Molecular Switches E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1401

Veröffentlichungsjahr: 2011

Beschreibung

The long-awaited second edition of the successful book covering molecular switches now in two volumes!

Providing principles and applications this book brings you everything you need to know about molecular switches - a hot topic in the nanoworld. The major classes of molecular switches including catenanes, rotaxanes, azobenzenes together with polymer and biomolecular switching systems and DNA based switches are covered. Chemists and material scientists interested in one of the most innovative areas of their science will benefit greatly from reading this book.

"This book will appeal most to organic chemists, because of the way new structures are introduced through their synthesis, but it will also provide a useful introduction for other scientists, provided they are conversant with molecular structures." (Organic and Biomolecular Chemistry)

"... a comprehensive and up-to-date insight ..." (Chemistry & Industry)

Leseprobe

Table of Contents

Related Titles

Title Page

Copyright

Preface

List of Contributors

Abbreviations

Part I: Molecular Switching

Chapter 1: Multifunctional Diarylethenes

1.1 Introduction

1.2 Electrochemical Ring-Closing and Ring-Opening of DTEs

1.3 Using Dithienylethenes to Modulate How Chemicals React or Interact with Others

1.4 Gated Photochromism

1.5 Reactivity-Gated Photochromism Using the Functional Group Effect

1.6 Conclusion

References

Chapter 2: Photoswitchable Molecular Systems Based on Spiropyrans and Spirooxazines

2.1 Introduction

2.2 Mechanism of the Photochromic Reaction

2.3 Switching of Physical Properties and Biological Activities via Photochromic Rearrangements of Functionalized Spiropyrans and Spirooxazines

2.4 Spiropyrans and Spirooxazines as Photodynamic Sensors for Metal Ions

2.5 Modulation of the Intramolecular Energy-Transfer Processes in SP/SPO-Containing Transition-Metal Complexes

2.6 Spiropyran-Containing Photoresponsive Polymers

2.7 Spiropyran/Spirooxazine-Containing Biphotochromic Systems

2.8 Concluding Remarks

Acknowledgement

References

Chapter 3: Fulgides and Related Compounds

3.1 IntroductionFulgides

3.2 Reviews Dealing with Fulgides

3.3 Introduction of New Fulgides towards Molecular Switches

3.4 Photophysics of Molecular Switches

3.5 Towards Optical Recording

3.6 Understanding of Molecular Structures from Calculations

3.7 Development of Photochromic Switches Closely Related to Fulgides

3.8 Perspectives of Research with Fulgides

References

Chapter 4: Transition Metal-Complexed Catenanes and Rotaxanes as Molecular Machine Prototypes

4.1 Introduction

4.2 Copper-Complexed [2]Catenanes in Motion: the Archetypes

4.3 Fighting the Kinetic Inertness of the First Copper-Based Machines; Fast-Moving Pirouetting Rotaxanes

4.4 Molecular Motions Driven by Chemical ReactionsUse of a Chemical Reaction to Induce the Contraction/Stretching Process of a Muscle-Like Rotaxane Dimer

4.5 Electrochemically Controlled Intramolecular Motion within a Heterodinuclear Bismacrocycle Transition-Metal Complex

4.6 Ru(II)-Complexes as Light-Driven Molecular Machine Prototypes

4.7 Conclusion and Prospective

References

Chapter 5: Chiroptical Molecular Switches

5.1 Introduction

5.2 Molecular Switching

5.3 Chiral Fulgides

5.4 Light-Driven Molecular Rotary Motors

5.5 Liquid Crystals

5.6 Gels

5.7 Conclusions and Perspectives

References

Chapter 6: Multistate/Multifunctional Molecular-Level Systems: Photochromic Flavylium Compounds

6.1 Introduction

6.2 Energy Stimulation

6.3 Photochromic Systems

6.4 Bistable and Multistable Systems

6.5 Nature of the Species Involved in the Chemistry of Flavylium Compounds

6.6 Thermal Reactions of the 4′-Methoxyflavylium Ion

6.7 Photochemical Behaviour of the 4′-Methoxyflavylium Ion

6.8 Flavylium Ions with OH Substituents

6.9 Flavylium Ions with Other Substituents

6.10 Energy-Level Diagrams

6.11 Chemical Process Networks

6.12 Conclusions

Acknowledgements

References

Chapter 7: Nucleic-Acid-Based Switches

7.1 Molecular Switches Made from DNA and RNA

7.2 Switchable Ribozymes

7.3 Regulatory RNA Molecules

7.4 Sensor Applications

7.5 DNA Computing

7.6 DNA Machines

7.7 Switchable Molecular Networks and Materials

7.8 Conclusion and Outlook

Acknowledgements

References

Part II: Switching in Containers, Polymers and Channels

Chapter 8: Switching Processes in Cavitands, Containers and Capsules

8.1 Introduction

8.2 Switchable Covalently Constructed Cavitands and Container Molecules

8.3 H-Bonded Molecular Capsules

8.4 Assembly and Disassembly of Metal-Ion-Coordination Cages

8.5 Conclusions

Acknowledgements

References

Chapter 9: Cyclodextrin-Based Switches

9.1 Introduction

9.2 In and Out Switching

9.3 Back and Forth Switching

9.4 Displacement Switching

9.5 Coordination Switching

9.6 Rearrangement Switching

9.7 Conclusion and Perspective

Acknowledgement

References

Chapter 10: Photoswitchable Polypeptides

10.1 Photoresponsive Polypeptides

10.2 Light-Induced Conformational Transitions

10.3 Photostimulated Aggregation–Disaggregation Effects

10.4 Photoeffects in Molecular and Thin Films

10.5 Photoresponsive Polypeptide Membranes

10.6 Summary and Recent Developments

10.7 Towards More Complex Biorelated Photoswitchable Polypetides

References

Chapter 11: Ion Translocation within Multisite Receptors

11.1 Introduction

11.2 Metal-Ion Translocation: Changing Metal's Oxidation State

11.3 Metal-Ion Translocation: Changing through a pH Variation the Coordinating Properties of One Receptor's Compartment

11.4 The Simultaneous Translocation of Two Metal Ions

11.5 Redox-Driven Anion Translocation

11.6 Anion Swapping in a Heteroditopic Receptor, Driven by a Concentration Gradient

11.7 Conclusions and Perspectives: Further Types of Molecular Machines?

References

Chapter 12: Optically Induced Processes in Azopolymers

12.1 Introduction

12.2 Azoaromatic Compounds: Synthesis, Functionality and Film Fabrication

12.3 Applications

12.4 Final Remarks and Prospects

Acknowledgements

References

Chapter 13: Photoresponsive Polymers

13.1 Introduction

13.2 Photo-Orientation by Photoisomerization

13.3 Photoisomerization and Photo-Orientation of Azo Dye in Films of Polymer: Molecular Interaction, Free Volume and Polymer Structural Effects

13.4 Photoisomerization Effects in Organic Nonlinear Optics: Photoassisted Poling and Depoling and Polarizability Switching

13.5 Conclusion

Acknowledgements

13.7 Appendix A Quantum-Yield Determination

13.8 Appendix B Derivation of Equations for Determination of Anisotropy

13.9 Appendix C From Molecular to Macroscopic Nonlinear Optical Properties

References

Chapter 14: Responsive Molecular Gels

14.1 Introduction

14.2 Chemoresponsive Gels

14.3 Physicoresponsive Gels

14.4 Conclusions

References

Chapter 15: Switchable Proteins and Channels

15.1 Introduction

15.2 Photoswitch Characteristics

15.3 Photoswitch Incorporation

15.4 Designing Photoswitchable Proteins

15.5 Photoswitchable Enzymes

15.6 Photoswitchable Ion Channels

15.7 Future Challenges

15.8 Concluding Remarks

References

Part III: Molecular Switching in Logic Systems and Electronics

Chapter 16: Reading and Powering Molecular Machines by Light

16.1 Introduction

16.2 Basic Concepts

16.3 Interlocked Molecular Species as Nanoscale Machines

16.4 Molecular Machines Monitored by Light

16.5 Molecular Machines Powered and Monitored by Light

16.6 Conclusion and Perspectives

Acknowledgements

References

Chapter 17: Photoinduced Motion Associated with Monolayers

17.1 Introduction

17.2 Background to Photoinduced Motion of Monolayers

17.3 Photoswitchable Flat Monolayers

17.4 Photoswitchable Surfaces with Controlled Roughness

17.5 Light-Guided Liquid Motion

17.6 Photoinduced Motion on Water Surface

17.7 Photoinduced Morphology and Switching at Nanometre Levels

17.8 Photoinduced Morphologies in Two-Component Systems

17.9 2D Block-Copolymer Systems

17.10 Summary

References

Chapter 18: Molecular Logic Systems

18.1 Introduction

18.2 YES Logic

18.3 NOT Logic

18.4 AND Logic

18.5 OR Logic

18.6 NAND Logic

18.7 INH Logic

18.8 NOR Logic

18.9 XOR Logic

18.10 Three-Input AND Logic

18.11 Three-Input NOR Logic

18.12 EnNOR Logic

18.13 Arithmetic and Gaming

18.14 An Application of Molecular Logic: Molecular Computational Identification (MCID)

18.15 Conclusion

Acknowledgements

References

Chapter 19: Electron- and Energy-Transfer Mechanisms for Fluorescence Modulation with Photochromic Switches

19.1 Fluorescence

19.2 Electron Transfer

19.3 Energy Transfer

19.4 Photochromism

19.5 Fluorescence Modulation in Fluorophore–Photochrome Conjugates

19.6 Fluorescence Modulation in Nanostructured Assemblies

19.7 Fluorescence Modulation in Multilayer Constructs

19.8 Conclusions

References

Chapter 20: Conductance Properties of Switchable Molecules

20.1 Introduction

20.2 Intrinsic Switches and Extrinsic Switching

20.3 Quantum Charge Transport through Molecular Junctions

20.4 Experimental Methods

20.5 Transport Studies on Switchable Molecules

20.6 Conclusions and Outlook

Acknowledgements

References

Index

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The Editors

Prof. Dr. Ben L. Feringa

Stratingh Institute for Chemistry

& Zernike Institute for

Advanced Materials

Faculty of Mathematics and

Natural Sciences

University of Groningen

Nijenborgh 4

9747 AG Groningen

The Netherlands

Dr. Wesley R. Browne

Stratingh Institute for Chemistry

& Zernike Institute for

Advanced Materials

Faculty of Mathematics and

Natural Sciences

University of Groningen

Nijenborgh 4

9747 AG Groningen

The Netherlands

Cover

The graphic material used in the cover illustration was kindly provided by the editors Ben L. Feringa and Wesley R. Browne (University of Groningen)

All books published by Wiley-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication Data

A catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche Nationalbibliothek

The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at <http://dnb.d-nb.de>.

© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

ISBN: 978-3-527-31365-5

ePDF: 978-3-527-63442-2

ePub: 978-3-527-63441-5

mobi: 978-3-527-63443-9

oBook: 978-3-527-63440-8

Preface

Nature has been particularly gracious to the molecular designers at the nanoscale by offering a myriad of examples of the most ingenious and complex dynamic systems. But at the same time it is fascinating to realise the elegance, effectiveness and apparent simplicity of several of its basic molecular concepts. When you read this sentence, the large collection of molecular switches that make this happen operate as a result of the simple photochemical cistrans isomerisation of a tiny olefin unit in the protein rhodopsin in your eye. The process of vision is arguably the most fantastic among nature's numerous systems that can be triggered by a switching process at the molecular level.

This work is about the design, functioning and application of molecular switches, in particular illustrating progress made over the past decade. Research on molecular switches covers a wide range of frontiers in science from molecular computing to sensors, displays and smart materials and from drug delivery to control of biomolecular processes. In the ongoing quest for nano-devices and molecular machines, the design of molecular switching elements integrated with a variety of functions is a formidable challenge. Research on molecular switches has been greatly stimulated by prospects of memory elements as small as the single molecule and their potential for information technology. It is particularly rewarding to see how this field has been flourishing with the first electronic devices based on molecular switching elements now demonstrated. On the other hand these developments also make clear how long and windy a road it can be from molecular function to functional device. But as the saying goes, it is a long road that has no turns.

The present two-volume work builds on the 2001 book Molecular Switches but is not simply a revised edition. Several chapters have been updated covering both basic principles and recent developments for completeness however for further background and those topics not fully covered, the reader is referred to the previous edition. As the field has seen spectacular development in the past years it is evident that we have tried to cover also many recent topics related to molecular switches in this second edition.

The chapters cover the structural diversity of molecular switches including discussion on various switching principles and methodology to the study their dynamic behaviour. Particular emphasis is on the dynamic control of function and materials properties. Furthermore, the use of molecular switches as trigger elements to control assembly, organization and function at different hierarchical levels and in macromolecular, mesoscopic and supramolecular systems is illustrated.

In the first section the focus is on different types of molecular switches including multilevel switching, nucleic acid based switches and molecular machines. The second section covers switchable containers, gels and polymers while chapters on switchable receptors, proteins and channels illustrate the potential in biomolecular sciences. In the third section, progress and prospects for molecular switching in logic systems and electronics and to control motion is discussed. The book ends with a chapter discussing the state of affairs with respect to photoresponsive molecular wires and devices, arguably one of the most rapidly developing areas of molecular switching in recent years.

The combination of topics demonstrates the multidisciplinary nature of research on molecular switches. Several contributions in this work also illustrate two other key aspects of research on molecular switches; first, it brings a responsive element to molecules and systems that allows triggering and control on command and second, the switching element is frequently part of a more complex molecular system with several components acting in concert. The lessons learned from the approaches described in these volumes hopefully will be also beneficial to numerous young researchers entering into molecular nanoscience, systems chemistry and synthetic biology. It was not our intention to be comprehensive and unfortunately not all relevant topics could be covered. However, we feel that this handbook gives a good perspective on the potential of the emerging field of molecular switches.

This second edition was only possible by the great efforts of the numerous contributors. We are particularly grateful to all authors for their excellent chapters. Join us on a fascinating journey through the dynamic scientific landscape opened by the introduction of molecular switches.

We hope your interest is switched on and that this book serves as a source of inspiration.

Centre for Systems Chemistry,

Wesley R. Browne,

University of Groningen

Ben L. Feringa

Groningen, May 2011

List of Contributors

Valeria Amendola

Università di Pavia

Dipartimento di Chimica

Viale Taramelli, 24

27100 Pavia

Italy

Vladimir A. Azov

Universität Bremen

Institut für Organische Chemie

Leobener Str. NW 2C

28334 Bremen

Germany

Débora T. Balogh

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

Vincenzo Balzani

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

Vincenzo Balzani

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

Matthew Banghart

Genentech, Inc.

1 DNA WaySouth San Francisco

CA 94080

USA

Tiziana Benelli

University of Miami

Department of Chemistry

Center for Supramolecular Science

1301 Memorial Drive

Coral Gables, FL 33146-0431

USA

Leonardo De Boni

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

Marco Bonizzoni

University of Alabama

Department of Chemistry

Tuscaloosa

AL 35487

USA

Neil R. Branda

Simon Fraser University

4D LABS

8888 University Drive

Burnaby BC, V5A 1S6

Canada

Simona Bronco

Università di Pisa

PolyLab-CNR

c/o Dipartimento di Chimica e Chimica Industriale

Via Risorgimento 35

56126 Pisa

Italy

Wesley R. Browne

University of Groningen

Stratingh Institute for Chemistry

& Zernike Institute for

Advanced Materials

Faculty of Mathematics and Natural Sciences

Nijenborgh 4

9747 AG Groningen

The Netherlands

Francesco Ciardelli

Università di Pisa

Dipartimento di Chimica e Chimica Industriale

Via Risorgimento 35

56126 Pisa

Italy

Alberto Credi

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

Françcois Diederich

Laboratorium für

Organische Chemie

ETH Zürich

Hönggerberg HCI

8093 Zürich

Switzerland

Jan van Esch

Delft University of Technology

Department of Chemical Engineering

Self Assembling Systems

Julianalaan 136

2628 BL Delft

The Netherlands

Luigi Fabbrizzi

Università di Pavia

Dipartimento di Chimica

Viale Taramelli, 24

27100 Pavia

Italy

Ben L. Feringa

University of Groningen

Stratingh Institute for Chemistry

& Zernike Institute for

Advanced Materials

Faculty of Mathematics and Natural Sciences

Nijenborgh 4

9747 AG Groningen

The Netherlands

Julien Frey

Swiss Federal Institute of Technology (EPFL)

Laboratory of Photonics & Interfaces

1015 Lausanne

Switzerland

Eike Friedrichs

Technische Universität München

Biomolecular Systems and Bionanotechnology

Physics Department and ZNN/WSI

Am Coulombwall 4a

85748 Garching

Germany

Raquel Gomes

Universidade Nova de Lisboa

REQUIMTE

Departamento de Química

Faculdade de Ciências e Tecnologia

2829-516, Monte de Caparica

Portugal

and

University of Gent

Department of Inorganic and Physical Chemistry

Physics and Chemistry of Nanostructures Group

Krijgslaan 281 (S3)

9000 Gent

Belgium

Tsuyoshi Gushiken

Yokohama National University

Graduate School of Engineering

Department of Advanced Materials Chemistry

Tokiwadai

Hodogaya

Yokohama 240-8501

Japan

Kunihiro Ichimura

Tokyo Institute of Technology

4259 Nagatsuta

Yokohama 226-8503

Japan

Jaap de Jong

University of Groningen

Stratingh Institute for Chemistry

Faculty of Mathematics and Natural Sciences

Nijenborgh 4

9497 AG Groningen

The Netherlands

Wolfgang Knoll

AIT Austrian Institute of Technology

Vienna

Austria

Vincent Lemieux

Simon Fraser University

4D LABS

8888 University Drive

Burnaby BC, V5A 1S6

Canada

Peter Liljeroth

University of Utrecht

Condensed Matter and Interfaces

Debye Institute for Nanomaterials Science

3508 TA Utrecht

The Netherlands

and

Aalto University School of Sciences

Department of Applied Physics

P.O. Box 15100

00076 Aalto

Finland

Mauro Maestri

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

Cleber R. Mendonça

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

Vladimir I. Minkin

Southern Federal University

Institute of Physical and Organic Chemistry

194/2 Stachka Ave

344090 Rostov on Don

Russian Federation

Sense Jan van der Molen

Leiden University

Niels Bohrweg 2

Kamerlingh Onnes Laboratorium

2333 CA Leiden

The Netherlands

Osvaldo N. Oliveira Jr.

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

A. Jorge Parola

Universidade Nova de Lisboa

REQUIMTE

Departamento de Química

Faculdade de Ciências e Tecnologia

2829-516 Monte de Caparica

Portugal

Osvaldo Pieroni

Università di Pisa

Dipartimento di Chimica e Chimica Industriale

Via Risorgimento 35

56126 Pisa

Italy

Fernando Pina

Universidade Nova de Lisboa

REQUIMTE

Departamento de Química

Faculdade de Ciências e Tecnologia

2829-516 Monte de Caparica

Portugal

Andrea Pucci

Università di Pisa

Dipartimento di Chimica e Chimica Industriale

Via Risorgimento 35

56126 Pisa

Italy

and

CNR NANO

Instituto Nanoscienze-CNR

piazza San Silverstro 12

56127 Pisa

Italy

Françisco M. Raymo

University of Miami

Department of Chemistry

Center for Supramolecular Science

1301 Memorial Drive

Coral Gables, FL 33146-0431

USA

David S. dos Santos Jr.

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

Zouheir Sekkat

Alakhawayn University in Ifrane

School of Science and Engineering

Hassan II Avenue

Ifrane 53000

Morocco

and

Osaka University

Department of Applied Physics

Yamada-oka 2-1, Suita

Osaka 565-0871

Japan

Jean Pierre Sauvage

Université de Strasbourg

CNRS UMR 7177

Institut de Chimie

Laboratoire de Chimie

Organo Minérale

4, rue Blaise Pascal

67070 Strasbourg Cedex

France

Takahiro Seki

Nagoya University

Graduate School of Engineering

Department of Molecular Design and Engineering

Furo-cho, Chikusa

Nagoya 464-8603

Japan

Monica Semeraro

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

A. Prasanna de Silva

Queen's University

School of Chemistry and Chemical Engineering

BT9 5AG Belfast

Northern Ireland

Friedrich C. Simmel

Technische Universität München

Biomolecular Systems and Bionanotechnology

Physics Department and ZNN/WSI

Am Coulombwall 4a

85748 Garching

Germany

Christian Tock

Luxinnovation

7, rue Alcide de Gasperi

1615 Luxembourg

Luxembourg

He Tian

East China University of

Science and Technology

Key Lab for Advanced Materials and Institute of Fine Chemicals

130 Meilong Road

Shanghai 20037

P.R. China

Massimiliano Tomasulo

University of Miami

Department of Chemistry

Center for Supramolecular Science

1301 Memorial Drive

Coral Gables, FL 33146-0431

USA

Dirk Trauner

University of Munich

Department of Chemistry and

Center of Integrated Protein Science

Butenandtstr. 5-13, Haus F

81377 München

Germany

Takashi Ubukata

Yokohama National University

Graduate School of Engineering

Department of Advanced Materials Chemistry

Tokiwadai

Hodogaya

Yokohama 240-8501

Japan

Thomas P. Vance

Queen's University

School of Chemistry and Chemical Engineering

BT9 5AG Belfast

Northern Ireland

Margherita Venturi

Università di Bologna

Dipartimento di Chimica

‘G. Ciamician’

Via Selmi 2

40126 Bologna

Italy

Matthew Volgraf

Department of Neurobiology

Harvard Medical School

Boston, MA 02115

USA

Qiao-Chun Wang

East China University of

Science and Technology

Key Lab for Advanced Materials and Institute of Fine Chemicals

130 Meilong Road

Shanghai 20037

P.R. China

Boontana Wannalerse

Queen's University

School of Chemistry and Chemical Engineering

BT9 5AG Belfast

Northern Ireland

and

Faculty of Science

Chulalongkorn University

Department of Chemistry

Bangkok 10330

Thailand

C. Chad Warford

Simon Fraser University

4D LABS

8888 University Drive

Burnaby BC, V5A 1S6

Canada

Matthew E.S. West

Queen's University

School of Chemistry and Chemical Engineering

BT9 5AG Belfast

Northern Ireland

Yasushi Yokoyama

Yokohama National University

Graduate School of Engineering

Department of Advanced Materials Chemistry

Tokiwadai

Hodogaya

Yokohama 240-8501

Japan

Valtencir Zucolotto

Universidade de São Paulo

Instituto de Física de São Carlos

CP 369

13560-970 São Carlos, São Paulo

Brazil

Abbreviations

α-HL α-Hemolysin

ABTS 2,2′-azino-bis3-ethylbenzthiazoline-6-sulfonic acid

ADA 1-adamantaneacetate

AFM atomic force microscopy

ANI 4-amino-1,8-naphthalimide

ANS 8-anilinonaphthalene-1-sulfonic acid

ATR attenuated total reflection

ATS 3-aminopropyltriethoxysilane

Az azobenzene

AzOH 4-(phenylazo)phenetyl alcohol

Azo-PUR azo-polyurethanes

BAM Brewster-angle microscopy

BCAII bovine carbonic anhydrase II

BN binaphthyl

BODIPY boron dipyromethene; 4,4-difluoro-4-bora-3a,4a-diaza-sindacene

BPB bromophenol blue

BPDN bipyridyl-dinitro oligophenylene-ethynylene dithiol

BSA Bovine serum albumin

CAP catabolite activator protein

cCMP cytidine 2′, 3′-cyclic monophosphate

CD circular dichroism

CN coordination number

CNDO/S complete neglect of differential overlap/spectroscopy

ConA concanavalin A

CPIMA center on polymer interfaces and macromolecular assemblies

CPK Corey, Pauling, Koltun

CRA calix[4]resorcinarenes

crRNA cis-repression RNA

CSTR continuous-stirred-tank reactor

CT charge transfer

CTAB cetyltrimethylammonium bromide

CV cyclic voltammetry

CyD cyclodextrins

DAC dodecyl ammonium chloride

DCE 1,2-dichloroethane

DE diarylethene

DFT density-functional theory

diMe-tpy 5, 5′′-dimethyl-2,2′:6′,2′′-terpyridine

DMF N,N-dimethylformamide

DNA deoxyribonucleic acid

DNP 1,5-dioxynaphthalene

DON dioxynaphthalene

dpp 2,9-diphenyl-1,10-phenanthroline

dppp 1,2-bis(diphenylphosphino)propane

DR1 disperse red one

DR19 disperse 19

DTE dithienylethene

dto dithiooxalate

ee enantiomeric excess

EET electronic energy transfer

EFIPE electric-field-induced Pockels effect

EFISH electric-field-induced second harmonic

en ethylenediamine

EO electro-optical

EPL expressed protein ligation

ES-MS electrospray mass spectroscopy

eT electron-transfer

FCS fluorescence correlation spectroscopy

FMN flavin mononucleotide

FRET fluorescence resonance energy transfer

FTIR Fourier transform infrared

FU functional unit

GDH glucose dehydrogenase

GFP green fluorescent protein

GIXR grazing-angle X-ray reflectivity

hCAI human carbonic anhydrase I

HCR hybridization chain reaction

HEK human embryonic kidney

HFP hexafluoro-2-propanol

HOMO highest occupied molecular orbital

HRP horseradish peroxidase

HTP helical twisting power

ICD induced circular dichroism

ICT internal charge transfer

IETS inelastic electron tunnelling spectroscopy

iGluR ionotropic glutamate receptor

imH imidazole

IPS 3-isocyanatopropyltriethoxysilane

IR infrared

LB Langmuir–Blodgett

LBD ligand-binding domain

LBK Langmuir–Blodgett–Kuhn

LbL layer-by-layer

LC liquid-crystal

LD-LISC ligand-driven light-induced spin change

LDOS local density of states

LF ligand field

LMOG low molecular mass gelators

LMW low molecular weight

LPL linearly polarized light

LUMO lowest unoccupied molecular orbital

MAQ maleimide, azobenzene and quaternary ammonium

MCBJs Mechanically controllable break-junctions

MEH-PPV poly[2-methoxy,5-(2′-ethyl-hexyloxy)-1,4-phenylenevinylene]

MLCT metal-to-ligand charge transfer

mRNA messenger RNA

MscL mechanosensitive channel of large conductance

nAChR nicotinic acetylcholine receptor

NCL native chemical ligation

NHS N-hydroxy succinimide

NLO nonlinear optical

NMTAA N-Methylthioacetamide

nNOS neuronal nitric oxide synthase

NOESY-NMR nuclear Overhauser effect spectroscopy nuclear magnetic resonance

OHB orientational hole burning

ONPC β-D-cellobioside

OPE oligo(phenylene ethynylene)

ORTEP Oak ridge thermal ellipsoid plot program

OTf triflate

PAH poly(allylamine hydrochloride)

PAL photoswitchable affinity labels

PAM 4-phenylazophenyl maleimide

PAP photoassisted poling

PAP phenylazophenylalanine

PCR polymerase chain reaction

PCS point-contact spectroscopy

2PE two-photon excitation

PEO poly(ethylene oxide)

PET photoinduced electron transfer

PHEMA poly(2-hydroxyethyl methacrylate)

phen 1,10-phenanthroline

PID photoinduced depoling

PMMA poly-methyl-methacrylate

PmPV poly[(m-phenylenevinylene)-co-(dioctoxy-p-phenylenevinylene)]

PS polystyrene

PSS photostationary states

PTL photoswitchable tethered ligands

PVA poly(vinyl alcohol)

QY quantum yield

RBS ribosome binding site

RCA rolling circle amplification

RCM ring-closing metathesis

REMD replica exchange molecular dynamics

RFID radiofrequency identification

RGD arginine-glycine-aspartate

SAM S-adenosyl-methionine

SAM self-assembled monolayer

SDS sodium dodecyl sulfate

SELEX systematic evolution of ligands by exponential enrichment

SEM scanning electron microscopy

SERS surface-enhanced Raman spectroscopy

SFVS sum-frequency vibrational spectroscopy

SHG second-harmonic generation

siRNA short interfering RNA

SNOM scanning near-field optical microscopy

SP spiropyrans

SPO spirooxazines

SRG surface-relief gratings

STM scanning tunnelling microscopy

STS scanning tunnelling spectroscopy

Taq Pol Thermus acquaticus polymerase

taRNA trans-activating RNA

TBDS tert-butyldiphenylchlorosilane

TE transverse electric

terpy 2, 2′, 6′, 2′′-terpyridine

TFA trifluoroacetic acid

TM transverse magnetic

TMD transmembrane domain

TMP trimethylphosphate

TPP thiamine pyrophosphate

TS transition state

TSPP tetrakis-sulfonatophenyl porphyrin

TTB tetra-tert-butyl

TTF tetrathiafulvalene

TX triple-crossover

UHV ultrahigh vacuum

UHV-STM ultrahigh-vacuum scanning tunnelling microscopy

UV ultraviolet

UV-Vis ultraviolet and visible

VT-NMR variable-temperature nuclear magnetic resonance

WLF Williams–Landel–Ferry

XOR eXclusive OR

XPS X-ray photoelectron spectroscopy

XR X-ray reflectivity

YFP yellow fluorescent protein

Part I

MOLECULAR SWITCHING