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.
1. [1]
  Xin XIONG , Qian CHEN , Quan XIE . First principles study of the photoelectric properties and magnetism of La and Yb doped AlN. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1519-1527. doi: 10.11862/CJIC.20240064
2. [2]
  Jin CHANG . Supercapacitor performance and first-principles calculation study of Co-doping Ni(OH)₂. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1697-1707. doi: 10.11862/CJIC.20240108
3. [3]
  Zhenming Xu , Mingbo Zheng , Zhenhui Liu , Duo Chen , Qingsheng Liu . Experimental Design of Project-Driven Teaching in Computational Materials Science: First-Principles Calculations of the LiFePO₄ Cathode Material for Lithium-Ion Batteries. University Chemistry, 2024, 39(4): 140-148. doi: 10.3866/PKU.DXHX202307022
4. [4]
  Xiaowu Zhang , Pai Liu , Qishen Huang , Shufeng Pang , Zhiming Gao , Yunhong Zhang . Acid-Base Dissociation Equilibrium in Multiphase System: Effect of Gas. University Chemistry, 2024, 39(4): 387-394. doi: 10.3866/PKU.DXHX202310021
5. [5]
  Cheng PENG , Jianwei WEI , Yating CHEN , Nan HU , Hui ZENG . First principles investigation about interference effects of electronic and optical properties of inorganic and lead-free perovskite Cs₃Bi₂X₉ (X=Cl, Br, I). Chinese Journal of Inorganic Chemistry, 2024, 40(3): 555-560. doi: 10.11862/CJIC.20230282
6. [6]
  Ruming Yuan , Pingping Wu , Laiying Zhang , Xiaoming Xu , Gang Fu . Patriotic Devotion, Upholding Integrity and Innovation, Wholeheartedly Nurturing the New: The Ideological and Political Design of the Experiment on Determining the Thermodynamic Functions of Chemical Reactions by Electromotive Force Method. University Chemistry, 2024, 39(4): 125-132. doi: 10.3866/PKU.DXHX202311057
7. [7]
  Chuanming GUO , Kaiyang ZHANG , Yun WU , Rui YAO , Qiang ZHAO , Jinping LI , Guang LIU . Performance of MnO₂-0.39IrO_x composite oxides for water oxidation reaction in acidic media. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1135-1142. doi: 10.11862/CJIC.20230459
8. [8]
  Ji-Quan Liu , Huilin Guo , Ying Yang , Xiaohui Guo . Calculation and Discussion of Electrode Potentials in Redox Reactions of Water. University Chemistry, 2024, 39(8): 351-358. doi: 10.3866/PKU.DXHX202401031
9. [9]
  Yanhui Zhong , Ran Wang , Zian Lin . Analysis of Halogenated Quinone Compounds in Environmental Water by Dispersive Solid-Phase Extraction with Liquid Chromatography-Triple Quadrupole Mass Spectrometry. University Chemistry, 2024, 39(11): 296-303. doi: 10.12461/PKU.DXHX202402017
10. [10]
  Haiyang Zhang , Yanzhao Dong , Haojie Li , Ruili Guo , Zhicheng Zhang , Jiangjiexing Wu . Exploring the Integration of Chemical Engineering Principle Experiment with Cutting-Edge Research Achievements. University Chemistry, 2024, 39(10): 308-313. doi: 10.12461/PKU.DXHX202405035
11. [11]
  Xiaofeng Zhu , Bingbing Xiao , Jiaxin Su , Shuai Wang , Qingran Zhang , Jun Wang . Transition Metal Oxides/Chalcogenides for Electrochemical Oxygen Reduction into Hydrogen Peroxides. Acta Physico-Chimica Sinica, 2024, 40(12): 2407005-. doi: 10.3866/PKU.WHXB202407005
12. [12]
  Tongyu Zheng , Teng Li , Xiaoyu Han , Yupei Chai , Kexin Zhao , Quan Liu , Xiaohui Ji . A DIY pH Detection Agent Using Persimmon Extract for Acid-Base Discoloration Popularization Experiment. University Chemistry, 2024, 39(5): 27-36. doi: 10.3866/PKU.DXHX202309107
13. [13]
  Kai CHEN , Fengshun WU , Shun XIAO , Jinbao ZHANG , Lihua ZHU . PtRu/nitrogen-doped carbon for electrocatalytic methanol oxidation and hydrogen evolution by water electrolysis. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1357-1367. doi: 10.11862/CJIC.20230350
14. [14]
  Qingqing SHEN , Xiangbowen DU , Kaicheng QIAN , Zhikang JIN , Zheng FANG , Tong WEI , Renhong LI . Self-supporting Cu/α-FeOOH/foam nickel composite catalyst for efficient hydrogen production by coupling methanol oxidation and water electrolysis. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1953-1964. doi: 10.11862/CJIC.20240028
15. [15]
  Yuena Yang , Xufang Hu , Yushan Liu , Yaya Kuang , Jian Ling , Qiue Cao , Chuanhua Zhou . The Realm of Smart Hydrogels. University Chemistry, 2024, 39(5): 172-183. doi: 10.3866/PKU.DXHX202310125
16. [16]
  Jiaxin Su , Jiaqi Zhang , Shuming Chai , Yankun Wang , Sibo Wang , Yuanxing Fang . Optimizing Poly(heptazine imide) Photoanodes Using Binary Molten Salt Synthesis for Water Oxidation Reaction. Acta Physico-Chimica Sinica, 2024, 40(12): 2408012-. doi: 10.3866/PKU.WHXB202408012
17. [17]
  Gaoyan Chen , Chaoyue Wang , Juanjuan Gao , Junke Wang , Yingxiao Zong , Kin Shing Chan . Heart to Heart: Exploring Cardiac CT. University Chemistry, 2024, 39(9): 146-150. doi: 10.12461/PKU.DXHX202402011
18. [18]
  Qin Hou , Jiayi Hou , Aiju Shi , Xingliang Xu , Yuanhong Zhang , Yijing Li , Juying Hou , Yanfang Wang . Preparation of Cuprous Iodide Coordination Polymer and Fluorescent Detection of Nitrite: A Comprehensive Chemical Design Experiment. University Chemistry, 2024, 39(8): 221-229. doi: 10.3866/PKU.DXHX202312056
19. [19]
  Limin Shao , Na Li . A Unified Equation Derived from the Charge Balance Equation for Constructing Acid-Base Titration Curve and Calculating Endpoint Error. University Chemistry, 2024, 39(11): 365-373. doi: 10.3866/PKU.DXHX202401086
20. [20]
  Yunting Shang , Yue Dai , Jianxin Zhang , Nan Zhu , Yan Su . Something about RGO (Reduced Graphene Oxide). University Chemistry, 2024, 39(9): 273-278. doi: 10.3866/PKU.DXHX202306050

Get Citation

PDF

XML

Metrics

PDF Downloads(1102)
Abstract views(2314)
HTML views(4)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142