A recently developed method for predicting binding affinities in ligand᎐receptor complexes, based on interaction energy averaging and conformational sampling by molecular dynamics simulation, is presented. Polar and nonpolar contributions to the binding free energy are approximated by a linear scali
Free energy of solvation from molecular dynamics simulations for low dielectric solvents
✍ Scribed by Paulo F. B. Gonçalves; Hubert Stassen
- Publisher
- John Wiley and Sons
- Year
- 2003
- Tongue
- English
- Weight
- 103 KB
- Volume
- 24
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
Using molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl~4~, CHCl~3~, benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute–solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie–Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1758–1765, 2003
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