2024
Subspace-Search Quantum Imaginary Time Evolution for Excited State Computations
Cianci C, Santos L, Batista V. Subspace-Search Quantum Imaginary Time Evolution for Excited State Computations. Journal Of Chemical Theory And Computation 2024, 20: 8940-8947. PMID: 39352769, DOI: 10.1021/acs.jctc.4c00915.Peer-Reviewed Original ResearchNoisy intermediate-scale quantumQuantum imaginary time evolutionImaginary time evolutionExcited statesQuantum (NISQStudy of excited statesComputation of excited statesLow-lying excited statesTime evolutionVariational quantum imaginary time evolutionCalculation of low-lying excited statesExcited state computationsQuantum systemsSmall molecular systemsVariational quantumLiH moleculeQuantum devicesGround stateQuantum computationQuantumMolecular systemsState algorithmState computationsLocal minimaVariational algorithmRapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C Nuclear Magnetic Resonance Spectrum
Li H, Tuttle M, Zilm K, Batista V. Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C Nuclear Magnetic Resonance Spectrum. Journal Of The American Chemical Society 2024, 146: 27542-27554. PMID: 39322561, DOI: 10.1021/jacs.4c08300.Peer-Reviewed Original ResearchConceptsSecondary structure compositionSecondary structureProtein secondary structure compositionEnsemble of secondary structuresSecondary structure elementsThree-dimensional foldC-NMR spectraSecondary structure contentProtein secondary structurePrimary sequenceProtein structureA-helixLiquid-liquid phase separationCharacterization of protein secondary structureMembrane-boundChemical shift assignmentsProteinBenchtop NMR spectrometersNuclear magnetic resonance spectraSolid-state NMRStructure contentRandom coilMagnetic resonance spectraB sheetsStructural compositionSimulating Cavity-Modified Electron Transfer Dynamics on NISQ Computers
Lyu N, Khazaei P, Geva E, Batista V. Simulating Cavity-Modified Electron Transfer Dynamics on NISQ Computers. The Journal Of Physical Chemistry Letters 2024, 15: 9535-9542. PMID: 39264851, DOI: 10.1021/acs.jpclett.4c02220.Peer-Reviewed Original ResearchElectron transfer dynamicsElectron transfer rateTransfer dynamicsIntramolecular electron transfer reactionElectron transfer reactionsNISQ computersCavity frequencyMolecular triadMolecular systemsTransfer reactionsQuantum (NISQ) computersNoisy Intermediate-Scale Quantum (NISQ) computersThermo field dynamicsIncreasing coupling strengthTetrahydrofuranTransfer rateCoupling strengthQuantum computationQuantum mechanicsEffect of couplingElectronNISQRate processesOscillatory dynamicsReactionSite-specific template generative approach for retrosynthetic planning
Shee Y, Li H, Zhang P, Nikolic A, Lu W, Kelly H, Manee V, Sreekumar S, Buono F, Song J, Newhouse T, Batista V. Site-specific template generative approach for retrosynthetic planning. Nature Communications 2024, 15: 7818. PMID: 39251606, PMCID: PMC11385523, DOI: 10.1038/s41467-024-52048-4.Peer-Reviewed Original ResearchComplexity of chemical spaceRetrosynthetic planningGenerative machine learning methodsChemical spaceTarget compoundsChemical transformationsChemical synthesisReaction templatesSynthetic pathwaySmall moleculesGenerative machine learningMoleculesReactionMachine learning methodsSynthesisUser selectionSynthonsLearning methodsMachine learningGeneration approachReactantsRetrosynthesisInterconversionCompoundsBeyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures
Perets E, Konstantinovsky D, Santiago T, Videla P, Tremblay M, Velarde L, Batista V, Hammes-Schiffer S, Yan E. Beyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures. The Journal Of Chemical Physics 2024, 161: 095104. PMID: 39230381, PMCID: PMC11377083, DOI: 10.1063/5.0220479.Peer-Reviewed Original ResearchConceptsChiral SFG spectraProbe water moleculeWater moleculesChiral SFG spectroscopyHydration shellSFG spectraMinor grooveSFG spectroscopyHydration shell water moleculesWater structureO-H stretching of waterSum frequency generation spectroscopyShell water moleculesPhosphate backboneN-H stretchingO-H stretchingDNA base pairsDNA minor grooveSpine of hydrationSpectra of DNAN-HVibrational spectroscopyO-HSFG responseSFG signalSimilarity Metrics for Subcellular Analysis of FRET Microscopy Videos
Burke M, Batista V, Davis C. Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos. The Journal Of Physical Chemistry B 2024, 128: 8344-8354. PMID: 39186078, DOI: 10.1021/acs.jpcb.4c02859.Peer-Reviewed Original ResearchForster resonance energy transferProtein-RNA interactionsHigh-resolution microscopySubcellular localizationResonance energy transferSpecialized compartmentsSubcellular analysisMicroscopy dataCellsMolecular populationsCompartmentHigh-resolution microscopy dataMolecular environmentMicroscopy videosDynamic heterogeneityA synergetic cocatalyst for conversion of carbon dioxide, sunlight, and water into methanol
Ye Z, Yang K, Zhang B, Navid I, Shen Y, Xiao Y, Pofelski A, Botton G, Ma T, Mondal S, Norris T, Batista V, Mi Z. A synergetic cocatalyst for conversion of carbon dioxide, sunlight, and water into methanol. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2408183121. PMID: 39172778, PMCID: PMC11363284, DOI: 10.1073/pnas.2408183121.Peer-Reviewed Original ResearchConversion of CO<sub>2</sub>Proton-coupled electron transfer pathwayConversion of carbon dioxideSynthesis of methanolTransfer of protonsElectron transfer pathwayVectorial transfer of protonsPhotocatalytic architecturesCore-shell nanoparticlesCore-shell interfaceCatalytic materialsProton reductionHydrogen spilloverProduct selectivityHydrogen atomsTransfer pathwayCore-shellAqueous solutionOxide shellHydrogenVectorial transferMethanolWireless systemsProtonSemiconducting nanowiresPhotoinduced Surface Oxidation of GaN Nanowires Facilitates Hydrogen Evolution
Menzel J, Dong W, Gruszecki E, Yang K, Mi Z, Batista V. Photoinduced Surface Oxidation of GaN Nanowires Facilitates Hydrogen Evolution. ACS Catalysis 2024, 14: 13314-13323. DOI: 10.1021/acscatal.4c00308.Peer-Reviewed Original ResearchHydrogen evolutionDensity functional theoryEffect of surface oxidationGaN NWsSurface oxidationPhotocatalytic hydrogen evolutionWater oxidation capabilityPhotoelectrochemical hydrogen evolutionLinear sweep voltammetrySolar energy storageCatalytic performanceGallium nitride nanowiresPhotocatalytic surfacesWater oxidationLight irradiationSweep voltammetryGallium oxynitrideFunctional theoryChronoamperometric measurementsElectronic structureValence band edge statesOxide surfaceAdsorbed hydroxideOxidation capabilityNitride nanowiresSimulating Chemistry on Bosonic Quantum Devices
Dutta R, Cabral D, Lyu N, Vu N, Wang Y, Allen B, Dan X, Cortiñas R, Khazaei P, Schäfer M, Albornoz A, Smart S, Nie S, Devoret M, Mazziotti D, Narang P, Wang C, Whitfield J, Wilson A, Hendrickson H, Lidar D, Pérez-Bernal F, Santos L, Kais S, Geva E, Batista V. Simulating Chemistry on Bosonic Quantum Devices. Journal Of Chemical Theory And Computation 2024, 20: 6426-6441. PMID: 39068594, DOI: 10.1021/acs.jctc.4c00544.Peer-Reviewed Original ResearchQuantum devicesQuantum two-level systemTwo-level systemMolecular vibronic spectraCalculations of electronic structureQuantum simulationBoson operatorsSystem HamiltonianQuantum computationVibronic spectraElectronic structureChemical dynamicsSolution-phaseReview recent progressGas-phaseChemical structureChemical problemsRecent progressCalculationsSimulate chemistryBosonsHamiltonianOscillationsDynamicsDevicesModeling Electrochemical Vacancy Regeneration in Single-Walled Carbon Nanotubes
Jelušić J, Menzel J, Bertrand Q, Crabtree R, Wang H, Brudvig G, Batista V. Modeling Electrochemical Vacancy Regeneration in Single-Walled Carbon Nanotubes. The Journal Of Physical Chemistry Letters 2024, 15: 7788-7792. PMID: 39048317, DOI: 10.1021/acs.jpclett.4c01293.Peer-Reviewed Original ResearchProton-coupled electron transferDensity functional theorySingle-walled carbon nanotubesC-H bondsQuantum mechanics/molecular mechanicsDiverse catalytic reactionsCarbene characterCarbon nanotubesC-HAdjacent carbonWater dissociationElectron transferCatalytic reactionsCatalytic intermediatesFunctional theoryHydrogen atomsKetone groupForce-fieldCarbon atomsHydroxyl groupsElectrochemical regenerationZigzag single-walled carbon nanotubesElectrochemical potentialKetonesVacancy defectsBenchmarking 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, 20: 6402-6413. 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, PMCID: PMC11294709, 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, 9: 2759-2759. 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