picoSpin 45 - Installation and Setup

picoSpin 45 - Installation and Setup
picoSpin 45 - Installation and Setup
Unpacking the Spectrometer
Avoid personal injury or equipment damage. Read
and understand the accompanying documentation
and all safety labels before attempting to install or
use this equipment.
Install detailed information about the picoSpin from the
documentation DVD that came with the system, or go to
1. Unpack the spectrometer.
2. Remove the shipping restraints.
a. Turn the spectrometer over on its top.
b. Turn the red thumbscrews counterclockwise until they can be
Figure 2. Bottom side of the spectrometer
CAUTION Eye protection should be worn at all
times while using this instrument. Please refer to
OSHA standards on EYE and FACE protection
when handling chemicals.
The Thermo Scientific™ picoSpin™ NMR spectrometer is a complete
pulsed Fourier transform liquid-phase proton NMR spectrometer. It
includes a capillary cartridge, a permanent magnet, radio-frequency
transmitters and receivers, digital data acquisition and signal
processing, a programmable pulse sequencer, and a web-server user
c. Remove black plugs from the plastic bag.
Figure 3. Remove red thumbscrews
What’s in the Box
Figure 1. Inside the box
Black plugs
Power cord
Ethernet cable
Power supply
d. Insert black plugs in the holes where the red thumbscrews
were removed.
Accessory kit
Revision A 269-298301
© 2013-2014 Thermo Fisher Scientific Inc.
All rights reserved.
Figure 4. Black plugs inserted
Figure 7. Connecting the spectrometer cables
e. Turn spectrometer over on its feet.
Spectrometer Components
Figure 5. Front of spectrometer
Power cord
Power supply
1. Plug the power cord into the power supply.
2. Plug the ethernet cable into the computer or into your LAN, and
connect the other end of the cable to the spectrometer.
3. Turn on the computer.
We recommend Mozilla’s free Firefox™ web browser for best
compatibility with our software, but most modern browsers will work
equally well, including Google Chrome™ and Safari™, and Internet
Explorer™ 10 and 11.
Ethernet Connection
Connecting through a LAN
In and Out ports
1. Switch on the unit while watching the front panel LCD display.
Figure 6. Back of the spectrometer
After about one minute an IP address appears on the front panel.
This address has been assigned by your LAN using DHCP. (See
“Setting up a Computer to Use a Static IP Address” if the address
displayed is
Type the IP address in the navigation toolbar of your web
Figure 8. picoSpin 45 welcome screen
DC Power
For example, if the address displayed is, type into the address field of the browser.
 Automatic assignment of the IP address by the LAN will only
be successful if the unit is switched on after it has been
connected to an active Ethernet port on your LAN, and then
only if your LAN has DHCP capability.
 If the unit is not assigned an IP address by DHCP it will
display a factory default IP address of
Windows 7 and Windows 8
1. Navigate to the networking configuration.
a. Select Control Panel > Network and Internet > Network and
Sharing Center.
b. Select Change adapter settings.
c. Select Local Area Connection.
In most cases, you will not be able to communicate through
your LAN to this address because LANs are configured to
communicate only with a subset of all IP addresses.
d. Select Internet Protocol Version 4 (TCP/IPv4).
e. Click Properties.
f. Select Alternate Configuration.
For example, your LAN might only allow communication
between IP addresses of the form 192.168.2.x, where x is a
number between 0 and 255. If you see the default IP address
and you are sure that your LAN does support DHCP, try
using the same cable to connect another device to the LAN
Ethernet port you have chosen to make sure it is active.
 If the unit is assigned an IP address by DHCP and you
cannot connect to it with your browser, then additional login
credentials may be required. For guidance, consult your IT
administrator on completing the LAN connection.
g. Select User configured.
2. Type in the following fields:
IP address: Subnet mask:
3. Click OK.
4. Click Close.
To check the configuration, launch the Command Prompt and
type ipconfig. The output should indicate the IP address you
entered above.
After the welcome screen has been displayed for a moment, it will
be replaced by the Run page, which is used to enter experiment
parameters, start experiments and monitor their progress.
Linux Debian
In Debian edit the file /etc/networking/interfaces for the wired
network interface card you intend to connect to the unit. For
computers with one network card the interface is typically called eth0
and that section would look like:
The orange text links at the upper right of the page are used to
navigate between pages.
If you are unable to connect to the spectrometer through your
LAN, make a direct connection.
iface eth0 inet static
Direct Connection
The computer must have an available Ethernet port with a working
network adapter. If you are unsure whether the Ethernet port is
working, try using it to connect to a network.
1. Turn the spectrometer power switch on.
2. After about a minute, the front panel LCD will display the
factory default IP address of
Magnet Temperature Control
3. Configure the Ethernet port on the computer so it can
communicate with the default IP address.
After start up, it may take from 20 minutes to 1 hour for the magnet
to stabilize at the setpoint temperature, depending on the starting
temperature of the magnet.
To do this, set the IP address of the computer to another address
on the same subnet. See “Setting up a Computer to Use a Static
IP Address.”
 To check the status of magnet temperature stabilization
For example, set the subnet mask to and the IP
address to
Click the Temperature link at the upper right to navigate to the
temperature controller page.
The details of setting up Ethernet ports and network adapters on
different computers vary widely. For help, consult your
computer’s documentation or your IT support staff. See “Setting
up a Computer to Use a Static IP Address.” for more detail.
A setpoint of 42.0 °C was used when the unit was tested at the
factory. Both the magnet Larmor frequency and the optimal shim
settings are a function of the magnet setpoint temperature, so it is
important to use the factory setpoint temperature for initial setup.
4. Once the port has been set up, type into
the address field of your browser.
If the magnet is not under temperature control, check the controller
Setting up a Computer to Use a Static IP Address
 To check the controller settings
In this section we outline how to set up your computer for a direct
Ethernet connection to the picoSpin. In this mode of operation you
must connect an Ethernet cable from the Ethernet port on the back
of the spectrometer directly to the Ethernet port on your computer.
On the Temperature page:
1. Click
near the top of the page to display the
temperature controller settings.
2. Verify the temperature controller parameters match those in
Figure 9.
Figure 10. Accessory packet
a. P = 10.2, I = 0.02
b. heater = on
c. closed loop = on
d. setpoint = 42
3. Click
Figure 9. Temperature page for a typical warm up
Inlet filter with
shipping plug
22 gauge
Drain PEEK plugs.
1 mL
Syringe port
CAUTION Avoid personal injury.
• Wear eye protection at all times when handling
liquid chemicals
• Do not breathe hazardous vapors
• Avoid skin contact with hazardous liquids and
• Eliminate ignition sources and prevent
significant waste volume buildup
Note For best performance and temperature stability, it is
recommended that the spectrometer be left turned on at all
Injecting a Sample
1. Remove the protective tape on the inlet and outlet fittings.
WARNING Avoid personal injury.
• Needles and syringes should be considered
regulated waste regardless of use
• Follow your local EH&S guidelines for disposal
• Never throw these items into the regular trash or
2. Insert the drain tube into the outlet fitting on the front panel.
3. Gently finger-tighten the PEEK nut.
The drain tube should be directed into a small bottle.
4. Remove the shipping plug from the inlet filter.
5. Screw the filter into the inlet fitting, tightening it gently.
6. Screw the syringe port into the inlet filter but do not tighten it.
7. Put the blunt-tip needle onto the syringe and draw a few hundred
microliters of fluid into the syringe, being careful not to draw up
any air bubbles.
Use water for initial shimming. Alternatively, you can use acetone
in place of water but note that the signal amplitude will be
reduced to 37% of the values in the test report.
8. Insert the needle into the syringe port and gently tighten it.
9. Gently inject fluid into the cartridge until you see it flowing out
of the outlet and no air bubbles are visible in the drain tube.
Figure 11. Injecting fluid into cartridge
A signal in the spectrum window appears as shown in Figure 14
a. Verify parameters match those in Figure 12.
 Do not change the pulse length, it is the optimized 90
degree pulse length for your instrument
 The test run box should remain checked
Note The auto tx and auto tx offset parameters allow the
spectrometer to track and change the transmitter frequency (tx
frequency) during shimming. • Auto tx uses the auto tx offset
parameter value to place the weighted average of signals at the
offset frequency.
• When checked, the tx frequency discovered using auto tx
becomes a global value that is shared with other experiment
scripts, such as the onePulse script.
NOTICE Do not exceed the 100 psi (700 kPa) maximum
pressure of the cartridge. This pressure corresponds to a force
of 3 lbf (1.4 kgf ) applied to the 1 mL syringe plunger. If you
use a syringe with a smaller plunger area, the maximum
pressure will be generated with a smaller force
• Turning off auto tx allows for manual control of the
transmitter frequency.
• Checking the test run box in the autoShim script overrides
auto tx selection even if checked. While test run is checked
auto tx will not make changes to the tx frequency.
 Take care not to inject air into the cartridge
 If an air bubble develops at or near the NMR RF coil, the
signal may be weak or it may be completely absent
 Any time you fail to find an expected signal keep in mind that
it could be due to an air bubble
• Test run is designed for evaluating parameter values without
changing them.
• Unchecking test run reestablishes auto tx control to discover
and change the tx frequency.
10. Remove the syringe port and the drain tube.
For shimming with water, the offset value should be set between
200 and 500 Hz. The default QuickStart auto tx offset value is set
to 200 Hz.
11. Plug the inlet and outlet with the two PEEK plugs from the
accessory package.
12. Gently finger-tighten the plugs to seal the ports.
b. Verify the signal appears in the spectrum window.
It should appear at the auto tx offset value.
NOTICE When the spectrometer is in continuous use it is
sufficient to plug just one of the ports. However, it is poor
practice to leave the instrument like this for long periods.
Cartridges will last longest if they are filled with clean solvent
and with both ports plugged.
c. If any parameters are changed click
The true signal position is indicated in the text window at the
bottom of the page; it is found next to the words spectral
center (Figure 13). The auto tx feature will change the tx
frequency after the second RF pulse and will write a new tx
frequency value to all experiment scripts when the script
completes, or when the script is aborted.
Finding the Signal
1. Go to the Temperature page and check that the magnet
temperature has stabilized to within a few millidegrees of the
The current temperature can be found in the upper left corner of
the magnet temperature plot.
2. Go to the Files page.
The Files page provides access to previously saved experiments,
together with their settings and data. It also allows you to select
shim settings files and experiment scripts.
3. Click the autoShim QuickStart saved run.
4. Click use these settings at Run.
You will be transferred to the Run page, which will display
settings similar to those shown in Figure 12.
5. Click
Figure 12. autoShim with QuickStart parameters
Figure 14. autoShim with QuickStart parameters
d. If no signal appears in the spectrum window, reinject water
and verify the bandwidth and min. and max freq. to plot
values (Figure 12).
e. Click
f. Change max iterations to 1.
g. Uncheck the test run box and click
Automatic Shimming
Your true transmitter frequency will now appear in the
tx frequency field. Proceed to the Automatic Shimming section.
Note Allow approximately 20 to 30 minutes for each 100
iterations run in the autoShim script.
Figure 13. Spectral center
1. If you are not already in the autoShim script, go to the Run page
and select the autoShim script from the scripts drop-down menu
at the top right of the page.
2. Verify parameters match those in Figure 15.
 Do not change the value of pulse length, it is the optimized
90 degree pulse length for your instrument
 The test run box should remain checked
 If any parameters are changed, click
Figure 15. Phase I autoShim script parameters
4. Click
to start phase I shimming.
5. Upon completion of phase I shimming, a screen similar to
Figure 16 appears.
6. Recheck the test run box.
7. Adjust the parameters to match those in Figure 17.
Figure 17. Phase II autoShim script parameters
3. Verify the signal appears in the spectrum window and looks
similar to Figure 14.
The signal appears at the auto tx offset value.
If any parameters are changed click
Figure 16. autoShim after phase I shimming
8. Click
9. Uncheck the test run box and click
to begin phase II
Upon successful completion of phase II shimming, a screen
similar to Figure 18 appears.
 To determine if the instrument is properly shimmed
1. Evaluate the FID and spectrum signal - look for a slow decay of
the FID (intensity of the FID should decay to half the initial
2. Spectrum peak height is reported in the text at the bottom of the
Run page upon completion of the autoShim script.
Compare the spectral peak height displayed in the message
window of the web browser to the value provided in the factory
test report. The spectrum peak height should be within ~15% of
the factory test report value; the factory spectrum peak height was
obtained fully relaxed water.
Tip If the unit has been moved, power cycled, or subjected to
temperature extremes since it was tested at the factory, it may
be necessary to run the autoShim script several times before
the performance found at the factory is reestablished.
 To save your shims
The autoShim script automatically saves the new shim values to the
working memory, but it does NOT save the shims to a named shim
file when it completes unless a name has been entered in the Shims
Name field.
3. Select the onePulse script from the scripts dialog window that
Tip It is recommended that you save a named shim file at least
once a week.
If this is the first time using the onePulse script, the factory
default onePusle QuickStart values will populate the parameter
1. When autoShim completes, save the shims by typing a name into
the Shims Name field and click Save.
If in doubt, go to the Files page, click the onePulse QuickStart
saved run, and click use these settings at Run.
The new shim file will then appear on the Files page.
NOTICE Anytime Start Run is pressed, shim values are
written to the shim electronics. If a file name is present in the
Shims Name field, clicking Start Run will also cause the
named shims file to be written and saved to memory. Saved
shim files can be overwritten if the Shims Name field is not
cleared; no file overwrite warning message will appear. It is
possible to overwrite good shim values by clicking Start Run
in execution and test run mode if the Shims Name field is not
You will see settings similar to those shown in Figure 19.
Figure 19. onePulse with QuickStart parameters
Figure 18. autoShim screen after Phase II shimming
4. Verify the parameters match those in Figure 19.
 Do not change the value of the pulse length, it is the
optimized 90 degree pulse length for your instrument
 If any parameters are changed, click
5. Click
and examine the plots.
Tip Plotting fewer points reduces the load on the server so
that live plots can be viewed during the run without
extending the desired recycle time. The plot settings have no
effect on the data that is saved.
Make adjustments to the auto tx offset value and phase correction
until the spectrum looks similar to Figure 20.
Keep the min. and max freq. to plot fixed at ±2 kHz and use the
interactive mouse zoom feature to zoom spectrum region of
Your First Spectrum
Note The auto tx feature uses a weighted average of signals
present in the full bandwidth, regardless of user supplied
min. and max freq. to plot values.
After shimming, if the auto tx box was checked, the tx frequency
discovered in the autoShim script will be written to the tx frequency
field in the onePulse script.
1. Follow the instructions on Injecting a Sample, fill the cartridge
capillary with the sample fluid.
Ethyl acetate is a good choice.
2. Click scripts in the upper right corner of the screen.
Figure 20. onePulse script with ethyl acetate
Every picoSpin comes with a one-year free license to the Mnova
NMR data analysis package from Mestrelab Research. Mnova is a
powerful package that makes all common NMR analysis tasks fast
and easy. To learn the basics of Mnova, download the manual from
the Mestrelab site and read the first 5 sections of Chapter VIII,
Processing Basics.
Figure 21. Ethyl acetate in Mnova
With a neat sample you will be able to see the main spectral
features from a single FID. In this case, we see a CH3 singlet, a
CH3 triplet, and a CH2 quartet.
Figure 21 shows the result of processing the EtOAc-neat-avg.jdx file
in Mnova as follows:
• open the JCAMP file
6. Once you have the desired settings, set scans to 10.
• set zero filling to 32,000
7. Name the Run, such as "EtOAc-neat."
8. Click
• LP filling: forward LP
• backward LP: -2 to 0
9. After the run finishes a Download Data button
) will appear next to Start Run button.
10. Click
• apodization: 0.5 First Point
• adjust zero-order phasing
and, in Firefox, a file dialog window will
• zoom axes
11. Select Save File and click OK.
• reference the methyl singlet to 2.0 ppm
This will save the file to your computer's download directory.
These steps were done manually but Mnova can perform these tasks
automatically with processing scripts and can perform many other
useful processing steps, including multiplet analysis, peak integration
and peak fitting.
Tip In Firefox, you can also select the option Open with, select
Mnova from the drop-down menu and check the Do this
automatically... and the files will automatically open in Mnova.
12. Open the file EtOH-neat-avg.jdx in Mnova; it contains the
10 scan averaged FID data in JCAMP-DX format.
Contact Information
For U.S. Technical Support, please contact:
Thermo Fisher Scientific
5225 Verona Road
Madison WI 53711-4495 U.S.A.
Telephone: 1 800 532 4752
E-mail: us.techsupport.analyze@thermofisher.com
For International Support, please contact:
Thermo Fisher Scientific
Telephone: +1 608 273 5017
E-mail: support.madison@thermofisher.com
Trademark Information
Microsoft, Windows and Internet Explorer are either trademarks or
registered trademarks of Microsoft Corporation in the United States
and/or other countries. Mnova is a trademark of Mestrelab Research,
Inc. and its subsidiaries. Safari is either a trademark or registered
trademark of Apple Inc. in the United States and/or other countries.
Firefox is a trademark of the Mozilla Foundation in the United States
and/or other countries. Google Chrome is a trademark of
Google Inc. All other trademarks are the property of Thermo Fisher
Scientific Inc. and its subsidiaries.
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