Literature DB >> 20001028

Approximate inclusion of quantum effects in transition path sampling.

Dimitri Antoniou1, Steven D Schwartz.   

Abstract

We propose a method for incorporating nuclear quantum effects in transition path sampling studies of systems that consist of a few degrees of freedom that must be treated quantum mechanically, while the rest are classical-like. We used the normal mode centroid method to describe the quantum subsystem, which is a method that is not CPU intensive but still reasonably accurate. We applied this mixed centroid/classical transition path sampling method to a model system that has nontrivial quantum behavior, and showed that it can capture the correct quantum dynamical features.

Mesh:

Year:  2009        PMID: 20001028      PMCID: PMC2802259          DOI: 10.1063/1.3272793

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

Review 1.  Quantum mechanical methods for enzyme kinetics.

Authors:  Jiali Gao; Donald G Truhlar
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study.

Authors:  Jodi E Basner; Steven D Schwartz
Journal:  J Am Chem Soc       Date:  2005-10-12       Impact factor: 15.419

3.  A refined ring polymer molecular dynamics theory of chemical reaction rates.

Authors:  Ian R Craig; David E Manolopoulos
Journal:  J Chem Phys       Date:  2005-07-15       Impact factor: 3.488

4.  Nuclear quantum effects on an enzyme-catalyzed reaction with reaction path potential: proton transfer in triosephosphate isomerase.

Authors:  Mingliang Wang; Zhenyu Lu; Weitao Yang
Journal:  J Chem Phys       Date:  2006-03-28       Impact factor: 3.488

5.  Illustration of transition path theory on a collection of simple examples.

Authors:  Philipp Metzner; Christof Schütte; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2006-08-28       Impact factor: 3.488

6.  On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy.

Authors:  Alexander Witt; Sergei D Ivanov; Motoyuki Shiga; Harald Forbert; Dominik Marx
Journal:  J Chem Phys       Date:  2009-05-21       Impact factor: 3.488

7.  Atomic detail of chemical transformation at the transition state of an enzymatic reaction.

Authors:  Suwipa Saen-Oon; Sara Quaytman-Machleder; Vern L Schramm; Steven D Schwartz
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-22       Impact factor: 11.205

8.  Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase.

Authors:  Suwipa Saen-Oon; Vern L Schramm; Steven D Schwartz
Journal:  Z Phys Chem (N F)       Date:  2008       Impact factor: 2.408

  8 in total
  6 in total

Review 1.  Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions.

Authors:  M W Dzierlenga; M J Varga; S D Schwartz
Journal:  Methods Enzymol       Date:  2016-06-16       Impact factor: 1.600

2.  Protein dynamics and enzymatic chemical barrier passage.

Authors:  Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2011-11-15       Impact factor: 2.991

3.  Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

Authors:  Matthew J Varga; Steven D Schwartz
Journal:  J Chem Theory Comput       Date:  2016-03-14       Impact factor: 6.006

Review 4.  Protein dynamics and the enzymatic reaction coordinate.

Authors:  Steven D Schwartz
Journal:  Top Curr Chem       Date:  2013

Review 5.  Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence.

Authors:  Vern L Schramm; Steven D Schwartz
Journal:  Biochemistry       Date:  2018-04-10       Impact factor: 3.162

6.  How Accurate Are Transition States from Simulations of Enzymatic Reactions?

Authors:  Dvir Doron; Amnon Kohen; Kwangho Nam; Dan Thomas Major
Journal:  J Chem Theory Comput       Date:  2014-04-23       Impact factor: 6.006

  6 in total

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