Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing

Journal of Computational Chemistry

Volumn 31, Issue 4, 2010, Pages 825-836

  Zhang, Laibin ^a   Li, Huifang ^a   Li, Jilai ^a   Chen, Xiaohua ^a   Bu, Yuxiang ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

Ab initio calculations; Excited states; Fluorescent properties; Pairing effect; Yy bases

Indexed keywords

ABSORPTION; ABSORPTION SPECTROSCOPY; EMISSION SPECTROSCOPY; EXCITED STATES; METHANOL;

AB INITIO CALCULATIONS; ABSORPTION AND EMISSION SPECTRA; BASE PAIRING; BLUE SHIFT; BLUESHIFTS; DNA BASIS; ELECTRONIC TRANSITION; EMISSION ENERGIES; EMISSION MAXIMA; FLUORESCENCE EMISSION; FLUORESCENCE MAXIMA; FLUORESCENT PROPERTY; GEOMETRICAL CHARACTERISTICS; LOW-LYING EXCITED STATE; MEASURED DATA; METHANOL SOLUTION; NATURAL BASIS; RED SHIFT; THEORETICAL STUDY;

FLUOROPHORES;

EID: 84962382976     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21376     Document Type: Article

References (93)

1. Cobb, A. J. A. Org Biomol Chem 2007, 5, 3260.
2. (a) Nielsen, P. E.; Egholm, M.; Buchart, O. Bioconjug Chem 1994, 5, 3;
3. (b) Egholm, M.; Buchart, O.; Christensen, L.; Behrens, C.; Freier, S. M.; Driver, D. A.; Berg, R. H.; Kim, S. K.; Norden, B.; Nielsen, P. E. Nature 1993, 365, 566.
4. Petersen, M.; Wengel, J. Trends Biotechnol 2003, 21, 74.
5. (a) .Eschenmoser, A. Science 1999, 284, 2118;
6. (b) Schoning, K.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.; Eschenmoser, A. Science 2000, 290, 1347.
7. (a) Ward, D. C.; Reich, E.; Stryer, L. J Biol Chem 1969, 244, 1228;
8. (b) Nordlund, T. M.; Andersson, S.; Nilsson, L.; Rigler, R.; Graslund, A.; McLaughlin, L. W. Biochemistry 1989, 28, 9095;
9. (c) Nordlund, T. M.; Xu, D.; Evans, K. O. Biochemistry 1993, 32, 12090.
10. (a) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710;
11. (b) Allan, B. W.; Reich, N. O.; Beechem, J. M. Biochemistry 1999, 38, 5308.
12. (a) Guest, C. R.; Hochstrasser, R. A.; Sowers, L. C.; Millar, D. P. Biochemistry 1991, 30, 3271;
13. (b) Bandwar, R. P.; Patel, S. S. J Biol Chem 2001, 276, 14075;
14. (c) Ujvari, A.; Martin, C. T. Biochemistry 1996, 35, 14574;
15. (d) Jia, Y.; Kumar, A.; Patel, S. S. J Biol Chem 1996, 271, 30451.
16. (a) Stivers, J. T. Nucleic Acids Res 1998, 26, 3837;
17. (b) Rachofsky, E. L.; Seibert, E.; Stivers, J. T.; Osman, R.; Ross, J. B. A. Biochemistry 2001, 40, 957.
18. Kool, E. T. Acc Chem Res 2002, 35, 936.
19. Krueger, A. T.; Lu, H.; Lee, A. H.; Kool, E. T. Acc Chem Res 2007, 40, 141.
20. Henry, A. A.; Romesberg, F. E. Curr Opin Chem Biol 2003, 7, 727.
21. Hirao, I. Curr Opin Chem Biol 2006, 10, 622.
22. (a) Liu, H.; Gao, J.; Lynch, S. R.; Saito, Y. D.; Maynard, L.; Kool, E. T. Science 2003, 302, 868;
23. (b) Gao, J.; Liu, H.; Kool, E. T. J Am Chem Soc 2004, 126, 11826;
24. (c) Liu, H.; Gao, J.; Kool, E. T. J Org Chem 2005, 70, 639;
25. (d) Liu, H.; Gao, J.; Maynard, L.; Saito, D.; Kool, E. T. J Am Chem Soc 2004, 126, 1102;
26. (e) Liu, H.; Gao, J.; Kool, E. T. J Am Chem Soc 2005, 127, 1396;
27. (f) Krueger, A. T.; Kool, E. T. J Am. Chem Soc 2008, 130, 3989.
28. (a) Lu, H.; He, K.; Kool, E. T. Angew Chem. Int Ed 2004, 43, 5834;
29. (b) Lee, A. H. F.; Kool, E. T. J Org Chem 2005, 70, 132;
30. (c) Lee, A. H. F.; Kool, E. T. J Am Chem Soc 2005, 127, 3332.
31. Lee, A. H. F.; Kool, E. T. J Am Chem Soc 2006, 128, 9219.
32. (a) Liu, C.; Martin, C. T. J Mol. Biol 2001, 308, 465;
33. (b) Liu, C.; Martin, C. T. J Biol Chem 2002, 277, 2725.
34. (a) Okamoto, A.; Tainaka, K.; Saito, I. J Am Chem Soc 2003, 125, 4972;
35. (b) Okamoto, A.; Tanaka, K.; Fukuta, T.; Saito, I. Chembiochem 2004, 5, 958;
36. (c) Okamoto, A.; Tainaka, K.; Saito, I. Tetrahedron Lett 2003, 44, 6871.
37. Coleman, R. S.; Madaras, M. L. J Org Chem 1998, 63, 5700.
38. (a) Zhang, J.; Cukier, R. I.; Bu, Y. J Phys Chem B 2007, 111, 8335;
39. (b) Han, L.; Li, H.; Cukier, R. I.; Bu, Y. J Phys Chem B 2009, 113, 4407.
40. (a) Barrio, J. R.; Secrist, J. A.,III; Leonard, N. J. Proc Natl Acad Sci USA 1972, 69, 2039;
41. (b) Secrist, J. A., III; Barrio, J. R.; Leonard, N. J. Science 1972, 175, 646.
42. (a) Godde, F.; Toulme, J. J.; Moreau, S. Biochemistry 1998, 37, 13765;
43. (b) Godde, F.; Toulme, J. J.; Moreau, S. Proc Natl Acad Sci USA 2000, 28, 2977.
44. (a) Mayer, A.; Neuenhofer, S. Angew Chem Int Ed Engl 1994, 33, 1044;
45. (b) Millar, D. P. Curr Opin Struct Biol 1996, 6, 322;
46. (c) Manuela, J. R.; Marino, J. P. Curr Org Chem 2002, 6, 775;
47. (d) Hawkins, M. E. Top Fluoresc Spectrosc 2003, 7, 151.
48. (a) Varsano, D.; Garbesi, A.; Felice, R. D. J Phys Chem B 2007, 111, 14012;
49. (b) Qu, Z.; Zhu, H.; May, V. J Phys Chem B 2009, 113, 4817.
50. (a) Zhang, L.; Bu, Y. J Phys Chem B 2008, 112, 10723;
51. (b) Zhang, L.; Li, H.; Chen, X.; Cukier, R. I.; Bu, Y. J Phys Chem B 2009, 113, 1173.
52. Laxer, A.; Major, D. T.; Gottlieb, H. E.; Fischer, B. J Org Chem 2001, 66, 5463.
53. (a) Vazquez-Mayagoita, A.; Huertas, O.; Fuentes-Cabrera, M.; Sumpter, B. G.; Orozco, M.; Luque, F. J. J Phys Chem B 2008, 112, 2179;
54. (b) Fuentes-Cabrera, M.; Sumpter, B. G.; Lipkowski, P.; Wells, J. C. J Phys Chem B 2006, 110, 6379.
55. Becke, A. D. J Chem Phys 1993, 98, 5648.
56. Lee, C.; Yang, W.; Parr, R. G. Phys Rev B Condens Matter 1988, 37, 785.
57. Foresman, J. B.; Head-Gordon, M.; Pople, J. A.; Frisch, M. J. J Phys Chem 1992, 96, 135.
58. (a) Broo, A.; Holmen, A. J Phys Chem A 1997, 101, 3589;
59. (b) Holmen, A.; Broo, A.; Norden, B. J Am Chem Soc 1997, 119, 12240.
60. (a) Shukla, M. K.; Leszczynski, J. J Phys Chem A 2002, 106, 4709;
61. (b) Shukla, M. K.; Leszczynski, J. J Phys Chem B 2005, 109, 17333.
62. (a) Hardman, S. J. O.; Thompson, K. C. Biochemistry 2006, 45, 9145;
63. (b) Thompson, K. C.; Miyake, N. J Phys Chem B 2005, 109, 6012.
64. (a) Shukla, M. K.; Leszczynski, J. J Comput Chem 2004, 25, 768;
65. (b) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J Phys Chem B 2007, 111, 8940;
66. (c) So, R.; Alavi, S. J. Comput Chem 2007, 28, 1776.
67. (a) Clark, A. E.; Qin, C.; Li, A. D. Q. J Am. Chem Soc 2007, 129, 7586;
68. (b) Kumar, A.; Sevilla, M. D. J Am Chem Soc 2008, 130, 2130.
69. (a) Miertus, S.; Scrocco, E.; Tomasi, J. Chem Phys 1981, 55, 117;
70. (b) Miertus, S.; Tomasi, J. Chem Phys 1982, 65, 239.
71. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Parkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortz, J. V.; Cui, Q.; Baboul, A. F.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanyakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision B.03; Gaussian. Inc.: Pittsburgh, PA, 2003.
72. Gorelsky, S. I. SWizard Program; CCRI, University Of Ottawa: Ottawa, Canada, 2008. Available at: http://www.sg-chem.net/.
73. Caut, E.; Dehareng, D.; Livin, J. J Phys Chem A 2006, 110, 9200.
74. Sobolewski, A. L.; Domcke, W.; Dedonder-Lardeux, C.; Jouvet, C. Phys Chem Chem Phys 2002, 4, 1093.
75. (a) Shukla, M. K.; Leszczynski, J. In Computational Chemistry: Reviews of Current Trends, Vol.8; Leszczynski, J., Ed.; World Scientific: Singapore, 2003; p. 249;
76. (b) Shukla, M. K.; Leszczynski, J. J Phys Chem A 2002, 106, 8642.
77. (a) Dreuw, A.; Weisman, J. L.; Head-Gordon, M. J Chem Phys 2003, 119, 2943;
78. (b) Dreuw, A.; Head-Gordon, M. Chem Rev 2005, 105, 4009.
79. (a) Bernasconi, L.; Sprik, M.; Hutter, J. J Chem Phys 2003, 119, 12417;
80. (b) Bernasconi, L.; Sprik, M.; Hutter, J. Chem Phys Lett 2004, 394, 141.
81. (a) Neugebauer, J.; Louwerse, M. J.; Baerends, E. J.; Wesolowski, T. A. J Chem Phys 2005, 122, 094115;
82. (b) Neugebauer, J.; Gritsenko, O.; Baerends, E. J. J Chem Phys 2006, 124, 214102.
83. (a) Lange, A.; Herbert, J. M. J Chem Theory Comput 2007, 3, 1680;
84. (b) Lange, A.; Herbert, J. M. J Am Chem Soc 2009, 131, 3913.
85. Peach, M. J. G.; Benfield, P.; Helgaker, T.; Tozer, D. J Chem Phys 2008, 128, 044118.
86. Crespo-Hernandez, C. E.; Cohen, B.; Kohler, B. Nature 2005, 436, 1141.
87. (a) Sobolewski, A. L.; Domcke, W. Phys Chem Chem Phys 2004, 6, 2763;
88. (b) Sobolewski, A. L.; Domcke, W. Chem Phys 2003, 294, 73;
89. (c) Sobolewski, A. L.; Domcke, W.; Hattig, C. Proc Natl Acad Sci USA 2005, 102, 17903.
90. Perun, S.; Sobolewski, A. L.; Domcke, W. J Phys Chem A 2006, 110, 9031.
91. Markwick, P. R. L.; Doltsinis, N. L. J Chem Phys 2007, 126, 175102.
92. Schultz, T.; Samoylova, E.; Tadloff, W.; Hertel, I. V.; Sobolewski, A. L.; Domcke, W. Science 2004, 306, 1765.
93. Schwalb, N. K.; Temps, F. J Am Chem Soc 2007, 129, 9272.