2020
Identification of a Na+‑Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II
Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudvig GW. Identification of a Na+‑Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II. Biochemistry 2020, 59: 2823-2831. PMID: 32650633, DOI: 10.1021/acs.biochem.0c00303.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexSpinach photosystem IIRedox-active Mn ionPhotosystem IIOxygen evolution activityQuantum mechanical calculationsOxomanganese clusterHydroxide anionCommon counterionCryo-electron microscopy mapMechanical calculationsAmino acid residuesMn ionsIonsElectrostatic simulationsMicroscopy mapsAcid residuesComplexesDeprotonationAnionsCounterionsNaChlorideSitesCl
2015
Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach
Send R, Suomivuori C, Kaila V, Sundholm D. Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach. The Journal Of Physical Chemistry B 2015, 119: 2933-2945. PMID: 25613980, DOI: 10.1021/jp5120898.Peer-Reviewed Original ResearchConceptsReduced virtual spaceProtonation stateExcited statesCoupled-clusterCalculation of excitation energiesMethods of theoretical chemistryExcitation energyCC2 excitation energiesCoupled-cluster studyCoupled-cluster singlesLowest excited stateQuantum mechanical calculationsExperimental absorption spectraCalculated energy splittingsStudy of excited statesQM regionVirtual orbitalsPhotoexcitation propertiesMechanical calculationsAbsorption spectraTheoretical chemistryEnergy splittingProtein modelsPredicted optical propertiesBiomolecular systems
2002
Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †
Wu Y, Batista V. Semiclassical Molecular Dynamics Simulations of the Excited State Photodissociation Dynamics of H2O in the AB1 Band †. The Journal Of Physical Chemistry B 2002, 106: 8271-8277. DOI: 10.1021/jp0207735.Peer-Reviewed Original ResearchPhotodissociation dynamicsFull quantum mechanical resultsFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState photodissociation dynamicsQuantum mechanical resultsExcited vibrational statesPhotodissociation cross sectionsTotal photodissociation cross sectionsQuantum mechanical calculationsSemiclassical initial value representation methodSemiclassical resultsSemiclassical approachVibrational statesMechanical calculationsCross sectionsH2O spectroscopyExcellent agreementMolecular dynamics simulationsMechanical resultsDynamics simulationsCalculationsBandDynamicsH2O
2000
Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2′-hydroxyphenyl)–oxazole. The Journal Of Chemical Physics 2000, 113: 9510-9522. DOI: 10.1063/1.1321049.Peer-Reviewed Original ResearchPotential energy surfaceExcited state potential energy surfacesFull-dimensional potential energy surfaceEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceProton transferVibrational energy redistributionProton transfer dynamicsQuantum mechanical calculationsSemiclassical initial value representation methodIntramolecular proton transferPlane vibrational modesSemiclassical resultsMolecular dynamics simulationsEnergy redistributionMechanical calculationsQuantum chemistryTransfer dynamicsCIS levelTautomerization reactionVibrational modesIsotopic substitutionDynamics simulationsNonadiabatic photodissociation dynamics of ICN in the à continuum: A semiclassical initial value representation study
Coronado E, Batista V, Miller W. Nonadiabatic photodissociation dynamics of ICN in the à continuum: A semiclassical initial value representation study. The Journal Of Chemical Physics 2000, 112: 5566-5575. DOI: 10.1063/1.481130.Peer-Reviewed Original ResearchFull quantum mechanical calculationsNonadiabatic photodissociation dynamicsPhotodissociation dynamicsMechanical calculationsQuantum mechanical calculationsSemiclassical initial value representation methodSemiclassical resultsNonadiabatic processesRotational distributionsSemiclassical techniquesAbsorption spectraModel HamiltonianExcellent agreementHamiltonianExperimental dataCalculationsContinuumDynamicsSpectraDirect comparisonQuantizationAgreementICN
1999
Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers
Guallar V, Batista V, Miller W. Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers. The Journal Of Chemical Physics 1999, 110: 9922-9936. DOI: 10.1063/1.478866.Peer-Reviewed Original ResearchExcited-state double proton transferState double proton transferDouble proton transferPotential energy surfaceInitial value representationProton transferExcited state potential energy surfacesEnergy surfaceFull quantum mechanical calculationsSemiclassical molecular dynamics simulationsState potential energy surfaceQuantum mechanical calculationsSemiclassical initial value representationMolecular dynamics simulationsUltrafast dynamicsSymmetric stretch vibrationSemiclassical resultsQuantum chemistryPopulation decayTautomerization reactionMechanical calculationsCIS levelMolecular systemsReduced dimensionalityIsotopic substitution
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