A Universal Organic Solvation Model.

2000 ◽  
Vol 65 (18) ◽  
pp. 5886-5886 ◽  
Author(s):  
David J. Giesen ◽  
Michael Z. Gu ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Solvation Model

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model

2016 ◽  
Vol 30 (11) ◽  
pp. 1007-1017 ◽  
Author(s):  
Sebastian Diaz-Rodriguez ◽  
Samantha M. Bozada ◽  
Jeremy R. Phifer ◽  
Andrew S. Paluch
Keyword(s):  
Water Distribution ◽  
Distribution Coefficients ◽  
Solvation Model

Erratum: “Density functional solvation model based on CM2 atomic charges” [J. Chem. Phys. 109, 9117 (1998); 111, 5624 (E) (1999)]

2000 ◽  
Vol 113 (9) ◽  
pp. 3930-3930
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Gregory D. Hawkins ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Density Functional ◽  
Chem Phys ◽  
Atomic Charges ◽  
Solvation Model ◽  
Model Based

scholarly journals Minimization and Eulerian Formulation of Differential Geormetry Based Nonpolar Multiscale Solvation Models

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Zhan Chen
Keyword(s):  
Phase Field ◽  
Phase Field Model ◽  
Lagrangian Formulation ◽  
Global Minimizer ◽  
Solvation Model ◽  
Phase Field Models ◽  
Eulerian Formulation ◽  
Solvation Models ◽  
Similarity And Difference ◽  
Nonpolar Solvation

AbstractIn this work, the existence of a global minimizer for the previous Lagrangian formulation of nonpolar solvation model proposed in [1] has been proved. One of the proofs involves a construction of a phase field model that converges to the Lagrangian formulation. Moreover, an Eulerian formulation of nonpolar solvation model is proposed and implemented under a similar parameterization scheme to that in [1]. By doing so, the connection, similarity and difference between the Eulerian formulation and its Lagrangian counterpart can be analyzed. It turns out that both of them have a great potential in solvation prediction for nonpolar molecules, while their decompositions of attractive and repulsive parts are different. That indicates a distinction between phase field models of solvation and our Eulerian formulation.

Multi-Phase Solvation Model for Biological Membranes: Molecular Action Mechanism of Amphotericin B

2017 ◽  
Vol 13 (7) ◽  
pp. 3388-3397 ◽  
Author(s):  
J. M. Falcón-González ◽  
G. Jiménez-Domínguez ◽  
I. Ortega-Blake ◽  
M. Carrillo-Tripp
Keyword(s):  
Amphotericin B ◽  
Biological Membranes ◽  
Action Mechanism ◽  
Solvation Model ◽  
Molecular Action ◽  
Multi Phase
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