Low mode search. An efficient, automated computational method for conformational analysis: Application to cyclic and acyclic alkanes and cyclic peptides

Journal of the American Chemical Society

Volumn 118, Issue 21, 1996, Pages 5011-5019

  Kolossváry, István ^a   Guida, Wayne C ^b  

^a BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATIONS; COMPUTER AIDED ANALYSIS; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; PROTEINS;

ACYCLIC PEPTIDES; COMPUTER ASSISTED MOLECULAR MODELING; CONFORMATIONAL ANALYSIS; CYCLIC PEPTIDES; LOW MODE SEARCH;

PARAFFINS;

ALKANE DERIVATIVE; CYCLOALKANE DERIVATIVE; CYCLOPEPTIDE;

ARTICLE; AUTOANALYSIS; CONFORMATION; ENERGY; MOLECULAR MODEL; SURFACE PROPERTY;

EID: 0142236572     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja952478m     Document Type: Article

References (70)

1. The importance of locating saddle points, as well as minima, has been described in the literature. See, for example: (a) Anet, F. A. L. J. Am. Chem. Soc. 1990, 112, 7172. (b) Kolossváry, I.; Guida, W. C. J. Am. Chem. Soc. 1993, 115, 2107.
2. The importance of locating saddle points, as well as minima, has been described in the literature. See, for example: (a) Anet, F. A. L. J. Am. Chem. Soc. 1990, 112, 7172. (b) Kolossváry, I.; Guida, W. C. J. Am. Chem. Soc. 1993, 115, 2107.
3. For reviews, see: (a) Howard, A. E.; Kollman, P. A. J. Med. Chem. 1988, 31, 1669. (b) Leech, A. In Reviews in Computational Chemistry: Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1991; Vol. 2, pp 1-47.
4. For reviews, see: (a) Howard, A. E.; Kollman, P. A. J. Med. Chem. 1988, 31, 1669. (b) Leech, A. In Reviews in Computational Chemistry: Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1991; Vol. 2, pp 1-47.
5. White, D. N. J.; Kitson, D. H. J. Mol. Graphics 1986, 4, 112.
6. Smith, G. M.; Veber, D. F. Biochem. Biophys. Res. Commun. 1986, 134, 907.
7. Fukazawa, Y.; Usui, S.; Uchio, Y.; Shiobara, Y.; Kodama, M. Tetrahedron Lett. 1986, 27, 1825.
8. Lipton, M.; Still, W. C. J. Comput. Chem. 1988, 9, 343.
9. Dammkoehler, R. A.; Karasek, S. F.; Shands, E. F. B.; Marshall, G. R. J. Comput.-Aided Mol. Des. 1989, 3, 3.
10. Goodman, J. M.; Still, W. C. J. Comput. Chem. 1991, 12, 1110.
11. Fine, R. M.; Wang, H.; Shenkin, P. S.; Yarmush, D. L.; Levinthal, C. Proteins: Struct., Funct. Genet. 1986, 1, 342.
12. Shenkin, P. S.; Yarmush, D. L.; Fine, R. M.; Wang, H.; Levinthal, C. Biopolymers 1987, 26, 2053.
13. Chang, G.; Guida, W. C.; Still, W. C. J. Am. Chem. Soc. 1989, 111, 4379.
14. Weinberg, N.; Wolfe, S. J. Am. Chem. Soc. 1994, 116, 9860.
15. Blommers, M. J. J.; Lucasius, C. B.; Kateman, G.; Kaptein, R. Biopolymers 1992, 32, 45.
16. McGarrah, D. B.; Judson, R. S. J. Comput. Chem. 1993, 14, 1385.
17. Judson, R. S.; Jaeger, E. P.; Treasurywala, A. M.; Peterson, M. L. J. Comput. Chem. 1993, 14, 1407.
18. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611.
19. von Freyberg, B.; Braun, W. J. Comput. Chem. 1991, 12, 1065.
20. Wilson, S. R.; Cui, W. Tetrahedron Lett. 1988, 29, 4373.
21. Wilson, S. R.; Cui, W. Biopolymers 1990, 29, 225.
22. Wilson, S. R.; Cui, W.; Moskowitz, J. W.; Schmidt, K. E. J. Comput. Chem. 1991, 12, 342.
23. Guarnieri, F.; Cui, W.; Wilson, S. R. J. Chem. Soc. Chem. Commun. 1991, 1542.
24. Guarnieri, F.; Wilson, S. R. Tetrahedron 1992, 48, 4271.
25. Saunders, M. J. Am. Chem. Soc. 1987, 109, 3150.
26. Saunders, M. J. Comput. Chem. 1989, 10, 203.
27. Saunders, M. J. Comput. Chem. 1991, 12, 645.
28. Ferguson, D. M.; Raber, D. J. J. Am. Chem. Soc. 1989, 111, 4371.
29. Ferguson, D. M.; Glauser, W. A.; Raber, D. J. J. Cumput. Chem. 1989, 10, 903.
30. Weiner, P. K.; Profeta, S.; Wipff, G.; Havel, T.; Kuntz, I. D.; Langridge, R.; Kollman, P. A. Tetrahedron 1983, 39, 1113.
31. Grippen, G. M.; Havel, T. F. Distance Geometry and Molecular Conformation; John Wiley: New York, 1988.
32. Havel, T. F. Prog. Biophys. Mol. Biol. 1991, 56, 43.
33. Peishoff, C. E.; Dixon, J. S. J. Comput. Chem. 1992, 13, 565.
34. Crippen, G. M. J. Comput. Chem. 1992, 13, 351.
35. Sun, Y.; Kollman, P. A. J. Comput. Chem. 1992, 13, 33.
36. Byrne, D.; Li, J.; Platt, E.; Robson, B.; Weiner, P. J. Comput.-Aided Mol. Des. 1994, 8, 67.
37. Goto, H.; Osawa, E. J. Am. Chem. Soc. 1989, 111, 8950.
38. Goto, H.; Osawa, E. Tetrahedron Lett. 1992, 33, 1343.
39. Goto, H.; Osawa, E. J. Chem. Soc., Perkin Trans. 2 1993, 187.
40. Kolossváry, I.; Guida, W. C. J. Comput. Chem. 1993, 14, 691.
41. Gerber, P. R.; Gubernator, K.; Müller, K. Helv. Chim. Acta 1988, 71, 1429.
42. Ghose, A. K.; Sanghvi, Y. S.; Larson, S. B.; Revankar, G. R.; Robins, R. K. J. Am. Chem. Soc. 1990, 112, 3622.
43. Nikiforovich, G. V.; Prakash, O.; Gehrig, C. A.; Hruby, V. J. J. Am. Chem. Soc. 1993, 115, 3399.
44. Gonnella, N. C.; Zhang, X.; Jin, Y.; Prakash, O.; Paris, C. G.; Kolossváry, I.; Guida, W. C.; Bohacek, R. S.; Vlattas, I.; Sytwu, T. Int. J. Peptide Protein Res. 1994, 43, 454.
45. Mierke, D. F.; Kurz, M.; Kessler, H. J. Am. Chem. Soc. 1994, 116, 1042.
46. Burgess, K.; Ho, K.-K.; Pettitt, B. M. J. Am. Chem. Soc. 1995, 117, 54.
47. Cicero, D. O.; Barbato, G.; Bazzo, R. J. Am. Chem. Soc. 1995, 117, 1027.
48. For a discussion of emerging challenges in computational chemistry, see: Stillinger, F. H.; Andersen, H. C.; Auslander, L.; Beveridge, D. L.; Davidson, E. R.; Guida, W. C.; Kollman, P. A.; Lester, W. A.; Martin, Y. C.; Schatz, G. C.; Schlick, T.; Scott, L. R.; Sumners, D. L.; Wolynes, P. G.; Houk, K. N.; Weidman, S. T. Mathematical Challenges from Theoretical/Computational Chemistry; National Academy Press: Washington, DC, 1995.
49. Cerjan, C. J.; Miller, W. H. J. Chem. Phys. 1981, 75, 2800.
50. Simons, J.; Jorgensen, P.; Taylor, H.; Ozment, J. J. Phys. Chem. 1983, 87, 2745.
51. O'Neal, D.; Taylor, H.; Simons, J. J. Phys. Chem. 1984, 88, 1510.
52. Banerjee, A.; Adams, N.; Simons, J.; Shepard, R. J. Phys. Chem. 1985, 89, 52.
53. Baker, J. J. Cumput. Chem. 1986, 7, 385.
54. Saunders, M.; Houk, K. N.; Wu, Y.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. J. Am. Chem. Soc. 1990, 112, 1419.
55. Still, W., C.; Galynker, I. Tetrahedron 1981, 37, 3981.
56. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MacroModel/BatchMin is available from W. Clark Still, Columbia University, New York, NY.
57. Ponder, J. W.; Richards, F. M. J. Comput. Chem. 1987, 8, 1016.
58. Schlick, T.; Overton, M. J. Comput. Chem. 1987, 8, 1025.
59. Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127.
60. Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. J. Am. Chem. Soc. 1989, 111, 8551.
61. Lii, J.-H.; Allinger, N. L. J. Am. Chem. Soc. 1989, 111, 8566.
62. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Sooc. 1984, 106, 765.
63. (61 ) The authors of the CSS paper misquoted our TFLEX/SUMM search results on cycloundecane and cyclododecane in Table 7 of ref 12.
64. The 121 conformers do not include structures containing pyramidal carbon atoms. In contrast to the study described in ref 12, we discarded such structures. Nonetheless, our present study found a number of such fully converged structures with the BatchMin warning message "rejected by distorted sp3 atom".
65. 12
66. 8 was also employed for cyclic structures, but the number of probe structures rejected by torsional memory was negligible compared to the large number of probe structures subject to ring closure violation.
67. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
68. Guarnieri, F.; Still, W. C. J. Comput. Chem. 1994, 15, 1302.
69. Senderowitz, H.; Guarnieri, F.; Still, W. C. J. Am. Chem. Soc. 1995, 117, 8211.
70. 54 program. We have provided the code for LMOD to Professor W. Clark Still. Columbia University, for inclusion in future releases of BatchMin.