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Quantum-chemical study of the effects of noncovalent interactions on the nuclear magnetic screening constants of pyrimidine base associates

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Abstract

The effects of weak noncovalent interactions on the nuclear magnetic screening (NMS) constants (σ 1H), (σ 13C) and charge distribution (q t ) on atoms in van der Waals model associates of unsubstituted and substituted pyrimidines and substituted uracil are considered. The NMS constants were calculated by the UB3LYP/6-31G(d,p) with GIAO functions. The correlation dependences of the 1H and 13C σ constants on the charge q on atoms whre constructed. It were shown that they can be represented as polynomials that include the terms that are linear and quadratic relative to the charge. The relations obtained in this way are similar in form and close in magnitude to the coefficients of the known Buckingham and Augspurger functions that describe the electric field effects on the nuclear magnetic screening constants. It was found that the coefficients in these polynomials have a definite physical sense in that they characterize nuclear magnetic screening and the “screening polarizability” tensor in the unperturbed molecule and associate, respectively. The NMS constants and charge distribution in pyrimidine base associates and accordingly the coefficients that reflect their values in polynomials depend on the form, size, and composition of the associate and can vary significantly depending on the position of the pyrimidine base in the associate.

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References

  1. R. Shenhar, H. Wang, R. E. Hoffman, et al., J. Am. Chem. Soc., 124, 4685–4692 (2002).

    Article  CAS  Google Scholar 

  2. D. M. Bassani and J.-M. Lehn, Bull. Soc. Chim. Fr., 134, 897–906 (1997).

    CAS  Google Scholar 

  3. J. Barberá, E. Cavero, M. Lehmann, et al., J. Am. Chem. Soc., 125, 4527–4533 (2003).

    Article  CAS  Google Scholar 

  4. J. A. R. Navarro, M. B. Janik, E. Freisinger, and B. Lippert, Inorg. Chem., 38, 426–432 (1999).

    Article  CAS  Google Scholar 

  5. P. F. H. Schwab, M. D. Levin, and J. Michl, Chem. Rev., 99, 1863–1933 (1999).

    Article  CAS  Google Scholar 

  6. M. D. Sindkhedkar, H. R. Mulla, and A. Cammers-Goodwin, J. Am. Chem. Soc., 122, 9271–9277 (2000).

    Article  CAS  Google Scholar 

  7. D. J. B. Folmer, R. P. Sijbesta, H. Kooijman, et al., ibid., 121, 9001–9007 (1999).

    Article  CAS  Google Scholar 

  8. M. Rapacioli, F. Calvo, F. Spiegelman, et al., J. Phys. Chem. A, 109, 2487–2497 (2005).

    Article  CAS  Google Scholar 

  9. T. Yamamoto, D. Komadurin, M. Arai, et al., J. Am. Chem. Soc., 120, 2047–2058 (1998).

    Article  CAS  Google Scholar 

  10. J. Murgich, Petr. Sci. Techn., 20, 983–997 (2002).

    Article  CAS  Google Scholar 

  11. K. S. Kim, S. B. Suh, J. C. Kim, et al., J. Am. Chem. Soc., 124, 14268–14279 (2002).

  12. L. Zhu, Y. Xiu, D. W. Hess, and C.-P. Wong, Nano Lett., 5, No. 12, 2641–2645 (2005).

    Article  CAS  Google Scholar 

  13. J. Gestel, A. R. A. Palmans, B. Titulaer, et al., J. Am. Chem. Soc., 127, 5490–5494 (2005).

    Article  CAS  Google Scholar 

  14. V. Germain, Li Jing, D. Ingert, et al., J. Phys. Chem. (B), 107, No. 34, 8717–8720 (2003).

    CAS  Google Scholar 

  15. L. M. Greig and D. Philp, Chem. Soc. Rev., 30, 287–302 (2001).

    Article  CAS  Google Scholar 

  16. I. Alkorta, I. Rozas, and J. Elguero, ibid., 27, 163–169 (1998).

    Article  CAS  Google Scholar 

  17. D. H. Williams and M. S. Westwell, ibid., 57–63.

  18. K. Müller-Dethlefs and P. Hobza, Chem. Rev., 100, 143–167 (2000).

    Article  CAS  Google Scholar 

  19. M. Orozco and F. J. Luque, ibid., 100, 4187–4225 (2000).

    CAS  Google Scholar 

  20. P. Hobza and J. Sponer, ibid., 99, 3247–3276 (1999).

    CAS  Google Scholar 

  21. K. S. Kim, P. Tarakeshwar, and J. Y. Lee, ibid., 100, 4145–4185 (2000).

    CAS  Google Scholar 

  22. D. M. Bishop, Int. Rev. Phys. Chem., 13, No. 1, 21–39 (1994).

    Article  CAS  Google Scholar 

  23. C. Dykstra, J. Am. Chem. Soc., 11, 6168–6174 (1989).

    Article  Google Scholar 

  24. J. A. N. F. Gomes and R. B. Mallion, Chem. Rev., 101, 1349–1383 (2001).

    Article  CAS  Google Scholar 

  25. M. Lee, M. J. Shephard, and S. M. Risser, J. Phys. Chem., 104A, 7593–7599 (2000).

    Google Scholar 

  26. P. Talukdar, G. Bollot, J. Mareda, et al., J. Am. Chem. Soc., 12, No. 18, 6528/6529 (2005).

    Google Scholar 

  27. K. Xiao, Y. Liu, T. Qi, et al., ibid., 127, No. 38, 13281–13286.

  28. Z. Xie, B. Yang, F. Li, et al., ibid., 14152/14153.

  29. M. Rueda, F. Luque, J. M. L. Javier, and M. Orozco, J. Phys. Chem. A, 105, 6575–6580 (2001).

    Article  CAS  Google Scholar 

  30. A. A. Voityuk and N. Rösch, J. Phys. Chem. B, 106, 3013–3018 (2002).

    Article  CAS  Google Scholar 

  31. K. S. Kim, P. Tarakeshwar, and J. Y. Lee, Chem. Rev., 100, 4145–4185 (2000).

    Article  CAS  Google Scholar 

  32. M. Lee, M. J. Shephard, S. M. Risser, et al., J. Phys. Chem. A, 104, 7593–7599 (2000).

    Article  CAS  Google Scholar 

  33. F. Salhi, B. Lee, C. Metz, et al., Org. Lett., 4, 3195–3198 (2002).

    Article  CAS  Google Scholar 

  34. J. F. Britten, O. P. Clements, and A. W. Cordes, Inorg. Chem., 40, 6820–6824 (2001).

    Article  CAS  Google Scholar 

  35. E. M. B. Boon and K. Jacqueline, Bioconjugate Chem., 14, 1140–1147 (2003).

    Article  CAS  Google Scholar 

  36. E. Z. Reineks and A. J. Berdis, Biochemistry, 43, 393–404 (2004).

    Article  CAS  Google Scholar 

  37. H. Hwang and J.-S. Taylor, ibid., 14612–14623.

  38. J. M. Warman, M. P. de Haas, G. Dicker, et al., Chem. Mater., 16, 4600–4609 (2004).

    Article  CAS  Google Scholar 

  39. T. M. Pappenfus, R. J. Chesterfield, C. D. Frisbie, et al., J. Am. Chem. Soc., 124, 4184/4185 (2002).

    Article  CAS  Google Scholar 

  40. T. Nakano and T. Yade, ibid., 125, 15474–15484 (2003).

  41. T. Ryu and S. Hiroshi, ibid., 15282/15283.

  42. D. A. Scherlis and N. Marzari, ibid., 3207–3212.

  43. D. E. Janzen, M. W. Burand, P. C. Ewbank, et al., ibid., 126, 15295-15308 (2004).

  44. M. A. O Neill and J. K. Barton, ibid., 11471–11483.

  45. M. W. Wong, J. Org. Chem., 70, 5487–5493 (2005).

    Article  CAS  Google Scholar 

  46. B. W. Gung, M. Patel, and X. J. Xue, J. Org. Chem., 70, No. 25, 1053–1057 (2005).

    Article  CAS  Google Scholar 

  47. M. Nakano, S. Yamada, M. Takahata, and K. Yamaguchi, J. Phys. Chem. A, 107, 4157–4164 (2003).

    Article  CAS  Google Scholar 

  48. E. M. Boon, N. M. Jackson, M. D. Wightman, et al., J. Phys. Chem. B, 107, 11805–11812 (2003).

    Google Scholar 

  49. C. Hecht, J. Friedrich, and T.-C. Chang, ibid., 108, 10241–10244 (2004).

  50. M. J. Fuller, L. E. Sinks, B. Rybtchinski, et al., J. Phys. Chem. A, 109, 970–975 (2005).

    Article  CAS  Google Scholar 

  51. W. S. Kim, J. Kim, J. K. Park, et al., J. Phys. Chem. B, 109, 2686–2692 (2005).

    Article  CAS  Google Scholar 

  52. K. B. Stark, J. M. Gallas, G. W. Zajac, et al., ibid., 1970–1977.

  53. P. Prins, K. Senthilkumar, F. C. Grozema, et al., ibid., 18267–18274.

  54. W. Zhang, A. F. Cozzolino, A. H. Mahmoudkhani, et al., ibid., 18378–18384.

  55. Y.-H. So, S. J. Martin, B. Bell, et al., Macromolecules, 36, 4699–4708 (2003).

    Article  CAS  Google Scholar 

  56. T. Yamamoto, M. Arai, H. Kokubo, S. Sasaki, ibid., 7986–7993.

  57. Y.-J. Sheng, H.-J. Lin, J. Z. Y. Chen, H.-K. Tsao, ibid., 37, 9631–9638 (2004).

    CAS  Google Scholar 

  58. G. Jiang, R. Jankowiak, N. Grubor, et al., Chem. Res. Toxicol., 17, 330–339 (2004).

    Article  CAS  Google Scholar 

  59. A. D. Buckingham, Can. J. Chem., 38, 300–307 (1960).

    Article  CAS  Google Scholar 

  60. A. D. Buckingham, T. Schaefer, and W. G. Schneider, J. Chem. Phys., 32, 1227–1233 (1960).

    Article  CAS  Google Scholar 

  61. R. A. Kromhout and B. Linder, J. Magn. Res., 1, 450–463 (1969).

    CAS  Google Scholar 

  62. F. R. Prado and C. Giessner-Prettre, ibid., 47, 103–117 (1982).

    Google Scholar 

  63. C. Giessner-Prettre and S. Ferchiou, ibid., 55, 64–77 (1983).

    CAS  Google Scholar 

  64. S. Ferchiou and C. Giessner-Prettre, ibid., 61, 262–271 (1985).

    CAS  Google Scholar 

  65. C. J. Giessner-Prettre, Biomol. Struct. Dyn., 4, No. 1, 99–110 (1986).

    CAS  Google Scholar 

  66. S. Ferchiou and C. Giessner-Prettre, Chem. Phys. Lett., 103, No. 2, 156–160 (1983).

    Article  CAS  Google Scholar 

  67. F. R. Prado, C. Giessner-Prettre, and A. Pullman, Theor. Chim. Acta (Berl.), 59, 55–69 (1981).

    Article  CAS  Google Scholar 

  68. J. Czernek, J. Phys. Chem. A, 107, 3952–3959 (2003).

    Article  CAS  Google Scholar 

  69. J. Czernek, ibid., 105, 1357–1365 (2001).

    Article  CAS  Google Scholar 

  70. J. D. Augspurger, J. G. Pearson, E. Olfield, et. al., J. Magn. Res., 100, 342–357 (1992).

    CAS  Google Scholar 

  71. J. D. Augspurger and C. E. Dykstra, J. Phys. Chem., 95, 9230 (1991).

    Article  CAS  Google Scholar 

  72. J. D. Augspurger, C. E. Dykstra, and E. Olfield, J. Am. Chem. Soc., 113, 2447 (1991).

    Article  CAS  Google Scholar 

  73. W. T. Raynes and R. Ratcliffe, Mol. Phys., 37, 571 (1979).

    Article  CAS  Google Scholar 

  74. W. T. Raynes, Encyclopedia of NMR, D. M. Grant and R. K. Harris (eds.), 1846–1856 (1996).

  75. M. Grayson and W. T. Raynes, Chem. Phys. Lett., 214, 473–480 (1993).

    Article  CAS  Google Scholar 

  76. M. Grayson and W. T. Raynes, Mol. Phys., 81, 533–545 (1994).

    Article  CAS  Google Scholar 

  77. M. Grayson and W. T. Raynes, Magn. Res. Chem., 33, 138–143 (1995).

    Article  CAS  Google Scholar 

  78. T. Schaefer and W. G. Schneider, Can. J. Chem., 40, 966–981 (1963).

    Article  Google Scholar 

  79. A. H. Gawer and B. P. Dailey, J. Chem. Phys., 42, 2658–2670 (1965).

    Article  CAS  Google Scholar 

  80. H. Spiescke and W. G. Schneiger, Tetrahedron Lett., 468 (1961).

  81. P. C. Lauterbur, J. Am. Chem. Soc., 83, 1838 (1961).

    Article  CAS  Google Scholar 

  82. M. Karplus and J. A. Pople, J. Chem. Phys., 38, 2803 (1963).

    Article  CAS  Google Scholar 

  83. P. C. Lauterbur, ibid., 43, 360 (1965).

    Article  CAS  Google Scholar 

  84. J. Feeney, I. H. Sutcliffe, and S. H. Walker, Mol. Phys., 11, 117 (1966).

    Article  CAS  Google Scholar 

  85. W. J. Horsley and H. Sternlicht, J. Am. Chem. Soc., 90, 3738–3748 (1968).

    Article  CAS  Google Scholar 

  86. T. Tokuhiro and G. Fraenkel, ibid., 91, 5005–5013 (1969).

    Article  CAS  Google Scholar 

  87. P. Lazzeretti and F. Tadei, Org. Magn. Res., 3, 113–125 (1971).

    Article  CAS  Google Scholar 

  88. J. G. Batchelor, J. H. Prestegard, R. J. Cushley, and J. Lipsky, J. Am. Chem. Soc., 19, 6378–6384 (1973).

    Google Scholar 

  89. J. G. Batchelor, J. Am. Chem. Soc., 97, 3410–3415 (1975).

    Article  CAS  Google Scholar 

  90. J. C. Facelli, D. M. Grant, and J. Michl, Acc. Chem. Res., 20, 152–158 (1987).

    Article  CAS  Google Scholar 

  91. A. S. Mikhailov, N. G. Pashkurov, V. S. Reznik, et al., Dokl. Ross. Akad. Nauk, 362, No. 5, 643/644 (1998).

    Google Scholar 

  92. U. Thewalt and C. E. Bugg, J. Am. Chem. Soc., 94, No. 25, 8892–8898 (1972).

    Article  CAS  Google Scholar 

  93. P. Hohenberg and W. Kohn, Phys. Rev. B, 136, 864 (1964).

    Article  Google Scholar 

  94. W. Kohn and L. J. Sham, Phys. Rev. A, 140, 1133 (1965).

    Article  Google Scholar 

  95. A. D. Becke, J. Chem. Phys., 98, 5648 (1993).

    Article  CAS  Google Scholar 

  96. C. Lee, W. Yang, and R. G. Parr, Phys. Rev. B, 37, 785–789 (1988).

    Article  CAS  Google Scholar 

  97. R. Ditchfield, Mol. Phys., 27, 789 (1974).

    Article  CAS  Google Scholar 

  98. Gaussian-98, Gaussian, Inc., Pittsburgh, PA (1998).

  99. V. G. Malkin, O. L. Malkina, M. E. Casida, and D. R. Salahub, J. Am. Chem. Soc., 116, 5898 (1994).

    Article  CAS  Google Scholar 

  100. C. J. Jameson and J. Mason, The Chemical Shift, Chapter 3, in: Multinuclear NMR, J. Mason (ed.) (1987).

  101. B. Shanker and J. Applequist, J. Phys. Chem., 100, 3879 (1966).

    Article  Google Scholar 

  102. A. R. Katrizky, K. Jug, and D. C. Oniciu, Chem. Rev., 101, 1421–1449 (2001).

    Article  CAS  Google Scholar 

  103. D. L. Bryce, J. Boisbouver, and A. Bax, J. Am. Chem. Soc., 126, 10820/10821 (2004).

    Google Scholar 

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  1. Kazan State University, Kazan

    A. A. Nafikova, R. M. Aminova & A. V. Aganov

  2. A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, Kazan

    V. S. Reznik

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  1. A. A. Nafikova
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  2. R. M. Aminova
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Correspondence to R. M. Aminova.

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Translated from Zhurnal Strukturnoi Khimii, Vol. 48, Supplement,pp. S71–S85, 2007.

Original Russian Text Copyright © 2007 by A. A. Nafikova, R. M. Aminova, A. V. Aganov, and V. S. Reznik

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Nafikova, A.A., Aminova, R.M., Aganov, A.V. et al. Quantum-chemical study of the effects of noncovalent interactions on the nuclear magnetic screening constants of pyrimidine base associates. J Struct Chem 48 (Suppl 1), S64–S78 (2007). https://doi.org/10.1007/s10947-007-0150-5

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