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
2023
Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Maschietto F, Morzan U, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro G, Nekrasov P, Brooks B, Loria J, Rivalta I, Batista V. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications 2023, 14: 2239. PMID: 37076500, PMCID: PMC10115891, DOI: 10.1038/s41467-023-37956-1.Peer-Reviewed Original ResearchConceptsEffector bindingImidazole Glycerol Phosphate SynthaseLocal amino acidsAmino acid dynamicsImidazole glycerolAllosteric drugsAllosteric activationAllosteric responsePhosphate synthaseAllosteric mechanismMode of activationEnzyme functionAmino acidsAllosteryDrug discoverySynthaseNuclear magnetic resonance spectroscopyBindingMolecular dynamics simulationsActivationAllostericCascadeDynamics simulations
2022
Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires
Neu J, Shipps CC, Guberman-Pfeffer MJ, Shen C, Srikanth V, Spies JA, Kirchhofer ND, Yalcin SE, Brudvig GW, Batista VS, Malvankar NS. Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires. Nature Communications 2022, 13: 5150. PMID: 36071037, PMCID: PMC9452534, DOI: 10.1038/s41467-022-32659-5.Peer-Reviewed Original ResearchConceptsUltrafast electron transferElectron transferPhotoconductive atomic force microscopyFemtosecond transient absorption spectroscopyQuantum dynamics simulationsMicrobial electron transferAtomic force microscopyTransient absorption spectroscopyValue-added chemicalsIndividual nanowiresWhole-cell catalysisPhotoconductive materialForce microscopyCarrier densityCatalytic performanceNanowiresAbsorption spectroscopyPhotoactive proteinsEfficient productionPhotoconductorsSynthetic photosensitizersDynamics simulationsGeobacter sulfurreducensBiodegradable materialsElectronic interface
2021
Functional Tensor-Train Chebyshev Method for Multidimensional Quantum Dynamics Simulations
Soley M, Bergold P, Gorodetsky A, Batista V. Functional Tensor-Train Chebyshev Method for Multidimensional Quantum Dynamics Simulations. Journal Of Chemical Theory And Computation 2021, 18: 25-36. PMID: 34898201, DOI: 10.1021/acs.jctc.1c00941.Peer-Reviewed Original ResearchQuantum dynamics simulationsQuantum dynamicsMultidimensional quantum dynamicsHydrogen-bonded DNA base pairsChebyshev methodQuantum effectsTensor train formatDynamics simulationsElectronic configurationRearrangement of protonsInitial stateTheoretical studyEfficient simulationPropagation schemeDNA base pairsChemical systemsProtonsSimulationsDynamics
2020
Allosteric Impact of the Variable Insert Loop in Vaccinia H1-Related (VHR) Phosphatase
Beaumont VA, Reiss K, Qu Z, Allen B, Batista VS, Loria JP. Allosteric Impact of the Variable Insert Loop in Vaccinia H1-Related (VHR) Phosphatase. Biochemistry 2020, 59: 1896-1908. PMID: 32348128, PMCID: PMC7364816, DOI: 10.1021/acs.biochem.0c00245.Peer-Reviewed Original ResearchConceptsAcid loopVariable insertActive siteActive-site hydrogen bondsInsert regionSolution nuclear magnetic resonanceNuclear magnetic resonanceMillisecond motionsActive site environmentNormal catalytic functionActive site altersMolecular dynamics simulationsActive site loopHydrogen bondsVaccinia H1Asparagine 74Protein tyrosineTyrosine phosphataseRapid kinetic measurementsAllosteric regionActivity of enzymesKinetic measurementsDynamics simulationsConformational motionsInsert loop
2019
Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II
Reiss K, Morzan U, Grigas A, Batista V. Water Network Dynamics Next to the Oxygen-Evolving Complex of Photosystem II. Inorganics 2019, 7: 39. DOI: 10.3390/inorganics7030039.Peer-Reviewed Original ResearchOxygen-evolving complexWater network dynamicsMolecular dynamics simulationsPhotosystem IICatalytic performanceHydrogen bondingProtein environmentLarge ionsS2 stateDynamics simulationsLarge channelsProton translocationWater diffusionComplexesPSII assemblyEigenvector centrality analysisWater networkGreat interestWater channelsDynamical natureBondingIonsWater transportMajor channelChloride
2017
Interfacial Structure and Electric Field Probed by in Situ Electrochemical Vibrational Stark Effect Spectroscopy and Computational Modeling
Ge A, Videla P, Lee G, Rudshteyn B, Song J, Kubiak C, Batista V, Lian T. Interfacial Structure and Electric Field Probed by in Situ Electrochemical Vibrational Stark Effect Spectroscopy and Computational Modeling. The Journal Of Physical Chemistry C 2017, 121: 18674-18682. DOI: 10.1021/acs.jpcc.7b05563.Peer-Reviewed Original ResearchSelf-assembled monolayersElectrolyte interfaceMolecular dynamics simulationsHelmholtz layerElectrochemical double-layer structureVibrational Stark effect spectroscopyElectrode/electrolyte interfaceVibrational sum frequency generation spectroscopySum frequency generation spectroscopyDensity functional theory calculationsDynamics simulationsAqueous electrolyte interfaceDirect spectroscopic methodFrequency generation spectroscopyStark tuning rateInterfacial structureFunctional theory calculationsStark effect spectroscopySolar energy conversionInterfacial electric fieldDetailed molecular levelElectrochemical interfaceModel complexesDouble-layer structureElectrolyte penetration
2016
Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulations Reveal a Rotationally Fluid Adsorption State of α‑Pinene on Silica
Ho J, Psciuk B, Chase H, Rudshteyn B, Upshur M, Fu L, Thomson R, Wang H, Geiger F, Batista V. Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulations Reveal a Rotationally Fluid Adsorption State of α‑Pinene on Silica. The Journal Of Physical Chemistry C 2016, 120: 12578-12589. DOI: 10.1021/acs.jpcc.6b03158.Peer-Reviewed Original ResearchMolecular dynamics simulationsΑ-pineneSum frequency generation spectroscopyDynamics simulationsHeterogeneous catalytic pathwayClassical molecular dynamics simulationsSum Frequency Generation StudyFrequency generation spectroscopyVan der Waals contactsFour-membered ringVibrational sum frequency generation studyAdsorption modePrimary oxidantSilica surfaceStrained hydrocarbonsCatalytic pathwayFine chemicalsAdsorption statesGeneration spectroscopyVibrational spectraMethylene groupWaals contactsVapor interfaceVibrational modesRotational diffusion constants
2015
Interfacial electron transfer in photoanodes based on phosphorus( v ) porphyrin sensitizers co-deposited on SnO 2 with the Ir(III)Cp* water oxidation precatalyst
Poddutoori P, Thomsen J, Milot R, Sheehan S, Negre C, Garapati V, Schmuttenmaer C, Batista V, Brudvig G, van der Est A. Interfacial electron transfer in photoanodes based on phosphorus( v ) porphyrin sensitizers co-deposited on SnO 2 with the Ir(III)Cp* water oxidation precatalyst. Journal Of Materials Chemistry A 2015, 3: 3868-3879. DOI: 10.1039/c4ta07018f.Peer-Reviewed Original ResearchInterfacial electron transferElectron paramagnetic resonanceQuantum dynamics simulationsElectron transferPhotoanode componentCatalytic water oxidationEfficient interfacial electron transferDynamics simulationsMetal oxide surfacesSolar cellsTime-resolved terahertz spectroscopy measurementsSteady-state fluorescenceTypes of porphyrinsTerahertz spectroscopy measurementsOxidation precatalystWater oxidationAxial coordinationChloride ligandsPorphyrin sensitizersOxidation stateCharge recombinationParamagnetic resonanceSnO 2Phosphorus porphyrinsSpectroscopy measurements
2014
Photoelectrochemical Hole Injection Revealed in Polyoxotitanate Nanocrystals Functionalized with Organic Adsorbates
Negre CF, Young KJ, Oviedo M, Allen LJ, Sánchez C, Jarzembska KN, Benedict JB, Crabtree RH, Coppens P, Brudvig GW, Batista VS. Photoelectrochemical Hole Injection Revealed in Polyoxotitanate Nanocrystals Functionalized with Organic Adsorbates. Journal Of The American Chemical Society 2014, 136: 16420-16429. PMID: 25337894, DOI: 10.1021/ja509270f.Peer-Reviewed Original ResearchOrganic adsorbatesVisible lightInterfacial charge transferQuantum dynamics simulationsEPR spectroscopyCharge transferPhotocathodic currentPhotoelectrochemical measurementsHole injectionCovalent attachmentCovalent bindingDynamics simulationsAdsorbatesNanocrystalsSurface statesThin layerAcetylacetonateNanoparticlesSpectroscopyElectrodeFirst timeTiO2FTO
2013
Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides
Poojari C, Xiao D, Batista V, Strodel B. Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides. Biophysical Journal 2013, 105: 2323-2332. PMID: 24268144, PMCID: PMC3838749, DOI: 10.1016/j.bpj.2013.09.045.Peer-Reviewed Original ResearchConceptsChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyMembrane/water interfaceFrequency generation spectroscopyΒ-sheet secondary structureChannel-forming proteinMolecular dynamics simulationsSimulated SFG spectraAmphiphilic propertiesHuman islet amyloidGeneration spectroscopySFG spectraWater interfaceΒ-sandwichHuman islet amyloid polypeptideIslet β-cellsAmyloid polypeptideWater permeationDynamics simulationsHIAPP aggregatesSecondary structureMembrane permeationIslet amyloid polypeptideΒ-cellsFibrillar structures
2011
Kepler Predictor–Corrector Algorithm: Scattering Dynamics with One-Over-R Singular Potentials
Markmann A, Graziani F, Batista V. Kepler Predictor–Corrector Algorithm: Scattering Dynamics with One-Over-R Singular Potentials. Journal Of Chemical Theory And Computation 2011, 8: 24-35. PMID: 26592868, DOI: 10.1021/ct200452h.Peer-Reviewed Original ResearchFull quantum dynamics calculationsQuantum dynamics calculationsInterstellar gas dynamicsTwo-body collisionsSemiclassical dynamics simulationTime-reversal symmetricTime-dependent pictureScattering dynamicsClassical simulationsScattering processR potentialClose encountersDynamics simulationsDynamics calculationsExcellent agreementCelestial mechanicsGas dynamicsKepler problemStandard numerical techniquesSingular potentialsParticlesPseudopotentialsCollisionsDynamicsSimulationsReengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
Watt ED, Rivalta I, Whittier SK, Batista VS, Loria JP. Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid. Biophysical Journal 2011, 101: 411-420. PMID: 21767494, PMCID: PMC3136797, DOI: 10.1016/j.bpj.2011.05.039.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsAmino acidsMeiboom-Gill (CPMG) relaxation dispersion experimentsWild-type ribonuclease AProtein energy landscapesNonnatural amino acidsRelaxation dispersion experimentsSingle residueProtein motionsMillisecond motionsConformational motionsEnzyme motionsHistidine-48Ribonuclease ACatalytic turnoverSimilar pH rangeRate limitingMolecular dynamics simulationsEnergy landscapeCorrelated motionAcidCatalytic cycleDispersion experimentsResiduesDynamics simulations
2010
Study of Redox Species and Oxygen Vacancy Defects at TiO2−Electrolyte Interfaces
da Silva R, Rego L, Freire J, Rodriguez J, Laria D, Batista V. Study of Redox Species and Oxygen Vacancy Defects at TiO2−Electrolyte Interfaces. The Journal Of Physical Chemistry C 2010, 114: 19433-19442. DOI: 10.1021/jp107385e.Peer-Reviewed Original ResearchRedox speciesElectronic structure calculationsDye-sensitized solar cellsStructure calculationsDifferent redox speciesFree energy barrierMolecular dynamics simulationsPyridine additivesRecombination of photoelectronsSolvent dynamicsTiO2 surfaceElectronic propertiesDynamics simulationsOxygen vacanciesSolar cellsSurface defectsElectrolyteAdsorptionDeeper insightInterfaceCalculationsMolecular processesAdditivesPhotoelectronVacancies
2009
Visible Light Sensitization of TiO2 Surfaces with Alq3 Complexes
Rego L, da Silva R, Freire J, Snoeberger R, Batista V. Visible Light Sensitization of TiO2 Surfaces with Alq3 Complexes. The Journal Of Physical Chemistry C 2009, 114: 1317-1325. DOI: 10.1021/jp9094479.Peer-Reviewed Original ResearchVisible light sensitizationSurface complexesAb initio DFT molecular dynamics simulationsLight sensitizationDFT molecular dynamics simulationsTransient electronic excitationsInterfacial electron transferInterfacial electron injectionTiO2 anatase (101) surfaceMolecular dynamics simulationsTris complexesMolecular assembliesElectron transferAlq3 complexesElectronic excitationTiO2 surfaceCovalent attachmentDynamics simulationsElectron injectionPair recombinationComplexesHost substrateSignificant interestOligothiophenesDerivatization
2003
Quantum Dynamics Simulations of Interfacial Electron Transfer in Sensitized TiO2 Semiconductors
Rego L, Batista V. Quantum Dynamics Simulations of Interfacial Electron Transfer in Sensitized TiO2 Semiconductors. Journal Of The American Chemical Society 2003, 125: 7989-7997. PMID: 12823021, DOI: 10.1021/ja0346330.Peer-Reviewed Original ResearchInterfacial electron transferElectron transferAb initio DFT molecular dynamics simulationsDFT molecular dynamics simulationsAnatase crystalsElectron injection eventsInterfacial electron transfer dynamicsQuantum dynamics calculationsQuantum dynamics simulationsDynamics simulationsElectron transfer dynamicsSurface charge separationMolecular dynamics simulationsCarrier relaxationCharge delocalizationElectronic relaxationAdsorbate moleculesAnatase nanostructuresElectronic statesCharge separationVacuum conditionsSurface ionsTiO2 semiconductorElectron injectionPhotovoltaic devices
2002
Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †
Wu Y, Batista V. Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †. The Journal Of Physical Chemistry B 2002, 106: 8271-8277. DOI: 10.1021/jp0207735.Peer-Reviewed Original ResearchPhotodissociation dynamicsFull quantum mechanical resultsFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState photodissociation dynamicsQuantum mechanical resultsExcited vibrational statesPhotodissociation cross sectionsTotal photodissociation cross sectionsQuantum mechanical calculationsSemiclassical initial value representation methodSemiclassical resultsSemiclassical approachVibrational statesMechanical calculationsCross sectionsH2O spectroscopyExcellent agreementMolecular dynamics simulationsMechanical resultsDynamics simulationsCalculationsBandDynamicsH2OProton-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
1998
Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone
Batista V, Miller W. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone. The Journal Of Chemical Physics 1998, 108: 498-510. DOI: 10.1063/1.475413.Peer-Reviewed Original ResearchElectronic potential energy surfacesSemiclassical molecular dynamics simulationsUltrafast photodissociation dynamicsChappuis bandsSemiclassical initial value representation methodTime-dependent picturePotential energy surfaceUltrafast dynamicsPhotodissociation dynamicsSemiclassical resultsExcited statesNonadiabatic processesMolecular dynamics simulationsEnergy surfaceModel HamiltonianVisible lightGas phaseDynamical featuresDynamics simulationsRealistic reactionsOzoneBandPredissociationPhotodissociationPhotoexcitation