Full experimental details of synthesis, crystallography, TGA and CO

Supporting Information
Ligand Flexibility and Framework Rearrangement in a New Family of Porous
Metal-Organic Frameworks
Samuel M. Hawxwell,a Guillermo Mínguez Espallargas,a Darren Bradshaw,b Matthew J.
Rosseinsky,b Timothy J. Prior,c Alastair J. Florence,d Jacco van de Streek e and Lee
Brammer*a
a
Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, S3 7HF, UK.
Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
c
Synchrotron Radiation Source, CCLRC Daresbury Laboratory, Daresbury, Warrington WA4
4AD, UK
d
Solid-State Research Group, Strathclyde Institute of Pharmacy and Biomedical Sciences,
University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, Scotland
e
Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK
b
Experimental
1. General
All chemicals were purchased from Aldrich or Lancaster and used as received. Infra-red spectra
were recorded on a Perkin-Elmer Spectrum RX I FT-IR spectrometer equipped with a SensIR
diamond attenuated total reflectance fitting. 1H NMR spectra were recorded on a Bruker AC-250
(250 MHz) or AMX-400 (400 MHz) supported by an Aspect 3000 data system. Chemical shifts
are reported in ppm with the solvent resonance as the internal standard (CHCl3: δ 7.27 ppm and
DMSO: δ 2.50 ppm). Data are reported as follows: chemical shift; multiplicity (s = singlet, d =
doublet, t = triplet, br = broad, m = multiplet); integration. 13C NMR spectra were recorded on a
Bruker AC-250 (62.9 MHz) or AMX-400 (100.6 MHz) with complete proton decoupling.
Chemical shifts are reported in ppm with the solvent resonance as the internal standard (CHCl3: δ
77.00 ppm and DMSO: δ 39.50 ppm). The electron ionisation mass spectra were obtained on a
VG Auto Spec Magnetic Sector machine working positive or negative ion mode. The elemental
analyses were conducted by the Elemental Analysis service, Department of Chemistry,
University of Sheffield. Powder diffraction data were obtained on a Bruker-AXS D8 Advance
powder diffractometer at the Strathclyde Institute of Pharmacy and Biomedical Science,
University of Strathclyde, using Cu Kα1 radiation (λ = 1.54056 Å).
2. Synthesis
2.1 Butane Tetraester (Me4L1)
S1
A mixture of dimethyl 5-hydroxyisophthalate (2.43 g, 11.6 mmol), 1,4-dibromobutane (1.08 g,
5.00 mmol) and K2CO3 (2.50 g, 18.1 mmol) were stirred in DMF (40 ml) at room temperature for
48 hours. After this time, the reaction mixture was poured into water (~400 ml) and stirred for a
further 15 minutes. The resulting white precipitate was collected and washed three times with
water. The precipitate was dissolved in CH2Cl2 (~150 ml) and then washed with a solution of 5 %
aqueous NaOH solution (2 x 100 ml portions). The CH2Cl2 solution was then dried over MgSO4,
filtered and reduced to give 1.79 g (75 %) of the butanetetraester Me4L1 as a white solid.
IR (ATR): ν 1723 cm-1 (carbonyl)
1
H NMR (CDCl3): δ 2.02 (m, 4H), 3.93 (s, 12H), 4.12 (m, 4H), 7.71 (d, 4H), 8.26 (t, 2H)
13
C NMR (CDCl3): δ 25.78, 52.44, 67.94, 119.79, 122.95, 131.73 (no 4º carbon signals
observed)
MS (ESI+): m/z calcd for C24H26O10 474, found 474
2.2 Butane Tetraacid (H4L1)
A mixture of butane tetraester Me4L1 (1.50 g, 3.16 mmol), KOH (0.710 g, 12.7 mmol), methanol
(25 ml) and distilled water (25 ml) were stirred under N2 at 60 ºC for 48 hours. After this time,
the reaction mixture was filtered to remove any unreacted starting materials. HCl (6 M, 25 ml)
was then added dropwise at 0 ºC. The precipitate was collected, washed with water and dried
under vacuum to give 1.04 g (79 %) of butanetetraacid H4L1 as a white solid.
IR (ATR): ν 1671 cm-1 (carbonyl)
1
H NMR (d6-DMSO): δ 1.91 (s, 4H), 4.15 (s, 4H), 7.63 (d, 4H), 8.06 (t, 2H), 13.27 (br, 4H)
13
C NMR (d6-DMSO): δ 25.62, 68.17, 119.53, 122.62, 132.98, 159.22, 166.83
MS (ESI-): m/z calcd for C20H18O10 418, found 417 [M – H]+
Elemental Analysis: calcd for C20H18O10 C 57.42 % H 4.54 % found C 56.75 % H 4.18 %
2.3 Butene Tetraester (Me4L2)
S2
A mixture of dimethyl 5-hydroxyisophthalate (2.10 g, 10.0 mmol), trans-1,4-dibromobut-2-ene
(1.05 g, 4.90 mmol), K2CO3 (2.21 g, 16.0 mmol) and dibenzo-18-crown-6 (0.10 g, 0.277 mmol)
were stirred in dry THF (40 ml) under N2 at 65 ºC for 24 hours. After this time, a solution of 1 %
aqueous Na2CO3 (20 ml) was added at 0 ºC. The resulting solid was collected, washed with water
and ether and dried under vacuum to give 2.17 g (94 %) of the butenetetraester Me4L2 as a white
solid.
IR (ATR): ν 1719 cm-1 (carbonyl)
1
H NMR (CDCl3): δ 3.92 (s, 12H), 4.68 (dd, 4H), 6.10 (dt, 2H), 7.75 (d, 4H), 8.26 (t, 2H)
13
C NMR (CDCl3): δ 52.48, 67.95, 120.00, 123.24, 128.00, 131.79 (no 4º carbon signals
observed)
MS (ESI+): m/z calcd for C24H24O10 472, found 472
2.4 Butene Tetraacid (H4L2)
A mixture of butene tetraester Me4L2 (1.00 g, 2.12 mmol), KOH (0.475 g, 8.46 mmol), methanol
(15 ml) and distilled water (15 ml) were stirred under N2 at 60 ºC for 48 hours. After this time,
the reaction mixture was filtered to remove any unreacted starting materials. HCl (6 M, 25 ml)
was then added dropwise at 0 ºC. The precipitate was collected, washed with water and dried
under vacuum to give 0.556 g (63 %) of butenetetraacid H4L2 as a white solid.
IR (ATR): ν 1686 cm-1 (carbonyl)
1
H NMR (d6-DMSO): δ 4.73 (s, 4H), 6.11 (s, 2H), 7.66 (s, 4H), 8.06 (s, 2H), 13.30 (br, 4H)
13
C NMR (d6-DMSO): δ 67.67, 119.28, 122.38, 132.58, 158.27, 166.32
MS (ESI-): m/z calcd for C20H16O10 416, found 415 [M – H]+
S3
Elemental Analysis: calcd for C20H18O11 (H42·H2O) C 55.30 % H 4.18 %, found C 55.49 % H
3.91 %
2.5 [Zn2(L1)(H2O)4]·2H2O (1)
Zn(ClO4)2·6H2O (0.112 g, 0.30 mmol) and butane tetraacid H4L2 (0.042 g, 0.10 mmol) were
added to a Parr 23 ml pressure vessel with Teflon liner followed by DMF (3 ml), ethanol (3 ml)
and distilled water (2 ml). The flask was sealed and heated at 95 ºC for 48 hours before being
cooled down to room temperature at 0.1 ºC min-1. The colourless crystalline product was
collected by filtration and included crystals suitable for single crystal diffraction study. Yield
0.039 g (59.7 %). Elemental analysis: calcd for Zn2C20H26O16 C 36.78 % H 4.01 %; found C
36.72 % H 3.74 %.
2.6 [Zn4(L2)2(DMF)3(H2O)3]·4H2O (2)
Zn(ClO4)2·6H2O (0.112 g, 0.30 mmol) and butene tetraacid H4L1 (0.042 g, 0.10 mmol) were
added to a Parr 23 ml pressure vessel with Teflon liner followed by DMF (3 ml), ethanol (3 ml)
and distilled water (2 ml). The flask was sealed and heated at 95 ºC for 48 hours before being
cooled down to room temperature at 0.1 ºC min-1. The colourless crystalline product was
collected by filtration and included crystals suitable for single crystal diffraction study. Yield
0.051 g (35.6 %). Elemental analysis: calcd for Zn4C49H59O30N3 C 41.11 % H 4.15 % N 2.94 %;
found C 40.64 % H 3.95 % N 2.56 %. The powder diffraction pattern of the bulk sample was
consistent with that calculated from the single crystal diffraction data.
3. Crystallography
3.1 Single Crystal Diffraction
Crystals of 1 and 2 were mounted using a viscous hydrocarbon oil to coat the crystal on a thin
carbon fibre attached to the end of a borosilicate glass capillary. X-ray data were collected on
synchrotron beam line 16.2smx at the Synchrotron Radiation Source at the CCLRC Daresbury
Laboratory at 100 K. For each compound, data were corrected for absorption using empirical
methods (SADABS) based upon symmetry equivalent reflections combined with measurements
at different azimuthal angles [1]. Crystal structures were solved and refined against all F2 values
using the SHELXTL suite of programs [2]. Non-hydrogen atoms were refined anisotropically
(when no disorder was present) and hydrogen atoms associated with oxygen atoms were located
from the difference map and the O–H distance fixed at 0.96 Å. All other hydrogen atoms were
placed in calculated positions with idealised geometries and refined using a riding model. In 2,
three of the four uncoordinated water molecules have the oxygen atom disordered over two sites
and have been modelled with 59(1):41(1), 72(2):28(2) and 58(2):42(2) ratios respectively.
Hydrogen atoms were not modelled on the disordered water molecules. Views of the two-fold
interpenetrated diamondoid network adopted by 2 are shown in Figures S1 and S2.
Table S1. Data collection, Structure Solution and Refinement Parameters for 1 and 2
Crystal colour
Formula
Mr
Crystal size (mm)
Crystal system
Space group, Z
a (Å)
1
Colourless
Zn2C20H26O16
326.57
0.06 x 0.06 x 0.06
Triclinic
P-1, 1
7.6916(15)
S4
2
Colourless
Zn4C49H59O30N3
1431.67
0.20 x 0.13 x 0.03
Triclinic
P-1, 2
13.0757(6)
b (Å)
8.5113(17)
14.1157(7)
c (Å)
9.827(2)
16.6631(8)
α (°)
68.56(3)
66.602(1)
β (°)
79.47(3)
87.138(1)
γ (°)
86.62(3)
89.757(1)
V (Å3)
588.7(2)
2818.7(2)
1.842
1.687
Calcd density
(Mg/m3)
λ (Å)
0.84600
0.84600
Temp (K)
100(2)
100(2)
µ (Mo-Kα) (mm–1)
2.121
1.779
3.81 to 32.87
3.74 to 31.00
θ range (deg)
Reflns collected
4270
19414
Independent reflns
2358 (0.0357)
10334 (0.0403)
(Rint)
Reflns used in
2358
10334
refinement, n
Restraints
0
0
L.S. parameters, p
172
811
R1(F)a, I > 2.0σ(I)
0.0460
0.0487
wR2(F2)a, all data
0.1268
0.1341
S(F2)a, all data
1.059
1.088
1.081
1.306
Max final ∆ρ (e. Å-3)
-1.163
-1.053
Min final ∆ρ (e. Å-3)
a
R1(F)= Σ(|Fo| – |Fc|)/Σ|Fo| ; wR2(F2) = [Σw(Fo2 – Fc2)2/ΣwFo4]½ ; S(F2) = [Σw(Fo2 – Fc2)2/(n – p)]½
Figure S1. Two-fold interpenetrated diamondoid network exhibited by 2. Separate networks
shown in green and red, Zn atoms shown in purple. Hydrogen atom, water molecules and DMF
molecules are not shown.
S5
Figure S2. Alternative view of two-fold interpenetrated diamondoid network exhibited by 2.
Colours as in Figure S1. Hydrogen atom, water molecules and DMF molecules are not shown.
3.2 Powder diffraction
The polycrystalline sample 3 was lightly ground in an agate mortar and pestle and filled into 1.0
mm borosilicate glass capillary prior to being mounted and aligned on a Bruker-AXS D8
Advance powder diffractometer, using Cu Kα1 radiation (λ = 1.54056 Å). One dataset (2θ = 3 –
65 º) was collected at room temperature using variable a count time (VCT) [3] scheme (3.00 –
43.00 º = 5 s/step; 43.00 – 65.00 º = 20 s/step) for 0.017 º steps. The diffraction pattern was
indexed using DICVOL91 [4] to a triclinic cell [F(18) = 54.5, M(18) = 24.1] and space group P-1
was assigned from volume considerations [5]. The presence of two, weak peaks at low angle
which were not accounted for by the indexed cell and space group indicate the presence of a
small amount of polycrystalline impurity in the sample. The dataset was background-subtracted
for Pawley refinement [6] and structure solution was performed using the simulated annealing
(SA) global optimization procedure, described previously [7], as implemented in the DASH
computer program [8]. Z-matrices describing the molecular topology of the fragments were
generated within DASH using analogous moieties taken from the CSD [9] and manually
modified using standard bond lengths and angles.
Global optimization of external (rotational for the half-ligand; translational for Zn and both water
oxygens) degrees of freedom against the extracted intensities was carried out with cooling rate set
to 0.01 and all other DASH SA control parameters set to default values. One hundred SA runs
with 2.5×107 SA moves per run were implemented for the structure determination. The SA
structure solution involved the optimisation of four independent fragments in the asymmetric unit
(one Zn2+ ion, one half-ligand and two water molecules), totalling 17 degrees of freedom. The
position of the half ligand was constrained to rotate around the origin using a dummy atom in the
z-matrix (reducing the external (rotational) degrees of freedom by 3. All degrees of freedom were
assigned random values at the start of the simulated annealing. The best SA solutions had
χ2(profile)/χ2(Pawley) ratio of 4.77 and a chemically reasonable packing arrangement. The solved
S6
structure was then refined against the data in the range 4 - 65 o 2θ using a restrained Rietveld
method as implemented in TOPAS v3.1 [10], where only the scale factor, background, zero error,
axial model, peak shape and unit cell parameters were refined. The Rwp fell to 0.06027 during the
refinement. All atomic positions (including H-atoms) for the structure of were refined, subject to
a series of restraints on bond lengths, bond angles and planarity. A spherical harmonics
correction of intensities for preferred orientation was applied in the final refinement [11]. The
observed and calculated diffraction patterns for the refined crystal structures are shown in Figure
S3. The crystal structure of 3 is shown in Figure S4.
Figure S3. Final observed (points), calculated (line) and difference plot [(Iobs – Icalc)/σ(Iobs)] from
the Rietveld refinement for 3 (2θ range 4.0 – 65.0 º).
S7
Figure S4. Crystal structure of 3 shown without water molecules in channels. Hydrogen atoms
on coordinated water molecules are omitted (and were not used in the model).
Table S2. Data collection, Structure Solution and Refinement Parameters for 3
3
White
Cylinder
12 × 1.0 × 1.0 mm
Triclinic
P-1, 1
9.5471(7)
7.8520(7)
8.4756(6)
91.891(4)
107.086(3)
100.815(4)
593.90(8)
1.695
298
3.139
3.0 to 65.0
0.0172
429
1.0 mm borosilicate
capillary
Transmission
Step
95
57
0.0478
0.0630
0.0164
Specimen colour
Specimen shape (mm)
Crystal system
Space group, Z
a (Å)
b (Å)
c (Å)
α (°)
β (°)
γ (°)
V (Å3)
Density (Mg/m3)
Temperature (K)
µ (mm–1)
2θ range (deg)
Increment in 2θ (deg)
reflns measured
Specimen mounting
Mode
Scan method
Parameters refined
No. of Restraints
Rp
Rwp
Rexp
4. CO2 Sorption Measurements
Sorption studies were carried out using a Hiden Isochema (Warrington, U. K.) Intelligent
Gravimetric Analyser (IGA) equipped with a micro-gram balance and 2, 100 and 20000 mbar
barotron pressure transducers. Temperature control was via a furnace for desolvation of the asS8
made phases, and by immersion of the reaction chamber into solid carbon dioxide contained in a
cryogenic vessel (at 198 K) during isotherm measurement. Samples were desolvated at 150°C
under high dynamic vacuum (10-7 mbar) until a constant mass had been reached; typically
overnight. The carbon-dioxide (SFC grade) used for this study was supplied by BOC gases. All
admittance pipe work was thoroughly decontaminated under high vacuum prior to the admission
of any gas, and an activated carbon standard of known surface area was used to validate all
measurement protocols. All isotherm data points were fitted by the IGASwin systems software
v.1.03.84 (Hiden Isochema 2002) using a linear driving force model, and all data were corrected
for buoyancy effects. The CO2 sorption and desorption isotherms for 1 are shown in Figure S5.
The corresponding isotherms for 2 can be found in Figure 3.
CO2 Uptake (% mass)
CO2 Sorption for 1
20
18
16
14
12
10
8
6
4
2
0
ads
desorp
0
0.1
0.2
0.3
P / P0
0.4
0.5
0.6
Figure S5. Sorption-desorption isotherm of 1 at 198 K obtained with CO2 gas over the pressure
range 2-1000 mbar (relative pressure range from 6 x 10-5 to 0.5)
5. TGA Measurements
Thermogravimetric analysis (TGA) was conducted using a Perkin-Elmer Pyris 1 TGA instrument
with heating under N2 at 5 ºC min-1 from room temperature to 600 ºC for 1 and 2. The TGA
traces for 1 and 2 are shown in Figures S6 and S7, respectively.
S9
Figure S6. TGA trace for 1 (heating under N2 at 5 ºC min-1 from room temperature to 600 ºC)
Figure S7. TGA trace for 2 (heating under N2 at 5 ºC min-1 from room temperature to 600 ºC)
5. References
[1] (a) G. M. Sheldrick, SADABS: Empirical absorption correction program, University of
Göttingen, 1995, based upon the method of Blessing [1b]; b) Blessing, R. H. Acta Crystallogr.
1995, A51, 33.
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[2] SHELXTL 5.1, Bruker Analytical X-Ray Instruments, Inc., 1998.
[3] (a) Shankland, K.; David, W. I. F.; Sivia, D. S. J. Mater. Chem. 1997, 7, 569; b) Hill, R. J.;
Madsen, I. C. Structure Determination from Powder Diffraction Data, 2002, edited by W. I. F.
David, K. Shankland, L. B. McCusker and Ch. Baerlocher, pp.114–116. Oxford University Press.
[4] Boultif, A.; Louër, D. J. Appl. Cryst. 1991, 24, 987.
[5] Markvardsen, A. J.; David,W. I. F.; Johnson, J. C.; Shankland, K. Acta Crystallogr. 2001,
A57, 47.
[6] Pawley, G. S. J. Appl. Crystallogr. 1981, 14, 357.
[7] David, W. I. F.; Shankland, K.; Shankland, N. J. Chem. Soc., Chem. Commun. 1998, 931.
[8] W. I. F David, K. Shankland, J. van de Streek, E. Pidcock, W. D. S. Motherwell and J. C.
Cole, J. Appl. Cryst. 2006, 39, 910.
[9] Allen, F. H. Acta Crystallogr. 2002, B58, 380.
[10] Coelho, A. A. (2003). TOPAS User Manual. Version 3.1. Bruker AXS GmbH
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