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Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations

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Abstract

Fused-sphere surfaces can be used to mimic a molecular ‘boundary’ associated with a constant value of the electron density. The simplest of such fused-sphere models are constructed by using the atomic radii for the spherical isodensity surfaces of individual atoms. In this work, we discuss the extension of this model to molecules containing atoms beyond the second row. In these many- electron systems, the computation of electron densities is usually simplified by adopting a pseudopotential (or effective-core potential) approach. Here, we discuss the performance of large- and small-core pseudo-potential calculations as a tool to derive atomic radii. Our results provide an optimum set of variable radii that can be used to build fused-sphere surfaces. This continuum of surfaces provides a simple approximation to the low-electron-density regions around molecules with heavy atoms.

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References

  1. Richards, F.M., Annu. Rev. Biophys. Bioeng., 6 (1977) 151.

    Google Scholar 

  2. Mezey, P.G., In Lipkowitz, K.B. and Boyd, D.B. (Eds.), Reviews in Computational Chemistry, Vol. 1, VCH Publishers, New York, NY, 1990, pp. 265–294.

    Google Scholar 

  3. Brinck, T., Murray, J.S. and Politzer, P., Mol. Phys., 76 (1992) 609.

    Google Scholar 

  4. Bader, R.F.W., Atoms in Molecules, Clarendon Press, Oxford, 1990.

    Google Scholar 

  5. a. Yang, W., Phys. Rev. Lett., 66 (1991) 1438. b. Yang, W. and Lee, T.-S., J. Chem. Phys., 103 (1995) 5674.

    Google Scholar 

  6. Walker, P.D., Arteca, G.A. and Mezey, P.G., J. Comput. Chem., 12 (1991) 220.

    Google Scholar 

  7. Grant, J.A. and Pickup, B.T., J. Phys. Chem., 99 (1995) 3503.

    Google Scholar 

  8. a. Walker, P.D. and Mezey, P.G., J. Am. Chem. Soc., 115 (1993) 12423. b. Walker, P.D. and Mezey, P.G., J. Am. Chem. Soc., 116 (1994) 12022.

    Google Scholar 

  9. Mezey, P.G., Shape in Chemistry, VCH Publishers, New York, NY, 1993.

    Google Scholar 

  10. Ooi, T., Oobatake, M., Némethy, G. and Scheraga, H.A., Proc. Natl. Acad. Sci. USA, 84 (1987) 3086.

    Google Scholar 

  11. Abraham, M.H., Chem. Soc. Rev., 22 (1993) 73.

    Google Scholar 

  12. a. Tuñón, I., Silla, E. and Pascual-Ahuir, J.L., Protein Eng., 5 (1992) 715. b. Tuñón, I., Silla, E. and Pascual-Ahuir, J.L., Chem. Phys. Lett., 203 (1993) 289.

    Google Scholar 

  13. Hansch, C. and Leo, A., Exploring QSAR, American Chemical Society, Washington, DC, 1995.

    Google Scholar 

  14. Mebane, R.C., Williams, C.D. and Rybolt, T.R., Fluid Phase Eq., 124 (1996) 111.

    Google Scholar 

  15. Politzer, P., Parr, R.G. and Murphy, D.R., J. Chem. Phys., 79 (1983) 3859.

    Google Scholar 

  16. Bader, R.F.W., Carroll, M.T., Cheeseman, J.R. and Chang, C., J. Am. Chem. Soc., 109 (1987) 7968.

    Google Scholar 

  17. Arteca, G.A., Grant, N.D. and Mezey, P.G., J. Comput. Chem., 12 (1991) 1198.

    Google Scholar 

  18. a. Ganguly, P., J. Am. Chem. Soc., 115 (1993) 9287. b. Ganguly, P., J. Am. Chem. Soc., 117 (1995) 2655.

    Google Scholar 

  19. García, A. and Cohen, M.L., Phys. Rev. B, 47 (1993) 4221.

    Google Scholar 

  20. Fernández Pacios, L., J. Comput. Chem., 16 (1995) 133.

    Google Scholar 

  21. Chattaraj, P.K., Cedillo, A. and Parr, R.G., J. Chem. Phys., 103 (1995) 10621.

    Google Scholar 

  22. Ghanty, T.K. and Ghosh, S.K., J. Phys. Chem., 100 (1996) 17429.

    Google Scholar 

  23. Du, Q. and Arteca, G.A., J. Comput. Chem., 17 (1996) 1258.

    Google Scholar 

  24. Gibbs, G.V., Tamada, O. and Boisen Jr., M.B., Phys. Chem. Minerals, 24 (1997) 432.

    Google Scholar 

  25. Yang, Z.-Z. and Davidson, E.R., Int. J. Quantum Chem., 62 (1997) 47.

    Google Scholar 

  26. Krauss, M. and Stevens, W.J., Annu. Rev. Phys. Chem., 35 (1984) 357.

    Google Scholar 

  27. Frenking, G., Antes, I., Böhme, M., Dapprich, S., Ehlers, A.W., Jonas, V., Neuhaus, A., Otto, M., Stegmann, R., Veldkamp, A. and Vyboishchikov, S.F., In Lipkowitz, K.B. and Boyd, D.B. (Eds.), Reviews in Computational Chemistry, Vol. 8, VCH Publishers, New York, NY, 1996, pp. 63–143.

    Google Scholar 

  28. Cundari, T.R., Benson, M.T., Lutz, M.L. and Sommerer, S.O., In Lipkowitz, K.B. and Boyd, D.B. (Eds.), Reviews in Computational Chemistry, Vol. 8, VCH Publishers, New York, NY, 1996, pp. 145–202.

    Google Scholar 

  29. Ganguly, P., J. Am. Chem. Soc., 117 (1995) 1777.

    Google Scholar 

  30. a. Zunger, A. and Cohen, M.L., Phys. Rev. B, 18 (1978) 5449. b. Zunger, A. and Cohen, M.L., 20 (1979) 4082.

    Google Scholar 

  31. Frisch, M.J., Trucks, G.W., Head-Gordon, M., Gill, P.M.W., Wong, M.W., Foresman, J.B., Johnson, B.G., Schlegel, H.B., Robb, M.A., Replogle, E.S., Gomperts, R., Andrés, J.L., Raghavachari, K., Binkley, J.S., González, C., Martin, R.L., Fox, D.J., Defrees, D. J., Baker, J., Stewart, J.J.P. and Pople, J.A., Gaussian 92 (Revision G.4), Gaussian, Inc., Pittsburgh, PA, 1992.

    Google Scholar 

  32. Hay, J.P. and Wadt, W.R., J. Chem. Phys., 82 (1985) 270.

    Google Scholar 

  33. Hay, J.P. and Wadt, W.R., J. Chem. Phys., 82 (1985) 299.

    Google Scholar 

  34. Bettega, M.H.F., Natalense, A.P.P., Lima, M.A.P. and Ferreira, L.G., Int. J. Quantum Chem., 60 (1996) 821.

    Google Scholar 

  35. Stevens, W.J., Krauss, M., Basch, H. and Jasien, P.G., Can. J. Chem., 70 (1992) 612.

    Google Scholar 

  36. Cundari, T.R., J. Am. Chem. Soc., 114 (1992) 7879.

    Google Scholar 

  37. a. Cundari, T.R. and Stevens, W.J., J. Chem. Phys., 98 (1993) 5555. b. Cundari, T.R., Sommerer, S.O. and Stevens, W.J., Chem. Phys., 178 (1993) 235.

    Google Scholar 

  38. Vyboishchikov, S.F., Sierraalta, A. and Frenking, G., J. Comput. Chem., 18 (1996) 416.

    Google Scholar 

  39. Bondi, A., J. Phys. Chem., 68 (1964) 441.

    Google Scholar 

  40. Gavezzotti, A., J. Am. Chem. Soc., 105 (1983) 5220.

    Google Scholar 

  41. Pauling, L., The Nature of the Chemical Bond, Cornell University Press, Ithaca, NY, 1960.

    Google Scholar 

  42. Weast, R.C. (Ed.), CRC Handbook of Chemistry and Physics, CRC Press, Boca Raton, FL, 1988, p. D-111.

    Google Scholar 

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Authors and Affiliations

  1. Département de Chimie et Biochimie Laurentian University, Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6

    Gustavo A. Arteca

  2. Department of Biology, Laurentian University, Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6

    Naomi D. Grant

Authors
  1. Gustavo A. Arteca
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  2. Naomi D. Grant
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Arteca, G.A., Grant, N.D. Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations. J Comput Aided Mol Des 13, 315–324 (1999). https://doi.org/10.1023/A:1008018802504

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