The impact of surface area, volume, curvature, and lennard–jones potential to solvation modeling
This article explores the impact of surface area, volume, curvature, and Lennard–Jones (LJ)
potential on solvation free energy predictions. Rigidity surfaces are utilized to generate …
potential on solvation free energy predictions. Rigidity surfaces are utilized to generate …
Breaking the polar‐nonpolar division in solvation free energy prediction
Implicit solvent models divide solvation free energies into polar and nonpolar additive
contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We …
contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We …
Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model
A Alibakhshi, B Hartke - Nature Communications, 2021 - nature.com
Theoretical estimation of solvation free energy by continuum solvation models, as a
standard approach in computational chemistry, is extensively applied by a broad range of …
standard approach in computational chemistry, is extensively applied by a broad range of …
Variational approach for nonpolar solvation analysis
Solvation analysis is one of the most important tasks in chemical and biological modeling.
Implicit solvent models are some of the most popular approaches. However, commonly used …
Implicit solvent models are some of the most popular approaches. However, commonly used …
Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies
Implicit solvent models are important tools for calculating solvation free energies for
chemical and biophysical studies since they require fewer computational resources but can …
chemical and biophysical studies since they require fewer computational resources but can …
[HTML][HTML] Parameter optimization in differential geometry based solvation models
Differential geometry (DG) based solvation models are a new class of variational implicit
solvent approaches that are able to avoid unphysical solvent-solute boundary definitions …
solvent approaches that are able to avoid unphysical solvent-solute boundary definitions …
Differential geometry based solvation model I: Eulerian formulation
This paper presents a differential geometry based model for the analysis and computation of
the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to …
the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to …
Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model
D Shivakumar, Y Deng, B Roux - Journal of Chemical Theory and …, 2009 - ACS Publications
Accurate determination of absolute solvation free energy plays a critical role in numerous
areas of biomolecular modeling and drug discovery. A quantitative representation of ligand …
areas of biomolecular modeling and drug discovery. A quantitative representation of ligand …
Solvation thermodynamics of solutes in water and ionic liquids using the multiscale solvation-layer interface condition continuum model
Molecular assembly processes are generally driven by thermodynamic properties in
solutions. Atomistic modeling can be very helpful in designing and understanding complex …
solutions. Atomistic modeling can be very helpful in designing and understanding complex …
Implicit nonpolar solvent models
C Tan, YH Tan, R Luo - The Journal of Physical Chemistry B, 2007 - ACS Publications
We have systematically analyzed a new nonpolar solvent model that separates nonpolar
solvation free energy into repulsive and attractive components. Our analysis shows that …
solvation free energy into repulsive and attractive components. Our analysis shows that …