First-principles density-functional theory calculations of electron-transfer rates in azurin dimers

Journal of Chemical Physics

Volumn 124, Issue 6, 2006, Pages

  Migliore, A ^a,b   Corni, S ^a   Di Felice, R ^a   Molinari, E ^a,b  

^a INFM   (Italy)

^b UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTABILITY AND DECIDABILITY; MATHEMATICAL MODELS; PROBABILITY DENSITY FUNCTION; PROTEINS;

ELECTRONIC COUPLINGS; MULTIELECTRON SCHEME;

ELECTRONIC STRUCTURE;

EID: 32644484895     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2166233     Document Type: Article

References (96)

1. A. Aviram, J. Am. Chem. Soc. 110, 5687 (1988).
2. A. Aviram, M. Ratner, and V. Mujica, Molecular Electronics II: Annals of the New York Academy of Sciences (The New York Academy of Sciences, New York, 2003), Vol. 960.
3. R. Rinaldi, A. Biasco, G. Maruccio, R. Cingolani, D. Alliata, L. Andolfi, P. Facci, F. De Rienzo, R. Di Felice, and E. Molinari, Adv. Mater. (Weinheim, Ger.) 14, 1453 (2002).
4. G. Maruccio, A. Biasco, P. Visconti, Adv. Mater. (Weinheim, Ger.) 17, 816 (2005).
5. A. Nitzan, Annu. Rev. Phys. Chem. 52, 681 (2001).
6. J. R. Heath and M. A. Ratner, Phys. Today 56 (5), 43 (2003).
7. S. Corni, F. De Rienzo, R. Di Felice, and E. Molinari, Int. J. Quantum Chem. 102, 328 (2005).
8. E. I. Solomon, R. K. Szilagyi, G. S. DeBeer, and L. Basumallick, Chem. Rev. (Washington, D.C.) 104, 419 (2004).
9. O. Farver, Ó. Einarsdóttir, and I. Pecht, Eur. J. Biochem. 267, 950 (2000).
10. G. W. Canters, H. A. O. Hill, N. A. Kitchen, and E. T. Adman, J. Magn. Reson. (1969-1992) 57, 1 (1984).
11. I. M. C. van Amsterdam, M. Ubbink, L. J. C. Jeuken, M. Ph. Verbeet, O. Einsle, A. Messerschmidt, and G. W. Canters, Chem.-Eur. J. 7, 2398 (2001).
12. I. M. C. van Amsterdam, M. Ubbink, O. Einsle, A. Messerschmidt, A. Merli, D. Cavazzini, G. L. Rossi, and G. W. Canters, Nat. Struct. Biol. 9, 48 (2002).
13. Q. Chi, J. Zhang, J. U. Nielsen, E. P. Friis, I. Chorkendorff, G. W. Canters, J. E. T. Andersen, and J. Ulstrup, J. Am. Chem. Soc. 12, 4047 (2000).
14. A. Alessandrini, M. Gerundi, G. W. Canters, M. Ph. Verbeet, and P. Facci, Chem. Phys. Lett. 376, 625 (2003).
15. A. Alessandrini, M. Salerno, S. Frabboni, and P. Facci, Appl. Phys. Lett. 86, 133902 (2005).
16. B. P. Paulson, L. A. Curtiss, B. Bal, G. L. Closs, and J. R. Miller, J. Am. Chem. Soc. 118, 378 (1996).
17. S. Corni, J. Phys. Chem. B 109, 3423 (2005).
18. T. R. Prytkova, I. V. Kurnikov, and D. N. Beratan, J. Phys. Chem. B 109, 1618 (2005).
19. A. Ferretti, Coord. Chem. Rev. 238-239, 127 (2003).
20. I. Cacelli, S. Campanile, G. Denti, A. Ferretti, and M. Sommovigo, Inorg. Chem. 43, 1379 (2004).
21. A. Farazdel, M. Dupuis, E. Clementi, and A. Aviram, J. Am. Chem. Soc. 112, 4206 (1990).
22. M. D. Newton, Chem. Rev. (Washington, D.C.) 91, 767 (1991).
23. L. Y. Zhang, R. A. Friesner, and R. B. Murphy, J. Chem. Phys. 107, 450 (1997).
24. L. M. Jones, I. V. Kurnikov, and D. N. Beratan, J. Phys. Chem. A 106, 2002 (2002).
25. A. A. Stuchebrukhov, Theor. Chem. Acc. 110, 291 (2003).
26. M. D. Newton, Theor. Chem. Acc. 110, 307 (2003).
27. H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, and T. Kakitani, J. Phys. Chem. B 109, 1978 (2005).
28. S. Corni, R. Di Felice, and E. Molinari, Chem. Phys. Lett. 393, 118 (2004).
29. N. Sutin, Acc. Chem. Res. 15, 275 (1982).
30. R. A. Marcus and N. Sutin, Biochim. Biophys. Acta 811, 265 (1985).
31. A. M. Kuznetsov and J. Ulstrup, Electron Transfer in Chemistry and Biology (Wiley, New York, 1999).
32. M. Bixon and J. Jortner, Adv. Chem. Phys. 106, 35 (1999).
33. S. S. Skourtis and D. N. Beratan, Adv. Chem. Phys. 106, 377 (1999).
34. J. J. Regan and J. N. Onuchic, Adv. Chem. Phys. 107, 497 (1999).
35. M. D. Newton, Int. J. Quantum Chem. 77, 255 (2000).
36. M. D. Newton, Coord. Chem. Rev. 238, 167 (2003).
37. A. A. Stuchebrukhov, J. Chem. Phys. 118, 7898 (2003).
38. C. Kobayashi, K. Baldridge, and J. N. Onuchic, J. Chem. Phys. 119, 3550 (2003).
39. X. H. Zheng and A. A. Stuchebrukhov, J. Phys. Chem. B 107, 9579 (2003).
40. A. Voityuk, N. Rösch, M. Bixon, and J. Jortner, J. Phys. Chem. B 104, 9740 (2000).
41. O. V. Prezhdo, J. T. Kindt, and J. C. Tully, J. Chem. Phys. 111, 7818 (1999).
42. I. V. Kurnikov and D. N. Beratan, J. Chem. Phys. 105, 9561 (1996).
43. H. Eyring, J. Chem. Phys. 0021-9606 10.1063/1.1749604 3, 107 (1935); H. Eyring, Chem. Rev. (Washington, D.C.) 17, 65 (1935).
44. H. Eyring, J. Chem. Phys. 0021-9606 10.1063/1.1749604 3, 107 (1935); H. Eyring, Chem. Rev. (Washington, D.C.) 17, 65 (1935).
45. D. S. Bendall, Protein Electron Transfer (Bios Scientific, Oxford, 1996).
46. L. D. Landau, Phys. Z. Sowjetunion 0369-9811 1, 88 (1932); L. D. Landau, Phys. Z. Sowjetunion 0369-9811 2, 46 (1932); C. Zener, Proc. R. Soc. London, Ser. A 0950-1207 137, 696 (1932); C. Zener, Proc. R. Soc. London, Ser. A 140, 660 (1933).
47. L. D. Landau, Phys. Z. Sowjetunion 0369-9811 1, 88 (1932); L. D. Landau, Phys. Z. Sowjetunion 0369-9811 2, 46 (1932); C. Zener, Proc. R. Soc. London, Ser. A 0950-1207 137, 696 (1932); C. Zener, Proc. R. Soc. London, Ser. A 140, 660 (1933).
48. L. D. Landau, Phys. Z. Sowjetunion 0369-9811 1, 88 (1932); L. D. Landau, Phys. Z. Sowjetunion 0369-9811 2, 46 (1932); C. Zener, Proc. R. Soc. London, Ser. A 0950-1207 137, 696 (1932); C. Zener, Proc. R. Soc. London, Ser. A 140, 660 (1933).
49. L. D. Landau, Phys. Z. Sowjetunion 0369-9811 1, 88 (1932); L. D. Landau, Phys. Z. Sowjetunion 0369-9811 2, 46 (1932); C. Zener, Proc. R. Soc. London, Ser. A 0950-1207 137, 696 (1932); C. Zener, Proc. R. Soc. London, Ser. A 140, 660 (1933).
50. M. Rust, J. Lappe, and R. J. Cave, J. Phys. Chem. A 106, 3930 (2002).
51. R. J. Cave and M. D. Newton, J. Chem. Phys. 106, 9213 (1997).
52. A. Ferretti, A. Ruini, G. Bussi, E. Molinari, M. J. Caldas, Phys. Rev. B 69, 205205 (2004); http://www.s3.infm.it/dti
53. A. Ferretti, A. Ruini, G. Bussi, E. Molinari, M. J. Caldas, Phys. Rev. B 69, 205205 (2004); http://www.s3.infm.it/dti
54. W. Koch and M. C. Holthausen, A Chemist's Guide to Density Functional Theory (Wiley, New York, 2000).
55. F. Jensen, Introduction to Computational Chemistry (Wiley, Chichester, 1999).
56. T. Hupp, B. Engels, F. Della Sala, and A. Görling, Chem. Phys. Lett. 360, 175 (2002).
57. F. Della Sala and A. Görling, J. Chem. Phys. 118, 10439 (2003).
58. J. Baker, A. Scheiner, and J. Andzelm, Chem. Phys. Lett. 216, 380 (1993).
59. G. J. Laming, N. C. Handy, and R. D. Amos, Mol. Phys. 80, 1121 (1993).
60. Actually, it has been argued that, apart from definition problems, the spin contamination of KS determinants should not be exactly zero. See J. A. Pople, P. M. W. Gill, and N. C. Handy, Int. J. Quantum Chem. 56, 303 (1995).
61. J. N. Gehlen, I. Daizadeh, A. A. Stuchebrukhov, and R. A. Marcus, Inorg. Chim. Acta 243, 271 (1996).
62. U. Ryde, M. H. M. Olsson, K. Pierloot, and B. O. Roos, J. Mol. Biol. 261, 586 (1996).
63. U. Ryde, M. H. M. Olsson, B. O. Roos, and A. C. Borin, Theor. Chem. Acc. 105, 452 (2001).
64. U. Ryde and M. H. M. Olsson, Int. J. Quantum Chem. 81, 335 (2001).
65. J. N. Onuchic, D. N. Beratan, and J. J. Hopfield, J. Phys. Chem. 90, 3707 (1986).
66. K. D. Jordan and M. N. Paddon-Row, J. Phys. Chem. 96, 1188 (1992).
67. C. X. Liang and M. D. Newton, J. Phys. Chem. 96, 2855 (1992).
68. C. C. Moser and P. L. Dutton, Biochim. Biophys. Acta 1101, 171 (1992).
69. C. C. Page, C. C. Moser, X. Chen, and P. L. Dutton, Nature (London) 402, 47 (1999).
70. D. N. Beratan, J. N. Betts, and J. N. Onuchic, Science 252, 1285 (1991).
71. D. N. Beratan, J. N. Betts, and J. N. Onuchic, J. Phys. Chem. 96, 2852 (1992).
72. J. J. Regan and J. N. Onuchic, Adv. Chem. Phys. 107, 497 (1999).
73. M. L. Jones, I. V. Kurnikov, and D. N. Beratan, J. Phys. Chem. A 106, 2002 (2002).
74. J. P. Perdew, J. A. Chevary, H. S. Vosko, K. A. Jackson, D. J. Singh, and C. Fiolhais, Phys. Rev. B 46, 6671 (1992).
75. S. Baroni, A. Dal Corso, S. de Gironcoli, and P. Giannozzi, http://www.pwscf.org
76. D. Vanderbilt, Phys. Rev. B 41, 7892 (1990).
77. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 98, Revision A.11.3, Gaussian, Inc., Pittsburgh, PA, 2002.
78. I. V. Kurnikov, HARLEM program, http://www.kurnikov.org/
79. E. Apr̀, T. L. Windus, T. P. Straatsma, NWCHEM, a computational chemistry package for parallel computers, Version 4.7, Pacific Northwest National Laboratory, Richland, Washington 99352-0999, 2005; R. A. Kendall, E. Apra, D. E. Bernholdt, Comput. Phys. Commun. 128, 260 (2000).
80. E. Apr̀, T. L. Windus, T. P. Straatsma, NWCHEM, a computational chemistry package for parallel computers, Version 4.7, Pacific Northwest National Laboratory, Richland, Washington 99352-0999, 2005; R. A. Kendall, E. Apra, D. E. Bernholdt, Comput. Phys. Commun. 128, 260 (2000).
81. D. N. Beratan and J. J. Hopfield, J. Am. Chem. Soc. 106, 1584 (1984).
82. R. J. Cave, D. V. Baxter, W. A. Goddard III, and J. D. Baldeschwieler, J. Chem. Phys. 87, 926 (1987).
83. I. Daizadeh, J. N. Gehlen, and A. A. Stuchebrukhov, J. Chem. Phys. 106, 5658 (1997).
84. J. P. Perdew, in Electronic Structure of Solids '91, edited by, P. Ziesche, and, H. Eschrig, (Akademie, Berlin, 1991).
85. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
86. E. Ruiz, M. Llunell, and P. Alemany, J. Solid State Chem. 176, 400 (2003).
87. X. Feng and N. M. Harrison, Phys. Rev. B 70, 092402 (2004).
88. J. R. Reimers, W. A. Shapley, N. Lambropoulos, and N. S. Hush, Ann. N.Y. Acad. Sci. 960, 100 (2002).
89. E. Ruiz, D. R. Salahub, and A. Vela, J. Phys. Chem. 100, 12265 (1996).
90. J. Wang and A. A. Stuchebrukhov, Int. J. Quantum Chem. 80, 591 (2000).
91. K. V. Mikkelsen, E. Dalgaard, and P. Swanstrom, J. Phys. Chem. 91, 3081 (1987).
92. K. V. Mikkelsen and M. A. Ratner, J. Chem. Phys. 90, 4237 (1989).
93. R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford University Press, New York, 1989).
94. A. J. Di Bilio, M. G. Hill, N. Bonander, B. G. Karlsson, R. M. Villahermosa, B. G. Malmström, J. R. Winkler, and H. B. Gray, J. Am. Chem. Soc. 0002-7863 119, 9921 (1997); H. B. Gray, B. G. Malmström, and R. J. P. Williams, JBIC, J. Biol. Inorg. Chem. 5, 551 (2000).
95. A. J. Di Bilio, M. G. Hill, N. Bonander, B. G. Karlsson, R. M. Villahermosa, B. G. Malmström, J. R. Winkler, and H. B. Gray, J. Am. Chem. Soc. 0002-7863 119, 9921 (1997); H. B. Gray, B. G. Malmström, and R. J. P. Williams, JBIC, J. Biol. Inorg. Chem. 5, 551 (2000).
96. R. P. Domingue and M. D. Fayer, J. Phys. Chem. 90, 5141 (1986).