Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5′-d(GCGAAGC)-3′ hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Journal of Physical Chemistry A

Volumn 109, Issue 6, 2005, Pages 1131-1136

  Dabkowska, Iwona ^a,b   Gonzalez, Haydee Valdes ^a   Jurečka, Petr ^a   Hobza, Pavel ^a  

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

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; CRYSTAL STRUCTURE; ENTHALPY; EXTRAPOLATION; FREE ENERGY; HYDROGEN BONDS; NUCLEAR MAGNETIC RESONANCE; OPTIMIZATION; QUANTUM THEORY; VACUUM APPLICATIONS;

BONDING ENERGY; QUANTUM CHEMISTRY; STABILIZATION ENERGIES; STACKED STRUCTURES;

DNA SEQUENCES;

ADENINE; CYTOSINE; GUANINE; THYMINE;

ALGORITHM; ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HYDROGEN BOND; METABOLISM; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; THERMODYNAMICS;

ADENINE; ALGORITHMS; BASE PAIRING; BASE SEQUENCE; CYTOSINE; GUANINE; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; THERMODYNAMICS; THYMINE;

EID: 14544274054     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp046738a     Document Type: Article

References (23)

1. Müller-Dethlefs, K.; Hobza, P. Chem. Rev. 2000, 100, 143.
2. Kool, E. T. Chem. Rev. 1997, 97, 1473.
3. Freier, S. M.; Sugimoto, N.; Sinclair, A.; Neilson, T.; Kieizek, R.; Caruthers, M. H.; Turner, D. H. Biochemistry 1986, 25, 3214.
4. Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Shells, C. J.; Paris, P. L.; Tahmassebi, D. C.; Kool, E. T. J. Am. Chem. Soc. 1996, 118, 8182.
5. Jurečka, P.; Hobza, P. J. Am. Chem. Soc. 2003, 125, 15608.
6. Gould, I. R.; Kollman, P. A. J. Am. Chem. Soc. 1994, 116, 2493.
7. Šponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590.
8. Yanson, I. K.; Teplitsky, A. B.; Sukhodub, L. F. Biopolymers 1979, 18, 1149.
9. Prive, G. G.; Yanagi, K.; Dickerson, R. E. J. Mol. Biol. 1991, 217, 177.
10. Soler-Lopez, M.; Malinina, L.; Subirana, J. A. J. Biol. Chem. 2000, 275, 23034.
11. Žídek. L.; Wu, H.; Feigon, J.; Sklenář, U. J. Biomol. NMR 2001, 21, 153.
12. Jurečka, P.; Nachtigall, P.; Hobza, P. Phys. Chem. Chem. Phys. 2001, 3, 4578.
13. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553.
14. Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Chem. Phys. Lett. 1998, 286, 243.
15. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796.
16. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165.
17. Jurečka, P.; Hobza, P. Chem. Phys. Lett. 2002, 365, 89.
18. Hobza, P.; Šponer, J. J. Am. Chem. Soc. 2002, 124, 11802.
19. MOLPRO, a package of ab initio programs designed by H.-J. Werner and P. J. Knowles version 2002.1: R. D. Amos, A. Bernhardsson, A. Berning, P. Celani, D. L. Cooper, M. J. O. Deegan, A. J. Dobbyn, F. Eckert, C. Hampel, G. Hetzer, P. J. Knowles, T. Korona, R. Lindh, A. W. Lloyd, S. J. McNicholas, F. R. Manby, W. Meyer, M. E. Mura, A. Nicklass, P. Palmieri, R. Pitzer, G. Rauhut, M. Schütz, U. Schumann, H. Stoll, A. J. Stone, R. Tarroni, T. Thorsteinsson, and H.-J. Werner.
20. Gaussian 03, Revision A.1: Frisch, M.J.; Trucks, G. W.; Schlegel, H. B.; Scuseria. G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa. J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, I. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Lin, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; 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.; Gonzalez, C.; Pople, J. A., Gaussian, Inc., Pittsburgh, PA, 2003.
21. Hobza, P.; Šponer, J., Reschel, T. J. Comput. Chem. 1995, 16, 1315.
22. Hobza, P.; Sponer, S. Chem. Phys. Lett. 1996, 261, 379.
23. Miller, J. L.; Kollman, P. A. J. Phys. Chem. 1996, 100, 8587.