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Free Energy of Solvation in the Energetic Perspective
AIP Conference Proceedings, 2007The theory of solutions in the energy representation is reformulated in the form of density‐functional theory. The Kirkwood charging formula is provided in the energy representation and the density‐functional defined over the energy distribution function is introduced through the Legendre transform.
Nobuyuki Matubayasi +2 more
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Solvation free energy arithmetic for small organic molecules
Journal of Computational Chemistry, 2023AbstractSolvent‐mediated interactions contribute to ligand binding affinities in computational drug design and provide a challenge for theoretical predictions. In this study, we analyze the solvation free energy of benzene derivatives in water to guide the development of predictive models for solvation free energies and solvent‐mediated interactions ...
Aleksandar Lazaric +4 more
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Scaling of Hydrophobic Solvation Free Energies
The Journal of Physical Chemistry B, 2001We have calculated the free energy of solvation for hard sphere solutes, as large as 20 A in diameter, in two simple-point-charge models of water. These results were obtained using umbrella sampling of ensembles with fixed, ambient temperature and pressure.
Huang, D.M. +2 more
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Proteins: Structure, Function, and Bioinformatics, 2004
AbstractSolvation energy calculation is one of the main difficulties for the estimation of protein–ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein–ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of protein ...
Jianfeng, Pei +3 more
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AbstractSolvation energy calculation is one of the main difficulties for the estimation of protein–ligand binding free energy and the correct scoring in docking studies. We have developed a new solvation energy estimation method for protein–ligand binding based on atomic solvation parameter (ASP), which has been shown to improve the power of protein ...
Jianfeng, Pei +3 more
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An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation
Science, 1992A model for absolute free energies of solvation of organic, small inorganic, and biological molecules in aqueous solution is described. This model has the following features: (i) the solute charge distribution is described by distributed monopoles, and solute screening of dielectric polarization is treated with no restrictions on solute shape; (ii) the
C J, Cramer, D G, Truhlar
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Calculation of Solvation Free Energies
1998Solvation effects play an important role in determining the properties and activities of biological molecules that function in a predominantly aqueous environment. To a good degree of approximation, a solvated molecule can be modeled as a set of point charges in a low-dielectric cavity that is embedded in a high-dielectric medium.
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Free energy of solvation of a small Lennard–Jones particle
Journal of Computational Chemistry, 1994AbstractIn molecular dynamics (MD) and Monte Carlo (MC) free energy calculations, the choices of the thermodynamic paths from state a to state b affect the accuracy of the result and the efficiency of the programs. Most of the problems occur at the initial stages of growing in a new particle into a solvent.
Ching-Lung Lin, Robert H. Wood
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Are Solvation Free Energies of Homogeneous Helical Peptides Additive?
The Journal of Physical Chemistry B, 2005We investigated the additivity of the solvation free energy of amino acids in homogeneous helices of different length in water and in chloroform. Solvation free energies were computed by multiconfiguration thermodynamic integration involving extended molecular dynamics simulations and by applying the generalized-born surface area solvation model to ...
Staritzbichler, R., GU, Wei, Helms, V.
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Predicting Aqueous Free Energies of Solvation as Functions of Temperature
The Journal of Physical Chemistry B, 2006This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem.
Adam C, Chamberlin +2 more
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Simulations of solvation free energies and solubilities in supercritical solvents
The Journal of Chemical Physics, 2006Computer simulations are used to study solvation free energies and solubilities in supercritical solvents. Solvation free energies are calculated using the particle insertion method. The equilibrium solvent configurations required for these calculations are based on molecular dynamics simulations employing model solvent potentials previously tuned to ...
Zemin, Su, Mark, Maroncelli
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