Molecular Devices and Machines - download.e-bookshelf.de · 9.10 Applications of Molecular Logic...
Transcript of Molecular Devices and Machines - download.e-bookshelf.de · 9.10 Applications of Molecular Logic...
-
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