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Literature DB >> 15936231

Implementation of the bisection sampling method in path integral simulations.

Abstract

A bisection sampling method is implemented in the framework of a quantized classical path algorithm to include nuclear quantum effects in path integral simulations. The present study examines the convergence of these calculations on two model systems with respect to the number of beads used in the polymer chain and the number of configurations both in free-particle sampling and in classical configuration sampling. The results will be useful for future studies of kinetic isotope effects in enzymatic reactions.

Entities: Chemical Disease

Mesh：

Substances：
Polymers

Year: 2005 PMID： 15936231 DOI： 10.1016/j.jmgm.2005.04.002

Source DB: PubMed Journal: J Mol Graph Model ISSN： 1093-3263 Impact factor: 2.518

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Cited

15 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

9. A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert's Variational Perturbation Theory.

Authors: Kin-Yiu Wong; Jiali Gao
Journal: J Chem Theory Comput Date: 2008-09-09 Impact factor: 6.006

10. Computation of kinetic isotope effects for enzymatic reactions.

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

Implementation of the bisection sampling method in path integral simulations.

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

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

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

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

Review 5. Hydrogen tunneling in enzymes and biomimetic models.

6. Connecting protein conformational dynamics with catalytic function as illustrated in dihydrofolate reductase.

7. Kinetic isotope effects of L-Dopa decarboxylase.

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

9. A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert's Variational Perturbation Theory.

10. Computation of kinetic isotope effects for enzymatic reactions.