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The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations.
Molecular dynamics simulations employing combined quantum mechanical and molecular mechanical (QM/MM) potentials have been carried out to investigate the reaction mechanism of the hydrolysis ofExpand
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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation
  • H. Gu, S. Zhang, +9 authors M. Harris
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences
  • 22 July 2013
Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis.Expand
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Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation.
Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing onlyExpand
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A Systematic Approach for Computing Zero-Point Energy, Quantum Partition Function, and Tunneling Effect Based on Kleinert's Variational Perturbation Theory.
  • Kin-Yiu Wong, J. Gao
  • Physics, Medicine
  • Journal of chemical theory and computation
  • 9 September 2008
In this paper, we describe an automated integration-free path-integral (AIF-PI) method, based on Kleinert's variational perturbation (KP) theory, to treat internuclear quantum-statistical effects inExpand
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Theoretical analysis of kinetic isotope effects on proton transfer reactions between substituted alpha-methoxystyrenes and substituted acetic acids.
Primary kinetic isotope effects (KIEs) on a series of carboxylic acid-catalyzed protonation reactions of aryl-substituted alpha-methoxystyrenes (X-1) to form oxocarbenium ions have been computedExpand
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An automated integration-free path-integral method based on Kleinert's variational perturbation theory.
Based on Kleinert's variational perturbation (KP) theory [Path Integrals in Quantum Mechanics, Statistics, Polymer Physics, and Financial Markets, 3rd ed. (World Scientific, Singapore, 2004)], weExpand
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Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.
We report results from combined quantum mechanical/molecular mechanical (QM/MM) free energy simulations to explore metal-assisted phosphoryl transfer and general acid catalysis in the extendedExpand
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Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water
TLDR
An integrated Feynman path integral‐free energy perturbation and umbrella sampling (PI‐FEP/UM) method has been used to investigate the kinetic isotope effects (KIEs) in the proton transfer reaction between nitroethane and acetate ion in water. Expand
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Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment.
The elucidation of the chemical mechanisms whereby biological molecules control, regulate and catalyze phosphoryl transfer reactions has profound implications for processes such as transcription,Expand
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Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.
TLDR
The variational free energy profile (vFEP) method is extended to two dimensions and tested with molecular simulation applications. Expand
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