The Quest for Chain-Link Hydrogen-Bonded ... - ACS Publications

The Quest for Chain-Link Hydrogen-Bonded Capsules: Self-Assembly of C-Methyl Calix[4]resorcinarene with 5,5′-Bipyrimidine Charles L. Barnes

CRYSTAL GROWTH & DESIGN 2005 VOL. 5, NO. 3 1049-1053

Department of Chemistry, University of Missouri, Columbia, Missouri 65211

Eric Bosch* Department of Chemistry, Southwest Missouri State University, Springfield, Missouri 65804 Received October 25, 2004;

Revised Manuscript Received January 16, 2005

ABSTRACT: The self-assembly of the tetradentate ligand 5,5′-bipyrimidine with C-methyl calix[4]resorcinarene is reported. The structures of three different three-dimensional hydrogen-bonded networks formed on self-assembly are presented. Two structures contain ligand-bridged resorcinarenes with a “chain-link” capsule motif. The third structure has the resorcinarenes diagonally cross-linked by the bipyrimidine ligand without forming distinct bridged capsules. Introduction The assembly of molecular capsules based on the concomitant formation of multiple hydrogen bonds between smaller molecular components has attracted wide interest recently.1 A particularly attractive building block is C-methyl calix[4]resorcinarene (1 in Chart 1) with eight pendant hydroxyl functional groups.2 This compound often crystallizes with a “bowl-like” conformation that has been exploited in the formation of various hydrogen-bonded networks. MacGillivray and Atwood first demonstrated the formation of “deepcavity” resorcinarenes by self-assembly with pyridine and other N-based heterocycles.3 The subsequent studies of Atwood, MacGillivray, and Coppens have exploited the self-assembly of resorcinarene 1 with various dipyridyl ligands to demonstrate the formation of hydrogenbonded networks that include guest molecules.3-5 For example, the self-assembly of C-methyl calix[4]resorcinarene with 4,4′-bipyridyl was shown to result in the formation of bipyridyl-bridged capsules.4,5 The group of Raston has also studied a variety of substituted resorcinarenes and most notably also reported the formation of a six-component molecular capsule based on selfassembly of 1 with a 4,4′′-terpyridine.6 There are several elegant examples of the self-assembly of resorcinarenes to form capsules. For example, Rissanen demonstrated the encapsulation of ammonium salts inside self-assembled resorcinarene capsules formed by a pair of resorcinarenes7 while Rebek demonstrated the encapsulation of organics in large capsules comprising six resorcinarene molecules.8 We initiated this study with the rather naı¨ve goal of forming chain-linked hydrogenbonded capsules by self-assembly of bipyrimidines with resorcinarenes. Our choice of pyrimidine-based ligands was guided by the presence of four hydrogen bond acceptor sites that we reasoned would allow these bis(pyrimidyl) units to bridge adjacent resorcinarenes, thereby forming a series of chain-linked capsules as shown in Chart 1. * To whom correspondence [email protected].

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The larger goal of the study is to predictably form “chain-link” capsules and modulate the volume and periphery of the cavity in a predictable fashion by changing the size, flexibility, and composition of the spacer between the pyrimidyl units. Our initial studies with 1,2-bis(5′-pyrimidyl)ethyne indicated that the basic idea is feasible but not trivial.9 In that paper we reported three distinct structures based on self-assembly of 1,2-bis(5′-pyrimidyl)ethyne with C-methyl calix[4]resorcinarene. In this paper we report our preliminary studies with the shorter ligand 5,5′-bipyrimidine. Experimental Section C-Methyl calix[4]resorcinarene, 1, and all the solvents were purchased from Aldrich and used as received. 5-Trimethylstannylpyrimidine was synthesized from 5-bromopyrimidine by treatment with lithium powder followed by trimethylstannylchloride: 1H NMR δ: 0.39 (s, 9 H), 8.71 (s, 2 H), 9.13 (s, 1 H). 5,5′-Bipyrimidine, 2, was synthesized by palladiumcatalyzed coupling of 5-bromopyrimidine and 5-trimethylstannylpyrimidine in 64% yield using the published general procedure.10 Synthesis. (a) Complex 3. A mixture of 1 (13.5 mg, 0.03 mmol) and 2 (4.7 mg, 0.03 mmol) and acetonitrile (0.5 mL) in a screw-cap vial was gently warmed until a clear solution was obtained. Diphenylmethane (0.25 mL) was added, and the warm solution allowed to cool to room temperature. After 24 h, rod-shaped crystals had formed. A crystal with dimensions 0.55 × 0.20 × 0.10 mm was selected for X-ray analysis. The remaining crystals were filtered and allowed to dry for 12 h. The experiment was repeated with exactly the same conditions, and the crystals were filtered after 1 week. The crystals were dried in air on filter paper for 5 min, weighed (13.4 mg), and then dissolved in DMSO-d6 for NMR analysis. Based on the NMR integrals listed below, the ratio of the components in the bulk crystalline material was determined to be 1/2/acetonitrile/diphenylmethane ) 1:1:5:1. Note that the peaks are assigned as RE ) 1, BP ) 2, AN ) acetonitrile, and DPM ) diphenylmethane. 1H NMR δ (DMSO-d6): 9.31 (s, 6H, BP), 8.56 (s, 8H, RE), 7.33-7.17 (m, 10H, DPM), 6.77 (s, 4H, RE), 6.15 (s, 4H, RE), 4.46 (q, J ) 6.8 Hz, 4H, RE), 3.94 (s, 2H, DPM), 2.07 (s, 15H, AN), 1.30 (d, J ) 6.8 Hz, 12H, RE). Elemental analyses are not reported because of solvent loss as the crystals slowly became opaque on exposure to the atmosphere.

10.1021/cg049639v CCC: $30.25 © 2005 American Chemical Society Published on Web 03/02/2005

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Barnes and Bosch Chart 1

Table 1. Crystal Data and Structure Refinement for 3-5 CCDC deposit no. formula fw crystal size (mm) crystal system space group a, Å b, Å c, Å R, deg β, deg γ, deg V, Å3 Z µ, mm-1 data/restraints/ parameters goodness-of-fit on F2 R (Fo) RW (Fo) largest diff peak and hole, e.Å-3

253644 C48H49N6O10 869.93 0.50×0.45×0.10 triclinic P1 h 12.1631(12) 12.4330(12) 14.9601(14) 83.957(2) 89.001(2) 83.130(2) 2233.6(4) 2 0.092 9400/3/601

253645 C63H65N9O8 1076.24 0.55×0.20×0.10 triclinic P1 h 15.5432(11) 15.8676(11) 15.9170(11) 94.9260(10) 117.3390(10) 115.9260(10) 2927.4 2 0.082 12618/0/762

253646 C40H43N4O9 723.78 0.45×0.35×0.15 triclinic P1 h 10.2272(8) 10.5430(8) 17.2047(14) 92.3970(10) 91.7660(10) 110.5190(10) 1733.8(2) 2 0.099 7407/0/524

1.028

1.000

1.016

0.0624 0.1688 1.135 and -0.566

0.0652 0.1562 0.422 and -0.309

0.442 0.1021 0.350 and -0.222

(b) Complex 4. A mixture of 1 (14.1 mg, 0.031 mmol) and 2 (5.1 mg, 0.032 mmol) and acetonitrile (1.5 mL) in a screwcap vial was gently warmed until a clear solution was obtained. Nitrobenzene (1.0 mL) was added, and the warm solution allowed to cool to room temperature. After 24 h, crystals had formed. A crystal with dimensions 0.50 × 0.45 × 0.10 mm was selected for X-ray analysis. The remaining crystals were dried in air on filter paper for 5 min, weighed (17.3 mg), and then dissolved in DMSO-d6 for NMR analysis. Based on the NMR integrals listed below, the ratio of the components in the bulk crystalline material was determined to be 1/2/acetonitrile/ nitrobenzene ) 2:1:6:2. Note that the peaks are assigned as RE ) 1, BP ) 2, AN ) acetonitrile, and NB ) nitrobenzene. 1H NMR δ (DMSO-d ): 9.31 (s, 6H, BP), 8.56 (s, 16H, RE), 6 8.25 (d, J ) 8.6 Hz, 4H, NB), 7.83 (br t, J ) 9.4 Hz, 2H, NB), 7.69 (br t, J ) 7.4 Hz, 4H, NB), 6.76 (s, 8H, RE), 6.15 (s, 8H, RE), 4.46 (q, J ) 6.6 Hz, 8H, RE), 2.08 (s, 18H, AN), 1.30 (d, J ) 6.8 Hz, 24H, RE). (c) Complex 5. A mixture of 1 (13.5 mg, 0.03 mmol) and 2 (4.7 mg, 0.03 mmol) and acetonitrile (1.5 mL) in a screw-cap vial was gently warmed until a clear solution was obtained. O-Nitrotoluene (0.3 mL) was added, and the warm solution cooled to room temperature. After 24 h, hexagonal-prismshaped crystals had formed. A crystal with dimensions 0.45 × 0.35 × 0.15 mm was selected for X-ray analysis. NMR analysis indicated that the o-nitrotoluene was not included in the crystalline solid. Identical solids were obtained with 4-nitrotoluene or ethylbenzoate in place of the 2-nitrotoluene. In fact the same crystalline solid was obtained on self-assembly of 1 (14.9 mg, 0.033 mmol) and 2 (5.5 mg, 0.033 mmol) and acetonitrile (1.5 mL). The crystals were dried in air on filter paper for 5 min, weighed (12.6 mg), and then dissolved in DMSO-d6 for NMR analysis. Based on the NMR integrals listed below, the ratio of the components in the bulk crystalline material was determined to be 1/2/acetonitrile ) 2:1:4. Note that the peaks are assigned as RE ) 1, BP ) 2, and AN ) acetonitrile. 1H NMR δ (DMSO-d6): 9.31 (s, 6H, BP), 8.56 (s, 16H, RE), 6.76 (s, 8H, RE), 6.15 (s, 8H, RE), 4.46 (q, J ) 6.4 Hz, 8H, RE), 2.08 (s, 12H, AN), 1.30 (d, J ) 7.0 Hz, 24H, RE).

Crystallography. In each case, crystals suitable for singlecrystal X-ray analysis were culled directly from the respective reaction mixtures. The X-ray data for each of the complexes described herein were collected on a Siemens CCD area detector-equipped diffractometer with Mo KR radiation. The structures were solved using SHELXS-9711 and refined using SHELXL-97.12 Hydrogen atoms were included in the calculated positions. The crystallographic data are collected in Table 1.

Results and Discussion A series of crystals were grown in a similar way: the bipyrimidine and resorcinarene were dissolved in warm acetonitrile, and then a second solvent (guest) was added and the mixture allowed to cool to room temperature. Large crystals were grown in this way from acetonitrile mixed with diphenylmethane (complex 3), nitrobenzene (complex 4), 2-nitrotoluene (complex 5), 4-nitrotoluene, 4-nitroanisole 4-chlorotoluene, isopropylbenzoate, methylbenzoate, and ethylbenzoate. In the structure of complex 3, there is one unique C-methyl calix[4]resorcinarene, one unique diphenylmethane, five unique acetonitrile molecules, and one unique 5,5′-bipyrimidine molecule. The resorcinarene adopts a symmetric bowl-shaped conformation with four intramolecular hydrogen bonds and two phenol hydrogen bond donors at opposite ends of the molecule.13 The four unique intramolecular hydrogen bonds have O- - -O and O- - -H distances in the range 2.8052.888(3) Å and 1.888 and 2.019 Å, respectively. The O-H- - -O angles range between 153.96 and 177.61°. Two resorcinarenes face each other to form a capsulelike structure bridged by a pair of 5,5′-bipyrimidine ligands on each side. It is noteworthy that the ligands are cofacially π-stacked in pairs with a centroidcentroid distance of adjacent pyrimidine rings of

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Figure 1. (A-C) Three mutually orthogonal views showing one of the string of linked capsules in complex 3. Two C-methyl calix[4]resorcinarenes are bridged by two 5,5′-bipyrimidyl ligands to form a molecular-sized capsule that contains four acetonitrile molecules (ref 14).

Figure 2. View of three capsules from one infinite chain of bipyrimidine-linked capsules.

4.07 Å and an interplanar distance of approximately 3.96 Å. These distances are similar to those observed for the related C-methyl resorcinarene complexes with 1,2-bis(5′-pyrimidyl)ethyne where we observed an interplanar distance of 3.88 Å.9 Coppens reported similar interplanar distances between the terpyridyl ligands in networks formed between C-methyl calix[4]resorcinarene and 2,4,6-tris(4-pyridyl)-1,3,5-triazine.5g These capsules are then linked together to form “chain-linked-capsules”. There are four, rather loosely packed, acetonitrile molecules included within each capsule as shown in Figure 1. The bipyrimidines bridge adjacent capsules to form extended chain-linked capsules as shown in Figure 2. There are four unique pyrimidine-phenol hydrogen bonds, O(3)-H(30)- - -N(2), O(4)-H(40)- - -N(3), O(7)-H(70)- - -N(4), and O(8)-H(80)- - -N(1) with O-N distances of 2.785(3), 2.782(7), 2.791(4), and 2.790(3) Å and H-N distances of 1.892, 1.876, 2.027, and 1.836 Å, respectively. The O-H- - -N angles are 177.61, 170.97, 170.96, and 166.65°, respectively. The diphenylmethanes are paired and form a dimeric unit that includes two C-H- - -π interactions as shown in Figure 4A. The H-centroid distance is 2.795 Å with a C-H- - -centroid angle of 157.9° and thus a C-centroid distance of 3.693 Å. There are two acetonitrile molecules nestled on either side of the plane formed by the pair of coplanar phenyl rings. There is a weak C-H- - -π interaction between the acetonitrile methyl moiety and the phenyl rings minimum with H- - -π distance of approximately 2.73 Å. In the structure of complex 4, there is one unique C-methyl calix[4]resorcinarene, one unique nitrobenzene, and three unique acetonitrile molecules and half of a 5,5′-bipyrimidine molecule is unique. The resorcinarene adopts the bowl-shaped conformation, and two resorcinarenes face each other to form a capsule-like structure that is diagonally bridged on each side by a single 5,5′-bipyrimidine ligand. The bipyrimidines bridge adjacent capsules to form extended chain-linked cap-

Figure 3. View showing the packing of the network 3. The circled areas show the incorporation of the diphenylmethane and acetonitrile molecules in the cavities between adjacent strands of bipyrimidyl-bridged resorcinarenes.

Figure 4. (A) View of the diphenylmethane dimeric unit showing the CH- - -π interactions. (B) Side view of the diphenylmethane dimeric unit showing the pairs of acetonitrile molecules nestled in the cavity.

sules. There are two unique pyrimidine-phenol hydrogen bonds, O(4)-H(40)- - -N(1) and O(7)-H(70)- - -N(2) with O-N distances of 2.741 and 2.716 Å and H-N distances of 1.825 and 1.874 Å, respectively. The O-H- - -N angles are 169.04 and 174.45°, respectively.

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Figure 5. (A, B) Two orthogonal views of the chain-link capsules formed by bipyrimidine-linked C-methyl calix[4]resorcinarenes that enclose a pair of nitrobenzene molecules within each cavity.

Figure 6. (A, B) Two orthogonal views of the pair of encapsulated nitrobenzene molecules showing the π-stacking and dipole-dipole matching.

Figure 8. View of the two eight-membered hydrogen-bonded rings that hold adjacent rows of resorcinarenes together.

Figure 7. (A, B) Two orthogonal views showing the hydrogenbonded connectivity between adjacent rows of resorcinarenes.

of 2.758-2.877 Å and 1.926-2.036 Å, respectively. The O-H- - -O angles vary from 156.47 to 164.98°. The acetonitrile molecules are not involved in any major hydrogen bonding and appear to merely fill the void-space in the three-dimensional structure. We reasoned that a guest slightly larger than nitrobenzene would result in the formation of a chain-linked complex with two bridging 5,5′-bipyrimidine ligands because this arrangement would slightly increase the encapsulated volume. Accordingly we prepared a variety of crystals using slightly larger guests such as 2-nitrotoluene, 4-nitrotoluene, and ethylbenzoate. In all cases, X-ray crystallography revealed that the crystals all had the same unit cell. The structure, 5, was solved from a crystal culled from a reaction mixture containing acetonitrile and 2-nitrotoluene as the two solvents/guests. In this structure there is one unique C-methyl resorcinarene molecule, one-half of a bipyrimidine molecule, two unique acetonitrile molecules, and an adventitious water molecule. The arrangement of the resorcinarenes is very different from our naı¨ve expectations shown in Chart 1. The resorcinarene does adopt the expected symmetric bowl-shaped conformation. Against our expectations, the bipyrimidine molecule bridges two bowlshaped resorcinarene molecules making a diagonal connection between the two resorcinarenes as shown in Figure 9. The water molecule bridges one pyrimidine nitrogen atom to the resorcinarene, while the other nitrogen is directly hydrogen-bonded to the resorcinarene. The pyrimidine-resorcinol hydrogen bond has O- - -N and H- - -N distances of 2.826(2) and 2.019 Å, respectively, with an O-H- - -N angle of 151.21°. The pyrimidinewater hydrogen bond has O- - -N and H- - -N distances of 2.932(3) and 2.050 Å, respectively, with an

Two nitrobenzenes are nestled inside the capsule formed by the bipyrimidine-linked resorcinarenes as shown in the two views in Figure 5. The nitrobenzenes pack in an offset fashion with opposing dipole moments. The nitrobenzenes have a centroid-to-centroid distance of 4.008 Å and an interplanar distance of approximately 3.65 Å. Adjacent chains of the pyrimidine-linked capsules are held together by hydrogen-bonding between two phenol OH groups from each of the neighboring resorcinarenes as shown in Figure 7. There two groups of four phenolic moieties involved in the hydrogen-bonded attachment as shown in Figure 8. There are four unique hydrogen bonds as shown in Figure 2 with O- - -O and O- - -H distances in the range

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encapsulated acetonitrile (#1) hydrogen bonds to the adjacent resorcinarene. Thus the acetonitrile in resorcinarene #2 is hydrogen-bonded to an OH group on resorcinarene #3 with N- - -H and N- - -O distances of 1.852 and 2.731(2) Å, respectively, and an N- - -H-O angle of 171.42°. The results presented here with 5,5′-bipyrimidine when coupled with our earlier results with 1,2-bis(5′-pyrimidyl)ethyne indicate that it is possible to form chain-linked capsules with variable internal volume. We will continue our efforts in this direction with bipyrimidine ligands since there is clearly still a lot of basic work to be done to understand the many factors that control this process in the solid state. Figure 9. (A, B) Two orthogonal views showing the linkages between the pyrimidine ligand, the water molecule, and the two resorcinarenes.

Acknowledgment. We thank the National Science Foundation for financial support of this research (Grant No. 0415711). Supporting Information Available: X-ray crystallographic data in CIF format. This material is available free of charge via the Internet at http://pubs.acs.org.

References

Figure 10. View showing the interactions between adjacent bipyrimidine-linked resorcinarenes and the included water and the two unique acetonitrile molecules.

O-H- - -N angle of 166.69°, while the water resorcinol hydrogen bond has O- - -O and H- - -Ow distances of 2.629(3) and 1.704 Å, respectively, with an O-H- - -Ow angle of 168.31°. Figure 10 shows the complex connectivity where the pairs of resorcinarenes labeled R#1 and R#2 are connected by the pyrimidine and water as shown in Figure 9. The resorcinarenes labeled R#3 and R#4 are connected in the same way. Note that one acetonitrile molecule labeled acetonitrile#1 is encapsulated within each resorcinarene and the second acetonitrile is placed vertically above the resorcinarene methyl groups. The terminal N of acetonitrile#2 is approximately 2.8 Å away from the methyl hydrogen atoms. The complex interconnection of the resorcinarenes labeled R#2 and R#3 involves π-stacking and resorcinol-resorcinol hydrogen bonding. Thus the pyrimidine ring is π-stacked with one resorcinarene ring as shown in Figure 9 as the π-π interaction. The centroid-centroid distance between the aromatic rings is 3.583 Å, and the interplanar distance is approximately 3.5 Å. There are two O-H- - -O hydrogen bonds between the resorcinarenes #2 and #3 with an O- - -O distance of 2.945(2) Å and an O- - -H distance of 2.122 Å with an O-H- - -O angle of 161.87°. In addition the

(1) (a) See for example: Calixarenes in Action; Mandolini, L., Ungaro, R., Eds.; Imperial College Press: London, 2000. (b) Shivanyuk, A.; Rebek, J., Jr. Chem. Commun. 2002, 2326. (c) Alarjarin, M.; Pastor, A.; Orenes, R.-A.; Steed, J. W. J. Org. Chem. 2002, 67, 7091. (d) Zadmard, R.; Schrader, T.; Grawe, T.; Kraft, A. Org. Lett. 2002, 4, 1687. (2) For a review see: Timmerman, P.; Verboom, W.; Reinhoudt, D. N. Tetrahedron 1996, 52, 2663-2704. (3) MacGillivray, L. R.; Atwood, J. L. Chem. Commun. 1999, 181-182. (b) MacGillivray, L. R.; Reid, J. L.; Ripmeester, J. A. CrystEngComm 1999, 1. (4) (a) MacGillivray, L. R.; Reid, J. L.; Ripmeester, J. A. Chem. Commun. 2001, 1034. (b) MacGillivray, L. R.; Reid, J. L.; Ripmeester, J. A. CrystEngComm 1999, 1. (c) MacGillivray, L. R.; Papaefstathiou, G. S.; Reid, J. L.; Ripmeester, J. A. Cryst. Growth Des. 2001, 1, 373. (d) MacGillivray, L. R.; Diamente, P. R.; Reid, J. L.; Ripmeester, J. A. Chem. Commun. 2000, 359. (e) Frisic, T.; MacGillivray, L. R. J. Organomet. Chem. 2003, 666, 43. (5) (a) Ma, B. Q.; Zhang, Y.; Coppens, P. CrystEngComm 2001, 20, 1. (b) Ma, B. Q.; Zhang, Y.; Coppens, P. Cryst. Growth Des. 2001, 1, 271. (c) Ma, B. Q.; Coppens, P. Chem. Commun. 2003, 5412. (d) Ma, B. Q.; Coppens, P. Chem. Commun. 2003, 504. (e) Ma, B. Q.; Coppens, P. Chem. Commun. 2004, 932. (f) Ma, B. Q.; Zhang, Y.; Coppens, P. Cryst. Growth Des. 2002, 2, 7. (g) Ma, B. Q.; Coppens, P. Cryst. Growth Des. 2004, 4, 211. (h) Ma, B. Q.; Zhang, Y.; Coppens, P. J. Org. Chem. 2003, 68, 9467. (6) (a) Cave, G. W. V.; Hardie, M. J.; Roberts, B. A.; Raston, C. L. Eur. J. Org. Chem. 2001, 3227. (b) Cave, G. W. V.; Raston, B. A. Eur. J. Chem. 2004, 10, 279. (7) (a) Mansikkama¨ki, H.; Nissinen, M.; Schalley, C. A.; Rissanen, K. New J. Chem. 2003, 88. (b) Mansikkama¨ki, H.; Nissinen, M.; Rissanen, K. Chem. Commun. 2002, 1902. (8) Shivanyuk, A.; Rebek, J., Jr. J. Am. Chem. Soc. 2003, 125, 3432. (9) Georgiev, I.; Barnes, C. L.; Draganjac, M.; Bosch, E. Cryst. Growth Des. 2004, 4, 235. (10) Sandosham, J.; Undheim, K. Tetrahedron 1994, 50, 275. (11) Sheldrick, G. M. SHELXS-97, Crystal Structure Solution; University of Go¨ttingen: Go¨ttingen, Germany, 1997. (12) Sheldrick, G. M. SHELXL-97, Crystal Structure Refinement; University of Go¨ttingen: Go¨ttingen, Germany, 1997. (13) Georgiev, I.; Bosch, E.; Barnes, C. L. J. Chem. Cryst. 2004, 34, 859. (14) Drawings prepared using the program X-seed developed by L. Barbour, see: Barbour, L.; Atwood, J. A. Cryst. Growth Des. 2003, 3, 3.

CG049639V