Out-of-Equilibrium (Supra)molecular Systems and Materials

441 Pages·2021·11.426 MB·English

by  Andreas Walther, Nicolas Giuseppone

Out-of-Equilibrium(Supra)molecularSystemsandMaterials
Out-of-Equilibrium (Supra)molecular Systems
and Materials
Edited by
Nicolas Giuseppone
Andreas Walther
Editors AllbookspublishedbyWILEY-VCH
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v
Contents
Foreword xiii
1 Out-of-Equilibrium(Supra)molecularSystemsandMaterials:
AnIntroduction 1
NicolasGiusepponeandAndreasWalther
1.1 GeneralDescriptionoftheField 1
1.1.1 Background,Motivation,andInterdisciplinaryNatureoftheTopic 1
1.1.2 FromEquilibriumSelf-AssemblytoFar-From-Equilibrium
Self-Organization 5
1.1.3 FromResponsiveMaterialstoAdaptiveandInteractiveMaterials
SystemswithLifelikeBehavior 7
1.1.4 AnOutlookonChallengesAhead 9
1.2 DescriptionoftheBookContent 10
Acknowledgments 14
References 14
2 LearningfromEmbryoDevelopmenttoEngineer
Self-organizingMaterials 21
AnisSenoussi,YuliiaVyborna,HélèneBerthoumieux,Jean-ChristopheGalas,
andAndréEstevez-Torres
2.1 TheEmbryoisaMaterialCapableofChemicalandMorphological
Differentiation 22
2.2 PatternFormationbyaReaction–DiffusionTuringInstability 24
2.2.1 ShortMathematicalAnalysisoftheTuringInstabilityinaTwo-species
System 26
2.2.2 TuringPatternsInVivo 27
2.2.3 TuringPatternsInVitro 28
2.2.4 SimplerthanTuring:Reaction–DiffusionWavesInVitro 29
2.2.4.1 MinProteinWaves 29
2.2.4.2 DNA/EnzymeWaves 31
2.3 PatternFormationbyPositionalInformation 32
2.3.1 ModelsofPositionalInformation 32
2.3.1.1 EquilibriumModel:Cooperativity 34
vi Contents
2.3.1.2 Reaction-onlyMechanism:TemporalBistability 34
2.3.1.3 Reaction–DiffusionMechanism:SpatialBistability 35
2.3.2 PositionalInformationInVivo:PatterningoftheDrosophila
blastoderm 35
2.3.3 PositionalInformationInVitro 36
2.3.3.1 DNAStrandDisplacementPatterns 36
2.3.3.2 PENDNA/EnzymePatterns 38
2.3.3.3 Transcription–TranslationPatterns 39
2.4 ForceGenerationandMorphogenesisinReconstitutedCytoskeletal
ActiveGels 40
2.4.1 CytoskeletalFilamentsandMolecularMotors,theBuildingBlocksof
ActiveGels 41
2.4.2 ActiveGelTheoryfora1DSystem 42
2.4.3 ActiveStructuresGeneratedbyCytoskeletalSystemsInVitro 45
2.4.3.1 GlidingFilaments 45
2.4.3.2 AsterFormation 45
2.4.3.3 Contractions 46
2.4.3.4 ActiveFlows 46
2.4.3.5 Corrugations 47
2.4.3.6 VesicleandDropletDeformationandMovement 47
2.5 ConclusionandPerspectives 48
Acknowledgment 49
References 50
3 FromClockstoSynchrony:TheDesignofBioinspired
Self-RegulationinChemicalSystems 61
AnnetteF.Taylor
3.1 Introduction 61
3.2 BioinspiredBehavior:InsightfromModels 62
3.3 FeedbackandClocks 63
3.3.1 ClockReactions 65
3.3.2 AutocatalysisinaClosedReactor 66
3.4 MaintainingSystemsFarfromEquilibrium 69
3.5 KineticSwitches 71
3.6 DesignofOscillators 72
3.7 WavesandPatterns 74
3.7.1 Fronts,Waves,andSpirals 74
3.7.2 StationaryConcentrationPatterns 76
3.8 SynchronizationandCollectiveBehavior 77
3.9 MaterialsSystems 78
3.9.1 CoupledReactionsandMaterials 78
3.9.2 FeedbackinPolymerizationandPrecipitationProcesses 79
3.10 Conclusions 81
References 82
Contents vii
4 DenovoDesignofChemicalReactionNetworksandOscillators
andTheirRelationtoEmergentProperties 91
SergeyN.Semenov
4.1 Introduction 91
4.2 TheRoleofOut-of-EquilibriumConditionsintheEmergenceofCRN
PropertiesandFunctions 94
4.3 TheRoleofStoichiometry,Connectivity,andKineticsforCRNs 96
4.4 DesignGuidelinesandNetworkMotifs 98
4.5 ExamplesofDenovoDesignedCRNsinWell-MixedSolutions 107
4.6 RecentAdvancesintheDesignofFlowSystems 112
4.7 ExamplesofDenovoDesignedReaction–DiffusionNetworks 112
4.8 AutocatalysisasanEmergentPropertyofCRNs 116
4.9 FutureChallengesandDirectionsinDesigningCRNs 119
References 120
5 KineticallyControlledSupramolecularPolymerization 131
KazunoriSugiyasu
5.1 Introduction 131
5.2 ThermodynamicModelsforSupramolecularPolymerization 134
5.3 SupramolecularPolymerizationUnderKineticControl 136
5.4 LivingSupramolecularPolymerization 139
5.5 SeededSupramolecularPolymerizationCoupledwithChemical
Reactions 147
5.6 Equipment-ControlledSupramolecularPolymerizations 151
5.7 Crystallization-DrivenSelf-AssemblyandOtherSystems 153
5.8 Conclusion 157
References 158
6 ChemicallyFueled,TransientSupramolecularPolymers 165
MichelleP.vanderHelm,JanH.vanEsch,andRienkEelkema
6.1 Introduction 165
6.2 NonlinearBehavior:ALessonfromBiology 167
6.3 WalkingUphillintheEnergyLandscape 169
6.4 TheNatureoftheChemicalFuel 171
6.5 ChemicallyFueled,TransientSupramolecularPolymerization
Systems 172
6.6 ConclusionandOutlook 184
References 185
7 DesignofChemicalFuel-DrivenSelf-AssemblyProcesses 191
KrishnenduDas,RuiChen,SushmithaChandrabhas,LucaGabrielli,and
LeonardJ.Prins
7.1 Introduction 191
7.2 ChemicallyFueledSelf-Assembly 191
viii Contents
7.3 TransientSignalGenerationUsingGoldNanoparticles 197
7.4 Self-AssemblyUnderDissipativeConditions 199
7.5 Out-of-EquilibriumSelf-Assembly 201
7.6 TowardChemicalFuel-DrivenSelf-Assembly 205
7.7 Outlook 209
References 210
8 DynamicCombinatorialChemistryOutofEquilibrium 215
KaiLiuandSijbrenOtto
8.1 Introduction 215
8.2 KineticControlinDCC 217
8.2.1 IntroducingIrreversibleReactionsintoDCLs 217
8.2.1.1 IrreversibleReactionsActingonaSpecificLibraryMember 218
8.2.1.2 IrreversibleReactionsActingonMultipleDCLMembers 221
8.2.2 KineticallyTrappedSelf-AssemblyinDCC 223
8.2.3 PhaseChangesinDCC 225
8.2.4 DCCUnderNon-equilibriumConditions 228
8.3 DissipativeDCC 230
8.3.1 ChemicallyFueledDCC 231
8.3.2 Light-DrivenDCC 231
8.4 ConclusionsandOutlook 234
References 236
9 ControllingSelf-AssemblyofNanoparticlesUsingLight 241
TongBian,ZonglinChu,andRafalKlajn
9.1 Introduction 241
9.2 NanoparticleSurface-FunctionalizedwithPhotoswitchable
Molecules 242
9.2.1 Azobenzene-FunctionalizedNanoparticles 242
9.2.2 Spiropyran-FunctionalizedNanoparticles 247
9.3 AssemblingNanoparticlesUsingPhotodimerizationReactions 251
9.4 (De)protonationofNanoparticle-BoundLigandsUsing
Photoacids/Photobases 253
9.5 Light-InducedAdsorptionofPhotoswitchableMolecules 256
9.5.1 PhotoswitchableHost–GuestInclusionComplexesonNanoparticle
Surfaces 256
9.5.2 NonselectiveAdsorptionofPhotoswitchableMolecules 259
9.6 PhaseTransitionsofThermoresponsivePolymersInducedbyPlasmonic
Nanoparticles 261
9.7 Light-InducedChemicalReductionofNanoparticle-Bound
Ligands 263
9.8 IrreversibleSelf-AssemblyofNanoparticles 265
9.9 ExtensiontoMicroparticles 266
9.10 SummaryandOutlook 268
References 269
Contents ix
10 PhotoswitchableComponentstoDriveMolecularSystems
AwayfromGlobalThermodynamicMinimumbyLight 275
MichaelKathanandStefanHecht
10.1 Introduction 275
10.2 Thermodynamicvs.PhotodynamicEquilibria 277
10.3 ManipulatingChemicalReactionsandEquilibriawithLight 281
10.4 FromShiftingEquilibriatoContinuousWorkPoweredbyLight 287
10.5 LighttoControlAssemblyandCreateOrder 296
10.6 Conclusion:FromRemoteControllingtoDrivingProcesses 297
References 299
11 Out-of-EquilibriumThreadedandInterlockedMolecular
Structures 305
MassimoBaroncini,AlbertoCredi,andSerenaSilvi
11.1 Introduction 305
11.1.1 Metastable,KineticallyTrapped,andDissipativeNon-equilibrium
States 307
11.1.2 EnergyInputs 309
11.1.2.1 ChemicalEnergy 309
11.1.2.2 ElectricalEnergy 310
11.1.2.3 LightEnergy 310
11.1.3 MechanicallyInterlockedMoleculesandTheirThreaded
Precursors 311
11.2 Pseudorotaxanes 312
11.2.1 Semirotaxane-BasedMolecularReservoirs 313
11.2.2 SupramolecularPumps 315
11.3 Rotaxanes 319
11.3.1 MolecularRatchets 319
11.3.2 GenerationofNon-equilibriumStatesbyAutonomousEnergy
Consumption 322
11.4 Catenanes 324
11.4.1 MolecularSwitchesandEnergyRatchets 325
11.4.2 AutonomousChemicallyFueledCatenaneRotaryMotors 327
11.5 Conclusions 331
Acknowledgments 332
References 332
12 Light-drivenRotaryMolecularMotorsforOut-of-Equilibrium
Systems 337
AnoukS.Lubbe,CosimaL.G.Stähler,andBenL.Feringa
12.1 Introduction 337
12.2 DesignandSynthesisofLight-drivenRotaryMotors 339
12.3 TuningthePropertiesofMolecularMotors 342
12.4 MolecularMotorsasOut-of-EquilibriumSystems 346
12.5 SingleMoleculesGeneratingWorkontheNanoscale 348
x Contents
12.5.1 MolecularStirring 349
12.5.2 AmplifyingMotorFunction 350
12.6 Immobilization 352
12.6.1 Surface-AttachedMolecularMotors 352
12.6.2 3DNetworks 355
12.7 LiquidCrystalsandPolymerDoping 358
12.7.1 LiquidCrystals 358
12.7.2 PolymerDoping 361
12.8 Self-assembledSystems 364
12.9 Conclusion 368
References 369
13 DesignofActiveNanosystemsIncorporatingBiomolecular
Motors 379
StanislavTsitkovandHenryHess
13.1 Introduction 379
13.2 ActiveNanosystemDesign 381
13.3 BiologicalComponentsofActiveNanosystems 384
13.3.1 Microtubules 385
13.3.2 Kinesin 387
13.3.3 Dynein 388
13.3.4 ActinFilaments 388
13.3.5 Myosin 389
13.4 InteractionsBetweenComponentsofActiveNanosystems 389
13.4.1 FilamentResponsetoExternalLoad 390
13.4.2 Motor–FilamentInteractions 390
13.4.3 Filament–FilamentInteractions 392
13.4.4 Filament–CargoInteractions 392
13.4.5 Motor–SurfaceInteractions 393
13.5 ImplementationsofActiveNanosystems 393
13.5.1 DeliveringCargoinActiveNanosystems 394
13.5.2 SensingUsingActiveNanosystems 396
13.5.2.1 Biosensors 396
13.5.2.2 SurfaceCharacterization 396
13.5.2.3 ForceMeasurements 397
13.5.3 ControllingtheBehaviorofActiveNanosystems 397
13.5.3.1 PassiveControl 397
13.5.3.2 ActiveControl 398
13.5.4 ExtendingtheLifetimeofActiveNanosystems 398
13.5.5 Higher-OrderStructureGeneration 399
13.5.6 SimulatingActiveNanosystemsintheInvertedMotility
Configuration 399
13.5.7 ActiveNanosystemsEmployingtheNativeMotilityConfiguration 401
13.5.7.1 BiologicalImportance 401
13.5.7.2 ActiveNanosystems 401
Contents xi
13.5.8 ActiveNematicGels 403
13.6 Conclusion 403
References 403
Index 423