2024
Beyond 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 signal
2022
Tensor-Train Split-Operator KSL (TT-SOKSL) Method for Quantum Dynamics Simulations
Lyu N, Soley M, Batista V. Tensor-Train Split-Operator KSL (TT-SOKSL) Method for Quantum Dynamics Simulations. Journal Of Chemical Theory And Computation 2022, 18: 3327-3346. PMID: 35649210, DOI: 10.1021/acs.jctc.2c00209.Peer-Reviewed Original Research
2015
Accurate Line Shapes from Sub‑1 cm–1 Resolution Sum Frequency Generation Vibrational Spectroscopy of α‑Pinene at Room Temperature
Mifflin A, Velarde L, Ho J, Psciuk B, Negre C, Ebben C, Upshur M, Lu Z, Strick B, Thomson R, Batista V, Wang H, Geiger F. Accurate Line Shapes from Sub‑1 cm–1 Resolution Sum Frequency Generation Vibrational Spectroscopy of α‑Pinene at Room Temperature. The Journal Of Physical Chemistry A 2015, 119: 1292-1302. PMID: 25647092, DOI: 10.1021/jp510700z.Peer-Reviewed Original ResearchMeSH KeywordsBicyclic MonoterpenesModels, ChemicalMolecular Dynamics SimulationMonoterpenesSpectrum AnalysisTemperatureVibrationConceptsVibrational spectroscopySum frequency generation vibrational spectroscopyGeneration vibrational spectroscopySum frequency generation spectraMolecular dynamics calculationsΑ-pineneVibrational energy relaxationSFG spectroscopyRoom temperaturePhase-resolved spectraAccurate line shapesVibrational spectraFourier transformMolecular surfaceHigh spectral resolutionSpectroscopyRaman spectraDynamics calculationsSame moleculeCommon terpenesNew spectroscopyVibrational coherenceEnergy relaxationGeneration spectraSpectral lines
2013
Chiral Sum Frequency Generation for In Situ Probing Proton Exchange in Antiparallel β‑Sheets at Interfaces
Fu L, Xiao D, Wang Z, Batista VS, Yan EC. Chiral Sum Frequency Generation for In Situ Probing Proton Exchange in Antiparallel β‑Sheets at Interfaces. Journal Of The American Chemical Society 2013, 135: 3592-3598. PMID: 23394622, PMCID: PMC9208335, DOI: 10.1021/ja3119527.Peer-Reviewed Original ResearchMeSH KeywordsDeuterium Exchange MeasurementPeptidesProtein Structure, SecondaryProtonsQuantum TheorySpectrum AnalysisConceptsD exchangeChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyHydrogen/deuterium exchangeSurface-selective methodFrequency generation spectroscopyVibrational modesAir/water interfaceAb initio simulationsWater OD stretch bandsH bondsPeptide backboneGeneration spectroscopyN stretchBulk solutionProton exchangeD stretchWater interfaceAntiparallel β-sheetDeuterium exchangeStretch bandFourier transformMass spectroscopyInitio simulations
2011
Amphiphilic Adsorption of Human Islet Amyloid Polypeptide Aggregates to Lipid/Aqueous Interfaces
Xiao D, Fu L, Liu J, Batista V, Yan E. Amphiphilic Adsorption of Human Islet Amyloid Polypeptide Aggregates to Lipid/Aqueous Interfaces. Journal Of Molecular Biology 2011, 421: 537-547. PMID: 22210153, PMCID: PMC3350761, DOI: 10.1016/j.jmb.2011.12.035.Peer-Reviewed Original ResearchConceptsLipid/aqueous interfaceAqueous interfaceΒ-sheet aggregatesAb initio quantum chemistry calculationsChiral sum frequency generation (SFG) spectroscopySum frequency generation spectroscopyQuantum chemistry calculationsFrequency generation spectroscopyHuman islet amyloid polypeptideHuman islet amyloid polypeptide aggregatesChemistry calculationsAmphiphilic propertiesGeneration spectroscopyΒ-sheetPolypeptide aggregatesIslet amyloid polypeptideΒ-strandsAggregatesAmyloid polypeptideAdsorbAdsorptionSpectroscopyAmyloid proteinInterfacePotential disruptive effects
2009
The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules
Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynthesis Research 2009, 102: 455-470. PMID: 19633920, PMCID: PMC2954272, DOI: 10.1007/s11120-009-9467-6.Peer-Reviewed Original ResearchMeSH KeywordsMacromolecular SubstancesMolecular Dynamics SimulationPhotosystem II Protein ComplexQuantum TheorySpectrum AnalysisWaterConceptsElectrostatic interactionsMM methodQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsForce fieldQM/MM hybrid methodsQM/MM methodologyQM/MM methodsMolecular mechanics force fieldQuantum chemistry techniquesMM force fieldsStructural refinementPhotosystem IIChemistry techniquesStructure/function relationsCharge transferQM layerMolecular fragmentsChemical modificationBiological macromoleculesSteric hindranceComputational protocolSpectroscopic dataMolecular domainsStructural propertiesHigh-resolution spectroscopic data
2007
Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. Current Opinion In Structural Biology 2007, 17: 173-180. PMID: 17395452, DOI: 10.1016/j.sbi.2007.03.015.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexPhotosystem IIWater oxidationOEC of PSIIQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsPhotocatalytic water oxidationGreen plant chloroplastsX-ray crystallographyX-ray absorption fine structure measurementsProcess of photosynthesisAmino acid residuesAbsorption fine structure measurementsExtended X-ray absorption fine structure (EXAFS) measurementsIntrinsic electronic propertiesComputational structural modelsFine structure measurementsOEC modelsAvailable mechanistic dataProtein environmentThylakoid membranesCatalytic mechanismX-ray diffraction modelElectronic propertiesInternal membranesCatalytic center
2006
Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine
Chen X, Batista V. Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine. The Journal Of Chemical Physics 2006, 125: 124313. PMID: 17014180, DOI: 10.1063/1.2356477.Peer-Reviewed Original ResearchConceptsNonadiabatic quantum dynamicsQuantum dynamicsFull-dimensional potential energy surfaceGradient-based optimization methodsSecond-order accuracyTime evolution operatorCoherent-state expansionNonadiabatic reaction dynamicsPhotoabsorption cross sectionsPotential energy surfacePhotoabsorption spectroscopyOrder accuracyTrotter expansionWave packetsReaction dynamicsExact simulationOptimization methodSurvival amplitudeModel HamiltonianPolyatomic systemsEnergy surfaceMultidimensional systemsCross sectionsPropagation schemeBenchmark calculations