Theoretical investigation of hydrogen bonding in Watson-Crick, Hoogestein and their reversed and other models: Comparison and analysis for configurations of adenine-thymine base pairs in 9 models

Journal of Molecular Structure: THEOCHEM

Volumn 714, Issue 1, 2005, Pages 43-60

  Monajjemi, Majid ^a   Chahkandi, Behzad ^b  

^a ISLAMIC AZAD UNIVERSITY   (Iran)

^b ISLAMIC AZAD UNIVERSITY   (Iran)

Author keywords

Ab initio; B3LYP; Hoogestein; NBO; PCM; Solvent effect; Watson Crick base pairs

Indexed keywords

ACETONE; ADENINE; ALCOHOL; HYDROGEN; METHANOL; THYMINE; WATER;

AB INITIO CALCULATION; ARTICLE; BASE PAIRING; CHEMICAL ANALYSIS; DIELECTRIC CONSTANT; ENTHALPY; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NUCLEOTIDE SEQUENCE; QUANTUM MECHANICS; STRUCTURE ANALYSIS; THEORETICAL MODEL;

EID: 84961980723     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theochem.2004.09.048     Document Type: Article

References (62)

1. G.A. Jeffrey, and W. Saenger Hydrogen Bonding in Biological Structures 1991 Springer Berlin
2. G.A. Jeffrey An Introduction to Hydrogen Bonding 1997 Oxford University Press New York (Chapter 10)
3. W. Saenger Principles of Nucleic Acid Structure 1984 Springer New York
4. J.D. Watson, and F.H.C. Crick Nature 171 1953 737
5. D. Voet, and A. Rich The crystal structures of purines, pyrimidines and their intermolecular complexes Prog. Nucleic Acid Res. Mol. Biol. 10 1970 183 265
6. L. Pauling The Nature of the Chemical Bond 1978 Cornell University Press Ithaca
7. S.N. Vinogradov, and R.H. Linnell Hydrogen Bonding 1971 Van Nostrand Reinhold New York
8. G.A. Jeffrey, and S. Takagi Hydrogen-bond structure in carbohydrate crystals Acc. Chem. Res. 11 1978 264 270
9. P.A. Kollman, and L.C. Allen The theory of the hydrogen bond Chem. Rev. 72 1972 283 303
10. H.A. Staab Einführung in die theoretische organishe Chemie 1962 Verlag Chemei Weinheim p. 270
11. J. Kroon, J.A. Kanters, J.G.C.M. van Duijneveldt-van De Rijdt, F.B. van Duijneveldt, and J.A. Vliegenthart O-H⋯O hydrogen bonds in molecular crystals. A statistical and quantum-chemical analysis J. Mol. Struct. 24 1975 109 129
12. Y. Kyogoku, R.C. Lord, and A. Rich Proc. Natl Acad. Sci. USA 57 1967 250
13. Y. Kyogoku, R.C. Lord, and A. Rich Biochem. Biophys. Acta 179 1969 10
14. H. Iwahashi, and Y. Kyogoku J. Am. Chem. Soc. 99 1977 7761
15. M. Watanabe, H. Sugeta, H. Iwahashi, Y. Kyogoku, and M. Kainosho Eur. J. Biochem. 117 1981 553
16. H. Iwahashi, H. Sugeta, and Y. Kyogoku Biochemistry 21 1982 631
17. R.A. Newmark, and C.R. Cantor J. Am. Chem. Soc. 90 1968 5010
18. S.B. Petersen, and J.J. Led J. Am. Chem. Soc. 103 1981 5308
19. L.D. Williams, B. Chawla, and B.R. Shaw Biopolymers 26 1987 591
20. N.G. Williams, L.D. Williams, and B.R. Shaw J. Am. Chem. Soc. 111 1989 7208
21. I.K. Yanson, A.B. Teplitsky, and L.F. Sukhodub Biopolymers 18 1979 1149
22. B. Pullman, P. Claverie, and J. Caillet Proc. Natl Acad. Sci. USA 55 1966 904
23. Z.G. Kudritskaya, and V.I. Danilov J. Theor. Biol. 59 1976 303
24. J. Langlet, P. Claverie, F. Caron, and J.C. Boeuve Int. J. Quantum Chem. 19 1981 299
25. P. Hobza, and C. Sandorfy J. Am. Chem. Soc. 109 1987 1302
26. M. Aida J. Comput. Chem. 9 1988 362
27. V.I. Danilov, I.S. Tolokh, V.I. Poltev, and G.G. Malenkov FEBS Lett. 167 1984 245
28. V.I. Danilov, I.S. Tolokh, and V.I. Poltev FEBS Lett. 171 1984 325
29. V.I. Danilov, and I.S. Tolokh FEBS Lett. 173 1984 347
30. J.T. Egan, S. Nir, R. Rein, and R.D. MacElroy Int. J. Quantum Chem. Quantum Biol. Symp. 5 1978 433
31. A. Pohorille, L.R. Pratt, S.K. Burt, and R.D. MacElroy J. Biomol. Struct. Dyn. 1 1984 1257
32. A. Pohorille, S.K. Burt, and R.D. MacElroy J. Am. Chem. Soc. 106 1984 402
33. P. Cieplak, and P.A. Kollman J. Am. Chem. Soc. 110 1988 3734
34. L.X. Dang, and P.A. Kollman J. Am. Chem. Soc. 112 1990 503
35. P. Gilli, V. Ferretti, V. Bertolasi, and G. Gilli M. Hargittai I. Hargittai Advances in Molecular Structure Research vol. 2 1996 JAI Press Greenwich, CT 67 102
36. G. Gilli, F. Bellucci, V. Ferretti, and V. Bertolasi J. Am. Chem. Soc. 111 1989 1023
37. G. Gilli, V. Bertolasi, V. Ferretti, and P. Gilli Acta Crystallogr. B49 1993 564
38. C.F. Guerra, F.M. Bickelhaupt, J.G. Snijders, and E.J. Baerends Chem. Eur. J. 5 1999 3581
39. C.F. Guerra, and F.M. Bickelhaupt Angew. Chem. 111 1999 3120
40. C.F. Guerra, and F.M. Bickelhaupt Angew. Chem. Int. Ed. 38 1999 2942
41. J. Maranon, A.F. Fantoni, and J.R. Grigera J. Mol. Liq. 79 1999 177
42. M. Meyer, and J. Sühnel J. Biomol. Struct. Dyn. 15 1997 619
43. S. Miertus, and E. Scrocco J. Chem. Phys. 55 1981 117
44. S. Miertus, and J. Tomasi J. Chem. Phys. 65 1982 239
45. R. Cammi B.Mennucci J. Chem. Phys. 110 1999 9877
46. M.J. Frisch, G.W. Trucks, and H.B. Schlegel gaussian 98, Revision A.7 1998 Gaussian, Inc Pittsburgh, PA
47. M.W. Wong, K.B. Wiberg, and M.J. Frisch J. Am. Chem. Soc 114 1992 1645
48. M. Cossi, V. Barone, R. Cammi, and J. Tomasi Chem. Phys. Lett. 255 1996 327
49. J.E. Carpenter, and F. Weinhold J. Mol. Struct. (THEOCHEM) 169 1988 41
50. J.P. Foster, and F. Weinhold J. Am. Chem. Soc. 102 1980 7211
51. A.E. Reed, and F. Weinhold J. Chem. Phys. 78 1983 4066
52. A.E. Reed, L.A. Curtiss, and F. Weinhold Chem. Rev. 88 1988 899
53. A.E. Reed, R.B. Weinstock, and F. Weinhold J. Chem. Phys. 83 1985 735
54. S.F. Boys, and F. Bernardi Mol. Phys. 19 1970 553
55. J. Sponer, P. Hobza, and J. Leszczynski J. Leszczynski Computational Chemistry, Reviews of Current Trends 1996 World Scientific Publisher Singapore 185 218
56. J. Sponer, and P. Hobza Int. J. Quantum Chem. 57 1996 959
57. E.L. Stewart, C.K. Foley, N.L. Allinger, and J.P. Bowen J. Am. Chem. Soc. 98 1994 1361
58. J. Sponer, J. Leszcynski, and P. Hobza J. Phys. Chem. 100 1997 1965
59. I.K. Yanson, A.B. Teplitsky, and L.F. Sukhodub Biopolymers 18 1979 1149
60. K. Lindauer, C. Bendic, and J. Sühnel Comput. Appl. Biosci. 12 1996 281
61. C.F. Guerra, F.M. Bickelhaupt, and J.G. Snijders Chem. Eur. J. 5 1999 3581
62. K. Brameld, S. Dasgupta, and W.A. Goddard III J. Phys. Chem. B 101 1997 4851