Literature DB >> 26626510

Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials.

Dan Thomas Major1, Mireia Garcia-Viloca1, Jiali Gao1.   

Abstract

A bisection sampling method was implemented in path integral simulations of chemical reactions in solution in the framework of the quantized classical path approach. In the present study, we employ a combined quantum mechanical and molecular mechanical (QM/MM) potential to describe the potential energy surface and the path integral method to incorporate nuclear quantum effects. We examine the convergence of the bisection method for two proton-transfer reactions in aqueous solution at room temperature. The first reaction involves the symmetrical proton transfer between an ammonium ion and an ammonia molecule. The second reaction is the ionization of nitroethane by an acetate ion. To account for nuclear quantum mechanical corrections, it is sufficient to quantize the transferring light atom in the ammonium ion-ammonia reaction, while it is necessary to also quantize the donor and acceptor atoms in the nitroethane-acetate ion reaction. Kinetic isotope effects have been computed for isotopic substitution of the transferring proton by a deuteron in the nitroethane-acetate reaction. In all computations, it is important to employ a sufficient number of polymer beads along with a large number of configurations to achieve convergence in these simulations.

Entities:  

Year:  2006        PMID: 26626510     DOI: 10.1021/ct050257t

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


  12 in total

Review 1.  Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

2.  Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water.

Authors:  Jiali Gao; Kin-Yiu Wong; Dan T Major
Journal:  J Comput Chem       Date:  2008-03       Impact factor: 3.376

3.  Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.

Authors:  Dan T Major; Annie Heroux; Allen M Orville; Michael P Valley; Paul F Fitzpatrick; Jiali Gao
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-19       Impact factor: 11.205

Review 4.  Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5'-phosphate dependent enzymes L-dopa decarboxylase and alanine racemase.

Authors:  Yen-Lin Lin; Jiali Gao; Amir Rubinstein; Dan Thomas Major
Journal:  Biochim Biophys Acta       Date:  2011-05-10

5.  Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

Authors:  J Gao
Journal:  Methods Enzymol       Date:  2016-07-22       Impact factor: 1.600

6.  Kinetic isotope effects of L-Dopa decarboxylase.

Authors:  Yen-lin Lin; Jiali Gao
Journal:  J Am Chem Soc       Date:  2011-03-02       Impact factor: 15.419

7.  Computation of kinetic isotope effects for enzymatic reactions.

Authors:  Jiali Gao
Journal:  Sci China Chem       Date:  2012-12       Impact factor: 9.445

Review 8.  Kinetic isotope effects and how to describe them.

Authors:  Konstantin Karandashev; Zhen-Hao Xu; Markus Meuwly; Jiří Vaníček; Jeremy O Richardson
Journal:  Struct Dyn       Date:  2017-12-13       Impact factor: 2.920

9.  Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.

Authors:  Meiyi Liu; Katelyn N Youmans; Jiali Gao
Journal:  Molecules       Date:  2018-10-15       Impact factor: 4.411

10.  Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Authors:  Suraj Kannath; Paweł Adamczyk; Langping Wu; Hans H Richnow; Agnieszka Dybala-Defratyka
Journal:  Int J Mol Sci       Date:  2019-11-26       Impact factor: 5.923

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