Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

Biophysical Chemistry

Volumn 78, Issue 1-2, 1999, Pages 147-155

  Li, Jiabo ^a   Cramer, Christopher J ^a   Truhlar, Donald G ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Continuum solvent; Dipole moment; Electrostatics; Free energy of solvation; Partial atomic charge; Partition coefficient; Polarizable solute

Indexed keywords

NUCLEIC ACID BASE;

CONFERENCE PAPER; DIPOLE; MODEL; MOLECULAR DYNAMICS; PARTITION COEFFICIENT; PRIORITY JOURNAL; QUANTUM MECHANICS; SOLVATION; SURFACE TENSION; THEORY;

EID: 0032968445     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(98)00228-2     Document Type: Conference Paper

References (47)

1. Rivail J.-L, Rinaldi D., Ruiz-Lopez M.F. NATO ASI Ser. C 339:1991;79.
2. Rivail J.-L., Rinaldi D. Comp. Chem. Rev. Curr. Trends. 1:1996;139.
3. Tomasi J., Persico M. Chem. Rev. 94:1994;2027.
4. Orozco M., Alhambra C., Barril X., Lopéz J.M., Busquest M.A., Luque F.J. J. Mol. Biol. 2:1996;1.
5. Cramer C.J., Truhlar D.G. Rev. Comp. Chem. 6:1995;1.
6. Cramer C.J., Truhlar D.G. Theor. Comp. Chem. 1:1994;9.
7. C.J. Cramer, D.G. Truhlar, in: O. Tapia, J. Bertrán (Eds.), Solvent Effects and Chemical Reactivity, Kluwer, Dordrecht, 1996, p. 1.
8. Cramer C.J., Truhlar D.G. J. Am. Chem. Soc. 113:1991;8305.
9. Cramer C.J., Truhlar D.G. Science. 256:1992;213.
10. Lee B., Richards F.M. J. Mol. Biol. 55:1971;379.
11. Hermann R.B. J. Phys. Chem. 76:1972;2754.
12. Cramer C.J., Truhlar D.G. J. Comput. Chem. 13:1992;1089.
13. Giesen D.J., Cramer C.J., Truhlar D.G. J. Phys. Chem. 99:1995;7137.
14. Chambers C.C., Hawkins G.D., Cramer C.J., Truhlar D.G. J. Phys. Chem. 100:1996;16385.
15. Giesen D.J., Gu M.Z., Cramer C.J., Truhlar D.G. J. Org. Chem. 61:1996;8720.
16. Giesen D.J., Chambers C.C., Cramer C.J., Truhlar D.G. J. Phys. Chem. 101:1997;2061.
17. Giesen D.J., Hawkins G.D., Liotard D.A., Cramer C.J., Truhlar D.G. Theor. Chem. Acc. 98:1997;85.
18. Hawkins G.D., Cramer C.J., Truhlar D.G. J. Phys. Chem. B. 101:1997;7147.
19. Hawkins G.D., Liotard D.A., Cramer C.J., Truhlar D.G. J. Org. Chem. 63:1998;4305.
20. Hawkins G.D., Cramer C.J., Truhlar D.G. J. Phys. Chem. B. 102:1998;3257.
21. Zhu T., Li J., Hawkins G.D., Cramer C.J., Truhlar D.G. J. Chem. Phys. 109:1998;9117.
22. Li J., Hawkins G.D., Cramer C.J., Truhlar D.G. Chem. Phys. Lett. 288:1998;293.
23. J. Li, T. Zhu, G.D. Hawkins, D.A. Liotard, C.J. Cramer, D.G. Truhlar, Theor. Chem. Acc., in press.
24. Dewar M.J.S., Zoebisch E.G., Healy E.F., Stewart J.J.P. J. Am. Chem. Soc. 107:1985;3902.
25. Thiel W., Voityuk A.A. J. Phys. Chem. 100:1996;616.
26. Easton R.E., Giesen D.J., Welch A., Cramer C.J., Truhlar D.G. Theor. Chim. Acta. 93:1996;281.
27. Francl M.M., Pietro W.J., Hehre W.J.et al. J. Chem. Phys. 77:1982;3654.
28. Li J., Zhu T., Cramer C.J., Truhlar D.G. J. Phys. Chem. A 102:1998;1820.
29. Becke A. Phys. Rev. A 38:1988;3098.
30. Perdew J.P., Burke K., Wang Y. Phys. Rev. B 54:1996;16533.
31. Stewart J.J.P. Rev. Comp. Chem. 1:1990;45.
32. Storer J.W., Giesen D.J., Cramer C.J., Truhlar D.G. J. Comput.-Aided Mol. Des. 9:1995;87.
33. Johnson R.C., Power T.D., Holt J.S., Immarapora B., Monat J.E., Sissoko A.A., Yanik M.M., Zagorodug A.V., Cybulski S.M. J. Phys. Chem. 100:1996;18875.
34. D.J. Giesen, C.C. Chambers, C.J. Cramer, D.G. Truhlar, J. Phys. Chem. B 101 (1997) 5084 and erratum to be published.
35. Hawkins G.D., Cramer C.J., Truhlar D.G. J. Chim. Phys. -Chim. Biol. 94:1997;1448.
36. J. Li, G.D. Hawkins, D.A. Liotard, C.J. Cramer, D.G. Truhlar, MN-GSM-version 98.2.3, University of Minnesota, Minneapolis, MN 55455-0431.
37. M.J. Frisch, G.W. Trucks, H.B. Schlegel et al., GAUSSIAN 94, Gaussian Inc., Pittsburgh, 1995.
38. J. Li, T. Zhu, G.D. Hawkins, D.A. Liotard, D. Rinaldi, C.J. Cramer, D.G. Truhlar, GAMESOL-version 2.0, University of Minnesota, Minneapolis, MN 55455-0431. http://comp.chem.umn.edu/gamesol.
39. Schmidt M.W., Baldridge K.K., Boatz J.A.et al. J. Comput. Chem. 14:1993;347.
40. G.D. Hawkins, D.J. Giesen, G.C. Lynch, C.C. Chambers, I. Rossi, J.W. Storer, J. Li, T. Zu, D.A. Liotard, C.J. Cramer, D.G. Truhlar, AMSOL-version 6.5.3, University of Minnesota, Minneapolis, MN 55455-0431. http://comp.chem.umn.edu/amsol.
41. R. Vasanwala, C. Hansch, C. Strong, C. Hansch, average of measurements, unpublished data, in: A.J. Leo (Ed.), MedChem Software Masterfile, BioByte Corp., Claremont, CA, 1994.
42. Shih P., Pedersen L.G., Gibbs P.R., Wolfenden R. J. Mol. Biol. 280:1998;421.
43. R. Wolfenden, P. Shih, personal communication.
44. A.J. Leo, personal communication.
45. Kwiatkowski J.S., Leszczyski J. J. Phys. Chem. 100:1996;941.
46. DeVoe H., Tinoco I. Jr. J. Mol. Biol. 4:1962;500.
47. Kulakaowska I., Geller M., Lesyng B., Bolewska K., Wierzchowski K.L. Biochim. Biophys. Acta. 407:1970;420.