XSOL, a Combined Integral Equation (XRISM) and Quantum Mechanical Solvation Model:  Free Energies of Hydration and Applications to Solvent Effects on Organic Equilibria

1998 ◽  
Vol 102 (50) ◽  
pp. 10366-10373 ◽  
Author(s):  
Lei Shao ◽  
Hsiang-Ai Yu ◽  
Jiali Gao
Keyword(s):  
Integral Equation ◽  
Solvent Effects ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Solvation Model ◽  
Model Free

The affinity of HGGG, GHGG, GGHG, and GGGH peptides for copper(II) and the structures of their complexes — An ab initio study

2009 ◽  
Vol 87 (7) ◽  
pp. 942-953 ◽  
Author(s):  
Stephen D. Barry ◽  
Gail A. Rickard ◽  
M. Jake Pushie ◽  
Arvi Rauk
Keyword(s):  
Geometry Optimization ◽  
Forward Direction ◽  
Ionic Species ◽  
Abundant Species ◽  
Coordination Pattern ◽  
Free Energies ◽  
Solvation Model ◽  
Model Free ◽  
C Terminus ◽  
Peptide Complexes

The structures and relative free energies in aqueous solution of the Cu(II) complexes of the “histidine walk” peptides, AcHGGGNH2, AcGHGGNH2, AcGGHGNH2, and AcGGGHNH2, were determined as a function of pH. Numerous structures of each species were found by gaseous- and solution-phase geometry optimization at the B3LYP/6–31G(d) level, and the effect of solvation estimated by the IEFPCM continuum solvation model. Free energies of solvation of the ionic species are large and favour structures with an extended peptide chain. In all Cu(II)–peptide complexes, deprotonation of two amide groups occurs readily at or below pH 7. In each system, the most abundant species at pH 7 is a neutral 1:1 complex with N3O1 coordination pattern. Binding in the forward direction toward the C terminus is preferred. The results are compared to recent experimental spectroscopic and potentiometric studies on related systems. Alternative explanations are offered for some of the experimental observations.

General Semiempirical Quantum Mechanical Solvation Model for Nonpolar Solvation Free Energies. n-Hexadecane

1995 ◽  
Vol 117 (3) ◽  
pp. 1057-1068 ◽  
Author(s):  
David J. Giesen ◽  
Joey W. Storer ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Quantum Mechanical ◽  
Free Energies ◽  
Solvation Model ◽  
Solvation Free Energies ◽  
Nonpolar Solvation

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>

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

On the quantum mechanical treatment of solvent effects

1980 ◽  
Vol 55 (4) ◽  
pp. 307-318 ◽  
Author(s):  
Bernard Theodoor Thole ◽  
Petrus Theodorus Duijnen
Keyword(s):  
Solvent Effects ◽  
Mechanical Treatment ◽  
Quantum Mechanical ◽  
Quantum Mechanical Treatment

Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations

1999 ◽  
Vol 110 (3) ◽  
pp. 1329-1337 ◽  
Author(s):  
Robert H. Wood ◽  
Eric M. Yezdimer ◽  
Shinichi Sakane ◽  
Jose A. Barriocanal ◽  
Douglas J. Doren
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Free Energies ◽  
Mechanical Interaction
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