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

Out-of-Equilibrium (Supra)molecular Systems and Materials A must-have resource that covers everything from out-of-equilibrium chemical systems to active materials Out-of-Equilibrium (Supra)molecular Systems and Materials presents a comprehensive overview of the synthetic approaches that use molecular and supramolecular bonds in various out-of-equilibrium situations. With contributions from noted experts on the topic, the text contains information on the design of dissipative chemical systems that adapt their structures in space and time when fueled by an external source of energy. The contributors also examine molecules, nanoscale objects and materials that can produce mechanical work based on molecular machines. Additionally, the book explores living supramolecular polymers that can be trapped in kinetically stable states, as well as out-of-equilibrium chemical networks and oscillators that are important to understand the emergence of complex behaviors and, in particular, the origin of life. This important book: Offers comprehensive coverage of fields from design of out-of-equilibrium self-assemblies to molecular machines and active materials Presents information on a highly emerging and interdisciplinary topic Includes contributions from internationally renowned scientists Written for chemists, physical chemists, biochemists, material scientists, Out-of-Equilibrium (Supra)molecular Systems and Materials is an indispensable resource written by top scientists in the field.

Table of Contents:
Foreword xiii 1 Out-of-Equilibrium (Supra)molecular Systems and Materials: An Introduction 1 Nicolas Giuseppone and Andreas Walther 1.1 General Description of the Field 1 1.1.1 Background, Motivation, and Interdisciplinary Nature of the Topic 1 1.1.2 From Equilibrium Self-Assembly to Far-From-Equilibrium Self-Organization 5 1.1.3 From Responsive Materials to Adaptive and Interactive Materials Systems with Life like Behavior 7 1.1.4 An Outlook on Challenges Ahead 9 1.2 Description of the Book Content 10 Acknowledgments 14 References 14 2 Learning from Embryo Development to Engineer Self-organizing Materials 21 Anis Senoussi, Yuliia Vyborna, Hélène Berthoumieux, Jean-Christophe Galas, and André Estevez-Torres 2.1 The Embryo is a Material Capable of Chemical and Morphological Differentiation 22 2.2 Pattern Formation by a Reaction–Diffusion Turing Instability 24 2.2.1 Short Mathematical Analysis of the Turing Instability in a Two-species System 26 2.2.2 Turing Patterns In Vivo 27 2.2.3 Turing Patterns In Vitro 28 2.2.4 Simpler than Turing: Reaction–Diffusion Waves In Vitro 29 2.2.4.1 Min Protein Waves 29 2.2.4.2 DNA/Enzyme Waves 31 2.3 Pattern Formation by Positional Information 32 2.3.1 Models of Positional Information 32 2.3.1.1 Equilibrium Model: Cooperativity 34 2.3.1.2 Reaction-only Mechanism: Temporal Bistability 34 2.3.1.3 Reaction–Diffusion Mechanism: Spatial Bistability 35 2.3.2 Positional Information In Vivo: Patterning of the Drosophila blastoderm 35 2.3.3 Positional Information In Vitro 36 2.3.3.1 DNA Strand Displacement Patterns 36 2.3.3.2 PEN DNA/Enzyme Patterns 38 2.3.3.3 Transcription–Translation Patterns 39 2.4 Force Generation and Morphogenesis in Reconstituted Cytoskeletal Active Gels 40 2.4.1 Cytoskeletal Filaments and Molecular Motors, the Building Blocks of Active Gels 41 2.4.2 Active Gel Theory for a 1D System 42 2.4.3 Active Structures Generated by Cytoskeletal Systems In Vitro 45 2.4.3.1 Gliding Filaments 45 2.4.3.2 Aster Formation 45 2.4.3.3 Contractions 46 2.4.3.4 Active Flows 46 2.4.3.5 Corrugations 47 2.4.3.6 Vesicle and Droplet Deformation and Movement 47 2.5 Conclusion and Perspectives 48 Acknowledgment 49 References 50 3 From Clocks to Synchrony: The Design of Bioinspired Self-Regulation in Chemical Systems 61 Annette F. Taylor 3.1 Introduction 61 3.2 Bioinspired Behavior: Insight from Models 62 3.3 Feedback and Clocks 63 3.3.1 Clock Reactions 65 3.3.2 Autocatalysis in a Closed Reactor 66 3.4 Maintaining Systems Far from Equilibrium 69 3.5 Kinetic Switches 71 3.6 Design of Oscillators 72 3.7 Waves and Patterns 74 3.7.1 Fronts, Waves, and Spirals 74 3.7.2 Stationary Concentration Patterns 76 3.8 Synchronization and Collective Behavior 77 3.9 Materials Systems 78 3.9.1 Coupled Reactions and Materials 78 3.9.2 Feedback in Polymerization and Precipitation Processes 79 3.10 Conclusions 81 References 82 4 De novo Design of Chemical Reaction Networks and Oscillators and Their Relation to Emergent Properties 91 Sergey N. Semenov 4.1 Introduction 91 4.2 The Role of Out-of-Equilibrium Conditions in the Emergence of CRN Properties and Functions 94 4.3 The Role of Stoichiometry, Connectivity, and Kinetics for CRNs 96 4.4 Design Guidelines and Network Motifs 98 4.5 Examples of De novo Designed CRNs in Well-Mixed Solutions 107 4.6 Recent Advances in the Design of Flow Systems 112 4.7 Examples of De novo Designed Reaction–Diffusion Networks 112 4.8 Autocatalysis as an Emergent Property of CRNs 116 4.9 Future Challenges and Directions in Designing CRNs 119 References 120 5 Kinetically Controlled Supramolecular Polymerization 131 Kazunori Sugiyasu 5.1 Introduction 131 5.2 Thermodynamic Models for Supramolecular Polymerization 134 5.3 Supramolecular Polymerization Under Kinetic Control 136 5.4 Living Supramolecular Polymerization 139 5.5 Seeded Supramolecular Polymerization Coupled with Chemical Reactions 147 5.6 Equipment-Controlled Supramolecular Polymerizations 151 5.7 Crystallization-Driven Self-Assembly and Other Systems 153 5.8 Conclusion 157 References 158 6 Chemically Fueled, Transient Supramolecular Polymers 165 Michelle P. van der Helm, Jan H. van Esch, and Rienk Eelkema 6.1 Introduction 165 6.2 Nonlinear Behavior: A Lesson from Biology 167 6.3 Walking Uphill in the Energy Landscape 169 6.4 The Nature of the Chemical Fuel 171 6.5 Chemically Fueled, Transient Supramolecular Polymerization Systems 172 6.6 Conclusion and Outlook 184 References 185 7 Design of Chemical Fuel-Driven Self-Assembly Processes 191 Krishnendu Das, Rui Chen, Sushmitha Chandrabhas, Luca Gabrielli, and Leonard J. Prins 7.1 Introduction 191 7.2 Chemically Fueled Self-Assembly 1917.3 Transient Signal Generation Using Gold Nanoparticles 197 7.4 Self-Assembly Under Dissipative Conditions 199 7.5 Out-of-Equilibrium Self-Assembly 201 7.6 Toward Chemical Fuel-Driven Self-Assembly 205 7.7 Outlook 209 References 210 8 Dynamic Combinatorial Chemistry Out of Equilibrium 215 Kai Liu and Sijbren Otto 8.1 Introduction 215 8.2 Kinetic Control in DCC 217 8.2.1 Introducing Irreversible Reactions into DCLs 217 8.2.1.1 Irreversible Reactions Acting on a Specific Library Member 218 8.2.1.2 Irreversible Reactions Acting on Multiple DCL Members 221 8.2.2 Kinetically Trapped Self-Assembly in DCC 223 8.2.3 Phase Changes in DCC 225 8.2.4 DCC Under Non-equilibrium Conditions 228 8.3 Dissipative DCC 230 8.3.1 Chemically Fueled DCC 231 8.3.2 Light-Driven DCC 231 8.4 Conclusions and Outlook 234 References 236 9 Controlling Self-Assembly of Nanoparticles Using Light 241 Tong Bian, Zonglin Chu, and Rafal Klajn 9.1 Introduction 241 9.2 Nanoparticle Surface-Functionalized with Photoswitchable Molecules 242 9.2.1 Azobenzene-Functionalized Nanoparticles 242 9.2.2 Spiropyran-Functionalized Nanoparticles 247 9.3 Assembling Nanoparticles Using Photodimerization Reactions 251 9.4 (De)protonation of Nanoparticle-Bound Ligands Using Photoacids/Photobases 253 9.5 Light-Induced Adsorption of Photoswitchable Molecules 256 9.5.1 Photoswitchable Host–Guest Inclusion Complexes on Nanoparticle Surfaces 256 9.5.2 Nonselective Adsorption of Photoswitchable Molecules 259 9.6 Phase Transitions of Thermoresponsive Polymers Induced by Plasmonic Nanoparticles 261 9.7 Light-Induced Chemical Reduction of Nanoparticle-Bound Ligands 263 9.8 Irreversible Self-Assembly of Nanoparticles 265 9.9 Extension to Microparticles 266 9.10 Summary and Outlook 268 References 269 10 Photoswitchable Components to Drive Molecular Systems Away from Global Thermodynamic Minimum by Light 275 Michael Kathan and Stefan Hecht 10.1 Introduction 275 10.2 Thermodynamic vs. Photodynamic Equilibria 277 10.3 Manipulating Chemical Reactions and Equilibria with Light 281 10.4 From Shifting Equilibria to Continuous Work Powered by Light 287 10.5 Light to Control Assembly and Create Order 296 10.6 Conclusion: From Remote Controlling to Driving Processes 297 References 299 11 Out-of-Equilibrium Threaded and Interlocked Molecular Structures 305 Massimo Baroncini, Alberto Credi, and Serena Silvi 11.1 Introduction 305 11.1.1 Metastable, Kinetically Trapped, and Dissipative Non-equilibrium States 307 11.1.2 Energy Inputs 309 11.1.2.1 Chemical Energy 309 11.1.2.2 Electrical Energy 310 11.1.2.3 Light Energy 310 11.1.3 Mechanically Interlocked Molecules and Their Threaded Precursors 311 11.2 Pseudorotaxanes 312 11.2.1 Semirotaxane-Based Molecular Reservoirs 313 11.2.2 Supramolecular Pumps 315 11.3 Rotaxanes 319 11.3.1 Molecular Ratchets 319 11.3.2 Generation of Non-equilibrium States by Autonomous Energy Consumption 322 11.4 Catenanes 324 11.4.1 Molecular Switches and Energy Ratchets 325 11.4.2 Autonomous Chemically Fueled Catenane Rotary Motors 327 11.5 Conclusions 331 Acknowledgments 332 References 332 12 Light-driven Rotary Molecular Motors for Out-of-Equilibrium Systems 337 Anouk S. Lubbe, Cosima L.G. Stähler, and Ben L. Feringa 12.1 Introduction 337 12.2 Design and Synthesis of Light-driven Rotary Motors 339 12.3 Tuning the Properties of Molecular Motors 342 12.4 Molecular Motors as Out-of-Equilibrium Systems 346 12.5 Single Molecules Generating Work on the Nanoscale 348 12.5.1 Molecular Stirring 349 12.5.2 Amplifying Motor Function 350 12.6 Immobilization 352 12.6.1 Surface-Attached Molecular Motors 352 12.6.2 3D Networks 355 12.7 Liquid Crystals and Polymer Doping 358 12.7.1 Liquid Crystals 358 12.7.2 Polymer Doping 361 12.8 Self-assembled Systems 364 12.9 Conclusion 368 References 369 13 Design of Active Nanosystems Incorporating Biomolecular Motors 379 Stanislav Tsitkov and Henry Hess 13.1 Introduction 379 13.2 Active Nanosystem Design 381 13.3 Biological Components of Active Nanosystems 384 13.3.1 Microtubules 385 13.3.2 Kinesin 387 13.3.3 Dynein 388 13.3.4 Actin Filaments 388 13.3.5 Myosin 389 13.4 Interactions Between Components of Active Nanosystems 389 13.4.1 Filament Response to External Load 390 13.4.2 Motor–Filament Interactions 390 13.4.3 Filament–Filament Interactions 392 13.4.4 Filament–Cargo Interactions 392 13.4.5 Motor–Surface Interactions 393 13.5 Implementations of Active Nanosystems 393 13.5.1 Delivering Cargo in Active Nanosystems 394 13.5.2 Sensing Using Active Nanosystems 396 13.5.2.1 Biosensors 396 13.5.2.2 Surface Characterization 396 13.5.2.3 Force Measurements 397 13.5.3 Controlling the Behavior of Active Nanosystems 397 13.5.3.1 Passive Control 397 13.5.3.2 Active Control 398 13.5.4 Extending the Lifetime of Active Nanosystems 398 13.5.5 Higher-Order Structure Generation 399 13.5.6 Simulating Active Nanosystems in the Inverted Motility Configuration 399 13.5.7 Active Nanosystems Employing the Native Motility Configuration 401 13.5.7.1 Biological Importance 401 13.5.7.2 Active Nanosystems 401 13.5.8 Active Nematic Gels 403 13.6 Conclusion 403 References 403 Index 423

About the Author :
Nicolas Giuseppone is Distinguished Professor of Chemistry (PREX2) at the University of Strasbourg, France. Andreas Walther is a Gutenberg Research Professor in the Department of Chemistry at the Johannes Gutenberg University of Mainz, Germany.