Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies PDF
Preview Ultrafast Dynamics at the Nanoscale: Biomolecules and Supramolecular Assemblies
Ultrafast Dynamics at the Nanoscale Pan Stanford Series on Renewable Energy — Volume 2 Ultrafast Dynamics at the Nanoscale Biomolecules and Supramolecular Assemblies edited by editors Irene Burghardt Preben Maegaard Anna Krenz Stefan Haacke Wolfgang Palz The Rise of Modern Wind Energy Wind Power for the World November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims Publishedby PanStanfordPublishingPte.Ltd. PenthouseLevel,SuntecTower3 8TemasekBoulevard Singapore038988 Email:[email protected] Web:www.panstanford.com BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary. UltrafastDynamicsattheNanoscale:Biomoleculesand SupramolecularAssemblies Copyright(cid:2)c 2017PanStanfordPublishingPte.Ltd. Allrightsreserved.Thisbook,orpartsthereof,maynotbereproducedinany form or by any means, electronic or mechanical, including photocopying, recordingoranyinformationstorageandretrievalsystemnowknownorto beinvented,withoutwrittenpermissionfromthepublisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not requiredfromthepublisher. ISBN978-981-4745-33-8(Hardcover) ISBN978-981-4745-34-5(eBook) PrintedintheUSA November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims Contents Preface xiii SECTIONI EXPERIMENT 1 ExcitedStatesofSingle-StrandedDNARevealedby FemtosecondTransientAbsorptionSpectroscopy 3 BernKohler 1.1 Introduction 4 1.1.1 Origins 5 1.2 TheTAExperiment 6 1.2.1 TheTASignal 8 1.2.2 DispersivePulseBroadeningandTemporal Walk-off 11 1.3 TransientAbsorptionSignalStrength 14 1.3.1 BleachRecoverySignals 18 1.3.2 DNATAExperiments 19 1.4 Excited-StateDynamicsofSingleDNAStrands 22 1.4.1 Structureof(dA) SingleStrands 25 n 1.4.2 TASignalsfrom(dA) SingleStrands 30 n 1.4.3 EstimatingQuantumYieldsfromBleach Signals 34 1.4.4 ExcitonDynamics 41 1.5 Summary 43 2 UltrafastLight-InducedProcessesinDNAPhotolyaseandIts Substrate-BoundComplex 65 KlausBrettel,MartinByrdin,andMartenH.Vos 2.1 Introduction 65 November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims vi Contents 2.2 EnergyTransfer 69 2.3 Photoactivation 70 2.4 Photorepair 75 3 DynamicsandMechanismsofUltraviolet-DamagedDNA RepairbyPhotolyases 91 ZheyunLiu,LijuanWang,andDongpingZhong 3.1 Introduction 92 3.2 ReactionMechanismofCPDRepairby Photolyase 94 3.3 ReactionMechanismof6-4PPRepairby Photolyase 101 3.4 Electron-TunnelingPathwaysinDNARestoration 106 3.5 ConcludingRemarks 117 4 PhotoactiveYellowProtein:ConvertingLightintoa MetastableStructuralChange 127 MarieLouiseGrootandKlaasJ.Hellingwerf 4.1 Introduction 128 4.2 UltrafastExperiments:Howto...? 131 4.3 TimescaleandMechanismofIsomerization 134 4.3.1 Timescales 134 4.3.2 Isomerization 136 4.3.2.1 Excitedstate 137 4.3.2.2 I state 137 0 4.3.2.3 I state 139 1 4.3.3 Mechanism 141 4.4 RoleofChargesintheProteinCavity 142 4.5 RoleofHydrogenBondstothePhenolRing andtheCarbonylGroupoftheChromophore 143 4.5.1 HydrogenBondstothePhenolRing 143 4.5.2 HydrogenBondstotheCarbonylGroup 146 4.6 RoleofWaterMolecules 147 4.7 EmergingPictureandOpenQuestions 148 4.8 ApplicationsofPYP:GeneralAspects 150 4.9 ApplicationsofPYP:Examples 152 November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims Contents vii 5 EnergyTransferMechanismsinNanobiohybridStructures BasedonQuantumDotsandPhotosensitiveMembrane Proteins 167 SvetlanaV.Sizova,VladimirA.Oleinikov, NicolasBouchonville,MichaelMolinari,PavelSamokhvalov, AlyonaSukhanova,andIgorNabiev 5.1 Introduction 168 5.2 PossibleEnergyTransferMechanismsin NanobiohybridStructuresBasedonPhotosensitive BiomoleculesandQuantumDots:Nonradiativeand RadiativeEnergyTransfer 169 5.3 TheQuantumDot–BacteriorhodopsinNanobiohybrid Structure 176 5.3.1 Bacteriorhodopsin:StructureandFunction 176 5.3.2 EnergyCouplingbetweenQuantumDotsand BacteriorhodopsininAqueousMedia 178 5.3.3 MethodsofFormingHeterostructures ContainingQuantumDot–Bacteriorhodopsin Complexes 182 5.3.4 QuantumDot–BacteriorhodopsinHybridsin DriedFilmsasMediaforSensingandOptical Applications 184 5.3.5 EnhancementoftheBiologicalFunctionsof BacteriorhodopsinbyMeansofCouplingwith QuantumDots 185 5.4 TheQuantumDot–PhotosyntheticReactionCenter NanobiohybridStructure 189 5.4.1 BacterialPhotosyntheticReactionCenters: StructureandProperties 189 5.4.2 EnergyTransferfromQuantumDotsto BacterialReactionCenters 192 5.5 ConclusionsandPerspectives 199 6 UltrafastFunctionalDynamicsinProteins:LocalMolecular ReportersandFemtosecond2DSpectroscopy 207 AndreaCannizzo,Je´re´mieLe´onard,andStefanHaacke 6.1 Introduction 208 November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims viii Contents 6.2 PhotoinducedChargeTranslocationandDynamic DielectricResponse 210 6.2.1 UltrafastResponseofAminoAcids:Exampleof RetinalProteins 210 6.2.2 PhotoinducedChargeTransferandDielectric DynamicsProbedbyTransientTrpAbsorption 214 6.3 LocalFluctuationandEnergyRedistributionin Biomolecules 216 6.3.1 SolvationandLocalFluctuation 216 6.3.2 DissipationandRedistributionofEnergyin Hemoproteins 218 6.4 TrackingDownConcertedMotionsinProteinsand MolecularDevices:AnOutlookonCoherentUV Spectroscopies 226 6.4.1 UVMultidimensionalSpectroscopies 226 6.4.2 PulseShapingandAutomatizedUV2D Spectrographs 233 6.4.3 All-OpticalChemicallySensitiveCoherent Spectroscopies 236 6.5 Conclusions/FinalRemarks 238 SECTIONII THEORY 7 UltrafastExcitonDynamicsinCorrelatedEnvironments 257 PeterNalbach 7.1 PhotosynthesisandEnergyTransfer 257 7.2 QuantumDynamicsinFluctuatingEnvironments 260 7.2.1 System–EnvironmentModels 261 7.2.1.1 QuantumLangevinequation 262 7.2.1.2 Spin-bosonmodel 264 7.2.1.3 Blochequations 266 7.2.2 Methods:RESPETandQUAPI 267 7.2.2.1 Weakcouplingapproximation 267 7.2.2.2 Correlatedenvironmentalfluctuations 269 7.3 ExcitationEnergyTransferDynamics 272 7.3.1 EnergyTransferinDonor–AcceptorSystems 274 7.3.1.1 Multiphonontransitions 275 November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims Contents ix 7.3.1.2 Coherenceduetotemporal correlations 277 7.3.1.3 Influenceofspatialcorrelations 278 7.3.2 ExcitonDynamicsintheFMOComplex 280 7.3.2.1 CoherencetimesintheFMOcomplex 283 7.3.2.2 High-energyvibrations 285 7.4 SummaryandOutlook 286 8 ExcitationEnergyTransferinLight-HarvestingSystems: Theory,Models,andApplication 293 PengfeiHuoandDavidF.Coker 8.1 Introduction 294 8.2 PartialLinearizedDensityMatrixPropagation 301 8.3 ModelHamiltonian 306 8.4 Short-TimeCoherentDynamicsandLong-Time ThermalEquilibriumfromPLDMPropagation 311 8.5 TheEight-SiteFMOComplex:AModelforinvivo InitialExcitation 316 8.6 StrengthofSystem–EnvironmentCouplingOptimizes EnergyTransferDynamicTurnoverBehavior 319 8.7 ExcitationDynamicsinPhycocyanin645 321 8.8 CorrelationsbetweenSiteEnergyFluctuations 324 8.9 ConcludingRemarks 329 9 BridgingtheGapbetweenCoherentandIncoherent ResonanceEnergyTransferDynamicsbyQuantumMaster EquationsinthePolaronPicture 337 SeogjooJang 9.1 Introduction 337 9.2 System–BathHamiltonianandFormallyExact QuantumMasterEquation 340 9.3 QMEintheWeakSystem–BathCouplingLimit 343 9.3.1 Time-NonlocalEquation 343 9.3.2 Time-LocalEquation 345 9.4 QMEinthePolaronPicture 346 9.5 PracticalIssues 354 9.5.1 PhysicalObservablesinthePolaronPicture 354 9.5.2 AssessmentofQuantumCoherence 356 November30,2016 13:32 PSPBook-9inx6in 00-Stefa-Haacke-Prelims x Contents 9.5.3 NumericalImplementation 356 9.6 ModelCalculations 357 9.6.1 Two-StateSystem 357 9.6.2 Three-StateSystem 361 9.7 Applications 364 9.8 SummaryandOutlook 366 10 TheoryofMetalNanoparticle–AffectedOpticaland TransportPropertiesinSupramolecularComplexes 371 YuanZhang,YaroslavZelinskyy,GeroldKyas, andVolkhardMay 10.1 Introduction 371 10.2 CollectiveExcitationsofMetalNanoparticle Electrons 376 10.2.1 DescriptionofDipolePlasmons 376 10.2.2 DescriptionofMultipolePlasmons 378 10.3 MoleculeMetalNanoparticleCoupling 381 10.4 DescriptionofaSphericalMNP 384 10.4.1 CouplingofanSCtoaSphericalMNP 384 10.5 PhotoinducedProcessesinaSupramolecular ComplexCoupledtoaMetalNanoparticle 385 10.5.1 DensityMatrixTheory 388 10.5.2 PhotoinducedExcitationEnergy Transfer 389 10.5.3 LinearAbsorption 393 10.5.4 Emission 395 10.6 ConcludingRemarks 401 11 UltrafastEnergyandChargeTransferinFunctional MolecularNanoscaleAggregates 407 HiroyukiTamura,KeithH.Hughes,RoccoMartinazzo, JanWahl,RobertBinder,andIreneBurghardt 11.1 Introduction 407 11.2 Electron–HoleLatticeHamiltonian 410 11.2.1 Electron–HoleBasis 410 11.2.2 WaveFunctionsandDensityMatrix Representation 412
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