Modeling chemical reactions for conformationally mobile systems with force field methods

Journal of Chemical Physics

Volumn 118, Issue 8, 2003, Pages 3523-3531

  Olsen, Per T ^a   Jensen, Frank ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

CALIBRATION; CHEMICAL BONDS; DEGREES OF FREEDOM (MECHANICS); LAGRANGE MULTIPLIERS; POTENTIAL ENERGY;

FORCE FIELD METHODS; TRANSITION STRUCTURES;

ELECTRONIC STRUCTURE;

EID: 0037460604     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1539033     Document Type: Article

References (54)

1. H. Eyring, J. Chem. Phys. 3, 107 (1935); D. G. Truhlar, B. C. Garrett, and S.J. Klippenstein, J. Phys. Chem. 100, 12771 (1996).
2. H. Eyring, J. Chem. Phys. 3, 107 (1935); D. G. Truhlar, B. C. Garrett, and S.J. Klippenstein, J. Phys. Chem. 100, 12771 (1996).
3. R. Czerminski and R. Elber, Int. J. Quantum Chem., Quantum Chem. Symp. 24, 167 (1990); T. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992); G. Henkelman, G. Johannesson, and H. Jonsson, Prog. Theor. Chem. Phys. 5, 269 (2000); G. Henkelman, B. P. Uberuaga, and H. Jonsson, J. Chem. Phys. 113, 9901 (2000).
4. R. Czerminski and R. Elber, Int. J. Quantum Chem., Quantum Chem. Symp. 24, 167 (1990); T. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992); G. Henkelman, G. Johannesson, and H. Jonsson, Prog. Theor. Chem. Phys. 5, 269 (2000); G. Henkelman, B. P. Uberuaga, and H. Jonsson, J. Chem. Phys. 113, 9901 (2000).
5. R. Czerminski and R. Elber, Int. J. Quantum Chem., Quantum Chem. Symp. 24, 167 (1990); T. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992); G. Henkelman, G. Johannesson, and H. Jonsson, Prog. Theor. Chem. Phys. 5, 269 (2000); G. Henkelman, B. P. Uberuaga, and H. Jonsson, J. Chem. Phys. 113, 9901 (2000).
6. R. Czerminski and R. Elber, Int. J. Quantum Chem., Quantum Chem. Symp. 24, 167 (1990); T. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992); G. Henkelman, G. Johannesson, and H. Jonsson, Prog. Theor. Chem. Phys. 5, 269 (2000); G. Henkelman, B. P. Uberuaga, and H. Jonsson, J. Chem. Phys. 113, 9901 (2000).
7. T. Helgaker, Chem. Phys. Lett. 182, 503 (1991); P. Culot, G. Dive, V. H. Nguyen, and J. M. Ghuysen, Theor. Chim. Acta 82, 189 (1992); J. Baker and F. Chan, J. Comput. Chem. 17, 888 (1996); B. Paizs, J. Baker, S. Suhai, and P. Pulay, J. Chem. Phys. 113, 6566 (2000).
8. T. Helgaker, Chem. Phys. Lett. 182, 503 (1991); P. Culot, G. Dive, V. H. Nguyen, and J. M. Ghuysen, Theor. Chim. Acta 82, 189 (1992); J. Baker and F. Chan, J. Comput. Chem. 17, 888 (1996); B. Paizs, J. Baker, S. Suhai, and P. Pulay, J. Chem. Phys. 113, 6566 (2000).
9. T. Helgaker, Chem. Phys. Lett. 182, 503 (1991); P. Culot, G. Dive, V. H. Nguyen, and J. M. Ghuysen, Theor. Chim. Acta 82, 189 (1992); J. Baker and F. Chan, J. Comput. Chem. 17, 888 (1996); B. Paizs, J. Baker, S. Suhai, and P. Pulay, J. Chem. Phys. 113, 6566 (2000).
10. T. Helgaker, Chem. Phys. Lett. 182, 503 (1991); P. Culot, G. Dive, V. H. Nguyen, and J. M. Ghuysen, Theor. Chim. Acta 82, 189 (1992); J. Baker and F. Chan, J. Comput. Chem. 17, 888 (1996); B. Paizs, J. Baker, S. Suhai, and P. Pulay, J. Chem. Phys. 113, 6566 (2000).
11. S. R. Billeter, A. J. Turner, and W. Theil, Phys. Chem. Chem. Phys. 2, 2177 (2000).
12. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
13. A. J. Turner, V. Moliner, and I. H. Williams, Phys. Chem. Chem. Phys. 1, 1323 (1999).
14. D. F. DeTar, J. Am. Chem. Soc. 96, 1255 (1974); D. F. DeTar, D. F. McMullen, and N. P. Luthra, ibid. 102, 4505 (1980).
15. D.F. DeTar, J. Am. Chem. Soc. 96, 1255 (1974); D. F. DeTar, D. F. McMullen, and N. P. Luthra, ibid. 102, 4505 (1980).
16. J. E. Eksterowies and K. N. Houk, Chem. Rev. 93, 2439 (1993).
17. P.-O. Norrby, J. Mol. Struct.: THEOCHEM 506, 9 (2000).
18. A. Warshel, J. Am. Chem. Soc. 102, 6218 (1980); A. Warshel, F. Sussman, and J.-K. Hwang, J. Mol. Biol. 201, 139 (1988); A. Yadav, R. M. Jackson, J. J. Holbrook, and A. Warshel, J. Am. Chem. Soc. 113, 4800 (1991).
19. A. Warshel, J. Am. Chem. Soc. 102, 6218 (1980); A. Warshel, F. Sussman, and J.-K. Hwang, J. Mol. Biol. 201, 139 (1988); A. Yadav, R. M. Jackson, J. J. Holbrook, and A. Warshel, J. Am. Chem. Soc. 113, 4800 (1991).
20. A. Warshel, J. Am. Chem. Soc. 102, 6218 (1980); A. Warshel, F. Sussman, and J.-K. Hwang, J. Mol. Biol. 201, 139 (1988); A. Yadav, R. M. Jackson, J. J. Holbrook, and A. Warshel, J. Am. Chem. Soc. 113, 4800 (1991).
21. Y. Kim, J. C. Corchado, J. Villa, J. Xing, and D. G. Truhlar, J. Chem. Phys. 112, 2718 (2000).
22. A. K. Rappe, M. A. Pietsch, D. C. Wiser, J. R. Hart, L. M. Bormann, and W. M. Skiff, Mol. Eng. 7, 385 (1997).
23. F. Jensen, J. Am. Chem. Soc. 114, 1596 (1992); F. Jensen, J. Comput. Chem. 15, 1199 (1994).
24. F. Jensen, J. Am. Chem. Soc. 114, 1596 (1992); F. Jensen, J. Comput. Chem. 15, 1199 (1994).
25. F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Canfield, G. Chang, T. Hendrickson, and W. C. Still, J. Comput. Chem. 11, 440 (1990).
26. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 98, Ganssian, Pittsburgh, PA, 1998.
27. S. Shaik and A. Shurki, Angew. Chem. Int. Ed. Engl. 38, 286 (1999).
28. F. Jensen, Introduction to Computational Chemistry (Wiley, Chichester, 1998).
29. J. J. P. Stewart, J. Comput. Chem. 10, 209 (1989); J. J. P. Stewart, ibid., 10, 221 (1989).
30. J. J. P. Stewart, J. Comput. Chem. 10, 209 (1989); J. J. P. Stewart, ibid., 10, 221 (1989).
31. P. M. Morse, Phys. Rev. 34, 57 (1929).
32. R. Rydberg, Z. Phys. 73, 376 (1931); P. Huxley and J. N. Murrell, J. Chem. Soc., Faraday Trans. 2 79, 323 (1983).
33. R. Rydberg, Z. Phys. 73, 376 (1931); P. Huxley and J. N. Murrell, J. Chem. Soc., Faraday Trans. 2 79, 323 (1983).
34. J. E. Lennard-Jones, Proc. R. Soc. London, Ser. A 106, 463 (1924).
35. J. R. Hart and A. K. Rappe, J. Chem. Phys. 97, 1109 (1992); T A. Halgren, J. Am. Chem. Soc. 114, 7827 (1992).
36. J. R. Hart and A. K. Rappe, J. Chem. Phys. 97, 1109 (1992); T A. Halgren, J. Am. Chem. Soc. 114, 7827 (1992).
37. T. A. Halgren, J. Comput. Chem. 17, 490 (1996).
38. N. L. Allinger, J. Am. Chem. Soc. 99, 8127 (1977); N. L. Allinger, Y. H. Yuh, and J. H. Lii, ibid. 111, 8551 (1989); N. L. Allinger, K. Chem, and J.-H. Lii, J. Comput. Chem. 17, 669 (1996).
39. N. L. Allinger, J. Am. Chem. Soc. 99, 8127 (1977); N. L. Allinger, Y. H. Yuh, and J. H. Lii, ibid. 111, 8551 (1989); N. L. Allinger, K. Chem, and J.-H. Lii, J. Comput. Chem. 17, 669 (1996).
40. N. L. Allinger, J. Am. Chem. Soc. 99, 8127 (1977); N. L. Allinger, Y. H. Yuh, and J. H. Lii, ibid. 111, 8551 (1989); N. L. Allinger, K. Chem, and J.-H. Lii, J. Comput. Chem. 17, 669 (1996).
41. R. T Pack, J. J. Valentini, C. H. Becker, R. J. Buss, and Y. T. Lee, J. Chem. Phys. 77, 5475 (1982); R. T Pack, J. J. Valentini, and J. B. Cross, ibid., 77, 5486 (1982).
42. R. T Pack, J. J. Valentini, C. H. Becker, R. J. Buss, and Y. T. Lee, J. Chem. Phys. 77, 5475 (1982); R. T Pack, J. J. Valentini, and J. B. Cross, ibid., 77, 5486 (1982).
43. W. D. Cornell, P. Cieplak, C. I. Bayly et al., J. Am. Chem. Soc. 117, 5179 (1995).
44. The well-depth for the AMBER and MMFF force fields is directly the parameter, but the well-depths for the MM2 and MM3 force fields are 1.17ε and 1.12ε, respectively. For comparing well-depths, the MM2 and MM3 ε parameters in Table II should thus be multiplied by a factor of 1.17 and 1.12, respectively.
45. E. Goldstein, B. Beno, and K. N. Houk, J. Am. Chem. Soc. 118, 6036 (1996); K. N. Honk, Y. Li, J. Storer, L. Raimondi, and B. Beno, J. Chem. Soc., Faraday Trans. 90, 1599 (1994).
46. E. Goldstein, B. Beno, and K. N. Houk, J. Am. Chem. Soc. 118, 6036 (1996); K. N. Honk, Y. Li, J. Storer, L. Raimondi, and B. Beno, J. Chem. Soc., Faraday Trans. 90, 1599 (1994).
47. D. A. Hrovat, J. Chen, K. N. Houk, and W. T. Borden, J. Am. Chem. Soc. 122, 7456 (2000); D. A. Hrovat, K. Morokuma, and W. T. Borden, ibid. 116, 1072 (1994).
48. D. A. Hrovat, J. Chen, K. N. Houk, and W. T. Borden, J. Am. Chem. Soc. 122, 7456 (2000); D. A. Hrovat, K. Morokuma, and W. T. Borden, ibid. 116, 1072 (1994).
49. R. L. Vance, N. G. Rondan, K. N. Honk, F. Jensen, W. T. Borden, A. Komornicki, and E. Wimmer, J. Am. Chem. Soc. 110, 2314 (1988); H. Y. Yoo and K. N. Houk, ibid. 119, 2877 (1997).
50. R. L. Vance, N. G. Rondan, K. N. Honk, F. Jensen, W. T. Borden, A. Komornicki, and E. Wimmer, J. Am. Chem. Soc. 110, 2314 (1988); H. Y. Yoo and K. N. Houk, ibid. 119, 2877 (1997).
51. S. Parthiban, G. de Oliveira, and J. M. L. Martin, J. Phys. Chem. A 105, 895 (2001).
52. G. Chang, W. C. Guida, and W. C. Still, J. Am. Chem. Soc. 111, 4379 (1989).
53. G. R. Kneller, Mol. Simul. 7, 113 (1991).
54. M. K. Diedrich, F.-G. Klärner, B. R. Beno, K. N. Houk, H. Senderowitz, and W. C. Still, J. Am. Chem. Soc. 119, 10255 (1997).