ArticleMethods in enzymology2016
Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.Molecules (Basel, Switzerland) · 2024Article
- Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations.The Journal of chemical physics · 2023Article
- Deuterium Isotope Effects on Acid-Base Equilibrium of Organic Compounds.Molecules (Basel, Switzerland) · 2021Article
- Article
- Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of COJournal of the American Chemical Society · 2021Article
- Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution.Journal of chemical theory and computation · 2020Article
- Use of Interaction Energies in QM/MM Free Energy Simulations.Journal of chemical theory and computation · 2019Article
- Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.Molecules (Basel, Switzerland) · 2018Article
- Path Integral-Free Energy Perturbation (PI-FEP) Simulations: Kinetic Isotope Effects of Proton/Deuteron Transfer Reactions in Aqueous Solution.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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1 author.
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Abstract
Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects.
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