Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
about
Biomolecular electrostatics and solvation: a computational perspectiveRecent advances in QM/MM free energy calculations using reference potentialsIndependent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulationsGeneralized Ensemble Sampling of Enzyme Reaction Free Energy PathwaysMicroscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis.Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion.Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase.Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive TrajectoriesBorn-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye.Theoretical frameworks for multiscale modeling and simulationAccelerating self-consistent field convergence with the augmented Roothaan-Hall energy function.Concerted O atom-proton transfer in the O-O bond forming step in water oxidation.Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions.Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine ModelAn implicit solvent model for SCC-DFTB with Charge-Dependent Radii.Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA).Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based modelsInvestigation of the acetylation mechanism by GCN5 histone acetyltransferase.Computing the Free Energy along a Reaction Coordinate Using Rigid Body DynamicsQuantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions.Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase.Ab initio QM/MM free-energy studies of arginine deiminase catalysis: the protonation state of the Cys nucleophileAutocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation.Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applicationsConical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics methodInsight into the phosphodiesterase mechanism from combined QM/MM free energy simulations.Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization.Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies.Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase.A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactionsComputational Investigation of the Interplay of Substrate Positioning and Reactivity in Catechol O-Methyltransferase.Hybrid dynamics simulation engine for metalloproteins.Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs
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Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
description
article científic
@ca
article scientifique
@fr
articolo scientifico
@it
artigo científico
@pt
bilimsel makale
@tr
scientific article published on January 2008
@en
vedecký článok
@sk
vetenskaplig artikel
@sv
videnskabelig artikel
@da
vědecký článek
@cs
name
Free energies of chemical reac ...... cs/molecular mechanics methods
@en
Free energies of chemical reac ...... s/molecular mechanics methods.
@nl
type
label
Free energies of chemical reac ...... cs/molecular mechanics methods
@en
Free energies of chemical reac ...... s/molecular mechanics methods.
@nl
prefLabel
Free energies of chemical reac ...... cs/molecular mechanics methods
@en
Free energies of chemical reac ...... s/molecular mechanics methods.
@nl
P2860
P1476
Free energies of chemical reac ...... cs/molecular mechanics methods
@en
P2093
P2860
P304
P356
10.1146/ANNUREV.PHYSCHEM.59.032607.093618
P577
2008-01-01T00:00:00Z