Crystal structure prediction by global optimization as a tool for evaluating potentials: Role of the dipole moment correction term in successful predictions

Journal of the American Chemical Society

Volumn 122, Issue 5, 2000, Pages 907-921

  Pillardy, Jaroslaw ^a   Wawak, Ryszard J ^a   Arnautova, Yelena A ^a   Czaplewski, Cezary ^a   Scheraga, Harold A ^a  

^a Department of Population Medicine and Diagnostic Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORMAMIDE; IMIDAZOLE; MALEIC ANHYDRIDE; SUCCINIC ANHYDRIDE;

ARTICLE; CALCULATION; CRYSTAL STRUCTURE; DIPOLE; ELECTRICITY; ENERGY TRANSFER; METHODOLOGY; PREDICTION; PROTEIN FOLDING;

EID: 0034624420     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja9929990     Document Type: Article

References (65)

1. Dzyabchenko, A. V.; Pivina, T. S.; Arnautova, E. A. J. Mol. Struct. 1996, 378, 67.
2. Chaka, A. M.; Zaniewski, R.; Youngs, W.; Tessier, C.; Klopman, G. Acta Crystallogr. 1996, B52, 165.
3. van Eijck, B. P.; Spek, A. L.; Mooij, W. T. M.; Kroon, I. Acta Crystallogr. 1998, B54, 291.
4. Williams, D. E. Acta Crystallogr. 1980, A36, 715.
5. Gavezzotti, A. J. Am. Chem. Soc. 1991, 113, 4622.
6. Holden, J. R.; Du, Z.; Ammon, H. L. J. Comp. Chem. 1993, 14, 422.
7. Dzyabchenko, A. V. Kristallografiya 1989, 34, 226.
8. Gibson, K. D.; Scheraga, H. A. J. Phys. Chem. 1995, 99, 3765.
9. Karfunkel, H. R.; Gdanitz, R. J. J. Comput. Chem. 1992, 13, 1171.
10. Williams, D. E. Acta Crystallogr. 1996, A52, 326.
11. Mooij, W. T. M.; van Eijck, B. P.; Price, S. L.; Verwer, P.; Kroon, J. J. Comput. Chem. 1998, 19, 459.
12. Wawak, R. J.; Gibson, K. D.; Liwo, A.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 1743.
13. Wawak, R. J.; Pillardy, J.; Liwo, A.; Gibson, K. D.; Scheraga, H. A. J. Phys. Chem. A 1998, 102, 2904.
14. Dzyabchenko, A. V.; Agafonov, V. Proc. Hawaii Int. Conf. Syst. Sci. 1995, 28, 237.
15. Molchanova, M. S.; Pivina, T. S.; Arnautova, E. A.; Zefirov, N. S. J. Mol. Struct. 1999, 465, 11.
16. For an average organic crystal structure (10 atoms in the molecule and 4 molecules in the unit cell), the number of interatomic interactions which must be computed approaches 300 000 for a cutoff consisting of three layers of unit cells on each side of the reference unit cell. To obtain a local minimum structure, one needs to carry out several hundred energy and gradient evaluations.
17. Ewald, P. Ann. Phys. 1921, 64, 253.
18. Allen, F. H.; Kennard, O.; Taylor, R. Acc. Chem. Res. 1983, 16, 146.
19. Kitaigorodsky, A. I. Molecular Crystals and Molecules; Academic Press: New York, 1973.
20. Pertsin, A. J.; Kitaigorodsky, A. I. The Atom-Atom Potential Method: Applications to Organic Molecular Solids; Springer: New York, 1987.
21. Belsky, V. K.; Zorkii, P. M. Acta Crystallogr. 1977, A33, 1004.
22. Mighell, A. D.; Himes, V. L.; Rodgers, J. D. Acta Crystallogr. 1983, A39, 737.
23. Chernikova, N. Yu.; Bel'skii, V. K; Zorkii, P. M. J. Struct. Chem. 1991, 31, 661.
24. Padmaja, N.; Ramakumar, S.; Viswamitra, M. A. Acta Crystallogr. 1990, A46, 725.
25. Brock, C. P.; Dunitz, J. D. Chem. Mater. 1994, 6, 1118.
26. Dzyabchenko, A. V. Zh. Strukt. Khim. 1984, 25, 85.
27. Pillardy, J.; Piela, L. J. Phys. Chem. 1995, 99, 11805.
28. Piela, L.; Kostrowicki, J.; Scheraga, H. A. J. Phys. Chem. 1989, 93, 3339.
29. Kostrowicki, J.; Piela, L.; Cherayil, B. J.; Scheraga, H. A. J. Phys. Chem. 1991, 95, 4113.
30. Kostrowicki, J.; Piela, L. J. Optimiz. Theory App. 1991, 69, 269.
31. Pillardy, J.; Olszewski, K. A.; Piela, L. J. Phys. Chem. 1992, 96, 4337.
32. Pillardy, J.; Olszewski, K. A.; Piela, L. J. Mol. Struct. 1992, 270, 277.
33. Amara, P.; Hsu, D.; Straub, J. E. J. Phys. Chem. 1993, 97, 6715.
34. Oresic̀, M.; Shalloway, D. J. Chem. Phys. 1994, 101, 9844.
35. Pappu, R. V.; Hart, R. K.; Ponder, J. W. J. Phys. Chem. B 1998, 102, 725.
36. Wawak, R. J.; Wimmer, M. M.; Scheraga, H. A. J. Phys. Chem. 1992, 96, 5138.
37. Pillardy, J.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. 1999, 103 A, 9370.
38. Pillardy, J.; Liwo, A.; Groth, M.; Scheraga, H. A. J. Phys. Chem. B 1999, 103, 7353.
39. Williams, D. E.; Starr, T. L. Comput. Chem. 1977, 1, 173.
40. Williams, D. E.; Weller, R. R. J. Am. Chem. Soc. 1983, 105, 4143.
41. Williams, D. E.; Houpt, D. J. Acta Crystallogr. 1986, B42, 286.
42. Hagler, A. T.; Huler, E.; Lifson, S. J. Am. Chem. Soc. 1974, 96, 5319.
43. Lifson, S.; Hagler, A. T.; Dauber, P. J. Am. Chem. Soc. 1979, 101, 5111.
44. Momany, F. A.; McGuire, R. F.; Burgess, A. W.; Scheraga, H. A. J. Phys. Chem. 1975, 79, 2361.
45. Gavezzotti, A.; Filippini, G. J. Phys. Chem. 1994, 98, 4831.
46. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
47. Stone, A. J.; Alderton, M. Mol. Phys. 1985, 56, 1047.
48. Le Sueur, C. R.; Stone, A. J. Mol. Phys. 1994, 83, 292.
49. Stone, A. J. Mol. Phys. 1985, 56, 1065.
50. Ewig, C. S.; Thacher, T. S.; Hagler, A. T. J. Phys. Chem. B 1999, 103, 6998.
51. de Leeuw, S. W.; Perram, J. W.; Smith, E. R. Proc. R. Soc. London 1980, A373, 27.
52. Smith, E. R. Proc. R. Soc. London 1981, A375, 475.
53. Deem, M. W.; Newsam, J. M.; Sinha, S. K. J. Phys. Chem. 1990, 94, 8356.
54. van Eijck, B. P.; Kroon, J. J. Phys. Chem. B 1997, 101, 1096.
55. Torrie, B. H.; O'Donovan, C.; Powell, B. M. Mol. Phys. 1994, 82, 643.
56. Martinez-Carrera, S. Acta Crystallogr. 1966, 20, 783.
57. Marsh, R. E.; Ubell, E.; Wilcox, H. E. Acta Crystallogr. 1962, 15, 35.
58. Ehrenberg, M. Acta Crystallogr. 1965, 19, 698.
59. Furberg, S.; Grøgaard, J.; Smedsrud, B. Acta Chem. Scand. 1979, B33, 715.
60. Nahringbauer, I. Acta Crystallogr. 1978, B34, 315.
61. Vedani, A.; Dunitz, J. D. J. Am. Chem. Soc. 1985, 107, 7653.
62. Klebe, G. Mol. Biol. 1994, 237, 212.
63. Lii, J.-H.; Allinger, N. L. J. Comput. Chem. 1998, 19, 1001.
64. Gay, D. M. ACM Trans. Math. Software 1983, 9, 503.
65. Dzyabchenko, A. V. Acta Crystallogr. 1994, B50, 414.