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• W2138325344 abstract "Previously unrecognized chiral and rotational twinning were revealed by optical microscopy, synchrotron white beam X-ray topography, and crystallography in the crystal structure of the inclusion compound of 2,12-tridecanedione/urea (see picture), which was otherwise intractable. Of the achiral substances in our world, only a small fraction are spontaneously resolved into enantiomorphic crystals that can be separated. Spontaneous resolution may occur when the molecular constituents of the crystal adopt chiral or skewed conformations or when molecules adopt chiral arrangements, such as a helices, which act as templates for further growth of the given enantiomorph. Certain inclusion compounds (such as those derived from urea and tri-o-thymotide) have received attention because spontaneous resolution of the inclusion compound leads to chiral discrimination between guest enantiomers.1, 2 For urea inclusion compounds (UICs), in which urea forms helical channels in the presence of long-chain guests,3 the literature has uniformly treated these materials as either right- or left-handed homochiral objects. In part, this misconception occurs because the typical needle morphology makes it difficult to observe the presence of enantiomorphic domains. Through the combined use of optical microscopy, synchrotron white beam X-ray topography (SWBXT), and crystallography, we demonstrate here the existence of two types of previously unrecognized macroscopic twinning in UICs. This work provides further support for our models of crystal growth4 and hydrogen-bond topologies in UICs containing bis(methyl ketone)s5 and provides a rationale for chiral (Brasil) twinning in these materials. This rationale may serve as a model for chiral twinning in other helical materials,6 especially those with double helices. Most urea inclusion compounds consist of well-defined host structures in which urea molecules are hydrogen-bonded to form honeycomb networks of nonintersecting hexagonal channels. Within these channels, long-chain guest molecules pack within van der Waals contact. Although UICs typically form high-symmetry, incommensurate (nonstoichiometric) structures,7 we have identified a series of commensurate UICs containing homologous bis(methyl ketone)s.3–5, 8 For such guests and their congeners, a reliable host–guest hydrogen-bonding motif can be used to control both internal symmetry and external shape of these crystals. In most bis(methyl ketone)/urea crystals that we have studied, urea molecules turn about their twofold axes to form hydrogen bonds with guest molecules in adjacent channels. Using this motif, we have developed a simple geometric model that allows us to use the host:guest stoichiometry, natural length of the guest, and the parity (odd or even) of the guest molecule's chain to restrict the possible host–guest hydrogen-bonding topologies. In the case of 2,12-tridecanedione/urea (1/urea), our prediction of the correct polymorphic structure was instrumental in our structure solution and refinement from the X-ray data.1 A description of helical wheels is given elsewhere,5 so only the salient features are presented here. Most UICs are chiral objects in which the two intertwined helices are of the same handedness and are related by C2 axes perpendicular to the channel. Each urea molecule in helix 1 (numbered 1, 2, and so on as one moves down the channel) has a counterpart directly across the channel (at the same z coordinate) in helix 2 (numbered 1′, 2′, and so on). These pairs of molecules (for example, 1 and 1′) lie parallel to each other. If the host:guest stoichiometry is known (or can be predicted), it is a simple matter to write down the relative positions of the urea molecules that are in position to use their syn N−H groups to form hydrogen bonds with the guest. For 1/urea, the natural length of the guest (18.8 Å)3, 4, 9 predicts a host:guest stoichiometry of 10:1, so the hydrogen-bonding motif requires that the two C=O groups of a given guest molecule are tethered to urea molecules in the first and eleventh positions in the channel (since half of a urea molecule is used at each end of the guest). The helical-wheel diagram shown in Figure 1 represents four possible combinations of host–guest connectivities (1–11, 1–11′, 1′–11, 1′–11′), the first and fourth of which are degenerate. Long arrows in the center of each diagram denote the orientations of the two carbonyl groups in one guest molecule and give a rough idea of the dihedral angle between them. Right-handed helical-wheel diagram showing four possible arrangements for host–guest hydrogen bonding in 1/urea. (An equivalent diagram can be drawn for a left-handed helix.) The numbered arrows around the periphery of the hexagon refer to the orientations of urea C=O groups. The C2 axis shared by A and D (which are degenerate) is shown in D. For this odd-chain guest, this simple model correctly predicts topology B (see Figure 4 e). For this odd-chain guest, whose natural length is slightly longer than the commensurate repeat of 18.36 Å, Figure 1 B predicts that a stable structure (with low torsional strain) can be formed. Indeed, the channel axis oscillation photograph indicates a commensurate structure with 3c=5c (urea: guest=10:1), and the crystals grow as thin {001} plates, as predicted for a commensurate structure in which guests are tethered to the host and offset from guests in adjacent channels by 0 Å.4 Further support for this structural motif came from atomic force microscopy (AFM), which showed that terraces on the {001} faces are molecularly smooth and offset along c by integral multiples of the guest length, with average height of 18.1(5) Å or a multiple thereof (Figure 2). Nevertheless, our early attempts to solve the structure from area detector data proved unsuccessful because of disorder of the guest. AFM images of the {001} face of 1/urea recorded in air on a Digital Nanoscope III instrument in tapping mode. The average step height for six different ledges was 18.1(5) Å or a multiple thereof. For a commensurate structure of 1/urea with 3c=5c one predicts that guests will be related by threefold (31) screw axes along the channels and that the crystals will therefore have uniaxial optical properties (that is, with no ferroelastic distortion in the ab plane).8 Photomicrographs can therefore reveal optical activity, which for most UICs is relatively insensitive to guest identity in the visible region of the spectrum.2b Because there were no previous reports of chiral twinning in UICs, we were surprised to find that in 1/urea and related materials (2-tridecanone/urea, 2,9-decanedione/urea,4 and mixed UICs of 2-undecanone and 6-undecanone), both dextrorotatory and levorotatory domains could be observed (Figure 3 a and b3). The twin boundaries that separate these domains occur every 60° and are coincident with the {110} faces of the crystal. a) Photomicrograph of 1/urea (0.26 mm thick) with polarized light at 546 nm and the analyzer rotated by +9° from the crossed position (dark=dextrorotatory). b) The same crystal with the analyzer rotated by −9° from the crossed position (dark=levorotatory). In each, the view is down the channel axis. Because the nature of the twin boundaries in UICs was important for our studies of domain switching in ferroelastic UICs8 (whose birefringence would mask any chiral twinning), we subjected this crystal to SWBXT at beamline X-19C at the National Synchrotron Light Source. In this technique, the highly collimated white beam provides topographic images with high spatial resolution for each Bragg reflection.10 The positions and intensities of the resulting images are sensitive to twinning, strain, dislocations, and differences in structure factors for reflections in different domains.11 After an exposure of 10–15 s, one obtains a Laue image corresponding to the most intense reflections in the diffraction pattern (Figure 4 a). For 1/urea, reflections occur in three separate sets, one of which shows no contrast. The other two sets form complementary images (labeled d and e) that reveal sectoring in addition to the chiral twinning described above (Figure 4 b and c4) and little or no apparent strain at any of the domain boundaries. a) SWBXT Laue image of 1/urea held with its {001} face perpendicular to the X-ray beam. Note complementary contrast in reflections labeled d and e. b) SWBXT of d1 reflection for 1/urea (g vector shown in upper right). Arrow on left denotes levorotatory region (2-(−)-d) used for X-ray crystal structure shown in Figure 4 d (see text). c) SWBXT of e1 reflection for 1/urea (g vector shown in upper right). Arrow on right denotes dextrorotatory region (7-(+)-e) used for X-ray crystal structure shown in Figure 4 e. Scale bar: 400 μm. d) and e) ORTEP diagrams (30 % ellipsoids) showing P3212 crystal structure of levorotatory fragment shown in Figure 4 b (d) and P3112 crystal structure of dextrorotatory fragment shown in Figure 4 c (e). The absolute configurations are not proven. In anticipation of a trigonal structure, we indexed the topograph with a nonprimitive, rhombohedral cell (a=55.96 Å, α=14.63°),12 and found that in the d and e reflections, the contrast pattern obeyed the conditions for obverse and reverse settings of a rhombohedral cell (−h+k+l=3 n and h−k+l=3 n). These unit cells are related by 180° (or equivalent 60°) rotation about the channel axis.13 Although this rotational (Dauphiné) twinning14 was invisible under the microscope, the X-ray topograph could be used as a guide for cleavage of this crystal into eleven fragments. Two complementary fragments [fragment 7-(+)-e (dextrorotatory type e) and fragment 2-(−)-d (levorotatory type d)] were used for X-ray data collection at −75 °C (see arrows in Figure 4 b and c4). Structure solution and refinement revealed that the apparent rhombohedral symmetry was only approximate, and that the structures could be solved in the trigonal space groups P3112 and P3212. Because there are no heavy atoms in these structures, the absolute structures could not be determined unambiguously with either Flack or Bijvoet methods,15 but the favored assignments (Figure 4 d and e4) agree with Schlenk's model-based correlation of positive optical rotation with the right-handed (31) sense of the urea helix.2b Nevertheless, the structures16 confirm that in the presence of host–guest hydrogen bonding, the helical-wheel method correctly predicts the observed polymorph (cf. Figures 1 B and 4 e). Facet indexing and correlation with the overall crystal morphology showed that the d and e domains are related to each other by 60° rotation about the channel axis. (For fragment 2-(−)-d, which was contaminated by a small amount of the adjacent type e domain, the largest peak in the difference Fourier map assumed the position of an oxygen atom in a guest carbonyl group rotated 58° about the channel axis.) This macroscopic rotational twinning is established during crystal growth, persists over a period of years, and is remarkable given the dynamic nature of guests in other UICs17 and the lack of ferroelastic distortion in 1/urea. (SWBXT of the upper right third of this crystal, which was held between −20 and 20 °C for two years after the initial topograph, showed no noticeable degradation in the Dauphiné twin boundaries.) Although chiral twinning is counterintuitive in a strongly hydrogen-bonded helical system, in which templated growth predominates, clues to the twinning mechanism in 1/urea come from our recent structures of a series of centrosymmetric UICs.18 For Br(CH2)6Br/urea and congeners (space group P21/n, b unique), the n-glide provides a convenient mechanism by which the structures on either side of certain (001)-type channel walls are related by mirror symmetry. In Br(CH2)6Br/urea, the n-glide generates a looplike topology of hydrogen bonds in which certain rows of urea molecules lying closest to the (001) plane are translated along the channel relative to their counterparts in helical structures. From a diagram based on our helical-wheel formalism, it is possible to show that the loop topology in Br(CH2)6Br/urea can serve as a template for the formation of enantiomorphic helices above and below the (001) plane (Figure 5). (No other primitive planes in the Br(CH2)6Br/urea structure can directly template both right- and left-handed helices.) Although the precise structure of the chiral twin boundaries is not available from SWBXT of 1/urea, support for this twinning mechanism comes from the structural correspondence between the {001} planes in Br(CH2)6Br/urea and the {110} planes of 1/urea, which exhibit chiral twinning.18 Modified helical-wheel diagram showing how the stacked loop structure of a centrosymmetric UIC (such as Br(CH2)6Br/urea) can serve as a template for the formation of left- and right-handed helices above and below the (001) plane. Arrows in the middle row of channels correspond to C=O axes for urea molecules in the P21/n structure found in numerous X(CH2)6X/urea inclusion compounds. The numbers correspond to the relative positions along the channel axis of those urea molecules. At the bottom of this centrosymmetric row, urea molecules 2 and 3 template the formation of a right-handed helix, in which the sequence 1, 2, 3, 4, 5, 6 leads in a clockwise sense away from the observer (down the channel). At the top, urea molecules 2 and 3 template the formation of a left-handed helix (counterclockwise from 1 through 6). These right- and left-handed helices correspond to the unprimed and primed helices described above in the helical-wheel formalism. Athough 1/urea is not ferroelastic, these results illuminate our studies of domain switching in ferroelastic crystals such as 2,10-undecanedione/urea, in which domain reorientation occurs under applied external anisotropic stress.8 Because the present work shows that chiral twinning may occur in helical urea systems, and that the most likely topology at this type of domain boundary is nonhelical, we anticipate that ferroelastic UICs containing such twin boundaries will have high barriers to domain wall motion.19 With the recent emergence of optical techniques for measuring chirality in biaxial crystals,20 identification of Brasil-type domain walls may soon be possible. 1/urea: A solution of 2,12-tridecanedione (0.301 g, 1.42 mmol, prepared by literature methods21), urea (0.857 g, 14.3 mmol, Baker AR) and MeOH (7.0 mL, Mallinckrodt) was allowed to evaporate at RT. After one day, thin plates (0.331 g) were collected. M.p. 134.5–135 °C, uncorrected; 1H NMR (400 MHz, [D6]DMSO): δ=5.41 (s, urea), 2.38 (t, 3J(H,H)=7.4 Hz), 2.04 (s), 1.41 (m), 1.20 (m), urea:guest (10.3:1); IR (Nujol): =1717 cm−1. Dedicated to Professor J. Michael McBride" @default.
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• W2138325344 date "2002-03-15" @default.
• W2138325344 modified "2023-10-17" @default.
• W2138325344 title "Template Effects, Asymmetry, and Twinning in Helical Inclusion Compounds" @default.
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