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Stacking Interactions in Benzene and Cytosine Dimers: From Molecular Electron Density Perspective

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Abstract

The stacking patterns of benzene and cytosine have been compared with the help of Bader’ theory of atoms in molecule using the conventional ab initio method. In addition, the differences in the stacking and hydrogen-bonded interactions in cytosine have also been quantified with the help of various topographical features of molecular electron density. The electron density at the bond critical point does not exhibit linear relationship with the strength of stacking interaction in various twisted cytosine dimers. However, the electron density and Laplacian of electron density at the cage critical point display good linear relationship with the stacking energy. The values of the electron density and Laplacian of electron density derived from AIM theory is highly useful in differentiating stacking and hydrogen-bonded interaction. The aromaticity of cytosine and cytosine stack has been compared with benzene and benzene stack employing NICS criteria.

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References

  1. Muller-Dethlefs, K.; Hobza, P. Chem. Rev. 2000, 100, 143.

    Article  PubMed  Google Scholar 

  2. Karlstrom, G.; Linse, P.; Wallqvist, A.; Jonsson, B. J. Am. Chem. Soc. 1983, 105, 3777.

    Article  Google Scholar 

  3. Carsky, P.; Selzle, H. L.; Schlag, E. W. Chem. Phys. 1988, 125, 165.

    Article  Google Scholar 

  4. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Chem. Phys. 1990, 93, 5893.

    Article  Google Scholar 

  5. Tsuzuki, S.; Uchimaru, T.; Tanabe, K. J. Mol. Struct. Theochem. 1994, 307, 107.

    Article  Google Scholar 

  6. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Am. Chem. Soc. 1994, 116, 3500.

    Article  Google Scholar 

  7. Jaffe, R. L.; Smith, G. D. J. Chem. Phys. 1996, 105, 2780.

    Article  Google Scholar 

  8. Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Phys. Chem. 1996, 100, 18790.

    Article  Google Scholar 

  9. Spirko, V.; Engkvist, O.; Soldán, P.; Selzle, H. L.; Schlag, E. W.; Hobza, P. J. Chem. Phys. 1999, 111, 572.

    Article  Google Scholar 

  10. Tsuzuki, S.; Uchimaru, T.; Sugawara, K.; Mikami, M. J. Chem. Phys. 2002, 117, 11216.

    Article  Google Scholar 

  11. Henson, B. F.; Hartland, G. V.; Venturo, V. A.; Felker, P. M. J. Chem. Phys. 1992, 97, 2189.

    Article  Google Scholar 

  12. Arunan, E.; Gutowsky, H. S. J. Chem. Phys. 1993, 98, 4294.

    Article  Google Scholar 

  13. Sponer, J.; Hobza, P. Chem. Rev. 1999, 99, 3247.

    Article  PubMed  Google Scholar 

  14. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.

    Google Scholar 

  15. Hunter, C. A. J. Mol. Biol. 1993, 230, 1025.

    Article  PubMed  Google Scholar 

  16. Jurecka, P.; Sponer, J.; Hobza, P. J. Phys. Chem. B. 2004, 108, 5466.

    Article  Google Scholar 

  17. Sponer, J.; Hobza, P. Chem. Phys. Letts. 1997, 267, 263.

    Article  Google Scholar 

  18. Sponer, J.; Gabb, H. A.; Leszczynski, J.; Hobza, P. Biophys. J. 1997, 73, 76.

    PubMed  Google Scholar 

  19. Sponer, J.; Leszczynski, J.; Hobza, P. Biopolymers 2002, 61, 3.

    Article  Google Scholar 

  20. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590.

    Article  Google Scholar 

  21. Sponer, J.; Leszczynski, J.; Hobza, P. J. Biomol. Struct. Dyn. 1996, 14, 117.

    PubMed  Google Scholar 

  22. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J. Am. Chem. Soc. 2002, 124, 104.

    Article  PubMed  Google Scholar 

  23. Hobza, P.; Sponer, J.; Polasek, M. J. Am. Chem. Soc. 1995, 117, 792.

    Article  Google Scholar 

  24. Amutha, R.; Subramanian, V.; Nair, B. U. Theor. Chem. Acc. 2002, 107, 343.

    Google Scholar 

  25. Sivanesan, D.; Babu, K.; Gadre, S. R.; Subramanian, V.; Ramasami, T. J. Phys. Chem. A. 2000, 104, 10887.

    Article  Google Scholar 

  26. Popelier, P. L. A.; Joubert, L. J. Am. Chem. Soc. 2002, 124, 8725.

    Article  PubMed  Google Scholar 

  27. Parthasarathi, R.; Amutha, R.; Subramanian, V.; Nair, B.U.; Ramasami, T. J. Phys. Chem. A. 2004, 108, 3817.

    Article  Google Scholar 

  28. Bader, R. F. W. Atoms in Molecules: A Quantum Theory; Oxford: Clarendon, 1990.

    Google Scholar 

  29. Bader, R. F. W. J. Phys. Chem. A. 1998, 102, 7314.

    Article  Google Scholar 

  30. Bone, R. G. A.; Bader, R. F. W. J. Phys. Chem. 1996, 100, 10892.

    Article  Google Scholar 

  31. Carroll, M. T.; Bader, R. F. W. Mol. Phys. 1988, 65, 695.

    Google Scholar 

  32. Bader, R. F. W.; Bayles, D. J. Phys. Chem. A. 2000, 104, 5579.

    Article  Google Scholar 

  33. Popelier, P. L. A. Atoms in Molecules: An Introduction; Prentice Hall: New York, 2000.

    Google Scholar 

  34. Popelier, P. L. A. Coord. Chem. Rev. 2000, 197, 169.

    Article  Google Scholar 

  35. Koch, U.; Popelier, P. L. A. J. Phys. Chem. 1995, 99, 9747.

    Article  Google Scholar 

  36. Popelier, P. L. A. J. Phys. Chem. A. 1998, 102, 1873.

    Article  Google Scholar 

  37. Popelier, P. L. A.; Joubert, L.; Kosov, D. S. J. Phys. Chem. A. 2001, 105, 8254.

    Article  Google Scholar 

  38. Grabowski, S. J. Chem. Phys. Lett. 1999, 312, 542.

    Article  Google Scholar 

  39. Grabowski, S. J. J. Phys. Chem. A. 2000, 104, 5551.

    Article  Google Scholar 

  40. Grabowski, S. J. J. Phys. Chem. A. 2001, 105, 10739.

    Article  Google Scholar 

  41. Grabowski, S. J. J. Mol. Struct. 2001, 562, 137.

    Article  Google Scholar 

  42. Scheiner, S.; Grabowski, S. J.; Kar, T. J. Phys. Chem. A. 2001, 105, 10607.

    Article  Google Scholar 

  43. Wojtulewski, S.; Grabowski, S. J. J. Mol. Struct. 2002, 605, 235.

    Article  Google Scholar 

  44. Grabowski, S. J. J. Mol. Struct. 2002, 615, 239.

    Article  Google Scholar 

  45. Wojtulewski, S.; Grabowski, S. J. J. Mol. Struct. 2003, 645, 287.

    Article  Google Scholar 

  46. Wojtulewski, S.; Grabowski, S. J. J. Mol. Struct. Theochem. 2003, 621, 285.

    Article  Google Scholar 

  47. Cubero. E.; Orozco, M.; Hobza, P.; Luque, F. J. J. Phys. Chem. A. 1999, 103, 6394.

    Article  Google Scholar 

  48. Malcom, N. O. J.; Popelier, P. L. A. J. Phys. Chem. A. 2001, 105, 7638.

    Article  Google Scholar 

  49. Hobza, P.; Sponer, J.; Cubero, E.; Orozco, M.; Luque, F. J. J. Phys. Chem. B. 2000, 104, 6286.

    Article  Google Scholar 

  50. Munoz, J.; Sponer, J.; Hobza, P.; Orozco, M.; Luque, F. J. J. Phys. Chem. B. 2001, 105, 6051.

    Article  Google Scholar 

  51. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 1965.

    Article  Google Scholar 

  52. Frisch, M. J. et al. Gaussian 98, Revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.

    Google Scholar 

  53. Biegler-Konig, F.; Schonbohm, J.; Derdau, R.; Bayles, Bader, R. W. F. D. AIM 2000, version 1; Bielefeld: Germany, 2000.

    Google Scholar 

  54. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553.

    Google Scholar 

  55. Schleyer, P. v. R.; Maercker, C.; Dransfield, A.; Jiao, H.; Hommes, N. J. R. v. E. J. Am. Chem. Soc. 1996, 118, 6317.

    Article  Google Scholar 

  56. Schleyer, P. v. R.; Jiao, H.; Hommes, N. J. R. v. E.; Malkin, V. G.; Malkina, O. L. J. Am. Chem. Soc. 1997, 119, 12669.

    Article  Google Scholar 

  57. Schleyer, P. v. R.; Manoharan, M.; Wang, Z. X.; Kiran, B.; Jiao, H.; Puchta, R.; Hommes, N. J. R. v. E. Org. Lett. 2001, 3, 2465.

    Article  PubMed  Google Scholar 

  58. Koristsanszky, T. S.; Mallion, R. B. Chem. Rev. 2001, 101, 1583.

    Article  PubMed  Google Scholar 

  59. Howard, S. T.; Krygowski, T. M. Can. J. Chem. 1997, 75, 7813.

    Google Scholar 

  60. Ranganathan, A.; Kulkarni, G. U. J. Phys. Chem. A. 2002, 106, 7813.

    Article  Google Scholar 

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  1. Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai, 600020, India

    R. Parthasarathi & V. Subramanian

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  1. R. Parthasarathi
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  2. V. Subramanian
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Correspondence to V. Subramanian.

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Parthasarathi, R., Subramanian, V. Stacking Interactions in Benzene and Cytosine Dimers: From Molecular Electron Density Perspective. Struct Chem 16, 243–255 (2005). https://doi.org/10.1007/s11224-005-4455-8

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  • DOI: https://doi.org/10.1007/s11224-005-4455-8

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