Vincenzo Balzani, Alberto Credi,and Margherita Venturi

Molecular Devices and Machines

Concepts and Perspectives for the Nanoworld

Second Edition

InnodataFile Attachment9783527621699.jpg

Vincenzo Balzani, Alberto Credi,and Margherita VenturiMolecular Devices and Machines

Related Titles

Kumar, C. S. S. R. (ed.)

Nanodevices for the Life Sciences

2006

ISBN 978-3-527-31384-6

Willner, I., Katz, E. (eds.)

BioelectronicsFrom Theory to Applications

2005

ISBN 978-3-527-30690-9

Schliwa, M. (ed.)

Molecular Motors

2003

ISBN 978-3-527-30594-0

Feringa, B. L. (ed.)

Molecular Switches

2000

ISBN 978-3-527-29965-2

Vincenzo Balzani, Alberto Credi,and Margherita Venturi

Molecular Devices and Machines

Concepts and Perspectives for the Nanoworld

Second Edition

The Authors

Prof. Vincenzo BalzaniDepartimento di chimica ‘‘G. Ciamician’’Università di BolognaVia Selmi 2040126 BolognaItaly

Prof. Alberto CrediDepartimento di chimica ‘‘G. Ciamician’’Università di BolognaVia Selmi 2040126 BolognaItaly

Prof. Margherita VenturiDepartimento di chimica ‘‘G. Ciamician’’Università di BolognaVia Selmi 2040126 BolognaItaly

CoverLeonardo da Vinci: “Two-wheel hoist”Codex Atlanticus (BAM), fol. 30v© Istituto e Museo di Storia della Scienza

Rotaxane Molecule (Alberto Credi)

All books published by Wiley-VCH are carefullyproduced. Nevertheless, authors, editors, andpublisher do not warrant the information containedin these books, including this book, to be free oferrors. Readers are advised to keep in mind thatstatements, data, illustrations, procedural details orother items may inadvertently be inaccurate.

Library of Congress Card No.:applied for

British Library Cataloguing-in-Publication DataA catalogue record for this book is available from theBritish Library.

Bibliographic information published bythe Deutsche NationalbibliothekDie Deutsche Nationalbibliothek lists thispublication in the Deutsche Nationalbibliografie;detailed bibliographic data are available in theInternet at .

# 2008 WILEY-VCH Verlag GmbH & Co. KGaA,Weinheim

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

Composition Thomson Digital, Noida, IndiaPrinting Strauss GmbH, MörlenbachBookbinding Litges & Dopf GmbH, HeppenheimCover Design Adam Design, Weinheim

Printed in the Federal Republic of GermanyPrinted on acid-free paper

ISBN: 978-3-527-31800-1

Contents

Preface to the Second Edition XVGlossary XVIIList of Abbreviations XXXIII

I General Concepts 1

1 Introduction 31.1 Devices and Machines at the Molecular Level 31.2 Nanoscience and Nanotechnology 51.3 Supramolecular (Multicomponent) Chemistry 71.4 Top-Down (Large-Downward) Approach 101.5 Bottom-Up (Small-Upward) Approach 101.6 Bottom-up Molecule-by-Molecule Approach 111.7 Self-Organization and Covalent Synthetic Design 131.8 Energy and Signals 15

2 Processing Energy and Signals by Molecular and SupramolecularSystems 23

2.1 Introduction 232.2 Molecular Electronics 252.3 Molecular Photonics 272.4 Molecular Chemionics 282.5 Molecular Electrophotonics 292.5.1 Solution Systems 302.5.2 Solid State 312.6 Molecular Electrochemionics 312.7 Molecular Photoelectronics 332.7.1 Photoinduced Electron Transfer in Homogeneous Systems 332.7.2 Photoinduced Potential Generation in Heterogeneous Systems 332.8 Molecular Photochemionics 342.8.1 Proton Release or Uptake 35

V

2.8.2 Metal Ion Release 352.8.3 Anion Release 362.8.4 Molecule Release 362.8.5 Configurational Changes 372.9 Molecular Chemiophotonics 382.10 Molecular Chemioelectronics 382.11 Multiple Input/Processes 392.11.1 A Sequence of Two Chemical and a Photonic Inputs

Generating Photon Emission 392.11.2 Two Electrochemical Inputs in Parallel Generating a

Chemical and a Photonic Process in a Sequence 392.11.3 A Photonic Input Generating Parallel and Serial Processes 40

II Molecular Devices for Processing Electrons andElectronic Energy 47

3 Fundamental Principles of Photoinduced Electron andEnergy Transfer 49

3.1 Molecular and Supramolecular Photochemistry 493.1.1 Molecular Photochemistry 493.1.2 Supramolecular Photochemistry 513.2 Electron Transfer 533.2.1 Marcus Theory 533.2.2 Quantum Mechanical Theory 563.2.2.1 The Electronic Factor 563.2.2.2 The Nuclear Factor 583.2.2.3 Optical Electron Transfer 593.3 Energy Transfer 603.3.1 Coulombic Mechanism 613.3.2 Exchange Mechanism 623.4 Role of the Bridge 63

4 Wires and Related Systems 694.1 Introduction 694.2 Conductivity Measurements 694.3 Electron-Transfer Processes at Electrodes 724.4 Wire-Type Systems Based on Photoinduced Charge Separation 734.4.1 Introduction 734.4.2 Dyads, Triads, and Larger Systems 734.4.3 Covalently Linked Systems Containing Metal Complexes 754.4.4 Covalently Linked Systems Containing Porphyrins 794.4.5 Covalently Linked Systems Based on Organic Compounds 834.4.6 DNA and Related Systems 864.5 Heterogeneous Photoinduced Electron Transfer 88

VI Contents

4.6 Energy Transfer 894.6.1 Covalently Linked Systems Containing Metal Complexes 894.6.2 Covalently Linked Systems Containing Porphyrins 934.6.3 Covalently Linked Systems Based on Organic Compounds 954.6.4 DNA and Related Systems 97

5 Switching Electron- and Energy-transfer Processes 1075.1 Introduction 1075.2 Switching of Electron-Transfer Processes 1085.2.1 Photon Inputs 1085.2.1.1 Long-Lived Switching 1095.2.1.2 Fast and Ultrafast Switching 1125.2.2 Redox Inputs 1165.2.3 Acid–Base Inputs 1175.2.4 Other Factors 1215.3 Switching of Energy-Transfer Processes 1225.3.1 Photon Inputs 1225.3.2 Redox Inputs 1255.3.3 Acid–Base Inputs 1255.3.4 Other Factors 127

6 Light Harvesting Antennae 1356.1 Introduction 1356.2 Natural Antenna Systems 1366.3 Dendrimers 1386.3.1 Porphyrin-Based Arrays and Dendrimers 1396.3.1.1 Arrays 1396.3.1.2 Dendrimers 1436.3.2 Dendrimers Containing Metal Complexes 1456.3.2.1 Metal Complexes as Cores 1456.3.2.2 Metal Complexes in Each Branching Center 1476.3.3 Dendrimers Based on Organic Chromophores 1506.3.3.1 Poly(arylether) Dendrimers 1506.3.3.2 Phenylacetylene Dendrons 1506.3.3.3 Polyphenylene and Oligo(p-Phenylene Vinylene) Dendrimers 1526.3.4 Host–Guest Systems 1536.3.4.1 Hosting Organic Molecules 1536.3.4.2 Hosting Metal Ions 1566.4 Other Systems 1596.4.1 Multichromophoric Cyclodextrins 1606.4.2 Phthalocyanines 1606.4.3 Metallosupramolecular Squares 1606.4.4 Rotaxanes 1616.4.5 Zeolites 1626.4.6 Polyelectrolytes 162

Contents VII

6.4.7 Polymers 1626.4.8 Self-Assembly of Biological Structures 164

7 Solar Energy Conversion 1717.1 Introduction 1717.2 Natural Photosynthesis 1737.2.1 Introduction 1737.2.2 Bacterial Photosynthesis 1747.2.3 Photosystem II 1777.3 Artificial Photosynthesis 1797.3.1 Introduction 1797.3.2 Hydrogen Economy 1797.3.3 Photochemical Water Splitting 1807.3.4 Coupling Artificial Antennas and Reaction-Center Building

Blocks 1827.3.4.1 Introduction 1827.3.4.2 Systems Based on Organic Compounds and Porphyrins 1837.3.4.3 Systems Based on Metal Complexes 1887.3.5 Coupling Single-Photon Charge-Separation with Multi-Electron

Redox Processes 1897.3.5.1 Introduction 1897.3.5.2 Coupling Electron and Proton Transfer for Oxygen Evolution 1907.3.5.3 Other Systems 1937.3.6 Assembly Strategies 1937.3.6.1 Introduction 1937.3.6.2 Self-Assembly 1937.3.6.3 Bilayer Membranes 1957.4 Hybrid Systems 1957.4.1 Hybrid Photosynthetic Reaction Center 1957.4.2 Conversion of Light to a Proton-Motive Force 1967.4.3 Light-Driven Production of ATP 1987.5 Conversion of Light into Electricity by Photoelectrochemical Cells 199

III Memories, Logic Gates, and Related Systems 209

8 Bistable and Multistable Systems 2118.1 Introduction 2118.2 Energy Stimulation 2128.2.1 Stimulation by Photons: Photochromic Systems 2138.2.2 Stimulation by Electrons: Electrochromic Systems 2168.3 Bistable Systems 2178.3.1 Modulation of Host–Guest Interactions 2178.3.2 Fluorescent Switches 2188.3.3 Chiroptical Switches 219

VIII Contents

8.3.4 Photochemical Biomolecular Switches 2228.3.5 Redox Switches 2238.3.6 Other Systems 2248.4 Multistable Systems 2258.4.1 Bi- and Multiphotochromic Supramolecular Systems 2258.4.2 Photochemical Inputs Coupled with other Stimuli 2268.4.2.1 Three-State Systems: Write–Lock–Read–Unlock–Erase Cycles 2278.4.2.2 Ortogonal Photochemical–Electrochemical Stimulations 2308.4.2.3 Ortogonal Photochemical–(Acid–Base) Stimulations 2338.4.3 Multielectron Redox Processes 2368.4.3.1 Systems with Equivalent Redox Units 2388.4.3.2 Systems with Nonequivalent Redox Units 2428.4.4 Electrochemical Inputs Coupled with Chemical Inputs 2458.4.5 Multiple Chemical Inputs 246

9 Logic Gates and Circuits 2599.1 Introduction 2599.1.1 Information Processing Based on Electronics 2599.1.2 Biological Information Processing 2609.1.3 The Chemical Computer 2609.2 Fundamental Concepts of Logic Gates 2619.3 Molecular Switches as Logic Gates 2639.3.1 Input/Output Signals 2639.3.2 Reconfiguration, Superposition, and Integration 2659.4 Basic Logic Gates 2669.4.1 YES and NOT Gates 2669.4.2 OR and NOR Gates 2679.4.3 AND and NAND Gates 2699.4.4 XOR and XNOR Gates 2729.4.5 INH Gate 2739.5 Combinational Logic Circuits 2749.5.1 EnOR and EnNOR Functions 2759.5.2 Other Functions 2769.5.3 Signal Communication Between Molecular Switches 2779.5.4 Half-Adder and Half-Subtractor 2799.5.5 Full-Adder and Full-Subtractor 2839.5.6 A Molecular 2-to-1 Digital Multiplexer 2879.6 Sequential Logic Circuits 2889.6.1 Molecular Memories 2899.6.2 A Molecular Keypad Lock 2909.7 Neural-Type Systems 2939.7.1 A Logic Device under Control of an Intrinsic ThresholdMechanism 2939.7.2 A Perceptron-Type Scheme 2959.8 Logic Devices Based on Biomolecules 2969.9 Heterogeneous Systems 299

Contents IX

9.10 Applications of Molecular Logic 3009.11 Conclusions 303

IV Molecular-Scale Mechanical Devices, Machines, and Motors 313

10 Basic Principles 31510.1 Introduction 31510.2 Biomolecular Machines and the Brownian Motion 31610.3 Artificial Systems 31710.3.1 Terms and Definitions 31910.3.2 Mechanical Devices 32010.3.3 Machines 32110.3.4 Motors 32210.4 Energy Supply 32210.4.1 Chemical Energy 32310.4.2 Light Energy 32410.4.3 Electrical Energy 32510.5 Other Features 32510.5.1 Motions 32510.5.2 Control and Monitoring 32610.5.3 Reset 32610.5.4 Timescale 32610.5.5 Functions 327

11 Spontaneous Mechanical-Like Motions 33111.1 Introduction 33111.2 Rotors 33111.3 Cogwheels 33211.4 Gears 33311.5 Paddle Wheels 33511.6 Turnstiles 33511.7 Brakes 33711.8 Ratchets 33811.9 Gyroscopes and Compasses 33811.10 Other Motions 340

12 Movements Related to Opening, Closing, and TranslocationFunctions 343

12.1 Introduction 34312.2 Allosteric Movements 34312.2.1 Allosteric Enzymes 34312.2.2 Artificial Allosteric Systems 34412.3 Tweezers and Harpoons 34612.3.1 Tweezers 346

X Contents

12.3.2 Harpoons and Related Systems 34912.4 Controlled Assembling–Disassembling of Host–Guest Systems 35112.4.1 Introduction 35112.4.2 Photoinduced Processes 35212.4.3 Redox-Induced Processes 35612.4.4 Chemically Induced Processes 36012.5 Molecular Locks 36112.6 Translocation of Metal Ions 36212.6.1 Redox-Driven Processes 36212.6.2 Acid–Base-Driven Processes 36312.7 Ion Channels 36412.7.1 Ion Transport in Nature 36412.7.2 A Natural Proton pump 36612.7.3 Artificial Ion Channels 36812.7.3.1 Introduction 36812.7.3.2 Modification of Natural Channel Formers 36812.7.3.3 Ion Channels Based on Biopolymers 36912.7.3.4 Synthetic Ion Channel Models 370

13 DNA-Based Nanomachines 38113.1 Introduction 38113.2 Important Features of DNA 38213.2.1 Structural and Functional Properties of Single- and

Double-Stranded DNA 38213.2.2 Construction of Multicomponent Nanostructures with DNA 38413.2.3 Experimental Methods for the Characterization of DNA

Nanodevices 38513.3 Simple Conformational Switches 38613.3.1 Twisters 38613.3.2 Tweezers 38813.3.3 Other Systems 39013.4 Walkers and Related Systems 39113.5 Rotary Devices 39413.6 Applications 395

14 Linear Movements 40114.1 Introduction 40114.2 Natural Linear Motors 40114.3 Threading-Dethreading Movements 40314.3.1 Introduction 40314.3.2 Chemically Driven Movements 40514.3.2.1 Systems Based on Metal–Ligand Bonds 40514.3.2.2 Systems Based on Hydrogen Bonds and Electrostatic

Interactions 40614.3.2.3 Systems Based on Donor–Acceptor Interactions 408

Contents XI

14.3.3 Electrochemically Driven Movements 41114.3.4 Photochemically Driven Movements 41414.4 Linear Motions in Rotaxanes 41814.4.1 Introduction 41814.4.2 Chemically Driven Movements 42014.4.2.1 Rotaxanes Based on Metal Complexes 42014.4.2.2 Rotaxanes Based on Hydrogen Bonds and Donor-Acceptor

Interactions 42214.4.2.3 Rotaxanes Based on Cucurbituril 42514.4.2.4 Rotaxanes Based on Cyclodextrins 42614.4.2.5 Other Systems 42714.4.3 Electrochemically Driven Movements 42714.4.4 Photochemically Driven Movements 43114.4.4.1 Rotaxanes Based on Metal Complexes 43114.4.4.2 Systems Based on Photoisomerization Reactions 43114.4.4.3 Systems Based on Photoinduced Electron Transfer 43314.4.5 Allowing/Preventing Ring Motion 437

15 Rotary Motions 45315.1 Introduction 45315.2 Natural Rotary Motors 45315.3 Hybrid Rotary Motors 45515.4 Rotary Movements in Artificial Systems 45715.4.1 Chemically Driven Processes 45815.4.1.1 Rotation Around a –C–C– Single Bond 45815.4.1.2 Ring Switching Processes in Rotaxanes and Catenanes 46015.4.1.3 Control of Rotation Around a Metal Ion in Sandwich-Type

Compounds 46415.4.2 Electrochemically Driven Processes 46615.4.2.1 Ring Switching Processes in Rotaxanes 46615.4.2.2 Ring-Switching Processes in Catenanes 46715.4.2.3 Control of Rotation Around a Metal Ion in Sandwich-Type

Compounds 47115.4.3 Photochemically Driven Processes 47215.4.3.1 Unidirectional Rotation Around a –C¼C– Double Bond 47215.4.3.2 Ring Switching Processes in Catenanes 47615.4.3.3 Unidirectional Rotation in Catenanes 477

16 From Solution to Heterogeneous Systems 48916.1 Introduction 48916.2 Rotary Motors on Surfaces 49016.3 Molecular Valves 49216.4 Molecular Muscles 49316.5 Molecular Motion Driven by STM 49516.6 Hybrid Bio-Nanodevices 498

XII Contents

16.7 Propelling Micrometer Objects 49816.8 Changing Surface Properties 50016.9 Threaded and Interlocked Compounds on Surfaces 50016.10 Interlocked Compounds in Solid State Devices 507

V Science and Society 517

17 The Role of Science in Our Time 51917.1 Introduction 51917.2 Science Will Never End 51917.3 A Fragile World 52017.4 An Unsustainable Growth 52117.5 An Unequal World 52117.6 The Role of Scientists 52217.7 Conclusions 523

Subject Index 527

Contents XIII

Preface to the Second Edition

A few years ago, because of the rapidly growing interest in supramolecular systemscapable of performing useful functions, we felt that a monograph was needed tocover the introductory features and present a unifying and stimulating overview ofthis new frontier of scientific research. We, therefore, decided to write MolecularDevices and Machines: A Journey into the Nanoworld, a book that was published byWiley-VCH in February 2003. The book was well received in the scientific commu-nity, as demonstrated by several flattering reviews published in the most importantscientific journals. In 2005 the book was translated in Chinese by Professors He Tianand Liming Wang (East China University, Shanghai) and published by ChineseChemical Industry Press (Beijing). A Japanese translation is going to be publishedvery soon by NTS, Inc., Tokyo.In the last few years, there has been a continuously growing interest in designing,

synthesizing, and operating artificial molecular devices and machines. New funda-mental concepts have emerged and a wealth of novel systems have been investi-gated. In Spring 2006, Wiley-VCH informed us that a few printed copies of our bookwere still available and suggested that, instead of making a reprint, it would havebeen more useful for the scientific community to produce a new edition of ourmonograph. After having consulted several colleagues, we indeed realized that it wasthe right time to revise and updateMolecular Devices and Machines: A Journey into theNanoworld. We have kept the title but changed the subtitle to emphasize that it isreally a new edition of the same book.Molecular Devices and Machines: Concepts and Perspectives for the Nanoworld indeed

maintains the fundamental structure of the previous book, while the content hasbeen substantially changed. The chapters and sections dealing with the fundamentalprinciples have been largely rewritten with the aim of helping the reader to realizeemerging trends, to find a sound discussion of fundamental processes like electronand energy transfer, to be cautious about naïve similarities with devices andmachines of the macroscopic world, and to understand that the nanoworld ischaracterized by some unfamiliar features that prevent the realization of nanoscaledevices and machines as described in science-fiction films, television series, andnovels. The chapters devoted to specific classes of devices and machines have beenrefreshed and updated, and new chapters have been added.

XV

As in the first edition, concepts that are then illustrated by paradigmatic modelsand enriched with examples taken from very recent publications have been empha-sized. Although this book mainly deals with artificial molecular-level devices andmachines, natural and biomimetic systems are also presented to give the reader anidea of the extremely different level of complexity between the ‘‘artificial’’ and‘‘natural,’’ and a flavor of the beauty of the chemical mechanisms responsible forthe material aspects of life. A chapter is dedicated to illustrate the most importantexamples of devices and machines based on heterogeneous or solid-state systems, afield closer to applications than that of systems in solution. The glossary in theappendix and the subject index have been revised and expanded.The most important feature of our book is the abundance of illustrations.

Cartoons and chemical formulas are, indeed, essential for understanding thecomposition and the way in which molecular devices and machines operate. Wehave tried to make it even better than in the previous edition, in which, ‘‘theillustrations alone are worth the price of the book,’’ as commented by Steven A.Edwards on p. 52 of his volume on The Nanotech Pioneers (Wiley-VCH, 2006).At the end of the book, we have added some comments on ‘‘Science and Society,’’

with our thoughts and reflections on being scientists in the present day. We dobelieve that scientists should play a more important role in the society, not forobtaining more funds but for leading the public opinion and helping the policymakers to build a more civilized and more peaceful world.We feel that this book can be useful not only for scientists engaged in research in

the fields of chemistry, physics, biology, and nanotechnology, but also as a basic textor a complementary reading source for graduate and postgraduate courses dealing,for example, with supramolecular chemistry, physical organic chemistry, photo-chemistry, electrochemistry, and energy- and electron-transfer processes. Indeed,the first edition of the book has already been used for teaching purposes. No doubtthat, in a few years, courses focusing on molecular-level devices and machines willbecome a must in all major universities.We are glad to thank the members of our research group for support, discussions,

suggestions and, even more, for their friendship. Giacomo Bergamini, MonicaSemeraro, and Serena Silvi have contributed with figure drawing and literaturesearching and Mara Monari has given secretarial help. We would like to warmlythank Professors J. Fraser Stoddart (UCLA) and Fritz Vögtle (Bonn University) forlong-lasting, profitable, and friendly collaborations on designing, making, andoperatingmolecular devices andmachines.We are also grateful to several colleaguesfrom all over the world who kindly supplied us with reprints and preprints of theirmost recent papers, and to the editors of several scientific journals for theirpermission to reproduce figures. Last but not the least, we would like to thank thestaff at Wiley-VCH for their outstanding professional capacity.

Bologna, July 2007 Vincenzo Balzani, Alberto Credi,and Margherita Venturi

XVI Preface to the Second Edition

GlossaryThe definitions given are not general but related to the content of this book.

absorption spectrum a diagram of the wavelength distribution of the absorption oflight by a substance

actin a threadlike protein related to the linear movement of myosinadduct a supramolecular species resulting from the association, driven by

intermolecular forces, of two simpler componentsallosteric effect the modification of the binding ability (or another property) of one

site in a molecule or supramolecular species derived from a conformationalrearrangement induced by binding at another remote site; allosteric effect can bepositive or negative

amphiphile a molecule that has two distinct zones, one water-soluble (hydrophilic)and the other soluble in organic media (hydrophobic or lipophilic)

antenna (molecular-level) see light-harvesting antennaaptamer a nucleic acid with specific recognition properties toward low-molecular-

weight substrates or macromolecules such as proteinsaspartate carbamoyltransferase an enzyme related to the synthesis of thymine and

cytosine in bacteriaassembler a general-purpose building nanorobotatomic force microscopy (AFM) see scanning probe microscopyATP synthase the enzyme that synthesizes ATP (see also F0F1-ATP synthase)attenuation parameter (b) a parameter related to the decrease in the rate of an

electron- (bel), hole- (bht), or energy- (ben) transfer process with increasingdistance

azacrown ether a crown ether in which one or more oxygen atoms are replaced bynitrogen

azobenzene amolecular unit containing an N¼Ndouble bond that can exist as twodifferent geometrical isomers called cis and trans; see also cis–trans isomers

back-electron transfer a term often used to indicate thermal reversal of a photo-induced electron-transfer reaction, restoring the donor and the acceptor in theiroriginal oxidation levels; see also charge recombination

battery (molecular-level) a molecule capable of accumulating charges

XVII

beacon (molecular-level) a hairpin-shaped oligonucleotide bearing an intramole-cularly quenched fluorophore whose fluorescence is restored upon binding to atarget nucleic acid; it is used to report the presence of specific nucleic acids insolution

bilayer membrane a membrane composed of two monolayers of amphiphilicmolecules (typically, phospholipids); the monolayers touch each other with theirhydrophobic side, while the hydrophilic zone is exposed

binary logic an algebraic representation in which variables can assume only twovalues (1 or 0, yes or no, true or false)

binary number system a representation for numbers using only the digits 0 and 1,in which successive digits are interpreted as coefficients of successive powers ofthe base 2

biomolecular switch a molecular-level switch that controls a biological functionbiphotochromic supramolecular system a supramolecular species containing two

photochromic componentsbistable molecule a molecule that can be reversibly switched between two different

stable states by some external stimulusblock copolymer a polymer whose chain is composed of different segments, each

composed of identical repeating unitsbottom-up approach (to miniaturization) the construction of nanometer objects,

devices, and machines starting from atoms or moleculesbridge (molecular-level) a molecular component in a supramolecular system that

is not directly involved in the function performed by the system but plays the roleof a connector between active components

bridging ligand a ligand capable of linking two metal ionsBrownianmotion the randommovement of molecules caused by collisions related

to thermal energycaged biomaterial a biologic material whose function has been blocked by chemi-

cal modificationcalixarene an aromatic macrocyclic molecule having the shape of a calixcarotenoids derivatives of carotene (a natural pigment) often used as electron

donors in multicomponent systemscatalyst a substance that accelerates a chemical reaction but is not altered in form

and amount at the end of the reactioncatenand a catenane-type ligandcatenane a supramolecular species consisting of two or more interlocked macro-

cyclic componentscatenate a catenane-type metal complexcharge pool (molecular-level) see batterycharge recombination the back-electron-transfer reaction that can follow charge

separation; see also back-electron transfercharge separation a chemical reaction, usually photoinduced, involving the trans-

fer of an electron in a supramolecular species from a neutral component toanother neutral component, leading to a speciesmade of positively and negativelycharged moieties

XVIII Glossary

charge shift a chemical reaction, usually photoinduced, involving the transfer of anelectron (or hole) in a supramolecular species from a charged to an unchargedmolecular components

charge transfer (CT) an electronic transition (and the related absorption band andexcited state) between orbitals predominantly localized in different componentsof a supramolecular species

charge transport a process moving a charge (either an electron or a hole) along awire-type supramolecular species

chemical computer a computer based on the properties of suitably designed andappropriately integrated molecular components

chemical stimulation the stimulation of a function of a molecular or supra-molecular species by the addition of an appropriate chemical reagent (e.g., ametal ion)

chemiluminescence light emission from an excited state resulting from a chemi-cal reaction

chimeric DNA a piece of oligodeoxynucleotide containing at least one ribonucleo-tide base

chiral molecule a molecule that can exist as two isomers that cannot be super-imposed (mirror images)

chiroptical switch a bistable chiral molecule; see also switchchromophore a light-absorbing molecular unitchronoamperometry an electrochemical technique particularly useful for measur-

ing the number of electrons exchanged in a redox processcircular dichroism a phenomenon related to the different absorption of left and

right circularly polarized light by chiral compoundscis–trans isomers two structures of the same molecule differing in the relative

positions of the substituents around a double bond; also called geometric isomerscofactor a small nonprotein molecular unit linked to the protein chain of an

enzyme that determines or improves the catalytic activitycolloid a heterogeneous system consisting of small (1–100 nm) particles sus-

pended in a solutioncombinational logic circuit a switching circuit whose output(s) is determined only

by the concurrent inputs; its logic function can be obtained by a suitablecombination of basic logic operations

complex (a) in coordination chemistry, a compound made of a metal atom or ametal ion surrounded by ligands; (b) in organic chemistry, a host–guest system;(c) in biological chemistry, a receptor–substrate adduct

complexes as metals/complexes as ligands strategy a synthetic strategy basedon the use of suitably designed metal complexes as building blocks forthe construction of metal-based dendrimers; a complex can be used as ametal when the metal coordination sphere is not saturated and as a ligandwhen the metal is coordinated to a bridging ligand carrying free coordinationsites

conjugated molecule a species containing alternated single and double bonds, inwhich p-electrons are delocalized over the entire molecule

Glossary XIX

convergent synthesis a synthetic procedure used to construct a dendrimer append-ing preformed dendrons to a core

coordination bond a bond between a metal or metal ion and a molecule or an ion;see also ligand and complex

copolymer a polymer made of different repeating unitscore the central unit in a dendrimercoulombic mechanism a mechanism for electronic energy transfer based on

coulombic interaction (also called resonance, through-space, or Förster mechan-ism)

covalent bonds strong atom–atom bonds that determine the structure of a mole-cule

CPK molecular models space-filling lego-type models for molecules (scale,1.25 cm: 1 Å)

crown ether a macrocyclic molecule containing oxygen atoms linked by organicspacers (typically, –CH2CH2– units)

cryptand amacrobicyclic host capable of surrounding a guest species; the resultingcomplex is called cryptate

cucurbituril a macrocyclic barrel-shaped compound prepared from acidic conden-sation of glycoluril and formaldehyde

cyclic voltammetry (CV) a very popular electrochemical technique for investigatingthe redox behavior of molecular and supramolecular species

cyclodextrin (CD) a cyclic oligosaccharide shaped like a truncated cone; a-CD, b-CD, and g-CD contain 6, 7, and 8 glucopyranoside units, respectively

cyclometalated complex ametal complex in which a heterocyclic aromatic ligand iscoordinated to a metal atom or a metal ion via a carbon and a nitrogen atoms

cyclophane a macrocyclic organic molecule with a bridged aromatic ringcytochromes afamilyofelectron-transferproteinshavingoneorseveralhemegroupsdenaturation structural changes of a protein (or of a nucleic acid) from the original

native state without alteration of the amino acid (or nucleotide) sequencedendrimer a well-defined macromolecule exhibiting a treelike structuredendron a dendrimer branchDexter mechanism see exchange mechanismdiastereoisomers stereoisomers that are not mirror images of each otherdifferential pulse voltammetry an electrochemical technique for investigating the

redox behavior of molecular and supramolecular speciesdiode (molecular-level) a two-terminal molecular switch that can turn a current on

or off as it attempts to pass through the diode; molecular rectifiers are a type ofmolecular-level diodes

ditopic receptor a supramolecular species with two binding sites, thus capable ofhosting two equal or different guests

divergent synthesis a synthetic procedure to construct a dendrimer starting fromits core by successive repetitive additions of building blocks

driving force term used to indicate the negative of the standard Gibbs energychange (DG0) of a reaction; reactions with a positive driving force (i.e., a negativeDG0) are spontaneous; see also free energy change

XX Glossary

dumbbell a molecular structure consisting of a threadlike component with twobulky groups at its extremities

dye term often used to indicate an organic molecule exhibiting absorption bandsin the visible spectral region

dynein a family of linear motor proteins in charge of intracellular transportefficiency (of a step, Z) the ratio between the rate of the step and the sum of the

rates of all the parallel steps that cause the disappearance of a specieselectrochemical sensor see sensorelectrochemical stimulation the stimulation of a function of a molecular or supra-

molecular species by an electrochemical inputelectrochemiluminescence light emission from an excited state resulting from a

redox reaction between electrochemically generated reactantselectrochromic molecule a molecule that can be reversibly interconverted by redox

processes between two or more forms exhibiting distinct absorption spectraelectrolysis exhaustive electrochemical reduction or oxidation of an ion, molecule,

or molecular componentelectromotive force a driving force based on an electrical potential differenceelectron acceptor an electron-deficient molecule (or molecular component in a

supramolecular species)electron donor an electron-rich molecule (or molecular component in a supramo-

lecular species)electron injection the transfer of a negative charge to a molecular or supramole-

cular species or to a semiconductorelectron transfer a process that involves the transfer of an electron from amolecule

(or a molecular component in a supramolecular species) to another; such aprocess is often called a redox reaction; it can be photoinduced, that is, inducedby light absorption in one of the two reaction partners; when the two partners areneutral, the process results in a charge separation into positively and negativelycharged molecules (or molecular components)

electron-transfer photosensitization see photosensitized processelectronic coupling (H) see electronic factorelectronic energy transfer see energy transferelectronic factor the electronic term in the Fermi ‘‘golden rule’’ expressions for the

rate constants of energy- (Hen) and electron- (Hel) transfer processeselectronic rearrangement a change in the electronic distribution caused by an

external stimulus (e.g., light absorption)electronically excited molecule a molecule in which the absorption of a photon has

caused a rearrangement in its electronic structure; see also excited stateemission the radiative deactivation of an excited stateemission spectrum a diagram of the wavelength distribution of the light emitted

by a substanceenantiomers stereoisomers that are mirror images of each otherenergy barrier (DG#) the activation energy of a chemical reactionenergy concentrator see light-harvesting antennaenergy-level diagram see state energy diagram

Glossary XXI

energy migration the transfer of electronic energy among identical molecularcomponents in a supramolecular species or monomeric units in a polymer; seealso energy-transfer and hopping mechanism

energy transfer a process that causes the transfer of electronic energy from anexcited state of a molecule (or a molecular component in a supramolecularspecies) to a another molecule (or molecular component)

enzyme protein capable of catalyzing biological processesexchange mechanism a mechanism for electronic energy transfer, based on

exchange interaction, that requires an overlap of the wave functions of the energydonor and the energy acceptor

excimer an excited dimer, dissociative in the ground state, resulting from thereaction of an excited molecule with a ground-state molecule of the same type

exciplex an excited complex, dissociative in the ground state, resulting from thereaction of an excited molecule with a ground-state molecule of a different type

excited state a higher energy state of a molecule (see also electronically excitedmolecule)

exciton a term used for polymers and solid-state systems to indicate an excitedstate (electron–hole pair)

F0F1-ATP synthase a natural molecular-scale machine consisting of two rotarymolecular motors (F0 and F1) attached to a common shaft; see also ATP synthase

fatigue term used for indicating the lack of reversibility, particularly with referenceto photochromic systems

Fermi ‘‘golden rule’’ expression a quantum mechanical expression for the rateconstant of energy- and electron-transfer processes

Fermi level the average between the highest occupied and the lowest unoccupiedlevels in a solid-state material

ferrocene an organometallic molecule that undergoes reversible one-electron oxi-dation, often used as a reference in electrochemical experiments

flash photolysis a pulsed irradiation technique used to produce and investigatetransient species

fluorescence the light emission caused by a spin-allowed radiative deactivation ofan excited state

fluorescent sensor see sensorfluorescent switch a compound existing in two forms that exhibit different fluor-

escence propertiesfluorophore a fluorescent molecular unitFörster mechanism see coulombic mechanismFranck–Condon factor (FC) the nuclear term in the Fermi ‘‘golden rule’’ expres-

sions for the rate constants of energy (FCen) and electron (FCel) transferfree-base porphyrin see porphyrinfree energy change (DG0) the thermodynamic quantity associated with a chemical

reaction that establishes whether such a reaction can occur (DG0 < 0); see alsodriving force

full adder a logic element that operates on two binary digits and a carry digit from apreceding stage, producing as output a sum digit and another carry digit

XXII Glossary

fullerene (C60) a spherical molecule consisting of 60 carbon (C) atomsfuzzy logic a logic in which propositions are not required to be either true or

false, but may be true or false to a different degree (in contrast to classicalbinary logic)

glucose oxidase an enzyme that catalyzes the oxidation of glucoseground state the lowest energy, stable electronic state of a moleculeguest an ion or a convexmolecule capable of being hosted into a concavemolecular

or supramolecular specieshalf adder (molecular-level) a molecular device capable of adding two one-digit

binary numbersheme group the complex between an iron(II) ion and a porphyrin ligand, which

constitutes a cofactor of many enzymes (e.g., cytochromes)hemicarceplex a host/guest complex in which the host (hemicarcerand) is a

species whose internal cavity is accessible only at high temperatureheterosupramolecular system a system consisting of molecular or supramolecular

species linked to a nanoscopic solid-state component (e.g., to a nanoparticle)hole burning the photobleaching of a feature within an inhomogeneous absorp-

tion or emission band caused by the disappearance of resonantly excited mole-cules as a result of a photochemical or photophysical process

hole injection the transfer of a positive charge to a molecular or supramolecularspecies or to a semiconductor

hole transfer the transfer of a positive charge from a molecule (or a molecularcomponent in a supramolecular species) to another; see also electron transfer

holography a technique used for three-dimensional optical image formationhopping mechanism a long range energy, electron, or hole transfer in a supramo-

lecular species taking place by successive steps which involve the bridging unitshost a molecular or supramolecular species, usually exhibiting a concave struc-

ture, capable of hosting an ion or a moleculehost–guest system see host and guesthybridization (of DNA) formation of the double helix by base pairing between

complementary DNA strandshydrogen bond a relatively weak chemical bond arising when a hydrogen atom

covalently linked to an atom X forms an additional bond with another atom Yeither in the same or in another molecule; strong hydrogen bonds are formedwhen X and Y are electronegative atoms (e.g., N, O)

induced fit an extensive rearrangement of a receptor aimed at optimization of ahost–guest interaction

inhibitor a substance that decreases the rate of a chemical reaction, but which isnot itself altered in form and amount at the end of the reaction

intermolecular forces weak attraction forces such as hydrogen bonds, electrondonor–acceptor and p–p interactions, and van der Waals forces that are respon-sible for molecular assembly

internal conversion a spin-allowed radiationless deactivation of an excited stateintersystem crossing a spin forbidden radiationless deactivation of an excited state

Glossary XXIII

intervalence transfer the transfer of an electron between two species that have thesame chemical nature but different oxidation state; see also mixed-valence state

ion channel a supramolecular system (in Nature, an allosteric protein) that allowsions to cross a membrane in a thermodynamically allowed direction

ion pump a supramolecular system (in Nature, an allosteric protein) that allowsions to cross amembrane against a thermodynamic gradient, by using a source ofenergy such as ATP or light

isoemissive point the wavelength at which the intensity of emission does notchange during a chemical reaction or physical change

isomerization the interconversion between isomersisomers molecules having the same composition but different structureisosbestic point the wavelength at which the absorbance does not change during a

chemical reaction or physical changekinesin a family of linear motor proteins in charge of intracellular transportLangmuir–Blodgett (LB) film a molecular mono- or multilayer obtained by orga-

nization of amphiphilic molecules at the air–water interface and deposited onto asolid surface

large-downward approach see top-down approachlargemolecule a chemical compound of large dimension in which it is not possible

to identify distinct molecular components, in contrast with supramolecularspecies

laser (acronym from light amplification by stimulated emission of radiation): asource of monochromatic and coherent light used in photochemistry for pulsedexcitation in very short timescales

Lewis acid a chemical compound capable of accepting an electron pairlifetime (t) the time needed by intrinsic, first-order deactivation processes to

reduce the concentration of a transient species (e.g., an excited state) to 1/e ofits initial value

ligand a molecule or an ion capable of binding to a metal ion or a metal atomligand centered the orbitals, electronic transitions, excited states, and absorption

bands of a ligand in a metal complexlight-emitting diode (LED) a device converting electric power into light by electro-

luminescencelight-harvesting antenna (molecular-level) an organized array of molecular com-

ponents (i.e., a supramolecular species) capable of absorbing light and deliveringthe resulting electronic energy to a predetermined component of the array; thisfunction is often called antenna effect

linker see bridgeliposome an aqueous compartment enclosed within a bilayer membraneliquid crystal a liquid that is not isotropic because of preferential orientation of

molecules in large domains; depending on the type of molecule and organiza-tion, liquid crystalline phases can be nematic, smectic, cholesteric, discotic, orlyotropic

logic gate (molecular-level) a molecular or supramolecular species capable ofperforming a logic operation

XXIV Glossary

logic operation an operation on logical quantities (0, 1; yes, not; true, false)luminescence the light emission caused by a radiative deactivation of an excited

stateluminophore a luminescent molecular unitmacrocycle a molecule or supramolecular species with closed, ring-type structureMarcus inverted process an electron- or energy-transfer process taking place in the

Marcus inverted region, that is, in a kinetic regime in which the rate constantdecreases with increasing driving force

Marcus theory a classical theory for electron- and energy-transfer processes inwhich the energy barrier (DG#) is related to the standard free energy change(DG0) and the nuclear reorganizational energy (l) by a quadratic equation.According to this theory, on increasing driving force, the reaction rate increaseswhen �DG0 < l (normal region), but it decreases when �DG0 > l (invertedregion)

memory (molecular-level) a molecule that can be switched between forms (write)that exhibit different properties (read); see also bistable molecule

mesogenic molecule a chemical species capable of generating a liquid crystalmetal-to-ligand charge transfer (MLCT) the electronic transitions (and related

excited states and absorption bands) that transfer electronic charge from metalto ligand(s) in metal complexes

methylviologen the common name for the 1,10-dimethyl-4,40-bipyridinium dica-tion

microtubule a threadlike protein-based structure, 18–25 nm in diameter, relatedto the linear movement of kinesin and dynein

mixed-valence state an excited state arising from an intervalence transfer transi-tion; it can be related to an absorption band

modular approach the use of repeating units to construct a supramolecular (mod-ular) system

molecular device an assembly of a discrete number of molecular components (i.e.,a supramolecular species) designed to perform a specific function

molecular electronics electronics based on molecular-level componentsmolecular machine a particular type of molecular device in which the component

parts display changes in their relative positions as a result of some externalstimulus

molecular recognition the ability of a molecule to recognize and associate withanother molecule, based on the presence of complementary chemical functional-ities

molecular-wire behavior a kinetic regime of electron-transfer reactions in supra-molecular species characterized by a very small decrease in the rate constant onincreasing distance

monolayer a one-molecule thick layermotor protein a complex biological species that plays the role of amotor inside cellsmulticomponent system see supramolecular systemmultiplexing optical system a system capable of processing two or more optical

signals simultaneously

Glossary XXV

multistate–multifunctional system a system capable of existing in three or moreforms that can be interconverted by means of different stimuli

myosin a family of linear motor proteinsnanoparticle a solid particle of nanometer size, usually a metal or semiconductor

nanocrystalnanostructured electrode an electrode made of synthesized nanoparticlesnanotechnology a new branch of technology, dealing with objects at the nanometer

(10�9 m) scalenanotube a tube at the molecular level a few nanometers in diameterneural-type system an artificial system capable of mimicking some elementary

properties of neuronsnonlinear optics the study of a particular class of phenomena dealing with the

interaction between light and matter, such as multiphoton processes and secondharmonic generation

nonradiative deactivation see radiationless decaynuclear factor see Franck–Condon factornuclear rearrangement a change in the relative positions of atoms in molecules or

components in supramolecular species caused by an external stimulus (e.g., lightabsorption)

nucleophile an electron-rich compoundnucleotide a chemical species formed by a heteroaromatic base, a sugar, and a

phosphate unitsoligonucleotide a polymer formed by a few nucleotides, essentially a fragment of a

nucleic acidoptical tweezer a laser technique to control the position of a small beadoptoelectronic device a device transducing an optical input into an electrical

outputorbital a one-electron wave function that explicitly depends on the spatial

coordinates and defines the region of space in which it is likely to find anelectron

oxidation the half reaction of a redox process concerning the release of one ormoreelectrons by a reactant

perceptron the artificial intelligence unit used to mimic the behavior of a neuronpersistence length (of a polymer) it is a measure of the stiffness of a polymer. It is a

value of chain length, lp, such that on a length scale smaller than or comparablewith lp, a polymer can be regarded as a rigid rod, whereas for lengths much largerthan lp, the polymer is flexible

pH jump a large change in the pH of a solution caused by a quick addition of acidor base

phase isomers the isomers generated in a supramolecular system by concertedconformational motions of its components

phosphorescence the light emission caused by a spin-forbidden radiative deactiva-tion of an excited state

photochemical stimulation the light stimulation of a function of a molecular orsupramolecular species

XXVI Glossary

photochemistry the branch of chemistry dealing with the interaction of light (farUV to IR) with matter; the absorption of light by a molecule causes the formationof an electronically excited state

photochromic molecule a molecule that can be reversibly interconverted, with atleast one of the reactions being induced by light absorption, between two formsexhibiting different absorption spectra

photocurrent an electric current generated by light absorptionphotoinduced electron transfer (PET) see electron transferphotoinduced redox reaction see electron transferphotoisomerization the photoinduced interconversion between isomersphotolithography a photochemical technique used in the top-down approach to

miniaturizationphotonic stimulation see photochemical stimulationphotonics the branch of science dealing with the use of light signals for infor-

mation processingphotophysical processes photoexcitation and subsequent events that lead from one

state of a molecular unit to another through radiative and radiationless transitionsphotorefractive material a material that undergoes a change in the refraction index

on light stimulationphotoresponsive polymer a polymer that undergoes a change in some of its

properties (e.g., its length) on light stimulationphotosensitized process a reaction of a nonabsorbing species induced by an

electron- or energy-transfer process involving an excited state of a light-absorbingspecies

photosensitizer a molecular unit capable of being photoexcited and of inducingexcitation or reaction in another molecular unit

photostationary state a chemical equilibrium reached under light excitationphotosynthesis a process that converts light energy into chemical energypolymer a chemical compound made of a large number of covalently linked

identical or different repeating unitspolynuclear complex a complex containing several metals or metal ions in its

structurepolypeptide a chain of amino acids; see also proteinpolypyridine ligand a ligand consisting of many pyridine unitsporphyrins a class of molecules based on a quadratic arrangement of four basic

nitrogen-containing pyrrole units. In free-base porphyrins, two nitrogens arelinked to hydrogen atoms; upon deprotonation, a metal ion can be coordinated bythe four nitrogens

p � p interactions weak, noncovalent interactions involving aromatic unitspreorganization a designed arrangement of functional groups or molecular units

aimed at facilitating the occurrence of a specific process or functionprotein a natural polymer made of a sequence of amino acidsprotein folding/unfolding the spontaneous (folding) or stimulated (unfolding)

rearrangements of protein chains related to their functional three-dimensionaltertiary structure

Glossary XXVII

proton a positively charged hydrogen atom; in solution, it is the species transferredin the so-called acid–base reactions

proton-motive force a driving force based on a proton energy gradientproton pump an ion pump for protonspseudorotaxane an inclusion complex in which amolecular thread is encircled by a

macrocyclic component; see also rotaxaneP-type photochromic system a photochemically reversible photochromic systemquantum yield (F) the ratio between the number of light-generated events and the

number of absorbed photons; for example, in the case of fluorescence, the ratiobetween the number of emitted and absorbed photons

quencher a molecule or molecular component in a supramolecular species thatdeactivates (quench) an excited state of another molecule or molecular compo-nent

quenching the deactivation of an excited state and, as a consequence, of all itsprocesses (e.g., luminescence) by a quencher

quinones electron-deficient aromatic molecules that can be reversibly reduced byone and two electrons

racemization a reaction that converts an enantiomer into its mirror image leadingeventually to equal population of the two enantiomers

radiationless decay the deactivation of an excited state via radiationless transitionswithout emission of a photon or a chemical change

radiationless transition an isoenergetic transition between two states of a mole-cular unit

radiative decay see luminescenceradiative transition a transition between two states of a system, the energy differ-

ence being emitted or absorbed as a photonrate constant a parameter used to express the specific rate of a processreaction center (RC) a supramolecular structure of natural photosynthetic systems

in which electronic energy is converted into chemical energy by means of acharge-separation reaction

receptor a term commonly used in biology to indicate a host speciesrectifier (molecular-level) a type of molecular-level diode in which current flow in

one direction is more difficult than in the opposite directionredox reaction a process resulting from coupled oxidation and reduction (half)

reactionsredox switch a compound that can be interconverted between two different forms

by a reversible redox reactionreduction the half reaction of a redox process concerning the uptake of one or

more electrons by a reactantrelay a chemical compound playing the role of charge carrier in a redox processreorganizational energy the energy (l in the Marcus equation) required for all the

structural adjustments (in reactants, li, and in the surrounding solvent mole-cules, lo) which are needed to obtain the reactive configuration for electron- andenergy-transfer processes

resonance mechanism see coulombic mechanism

XXVIII Glossary