0000000000646275

AUTHOR

James T. Hynes

showing 3 related works from this author

A simple model for barrier frequencies for enzymatic reactions.

2010

We present a simple model to rationalize the effects of environment on the reaction barrier frequencies derived from free energy profiles. These frequencies are relevant in deviations of a rate constant from its transition state theory value and in determining which environmental dynamics participate in the reaction. In particular, this simple model can be used to understand the changes in the reaction barrier frequencies of an enzymatic catalyzed reaction and the corresponding uncatalyzed process in aqueous solution, a change which has implications for dynamical environmental effects on the enzymatic reaction. Two possible cases are analyzed, in which the polarity (charge separation/locali…

Aqueous solutionMolecular StructureChemistryPolarity (physics)ThermodynamicsInverseAtomic and Molecular Physics and OpticsTransition stateEnzyme catalysisCatalysisEnzymesTransition state theoryReaction rate constantModels ChemicalBiocatalysisPhysical chemistryThermodynamicsPhysical and Theoretical ChemistryNuclear ExperimentChemphyschem : a European journal of chemical physics and physical chemistry
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Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.

2015

Highlights • The possible role of enzymatic reaction dynamical effects is examined. • Solution reactions usefully inform the issue of dynamical effects in enzymes. • Division into regions containing and away from the transition state is important. • Motions in passage to/from the transition state need not lead to dynamical effects. • Transition State Theory is usually a reasonable description of enzyme kinetics.

StereochemistryProtein ConformationBiophysicsBiochemistryModels BiologicalVibrationArticleEnzyme catalysisDiffusionTransition state theoryTransition State TheoryEscherichia coli[CHIM]Chemical SciencesStatistical physicsMolecular BiologyQuantumNuclear motionChemistryQuantitative Biology::Molecular Networksdigestive oral and skin physiologyEnzyme catalysisEnzymesEnzyme ActivationKineticsTetrahydrofolate DehydrogenaseDynamical effectsBiocatalysisQuantum TheoryTetrahydrofolate dehydrogenaseProtonsArchives of biochemistry and biophysics
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Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach

2008

We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nu…

Models MolecularReaction ratesMechanicsBiochemistryChemical reactionCatalysisReaction coordinateReaction rateMolecular dynamicsCharge transferChalconesColloid and Surface ChemistryNucleophileComputational chemistryChemical reactionsFreezingIntramolecular LyasesReaction kineticsFourier AnalysisChemistryIntermolecular forceWaterGeneral ChemistryCarbonDynamicsKineticsModels ChemicalReaction dynamicsChemical physicsIntramolecular forceFlavanonesQuantum TheoryThermodynamicsIon exchangeJournal of the American Chemical Society
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