An AIMD study of the CPD repair mechanism in water: Reaction free energy surface and mechanistic implications

Journal of Physical Chemistry B

Volumn 115, Issue 14, 2011, Pages 3848-3859

  Hassanali, Ali A ^a   Zhong, Dongping ^a   Singer, Sherwin J ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BUTANE; CALCULATIONS; ELECTRON TRANSITIONS; FREE ENERGY; IONS; MOLECULAR DYNAMICS; REACTION KINETICS; REPAIR; SOLVENTS; SURFACE REACTIONS; TWO DIMENSIONAL;

AB INITIO MOLECULAR DYNAMICS SIMULATION; AQUEOUS SOLVENTS; BACK ELECTRON TRANSFER; CYCLOBUTANE PYRIMIDINE DIMERS; CYCLOBUTANES; FREE ENERGY SURFACE; NEUTRAL SURFACES; PICOSECOND TIME SCALE; REACTION FREE ENERGY; REPAIR MECHANISM; SOLVENT POLARITY; SPLITTING PROCESS; TRANSITION STATE; UMBRELLA SAMPLING;

DIMERS;

EID: 79953784392     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp107722z     Document Type: Article

References (65)

1. Sancar, A. Biochemistry 1994, 33 (1) 2-9
2. Carell, T.; Burgdorf, L. T.; Kundu, L. M.; Cichon, M. Curr. Opin. Chem. Biol. 2001, 5 (5) 491-498
3. Sancar, A. Chem. Rev. 2003, 103 (6) 2203-2237
4. You, Y.-H.; Lee, D.-H.; Yoon, J.-H.; Nakajima, S.; Yasui, A.; Pfeifer, G. P. J. Biol. Chem. 2001, 276 (48) 44688-44694
5. Lima-Bessa, K. M.; Menck, C. F. Curr. Biol. 2005, 15 (2) R58-R61
6. Jans, J.; Schul, W.; Sert, Y.-G.; Rijksen, Y.; Rebel, H.; Eker, A. P. M.; Nakajima, S.; van Steeg, H.; de Gruijl, F. R.; Yasui, A.; Hoeijmakers, J. H. J.; van der Horst, G. T. J. Curr. Biol. 2005, 15 (2) 105-115
7. MacFarlane; Stanley, R. J. Biochemistry 2003, 42 (28) 8558-8568
8. Kao, Y.-T.; Saxena, C.; Wang, L.; Sancar, A.; Zhong, D. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (45) 16128-16132
9. Kim, S.-T.; Rose, S. D. Photochem. Photobiol. 1988, 47 (5) 725-729
10. Song, Q.-H.; Tang, W.-J.; Hei, X.-M.; Wang, H.-B.; Guo, Q.-X.; Yu, S.-Q. Eur. J. Org. Chem. 2005, 2005 (6) 1097-1106
11. Song, Q.-H.; Tang, W.-J.; Ji, X.-B.; Wang, H.-B.; Guo, Q.-X. Chem. - Eur. J. 2007, 13 (27) 7762-7770
12. Voityuk, A. A.; Michel-Beyerle, M.-E.; Rösch, N. J. Am. Chem. Soc. 1996, 118 (40) 9750-9758
13. Masson, F.; Laino, T.; Tavernelli, I.; Rothlisberger, U.; Hutter, J. J. Am. Chem. Soc. 2008, 130 (11) 3443-3450
14. Saettel, N. J.; Wiest, O. J. Am. Chem. Soc. 2001, 123 (11) 2693-2694
15. Masson, F.; Laino, T.; Rothlisberger, U.; Hutter, J. ChemPhysChem 2009, 10 (2) 400-410
16. Tachikawa, H.; Kawabata, H. J. Phys. Chem. 2008, B112 (24) 7315-7319
17. Begley, T. P. Acc. Chem. Res. 1994, 27 (12) 394-401
18. Heelis, P. F.; Hartman, R. F.; Rose, S. D. Chem. Soc. Rev. 1995, 24 (4) 289-297
19. Carell, T.; Epple, R. Eur. J. Org. Chem. 1998, 1998 (7) 1245-1258
20. Podmore, I.; Heelis, P.; Symons, M.; Pezeshk, A. J. Chem. Soc., Chem. Commun. 1994, 1994 (8) 1005-1006
21. Pezeshk, A.; Podmore, I.; Heelis, P.; Symons, M. J. Phys. Chem. 1996, 100 (50) 19714-19718
22. Kim, S.-T.; Hartman, R. F.; Rose, S. D. Photochem. Photobiol. 1990, 52 (4) 789-794
23. Hartzfeld, D. G.; Rose, S. D. J. Am. Chem. Soc. 1993, 115 (3) 850-854
24. Tang, W.-J.; Guo, Q.-X.; Song, Q.-H. J. Phys. Chem. 2009, B113 (20) 7205-7210
25. Yeh, S. R.; Falvey, D. E. J. Am. Chem. Soc. 1991, 113 (22) 8557-8558
26. Chatgilialoglu, C.; Guerra, M.; Kaloudis, P.; Houée-Lévin, C.; Marignier, J.-L.; Swaminathan, V. N.; Carell, T. Chem. - Eur. J. 2007, 13 (32) 8979-8984
27. CP2K website, http://cp2k.berlios.de.
28. VandeVondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167 (2) 103-128
29. VandeVondele, J.; Hutter, J. J. Chem. Phys. 2003, 118 (10) 4365-4369
30. Pulay, P. Chem. Phys. Lett. 1980, 73 (2) 393-398
31. Pulay, P. J. Comput. Chem. 1982, 3 (4) 556-560
32. Becke, A. D. Phys. Rev. 1988, A38 (6) 3098-3100
33. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37 (2) 785-789
34. Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. 1996, B54 (3) 1703-1710
35. VandeVondele, J.; Hutter, J. J. Chem. Phys. 2007, 127 (11) 114105
36. Jursic, B. S. THEOCHEM J. Mol. Struct. 1998, 430 (1-3) 17-22
37. Wiener, J. J. M.; Politzer, P. THEOCHEM J. Mol. Struct. 1998, 427 (1-3) 171-174
38. Hassanali, A. A.; Zhong, D.; Singer, S. J. J. Phys. Chem. B 2011, in press.
39. Nosé, S. Mol. Phys. 1984, 52 (2) 255-268
40. Hoover, W. G. Phys. Rev. 1985, A31 (3) 1695-1697
41. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23 (2) 187-199
42. Jarzynski, C. Phys. Rev. Lett. 1997, 78 (14) 2690-2693
43. Darve, E.; Pohorille, A. J. Chem. Phys. 2001, 115 (20) 9169-9183
44. Rodriguez-Gomez, D.; Darve, E.; Pohorille, A. J. Chem. Phys. 2004, 120 (8) 3563-3578
45. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90 (23) 238302
46. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. J. Comput. Chem. 1992, 13 (8) 1011-1021
47. Ferrenberg, A. M.; Swendsen, R. H. Phys. Rev. Lett. 1989, 63 (12) 1195-1198
48. Roux, B. Comput. Phys. Commun. 1995, 91 (1-3) 275-282
49. Souaille, M.; Roux, B. Comput. Phys. Commun. 2001, 135 (1) 40-57
50. Voityuk, A. A.; Rösch, N. J. Phys. Chem. 1997, A101 (44) 8335-8338
51. Harrison, C. B.; ONeil, L. L.; Wiest, O. J. Phys. Chem. 2005, A109 (32) 7001-7012
52. Bond lengths were constrained at the following distances: 1.694, 1.746, 1.799, 1.852, 1.905, 1.958, 2.011, 2.064, 2.117, 2.170, 2.223, 2.276, 2.329, 2.382, 2.435, 2.488, 2.541, 2.593 Å.
53. Bond lengths were constrained at the following distances: 1.588, 1.614, 1.641, 1.667, 1.694, 1.720, 1.746, 1.773, 1.799, 1.826, 1.852, 1.905, 1.958, 2.011, 2.064, 2.117, 2.170, 2.223, 2.276, 2.329, 2.382, 2.435, 2.488, 2.541, 2.593, 2.646, 2.699, 2.752, 2.805, 2.858, 2.911, 2.964, 3.017 Å.
54. Bond lengths were constrained at the following distances: 1.641, 1.667, 1.694, 1.720, 1.746, 1.773, 1.799, 1.826, 1.852, 1.905, 1.958, 2.011, 2.064, 2.117, 2.170, 2.223, 2.276, 2.329, 2.382, 2.435, 2.488, 2.541, 2.593, 2.646, 2.699, 2.752 Å.
55. Durbeej, B.; Eriksson, L. A. J. Am. Chem. Soc. 2000, 122 (41) 10126-10132
56. Scannell, M. P.; Fenick, D. J.; Yeh, S. R.; Falvey, D. E. J. Am. Chem. Soc. 1997, 119 (8) 1971-1977
57. Schreier, W. J.; Schrader, T. E.; Koller, F. O.; Gilch, P.; Crespo-Hernb andez, C. E.; Swaminathan, V. N.; Carell, T.; Zinth, W.; Kohler, B. Science 2007, 315 (5812) 625-629
58. Boggio-Pasqua, M.; Groenhof, G.; Schäfer, L. V.; Grubmüller, H.; Robb, M. A. J. Am. Chem. Soc. 2007, 129 (36) 10996-10997
59. Diogo, H. P.; Dias, A. R.; Dhalla, A.; Minas da Piedade, M. E.; Begley, T. P. J. Org. Chem. 1991, 56 (26) 7340-7341
60. Smets, J.; Smith, D. M. A.; Elkadi, Y.; Adamowicz, L. J. Phys. Chem. 1997, A101 (48) 9152-9156
61. Hochstrasser, R. M.; Weisman, R. B. In Radiationless Transitions; Lin, S. H., Ed.; Academic: New York, 1980; pp 317 - 362.
62. Jortner, J.; Bixon, M. J. Chem. Phys. 1988, 88 (1) 167-170
63. Walker, G. C.; Åakesson, E.; Johnson, A. E.; Levinger, N. E.; Barbara, P. F. J. Phys. Chem. 1992, 96 (9) 3728-3736
64. Savéant, J.-M. J. Am. Chem. Soc. 1987, 109 (22) 6788-6795
65. Reid, P. J.; Barbara, P. F. J. Am. Chem. Soc. 1995, 99 (11) 3554-3565