Literature DB >> 17004821

Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases.

Gongyi Hong1, Edina Rosta, Arieh Warshel.   

Abstract

The empirical valence bond (EVB) model provides an extremely powerful way for modeling and analyzing chemical reactions in solutions and proteins. However, this model is based on the unverified assumption that the off diagonal elements of the EVB Hamiltonian do not change significantly upon transfer of the reacting system from one phase to another. This ad hoc assumption has been rationalized by its consistency with empirically observed linear free energy relationships, as well as by other qualitative considerations. Nevertheless, this assumption has not been rigorously established. The present work explores the validity of the above EVB key assumption by a rigorous numerical approach. This is done by exploiting the ability of the frozen density functional theory (FDFT) and the constrained density functional theory (CDFT) models to generate convenient diabatic states for QM/MM treatments, and thus to examine the relationship between the diabatic and adiabatic surfaces, as well as the corresponding effective off diagonal elements. It is found that, at least for the test case of S(N)()2 reactions, the off diagonal element does not change significantly upon moving from the gas phase to solutions and thus the EVB assumption is valid and extremely useful.

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Year:  2006        PMID: 17004821     DOI: 10.1021/jp0625199

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  17 in total

Review 1.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 2.  Biochemistry and theory of proton-coupled electron transfer.

Authors:  Agostino Migliore; Nicholas F Polizzi; Michael J Therien; David N Beratan
Journal:  Chem Rev       Date:  2014-04-01       Impact factor: 60.622

3.  Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Authors:  Nikolay V Plotnikov; Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Chem B       Date:  2011-05-27       Impact factor: 2.991

4.  On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions.

Authors:  Edina Rosta; Arieh Warshel
Journal:  J Chem Theory Comput       Date:  2012-03-29       Impact factor: 6.006

5.  On unjustifiably misrepresenting the EVB approach while simultaneously adopting it.

Authors:  Shina C L Kamerlin; Jie Cao; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-08-06       Impact factor: 2.991

6.  On the construction of diabatic and adiabatic potential energy surfaces based on ab initio valence bond theory.

Authors:  Lingchun Song; Jiali Gao
Journal:  J Phys Chem A       Date:  2008-12-18       Impact factor: 2.781

Review 7.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

8.  The EVB as a quantitative tool for formulating simulations and analyzing biological and chemical reactions.

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Faraday Discuss       Date:  2010       Impact factor: 4.008

9.  An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane.

Authors:  Lingchun Song; Yirong Mo; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2009-01-01       Impact factor: 6.006

10.  Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane.

Authors:  Rosendo Valero; Lingchun Song; Jiali Gao; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2009-01-01       Impact factor: 6.006

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