2.2 [3+2] Organic Cages
all 28 conditions, two polymorphs of C1 were identified, crystallising from DCM and hexane, and the second polymorph DCM and m-xylene The first structure
was isostructural to B1, however the second crystal structure of C1 showed hexagonal channels throughout the cage molecules.
During refinement, all non-H atoms were refined anisotropically unless stated otherwise, the H-atoms were located using the difference map and
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refined using the riding model. The crystal structure was solved using SHELXT68 and refined using SHELXL69. All adsorption corrections were performed using SAINT70. For an improved model, RIGU71 was applied to the cage molecule to improve the atomic displacement parameters (ADP), but not necessary for the disordered dichloromethane solvent which was modelled in the final structural solution. C1.DCM.Hexane was grown via vapour diffusion in an incubator at 15°C. Crystals were well-refined, with minimal structural disorder except for the solvent. The water which was modelled from residual electron density was refined isotropically and their combined occupancy total 70%. The disordered DCM was modelled at 50% occupancy over 2 sites. The displacement ellipsoid plot can be seen in Figure 7A, with solvent and hydrogen atoms removed for clarity.
The overlaid structures from the single crystal structure of
C1.CH2Cl2.0.7(H2O) and the calculated structures shows almost perfect agreement. The phenyl rings in the linkers are in the same positions, as well as the ethyl chains on the triamine. The RMSD between the structures is only 0.12 Å, further demonstrating the reliability between the calculated and experimental structures.
Figure 7 A) Displacement ellipsoid plot from the single crystal structure C1.CH2Cl2.0.7(H2O). Ellipsoids are displayed at 50% probability. The water was omitted from the figure for clarity; B) Overlay of the calculated cage and the experimental crystal structure of C1 (red).
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The other polymorph of C1 was recrystallised from DCM and m-xylene. The displacement ellipsoid plot for C1.CH2Cl2.3(C8H10) can be seen in Figure
8. C1.CH2Cl2.0.7(H2O) (left, Figure 9), shows WTE packing, arising from the T-shaped − stacking at a distance of 3.84 Å. The anti-solvent for this crystal structure was hexane, however in the crystal structure, the solvent modelled was CH2Cl2 and water, implying that C6H14 had little impact on directionality in the crystal packing. Comparatively, C1.CH2Cl2.3(C8H10).(H2O) crystallised with hexagonal channels throughout the structure due to preferential − stacking between cage and m-xylene solvent. The cage linkers showed parallel- displaced − stacking, with one m-xylene per cage, at a distance of approximately 4.02 Å.
Figure 8 Displacement ellipsoid plot from the single crystal structure of C1.CH2Cl2.3(C8H10).(H2O). Each m-xylene molecule was modelled with 33.3% occupancy. Ellipsoids are displayed at 50% probability. Labels were omitted for clarity.
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Figure 9 Comparison between the crystal packing of C1.(CH2Cl2).0.7(H2O) on the left, and C1.(CH2Cl2).3(C8H10).(H2 on the right. Viewing along the a-, b- and
c-axes (top to bottom). Recrystallisation using hexane shows edge-to-edge
packing with minimal interactions between the cages, comparatively using m- xylene, the cage forms hexagonal channels which are directed by the − interactions between the cages and the m-xylene solvent, which has been omitted for clarity.
There are currently several examples of solvent directed crystal packing, with CC1 shown to be a solvatomorphic POC, as well as CC3 exhibiting guest controlled directed packing.65,72,73 Crystal packing can be
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directed by taking advantage of stronger interactions between the solvent and the cage.
Cages packed in the crystal structure tend to have weak, non-covalent interactions which are typically less directional compared to other porous molecular solids.50,51,74,75 Introduction of certain solvents can either promote, or interrupt these weak, WTW interactions and directs the packing towards a porous or non-porous solid respectively.73 Cage C1 formed a [3+2] cage regardless of the crystallisation method, comparatively when using m-xylene the − interactions between the solvent and the cage encourage the formation of one-dimensional channels throughout the structure, shown in
Figure 10.
Figure 10 Solvent m-xylene in the pseudo-pore of C1, modelled as green for
clarity.
2.2.3 [3+2] Organic Cage C14
C14 was synthesised from (2,4,6-triethylbenzene-1,3,5- triyl)trimethanamine and anthracene-9,10-dicarboxylic acid. The single crystal was grown from DCM and THF. The calculated structure for C14 can be seen overlaid with the single crystal structure of C14.(CH2Cl2).1.5(C4H8O), showing there is some variation in the imine angles, and the position of the anthracene aldehyde linker. Calculations revealed that the [6+4] age was energetically
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more favourable based on formation energy per bond than the [3+2]. The [6+4] cage was around -23.5 kJ mol-1 per bond, whereas the [3+2] cage was = 20.1 kJ mol-1. The RMSD between the calculated and experimental structure was 1.74 Å, which is a considerable difference. The imine angle, which determine the position of the anthracene linkers differ between the two, leading to the difference in the overlaid structures.
Figure 11 A) Displacement ellipsoid plot from the single crystal structure of C14.(CH2Cl2).1.5(C4H8O), showing disorder on the imines of N4 and N5, and N6 and N7. Other atom labels and all hydrogen atoms are omitted for clarity. Ellipsoids are displayed with 50% probability; B) Overlay of the single crystal structure of C14 (red) and the calculated structure.
The asymmetric unit comprises one complete C14 cage and two THF molecules. Due to disorder, diffuse scatter beyond 0.85 Å was omitted during refinement (PLAT027_ALERT_3_A checkCIF alert), and two -CH2=N-CH- groups were modelled over two positions. In the crystal structure two reasonably well ordered THF molecules were located between C14 cages and modelled with 50% occupancy. Due to slight disorder, one of these THF molecules was refined with a rigid bond restraint (RIGU in SHELX), and for this molecule one -O-CH2- group was modelled over two positions. N6 and N7 were modelled with 50% occupancy each, N4 40% and N5 60% occupancy.
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Disordered THF was modelled with 100% occupancy for one well-ordered molecule, and 50% for the more disordered. Despite only having seen the [2+3] cages experimentally, both from synthesis and crystallisation, calculations revealed that the [4+6] cage was in fact energetically favoured by approximately 22 kJ mol-1.
For most of the cages in this study, we have seen good agreement between computational and experimental results. However, for a few examples there were discrepancies between experimental and computational results. In this case, despite the [6+4] cage being predicted to be energetically more favourable and stable, the [3+2] cage was found experimentally. The − stacking interactions, at a distance of 3.483 Å, direct the formation of the [3+2] cage, as seen in Figure 12.
Figure 12 C14.(CH2Cl2).1.5(C4H8O) viewed along the a-, b- and c-axes (top left clockwise).
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