Literature DB >> 18512970

A universal approach to solvation modeling.

Christopher J Cramer1, Donald G Truhlar.   

Abstract

Continuum mean-field models that have been carefully designed to address the various electrostatic and nonelectrostatic interactions that develop between a molecule and a surrounding medium are particularly efficient tools for studying the effects of condensed phases on molecular structure, energetics, properties, spectra, interaction potentials, and dynamics. The SM8 model may be combined with density functional theory or Hartree-Fock theory to describe a solute's electronic structure and its self-consistent-field polarization by a solvent. A key feature is the use of class IV charge models to obtain accurate charge distributions (either in the vapor phase or in solution), even when using small basis sets that are affordable for large systems. A second key feature is that nonelectrostatic effects due to cavity formation, dispersion interactions, and changes in solvent structure are included in terms of empirical atomic surface tensions that depend on geometry but do not require atom-type assignments by the user. Use of an analytic surface area algorithm provides very stable energy gradients that allow geometry optimization in solution. The SM8 continuum model, the culmination of a series of SMx models (x = 1-8), permits the modeling of such diverse media as aqueous and organic solvents, soils, lipid bilayers, and air-water interfaces. In addition to predicting accurate transfer free energies between gaseous and condensed phases or between two different condensed phases, SMx models have been useful for predicting the significant influence of condensed phases on processes associated with a change in molecular charge, including acid/base equilibria and oxidation/reduction processes. In this Account, we provide an overview of the algorithms associated with the computation of free energies of solvation in the SM8 model. We also compare the accuracies of the SM8 model with those of other continuum solvation models. Finally, we highlight applications of the SM8 models to compute ionic solvation free energies, oxidation and reduction potentials, and pK(a) values.

Entities:  

Year:  2008        PMID: 18512970     DOI: 10.1021/ar800019z

Source DB:  PubMed          Journal:  Acc Chem Res        ISSN: 0001-4842            Impact factor:   22.384


  61 in total

1.  A fragment-based approach to the SAMPL3 Challenge.

Authors:  John L Kulp; Seth N Blumenthal; Qiang Wang; Richard L Bryan; Frank Guarnieri
Journal:  J Comput Aided Mol Des       Date:  2012-05       Impact factor: 3.686

2.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

3.  Analysis of SM8 and Zap TK calculations and their geometric sensitivity.

Authors:  Benjamin A Ellingson; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-30       Impact factor: 3.686

4.  Tautomers and reference 3D-structures: the orphans of in silico drug design.

Authors:  Timothy Clark
Journal:  J Comput Aided Mol Des       Date:  2010-03-27       Impact factor: 3.686

5.  Structures and formation mechanisms of aquo/hydroxo oligomeric beryllium in aqueous solution: a density functional theory study.

Authors:  Xiaoyan Jin; Rongbao Liao; Hai Wu; Zhengjie Huang; Hong Zhang
Journal:  J Mol Model       Date:  2015-08-14       Impact factor: 1.810

Review 6.  Quantum mechanical investigations of organocatalysis: mechanisms, reactivities, and selectivities.

Authors:  Paul Ha-Yeon Cheong; Claude Y Legault; Joann M Um; Nihan Çelebi-Ölçüm; K N Houk
Journal:  Chem Rev       Date:  2011-06-28       Impact factor: 60.622

7.  Role of hydration in collagen recognition by bacterial adhesins.

Authors:  Luigi Vitagliano; Rita Berisio; Alfonso De Simone
Journal:  Biophys J       Date:  2011-05-04       Impact factor: 4.033

8.  Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

Authors:  Andrei L Lomize; Irina D Pogozheva; Henry I Mosberg
Journal:  J Chem Inf Model       Date:  2011-03-25       Impact factor: 4.956

Review 9.  Perspectives on computational organic chemistry.

Authors:  Andrew Streitwieser
Journal:  J Org Chem       Date:  2009-06-19       Impact factor: 4.354

10.  Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Authors:  Gerhard König; Ye Mei; Frank C Pickard; Andrew C Simmonett; Benjamin T Miller; John M Herbert; H Lee Woodcock; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2015-12-11       Impact factor: 6.006

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