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The crystal structure of a heptiptycene-chlorobenzene clathrate
Tetrahedron Letters, Vol. 36, No. 14, pp. 2419-2422, 1995
Pergamon
Elsevier Science Ltd Printed in Great Britain 0040-4039/95 $9.50+0.00
0040-4039(95)00318-5
The Crystal Structure of a Heptiptycene-Chlorobenzene
Clathrate
Paloth Venugopalan, Hans-Beat Btirgi,* Natia L. Frank, Kim K. Baidridge, and Jay S. Siegel* San Diego Supereomputer Center, P.O. Box 85608, San Diego, California, 92186-9784; Department of Chemistry, University of California, San Diego, La Jolla, California, 92093-0358, Laboratorium fiir Chemische und MineralogischeKristalographie, Universit~tBern, Bern, Switzerland, CH-3012.
Abstract: Crystalline heptiptycene 1 forms a 1:1 complex with chlorobenzene in which the solvent molecule pack in channels between ribbons of molecules of 1. The X-ray structure shows that 1 is distorted from D3h symmetry in the packing, but show almost no bond localization in the central ring. The calculated moleculargeometryof I (Hartree-Fock(6-31G(D)) and local density methods) compares well with the experimental one. The synthetic methodologies developed by Hart have led to the iptycenes, a large family of triptycenebased hosts with a wide variety of topologies (1-3).! These molecules contain arene-lined cavities, and show a strong ability to complex solvent molecules. For example, tritriptycene 3 forms an ordered 1:1 crystalline complex with acetone in which the carbonyl-carbon lies near the center of a tetra-arene "U-shaped" cavity .2 The structural elucidation of several related molecules has been impeded by disorder in their inclusion complexes, l Crystals of supertriptycene 2, grown from ethyl acetate-tetrachloroethane include disordered solvent to such an extent that it has not been possible to solve the X-ray structure. 3 The preliminary crystallographic investigation of heptiptycene 1,4 did not yield a structural model. 5 We have reinvestigated the crystal structure of 1.chlorobenzene clathrate and performed split-valence level ab initio (HF) and Density Functional Theory (DFT) computations on the molecular structure of 1.
1
2
3
Single crystals of 1. chlorobenzene suitable for diffraction studies were obtained by slow evaporation of a solution of 1 in chlorobenzene at room temperature. The structure was solved by direct methods and refined successfully in space group Cmc21. 6,7 There are 4 mirror symmetric, symmetry related heptiptycene molecules 2419
2420
in the unit cell. They are packed in zigzag ribbons along the c-axis which are separated by channels filled with chiorobermene (figure 1). Within each heptaiptycene molecule, six flanking benzene rings define two clefts. One of these rings acts as a tab which fills a cleft of the next molecule along the ribbon. A solvent of crystallization fills the cleft on the other side of the molecule, exterior to the zigzag ribbon. The hydrogens of chlorobenzene can interact in a T-shape fashion with the aromatic rings of 1, whereas the chlorine of the chiorobenzene juts out away from the host. 8 The chlorobenzenes of consecutive ribbons along the b-axis interleave in a zipper motif. Despite the specificity with which the chiorobenzene molecules pack in the lattice, they are heavily disordered about their principal molecular axis and thus no precise information about the interribbon interactions in the b, c-plane can be obtained.
ribbon
solvent channel {
ribbon
Figure 1. Packing diagrams of 1.chlorobenzene: (a) the b,c-plane (c horizontal), with solvent; (b) the a,b-plane (a horizontal), without solvent. The crystal packing distorts the molecular structure of I away from the idealized D3h form expected for the isolated molecule. Rigorously speaking, the molecular symmetry is reduced to Cs within the crystal lattice, but the molecular geometry is close to C3v. The principal distortion comes from the differential fillings of the two clefts of 1. The rings defining the solvent-filled cleft are bent inward around the solvent molecule while the others are splayed apart by the "tab" inserted from an adjacent host. The widths of the two clefts differ by over 1.2/~ and their depths by about 0.6/~ (figure 2), indicating a large degree of flexibility in the molecular skeleton. The average opening of the two clefts, as gauged by the distance between rim carbon atoms related by the molecular threefold axis, is 7.75/~ [(7.08+7.14+7.18+8.24+8.31+8.53)/6]. DFT and HF computations9 predict a D3h structure for 1. In the former method, the cleft opening is 7.15/~, and its depth is 3.47/~, whereas in the latter method the opening is 7.91 A. and the depth is 3.29/~.
2421
3.6/~{
~
1
1
2
~
°
A
eXO
endo Figure 2.
Distortion of 1 showing differential splaying of triptycene wings in the crystal lattice.
The structure of 1 can also be analyzed for bond alternation in the central benzene ring as a function of annelating substituents.13 This ring of heptiptycene is essentially planar (0.008/~ average deviation from plane). Average lengths of the two constitutionally different C-C bonds in the approximately planar central sixmembered ring differ by 0.022(9)/~ (Table). A comparison with calculated geometries shows that, within the rather large experimental uncertainty, the extent of bond alternation is closely reproduced by DFT methods but overestimated by HF/6-31G(D) theory. 024
G14~ 1 C15
Figure 3. Stereoview of 1 showing atomic numbering and anisotropic displacement parameters (20% probability level). Table 1. Calculated (HF and DFT) and Experimental Bond Lengths in the Central Ring of 1, C-C Bond C1-C1 C2-C3 (endo) C1-C2 C3-C3 (exo) Bond Alternation
HF (6-31G(D)) 1.418 1.363 0.055
Bond Lengths (/~) DF X-ray 1.407 1.414(8),1.396(8), 1.396(8) 1.369 1.375(8), 1.375(8), 1.390(8) 0.038 0.022 (9)
2422
Acknowledgments: This work was supported by the National Science Foundation (CHE-9307582; ASC8902827), the Alfred P. Sloan Foundation (JSS), and the Schweitzerischer Nationalfonds.
References and Notes 1.
Hart, H. Pure and Appl. Chem. 1993, 65, 27-34.
2.
Bashir-Hashemi, A.; Hart, H.; Ward, D. J. Am. Chem. Soc. 1986, 108, 6675-6679.
3.
(a) Shahlai, K.; Hart, H. J. Org. Chem. 1991, 56, 6905-6912, (b) Shahlai, K.; Hart, H. J. Am.
4.
Hart, H.; Shamouilian, S.; Takehira, T.J. Org. Chem. 1981,46, 4427-4432.
Chem. Soc. 1990, 112, 3687-3688. 5.
Huebner, C. F.; Puckett, R. T.; Brzechffa, M.; Schwartz, S. L. Tetrahedron Lett. 1970, 359-362.
6.
X-ray Crystallography: Crystal Data and final coordinates deposited in the Cambridge Crystallographic Data Center. Data Summary for 1.chlorobenzene: Orthorhombic (Cmc20; a = 17.116(2)/~, b = 21.227(4)A, c = 10.619(2)/~; Z = 4; V = 3858(1) A 3, p = 1.179 g/cm3; R(IFI) = 5.6%, wR (IFI)= 7.7% ; 1548 reflections (>6if(F)); and 282 parameters.
7.
Hubner et al. proposed5 that the space group of 1.chlorobenzene might be Cmcm, Cmc2, or C2cm (the middle assignment does not correspond to any of the 230 groups listed in the International Tables).
8.
For a recent discussion of the importance of T-shaped benzene interactions in the orientation of included benzene, see: Klebe, G.; Diederich, F. Phil. Trans. R. Sac. Lond. A. 1993, 345, 37.
9.
Computational Methods: The molecular structure of 1 has been determined with the split valence 631G(D) 10 basis set, at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory. This basis set includes a set of six d polarization functions on all heavy atoms. These calculations were performed with the aid of the analytically determined gradients and the search algorithms contained in GAMESS. 11 Additional calculations were performed on 1 using Density Functional Techniques, employing a double numerical basis set augmented by polarization functions with the aid of numerical methods within DMol. 12 This basis set is comparable in size to the 6-31G(D) basis set.
10. 11. 12. 13.
a) Hariharan, P.C.; Pople, J.A. Theor. Chim. Acta 1982, 28,213. b) Gordon, M.S. Chem. Phys. Lett. 1980, 76, 163. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Jensen, J. H.; Koseki, S.; Gordon, M. S.; Nguyen, K. A.; Windus, T. L.; Elbert, S. T. QCPE Bull. 1990, 10, 52. a) Delley, B. J. Chem. Phys. 1990, 92, 508. DMol is available commercially from BIOSYM Technologies, San Diego, CA. b) Delley, B. J. Chem. Phys. 1991, 94, 7245. The slight degree of bond alternation seen in the central ring of 1 is caused by the exocyclic strain inherent in the triptycene system, commonly referred to as "the Mills-Nixon Effect." For further discussion, see: Frank, N. L.; Siegel, J. S. "Mills-Nixon Effects?" in Adv. Theoretically Interesting Molecules", Thummel, R., Ed., JAI Press, 1995.
(Received in USA 11 January 1995; revised 8 February 1995; accepted 10 February 1995)
Pergamon
Elsevier Science Ltd Printed in Great Britain 0040-4039/95 $9.50+0.00
0040-4039(95)00318-5
The Crystal Structure of a Heptiptycene-Chlorobenzene
Clathrate
Paloth Venugopalan, Hans-Beat Btirgi,* Natia L. Frank, Kim K. Baidridge, and Jay S. Siegel* San Diego Supereomputer Center, P.O. Box 85608, San Diego, California, 92186-9784; Department of Chemistry, University of California, San Diego, La Jolla, California, 92093-0358, Laboratorium fiir Chemische und MineralogischeKristalographie, Universit~tBern, Bern, Switzerland, CH-3012.
Abstract: Crystalline heptiptycene 1 forms a 1:1 complex with chlorobenzene in which the solvent molecule pack in channels between ribbons of molecules of 1. The X-ray structure shows that 1 is distorted from D3h symmetry in the packing, but show almost no bond localization in the central ring. The calculated moleculargeometryof I (Hartree-Fock(6-31G(D)) and local density methods) compares well with the experimental one. The synthetic methodologies developed by Hart have led to the iptycenes, a large family of triptycenebased hosts with a wide variety of topologies (1-3).! These molecules contain arene-lined cavities, and show a strong ability to complex solvent molecules. For example, tritriptycene 3 forms an ordered 1:1 crystalline complex with acetone in which the carbonyl-carbon lies near the center of a tetra-arene "U-shaped" cavity .2 The structural elucidation of several related molecules has been impeded by disorder in their inclusion complexes, l Crystals of supertriptycene 2, grown from ethyl acetate-tetrachloroethane include disordered solvent to such an extent that it has not been possible to solve the X-ray structure. 3 The preliminary crystallographic investigation of heptiptycene 1,4 did not yield a structural model. 5 We have reinvestigated the crystal structure of 1.chlorobenzene clathrate and performed split-valence level ab initio (HF) and Density Functional Theory (DFT) computations on the molecular structure of 1.
1
2
3
Single crystals of 1. chlorobenzene suitable for diffraction studies were obtained by slow evaporation of a solution of 1 in chlorobenzene at room temperature. The structure was solved by direct methods and refined successfully in space group Cmc21. 6,7 There are 4 mirror symmetric, symmetry related heptiptycene molecules 2419
2420
in the unit cell. They are packed in zigzag ribbons along the c-axis which are separated by channels filled with chiorobermene (figure 1). Within each heptaiptycene molecule, six flanking benzene rings define two clefts. One of these rings acts as a tab which fills a cleft of the next molecule along the ribbon. A solvent of crystallization fills the cleft on the other side of the molecule, exterior to the zigzag ribbon. The hydrogens of chlorobenzene can interact in a T-shape fashion with the aromatic rings of 1, whereas the chlorine of the chiorobenzene juts out away from the host. 8 The chlorobenzenes of consecutive ribbons along the b-axis interleave in a zipper motif. Despite the specificity with which the chiorobenzene molecules pack in the lattice, they are heavily disordered about their principal molecular axis and thus no precise information about the interribbon interactions in the b, c-plane can be obtained.
ribbon
solvent channel {
ribbon
Figure 1. Packing diagrams of 1.chlorobenzene: (a) the b,c-plane (c horizontal), with solvent; (b) the a,b-plane (a horizontal), without solvent. The crystal packing distorts the molecular structure of I away from the idealized D3h form expected for the isolated molecule. Rigorously speaking, the molecular symmetry is reduced to Cs within the crystal lattice, but the molecular geometry is close to C3v. The principal distortion comes from the differential fillings of the two clefts of 1. The rings defining the solvent-filled cleft are bent inward around the solvent molecule while the others are splayed apart by the "tab" inserted from an adjacent host. The widths of the two clefts differ by over 1.2/~ and their depths by about 0.6/~ (figure 2), indicating a large degree of flexibility in the molecular skeleton. The average opening of the two clefts, as gauged by the distance between rim carbon atoms related by the molecular threefold axis, is 7.75/~ [(7.08+7.14+7.18+8.24+8.31+8.53)/6]. DFT and HF computations9 predict a D3h structure for 1. In the former method, the cleft opening is 7.15/~, and its depth is 3.47/~, whereas in the latter method the opening is 7.91 A. and the depth is 3.29/~.
2421
3.6/~{
~
1
1
2
~
°
A
eXO
endo Figure 2.
Distortion of 1 showing differential splaying of triptycene wings in the crystal lattice.
The structure of 1 can also be analyzed for bond alternation in the central benzene ring as a function of annelating substituents.13 This ring of heptiptycene is essentially planar (0.008/~ average deviation from plane). Average lengths of the two constitutionally different C-C bonds in the approximately planar central sixmembered ring differ by 0.022(9)/~ (Table). A comparison with calculated geometries shows that, within the rather large experimental uncertainty, the extent of bond alternation is closely reproduced by DFT methods but overestimated by HF/6-31G(D) theory. 024
G14~ 1 C15
Figure 3. Stereoview of 1 showing atomic numbering and anisotropic displacement parameters (20% probability level). Table 1. Calculated (HF and DFT) and Experimental Bond Lengths in the Central Ring of 1, C-C Bond C1-C1 C2-C3 (endo) C1-C2 C3-C3 (exo) Bond Alternation
HF (6-31G(D)) 1.418 1.363 0.055
Bond Lengths (/~) DF X-ray 1.407 1.414(8),1.396(8), 1.396(8) 1.369 1.375(8), 1.375(8), 1.390(8) 0.038 0.022 (9)
2422
Acknowledgments: This work was supported by the National Science Foundation (CHE-9307582; ASC8902827), the Alfred P. Sloan Foundation (JSS), and the Schweitzerischer Nationalfonds.
References and Notes 1.
Hart, H. Pure and Appl. Chem. 1993, 65, 27-34.
2.
Bashir-Hashemi, A.; Hart, H.; Ward, D. J. Am. Chem. Soc. 1986, 108, 6675-6679.
3.
(a) Shahlai, K.; Hart, H. J. Org. Chem. 1991, 56, 6905-6912, (b) Shahlai, K.; Hart, H. J. Am.
4.
Hart, H.; Shamouilian, S.; Takehira, T.J. Org. Chem. 1981,46, 4427-4432.
Chem. Soc. 1990, 112, 3687-3688. 5.
Huebner, C. F.; Puckett, R. T.; Brzechffa, M.; Schwartz, S. L. Tetrahedron Lett. 1970, 359-362.
6.
X-ray Crystallography: Crystal Data and final coordinates deposited in the Cambridge Crystallographic Data Center. Data Summary for 1.chlorobenzene: Orthorhombic (Cmc20; a = 17.116(2)/~, b = 21.227(4)A, c = 10.619(2)/~; Z = 4; V = 3858(1) A 3, p = 1.179 g/cm3; R(IFI) = 5.6%, wR (IFI)= 7.7% ; 1548 reflections (>6if(F)); and 282 parameters.
7.
Hubner et al. proposed5 that the space group of 1.chlorobenzene might be Cmcm, Cmc2, or C2cm (the middle assignment does not correspond to any of the 230 groups listed in the International Tables).
8.
For a recent discussion of the importance of T-shaped benzene interactions in the orientation of included benzene, see: Klebe, G.; Diederich, F. Phil. Trans. R. Sac. Lond. A. 1993, 345, 37.
9.
Computational Methods: The molecular structure of 1 has been determined with the split valence 631G(D) 10 basis set, at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory. This basis set includes a set of six d polarization functions on all heavy atoms. These calculations were performed with the aid of the analytically determined gradients and the search algorithms contained in GAMESS. 11 Additional calculations were performed on 1 using Density Functional Techniques, employing a double numerical basis set augmented by polarization functions with the aid of numerical methods within DMol. 12 This basis set is comparable in size to the 6-31G(D) basis set.
10. 11. 12. 13.
a) Hariharan, P.C.; Pople, J.A. Theor. Chim. Acta 1982, 28,213. b) Gordon, M.S. Chem. Phys. Lett. 1980, 76, 163. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Jensen, J. H.; Koseki, S.; Gordon, M. S.; Nguyen, K. A.; Windus, T. L.; Elbert, S. T. QCPE Bull. 1990, 10, 52. a) Delley, B. J. Chem. Phys. 1990, 92, 508. DMol is available commercially from BIOSYM Technologies, San Diego, CA. b) Delley, B. J. Chem. Phys. 1991, 94, 7245. The slight degree of bond alternation seen in the central ring of 1 is caused by the exocyclic strain inherent in the triptycene system, commonly referred to as "the Mills-Nixon Effect." For further discussion, see: Frank, N. L.; Siegel, J. S. "Mills-Nixon Effects?" in Adv. Theoretically Interesting Molecules", Thummel, R., Ed., JAI Press, 1995.
(Received in USA 11 January 1995; revised 8 February 1995; accepted 10 February 1995)