New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms [PDF]
Journal of Cheminformatics, 2013 Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors.
Choi Hwanho, Kang Hongsuk, Park Hwangseo
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Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model [PDF]
Nature Communications, 2021 Accurate theoretical evaluation of solvation free energy is challenging. Here the authors introduce a machine-learning based polarizable continuum solvation approach to improve the accuracy of widely accepted continuum solvation models by almost one ...
Amin Alibakhshi, Bernd Hartke
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MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning [PDF]
Journal of Cheminformatics, 2021 Recent advances in machine learning technologies and their applications have led to the development of diverse structure–property relationship models for crucial chemical properties. The solvation free energy is one of them. Here, we introduce a novel ML-
Hyuntae Lim, YounJoon Jung
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GAFF/IPolQ-Mod+LJ-Fit: Optimized force field parameters for solvation free energy predictions [PDF]
ADMET and DMPK, 2020 Rational drug design featuring explicit solubility considerations can greatly benefit from molecular dynamics simulations, as they allow for the prediction of the Gibbs free energy of solvation and thus relative solubilities.
Andreas Mecklenfeld, Gabriele Raabe
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Solvation free energy in governing equations for DNA hybridization, protein–ligand binding, and protein folding [PDF]
FEBS Open BioThis work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the equilibria. In the first example, the binding affinities of two DNA duplexes, one of nine and one
Caroline Harmon +6 more
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Solvation Free Energy Simulation for Rosmarinic Acid Extraction from Orthosiphon stamineus [PDF]
Methods and Protocols, 2019 This study was aimed to extract rosmarinic acid from Orthosiphon stamineus Benth. (Lamiaceae) in high yield. The mixture of chloroform−ethyl acetate (70:30) was chosen as the solvent system because rosmarinic acid gave the lowest solvation free ...
Cher Haan Lau, Lee Suan Chua
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Accurate determination of solvation free energies of neutral organic compounds from first principles
Nature Communications, 2022 Theoretical estimations of solvation free energy by continuum solvation models are generally not accurate. Here the authors report a polarizable force field fitted entirely to first-principles calculations for the estimation of free energy of solvation ...
Leonid Pereyaslavets +24 more
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Free energy and enthalpy data of neutral and protonated clusters in the solvent phase
Data in Brief, 2021 Structures of neutral and protonated acetonitrile in the solvent phase are important to describe proton behavior and to calculate thermodynamic quantities related to the solvation of ions or molecules in acetonitrile.
Alhadji Malloum, Jeanet Conradie
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J, 2021 The three-dimensional reference interaction site model of the molecular solvation theory with the Kovalenko–Hirata closure is used to calculate the free energy of solvation of organic solutes in liquid aliphatic ketones.
Dipankar Roy, Andriy Kovalenko
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Solvation free energy of light alkanes in polar and amphiphilic environments
Bibechana, 2018 Computer simulations of molecular models are powerful technique that have improved the under- standing of many biochemical phenomena. The method is frequently applied to study the motions of biological macromolecules such as protein and nucleic acids ...
Sunil Pokharel +2 more
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