2024
A Roadmap for Simulating Chemical Dynamics on a Parametrically Driven Bosonic Quantum Device
Cabral D, Khazaei P, Allen B, Videla P, Schäfer M, Cortiñas R, de Albornoz A, Chávez-Carlos J, Santos L, Geva E, Batista V. A Roadmap for Simulating Chemical Dynamics on a Parametrically Driven Bosonic Quantum Device. The Journal Of Physical Chemistry Letters 2024, 15: 12042-12050. PMID: 39589318, DOI: 10.1021/acs.jpclett.4c02864.Peer-Reviewed Original ResearchZero-point energy motionTransition-state theoryQuantum devicesQuantum effectsThermal bathCoupling strengthReaction dynamicsDegrees of freedomReactive fluxChemical dynamicsHydrogen-bonded dimersProton-transfer reactionsFree energy profilesFree energy barrierDNA base pairsReaction coordinateRate theoryEnergy barrierEnergy profilesChemical reactionsReactionDynamicsTheoryParametrizationCouplingChemiexcitation in preventing macular degeneration
Brash D, Gaillard E. Chemiexcitation in preventing macular degeneration. Frontiers In Photonics 2024, 5: 1451857. DOI: 10.3389/fphot.2024.1451857.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsExcited statesGround-state chemical reactionsExcited-state wavefunctionsHigh-energy statesQuantum biologyMagnetic fieldEnergy statesChemiexcitation processEnergy barrierChemiexcitationElectronReaction productsChemical reactionsWavefunctionsEnergyQuantumStateTransient mixingReactionIntermediate moleculesMoleculesGroundField
2022
Ultrafast 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
2020
Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems
Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chemical Biology 2020, 27: 1063-1072.e7. PMID: 32698018, PMCID: PMC7483975, DOI: 10.1016/j.chembiol.2020.07.001.Peer-Reviewed Original ResearchConceptsBiological systemsChemical toolsRational designChemical reactionsPhotosensitizerElectron microscopyChromophore-assisted light inactivationNumerous biological experimentsHigh-resolution imagingPowerful methodPhotopolymerizationReactive oxygen speciesRhodamineOxygen speciesSynthesisTargeted destructionReactionBiological experimentsBroad rangeMicroscopyCharacterizationCell ablationDiaminobenzidine
2018
Crystallographic evidence for two‐metal‐ion catalysis in human pol η
Wang J, Smithline ZB. Crystallographic evidence for two‐metal‐ion catalysis in human pol η. Protein Science 2018, 28: 439-447. PMID: 30368948, PMCID: PMC6319759, DOI: 10.1002/pro.3541.Peer-Reviewed Original ResearchConceptsMetal ionsProduct pyrophosphateChemical reactionsTwo-metal-ion catalysisTwo-metal-ion catalytic mechanismThird metal ionPhosphoryl transfer reactionsTransfer reactionsCrystallographic dataCatalytic mechanismCrystal structureCrystallographic evidenceHuman Pol ηMeal ionsIonsHuman polymerase ηCatalysisReactionComplexesSubPyrophosphateBindingProductsDNA polymeraseCrystalsFormation of flavorant–propylene Glycol Adducts With Novel Toxicological Properties in Chemically Unstable E-Cigarette Liquids
Erythropel HC, Jabba SV, DeWinter TM, Mendizabal M, Anastas PT, Jordt SE, Zimmerman JB. Formation of flavorant–propylene Glycol Adducts With Novel Toxicological Properties in Chemically Unstable E-Cigarette Liquids. Nicotine & Tobacco Research 2018, 21: 1248-1258. PMID: 30335174, PMCID: PMC6698951, DOI: 10.1093/ntr/nty192.Peer-Reviewed Original ResearchConceptsFlavor aldehydesSolvent componentsNuclear magnetic resonance spectroscopyNovel chemical speciesReaction productsPhysiological aqueous solutionE-cigarette liquidsReactive chemical systemsToxicological propertiesCommercial e-liquidsMagnetic resonance spectroscopyE-liquidsAqueous mediaPropylene glycolAqueous solutionPotential toxicological effectsNew compoundsUltraviolet spectroscopyChemical speciesChemical reactionsGas chromatographyChemical systemsResonance spectroscopyToxicological effectsAldehydes
2016
Aspartyl Oxidation Catalysts That Dial In Functional Group Selectivity, along with Regio- and Stereoselectivity
Alford JS, Abascal NC, Shugrue CR, Colvin SM, Romney DK, Miller SJ. Aspartyl Oxidation Catalysts That Dial In Functional Group Selectivity, along with Regio- and Stereoselectivity. ACS Central Science 2016, 2: 733-739. PMID: 27800556, PMCID: PMC5084076, DOI: 10.1021/acscentsci.6b00237.Peer-Reviewed Original ResearchBaeyer-Villiger oxidationAlkene epoxidationSmall-molecule catalystsModes of reactivityOrthogonal chemical reactivityFunctional group selectivityCarboxylic acid groupsCatalytic functional groupsLate-stage diversificationDifferent chemical reactionsActive site carboxylatesMacromolecular architecturesPolyfunctional moleculesChemical reactivityChemical selectivityElectrophilic oxidantSelective reactionGroup selectivityAmide bondAcid groupsFunctional groupsActive siteCatalytic mechanismChemical reactionsCatalyst
2013
A molecular dynamics simulation of DNA damage induction by ionizing radiation
Abolfath RM, Carlson DJ, Chen ZJ, Nath R. A molecular dynamics simulation of DNA damage induction by ionizing radiation. Physics In Medicine And Biology 2013, 58: 7143-7157. PMID: 24052159, DOI: 10.1088/0031-9155/58/20/7143.Peer-Reviewed Original ResearchConceptsMolecular dynamics simulationsChemical reactionsDynamics simulationsChemical bond breaksWater moleculesMolecular dynamics softwareHydrogen abstractionHydroxyl free radicalsBond breaksChemical eventsCollection of ionsSingle protonRadicalsLow-energy electronsDNA moleculesProtonsBackbone damageFree radicalsMulti-scale simulationsIonsMoleculesReactionElectronsBroken bondsEnergy electronsTH‐F‐105‐02: Molecular Dynamics Simulation of DNA Damage Induction by Ionizing Radiation
Abolfath R, Carlson D, Chen Z, Nath R. TH‐F‐105‐02: Molecular Dynamics Simulation of DNA Damage Induction by Ionizing Radiation. Medical Physics 2013, 40: 552-552. DOI: 10.1118/1.4815815.Peer-Reviewed Original ResearchWater moleculesOH radicalsMD simulationsChemical reactionsMolecular dynamicsReaxFF molecular dynamicsHydrogen bond disruptionDynamics of OHMolecular dynamics simulationsChemical pathwaysPair of ionsResult of ionizationSuch computational approachesBond disruptionDynamics simulationsSingle protonMoleculesProtonsBeam of electronsIon distributionOHReactionElectronsIonizationComputational approachChemical Tailoring of Teicoplanin with Site-Selective Reactions
Pathak TP, Miller SJ. Chemical Tailoring of Teicoplanin with Site-Selective Reactions. Journal Of The American Chemical Society 2013, 135: 8415-8422. PMID: 23692563, PMCID: PMC3800266, DOI: 10.1021/ja4038998.Peer-Reviewed Original ResearchConceptsNew compoundsSelective cross-coupling reactionsChemical reactionsOrthogonal chemical reactionsSite-selective reactionsTotal chemical synthesisCross-coupling reactionsNatural product derivativesTwo-step accessChemical tailoringChemical synthesisProduct derivativesChemical modificationPoor selectivityAntibacterial propertiesAntibiotic teicoplaninReactionChemical alterationImproved analoguesCompoundsUnmet challengeAnaloguesSelectivitySemisynthesisComplex structure
2012
Modeling cellular signaling: taking space into the computation
Sneddon MW, Emonet T. Modeling cellular signaling: taking space into the computation. Nature Methods 2012, 9: 239-242. PMID: 22373909, PMCID: PMC4713026, DOI: 10.1038/nmeth.1900.Peer-Reviewed Original Research
2008
2 The Neuron Simulation Environment in Epilepsy Research
Carnevale N, Hines M. 2 The Neuron Simulation Environment in Epilepsy Research. 2008, 18-33. DOI: 10.1016/b978-012373649-9.50005-3.Peer-Reviewed Original ResearchLigand-dependent ion channelsIon accumulationExtracellular ion accumulationIon channelsCell membraneSingle cellsBiophysical propertiesBiophysical mechanismsSubcellular mechanismsExtracellular stimulationMechanistic modelStochastic gatingElectrical fieldCellsDomainAccumulationBiologyNeuronsMechanismChemical reactionsLocal concentrationSpecial programming languageComputational detailsMembraneIndividual neurons
2005
Mechanistic Comparisons Between Photosystem II and Cytochrome c Oxidase
Brudvig G, Wikström M. Mechanistic Comparisons Between Photosystem II and Cytochrome c Oxidase. Advances In Photosynthesis And Respiration 2005, 22: 697-713. DOI: 10.1007/1-4020-4254-x_32.Peer-Reviewed Original ResearchFour-electron reductionSingle reaction stepSame chemical reactionPhotosystem IIRole of protonsOxygen reductionProton transferMolecular oxygenReaction mechanismReaction stepsActive siteWater reactionChemical reactionsRequirement of electronsMechanistic comparisonReverse reactionReactionCytochrome c oxidaseProtonsC oxidaseMechanistic similaritiesChemistryElectronsWaterRespiratory enzymes
2004
Chapter 4 Enzymes
Silverman R. Chapter 4 Enzymes. 2004, 173-225. DOI: 10.1016/b978-0-08-051337-9.50009-2.Peer-Reviewed Original ResearchCatalyze hydrolytic reactionsCytosol of cellsMechanisms of enzyme catalysisEnzyme-substrate complexSubstrate to productGenetic engineering techniquesEnzyme-catalyzed reactionsEnzyme functionActive enzymeTransition state energiesEnzyme instabilityCatalyze chemical reactionsEnzyme catalysisState energyEnzymeNatural proteinsBond vibrationsTransition stateHigh-energy statesActive siteHydrolytic reactionChemical reactionsEnergetic intermediatesCatalysisReaction
2001
In Vitro Selection of Kinase and Ligase Deoxyribozymes
Li Y, Breaker R. In Vitro Selection of Kinase and Ligase Deoxyribozymes. Methods 2001, 23: 179-190. PMID: 11181037, DOI: 10.1006/meth.2000.1119.Peer-Reviewed Original ResearchConceptsDNA ligationModern living systemsDNA kinaseEnzymatic functionRandom sequence populationVitro SelectionProtein enzymesConstruction of DNADNA constructsDNA phosphorylationDNADeoxyribozymesKinaseLiving systemsFundamental roleChemical reactionsAdenylationFundamental questionsBiocatalysisPhosphorylationEnzymeBiotechnologySelection strategyDiscoveryDetailed overview
2000
Neuronal Protection by Nitric Oxide-Related Species
Lipton S, Choi Y, Sucher N, Chen H. Neuronal Protection by Nitric Oxide-Related Species. 2000, 143-152. DOI: 10.1007/978-4-431-67949-3_9.Peer-Reviewed Original ResearchRedox-related speciesFree sulfhydryl groupsSufficient redox potentialNO groupSulfhydryl groupsOrganic synthesisProtein cysteine residuesSingle sulfhydryl groupRedox potentialChemical reactionsRedox agentsCysteine sulfhydrylsDistinctive chemistryAdditional electronLess electronBiological systemsRedox modulationOxideDisulfide bondsCysteine residuesEndogenous redox agentsDifferent biological effectsChemistryElectronsLipoic acidChapter 29 Role of Nitric Oxide in Neuronal Protection versus Apoptosis
Lipton S. Chapter 29 Role of Nitric Oxide in Neuronal Protection versus Apoptosis. 2000, 453-464. DOI: 10.1016/b978-012370420-7/50030-7.Peer-Reviewed Original ResearchDifferent chemical statesPossible chemical reactionsRedox reactionsChapter 29 RoleChemical stateRelated reactionsFurther oxidationDistinct reactivityActive siteChemical reactionsCysteine residue presentThiol groupsOxide groupsAdditional electronBiological activityNitroxyl anionS-nitrosylationReactionRedox stateCaspase enzymesCritical thiolsCysteine residuesCritical cysteine residuesResidue presentAnionsMetabolic Control From The Back Benches: Biochemistry Towards Biocomplexity
Westerhoff H, Teusink B, Mensonides F, Reijenga K, Esgalhado E, Kholodenko B, Somsen O, Van Heeswijk W, Boogerd F, Bruggeman F, Snoep J. Metabolic Control From The Back Benches: Biochemistry Towards Biocomplexity. NATO Science Partnership Subseries: 3 2000, 235-242. DOI: 10.1007/978-94-011-4072-0_26.Peer-Reviewed Original ResearchBacterial inner membraneElectron transfer chainImportant metabolic processesBiological free energy transductionFermentation of glucoseInner membraneATP hydrolysisPhysiological processesMetabolic processesMolecular biologyProton pumpLiving cellsStudy of metabolismProtein fractionsBiochemical reactionsIndependent chemical reactionsFree energy transductionBiochemistryChemical reactionsTransductionYeastBiocomplexityReactionBiologySubstantial progress
1999
Nucleic acid molecular switches
Soukup G, Breaker R. Nucleic acid molecular switches. Trends In Biotechnology 1999, 17: 469-476. PMID: 10557159, DOI: 10.1016/s0167-7799(99)01383-9.Peer-Reviewed Original ResearchDeoxyribozymes: New players in the ancient game of biocatalysis
Li Y, Breaker R. Deoxyribozymes: New players in the ancient game of biocatalysis. Current Opinion In Structural Biology 1999, 9: 315-323. PMID: 10361095, DOI: 10.1016/s0959-440x(99)80042-6.Peer-Reviewed Original ResearchConceptsSubstrate recognitionGenetic informationIdeal storage systemBiological catalysisRNA counterpartsInert characterChemical reactionsDNANovel chemicalRate enhancementSubstantial untapped potentialNew playersArtificial DNAHelical structurePolynucleotide chainSurprising varietyDeoxyribozymesRecent studiesStructure formationProteinCatalysisBiocatalysisStorage systemReactionChemicals
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