Mechanistic study of the deamination reaction of guanine: A computational study

Journal of Physical Chemistry A

Volumn 115, Issue 10, 2011, Pages 2065-2076

  Uddin, Kabir M ^a   Almatarneh, Mansour H ^a   Shaw, Dawn M ^a   Poirier, Raymond A ^a  

^a MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATIONS; B3LYP/6-31G; CBS-QB3; COMPUTATIONAL STUDIES; DEAMINATION REACTION; INTRINSIC REACTION COORDINATE; MECHANISTIC STUDIES; MP2/6-31G; OPTIMIZED GEOMETRIES; RHF/6-31G; TETRAHEDRAL INTERMEDIATES; TRANSITION STATE;

AMINES; CALCULATIONS; POSITIVE IONS; QUANTUM CHEMISTRY;

ACTIVATION ENERGY;

GUANINE; HYDROXIDE; HYDROXIDE ION; PROTON; WATER;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DEAMINATION; QUANTUM THEORY; THERMODYNAMICS;

DEAMINATION; GUANINE; HYDROXIDES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTONS; QUANTUM THEORY; THERMODYNAMICS; WATER;

EID: 79952614481     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp1120806     Document Type: Article

References (55)

1. Neidle, S. Oxford Hand Book of Nucleic Acid Structure; Oxford University Press Inc.: New York, 1999.
2. Strazewski, P. Nucleic Acids Res. 1988, 16, 9377
3. Topal, M. B.; Fresco, J. R. Nature 1976, 263, 285
4. Friedberg, E. C.; Walker, G. C.; Siede, W. DNA Repair and Mutagenesis: American Society for Microbiology: Washington, DC, 1995.
5. Burrows, C. J.; Muller, J. G. Chem. Rev. 1998, 98, 1109-1151
6. Wakabayashi, K., In Mutation and the Environment; Albertini, R. J., Ed.; Wiley-Liss: New York, 1990; Part E, pp 107 - 116.
7. Streckers, A. Liebigs Ann. Chem. 1861, 118, 151-156
8. Kossel, A.; Neumann, A. Z. Physiol. Chem. 1894, 27, 950-955
9. Kossel, A. Berichte 1985, 18, 1929-1930
10. Geiduschek, E. P. Proc. Natl. Acad. Sci. U.S.A. 1961, 47, 950-955
11. Geiduschek, E. P. J. Mol. Biol. 1962, 4, 467-487
12. Caulfield, J. L.; Wishnok, J. S.; Tannenbaum, S. R. Chem. Res. Toxicol. 2003, 16, 571-574
13. Chen, H.; Shaw, B. R. Biochemistry 1993, 32, 3535-3539
14. Shapiro, R.; Servis, R. E.; Welcher, M. J. Am. Chem. Soc. 1970, 92, 422-424
15. Slae, S.; Shapiro, R. J. Org. Chem. 1978, 43, 1721-1726
16. Ehrlich, M.; Norris, K. F.; Wang, R. Y.H.; Kuo, K. C.; Gehrke, C. W. Biosci. Rep. 1986, 6, 387-393
17. Ullmann, J. S.; McCarthy, B. J. Biochim. Biophys. Acta 1973, 294, 396-404
18. Shapiro, R.; Klein, R. S. Biochemistry 1967, 11, 3576-3582
19. Yao, L.; Cukier, R. I.; Yan, H. J. Phys. Chem. B 2007, 111, 4200-4210
20. Nygaard, P.; Bested, S. M.; Andersen, K. A. K.; Saxild, H. H. Microbiology 2000, 146, 3061-3069
21. Yao, L.; Li, Y.; Wu, Y.; Liu, A.; Yan, H. Biochemistry 2005, 44, 5940-5947
22. Zhang, A.; Yang, B.; Li, Z. J. Mol. Struct. 2007, 819, 95-10
23. Sponer, J. E.; Miguel, P. J.; Rodriguez-Santiago, Erxleben, A.; Krumm, M.; Sodupe, M.; Sponer, J.; Lippert, B. Angew. Chem., Int. Ed. 2004, 43, 5396-5399
24. Frederico, L. A.; Kunkel, T. A.; Shaw, B. R. Biochemistry 1990, 29, 2532-2537
25. Lindahl, T.; Nyberg, B. Biochemistry 1974, 13, 3405-3410
26. Rayat, S.; Wu, Z.; Glaser, R. Chem. Res. Toxicol. 2004, 17, 1157-1169
27. Rayat, S.; Qian, M.; Glaser, R. Chem. Res. Toxicol. 2005, 18, 1211-1218
28. Glaser, R.; Wu, H.; Lewis, M. J. Am. Chem. Soc. 2005, 127, 7346-7358
29. Matsubara, T.; Ishikura, M.; Aida, M. J. Chem. Inf. Model. 2006, 46, 1276-1285
30. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O. M.; Nakai, H.; Vreven, T.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; R.; Bearpark; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; J. C.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Revision A.02, Gaussian, Inc.: Wallingford, CT, 2009.
31. Almatarneh, M. H.; Flinn, C. G.; Poirier, R. A. Can. J. Chem. 2005, 83, 2082-2090
32. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K.; Rassolov, V.; Pople, J. A. J. Chem. Phys. 1999, 110, 4703-4709
33. Baboul, A. G.; Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys. 1999, 110, 7650-7657
34. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys. 2007, 126, 084108:1-12
35. Curtiss, L. A.; Redfern, P. C.; Raghavachari, K. J. Chem. Phys. 2007, 127, 124105:1-8
36. Wood, G. P. F.; Radom, L.; Petersson, G. A.; Barnes, E. C.; Frisch, M. J.; Montgomery, J., Jr. J. Chem. Phys. 2006, 125, 094106:1-16
37. Yanai, T.; Tew, D.; Handy, N. Chem. Phys. Lett. 2004, 393, 51-57
38. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 364-382
39. Almatarneh, M. H.; Flinn, C. G.; Poirier, R. A.; Sokalski, W. A. J. Phys. Chem. A 2006, 110, 8227-8234
40. Chen, X.; Syrstad, E. A.; Nguyen, M. T.; Gerbaux, P.; Turecek, F. J. Phys. Chem. A 2004, 108, 9283-9293
41. Chen, X.; Syrstad, E. A.; Nguyen, M. T.; Gerbaux, P.; Turecek, F. J. Phys. Chem. A 2005, 109, 8121-8132
42. Jang, Y. H.; Goddard, W. A., III; Noyes, K. T.; Sowers, L. C.; Hwang, S.; Chung, D. S. J. Phys. Chem. B 2003, 107, 344-357
43. Zhachkina, A.; Liu, M.; Sun, X.; Amegayibor, F. S.; Lee, J. K. J. Org. Chem. 2009, 74, 7429-7440
44. Chandra, A. K.; Nguyen, M. T.; Uchimaru, T; Zeegers-Huyskens, T. J. Phys. Chem. A 1999, 103, 8853-8860
45. Hohenstein, E. G.; Chill, S. T.; Sherrill, C. D. J. Chem. Theory Comput. 2008, 4, 1996-2000
46. Tsuzuki, S.; Lüthi, H. P. J. Chem. Phys. 2001, 114, 3949-3957
47. Ĉerný, J.; Hobza, P. Phys. Chem. Chem. Phys. 2005, 7, 1624-1626
48. Hobza, P.; Sponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315-1325
49. Johnson, E. R.; Wolkow, R. A.; DiLabio, G. A. Chem. Phys. Lett. 2004, 394, 334-338
50. Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215-241
51. RodrPguez-Santiago, L.; Vendrell, O.; Tejero, I.; Sodupe, M.; Bertran, J. Chem. Phys. Lett. 2001, 334, 112-118
52. Almatarneh, M. H.; Flinn, C. G.; Poirier, R. A. J. Chem. Inf. Model. 2008, 48, 831-843
53. Wang, B.; Cao, Z. J. Phys. Chem. A 2010, 114, 12918-12927
54. Wu, Y.; Jin, L.; Xue, Y.; Xie, D. Q.; Kim, C. K.; Guo, Y.; Yan, S. Y. J. Comput. Chem. 2008, 29, 1222-1232
55. Chen, Z.; Xue, Y. J. Phys. Chem. B 2010, 114, 12641-12654