A TDDFT study of the optical response of DNA bases, base pairs, and their tautomers in the gas phase

Journal of Physical Chemistry A

Volumn 109, Issue 10, 2005, Pages 2373-2380

  Tsolakidis, Argyrios ^a   Kaxiras, Efthimios ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; PHOTOCHEMICAL DECAY; TAUTOMERS; TIME-DEPENDENT DENSITY FUNCTIONAL THEORY (TDDFT);

CARRIER CONCENTRATION; CHARGE TRANSFER; DNA; ELECTRON ENERGY LEVELS; ELECTRON TRANSITIONS; HYDROGEN BONDS; PERTURBATION TECHNIQUES; PHASE TRANSITIONS; PROBABILITY DENSITY FUNCTION; REACTION KINETICS;

PHOTOCHEMICAL REACTIONS;

ADENINE; CYTOSINE; DNA; GUANINE; THYMINE;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; DNA BASE COMPOSITION; GAS; LIGHT; PHASE TRANSITION; QUANTUM THEORY; RADIATION EXPOSURE; SPECTROSCOPY; STEREOISOMERISM;

ADENINE; BASE COMPOSITION; BASE PAIRING; CYTOSINE; DNA; GASES; GUANINE; LIGHT; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PHASE TRANSITION; QUANTUM THEORY; SPECTRUM ANALYSIS; STEREOISOMERISM; THYMINE;

EID: 15944388901     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp044729w     Document Type: Article

References (101)

1. Ruzsicska, B. P.; Lemaire, D. G. E. in CRC Handbook of Organic Photochemistry and Photobiology. Horspool, W. M., Song, P. S.; Eds.; CRC Press: Boca Raton, FL, 1995; p 1289.
2. Vigny, P.; Duquesne, M. in Excited States of Biological Molecules; Birks, J. B.; Wiley: New York, 1976; Vol. 3, p 167.
3. Daniels, M. in Photochemistry and Photobiology of Nucleic Acids; Wang, S. Y., Ed.; Academic Press: New York, 1976; Vol. 1, p 23.
4. Daniels, M. Photochem. Photobio. 1983, 37, 691.
5. Callis, P. R. Amu. Rev. Phys. Chem. 1983, 37, 691.
6. Crespo-Hernández, C. E.; Cohen, B.; Hare, P. M.; Kohler, B. Chem. Rev. 2004, 104, 1977.
7. Miller, D. L.; Weinstock, M. A. J. Am. Acad. Dermatol 1994, 30, 774.
8. Kraemer, K. H. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 11.
9. Foresman, J. B.; Head-Gordon, M.; Pople, J. A.; Frisch, M. J. J. Phys. Chem. 1992, 96, 135.
10. Anderson, K.; Malmqvist, P. A.; Roos, B. O. J. Chem. Phys. 1992, 96, 1218.
11. Fülscher, M. P.; Anderson, K.; Roos, B. O. J. Phys. Chem. 1992, 96, 9204.
12. Huron, B.; Malrieu, J.-P.; Rancurel, P. J. Chem. Phys. 1973, 58, 5745.
13. Evangelisti, S.; Daudey, J.; Malrieu, J.-P. Chem. Phys. 1983, 75, 91.
14. Spiegelmann, F.; Malrieu, J.-P. J. Phys. B 1984, 17, 1235.
15. Cimiraglia, R. J. J. Chem. Phys. 1985, 83, 1746.
16. Cimiraglia, R.; Persico, M. J. Comput. Chem. 1987, 8, 39.
17. Runge, E.; Gross, E. K. U. Phys. Rev. Lett. 1984, 52, 997.
18. Gross, E. K. U.; Ullrich, C. A.; Gossmann, U. J. in Density Functional Theory, Gross, E. K. U., Dreizler, R. M.; Eds.; Plenum Press: New York, 1995.
19. Gross, E. K. U.; Dobson, J. F.; Petersilka, M. in Topics in Current Chemistry: Nalewajski, R. F., Ed.; Springer-Verlag: Berlin, 1996; Vol. 181.
20. Holmén, A.; Broo, A.; Albinsson, B.; Nordén, B. J. Am. Chem. Soc. 1997, 119, 12240.
21. Mennucci, B.; Toniolo, A.; Tomasi, J. J. Phys. Chem. 2001, 105, 4749.
22. Sobolewski, A. L.; Domcke, W. Eur. Phys. J. D 2002, 20, 369.
23. Fülscher, M. P.; Serano-Andres, L.; Roos, B. O. J. Am. Chem. Soc. 1997, 119, 6168.
24. Mishra, S. K.; Shukla, M. K.; Mishra, P. C. Spectrochim. Acta Part A 2000, 56, 1355.
25. Broo, A.; Holmén, A. J. Phys. Chem. A 1997, 101, 3589.
26. Shukla, M. K.; Mishra, S. K.; Kumar, A.; Mishra, P. C. J. Comput. Chem. 2000, 21, 826.
27. Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 11338.
28. Lührs, D. C.; Viallon, J.; Fischer, I. Phys. Chem. Chem. Phys. 2001, 3, 1827.
29. Cohen, B.; Hare, P. M.; Kohler, B. J. Am. Chem. Soc. 2003, 125, 13594.
30. Dreyfus, M.; Dodin, G.; Bensaude, O.; Dubois, J. E. J. Am. Chem. Soc. 1975, 97, 2369.
31. Holmén, A.; Broo, A. Int. J. Quantum Chem. 1995, 22, 113.
32. Langer, H.; Doltsinis, N. L. J. Chem. Phys. 2003, 118, 5400.
33. Broo, A. J. Phys. Chem. A 1998, 102, 526.
34. Shukla, M. K.; Mishra, P. C. Chem. Phys. 1999, 240, 319.
35. Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 1011.
36. Shukla, M. K.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 4709.
37. Sobolewski, A. L.; Domcke, W. Phys. Chem. Chem. Phys. 2004, 6, 2763.
38. Kumar, A.; Knapp-Mohammady, M.; Mishra, P. C.; Suhai, S. J. Comput. Chem. 2004, 25, 1047.
39. Joubert, L.; Popelier, P. L. A. Phys. Chem. Chem. Phys. 2002, 4, 4353.
40. Podolyan, Y.; Rubin, Y. V.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 9964.
41. Komarov, V. M. J. Biol. Phys. 1999, 24, 167.
42. Sponer, J.; Hobza, P. Chem. Phys. 1996, 204, 365.
43. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 1965.
44. Yanov, I.; Leszczynski, J. J. Quantum Chem. 2004, 96, 436.
45. Hobza, P.; Šponer, J. Chem. Phys. Lett. 1996, 261, 379.
46. Hobza, P.; Sandorfy, C. J. Am. Chem. Soc. 1987, 109, 1302.
47. Sivanesan, D.; Sumathi, I.; Welsh, W. J. Chem. Phys. Lett. 2003, 367, 351.
48. Jurečka, P.; Nachtigall, P.; Hobza, P. Phys. Chem. Chem. Phys. 2001, 3, 4578.
49. Florián, J.; Leszczynski, J.; Johnson, B. G. J. Mol. Struct. 1995, 349, 421.
50. Seeman, N. C. Nature 2003, 421, 427.
51. Jasíen, P. G.; Fitzgerald, G. J. Chem. Phys. 1990, 93, 2554.
52. Guallar, V.; Douhal, A.; Moreno, M.; Lluch, J. M. J. Phys. Chem. A 1999, 103, 6251.
53. Scheiner, S.; Kern, C. W. J. Am. Chem. Soc. 1979, 101, 4081.
54. Burda, J. V.; Šponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. B 1997, 101, 9670.
55. Tsolakidis, A.; Sánchez-Portal, D.; Martin, R. M. Phys. Rev. B 2002, 66, 235416.
56. Sanchez-Portal, D.; Ordejón, P.; Artacho, E.; Soler, J. M. Int. J. Quantum Chem. 1997, 65, 453.
57. Artacho, E.; Sánchez-Portal, D.; Ordejón, P.; García, A.; Soler, J. M. Phys. Status Solidi B 1999, 215, 809.
58. Ordejón, P. Phys. Status Solidi B 2000, 217, 335.
59. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993.
60. Kleinman, L.; Bylander, D. M. Phys. Rev. Lett. 1982, 48, 1425.
61. Sankey, O. F.; Niklewski, D. J. Phys. Rev. B 1989, 40, 3979. Sanchez-Portal, D.; Artacho, E.; Soler, J. M. J. Phys.: Condens. Matter 1996, 8, 3859.
62. Sankey, O. F.; Niklewski, D. J. Phys. Rev. B 1989, 40, 3979. Sanchez-Portal, D.; Artacho, E.; Soler, J. M. J. Phys.: Condens. Matter 1996, 8, 3859.
63. Fülscher, M. P.; Malmqvist, P. Å; Roos, B. O. Ab Initio Quantum Chemical Calculations of Excitation Energies and Transition Moments for the Nucleic Acid Base Monomers, in Time-Resolved Laser Spectroscopy in Biochemistry II; Lakowicz, J., Ed.; SPIE: Belingham, WA, 1990; p 1204.
64. Jensen, H. J. A.; Koch, H.; Jørgensen, P.; Olsen, J. Chem. Phys. 1998, 119, 297.
65. Matos, J. M. O.; Roos, B. O. J. Am. Chem. Soc. 1988, 110, 7664.
66. Pelke, J. D.; Maggiora, G. M.; Christoffersen, R. E. J. Am. Chem. Soc. 1990, 112, 5452.
67. Petke, J. D.; Maggiora, G. M.; Christoffersen, R. E. J. Phys. Chem. 1992, 96, 6992.
68. Fülscher, M. P.; Roos, B. O. J. Am. Chem. Soc. 1995, 117, 2089.
69. Lorentzon, J.; Fülscher, M. P.; Roos, B. O. J. Am. Chem. Soc. 1995, 117, 9265.
70. Mennucci, B.; Toniolo, A.; Tomasi, J. J. Phys. Chem. 2001, 105, 7126.
71. Shukla, M. K.; Leszczynski, J. J. Comput. Chem. 2004, 25, 768.
72. Merchán, M.; Serrano-Andrés, L. J. Am. Chem. Soc. 2003, 125, 8108.
73. Kaito, A.; Hatano, M.; Ueda, T.; Shibuya, S. Bull. Chem. Soc. Jpn. 1980, 53, 3073.
74. Clark, L. B.; Peschel, G. G.; Tinoco, I., Jr. J. Phys. Chem. 1965, 69, 3615.
75. Voet, D.; Gratzer, W. B.; Cox, R. A.; Doty, P. Biopolymers 1963, 1, 193.
76. Voelter, W.; Records, R.; Bunnenberg, E.; Djerassi, C. J. Am. Chem. Soc. 1968, 90, 6163.
77. Yamada, T.; Fukutome, H. Biopolymers 1968, 6, 43.
78. Matsuoka, Y.; Nordén, B. J. Phys. Chem. 1982, 86, 1378.
79. Sprecher, C. A.; Johnson, W. C., Jr. Biopolymers 1977, 16, 2243.
80. Brunner, W. C.; Maestre, M. F. Biopolymers 1975, 14, 555.
81. Sutherland, J. C.; Griffin, K. Biopolymers 1984, 23, 2715.
82. Isaacson, M. J. Chem. Phys. 1972, 56, 1803.
83. Zaloudek, F.; Novros, J. S.; Clark, L. B. J. Am. Chem. Soc. 1985, 107, 7344.
84. Raksányi, K.; Földváry, J.; Fidy, J.; Kittler, L. Biopolymers 1978, 17, 887.
85. Morita, H.; Nagakura, S. Theor. Chim. Acta 1968, 11, 279.
86. Clark, L. B. J. Am. Chem. Soc. 1977, 99, 3934.
87. Miles, D. W.; Hahn, S. J.; Robins, R. K.; Eyring, H. J. Phys. Chem. 1968, 72, 1483.
88. Clark, L. B.; Tinoco, I., Jr. J. Am. Chem. Soc. 1965, 87, 11.
89. Chin, W.; Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M. Eur. Phys. J. D 2002, 20, 347.
90. Nir, E.; Plutzer, C.; Kleinermanns, K.; de Vries, M. Eur. Phys. J. D 2002, 20, 317.
91. Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M. J. Phys. Chem. A 2002, 106, 5088.
92. Watson, J. H. D.; Crick, F. H. C. Nature 1953, 171, 737.
93. Löwdin, P. O. Adv. Quantum Chem. 1965, 2, 213.
94. Nikogosyan, D. N.; Angelov, D.; Soeb, B.; Lindqvist, L. Chem. Phys. Lett. 1996, 252, 322.
95. Pecourt, J.-M. L.; Peon, J.; Kohler, B. J. Am. Chem. Soc. 2001, 123, 10370.
96. Peon, J.; Zewail, A. H. Chem. Phys. Lett. 2001, 348, 255.
97. Onidas, D.; Markovitsi, D.; Marguet, S.; Sharonov, A.; Gustavsson, T. J. Phys. Chem. B 2002, 106, 11367.
98. Hall, D. B.; Holmlin, R. E.; Barton, J. K. Nature 1996, 384, 731.
99. Steenken, S. Chem. Rev. 1989, 89, 503.
100. Brealey, G. J.; Kasha, M. J. Am. Chem. Soc. 1955, 77, 4462.
101. Dreuw, A.; Weisman, J. L.; Head-Gordon, M. J. Chem. Phys. 2003, 119, 2943.