2022
Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers
Wei R, Khaniya U, Mao J, Liu J, Batista V, Gunner M. Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers. Photosynthesis Research 2022, 156: 101-112. PMID: 36307598, DOI: 10.1007/s11120-022-00973-0.Peer-Reviewed Original ResearchConceptsProtonation stateMolecular dynamicsProton affinityReaction centersSide chainsElectron transfer reactionsProton transfer pathwayHydroxy side chainsBacterial reaction centersProton-transfer networkPhotosynthetic reaction centersChains of waterGrotthuss mechanismTransfer reactionsActive siteTransfer pathwayQB siteProton bindingProtein conformationTransmembrane electrochemical gradientUltrafast Charge Relocation Dynamics in Enol–Keto Tautomerization Monitored with a Local Soft-X-ray Probe
Soley M, Videla P, Nibbering E, Batista V. Ultrafast Charge Relocation Dynamics in Enol–Keto Tautomerization Monitored with a Local Soft-X-ray Probe. The Journal Of Physical Chemistry Letters 2022, 13: 8254-8263. PMID: 36018775, PMCID: PMC9465716, DOI: 10.1021/acs.jpclett.2c02037.Peer-Reviewed Original ResearchConceptsSoft X-ray probeSoft X-ray spectroscopyFull quantum treatmentPump-probe spectroscopyUltrafast time scaleQuantum treatmentHydrogen fuel cellsNuclear dynamicsElectronic excitationEnol-keto tautomerizationPCET mechanismOxygen reductionInterplay of protonsFrontier orbitalsWater splittingCharge relocationElectron transferElectronic structure rearrangementLocal excitationTautomerization reactionImportant reactionsFuel cellsElementary stepsChemical reactionsH atoms
2021
Proton exit pathways surrounding the oxygen evolving complex of photosystem II
Kaur D, Zhang Y, Reiss KM, Mandal M, Brudvig GW, Batista VS, Gunner MR. Proton exit pathways surrounding the oxygen evolving complex of photosystem II. Biochimica Et Biophysica Acta (BBA) - Bioenergetics 2021, 1862: 148446. PMID: 33964279, DOI: 10.1016/j.bbabio.2021.148446.Peer-Reviewed Original ResearchConceptsOxygen-Evolving ComplexMulti-Conformation Continuum ElectrostaticsWater-filled channelsMolecular dynamicsSubstrate water moleculesHydrogen bond network analysisProton exit pathwayPhotosynthetic electron transfer chainProton transfer pathPhotosystem IISimilar free energiesInorganic coreWater chainWater moleculesAqueous surfaceElectron transfer chainContinuum electrostaticsProduct oxygenFree energyTransfer chainLarge channelsLikely exitTransfer pathLumenal sideComplexes
2013
Electrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II
Amin M, Vogt L, Vassiliev S, Rivalta I, Sultan MM, Bruce D, Brudvig GW, Batista VS, Gunner MR. Electrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II. The Journal Of Physical Chemistry B 2013, 117: 6217-6226. PMID: 23570540, PMCID: PMC3753004, DOI: 10.1021/jp403321b.Peer-Reviewed Original ResearchConceptsOxomanganese complexesElectron transferOxygen-evolving complexComplexes 6Electrostatic effectsΜ-oxo bridgeDensity functional theory levelTerminal water ligandsBiomimetic oxomanganese complexesPhotosystem IIOxidation state transitionsContinuum electrostatic modelWater ligandsLigand substituentsOxidation midpoint potentialsOxo bridgeCalculated pKaProton transferElectrostatic interactionsTheory levelElectrostatic contributionMidpoint potentialMn oxidationElectrostatic modelFree energyChiral 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 ResearchConceptsD 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
Structural–Functional Role of Chloride in Photosystem II
Rivalta I, Amin M, Luber S, Vassiliev S, Pokhrel R, Umena Y, Kawakami K, Shen JR, Kamiya N, Bruce D, Brudvig GW, Gunner MR, Batista VS. Structural–Functional Role of Chloride in Photosystem II. Biochemistry 2011, 50: 6312-6315. PMID: 21678923, PMCID: PMC3140697, DOI: 10.1021/bi200685w.Peer-Reviewed Original Research
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
2002
Proton-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