DOI: 10.1021/cg901244v
Generation of Square-Shaped Cyclic Dimers vs Zigzag HydrogenBonding Networks and Pseudoconformational Polymorphism of Tethered Benzoic Acids
2009, Vol. 9 5017–5020
Shigeo Kohmoto,*,† Yu Kuroda,† Keiki Kishikawa,† Hyuma Masu,‡ and Isao Azumaya‡ †
Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan, and ‡Faculty of Pharmaceutical Science at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan Received October 8, 2009
ABSTRACT: Two approaches to create hydrogen-bonding (H-bonding) cyclic dimers of tethered benzoic acids in a crystalline state were examined. The cyclic dimers of the methoxy derivative 1 were generated by inclusion of aromatic guest molecules: benzene or benzonitrile. Depending on the size of the guests, the conformation of the pentylene linker of 1 took either the all-trans or 1,2- and 4,5-gauche conformation to adjust the size of the cavity for the guest. The tethered benzoic acids 2 possessing benzyloxy groups as pendants generated a poly(pseudo)rotaxane-like structure in which pendants were included in the cavity of the cyclic dimer itself. In contrast, 1 afforded a zigzag H-bonding network by recrystallization from methanol or ethanol. Incorporation of methanol in the zigzag network was observed when 1 was recrystallized from methanol.
*Corresponding author. Telehone: þ81-43-290-3420. Fax: þ81-2903422. E-mail:
[email protected].
and 2,3- and 4,5-gauche (conformation C), are shown in Figure 1. In conformation A, two carboxy moieties direct opposite for H-bonding. On the contrary, they direct the same direction in conformations B and C. The former is responsible for the formation of the linear H-bonding network, and the latter two are responsible for the cyclic dimer formation, respectively. When 1 was recrystallized from ethanol, the zigzag H-bonding network was created employing the benzoic acid dimer motif (Figure 2a). The linker adopts the gauche conformation around C1-C2 and C4-C5 bonds (conformation A), in which two carboxy moieties are opposite in direction. It was reported that the carboxylic acid dimer motif was unfavorable compared to that of the catemer motif in benzoic acid derivatives with bulky substituents.11 However, those with a relatively long tether (C4) were reported to have a propensity to favor the dimer motif.12 Recrystallization of 1 from methanol afforded a similar zigzag Hbonding network, but with incorporation of methanol molecules in the ratio of 1/methanol = 1/2 (Figure 2b). Methanol molecules are wedged into the H-bonding between carboxys. In contrast, when 1 was recrystallized from benzene/ethanol solution, the H-bonding cyclic dimer (1 3 1/2C6H6) was generated by the inclusion of one molecule of benzene in its cavity. Inclusion of a benzene molecule in a H-bonding cyclic host was reported by Etter et al. in the formation of a 6:1 cyclohexanedione/benzene cyclamer.13 Single crystal X-ray analysis of it showed that 1 has an all-trans conformation (conformation B). The cyclic dimer possesses a flat framework with an almost square-shaped cavity with dimensions of ca. 8.3 A˚ 8.7 A˚ (Figure 3a). The benzene molecule is well fitted in the cavity. Its packing diagram shows that the dimers are laminated with the layer distance of 3.3 A˚. The CH/π interaction is observed between the benzene molecule and one of the methylene protons of the neighboring dimer with the centroid(benzene)-proton distance of 2.9 A˚. An oblique channel structure is observed in a tilt angle of 59° to the perpendicular (Figure 3b). Recrystallization from benzonitrile/ethanol also afforded inclusion crystals. As observed in the X-ray structure of 1 3 1/2C6H6 (Figure 3a), a benzene molecule is well fitted in the cavity of the cyclic dimer and no extra space exists to locate the nitrile group in there. Therefore, a different type of cyclic dimers is expected for the benzonitrile-included crystals. The single crystal X-ray structure of the benzonitrile-included crystal (1 3 1/2C7H5N) shows that the acid 1 takes a 2,3- and 4,5-gauche conformation (conformation
r 2009 American Chemical Society
Published on Web 10/27/2009
Recently, much attention has been paid to cyclic self-assemblies in crystal engineering,1 which can be applied to the creation of channel structures and porous crystals via H-bondings,2 ionic interactions,3 metal coordinations,4 or even covalent bonds.5 Cyclic assemblies have also been utilized in a spherical way to prepare molecular capsules with multiple interactive sites.6 However, the simple self-assembled cyclic dimer of a square or a rectangular type is hardly reported. These types of dimers can be generated by the self-assembly of bifunctional molecules possessing interactive sites at both ends of the molecules. If the molecules are flexible, linear assemblies are also possible in addition to cyclic assemblies depending on their molecular shapes: transoids or cisoids.7 In relation to the recent interest in conformational polymorphism,8 it is worthwhile to control these assemblies in a conformational way, which contributes to the designing of organic crystals. We planned to carry out the cyclic assembly of flexible linear molecules possessing carboxy moieties at both ends of the molecule. A dimer motif of carboxylic acid has been employed as an H-bonding building block. Herein, we report on our approach to fabricate square-shaped cyclic dimers of tethered benzoic acid derivatives. Figure 1 depicts our approach to create the cyclic dimer of the molecules possessing two H-bonding sites at the molecular termini. It is commonly considered that the existence of void spaces in crystals is unfavorable due to implosion. Without filling the space, the linearly arrayed zigzag H-bonding network will be created (path a). Our idea for cyclic dimer formation is to fill the cavity space in two ways. The first approach is an inclusion of a guest molecule as a template in the cavity (path b). The second approach is an unusual one which involves the inclusion of pendant groups in the cavity. If the size of the pendant group fits the size of the cavity, the inclusion of the pendant group will stabilize the cyclic dimer. This gives the novel poly(pseudo)rotaxane-like network9 (path c). The tethered benzoic acids without and with pendant groups, 1 (R = Me) and 2 (R = Bn), respectively, were prepared as model compounds and subjected to X-ray crystallographic study. Because of the flexibility of the pentylene linker, several conformations of them could exist. Three possible conformations of them, 1,2- and 4,5-gauch (conformation A), all-trans (conformation B),
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Figure 3. Single crystal X-ray structure of the H-bonding cyclic dimer of 1 with an all-trans conformation (conformation B). (a) Inclusion of a benzene molecule in its cavity and (b) the packing structure showing oblique channels.
Figure 1. Schematic representation of the zigzag vs cyclic selfassemblies, and compounds 1, 2, and their three conformers. The moieties colored pink, yellow, blue, and red designate the molecular framework, the H-bonding sites, the pendant groups, and the guest molecule, respectively. The formation of the zigzag H-bonding network (path a), the cylic dimer with inclusion of a guest molecule (path b), and the linear array of the cyclic dimer with inclusion of the pendant groups (path c). Three possible conformations of the tethered benzoic acids, 1,2- and 4,5-gauche (conformation A), all-trans (conformation B), and 2,3and 4,5-gauche (conformation C). Arrows show the direction of H-bonding.
Figure 2. Single crystal X-ray structures of 1. The zigzag H-bonding network adopted conformation A. (a) Crystal structure obtained by recrystallization from ethanol. (b) Methanol incorporated structure, 1 3 2CH3OH. Hydrogen bonds are indicated with black dotted lines.
C) to create a cyclic dimer (Figure 4a). Unlike the benzene inclusion complex, the cyclic dimer of benzonitrile inclusion does not have a flat structure due to the conformation of the pentylene linker. It has a step, and its cavity is slightly distorted to create enough space for the nitrile group. Disorder of the included benzonitrile molecules is observed due to the two possible orientations of them in the cavity. Stacking of cyclic dimers gives the oblique channel structure. Several CH/O interactions are observed between the cyclic dimers (Figure 4b). As we observed a benzene molecule was an effective template for the creation of the cyclic dimer, we considered to replace a methoxy with a benzyloxy moiety as a pendant. We expected that the size of the benzyl moiety similar to that of benzene was suitable to be included in the cavity of the cyclic dimer as a template. This second approach to create the H-bonding cyclic dimer was successful. A single crystal of 2 was obtained by recrystallization from chloroform. The single crystal X-ray structure of 2 shows a poly(pseudo)rotaxane-like structure. The square-shaped cyclic dimer was created by H-bonding, similar to the benzene inclusion complex of 1 with conformation B (Figure 5a). Two of the benzyloxy moieties out of four in the dimer pop out upward and downward. They play a role as pendant groups. Unlike the benzene inclusion complex of 1, in which one molecule of benzene was included in the cavity of the dimer, two benzyloxy moieties of the neighboring molecules are included in the cavity. In the former case, the benzene molecule is located in the cavity nearly parallel to the plane of the cyclic dimer of 1 at a tilt angle of 11°. However, the phenyl moiety of the benzyloxy of 2 is almost perpendicular to the plane of the dimer at a tilt angle of 78°. Half of its benzene moiety is included in the cavity. The remaining two benzyloxy moieties have a flat structure and are settled on the same plane of the cyclic framework. The dimer possesses a cavity of ca. 8.1 8.9 A˚ dimension. This inclusion occurs in a sequential way to form a poly(pseudo)rotaxane-like network (Figure 5b). The layer distance between the dimers is 3.5 A˚. The distance between the two benzene rings of the benzyl moieties is 3.5 A˚. The CH/π interaction is observed between the hydrogen atoms at the para-position of the benzyloxy moiety and the benzene ring of the benzoic acid part. We have shown a novel design of the H-bonded cyclic dimer of the tethered benzoic acid based on two approaches: inclusion of a
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guest molecule or a pendant group as a template to be filled in the cavity of the dimer. The latter approach gives a network of poly(pseudo)rotaxane-like structure. The lack of template results in the formation of the zigzag H-bonding network. An interesting guest-molecule induced pseudoconfomational polymorphism was observed to give the three conformations of the pentylene linker. Supporting Information Available: Preparation information and spectral data of 1 and 2, and crystallographic information files (CIF) of 1, 1 3 2CH3OH, 1 3 1/2C6H6, 1 3 1/2C7H5N, and 2. This material is available free of charge via the Internet at http://pubs. acs.org.
References
Figure 4. Single crystal X-ray structure of the H-bonding cyclic dimer of 1 with a 2,3- and 4,5-gauche conformation (conformation C) including a benzonitrile molecule in its cavity. Benzonitrile molecules are disordered with two orientations. One of them is presented in each cavity. (a) Packing structure showing oblique channels and (b) short contacts (CH/O) between dimers indicated with black dotted lines.
Figure 5. Single crystal X-ray structure of 2. (a) The included phenyl rings in a cavity are presented in a space-filling model colored with pink and green, respectively. (b) Schematic representation of the poly(pseudo)rotaxane-like structure.
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(b) Crystal data for 1 3 2CH3OH: C23H32O20, Mr = 468.49, 0.30 0.15 0.10 mm3, monoclinic, P2/c, a = 18.241(8), b = 4.491(2), c = 15.404(7) A˚, β = 113.219(7)°, V = 1159.6(9) A˚3, Z = 2, Fcalcd = 1.342 g cm-3, μ = 0.105 mm-1, T = 90 K, 2θmax = 56.70°, 6257 reflections, 2687 unique (Rint = 0.0666), R1 = 0.0682, wR2 = 0.1786 (I > 2σ(I)). (c) Crystal data for 1 3 1/2C6H6: C24H27O8, Mr = 443.46, 0.50 0.30 0.03 mm3, triclinic, P1, a = 5.4919(6), b = 12.596(1), c = 17.208(2) A˚, R = 71.111(1), β = 86.297(1), γ = 85.830(1)°, V = 1122.2(2) A˚3, Z = 2, Fcalcd = 1.312 g cm-3, μ = 0.099 mm-1, T = 200 K, 2θmax = 54.24°, 5612 reflections, 4297 unique (Rint = 0.0093), R1 = 0.0414, wR2 = 0.1071 (I > 2σ(I)). (d) Crystal data for 1 3 1/2C7H5N: C24.5H26.5N0.5O8, Mr = 455.96, 0.45 0.10 0.05 mm3, triclinic, P1, a = 5.2438(6), b = 12.401(1), c = 17.403(2) A˚, R = 79.855(1)°, β = 89.499(1)°, γ = 89.383(2)°,
Kohmoto et al. V = 1113.9(2) A˚3, Z = 2, Fcalcd = 1.359 g cm-3, μ = 0.102 mm-1, T = 200 K, 2θmax = 54.06°, 5538 reflections, 4252 unique (Rint = 0.0139), R1 = 0.0458, wR2 = 0.1163 (I > 2σ(I)). (e) Crystal data for 2: C33H32O8, Mr = 556.59, 0.20 0.10 0.05 mm3, triclinic, P1, a = 10.016(6), b = 11.027(7), c = 14.051(8) A˚, R = 79.032(8), β = 75.086(8), γ = 67.286(7)°, V = 1376(1) A˚3, Z = 2, Fcalcd = 1.343 g cm-3, μ = 0.096 mm-1, T = 90 K, 2θmax = 54.34°, 6706 reflections, 5185 unique (Rint = 0.0519), R1 = 0.0789, wR2 = 0.1601 (I > 2σ(I)). (11) Moorthy, J. N.; Natrajan, P. J. Mol. Struct. 2008, 885, 139–148. (12) Moorthy, J. N.; Natarajan, P. Cryst. Growth Des. 2008, 8, 3360– 3367. (13) Etter, C. M.; Urba nczyk-Lipkowska, Z.; Jahn, D. A.; Frye, J. S. J. Am. Chem. Soc. 1986, 108, 5871–5876.
