Predicting crystalline packing arrangements of molecules that form hydrogen-bonded tapes

Journal of the American Chemical Society

Volumn 121, Issue 10, 1999, Pages 2115-2122

  Chin, Donovan N ^a   Palmore, G Tayhas R ^b   Whitesides, George M ^c  

^a Moldyn Inc   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PIPERAZINEDIONE;

ARTICLE; CHEMICAL REACTION; CONFORMATION; CRYSTAL STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; REACTION ANALYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 0033577316     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja983163k     Document Type: Article

References (69)

1. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
2. Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem. Soc. 1992, 114, 5473-5475.
3. Zerkowski, J. A.; Mathias, J. P.; Whitesides, G. M. J. Am. Chem. Soc. 1994, 116, 4305-4315.
4. Zerkowski, J. A.; Whitesides, G. M. J. Am. Chem. Soc. 1994, 116, 4298-4304.
5. Zerkowski, J. A.; MacDonald, J. C.; Seto, C. T.; Wierda, D. A.; Whitesides, G. M. J. Am. Chem. Soc. 1994, 116, 2382.
6. Schwiebert, K. E.; Chin, D. N.; MacDonald, J. C.; Whitesides, G. M. J. Am. Chem. Soc. 1996, 118, 4018-4029.
7. Palacin, S.; Chin, D. N.; Simanek, E. E.; MacDonald, J. C.; Whitesides, G. M.; McBride, M. T.; Palmore, G. T. R. J. Am. Chem. Soc. 1997, 119, 11807-11816.
8. Russell, V. A.; Evans, C. C.; Li, W.; Ward, M. D. Science 1997, 276 (5312), 575-579.
9. Russell, V. A.; Ward, M. D. J. Mater. Chem. 1997, 7, 1123-1133.
10. Russell, V.; Ward, M. D. Chem. Mater. 1996, 8, 1654-1666.
11. Palmore, G. T. R.; McBride, M. T. Chem. Commun. 1998, 145-146.
12. Hollingsworth, M. D.; Ward, M. D. In Structure and Chemistry of the Organic Solid State; Hollingsworth, M. D., Ward, M. D., Eds.; American Chemical Society: Washington, DC, 1994; Vol. 6.
13. Fan, E.; Vicent, C.; Geib, S. J.; Hamilton, A. D. Chem. Mater. 1994, 6, 1113-1117.
14. Aakeroy, C. B.; Nieuwenhuyzen, M. J. Am. Chem. Soc. 1994, 116, 10983-10991.
15. Aakeroy, C. B.; Hughes, D. P.; Nieuwenhuyzen, M. J. Am. Chem. Soc. 1996, 118, 10134-10140.
16. MacGillivray, L. R.; Atwood, J. L. J. Am. Chem. Soc. 1997, 119, 6931-6932.
17. Ghadiri, M. R.; Granja, J. R.; Milligan, R. A.; McRee, D. E.; Khazanovich, N. Nature 1993, 366, 324.
18. Bertolasi, V.; Gilli, P.; Ferretti, V.; Gilli, G. Acta Crystallogr., Sect. B: Struct. Sci. 1998, B54, 50-65.
19. Bernstein, J. J. Phys. D: Appl. Phys. 1993, 26, B66-B76.
20. Haleblian, J.; McCrone, W. J. Pharm. Sci. 1969, 58, 911-929.
21. Gavezzotti, A. J. Am. Chem. Soc. 1991, 113, 4622-4629.
22. Holden, J. R.; Du, Z.; Ammon, H. L. J. Comput. Chem. 1993, 14, 422-437.
23. Perlstein, J. J. Am. Chem. Soc. 1992, 114, 1955-1963.
24. Perlstein, J. J. Am. Chem. Soc. 1994, 116, 455-470.
25. Hofmann, D. W. M.; Lengauer, T. Acta Crystallogr. 1997, A53, 225-235.
26. Wawak, R. J.; Gibson, K. D.; Liwo, A.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 1743-1746.
27. Karfunkel, H. R.; Gdanitz, R. J. J. Comput. Chem. 1992, 13, 1171-1183.
28. Maddox, J. Nature 1988, 335, 201.
29. Desiraju, G. R. Angew. Chem., Int. Ed. Engl. 1995, 34, 2311-2327.
30. Desiraju, G. R. Crystal Engineering: The Design of Organic Solids; Elsevier: New York, 1989.
31. Gavezzotti, A. Acc. Chem. Res. 1994, 27, 309-314.
32. Straub, J. E. In Optimization Techniques with Applications to Proteins; Elber, R., Ed.; World Scientific: Singapore, 1996.
33. Dunitz, J. D.; Bernstein, J. Acc. Chem. Res. 1995, 28, 193.
34. Khoshkhoo, S.; Anwar, J. J. Phys. D: Appl. Phys 1993, 26, B90-B93.
35. Dunitz, J. D. Acta Crystallogr. 1995, B51, 619-631.
36. Bernstein, J. J. Phys. D: Appl. Phys. 1993, 26, B66-B76.
37. McCrone, W. C. In Polymorphism, Fox, D., Labes, M. M., Weissberger, A., Eds.; John Wiley & Sons: New York, 1965; Vol. 2, pp 725-767.
38. Sato, K. J. Phys. D: Appl. Phys. 1993, B77-B84.
39. Sangwal, K. J. Cryst. Growth 1989, 393-405.
40. Chin, D. N.; Zerkowski, J. A.; MacDonald, J. C.; Whitesides, G. M. In Strategies for the Design and Assembly of Hydrogen-bonded Aggregates in the Solid State; Whitesell, J. T., Ed.; John Wiley & Sons: London, 1998. In press.
41. MacDonald, J. C.; Whitesides, G. M. Chem. Rev. 1994, 94, 383-420.
42. For example, torsions where the barriers of rotation are on the order of kT (0.6 kcal/mol).
43. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Clarendon Press: Oxford, 1987.
44. Allen, F. H.; Kennard, O.; Taylor, R. Acc. Chem. Res. 1983, 16, 146-156.
45. Brock, C. P.; Dunitz, J. D. Chem. Mater. 1994, 6, 1118-1127.
46. MSI, QUANTA Molecular Modeling Program; MSI: San Diego, CA, 1995.
47. The molecular frame of reference can be conveniently represented by placing "dummy" atoms on a Cartesian axis proximate to the molecule. These dummy atoms are not included in the calculations of the energy, but their presence conveniently faciliates the molecular rotation commands in CHARMM.
48. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611-6615.
49. Etter, M. C.; Huang, K. S. Chem. Mater. 1992, 4, 824.
50. Etter, M. C.; Urfanczyk-Lipkowska, Z.; Zia-Ebrahimi, M.; Panunto, T. W. J. Am. Chem. Soc. 1990, 112, 8415-8426.
51. Etter, M. C. J. Phys. Chem. 1991, 95, 4601-4610.
52. A value of 90° was chosen to allow some flexibility in the connecting hydrogen bonds.
53. MSI, Cerius 2 Molecular Modeling Program; MSI: San Diego, CA, 1995.
54. Cerius2 was used because it produced better hydrogen-bond geometries during its minimizations than CHARMM/QUANTA4.1.
55. m for some functional groups and does not provide a sufficiently extensive range for general use among many organic compounds.
56. Kitaigorodskii, A. I. Molecular Crystals and Molecules; Academic Press: New York, 1973.
57. Spek, A. L. In Platon 92; Spek, A. L., Ed.; University of Utrecht: Utrecht, Netherlands, 1992.
58. Karfunkel, H. R.; Rohde, B.; Leusen, F. J. J.; Gdanitz, R. J.; Rihs, G. J. Comput. Chem. 1993, 14, 1125-1135.
59. Cullity, B. D. Elements of X-ray Diffraction; Addison-Wesley: Reading, MA, 1978.
60. Powder diffraction patterns were calculated using Cerius2 from Molecular Simulations/Biosym.
61. E.g., the difference plot for the C5DKP structure before and after energy minimization shows enormous differences, the Rp was 62%, yet the structures are visually very close (shown in the Supporting Information).
62. Giacovazzo, C. In Fundamentals of Crystallography; Giacovazzo, C., Ed.; Oxford University Press: Oxford, 1992; pp 109-111.
63. For example, Z = 1 for the space group P1. P1 has two symmetry operators - translation and inversion - which implies that there is one-half of a molecule for the asymmetric unit (number of operatators x molecule in the unit cell = Z). In our prediction program, Z = 1 for the space group P1; that is, one symmetry operator x one molecule for the asymmetric unit = Z.
64. Lehn, J. M. Supramolecular Chemistry; VCH: Weinheim, 1995.
65. Perlstein, J.; Steppe, K.; Vaday, S.; Ndip, E. M. N. J. Am. Chem. Soc. 1996, 118, 8433-8443.
66. Chin, D. N. In Improving the Efficiency Of Predicting Hydrogen-Bonded Organic Molecules; Zaworotko, M., Rodgers, R., Eds.; MRS Transactions: Washington, DC. In press.
67. Price, S. L. Intermolecular Forces-from the Molecular Charge Distribution to the Molecular Packing; Gavezzotti, Ed.; John Wiley & Sons: Chichester, 1997; Vol. 1. pp 31-60.
68. Gavezzotti, G. Theoretical Aspects and Computer Modeling of the Molecular Solid State; Gavezzotti, G., Ed.; John Wiley & Sons: New York, 1997; Vol. 1.
69. Beazley, D. M.; Lomdahl, P. S. Comput. Phys. 1997, 11, 231-237.