Effects of hydrogen bonding on the acidity of uracil

Journal of Physical Chemistry A

Volumn 107, Issue 48, 2003, Pages 10406-10413

  Di Laudo, Mariana ^a   Whittleton, Sarah R ^a   Wetmore, Stacey D ^a  

^a MOUNT ALLISON UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA GLYCOSYLASE; HYDROGEN BONDING INTERACTIONS; HYDROGEN FLUORIDE; URACIL;

ACIDITY; BINDING ENERGY; BIOCHEMISTRY; BOND STRENGTH (CHEMICAL); DNA; ENZYMES; HYDROGEN BONDS; MOLECULAR STRUCTURE; NEGATIVE IONS; PROBABILITY DENSITY FUNCTION;

HYDROCARBONS;

EID: 0346947348     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp035496w     Document Type: Article

References (91)

1. For a review of hydrogen bonding in biological systems, see: Jeffrey, G. A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: New York, 1994.
2. Port, G. N. J.; Pullman, A. FEBS Lett. 1973, 31, 70-74.
3. Pullman, B.; Miertus, Š.; Perahia, D.; Theor. Chim. Acta 1979, 50, 317.
4. Del Bene, J. E. J. Comput. Chem. 1981, 2, 188.
5. Scheiner, S. Biopolymers 1983, 22, 731.
6. Del Bene, J. E. J. Comput. Chem. 1983, 4, 226.
7. Sagarik, K.; Corongiu, G.; Clementi, E. J. Mol. Struct. (THEOCHEM) 1991, 81, 355.
8. Rybak, S.; Szalewicz, K.; Jeziorski, B.; Corongiu, G. Chem. Phys. Lett. 1992, 199, 567-573.
9. Ghomi, M.; Aamouche, A.; Cadioli, B.; Berthier, G.; Grajcar, L.; Baron, M. H. J. Mol. Struct. 1997, 410, 323-326.
10. Aamouche, A.; Berthier, G.; Cadioli, B.; Gallinella, E.; Ghomi, M. J. Mol. Struct. (THEOCHEM) 1998, 426, 307-312.
11. Nguyen, M. T.; Chandra, A. K.; Zeegers-Huyskens, T. J. Chem. Soc., Faraday Trans. 1998, 94, 1277-1280.
12. Chandra, A. K.; Nguyen, M. T.; Zeegers-Huyskens, T. J. Phys. Chem. A 1998, 102, 6010-6016.
13. Chandra, A. K.; Nguyen, M. T.; Uchimaru, T.; Zeegers-Huyskens, T. J. Phys. Chem. A 1999, 103, 8853-8860.
14. van Mourik, T.; Price, S. L.; Clary, D. C. J. Phys. Chem. A 1999, 103, 1611-1618.
15. Bencivenni, L.; Ramondo, F.; Pieretti, A.; Sanna, N. J. Chem. Soc., Perkin Trans. 2 2000, 1685-1693.
16. Gadre, S. R.; Babu, K.; Rendell, A. P. J. Phys. Chem. A 2000, 104, 8976-8982.
17. van Mourik, T.; Benoit, D. M.; Price, S. L.; Clary, D. C. Phys. Chem. Chem. Phys. 2000, 2, 1281-1290.
18. Shishkin, O. V.; Gorb, L.; Leszczynski, J. Int. J. Mol. Sci. 2000, 1, 17-27.
19. van Mourik, T. Phys. Chem. Chem. Phys. 2001, 3, 2886-2892.
20. Gaigeot, M.-P.; Kadri, C.; Ghomi, M. J. Mol. Struct. (THEOCHEM) 2001, 565-566, 469-473.
21. Gaigeot, M. P.; Ghomi, M. J. Phys. Chem. B 2001, 105, 5007-5017.
22. Kryachko, E.; Nguyen, M. T.; Zeegers-Huyskens, T. J. Phys. Chem. A 2001, 105, 1934-1943.
23. Chandra, A. K.; Uchimaru, T.; Zeegers-Huyskens, T. J. Mol. Struct. 2002, 605, 213-220.
24. Kryachko, E.; Nguyen, M.T.; Zeegers-Huyskens, T. J. Phys. Chem. A 2001, 105, 3379-3387.
25. Shishkin, O. V.; Sukhanov, O. S.; Leszczynski, J. J. Phys. Chem. A 2002, 106, 7828-7833.
26. (a) Smets, J.; McCarthy, W. J.; Adamowicz, L. J. Phys. Chem. 1996, 100, 14655-14660.
27. (b) Smets, J.; Smith, D. M. A.; Elkadi, Y.; Adamowicz L. J. Phys. Chem. A. 1997, 101, 9152-9156.
28. Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V. J. Phys. Chem. A 1999, 103, 7912-7917.
29. For general reviews on the mechanisms of action of DNA glycosylases, see, for example: (a) Dodson, M. L.; Michaels, M. L.; Lloyd, R. S. J. Biol. Chem. 1994, 269, 32709-32712.
30. (b) McCullough, A. K.; Dodson, M. L.; Lloyd, R. S. Annu. Rev. Biochem. 1999, 68, 255-285.
31. (c) Stivers, J. T.; Drohat, A. C. Arch. Biochem. Biophys. 2001, 396, 1-9.
32. (a) Savva, R.; McAulley-Hecht, K.; Brown, T.; Pearl, L. Nature 1995, 373, 487-493.
33. (b) Kimura, E.; Kitamura, H.; Koike, T.; Shiro, M. J. Am. Chem. Soc. 1997, 119, 10909-10919.
34. (c) Parikh, S. S.; Walcher, G.; Jones, G. D.; Shupphaug, G.; Krokan, H. E.; Blackburn, G. M.; Tainer, J. A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5083-5088.
35. (d) Werner, R. M.; Jiang, Y. L.; Gordley, R. G.; Jagadeesh, G. J.; Ladner, J. E.; Xiao, G.; Tordova, M.; Gilliland, G. L.; Stivers, J. T. Biochemistry 2000, 39, 12585-12594.
36. (e) Werner, R. M.; Stivers, J. T. Biochemistry 2000, 39, 14054-14064.
37. (f) Dinner, A. R.; Blackburn, G. M.; Karplus, M. Nature 2001, 412, 752-755.
38. (g) Jiang, Y. L.; Ichikawa, Y.; Stivers, J. T. Biochemistry 2002, 41, 7116-7124.
39. (h) Jiang, Y. L.; Drohat, A. C.; Ichikawa, Y.; Stivers, J. T. J. Biol. Chem. 2002, 277, 15385-15392 and references therein.
40. Kurinovich, M. A.; Lee, J. K. J. Am. Chem. Soc. 2000, 122, 6258-6262.
41. Kurinovich, M. A.; Lee, J. K. J. Am. Soc. Mass. Spectrom. 2002, 13, 985-995.
42. Drohat, A. C.; Stivers, J. T. J. Am. Chem. Soc. 2000, 122, 1840-1841.
43. Latajka, Z.; Ratajczak, H.; Zeegers-Huykens, T.; Scheiner, S. J. Mol. Struct. (THEOCHEM) 1991, 235, 409-415.
44. (a) Dabkowska, I.; Rak, J.; Gutowski, M. J. Phys. Chem. A 2002, 106, 7423-7433.
45. (b) Dabkowska, I.; Gutowski, M.; Rak, J. Polish J. Chem. 2002, 76, 1243-1247.
46. Jalbout, A. F.; Hall-Black, C. S.; Adamowicz, L. Chem. Phys. Lett. 2002, 354, 128-133.
47. Gutowski, M.; Dabkowska, I.; Rak, J.; Xu, S.; Nilles, J.M.; Radisic, D.; Bowen, K. H., Jr. Eur. Phys. J. D 2002, 20, 431-439.
48. Harańczyk, M.; Bachorz, R.; Rak, J.; Gutowski, M.; Radisic, D.; Stockes, S. T.; Nilles, J. M.; Bowen, K. M., Jr. J. Phys. Chem. B 2003, 107, 7889-7895.
49. -1, respectively.
50. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 553.
51. (a) Hobza, P.; Sponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315.
52. (b) Del Bene, J. E.; Person, W. B.; Szczepaniak, K. J. Phys. Chem. 1995, 99, 10705.
53. (c) Civalleri, B.; Garrone, E.; Ugliengo, P. J. Mol. Struct. (THEOCHEM) 1997, 419, 227.
54. (d) Maerker, C.; von Ragué Schleyer, P.; Leidl, K. R.; Ha, T.-K.; Quack, M.; Suhm, M. A. J. Comput. Chem. 1997, 18, 1695.
55. (e) Paizs, B.; Suhai, S. J. Comput. Chem. 1998, 19, 575.
56. (f) Rappé, A. K.; Bernstein, E. R. J. Phys. Chem. A 2000, 104, 6117.
57. (a) Sim, F.; St-Amant, A.; Pápai, I.; Salahub, D. R. J. Am. Chem. Soc. 1992, 114, 4391.
58. (b) Keininger, M.; Suhai, S. Int. J. Quantum Chem. 1994, 52, 465.
59. (c) Kim, K.; Jordan, K. D. J. Phys. Chem. 1994, 98, 10089.
60. (d) Latajka, Z.; Bouteiller, Y. J. Chem. Phys. 1994, 101, 9793.
61. (e) Mele, F.; Mineva, T.; Russo, N. Toscano, M. Theor. Chim. Acta 1995, 91, 169.
62. (f) Han, W.-G.; Suhai, J. Phys. Chem. 1996, 100, 3942.
63. (g) Lozynski, M.; Rusinska-Roszak, D.; Mack, H.-G. J. Phys. Chem. A 1998, 102, 2899.
64. (h) Lundell, J.; Latajka, Z. J. Phys. Chem. A 1997, 101, 5004.
65. (i) Chandra, A. K.; Nguyen, M. T. J. Chem. Res. 1997, 216.
66. (j) Chandra, A. K.; Nguyen, M. T. Chem. Phys. 1998, 232, 299.
67. (k) McAllister, M. A. J. Mol. Struct. (THEOCHEM) 1998, 427, 39.
68. (l) Rablen, P. R.; Lockman, J. W.; Jorgensen, W. L. J. Phys. Chem. A 1998, 102, 3782.
69. (m) Pan, Y.; McAllister, M. A. J. Mol. Struct. (THEOCHEM) 1998, 427, 221
70. Lundell, J.; Latajka, Z. J. Phys. Chem. A 1997, 101, 5004.
71. (a) Hartmann, M.; Radom, L. J. Phys. Chem. 2000, 104, 968.
72. (b) Hartmann, M.; Wetmore, S. D.; Radom, L. J. Phys. Chem. A 2001, 115, 4470-4479.
73. (c) Wetmore, S. D.; Schofield, R.; Smith, D. M.; Radom, L. J. Phys. Chem. A 2001, 105, 8718-8726.
74. Sponer, J.; Leszczynski, J. J. Phys. Chem. 1996, 100, 1965.
75. We note that calculations suggest a proton adds to the O2 or O4 position of uracil in the molecular plane and that the proton will align in one of two directions at each site (for example, addition to the O2 position can be directed towards N1 or N3).
76. Podolyan, Y.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 7346-7352.
77. We also note that in DNA the hydrogen at N1 is replaced by a sugar moiety. Therefore, the O2(N1) complex is not possible if interactions with DNA, such as those at the active site of uracil DNA glycosylase, are being considered, which is one of the driving forces for the present study. Furthermore, hydrogen bonding at O2(N1) will likely greatly stabilize the uracil (N1) anion due to direct interactions with N1 and thus prevent a fair comparison of the effects of hydrogen bonding at different tracil sites.
78. For earlier computational and experimental discussions, see, for example: (a) D'Albis, A.; Wickens, M. P.; Gratzer, W. B. Biopolymers 1975, 14, 1423.
79. (b) Scheiner, S. Biopolymers 1983, 22, 731.
80. (c) Falk, M.; Hartmann, K. A.; Lord, R. C. J. Am. Chem. Soc. 1983, 85, 387.
81. (c) Spencer, J. N.; Barton, S. W.; Smith, W. S.; Wolbach, J. F.; Powell, J. F.; Kirshenbaum, M. R.; Firth, D. W.; Harris, E. M.; Judge, T. A. Can. J. Chem. 1983, 61, 2695.
82. (d) Kasende, O.; Zeegers-Huyskens, T. J. Phys. Chem. 1984, 88, 2636.
83. (e) Pranata, J.; Wierschke, S. G.; Jorgensen, W. J. J. Am. Chem. Soc. 1991, 113, 2810.
84. Russo, N.; Toscano, M.; Grand, A.; Jolibois, F. J. Comput. Chem. 1998, 19, 989.
85. Kurinovich, M. A.; Phillips, L. M.; Sharma, S.; Lee, J. K. Chem. Commun. 2002, 2354-2355.
86. Gronert, S.; Feng, W. Y.; Chew, F.; Wu, W. Int. J. Mass Spectrom. 2000, 196, 251-258.
87. -1).
88. -1).
89. We note that Zeegers-Huyskens et al. investigated the O2(N1) complex rather than the O4(C5) complex. It has been widely concluded that the strongest binding to uracil occurs at O2(N1).
90. -1), which is likely due to competing interactions with the N3 hydrogen.
91. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Rega, N.; Salvador, P.; Dannenberg, J. J.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, revision A.11.3; Gaussian, Inc.: Pittsburgh, PA, 2002.