Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and Ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results

Journal of Computational Chemistry

Volumn 18, Issue 9, 1997, Pages 1136-1150

  Hobza, Pavel ^a   Kabeláč, Martin ^a   Šponer, Jiří ^a   Mejzlík, Petr ^b   Vondrášek, Jiří ^c  

^a J HEYROVSKÝ INSTITUTE OF PHYSICAL CHEMISTRY   (Czech Republic)

^b MASARYK UNIVERSITY   (Czech Republic)

^c INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

Author keywords

Ab initio SCF with dispersion energy; Empirical force fields; H bonded and stacked DNA base pairs; Semiempirical quantum chemical methods

Indexed keywords

EID: 0343213055     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19970715)18:9<1136::AID-JCC3>3.0.CO;2-S     Document Type: Article

References (50)

1. T. J. Zielinski and M. Shibata, Biopolymers, 29, 1027 (1990).
2. S. Swaminathan, G. Ravisheanker, and D. L. Beveridge, J. Am. Chem. Soc., 113, 5027 (1991).
3. K. Miaskiewicz, R. Osman, and H. Weinstein, J. Am. Chem. Soc., 115, 1526 (1993).
4. I. K. Yanson, A. B. Teplitsky, and L. F. Sukhodub, Biopolymers, 18, 1149 (1979).
5. M. Dey, J. Grotenmeyer, and E. W. Schlag, Z. Naturforsch., 49a, 776 (1994).
6. P. Hobza and C. Sandorfy, J. Am. Chem. Soc., 109, 1302 (1987).
7. I. R. Gould and P. Kollman, J. Am. Chem. Soc., 116, 2493 (1994).
8. M. Aida and C. Nagata, Int. J. Quantum Chem., 29, 1253 (1986).
9. (a) P. Hobza, J. Šponer, and M. Polášek, J. Am. Chem. Soc., 117, 792 (1995)
10. (b) J. Šponer, J. Leszczynski, and P. Hobza, J. Phys. Chem., 100, 1965 (1996)
11. (c) J. Šponer, J. Leszczynski, and P. Hobza, J. Phys. Chem., 100, 5590 (1996)
12. (d) J. Šponer, J. Florian, P. Hobza, and J. Leszczynski, J. Biomol. Struc. Dyn., 13, 827 (1996)
13. (e) J. Šponer, J. Leszczynski, and P. Hobza, J. Comput. Chem., 12, 841 (1996)
14. (f) J. Šponer, J. Leszczynski, V. Vetterl, and P. Hobza, J. Biomol. Struct. Dyn., 13, 695 (1996)
15. (g) J. Šponer, J. Leszczynski, and P. Hobza, J. Biomol. Struct. Dyn., 14, 117 (1996).
16. P. Hobza, F. Hubálek, M. Kabeláč, P. Mejzlík, J. Šponer, and J. Vondrášek, Chem. Phys. Lett., 257, 31 (1996).
17. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman, AMBER 4.1, University of California, San Francisco, 1995.
18. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc., 117, 5179 (1995).
19. (a) S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, D. S. Profeta, Jr., P. J. Weiner, J. Am. Chem. Soc., 106, 765 (1984)
20. (b) S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230 (1986).
21. Discover, Versions 2.9.5 & 94.0, Biosym Technologies, San Diego, CA, May 1994.
22. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983).
23. A. D. MacKerell, Jr., J. Wiórkiewicz-Kuczera, and M. Karplus, J. Am. Chem. Soc., 117, 11946 (1995).
24. (a) J. R. Maple, M.-J. Hwang, T. P. Stockfisch, U. Dinur, M. Waldman, C. S. Ewig, and A. T. Hagler, J. Am. Chem. Soc., 115, 162 (1994)
25. (b) T. P. Stockfisch and C. S. Ewig, manuscript in preparation.
26. A. T. Hagler and C. S. Ewig, Camp. Phys. Commun., 84, 131 (1994).
27. U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2949 (1989) and 91, 2959 (1989).
28. U. Dinur and A. T. Hagler, J. Chem. Phys., 91, 2949 (1989) and 91, 2959 (1989).
29. F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, C. Caufield, G. Chang, T. Hendrickson, and W. C. Still, Macro Model V. 4.0, J. Comput. Chem., 11, 440 (1990).
30. (a) W. L. Jorgensen and J. Tirado Rives, J. Am. Chem. Soc., 110, 1657 (1988)
31. (b) W. L. Jorgensen, J. M. Briggs, and M. L. Contreras, J. Phys. Chem., 94, 1683 (1990).
32. J. Pranata, S. G. Wierschke, and W. L. Jorgensen, J. Am. Chem. Soc., 113, 2810 (1991).
33. V. B. Zhurkin, V. I. Poltev, and V. L. Florentov, Mol. Biol. (USSR), 14, 1116 (1980).
34. V. I. Poltev and N. V. Shulvupina, J. Biomol. Struc. Dyn., 3, 739 (1986).
35. M. J. S. Dewar and W. Thiel, J. Am. Chem. Soc., 99, 4899 (1977).
36. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc., 107, 3902 (1985).
37. J. J. P. Stewart, J. Comput. Chem., 10, 209 (1989).
38. A. A. Blizniuk and A. A. Voityuk, Zh. Str. Chim., 29(2), 31 (1988).
39. M. W. Jurena and G. C. Shields, J. Comput. Chem., 14, 89 (1993).
40. S. F. Boys and F. Bernardi, Mol. Phys., 19, 553 (1970).
41. J. Šponer and P. Hobza, Chem. Phys., 204, 365 (1996).
42. (a) J. Šponer and J. Kypr, In Theoretical Biochemistry & Molecular Biophysics, D. L. Beveridge and R. Lavery, Eds., Adenine Press, Guiderland, NY, 1990, p. 271
43. (b) J. Šponer and J. Kypr, J. Biomol. Struc. Dyn., 11, 277 (1993).
44. G. G. K. Prive, K. Yanagi, and R. E. Dickerson, J. Mol. Biol., 217, 177 (1991).
45. (a) P. Hobza and J. Sponer, J. Mol. Struc. (Theochem.), 388, 115 (1996)
46. (b) cf. S. Suhai, J. Chem. Phys., 103, 7030 (1995).
47. H.-J. Werner, unpublished data, 1994.
48. P. Hobza, H. L. Selzle, and E. W. Schlag, J. Phys. Chem. 100, 18790 (1996), G. D. Smith and R. L. Jaffe, J. Phys. Chem., 100, 9624 (1996).
49. P. Hobza, H. L. Selzle, and E. W. Schlag, J. Phys. Chem. 100, 18790 (1996), G. D. Smith and R. L. Jaffe, J. Phys. Chem., 100, 9624 (1996).
50. J. Šponer and P. Hobza, Chem. Phys. Lett., 267 263 (1997).