第一性原理方法预测水相核酸碱基及其代谢物的氧化还原电动势

doi:10.3866/PKU.WHXB20110333

Abstract

Abstract:

Redox potentials are of importance in understanding the charge/electron transfer processes involved in nucleic acids. In this study, the protocol of the B3LYP/6-311++G(2df,2p)//B3LYP/6-31+G(d) in gas phase and the HF-COSMORS/UAHF for the solvation energy calculations at the HF-CPCM/UAHF re-optimized solution geometries in aqueous solution, as implemented in the Gaussian 03 programs, has been established to predict the redox potentials of the aromatic compounds in aqueous solution. In comparison with the 82 experimental redox potentials, the root mean square deviation (RMSD) is only 0.124 V. This scheme has been employed successfully to calculate the redox potentials of various nucleobases and the metabolites. The structural and charge/electron transfer impact on the redox potentials was discussed. The implications to the design of new redox-active nucleobase derivatives were suggested.

Key words: First-principles method, Redox potential, Nucleobases, Metabolites, Aqueous solution

MSC2000:

O641

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LI Min-Jie, LIU Wei-Xia, PENG Chun-Rong, LU Wen-Cong. A First-Principles Method for Predicting Redox Potentials of Nucleobases and the Metabolites in Aqueous Solution[J].Acta Phys. -Chim. Sin., 2011, 27(03): 595-603.

References

(1) Steenken, S.; Telo, J. P.; Novais, H. M.; Candeias, L. P. J. Am. Chem. Soc. 1992, 114, 4701.
(2) (a) Colson, A. O.; Sevilla, M. D. Int. J. Radiat. Biol. 1995, 67, 627. (b) Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2001, 105, 10115. (c) Li, X.; Sevilla, M. D.; Sanche, L. J. Phys. Chem. B 2004, 108, 5472. (d) Li, X.; Sanche, L.; Sevilla, M. D. J. Phys. Chem. B 2004, 108, 19013.
(3) Desfrancois, D.; Abdoul-Carime, H.; Schermann, J. P. J. Chem.Phys. 1996, 104, 7792.
(4) Huels, M. A.; Hahndorf, I.; Illengerger, E.; Sanche, L. J. Chem. Phys. 1998, 108, 1309.
(5) (a) Li, M. J.; Liu, L.; Wei, K.; Fu, Y.; Guo, Q. X. J. Phys. Chem. B 2006, 110, 13582. (b) Li, M. J.; Liu, L.; Fu, Y.; Guo, Q. X. J. Phys. Chem. B 2005, 109, 13818.
(6) Burrows, C. J.; Muller, J. G.; Chem. Rev. 1998, 98, 1109.
(7) Kelley, S. O.; Barton, J. K. Science 1999, 283, 375.
(8) Berlin, Y. A.; Burin, A. L.; Ratner, M. A. J. Am. Chem. Soc. 2001, 123, 260.
(9) (a) Giese, B.; Amaudrut, J.; K?hler, A. K.; Spormann, M.; Wessely, S. Nature 2001, 412, 318. (b) Giese, B. Accounts Chem. Res. 2000, 33, 631.
(10) (a) Anusiewicz, I.; Berdys-Kochanska, J.; Sobczyk, M.; Skurski, P.; Simons, J. J. Phys. Chem. A 2004, 108, 11381. (b) Anusiewicz, I.; Sobczyk, M.; Berdys-Kochanska, J.; Skurski, P.; Simons, J. J. Phys. Chem. A 2005, 109, 484.
(11) LaVerne, J. A.; Pimblott, S. M. Radiat. Res. 1995, 141, 208.
(12) (a) Gu, J. D.; Xie, Y. M.; Schaefer, H. F. J. Am. Chem. Soc. 2005, 127, 1053. (b) Hou, R.; Gu, J.; Xie, Y.; Yi, X.; Schaefer, H. F. J. Phys. Chem. B 2005, 109, 22053. (c) Gu, J. D.; Xie, Y. M.; Schaefer, H. F. J. Am. Chem. Soc. 2006, 128, 1250. (d) Gu, J. D.; Xie, Y. M.; Schaefer, H. F. Nucleic Acids Res. 2007, 35, 5165. (e) Lyngdoh, R. H. D.; Schaefer, H. F. Accounts Chem. Res. 2009, 42, 563. (f) Jaeger H. M. and Schaefer, H. F. J. Phys. Chem. B 2009, 113, 8142.
(13) Li, X.; Sevilla, M. D.; Sanche, L. J. Am. Chem. Soc. 2003, 125, 13668.
(14) (a) Berdys, J.; Anusiewicz, I.; Skurski, P.; Simons, J. J. Am. Chem. Soc. 2004, 126, 6441. (b) Berdys, J.; Skurski, P.; Simons, J. J. Phys. Chem. B 2004, 108, 5800.
(15) Hendricks, J. H.; Lyapustina, S. A.; de Clercq, H. L.; Bowen, K. H. J. Chem. Phys. 1998, 108, 8.
(16) (a) Fu, Y.; Liu, L.; Yu, H. Z.; Wang, Y. M.; Guo, Q. X. J. Am. Chem. Soc. 2005, 127, 7227. (b) Fu, Y.; Liu, L.; Wang, Y. M.; Li, J. N.; Yu, T. Q.; Guo, Q. X. J. Phys. Chem. A 2006, 110, 5874. (c) Feng, Y.; Liu, L.; Fang, Y.; Guo, Q. X. J. Phys. Chem. A 2002, 106, 11518.
(17) Abraham, J.; Gosh, A. K.; Schuster, G. B. J. Am. Chem. Soc. 2006, 128, 5346.
(18) Becker, D.; Sevilla, M. D. Adv. Radiat. Biol. 1993, 17, 121.
(19) Baik, M. H.; Silverman, J. S.; Yang, I. V.; Ropp, P. A.; Szalai, V. A.;Yang, W. T.; Thorp, H. H. J. Phys. Chem. B 2001, 105, 6437.
(20) Baik, M.-H.; Ziegler, T.; Schauer, C. K. J. Am. Chem. Soc. 2000, 122, 9143.
(21) Kettle, L. J.; Bates, S. P.; Mount, A. R. Phys. Chem. Chem. Phys. 2000, 2, 195.
(22) Trasatti, S. Pure Appl. Chem. 1986, 58, 955.
(23) (a) Kawai, K.; Wata, Y.; Ichinose, N.; Majima, T. Angew. Chem. Int. Edit. 2000, 39, 4327. (b) Kawai, K.; Wata, Y.; Hara, M.; Tojo, S.; Majima, T. J. Am. Chem. Soc. 2002, 124, 3586. (c) Kawai, K.; Takada, T.; Tojo, S.; Ichinose, N.; Majima, T. J. Am. Chem. Soc. 2001, 123, 12688.
(24) (a) Caruso, T.; Carotenuto, M.; Vasca, E.; Peluso, A. J. Am. Chem. Soc. 2005, 127, 15040. (b) Caruso, T.; Capobianco, A.; Peluso, A. J. Am. Chem. Soc. 2007, 129, 15347.
(25) (a) Lewis, F. D. Photochem. Photobiol. 2005, 81, 65. (b) Lewis, F. D.; Letsinger, R. L.; Wasielewski, M. R. Accounts Chem. Res. 2001, 34, 159.
(26) (a) Steenken, S.; Jovanovic, S. V.; Bietti, M.; Bernhard, K. J. Am. Chem. Soc. 2000, 122, 2373. (b) Steenken, S. Biol. Chem. 1997, 378, 1293. (c) Steenken, S. Chem. Rev. 1989, 89, 503. (d) Jovanovic, S. V.; Simic, M. G. J. Phys. Chem. 1986, 90, 974.
(27) Steenken, S.; Jovanovic, S. V. J. Am. Chem. Soc. 1997, 119, 617.
(28) (a) Close, D. M. J. Phys. Chem. A 2004, 108, 10376. (b) Crespo-Hernández, C. E.; Arce, R.; Ishikawa, Y.; Gorb, L.; Leszczynski, J.; Close, D. M. J. Phys. Chem. A 2004, 108, 6373. (c) Close, D. M.; Øhman, K. T. J. Phys. Chem. A 2008, 112, 11207. (d) Close, D. M. J. Phys. Chem. A, 2008, 112, 8411. (e) Close, D. M.; Crespo-Hernández, C. E.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2006, 110, 7485.
(29) Fukuzumi, S.; Miyao, H.; Ohkubo, K.; Suenobu, T. J. Phys. Chem. A 2005, 109, 3285.
(30) Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem. 1996, 100, 5541.
(31) Lecomte, J. P.; Kirsch-De Mesmaeker, A.; Kelly, J. M.; Tossi, A. B.; Görner, H. Photochem. Photobiol. 1992, 55, 681.
(32) Langmaier, J.; Samec, Z.; Samcová, E.; Hobza, P.; Reha, D. J. Phys. Chem. B 2004, 108, 15896.
(33) Kittler, L.; L?ber, G.; Gollmick, F.; Berg, H. J. Electroanal. Chem. 1980, 116, 503.
(34) Oliveira-Brett, A. M.; Piedade, J. A. P.; Silva, L. A.; Diculescu, V. C. Anal. Biochem. 2004, 332, 321.
(35) Guirado, G.; Fleming, C. N.; Lingenfelter, T. G.; Williams, M. L.; Zuihof, H.; Dinnocenzo, J. P. J. Am. Chem. Soc. 2004, 126, 14086.
(36) Fiebig, T.; Wan, C.; Zewail, A. H. Chem. Phys. Chem. 2002, 3,781.
(37) Crespo-Hernández, C. E.; Close, D. M.; Gorb, L.; Leszczynski, J. J. Phys. Chem. B 2007, 111, 5386.
(38) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B. et al. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004
(39) Klamt, A.; Schüürmann, G. J. Chem. Soc. Perkin Trans. 1993, 2, 799.
(40) (a) Barone, V.; Cossi, M. J. Phem. Chem. A 1998, 102, 1995. (b) Fu, Y.; Wang, H. J.; Chong, S. S.; Guo, Q. X.; Liu, L. J. Org. Chem. 2009, 74, 810. (c) Fu, Y.; Liu, L.; Li, R. Q.; Liu, R.; Guo, Q. X. J. Am. Chem. Soc. 2004, 126, 814.
(41) Liptak, D.; Gross, K. C.; Seybold, P. G.; Feldgus, S.; Shields, G. C. J. Am. Chem. Soc. 2002, 124, 6421.
(42) Suatoni, J. C.; Snyder, R. E.; Clark, R. O. Anal. Chem. 1961, 33, 1894
(43) Faraggi, M.; Broitman, F.; Trent, J. B.; Klapper, M. H. J. Phys. Chem. 1996, 100, 14751.
(44) Lias, S. G.; Bartmess, J. E.; Liebman, J. F.; Holmes, J. L.; Levin R. D.; Mallard, W. G. J. Phys. Chem. Ref. Data, 1988, 17, Supplement 1.
(45) Prat, F.; Houk, K. N.; Foote, C. S. J. Am. Chem. Soc. 1998, 120, 845.
(46) Grinstaff, M. W. Angew. Chem. Int. Edit. 1999, 38, 3629.
(47) Schuster, G. B. Accounts Chem. Res. 2000, 33, 253.

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A First-Principles Method for Predicting Redox Potentials of Nucleobases and the Metabolites in Aqueous Solution

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