Merck molecular force field. IV. Conformational energies and geometries for MMFF94

Journal of Computational Chemistry

Volumn 17, Issue 5-6, 1996, Pages 587-615

  Halgren, Thomas A ^a   Nachbar, Robert B ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001061464     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199604)17:5/6<587::AID-JCC4>3.0.CO;2-Q     Document Type: Article

References (92)

1. Part I: T. A. Halgren, J. Comput. Chem, (this issue).
2. Part II: T. A. Halgren, J. Comput. Chem. (this issue).
3. Part III: T. A. Halgren, J. Comput. Chem. (this issue).
4. Part V: T. A. Halgren, J. Comput. Chem. (this issue).
5. M. K. Holloway, J. M. Wai, T. A. Halgren, P. M. D. Fitzgerald, J. P. Vacca, B. D. Dorsey, R. B. Levin, W. J. Thompson, L. J. Chen, S. J. deSolms, N. Gaffin, A. K. Ghosh, E. A. Giuliani, S. L. Graham, J. P. Guare, R. W. Hungate, T. A. Lyle, W. M. Sanders, T. J. Tucker, M. Wiggins, C. M. Wiscount, O. W. Woltersdorf, S. D. Young, P. L. Darke, and J. A. Zugay, J. Med. Chem., 38, 305-317 (1995).
6. (a) N. L. Allinger, J. Am. Chem. Soc., 89, 8127 (1977);
7. (b) U. Bukert and N. L. Allinger, Molecular Mechanics, American Chemical Society, Washington, DC, 1982;
8. (c) N. L. Allinger and Y. Yuh, QCPE, 12, 395 (1980).
9. N. L. Allinger, Y. H. Yuh, and J.-H. Lu, J. Am. Chem. Soc., 111, 8551-8566 (1989).
10. M. J. Frisch, M. Head-Gordon, H. B. Schlegel, K. Raghavachari, J. S. Binkley, C. Gonzalez, D. J. Defrees, D. J. Fox, R. A. Whiteside, R. Seeger, C. F. Melius, J. Baker, R. L. Martin, L. R. Kahn, J. J. P. Stewart, E. M. Fluder, S. Topiol, and J. A. Pople, Gaussian 88, Gaussian, Inc., Pittsburgh, PA, 1988, as modified at Merck for improved I/O performance by E. M. Fluder.
11. M. J. Frisch, M. Head-Gordon, G. W. Trucks, J. B. Foresman, H. B. Schlegel, K. Raghavachari, M. Robb, J. S. Binkley, C. Gonzalez, D. J. Defrees, D. J. Fox, R. A. Whiteside, R. Seeger, C. F. Melius, J. Baker, R. L. Martin, L. R. Kahn, J. J. P. Stewart, S. Topiol, and J. A. Pople, Gaussian 90 (Revision J), Gaussian, Inc., Pittsburgh, PA, 1990.
12. M. J. Frisch, G. W. Trucks, M. Head-Gordon, P. M. W. Gill, M. W. Wong, J. B. Foresman, B. G. Johnson, H. B. Schlegel, M. A. Robb, E. S. Replogle, R. Gomperts, J. L. Andres, K. Raghavachari, J. S. Binkley, C. Gonzalez, R. L. Martin, D. J. Fox, D. J. Defrees, J. Baker, J. J. P. Stewart, and J. A. Pople, Gaussian 92 (Revision C), Gaussian, Inc., Pittsburgh, PA, 1992.
13. R. Krishnan, M. J. Frisch, and J. A. Pople, J. Chem. Phys., 72, 4244-4245 (1980); R. Krishnan and J. A. Pople, Int. J. Quan. Chem., 14, 91 (1978).
14. R. Krishnan, M. J. Frisch, and J. A. Pople, J. Chem. Phys., 72, 4244-4245 (1980); R. Krishnan and J. A. Pople, Int. J. Quan. Chem., 14, 91 (1978).
15. W. J. Hehre, L. Radom, P. v. R. Schleyer, and J. A. Pople, Ab Initio Molecular Orbital Theory, Wiley, New York, 1986, Chapter 4. The 6-31G* and 6-31 + G** basis sets are also known as 6-31G(d) and 6-31 + G(p, d), respectively.
16. T. H. Dunning Jr., J. Chem. Phys., 55, 716-723 (1971).
17. A. D. McLean and G. S. Chandler, J. Chem. Phys., 72, 5639-5648 (1980).
18. T. H. Dunning Jr., J. Chem. Phys., 90, 1007-1023 (1989).
19. B. Roos and P. Siegbahn, Theoret. Chim. Acta, 17, 199-208 (1970).
20. M. Frisch and J. A. Pople, J. Chem. Phys., 80, 3265-3269 (1984); R. Krioshnan, J. S. Binkley, R. Seeger, and J. A. Pople, J. Chem. Phys., 72, 650-654 (1980).
21. M. Frisch and J. A. Pople, J. Chem. Phys., 80, 3265-3269 (1984); R. Krioshnan, J. S. Binkley, R. Seeger, and J. A. Pople, J. Chem. Phys., 72, 650-654 (1980).
22. 2.
23. A. St.-Amant, W. D. Cornell, T. A. Halgren, and P. A. Kollman, J. Comput. Chem., 16, 1483-1506 (1995).
24. J. P. Bowen, A. Pathiaseril, S. Profeta, Jr., and N. L. Allinger, J. Org. Chem., 52, 5162-5166 (1987).
25. The QCISD(T) (quadratic configuration interaction) method as implemented in Gaussian 92 (ref. 10) includes the fourth-order triples contribution to the energy; these contributions are computed after the QCISD energy has converged.
26. T. H. Dunning Jr. and P. J. Hay, Modern Theoretical Chemistry, Plenum, New York, 1976, Chapter 1.
27. This work was done on the Merck Research Laboratories' Cray YMP8i 4/128.
28. Appendix A is available in Supplementary Material (see footnote * on the first page of this article).
29. As discussed in the "MMFF Torsion Parameters" section, each torsion parameter actually carries a fifth numerical index corresponding to the "torsion type." For simplicity, this dependence is suppressed in the present context.
30. 0 represents the change needed in the MMFF torsional energy contribution.
31. For MM2X, we omitted eight comparisons for structures near the "syn" and "anti" transition states for C-N rotation in N-methylformamide used in parameterizing and evaluating MMFF. MM2X gives reasonable energies for some of these structures, but others collapse to structures not representative of the transition state region. Inclusion of these structures would increase the rms deviation and the rms value for "conformational energies" to 2.07 and 3.99 kcal/mol, respectively.
32. T. Head-Gordon, M. Head-Gordon, M. J. Frisch, C. L. Brooks III, and J. A. Pople, J. Am. Chem. Soc., 113, 5989-5997 (1991).
33. (a) K. Gundertofte, T. Liljefors, P.-O. Norrby, and I. Pettersson, J. Comput. Chem. (in press);
34. (b) K. Gundertofte, J. Palm, I. Petterson, and A. Stamvik, J. Comput. Chem., 11, 200-208 (1991).
35. C. J. Casewit, K. S. Colwell, and A. K. Rappé, J. Am. Chem. Soc., 114, 10035-10046 (1992).
36. F. A. Momany and R. Rone, J. Comput. Chem., 13, 888-900 (1992).
37. S. Ataka, H. Takeuchi, and M. Tasumi, J. mol. Struct., 113, 147-160 (1984).
38. T. Drakenberg and S. Forsen, J. Chem. Soc. Chem. Commun., 1404-1405 (1971).
39. J.-H. Lii and N. L. Allinger, J. Comput. Chem., 12, 186-199 (1991).
40. N. L. Allinger, Z. S. Zhu, and K. Chen, J. Am. Chem. Soc., 114, 6120-6133 (1992).
41. Averages for each of two disparate sets of experimental values cited by: J. P. Bowen, A. Pathiaresil, S. Profeta Jr., and N. L. Allinger, J. Org. Chem., 52, 5162-5166 (1987).
42. K. B. Wiberg and E. Martin, J. Am. Chem. Soc., 107, 5035-5041 (1985).
43. D. A. Dixon and B. E. Smart, J. Phys. Chem., 92, 2729-2733 (1988).
44. D. A. Dixon, N. Matsuzawa, and S. C. Walker, J. Phys. Chem., 96, 10740-10746 (1987).
45. J. R. Durig, S. E. Godbey, and J. F. Sullivan, J. Chem. Phys., 80, 5983-5993 (1984).
46. K. Yamanouchi, M. Sugie, H. Takeo, C. Matsumura, and K. Kuchitsu, J. Phys. Chem., 88, 2315-2320 (1984).
47. Y. Ogawa, S. Imazeki, H. Yamaguchi, H. Matsuura, I. Harada, and T. Shimanouchi, Bull. Chem. Soc. Jpn., 51, 748-767 (1978).
48. N. L. Allinger, M. Rahman, and J.-H. Lii, J. Am. Chem. Soc., 112, 8293-8307 (1990).
49. H. Booth and M. L. Jozefowicz, J. Chem. Soc. Perkin Trans. 2, 895-901 (1976).
50. J. R. Durig, W. E. Bucy, C. J. Wurrey, and L. A. Carreira, J. Phys. Chem., 79, 988-993 (1975).
51. R. K. Kakar and C. R. Quade, J. Chem. Phys., 72, 4300-4307 (1980).
52. F. A. L. Anet and V. J. Basus, J. Am. Chem. Soc., 95, 4424-4426 (1973).
53. Evaluated using Ermer's formulation; cf. O. Ermer, Aspekte von Kraftfeldrechnungen, Wolfgang Baur Verlag, München, 1981, p. 59. We note that the Sro, coefficient of 1.287 following eq. (10b) should be 2.287.
54. J. B. Hendrickson, J. Am. Chem. Soc., 89, 7036-7043 (1967).
55. For the notation used, see J. Dale, Top. Stereochem., 9, 199 (1976).
56. F. A. L. Anet and J. Krane, Isr. J. Chem., 20, 72-83 (1980).
57. N. L. Allinger, K. Chen, and J.-H. Lii, J. Comput. Chem. (this issue).
58. We thank K. Chen and N. L. Allinger for alerting us to the possible role of this conformer and for providing a MM4-optimized geometry prior to publication (ref. 52). In recent work, Anet has referred to this species as "TCTC" (cf. F. A. L. Anet, J. Am. Chem. Soc., 112, 7172 [1990]).
59. A. K. Rappé, C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff, J. Am. Chem. Soc., 114, 10024-10035 (1992).
60. N. L. Allinger, R. S. Grev, B. F. Yates, and H. F. Schaefer III, J. Am. Chem. Soc., 112, 114-118 (1990), and references therein.
61. See K. B. Wiberg, P. R. Rablen, and M. Marquez, J. Am. Chem. Soc., 114, 8654-8668 (1992).
62. N. L. Allinger, F. Li, and L. Yan, J. Comput. Chem., 11, 868-895 (1990).
63. L. A. Carriera, J. Chem. Phys., 62, 3851-3854 (1975).
64. Y. N. Panchenko, A. V. Abramenkov, and C. W. Bock, J. Mol. Struct., 140, 87-92 (1986).
65. C. W. Bock, P. George, M. Trachtman, and M. Zanger, J. Chem. Soc. Perkin Trans. II, 26-34 (1979).
66. K. Wiberg and R. E. Rosenberg, J. Am. Chem. Soc., 112, 1509 (1990).
67. Y. Furakawa, H. Takenchi, I. Harada, and M. Tasumi, Bull. Chem. Soc. Jpn., 56, 392 (1983).
68. D. C. Spellmeyer, P. D. J. Grootenhuis, M. D. Miller, L. F. Kuyper, and P. A. Kollman, J. Phys. Chem., 94, 4483-4491 (1990).
69. M. A. Vincent and I. H. Hillier, Chem. Phys., 140, 35 (1990). Note: Allinger and co-workers (cf. ref. 65) cite an experimental barrier for anisole of 2.4 kcal/mol and reference the article by Vincent and Hillier. However, the barrier cited was in fact obtained by ab initio calculation.
70. N. L. Allinger and L. Yan, J. Am. Chem. Soc., 115, 11918-11925 (1993).
71. J. R. Durig, H. D. Bist, K. Furic, J. Qui, and T. S. Little, J. Mol. Spectrosc., 129, 45-56 (1985).
72. T. Drakenberg, J. Sommer, and R. Jost, J. Chem. Soc., Perkin Trans. II, 363-369 (1980).
73. W. N. Hubbard, D. R. Douslin, J. P. McCullough, D. W. Scott, S. S. Todd, J. F. Messerly, I. A. Hossenlopp, A. George, and G. Waddington, J. Am. Chem. Soc., 80, 3547-3554 (1958).
74. K. Chen and N. L. Allinger, J. Phys. Org. Chem., 4, 659-666 (1991).
75. (a) M.-J. Hwang, T. P. Stockfish, and A. T. Hagler, J. Am. Chem. Soc., 116, 2515-2525 (1994);
76. (b) J. R. Maple, M.-J. Hwang, T. P. Stockfish, U. Dinur, M. Waldman, C. S. Ewig, and A. T. Hagler, J. Comput. Chem., 15, 161-182 (1994).
77. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta Jr., and P. Weiner, J. Am. Chem. Soc., 106, 765-784 (1984).
78. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187-217 (1983).
79. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230-252 (1986).
80. P. Dauber-Osguthoorpe, V. A. Roberts, D. J. Osguthorpe, J. Wolff, M. Genest, and A. T. Hagler, Proteins, 4, 31-47 (1988).
81. J. C. Smith and M. Karplus, J. Am. Chem. Soc., 114, 801-812 (1992).
82. A. K. Rappé and W. A. Goddard III, J. Phys. Chem., 95, 3558-3563 (1991).
83. Y. Sun, D. Spellmeyer, D. A. Pearlman, and P. Kollman, J. Am. Chem. Soc., 114, 6798-6801 (1992); C. I. Bayly and P. A. Kollman, J. Am. Chem. Soc., 115, 9620-9631 (1993).
84. Y. Sun, D. Spellmeyer, D. A. Pearlman, and P. Kollman, J. Am. Chem. Soc., 114, 6798-6801 (1992); C. I. Bayly and P. A. Kollman, J. Am. Chem. Soc., 115, 9620-9631 (1993).
85. i -10 were used in eq. (2) to ensure that the torsion parameters would reproduce the conformational energy differences for cyclohexanol as well as possible.
86. W. L. Jorgensen, J. Chandrasekhar, and J. D. Madura, J. Chem. Phys., 79, 926-935 (1983).
87. The MMFF94 parameters are included in Appendix B in the Supplementary Material for part I (ref. 1) and are available in computer-readable ASCII format.
88. In the current OPTIMOL implementation, these quantities are set to 6 and 136, respectively, to insure that the maximum value computed for CXT will fit within a 32-bit integer word.
89. 1 for citations to some of this work.
90. U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2949-2958 (1989); U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2959-2970 (1989).
91. U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2949-2958 (1989); U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2959-2970 (1989).
92. D. E. Williams, in Reviews in Computational Chemistry, Vol. 2, K. B. Lipkowitz and D. B. Boyd, Eds., VCH, New York, 1991, pp. 219-271.