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Aug 31, 2009 - Centre for Strategic Nano-Fabrication School of Biomedical, ... are 1:1 polymorphs (R and β), both with the calix[5]arenes packed in a...
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DOI: 10.1021/cg900682c

Aromatic Solvent Specific Induced Arrays of Calix[5]arenes

2009, Vol. 9 4864–4871

Adam D. Martin, Thomas E. Clark, Mohamed Makha, Alexandre N. Sobolev, and Colin L. Raston* Centre for Strategic Nano-Fabrication School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Hwy, Crawley, Western Australia 6009, Australia Received June 18, 2009; Revised Manuscript Received July 26, 2009

ABSTRACT: Calix[5]arene forms three inclusion complexes with benzene, which have been structurally authenticated and studied by Hirshfeld surface analysis. Two of them are 1:1 polymorphs (R and β), both with the calix[5]arenes packed in a backto-back style arrangement. In the R polymorph, three 1:1 supermolecules, [calix[5]arene∩benzene], cooperate in creating a large cavity containing three solvent molecules. In the β polymorph, the calix[5]arenes alternate in an up and down orientation, resulting in a less dense arrangement. The other inclusion complex is 1:2 ([calix[5]arene∩benzene] 3 benzene) which has a benzene molecule endo and exo relative to the calix[5]arene cavity. Hirshfeld surface analyses are effective in differentiating the intermolecular contacts between this structure and the R and β polymorphs, both for the calix[5]arene and the included benzene guest molecules.

Introduction Calixarenes are an extensively studied class of macrocycles that have a wide variety of applications due to their flexibility in functionalization of the upper rim,1 lower rim,2 and ring sizes.3 Such ease in chemical elaboration allows calixarenes to be constructed to include a wide variety of guests inside the cavity, from metal ions4 to larger guests such as fullerenes5 and carboranes.6 Calix[5]arene is a less studied macrocycle compared to the even numbered calixarene homologues due to its more challenging and lower yielding synthesis,7 yet it is a remarkably versatile molecule for many applications such as gas sorption8 and cation inclusion.9 Calix[5]arene has been shown to form a variety of supramolecular arrays with different guest molecules such as ferrocene10 and acetone.11 Variants of calix[5]arene such as the para-benzyl and para-phenyl12 analogues can also form inclusion compounds with solvent molecules such as pyridine13 and toluene.14 It is also noteworthy that the parent para-tert-butylcalix[5]arene, which is the synthetic precursor to calix[5]arene, forms inclusion complexes with DMF,15 ethyl acetate,16 and hexane.17 Hirshfeld surface analysis is rapidly gaining prominence in mapping out the interactions within a complex construct between neighboring atoms, taking into account their electron density. These generated surfaces can display a variety of parameters, including distances to atoms inside or outside of the Hirshfeld surface (di and de, respectively),18 distances between atoms inside and outside of the surface (dnorm, which is very useful for visualizing short contacts),19 and even parameters such as shape index, which allows for visualization of the packing between molecules through the different contours and colors of the surface. Hirshfeld surfaces have been used to model the interactions between O-alkylated calix[6]arenes,20 polymorphs of aromatic molecules such as 2-chloro-4-nitrobenzoic acid,21 phosphonated calix[4]arenes bound to calcium ions,22 and the encapsulation of C70 by extended arm calixarenes.23 *To whom correspondence should be addressed. Tel: þ618 6488 3045. Fax: þ618 6488 1005. E-mail: [email protected]. pubs.acs.org/crystal

Published on Web 08/31/2009

Scheme 1. General Procedure for Preparation of Complexes 1-3 (eq 1)

Recently, we reported the Hirshfeld surface analysis of four different halobenzene inclusion complexes of calix[5]arene.24 The fluoro-, chloro-, and bromo-benzene complexes are very similar, with that of iodo-benzene being distinctly different in its intermolecular contacts, which is reflected in the dnorm surface and unique fingerprint plot. Herein we report the structure determination of three benzene inclusion complexes, two of which are polymorphs, with all of them based on the assembly of perched host-guest supermolecule [calix[5]arene∩benzene]. Results and Discussion The 1:1 [calix[5]arene∩benzene] inclusion polymorphs R and β, complexes 1 and 2, respectively, were prepared by slow evaporation of the benzene from a pure solution of calix[5]arene, with crystals suitable for single crystal diffraction studies forming over a period of 2 h to 6 days, eq 1 (Scheme 1). The polymorphs are remarkably different, with the R-polymorph having three supermolecules, [calix[5]arene∩benzene], in the asymmetric unit whereas the β-polymorph has two such supermolecules. Interestingly, the R-polymorph is isostructural with the 1:1 toluene complex, [toluene∩calix[5]arene], despite now with the presence of the methyl substituent on the benzene ring.13 Clearly, the cavity of calix[5]arene is rather versatile r 2009 American Chemical Society

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Figure 1. Complex 1: (A) Asymmetric unit showing supermolecules 1-3, (B) extended packing showing the hexagonal close packing arrangement (pink) and the star shape motif (yellow), (C) extended packing showing the differing columnar arrangement (supermolecule 1 (gold), supermolecule 2 (purple), supermolecule 3 (blue) and benzene (yellow)), and (D) the interplay of the three supermolecules cooperatively forming a larger cavity containing the three solvent molecules, with the supermolecules forming the columnar arrays. General coloring scheme purple for calix[5]arene carbons and green for benzene carbons except for spacefilling view in (C).

in being able to accommodate a wide variety of different sized guests. For all of the complexes, the calix[5]arene maintains the cone conformation, with the five hydroxyl groups forming the expected hydrogen-bonded network, albeit with the hydrogen atoms disordered in both directions around the lower rim. This is in contrast to the sublimed form of calix[5]arene (a so-called R-form),25 which adopts an inverted cone conformation, forming helical stacks in the extended structure, and having hydrogen bonded chains involving the hydroxyl groups. The β-polymorph of calix[5]arene in the present study has the calixarenes in the cone conformation. These are arranged the same as in another sublimed form of calix[5]arene (the so-called β-form), which is active toward CO2 sorption.25 Complex 1 crystallizes in the space group P31c with three supermolecules, [benzene∩calix[5]arene], as perched host-guest complexes in the asymmetric unit. The calix[5]arenes have a slightly distorted cone conformation as evident by analysis of the angles between the least-squares planes of the five “O” centers and phenyl rings, which vary from 127.1 to 140.4°. The supermolecules have approximately m symmetry with the interplay of the two components involving three C-H 3 3 3 π interactions which range in distance from 2.58 to 3.31 A˚. The benzene molecules sit in the cavity with the aromatic ring directed toward the bottom of the cavity, Figure 1A, the dihedral angle θ between the principal axis of the calix[5]arenes and the principal axis of the benzene molecules being 152.1, 153.2, and 153.0° ((0.5°) for supermolecules 1, 2, and 3, respectively. A measure of how deep the benzene resides in the cavity of the calix[5]arene is the distance between the center of the aromatic ring of the benzene and the centroid of the five O-centers, which varies slightly from 4.05 to 4.07 A˚. The organization of the supermolecules involves methylene C-H 3 3 3 π and aromatic C-H 3 3 3 π interactions at 3.16 and 3.13 A˚, respectively, between supermolecules 1 and 2.

Supermolecules 2 and 3 have back to back contacts of their lower rims offset by about half the radius of the lower rim itself, the closest contacts, O 3 3 3 O, being 3.00 and 3.07 A˚ ((0.01 A˚). The extended structure can be considered as built of columnar arrays of supermolecules which are located around 3 symmetry axes, the peripheral of each column being lined with the lower rim of the calix[5]arenes. The guest molecules are embedded in the columnar arrays, Figure 1B, and this is reminiscent of the arrangement of the component molecules in the 1:1 complex of fullerene C60 and calix[5]arene.4 The principal axes of the calix[5]arenes are not orthogonal to the principal axis of the columns, being skewed by 51.5, 50.3, and 49.0° ((0.5°) for supermolecules 1, 2, and 3, respectively. The columns form a hexagonal closed packed arrangement with one of the supermolecules forming a downward facing column, while the other two supermolecules form an upward facing column as viewed down the c axis, Figure 1C. Each downward facing column is surrounded by six upward facing columns with numerous aromatic and methylene C-H 3 3 3 π interactions between columns, ranging from 2.89 to 3.13 A˚. The reversal in column direction is due to back to back stacking between calix[5]arenes in neighboring columns. Each hexagon contains one full column and one-third of six columns giving three columns in total, and the circumferences of the fractional columns in a hexagon create the outline of a star shape motif, Figure 1B. The columns are composed of a repeating unit of two segments with the two segments offset by 60° relative to each other. Each segment is comprised of three calix[5]arenes, and there are no obvious hydrogen bonding interactions between the supermolecules in a segment, Figure 1D. The segments in the repeating unit are held together via aromatic C-H 3 3 3 π interactions between calix[5]arenes, at 3.04 to 3.06 A˚, and methylene and aromatic C-H 3 3 3 π interactions between

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Figure 2. Complex 2: (A) The asymmetric unit, with the two supermolecules and the CH 3 3 3 π interactions present between the benzene molecule and the calix[5]arene, and (B) packing of the supermolecules, as projected down the c axis, showing the layered arrangement of the calix[5]arenes.

calix[5]arenes and benzene molecules, at 3.16-3.37 and 2.91-3.13 A˚, respectively. Complex 2 crystallizes in the space group P21/c, with the asymmetric unit containing two supermolecules of [calix[5]arene∩benzene]. The benzene molecule sits in the cavity with its aromatic ring directed toward the phenolic oxygens of the calix[5]arene. The distance from the center of the benzene molecule to a plane containing the five phenolic oxygens is 3.94 and 3.90 A˚ for supermolecules 1 and 2, respectively, with both of these distances being slightly shorter than for the R polymorph, and thus the molecule resides deeper in the cavity relative to this complex. The calix[5]arene molecules are in a slightly pinched cone formation, with the angles between the least-squares planes of the “O” centers and phenyl rings varying from 127.3 to 143.9° for supermolecule 1, and 130.0 to 144.0° for supermolecule 2. The pinched conformation is associated with interplay with a neighboring calix[5]arene molecule, in addition to the benzene molecule in the cavity of the calix[5]arene. For supermolecule 1, the CH 3 3 3 π interaction distances between the phenyl rings of the calix[5]arene and the benzene vary from 2.67 to 3.05 A˚, whereas for supermolecule 2 these distances vary from 2.68 to 2.97 A˚, Figure 2A. The supermolecules pack into an alternating array of calix[5]arenes, stacked in a back-to-back type fashion down both the a and b axes. Down the b axis there is a 2-fold symmetry axis that cuts through the plane created by the phenolic oxygens of the calix[5]arenes. A projection down the c axis shows that the calix[5]arenes are organized into layers, Figure 2B, as opposed to the traditional bilayer arrangement of calixarenes in general.26 The layers are made up of four uniquely oriented calix[5]arenes in an up, down, down, up fashion, Figure 2B with neighboring calix[5]arenes of similar orientation separated by glide planes. The distance between layers is 9.62 A˚ ((0.02), as measured between similar molecules in different layers. Notable interactions between the supermolecules within these layers are due to H 3 3 3 H contacts, where methylene protons from one “up” oriented calix[5]arene interact with methylene protons from a neighboring “down” oriented calix[5]arene, at a distance of 2.38 A˚. CH 3 3 3 π interactions are also present within the layers, with a meta-hydrogen from an “up” calix[5]arene interacting with a phenyl ring from a “down” calix[5]arene, and an interaction that arises between a para-hydrogen and a phenyl ring from two similarly oriented

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Figure 3. Complex 3: (A) The asymmetric unit, showing the endo and exo benzene molecules and close host-guest contacts, and (B) packing projected down the c axis, showing the layered arrangement of the calix[5]arenes and the S-shaped motif.

calix[5]arenes. These interactions have CH 3 3 3 π distances of 3.32 and 3.34 A˚, respectively. Some π 3 3 3 π stacking is also present throughout the layers, at a distance of 3.93 A˚. Complex 3 crystallizes in the space group P21/n, with the asymmetric unit comprised of one calix[5]arene molecule and two benzene molecules, one endo relative to the calix[5]arene, the other exo. The exo benzene interacts with the calix[5]arene through a H 3 3 3 H close contact with the methylene hydrogen of the calix[5]arene at 2.45 A˚. The distance from the benzene molecule centroid to a plane containing the phenolic oxygens is 3.85 A˚, and thus the benzene molecule is deeper in the cavity in complex 3 relative to that in either the R or β polymorphs. CH 3 3 3 π interactions are present in complex 3 between the calix[5]arene and endo benzene, with distances ranging from 2.75 to 3.02 A˚. The conformation of this calix[5]arene has the least pinched of all the structures, with the angles between the least-squares planes of the “O” centers and phenyl rings varying from only 133.6 to 142.1°. Packing of complex 3 shows back-to-back arrangements of calix[5]arenes when projected down the a and b axes, in a manner similar to that for complex 2. However, projection down the c axis of the structure shows S-shaped channels in between calix[5]arenes, which are also arranged in an S shaped arrangement. Similar to complex 2, the calix[5]arenes are packed into layers as oppositely orientated bilayers, with the distance between the layers being 7.09 A˚. Figure 4 shows the Hirshfeld surfaces and fingerprint plots of the three benzene molecules in the R-polymorph, complex 1. These are crystallographically independent but have similar intermolecular contacts as evident by the similarity in their fingerprint plots and surfaces. The de surface, Figure 4A, shows three major red spots due to two ArH 3 3 3 π and one CH2 3 3 3 π interactions at distances of 2.8 and 3.0 A˚, 2.6 and 3.2 A˚, 2.7 and 3.3 A˚ for molecules 1, 2, and 3, respectively. The C-H 3 3 3 π contacts are viewed as diffuse wing shaped features with a more prominent C-H 3 3 3 π donor than C-H 3 3 3 π acceptor component, Figure 4D. This is consistent with six hydrogen atoms per benzene molecule that can contribute to C-H 3 3 3 π interactions, as opposed to only one C-H 3 3 3 π acceptor contact per benzene molecule. The interactions between supermolecules involve C-H 3 3 3 π acceptor contacts on the benzene molecules and a breakdown of the plots shows 14.0, 14.0, and 13.9% of the benzene surfaces to be involved in such contacts for supermolecules 1, 2, and 3, respectively. The interactions between benzene and calix[5]arene within a supermolecule involves C-H 3 3 3 π donor contacts on the benzene molecule, with contributions of 31.2, 32.9, and 30.4%

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Figure 4. Hirshfeld surfaces and fingerprint plots for the three benzene molecules in complex 1: (A) The de surface of benzene looking into the calix[5]arene cavity, (B) the di surface of benzene looking away from the calix[5]arene cavity, (C) fingerprint plots showing the relative frequency of all intermolecular contacts, and (D) fingerprint plots highlighting the C-H 3 3 3 π interactions.

for supermolecules 1, 2, and 3, respectively. This is shown on the di surface, Figure 4B, with four red spots due to three C-H 3 3 3 π interactions, at distances of 2.7 to 3.0 A˚ for supermolecules 1, 2, and 3; the fourth spot is due to a C-H 3 3 3 π contact at a dihedral angle at the hydrogen atoms 2σ(I)) = 5527, R = 0.1618, wR2 = 0.3625 (A, B = 0.19, 135.00), GOF = 1.002, |ΔFmax| = 1.37(16) e A˚-3. Crystal/refinement details for complex 2 (β-benzene): C41H36O5, M = 608.70, F(000) = 2576 e, monoclinic, P21/c, Z = 8, T = 100(2) K, a = 16.9082(5), b = 23.1298(5), c = 17.4876(5) A˚, β = 109.975(3) °, V = 6427.7(3) A˚3, Dc = 1.258 g/cm3, sin θ/λmax = 0.5946, N(unique) = 11279 (merged from 37255, Rint = 0.0579, Rsig = 0.1687), No (I > 2σ(I)) = 4789, R = 0.0406, wR2 = 0.0483 (A, B = 0.01, 0.00), GOF = 1.001, |ΔFmax| = 0.23(5) e A˚-3. Crystal/refinement details for complex 3: C47H42O5, M = 686.81, F(000) = 1456 e, monoclinic, P21/n, Z = 4, T = 100(2) K, a = 15.3711(2), b = 14.1732(2), c = 16.7267(2) A˚, β = 94.227(1) °, V = 3634.13(8) A˚3, Dc = 1.255 g/cm3, sin θ/λmax = 0.6497, N(unique) = 8302 (merged from 56616, Rint = 0.0371, Rsig = 0.0280), No (I > 2σ(I)) = 6415, R = 0.0462, wR2 = 0.1166 (A, B = 0.07, 1.3), GOF = 1.002, |ΔFmax| = 0.42(5) e A˚-3. Supporting Information Available: Crystallographic information files are available free of charge via the Internet at http://pubs.acs.org.

References (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) (11) (12)

Crystallography

)

The X-ray diffracted intensities were measured from single crystals at about 100 K on an Oxford Diffraction Xcalibur CCD diffractometer using monochromatized Mo-KR (λ = 0.71073 A˚). Data were corrected for Lorentz and polarization effects and absorption correction applied using multiple symmetry equivalent reflections. The structure were solved by direct method and refined on F2 using SHELX-97 crystallographic package28 and X-Seed interface.29 A full matrix leastsquares refinement procedure was used, minimizing w(Fo2 Fc2), with w = [σ2(Fo2) þ (AP)2 þ BP]-1, where P = (Fo2 þ 2Fc2)/3. Agreement factors (R = Σ Fo| - |Fc /Σ|Fo|, wR2 = {Σ[w(Fo2 - Fc2)2]/Σ[w(Fo2)2]}1/2 and GOF = {Σ[w(Fo2 Fc2)2]/(n - p)}1/2 are cited, where n is the number of reflections and p is the total number of parameters refined). Non-hydrogen atoms were refined anisotropically using a unique set of all reflections. The positions of hydrogen atoms calculated from geometrical consideration and their atomic parameters were )

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(13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23)

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(27) Arduini, A.; Casnati, A. Macrocycle Synthesis, 1st ed; Parker, D., Ed.; Oxford University Press: New York, 1996. (28) Sheldrick, G. M. Acta Crystallogr. 2008, A64, 112. (29) Barbour, L. J. J. Supramol. Chem. 2001, 1, 189. (30) Grimwood, D. J.; Jayatilaka, D.; McKinnon, J. J.; Spackman, M. A.; Wolff, S. K. CrystalExplorer; The University of Western Australia, 2008.