Ab Initio QM/MM Simulations with a Molecular Orbital-Valence Bond (MOVB) Method: Application to an SN2 Reaction in Water

Journal of Computational Chemistry

Volumn 21, Issue 16, 2000, Pages 1458-1469

  Mo, Yirong ^a   Gao, Jiali ^a  

^a UNIVERSITY OF OVIEDO   (Spain)

Author keywords

Combined QM MM method; Mixed molecular orbital and valence bond method; Monte Carlo simulations of chemical reaction in solution; Solvent effects on SN2 reaction; Valence bond theory

Indexed keywords

EID: 0000342940     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/1096-987X(200012)21:16<1458::AID-JCC4>3.0.CO;2-2     Document Type: Article

References (71)

1. Gao, J. Acc Chem Res 1996, 29, 298.
2. Åqvist, J.; Warshel, A. Chem Rev (Washington) 1993, 93, 2523.
3. Amara, P.; Field, M. J. In Computational Molecular Biology; Leszczynski, J., Ed.; Elsevier: Amsterdam, 1999, p. 1.
4. Bash, P. A.; Field, M. J.; Davenport, R. C.; Petsko, G. A.; Ringe, D.; Karplus, M. Biochemistry 1991, 30, 5826.
5. Gao, J.; Thompson, M. A., Eds.; Combined Quantum Mechanical and Molecular Mechanical Methods; American Chemical Society: Washington, DC, 1998.
6. Alhambra, C.; Wu, L.; Zhang, Z.-Y.; Gao, J. J Am Chem Soc 1998, 120, 3858.
7. Hartsough, D. S.; Merz, K. M., Jr. J Phys Chem 1995, 99, 384.
8. Merz, K. M., Jr.; Banci, L. J Phys Chem 1996, 100, 17414.
9. Assfeld, X.; Ferre, N.; Rivail, J.-L. ACS Symp Ser 1998, 712, 234.
10. Liu, H.; Mueller-Plathe, F.; van Gunsteren, W. F. J Mol Biol 1996, 261, 454.
11. Chatfield, D. C.; Brooks, B. R. J Am Chem Soc 1995, 117, 5561.
12. Alhambra, C.; Gao, J.; Corchado, J. C.; Villa, J.; Truhlar, D. G. J Am Chem Soc 1999, 121, 2253.
13. Wu, N.; Mo, Y.; Gao, J.; Pai, E. F. Proc Natl Acad Sci USA 2000, 97, 2017.
14. Warshel, A.; Levitt, M. J Mol Biol 1976, 103, 227.
15. Gao, J. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH: New York, 1995, p. 119, vol. 7.
16. Singh, U. C.; Kollman, P. A. J Comput Chem 1986, 7, 718.
17. Weiner, S. J.; Singh, U. C.; Kollman, P. A. J Am Chem Soc 1985, 107, 2219.
18. Tapia, O.; Lluch, J. M.; Cardenas, R.; Andres, J. J Am Chem Soc 1989, 111, 829.
19. Bash, P. A.; Field, M. J.; Karplus, M. J Am Chem Soc 1987, 109, 8092.
20. Field, M. J.; Bash, P. A.; Karplus, M. J Comput Chem 1990, 11, 700.
21. Gao, J.; Xia, X. Science 1992, 258, 631.
22. Freindorf, M.; Gao, J. J Comput Chem 1996, 17, 386.
23. Gao, J.; Freindorf, M. J Phys Chem A 1997, 101, 3182.
24. Alhambra, C.; Byun, K.; Gao, J. ACS Symp Ser 1998, 712, 35.
25. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J Am Chem Soc 1984, 106, 3049.
26. Chandrasekhar, J.; Jorgensen, W. L. J Am Chem Soc 1985, 107, 2974.
27. Van der Zwan, G.; Hynes, J. T. J Chem Phys 1983, 78, 4174.
28. Gertner, B. J.; Bergsma, J. P.; Wilson, K. R.; Lee, S.; Hynes, J. T. J Chem Phys 1987, 86, 1377.
29. Bergsma, J. P.; Gertner, B. J.; Wilson, K. R.; Hynes, J. T. J Chem Phys 1987, 86, 1356.
30. Muller, R. P.; Warshel, A. J Phys Chem 1995, 99, 17516.
31. Geissler, P. L.; Dellago, C.; Chandler, D. J Phys Chem B 1999, 103, 3706.
32. Truhlar, D. G.; Garrett, B. C. J Phys Chem B 2000, 104, 1069.
33. Mo, Y.; Gao, J. J Phys Chem A 2000, 104, 3012.
34. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; Wiley: New York, 1991.
35. Mo, Y.; Peyerimhoff, S. D. J Chem Phys 1998, 109, 1687.
36. Mo, Y.; Zhang, Y.; Gao, J. J Am Chem Soc 1999, 121, 5737.
37. Mo, Y.; Gao, J.; Peyerimhoff, S. D. J Chem Phys 2000, 112, 5530.
38. Gerratt, J.; Cooper, D. L.; Karadakov, P. B.; Raimondi, M. Chem Soc Rev 1997, 26, 87.
39. Cooper, D. L.; Gerratt, J.; Raimondi, M. Chem Rev 1991, 91, 929.
40. McWeeny, R. Pure Appl Chem 1989, 61, 2087.
41. Cooper, D. L.; Gerratt, J.; Raimondi, M. Adv Chem Phys 1987, 69, 319.
42. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J Am Chem Soc 1985, 107, 154.
43. Vande Linde, S. R.; Hase, W. L. J Chem Phys 1990, 93, 7962.
44. Zhao, X. G.; Tucker, S. C.; Truhlar, D. G. J Am Chem Soc 1991, 113, 826.
45. Shaik, S. S.; Schlegel, H. B.; Wolfe, S. Theoretical Aspects of Physical Organic Chemistry: The SN2 Mechanism; Wiley: New York, 1992.
46. Shi, Z.; Boyd, R. J. J Am Chem Soc 1991, 113, 2434.
47. Glukhovtsev, M. N.; Pross, B. A.; Radom, L. J Am Chem Soc 1995, 117, 2024.
48. Glukhovtsev, M. N.; Pross, B. A.; Radom, L. J Am Chem Soc 1995, 117, 9012.
49. Gianinetti, E.; Raimondi, M.; Tornaghi, E. Int J Quantum Chem 1996, 60, 157.
50. Mo, Y.; Gao, J. BLW; Version 0.2; SUNY: Buffalo, NY, 1999.
51. Hwang, J. K.; King, G.; Creighton, S.; Warshel, A. J Am Chem Soc 1989, 110, 5297.
52. Hiberty, P. C.; Flament, J. P.; Noizet, E. Chem Phys Lett 1992, 189, 259.
53. Hiberty, P. C.; Humbel, S.; Archirel, P. J Phys Chem 1994, 98, 11697.
54. Shurki, A.; Hiberty, P. C.; Shaik, S. J Am Chem Soc 1999, 121, 822.
55. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J Chem Phys 1998, 108, 1964.
56. Dellago, C.; Bolhuis, P. G.; Chandler, D. J Chem Phys 1999, 110, 6617.
57. Zwanzig, R. J Chem Phys 1961, 34, 1931.
58. Valleau, J. P.; Torrie, G. M. In Modern Theoretical Chemistry; Berne, B. J., Ed.; Plenum: New York, 1977, p. 169, vol. 5.
59. Wu, W.; Mo, Y.; Zhang, Q. Xiamen University: Xiamen, 1998.
60. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. S. GAMESS; Version 11; Iowa State University: Anes, Iowa, 1993.
61. Gao, J. MCQUB; Version 3.0; Buffalo, NY, 1998.
62. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Oritz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Grodon, M.; Gonzalez, C.; Pople, J. A. GAUSSIAN 94; E2 ed.; Gaussian, Inc.: Pittsburgh, PA, 1994.
63. Olmstead, W. N.; Brauman, J. I. J Am Chem Soc 1977, 99, 4219.
64. Pellerite, M. J.; Brauman, J. I. J Am Chem Soc 1980, 102, 5993.
65. Dougherty, R. C.; Roberts, J. D. Org Mass Spectrom 1974, 8, 81.
66. Wladkowski, B. D.; Brauman, J. I. J Phys Chem 1993, 97, 13158.
67. Barlow, S. E.; Van Doren, J. M.; Bierbaum, V. M. J Am Chem Soc 1988, 110, 7240.
68. Shaik, S. S.; Pross, A. J Am Chem Soc 1982, 104, 2708.
69. Shaik, S. S.; Shurki, A. Angew Chem Int Ed 1999, 38, 587.
70. Albery, W. J.; Kreevoy, M. M. Adv Phys Org Chem 1978, 16, 87.
71. Bentzien, J.; Muller, R. P.; Florian, J.; Warshel, A. J Phys Chem B 1998, 102, 2293.