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· Katsuhiko Ariga Toyoki Kunitake Supramolecular Chemistry – Fundamentals and Applications Advanced Textbook With173Figures 123 KatsuhikoAriga SupermoleculesGroup NationalInstituteforMaterialsScience Namiki1-1 305-0044Ibaraki,Japan e-mail:[email protected] ToyokiKunitake TopochemicalDesignLab. FRS,RIKEN Hirosawa,Wako-shi2-1 351-0198Saitama,Japan e-mail:[email protected] LibraryofCongressControlNumber:2006920777 ISBN-10 3-540-01298-2 SpringerBerlinHeidelbergNewYork ISBN-13 978-3-540-01298-6 SpringerBerlinHeidelbergNewYork DOI: 10.1007/b84082 Thisworkissubjecttocopyright.Allrightsreserved,whetherthewholeorpartofthematerialisconcerned, specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmorinanyotherway,andstorageindatabanks.Duplicationofthispublicationorpartsthereof ispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965,initscurrent version,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliableforprosecution undertheGermanCopyrightLaw. SpringerisapartofSpringerScience+BusinessMedia springer.com ©Springer-VerlagBerlinHeidelberg2006 PrintedinGermany CHOBUNSHIKAGAKUHENOTENKAI ByKatsuhikoArigaandToyokiKunitake Copyright©2000byKatsuhikoArigaandToyokiKunitake OriginallypublishedinJapanesein2000 ByIwanamiShoten,Publishers,Tokyo ThisEnglisheditionpublished2006 BySpringer-VerlagHeidelberg Theuseofgeneraldescriptivenames,registerednames,trademarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandthereforefreeforgeneraluse. 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 consultingtherelevantliterature. Coverdesign:design&productionGmbH,Heidelberg Typesettingandproduction:LE-TEXJelonek,Schmidt&VöcklerGbR,Leipzig,Germany Printedonacid-freepaper 2/3141/YL-543210 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.Avastnumberofmoleculesofdifferentsizesandstructuresareknown, rangingfromthesimplesthydrogenmoleculetohigh-molecular-weightman- madepolymersandsophisticatedbiologicalmacromoleculessuchasproteins and DNA. Indeed,allliving matter, natural mineralsand artificial materials, howevercomplexandnumeroustheyare,arecombinationsofsomeofthese tensofmillionsofmolecules.Wemaythereforebetemptedtobelievethatthe structures and properties of these materials and compounds can be directly relatedtothoseoftheindividualmoleculesthatcomprisetheminastraight- forward way. Unfortunately, this notion is not correct. However deeply we understandthenatureofindividualmolecules,thisknowledgeisnotenough toexplainthestructuresandfunctionsofmaterialsandmolecularassemblies thatarederivedasaresultoforganizingindividualmolecules.Thisispartic- ularlytruewithbiologicalmolecularsystemsthatarederivedfromthespatial andtemporalorganizationofcomponentmolecules. 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 othermolecules.Themoleculesthatcomprisethesupermoleculeinteractwith eachotherviaweakinteractionssuchashydrogenbonding,hydrophobicin- teractions and coordination to form new entities with novel properties and functions that cannot be deduced by a simple summation of the properties of the individual molecules. This monograph is intended to convey the rele- vanceandfascinationofthefast-growingfieldofsupramolecularchemistryto advancedundergraduatestudents,andtoprovideanoverviewofittoyoung scientists and engineers. Readers will find that supramolecular chemistry is associatedwithmanyattractivedisciplinesofchemistry,includingmolecular recognition,moleculartopology,self-organization,ultrathinfilms,molecular devices and biomolecular systems. As described in Chap. 1, supramolecular chemistryisstillaveryyoungfield,andsoitisdifficulttopredictitsfuture,but ithasalreadysecuredafirmpositioninthechemicalsciences.Forexample, biotechnologyandnanotechnologyareexpectedtoleadtotechnologicalrevo- VI Preface lutionsinnearfuturethatwilldramaticallyaffectourlifestylesandeconomies. Supramolecularchemistryisanindispensabletoolinthesetechnologies. ThisbookwasoriginallywrittenaspartofaseriesofJapanesechemistry textbooks. The authors hope that this book be warmly accepted by English- languagereadersaswell. IbarakiandSaitama,January 2006 KatsuhikoAriga, ToyokiKunitake Contents 1 Overview–WhatisSupramolecularChemistry? . . . . . . . . . . 1 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2 TheChemistryofMolecularRecognition– HostMoleculesandGuestMolecules . . . . . . . . . . . . . . . 7 2.1 MolecularRecognitionastheBasis forSupramolecularChemistry . . . . . . . . . . . . . . . . . 9 2.2 MolecularInteractionsinMolecularRecognition . . . . . . . 10 2.3 CrownEthersandRelatedHosts– TheFirstClassofArtificialHost . . . . . . . . . . . . . . . . 12 2.4 SignalInput/OutputinCrownEtherSystems . . . . . . . . . 14 2.5 ChiralRecognitionbyCrownEthers . . . . . . . . . . . . . . 17 2.6 MacrocyclicPolyamines–Nitrogen-BasedCyclicHosts . . . 18 2.7 Cyclodextrin–ANaturallyOccurringCyclicHost . . . . . . 21 2.8 Calixarene–AVersatileHost . . . . . . . . . . . . . . . . . . 24 2.9 OtherHostMolecules–Building Three-DimensionalCavities . . . . . . . . . . . . . . . . . . 28 2.10 EndoreceptorsandExoreceptors . . . . . . . . . . . . . . . . 30 2.11 MolecularRecognitionatInterfaces–TheKey toUnderstandingBiologicalRecognition . . . . . . . . . . . 32 2.12 VariousDesignsofMolecularRecognitionSitesatInterfaces . 34 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3 ControllingSupramolecularTopology– TheArtofBuildingSupermolecules . . . . . . . . . . . . . . . . 45 3.1 Fullerenes–CarbonSoccerBalls . . . . . . . . . . . . . . . . 46 3.2 CarbonNanotubes–TheSmallestTubularMolecules. . . . . 49 3.3 Dendrimers–MolecularTrees . . . . . . . . . . . . . . . . . 52 3.4 Rotaxanes–ThreadingMolecularRings . . . . . . . . . . . . 59 3.5 CatenanesandMolecularCapsules– ComplexMolecularAssociations . . . . . . . . . . . . . . . . 63 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 VIII Contents 4 MolecularSelf-Assembly– HowtoBuildtheLargeSupermolecules . . . . . . . . . . . . . . 75 4.1 ProgrammedSupramolecularAssembly . . . . . . . . . . . . 77 4.2 SupramolecularCrystals . . . . . . . . . . . . . . . . . . . . 83 4.3 MacroscopicModelsofSupramolecularAssembly . . . . . . 87 4.4 SupermolecularAssemblythroughFuzzyInteractions . . . . 88 4.5 StructuresandFormationMechanismsofCellMembranes . . 89 4.6 Micelles–DynamicSupramolecularAssemblies . . . . . . . 90 4.7 Liposomes,Vesicles,andCastFilms– SupramolecularAssemblyBasedonLipidBilayers . . . . . . 93 4.8 MonolayersandLBFilms–ControllableLayeredAssembly . 101 4.9 Self-AssembledMonolayers– MonolayersStronglyBoundtoSurfaces . . . . . . . . . . . . 106 4.10 AlternateLayer-by-LayerAssembly–Supramolecular ArchitectureObtainedwithBeakersandTweezers . . . . . . 110 4.11 HierarchicalHigherOrganization– FromBilayerstoFibersandRods . . . . . . . . . . . . . . . . 113 4.12 ArtificialMolecularPatterns– ArtificiallyDesignedMolecularArrangement . . . . . . . . . 117 4.13 ArtificialArrangementofMoleculesinaPlane– Two-DimensionalMolecularPatterning . . . . . . . . . . . . 119 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 5 ApplicationsofSupermolecules– MolecularDevicesandNanotechnology . . . . . . . . . . . . . . 137 5.1 WhatisaMolecularDevice? . . . . . . . . . . . . . . . . . . 138 5.2 ReadingSignalsfromMolecularDevice . . . . . . . . . . . . 140 5.3 MolecularElectronicDevices– ControllingElectricityUsingSupermolecules . . . . . . . . . 144 5.4 MolecularPhotonicDevices– ControllingLightwithSupermolecules . . . . . . . . . . . . 149 5.5 MolecularComputers– SupermoleculesthatcanThinkandCalculate . . . . . . . . . 150 5.6 MolecularMachines– SupermoleculesthatcanCatchObjects,MoveandRotate. . . 155 5.7 MolecularDeviceswithDirectionalFunctionality– SupermoleculesthatTransmitSignalsinaDesiredDirection 161 5.8 SupramolecularChemistry&NanotechnologytowardFuture 166 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 Contents IX 6 BiologicalSupermolecules–LearningfromNature . . . . . . . . 175 6.1 SupramolecularSystemsSeenintheBiologicalWorld . . . . 177 6.2 ControllingMaterialTransport–IonChannels . . . . . . . . 179 6.3 InformationConversionandAmplification– 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 CombinatorialChemistry andEvolutionaryMolecularEngineering . . . . . . . . . . . 194 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196 SubjectIndex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205 1 Overview–WhatisSupramolecularChemistry? “Supramolecularchemistry”isoftendefinedasbeing“chemistrybeyondthe molecule”, which is rather vague and mysterious expression. Therefore, in ordertogetacrossthebasicconceptsof“supermolecules”and“supramolec- ular chemistry”, it is worth using an analogy from daily life. Many sports involve teams of players. One of the main objectives in such sports is to or- ganizetheteamsuchthattheperformanceoftheteamissignificantlygreater that that the sum of the performances of each team-member. This concept of a “good teambeinggreater thanthesumof itsparts” canalso beapplied to a supermolecule. According to Dr. Lehn, who invented the term, a super- moleculeisanorganized,complexentitythatiscreatedfromtheassociation of two or more chemical species held together by intermolecular forces. Su- permoleculestructuresaretheresultofnotonlyadditivebutalsocooperative interactions, including hydrogen bonding, hydrophobic interactions and co- ordination, and their properties are different (often better) than the sum of thepropertiesofeachindividualcomponent.Thepurposesofthisbookisto explore fundamental supramolecular phenomena and to explain highly so- phisticatedcharacteristicsandfunctionsofsupramolecularsystems.Wewill seethatgoodorganizationandawell-selectedcombinationofsupramolecular elements leads to systems with incredible performance. The huge variety of supermoleculesavailablemaysurprisemanyreaders.Inthissection,wegive an outline of supramolecular chemistry and relate it to the contents of this book(Fig.1.1). Supramolecularchemistryisstillayoungfield,meaningthatitcanberather difficult to define exactly what it encompasses – indeed it is a field that has developedrapidlyduetocontributionsfromavarietyofrelatedfields.There- fore,thesubjectneedstobetackledfromvariouspointsofview.Inthisbook, supramolecularchemistryisclassifiedintothreecategories:(i)thechemistry associatedwithamoleculerecognizingapartnermolecule(molecularrecog- nitionchemistry);(ii)thechemistryofmoleculesbuilttospecificshapes;(iii) thechemistryofmolecularassemblyfromnumerousmolecules.Thisclassifi- cationisdeeplyrelatedtothesizeofthetarget molecularsystem.Molecular recognition chemistry generally deals with the smallest supramolecular sys- tems,andencompassesinteractionsbetweenjustafewmolecules.Incontrast, 2 1 Overview–WhatisSupramolecularChemistry? Figure1.1. Worldofsupermolecules the chemistry of molecular assemblies can include molecular systems made fromcountlessnumbersofmolecules.Thisclassificationschemeisreflectedin Chaps.2to4,whichcoverthebasicsofsupramolecularchemistry,fromsmall supermoleculesinChap.2tolargeonesinChap.2. 1 Overview–WhatisSupramolecularChemistry? 3 InChap.2,wediscussmolecularrecognitionchemistryanddescribevari- ouskindsofhostmoleculesandrelatedfunctions.Themolecularrecognition described in Chap. 2 can be regarded in many ways as the most fundamen- tal kind of supramolecular chemistry, because all supramolecular chemistry is based on how to recognize molecules, how to influence molecules, and how to express specific functions due to molecular interactions. The im- portance of molecular recognition first came to light in the middle of the nineteenthcentury–considerablybeforetheconceptofsupermoleculeswas established. For example, Pasteur noticed during microscopic observations that crystals of tartaric acid occurred in two types, that were mirror im- ages of each other, and found that mold and yeast recognize and utilize only one of these types. The origin of “molecular recognition” is often said to be the “lock and key” principle proposed by Emil Fischer in 1894. This concept proposed that the mechanism by which an enzyme recognizes and interacts with a substrate can be likened to a lock and a key system. The presenceofnaturalproductsthatcanrecognizeparticularmoleculeswasal- ready known by the 1950s: for example, the recognition capabilities of the cyclicoligosaccharide cyclodextrinand those of the cyclic oligopeptidevali- nomycin. In 1967, Pedersen observed that crown ether showed molecular recogni- tion–thefirstartificialmoleculefoundtodoso.Cramdevelopedthisconcept to cover a wide range of molecular systems and established a new field of chemistry,host–guestchemistry,wherethehostmoleculecanaccommodate another molecule, called the guest molecule. In 1978, Lehn attempted to or- ganizethesenovelchemistries,andfirstproposedtheterm“supramolecular chemistry”.Thisrepresentedthemomentthatsupramolecularchemistrywas clearly established. Together, Pedersen, Cram and Lehn received the Nobel PrizeforChemistryin1987. InChap.3,medium-sizedsupermoleculescomposedfromasmallnumber ofmoleculesareintroduced.Suchsupermoleculeshavegeometricallyspecific shapes, and readers may well be impressed by their uniqueness and variety. Thesupermoleculesthatappearinthischapterhaveinterestingcharacteristics fromatopologicalviewpoint:forexample,rotaxanecontainscyclicmolecules thatarethreadedbylinearmolecules,andcatenanecontainsentangledmolec- ularrings.Theseentangledmoleculescanbeobtained(withquitelowyields) as the products from accidental phenomena. Introducing a strategy based onsupramolecularchemistrydrasticallyimprovestheiryield.Fixingspecific supramolecular interaction sites that give controlled ring closure results in as-designed entangled molecules. Relatively large single molecules with ge- ometrically attractive shapes are also introduced in this chapter. Fullerenes are closed spheres formed from carbon pentagons and carbon hexagons, someofwhichcouldbedescribedas“molecularsoccerballs”.Fusingcarbon pentagons and hexagons also yields carbon nanotubes, which are molecular tubes with nanoscale diameters. Controlled branching in molecules results
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