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Article
Variable Atomic Radii for Continuum-Solvent Electrostatics Calculation
Journal of Chemical Physics (2008)
  • Baojing Zhou, University of Missouri–St. Louis
  • Manish Agarwal, University of Missouri–St. Louis
  • Chung F. Wong, University of Missouri–St. Louis
Abstract
We have developed a method to improve the description of solute cavity defined by the interlocking-sphere model for continuum-solvent electrostatics calculations. Many models choose atomic radii from a finite set of atom types or uses an even smaller set developed by Bondi [J. Phys. Chem. 68, 441 (1964)]. The new model presented here allowed each atom to adapt its radius according to its chemical environment. This was achieved by first approximating the electron density of a molecule by a superposition of atom-centered spherical Gaussian functions. The parameters of the Gaussian functions were then determined by optimizing a function that minimized the difference between the properties from the model and those from ab initio quantum calculations. These properties included the electrostatics potential on molecular surface and the electron density within the core of each atom. The size of each atom was then determined by finding the radius at which the electron density associated with the atom fell to a prechosen value. This value was different for different chemical elements and was chosen such that the averaged radius for each chemical element in a training set of molecules matched its Bondi radius. Thus, our model utilized only a few adjustable parameters—the above density cutoff values for different chemical elements—but had the flexibility of allowing every atom to adapt its radius according to its chemical environment. This variable-radii model gave better solvation energy for 31 small neutral molecules than the Bondi radii did, especially for a quantum mechanics/Poisson–Boltzmann approach we developed earlier. The improvement was most significant for molecules with large dipole moment. Future directions for further improvement are also discussed.

Publication Date
July 7, 2008
DOI
10.1063/1.2949821
Publisher Statement
This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in [Zhou, B., Agarwal, M., and Wong, C.F. (2008). Variable atomic radii for continuum-solvent electrostatics calculation. The Journal of Chemical Physics 129, 014509.] and may be found at https://doi.org/10.1063/1.2949821.
Citation Information
Baojing Zhou, Manish Agarwal and Chung F. Wong. "Variable Atomic Radii for Continuum-Solvent Electrostatics Calculation" Journal of Chemical Physics Vol. 129 Iss. 1 (2008) p. 14509 - 14509
Available at: http://works.bepress.com/chung-wong/29/