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Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

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journal contribution
posted on 04.06.2009, 00:00 by Eirik F. da Silva, Hallvard F. Svendsen, Kenneth M. Merz
A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster, and the solvation free energy of the cluster was calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson−Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson−Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a rmsd of 2.6 kcal/mol for anions; for cations the unsigned average error was 2.8 kcal/mol and the rmsd 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model.