Victor Batista
John Gamble Kirkwood Professor of ChemistryCards
About
Research
Publications
Benchmarking various nonadiabatic semiclassical mapping dynamics methods with tensor-train thermo-field dynamics
Liu Z, Lyu N, Hu Z, Zeng H, Batista V, Sun X. Benchmarking various nonadiabatic semiclassical mapping dynamics methods with tensor-train thermo-field dynamics. The Journal Of Chemical Physics 2024, 161: 024102. PMID: 38980091, DOI: 10.1063/5.0208708.Peer-Reviewed Original ResearchNonadiabatic dynamics methodsZero-point energy parameterOne-dimensional scattering modelLinear vibronic coupling modelEhrenfest mean-fieldSpin-boson modelThermo field dynamicsZero-temperature dynamicsAccurate quantum dynamics simulationsNumerically exact calculationsVibronic coupling modelFinite-temperature dynamicsZero-point energyDynamics methodStudy of electron transferNonadiabatic dynamicsQuasiclassical dynamicsNonadiabatic processesConical intersectionMean-fieldExact calculationsElectronic transitionsElectron transferCondensed phasePhotochemical reactionsHolographic Gaussian Boson Sampling with Matrix Product States on 3D cQED Processors
Lyu N, Bergold P, Soley M, Wang C, Batista V. Holographic Gaussian Boson Sampling with Matrix Product States on 3D cQED Processors. Journal Of Chemical Theory And Computation 2024 PMID: 38968605, DOI: 10.1021/acs.jctc.4c00384.Peer-Reviewed Original ResearchGaussian boson samplingCircuit quantum electrodynamicsBoson samplingMatrix product state representationQubit-based quantum computersCircuit quantum electrodynamics devicesMatrix product statesFock statesQuantum electrodynamicsHolographic approachQuantum circuitsQuantum computationProduct statesState representationTruncated expansionElectrodynamicsSimulation of molecular dockingState vectorModeStateSulfonamide ligandsMolecular dockingCircuitSimulationMutation-induced shift of the photosystem II active site reveals insight into conserved water channels
Flesher D, Liu J, Wang J, Gisriel C, Yang K, Batista V, Debus R, Brudvig G. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Journal Of Biological Chemistry 2024, 300: 107475. PMID: 38879008, DOI: 10.1016/j.jbc.2024.107475.Peer-Reviewed Original ResearchOxygen-evolving complexPhotosystem II active sitePhotosystem IIJahn-Teller distortionPhotosystem II complexD1-Asp170Jahn-TellerResolution cryo-EM structureMutation-induced structural changesCryo-EM structureMagnetic propertiesD1 subunitActive siteOxygenic photosynthesisMutagenesis studiesLight-driven water oxidationSpectroscopic propertiesStructural basisSpectroscopic dataAmino acidsWater oxidation mechanismPhotosystemMutationsMutation-induced shiftWater oxidationWater Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II
Liu J, Yang K, Long Z, Armstrong W, Brudvig G, Batista V. Water Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II. Journal Of The American Chemical Society 2024, 146: 15986-15999. PMID: 38833517, DOI: 10.1021/jacs.4c02926.Peer-Reviewed Original ResearchProton-coupled electron transferOxygen-evolving complexWater insertionWater ligandsCatalytic cycleMolecular dynamicsO-O bondQuantum mechanics/molecular mechanicsConformational changesFree energy changeLigand environmentElectron transferLigand exchangePhotosystem IIOxygen evolutionWater binding mechanismsEnergy changeLigandBinding mechanismAqueous environmentRedoxWater bindingLigand bindingCatalystIsomerizationQuantum-to-Classical Neural Network Transfer Learning Applied to Drug Toxicity Prediction
Smaldone A, Batista V. Quantum-to-Classical Neural Network Transfer Learning Applied to Drug Toxicity Prediction. Journal Of Chemical Theory And Computation 2024, 20: 4901-4908. PMID: 38795030, DOI: 10.1021/acs.jctc.4c00432.Peer-Reviewed Original ResearchScalable machine learning modelVastness of chemical spaceInner product estimationDrug toxicity predictionMachine learning modelsLearnable weightsLearning AppliedDeep learningQuantum phase estimationTox21 dataHadamard testLearning modelsMatrix multiplicationReduced complexityNeural behaviorQuantum circuit designLife-saving applicationsQuantum advantagePrediction accuracyQuantumPhase estimationSwap testChemical spaceToxicity predictionCircuit designA salt bridge of the C‐terminal carboxyl group regulates PHPT1 substrate affinity and catalytic activity
Zavala E, Dansereau S, Burke M, Lipchock J, Maschietto F, Batista V, Loria J. A salt bridge of the C‐terminal carboxyl group regulates PHPT1 substrate affinity and catalytic activity. Protein Science 2024, 33: e5009. PMID: 38747379, PMCID: PMC11094782, DOI: 10.1002/pro.5009.Peer-Reviewed Original ResearchConceptsCatalytic activityPhenylphosphonic acidAnalysis of molecular dynamics trajectoriesNMR chemical shiftsSalt bridgesMolecular dynamics trajectoriesC-terminal carboxyl groupChemical shiftsCombination of solution NMRMolecular dynamicsGuanidinium moietyCarboxyl groupsPara-nitrophenylphosphateSolution NMRActive site inhibitorsHistidine phosphataseActive siteElectrostatic interactionsDynamics trajectoriesEnzymatic functionC-terminusGlycine residuesSubstrate affinityBiochemical experimentsBinding affinityDemystifying metal-assisted chemical etching of GaN and related heterojunctions
Chan C, Menzel J, Dong Y, Long Z, Waseem A, Wu X, Xiao Y, Xie J, Chow E, Rakheja S, Batista V, Mi Z, Li X. Demystifying metal-assisted chemical etching of GaN and related heterojunctions. Applied Physics Reviews 2024, 11: 021416. DOI: 10.1063/5.0186709.Peer-Reviewed Original ResearchReactive ion etchingDevice structureMetal-assisted chemical etchingMechanisms of carrier generationPhotocatalytic reactionAnisotropic etching methodPhotoelectrochemical processesElectrochemical mechanismEnergy-band alignmentPlasma-induced damageElectronic mechanismPower electronicsAnode designPrediction of system behaviorLocal cathodesPassive devicesNano-structuresCarrier generationAnisotropic etchingEtching methodIon etchingSolution chemistryExperimental investigationChemical etchingBandgap materialsAuthor Correction: Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity
Gu Y, Guberman-Pfeffer M, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey F, Batista V, Malvankar N. Author Correction: Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nature Microbiology 2024, 1-1. PMID: 38684912, DOI: 10.1038/s41564-024-01702-0.Peer-Reviewed Original ResearchBreaking a Molecular Scaling Relationship Using an Iron–Iron Fused Porphyrin Electrocatalyst for Oxygen Reduction
Nishiori D, Menzel J, Armada N, Cruz E, Nannenga B, Batista V, Moore G. Breaking a Molecular Scaling Relationship Using an Iron–Iron Fused Porphyrin Electrocatalyst for Oxygen Reduction. Journal Of The American Chemical Society 2024, 146: 11622-11633. PMID: 38639470, DOI: 10.1021/jacs.3c08586.Peer-Reviewed Original ResearchOxygen reduction reactionBinuclear catalystsElectrophilic characterDesign of efficient electrocatalystsCatalytic turnover frequencySynthetic design strategiesMacrocyclic ligandCoordination sphereLigand designTurnover frequencyElectronic conjugationEfficient electrocatalystsReduction reactionOxygen reductionMolecular scaffoldsCatalystCatalytic centerIron-ironCharged sitesElectrocatalystsElectrocatalysisLigandBioinspired applicationsDesign strategyScaling relationshipsA Resilient Platform for the Discrete Functionalization of Gold Surfaces Based on N‑Heterocyclic Carbene Self-Assembled Monolayers
Palasz J, Long Z, Meng J, Videla P, Kelly H, Lian T, Batista V, Kubiak C. A Resilient Platform for the Discrete Functionalization of Gold Surfaces Based on N‑Heterocyclic Carbene Self-Assembled Monolayers. Journal Of The American Chemical Society 2024, 146: 10489-10497. PMID: 38584354, DOI: 10.1021/jacs.3c14113.Peer-Reviewed Original ResearchN-heterocyclic carbeneSelf-assembled monolayersCalculations of vibrational spectraAu(I) complexesLigand exchange reactionFunctionalization of gold surfacesX-ray photoelectron spectroscopyDensity functional theoryExperimental spectroscopic signaturesSurface-enhanced Raman spectroscopyVibrational spectraBinding geometryFunctional theoryBinding modePhotoelectron spectroscopyExchange reactionGold surfaceOn-surfaceSpectroscopic signaturesRaman spectroscopyX-rayAmbient conditionsCarbeneSpectroscopyAcid-base