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SUPPLEMENTARY INFORMATIONdoi: 10.1038/nmat2545

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Porous Organic Cages

Tomokazu Tozawa,1,2 James T. A. Jones,1 Shashikala I. Swamy,1 Shan Jiang,1 Dave J. Adams,1

Stephen Shakespeare,1 Rob Clowes,1 Darren Bradshaw,1 Tom Hasell,1 Samantha Y. Chong,1 Chiu

Tang,3 Stephen Thompson,3 Julia Parker,3 Abbie Trewin,1 John Bacsa,1 Alexandra M. Z. Slawin,4

Alexander Steiner1 and Andrew I. Cooper1*

1 Department of Chemistry and Centre for Materials Discovery, University of Liverpool, Crown

Street, Liverpool L69 7ZD, United Kingdom

2 Kaneka Corporation, Japan

3 I11 Beamline, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton,

Didcot, Oxfordshire OX11 0DE, UK.

4 School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST,

Scotland, United Kingdom

* To whom correspondence should be addressed: [email protected]

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2 nature materials | www.nature.com/naturematerials

SUPPLEMENTARY INFORMATION doi: 10.1038/nmat2545

2

Experimental

Materials. 1,3,5-Triformylbenzene was prepared by standard literature procedures1 or purchased from Waterstone Technology, USA or Manchester Organics, UK. All other chemicals were purchased from Sigma-Aldrich and used as received.

Synthesis of Cage 1

Ethyl acetate (35 mL) was added to 1,3,5-triformylbenzene (50 mg, 0.31 mmol) in a beaker at room temperature. After 5 minutes, a solution of ethlylene diamine (28 mg, 0.47 mmol) in EtOAc (5 mL) was added. The resulting mixture was left covered for 60 h without stirring. A turbid solution was observed to form within 5 min after ethylene diamine addition to the partially dissolved trialdehyde. This was followed by precipitation of a solid after around 5–6 h and, finally, pale white needles of cage 1 were observed to crystallize from solution after around 60 h. The product obtained was a mixture of needle-like crystals which adhered to the sides of the reaction flask (major component) and a thin layer of amorphous material at the bottom of the flask (minor component). The crystals were harvested carefully from the sides of the flask using a spatula without disturbing the amorphous layer, washed with ethyl acetate, and air dried to give the ethyl acetate solvate of cage 1.

1H NMR (CDCl3, 400 MHz) δ 8.18 (s, 12H, -CH=N), 7.92 (s, 12H, -ArH), 4.12 (q, J = 7.2 Hz, 5H, 2.5 x -OCH2), 4.02 (br s, 24H, -NCH2), 2.04 (s, 7.5H, -2.5 x -COCH3), 1.25 (t, J = 7.2 Hz, 7.5H, 2.5 x CH3) ppm. 13C NMR (CDCl3, 100 MHz) δ 171.1, 161.2, 136.4, 129.6, 61.6, 60.4, 21.04, 14.2 ppm. IR (KBr pellet, ν) 2917 (s), 2389 (s), 1739 (s), 1648 (s), 1598 (m), 1433 (m), 1335 (s), 1238 (s), 1155 (s), 1108 (m) 1048 (s), 991 (m), 911 (m), 694 (m) cm-1. ESI-MS (CH3OH) m/z: 793 [M+H]+ for C48H48N12, 815 [M+Na]+.

To desolvate cage 1, a sample was heated to 100 °C for 6 hours with a dry nitrogen flow and then evacuated at 80 °C for a further 6 hours (final isolated yield 35 %).

1H NMR (CDCl3, 400 MHz) δ 8.18 (s, 12H, -CH=N), 7.92 (s, 12H, -ArH), 4.02 (br s, 24H, -NCH2) ppm. 13C NMR (CDCl3, 100 MHz) δ 161.2, 136.4, 129.6, 61.6 ppm. IR (KBr pellet, ν) 2917 (s), 2340 (s), 1648 (s), 1598 (m), 1439 (m), 1361 (m), 1252 (w), 1156 (m), 1109 (w) 1050 (m), 909 (m), 692 (m) cm-1. ESI-MS (CH3OH) m/z: 793 [M+H]+ for C48H48N12, 815 [M+Na]+. Accurate mass calculated for C48H49N12: 793.4203. Found: 793.4234.

Synthesis of Cage 2

This was prepared in a similar manner to cage 1. Acetonitrile (15 mL) was added to 1, 3, 5-triformylbenzene (50 mg, 0.31 mmol) in a beaker at room temperature. After 5 minutes, a solution of 1,2-diaminopropane (34 mg, 0.47 mmol) in CH3CN (5 mL) was added. The resulting mixture was left covered for 60 h without stirring. A turbid solution was observed to form within 5 minutes after 1,2-diaminopropane was added to the partially dissolved trialdehyde. This was followed by precipitation of a solid after around 5–6 h and, finally, pale white needles of cage 2 were observed to crystallize from solution after around 60 h. As for 1, the product obtained was a mixture of needle crystals which adhered to the sides of the reaction flask (major component) and a thin layer of amorphous material at the bottom of the flask (minor component). The crystals were separated



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carefully from the flask walls using a spatula without disturbing the amorphous layer, washed with acetonitrile and air dried to give the acetonitrile solvate of cage 2.

1H NMR (CDCl3, 400 MHz) δ 8.17-8.13 (m, 12H, -CH=N), 7.92-7.88 (m, 12H, -ArH), 4.09-4.06 (m, 6H, 6 x -NCH), 3.84 (m, 6H, -NCH), 3.52-3.47 (m, 6H, 6x -NCH), 2.01 (s, 3H nCH3CN),1.32 (d, J = 5.2 Hz, 18H, 18 x -CH3) ppm. 13C NMR (CDCl3, 100 MHz) δ 161.0, 160.9, 159.3, 159.1, 136.5, 129.7, 129.6, 129.5, 129.4, 104.6, 68.4, 66.8, 20.9, 1.9 ppm. IR (KBr pellet, ν) 2967 (m), 2855 (s), 2360 (w), 1649 (s), 1446 (m), 1369 (m), 1252 (m), 1135 (m), 888 (w), 796 (w),692 (w) cm-1. ESI-MS (CH3OH) m/z: 877 [M+H]+ for C54H60N12, 899 [M+Na]+.

To desolvate cage 2, a sample was heated to 120 °C for 6 hours with a dry nitrogen flow and then evacuated at 80 °C for a further 6 hours (final isolated yield 37 %).

1H NMR (CDCl3, 400 MHz) δ 8.17-8.13 (m, 12H, -CH=N), 7.92-7.88 (m, 12H, -ArH), 4.09-4.06 (m, 6H, 6 x -NCH), 3.84 (m, 6H, -NCH), 3.52-3.47 (m, 6H, 6x -NCH), 1.32 (d, J = 5.2 Hz, 18H, 18 x -CH3) ppm. 13C NMR (CDCl3, 100 MHz) δ 161.0, 160.9, 159.3, 159.1, 136.5, 129.7, 129.6,129.5, 129.4, 68.4, 66.8, 20.9 ppm. IR (KBr pellet, ν) 2967 (m), 2855 (s), 2360 (w), 1650 (s), 1446 (m), 1369 (m), 1342 (m), 1252 (m), 1135 (m), 888 (w), 796 (w) and 692 (w) cm-1. ESI-MS (CH3OH) m/z: 877 [M+H]+ for C54H60N12, 899 [M+Na]+. Accurate mass calculated for C54H61N12: 877.5142. Found: 877.5178.

Synthesis of Cage 3

1,3,5-Triformylbenzene (81 mg, 0.5 mmol) was dissolved in dichloromethane (3 mL) and added to a solution of (R,R)-1,2-diaminocyclohexane (85 mg, 0.75 mmol) in dichloromethane (3 mL). After 2 days at room temperature, transparent prism-like crystals were formed. The solvent was decanted, and fresh dichloromethane (3 mL) added which was then quickly decanted. A further aliquot of dichloromethane (8 mL) was added and the solution stirred to re-dissolve the crystalline material, filtered through a 200 nm PTFE filter (Millex-FG) and the solvent allowed to evaporate to afford a white, microcrystalline powder in low yield (25 mg, 18 %). Crystals suitable for X-ray crystallography were either removed directly from the reaction flask after 2 days prior to the washing step described above or, alternatively, by carrying out the reaction in chloroform instead of dichloromethane and simply allowing the solvent to evaporate slowly over several days.

1H NMR (CDCl3) δ 8.15 (s, CH=N, 12H), 7.89 (s, ArH, 12H), 3.33 (m, CHN, 12H), 1.9 – 1.4 (m, CH2, 48H) ppm. 13C NMR (CDCl3) δ 159.1, 136.7, 129.5, 74.7, 33.0, 24.4 ppm. IR (KBr pellet, ν) 2929 (s), 2858 (s), 1649 (s), 1601 (w), 1448 (m), 1372 (w), 1342 (w), 1306 (w), 1157 (m), 1092 (m), 1041 (w), 990 (w), 937 (w), 885 (w), 863 (w), 691 (m), 671 (m), 520 (w), 458 (w), 439 (w) cm-

1. MS (ES+) 1118 ([M+H]+). Accurate mass calculated for C72H85N12: 1117.7020. Found: 1117.7065.

Recrystallisation of Cage 1 from o-xylene / dicholoromethane mixtures

Cage 1 was synthesized as before in EtOAc and desolvated under a dry N2 flow and subsequent application of vacuum at 80 °C. The de-solvated sample (46.9 mg) was then dissolved in



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dichloromethane (6 mL), filtered to remove any undissolved material, and ortho-Xylene (0.25 mL) was added to the solution. The solvent was then evaporated to dryness at room temperature under a dry N2 flow in a dessicator. The material was then desolvated as before by heating at 80 °C under a flow of dry N2 followed by heating to 100–130 °C under dynamic vacuum overnight. The recrystallisation procedure was conducted five times in parallel to obtain sufficient material for gas sorption analysis and to confirm reproducibility of the crystallisation. The same PXRD pattern was obtained for all five repeat crystallisations.

Methods

NMR. Solution 1H NMR spectra were recorded at 400.13 MHz using a Bruker Avance 400 NMR spectrometer. 13C NMR spectra were recorded at 100.6 MHz.

Fourier Transform Infrared Spectroscopy (FTIR). IR spectra were collected on a Bruker Tensor 27 spectrometer. Samples were analyzed as KBr disks for 16 scans with a resolution of 4 cm-1. Spectra were recorded in transmission mode.

Optical Microscopy: Imaging was achieved using a Meiji Techno MX9300 optical microscope fitted with an Infinity1 digital camera. Images were collected using either 4x, 10x or 25x magnification lenses. Images were processed using Infinity Analyze software 4.6.0 (Lumenera Corporation) calibrated against a stage micrometer (Agar Scientific).

Scanning Electron Microscopy. High resolution imaging of the crystal morphology was achieved using a Hitachi S-4800 cold Field Emission Scanning Electron Microscope (FE-SEM). The dry samples were prepared on 15 mm Hitachi M4 aluminium stubs using either silver dag or an adhesive high purity carbon tab. The samples were then coated with a 2 nm layer of gold using an Emitech K550X automated sputter coater. The FE-SEM measurement scale bar was calibrated using certified SIRA calibration standards. Imaging was conducted at a working distance of 8 mm and a working voltage of 3 kV using a mix of upper and lower secondary electron detectors.

Thermogravimetric Analysis. TGA analysis was carried out using a Q5000IR analyzer (TA instruments) with an automated vertical overhead thermobalance. The samples were heated at the rate of 5 oC /min.

Powder X-ray Diffraction. Powder X-ray diffraction data were collected on a Panalytical X’pert pro multi-purpose diffractometer (MPD) in reflection Bragg-Brentano geometry operating with a Cu anode at 40 kV 40 mA. Samples were mounted as loose powder onto a silicon zero background holder. PXRD patterns were collected in 16 1 hour scans with a step size of 0.00657 degrees 2 theta and scan time of 115 s/step over 2 – 50 deg 2 theta on a sample stage rotating at 2s/rotation. The incident X-ray beam was conditioned with 0.04 rad Soller slits, automatic divergence slit (5 mm), mask (5 mm) and anti-scatter slit of 1 deg. The diffracted beam passed through an automatic antiscatter slit (5 mm), 0.04 rad Soller slits and Ni filter before processing by the PIXcel detector operating in scanning mode.

For cage 1 desolvated: a microcrystalline powder sample of desolvated 1 was introduced into a 1.5 mm diameter capillary. The powder diffraction data were collected at ambient temperature in transmission mode using a capillary spinner on the I11 beamline at the Diamond Light Source (λ =



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0.827231 Å, Si{111} monochromated radiation). Nine 60 min scans were collected in the range 2θ = 3 – 120 ° with a step size of 0.001°. The single crystal solution was used as the initial model for Rietveld refinement carried out using the TOPAS-Academic[R]2 software on a truncated dataset of nine combined scans rebinned to a step size of 0.002°, with soft constraints applied to intramolecular bond lengths and angles. Anisotropic line broadening was accounted for using the Stephens’ microstrain model[R]3 with preferred orientation modelled using a 4th order spherical harmonics series.

Single Crystal X-ray Diffraction. X-ray diffraction data for the cage 1 ethyl acetate solvate, desolvated cage 3 and a cage 3 chloroform solvate and were collected on a Bruker Apex diffractometer and 1.5 kW graphite monochromated Mo radiation (λ = 0.71073 Å) using 0.3° ω scan steps spanning at least a hemisphere of reciprocal space for all structures. The frames were integrated with the SAINT v6.45a (Bruker, 2005).4 A semi-empirical absorption correction using multiple-reflections was carried out using the program SADABS V2008-1.5

X-ray diffraction data for cage 1 (desolvated) were collected at 173 K using a Rigaku MM007/Saturn92 diffractometer (confocal optics Cu-K∝ radiation). Intensity data were collected using ω steps accumulating area detector frames spanning at least a hemisphere of reciprocal space for all structures (data were integrated using CrystalClear).6 All data were corrected for Lorentz, polarisation and long-term intensity fluctuations (using CrystalClear). Absorption effects were corrected on the basis of multiple equivalent reflections.

X-ray diffraction data for cage 2 were performed at 173 K using a Rigaku MM007/Mercury diffractometer (confocal optics Mo-K∝ radiation). Intensity data were collected using ω steps accumulating area detector frames spanning at least a hemisphere of reciprocal space for all structures (data were integrated using CrystalClear). All data were corrected for Lorentz, polarisation and long-term intensity fluctuations (using CrystalClear). Absorption effects were corrected on the basis of multiple equivalent reflections.

Crystal structures were refined by full-matrix least squares using SHELX97 against F2 for all structures.7

Crystal data for cage 1 solvate: (C48H48N12)•2.5(C4H8O2) (composition as determined by 1H NMR), colourless needle, 0.30 × 0.10 × 0.02 mm3, monoclinic, space group C2/c (No. 15), a = 28.32(2), b = 10.976(10), c = 36.46(3) Å, β = 93.265(15)°, V = 11317(17) Å3, Z = 8, Dc = 1.241 g/cm3, F000 = 4512, MoK∝ radiation,λ = 0.71073 Å, T = 100(2)K, 2θmax = 39.8º, 16509 reflections collected, 5190 unique. Final R1 = 0.0793, wR2 = 0.0897. R indices based on 1018 reflections with I >2sigma(I) (refinement on F2).

Crystals of cage 1 solvate were small (< 100 μm width, see fig. S1) and contained areas of diffuse solvent; these crystals therefore diffracted to only low resolution. The cage encapsulated C4H8O2 molecule could be located and refined with certainty, while the others were diffuse and disordered. The SQUEEZE routine in PLATON8 was used for removing the contributions of diffuse solvent from diffraction intensities. The unit cell was found to contain 4 solvent accessible voids, with a volume 495 Å3 and a total of 195 electrons for each a void equivalent to 4 C4H8O2 molecules, 2 in the asymmetric unit. NMR data suggests a cage-to-solvent ratio of (C48H48N12)•2.5(C4H8O2) and it is likely that excess electrons calculated in PLATON can be ascribed to encapsulate H2O which is



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the condensate in the synthesis and can be observed both in the NMR and FTIR for the solvate.

Crystal data for cage 1 (desolvated): C48H48N12, M = 792.98, colourless needle, 0.28 × 0.02 × 0.02 mm3, monoclinic, space group P21/c (No. 14), a = 12.810(3), b = 10.910(3), c = 36.810(10) Å, β = 97.490(5)°, V = 5101(2) Å3, Z = 4, Dc = 1.033 g/cm3, F000 = 1680, CuKα radiation, λ = 1.54190 Å, T = 173(2)K, 2θmax = 61.9º, 9414 reflections collected, 1576 unique. Final R1 = 0.1733, wR2 = 0.4127, R indices based on 747 reflections with I >2sigma(I) (refinement on F2).

Crystals cage 1 (desolvated) were obtained by slowly heating crystals of cage 1 solvate with complete removal of the solvent. The crystals retained their crystallinity, even though all the ethyl acetate molecules were lost (25% of the sample mass is removed), and the space group symmetry changes from C2/c to P21/c. This large transformation of the crystal structure involves both loss of solvent and substantial rearrangement of the cage molecules. Successful single crystal-crystal reactions proceed with either the least amount of motion or a minimal distortion of the reaction cavity (the topochemical postulate). This transformation proceeds with movement of ethyl acetate out of the cages, migration of solvent through the crystal via transient free volume in the crystal, and the translation/rotation of the cages. The cage units move closer together to compensate for loss of the guest molecules. This reaction is therefore highly unusual since a single crystal-crystal transformation has proceeded with large scale movement of component molecules, although the crystal quality is poor (highly mosaic). The crystals are very small and they lack heavy atoms (N being the heaviest), resulting in very low resolution data and larger than usual R indices. However, the present data give an adequate model, also supported by powder X-ray diffraction and Rietveld refinement (see below; fig. S22), describing the unit cell and the structure of the cage. The principal molecular cage structure is also described in the solvated crystal structures and this appears to be essentially unchanged upon desolvation.

Crystal data for cage 2 hydrate: (C54H60N12)•6(H2O), M = 987.25, colorless needle, 0.80 × 0.03 × 0.03 mm3, trigonal, space group P-3 (No. 147), a = b = 18.770(3), c = 10.921(2) Å, V = 3332.1(10) Å3, Z = 2, Dc = 0.984 g/cm3, F000 = 1060, MoKα radiation, λ = 0.71073 Å, T = 100(2)K, 2θmax = 40.0º, 9959 reflections collected, 2053 unique (Rint = 0.1558). Final R1 = 0.0909, wR2 = 0.1811, R indices based on 921 reflections with I >2sigma(I) (refinement on F2).

Crystals of cage 2, grown from acetonitrile, were also small (< 50 μm width; see fig. S2). The crystals lost solvent readily even without deliberate desolvation, most likely as a result of the connected pore channels in the material. The material contained diffuse electron density only and diffracted to low resolution. No ordered guests could be located and refined in the channels. Other analytical techniques (TGA, Figure S19 and FTIR, Figure S14) showed no acetonitrile, but water molecules only (NMR showed the presence of approximately 6 H2O / cage with approximately 0.1 CH3CN / cage). The unit cell was found to contain three solvent accessible voids, two smaller ones with a volume 158 Å3 inside the cage molecules, and a larger void corresponding to the channel also with a volume 568 Å3 per unit cell. Contoured electron density maps were used to visualise the electron density inside the channels and the cages. A large region of diffuse electron density exists in the interior of the cage with a maximum peak height = 0.88 e-Å-3, but this could not refined as ordered H2O or acetonitrile molecules. Columns of electron density were also found in the 1-D pore channels, maximum peak height = 0.65 e-Å-3. The centre of the 1-D pore channels was found to have no electron density. SQUEEZE routine in PLATON8 calculates a total of 100 electrons



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ascribed to diffuse guests, which coupled with other characterisation methods such as 1H NMR leads to an estimate of approximately 6 H2O molecules per asymmetric unit. This was then used to remove the diffuse guest contribution from the diffraction intensities in the final refinements.

Crystal data for cage 3 solvate (as synthesized from CHCl3 solution) collected at 100 K: C72H84N12•3(CHCl3) M = 1475.62, colourless prism, 0.60 × 0.50 × 0.30 mm3, cubic, space group F4132 (No. 210), a = 25.0157(16), V = 15090(12) Å3, Z = 8, Dc = 1.252 g/cm3, F000 = 6192, MoKα radiation, λ = 0.71073 Å, T = 100(2)K, 2θmax = 45.4º, 7282 reflections collected, 848 unique (Rint = 0.0232). Final GooF = 1.056, R1 = 0.0948, wR2 = 0.2720, R indices based on 653 reflections with I >2sigma(I) (refinement on F2), 65 parameters, 0 restraints. Lp and absorption corrections applied, μ = 0.37 mm-1. Diffracted to rather low resolution, diffuse scattering very strong due to diffuse solvent. The crystal has large solvent accessible voids, and it was obvious that much of the crystal/included solvent was scattering diffusely (indeed, the crystal behaved as though it was fluorescing in the X-ray beam). SQUEEZE calculates 1414 electrons/unit cell corresponding to an estimated 24 CHCl3 molecules. However, since much of the solvent appears to scatter diffusely with a concomitantly reduced contribution to the observed structure factors, the true solvent count may be larger. This diffuse scatter may also responsible for the higher than expected R-indices.

The diffraction data obtained at 400 K gave much better R-values, since all of the diffuse solvent contribution was removed. Crystal data for cage 3 (desolvated) collected at 400K: C72H84N12, M = 1117.55, colourless prism, 0.60 × 0.50 × 0.30 mm3, cubic, space group F4132 (No. 210), a = 24.80(5), V = 15256(49) Å3, Z = 8, Dc = 0.973 g/cm3, F000 = 4800, MoKα radiation, λ = 0.71073 Å, T = 400(2)K, 2θmax = 41.5º, 6326 reflections collected, 684 unique (Rint = 0.0638). Final GooF = 1.040, R1 = 0.0577, wR2 = 0.1308, R indices based on 466 reflections with I >2sigma(I) (refinement on F2), 64 parameters, 9 restraints. Lp and absorption corrections applied, μ = 0.059 mm-1.

Crystallographic data have been submitted to the Cambridge Crystallographic Database with reference numbers CCDC 707056 (1, EtOAc solvate), CCDC 720848 (1, desolvated), CCDC 720849 (2, desolvated), CCDC 720851 (3, CHCl3 solvate) and CCDC 720850 (3, desolvated, data collected at 400 K) and are available free of charge at www.ccdc.cam.ac.uk/data_request/cif.

Gas Sorption Analysis. All samples were tested with gases of the following purities: hydrogen (99.9995% - BOC gases), carbon dioxide (SCF grade – BOC gases) and methane (ultrahigh purity - BOC). Surface areas and pore size distributions were measured by nitrogen adsorption and desorption at 77.3 K using a Micromeritics ASAP 2020 volumetric adsorption analyzer. Samples were degassed at offline at 80 °C for 15 h under vacuum (10-5 bar) before analysis, followed by degassing on the analysis port under vacuum, also at 80 °C. Both methane and carbon dioxide isotherms were measured at both 275 and 289K using a Micromeritics 2420 volumetric adsorption analyzer using the same degassing procedure. Gravimetric sorption isotherms were obtained using a HidenIsochema (Warrington, U. K.) Intelligent Gravimetric Analyzer (IGA) equipped with a micro-gram balance and 2, 100 and 20000 mbar barotron pressure transducers. All samples were activated by outgassing at 60°C at 10-10 bar until a constant mass had been reached (typically overnight). Isotherms for carbon dioxide and methane were obtained at ambient temperature while those of hydrogen were measured at 77.3 K (liquid N2). All data points were measured to 98% equilibration and fitted to a linear driving force model using the IGASWIN software (v1.03.148). All data were



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corrected for buoyancy effects of the system and samples, employing the calculated crystallographic densities for the desolvated materials assuming complete outgassing: cage 1 (1.033 cm3g-1), cage 2 (0.874 cm3g-1) and cage 3 (0.973 cm3g-1).

Atomistic Simulations. Molecular models were generated from X-ray crystallographic data structure using Materials Studio 4.0 (Accelrys). Connolly surfaces were calculated by rolling a probe molecule across the substrate, the interface taken from the contact point of the probe molecule.9 Solvent accessible surfaces were calculated from the centre of the probe and take into account free volume which can be accessed from at least one of the six sides of the simulation cell. Free volumes and consequently packing coefficients were obtained from the Connolly surfaces. Free volumes were calculated by removal of the solvent guests to leave vacant channels (keeping the cage atom positions fixed). The free volume associated with the cage and interstitial sites, respectively, were calculated by removing solvent from each site in turn and calculating the difference between the remaining available free volume and the total free volume. Packing coefficients were determined from the ratio of the van der Waals volume of the solvent and the free volume available.10 Most favourable sorption sites in 2 and saturation gas uptakes were calculated by molecular simulations employing the Sorption Locator module within Materials Studio 4.0.



Figures and Tables

Figure S1. Electron micrographs (top) and optical microscope images (bottom) for desolvated crystals of 1.

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Figure S4. 1-D NMR data for cages 1-3. Left: 1H NMR (CDCl3); Right, 13C NMR (CDCl3).

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Figure S5. 1H COSY NMR spectrum for 1.

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Figure S6. Heteronuclear single quantum correlation (HSQC) NMR for 1.

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Figure S7. Heteronuclear multiple bond correlation (HMBC) NMR for 1.

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Figure S8. 1H COSY NMR for 2. A 3J vicinal coupling between the CH3 protons and the CH proton, H2, is observed. A 2J geminal coupling between the CH2 group protons, H1 and H3, is also observed. A 3J vicinal coupling is seen between H2 and the CH2 proton trans to this (H1). The 1-D 1H NMR (fig. S4) is also consistent with this assignment since the H3 site is a symmetrical doublet coupled to only one other spin ½ nucleus.

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Figure S9. HSQC NMR for 2 confirms the CH and CH2 assignment and correlates well with the COSY experiment.

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Figure S10. Heteronuclear multiple bond correlation (HMBC) NMR for 2.

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Figure S11. 1H COSY NMR for 3.

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Figure S12. HSQC NMR for 3.

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Figure S13. HMBC NMR for 3.

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Figure S14. FTIR data for cages 1-3, both as directly prepared (solvates; EtOAc, CH3CN and CH2Cl2, respectively) and after desolvation (de-solvate). For cages 2 and 3, desolvation occurs spontaneously at ambient temperature (see also TGA data; Figures S15 and S19). As such, for 2 and 3, some solvent is inevitably lost prior to FTIR analysis of the “solvates” – indeed, no acetonitrile peak can be observed in the sample of 2 prior to desolvation by heating (see also figs. S15, S17 & S19). Cage 1 by contrast forms a much more stable solvate with EtOAc (fig. S16) which also exhibits a strong IR vibration at 1740 cm-1 corresponding to the carbonyl in the solvent guest.

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Figure S15. FTIR data for a sample of 2 removed from acetonitrile and mounted immediately on the FTIR sample stage. Repeat scans were taken over 1 hour. The spectrum does not change significantly apart from the complete loss of the FTIR bands associated with the solvent, CH3CN. These spectra suggest that essentially all of the solvent is lost from the structure within a period of < 20 minutes upon simple standing in air. This rapid loss of solvent from the pore structure in 2 was further confirmed by thermogravimetric analysis under a nitrogen flow (see fig. S19).

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Figure S16. Thermogravimetric analysis (TGA) data for cage 1 (nitrogen flow, heating rate = 5 °C / min). The weight loss for the solvate at 300 °C is 20 wt. % which equates to a formula of 1•2.25 EtOAc, in broad agreement with the solvent content estimated from the electron count measured by X-ray diffraction. The fully desolvated sample (desolvated by heating to 80 ºC under nitrogen flow for 8 hours) shows only 1% weight loss up to 300 °C and onset of decomposition at 337 °C (610 K).

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Figure S17. Thermogravimetric analysis (TGA) data for cage 2 (nitrogen flow, heating rate = 5 °C / min). This material desolvates rapidly and spontaneously at ambient temperature to lose the solvent, CH3CN. As such, the TGA analyses are similar for both samples, quite unlike cage 1 (fig. S16). The small mass loss observed for the as-synthesized sample is most likely attributable to more strongly physisorbed water molecules. The onset of decomposition for the desolvated sample occurs at 349 °C (622 K).

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Figure S18. Thermogravimetric analysis (TGA) data for cage 3 (nitrogen flow, heating rate = 5 °C / min). The dichloromethane solvate of cage 3 is more stable than in the case of 2/CH3CN (fig. S17) but all of the solvent (estimated 17 wt. %) is removed by heating to 200 °C under these conditions. The desolvated sample loses 4.2 wt. % between ambient temperature and 60 °C possibly due to the removal of a small amount of physisorbed water vapour. The onset of decomposition for desolvated 3 occurs at 398 °C (671 K).

26



Figure S19. Time-resolved TGA data for samples of cages 1 – 3. In all cases, the crystals were removed directly from solvent (EtOAc, CH3CN and CH2Cl2, respectively) and quickly mounted in the TGA apparatus. The data was then collected over time under a flow of N2 (25 ml/min). In all cases, there was a rapid initial decrease in mass which can be ascribed to the evaporation of bulk solvent on the surface the crystals. For cage 1, the mass then stabilised at ambient temperature after this initial rapid loss, consistent with a relatively stable EtOAc solvate. Upon heating, a further mass loss of 21.5 wt. % (based on mass after evaporation of external solvent) was observed, corresponding to desolvation of the sample. For cage 2, initial evaporation was followed by a rapid desolvation at ambient temperature in less than 25 min after which the sample reach constant weight. Only a very small additional mass loss was observed upon heating (1.4 wt. %), most likely due to the removal of physisorbed water. This is in good agreement with the timescale for desolvation at ambient temperature suggested by FTIR experiments (fig. S15). For cage 3, CH2Cl2 solvent loss occurs at ambient temperature but much more slowly than for 2/CH3CN, suggesting a more stable solvate. The material was fully desolvated by heating to 125 °C. The desolvation rate may also be affected by crystal size since 3 is composed of significantly larger crystals than 2 (c.f., Figs. S1 & S3).

27



3

11

1

2 2

2

0

1 1

2

2

3

21

0

3111 2220

2211 3210

(C3) (C3)

(C1) (C1)

N

N

N=

Figure S20. Cage 2 positional isomers. The methyl groups of the propyl vertices in cage 2 (shown

here in bold) are disordered over the exo-positions of the two bridging carbon atoms. The positional

disorder gives rise to the four isomers 3111, 2220, 2211 and 3210 (this equates to eight enantiomers

since the cage structure is chiral). The four digit numbers indicate how many of the adjacent C-

atoms of each C6H3(CN)3 unit carry a methyl group (that is, 3, 2, 1 or none).

28



Figure S21. The cage window diameter was measured for cages 1, 2, and 3 by first creating a centroid, c from the three surrounding arene hydrogens for each cage window. The distance from the centroid to the arene-H less half the van der Waals radius for H was taken to be the radius, r, of the largest sphere that could pass through the window (assuming that the cage is static) and this was taken as the maximum window radius. The average radius for each cage was simply doubled to obtain the window diameter.

29



Figure S22. Powder X-ray diffraction patterns for desolvated cage 1. A) Simulated from single crystal data (bottom) and experimental PXRD (top), data collected at the Diamond Light Source. B) Le Bail fitting agreement factors: a =12.87182(6), b = 10.91512(3), c = 37.0665(1) Å, β = 97.0595(3) °, V = 5168.27(3) Å3. Rwp = 1.73%, Rp = 1.28%, χ2 = 4.17. C) Rietveld fitting with agreement factors (data from Diamond Light Source): a = 12.87049(8), b = 10.91378(4), c = 37.0626(2) Å, β = 97.0614(6) °, V = 5166.53(4) Å3, Rwp = 2.08%, Rp = 1.62%, χ2 = 5.03.

30



Figure S23. Powder X-ray diffraction patterns for desolvated cage 2, as simulated from single crystal X-ray diffraction data for the as-synthesized sample (bottom) compared with the experimental data for the bulk as-synthesized sample before (middle) and after (top) gas sorption analysis. The X-ray pattern is essentially unchanged after gas sorption analysis. While the as-synthesized sample contained a small amount of solvent (acetonitrile), this was quite readily lost even by evaporation at room temperature (see figs. S15 & S19). This explains the close correspondence of the PXRD data before and after sorption analysis, as well as the very small mass decrease (5.7 %) which is observed when the sample is degassed prior to sorption analysis. FTIR spectra, PXRD data, and 1H NMR measurements for samples of 2 dissolved in anyhydrous deuterated solvents suggest that there is physisorbed water in the pore channels of the material prior to degassing.

Lattice constants from single crystal data measured at 173 K: a = b = 18.770(3), c = 10.921(2) Å, V = 3332.1(10) Å3, lattice constants from powder data for desolvated cage 2 at 298 K: a = b = 18.83(3), c = 10.83(1) Å, V = 3326(10) Å3.

31



Figure S24. Powder X-ray diffraction patterns for desolvated cage 3 as simulated from single crystal data (bottom) compared with experimental data (top) showing correspondence between bulk material and the single crystal selected for diffraction.

32



Figure S25. The rigid cage structure locks the six vertex groups in a staggered conformation with fixed exo/endo sites. The exo positions point away from the cage. Substituents other than hydrogen occupy exclusively the exo-sites in cages 2 and 3.

33



Figure S26. (A–C) Packing structures for cages 1-3, respectively, to supplement Fig. 3. (A) Cage 1. (B) Cage 2; the pore necks (as highlighted by dashed yellow circles here) are defined by the methyl groups (green). (C) Cage 3; this structural representation illustrates the packing of the cyclohexyl groups in 3 between the diamondoid pore channels.

Figure S27. Alternative view of diamondoid channel structure in 3 (to supplement Fig. 3C). 34



Figure S28. Non local density functional theory (NL-DFT) pore size distribution curves obtained from the N2 adsorption branch of the isotherm at 77.3 K for cages 2 and 3

35



36

Table S1. Gas sorption data as determined by volumetric sorption for cages 1 to 3.

N2(mmol g-1,

P/P0 = 0.998,

77.3 K)

CO2(mmol g-1,

1 bar)

CH4(mmol g-1,

1 bar)

H2(mmol/g, 77.3 K)

SALANG (m2 g-1,

N2)

SABET (m2 g-1,

N2)

Vmicro (cm3/g, N2, P/P0 =

0.998)

275 K 289 K 275 K 289 K 1 bar

1 1.08 1.27 1.03 0.55 0.44 0.76 40 231 0.04

2 7.52 3.0 2.21 1.13 0.95 5.9 600 533 0.26

3 8.17 2.47 1.94 1.53 1.15 5.0 730 624 0.28

1 The resulting C value here was negative and this measurement should therefore be treated with

caution. As is clear from Fig. 4A, cage 1 shows very low conventional permanent porosity when

analyzed under these conditions. Cages 2 and 3 cage excellent BET and Langmuir plots, see

fig. S19.

Table S2. Sorption data for molecular cages 1-3 as determined using a gravimetric sorption

balance.

CO2 (mmol g-1, 12 bar, 289 K)

CH4 (mmol g-1, 12 bar, 289 K)

H2 (mmol/g, 7 bar 77.3 K)

1 – 1.14 –

2 5.48 3.06 8.88

3 4.46 2.90 7.50

Table S3. Data derived from Brunauer-Emmett-Teller (BET) and Langmuir surface area plots for

cages 2 and 3 (fitted using 8 points).).

P/P0 range SABET (m2 g-1)

R2 C value SALANG (m2 g-1)

R2

2 0.01 – 0.1 533 0.9999 2372 600 0.9998 3 0.01 – 0.1 624 0.9999 2825 730 0.9999



.

Figure S29. Molecular simulations of guest sorption in cage 2. (a, b) Simulations for water guests; (c, d) Simulations for dinitrogen guests; (e,f) Simulations for acetonitrile guests; (a, c, d) Simulated density field (blue) shows all favourable binding sites available at saturation; (b, d, f) Density field shows the potential energy of each binding site coloured from yellow to blue representing the lowest energy binding sites; (g) Electron density map measured by X-ray diffraction for disordered physisorbed water guests in 2; (h) Lowest energy binding site for water in 0-D cage void as calculated by molecular simulations; (i) Lowest energy binding site for water in 1-D pore channel as calculated by molecular simulations.

37



Figure S30. Volumetric CO2 adsorption isotherms at 289 K for cages 1-3.

Figure S31. Volumetric CH4 adsorption isotherms at 275 K for cages 1-3.

38



Figure S32. Gravimetric CH4 adsorption isotherms at 290 K for cages 1-3 measured using a HidenIsochema (Warrington, U. K.) Intelligent Gravimetric Analyzer (IGA).

Figure S33. Gravimetric H2 adsorption isotherms at 77.3 K for cages 2 and 3 measured using a HidenIsochema (Warrington, U. K.) Intelligent Gravimetric Analyzer (IGA).

39



Figure S34. Gravimetric CO2 adsorption isotherms at 290 K for cages 2 and 3 measured using a HidenIsochema (Warrington, U. K.) Intelligent Gravimetric Analyzer (IGA).

Figure S35. Comparison of CO2 adsorption isotherms at 290 K for cages 2 and 3 as measured using gravimetric and volumetric methods on two separate instruments (HidenIsochema IGA and Micromeritics 2050, respectively). The filled and open symbols represent volumetric and gravimetric experiments.

40



Figure S36. Comparison of CO2 adsorption isotherms at 290 K for cages 1-3 as measured using gravimetric and volumetric methods on two separate instruments (HidenIsochema IGA and Micromeritics 2050, respectively). The filled and open symbols represent volumetric and gravimetric experiments.

41



Figure S37. (A, C) Derivation of surface area from N2 sorption isotherms at 77.3 K using the BET method for cages 2 and 3, respectively. (B, D) Derivation of Langmuir surface areas from N2 sorption isotherms at 77.3 K for cages 2 and 3, respectively.

42



0

20

40

60

80

100

120

0 5 10 15 20 25 30 35 40

Pressure (bar)

Volu

met

ric C

H4

upta

ke (v

ol(S

TP)/v

ol)

Cage 3

COF-102

COF-103

0

20

40

60

80

100

120

0 5 10 15 20 25 30 35 40

Pressure (bar)

Volu

met

ric C

H4

upta

ke (v

ol(S

TP)/v

ol)

Cage 3

COF-102

COF-103

Figure S38. Volumetric CH4 uptakes for cage 3 and the crystalline organic networks, COF-102 and COF-103 (data for COFs replotted in volumetric units from ref. 38). The cage material is more competitive in terms of volumetric uptakes at lower pressures because it comprises small micropores while the larger-pore, much higher surface area COFs dominate at higher pressures. The BET surface areas of 3, COF-102 and COF-103 are 624, 4650 and 4630 m2/g, respectively. It should be noted that the temperature used in these experiments differs by 9 K (289 K for 3 versus 298 K for the COFs) and that the COF networks would be expected to adsorb somewhat more methane at the lower temperature.

43



Figure S39. PXRD characterisation for porous polymorph of 1 formed by recrystallization from dichloromethane (DCM) / o-xylene mixture. (a) Comparison of PXRD data for porous polymorph (upper) with simulated PXRD pattern (lower) produced by packing 1, as shown in (c). This packing mode is analogous to that found in 2 when synthesized in CH3CN (see Fig. 3, main text). (b) Le Bail fitting for the desolvated cage 1 porous polymorph to a monoclinic cell, space group P21, with cell constants: a = 18.4189(6), b = 30.359(3), c = 11.0236(4) Å, β = 111.059(6)°, V = 5752.5(7) Å3. Agreement factors, Rwp = 1.89%, Rp = 1.46%, χ2 = 1.27). Broadening and splitting of reflections indicates a lowering of symmetry, consistent with a monoclinic cell. These data could also be reasonably fitted to other monoclinic space groups related to the cage 2 packing mode. (c) Projection on (001) representing relationship between size of idealised trigonal cell (based on cage 2, a = 7.485, b = 10.739Å from indexing) and monoclinic cell obtained from fitting of PXRD data.

44



Figure S40. Characterisation data for porous polymorph of 1 formed by recrystallization from dichloromethane (DCM) / o-xylene mixture. (a) Electron microscopy shows intergrown, striated crystals with a morphology which differs from cage 1 / EtOAc (see Fig. S1). (b) Thermogravimetric analysis for solvated and desolvated crystals of the porous cage 1 polymorph. The thermal stability of the desolvated crystals is comparable to the non-porous polymorph of 1 (see fig. S16). (c) Comparison of micropore size distributions for cages 2, 3 and the porous polymorph of 1 as calculated using non-local density functional theory.

45



46

References

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2. A. A. Coelho (2007), TOPAS-Academic v. 4.1, http://www.topas-academic.net/.

3. P. W. Stephens, J. Appl. Cryst., 32, 281 (1999)

4. Bruker, SAINT V6.45a, BRUKER AXS Inc., Madison, WI, USA (2005).

5. Bruker, SADABS V2008-1, BRUKER AXS Inc., Madison, WI, USA (2008).

6. Rigaku, CrystalClear, Rigaku Inc., The Woodlands, TX, USA (2007).

7. G. M. Sheldrick, Acta Crystallogr. A64, 112 (2008).

8. A. L. Spek, PLATON, A Multipurpose Crystallographic Tool, Utrecht University, Utrecht, The Netherlands (2005).

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