2024
Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations
Kaur D, Reiss K, Wang J, Batista V, Brudvig G, Gunner M. Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations. The Journal Of Physical Chemistry B 2024, 128: 2236-2248. PMID: 38377592, DOI: 10.1021/acs.jpcb.3c05367.Peer-Reviewed Original ResearchOxygen-evolving centerWater moleculesPhotosystem IIPositions of water moleculesAnalysis of water moleculesCatalyze water oxidationHydrogen bond networkOccupancy of water moleculesMolecular dynamics simulationsD1-D61Electron density mapsMolecular dynamics analysisProton transferWater oxidationCrystallographic dataIce latticeMD simulationsMolecular dynamicsStructural transitionDynamics simulationsSubstrate waterOxygen-evolvingRoom temperatureProtein residuesMolecules
2015
Photoinduced Water Oxidation at the Aqueous GaN (101̅0) Interface: Deprotonation Kinetics of the First Proton-Coupled Electron-Transfer Step
Ertem M, Kharche N, Batista V, Hybertsen M, Tully J, Muckerman J. Photoinduced Water Oxidation at the Aqueous GaN (101̅0) Interface: Deprotonation Kinetics of the First Proton-Coupled Electron-Transfer Step. ACS Catalysis 2015, 5: 2317-2323. DOI: 10.1021/acscatal.5b00054.Peer-Reviewed Original ResearchWater oxidation mechanismElectron transfer stepWater oxidationProton transferFree energy changeElectron transferProton-coupled electron transfer stepsOxidation mechanismOverall water splitting reactionAb initio molecular dynamicsPhotoinduced water oxidationHydrogen bonding interactionsRadical ion intermediatesFirst solvation shellWater splitting reactionInitio molecular dynamicsPhotoelectrochemical water splittingCluster model approachPCET stepsProton reductionBonding interactionsSplitting reactionWater dissociationHydrogen bondingSolvation shell
2013
Photoinduced Proton Coupled Electron Transfer in 2‑(2′-Hydroxyphenyl)-Benzothiazole
Luber S, Adamczyk K, Nibbering E, Batista V. Photoinduced Proton Coupled Electron Transfer in 2‑(2′-Hydroxyphenyl)-Benzothiazole. The Journal Of Physical Chemistry A 2013, 117: 5269-5279. PMID: 23718689, DOI: 10.1021/jp403342w.Peer-Reviewed Original ResearchExcited-state intramolecular proton transferElectron transferState intramolecular proton transferTime-dependent density functional theoryQuantum chemical modelingIR-probe spectroscopyIntramolecular proton transferConjugated double bondsDensity functional theoryEnol-keto tautomerizationPhotoinduced ProtonBenzothiazole ringNonpolar solventsProton transferChemical modelingMid-infrared spectroscopyMolecular chromophoresMarker modesPrototypical moleculeDouble bondElectronic changesIsomerization dynamicsElectronic chargeFunctional theoryBenzothiazoleElectrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II
Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR. Electrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II. The Journal Of Physical Chemistry B 2013, 117: 6217-6226. PMID: 23570540, PMCID: PMC3753004, DOI: 10.1021/jp403321b.Peer-Reviewed Original ResearchConceptsOxomanganese complexesElectron transferOxygen-evolving complexComplexes 6Electrostatic effectsΜ-oxo bridgeDensity functional theory levelTerminal water ligandsBiomimetic oxomanganese complexesPhotosystem IIOxidation state transitionsContinuum electrostatic modelWater ligandsLigand substituentsOxidation midpoint potentialsOxo bridgeCalculated pKaProton transferElectrostatic interactionsTheory levelElectrostatic contributionMidpoint potentialMn oxidationElectrostatic modelFree energy
2012
Tunneling through Coulombic barriers: quantum control of nuclear fusion
Saha R, Markmann A, Batista V. Tunneling through Coulombic barriers: quantum control of nuclear fusion. Molecular Physics 2012, 110: 995-999. DOI: 10.1080/00268976.2012.679635.Peer-Reviewed Original ResearchNuclear fusionCoherent control schemeLow-energy collisionsQuantum control scenariosQuantum dynamicsIonization pulseQuantum tunnelingEnergy collisionsReactive scatteringCoulombic barrierInterference phenomenaForbidden regionsProton transferConfiguration spaceSimple modelPossible enhancementScatteringTunnelingPulsesCollisionsProtonsDynamics
2009
Quantum Dynamics of the Excited‐State Intramolecular Proton Transfer in 2‐(2′‐Hydroxyphenyl)benzothiazole
Kim J, Wu Y, Brédas J, Batista V. Quantum Dynamics of the Excited‐State Intramolecular Proton Transfer in 2‐(2′‐Hydroxyphenyl)benzothiazole. Israel Journal Of Chemistry 2009, 49: 187-197. DOI: 10.1560/ijc.49.2.187.Peer-Reviewed Original ResearchReaction dynamicsExcited state intramolecular proton transfer (ESIPT) dynamicsExcited state potential energy surfacesExcited-state reaction dynamicsReaction surface HamiltonianExcited-state intramolecular proton transferUltrafast reaction dynamicsCoherent-state expansionProton transfer dynamicsPotential energy surfaceIntramolecular proton transferQuantum dynamicsTime evolution operatorSurface HamiltonianWave packetsSurvival amplitudeTrotter expansionPolyatomic systemsEnergy surfacePropagation methodProton transferTautomerization reactionExperimental dataFourier transform methodPropagation scheme
2002
Coherent Control in the Presence of Intrinsic Decoherence: Proton Transfer in Large Molecular Systems
Batista V, Brumer P. Coherent Control in the Presence of Intrinsic Decoherence: Proton Transfer in Large Molecular Systems. Physical Review Letters 2002, 89: 143201. PMID: 12366043, DOI: 10.1103/physrevlett.89.143201.Peer-Reviewed Original ResearchCoherent controlExcited-state proton transfer dynamicsCoherent control scenarioProton transfer dynamicsDecoherence phenomenaDecoherence measuresSemiclassical approachIntrinsic decoherenceLarge molecular systemsExperimental interestTransfer dynamicsMolecular systemsProton transferTautomerization reactionDecoherenceLarge moleculesPhotoexcitationProton-Transfer Dynamics in the Activation of Cytochrome P450eryF
Guallar V, Harris D, Batista V, Miller W. Proton-Transfer Dynamics in the Activation of Cytochrome P450eryF. Journal Of The American Chemical Society 2002, 124: 1430-1437. PMID: 11841312, DOI: 10.1021/ja016474v.Peer-Reviewed Original ResearchConceptsProton transfer eventsProton transfer dynamicsCytochrome P450eryFQuantum chemistry calculationsHydrogen bond networkMechanism of oxidationUltrafast proton transferMolecular dynamics simulationsProton transfer energy profileChemistry calculationsDistal oxygenOxyferrous stateBond networkProton transferEnergy profilesDynamics simulationsHeme groupEnzymatic efficacyP450eryFEnzymatic activationOxidationOxygen speciesReactionOxygenCytochrome P450
2000
Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole. The Journal Of Chemical Physics 2000, 113: 9510-9522. DOI: 10.1063/1.1321049.Peer-Reviewed Original ResearchPotential energy surfaceExcited state potential energy surfacesFull-dimensional potential energy surfaceEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceProton transferVibrational energy redistributionProton transfer dynamicsQuantum mechanical calculationsSemiclassical initial value representation methodIntramolecular proton transferPlane vibrational modesSemiclassical resultsMolecular dynamics simulationsEnergy redistributionMechanical calculationsQuantum chemistryTransfer dynamicsCIS levelTautomerization reactionVibrational modesIsotopic substitutionDynamics simulations
1999
Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers. The Journal Of Chemical Physics 1999, 110: 9922-9936. DOI: 10.1063/1.478866.Peer-Reviewed Original ResearchExcited-state double proton transferState double proton transferDouble proton transferPotential energy surfaceInitial value representationProton transferExcited state potential energy surfacesEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceQuantum mechanical calculationsSemiclassical initial value representationMolecular dynamics simulationsUltrafast dynamicsSymmetric stretch vibrationSemiclassical resultsQuantum chemistryPopulation decayTautomerization reactionMechanical calculationsCIS levelMolecular systemsReduced dimensionalityIsotopic substitution