2024
Site-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 approachReactantsRetrosynthesisInterconversionCompoundsOccupancy 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 residuesMoleculesChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
Kyro G, Morgunov A, Brent R, Batista V. ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation. Journal Of Chemical Information And Modeling 2024, 64: 653-665. PMID: 38287889, DOI: 10.1021/acs.jcim.3c01456.Peer-Reviewed Original ResearchConceptsVastness of chemical spaceMolecular generationDomain of drug discoveryArtificial intelligence modelsChemical spaceIntelligence modelsLearning methodologyPython packageDrug discoverySmall molecule inhibitorsActive learning methodologiesFDA-approved small molecule inhibitorsMoleculesEfficient methodDomainSoftwareC-Abl kinase
2023
ChemSpaceAL: An efficient active learning methodology applied to protein-specific molecular generation
Kyro G, Morgunov A, Brent R, Batista V. ChemSpaceAL: An efficient active learning methodology applied to protein-specific molecular generation. Biophysical Journal 2023, 123: 283a. PMID: 37744464, PMCID: PMC10516108, DOI: 10.1016/j.bpj.2023.11.1763.Peer-Reviewed Original ResearchMolecular generationVastness of chemical spaceLearning methodologyActive learning methodologiesDomain of drug discoveryArtificial intelligence modelsChemical spaceGenerative modelIntelligence modelsPython packageDrug discoverySample spaceSmall molecule inhibitorsFDA-approved small molecule inhibitorsMoleculesEfficient methodDomainSoftwareApplicationsMethodologyC-Abl kinaseImplementationSpaceMethod
2017
Ultrafast photo-induced charge transfer of 1-naphthol and 2-naphthol to halocarbon solvents
Chaudhuri S, Rudshteyn B, Prémont-Schwarz M, Pines D, Pines E, Huppert D, Nibbering E, Batista V. Ultrafast photo-induced charge transfer of 1-naphthol and 2-naphthol to halocarbon solvents. Chemical Physics Letters 2017, 683: 49-56. DOI: 10.1016/j.cplett.2017.03.080.Peer-Reviewed Original ResearchHalocarbon solventsPhoto-induced charge transferFirst solvation shellQuantum chemistry computationsFemtosecond IR spectroscopyClose contact interactionsIR spectroscopyHalocarbon moleculesSolvation shellElectron transferChemistry computationsCharge transferFluorescence quenchingElectronic structureSolventDe-excitation mechanismNaphtholMoleculesTransferDecay rateQuenchingFaster decay rateInteractionShellStructure
2016
Ab initio tensorial electronic friction for molecules on metal surfaces: Nonadiabatic vibrational relaxation
Maurer R, Askerka M, Batista V, Tully J. Ab initio tensorial electronic friction for molecules on metal surfaces: Nonadiabatic vibrational relaxation. Physical Review B 2016, 94: 115432. DOI: 10.1103/physrevb.94.115432.Peer-Reviewed Original ResearchMetal surfaceElectronic frictionElectron-hole pair excitationsVibrational relaxationDensity functional theoryMolecular adsorbatesNonadiabatic coupling matrix elementsCoupling matrix elementsVibrational relaxation rateFunctional theoryAtomic orbital basis setsBasis setKohn-Sham density functional theoryEnergy transferAdsorbatesDiatomic moleculesPair excitationsMoleculesRelaxation rateTensorial propertiesSurfaceExperimental findingsChemistryFriction tensorCOSurface-Induced Anisotropic Binding of a Rhenium CO2‑Reduction Catalyst on Rutile TiO2(110) Surfaces
Ge A, Rudshteyn B, Psciuk B, Xiao D, Song J, Anfuso C, Ricks A, Batista V, Lian T. Surface-Induced Anisotropic Binding of a Rhenium CO2‑Reduction Catalyst on Rutile TiO2(110) Surfaces. The Journal Of Physical Chemistry C 2016, 120: 20970-20977. DOI: 10.1021/acs.jpcc.6b03165.Peer-Reviewed Original ResearchVibrational sum frequency generation spectroscopySum frequency generation spectroscopyCO2 reduction catalystsDensity functional theory levelFrequency generation spectroscopyHigh surface coverageProper hydrogen bondingHydrogen bondingCarboxylate groupsSingle-crystalline TiO2Water moleculesGeneration spectroscopyTheory levelSurface coverageSFG intensityOptical anisotropyIsotropic distributionAnisotropic distributionRing angleCatalystNearest-neighbor effectsMoleculesPlane rotationSurfaceTilt angle
2014
High-Conductance Conformers in Histograms of Single-Molecule Current–Voltage Characteristics
Ding W, Negre C, Vogt L, Batista V. High-Conductance Conformers in Histograms of Single-Molecule Current–Voltage Characteristics. The Journal Of Physical Chemistry C 2014, 118: 8316-8321. DOI: 10.1021/jp503193m.Peer-Reviewed Original ResearchOptimal charge transport propertiesFavorable electronic couplingSingle molecular junctionCharge transport propertiesBroadening of bandsBreak-junction experimentsMolecular assembliesMolecular conductanceChemical stabilityElectronic couplingMolecular conformationTransport propertiesMolecular junctionsSingle moleculesRational designMolecular orientationExperimental transport propertiesCharge transportElectronic statesMinimum energy configurationNonequilibrium Green's function methodConformationMoleculesEnergy configurationComputational methodology
2013
Efficiency of Interfacial Electron Transfer from Zn-Porphyrin Dyes into TiO2 Correlated to the Linker Single Molecule Conductance
Negre C, Milot R, Martini L, Ding W, Crabtree R, Schmuttenmaer C, Batista V. Efficiency of Interfacial Electron Transfer from Zn-Porphyrin Dyes into TiO2 Correlated to the Linker Single Molecule Conductance. The Journal Of Physical Chemistry C 2013, 117: 24462-24470. DOI: 10.1021/jp408738b.Peer-Reviewed Original ResearchDye-sensitized solar cellsSingle-molecule conductanceElectron injection efficiencyZn-porphyrin dyeMolecule conductanceLinker moleculesHigh performance dye-sensitized solar cellsZn-porphyrin complexInterfacial electron transferEfficient electron transportInjection efficiencyMolecular conductanceAdsorbate complexesElectron transferMolecular linkersSame chromophoreTiO2 nanoparticlesSolar cellsDyeModular assemblyMoleculesSpectroscopySemiconductor interfaceLinkerElectron transport
2010
Single-Molecule Interfacial Electron Transfer in Donor-Bridge-Nanoparticle Acceptor Complexes
Jin S, Snoeberger R, Issac A, Stockwell D, Batista V, Lian T. Single-Molecule Interfacial Electron Transfer in Donor-Bridge-Nanoparticle Acceptor Complexes. The Journal Of Physical Chemistry B 2010, 114: 14309-14319. PMID: 20225886, DOI: 10.1021/jp911662g.Peer-Reviewed Original ResearchInterfacial electron transferElectron transferAcceptor complexesSingle moleculesSingle-molecule conditionsSingle-molecule levelET ratesElectronic coupling strengthEnsemble average levelFluorescence lifetimeDonor–BridgeShort fluorescence lifetimeMolecular conformationMolecule levelMolecule conditionsDifferent moleculesMoleculesFluorescence decayComplexesSulforhodamine BConformationComplete samplingSRHBComputational modelingTransfer