Comparison of two simulation methods to compute solvation free energies and partition coefficients

2012 ◽  
Vol 34 (4) ◽  
pp. 284-293 ◽  
Author(s):  
Li Yang ◽  
Alauddin Ahmed ◽  
Stanley I. Sandler
Keyword(s):  
Partition Coefficients ◽  
Simulation Methods ◽  
Free Energies ◽  
Solvation Free Energies

scholarly journals 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies

2009 ◽  
Vol 5 (9) ◽  
pp. 2436-2446 ◽  
Author(s):  
Nuno M. Garrido ◽  
António J. Queimada ◽  
Miguel Jorge ◽  
Eugénia A. Macedo ◽  
Ioannis G. Economou
Keyword(s):  
Partition Coefficients ◽  
Molecular Simulations ◽  
Free Energies ◽  
Solvation Free Energies

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>

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

A QM/MM study combined with the theory of energy representation: Solvation free energies for anti/syn acetic acids in aqueous solution

2006 ◽  
Vol 419 (1-3) ◽  
pp. 240-244 ◽  
Author(s):  
Takumi Hori ◽  
Hideaki Takahashi ◽  
Masayoshi Nakano ◽  
Tomoshige Nitta ◽  
Weitao Yang
Keyword(s):  
Aqueous Solution ◽  
Free Energies ◽  
Solvation Free Energies ◽  
Acetic Acids

scholarly journals Blind prediction of solvation free energies from the SAMPL4 challenge

2014 ◽  
Vol 28 (3) ◽  
pp. 135-150 ◽  
Author(s):  
David L. Mobley ◽  
Karisa L. Wymer ◽  
Nathan M. Lim ◽  
J. Peter Guthrie
Keyword(s):  
Free Energies ◽  
Blind Prediction ◽  
Solvation Free Energies
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