Literature DB >> 16108048

Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA.

Daniel J Price1, Charles L Brooks.   

Abstract

Modern classical force fields have been traditionally parameterized by attempting to maximize agreement to any number of experimental and/or quantum mechanical target properties. As these force fields are pushed towards obtaining quantitative estimates of often subtle energetic differences, stringent and consistent parameterization criteria, particularly in regard to charge distributions, are required to ensure that systematic errors cancel, that parameters are transferable between molecules, and that performance does not significantly deteriorate when using more approximate methods, such as with continuum solvent models. Relative free energies of hydration are presented here for 40 mono- and disubstituted benzenes modeled with the OPLS-AA force field; heats of vaporization and pure liquid densities at standard conditions are presented when experimental data is available. Overall agreement between OPLS-AA and experiment is remarkable (average error = 0.5 kcal/mol for DeltaDeltaG(hydration), 1.0 kcal/mol for DeltaH(vap) (0), 0.02 g/mL for densities), yet several functional groups are identified as having consistent and correctable errors (alkyl-, nitro-, and thiobenzenes). Relative free energies of hydration obtained with rigorous free energy perturbations using explicit solvent are also compared with energies from minimizations using a generalized Born model (GB). There is high correlation between these estimates (R = 0.99), and as demonstrated here, reparameterization of the aforementioned groups can be guided with rapid GB calculations.

Entities:  

Mesh:

Substances:

Year:  2005        PMID: 16108048     DOI: 10.1002/jcc.20284

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  6 in total

1.  Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.

Authors:  Maneesh K Yadav; Luke J Leman; Daniel J Price; Charles L Brooks; C David Stout; M Reza Ghadiri
Journal:  Biochemistry       Date:  2006-04-11       Impact factor: 3.162

2.  Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria.

Authors:  William L Jorgensen; Laura L Thomas
Journal:  J Chem Theory Comput       Date:  2008-05-09       Impact factor: 6.006

3.  Application of Molecular Dynamics Simulations in Molecular Property Prediction I: Density and Heat of Vaporization.

Authors:  Junmei Wang; Hou Tingjun
Journal:  J Chem Theory Comput       Date:  2011-07-12       Impact factor: 6.006

4.  Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion.

Authors:  William L Jorgensen; Kasper P Jensen; Anastassia N Alexandrova
Journal:  J Chem Theory Comput       Date:  2007-11-01       Impact factor: 6.006

5.  Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design.

Authors:  Jennifer L Knight; Charles L Brooks
Journal:  J Chem Theory Comput       Date:  2009       Impact factor: 6.006

6.  A new view of the bacterial cytosol environment.

Authors:  Benjamin P Cossins; Matthew P Jacobson; Victor Guallar
Journal:  PLoS Comput Biol       Date:  2011-06-09       Impact factor: 4.475

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.