer that supports the MacOS can convert
QuickDraw representations into printed output.
However, QuickDraw does not support some features (for example, high-resolution printing) that
are available only on some printers.
If you are transferring information to another
application from which you print ChemDraw pictures, you should consider including PostScript
commands and the ChemDraw LaserPrep File
with the pictures. For information about special
situations to consider, see “Transferring PostScript
(Macintosh)” on page 167.
Optimize Pictures for High-Resolution
Non-PostScript Printing
The Macintosh High Resolution Clipboard supports high-resolution printers. Most applications
support the High Resolution Clipboard. Because
this was not always the case in the past, this preference continues to be available for users to turn off
CambridgeSoft
Overview
if an application being used does not support the
High Resolution Clipboard.
If you are unsure if the application uses a High
Resolution Clipboard, try transferring pictures with
this check box selected and deselected, and see
which picture prints with higher quality.
If you are printing to a non-PostScript printer,
deselect Include ChemDraw LaserPrep and Include
PostScript to reduce the size of each picture. Do
not deselect this option if the document will ever
be printed to a PostScript printer.
Printers that use the PostScript page definition language use the PostScript representation. The PostScript representation describes objects by using
mathematical shapes that can be precisely imaged
at whatever resolution is used by your printer. The
PostScript representation created by ChemDraw is
composed of two parts, the PostScript commands
and the ChemDraw Laser Prep. The ChemDraw
Laser Prep contains specific instructions that
enable the printer to interpret the PostScript commands contained in a ChemDraw document.
Include PostScript
To transfer ChemDraw pictures to another document that will be printed on a PostScript printer:
1. Click Preferences on the File menu.
2. Click Include PostScript.
ChemDraw 10
3. Click OK.
When Include PostScript is deselected, no PostScript commands are generated. This usually
results in lower quality printing, particularly of
drawings cut and pasted into other applications.
However, because the representation used for
printing when Include PostScript is not selected is
the same as that used for drawing to the screen,
better correspondence between the screen and
printed output may be observed.
For more information, see “Transferring PostScript (Macintosh)” on page 167.
Include ChemDraw Laser Prep
Selecting the include ChemDraw Laser Prep allows
you to print to a printer that cannot be initialized
using ChemDraw. If you create drawings with this
option off, they will not print on PostScript printers without the use of ChemDraw.
To Include ChemDraw Laser Prep:
1. Click Preferences on the File menu.
2. Click Include ChemDraw Laser Prep.
3. Click OK.
NOTE: When you select Include ChemDraw Laser Prep,
you should also select Include PostScript.
For more information, see “Transferring PostScript (Macintosh)” on page 167.
Customizing ChemDraw
Overview
• 215
Administrator
216•
Customizing ChemDraw
CambridgeSoft
Overview
Appendix B: Document Settings
Creating Style Sheets or
Stationery Pads
e. Type a name for the document.
f. Select the ChemDraw Items folder as the
location for saving the template.
5. Click OK or Save.
To create your own Style Sheet or Stationery Pad:
1. Create a new document.
2. Enter the settings in the Page Setup, Drawing,
Text Settings, and Color Palette dialog boxes.
3. Click Save As on the File menu.
4. In the Save As dialog box:
d. Select the CD Style Sheet or Stationery Pad
file format.
ChemDraw Style Sheets or
Stationery Pads
This following table contains drawing settings and
a sample structure for each of the Style Sheets or
Stationery Pads ChemDraw provides.
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
ACS 1996
ACS 1996
O
HO
N
H
Morphine
ChemDraw 10
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 14.4 pt
Bold Width: 2 pt
Line Width: 0.6 pt
Margin Width: 1.6 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 18
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 10 pt
Drawing Area (Width x Height): 540 pt x 720 pt
Page Size: US Letter
Reduction (%): 100
Document Settings
Creating Style Sheets or Stationery Pads
• 217
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
Administrator
Adv.Synth Catal.
Adv. Synth. Catal.
HO
O
HO
N
H
Morphine
J.Chin. Chem. Soc.
J. Chin. Chem. Soc.
HO
O
HO
N
H
Morphine
218•
Document Settings
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 17 pt
Bold Width: 2 pt
Line Width: 1 pt
Margin Width: 1.6 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 18
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Times New
Roman/Times
Caption Size: 12 pt
Drawing Area (Width x Height): 540 pt x 720 pt
Page Size: US Letter
Reduction (%): 100
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 18 pt
Bold Width: 2.5 pt
Line Width: 1 pt
Margin Width: 2 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 20
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 12 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 12 pt
Drawing Area (Width x Height): 693 pt x 918 pt
Page Size: US Letter
Reduction (%): 80
CambridgeSoft
Creating Style Sheets or Stationery Pads
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
J. Mol. Mod.
J. Mol. Mod.
O
HO
N
H
Morphine
•
•
•
•
•
•
•
•
•
•
•
•
•
•
ChemDraw 10
Fixed Length: 14.4 pt
Bold Width: 2 pt
Line Width: 0.6 pt
Margin Width: 1.6 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 18
Atom Label Font (Win/Mac): Times New
Roman/Times
Atom Label Size: 10 pt
Caption Font (Win/Mac): Times New Roman/Times
Caption Size: 10 pt
Drawing Area (Width x Height): 8.5 cm x 25.4 cm (1
column); 17 cm x 25.4 cm (2 column)
Page Size: US Letter
Reduction (%): 100
Document Settings
Creating Style Sheets or Stationery Pads
• 219
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
Administrator
New Document
New Document
OH
O
OH
N
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 30 pt
Bold Width: 2 pt
Line Width: 1 pt
Margin Width: 2 pt
Hash Spacing: 2.7 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 12
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Times New
Roman/Times
Caption Size: 12 pt
Drawing Area (Width x Height): 7.5 in x 10 in
Page Size: US Letter or A4 (as selected)
Reduction (%): 100
H
Morphine
220•
Document Settings
CambridgeSoft
Creating Style Sheets or Stationery Pads
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
New Slide
•
•
•
•
•
•
•
•
•
•
•
•
•
•
ChemDraw 10
Fixed Length: 30 pt
Bold Width: 4 pt
Line Width: 1.6 pt
Margin Width: 2 pt
Hash Spacing: 2.7 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 15
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 12 pt
Caption Font (Win/Mac): Times New
Roman/Times
Caption Size: 16 pt
Drawing Area (Width x Height): 7.5 in x 10 in
Page Size: US Letter
Reduction (%): 100
Document Settings
Creating Style Sheets or Stationery Pads
• 221
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
Administrator
Phytomedicine
Phytomedicine
O
HO
N
H
Morphine
RSC
RSC (1 and 2 column)
O
HO
N
H
Morphine
222•
Document Settings
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 20 pt
Bold Width: 1.33 pt
Line Width: 1pt
Margin Width: 1.25 pt
Hash Spacing: 3 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 8
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 12 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 12 pt
Drawing Area (Width x Height): 540 pt x 720 pt
Page Size: US Letter
Reduction (%): 100
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 0.43 cm
Bold Width: 0.056 cm
Line Width: 0.016 cm
Margin Width: 0.044 cm
Hash Spacing: 0.062 cm
Chain Angle (degrees): 120
Bond Spacing (% of length): 20
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 9 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 9 pt
Drawing Area (Width x Height): 8.9 cm x 25.4 cm (1
column); 19 cm x 27.7 cm
• Page Size: US Letter
• Reduction (%): 100
CambridgeSoft
Creating Style Sheets or Stationery Pads
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
Science of Synthesis
Science of Synthesis
O
HO
N
H
Morphine
Synthesis, Synlett
SYNTHESIS, SYNLETT
O
HO
Na
H
Morphine
ChemDraw 10
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 17 pt
Bold Width: 2 pt
Line Width: 0.8 pt
Margin Width: 2.25 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 18
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 10 pt
Drawing Area (Width x Height): 19.79 cm x 27.15 cm
Page Size: A4
Reduction (%): 100
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 17 pt
Bold Width: 2 pt
Line Width: 0.8 pt
Margin Width: 1.3 pt
Hash Spacing: 2.5 pt
Chain Angle (degrees): 120
Bond Spacing (% of length): 18
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 10 pt
Drawing Area (Width x Height): 12 cm x 26.7 cm
Page Size: A4
Reduction (%): 100
Document Settings
Creating Style Sheets or Stationery Pads
• 223
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery
Pads
Administrator
Verlag Helvetica Chimica Acta
Verlag Helvetica Chimica Acta
HO
O
HO
N
H
Morphine
Wiley Document
Wiley Document
O
HO
N
H
Morphine
224•
Document Settings
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 17 pt
Bold Width: 2.9 pt
Line Width: 0.54 pt
Margin Width: 2 pt
Hash Spacing: 2 pt
Chain Angle (degrees): 120
Bond Spacing (% of length):14
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 10 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 12 pt
Drawing Area (Width x Height): 368 x 720 pts
Page Size: US Letter
Reduction (%): 100
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Fixed Length: 17 pt
Bold Width:2.6 pt
Line Width:0.75 pt
Margin Width: 2 pt
Hash Spacing: 2.6 pt
Chain Angle (degrees): 120
Bond Spacing (% of length):18
Atom Label Font (Win/Mac): Arial/Helvetica
Atom Label Size: 12 pt
Caption Font (Win/Mac): Arial/Helvetica
Caption Size: 12 pt
Drawing Area (Width x Height): 19.79 x 27.15 cm
Page Size: A4
Reduction (%): 100
CambridgeSoft
Creating Style Sheets or Stationery Pads
Appendix C: Chemistry File Formats
File formats other than ChemDraw may not preserve all of your data. ChemDraw can create many
types of items—particularly graphical objects such
as boxes and curves—that cannot be saved into
chemical file formats.
Other file formats sometimes contain data that
cannot be interpreted by ChemDraw. ChemDraw
always tries to interpret other file formats so that as
much chemically-relevant data is preserved as possible, even if that causes the actual appearance of
the file to change when it is saved and reopened.
Most file formats supported by ChemDraw are
proprietary or extremely complex and are documented more thoroughly elsewhere. For example,
you can find more information about CambridgeSoft’s CDX file format at: sdk.cambridgesoft.com
Connection Table File
Format
The connection table format file described in this
section is generated for the cyclohexanol structure
shown below. All references to atom serial numbers are based on the Atom Numbering shown.
Figure C.59: Atom numbering used in the following
examples
7
OH
1
6
2
5
3
4
Table 23 is a sample Connection Table file produced for cyclohexanol using ChemDraw. The line
ChemDraw 10
numbers are added for purposes of discussion
only.
Table 23: Sample connection table for cyclohexanol
Line 1
Cyclohexanol
Line 2
77
Line 3
0.0000
0.5000
0.0000
C
Line 4
-0.8667
0.0000
0.0000
C
Line 5
-0.8667
-1.0000
0.0000
C
Line 6
0.0000
-1.5000
0.0000
C
Line 7
0.8667
-1.0000
0.0000
C
Line 8
0.8667
0.0000
0.0000
C
Line 9
0.0000
1.5000
0.0000
O
Line 10
1211
Line 11
2311
Line 12
3411
Line 13
4511
Line 14
5611
Line 15
1611
Line 16
6711
Each line represents a data record containing one
or more fields of information about the structure.
Individual fields are delimited by space(s) or a tab.
The fields in the Connection Table format file used
by ChemDraw are discussed below. The field value
for Carbon 6 from the example file is included in
parentheses for reference.
• Line 1 is the molecule name. The molecule
name is the file name when the file was created
using ChemDraw.
• Line 2 contains two fields: the first field is the
number of atom labels, and the second field is
the number of bonds. These fields must be
separated by at least one space.
Chemistry File Formats
• 225
Administrator
• Lines 3. 9 each contain 4 fields describing
information about the individual atoms: the
first field is the X Cartesian coordinate
(0.8667), the second field is the Y Cartesian
coordinate (0.0000), the third field is the Z Cartesian coordinate (0.0000), and the fourth field
is the atom label (C).
The spacing of these fields is very important.
Any data outside the following columns (especially data overlapping the ranges) may render
a file unreadable.
• Field 1: Columns 0. 9
• Field 2: Columns 10. 19
• Field 3: Columns 20. 29
• Field 4: Columns 31. end
• Lines 10. 16 each contain four fields describing
information about the individual bonds
between the atoms: the first two fields represent the serial numbers of the atoms that are
connected by this bond (atom 1 and atom 6),
the third field is the bond order (1) and the
fourth field is the bond type (1).
The bond types for the Connection Table format
are listed in Table 24:
Table 24: Encoding for bond types
value
bond type
6
Bold.
7
Wedged with first atom at
narrow end.
8
Wedged with second atom at
narrow end.
9
Wavy.
10
Hollow wedge with narrow end
towards 1st atom.
11
Hollow wedge with narrow end
towards 2nd atom.
12
Dative bond with arrow
towards 2nd atom.
13
Dative bond with arrow
towards 1st atom.
Table 24: Encoding for bond types
value
bond type
14
Any (bond property).
1
Single.
15
2
Dashed.
Single/Double (bond property).
3
Hashed.
16
Double/Aromatic (bond property).
4
Wedged hash with first atom at
narrow end.
17
Single/Aromatic (bond property).
5
Wedged hash with second
atom at narrow end.
Double bonds are bit encoded using a bitmask.
The default value (0) indicates a normal (two solid
lines) double bond, with the second line on the
226•
Chemistry File Formats
CambridgeSoft
right (looking from the first atom to the second).
Other values are listed in Table 25:
Table 25: Encoding of double bonds
Table 25: Encoding of double bonds
value
bond type/position
value
bond type/position
16
A double bond with one bold
and one solid line.
1
The second line is on the left
(looking from the first atom to
the second).
32
A crossed bond.
64
2
The two lines are centered.
A double bond with two
dashed lines.
4
A double bond with one
dashed and one solid line.
8
A modifier to the previous two
values, indicating that the user
specifically set the positioning.
If this bit is not present, ChemDraw calculated the positioning automatically.
ChemDraw 10
So, for example, a bitmask value of 13 (= 1 + 4 +
8) means a double bond with one dashed and one
solid line (4), where the user specifically wants (8)
the second line to be on the left (1).
NOTE: This connection table format is obsolete, and is
documented here for historical purposes only. This format
should never be used for critical work where chemical information is important.
Chemistry File Formats
• 227
Administrator
228•
Chemistry File Formats
CambridgeSoft
Appendix D: ChemDraw Chemistry
ChemDraw automatically converts lines, characters, and other symbols into chemically meaningful
figures as you work. This work occurs in the background, but you can choose to view this chemical
data using Check Structure, Analyze Structure, and
Expand Atom Labels. ChemDraw also uses this
chemical data when exporting to file formats that
support only a subset of the notations that ChemDraw does.
This appendix describes how ChemDraw interprets what you draw and how you can help ChemDraw better interpret what you mean.
Chemical Intelligence in
ChemDraw
ChemDraw was designed as a tool to aid in chemical communication. Most chemists would understand AcOo-C6H4COOH immediately, whether or
not they recognized it as aspirin. Most computer
programs, however, require what is known as a
“complete connection table,” in this case, a collection of 21 atoms connected by 5 double bonds and
16 single bonds in a specific pattern. ChemDraw
takes what makes sense to a chemist and converts
it into what makes sense to another application.
This chemical intelligence can be used as a sophisticated “spelling” checker for chemical compounds. For example, if you’re investigating
organic acids, a compound with the structural formula CH3COO would probably represent acetic
acid. Present the same formula in a paper on transition metal chemistry, and you might be describing a novel methylated cobalt oxide. If you had
asked ChemDraw to interpret it beforehand, you
would have received a message reporting a valence
ChemDraw 10
error, and you might have been prompted either to
add a negative charge or to change the capitalization.
ChemDraw can offer only suggestions. If you and
your audience understand what you are trying to
depict, then you can ignore these suggestions. In
many cases, you can teach ChemDraw to understand the notation you’re using. For more information, see “Applying Nicknames” on page 82.
Database Conventions
Most databases require not only that you draw a
structure in a way that makes sense, but that you
draw it in the way that the database expects it.
Consider ferrocene, which is represented in at least
four different ways in major databases:
Figure D.60: Representations of ferrocene
Merck Index
and 3 other isomers
Beilstein
A successful search in one database might not produce any hits in another. When in doubt, consult
the documentation for your database, and see if it
offers any clues to the conventions used.
ChemDraw Chemistry
• 229
Chemical Conventions
Administrator
The following table describes the chemical conventions understood by ChemDraw.
A single bond near a closed circle is recognized as
aromatic:
Figure D.61: Aromatic examples
Table 26: Bond conventions in ChemDraw
Bond
Description
Single bond, unspecified stereochemistry.
Single bond, “down” stereochemistry (into the plane of the paper,
away from the viewer), from the first
drawn atom to the second drawn
atom.
Atom Labels
A simple atom label may contain any of the following:
Table 27: Atom label examples
A single element.
Single bond, “up” stereochemistry
(out of the plane of the paper,
toward the viewer), from the first
drawn atom to the second drawn
atom.
An element and some
number of hydrogen
atoms.
Single bond, mixture of “up” and
“down” stereochemistries in some
unspecified proportion.
A nickname.
Dative bond. Often used to indicate polar bonds, such as the N-O
bond in pyridine N-oxide.
Repeating units within
parentheses.
Double bond, with cis/trans stereochemistry as drawn.
Double bond, with cis/trans stereochemistry unknown.
Tautomeric bond, either single or
double according to rules of
tautomerism.
Aromatic bond, part of a delocalized resonance system.
Triple bond.
Quadruple Bond.
230•
ChemDraw Chemistry
+*/
A series of any combination of the above.
When analyzing an atom label, ChemDraw starts at
the left and continues to the right, applying standard rules of valence to determine which atoms are
bound to which. The exception is with an atom
label in Automatic alignment on the left side of a
compound. This sort of atom label is displayed
“backwards” (H3CO instead OCH3) and is there-
CambridgeSoft
fore parsed from right to left. Standard valences
for each atom are defined in the Isotopes Table.
By definition, a “simple” atom label has all bonds
attached to the first (or last) character. A multiattached atom label has bonds connected to more
than one character, or has all of its bonds attached
to a specific character in the middle of the atom
label. Multi-attached atom labels are always parsed
from beginning to end, but again the beginning
might be on the right if the atom label was in Automatic style and on the left side of the original structure:
Table 28: Multi-attached labels
A multi-attached label that
is parsed from left to right.
A multi-attached label that
is parsed from right to left.
Table 29: Multiple fragments
Explicitly, using a space,
period (unsuperscripted
or unsubscripted), bullet,
or combination.
An unsuperscripted,
unsubscripted integer at
the start of a fragment is
recognized as a stoichiometric multiplier and is
treated as if the appropriate number of fragments were drawn
explicitly.
Chemically Significant Text
A bond attached to the
open parenthesis of a
repeating group is treated
as if bonded to the first of
those groups.
A bond attached to the
close parenthesis or repeat
count of a repeating group
is treated as if bonded to
the last of those groups.
Multiple fragments within a single label can be
specified in the following ways:
Table 29: Multiple fragments
Implicitly, using standard valence rules.
ChemDraw 10
Often it is simpler to write a chemical formula like
MeOH or H2O than it is to draw out an entire
atoms-and-bonds structure. ChemDraw correctly
interprets any unambiguous structural formula. For
example, CH3COCH2CH3 is recognized as methyl
ethyl ketone and MeOH is recognized as methanol.
On the other hand, C6H6 might mean benzene, or
it might mean one of over 200 other isomers.
C6H6 is not recognized by ChemDraw, and generates an error message if you try to analyze it. Generally, empirical formulas (C2H6 and H2SO4) are
not recognized, but structural formulas (CH3CH3
and HOSO2OH) are.
Molecular weight and elemental analyses of empirical structures is possible, but the Expand Label
command does not work with them. Empirical
structures are discarded when they are transferred
to other applications that require unambiguous
structures.
ChemDraw Chemistry
• 231
Administrator
Chemically-significant text must be entirely in Formula or, for isotopes and charges, Superscript
style. ChemDraw does not recognize a chemical
formula embedded within a larger block of text.
Table 30: Chemically significant text
NH4+
H 2O
If you draw a bond, add an atom
label, and then delete the bond,
you have a chemically meaningful text block whose font,
size, and style match other atom
labels.
If you create a caption with the
text tool and set it to Formula
style, you have a chemically
meaningful text block whose
font, size, and style match other
captions.
Charges
Charges may be created as part of a textual atom
label or with the appropriate symbol from the
Chemical Symbols Palette. Charges are always
assigned to a specific element in the atom label,
whose acceptable valences become those of the
similar isoelectronic neutral element.
Table 31: Charge examples
A charge following an element
is assigned to that element.
A charge that does not follow
an element is assigned to the
next element.
Table 31: Charge examples
Charges that follow other
repeating units are distributed
among those units.
Charges may be superscripted.
Multiple charges are recognized appropriately.
Charges may have repeat
counts as long as both the
charge and the repeat count are
superscripted.
A “floating” charge placed with
the Chemical Symbols Tool is
assigned to the nearest atom. If
no atom is within the distance
set as the Fixed Length, the
charge is ignored and not
assigned to any atom.
A “floating” charge placed
within a delocalized system is
recognized by the Analyze
Structure function, but is
discarded when saved to
formats that require all charges
to be associated with specific
atoms.
Isotopes and Elements
By default, ChemDraw correctly recognizes all isotopes in the full Table of the Elements. This data is
provided by CRC Press, Inc. Isotopes are defined
Charges that follow a monovalent element with a repeat
count are assigned to the
element before that element.
232•
ChemDraw Chemistry
CambridgeSoft
in the Isotopes Table file. You can edit this file to
add new isotopes in any text editor.
Table 32: Isotope examples
A superscripted number
before the element
symbol indicates isotope
numbers.
Isotopes can be
included anywhere that
regular elements can.
Deuterium and Tritium
can be indicated by their
one-letter symbols.
Radicals
Radicals are indicated with the appropriate symbol
from the Chemical Symbols Palette. As with
charges, they are assigned to the nearest atom.
Radicals always occupy one free valence, in addition to any charge effects.
Complexes
Compounds with electron pairs can act as Lewis
bases, bonding with Lewis acids that are electrondeficient. Similar behavior can be seen between
lone pairs and metals.
The best representation of these types of interaction is with a dative bond from the electron-pair
donor to the acceptor. With a plain bond instead
of the dative bond, ChemDraw would report a
valence error. The dative bond more accurately
represents the electron donation.
Complexes may also be represented with explicit
lone pairs and without any bonds.
If you use a plain bond to indicate a complex, you
may want to set Abnormal Valence to Allowed in
the Atom Properties dialog.
Table 33: Complexes
F3B
NH3
O
Figure D.62: Radical examples
Boron trifluorideacetic acid
complex.
HO
Ph
Ph
Boron trifluorideammonia complex.
C
C
B
O
F
Ph
F
F
H-Dot/H-Dash
H-Dot and H-Dash symbols from the Chemical
Symbols Palette indicate the stereochemistry of a
single hydrogen atom. These symbols are most
commonly used in fused systems.
Figure D.63: H-dot example
N
N
Fe
N
HO
N
Heme, a
compound with
two formal covalent bonds and two
formal donoracceptor pairs.
O
H
H
ChemDraw 10
ChemDraw Chemistry
• 233
Figure D.67η-C5H5Mn(CO)3
Table 33: Complexes
Another representation of heme.
Administrator
Fe
CO
Mn
N
N
OC
CO
N
N
HO
O
Stereochemistry
Multi-center Attachments
Multi-center attachments are meaningful only
when created using Add Multi-Center Attachment
from the Structure Menu. This command creates a
pseudo-atom that is disregarded during chemical
calculations, but still allows you to create diagrams
that look meaningful to an experienced chemist.
Figure D.64: η3 or π-Allyl complex
M
Figure D.65: Ferrocene, a π-Aryl complex
Fe
Figure D.66: Cp2TiCl2, another π-Aryl complex
Cl
Cl
Ti
234•
ChemDraw Chemistry
Absolute stereochemistry is calculated for tetrahedral atoms and double bonds according to the
Cahn-Ingold-Prelog (CIP) priority rules. The CIP
rules are designed to order ligands by their priority
and determine a descriptor based on the orientation of the ordered ligands in space.
A ligand is an entity attached to a stereocenter. For
example, a tetrahedral carbon has four ligands corresponding to its four substituents. When a tetrahedral carbon is in a ring, it still has four ligands:
the two ligands outside the ring, a third consisting
of the ring “unpeeled” clockwise, and a fourth
consisting of the ring “unpeeled” counterclockwise.
Five rules are used to determine the priority of
ligands are summarized below in simplified form.
For more detailed information, see the references.
They are checked sequentially as follows:
• Rule 1—Higher atomic number precedes
lower
• Rule 2—Higher atomic mass precedes lower
• Rule 3—cis precedes trans
• Rule 4—Like pairs of descriptors precede
unlike pairs
• Rule 5—R precedes S
ChemDraw checks differences up to 15 atoms distant from the stereocenter.
CambridgeSoft
assigned as shown in the following table.1
centers. Stereochemical flags apply to the nearest
structure; if no structure is within the distance
specified by the Fixed Length value, the stereochemical flag is not assigned to any structure.
Table 34: Ligand ranking in stereochemistry
Table 35: Stereochemical flags
Stereochemical Indicators
After the ligands are ranked, an indicator is
Stereocenter
Indicator
Double bond
Z if the highest ranking ligand
of each pair are on the same
side of the bond; otherwise E.
The Absolute
flag indicates
the exact stereoisomer as
drawn.
Abs
COOH
NH2
COOH
NH2
Tetrahedral atom When the lowest-ranking ligand
is located behind the central
atom:
Rel
COOH
NH2
• R when remaining 3
ligands are arranged clockwise in descending order
• S when remaining 3 ligands
are arranged counterclockwise in descending order
• r or s is used for pseudo
asymmetric atoms
COOH
NH2
1. R.S. Cahn, C.K. Ingold, and V. Prelog, “Specification of Molecular Chirality”, Angew. Chem.,
Int. Ed. Engl. 1966, 5, 385-414 (errata: 1966, 5,
511); Angew. Chem. 1966, 78, 413-447.
V. Prelog and G. Helmchen, “Basic Principals of
the CIP-System and Proposals for a Revision”,
Angew. Chem. 1982, 94, 614-631; Angew. Chem.
Int. Ed. Engl. 1982, 21, 567-583.
P. Mata, A.M. Lobo, C. Marshall, and A.P.
Johnson, “The CIP Sequence Rules: Analysis and
Proposal for a Revision.” Tetrahedron:Asymmetry. 1993, 4, 657-668.
ChemDraw 10
NH2
Rac
COOH
NH2
Stereochemical Flags
While the chirality of a specific stereocenter can be
indicated with the appropriate wedged, hashed, or
plain bond, sometimes it is useful to indicate the
relative stereochemistry of a molecule as a whole,
considering the relationship between all stereo-
COOH
OR
The Relative
flag indicates
the exact stereoisomer as
drawn, or its
enantiomer.
COOH
NH2
COOH
AND
The Racemic
flag indicates a
mixture of the
exact stereoisomer as drawn
and its enantiomer.
NH2
Polymer Representations
Brackets are used to enclose repeated structures or
structural fragments. ChemDraw provides bracket
properties to specify the orientation and context of
the repeating units. An explanation of the bracket
properties is given in “Representing Polymers and
Other Repeating Units” on page 99.
References
“Graphic Representations (Chemical Formulae) of
Macromolecules (Recommendations 1994)” Pure
Appl. Chem., 66, 2469-2482 (1994).
ChemDraw Chemistry
• 235
“Source-Based Nomenclature for Copolymers
(Recommendations 1985)” Pure Appl. Chem., 57,
1427-1440 (1985). Also available at:
Administrator
http://www.iupac.org/publications/books/pbook/PurpleBook-C7.pdf.
“Basic Definitions of Terms Relating to Polymers
(1974)” Pure Appl. Chem., 40, 479-491 (1974) Also
available at:
http://www.iupac.org/reports/1996/6812jenkins/inde
x.html).
Also see the Guide for the authors of papers and
reports in polymer science and technology from
IUPAC.
• Critical messages that may affect the final analysis
Table 36: Analysis messages
Message
Description
There are too
many bonds to
this unlabeled
Carbon.
Displayed for every unlabeled
atom with more than 4 filled
valences. Filled valences
include sum of bond orders,
charge, radicals, and free sites.
Aromatic bonds count 1.5
each, rounded down unless it is
the only bond to the atom.
Charge is signed and includes
charge implied by dative
bonds. The Substituents query
property treats Free Sites, Up
to and Exactly the same way:
an atom with 2 explicit bonds
and “Substituents: Up To 3” or
“Substituents: Exactly 3” or
“Substituents: Free Sites 1” has
three filled valences.
An atom in this
label has an
invalid valence.
Displayed in a variety of cases
where ChemDraw cannot find
a place to put a bond or cannot
find a bond to put on an atom.
Valid valences for each
element are listed in the
Isotopes Table file.
Query Properties
By their nature, query properties do not represent
actual chemical features, but describe broad classes
or groups of features. For information on using
query properties, see Chapter 5: Query Structures.
Analysis Messages
When ChemDraw is unable to analyze your structure fully, two general types of messages are displayed:
• Status messages that report a problem that may
not affect the final analysis
ChemDraw can’t Displayed when ChemDraw
interpret this
finds text that it cannot identify
label.
as an element, nickname,
generic nickname, or alternative group name.
236•
ChemDraw Chemistry
CambridgeSoft
Table 36: Analysis messages
Message
Description
Parentheses don’t Displayed when parentheses
match.
cannot be matched into nested
open-close pairs.
This label has
conflicting or
unassignable
charges.
Displayed when a plus and
minus charge have been
assigned to the same element,
charges have been assigned in
more than one way, or a charge
has been assigned to a nickname, generic nickname, or
Alternative Group name.
Formula cannot Displayed for every label that
be computed for contains a generic nickname,
queries.
an element list or an alternative
group. This is a status message
only; analysis continues as if
the problematic label were not
selected.
Text not in
Formula style
won’t be interpreted.
Displayed for the first caption
that is not an atom label or
Alternative Group name, and
which contains any text not in
Formula, Subscript, or Superscript style. This is a status
message only, and appears only
once regardless of how many
captions are in the selection.
This named alternative group
contains no
attachment point.
Displayed for any structure
within an Alternative Group
Box where the structure lacks
an attachment point. This is a
status message only.
ChemDraw 10
Table 36: Analysis messages
Message
Description
This named alternative group
contains fragments with
inconsistent
valences.
Displayed for any Alternative
Group Box whose contained
structures have varying
numbers of attachment points.
Since all structures within an
Alternative Group Box are to
be used interchangeably, they
must have the same number of
attachments. This is a status
message only.
This named alter- Displayed for any Alternative
native group
Group Box that is empty. This
contains no frag- is a status message only.
ment.
Part of a molecule is outside of
the alternative
group definition.
Displayed for any Alternative
Group Box whose border
crosses part of a structure. This
is a status message only.
This isolated
bond is probably
not intended to
have chemical
significance.
Displayed for unlabeled single
bonds unattached to other
bonds. All bonds are interpreted chemically, usually as
C2H6, and may cause unexpected results if intended as a
graphical line only. This is a
status message only.
The atom is very Displayed for any atom that is
close to another nearly touching another atom
atom or bond.
or bond but not bound to it. If
a bond really was intended, the
analysis of the structure
produces incorrect results.
This is s status message only.
ChemDraw Chemistry
• 237
Table 36: Analysis messages
Message
Description
Administrator
The stereocenter Displayed for any asymmetric
has no stereocenter without attached
bonds specified. wedged, hashed, dashed, or
bold bonds. This is a status
message only, and appears only
when Show Stereochemistry is
tuned on and there is at least
one other wedged, hashed,
dashed, or bold bond in the
structure.
There is a valence
and charge error
somewhere in
this aromatic
system.
Displayed for any
odd-membered ring drawn as a
delocalized system (with a
circle in the middle), where
there is no corresponding associated charge. For example, a
delocalized representation of
cyclopentadiene must include
either a negative charge or a
multicenter attachment.
The stereocenter
has conflicting or
ambiguous stereobonds specified.
Displayed for any stereocenter
(tetrahedral atom, asymmetric
double bond, etc.) where the
absolute stereochemistry
cannot be determined from the
structure as drawn. For
example, this message would
be shown for a carbon atom
attached by bold bonds to four
different ligands. This message
is displayed only when Show
Stereochemistry is also turned
on.
238•
ChemDraw Chemistry
Table 36: Analysis messages
Message
Description
This label has an Displayed for every label that
unrecognized
has a numeric superscript
isotopic mass.
immediately preceding an
atomic symbol, where the
superscripted number does not
correspond to a recognized
isotope. For example, 24CH3.
CambridgeSoft
Appendix E: How ChemProp Works
ChemProp Values
Henry’s Law
ChemProp enables you to calculate predicted values of selected physical and thermodynamic properties for structures of up to 100 atoms. The
following topics describe how ChemProp obtains
its values.
Henry’s Law Constant—The air to water partition coefficient that is expressed as ratio of vapor
pressure to water solubility or as a unitless distribution coefficient that can be evaluated as a ratio of
the concentration in air to the concentration in
water.
Two methods are used to predict Henry’s Law
constant.
1. The first is an approach based on the bond
contribution method. This method uses 59
bond contribution values and 15 correction
factors. The contributions were calculated by
least squares analysis using a data set of 345
chemicals. This method estimates with a mean
error of 0.30 units and a standard deviation of
0.45 units and can handle molecules containing
carbon, hydrogen, oxygen, nitrogen, sulfur,
phosphorus and halogens.
2. In the second method, Henry’s Law constant is
estimated from an equation found using linear
regression. Multifunctional compounds were
omitted from this study. This method should
not be used for compounds where distant polar
interaction is present.
LogP
LogP (partition coefficient for n-octanol/water)—
three fragmentation methods are used to predict
the logP values.
Method one is based on 94 atomic contributions
evaluated from 830 molecules by least squares
analysis. This method works with a standard deviation of 0.47 logP units and can handle molecules
containing hydrogen, oxygen, nitrogen, sulfur and
halogens.
6. Method two is an extension of method one
that is based on 120 atomic contributions evaluated from 893 molecules by least squares analysis. In addition to the atoms introduced for
method one, it can handle molecules that contain phosphorus and selenium atoms. This
method works with a standard deviation of
0.50 logP units.
7. Method three is based on 222 atomic contributions calculated from 1868 molecules by least
squares analysis. This method allows a calculation of logP with a standard deviation of 0.43
logP units and can handle molecules containing
hydrogen, oxygen, nitrogen, sulfur, halogens
and phosphorus atoms. If this method is
applied to molecules with internal hydrogen
bonds, the standard deviation is 0.83 logP
units.
ChemDraw 10
Molar Refractivity
Molar refractivity—Two fragmentation methods
are used to estimate the molar refractivity value.
1. Method one includes 93 atomic contributions
evaluated from 504 molecules by using a constrained least squares technique. This method
works with a standard deviation 1.27 cm3/mol
and can handle molecules containing hydrogen, oxygen, nitrogen, sulfur and halogens.
How ChemProp Works
ChemProp Values
• 239
Administrator
2. The second method is an extension of method
one that includes 120 atomic contributions
evaluated from 538 molecules by using a constrained least squares analysis technique. In
addition to the atoms introduced for method
one, this method can handle molecules with
phosphorus and selenium atoms. This method
works with a standard deviation of 0.77
cm3/mol.
Ultra
ClogP and CMR
Specific algorithms for calculating LogP and molar
refractivity from fragment-based methods developed by the Medicinal Chemistry Project and BioByte.
For more information, see: http://www.biobyte.com
Topological Polar Surface Area
The polar surface area of a molecule (measured in
square Angstroms) is an important property that
can be used for the prediction of pharmaceutical
transport properties in the body. Historically, this
property has been calculated using time-consuming
240•
How ChemProp Works
3D techniques, but a recent paper1 has provided a
remarkably accurate way of predicting it very rapidly. ChemDraw implements this algorithm, and
displays it on the Chemical Properties window.
Other Properties
Heat of Formation, Gibbs Free Energy, Ideal
Gas Thermal Capacity, Freezing Point, Critical
Temperature, Critical Pressure, and Critical
Volume are estimated using Joback’s fragmentation method.
Normal Boiling Point and Melting Point—
Estimated in K using two methods.
1. Joback's fragmentation method.
2. The Joback method as modified by Stein. All
boiling points are estimated at a pressure of
1 atm.
1. Ertl, P., Rohde, B., and Selzer, P., 2000. Fast
Calculation of Molecular Polar Surface Area as a
Sum of Fragment Based Contributions and Its
Application to the Prediction of Drug Transport
Properties. J.Med. Chem.43: 3714-3717.
CambridgeSoft
ChemProp Values
Appendix F: How ChemNMR Works
ChemNMR estimates chemical shifts for all hydrogen or carbon atoms for which additivity rules are
available. Following a hierarchical list, it first identifies key substructures of a molecule. A substructure provides the base value for the estimated shift.
For example, benzene would be identified as the
key substructure of trinitrotoluene.
When a substructure happens to be a ring system
not available in the data, ChemNMR approximates
its base shift using embedded rings and, if necessary, it will even disassemble the ring into acyclic
substructures.
ChemNMR views remaining parts of the molecule
as substituents of a substructure. Each substituent
adds to or subtracts from the base shift of the substructure to which it is attached. Additivity rules
determine the increment of each contribution. If
an increment for a substituent cannot be determined, ChemNMR uses embedded substituents—
smaller structural units with the same neighboring
atoms. Or, it will use increments of identical or
embedded substituents of a corresponding substructure by assuming that the effects of the substituents are of the same magnitude.
ChemNMR provides a detailed protocol of the
estimation process applied. It gives substructures
as names, compound classes in most cases, substituents in form of a linear code, respectively.
The data set for the 1H NMR Shift tool currently
contains 700 base values and about 2000 increments. The 13C NMR Shift tool is based on 4000
parameters. It also implements models for ethylenes (cis/trans) and cyclohexanes (equatorial/axial).
H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si,
P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni,
Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb,
Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe,
Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy,
Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au,
Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U,
Nep, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr.
Functional groups are expanded automatically.
In case of 1H NMR, it estimates shifts of about
90% of all CHx-groups with a standard deviation
of
0.2. 0.3 ppm. The use of polar solvents may
strongly increase these deviations. It does not estimate shifts of hydrogen atoms bonded to heteroatoms because they are significantly affected by
solvents, concentration, impurities, and steric
effects.
In case of 13C NMR, it estimates over 95% of the
shifts with a mean deviation of -0.29 ppm and
standard deviation of 2.8 ppm.
For more information see:
Fürst, A.; Pretsch, E. Anal. Chim. Acta 1990, 229,
17.
Pretsch, E.; Fürst, A.; Badertscher M.; Bürgin, R.;
Munk, M. E. J. Chem. Inf. Comp. Sci. 1992, 32, 291295.
Bürgin Schaller, R.; Pretsch, E. Anal. Chim. Acta
1994, 290, 295.
Bürgin Schaller, R.; Arnold, C.; Pretsch, E. Anal.
Chim. Acta 1995, 312, 95-105.
Bürgin Schaller, R.; Munk, M. E.; Pretsch, E.
J. Chem. Inf. Comput. Sci.1996, 36, 239-243.
ChemNMR Limitations
The program handles the following elements:
ChemDraw 10
How ChemNMR Works
• 241
Administrator
242•
How ChemNMR Works
CambridgeSoft
Appendix CS-1: Technical Support
Overview
CambridgeSoft Corporation (CS) provides technical support to all registered users of this software
through the internet, and through our Technical
Support department.
Our Technical Support webpages contain answers
to frequently asked questions (FAQs) and general
information about our software. You can access
our Technical Support page using the following
address: http://www.cambridgesoft.com/services/
If you don’t find the answers you need on our
website, please do the following before contacting
Technical Support.
1. Check the ReadMe file for known limitations
or conflicts.
2. Check the system requirements for the software at the beginning of this User’s Guide.
3. Read the Troubleshooting section of this
appendix and follow the possible resolution
tactics outlined there.
4. If all your attempts to resolve a problem fail, fill
out a copy of the CS Software Problem Report
Form at the back of this User’s Guide. This
form is also available on-line at:
http://www.cambridgesoft.com/services/mail
• Try to reproduce the problem before con-
tacting us. If you can reproduce the problem, please record the exact steps that you
took to do so.
• Record the exact wording of any error messages that appear.
• Record anything that you have tried to correct the problem.
ChemOffice 2006/ChemFinderTechnical Support
Overview
You can deliver your CS Software Problem Report
Form to Technical Support by the following methods:
Internet: http://www.cambridgesoft.com/services/mail
Email: [email protected]
Fax: 617 588-9360
Mail: CambridgeSoft Corporation
ATTN: Technical Support
100 CambridgePark Drive
Cambridge, MA 02140 USA
Serial Numbers
When contacting Technical Support, you must
always provide your serial number. This serial number was on the outside of the original application
box, and is the number that you entered when you
launched your CambridgeSoft application for the
first time. If you have thrown away your box and
lost your installation instructions, you can find the
serial number in the following way:
• Choose About CS <application name> from the
Help menu. The serial number appears at the
bottom left of the About box.
For more information on obtaining serial numbers
and registration codes see: http://www.cambridgesoft.com/services/codes.cfm
Troubleshooting
This section describes steps you can take that
affect the overall performance of s Desktop Applications, as well as steps to follow if your computer
crashes when using a CS software product.
• 243
Performance
Administrator
Below are some ways you can optimize the performance of CambridgeSoft Desktop Applications:
• In the Performance tab in the System control
panel, allocate more processor time to the
application.
• Install more physical RAM. The more you
have, the less ChemOffice Desktop Applications will have to access your hard disk to use
Virtual Memory.
• Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
your hard disk to be used as RAM. However,
the time for swapping between the application
and the hard disk is slower than swapping with
physical RAM.
Change the VM as follows:
• System control panel, Performance tab.
System Crashes
CambridgeSoft Desktop Applications should
never crash, but below are the steps you should go
through to try to resolve issues that cause computer crashes while using a CS software product.
1. Restart Windows and try to reproduce the
problem. If the problem recurs, continue with
the following steps.
2. The most common conflicts concern Video
Drivers, Printer Drivers, screen savers, and
virus protection. If you do need to contact us,
be sure to determine what type and version of
drivers you are using.
244•Technical SupportCambridgeSoft
Overview
• Video Driver related problems: If you are
having problems with the display of any
CambridgeSoft Desktop Application, try
switching to the VGA video driver in the
display Control Panel (or System Setup, and
then retest the problems. If using a different
driver helps, your original driver may need
to be updated–contact the maker of the
driver and obtain the most up-to-date
driver. If you still have trouble contact us
with the relevant details about the original
driver and the resulting problem.
• Printer Driver related problems: Try
using a different printer driver. If using a different driver helps, your original driver may
need to be updated–contact the maker of
the driver and obtain the most up-to-date
driver. If you still have trouble contact us
with the relevant details about the original
driver and the resulting problem.
3. Try reinstalling the software. Before you reinstall, uninstall the software and disable all background applications, including screen savers
and virus protection. See the complete uninstall instructions on the CambridgeSoft Technical Support web page.
4. If the problem still occurs, use our contact
form at: http://www.cambridgesoft.com/services/mail and provide the details of the problem to Technical Support.
Appendix CS-2: Accessing the CambridgeSoft Web Site
Online Menu Overview
The ChemFinder Online menu gives you quick
access to the CambridgeSoft web site from within
ChemFinder. With the Online menu, you can:
• Register your software.
• Search for compounds by name or ACX number and insert the structure in a worksheet
• Use ACX numbers, or names or structures in
the worksheet, to search for chemical information
• Browse the CambridgeSoft website for technical support, documentation, software updates,
and more
To use the Online menu, you must have internet
access.
If your serial number is invalid for any reason, or if
you do not have an internet connection, you will
have to contact CambridgeSoft Support to receive
a registration code.
You may use your ChemOffice application a limited number of times while waiting for the registration process to be completed. Once the application
times out, you must register to activate the software.
In addition to registering your software, you can
request literature, or register for limited free access
to ChemFinder.com, ChemACX.com, ChemClub.com, and the email edition of ChemNews
from the Register Online link of the Online menu.
This link connects you to the CambridgeSoft Professional Services page. From this page you can
link to a registration form.
To register online:
1. From the Online menu, choose Register Online.
The CambridgeSoft Professional Services page
opens in your browser.
Register tab
Registering Online
ChemOffice 2006 applications utilize a new security scheme. In order to activate any ChemOffice
application, you must register with the CambridgeSoft website to receive a registration code. Upon
filling out a registration form, the registration code
is sent to you by email. This registration scheme
does not apply to site licenses.
2. Select the Register tab.
Accessing the Online
ChemDraw User’s Guide
The Online menu link Browse CS ChemDraw Documentation opens the CambridgeSoft Desktop Manuals page, where you can access current and
ChemOffice 2006/ChemFinderAccessing the CambridgeSoft Web Site
Online Menu Overview
• 245
Administrator
previous versions of the ChemFinder User’s
Guide.
To access the CambridgeSoft Manuals page:
1. From the Online menu, choose Browse
CS ChemDraw Documentation.
The Desktop Manuals page appears. PDF versions of the CambridgeSoft manuals can be
accessed from this page.
NOTE: If you do not have a CambridgeSoft User
account, you will be directed to a sign-up page first.
2. Click version of the manual to view.
Accessing CambridgeSoft
Technical Support
The Online menu link Browse CS ChemFinder
Technical Support also opens the CambridgeSoft
Professional Services page. There are a number of
links on this page for Troubleshooting, Downloads, Q&A (the ChemOffice FAQ), Contact, and
so forth.
Finding Information on
ChemFinder.com
The Find Information on ChemFinder.com menu
item links your browser to the ChemFinder database record of the compound you have selected.
246•Accessing the CambridgeSoft Web SiteCambridgeSoft
Online Menu Overview
ChemFinder is the public-access database on the
ChemFinder.com website. It contains physical,
regulatory, and reference data for organic and inorganic compounds.
To access ChemFinder.com:
1. In ChemFinder, select a structure you want to
look up.
2. From the Online menu, choose Find Information
on ChemFinder.com.
The ChemFinder.com page opens in your
browser with information on the selected
structure.
In ChemFinder.com you can search for chemical
information by name (including trade names), CAS
number, molecular formula, or molecular weight.
Follow the links to do substructure queries.The
following illustration shows part of the page for
Benzene.
Finding Chemical Suppliers
on ACX.com
Finding ACX Structures and
Numbers
The Find Suppliers on ChemStore.Com menu item
links your browser to the chemacx.com database
record of suppliers of the compound you have
selected.
ChemACX (Available Chemicals Exchange) is a
Webserver application that accesses a database of
commercially available chemicals. The database
contains catalogs from research and industrial
chemical vendors.
ChemACX allows the user to search for particular
chemicals and view a list of vendors providing
those chemicals.
To use Find Suppliers on ChemStore.Com menu
access:
1. In ChemFinder, select a structure you want to
look up.
2. From the Online menu, choose Find Suppliers
on ChemStore.com.
The ChemACX.Com page opens in your
browser with information on the selected
structure.
For example the ChemACX.com page for Benzene
is shown below.
ChemFinder searches ACX and returns information about related structures and numbers. You
can place the returned information in your document.
ACX Structures
There are two ways to find ACX structures: by
ACX number or by name.
To find a structure that corresponds to an ACX
number:
1. From the Online menu, choose Find Structure
from ACX Number.
The Find Structure from ACX number dialog box
appears.
2. Type the ACX registry number.
3. Click the OK button.
The Structure appears in your document.
To find a structure from a name
1. From the Online menu, choose Find Structure
from Name at ChemACX.com.
The Find Structure from Name dialog box
appears.
For more information on using the ChemACX
website, see the ChemOffice Enterprise Workgroup & Databases Manual.
ChemOffice 2006/ChemFinderAccessing the CambridgeSoft Web Site
Online Menu Overview
• 247
2. Type in a name. As with ChemFinder.com, you
Administrator
can use a chemical name or a trade name.
3. Click the OK button.
The Structure appears in your document.
The ChemStore.Com page opens in your
browser.
ACX Numbers
To Find an ACX number for a structure:
1. In a ChemFinder document, select the structure for which you want to find an ACX number.
2. From the Online menu, choose Find ACX Numbers from Structure.
The ACX number appears in the Find ACX
Numbers from Structure dialog box.
You can search ChemStore.Com for chemicals, lab
supplies, chemistry-related software, and other
items you want to buy. You can access
ChemACX.Com, LabEqwip.Com, and other pages
from ChemStore.Com.
Browsing
CambridgeSoft.com
Browsing ChemStore.com
Browse ChemStore.com opens the ChemStore
page of the CambridgeSoft web site.
To access Browse ChemStore.com:
From the Online menu, choose Browse ChemStore.com.
248•Accessing the CambridgeSoft Web SiteCambridgeSoft
Online Menu Overview
Browse CambridgeSoft.com opens the Home page
of the CambridgeSoft web site.
To access the CambridgeSoft Home Page:
From the Online menu, choose Browse CambridgeSoft.com.
The CambridgeSoft web site in your browser.
Check the CambridgeSoft web site for new product information. You can also get to ChemStore.Com, ChemNews.Com, and other pages
through CambridgeSoft.Com.
Using the ChemOffice SDK
The ChemOffice Software Developer’s Kit (SDK)
enables you to customize your applications.
To browse the ChemOffice SDK:
From the Online menu, choose Browse
ChemOffice SDK.
The CS ChemOffice SDK page opens in your
browser.
The ChemOffice SDK page contains documentation, sample code, and other resources for the
Application Programming Interfaces (APIs).
ChemOffice 2006/ChemFinderAccessing the CambridgeSoft Web Site
Online Menu Overview
• 249
Administrator
250•Accessing the CambridgeSoft Web SiteCambridgeSoft
Online Menu Overview
Index
Numerics
C, H shifts, estimating 128
35 mm Slide Boundary lines 152
3D models 115
3D query properties 94
13
1
A
Abnormal valence 90
Abnormally shaped arrows, creating 144
Absolute flag, drawing 96
Actual Size command 153
Acyclic chains
adding 52
changing direction 53
length 53
Add
3D query property 94
chemical names 121
to selection 64
Add Frame 140
Adding
column to template 81
row to template 81
structures in ChemDraw/Excel 184
Adjustment handles 136, 139
Aligning objects
Align Submenu 156
overview 156
rulers 154
with crosshair 155
Aligning Structures 28
Alternative groups
attachment point numbering 104
attachment point symbol 103
attachment Rank indicators 103
defining 102
description 102
ChemDraw 10
Alternative groups (continued)
multiple attachment points 103
Always display and print atom mapping 105
Analysis
information 111
messages 236
Analysis window 18
Anion, drawing 135
Anonymous alternative groups 104
Apply settings command 202
Arc Tool 141
Arcs 141
drawing 137, 141
resizing 141
Arrows
adjustment handles 136
autoscaling 166
changing direction 137
created with curves 144
cursor types 136
disequilibrium, modifying 136
equilibrium 136
hollow arrows 137
new arrow types 136
rotating 138
snapping 138
undo 137
Arrows see also Tools
see also
Assigning
atom mapping 105
structures to spectra 127
Asymmetry, see Stereochemistry indicators
Atom
numbers 75–76
query properties 85
Atom label text boxes, closing 199
•
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Atom Labels
specification 230
Atom labels
automatic justification 208
creating 58
deleting 59
editing 59
editing with a bond or ring tool 59
justification 207
layering 209
margin width 209
multi-attached 71
overview 56
repeating 60
text boxes, creating new line 199
using HotKeys 60
white space 209
Atom numbers
editing 75
position 75
showing and hiding 75
Atom properties
abnormal valence 90
description 87
implicit hydrogens 87
in query structures 85
reaction changes 89
reaction stereo 89
resetting defaults 86
ring bond count 88
substituents 87
unsaturation 88
viewing 86
Atoms
moving 64
Atom-to-atom mapping 105
Attached data 169
Attachment point
defining 102
numbering 104
symbol 103
ii
•
Attachment point (continued)
tool 135
Attachment point tool 102
Attachment points, multiple 103
Attachment points, viewing 74
Attachment rank indicators, showing 104
Auto update 122
Automatic
drawing of structure 122
justification, atom labels 208
mapping 105
Autosave 198
Autoscale
bonds 166
empty document window 166
template color 214
when transferring 165
B
Background color, printing 214
Baseline style, captions 206
Benzene ring tool 50
Benzene ring, changing orientation 52
Benzene rings, drawing 52
Bézier curves 142
Bicyclics, see Other toolbars command
BioDraw 20, 193
drawing a helix protein 196
drawing a membrane arc 195
drawing a membrane line 195
drawing DNA 196
BioDraw objects
color 20, 193
customizing 21, 194
line and fill properties 20, 193
Bitmap fonts, using when available 199
BitMap, see File formats 171
Bitmapped
printing quality 201
BMP, see File formats 171
Boiling point, calculation 240
CambridgeSoft
Boiling point, definition 117
Bold width 204
Bond crossings
white space 204
Bond crossings, changing 55
Bond order, changing 55
Bond properties
defining 90
descriptors 91
reaction center 94
removing 91
topology 93
types 92
viewing 91
Bond query indicators 91
Bond spacing, description 203
Bond tool
repeating a label 60
Bonds
adding to an atom label 72
autoscaling 166
bond orientation for dative or wedged bonds
49
changing orientation 54
changing type 53
double either 93
drawing 47
drawing by clicking 49
drawing by dragging 50
editing 53
fixed angle 48
fixed length 47
layering 55
margin width 204
multi center attachment 73
quadruple 49
selecting 63
types 230
Bonds see also Tools
see also
Border of page 149
ChemDraw 10
Boxes
drawing 139
Braces 140
Bracket
usage 100
Brackets
drawing 140
paired 140
setting properties 99
single 140
tool 140
using to represent polymers 99
Brackets see also Tools
see also
Bring to Front command 157
Bruker JCAMP file format 174
C
Calculating
chemical properties 115
elemental analysis 112
exact mass 112
formula 112
molecular weight 112
Calculations see ChemProp
Caption text boxes
closing 199
creating new line 199
Captions 57
analysis information 112
autoscaling 166
chemical significance of 57
coloring 57
converting to structures 123
creating tables 160
editing 58
formula 206
inserting from structure 121
inserting rows in tables 162
justification 207
setting font, size and styles 208
•
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Captions 57 (continued)
subscript 206
superscript 206
Table column spacing 161
width 58
Carbon-13 shifts, see 13C, 1H shifts, estimating
Cation, drawing 135
CCITT group 3 and 4 176
CDS, see File formats
CDX see File formats
CDX, see File formats
CDXML, see File formats
Center on Page command 156
Centering objects 156
Chain angle, description 203
Changing
bond orientation 54
default settings 201
perspective 153
settings when transferring 167
tolerance 200
Changing bond type 53
Character Map 19
Charges
specifications 232
symbols, drawing 135
Check structure
overview 111
when copying 111
Checking chemistry 111
Chem3D 115
Chem3D objects, caution when sharing files 172
ChemDraw
2.x file format 172
3.5 file format 172
CDX format 171
CTP, CTR file formats 171
customizing 21, 197
HotKeys file 210
ChemDraw Items folder
isotope table 90
iv
•
ChemDraw items folder
description 200
nicknames 81
open special 200
scripts 202
templates 78
window menu 200
ChemDraw laser prep 214
ChemDraw template 171
ChemDraw/Excel
adding structure files 184
adding structures 184
adding structures as SMILES 185
adding structures by name 185
adding structures with ChemDraw 184
aligning structures 188
converting old worksheets 182
exporting to SDFiles 183
get ChemDraw list command 183
import hit list error messages 183
importing tables 181
inserting functions in worksheets 191
naming molecules 187
overview 181
searching 186
starting 181
Chemical Intelligence in ChemDraw 229
Chemical name, structure from 122
Chemical properties
calculating 116
ChemProp 115
Chemical Properties window 18
Chemical properties window 116
Chemical Symbols
palette 134
rotating 136
tool 134
Chemical symbols see also Tools
see also
Chemical syntax checking 55
CambridgeSoft
Chemical warnings 55
suppressing 25, 55
Chemically significant text 231
Chemistry
of ChemDraw 229
Chemistry checking 111
ChemNMR
description 241
using 128
ChemProp
boiling point 240
calculations 239
ClogP 240
CMR 240
critical pressure 240
Critical temperature 240
critical volume 240
description 239
Freezing point 240
Gibbs Free Energy 240
Heat of Formation 240
Henry’s Law 239
Ideal Gas Thermal Capacity 240
logP 239
molar refractivity 239
Thermal Capacity 240
TPSA 240
using 115
ChemProp, using with ChemDraw/Excel 191
Chirality, see Stereochemistry, flags
CHM, see File formats
CIP Rules 234
Circles
resizing 139
Clearing
mapping 106
spectrum-structure assignments 128
stereochemical markers 113
Click to select objects 63
Clipart, see Other toolbars command
ChemDraw 10
Clipboard 163
check structure 111
Clipping files 165
CLogP 117
ClogP 240
Closed style, shapes 144
CML, see File formats
CMR 117
CMYK, planar and contiguous 173
Color
autoscaling 166
menu 211
overview 210
saving settings 214
Color dialog box 212
Color palette 212
Coloring
captions 57
objects 211
Colors, maximum number of 166, 210, 212
Column spacing 161
Commands
new 21
open 22
save 22
save as 22
Compression 176
Conformers, Other toolbars command
Connection Table
example file 225
file format 225
Connection table
file format 172
Contracting labels 71
Conventions 10
Convert name to structure, limitations 122
Convert structure to name, automatic captions
121
Converting
name to structure 123
Converting names to structures 123
•
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Converting to 3D 115
Copy
and check structure 111
as SLN command 164
as SMILES command 163
with clipboard 163
with drag and drop 165
Copy, see also Duplicating
see also
Creating
atom labels 58
HotKeys 210
mirror images 70
SLN strings 164
tables 160
templates 80
Creating text 56
Critical pressure, calculation 240
Critical pressure, definition 117
Critical temperature, calculation 240
Critical temperature, definition 117
Critical volume, calculation 240
Critical volume, definition 117
Crosshair
displaying 155
moving 155
using to align objects 155
CT, see File formats
CTP, see File formats
CTR, see File formats
CTS, see File formats
Curves
autoscaling 166
for creating arrows 144
segment, deleting 143
Custom templates 79
Customized settings, saving 201
Customizing
ChemDraw 197
saving document settings 201
Customizing ChemDraw 21
vi
•
Cycloalkane rings, converting to delocalized rings
51
Cyclohexane chair ring tool 50
orientation 51
Cyclohexane ring tool 50
Cyclooctane ring tool 50
Cyclopentadiene ring tool 50
Cyclopentadiene ring, changing orientation 52
Cyclopentadiene rings, drawing 52
Cyclopentane ring tool 50
Cyclopropane ring tool 50
D
Daggers 140
Data SGroup, support for 169
Database conventions, in structure drawings 229
Databases
support for query structures 85
Dative bonds, drawing 49
Default
atom properties, resetting 86
bond properties, resetting 91
changing 201
document location 197
file format 197
stationery pad 213
Default save file format 199
Deflate compression 176
Delete column, from template 81
Delete row, from template 81
Deleting
atom labels 59
curve segment 143
delete key 65
nicknames 83
objects 65
Pen tool shapes 143
Delocalized rings, drawing 51
Deselecting objects 63
Detecting errors
automatic error checking 55
CambridgeSoft
Detecting errors (continued)
check structure command 111
Disable chemical warnings 25, 55
Discarding changes 22
Displaying
atom mapping 105
cross hairs 155
entire page 153
reaction mapping 105
rulers 154
Dissociation tool 78
Distributing Objects 156
Distributing objects 156
DNA templates, see Other toolbars command
Document
location, default 197
multi-paged 149
posters 150
reverting to last saved 22
Stationery pad settings 217
style sheet settings 217
Document Settings
ACS Document 1996 217
Adv. Synth.Catal. 218
J. Mol. Mod. 219
J.Chin.Chem. Soc. 218
New Document 220
New Slide 221
Phytomedicine 222
RSC Document 222
Science of Synthesis 223
Synthesis/Synlett Document 223
Verlag Helvetica Chimica Acta 224
Wiley Document 224
Document Settings, overview 200
Document Setup
Posters 150
Document setup
multiple-paged documents 149
Document window
drawing area 149
ChemDraw 10
Document window (continued)
enlarging 149
orientation 152
reducing 149
Documents
creating 21
saving 22
D-orbitals, drawing 133
Double bond
changing type 53
Double bond orientation 54
Double bonds, drawing 48
Double either bonds, drawing 49
Drag and drop 165
Drawing
acyclic chains 52
arcs 141
benzene and cyclopentadiene rings 52
bonds by clicking 49
bonds by dragging 50
boxes 139
charge symbols 135
database conventions 229
d-orbitals 133
double bonds 48
double either bonds 49
dz2-orbitals 133
fixed angle bonds 48
fixed length bonds 47
free sites 97
H-Dash Symbol 134
H-Dot Symbol 134
hybrid orbitals 133
mirror images 70
orbitals 131
p-orbitals 133
quadruple bonds 49
radicals 135
resonance delocalized rings 51
rings 50
rings with fixed length 50
•
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Drawing (continued)
sigma orbitals 132
single bonds 47
single lobe orbitals 132
s-orbitals 132
stereochemical symbols 96
structure automatically from name 122
triple bonds 49
with templates 79
Drawing area 149
Drawing daggers 140
Drawing Elements
color 139
fill patterns 139
Drawing elements
autoscaling 166
Drawing elements see also Tools
see also
Drawing settings
changing defaults 201
margin width, effect on atom labels 209
margin width, effect on bond crossing 204
Duplicate, see also Copy
see also
Duplicating
labels 60
Duplicating objects 65
DX, see File formats
Dz2- orbitals, drawing 133
E
Editing
atom labels 59
atom numbers 75
bond orientation 54
bond type 53
bonds 53
captions 58
embedded objects 167
generic nickname file 97
query indicators 96
viii •
Element
recognized 232
Element lists 98
Element not-lists 98
Elemental analysis
caption 112
description 112
Embedded objects 177
Embedding objects 167
Empirical formulas 231
Enantiomers, describing 114
Encapsulated PostScript, see File formats
Enclosing objects 140
Enlarge
document window 149
page size 152
EPS, see File formats
Eraser see Tools
Eraser tool, changing bond order with 55
Error checking 55
Error Messages 236
Exact mass
caption 112
definition 112
Excel add-in, see ChemDraw/Excel 181
Expanding labels 70
Exporting
checking structure 111
compatibility 107
mapping 107
PNG 175
query properties 107
query structures 107
tiff 176
using file formats 168
F
FAQ, technical support 243
File format
connection table 225
WMF 176
CambridgeSoft
File formats
bitmap 171
CDX 22
CDXML 172
ChemDraw 171
ChemDraw 3.5 172
ChemDraw stationery 172
CML 172
connection table 172
CT 172
CTP 171
CTR 171
CTS 176
DX 174
EPS (text) 172
GIF 173
ISIS 173
ISIS/reactions 174
JCAMP 174
JDX 174
JPEG 174
MDL MolFile 174
MDL MolFile V3000 169
MDL RGFile 174
MSI MolFile 175
native 22
pict 175
Pict scaled 4x 175
PNG 175
rxn 174
SKC 173
SMD 175
SPC 175
stationery pad 172
style sheet 172
template 171
TGF 173
TIFF 176
TPL style sheet 176
File formats, table 170
Files, inserting 177
ChemDraw 10
Filled style, shapes 144
Filtering tables 186
Fit to Window 153
Fixed angle bonds 48
Fixed angles, toggling on/off 48
Fixed length bonds 47
Fixed lengths
description 203
scaling 69
Fixed lengths, toggling on/off 48
Flatten command 76
Flip horizontal command 70
Flip type 102
Flip vertical command 70
Flush left justification 207
Flush right justification 207
Font
imaging speed 199
new captions 208
Font substitution 57
Footers, creating 150
Format
atom labels 207
text 206
Formula command
description 112
using 206
Fragmentation see also Tools
see also
Free Energy, calculation 240
Free energy, definition 117
Free sites
drawing 97
in queries 87
Freezing Point, calculation 240
Front to Back ordering 156
Fusing templates 79
G
G groups 102
Galactic Industries, see File formats, SPC
•
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Generic groups 102
Generic nicknames 97
description 97
Generic structures, expanding 119
Get ChemDraw/Excel list 183
Getting started tutorial 25
Gibbs free energy, definition 117
GIF, see File formats
GRAMS software 175
Graphical User Interface 13
Grouping objects 68
Grouping orbitals 131
Groups
integral 69
GUI, see Graphical User Interface
H
Hard coded HotKeys 210
Hash spacing, description 204
H-Dash Symbol, drawing 134
H-Dot and H-Dash, specification 233
H-Dot Symbol, drawing 134
Headers, creating 150
Heat of formation, definition 117
Help
Windows 11
Henry’s Law 239
Henry’s law, definition 117
Hide Crosshair command 155
Hide Rulers command 155
Hiding atom numbers 75
Hiding palettes 17
High resolution
non-PostScript printing 201
High resolution printing 214
Highlight box
selecting 63
HotKeys
“sticky” behavior 61
labeling by pointing 61
labeling multiple atoms 61
x
•
HotKeys (continued)
labeling the last atom drawn 60
quick reference 10
Hotkeys
creating 210
file 210
hard-coded 210
Hot-linked properties 122
How to use this guide 9
Hybrid orbitals, drawing 133
Hydrogen labels, implicit 60
Hydrogens, implicit 87
Hyphens, font submenu 206
I
Implicit hydrogens 87
Implicit hydrogens, hiding 60
Imported objects, selecting 63
Imported picture 172
Importing
spectral data 174, 175
using file formats 168
Importing tables to ChemDraw/Excel 181
InChI strings, copy as 163
InChI strings, creating 165
Include ChemDraw LaserPrep 168
Indicators
atom numbering 75
query 96
query, editing 96
query, positioning 96
stereochemical 235
stereochemistry 113, 235
stereochemistry, positioning 113
Indicators, stereochemical 96
Info window 18
displaying fixed angles 48
Insert name as structure 122
Inserting
files 177
name as structure 122
CambridgeSoft
Inserting (continued)
objects 177
rows in tables 162
Integral groups, creating 69
IR spectra, see spectra
ISIS
reactions 174
SKC file format 173
TGF file format 173
V3000 support 169
Isotopes
specifications 232
Isotopes table file 90
Isotopes text file 90
Isotopic abundance 90
J
JCAMP, see File formats
JDX, see File formats
Joback’s Fragmentation Method 240
Joining objects 67
Joining structures 67
JPEG, see File formats
Justification
atom labels 207
captions 207
K
Kekule structures 51
Keyboard shortcuts, quick reference 10
L
Labels
automatic terminal carbons 205
auto-update 122
contracting 71
expanding 70
Landscape page orientation 152
Lasso tool
selecting objects 62
ChemDraw 10
Layering
atom labels 209
objects 156
Layout, page 149
Lewis dot symbol, see Lone Pair Symbol
Ligand, defined 234
Limitations, name-to-structure 122
Line width 204
Lines, drawing 140
Link nodes 99
LogP 239
Lone Pair Symbol 134
M
m/z, displaying 112
Magnifying
with Magnification control 153
with View menu 153
Make spectrum-structure assignment 127
Manual mapping
clearing 106
overview 106
Mapping
atom 105
automatic 105
clearing 106
exporting 107
manual 106
reaction 105
Margin Width
description 204
Margin width
adjusting 204
effect on Bond crossings 204
specifying 209
Margin width, specifying 209
Marquee tool 63
Mass fragmentation tool 76
Mass spectra
importing as JDX 174
importing as SPC 175
•
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Administrator
mass/charge, displaying 112
Maximize objects 153
MDL MolFile, see File formats
MDL RGFile, see File formats
Melting point, definition 117
Menus
view 17
Menus and toolbars 17
Messages
analysis 236
status 236
Mirror images, creating 70
Molar refractivity 239
Molecular mass, definition 112
Molecular Weight
display in status bar 18
Molecular weight
caption 112
definition 112
how calculated 112
molfile, see File formats
Monochrome 173
Moving
atoms 54, 64
crosshair 155
in tables 161
objects 64
MS, see spectra
MSI MolFile, see File formats
Multi-attached atom labels command 71
Multi-Center Attachments
overview 234
Multi-center attachments 73
Multi-center attachments, see also Variable attachments
see also
Multiple attachment points 103
Multiple Bond tool 48
Multiple selection 62
Multiple-paged documents, setup 149
xii
•
N
Name
inserting as structure 122
of structure, inserting 121
Name to structure see Name=Struct
Name, automatic structure from 122
Name=Struct 122
converting 123
limitations 122
paste special 123
with German names 123
Nanotubes, see Other toolbars command
Native file format 22
New color button 212
New template, creating 79
Nicknames 81
applying 82
defining 82
defining peptides 83
deleting 83
generic 97
quick reference 10
troubleshooting 83
Nicknames, generic
description 97
NMR, see ChemNMR, spectra
Non-PostScript printing
high resolution 201
Macintosh 168
Normal view 153
Numbering atoms 75
O
Object
Add Frame 140
Align 28
Distribute 156
Objects
3D rotation 139
adjusting 139
aligning 155
CambridgeSoft
Objects (continued)
centering 156
deleting 65
Distributing 156
distributing 156
grouping 68
joining 67
moving 64
multiple selection 62
ordering 156
reflecting 69
selecting all 64
ungrouping 68
using crosshair with 155
using rulers with 154
Objects, embedding 177
OLE 167
Online Help, see Help
Opening
ChemDraw/Excel 181
Orbitals see also Tools
see also
Orbitals, drawing 131
Orbitals, grouping 131
Ordering objects 156
Orientation
benzene ring tool 52
cyclopentadiene ring tool 52
double bonds 54
of page 152
rings 50
Orientation of cyclohexane chairs 51
Orientation, of templates 79
Orientation, of user-defined templates 80
Original view 153
Other toolbars command 21
Ovals
adjusting 139
Overlap, multipaged documents 150
ChemDraw 10
P
Packbits, compression 176
Page
border 149
layout 149
orientation 152
overlap 150
setup 151
Page definition language
QuickDraw 201
Page Setup
page layout 151
saving settings 152
Paged documents 149
Paired brackets 140
Palette
arcs 141
Brackets 140
Chemical Symbols 134
color 212
orbital tools 131
query tools 95
single bonds 47
Palettes
showing 17
tearing off 17
Paper Size 151
Parentheses 140
Paste special
name as structure 123
SMILES 164
Pen see Tools
Pen tool shapes
deleting segments 143
Pen tool, Bézier curves 142
Pen tool, drawing by clicking 142
Pen tool, selecting shapes 143
Peptides, defining with nicknames 83
Performance, optimizing 244
Periodic Table 19
Perspectives, changing 153
•
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PICT, see File formats 175
Picture layers
atom labels 209
Plain style, shapes 144
PNG, see File formats
Polyhedra, see Other toolbars command
Polymers
flip type 102
repeat pattern 101
source-based 100
structure-based 100
P-orbitals, drawing 133
Portrait page orientation 152
Positioning
atom number indicators 75
by small increments 64
constrained to axes 64, 65
crosshair 155
objects 64
query indicators 96
rulers 154
stereochemistry indicators 113
Posters, setup 150
PostScript
commands 167
EPS (text) 172
printing 202
Preferences
check structure 111
drawing, see Drawing settings 201
include ChemDraw LaserPrep 168
include PostScript 168
initialize PostScript printer 168
overview 197
print 214
require CTRL+ENTER 199
require Option+Return 199
text, see Text settings 201
use bitmap fonts when available 199
Print quality 200
xiv
•
Printing
atom mapping 105
background color 214
ChemDraw laser prep 214
drawing elements fill 139
effect of PostScript commands 167
high-resolution non-PostScript 201
orientation (of page) 152
overview 162, 214
page setup 151
paper size 151
PostScript atom labels 214
preferences 214
reaction mapping 105
Properties
atom in searching 85
atom, abnormal valence 90
atom, description 87
atom, implicit hydrogens 87
atom, query 85
atom, reaction changes 89
atom, reaction stereo 89
atom, resetting defaults 86
atom, ring bond count 88
atom, substituents 87
atom, unsaturation 88
atom, viewing values 86
bond 90
bond descriptors 91
bond types 92
bond, reaction center 94
bond, removing 91
bond, topology 93
bond, viewing 91
brackets 99
calculating 116
Proton shifts, see 13C, 1H shifts, estimating
Q
Quadruple bonds 49
CambridgeSoft
Queries
multiple rings 99
Queries, see searching
Query indicators
editing 96
overview 96
Query properties
3D 94
exported 107
overview 236
Query structures
description 85
exporting 107
Query tools palette 95
Quick Reference 10
Quick Reference Card, description 11
QuickDraw
bitmapped image 201
print quality 200
R
R groups 102
Racemic flag, drawing 96
Radicals
drawing 135
specification 233
Reaction atom-atom map tool 105
Reaction atom-to-atom mapping 105
Reaction center 94
Reaction changes 89
Reaction mapping
always display and print 105
automatic 105
clearing 106
exporting 107
manual 106
overview 105
Reaction stereo 89
Rectangles
adjusting 139
Red boxes on objects 55
ChemDraw 10
Redo 199
Reduce
document window 149
object 153
page size 152
Reflection through a plane 70
Registration marks 150
Relative flag, drawing 96
Relative stereochemistry 114
Remove
colors 213
rulers 155
Remove color button 212
Repeat command, rotations 66
Repeating a label 60
Repeating actions 23
Repositioning
query indicators 96
stereochemistry indicators 113
Require ctrl+enter to create new line in atom labels 199
Require ctrl+enter to create new line in captions
199
Requirements
windows 11
Reset defaults
atom properties 86
bond properties 91
Resizing
arcs 141
objects 62
objects, with distortion 62
template panes 81
Resizing see also Scaling
see also
Resolution, tiff 176
Resonance delocalized rings, drawing 51
Retrosynthesis see also Tools
see also
Retrosynthesis tool 78
Reversing actions 23
•
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Administrator
Revert command 22
RGB Indexed color 173
RGFile, see File formats
Ring bond count 88
Ring pointer icon appearance 50
Rings
drawing 50
drawing with fixed length 50
orientation 50
RNA templates, see Other toolbars command
Rotate
chemical symbols 136
command 66
dialog box 66
objects 65
RS, see Stereochemistry indicators
Ruler Guides 154
Rulers
hiding 155
showing 154
RXN, see File formats
S
Save command
default file format 199
Saving
defaults 201
structures in ChemDraw/Excel 185
template documents 81
Saving changes automatically 198
Saving customized settings 201
Scaling
by a percentage 69
fixed length 69
objects 69
when transferring information 165
Scrap files 165
Searching
ChemDraw/Excel 186
databases 85
export compatibility 107
xvi
•
Searching (continued)
query properties supported 85
Select All command 64
Selecting
all 64
bonds 63
entire structure 63
pen tool shapes 143
several objects 64
with lasso 62
with marquee 63
Selection rectangle
rotation handle 62
Selection see also Tools
see also
Selection Tool
highlight box 63
selecting several objects 64
Selection tool
deleting 65
deselecting objects 63, 64
joining 67
selecting all 64
using 61
Selection tools 61
Selection, adding to 64
Send to Back command 157
Serial number 243
Set color button 212
Setting
margin width 209
preferences 197
Settings
document 200
Shaded style, shapes 144
Shapes
closed 144
filled 144
plain 144
shaded style 144
Sharing information 163
CambridgeSoft
Shortcuts, see Keyboard shortcuts
Show
atom numbering 75
Show Crosshair 155
Show Page 153
Show Rulers command 154
Show stereochemistry 113
Showing palettes 17
Sigma orbitals, drawing 132
Similarity searching
in ChemDraw/Excel 187
Single bonds, drawing 47
Single brackets 140
Single lobe orbitals, drawing 132
SKC, see File formats
SLN strings 164
SLN strings, copy as 163
SMD, see File formats
SMILES
creating 164
overview 163
paste 164
viewing clipboard 164
SMILES strings, copy as 163
SMIRKS, overview 163
S-orbitals, drawing 132
SPC, see File formats
Spectra
assigning structures 127
exporting 174
importing 174, 175
importing as JDX 174
importing as SPC 175
removing assignments 128
Spectrum-structure assignments
making 127
removing 128
viewing 127
Spiro linkage, templates 79
Squiggly Bond tool see Tools, wavy bond
ChemDraw 10
Starting
ChemDraw/Excel 181
Stationery documents 21
Stationery Pad
saving document settings 199
Stationery pad
default 213
document settings 213
file format 172
Page Setup settings 152
Stationery Pads
creating 217
provided 217
Status bar 18
Status messages 236
Stereochemical symbols, drawing 96
Stereochemistry
drawing mirror images 70
flags 235
how calculated 234
indicators 113, 235
indicators, repositioning 113
removing markers 113
showing 113
terms supported 113
Stereochemistry, relative 114
Stereochemistry, see also Indicators, stereochemical
see also
Stoichiometry grid 118
Stoichiometry grid, editing with the context
menu 119
Stoichiometry grid, setting the limiting compound 118
Struct=Name 121–??, 121, ??–122
Struct=Name, structure types supported 124
Structure
automatic error checking 55
checking 111
cleanup command 72
converting to name 121
• xvii
Administrator
Structure (continued)
diagram generation 72
selecting 63
show stereochemistry 113
Structure Perspective tool, using with objects 139
Structure searching, in ChemDraw/Excel 186
Structures
3D 115
Aligning 28
multiple selection 62
Style Sheet
file format 172
Page Setup settings 152
saving document settings 201
Style sheet
document settings 200
Style Sheets
creating 217
provided 217
Style sheets 21
color palette 214
Style, caption 206
Subscript command 206
Substituents 87
Substructure searching, in ChemDraw/Excel
186
Superatom, ISIS 173
Superscript command 206
Suppress chemical warnings 25, 55
Supramolecules, see Other toolbars command
Syntax checking 111
System crashes 244
System requirements 11
T
Table
adjusting rows and columns 159
adjusting the whole table 159
alignment 159
clearing cells 159
fit to cells 159
xviii •
Table tool 157
Tables
column spacing 161
creating 160
creating with Table tool 157
inserting rows 162
moving in 161
Tables see also Tools
see also
TCL spots
crescent 146
Template panels 81
Template tool 78
Templates
autoscaling 79
coloring 214
creating 79, 80
drawing with 79
file format 176
fusing 79
fusing with existing structure 79
orientation 79, 80
overview 78
panel 81
resizing panes 81
reusing 79
saving template documents 81
spiro linkage 79
Templates, see Other toolbars command
Terminal carbons, labeling 59
Text
atom label format 207
atom label textbox 58
atom labels, automatic justification 208
atom labels, editing 59
caption, creating tables 160
coloring 57
creating 56
editing captions 58
formatting 206
types 56
CambridgeSoft
Text box
closing 199
creating new line 199
Text see also Tools
see also
Text settings
captions, font, size, and style 208
changing defaults 201
Text tool
atom labels 58
TGF, see File formats
TIFF
options 176
resolution 176
TIFF, see File formats
TLC see also Tools
see also
TLC spots
custom, about 146
custom, adding 145
display or set Rf 145
enlarged 146
resizing 146
Rf, about 146
tails 146
wide 146
TLC tool 144
Toggling
between tools 61
Toggling fixed lengths and angles 48
Toggling the text tool with lasso tool 60
Tolerance
effect on highlight box 200
Tool
reaction atom-to-atom mapping 105
Toolbars
docking 17
Main Tools Palette 14
Toolbars and Menus 17
Tools
acyclic chain 16, 52
ChemDraw 10
Tools (continued)
alternative group 102
arc 16, 141
arrow 16
attachment point 102
benzene ring 50
BioDraw 20
bold bond 47
bold wedge bond 47
bond 15, 47
Bracket 140
brackets 16
Chemical Symbol 134
chemical symbols 16
cyclohexane chair 50
cyclohexane ring 50
cyclooctane ring 50
cyclopentadiene ring 50
cyclopentane ring 50
cyclopropane ring 50
dashed bond 47
dative bond 47
dissociation 78
Drawing Elements 138
drawing elements 16
eraser 15
hashed bond 47
hashed wedge bond 47
hollow wedge bond 47
lasso 15, 61, 62
marquee 15, 61, 63
mass fragmentation 76
multiple bond 48
multiple bonds 15
orbital 16
orbitals 131
pen 16, 141
query 95
retrosynthesis 78
ring 16
structure perspective 15, 76
•
xix
Administrator
Tools (continued)
Table 157
table 16
template 16
templates 78
text 16, 56
TLC plate 16
wavy bond 47
Topological Polar Surface Area 240
Topology 93
TPL style sheet, see File formats
Trackball tool 76
Trackball tool see Tools
seetructure perspective
Transferring information
across platforms 178
keeping in scale 165
Translation (query property) 89
Triple bonds, drawing 49
Troubleshooting 243
Tutorial 25
Types of bonds 230
Viewing (continued)
atom properties 86
bond properties 91
chemical properties 116
spectrum-structure assignments 127
W
Warnings, chemical 55
Wedged bonds, drawing 49
What’s New 10
White space, adjusting in atom labels 209
Window
analysis 111
chemical properties 116
Window menu 23
Windows Help 11
Windows metafile 176
WMF, see File formats 176
Z
Zooming, see Changing Perspectives
U
Undo 23
Undo command 198
Ungroup command 68
Unsaturation 88
Unspecified atom properties, in queries 87
Up to, in queries 87
Use defaults
atom properties 86
bond properties 91
bracket properties 99
User-defined templates 79
V
V3000, support for 169
View menu 17
Viewing
analysis information 111
xx
•
CambridgeSoft
CambridgeSoft
Solutions
D ESKTOP S OFTWARE
E NTERPRISE S OLUTIONS
C HEMICAL I NFORMATICS
B IOLOGICAL I NFORMATICS
K NOWLEDGE M ANAGEMENT
S CIENTIFIC D ATABASES
CAMBRIDGESOFT
ChemOffice Desktop to
KNOWLEDGE
MANAGEMENT
CHEMICAL
INFORMATICS
Desktop
E-Notebook
Enterprise
CombiChem
Enterprise
Inventory
Enterprise
E-Signatures
IP Protection
21CFR11
Compliance
GxP
Validation
Registration
Enterprise
Enterprise
WebServer
DESKTOP TO ENTERPRISE
Chem & Bio Office
ChemOffice Workgroup
ChemOffice Enterprise
Just as Chem & Bio Office supports the daily work of the individual scientist,
ChemOffice Enterprise, with Oracle Cartridge, and ChemOffice Workgroup, based
on SQL Server, help organizations from small workgroups to large enterprises
collaborate and share information more effectively.
KNOWLEDGE MANAGEMENT
E-Notebook Enterprise
Reaction Explorer
CombiChem Enterprise
E-Signatures
21CFR11 Compliance
Research organizations thrive when information is easily captured, well organized, and
readily available. E-Notebook Enterprise streamlines record keeping with rigorous
security and efficient archiving, and facilitates text and structure searching. Reaction
Explorer can display the ancestors and descendants of a particular batch in seconds,
while CombiChem Enterprise provides the power of combinatorial chemistry.
E-Signatures provides intellectual property protection and 21CFR11 Compliance
implements an organization’s regulatory compliance process.
CHEMICAL INFORMATICS
Inventory Enterprise
GxP Validation
Registration Enterprise
DocManager Enterprise
Oracle Cartridge
Managing huge data streams is a key challenge. Registration Enterprise organizes
information about new compounds according to an organization's business rules,
while Inventory Enterprise provides complete management of chemical and biological
inventories, including GxP validation. DocManager Enterprise is an important part
of collaborative research data management. Oracle Cartridge adds chemically
intelligent searching to Oracle, integrating with ChemOffice Enterprise applications.
SOLUTIONS
Enterprise Solutions
BIOLOGICAL
INFORMATICS
DocManager
Enterprise
Oracle Cartridge
or SQL DB
SCIENTIFIC
DATABASES
BioAssay
& BioViz
ChemACX
Database
The Merck
Index
BioSAR
Enterprise
Sigma-Aldrich
MSDS
Scientific
Databases
BIOLOGICAL INFORMATICS
BioAssay Enterprise
BioViz
BioSAR Enterprise
BioDraw
Finding structural determinants of biological activity requires processing masses of
biological assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set
up biological models and visualize information, to generate spreadsheets correlating
structure and activity, and to search by structure. The BioViz application allows you to
create graphical representations of data.
DESKTOP SOFTWARE
ChemDraw & Chem3D
ChemFinder & ChemInfo
BioAssay & BioViz
BioDraw
Inventory & E-Notebook
Success begins at the desktop, where scientists use ChemDraw, ChemOffice, and
BioOffice to pursue ideas and communicate with the natural language of chemical
structures, biological pathways, and models. Scientists organize information and
manage data with E-Notebook and Inventory. Chem3D provides modeling, ChemFinder
aids searching, while BioOffice adds BioAssay, BioViz and BioDraw. Integrated with
Microsoft Office to speed research tasks.
SCIENTIFIC DATABASES
The Merck Index
Scientific Databases
ChemACX Database
Sigma-Aldrich MSDS
Development
Training & Support
Good research depends on reference information, starting with the structuresearchable ChemACX Database of commercially available chemicals and SigmaAldrich MSDS. The Merck Index and other scientific databases provide necessary
background about chemicals, their properties, and reactions.
PROFESSIONAL SERVICES
CambridgeSoft's scientific staff has the industry experience, and chemical and
biological knowledge to maximize the effectiveness of your information systems.
Av
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Includes
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a
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a
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a
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s
Databases
Applications & Features
Software
*ChemDraw Ultra
Win/Mac
*ChemDraw Pro
Win/Mac
*ChemDraw Std
Win/Mac
*ChemDraw ActiveX/Plugin Pro
Win/Mac
*Chem3D Ultra
Win
*Chem3D ActiveX Pro
Win
*Chem3D & E-Notebook Pro
Chem3D & E-Notebook Std
ChemFinder Pro
ChemFinder Std
Win
Win
Win
Win
*BioDraw Pro (Pathworks)
*BioAssay Pro
*Inventory Pro
Win
Win
Win
*E-Notebook Ultra
Win
BioViz/Chem & Bio Finder
Win
CombiChem/Excel
ChemFinder/Oracle
Win
Win
ChemFinder/Office
Win
ChemDraw/Excel
Struct<=>Name
ChemNMR & ClogP
Stoichiometry Grid
Win
Win/Mac
Win/Mac
Win/Mac
TLC PLate Tool
Mass Fragmentation Tool
Structure Clean Up
Win/Mac
Win/Mac
Win/Mac
Polymer Draw
Win/Mac
LabArt & BioArt
Win/Mac
Tinker/Chem3D
Win
MOPAC Client
Win
GAMESS Client
Gaussian Client
Jaguar Client
Win
Win
Win
The Merck Index
Win/Mac
*ChemACX Ultra (1 Year)
Win
*ChemINDEX Ultra
Win
ChemRXN, NCI & AIDS
*Available Separately
Win
Chem & Bio Office
Software Standard for Scientists
the ultimate
software suite
for scientists
ChemOffice is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder
and ChemACX for chemists, BioOffice, BioAssay, BioViz, and BioDraw for biologists, and
Inventory, E-Notebook and The Merck Index for scientists. ChemOffice and BioOffice are available
for Microsoft Windows.
the standard
achieves the
ultimate
ChemDraw includes Struct <=> Name, ChemDraw/Excel and ChemNMR. Create stereochemically correct structures from chemical names, and get accurate IUPAC names for structures.
Estimate NMR spectra from a ChemDraw structure with direct atom to spectral correlation.
The ChemDraw ActiveX/ Plugin adds chemical intelligence to your browser for querying databases
and displaying information.
computational
chemistry
made easy
Chem3D provides visualization and display of molecular surfaces, orbitals, electrostatic potentials,
charge densities and spin densities. Chem3D utilizes MOPAC, Gaussian, GAMESS and extended
Hückel to compute molecular properties. ChemProp computes Connolly surface areas, molecular
volumes and properties, including Tinker, ClogP, molar refractivity, critical temperature & pressure.
desktop to
enterprise
searching
ChemFinder is a chemically intelligent database manager and search engine. ChemDraw/Excel
creates searchable spreadsheets. ChemFinder/Word searches documents, spreadsheets, and files for
chemical structures and references. ChemFinder includes CombiChem/Excel for combinatorial library
generation in chemical spreadsheets. ChemFinder/Oracle provides enterprise solution integration.
ultimate suite
for biologists
BioOffice is the ultimate suite for management, analysis and visualization of biological data
using BioAssay and BioViz. Use BioDraw for drawing pathways. Includes Chem3D, Inventory
and E-Notebook.
draw
pathways
BioDraw, formerly called Pathworks, makes drawing and annotating your biological pathways straight-forward and quick, adding a level of uniformity and detail which is unmatched.
screening
data
BioAssay manages both high and low throughput biological screening data. Designed for
complex lead optimization experiments, the software supports the quick set-up of biological models.
visualize
data
BioViz offers automated calculations, curve fitting, and customized structure activity reports,
including a user friendly interface for importing, viewing, validating & plotting biological assay data.
handle
reagent
tracking
Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop
database, you organize, store and search over your inventory. Inventory integrates with the
ChemACX database of available chemicals and ChemMSDX safety data providing chemical
sourcing and purchasing.
efficient
notebook
keeping
E-Notebook is the efficient, accurate way to write lab notebooks. It stores MS Office documents, ChemDraw structures and reaction drawings, and related data in a notebook searchable
by text or chemical structure. Organize pages by project, experiment, or in your own style. Use
CombiChem/Excel to build libraries.
access info
with ease
Databases include The Merck Index and ChemINDEX, including the NCI and AIDS databases.
The ChemACX Database contains nearly 400 catalogs from leading suppliers and ChemMSDX
Database contains over 20,000 material safety data sheets for commonly used laboratory chemicals.
ENTERPRISE &
Chem & Bio Office Workgroup
Integrated Research, Discovery, Development,
Research & Discovery - Search for Products
Since the company’s founding, CambridgeSoft’s
desktop software, starting with its industry-leading
ChemDraw, has been the cornerstone application for
scientists who draw and annotate molecules, reactions,
and pathways. The suite of applications has developed and CambridgeSoft now provides solutions in
virtually all areas of discovery. Researchers can record
and share their experimental information using
E-Notebook, while protecting intellectual property
with digital signatures and 21CFR11 compliance.
They can design both single experiments or design
combinatorial libraries of compounds. They find
and purchase reagents in ChemACX database, store
ChemOffice
En
ter
Includes
pr
Ul ise
tra
En
ter
and use them from Inventory, record newly made
compounds within a proprietary Registration system,
record the results from biological testing in BioAssay,
analyze the results with BioViz, and generate reports
linking activity and structure with BioSAR.
Virtually every aspect of discovery—from synthesis
planning, library enumeration, reagent selection,
primary and secondary screening, in vivo testing,
through to analysis of results and reporting is covered
by this integrated application suite.
Development - Converting Leads into Testing
Building on productivity software, CambridgeSoft
created enterprise applications to meet the needs of an
En
pr
is
Pr e
o
ter
W
W
W
or
or
or
k
k
kg
gr
gr
pr
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o
E-Notebook Enterprise or Workgroup
BioAssay Enterprise or Workgroup
BioSAR Enterprise
BioViz Desktop
Registration Enterprise
Inventory Enterprise or Workgroup
ChemACX Database
ChemINDEX Database
Oracle Cartridge
SQL Server Compatible
ChemFinder Ultra
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
WORKGROUP
and Enterprise Solutions
Trials and Manufacturing Workflow
ever expanding research and development community
that relies on data sharing across scientific disciplines,
research campuses, and even oceans as globalization
has increased demands. Since it is web-based, the
software is deployed readily throughout a research
and development organization. Using Registration, ENotebook, BioAssay, and BioViz, in conjunction with
DocManager and DrugDeg, scientific teams are well
armed to solve the daily challenges of development.
These teams include scientists who scale up and
design manufacturing procedures, toxicologists who
determine the metabolic fate of drug candidates, formulation scientists who determine drug dosing and
delivery systems, as well as many others.
Trials & Manufacturing - Last Steps to Success
A suitable drug candidate is one that has the desired
activity to provide disease therapy while still meeting
drug safety requirements, can be manufactured in a
cost effective and reproducible fashion under
21CFR11 and GMP guidelines, and is stable under
normal formulation and storage conditions. With a
drug candidate in hand, the final challenge is to determine safety and efficacy, beyond the laboratory, in a
patient population.
Manufacturing requires the hand off of data and
batch process records from the pilot plant studies
using Inventory, E-Notebook, and Registration systems
under Good Laboratory and Manufacturing
Processes (GxP).
The handling of materials, including chain of custody
requirements, material documentation, material
workflow, such as availability states and recertification
dates, are tracked and handling by the system. The
systems meet these requirements and provide the
basis to manage materials and records during clinical
trials. Clinicians can design and record results from
protocols, and all of these web based software systems
provide the access required by clinicians who are
removed from the sponsoring company.
ChemOffice Enterprise is a comprehensive
knowledge management and informatics solution,
covering electronic notebooks, biological screening,
chemical registration and more over your intranet.
Enterprise Ultra includes E-Notebook for record keeping, BioAssay for low and high throughput screening
with integrated plate inventory, BioSAR for SAR
reports, Registration system, Inventory for reagents
and ChemACX database of available chemicals.
Technologies include ChemDraw ActiveX and Oracle
Cartridge.
ChemOffice Workgroup is a comprehensive
knowledge management and informatics solution,
covering electronic notebooks, biological screening
and more over your intranet. Workgroup Ultra
includes E-Notebook for record keeping, BioAssay for
low and high-throughput screening, BioViz for
visualization, Inventory for reagents and ChemACX
database of available chemicals. Technologies include
SQL Server for affordability and ease of administration.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
KNOWLEDGE
E-Notebook, Reaction Explorer,
Electronic Journal and Record Keeping
E-Notebook
E-Notebook provides a smooth web-based interface
designed to replace paper laboratory notebooks, with
a fully configurable, secure system for organizing the
flow of information generated by your organization.
You can enter reactions, Microsoft Word documents,
spectra and other types of data, and search this data
by text, substructure or meta data. You can organize
your electronic pages by projects, experiments or any
other classification that conforms to your workflow.
• E-Notebook offers custom organization of
notebook pages at personal or enterprise levels
• Quick access to important data by searching
on keywords, dates, chemical structures and
more
• Reaction Explorer can display the ancestors
and descendants of a batch in seconds
E-Notebook Ultra
E-Notebook Enterprise
E-Notebook Enterprise edition integrates notebook
keeping at group and enterprise levels to promote lab
productivity and information sharing. Oracle
Cartridge manages chemical structures in a common
data repository with detailed security and 21CFR11
Compliance. The enterprise edition also works with
procurement and inventory management systems to
save time locating chemicals and entering structures.
E-Notebook Workgroup
E-Notebook Workgroup, intended for use with a
medium number of users, offers much of the functionality delivered in E-Notebook Enterprise while
using SQL Server as the database. Learning to use
and administer the application is quick and straightforward. E-Notebook applies various data types to
suit different disciplines with an unlimited number
of workflows.
E-Notebook Ultra is the efficient, accurate way to
write lab notebooks entries as you work. It stores
Microsoft Office documents, ChemDraw structures
and reaction drawings, and related data in an electronic notebook you can search by text or chemical
structure. Organize pages by project, experiment or
your own style with the MSDE database.
CombiChem/Excel builds combinatorial libraries.
Reaction Explorer
Reaction Explorer is a powerful application that
assembles a vast amount of information into a lucid
synthesis map. The map provides reaction information, as well as quick access to experiments. Reaction
Explorer displays two types of relationships between
compounds: relationships grouped by batch and
those grouped by compound. Both types of displays
are configurable, allowing scientists to create a look
and feel that they are comfortable with.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
MANAGEMENT
E-Signatures & 21CFR11 Compliance
Property Protection and Regulatory Compliance
The batch display tracks the history of a particular
entity through several subsequent reactions and
experiments. This might be of interest to a chemical
auditor or patent attorney needing to track down the
original source of material.
E-Notebook also provides the capability to scale reactions by virtually any parameter from reagent
amount to vessel size. Individual reactions may be
scaled as well as total syntheses. Batch procedures created with E-Notebook can be used to produce automatically batch record worksheets.
The compound display is more general, and shows all
possible pathways to and from a compound. This is
ideal for chemists working to optimize a process, or a
patent attorney trying to link a product to discovery,
or a scientist trying to compile work done by several
other scientists.
Process Chemistry
The objective of process research is
to identify efficient processes for the
synthesis of active pharmaceutical
agents at the scale required for
clinical trials and commercial use. It
is necessary to provide precise
descriptions of these processes so
that they can be executed by different groups in different locations.
E-Notebook’s process chemistry modules are designed to support these
dual workflow and regulatorycompliance needs of process
chemists. After the steps in a synthesis have been optimized, either individual steps or the entire synthesis
must be scaled.
Display Ancestors
Authenticate Work
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
KNOWLEDGE
E-Notebook, Reaction Explorer,
Electronic Journal and Record Keeping
CombiChem Enterprise
Combinatorial chemistry, in particular the technique
of parallel synthesis, has become an essential element
of the drug discovery process. By using parallel
synthesis techniques, chemists are able to multiply
their productivity by a factor of between 5 and 100.
CombiChem Enterprise has been developed to provide
the tools required by the combinatorial chemist
to manage and document parallel synthesis
experiments.
Flexibility is the key when dealing with databases of
chemical compounds. CombiChem Enterprise can use
reagent lists from a variety of different sources: SD
files, ChemFinder databases, ChemFinder hit lists,
ChemACX Database, or directly from the user via
ChemDraw. Regardless of the source, CombiChem
produces a list of reagents which match a particular
generic reactant.
E-Signatures IP Protection
E-Signatures provides data storage and access functions for electronic records. It is used in conjunction
with E-Notebook as a long-term storage system.
While E-Notebook is intended to capture and record
data as the experiments are carried out, E-Signatures
serves as the repository for finished experiments and
other documents. Electronic records must be
available indefinitely, and their authenticity must be
verifiable independently of the E-Notebook system. In
addition to the record, E-Signatures’ long-term
archive includes a digital signature, a timestamp, and
• Highly flexible and configurable to match
an organization’s workflow
• Consulting teams analyze and adapt
existing procedures to comply with new
regulations
• Systems include authentication and digital
signatures and adapt to changing
regulations and demands for intellectual
property protection
associated metadata. Managers, patent attorneys,
and scientists can retrieve records based on searches
over the metadata.
E-Signatures also manages the signature workflow for
electronic records and documents in process. Digital
signatures are captured at the time of record
creation, which can later serve to prove the authenticity of the stored electronic records. Reviewers,
witnesses, and other individuals can countersign
records for various business purposes, including witness records necessary to meet the needs of 37 CFR
and similar regulations worldwide.
21CFR11 Compliance
Large and growing enterprises are facing a challenge
to their core missions of developing and producing
new products including food, therapeutic pharmaceuticals, medical devices, cosmetics or other health
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
MANAGEMENT
E-Signatures & 21CFR11 Compliance
Property Protection and Regulatory Compliance
enhancing items. The complexity lies in complying
with government regulations designed to protect
public health and safety. The most notable of these
is Title 21 of the Code of Federal Regulations
governing Electronic Records and Signatures
(21CFR11).
Once you have determined how your enterprise will
comply with these new regulations, implementing
those decisions needs to be done quickly, efficiently
and with the understanding that the rules for
compliance are in flux. In order to succeed, you must
be able to respond to change. CambridgeSoft’s
21CFR11 Compliance consulting has both the tools
and the expertise to provide complete solutions, carry
out integration with existing systems, and help execute the process as quickly as your organization
demands.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
CHEMICAL
Inventory, Registration,
Chem and Bio Inventory and Registration
Chem & Bio Inventory
Inventory is an application designed to manage the
chemical and reagent tracking needs of laboratories
and research centers. The system manages data
associated with both commercially procured and
internally produced chemical substances from
procurement or initial production through depletion
and disposal. To meet the needs of institutions
of all sizes, Inventory comes in an Enterprise edition,
a Workgroup edition and two Desktop editions.
Inventory Enterprise is an Oracle-based, ChemOffice
Enterprise product. Designed for large organizations,
it comprises a number of features not included in the
desktop or workgroup versions. Inventory Enterprise
conveniently manages plate information. In addition
to storing, moving, and deleting plates, the application allows users to create daughter plates and
reformat plates. Inventory Enterprise can be tightly
integrated with Registration Enterprise and ChemACX
Database.
Inventory Workgroup is a thick-client SQL Serverbased product. This version is suitable for larger
organizations that do not have the interest or desire to
maintain an Oracle server.
Inventory Ultra is the same MSDE based product,
while also including the ChemACX Database,
CambridgeSoft’s collection of nearly 400 catalogs
from suppliers of chemical reagents.
• Inventory offers plate handling for highthroughput experimentation
• Inventory is GxP Compliant with validated
audit trails
• Registration has flexible business rules for
registration, salt handling, and batch fields
with chemical intelligence that includes
advanced stereochemistry
Inventory Pro is an all-inclusive desktop product. It
includes Microsoft SQL Server Desktop Edition
(MSDE ), the re-distributable database for SQL
Server. No additional licensing is required.
Registration Enterprise
Registration Enterprise includes a robust data model
for pure compounds, batches, salt management,
automatic duplicate checking and unique ID assignments. Compounds may be entered individually or
through the use of a batch loader. The data model
resides entirely in Oracle and uses Oracle’s security
and transaction framework. Registration is easily
adapted to any workflow.
New compound chemical and non-chemical data is
entered into a temporary storage area through a web
form. When the compound is registered, it is
compared for uniqueness via a configurable, stereoselective duplicate check, and assigned a registry
All specifications subject to change without notice.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
I N F O R M AT I C S
DocManager & Oracle Cartridge
Document Searching and Enterprise Infrastructure
number. All information about the compound,
including its test data and other syntheses, is tracked
by the registry number. When a compound is registered, the structure is checked for novelty. If a duplicate already exists in the database, the user can elect
to register the information as a new batch of the
existing compound, or assign it a unique registry
number.
systems are designed for registration of single molecules, with little thought for the world of formulations
and mixtures. CambridgeSoft has developed a system
specifically designed for this registration need called
Formulations & Mixtures.
Registration Enterprise is the only true n-tiered application of its kind that is designed around thin clients
and thin servers. This translates into ultimate flexibility on both the client and server side. Oracle is
supported on a variety of platforms and operating
systems. Using Oracle keeps your proprietary data
secure through the use of Oracle’s
role based security and allows all
chemical and non-chemical data to
be stored directly in the Oracle
tables.
Index Documents
Formulations & Mixtures
Formulation scientists face different
challenges from those working with
individual molecules, yet many of
the tools they are forced to use
emerge from the drug-discovery
world, where single-molecule
research is the norm. Take an essential task such as compound registration and you will find that most
Manage your Inventory
All specifications subject to change without notice.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
CHEMICAL
Inventory, Registration,
Chem and Bio Inventory and Registration
DocManager Enterprise
Web browser based, DocManager Enterprise extends
the capability of standard search engines to include
full free text searching and chemically intelligent
structure searching of electronic documents including Text, Microsoft Word, Excel, PowerPoint, and
Adobe PDF.
The DocManager Enterprise interface allows users to
easily submit documents through a series of simple to
navigate web forms. When a new document is
submitted, DocManager builds a free-text index of
the document, and extracts chemical information
into a chemically-aware, substructure searchable
database. Chemical information can originate from
either ChemDraw or ISIS Draw.
DocManager Enterprise includes a batch loading
utility for administration level users to load multiple
documents at one time. The system can be
configured to submit a batch of documents as one
event, or as a reoccurring submission to be executed
daily. The administrator simply specifies a time
for the submission to take place and the location of
the files.
DocManager Enterprise utilizes the searching intelligence of the ChemOffice Enterprise suite. In addition
to standard textual and numerical searching,
DocManager searches the submitted documents for
chemical structure or reaction.
• DocManager parses Word, Excel and
PowerPoint documents, including free text
• DocManager has a web based interface and
a file drop folder for quick submissions
• Oracle Cartridge is compatible with Linux,
Solaris, AIX and Windows and includes
structure searching, property predictions
and nomenclature
Oracle Cartridge
The CambridgeSoft Oracle Cartridge is used by all
ChemOffice Enterprise applications for storing, searching over, and analyzing chemical data. It can also be
used in the development of your custom Oracle
applications. Chemical structure information is
difficult to manipulate without utilizing special
software. Oracle data cartridges define new, recognized
datatypes. CambridgeSoft’s Oracle Cartridge utilizes
this technology making it possible to manipulate
chemical structure and reaction data from within
Oracle, improving portability and consistency in
applications. Since the Oracle Cartridge is accessed
through Oracle, this allows the programmer to interact
with chemical structure data directly in Oracle. The
CambridgeSoft Oracle Cartridge supports CDX ,
CDXML , MolFile, RXN , and SMILES formats
making it flexible enough to be included with both
new and legacy data, without the need for conversion.
All specifications subject to change without notice.
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FAX
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EU
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
I N F O R M AT I C S
DocManager & Oracle Cartridge
Document Searching and Enterprise Infrastructure
ChemFinder Enterprise
ChemFinder Enterprise is a multiple-user system
designed for sites with heavy-duty chemical and
biological data needs. ChemFinder Enterprise contains
its own engine for working with local and shared
databases and it is also delivered with the
CambridgeSoft Oracle Cartridge, the powerful
Oracle-hosted structure engine based on ChemFinder
search technology. So, the face of ChemFinder
Enterprise is the same friendly form-oriented interface
as the desktop version, but underneath is a fast direct
connection to Oracle and the robust, scalable Oracle
Cartridge running on the server.
All specifications subject to change without notice.
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1 800 315–7300
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FAX
1 617 588–9390
EMAIL
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EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioAssay
Biological assay data comes in many forms, from a
scientist’s observations to output from a plate reader.
Software designed to store and analyze this data must
provide a solution for both the ultra-high volume
laboratories, including laboratory automation,
calculation, and statistics, as well as the very complicated low and medium throughput assays such as
animal models and in vivo experiments. Organizing,
analyzing, and sharing data can be a challenge for
screening biologists, regardless of the amount of
automation or manual data manipulation employed.
• BioAssay effectively manages data from complex biological assays involved with lead
optimization
• BioViz provides a flexible reporting and plotting engine for your scientific data
• BioViz integrates with BioSAR for one step indepth data analysis from a BioSAR report
BioAssay was designed to tackle the needs of high and
low throughput screening biologists alike by providing an application flexible enough to model any
assay, regardless of complexity, while robust enough
to provide an easy to use interface for importing,
storing and analyzing the data. The software supports
the quick set-up of biological models, automated calculations and curve fitting, data validation, and the
creation of customized structure activity reports.
BioAssay Workgroup, intended for single site deployment, uses SQL Server as a database, instead of
Oracle. This solution offers affordability and ease of
maintenance, but still remains a robust solution suitable for a smaller group’s needs. Organize and share
your biological screening data with minimal administrative costs.
BioAssay Enterprise offers a scalable, flexible biological
screening solution utilizing Oracle’s role based security and the Oracle Cartridge. As part of ChemOffice
Enterprise, BioAssay is easily integrated with Inventory
Enterprise for plate tracking and management,
Registration Enterprise for the registration of new
compounds and BioSAR Enterprise for customized
reporting.
BioAssay Ultra is designed to deliver much of the functionality of our enterprise level applications, without
a widespread roll out. MSDE database compatible,
BioAssay Ultra, coupled with BioViz, offers a user
friendly interface for importing, viewing, validating,
and plotting your biological assay data from your
desktop.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
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EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
I N F O R M AT I C S
BioSAR & BioDraw
Data Mining and Pathway Drawing
BioViz
BioViz, with ChemFinder, transforms the numbers in
your database into graphics on your screen. Retrieve
or search for a set of compounds, choose the data you
want to see, whether it is biological test results in
Oracle tables, physical property values calculated
automatically or prices in a catalog, and BioViz will
generate an interactive window showing a scatterplot,
histogram, or other useful data graphic.
The Plot Window, the key to data visualization in
BioViz, shows two variables plotted against each
other in a scatterplot with each point representing a
structure from the current hit list.
If you modify the list, for example
by performing a search, the plot
updates to show the new set of
points. You can drag a rectangle
around a set of points to select
them, or zoom in to see them
more closely.
Draw Biological Pathways
Plot Assay Data
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
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EU
00 800 875 20000
UK
JP
0120 731 800
WWW
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+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioSAR
BioSAR Enterprise, a strategic must for any discovery
organization interested in serious data mining, is a
data-dictionary driven structure-activity analysis
program. Users may choose among assays registered
in the dictionary or search for assays of interest. The
power of BioSAR lies in the researcher’s freedom from
dependence on IT support. Once an assay is
registered into the data-dictionary, it is automatically
included in the powerful analysis framework. By
reducing the time between question and answer,
BioSAR gives researchers the ability to explore new
ideas, the bottom line for discovery information systems. Systems that provide answers after questions
have become irrelevant are of no use. BioSAR avoids
this issue by placing application development in the
researcher’s control.
BioSAR Enterprise allows the researcher to create custom reports and views of their data. You decide what
is displayed, and BioSAR takes care of the rest. While
most SAR tools provide only a table-based interface,
BioSAR provides a both a form view and table view.
The form view provides highly detailed information
about one compound, whereas the tabular view
makes viewing comparisons between compounds
more feasible. There is often a tradeoff between
power and simplicity, and most SAR tools opt for the
former at the expense of the latter. BioSAR, however,
merges the sophistication of a powerful data catalog
technique with knowledge gained through years of
• BioSAR is a catalog driven data mining and
structure- activity analysis program
• BioSAR provides both form and table views
within a simple and powerful web interface
• BioDraw makes it easy to draw and annotate
biological pathways including common
elements such as membranes, enzymes,
receptors and DNA
working closely with users. The result is a SAR
application that is as intuitive as it is powerful.
Security within BioSAR Enterprise is highly granular.
Different roles exist for administrators, publishers,
and browsers. Administrators may add assays to the
data catalog engine, publishers may create reports
and publish them, and browsers may use data query
and analysis. Most data mining tools provide a
mechanism to store queries, but the interface for
creating queries is too complex. With BioSAR, each
set of assays is a complete report with a query form,
a view form, and a table view, combining the
convenience of a ChemFinder or ISIS application with
the power and flexibility of a data catalog-driven
mining program.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
I N F O R M AT I C S
BioSAR & BioDraw
Data Mining and Pathway Drawing
BioDraw
Reporting on and presenting findings is a task familiar
to every biologist. Making this process easier and
more effective benefits everyone involved. BioDraw,
formerly called Pathworks, is doing for biologists
what ChemDraw has done for chemists for years—
saving time, and resulting in a more professional
representation of the science at hand.
The drawing and data organization offered by
BioDraw gives any biologist an advantage. Sharing
this advantage assists the community as a whole.
BioDraw offers many ways to share your drawings
and accompanying data. Users can export data to
Microsoft Office applications for inclusion in
presentations and grant proposals or save data as an
image file for use in journal article submission.
BioDraw makes drawing and annotating biological
pathways quick and easy, adding a level of uniformity and detail which is unmatched. Typical drawings
of biological pathways include many elements that
are difficult to draw with the standard presentation
and word processing software that is on the market.
Common pathway elements such as membranes,
enzymes, receptors, DNA and reaction arrows are
built into the BioDraw toolbar. BioDraw also allows
users to import images in GIF, PNG or JPEG format.
Keeping data organized is of utmost importance in
any lab. BioDraw reflects that importance by allowing users to store annotations for each element in a
drawing. Annotation data ranges from manually
entered text to attached documents, restriction maps,
microarrays, sequence information, literature references, or links. Any data, regardless of format, is
stored side-by-side with the drawing for future
retrieval.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
DESKTOP
ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemDraw Ultra adds Struct<=>Name,
ChemDraw/Excel, ChemNMR, CLogP, tPSA and
ChemFinder/Word to ChemDraw Pro. With rich
polymer notation, atom numbering, BioArt templates,
and modern user interface, ChemDraw is more
powerful than ever before. Create tables of structures,
identify and label stereochemistry, estimate NMR
spectra from a ChemDraw structure with structureto-spectrum correlation, obtain structures from
chemical names, assign names from structures, and
create multi-page documents and posters.
ChemDraw Pro will boost your productivity
more than ever. Draw publication-quality structures
and reactions. Publish on the web using the
ChemDraw Plugin. Create precise database queries by
specifying atom and bond properties and include
stereochemistry. Display spectra, structures, and
annotations on the same page. Use the Online Menu
to query ChemACX.Com by structure and identify
available vendors.
Struct<=>Name contains the leading comprehensive methods for converting chemical structures
into chemical names and names to structures. It can
be used for many types of compounds, including
charged compounds and salts, highly symmetric
structures and many other types of inorganic and
organometallics. Struct<=>Name is available in two
forms: a batch application, and an interactive version
that is also available in ChemDraw Ultra.
• ChemDraw’s improved Struct<=>Name
feature produces names for more types of
compounds
• Live ChemDraw window embedded in
Chem3D application allows simultaneous
2D and 3D editing
• Chem3D brings workstation-quality
molecular graphics and rigorous
computational methods to your desktop
ChemDraw/Excel allows the user to create
chemically knowledgeable spreadsheets within the
familiar Microsoft Excel environment. You can build
and manipulate chemical structures within Excel,
compute chemical properties and perform database
searches.
ChemNMR can be used to accurately estimate 13C
and 1H (proton) chemical shifts. The molecule and
the spectrum appear in a new window. The chemical
shifts are displayed on the molecule and the spectrum
is linked to the structure so that clicking on a peak in
the spectrum highlights the related fragment on the
molecule.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
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EU
00 800 875 20000
UK
JP
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
S O F T WA R E
ChemFinder & ChemInfo
Structure Searching and Scientific Databases
Chem3D Ultra includes a number of molecular
modeling capabilities such as molecular overlay,
conformational searching and dihedral driver support.
It also includes interfaces for optional use of
MOPAC , Gaussian and GAMESS . The user can also
compute advanced physical properties such as CLogP
and ChemProp. These properties can be used to
create SAR tables. ChemSAR/Excel can then be used
to explore structure activity relationships. High
quality Chem3D graphics can be viewed on the web
using the Chem3D ActiveX.
It can also be used to predict a number of chemical
and physical properties. Chem3D contains an
interface to the MOPAC package.
Gaussian is a collection of semi-empirical and
ab initio molecular orbital (MO) computational
methods which can be used to predict energies,
molecular structures, molecular properties, as well
as molecular spectra. Chem3D enables the user to
transparently create input and analyze output resulting
from Gaussian.
Chem3D Pro brings workstation quality molecular
visualization and display to your desktop. Convert
ChemDraw and ISIS/Draw sketches into 3D models.
View molecular surfaces, orbitals, electrostatic
potentials, charge densities and
spin densities. Use built-in extended
Hückel to compute partial atomic
charges. Use MM2 to perform
rapid energy minimizations and
molecular dynamics simulations.
ChemProp estimates physical properties such as logP, boiling point,
melting point and more. Visualize
Connolly surface areas and molecular volumes.
MOPAC is a semi-empirical
quantum mechanics package which
can be applied to the study of
chemical properties and reactions.
Molecular Modeling
Estimate Spectra
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
DESKTOP
ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemFinder Enterprise is a multiple-user
system designed for chemical and biological data
management. ChemFinder Enterprise contains its own
engine for working with local and shared databases
and it is also delivered with the CambridgeSoft
Oracle Cartridge, the powerful Oracle-hosted
structure engine based on ChemFinder search
technology. So, the face of ChemFinder Enterprise is
the same friendly form-oriented interface as the desktop version, but underneath is a fast direct connection to Oracle and the robust, scalable Oracle
Cartridge running on the server.
• ChemFinder offers improved searching and
hitlist management, along with new property
generation
• ChemFinder is tightly integrated with
CambridgeSoft’s Oracle Cartridge
• Search ChemACX and other CambridgeSoft
databases for important chemical information
BioViz, included in ChemFinder Enterprise, provides
a new set of data visualization features. These features
allow you to plot structural and biological data in a
variety of styles, filter plots based on your criteria,
highlight lists and intersecting sets on plots, generate
histograms of data distributions, and more.
The Merck Index is an encyclopedia of chemicals, drugs and biologicals, with over 10,000 monographs covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses and more.
ChemFinder Pro is a fast, chemically intelligent,
relational database search engine for desktop, workgroup or enterprise applications. Extended integration with Microsoft Excel and Word adds chemical
searching and database capability to spreadsheets and
documents.
ChemACX Database includes 500,000 chemical products from nearly 400 supplier catalogs,
searchable with a single query by structure, substructure, name, synonym, partial name, and other text
and numeric criteria. ChemSCX is a compilation of
searchable catalogs from leading screening compound
suppliers.
Today, an ever-increasing number of chemical databases are available in ChemFinder format. Compatibility
with MDL ISIS databases is provided by SDfile and
RDfile import/export. ChemFinder provides network
server workgroup functionality when used with
ChemOffice Workgroup and Enterprise.
ChemMSDX Database provides material safety data sheets for 7,000 pure compounds.
ChemINDEX Database includes 100,000
chemicals, public NCI compounds, AIDS data, and
more.
All specifications subject to change without notice.
US
1 800 315–7300
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FAX
1 617 588–9390
EMAIL
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EU
00 800 875 20000
UK
JP
0120 731 800
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MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
S O F T WA R E
ChemFinder & ChemInfo
Structure Searching and Scientific Databases
NCI Database contains over 200,000 compounds with anti-cancer drug dose-response data.
AIDS Database is an NCI compiled database for
AIDS anti-viral compounds.
ChemRXN Database is a collection of 30,000
fully atom-mapped reactions selected and refined from
the chemical literature. It includes reactions from
InfoChem’s ChemSelect database and ISI’s
ChemPrep database.
ChemFinder.Com is the award-winning web site
with information and WWW links for over 100,000
chemicals. Users can search by name or partial name,
view structure drawings, or use the ChemDraw
ActiveX/Plugin for structure and substructure searches. In addition, users can view live ChemDraw files on
Windows and Macintosh clients.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
DESKTOP
BioDraw, BioAssay, BioViz
Pathways, Biological Assay and Visualization
BioAssay Ultra
BioAssay Ultra, the cornerstone of BioOffice, provides
flexible storage, retrieval, and analysis of biological
data. BioAssay easily manages both high and low
throughput biological screening data. Designed for
complex lead optimization experiments, the software
supports the quick set-up of biological models, automated calculations and curve fitting, and the creation
of customized structure activity reports. BioAssay
brings all of this functionality to your desktop.
BioAssay Ultra, compatible with MSDE database,
offers a user friendly interface for importing, viewing,
validating and plotting your biological assay data.
BioViz
Combining biological data with the chemical
structure is of utmost importance in any drug discovery
environment. BioViz allows you to analyze structurerelated data combined with biological data visually.
BioViz, within ChemFinder, provides a graphical representation of the data loaded into a ChemFinder
form. Users can search over data and construct a
scatterplot, histogram, or other useful data charts.
Plots are interactive to allow you to select subsets of
your data.
BioDraw
BioDraw, formerly called Pathworks, makes drawing
and annotating your biological pathways quick and
easy, adding a level of uniformity and detail which is
unmatched. Typical drawings of biological pathways
include many elements that are difficult to draw with
• BioAssay offers flexible storage, retrieval and
analysis of biological data
• BioViz provides a graphical representation of
the data loaded into a ChemFinder form
• BioDraw allows for quick and easy drawing
and annotating of biological pathways, including importing of images in GIF , PNG or
JPEG format
the standard presentation and word processing
software on the market. Common pathway elements
such as membranes, enzymes, receptors, DNA and
reaction arrows are built into the BioDraw toolbar
and including them in your document is as easy as
including a rectangle. Click on the toolbar shortcut
and drop the element into your document. Resize
and move elements by clicking and dragging and
create an accurate and concise drawing in minutes.
BioDraw allows the import of images in GIF , PNG
or JPEG format. ChemDraw users are also able to
include ChemDraw structures in drawings without
difficulty.
Keeping data organized is of utmost importance in
any lab. The BioDraw application reflects that importance by allowing you to store annotations for each
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
S O F T WA R E
Inventory & E-Notebook
Materials Management and Electronic Journal
element in your drawing. Annotation data ranges
from manually entered text to attached documents,
literature references, or links. Any data, regardless of
format, is stored side-by-side with the drawing for
future retrieval.
The drawing and data organization offered by
BioDraw gives any biologist an advantage. Sharing
this advantage assists the community as a whole.
BioDraw offers many ways to share your drawings
and accompanying data.
Notebook Pages
Data Visualization
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
DESKTOP
BioDraw, BioAssay, BioViz
Pathways, Biological Assay and Visualization
Inventory Ultra
Inventory is an application designed to manage the
chemical and reagent tracking needs of laboratories
and research centers. The system manages data
associated with both commercially procured and
internally produced chemical substances from their
procurement or initial production through their
depletion and disposal.
Inventory Ultra is an MSDE based product and
includes the ChemACX Database with nearly 400
catalogs of chemical reagents. The three primary
entities in an Inventory system are locations, containers,
and substances. Users or administrators configure
a network of locations, which represent locations
within an organization.
Containers are created to represent actual containers
in your facility. Each container is assigned a unique
barcode, which can be printed, using a customized
template, from the Inventory interface. Each container
stores a substance. Additional text fields are available
to track other chemical contents such as the solvent,
and custom fields may also be defined. To keep
track of substances, the system maintains its own
internal chemical structure database containing
unique substances that can be associated with
inventory containers. Advanced duplicate checking is
incorporated in the system.
Every field in a record, including chemical structure,
molecular formula and molecular weight are search-
• Inventory manages the chemical and reagent
tracking needs of laboratories and research
centers
• Inventory maintains its own internal chemical
structure database with advanced duplicate
checking
• E-Notebook stores Microsoft Office documents,
ChemDraw structures, reaction drawings and
related data in a convenient, searchable format
able. The application includes a number of specially
designed inventory search forms. Search results are
returned in list form and can be exported into a document (PDF , RTF , HTML ) using the report engine.
The Inventory interface allows for printing labels as
well as generating elaborate reports. Inventory uses a
report application that incorporates wizards that allow
for the quick creation of simple report and label
templates that can be shared across an organization.
Inventory Pro
Inventory Pro contains the same features as Inventory
Ultra without the ChemACX Database.
E-Notebook Ultra
E-Notebook Ultra is the efficient, accurate way to
write lab notebooks entries as you work. It stores
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
S O F T WA R E
Inventory & E-Notebook
Materials Management and Electronic Journal
Microsoft Office documents, ChemDraw structures
and reaction drawings, and related data in an electronic notebook that is searchable by text or chemical structure. You can organize pages by project,
experiment, or in your own style with the MSDE
database . CombiChem/Excel builds combinatorial
libraries.
E-Notebook is configured exactly like a chemist would
like his or her own notebook to be. Reactions can be
easily drawn into the reaction template by either
selecting from the generous list of preloaded reagents
or by entering or drawing one’s own chemicals.
Commonly used reagents can be stored in a separate
folder for easy access. Another fantastic feature is the
procedural section. This section contains prewritten
procedural sentences with the ability to easily drop in
the specific names of reagent chemicals present in the
reaction. One can also easily add other data to the
notebook page such as spectra and Word or Excel
documents.
CombiChem/Excel
CambridgeSoft provides you with the tools to effectively plan combinatorial chemistry experiments in
Excel. The CombiChem/Excel add-in introduces additional functionality for handling combinatorial
chemistry. Users can generate products from a reaction and lists of reagents, you can view all the products arising from a given reagent or all the reagents of
a given product, and you can lay out reagent and
reaction plates.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
SCIENTIFIC
The Merck Index, NCI, AIDS,
Scientific Reference, Chemical Reactions and Patents
The Merck Index
Among printed chemical reference works, one that
stands out for its integrity, detail and longevity is The
Merck Index. The Merck Index database is a structuresearchable encyclopedia of chemicals, drugs, and
biological agents which includes the complete
10,250 monographs of the 13th edition, 230 new
monographs unavailable anywhere else, as well as 540
monographs retired from the 12th Edition.
The Merck Index is available in many forms to suit the
various needs of both individuals and institutions.
Personal subscriptions are available in one-year and
one-month time periods. A stand-alone package,
requiring no other applications, is also available for
personal use.
The subjects covered include human and veterinary
drugs, biological agents and natural products, industrial and laboratory chemicals, and environmentally
significant compounds. In addition to the standard
searches, compound monographs can be searched by
ChemDraw structure as well as substructure.
Traditional Chinese Medicines
Many of today’s well-known drugs have their origins
from natural sources. Access to this wealth of
knowledge is now available with the Traditional
Chinese Medicines database. The database consists of
monographs for 10,458 chemicals isolated from 4,625
natural sources used in traditional Chinese remedies.
The monographs feature bio-activity data for many
• The Merck Index offers encyclopedic reference
for over 10,000 chemicals, drugs and
biological agents
• Traditional Chinese Medicines provides
chemical information and their biological
effects of complex compounds isolated from
natural sources
• All electronic databases are updated,
contain information unavailable in print,
and are searchable by structure, as well
as text and numeric range
of the compounds, effects and indications of the
medicines, English, Latin, and Chinese names for the
natural sources, and over 2,000 references. This
information is also available as an SD file to facilitate
in silico research.
ChemINDEX
The ability to quickly look up data such as chemical
properties, biological assay results and toxicological
information is no longer a luxury item, but instead a
requirement. Scientists have used the award-winning
ChemFinder.Com database since 1995. Now, the data
on ChemFinder.Com is integrated into ChemOffice as
ChemINDEX. ChemINDEX contains data on over
75,000 compounds including structures, names and
synonyms, physical properties, and Internet links.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
D ATA B A S E S
ChemACX & Sigma-Aldrich MSDS
Available Chemicals and Material Safety Data Sheets
NCI, AIDS & Cancer
Three informative databases have been integrated
into one powerful application with the NCI and
AIDS database collections. The application starts
with a collection of over 200,000 molecules collected
by the National Cancer Institute. Searchable fields
include structure, synonym, CAS RN, formula, and
molecular weight.
ChemReact68
ChemReact68, from InfoChem GmbH, is a database of
sample reactions comprising essential information on
68,000 reactions. These reactions have been selected
because they have greater than 50% yield and have
appeared in more than five example reactions.
The database consists of reaction information and
literature references.
ChemRXN
ChemPrep and ChemSelect are the two reactions databases that make up ChemRXN.
ChemPrep is a reaction database assembled
by the Institute for Scientific Information
(ISI). This reaction database is designed to
help organic chemists find reactions easily.
It includes full literature citations.
ChemSelect, licensed from InfoChem
GmbH, is a reaction database containing
13,000 important organic reactions.
ChemSynth
Scientific Databases
REFERENCE DATA
The Merck Index
11,000 monographs
Traditional Chinese Medicines
10,000 substances
ChemINDEX Database
75,000 substances
NCI, AIDS & Cancer
270,000 substances
Drugs: Synonyms & Properties
8,000 drugs
Medicinal Chemistry
540,000 substances
SOURCING & SAFETY DATA
ChemSynth, from InfoChem GmbH, is a
database of sample reactions comprising
essential information on 180,000 reactions.
These reactions have been selected because
they have greater than 50% yield and have
been sited in leading journals more than
once. The database consists of reaction
information and literature reference.
ChemACX Database
380 catalogs
ChemMSDX Database
23,000 MSDSs
Sigma-Aldrich MSDS
130,000 MSDSs
REACTION & SYNTHESIS DATA
ChemRXN Database
28,000 reactions
ChemSynth
178,000 reactions
ChemReact68
68,000 reactions
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
In order to provide our customers with a total
solution for scientific informatics, CambridgeSoft
offers the following services to assist our clients in
maximizing the productivity of their research and
discovery organizations.
Informatics Planning
With custom development, CambridgeSoft
works collaboratively with your team to create
a system that meets your needs while executing
our quality driven software development
process. We deliver what you need, on time
and within budget, without surprises.
Strategic and Operational Planning
A formal analysis is conducted to provide a roadmap
for successful technology utilization. This process
includes:
· An analysis of the current state of the science
technology environment, including architecture and
operational processes
· A view of the strategic goals and the barriers to
achievement
· The delivery of a phased technology transition plan
Is your project set up for success? Is it well defined
into measurable deliverables? Are the roles of project
members clearly defined? CambridgeSoft’s Project
Readiness Assessment has one goal in mind—
to create or assess current plans and make recommendations to ensure that results are achieved.
Requirements Analysis & Proof of Concept
21CFR11 Compliance
CambridgeSoft consultants can create or refine
requirements to produce an environment that will
ensure success. With years of experience meeting the
needs of the scientific community, CambridgeSoft
understands the user. The prototyping process
allows definition and testing of the functional and
technical feasibility of potential technology solutions.
The process provides a baseline for the future
development and deployment of a tailored solution.
Users gain valuable first hand knowledge in
experiencing how the system can help achieve
individual and workgroup goals.
Successfully implemented, a traceable and usable
system is essential to any organization involved in the
creation and management of data in a regulated
environment. As an integral part in creating 21CFR11
and GxP validated applications, CambridgeSoft offers
services to:
Project Readiness Assessment
· Audit the software and process
· Create conforming systems design specifications
· Generate test plans and validation matrices
· Insure systems compliance with functional guidelines
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
SERVICES
Training & Support
Educational Training and Technical Support
Product Development
Data Conversion and Integration
When developing a new system, the process of
converting existing data and creating interfaces with
other data systems is an essential part of the process.
CambridgeSoft’s professional services staff is equipped
to seamlessly incorporate existing data into the development of a new enterprise system. Organizations
will be able to capitalize on historical scientific data
while setting the platform for future success.
Custom Development
You have discovered a unique application
need in your organization, but cannot find a
solution that will meet your functionality or
cost requirements. With custom development,
CambridgeSoft works collaboratively with
your team to create a system that meets your
needs, while executing our quality driven
software development process. We deliver
what you need, on time and within budget,
without surprises.
Product Tailoring
Your organization can see the benefit from
implementing a CambridgeSoft application,
Installation and Configuration
CambridgeSoft will install and configure applications
to meet the needs of your user community. For
unique environments, we build custom installers that
allow us to productively deploy software across an
enterprise.
PLANNING
DEVELOPMENT
DEPLOYMENT
MANAGEMENT
Strategic/Op
Planning
Data
Integration
Installation &
Configuration
Managed
Informatics
Requirements
Analysis
Proof of
Concept
Systems Integration
The ability to integrate core applications
with other systems in the technology environment is a competency required to deliver
the functionality of a new application.
but would like to customize it for a unique environment. Our professional services teams can provide
those specific features by making custom modifications that will be supported in the future.
Systems Deployment
Project
Readiness
21CFR11
Compliance
Custom
Application
Development
Systems
Integration
Product
Tailoring
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
Systems
Optimization
Pre-Release
Programs
Software
Evaluations
Training
Services
Ultra
Services
Plans
Technical
Support
Remote DBA
Services
PROFESSIONAL
Development, Deployment,
Custom Development and System Deployment
Systems Optimization
CambridgeSoft’s systems deployment team will work
with you to make sure that your computing environment has been optimized for high performance.
Your systems, networks, applications and databases
are assessed and designed to deliver maximum
achievement.
Managed Informatics allows your organization
to focus on science, allowing CambridgeSoft to
plan, implement and manage your technology
environment.
Beta and Pre-Release Programs
CambridgeSoft is committed to maximizing your
productivity through the use of our products, as well
as exposing you to the newest technologies. Our beta
and pre-release programs provide you with that
knowledge, allowing CambridgeSoft to improve
applications with your customer feedback.
sional services staff supporting your systems
environment
· On-site formal classroom training
· Webinars for multi-location instruction
· Off-site at CambridgeSoft facilities
Systems Management
Pilot Software Evaluations
Managed Informatics
It often makes sense to pilot an application before a
major commitment for an enterprise wide implementation is made. CambridgeSoft will work closely with
you to plan the evaluation, deploy the application,
and gather critical feedback regarding systems design,
API’s and technology specifications.
There is no longer a need to worry about licensing
fees, maintenance contracts, systems administration
work or database support. Informatics Outsourcing
provides the people, processes and technology to
develop a unique level of service for your organization.
For a monthly fee, CambridgeSoft will deliver the
informatics applications and the technology staff
required to maximize productivity. This service
allows your organization to focus on science, while
CambridgeSoft plans, implements and manages your
technology environment.
Training
Effective user, administrator and help desk training is
often an afterthought in many systems deployments.
However, the productivity returns generated by
an investment in systems training can provide
dramatic returns. CambridgeSoft offers training in
the following ways:
· On-site “real time” training through our profes-
Ultra Services
The Ultra Services program is CambridgeSoft’s
personalized, premium service for supporting our
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
SERVICES
Training & Support
Educational Training and Technical Support
customers. Organizations can take advantage of both
telephone and electronic access to CambridgeSoft’s
support scientists who can address:
· Usage and installation questions
· Product compatibility and interoperability
questions
· Diagnostic review to help isolate the cause of a
problem
· Configuration assistance
· Planning information for software updates and
upgrades
· Assistance with problem resolution
Technical Support & Remote DBA Services
To complete our Management Services offerings,
Technical Support and Remote DBA Services, for
Oracle and SQL Server, are also available.
All specifications subject to change without notice.
US
1 800 315–7300
INT’L 1 617 588–9300
FAX
1 617 588–9390
EMAIL
[email protected]
EU
00 800 875 20000
UK
JP
0120 731 800
WWW
www.cambridgesoft.com
+44 1223 464900
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, Massachusetts 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation ©2005
Chem & Bio Office
Desktop Software to Enterprise Solutions
CHEMICAL
INFORMATICS
KNOWLEDGE
MANAGEMENT
BIOLOGICAL
INFORMATICS
SCIENTIFIC
DATABASES
Desktop
E-Notebook
Enterprise
CombiChem
Enterprise
Inventory
Enterprise
E-Signatures
IP Protection
21CFR11
Compliance
GxP
Validation
Enterprise
Registration
Enterprise
DocManager
Enterprise
Oracle Cartridge
or SQL DB
BioAssay
& BioViz
ChemACX
Database
The Merck
Index
BioSAR
Enterprise
Sigma-Aldrich
MSDS
Scientific
Databases
Enterprise
Research, Discovery, Development, Trials & Manufacturing
Enterprise Solutions include ChemOffice, with Oracle Cartridge, and ChemOffice Workgroup, based on SQL Server to help
organizations from small workgroups to large enterprises collaborate and share information more effectively.
Desktop Software includes ChemOffice, a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and
ChemACX for chemists, BioDraw, BioAssay and BioViz for biologists, and Inventory and E-Notebook.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management
of chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
BioIogical Informatics scientists use BioAssay, BioViz, BioSAR and BioDraw to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS.
The Merck Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services includes custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.
Web
Email
[email protected]
America 1 800 315–7300
UK
+44 1223 464900
Europe
00 800 875 20000
Germany
+49 69 2222 2280
Japan
0120 731 800
France
+33 1 70 71 98 80
www.cambridgesoft.com
CS Software Problem Report
For faster response and accuracy, use the Web:
www.cambridgesoft.com/services/mail
USER INFORMATION (Please Print Legibly)
Name
WWW
EMAIL
FAX
MAIL
Title
Firm
Street
City
Submit this form via…
State
Zip
Country
Tel
Fax
Email
DETAILS OF THE PROBLEM
SYSTEM CONFIGURATION
SOFTWARE
Application Name
!
Please cut here or photocopy page.
Version Number
Serial Number
SYSTEM
Windows (version)
MacOs (version)
Web Browser(s) (version)
US
1 617 588-9300
FAX
1 617 588–9390
WWW
EU
00 800 875 20000
FAX
+44 1223 464990
EMAIL
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
www.cambridgesoft.com
[email protected]
www.cambridgesoft.com/services/mail
[email protected]
1 617 588–9360
CambridgeSoft, 100 CambridgePark Dr.
Cambridge, MA 02140 USA
ChemBioOffice.Com
CS ChemDraw
®
for Windows
Quick Reference
SCREEN ELEMENTS
Magnification controls
Title Bar
Object Toolbar
Menu Bar
General
Toolbar
®
Lasso
Structure Perspective
Solid Bond
Multiple Bonds
Dashed Bond
Hashed Bond
Hashed Wedged Bond
Bold Bond
Bold Wedged Bond
Hollow Wedged Bond
Wavy Bond
Table
Acyclic Chain
Cyclopropane Ring
Cyclopentane Ring
Cycloheptane Ring
Cyclohexane chair 1
Cyclopentadiene Ring
1-substrate enzyme
2-substrate enzyme
Receptor
Ion Channel
Helix Protein
Membrane (line)
Membrane (arc)
Golgi Body
Cloud
Marquee
Fragmentation tools
Eraser
Text
Pen
Arrows
Orbitals
Drawing Elements
Brackets
Chemical Symbols
Query tools
TLC plate
Templates
Cyclobutane Ring
Cyclohexane Ring
Cyclooctane Ring
Cyclohexane chair 2
Benzine Ring
G-protein (alpha subunit)
Rotation Handle
Text Style Toolbar
Resize Handles
Selection Box
G-protein (beta subunit)
G-protein (gamma subunit)
Immunoglobulin
DNA
Micelle
Membrane (ellipse)
Endoplasmic Reticulum
Mitochondrion
Status Bar
Resize
WORKING WITH SELECTIONS
If you want to …
Here’s how …
Add items to a selection
SHIFT+select items not currently selected
Remove items from a selection
SHIFT+select items currently selected
Duplicate a selection
CTRL+drag Selection Rectangle
Constrain dragging to X or Y direction
SHIFT+drag Selection Rectangle
Duplicate and constrain dragging
SHIFT+CTRL+drag Selection Rectangle
Switch between selection and another tool
CTRL+ALT+TAB
Resize selection excluding atom labels
Drag Resize handle of Selection Rectangle
Resize selection including atom labels
CTRL+drag Resize handle of Selection Rectangle
Rotate selection excluding atom labels
Drag Rotation handle of Selection Rectangle
Rotate selection including atom labels
CTRL+drag Rotation handle of Selection Rectangle
Distort aspect ratio of selection
Drag sides of the Selection Rectangle
Resize without distortion
Drag corners of the Selection Rectangle
Free Resize
SHIFT + drag corners of the Selection Rectangle
Open Rotate or Resize dialog box
Double-click Resize handle or Rotation handle
DRAWING TECHNIQUES
Draw a first bond
Drag to draw the bond
Add a bond to a structure
Click an atom or drag from an atom
Label an atom using a bond or ring tool
Double-click an atom (triple-click to repeat last label)
Label an atom using the Text tool
Click an atom (double-click to repeat last label)
Label an atom using a HotKey
Point at an atom and press a HotKey (e.g., “c”)
Draw a double bond (solid, dashed, bold only)
Select bond type from context menu
Draw a triple bond (solid only)
Select bond type from context menu
Reduce bond order using Eraser tool
Click once
Change double bond alignment
Click center of double bond using any bond tool
Change double bond type
Click center of double bond using different bond tool
Move an atom
SHIFT+drag an atom using a bond tool
Change bond type
Click center of bond using different bond tool
Change bond layering using bond tool
Double-click center of bond you want forward
Draw a ring
Click or drag using a Ring tool
Create a spiro-linkage
Click or drag from an atom using a Ring tool
Create a fused ring
Click a bond using a Ring tool
Change size of non-bond object
Drag starting point of object (e.g., arrowhead)
We b
America
Europe
Japan
IWE 05652 0512
w w w. c a m b r i d g e s o f t . c o m
1 800 315–7300
00 800 875 20000
0120 731 800
Email
UK
[email protected]
+44 1223 464900
Germany
+49 69 2222 2280
France
+33 1 70 71 98 80
ChemBioOffice.Com
CS ChemDraw
®
for Macintosh
Quick Reference
SCREEN ELEMENTS
General
Toolbar
Menu Bar
Title Bar
Magnification controls
Object Toolbar
Lasso
Structure Perspective
Solid Bond
Fragmentation tools
Eraser
Multiple Bonds
Text
Dashed Bond
Hashed Bond
Pen
®
Hashed Wedged Bond
Bold Bond
Bold Wedged Bond
Hollow Wedged Bond
Wavy Bond
Table
Acyclic Chain
Cyclopropane Ring
Cyclopentane Ring
Cycloheptane Ring
Cyclohexane chair 1
Cyclopentadiene Ring
1-substrate enzyme
2-substrate enzyme
Receptor
Ion Channel
Helix Protein
Arrows
Orbitals
Drawing Elements
Brackets
Rotation Handle
Resize Handles
Chemical Symbols
Query tools
TLC plate
Templates
Cyclobutane Ring
Cyclohexane Ring
Selection Box
Cyclooctane Ring
Cyclohexane chair 2
Benzine Ring
G-protein (alpha subunit)
G-protein (beta subunit)
G-protein (gamma subunit)
Scroll bar
Immunoglobulin
DNA
Membrane (line)
Micelle
Membrane (arc)
Golgi Body
Membrane (ellipse)
Cloud
Text Style Toolbar
Endoplasmic Reticulum
Mitochondrion
Resize
WORKING WITH SELECTIONS
If you want to …
Here’s how …
Add items to a selection
SHIFT+select items not currently selected
Remove items from a selection
SHIFT+select items currently selected
Duplicate a selection
APPLE+drag Selection Rectangle
Constrain dragging to X or Y direction
SHIFT+drag Selection Rectangle
Duplicate and constrain dragging
SHIFT+APPLE+drag Selection Rectangle
Switch between selection and another tool
CTRL+APPLE+TAB
Resize selection excluding atom labels
Drag Resize handle of Selection Rectangle
Resize selection including atom labels
APPLE+drag Resize handle of Selection Rectangle
Rotate selection excluding atom labels
Drag Rotation handle of Selection Rectangle
Rotate selection including atom labels
APPLE+drag Rotation handle of Selection Rectangle
Distort aspect ratio of selection
Drag sides of the Selection Rectangle
Resize without distortion
Drag corners of the Selection Rectangle
Free Resize
SHIFT + drag corners of the Selection Rectangle
Open Rotate or Resize dialog box
Double-click Resize handle or Rotation handle
DRAWING TECHNIQUES
Draw a first bond
Drag to draw the bond
Add a bond to a structure
Click an atom or drag from an atom
Label an atom using a bond or ring tool
Double-click an atom (triple-click to repeat last label)
Label an atom using the Text tool
Click an atom (double-click to repeat last label)
Label an atom using a HotKey
Point at an atom and press a HotKey (e.g., “c”)
Draw a double bond (solid, dashed, bold only)
Select bond type from context menu
Draw a triple bond (solid only)
Select bond type from context menu
Reduce bond order using Eraser tool
Click once
Change double bond alignment
Click center of double bond using any bond tool
Change double bond type
Click center of double bond using different bond tool
Move an atom
SHIFT+drag an atom using a bond tool
Change bond type
Click center of bond using different bond tool
Change bond layering using bond tool
Double-click center of bond you want forward
Draw a ring
Click or drag using a Ring tool
Create a spiro-linkage
Click or drag from an atom using a Ring tool
Create a fused ring
Click a bond using a Ring tool
Change size of non-bond object
Drag starting point of object (e.g., arrowhead)
We b
America
Europe
Japan
IME 05812 0512
w w w. c a m b r i d g e s o f t . c o m
1 800 315–7300
00 800 875 20000
0120 731 800
Email
UK
[email protected]
+44 1223 464900
Germany
+49 69 2222 2280
France
+33 1 70 71 98 80
ChemBioOffice.Com
CS ChemDraw
for Excel
®
for Windows
Quick Reference
SCREEN ELEMENTS
Title bar
ChemDraw menu
ChemDraw for Excel functions
Excel menu bar
Excel toolbar
ChemDraw
toolbar
®
ChemDraw
structure
TOOLBAR
1
2
3
4
5
6
7
8
9
10
11
12 13 14
15 16 17
18 19
1. New ChemDraw Worksheet — Create a new
worksheet.
11. Show Pictures — Display molecules.
2. Import Table — Import an SDFile or a
ChemFinder database.
13. Resize Pictures — Resize molecules using
the resize handles.
3. Export Table — Export selected cells or the entire
spreadsheet to an SDFile or ChemFinder database.
14. Align All Pictures — Enlarge cells or reposition the
molecules within the cells.
4. Import ChemFinder list — Import an open hitlist.
15. Normal Search — Search for exact structures and
substructure using the Search Query dialog box.
5. Load Molecule — Load a single molecule from a file.
6. Save Molecule — Save a single molecule to a file.
7. Cut Molecule — Remove a molecule and place it
on the clipboard.
8. Copy Molecule — Copy a molecule and place it on the
clipboard.
9. Paste Molecule — Paste a molecule from the clipboard.
10. Name Molecule — Name a molecule.
12. Hide Pictures — Hide molecules.
16. Similarity Search — Search for similar structures using
the Similarity Query dialog box.
17. R-Group Analysis — Shows groups attached to the query
structure.
18. Convert SMILES to Molecule — Convert a valid
SMILES string to a molecule.
19. Convert Name to Molecule — Convert a name
into a molecule.
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