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Supramolecular Chemistry – Fundamentals and Applications Advanced Textbook Katsuhiko Ariga · Toyoki Kunitake Supramolecular Chemistry – Fundamentals and Applications Advanced Textbook With 173 Figures 123 Katsuhiko Ariga Supermolecules Group National Institute for Materials Science Namiki 1-1 305-0044 Ibaraki, Japan e-mail: [email protected] Toyoki Kunitake Topochemical Design Lab. FRS, RIKEN Hirosawa, Wako-shi 2-1 351-0198 Saitama, Japan e-mail: [email protected] Library of Congress Control Number: 2006920777 ISBN-10 3-540-01298-2 Springer Berlin Heidelberg New York ISBN-13 978-3-540-01298-6 Springer Berlin Heidelberg New York DOI: 10.1007/b84082 This work is subject to copyright. All rights reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer.com © Springer-Verlag Berlin Heidelberg 2006 Printed in Germany CHOBUNSHI KAGAKU HE NO TENKAI By Katsuhiko Ariga and Toyoki Kunitake Copyright © 2000 by Katsuhiko Ariga and Toyoki Kunitake Originally published in Japanese in 2000 By Iwanami Shoten, Publishers, Tokyo This English edition published 2006 By Springer-Verlag Heidelberg The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product liability: The publishers cannot guarantee the accuracy of any information about dosage and application contained in this book. In every individual case the user must check such information by consulting the relevant literature. Cover design: design & production GmbH, Heidelberg Typesetting and production: LE-TEX Jelonek, Schmidt & Vöckler GbR, Leipzig, Germany Printed on acid-free paper 2/3141/YL - 5 4 3 2 1 0 Preface Molecules are created by the covalent bonding of atoms. However, although a molecule is created from a multitude of atoms, it behaves as an individual entity. A vast number of molecules of different sizes and structures are known, ranging from the simplest hydrogen molecule to high-molecular-weight man- made polymers and sophisticated biological macromolecules such as proteins and DNA. Indeed, all living matter, natural minerals and artificial materials, however complex and numerous they are, are combinations of some of these tens of millions of molecules. We may therefore be tempted to believe that the structures and properties of these materials and compounds can be directly related to those of the individual molecules that comprise them in a straight- forward way. Unfortunately, this notion is not correct. However deeply we understand the nature of individual molecules, this knowledge is not enough to explain the structures and functions of materials and molecular assemblies that are derived as a result of organizing individual molecules. This is partic- ularly true with biological molecular systems that are derived from the spatial and temporal organization of component molecules. In this book we delve into the field of supramolecular chemistry, which deals with supermolecules. A supermolecule in this sense can be defined as a “molecule beyond a molecule” – a large and complex entity formed from other molecules. The molecules that comprise the supermolecule interact with each other via weak interactions such as hydrogen bonding, hydrophobic in- teractions and coordination to form new entities with novel properties and functionsthatcannotbededucedbyasimplesummationoftheproperties of the individual molecules. This monograph is intended to convey the rele- vance and fascination of the fast-growing field of supramolecular chemistry to advanced undergraduate students, and to provide an overview of it to young scientists and engineers. Readers will find that supramolecular chemistry is associated with many attractive disciplines of chemistry, including molecular recognition, molecular topology, self-organization, ultrathin films, molecular devices and biomolecular systems. As described in Chap. 1, supramolecular chemistry is still a very young field, and so it is difficult to predict its future, but it has already secured a firm position in the chemical sciences. For example, biotechnology and nanotechnology are expected to lead to technological revo- VI Preface lutions in near future that will dramatically affect our lifestyles and economies. Supramolecular chemistry is an indispensable tool in these technologies. This book was originally written as part of a series of Japanese chemistry textbooks. The authors hope that this book be warmly accepted by English- language readers as well. Ibaraki and Saitama, January 2006 Katsuhiko Ariga, Toyoki Kunitake Contents 1 Overview – What is Supramolecular Chemistry? .......... 1 References............................ 6 2 The Chemistry of Molecular Recognition – Host Molecules and Guest Molecules ............... 7 2.1 Molecular Recognition as the Basis forSupramolecularChemistry................. 9 2.2 MolecularInteractionsinMolecularRecognition....... 10 2.3 Crown Ethers and Related Hosts – TheFirstClassofArtificialHost................ 12 2.4 SignalInput/OutputinCrownEtherSystems......... 14 2.5 ChiralRecognitionbyCrownEthers.............. 17 2.6 Macrocyclic Polyamines – Nitrogen-Based Cyclic Hosts . 18 2.7 Cyclodextrin–ANaturallyOccurringCyclicHost...... 21 2.8 Calixarene–AVersatileHost.................. 24 2.9 Other Host Molecules – Building Three-DimensionalCavities.................. 28 2.10 EndoreceptorsandExoreceptors................ 30 2.11 Molecular Recognition at Interfaces – The Key toUnderstandingBiologicalRecognition........... 32 2.12 Various Designs of Molecular Recognition Sites at Interfaces . 34 References............................ 38 3 Controlling Supramolecular Topology – The Art of Building Supermolecules ................ 45 3.1 Fullerenes–CarbonSoccerBalls................ 46 3.2 Carbon Nanotubes – The Smallest Tubular Molecules ..... 49 3.3 Dendrimers–MolecularTrees................. 52 3.4 Rotaxanes–ThreadingMolecularRings............ 59 3.5 Catenanes and Molecular Capsules – ComplexMolecularAssociations................ 63 References............................ 70 VIII Contents 4 Molecular Self-Assembly – How to Build the Large Supermolecules .............. 75 4.1 ProgrammedSupramolecularAssembly............ 77 4.2 SupramolecularCrystals.................... 83 4.3 Macroscopic Models of Supramolecular Assembly ...... 87 4.4 SupermolecularAssemblythroughFuzzyInteractions.... 88 4.5 Structures and Formation Mechanisms of Cell Membranes . 89 4.6 Micelles – Dynamic Supramolecular Assemblies ....... 90 4.7 Liposomes, Vesicles, and Cast Films – Supramolecular Assembly Based on Lipid Bilayers ...... 93 4.8 Monolayers and LB Films – Controllable Layered Assembly . 101 4.9 Self-Assembled Monolayers – MonolayersStronglyBoundtoSurfaces............ 106 4.10 Alternate Layer-by-Layer Assembly – Supramolecular ArchitectureObtainedwithBeakersandTweezers...... 110 4.11 Hierarchical Higher Organization – FromBilayerstoFibersandRods................ 113 4.12 Artificial Molecular Patterns – ArtificiallyDesignedMolecularArrangement......... 117 4.13 Artificial Arrangement of Molecules in a Plane – Two-Dimensional Molecular Patterning ............ 119 References............................ 125 5 Applications of Supermolecules – Molecular Devices and Nanotechnology .............. 137 5.1 WhatisaMolecularDevice?.................. 138 5.2 ReadingSignalsfromMolecularDevice............ 140 5.3 Molecular Electronic Devices – ControllingElectricityUsingSupermolecules......... 144 5.4 Molecular Photonic Devices – ControllingLightwithSupermolecules............ 149 5.5 Molecular Computers – SupermoleculesthatcanThinkandCalculate......... 150 5.6 Molecular Machines – Supermolecules that can Catch Objects, Move and Rotate . 155 5.7 Molecular Devices with Directional Functionality – Supermolecules that Transmit Signals in a Desired Direction 161 5.8 Supramolecular Chemistry & Nanotechnology toward Future 166 References............................ 167 Contents IX 6 Biological Supermolecules – Learning from Nature ........ 175 6.1 Supramolecular Systems Seen in the Biological World .... 177 6.2 ControllingMaterialTransport–IonChannels........ 179 6.3 Information Conversion and Amplification – SignalTransduction....................... 181 6.4 EnergyConversion–Photosynthesis.............. 183 6.5 MaterialConversion–NaturalandArtificialEnzymes.... 185 6.6 CleavingGenes–RestrictionEnzymes............. 188 6.7 Tailor-MadeEnzymes–CatalyticAntibodies......... 191 6.8 KeytotheOriginofLife–Ribozymes............. 193 6.9 Combinatorial Chemistry andEvolutionaryMolecularEngineering........... 194 References............................ 196 Subject Index ................................ 205.

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