A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution

Journal of Chemical Physics

Volumn 123, Issue 12, 2005, Pages

  Takahashi, Hideaki ^a   Kawashima, Yuko ^a   Nitta, Tomoshige ^a   Matubayasi, Nobuyuki ^b  

^a OSAKA UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; ISOMERIZATION; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; POLARIZATION;

QUANTUM MECHANICAL/MOLECULAR MECHANICAL (QM/MM) APPROACH; SOLVATION; SOLVATION FREE ENERGY; THEORY OF ENERGY REPRESENTATION;

QUANTUM THEORY;

EID: 26044444932     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2008234     Document Type: Article

References (48)

1. A. Szabo and N. S. Ostlund, Modern Quantum Chemistry (Macmillan, New York, 1982).
2. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, Oxford, 1987).
3. J. P. Hansen and I. R. McDonald, Theory of Simple Liquids (Academic, London, 1986).
4. H. Takahashi, N. Matubayasi, T. Nitta, and M. Nakahara, J. Chem. Phys. 121, 3989 (2004).
5. Combined Quantum Mechanical and Molecular Mechanical Methods, edited by, J. Gao, and, M. A. Thompson, (American Chemical Society, Washington, D.C. 1998).
6. Combined QM/MM Calculations in Chemistry and Biochemistry, edited by, M. F. Ruiz-Lopez, J. Mol. Struct. 632 (2003), special issue.
7. N. Matubayasi and M. Nakahara, J. Chem. Phys. 113, 6070 (2000).
8. H. Takahashi, T. Hori, T. Wakabayashi, and T. Nitta, Chem. Lett. 3, 222 (2000).
9. H. Takahashi, T. Hori, T. Wakabayashi, and T. Nitta, J. Phys. Chem. A 105, 4351 (2001).
10. H. Takahashi, T. Hori, H. Hashimoto, and T. Nitta, J. Comput. Chem. 22, 1252 (2001).
11. H. Takahashi, H. Hashimoto, and T. Nitta, J. Chem. Phys. 119, 7964 (2003).
12. T. Hori, H. Takahashi, and T. Nitta, J. Chem. Phys. 119, 8492 (2003).
13. H. Takahashi, W. Satou, and T. Nitta, J. Chem. Phys. 122, 044504 (2004).
14. N. Matubayasi and M. Nakahara, J. Chem. Phys. 0021-9606 10.1063/1.1495850 117, 3605 (2002); N. Matubayasi and M. Nakahara, J. Chem. Phys. 118, 2446 (2003).
15. N. Matubayasi and M. Nakahara, J. Chem. Phys. 0021-9606 10.1063/1.1495850 117, 3605 (2002); N. Matubayasi and M. Nakahara, J. Chem. Phys. 118, 2446 (2003).
16. N. Matubayasi and M. Nakahara, J. Chem. Phys. 119, 9686 (2003).
17. R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954).
18. Y. Ding and K. K-Jespersen, Chem. Phys. Lett. 199, 261 (1992).
19. T. N. Truong and E. V. Stefanovich, J. Chem. Phys. 103, 3709 (1995).
20. J. Andzelm, C. Kölmel, and A. Klamt, J. Chem. Phys. 103, 9312 (1995).
21. F. R. Tortonda, J. L. Pascual-Ahuir, E. Silla, I. Tuñón, and F. Ramírez, J. Chem. Phys. 109, 592 (1998).
22. M. Nagaoka, N. Okuyama-Yoshida, and T. Yamabe, J. Phys. Chem. A 102, 8202 (1998).
23. I. Tuñón, E. Silla, and M. F. Ruiz-López, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(00)00365-1 321, 433 (2000); I. Tuñón, E. Silla, C. Millot, M. T. C. Martins-Costa, and M. F. Ruiz-López, J. Phys. Chem. A 102, 8673 (1998).
24. I. Tuñón, E. Silla, and M. F. Ruiz-López, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(00)00365-1 321, 433 (2000); I. Tuñón, E. Silla, C. Millot, M. T. C. Martins-Costa, and M. F. Ruiz-López, J. Phys. Chem. A 102, 8673 (1998).
25. Q. Cui, J. Chem. Phys. 117, 4720 (2002).
26. J. S. Gaffney, R. C. Pierce, and L. Friedman, J. Am. Chem. Soc. 99, 4293 (1977).
27. P. Haberfield, J. Chem. Educ. 57, 346 (1980).
28. G. Wada, E. Tamura, M. Okina, and M. Nakamura, Bull. Chem. Soc. Jpn. 55, 3064 (1982).
29. S. Xu, J. M. Nilles, and K. H. Bowen, Jr., J. Chem. Phys. 119, 10696 (2003).
30. J. Tomasi and M. Persico, Chem. Rev. (Washington, D.C.) 94, 2027 (1994).
31. V. Barone and M. Cossi, J. Phys. Chem. A 102, 1995 (1998).
32. A. Klamt and G. Schüürmann, J. Chem. Soc., Perkin Trans. 2 1993, 799 (1993).
33. GAUSSIAN03, Revision B.05, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2003.
34. P. Hohenberg and W. Kohn, Phys. Rev. 136, B864 (1964).
35. W. Kohn and L. Sham, Phys. Rev. 140, A1133 (1965).
36. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
37. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 37, 785 (1988).
38. T. H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989).
39. T. Ono and K. Hirose, Phys. Rev. Lett. 82, 5016 (1999).
40. J. R. Chelikowsky, N. Troullier, and Y. Saad, Phys. Rev. Lett. 72, 1240 (1994).
41. J. R. Chelikowsky, N. Troullier, K. Wu, and Y. Saad, Phys. Rev. B 50, 11355 (1994).
42. X. Jing, N. Troullier, D. Dean, N. Binggeli, J. R. Chelikowsky, K. Wu, and Y. Saad, Phys. Rev. B 50, 12234 (1994).
43. L. Kleinman and D. M. Bylander, Phys. Rev. Lett. 48, 1425 (1982).
44. A. D. Becke, Phys. Rev. A 38, 3098 (1988).
45. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
46. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, Journal 117, 5179 (1995).
47. P. Ewald, Ann. Phys. (Paris) 64, 253 (1921).
48. H. Takahashi, S. Takei, T. Hori, and T. Nitta, J. Mol. Struct.: THEOCHEM 632, 185 (2003).