Tautomerism of 1-methyl derivatives of uracil, thymine, and 5-bromouracil. Is tautomerism the basis for the mutagenicity of 5-bromouridine?

Journal of Physical Chemistry B

Volumn 102, Issue 26, 1998, Pages 5228-5233

  Orozco, Modesto ^a   Hernández, Begoña ^a   Luque, F Javier ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84962469231     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp981005+     Document Type: Article

References (66)

1. (a) Blackburn, G. M. In Nucleic Acids in Chemistry and Biology; Blackburn, G. N., Gait, M. J., Eds.; IRL Press: Oxford, 1990; Chapter 2.
2. (b) Saenger, W. In Principles of Nucleic Acid Structure; Springer-Verlag; New York, 1988.
3. (c) Sinden, R. R. In DNA Structure and Function; Academic Press: San Diego, 1994.
4. Topal, M. D.; Fresco, J. R. Nature 1976, 263, 285.
5. Sowers, L. C.; Fazakerley, G. C.; Eritja, R.; Kaplan, B. E.; Goodman, M. F. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 5434.
6. Sowers, L. C.; Goodman, M. F.; Eritja, R.; Kaplan, B. E.; Fazakerley, G. C. J. Mol. Biol. 1989, 205, 437.
7. Goodman, N. F. Proc. Natl. Acad Sci. U.S.A. 1997, 94, 10493.
8. (a) Piccirilli, J. A.; Moroney, S. E.; Benner, S. A. Biochemistry 1991, 30, 10350.
9. (b) Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature 1990, 343, 33.
10. (c) Benner, S. A.; Ellington, A. D.; Tauer, A. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 7054.
11. Söll, D.; Rajbhandary, U. In Nucleic Acids in Chemistry and Biology; Blackburn, G. N., Gait, M. J., Eds.; IRL Press: Oxford, 1990; Chapter 6.
12. McCloskey, J. A.; Nishimura, S. Acc. Chem. Res. 1977, 10, 403.
13. Schweitzer, B. A.; Kool, E. T. J. Am. Chem. Soc. 1995, 117, 1863.
14. Danenberg, P. V.; Heidelberger, C.; Mulkins, M. A.; Peterson, A. R. Biochem. Biophys. Res., Commun. 1981, 102, 617.
15. Moran, S.; Ren, R.; Kool, E. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10506.
16. Yu, H.; Eritja, R.; Bloom, L. B.; Goodman, M. F. J. Biol. Chem. 1993, 268, 15935.
17. (a) Sowers, L. C.; Eritja, R.; Kaplan, B. E.; Goodman, M. F.; Fazakerley, G. V. J. Biol. Chem. 1987, 202, 15436.
18. (b) Fazakerley, G. V.; Sowers, L. C.; Eritja, R.; Kaplan, B. E.; Goodman, M. F. J. Biomol. Struct. Dyn. 1987, 5, 639.
19. McLean, A. D.; Chandler, G. S. J. Chem. Phys. 1980, 72, 5639.
20. Möller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618.
21. Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta 1978, 28, 213.
22. (a) Alhambra, C.; Luque, F. J.; Estelrich, J.; Orozco, M. J. Org. Chem. 1995, 60, 969.
23. (b) Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 118, 6811.
24. (c) Luque, F. J.; Lopez-Bes, J. M.; Cemeli, J.; Aroztegui, M.; Orozco, M. Theor. Chem. Acc. 1997, 96, 105.
25. Frisch, M. J.; Trucks, G. W.; Schelgel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T. A.; Petersson, G. A.; Montgomery. G. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.,; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian-94, Revision D.3; Gaussian Inc.: Pittsburgh, PA, 1995.
26. (a) Bachs, M.; Luque, F. J.; Orozco, M. J. Comput. Chem. 1994, 15, 446.
27. (b) Luque, F. J.; Bachs, M.; Orozco, M. J. Comput. Chem. 1994, 15, 847.
28. (c) Orozco, M.; Bachs, M.; Luque, F. J. J. Comput. Chem. 1995, 16, 563.
29. (a) Miertus, S.; Scrocco, E.; Tomasi, J. Chem. Phys. 1981, 55, 117.
30. (b) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239.
31. (a) Orozco, M.; Luque, F. J. J. Am. Chem. Soc. 1995, 117, 1378.
32. (b) Hernandez, B.; Luque, F. J.; Orozco, M. J. Org. Chem. 1996, 61, 5964.
33. (c) Hernandez, B.; Orozco, M.; Luque, F. J. J. Comput. Aided Mol. Des. 1996, 10, 535.
34. (d) Hernandez, B.; Orozco, M.; Luque, F. J. J. Comput. Aided Mol. Des. 1997, 11, 153.
35. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420.
36. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
37. (a) Bonaccorsi, R.; Scrocco, E.; Petrongolo, C.; Tomasi, J. Theor. Chim. Acta 1971, 20, 331.
38. (b) Momany, F. A. J. Phys. Chem. 1978, 82, 592.
39. (c) Orozco, M.; Luque, F. J. J. Comput. Aided Mol. Des. 1990, 4, 31.
40. Pranata, J.; Wierschke, S. G.; Jorgensen, W. L. J. Am. Chem. Soc. 1991, 113, 2810.
41. 3Br molecule. SCF values were corrected for basis set superposition error using the counterpoise method. A total of 15 configurations for the dimer, corresponding to different Br-O distances, were selected. The error in the location of the minima was 0.0 Å (in Br-O distance), the error at the minimum was 0.1 kcal/mol, and the rms error in the fitting was 0.5 kcal/mol.
42. (a) Gilson, M. K.; Honig, P. H. Nature 1987, 330, 84.
43. (b) Gilson, M. K.; Honig, P. H. Proteins 1988, 4, 7.
44. (c) DELPHI (computer program); Biosym Co.: San Diego, 1994.
45. Arnott, S.; Hukins, D. W. L. Biochem. Biophys. Res. Commun. 1972, 47, 1504.
46. Peterson, M.; Poirier, R. MONSTERGAUSS; Department of Chemistry, University of Toronto: Canda (version modified by Cammi, R.; Bonaccorsi, R.; Tomasi, J. in 1987 and by Luque, F. J.; Orozco, N. in 1995).
47. Dupuis, M.; Farazdel, A.; Karma, S. A.; Maluendes, S. HONDO-8, IBM Corporation Scientific and Engineering Computations; IBM Corporation: Kingston, NY (modified by Cossi, M.; Cammi, R.; Tomasi, J. in 1994).
48. Luque, F. J.; Orozco, M. MOPETE/MOPFIT (computer programs); University of Barcelona: Spain, 1998.
49. Jorgensen, W. L. BOSS 3.4 (computer program); Yale University: New Haven, CT, 1993.
50. (a) Green, D. W.; Mathews, F. S.; Rich, A. J. Biol. Chem. 1962, 237, 3573.
51. (b) Shugar, D.; Szczepaniak, J. Int. J. Quantum Chem. 1981, 20, 573.
52. (c) Beak, P.; White, J. M. J. Am. Chem. Soc. 1982, 104, 7073.
53. (d) Fujii, M.; Tamura, T.; Mikami, N.; Ito, M. Chem. Phys. Lett. 1986, 126, 583.
54. (e) Brady, B. H.; Peteanu, L. A.; Levy, D. H. Chem. Phys. Lett. 1986, 126, 583.
55. (f) Tsuchiya, Y.; Tamura, T.; Fujii, M.; Ito, M. J. Phys. Chem. 1988, 92, 1760.
56. (g) Zwierzchowska, Z.; Dobrosz-Teperek, K.; Lewandowski, W.; Kolos, R.; Bajdor, K.; Dobrowolski, J. C.; Mazurek, A. P. J. Mol. Struct. 1997, 410, 415.
57. (a) Leszcynski, J. Int. J. Quantum Chem., Quantum Biol. Symp. 1991, 18, 9.
58. (b) Leszcynski, J. J. Phys. Chem. 1992, 96, 1649 and references therein.
59. (c) Boughton, J. W.; Pulay, P. Int. J. Quantum Chem. 1993, 47, 49.
60. (d) Gould, I. R.; Burton, N. A.; Hall, R. J.; Hillier, I. H. J. Mol. Struct.: THEOCHEM 1995, 331, 147.
61. (e) Marino, T.; Russo, N.; Toscano, M. Int. J. Quantum Chem. 1997, 62, 459.
62. (a) Marshall, J. R.; Walker, J. J. Chem. Soc. 1951, 1005.
63. (b) Katritzky, A. R.; Waring, A. J. J. Chem. Soc. 1962, 1540.
64. (c) Poulter, C. D.; Frederick, G. D. Tetrahedron Lett. 1975, 2171.
65. Poisson Boltzman calculations give only the electrostatic contribution to the solvation free energy. PB is probably less precise than MC-FEP or MST calculations owing to the use of a rigid geometry and a rigid and oversimplified expression of the solute charge distribution. It is not simple to compare PB with MC-FEP or MST calculations. But as a reference, the electrostatic contribution to the free energy of solvation computed from PB calculations for the N3 forms considered here ranges from -22 to -24 kcal/mol (∈ = 1 for solute) and from -12 to -13 kcal/mol (∈ = 2 for the solute). The equivalent MST estimates range between -15 and -17 kcal/ mol.
66. Orozco, M.; Hernandez, B.; Luque, F. J. To be published.