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Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA

  • Invited Paper
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Central European Journal of Chemistry

Abstract

We have theoretically analyzed mimics of Watson-Crick AT and GC base pairs in which N-H···O hydrogen bonds are replaced by N-H···S, using the generalized gradient approximation (GGA) of density functional theory at BP86/TZ2P level. The general effect of the above substitutions is an elongation and a slight weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many, and in particular, on which hydrogen bonds AT and GC are substituted.. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the hydrogen bonds involved in the mimics, using a quantitative bond energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these hydrogen bonds is found to contribute more than 40% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction.

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References

  1. P. Karran, Br. Med. Bull., 79–80, 153 (2006)

    Article  CAS  Google Scholar 

  2. L. J. J. Derijks, L. P. L. Gilissen, P. M. Hooymans, D. W. Hommes, Aliment. Pharmacol. Ther., 24, 715 (2006)

    Article  CAS  Google Scholar 

  3. E. B. Astwood, JAMA, 122 (1943) 78

    CAS  Google Scholar 

  4. L. Somerville et al., J. Biol. Chem., 278, 1005 (2003)

    Article  CAS  Google Scholar 

  5. N. Spackova, E. Cubero, J. Sponer, M. Orozco, J. Amer. Chem. Soc., 126, 146421 (2004)

    Article  CAS  Google Scholar 

  6. J. Sponer, J. Leszczynski, P. Hobza, J. Phys. Chem. A, 101, 9489 (1997)

    Article  CAS  Google Scholar 

  7. S. Kawahara, T. Uchimaru, Eur. J. Org. Chem. 2577 (2003)

  8. S. Kawahara, T. Uchimaru, K. Taira, M. Sekine, J. Phys. Chem. A, 106, 3207 (2002)

    Article  CAS  Google Scholar 

  9. I. Dabkowska, P. Jurecka, P. Hobza, J. Chem. Phys. 122, art. 204322 (2005)

    Google Scholar 

  10. J. Sponer, P. Jurecka, P. Hobza, J. Am. Chem. Soc. 126, 10142 (2004)

    Article  CAS  Google Scholar 

  11. P. Hobza, J. Sponer, Chem. Rev. 99, 3247 (1999)

    Article  CAS  Google Scholar 

  12. J. Bertran, A. Oliva, L. Rodríguez-Santiago, M. Sodupe, J. Am. Chem. Soc. 120, 8159 (1998)

    Article  CAS  Google Scholar 

  13. K. Brameld, S. Dasgupta, W. A. Goddard III, J. Phys. Chem. B 101, 4851 (1997)

    Article  CAS  Google Scholar 

  14. J. Sponer, J. Leszczynski, P. Hobza, J. Phys. Chem., 100, 1965 (1996)

    Article  CAS  Google Scholar 

  15. I. R. Gould, P. A. Kollman, J. Am. Chem. Soc., 116, 2493 (1994)

    Article  CAS  Google Scholar 

  16. R. Santamaria, A. Vázquez, J. Comp. Chem., 15, 981 (1994)

    Article  CAS  Google Scholar 

  17. J. Sponer, P. Hobza, J. Phys. Chem. A, 104, 4592 (2000)

    Article  CAS  Google Scholar 

  18. P. Hobza, J. Sponer, E. Cubero, M. Orozco, F. J. Luque, J. Phys. Chem. B, 104, 6286 (2000)

    Article  CAS  Google Scholar 

  19. J. Poater, X. Fradera, M. Solà, M. Duran, S. Simon, Chem. Phys. Lett., 369, 248 (2003)

    Article  CAS  Google Scholar 

  20. C. Fonseca Guerra, F. M. Bickelhaupt, Angew. Chem., 111, 3120 (1999)

    Article  Google Scholar 

  21. C. Fonseca Guerra, F. M. Bickelhaupt, Angew. Chem. Int. Ed., 38, 2942 (1999)

    Article  Google Scholar 

  22. C. Fonseca Guerra, F. M. Bickelhaupt, J. G. Snijders, E. J. Baerends, J. Am. Chem. Soc., 122, 4117 (2000)

    Article  CAS  Google Scholar 

  23. C. Fonseca Guerra, F. M. Bickelhaupt, J. G. Snijders, E. J. Baerends, Chem. Eur. J., 5, 3581 (1999)

    Article  Google Scholar 

  24. C. Fonseca Guerra, E. J. Baerends and F. M Bickelhaupt, Crystal Growth & Design, 2, 239 (2002)

    Article  CAS  Google Scholar 

  25. C. Fonseca Guerra, T. van der Wijst, F. M. Bickelhaupt, Chem. Eur. J., 12, 3032 (2006)

    Article  CAS  Google Scholar 

  26. F. M. Bickelhaupt, E. J. Baerends, In: K. B. Lipkowitz and D. B. Boyd (Eds.) Rev. Comput. Chem. (Wiley-VCH: New York, 2000) 15, 1

    Google Scholar 

  27. L. Stryer, Biochemistry (W.H. Freeman and Company, New York, 1988) Chapter 1

    Google Scholar 

  28. D. Voet, J. G. Voet, Biochemistry (Wiley, New York, 1995) Chapter 2

    Google Scholar 

  29. G. A. Jeffrey, W. Saenger, Hydrogen Bonding in Biological Structures (Springer-Verlag, Berlin, 1991,) Chapter 2

    Google Scholar 

  30. G. A. Jeffrey, An Introduction to Hydrogen Bonding (Oxford University Press, New York, 1997) Chapter 2

    Google Scholar 

  31. G. R. Desiraju, T. Steiner, The Weak Hydrogen Bond (Oxford University Press, New York, 1999) Chapter 1

    Google Scholar 

  32. C. Fonseca Guerra, F. M. Bickelhaupt, Angew. Chem., 114, 2194 (2002)

    Article  Google Scholar 

  33. C. Fonseca Guerra, F. M. Bickelhaupt, Angew. Chem. Int. Ed., 41, 2092 (2002)

    Article  Google Scholar 

  34. C. Fonseca Guerra, F. M. Bickelhaupt, J. Chem. Phys., 119, 4262 (2003)

    Article  CAS  Google Scholar 

  35. C. Fonseca Guerra, F. M. Bickelhaupt, E. J. Baerends, ChemPhysChem, 5, 481 (2004)

    Article  CAS  Google Scholar 

  36. G. te Velde et al., J. Comput. Chem., 22, 931 (2001)

    Article  Google Scholar 

  37. C. Fonseca Guerra, O. Visser, J. G. Snijders, G. te Velde, E. J. Baerends, In: E. Clementi and G. Corongiu (Eds.) Methods and Techniques for Computational Chemistry (STEF: Cagliari, 1995) 305

    Google Scholar 

  38. E. J. Baerends, D. E. Ellis, P. Ros, Chem. Phys., 2, 41 (1973)

    Article  CAS  Google Scholar 

  39. E. J. Baerends, P. Ros, Chem. Phys., 8, 412 (1975)

    Article  CAS  Google Scholar 

  40. E. J. Baerends, P. Ros, Int. J. Quantum. Chem. Symp., 12, 169 (1978)

    CAS  Google Scholar 

  41. C. Fonseca Guerra, J. G. Snijders, G. te Velde, E. J. Baerends, Theor. Chem. Acc., 99 391 (1998)

    Article  Google Scholar 

  42. P. M. Boerrigter, G. te Velde, E. J. Baerends, Int. J. Quantum Chem., 33, 87 (1988)

    Article  CAS  Google Scholar 

  43. G. te Velde, E. J. Baerends, J. Comp. Phys. 99, 84 (1992)

    Article  Google Scholar 

  44. J. G. Snijders, E. J. Baerends, P. Vernooijs, At. Nucl. Data Tables, 26, 483 (1982)

    Article  Google Scholar 

  45. J. Krijn, E. J. Baerends, Fit-Functions in the HFS-Method; Internal Report (in Dutch), Vrije Universiteit, Amsterdam, 1984

    Google Scholar 

  46. L. Versluis, T. Ziegler, J. Chem. Phys. 88, 322 (1988)

    Article  CAS  Google Scholar 

  47. J. C. Slater, Quantum Theory of Molecules and Solids, Vol. 4, (McGraw-Hill, New York, 1974)

    Google Scholar 

  48. A. D. Becke, J. Chem. Phys., 84, 4524 (1986)

    Article  CAS  Google Scholar 

  49. A. D. Becke, Phys. Rev. A, 38, 3098 (1988)

    Article  CAS  Google Scholar 

  50. S. H. Vosko, L. Wilk, M. Nusair, Can. J. Phys., 58, 1200 (1980)

    Article  CAS  Google Scholar 

  51. J. P. Perdew, Phys. Rev. B, 33, 8822 (1986) (Erratum: Phys. Rev. B, 34, 7406 (1986)

    Article  Google Scholar 

  52. L. Fan, T. Ziegler, J. Chem. Phys., 94, 6057 (1991)

    Article  CAS  Google Scholar 

  53. M. Swart, F.M. Bickelhaupt, J. Comput. Chem., (in press)

  54. K. Morokuma, J. Chem. Phys., 55, 1236 (1971)

    Article  CAS  Google Scholar 

  55. K. Kitaura, K. Morokuma, Int. J. Quantum. Chem., 10, 325 (1976)

    Article  CAS  Google Scholar 

  56. T. Ziegler, A. Rauk, Inorg. Chem., 18, 1755 (1979)

    Article  CAS  Google Scholar 

  57. T. Ziegler, A. Rauk, Inorg. Chem, 18, 1558 (1979)

    Article  CAS  Google Scholar 

  58. T. Ziegler, A. Rauk, Theor. Chim. Acta, 46, 1 (1977)

    CAS  Google Scholar 

  59. F. M. Bickelhaupt, N. J. R. van Eikema Hommes, C. Fonseca Guerra, E. J. Baerends, Organometallics, 15, 2923 (1996)

    Article  CAS  Google Scholar 

  60. C. Kittel, Introduction to Solid State Physics; Wiley: New York, (1986)

    Google Scholar 

  61. T. van der Wijst, C. Fonseca Guerra, M. Swart, F.M. Bickelhaupt, Chem. Phys. Lett., 426, 415 (2006)

    Article  CAS  Google Scholar 

  62. For a proper comparison between theoretical A-T and G-C base-pairing enthalpies and mass spectrometric values, the latter must be corrected for the fact that they refer to a mixture of isomeric AT and GC complexes, respectively, which causes the experimental values to overestimate the Watson-Crick base-pairing enthalpies by about 1 kcal/mol (see ref [13], [22] and I. K. Yanson, A. B. Teplitsky, L. F. Sukhodup, Biopolymers, 18, 1149 (1979)

    Article  CAS  Google Scholar 

  63. M. Swart, C. Fonseca Guerra, F. M. Bickelhaupt, J. Amer. Chem. Soc., 126, 16718 (2004)

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV, Amsterdam, The Netherlands

    Célia Fonseca Guerra, Evert Jan Baerends & F. Matthias Bickelhaupt

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  1. Célia Fonseca Guerra
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  2. Evert Jan Baerends
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  3. F. Matthias Bickelhaupt
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Correspondence to F. Matthias Bickelhaupt.

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Guerra, C.F., Baerends, E.J. & Bickelhaupt, F.M. Watson-crick base pairs with thiocarbonyl groups: How sulfur changes the hydrogen bonds in DNA. cent.eur.j.chem. 6, 15–21 (2008). https://doi.org/10.2478/s11532-007-0068-y

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  • DOI: https://doi.org/10.2478/s11532-007-0068-y

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