Molecular mechanical solvation energy

H. Liu, F. Mulle Plathe, and W. F. van Gunsteren, /. Chem. Phys., 102, 1702 (1995). A Molecular Dynamics Simulation Study with a Combined Quantum Medianical and Molecular Mechanical Potential Energy Function Solvation Effects of the Conformational Equilibrium of Dimethoxyethane. 

W C, A Tempcz)rrk, R C Hawley and T Hendrickson 1990. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. Journal of the American Chemical Society 112 6127-6129. ensson M, S Humbel, R D J Froese, T Matsubara, S Sieber and K Morokuma 1996. ONIOM A Multilayered Integrated MO + MM Method for Geometry Optimisations and Single Point Energy Predictions. A Test for Diels-Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition. Journal of Physical Chemistry 100 19357-19363. 

Shirts, M. R. Pande, V. S., Solvation free energies of amino acid side chain analogs for common molecular mechanics water models, J. Chem. Phys. 2005,122, 134508. 

A solvated MD simulation is performed to determine an ensemble of conformations for the molecule of interest. This ensemble is then used to calculate the terms in this equation. Vm is the standard molecular mechanics energy for each member of the ensemble (calculated after removing the solvent water). G PB is the solvation free energy calculated by numerical integration of the Poisson-Boltzmann equation plus a simple surface energy term to estimate the nonpolar free energy contribution. T is the absolute temperature. S mm is the entropy, which is estimated using... 

The background theory that underlies the FEP method as well as the molecular mechanics force fields that relate molecular structure to energy are reviewed in section one of the book. Section two describes the use of free energy calculations for determining molecular properties of ligands, including solvation, as calculated using both implicit and explicit water... 

The N,N -diphenylguanidinium (dpg+) has been foimd to adopt different conformations both in aqueous solutions [9] and in several salts that are being reviewed in this paper. The conformation of dpg+ is very sensitive to the counter-ion, and this effect has been the subject of ab-initio quantum mechanical and molecular mechanics calculations [10]. Stabilization of a particular conformation depends critically on intermolecular interactions with the solvent, since the energetic cost of rotation of the phenyl rings is much lower than typical solvation energies. 

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