Molecular mechanics for chemical reactions: A standard strategy for using multiconfiguration molecular mechanics for variational transition state theory with optimized multidimensional tunneling

Journal of Physical Chemistry A

Volumn 105, Issue 37, 2001, Pages 8465-8487

  Albu, Titus V ^a   Corchado, José C ^a   Truhlar, Donald G ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MECHANICS;

CHEMICAL REACTIONS; ELECTRONIC STRUCTURE; HYDROGEN; POTENTIAL ENERGY; RATE CONSTANTS;

MOLECULAR DYNAMICS;

EID: 0035922555     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp011951h     Document Type: Article

References (142)

1. Garrett, B. C.; Truhlar, D. G. J. Chem. Phys. 1984, 81, 309.
2. Truhlar, D. G.; Garrett, B. C.; Hipes, P. G.; Kuppermann, A. J. Chem. Phys. 1984, 81, 3542.
3. Truhlar, D. G.; Isaacson, A. D.; Garrett, B. C. In Theory of Chemical Reaction Dynamics; Baer, M., Ed.; CRC Press: Boca Raton, FL, 1985; Vol. 4; p 65.
4. Kreevoy, M. M.; Truhlar, D. G. In Investigation of Rates and Mechanisms of Reactions; Bernasconi, C. F., Ed.; John Wiley & Sons: New York, 1986; Vol. 6; p 13.
5. Tucker, S. C.; Truhlar, D. G. In New Theoretical Concepts Understanding Organic Reactions; J. Bertran, I. G. C., Ed.; Kluwer Academic Publishers: Dordrecht, 1989; Vol. 267; p 291.
6. Truhlar, D. G.; Garrett, B. C.; Klippenstein, S. J. J. Phys. Chem. 1996, 100, 12 771.
7. Warshel, A.; Karplus, M. Chem. Phys. Lett. 1975, 32, 11.
8. Leforestier, C. J. Chem. Phys. 1978, 68, 4406.
9. Truhlar, D. G.; Duff, J. W.; Blais, N. C.; Tully, J. C.; Garrett, B. C. J. Chem. Phys. 1982, 77, 764.
10. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471.
11. Baldridge, K. K.; Gordon, M. S.; Steckler, R.; Truhlar, D. G. J. Phys. Chem. 1989, 93, 5107.
12. Truhlar, D. G.; Gordon, M. S. Science 1990, 249, 491.
13. Galli, G.; Parrinello, M. NATO ASI Ser., Ser. E 1991, 205, 283.
14. Gonzalez-Lafont, A.; Truong, T. N.; Truhlar, D. G. J. Phys. Chem. 1991, 95, 4618.
15. Hartke, B.; Carter, E. A. J. Chem. Phys. 1992, 97, 6569.
16. Lu, D.-h.; Truong, T. N.; Melissas, V. S.; Lynch, G. C.; Liu, Y.-P.; Garrett, B. C.; Steckler, R.; Isaacson, A. D.; Rai, S. N.; Hancock, G. C.; Laudenlale, J. G.; Joseph, T.; Truhlar, D. G. Comput. Phys. Commun. 1992, 71, 235.
17. Liu, Y. P.; Lynch, G. C.; Truong, T. N.; Lu, D. H.; Truhlar, D. G.; Garrett, B. C. J. Am. Chem. Soc. 1993, 115, 2408.
18. Liu, Y. P.; Lu, D. H.; Gonzalez-Lafont, A.; Truhlar, D. G.; Garrett, B. C. J. Am. Chem. Soc. 1993, 115, 7806.
19. Truong, T. N.; Lu, D.-h.; Lynch, G. C.; Liu, Y.-P.; Melissas, V. S.; Stewart, J. J. P.; Steckler, R.; Garrett, B. C.; Isaacson, A. D.; Gonzalez-Lafont, A.; Rai, S. N.; Hancock, G. C.; Joseph, T.; Truhlar, D. G. Comput. Phys. Commun. 1993, 75, 143.
20. Truhlar, D. G. In The Reaction Path in Chemistry: Current Approaches and Perspectives; Heidrich, D., Ed.; Kluwer Dordrecht, 1995; Vol. 16; p 229.
21. Cheng, H. P.; Barnett, R. N.; Landman, U. Chem. Phys. Lett. 1995, 237, 161.
22. Jackels, C. F.; Gu, Z.; Truhlar, D. G. J. Chem. Phys. 1995, 102, 3188.
23. Truong, T. N. J. Chem. Phys. 1995, 102, 5335.
24. Gordon, M. S.; Chaban, G.; Taketsugu, T. J. Phys. Chem. 1996, 100, 11 512.
25. Bueker, H.-H.; Helgaker, T.; Ruud, K.; Uggerud, E. J. Phys. Chem. 1996, 100, 15 388.
26. Cheng, H.-P.; Krause, J. L. J. Chem. Phys. 1997, 107, 8461.
27. Aida, M.; Yamataka, H.; Dupuis, M. Chem. Phys. Lett. 1998, 292, 474.
28. Duncan, W. T.; Bell, R. L.; Truong, T. N. J. Comput. Chem. 1998, 19, 1039.
29. Roberto-Neto, O.; Coitino, E. L.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 4568.
30. Corchado, J. C.; Espinosa-Garcia, J.; Roberto-Neto, O.; Chuang, Y.-Y.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 4899.
31. Bolton, K.; Bernhard Schlegel, H.; Hase, W. L.; Song, K. Phys. Chem. Chem. Phys. 1999, 1, 999.
32. Truong, T. N.; Maity, D. K. Comput. Chem. (Singapore, Singapore) 2000, 5, 211.
33. Pople, J. A.; Binkley, J. S.; Seeger, R. Int. J. Quantum Chem., Symp. 1976, 10, 1.
34. Purvis, G. D.; III; Bartlett, R. J. J. Chem. Phys. 1982, 76, 1910.
35. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. Chem. Phys. Lett. 1989, 157, 479.
36. Hirao, K. Chem. Phys. Lett. 1992, 190, 374.
37. Raghavachari, K.; Anderson, J. B. J. Phys. Chem. 1996, 100, 12 960.
38. Chemical Applications of Density-Functional Theory; Laird, B. B.; Ross, R. B.; Ziegler, T., Eds.; ACS Symposium series 629. American Chemical Society: Washington, DC, 1996.
39. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Rassolov, V.; Pople, J. A. J. Chem. Phys. 1998, 109, 7764.
40. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J. Chem. Phys. 2000, 112, 1125.
41. Fast, P. L.; Sanchez, M. L.; Truhlar, D. G. Chem. Phys. Lett. 1999, 306, 407.
42. Fast, P. L.; Corchado, J. C.; Sanchez, M. L.; Truhlar, D. G. J. Phys. Chem. A 1999, 103, 5129.
43. Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. J. Phys. Chem. A 2000, 104, 4811.
44. Garrett, B. C.; Truhlar, D. G.; Wagner, A. F.; Dunning, T. H., Jr. J. Chem. Phys. 1983, 78, 4400.
45. Bondi, D. K.; Connor, J. N. L.; Garrett, B. C.; Truhlar, D. G. J. Chem. Phys. 1983, 78, 5981.
46. Garrett, B. C.; Abusalbi, N.; Kouri, D. J.; Truhlar, D. G. J. Chem. Phys. 1985, 83, 2252.
47. Garrett, B. C.; Joseph, T.; Truong, T. N.; Truhlar, D. G. Chem. Phys. 1989, 136, 271.
48. Kreevoy, M. M.; Ostovic, D.; Truhlar, D. G.; Garrett, B. C. J. Phys. Chem. 1986, 90, 3766.
49. Truhlar, D. G.; Garrett, B. C. Journal de Chimie Physique 1987, 84, 365.
50. Fernandez-Ramos, A.; Truhlar, D. G. J. Chem. Phys. 2001, 114, 1491.
51. Truhlar, D. G.; Kilpatrick, N. J.; Garrett, B. C. J. Chem. Phys. 1983, 78, 2438.
52. Gonzalez-Lafont, A.; Truong, T. N.; Truhlar, D. G. J. Chem. Phys. 1991, 95, 8875.
53. Melissas, V. S.; Truhlar, D. G. J. Chem. Phys. 1993, 99, 1013.
54. Hu, W. P.; Liu, Y. P.; Truhlar, D. G. J. Chem. Soc., Faraday Trans. 1994, 90, 1715.
55. Ischtwan, J.; Collins, M. A. J. Chem. Phys. 1994, 100, 8080.
56. Nguyen, K. A.; Rossi, I.; Truhlar, D. G. J. Chem. Phys. 1995, 103, 5522.
57. Ishida, T.; Schatz, G. C. J. Chem. Phys. 1997, 107, 3558.
58. Corchado, J. C.; Coitino, E. L.; Chuang, Y.-Y.; Fast, P. L.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 2424.
59. Hollebeek, T.; Ho, T.-S.; Rabitz, H. Annu. Rev. Phys. Chem. 1999, 50, 537.
60. Kim, Y.; Corchado, J. C.; Villa, J.; Xing, J.; Truhlar, D. G. J. Chem. Phys. 2000, 112, 2718.
61. Huang, C.-H.; You, R.-M.; Lian, P.-Y.; Hu, W.-P. J. Phys. Chem. A 2000, 104, 7200.
62. Hollebeek, T.; Ho, T.-S.; Rabitz, H. J. Chem. Phys. 2001, 114, 3940.
63. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
64. Allinger, N. L.; Yuh, Y. H.; Lu, J. H. J. Am. Chem. Soc. 1989, 111, 8551.
65. Lu, J. H.; Allinger, N. L. J. Am. Chem. Soc. 1989, 111, 8566.
66. Lu, J. H.; Allinger, N. L. J. Am. Chem. Soc. 1989, 111, 8576.
67. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 97, 1.
68. Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
69. London, F. Z. Electrochem. 1929, 35, 552.
70. Ellison, F. O. J. Am. Chem. Soc. 1963, 85, 3540.
71. Blais, N. C.; Truhlar, D. G. J. Chem. Phys. 1973, 58, 1090.
72. Tully, J. C. In Semiempirical Methods of Electronic Structure Theory, Part A: Techniques; Segal, G. A., Ed.; Plenum: New York, 1977; p 173.
73. Truhlar, D. G.; Wyatt, R. E. Adv. Chem. Phys. 1977, 36, 141.
74. Kuntz, P. J. In Atom-Molecule Collision Theory; Bernstein, R. B., Ed.; Plenum: New York, 1979; p 79.
75. Faist, M. B.; Muckerman, J. T. J. Chem. Phys. 1979, 71, 225.
76. Vila, C. L.; Kinsey, J. L.; Ross, J.; Schatz, G. C. J. Chem. Phys. 1979, 70, 2414.
77. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218.
78. Zeiri, Y.; Shapiro, M. J. Chem. Phys. 1981, 75, 1170.
79. Pross, A.; Shaik, S. S. Acc. Chem. Res. 1983, 16, 363.
80. Duggan, J. J.; Grice, R. J. Chem. Soc., Faraday Trans. 2 1984, 80, 739.
81. Garrett, B. C.; Truhlar, D. G. J. Chem. Phys. 1985, 82, 4543.
82. Sevin, A. NATO ASI Ser., Ser. C 1986, 176, 235.
83. Bernardi, F.; McDouall, J. J. W.; Robb, M. A. J. Comput. Chem. 1987, 8, 296.
84. Bernardi, F.; Olivucci, M.; McDouall, J. J. W.; Robb, M. A. J. Am. Chem. Soc. 1987, 109, 544.
85. Warshel, A.; Sussman, F.; Hwang, J. K. J. Mol. Biol. 1988, 201, 139.
86. Chang, Y. T.; Miller, W. H. J. Phys. Chem. 1990, 94, 5884.
87. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions; John Wiley & Sons: New York, 1991.
88. Yadav, A.; Jackson, R. M.; Holbrook, J. J.; Warshel, A. J. Am. Chem. Soc. 1991, 113, 4800.
89. Kabbaj, O. K.; Lepetit, M. B.; Malrieu, J. P.; Sini, G.; Hiberty, P. C. J. Am. Chem. Soc. 1991, 113, 5619.
90. Cimiraglia, R. NATO ASI Ser., Ser. B 1992, 299, 11.
91. Chang, Y. T.; Minichino, C.; Miller, W. H. J. Chem. Phys. 1992, 96, 4341.
92. Benneyworth, P. R.; Balint-Kurti, G. G.; Davis, M. J.; Williams, I. H. J. Phys. Chem. 1992, 96, 4346.
93. Aaqvist, J.; Warshel, A. Chem. Rev. 1993, 93, 2523.
94. Shaik, S.; Reddy, A. C. J. Chem. Soc., Faraday Trans. 1994, 90, 1631.
95. Mathis, J. R.; Bianco, R.; Hynes, J. T. J. Mol. Liq. 1994, 61, 81.
96. Kong, Y. S.; Warshel, A. J. Am. Chem. Soc. 1995, 117, 6234.
97. Mestres, J.; Hiberty, P. C. New J. Chem. 1996, 20, 1213.
98. Aaqvist, J. In Computational Approaches to Biochemical Reactivity; Naray-Szabo, G.; Warshel, A., Eds.; Kluwer Academic: Dordrecht, 1997; Vol. 19; p 341.
99. Allison, T. C.; Mielke, S. L.; Schwenke, D. W.; Truhlar, D. G. J. Chem. Soc., Faraday Trans. 1997, 93, 825.
100. Minichino, C.; Voth, G. A. J. Phys. Chem. B 1997, 101, 4544.
101. Cattaneo, P.; Persico, M. Chem. Phys. 1997, 214, 49.
102. Bottoni, A. J. Phys. Chem. A 1998, 102, 10 142.
103. Dobrovsky, I.; Levine, R. D. Chem. Phys. Lett. 1998, 286, 155.
104. Kolmodin, K.; Hansson, T.; Danielsson, J.; Aqvist, J. ACS Symp. Ser. 1999, 721, 370.
105. Anglada, J. M.; Besalu, E.; Bofill, J. M.; Crehuet, R. J. Comput. Chem. 1999, 20, 1112.
106. Anglada, J. M.; Besalu, E.; Bofill, J. M.; Crehuet, R. J. Comput. Chem. 1999, 20, 1130.
107. Mo, Y.; Gao, J. J. Phys. Chem. A 2000, 104, 3012.
108. Garrett, B. C.; Truhlar, D. G. J. Phys. Chem. 1979, 83, 2921.
109. Garrett, B. C.; Truhlar, D. G. J. Phys. Chem. 1979, 83, 1079.
110. Garrett, B. C.; Truhlar, D. G. J. Am. Chem. Soc. 1979, 101, 4534.
111. Garrett, B. C.; Truhlar, D. G.; Grev, R. S.; Magnuson, A. W. J. Phys. Chem. 1980, 84, 1730.
112. Truhlar, D. G.; Garrett, B. C. Acc. Chem. Res. 1980, 13, 440.
113. Isaacson, A. D.; Truhlar, D. G. J. Chem. Phys. 1982, 76, 1380.
114. Allison, T. C.; Truhlar, D. G. In Modern Methods for Multidimensional Dynamics Computations in Chemistry; Thompson, D. L., Ed.; World Scientific: Singapore, 1998; p 618.
115. Nguyen, K. A.; Jackels, C. F.; Truhlar, D. G. J. Chem. Phys. 1996, 104, 6491.
116. Chuang, Y.-Y.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 242.
117. Downing, J. W.; Michl, J. In Potential Energy Surfaces and Dynamics Calculations; Truhlar, D. G., Ed.; Plenum: New York, 1981; p 199.
118. Chen, Z. Theor. Chim. Acta 1989, 75, 481.
119. Corchado, J. C.; Kim, Y.; Villa, J.; Albu, T. V.; Xing, J.; Truhlar, D. G. TINKERATE 8.5 University of Minnesota, Minneapolis, 2000.
120. Corchado, J. C.; Chuang, Y.-Y.; Fast, P. L.; Villa, J.; Hu, W.-P.; Liu, Y.-P.; Lynch, G. C.; Nguyen, K. A.; Jackels, C. F.; Melissas, V. S.; Lynch, B. J.; Rossi, I.; Coitiño, E. L.; Fernandez-Ramos, A.; Steekler, R.; Garrett, B. C.; Isaacson, A. D.; Truhlar, D. G. POLYRATE 8.5.1 University of Minnesota, Minneapolis, 2000.
121. Ponder, J. W. TINKER 3.5 Washington University, St. Louis, MO, 1997.
122. Corchado, J. C.; Chuang, Y.-Y.; Coitiño, E. L.; Truhlar, D. G. GAUSSRATE 8.6 University of Minnesota, Minneapolis, 2000.
123. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian98 (Revision A.9); Gaussian, Inc.: Pittsburgh, PA, 1998.
124. Page, M.; McIver, J. W., Jr. J. Chem. Phys. 1988, 88, 922.
125. Chuang, Y.-Y.; Truhlar, D. G. J. Chem. Phys. 2000, 112, 1221.
126. Glasstone, S.; Laidler, K.; Eyring, H. The Theory of Rate Processes; McGraw-Hill: New York, 1941.
127. Cohen, N.; Westberg, K. R. Int. J. Chem. Kinet. 1986, 18, 99.
128. Cohen, N. Int. J. Chem. Kinet. 1986, 18, 59.
129. Sutherland, J. W.; Michael, J. V.; Klemm, R. B. J. Phys. Chem. 1986, 90, 5941.
130. Herron, J. T. J. Phys. Chem. Ref. Data 1988, 17, 967.
131. Baulch, D. L.; Cobos, C. J.; Cox, R. A.; Esser, C.; Frank, P.; Just, T.; Kerr, J. A.; Pilling, M. J.; Troe, J. J. Phys. Chem. Ref. Data 1992, 21, 411.
132. Clary, D. C. Phys. Chem. Chem. Phys. 1999, 1, 1173.
133. Roberto-Neto, O.; Machado, F. B. C.; Truhlar, D. G. J. Chem. Phys. 1999, 111, 10 046.
134. Bersuker, I. B. The Jahn-Teller Effect and Vibronic Interactions in Modern Chemistry; Plenum Press: New York, 1984.
135. Gonzalez, C.; McDouall, J. J. W.; Schlegel, H. B. J. Phys. Chem. 1990, 94, 7467.
136. Espinosa-Garcia, J.; Garcia-Bernaldez, J. C. Phys. Chem. Chem. Phys. 2000, 2, 2345.
137. Truong, T. N.; Truhlar, D. G. J. Chem. Phys. 1990, 93, 1761.
138. Melissas, V. S.; Truhlar, D. G. J. Chem. Phys. 1993, 99, 3542.
139. Chuang, Y.-Y.; Corchado, J. C.; Truhlar, D. G. J. Phys. Chem. A 1999, 103, 1140.
140. Espinosa-Garcia, J.; Corchado, J. C. J. Chem. Phys. 2000, 112, 5731.
141. Masgrau, L.; Gonzalez-Lafont, A.; Lluch, I. M. J. Chem. Phys. 2001, 114, 2154.
142. CRC Handbook of Chemistry and Physics, 75th ed.; Lide, D. R., Ed.; CRC Press: Boca Raton, FL, 1994.