Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach

Journal of Chemical Physics

Volumn 128, Issue 12, 2008, Pages

  Zeng, Xiancheng ^a   Hu, Hao ^a   Hu, Xiangqian ^a   Cohen, Aron J ^a   Yang, Weitao ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; ELECTRON TRANSITIONS; FREE ENERGY; MOLECULAR DYNAMICS; QUANTUM THEORY;

ELECTRON TRANSFER (ET) REACTIONS; FRACTIONAL NUMBER;

MOLECULAR MECHANICS;

FERRIC ION; FERROUS ION; RUTHENIUM; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ELECTRON; OXIDATION REDUCTION REACTION; QUANTUM THEORY;

COMPUTER SIMULATION; ELECTRONS; FERRIC COMPOUNDS; FERROUS COMPOUNDS; MODELS, CHEMICAL; OXIDATION-REDUCTION; QUANTUM THEORY; RUTHENIUM; WATER;

EID: 41549112442     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2832946     Document Type: Article

References (69)

1. M. Bixon and J. Jortner, Adv. Chem. Phys. 0065-2385 10.1002/ 9780470141656.ch1 106, 1 (1999).
2. R. A. Marcus, J. Chem. Phys. 0021-9606 10.1063/1.1742723 24, 966 (1956).
3. R. A. Marcus, J. Chem. Phys. 0021-9606 10.1063/1.1742724 24, 979 (1956).
4. R. A. Marcus, J. Chem. Phys. 0021-9606 10.1063/1.1743423 26, 867 (1957).
5. R. A. Marcus, J. Chem. Phys. 0021-9606 10.1063/1.1743424 26, 872 (1957).
6. E. A. Carter and J. T. Hynes, J. Phys. Chem. 0022-3654 10.1021/j100343a002 93, 2184 (1989).
7. P. Jaque, A. Marenich, C. Cramer, and D. Truhlar, J. Phys. Chem. C 1932-7447 10.1021/jp066765w 111, 5783 (2007).
8. K. Rosso and J. Rustad, J. Phys. Chem. A 1089-5639 10.1021/jp994164h 104, 6718 (2000).
9. M. Uudsemaa and T. Tamm, J. Phys. Chem. 107, 9997 (2003). 0022-3654
10. A. Warshel, J. Phys. Chem. 0022-3654 10.1021/j100209a016 86, 2218 (1982).
11. A. Warshel and J. -K. Hwang, J. Chem. Phys. 0021-9606 10.1063/1.449981 84, 4938 (1986).
12. J. -K. Hwang and A. Warshel, J. Am. Chem. Soc. 0002-7863 10.1021/ja00237a013 109, 715 (1987).
13. J. K. Hwang, G. King, S. Greighton, and A. Warshel, J. Am. Chem. Soc. 0002-7863 10.1021/ja00224a011 110, 5297 (1988).
14. R. A. Kuharski, J. S. Bader, D. Chandler, M. Sprik, M. L. Klein, and R. W. Impey, J. Chem. Phys. 0021-9606 10.1063/1.454929 89, 3248 (1988).
15. J. Blumberger and M. Sprik, Theor. Chem. Acc. 1432-881X 10.1007/s00214-005-0058-0 115, 113 (2006).
16. R. Car and M. Parrinello, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett. 55.2471 55, 2471 (1985).
17. J. Blumberger and M. Sprik, J. Phys. Chem. B 1089-5647 10.1021/jp036610d 108, 6529 (2004).
18. J. Blumberger, L. Bernasconi, I. Tavernelli, R. Vuilleumier, and M. Sprik, J. Am. Chem. Soc. 0002-7863 10.1021/ja0390754 126, 3928 (2004).
19. J. Blumberger and M. Sprik, J. Phys. Chem. B 1089-5647 10.1021/jp0455879 109, 6793 (2005).
20. Y. Tateyama, J. Blumberger, M. Sprik, and I. Tavernelli, J. Chem. Phys. 0021-9606 10.1063/1.1938192 122, 234505 (2005).
21. J. Blumberger, I. Tavernelli, M. L. Klein, and M. Sprik, J. Chem. Phys. 0021-9606 10.1063/1.2162881 124, 064507 (2006).
22. M. Sulpizi, S. Raugei, J. VandeVondele, P. Carloni, and M. Sprik, J. Phys. Chem. B 1089-5647 10.1021/jp067387y 111, 3969 (2007).
23. A. Warshel and M. Levitt, J. Mol. Biol. 0022-2836 10.1016/0022-2836(76) 90311-9 103, 227 (1976).
24. Y. Zhang, H. Liu, and W. Yang, J. Chem. Phys. 0021-9606 10.1063/1.480503 112, 3483 (2000).
25. H. Hu and W. Yang, Annu. Rev. Phys. Chem. 59, 034105 (2008). 0066-426X
26. M. Olsson, G. Hong, and A. Warshel, J. Am. Chem. Soc. 0002-7863 10.1021/ja0212157 125, 5025 (2003).
27. G. Li, X. Zhang, and Q. Cui, J. Phys. Chem. B 1089-5647 10.1021/jp034286g 107, 8643 (2003).
28. M. Cascella, A. Magistrato, I. Tavernelli, P. Carloni, and U. Rothlisberger, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 10.1073/pnas.0607890103 103, 19641 (2006).
29. S. Wang, P. Hu, and Y. Zhang, J. Phys. Chem. B 1089-5647 10.1021/jp067147i 111, 3758 (2007).
30. R. A. Marcus, J. Phys. Chem. 0022-3654 10.1021/j100798a033 67, 853 (1963).
31. P. H.-L. Sit, M. Cococcioni, and N. Marzari, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.97.028303 97, 028303 (2006).
32. R. Zwanzig, J. Chem. Phys. 0021-9606 10.1063/1.1740409 22, 1420 (1954).
33. J. G. Kirkwood, J. Chem. Phys. 0021-9606 10.1063/1.1749657 3, 300 (1935).
34. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 0021-9991 10.1016/0021-9991(77)90121-8 23, 187 (1977).
35. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 0021-9606 10.1063/1.476378 108, 9236 (1998).
36. R. Vuilleumier, M. Sprik, and A. Alavi, J. Mol. Struct. 506, 343 (2000). 0022-2860
37. I. Tavernelli, R. Vuilleumier, and M. Sprik, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.88.213002 88, 213002 (2002).
38. J. P. Perdew, R. G. Parr, M. Levy, and J. L. Balduz, Jr., Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.49.1691 49, 1691 (1982).
39. W. Yang, Y. Zhang, and P. Ayers, Phys. Rev. Lett. 0031-9007 10.1103/PhysRevLett.84.5172 84, 5172 (2000).
40. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
41. O. A. von Lilienfeld and M. E. Tuckerman, J. Chem. Phys. 0021-9606 10.1063/1.2338537 125, 154104 (2006).
42. A. J. Cohen, P. Mori-Sanchez, and W. Yang, Phys. Rev. B (to be published).
43. P. Mori-Sanchez, A. J. Cohen, and W. Yang, arXiv:0708.3688v1 cond-mat.mtrl-sci, 2007.
44. P. Bernhard, H. B. Buergi, J. Hauser, H. Lehmann, and A. Ludi, Inorg. Chem. 21, 3936 (1982). 0020-1669
45. W. Bottcher, G. M. Brown, and N. Sutin, Inorg. Chem. 0020-1669 10.1021/ic50196a008 18, 1447 (1979).
46. B. S. Brunschwig, J. Logan, M. D. Newton, and N. Sutin, J. Am. Chem. Soc. 0002-7863 10.1021/ja00538a017 102, 5798 (1980).
47. J. Silverman and R. W. Dodson, J. Phys. Chem. 0022-3654 10.1021/j150499a007 56, 846 (1952).
48. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 0021-9606 10.1063/1.445869 79, 926 (1983).
49. H. Hu, M. Elstner, and J. Hermans, Proteins Struct. Funct. Genet. 50, 451 (2003). 0887-3585
50. G. Mann, R. H. Yun, L. Nyland, J. Prins, J. Board, and J. Hermans, Computational Methods for Macromolecules: Challenges and Applications- Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling (Springer, Berlin, 2002).
51. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 03, Revision D.02, Gaussian, Inc., Wallingford, CT, 2004.
52. H. Hu, Z. Lu, and W. Yang, J. Chem. Theory Comput. 1549-9618 10.1021/ct600240y 3, 390 (2007).
53. A. D. Becke, Phys. Rev. A 1050-2947 10.1103/PhysRevA.38.3098 38, 3098 (1988).
54. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B 0163-1829 10.1103/PhysRevB.37.785 37, 785 (1988).
55. P. J. Hay and W. R. Wadt, J. Chem. Phys. 0021-9606 10.1063/1.448799 82, 270 (1985).
56. A. MacKerell, D. Bashford, M. Bellott, R. Dunbrack, J. Evanseck, M. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 1089-5647 10.1021/jp973084f 102, 3586 (1998).
57. P. Brandt, T. Norrby, B. Akermark, and P. -O. Norrby, Inorg. Chem. 37, 4120 (1998). 0020-1669
58. U. C. Singh and P. A. Kollman, J. Comput. Chem. 0192-8651 10.1002/jcc.540050204 5, 129 (1984).
59. B. H. Besler, K. M. Merz, Jr., and P. A. Kollman, J. Comput. Chem. 0192-8651 10.1002/jcc.540110404 11, 431 (1990).
60. H. Reiss, J. Phys. Chem. 0022-3654 10.1021/j100266a013 89, 4207 (1985).
61. P. Delahay, K. V. Burg, and A. Dziedzic, Chem. Phys. Lett. 0009-2614 10.1016/0009-2614(81)85309-2 79, 157 (1981).
62. P. Delahay, Chem. Phys. Lett. 0009-2614 10.1016/0009-2614(82)83188-6 87, 607 (1982).
63. P. Delahay, Chem. Phys. Lett. 99, 87 (1983). 0009-2614
64. B. S. Brunschwig, C. Creutz, D. H. Macartney, T. -K. Sham, and N. Sutin, Faraday Discuss. Chem. Soc. 0301-7249 10.1039/dc9827400113 74, 113 (1982).
65. B. L. Tembe, H. L. Friedman, and M. D. Newton, J. Chem. Phys. 0021-9606 10.1063/1.443110 76, 1490 (1982).
66. J. S. Bader, R. A. Kuharski, and D. Chandler, J. Chem. Phys. 0021-9606 10.1063/1.459596 93, 230 (1990).
67. J. S. Bader and D. Chandler, J. Phys. Chem. 0022-3654 10.1021/j100194a059 96, 6423 (1992).
68. Handbook of Chemistry and Physics (CRC Press, Boca Raton, FL, 2006).
69. S. U. M. Khan and J. O. Bockris, Chem. Phys. Lett. 99, 83 (1983). 0009-2614