Citation: 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 Physico-Chimica Sinica, ;2011, 27(03): 595-603. doi: 10.3866/PKU.WHXB20110333 shu

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

1.
Department of Chemistry, Shanghai University, Shanghai 200444, P. R. China

Received Date: 2 November 2010
Available Online: 17 February 2011
Fund Project: 国家自然科学基金青年基金(20902056) (20902056) 上海大学创新基金(A.10-0101-08-423) (A.10-0101-08-423)上海市教委第五期重点学科建设项目(J50101)资助 (J50101)

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.
- First-principles method,
- Redox potential,
- Nucleobases,
- Metabolites,
- Aqueous solution
1. [1]
  
  (1) Steenken, S.; Telo, J. P.; Novais, H. M.; Candeias, L. P. J. Am. Chem. Soc. 1992, 114, 4701.
2. [2]
  (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. [3]
  (3) Desfrancois, D.; Abdoul-Carime, H.; Schermann, J. P. J. Chem.Phys. 1996, 104, 7792.
4. [4]
  (4) Huels, M. A.; Hahndorf, I.; Illengerger, E.; Sanche, L. J. Chem. Phys. 1998, 108, 1309.
5. [5]
  (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. [6]
  (6) Burrows, C. J.; Muller, J. G.; Chem. Rev. 1998, 98, 1109.
7. [7]
  (7) Kelley, S. O.; Barton, J. K. Science 1999, 283, 375.
8. [8]
  (8) Berlin, Y. A.; Burin, A. L.; Ratner, M. A. J. Am. Chem. Soc. 2001, 123, 260.
9. [9]
  (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. [10]
  (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. [11]
  (11) LaVerne, J. A.; Pimblott, S. M. Radiat. Res. 1995, 141, 208.
12. [12]
  (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. [13]
  (13) Li, X.; Sevilla, M. D.; Sanche, L. J. Am. Chem. Soc. 2003, 125, 13668.
14. [14]
  (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. [15]
  (15) Hendricks, J. H.; Lyapustina, S. A.; de Clercq, H. L.; Bowen, K. H. J. Chem. Phys. 1998, 108, 8.
16. [16]
  (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. [17]
  (17) Abraham, J.; sh, A. K.; Schuster, G. B. J. Am. Chem. Soc. 2006, 128, 5346.
18. [18]
  (18) Becker, D.; Sevilla, M. D. Adv. Radiat. Biol. 1993, 17, 121.
19. [19]
  (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. [20]
  (20) Baik, M.-H.; Ziegler, T.; Schauer, C. K. J. Am. Chem. Soc. 2000, 122, 9143.
21. [21]
  (21) Kettle, L. J.; Bates, S. P.; Mount, A. R. Phys. Chem. Chem. Phys. 2000, 2, 195.
22. [22]
  (22) Trasatti, S. Pure Appl. Chem. 1986, 58, 955.
23. [23]
  (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. [24]
  (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. [25]
  (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. [26]
  (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. [27]
  (27) Steenken, S.; Jovanovic, S. V. J. Am. Chem. Soc. 1997, 119, 617.
28. [28]
  (28) (a) Close, D. M. J. Phys. Chem. A 2004, 108, 10376. (b) Crespo-Hernández, C. E.; Arce, R.; Ishikawa, Y.; rb, 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.; rb, L.; Leszczynski, J. J. Phys. Chem. A 2006, 110, 7485.
29. [29]
  (29) Fukuzumi, S.; Miyao, H.; Ohkubo, K.; Suenobu, T. J. Phys. Chem. A 2005, 109, 3285.
30. [30]
  (30) Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem. 1996, 100, 5541.
31. [31]
  (31) Lecomte, J. P.; Kirsch-De Mesmaeker, A.; Kelly, J. M.; Tossi, A. B.; Görner, H. Photochem. Photobiol. 1992, 55, 681.
32. [32]
  (32) Langmaier, J.; Samec, Z.; Samcová, E.; Hobza, P.; Reha, D. J. Phys. Chem. B 2004, 108, 15896.
33. [33]
  (33) Kittler, L.; L?ber, G.; llmick, F.; Berg, H. J. Electroanal. Chem. 1980, 116, 503.
34. [34]
  (34) Oliveira-Brett, A. M.; Piedade, J. A. P.; Silva, L. A.; Diculescu, V. C. Anal. Biochem. 2004, 332, 321.
35. [35]
  (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. [36]
  (36) Fiebig, T.; Wan, C.; Zewail, A. H. Chem. Phys. Chem. 2002, 3,781.
37. [37]
  (37) Crespo-Hernández, C. E.; Close, D. M.; rb, L.; Leszczynski, J. J. Phys. Chem. B 2007, 111, 5386.
38. [38]
  (38) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B. et al. Gaussian 03, Revision C.02; Gaussian, Inc.: Wallingford, CT, 2004
39. [39]
  (39) Klamt, A.; Schüürmann, G. J. Chem. Soc. Perkin Trans. 1993, 2, 799.
40. [40]
  (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. [41]
  (41) Liptak, D.; Gross, K. C.; Seybold, P. G.; Feldgus, S.; Shields, G. C. J. Am. Chem. Soc. 2002, 124, 6421.
42. [42]
  (42) Suatoni, J. C.; Snyder, R. E.; Clark, R. O. Anal. Chem. 1961, 33, 1894
43. [43]
  (43) Faraggi, M.; Broitman, F.; Trent, J. B.; Klapper, M. H. J. Phys. Chem. 1996, 100, 14751.
44. [44]
  (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. [45]
  (45) Prat, F.; Houk, K. N.; Foote, C. S. J. Am. Chem. Soc. 1998, 120, 845.
46. [46]
  (46) Grinstaff, M. W. Angew. Chem. Int. Edit. 1999, 38, 3629.
47. [47]
  (47) Schuster, G. B. Accounts Chem. Res. 2000, 33, 253.
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