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 signalOccupancy 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 residuesMolecules
2021
Do crystallographic XFEL data support binding of a water molecule to the oxygen-evolving complex of photosystem II exposed to two flashes of light?
Wang J, Armstrong WH, Batista VS. Do crystallographic XFEL data support binding of a water molecule to the oxygen-evolving complex of photosystem II exposed to two flashes of light? Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2023982118. PMID: 34117119, PMCID: PMC8214663, DOI: 10.1073/pnas.2023982118.Peer-Reviewed Original ResearchProton 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
2018
Behavior of Ru–bda Water‐Oxidation Catalysts in Low Oxidation States
Matheu R, Ghaderian A, Francàs L, Chernev P, Ertem M, Benet‐Buchholz J, Batista V, Haumann M, Gimbert‐Suriñach C, Sala X, Llobet A. Behavior of Ru–bda Water‐Oxidation Catalysts in Low Oxidation States. Chemistry - A European Journal 2018, 24: 12838-12847. PMID: 29897655, DOI: 10.1002/chem.201801236.Peer-Reviewed Original ResearchCoordination modeRu centerRu complexesWater moleculesVariable-temperature NMR spectroscopyHydrogen-bonded water moleculesX-ray absorption spectroscopyPseudo-octahedral geometryAdditional water moleculesMain coordination modesNew Ru complexesLower oxidation statesSingle crystal XRDSecond coordination sphereComplex 1 reactsAcidic aqueous solutionExcess of NOTridentate mannerAniline ligandNew RuO ligandsCoordination sphereNMR spectroscopySynthetic intermediatesCarboxylate groups
2016
Surface-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
2015
Triplet Oxygen Evolution Catalyzed by a Biomimetic Oxomanganese Complex: Functional Role of the Carboxylate Buffer
Rivalta I, Yang K, Brudvig G, Batista V. Triplet Oxygen Evolution Catalyzed by a Biomimetic Oxomanganese Complex: Functional Role of the Carboxylate Buffer. ACS Catalysis 2015, 5: 2384-2390. DOI: 10.1021/acscatal.5b00048.Peer-Reviewed Original ResearchOxomanganese complexesTriplet oxygenOxygen evolutionWater splittingCatalytic oxygen evolutionO bond formationBiomimetic oxomanganese complexesNucleophilic water moleculeUnderlying reaction mechanismGreen plant chloroplastsPhotosynthetic oxygen evolutionWater ligandsCarboxylate ligandsInorganic coreMn complexesSuperoxo speciesNoninnocent roleCarboxylate groupsWater moleculesSubstrate waterBond formationSynthetic complexesCarboxylate buffersNucleophilic attackRedox potential
2013
S0‑State Model of the Oxygen-Evolving Complex of Photosystem II
Pal R, Negre CF, Vogt L, Pokhrel R, Ertem MZ, Brudvig GW, Batista VS. S0‑State Model of the Oxygen-Evolving Complex of Photosystem II. Biochemistry 2013, 52: 7703-7706. PMID: 24125018, DOI: 10.1021/bi401214v.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexS1 transitionQuantum mechanics/molecular mechanics modelsX-ray absorption fine structure spectroscopyExtended X-ray absorption fine structure (EXAFS) spectroscopyQM/MM modelAbsorption fine structure spectroscopyElectron transfer processHydrogen bonding networkFine structure spectroscopyPhotosystem IIX-ray diffraction dataMolecular mechanics modelPCET mechanismKok cycleWater moleculesWater splittingBonding networkS1 stateMn centersStructure spectroscopyS0 stateDiffraction dataMM modelSignificant rearrangement
2008
Quantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II
Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II. Journal Of The American Chemical Society 2008, 130: 3428-3442. PMID: 18290643, DOI: 10.1021/ja076130q.Peer-Reviewed Original ResearchConceptsSubstrate water moleculesWater moleculesMu-oxo bridgeOxygen-evolving complexWater splittingQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsQuantum Mechanics/Molecular Mechanics StudySolar fuel production systemsPhotosystem IIX-ray diffraction structureMolecular mechanics studySecond coordination shellCyanobacterium Thermosynechococcus elongatusOxomanganese clusterDioxygen evolutionTerminal ligandsXRD structureCatalytic clustersCP43-R357Ligand exchangeCatalytic reactionCatalytic cycleReaction intermediatesS0 stateNucleophilic attack
2007
QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II
Sproviero EM, Shinopoulos K, Gascn J, McEvoy JP, Brudvig GW, Batista VS. QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II. Philosophical Transactions Of The Royal Society B Biological Sciences 2007, 363: 1149-1156. PMID: 17971333, PMCID: PMC2614095, DOI: 10.1098/rstb.2007.2210.Peer-Reviewed Original ResearchConceptsOxygen-evolving centerWater moleculesSubstrate waterElectrostatic potential atomic chargesQM/MM computational studiesPhotosystem IIComputational studyX-ray crystal structureCharge transfer interactionFormal oxidation stateCyanobacterium Thermosynechococcus elongatusDioxygen formationMetal centerModel complexesOxidation stateWater exchange rateAtomic chargesMetal clustersSubstrate moleculesMn ionsCrystal structureEnergy barrierThermosynechococcus elongatusManganese ionsWater binding
2006
Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin
Gascón J, Sproviero E, Batista V. Computational Studies of the Primary Phototransduction Event in Visual Rhodopsin. Accounts Of Chemical Research 2006, 39: 184-193. PMID: 16548507, DOI: 10.1021/ar050027t.Peer-Reviewed Original ResearchConceptsG protein-coupled receptorsRecent computational studiesPrimary photochemical eventQuantum mechanics/molecular mechanics (QM/MM) hybrid methodsComputational studyPhotochemical eventsEnergy storage mechanismPrototypical G protein-coupled receptorX-ray structureVisual rhodopsinHigh-resolution X-ray structuresBovine visual rhodopsinWater moleculesSpectroscopic changesRetinyl chromophoreStorage mechanismActive siteMolecular rearrangementTrans isomerizationPhototransduction eventsMolecular originIndividual residuesStructural refinementPhototransduction mechanismChromophore