Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

Journal of the American Chemical Society

Volumn 124, Issue 39, 2002, Pages 11802-11808

  Hobza, Pavel ^a   Šponer, Jiří ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC STACKING;

CALIBRATION; CHEMICAL BONDS; DIMERS; EXTRAPOLATION; RNA;

DNA;

CYTOSINE; DIMER; DNA BASE; GUANINE; NUCLEIC ACID BASE; PYRIMIDINE; URACIL;

ACCURACY; ARTICLE; BASE PAIRING; CALCULATION; CORRELATION FUNCTION; ENERGY; GEOMETRY; HYDROGEN BOND; MOLECULAR STABILITY; POLARIZATION;

CYTOSINE; DNA; ELECTROSTATICS; GUANINE; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PYRIMIDINE DIMERS; THERMODYNAMICS; URACIL;

EID: 0037010001     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja026759n     Document Type: Article

References (66)

1. (a) Mathews, D. H.; Sabina, J.; Zuker, M.; Turner, D. H. J. Mol. Biol. 1999, 288, 911-940.
2. (b) Bommarito, S.; Peyret, N.; SantaLucia, J. Nucleic Acids Res. 2000, 28, 1929-1934.
3. (c) Suzuki, M.; Amano, N.; Kakinuma, J.; Tateno, M. J. Mol. Biol. 1997, 274, 421-435.
4. (a) Hobza, P.; Šponer, J. Chem. Rev. 1999, 99, 3247-3276.
5. (b) Šponer, J.; Leszczynski, J.; Hobza, P. Biopolymers 2001, 61, 3-31.
6. (a) Šponer J.; Leszczynski, J.; Hobza. P. J. Phys. Chem. 1996, 100, 5590-5596.
7. (b) Šponer, J.; Gabb, H. A.; Leszczynski, J.; Hobza, P. Biophys. J. 1997, 73, 76-87.
8. (c) Šponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. A 1997, 101, 9489-9495.
9. (a) Šponer, J.; Leszczynski, J.; Hobza, P. J. Comput. Chem. 1996, 17, 841-850.
10. (b) Adamo, C.; Barone, V. J. Chem. Phys. 1998, 108, 664-675.
11. (c) Wesolowski, T. A.; Parisel, O.; Ellinger, Y.; Weber, J. J. Phys. Chem. A 1997, 101, 7818-7825.
12. (d) Williams, H. L.; Chabalowski, C. F. J. Phys. Chem. A 2001, 105, 646-659.
13. (e) Kurita, N.; Kobayashi, K. Comput. Chem. 2000, 24, 351-357.
14. (f) Kurita, N.; Araki, M.; Nakao, K.; Kobayashi, K. Chem. Phys. Lett. 1999, 313, 693-700.
15. (g) Wesolowski, T. A.; Morgantini, P. Y.; Weber, J. J. Chem. Phys. 2002, 116, 6411-6421.
16. (h) Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. J. Chem. Phys. 2001, 114, 5149-5155.
17. Šponer, J.; Hobza, P. Chem. Phys. Lett. 1997, 267, 263-270.
18. Kroon-Batenburg, L. M. J.; van Duijneveldt. F. B. J. Mol. Struct. THEOCHEM 1985, 121, 185-199.
19. Leininger, M. L.; Nielsen, I. M. B.; Colvin, M. E.; Janssen, C. L. J. Phys. Chem. A 2002, 106, 3850-3854.
20. (a) Feyereisen, M.; Fitzgerald, G.; Komomicki, A. Chem. Phys. Lett. 1993, 208, 359-363.
21. (b) Vahtras, O.; Almlöf, J.; Feyereisen, M. W. Chem. Phys. Lett. 1993, 213, 514-518.
22. (c) Bernholdt, D. E.; Harrison, R. J. Chem. Phys. Lett. 1996, 250, 477-484.
23. (d) Jurečka, P.; Nachtigall, P.; Hobza, P. Phys. Chem. Chem. Phys. 2001, 3, 4578-4582.
24. (a) Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries. M. S. Phys. Chem. Chem. Phys. 2002, 4, 732-739.
25. (b) Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. Phys. Chem. Chem. Phys. 2002, 4, 740-750.
26. (c) Desfrancois, C.; Abdoul-Carime, H.; Schultz, L. P.; Schermann, J. P. Science 1995, 269, 1707-1709.
27. (d) Schnier, P. D.; Klassen, J. S.; Strittmatter, E. E.; Williams, E. R. J. Am. Chem. Soc. 1998, 120, 9605-9613.
28. (e) Dunger, A.; Limbach, H.-H.; Weisz, K. J. Am. Chem. Soc. 2000, 122, 10109-10114.
29. (a) Hobza, P.; Šponer; J. Chem. Phys. Lett. 1998, 288, 7-14.
30. (b) Kratochvíl, M.; Engkvist, O.; Šponer, J.; Jungwirth, P.; Hobza, P. J. Phys. Chem. A 1998, 102, 6921-6926.
31. 2-4 Further, the pronounced out-of-plane deformations of bases seen in the isolated dimers should be eliminated inside DNA as bases have stacking partners at either side.
32. (a) Truhlar, D. G. Chem. Phys. Lett. 1998, 294, 45-48.
33. Slavíček, P.; Kalus, R.; Paška, P.; Odvárková, I.; Hobza, P.; Malijevský, A. J. Chem. Phys.. submitted.
34. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, J. S.; Pople, J. A. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
35. MOLPRO is a package of ab initio programs written by H.-J. Werner and P. J. Knowles, with contributions from J. Almlof, R. D. Amos, A. Berning, P. Celani, D. L. Cooper, M. J. O. Deegan, A. J. Dobbyn, F. Eckert, S. T. Elbert, C. Hampel, G. Hetzer, R. Lindh, A. W. Lloyd, W. Meyer, A. Nicklass, T. Korona, K. Peterson, R. Pitzer, G. Rauhut, A. J. Stone, P. R. Taylor, M. E. Mura, P. Pulay, M. Schutz, H. Stoll, and T. Thorsteinsson.
36. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kö, C. Chem. Phys. Lett. 1989, 162, 165-169.
37. (a) Woon, D. E.; Dunning, T. H., Jr. J. Chem. Phys. 1993, 98, 1358-1371.
38. (b) Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796-6806.
39. (c) Schaefer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571-2573.
40. Schaefer, A.; Huber, C.; Ahlrichs, R. J. Chem. Phys. 1994, 100, 5829-5835.
41. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553-574.
42. The calculation illustrates capability of bond functions in stacking calculations, although their common utilization is hampered by lack of general rules regarding where to place the bond function centers for displaced geometries, dimers with irregular shape, dimers with noncoplanar bases, and others.
43. Calculations lacking any polarization functions (6-31G, 6-311G, 6-311+G basis sets; not shown) yield this difference around 1 kcal/mol.
44. (a) Řeha, D.; Kabeláč, M.; Ryjáček, F.;Šponer, J.; Šponer, J. E.; Elstner, M.; Suhai, S.; Hobza, P. J. Am. Chem. Soc. 2002, 124, 3366-3376.
45. (b) Bondarev, D. A.; Skawinski, W. J.; Venanzi, C. A. J. Phys. Chem. B 2000, 104, 815-822.
46. Truhlar's extrapolation was used, except of guanine dimer.
47. (a) Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Phys. Chem. 1996, 100, 18790-18794.
48. (b) Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J. Am. Chem. Soc. 2002, 124, 104-112.
49. Johnson, R. C.; Power, T. D.; Holt, J. S.; Immaraporn, B.; Monat, J. E.; Sissoko, A. A.; Yanik, M. M.; Zagorodny, A. V.; Cybulski, S. M. J. Phys. Chem. 1996, 100, 18875-18881.
50. Fomine, S.; Tlenkopatchev, M.; Martinez, S.; Fomina, L. J. Phys. Chem. A 2002, 104, 4817-4824.
51. Cheatham, T. E., III: Kollman, P. A. In Structure, Motion, Interactions and Expression ofBiological Macromolecules; Sarma, R. H, Sarma, M. H., Eds.; Adenine Press: Albany, NY, 1998; pp 99-116.
52. Cornell, W. D,; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T,; Caldwell, J. W.; Kollman, P. A J. Am. Chem. Soc. 1995, 117, 5179-5197.
53. Šponer, J.; Hobza, P. J. Phys. Chem, A 2000, 104, 4592-4597.
54. (a) Kabeláč, M.; Hobza, P. J. Phys. Chem. B 2001, 105, 5804-5817.
55. (b) Florián, J.; Šponer, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 884-892.
56. (c) Kabeláč, M.; Hobza, P. Chem. Eur. J. 2001, 7, 2064-2974.
57. (d) Kratochvíl, M.; Šponer, J.; Hobza, P. J. Am. Chem. Soc. 2000, 122, 3495-3499.
58. (e) Luo, R.; Gilson, H. S. R.; Porter, M. J.; Gilson, M. K. Biophys. J. 2001, 80, 140-148.
59. (a) Šponer, J.; Berger, I.; Špačková, N.; Leszczynski, J.; Hobza, P. J. Biomol. Struct. Dyn. 2000, S2 (11th Conversation Special Issue), 383-407.
60. (b) Lankaš, F.; Cheatham, T. E., III; Spačková, N.; Hobza, P.; Langowski, J.; Šponer, J. Biophys. J. 2002, 82, 2592-2609.
61. (c) Chou, S. H.; Chin, K. H. J. Mol. Biol. 2001, 314, 139-152.
62. (a) Špačková, N.; Berger, I.; Egli, M.; Šponer, J. J. Am. Chem. Soc. 1998, 120, 6147-6151.
63. (b) Leroy, J. L.; Snoussi, K.; Gueron, M. Magn. Reson. Chem. 2001, 39 (Special Issue), S171-S176.
64. (c) Gallego, J.; Golden, E. B.; Stanley, D. E.; Reid, B. R. J. Mol. Biol. 1999, 285, 1039-1052.
65. (d) Gehring, K.; Leroy, J. L.; Gueron, M. Nature 1993, 363, 561-565.
66. Soliva, R.; Laughton, C. A.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1998, 120, 11226-11233 and references therein.