Application of a universal solvation model to nucleic acid bases: Comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory

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Abstract

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution. Copyright (C) 1999 Elsevier Science B.V. All rights reserved.

Original languageEnglish (US)
Pages (from-to)147-155
Number of pages9
JournalBiophysical Chemistry
Volume78
Issue number1-2
DOIs
StatePublished - Apr 5 1999

Bibliographical note

Funding Information:
The authors are grateful to Paul Winget for helpful discussions and assistance and to Albert J. Leo, Richard Wolfenden, and Phoebe Shih for helpful correspondence. This work was supported in part by the National Science Foundation.

Keywords

  • Continuum solvent
  • Dipole moment
  • Electrostatics
  • Free energy of solvation
  • Partial atomic charge
  • Partition coefficient
  • Polarizable solute

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