Literature DB >> 20047005

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

Rosendo Valero1, Lingchun Song, Jiali Gao, Donald G Truhlar.   

Abstract

Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (S(N)2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i-v. These comparisons show the danger of basing the diabatic states on molecular mechanics without the explicit calculation of electronic wave functions. Furthermore, comparison of schemes i-v with one another shows that significantly different quantitative results can be obtained by using different methods for extracting diabatic states from wave function calculations, and it is important for each user to justify the choice of diabatization method in the context of its intended use.

Entities:  

Year:  2009        PMID: 20047005      PMCID: PMC2658610          DOI: 10.1021/ct800318h

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  64 in total

1.  Empirical Valence-Bond Models for Reactive Potential Energy Surfaces Using Distributed Gaussians.

Authors:  H Bernhard Schlegel; Jason L Sonnenberg
Journal:  J Chem Theory Comput       Date:  2006-07       Impact factor: 6.006

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

Authors:  Gongyi Hong; Edina Rosta; Arieh Warshel
Journal:  J Phys Chem B       Date:  2006-10-05       Impact factor: 2.991

3.  The Menshutkin reaction in the gas phase and in aqueous solution: a valence bond study.

Authors:  Peifeng Su; Fuming Ying; Wei Wu; Philippe C Hiberty; Sason Shaik
Journal:  Chemphyschem       Date:  2007-12-21       Impact factor: 3.102

4.  Diabatic free energy curves and coordination fluctuations for the aqueous Ag+Ag2+ redox couple: a biased Born-Oppenheimer molecular dynamics investigation.

Authors:  Jochen Blumberger; Ivano Tavernelli; Michael L Klein; Michiel Sprik
Journal:  J Chem Phys       Date:  2006-02-14       Impact factor: 3.488

5.  Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

Authors:  S R Billeter; S P Webb; P K Agarwal; T Iordanov; S Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2001-11-14       Impact factor: 15.419

6.  Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction.

Authors:  A Lewandowicz; J Rudziński; L Tronstad; M Widersten; P Ryberg; O Matsson; P Paneth
Journal:  J Am Chem Soc       Date:  2001-05-16       Impact factor: 15.419

7.  Haloalkane dehalogenases: steady-state kinetics and halide inhibition.

Authors:  J F Schindler; P A Naranjo; D A Honaberger; C H Chang; J R Brainard; L A Vanderberg; C J Unkefer
Journal:  Biochemistry       Date:  1999-05-04       Impact factor: 3.162

8.  The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase.

Authors:  E Y Lau; K Kahn; P A Bash; T C Bruice
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

9.  Dynamic and electrostatic effects in enzymatic processes. An analysis of the nucleophilic substitution reaction in haloalkane dehalogenase.

Authors:  Alejandro Soriano; Estanislao Silla; Iñaki Tuñón; Manuel F Ruiz-López
Journal:  J Am Chem Soc       Date:  2005-02-16       Impact factor: 15.419

10.  Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site.

Authors:  G H Krooshof; I S Ridder; A W Tepper; G J Vos; H J Rozeboom; K H Kalk; B W Dijkstra; D B Janssen
Journal:  Biochemistry       Date:  1998-10-27       Impact factor: 3.162

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  10 in total

1.  Multistate Density Functional Theory for Effective Diabatic Electronic Coupling.

Authors:  Haisheng Ren; Makenzie R Provorse; Peng Bao; Zexing Qu; Jiali Gao
Journal:  J Phys Chem Lett       Date:  2016-06-07       Impact factor: 6.475

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.  Diabatic-At-Construction Method for Diabatic and Adiabatic Ground and Excited States Based on Multistate Density Functional Theory.

Authors:  Adam Grofe; Zexing Qu; Donald G Truhlar; Hui Li; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2017-02-13       Impact factor: 6.006

4.  On the Interfragment Exchange in the X-Pol Method.

Authors:  Alessandro Cembran; Peng Bao; Yingjie Wang; Lingchun Song; Donald G Truhlar; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2010       Impact factor: 6.006

Review 5.  Energy decomposition analysis based on a block-localized wavefunction and multistate density functional theory.

Authors:  Yirong Mo; Peng Bao; Jiali Gao
Journal:  Phys Chem Chem Phys       Date:  2011-03-02       Impact factor: 3.676

6.  Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces.

Authors:  Alessandro Cembran; Lingchun Song; Yirong Mo; Jiali Gao
Journal:  J Chem Theory Comput       Date:  2009-10-13       Impact factor: 6.006

7.  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

Review 8.  At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  Proteins       Date:  2010-05-01

9.  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

Review 10.  Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent.

Authors:  Trevor A Hamlin; Marcel Swart; F Matthias Bickelhaupt
Journal:  Chemphyschem       Date:  2018-04-19       Impact factor: 3.102

  10 in total

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