Structure, energetics, vibrational frequencies and charge transfer of base pairs, nucleoside pairs, nucleotide pairs and b-dna pairs of trinucleotides: Ab initio hf/mini-1 and empirical force field study

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 6, 2000, Pages 1077-1086

  Kabeláč, Martin ^a   Kratochvíl, Martin ^a   Šponer, Jiří ^a   Hobza, Pavel ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

DNA B; HYDROGEN; NUCLEOSIDE; NUCLEOTIDE; TRINUCLEOTIDE;

ANALYTIC METHOD; ARTICLE; BASE PAIRING; DNA STRUCTURE; ELECTRON TRANSPORT; ENERGY TRANSFER; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REACTION ANALYSIS; RELIABILITY; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

EID: 0033913465     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2000.10506593     Document Type: Article

References (15)

1. Gould, I. R., and Kollman, P. A., 1994. J. Am. Chem. Soc., 116:2493
2. Šponer, J., Leszczynski, J., and Hobza, P., 1996. J. Comput. Chem., 17:841
3. Sponer, J., Leszczynski, J., and Hobza, P., 1996. J. Phys. Chem., 100:1965
4. Šponer, J., Leszczynski, J., and Hobza, P., 1996. J. Phys. Chem., 100:5590 (b) J. Šponer, P. Hobza, Chem. Phys. Lett., 267, 263 (1997) (c) K. Brameld, S. Dasgupta, W.A. Goddard III J. Phys. Chem. B, 101, 4851 (1997)
5. Šponer, J., and Hobza, P., 1996. Chem. Phys., 204:365
6. Hobza, P., Kabeláý, M., Šponer, J., Mejzlík, P., and Vondrásek, J., 1997. J. Comp. Chem., 18:1136
7. Cornell, W. D., Cieplak, P., Bayly, Ch. I., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179
8. Špirko, V., Šponer, J., and Hobza, P., 1997. J. Chem. Phys., 106:1472
9. Urabe, H., and Tominaga, Y., 1982. Biopolymers, 21:2477
10. Lindslay, S. M., Powell, J. W., and Rupprecht, A., 1984. Phys. Rev. Letters, 53:1853
11. Painter, P. C., Mosher, L., and Rhoads, C., 1981. Biopolymers, 20:243
12. Volkov, S. N., and Kosevich, A. M., 1991. J. Biomol. Struct. Dyn., 8:1060
13. Lisý, V., Miškovský, P., and Schreiber, P., 1996. J. Biomol. Struct. Dyn., 13:707
14. Pearlman, D. A., Case, D. A., Caldwelll, J. W., Ross, W. S., Cheatham, T. E., III, Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1995. AMBER 4.1. San Francisco:University of California.
15. Arnott, S., Chandrasekaran, Z., Birdsall, D. L., Leslie, A. G.W., and Ratliff, R. L., 1980. Nature, 283:743