On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

Journal of Chemical Physics

Volumn 122, Issue 20, 2005, Pages

  Da̧bkowska, Iwona ^a,b   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

DIMERS; HYDROGEN BONDS; MOLECULAR ORIENTATION; MOLECULAR STRUCTURE; OPTIMIZATION; PERTURBATION TECHNIQUES; PROBABILITY DENSITY FUNCTION;

ADENINE; NUCLEIC ACID BASE PAIRS; THYMINE; URACIL;

NUCLEIC ACIDS;

ADENINE; NUCLEOTIDE;

ARTICLE; BASE PAIRING; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; HYDROGEN BOND; QUANTUM THEORY;

ADENINE; BASE PAIRING; COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; QUANTUM THEORY;

EID: 20844449600     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1906205     Document Type: Article

References (31)

1. K. Müller-Dethlefs and P. Hobza, Chem. Rev. (Washington, D.C.) 100, 143 (2000).
2. P. Jurečka and P. Hobza, J. Am. Chem. Soc. 0002-7863 10.1021/ja036611j 125, 15608 (2003); P. Jurečka, J. Šponer, and P. Hobza, J. Phys. Chem. B 1089-5647 108, 5466 (2004); J. Šponer, P. Jurečka, and P. Hobza, J. Am. Chem. Soc. 0002-7863 126, 10142 (2004); I. Da̧bkowska, H. Valdes, P. Jurečka, and P. Hobza, J. Phys. Chem. A 109, 1131 (2005).
3. P. Jurečka and P. Hobza, J. Am. Chem. Soc. 0002-7863 10.1021/ja036611j 125, 15608 (2003); P. Jurečka, J. Šponer, and P. Hobza, J. Phys. Chem. B 1089-5647 108, 5466 (2004); J. Šponer, P. Jurečka, and P. Hobza, J. Am. Chem. Soc. 0002-7863 126, 10142 (2004); I. Da̧bkowska, H. Valdes, P. Jurečka, and P. Hobza, J. Phys. Chem. A 109, 1131 (2005).
4. P. Jurečka and P. Hobza, J. Am. Chem. Soc. 0002-7863 10.1021/ja036611j 125, 15608 (2003); P. Jurečka, J. Šponer, and P. Hobza, J. Phys. Chem. B 1089-5647 108, 5466 (2004); J. Šponer, P. Jurečka, and P. Hobza, J. Am. Chem. Soc. 0002-7863 126, 10142 (2004); I. Da̧bkowska, H. Valdes, P. Jurečka, and P. Hobza, J. Phys. Chem. A 109, 1131 (2005).
5. P. Jurečka and P. Hobza, J. Am. Chem. Soc. 0002-7863 10.1021/ja036611j 125, 15608 (2003); P. Jurečka, J. Šponer, and P. Hobza, J. Phys. Chem. B 1089-5647 108, 5466 (2004); J. Šponer, P. Jurečka, and P. Hobza, J. Am. Chem. Soc. 0002-7863 126, 10142 (2004); I. Da̧bkowska, H. Valdes, P. Jurečka, and P. Hobza, J. Phys. Chem. A 109, 1131 (2005).
6. (a) D. Feller, J. Chem. Phys. 0021-9606 10.1063/1.462652 96, 6104 (1992); (b) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, O. Jeppe, and A. K. Wilson, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(98) 00111-0 286, 243 (1998); (c) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, and J. Olsen, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)00179-7 302, 437 (1999); (d) D. G. Truhlar, Chem. Phys. Lett. 294, 45 (1998).
7. (a) D. Feller, J. Chem. Phys. 0021-9606 10.1063/1.462652 96, 6104 (1992); (b) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, O. Jeppe, and A. K. Wilson, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(98) 00111-0 286, 243 (1998); (c) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, and J. Olsen, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)00179-7 302, 437 (1999); (d) D. G. Truhlar, Chem. Phys. Lett. 294, 45 (1998).
8. (a) D. Feller, J. Chem. Phys. 0021-9606 10.1063/1.462652 96, 6104 (1992); (b) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, O. Jeppe, and A. K. Wilson, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(98) 00111-0 286, 243 (1998); (c) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, and J. Olsen, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)00179-7 302, 437 (1999); (d) D. G. Truhlar, Chem. Phys. Lett. 294, 45 (1998).
9. (a) D. Feller, J. Chem. Phys. 0021-9606 10.1063/1.462652 96, 6104 (1992); (b) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, H. Koch, O. Jeppe, and A. K. Wilson, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(98) 00111-0 286, 243 (1998); (c) A. Halkier, T. Helgaker, P. Jørgensen, W. Klopper, and J. Olsen, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(99)00179-7 302, 437 (1999); (d) D. G. Truhlar, Chem. Phys. Lett. 294, 45 (1998).
10. P. Jurečka and P. Hobza, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(02)01423-9 365, 89 (2002); P. Hobza and J. Šponer, J. Am. Chem. Soc. 124, 11802 (2002).
11. P. Jurečka and P. Hobza, Chem. Phys. Lett. 0009-2614 10.1016/S0009-2614(02)01423-9 365, 89 (2002); P. Hobza and J. Šponer, J. Am. Chem. Soc. 124, 11802 (2002).
12. S. F. Boys and F. Bernardi, Mol. Phys. 19, 553 (1970).
13. S. Simon, M. Duran, and J. J. Dannenberg, J. Chem. Phys. 0021-9606 10.1063/1.472902 105, 11024 (1996); P. Hobza and Z. Havlas, Theor. Chem. Acc. 1432-881X 10.1007/s002140050018 99, 372 (1998); P. Hobza, O. Bludský, and S. Suhai, Phys. Chem. Chem. Phys. 1463-9076 10.1039/a902109d 1, 3073 (1999); P. K. Wawrzyniak, J. Panek, Z. Latajka, and J. Lundell, J. Mol. Struct. 704, 297 (2004).
14. S. Simon, M. Duran, and J. J. Dannenberg, J. Chem. Phys. 0021-9606 10.1063/1.472902 105, 11024 (1996); P. Hobza and Z. Havlas, Theor. Chem. Acc. 1432-881X 10.1007/s002140050018 99, 372 (1998); P. Hobza, O. Bludský, and S. Suhai, Phys. Chem. Chem. Phys. 1463-9076 10.1039/a902109d 1, 3073 (1999); P. K. Wawrzyniak, J. Panek, Z. Latajka, and J. Lundell, J. Mol. Struct. 704, 297 (2004).
15. S. Simon, M. Duran, and J. J. Dannenberg, J. Chem. Phys. 0021-9606 10.1063/1.472902 105, 11024 (1996); P. Hobza and Z. Havlas, Theor. Chem. Acc. 1432-881X 10.1007/s002140050018 99, 372 (1998); P. Hobza, O. Bludský, and S. Suhai, Phys. Chem. Chem. Phys. 1463-9076 10.1039/a902109d 1, 3073 (1999); P. K. Wawrzyniak, J. Panek, Z. Latajka, and J. Lundell, J. Mol. Struct. 704, 297 (2004).
16. S. Simon, M. Duran, and J. J. Dannenberg, J. Chem. Phys. 0021-9606 10.1063/1.472902 105, 11024 (1996); P. Hobza and Z. Havlas, Theor. Chem. Acc. 1432-881X 10.1007/s002140050018 99, 372 (1998); P. Hobza, O. Bludský, and S. Suhai, Phys. Chem. Chem. Phys. 1463-9076 10.1039/a902109d 1, 3073 (1999); P. K. Wawrzyniak, J. Panek, Z. Latajka, and J. Lundell, J. Mol. Struct. 704, 297 (2004).
17. (a) P. Hobza, J. Šponer, and T. Reschel, J. Comput. Chem. 0192-8651 10.1002/jcc.540161102 16, 1315 (1995); (b) J. Šponer and P. Hobza, Collect. Czech. Chem. Commun. 0010-0765 68, 2231 (2003); (c) J. Černý and P. Hobza, Phys. Chem. Chem. Phys. 7, 1624 (2005).
18. (a) P. Hobza, J. Šponer, and T. Reschel, J. Comput. Chem. 0192-8651 10.1002/jcc.540161102 16, 1315 (1995); (b) J. Šponer and P. Hobza, Collect. Czech. Chem. Commun. 0010-0765 68, 2231 (2003); (c) J. Černý and P. Hobza, Phys. Chem. Chem. Phys. 7, 1624 (2005).
19. (a) P. Hobza, J. Šponer, and T. Reschel, J. Comput. Chem. 0192-8651 10.1002/jcc.540161102 16, 1315 (1995); (b) J. Šponer and P. Hobza, Collect. Czech. Chem. Commun. 0010-0765 68, 2231 (2003); (c) J. Černý and P. Hobza, Phys. Chem. Chem. Phys. 7, 1624 (2005).
20. (a) M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 0163-1829 10.1103/PhysRevB.58.7260 58, 7260 (1998); (b) M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, and E. Kaxiras, J. Chem. Phys. 0021-9606 10.1063/1.1329889 114, 5149 (2001); (c) D. Reha, M. Kabeláč, F. Ryjacek, J. Šponer, J. E. Šponer, M. Elstner, S. Suhai, and P. Hobza, J. Am. Chem. Soc. 124, 336 (2002).
21. (a) M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 0163-1829 10.1103/PhysRevB.58.7260 58, 7260 (1998); (b) M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, and E. Kaxiras, J. Chem. Phys. 0021-9606 10.1063/1.1329889 114, 5149 (2001); (c) D. Reha, M. Kabeláč, F. Ryjacek, J. Šponer, J. E. Šponer, M. Elstner, S. Suhai, and P. Hobza, J. Am. Chem. Soc. 124, 336 (2002).
22. (a) M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 0163-1829 10.1103/PhysRevB.58.7260 58, 7260 (1998); (b) M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, and E. Kaxiras, J. Chem. Phys. 0021-9606 10.1063/1.1329889 114, 5149 (2001); (c) D. Reha, M. Kabeláč, F. Ryjacek, J. Šponer, J. E. Šponer, M. Elstner, S. Suhai, and P. Hobza, J. Am. Chem. Soc. 124, 336 (2002).
23. T. A. Halgren, J. Am. Chem. Soc. 114, 7827 (1992).
24. M. J. Frisch, G. W. Trucks, H. B. Schlegel, GAUSSIAN 03, Revision A.1, Gaussian, Inc., Pittsburgh, PA, 2003.
25. R. Ahlrichs, M. Bär, M. Häser, H. Horn, and C. Kölmel, Chem. Phys. Lett. 162, 165 (1989).
26. R. D. Amos, A. Bernhardsson, A. Berning, MOLPRO, a package of ab initio programs designed by, H.-J. Werner, and, P. J. Knowles, version 2002.1.
27. J. Šponer and P. Hobza, J. Phys. Chem. A 104, 4592 (2000).
28. P. Hobza and J. Šponer, Chem. Rev. (Washington, D.C.) 99, 3247 (1999).
29. L. M. J. Kroon-Batenburg and F. B. van Duijneveldt, J. Mol. Struct. 121, 185 (1985).
30. P. Hobza and R. Zahradník, Chem. Rev. (Washington, D.C.) 88, 871 (1988).
31. J. Vondrášek, L. Bendová, V. Klusák, and P. Hobza, J. Am. Chem. Soc. 127, 2615 (2005).