Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges

Journal of Computational Chemistry
A LaraEsteban Vöhringer-Martinez

Abstract

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is ...Continue Reading

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Citations

Jan 22, 2020·Journal of Computer-aided Molecular Design·Maximiliano Riquelme, Esteban Vöhringer-Martinez
Jun 25, 2021·Journal of Chemical Information and Modeling·Panagiotis C PetrisJohannes G E M Fraaije

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