Hole migration in DNA: A theoretical analysis of the role of structural fluctuations

Journal of Physical Chemistry B

Volumn 106, Issue 8, 2002, Pages 2093-2101

  Troisi, Alessandro ^a   Orlandi, Giorgio ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONIC COUPLINGS; STRUCTURAL FLUCTUATIONS;

COMPOSITION EFFECTS; COMPUTER SIMULATION; DNA; HOLE MOBILITY; MOLECULAR DYNAMICS;

CHARGE TRANSFER;

EID: 0037187105     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0133182     Document Type: Article

References (68)

1. Marcus, R.A. J. Chem. Phys. 1956, 24, 979.
2. Hush, N.S. Trans. Faraday Soc. 1961, 57, 155.
3. Jortner, J. J. Chem. Phys. 1976, 64, 4860.
4. Bixon, M.; Jortner, J. Adv. Chem. Phys 1999, 106, 35.
5. Newton, M.D. Adv. Chem. Phys 1999, 106, 303.
6. Ratner, M.A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 387.
7. Castner, E.W.; Kennedy, D.; Cave, R.J. J. Phys. Chem. A 2000, 104, 2869.
8. (a) Schlag, E.W.; Sheu, S.Y.; Yang, D.Y.; Selzle, H.L.; Lin, S.H.; Proc. Nat. Acad. Sci. U.S.A. 2000, 97, 1068.
9. (b) Schlag, E.W.; Yang, D.Y.; Sheu, S.Y.; Selzle, H.L.; Lin, S.H.; Rentzepis, P.M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9849.
10. (a) Han, J.; Zimmt, M. J. Am. Chem. Soc. 1998, 120, 8001.
11. (b) Kaplan, R.W.; Napper, A.M.; Waldeck, D.H.; Zimmt, M. J. Am. Chem. Soc. 2000, 122, 12039.
12. Vath, P.; Zimmt, M.B.; Matyushov, D.V.; Voth, G.A. J. Phys. Chem. B 2000, 103, 9130.
13. Barbara, P.F.; Olson, E.J.C. Adv. Chem. Phys. 1999, 107, 647.
14. (a) Murphy, C.J.; Arkin, M.R.; Jenkins, Y.; Ghatlia, N.D.; Bossman, S.H.; Turro, N.J.; Barton, J.K. Science 1993, 262, 1025.
15. (b) Kelley, S.O.; Jackson, N.M.; Hill, M.G.; Barton, J.K. Angew. Chem., Int. Ed. Engl. 1999, 38, 8, 941.
16. (c) Williams, T.T.; Odom, D.T.; Barton, J.K. J. Am. Chem. Soc 2000, 122, 9048.
17. (d) Wagenknecht, H.A.; Rajski, S.T.; Pascaly, M.; Stemp, E.D.A.; Barton, J.K. J. Am. Chem. Soc. 2001, 123, 4400.
18. (a) Henderson, P.T.; Jones, D.; Hampikian, G.; Kan, Y.Z.; Schuster, G.B. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 8353.
19. (b) Sanii, L.; Schuster, G.B.; J. Am. Chem. Soc. 2000, 122, 11545.
20. (a) Meggers, E.; Michel-Beyerle, M.E.; Giese, B. J. Am. Chem. Soc. 1995, 120, 12950.
21. (b) Giese, B. Wessely, S. Spormann, M. Lindemann, U. Meggers, E. Michel-Beyerle, M.E. Angew. Chem., Int. Ed. Engl. 1999, 38, 996.
22. (c) Davis, W.B. Naydenova, I. Haselsberger, R. Ogrodnik, A. Giese, B. Michel-Beyerle, M.E. Angew. Chem., Int. Ed. 2000, 39, 3649.
23. (d) Giese, B.; Spichty, M. Chem. Phys. Chem. 2000, 1, 195.
24. (a) Wan, C.Z.; Fiebig, T.; Kelley, S.O.; Treadway, C.R.; Barton, J.K.; Zewail, A.H.; Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6014.
25. (b) Wan, C.Z.; Fiebig, T.; Schiemann, O.; Barton, J.K.; Zewail, A.H.; Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14052.
26. Harriman, A. Angew. Chem., Int. Ed. Engl. 1999, 38, 8, 945.
27. Fukui, K.C.; Tanaka, K. Angew. Chem., Int. Ed. Engl. 1998, 37, 158.
28. (a) Lewis, F.D.; Wu, T., Zhang, Y., Letsinger, R.L., Greenfield, S.R., Wasielewsky, M.R. Science 1997, 277, 673.
29. (b) Lewis, F.D.; Liu, X.Y.; Liu, J.Q.; Miller, S.E.; Hayes, R.T.; Wasielewsky, M.R. Nature 2000, 406, 51.
30. (c) Lewis, F.D.; Wu, T.F.; Liu, X.Y.; Letsinger, R.L.; Greenfield, S.R.; Miller, S.E.; Wasielewsky, M.R. J. Am. Chem. Soc. 2000, 122, 2889.
31. (c) Lewis, F.D.; Kalgutkar, R.S.; Wu, Y.S.; Lin, X.Y.; Liu, J.Q.; Hayes, R.T.; Miller, S.E.; Wasielewsky, M.R. J. Am. Chem. Soc. 2000, 122, 2000, 12346.
32. Schoonveld, W.A.; Vrijmoeth, J.; Klapwijk, T.M. Appl. Phys. Lett. 1998, 73, 3884.
33. Bixon, M.; Giese, B.; Wessely, S.; Langenbacher, T.; Michel-Beyerle, M.E., Jortner, J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11713.
34. Priyadanshy, S.; Risser, S.M.; Beratan, D.N. J. Phys. Chem. 1996, 100, 0, 17678.
35. Voityuk, A.A.; Jortner, J.; Bixon, M.; Rösch, N. Chem. Phys. Lett. 2000, 324, 427.
36. Saito, I.; Nakamura, T.; Nakatani, K.; Yoshioka, Y.; Yamaguchi, K.; Sugiyama, H. J. Am. Chem. Soc. 1998, 120, 12686.
37. (a) Berlin, Y.A.; Burin, A.L.; Ratner, M.A. J. Phys. Chem. A 2000, 104, 443.
38. (b) Berlin, Y.A.; Burin, A.L. Ratner, M.A. J. Am. Chem. Soc. 2001, 123, 260.
39. Grozema, F.G.; Berlin, Y.A.; Siebbeles, L.D.A. J. Am. Chem. Soc. 2000, 122, 10903.
40. (a) Voityuk, A.A.; Rösch, N.; Bixon, M.; Jortner, J. J. Phys. Chem. B 2000, 104, 9740.
41. (b) Voityuk, A.A.; Jortner, J.; Bixon, M.; Rösch, J. Chem. Phys. 2001, 114, 5614.
42. Troisi, A.; Orlandi, G. Chem. Phys. Lett. 2001, 344, 509.
43. Bruinsma, R.; Gruner, G.; D'Orsogna, M.R.; Rudnick, J. Phys. Rev. Lett. 2000, 85, 4393.
44. Ratner, M.A. J. Phys. Chem. 1990, 94, 4877.
45. Skourtis, S.S.; Beratan, D.N. Adv. Chem. Phys. 1999, 106, 377.
46. (a) Löwdin, P.O. J. Math. Phys. 1962, 3, 969.
47. (b) Priyadarshy, S.; Skourtis, S.; Risser, S.M.; Beratan, D.N. J. Chem. Phys. 1996, 104, 9673.
48. McConnell, H.M. J. Chem. Phys 1961, 35, 508.
49. (a) Cheatman, T.E.; Kollman, P.E. Annu. Rev. Phys. Chem. 2000, 51, 435.
50. (b) Ravishanker, G.; Auffinger, P.; Langley, D.R.; Bhyravabhotla, J.; Matthew, A.Y.; Beveridge, D.L. Rev. Comput. Chem. 1997, 11, 317.
51. Orlandi, G.; Troisi, A.; Zerbetto, F. J. Am. Chem. Soc. 1999, 121, 5392.
52. Pople, J.A.; Beveridge, D.L. Approximate Molecular Orbital Theory; McGraw-Hill: NewYork, 1970.
53. Mulliken, R.S. J. Phys. Chem. 1952, 56, 295.
54. (a) Dudek, M.J.; Ponder, J.W. J. Comput. Chem. 1995, 16, 791.
55. (b) Kundrot, C.E.; Ponder, J.W.; Richards, F.M. J. Comput. Chem. 1991, 12, 402.
56. (c) Ponder, J.W.; Richards, F.M. J. Comput. Chem. 1987, 8, 1016.
57. Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. J. Am. Chem. Soc. 1995, 117, 5179.
58. Jorgensen, W.L.; Chandresekhar, J.; Madura, J.; Impey, R.W.; Klein, M. J. Chem. Phys 1983, 79, 926.
59. Darden, T.; York, D.; Pedersen, L.G. J. Chem. Phys. 1993, 98, 10089.
60. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; DiNola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684.
61. Andersen, H.C. J. Comput. Phys. 1983, 52, 24.
62. Heinemann, U.; Hahn, M. J. Biol. Chem. 1992, 267, 7332.
63. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Zakrzewski, V.G.; J.A. Montgomery, J.; 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.; Lin, 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. Gaussian 98, Revision A.5; Gaussian, Inc.: Pittsburgh, PA, 1998.
64. Orlov, V.M.; Smirnov, A.N.; Vershavsky, Y.M. Tetrahedron Lett. 1976, 48, 4377.
65. Hush, N.S.; Cheung, A.S. Chem. Phys. Lett. 1975, 34, 11.
66. (a) Herzberg, G.; Teller, E.Z. Phys. Chem. (Leipzig) 1933, B21, 410.
67. (b) Herzberg, G. Electronic Spectra of Polyatomic Molecules; Van Nostrand: Princeton, 1966.
68. Conwell, E.M.; Rakmanova, S.V. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 4556.