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(BQ) Part 2 book Supramolecular chemistry has contents: Network Solids, self assembly, molecular devices, biological mimics and supramolecular catalysis, interfaces and liquid assemblies, supramolecular polymers, gels and fibres, nanochemistry.
9 Network Solids Laws are generally found to be nets of such a texture as the little creep through, the great break through, and the middle-sized are alone entangled in. William Shenstone (17141763), Essays on Men and Manners On Politics Network Solids 538 9.1 What Are Network Solids? 9.1.1 Concepts and Classication Moulton, B and Zaworotko, M J., From molecules to crystal engineering: Supramolecular isomerism and polymorphism in network solids, Chem Rev 2001, 101, 16291658 So far we have been predominantly focused on the host-guest paradigm of supramolecular chemistry In Chapters 36 we looked at discrete, solution phase hosts for various guests In Chapter we focused on (predominantly organic) molecular crystalline solids with guest binding cavities or channels and in the last chapter we developed this solid state chemistry into crystal engineering designer solids based on supramolecular interactions Now that we have seen that it is possible to understand and engineer molecular solids we turn to infinite solid-state networks where, formally, there are no discrete molecules and the entire solid is either all one molecule (as in diamond) or made up of relatively few infinite polymeric strands linked together by strong covalent, or more commonly, dative coordination bonds Into this category fall naturally occurring inorganic materials such as zeolites as well as a vast range of coordination polymers infinite coordination complexes in which metal ions are bridged by multidentate ligands into an infinite line or array Some of these materials (e.g zeolites) have cavities and are porous and so act as hosts for guests in the way we saw organic hosts in Chapter Others are not hosts but are still interesting from the point of view of materials design using supramolecular interactions or templating In this chapter we progress from frameworks for capture, storage or transport that are often only stable in the presence of guests (i.e clathration the process of transforming a dense crystal form to an open structure containing the guest) to materials that take up guests reversibly without a major alteration in host structure (i.e sorption relatively facile diffusion of guests into a structure with permanent void space) At the interface between these extremes is nascent interest in host materials that respond to an external stimulus in a controlled fashion This kind of dynamic smart sorbent exhibits more complicated behaviour with significant changes at both the crystal and molecular levels In this chapter we begin with some relatively classical materials that are well-known and move on to the latest research in coordination polymers, particularly metal-organic frameworks that exhibit remarkable structural robustness in comparison to traditional clathrates, yet are highly amenable to design and modification, in contrast to the inorganic zeolites In reaching this point we have come on a long journey following the science of non-covalent interactions, from solution host-guest chemistry, which has been traditionally the preserve of synthetic organic chemists or coordination chemists, through the physical organic chemistry of clathrates all the way to what is really a branch of modern materials science This breadth of supramolecular chemistry is at once one of its most daunting yet exciting features For convenience we will classify network solids according to the dimensionality of their connectivity as listed below, where connectivity in this context refers to a strong covalent or coordination bond Some examples are shown in Figure 9.1 0D solids comprise discrete molecules these are the kinds of compound we considered in the last chapter 1D solids comprise infinite thread-like strands The solid is then made up of the non-covalent packing of these strands 2D solids are made up of sheet-like components that are infinite in two dimensions and pack together via non-covalent interactions in the third Supramolecular Chemistry, 2nd edition J W Steed and J L Atwood â 2009 John Wiley & Sons, Ltd ISBN: 978-0-470-51233-3 What Are Network Solids? 539 3D solids are fully three-dimensionally interconnected covalent or coordination compounds in which the entire crystal is formally a single molecule Figure 9.1 Schematic representation of some of the simple network architectures structurally characterised for metal-organic polymers: (a) 2D honeycomb, (b) 1D ladder, (c) 3D octahedral, (d) 3D hexagonal diamondoid, (e) 2D square grid, and (f) 1D zigzag chain (reprinted from Section Key Reference â The American Chemical Society) Within these categories we will also distinguish between materials that are either porous or non-porous according to strict definitions that we will discuss in Section 9.1.3, and whether or not individual networks are interpenetrated (in one, two or three dimensions) with other networks i.e whether they are mutually topologically entangled in such a way that they could not be separated without breaking bonds We begin with a description of nomenclature that we will use to describe network topology 9.1.2 Network Topology Robson, R., A net-based approach to coordination polymers, J Chem Soc., Dalton Trans 2000, 37353744 Topology is a basic field of mathematics in which any network is reduced to a series of nodes (connection points) and connections Networks are said to be topologically equivalent unless they cannot be deformed into one another without cutting or glueing Thus the topology of networks depends on the way in which they are connected, not on the shape or size of the individual components The science of topology began with Leonhard Eulers solution to the seven bridges of Kửnigsberg problem Kửnigsberg (now Kaliningrad in Russia) was the capital of East Prussia and is built on the River Pregel at the junction with another river The island of Kniephof is situated at the conflux of the two rivers The island and different parts of the mainland are mutually linked by a total of seven bridges, Figure 9.2 The problem Figure 9.2 (a) The City of Kửnigsberg showing the seven bridges The island of Kniephof is in the centre (b) simplified map and, (c) topological representation where land masses are reduced to nodes and bridges are reduced to lines Network Solids 540 is to cross all seven bridges without crossing any one twice In 1735, Euler presented the solution to the problem to the Russian Academy, proving that crossing all seven bridges without crossing a bridge twice is impossible Eulers solution was based on his invention of graph theory, from which, in turn topology developed He reasoned that every land mass muct have an even number of bridges allowing a traveller to get on and off again In fact each land mass has an odd number As far as real network solids go, we can reduce chemical entities such as metal centres or small clusters of metals (termed secondary building units or SBUs) to nodes, and bridging ligands to connections It then becomes possible to describe the topology of a chemical network material In a famous book published in 1977 A F Wells identified a number of commonly occurring chemical network topologies1 and many more are now known, although presumably more remain to be discovered Network topologies may be described by two somewhat related sets of symbols or notation, and it is easy to become confused between them Wells notation takes the form (n, p)-net where n and p are integers that describe, respectively, the shortest route in terms of number of nodes to complete a circuit back to the starting place and the connectivity of a given node Thus a (6,3)-net contains hexagonal holes (or, if irregular, holes that form a six-sided polygon; a 6-gon; n 6) and each node is 3-connected (p 3) A Schlọfli symbol describes the length of the shortest routes, in terms of number of nodes, from one node back to itself based on each pair of connections at the node For example, the Schlọfl i symbol 63 means that 6-gons are the shortest circuit of connecting nodes that can be formed, and that there are three of these circuits radiating out in different directions from each node Similarly the symbol 4.82 indicates that the shortest circuit back to a three-connected node is a 4-gon between one pair of connections and two 8-gons between the other two pairs Some common network topologies and their Schlọfli symbols are given below Note how the hexagonal grid and brick wall patterns are topologically identical they are both 63 (or (6,3) in Wells system) networks The two sets of symbols are not always the same, however For a square grid based on a square planar metal centre node for example, the Wells nomenclature is (4,4) In the Schlọfli nomenclature this network would be described as 4.62 there are four pairs of cis related connections giving four 4-gons (squares in the example shown in Figure 9.3 but there are also two pairs of trans related connections giving fourfold helix perpendicular to page hexagonal grid 63 4.82 'brick wall' 44.62 10-gon 103-a Figure 9.3 Examples of network topologies along with their Schlọfli symbols The corresponding Wells symbols are (6,3), (4,82), (4,4) and (10,3)-a What Are Network Solids? 541 Figure 9.4 Common nets exhibited by simple materials along with their generic names Characteristic rings are shaded The SrSi2 structure is a (10,3)-a net (reproduced with permission from The Royal Society of Chemistry) See plate section for colour version of this image two 6-gons (rectangles) The Wells and Schlọfl i nomenclature can become complicated in three dimensions and for complex topologies, particularly when more than one topologically distinct type of node is present (the nets shown in Figure 9.3 are all examples of uninodal nets; nets with two, three or more types of node are termed binodal, trinodal etc.) For nets that are common, recognised types a trivial name based on the simplest representative member of the series is often adopted (Figure 9.4) For example diamondoid (4-connected tetrahedral centres, Section 8.12), -polonium (or NaCl, with 6-connecting, octahedral centres), the NbO net (square planar 4-connecting centres with a 90 o rotation along each connection); the PtS net (with a : ratio of tetrahedral and square planar nodes), the rutile net (octahedral and trigonal centres in a : ratio); the Pt 3O4 net (with square planar and trigonal nodes in a : ratio) and the Ge3N4 net (with tetrahedral and trigonal nodes in a : ratio) Another interesting net is the cubic (10,3)-a (Wells) or 103-a (Schlọfli) net exhibited by SrSi2 This may be regarded as a three-connected analogue of the four-connected, cubic diamondoid net The a refers to the most symmetrical variant of (10,3) nets identified by Wells The (10,3)-a net is chiral with fourfold screw axes (Box 8.2) running through the structure An nice example is the zinc(II) tripyridyltriazine (9.1) complex [Zn(9.1)2/3 (SiF6)(H2O)2 (MeOH)] ã solvent In this case the Zn(II) ions are each bound to two tripyridyltriazine ligands and so act as essentially linear connectors (the zinc coordination environment is completed by bonds to two water molecules, the SiF62 anion and a methanol molecule, none of which matter from a topological point of view) As a result it is the tripyridyltriazine ligands that we think of as being the 3-connected nodes The network structure actually comprises eight interpenetrating (10,3)-a nets, four of each handedness The environment about one of the fourfold helices is shown in Figure 9.5 Recently there have been significant advances in mathematical tiling theory which have been applied to more rigorous descriptions of complex 3D (or 3-periodic) network topologies The reader is referred to the literature for a complete description of these powerful new methods.3, Network Solids 542 Figure 9.5 The view along the fourfold helix in one of the eight interpenetrating (10,3)-a nets in [Zn(9.1)2/3 (SiF6)(H2O)2 (MeOH)]ãsolvent Helices are highlighted by imaginary poles running along the selected helical axes (reproduced with permission from The Royal Society of Chemistry) 9.1.3 Porosity Barbour, L J., Crystal porosity and the burden of proof, Chem Commun 2006, 11631168 The presence or absence of porosity in solids is of crucial interest in their ability to function as host materials for any substance, be it liquid, solid or gas under ambient conditions Porous materials have very broad applications in catalysis, separations and sequestration applications and are an area of tremendous current interest Len Barbour of the University of Stellenbosch, South Africa, identifies two key criteria (listed below) that must be fulfilled if a material is to be described as porous Permeability should be demonstrated (e.g by gas sorption measurements, spectroscopic evidence of guest exchange or crystallography) The term porous should apply to a specific host phase and not simply to the host molecules as an amorphous or mutating collective Therefore, in principle, the host framework should remain substantially unaffected by guest uptake and removal This requirement means that we not describe, for example, the close-packed, tetragonal -phase of urea as porous, however the description would be appropriate for an empty, hexagonal urea apohost phase (Section 7.3) Given these requirements Barbour identifies three kinds of porosity in the current literature: porosity without pores, conventional porosity, virtual porosity We have already seen in Section 7.9 a number of systems exhibiting porosity without pores This term applies to generally relatively soft solids such as molecular clathrates that can deform in such a way as to allow the ingress and egress of guest molecules without any obvious channel or port in the Zeolites 543 conventional space-filling representation of the structure of the material Porosity without pores is a real and useful phenomenon and the reader is referred to Section 7.9 for a description of some of the fascinating compounds exhibiting this kind of behaviour In this chapter we will focus much more on conventional porosity Conventional porosity requires the existence of permanent, linked gaps or holes in a solid with a minimum diameter of about , and a size typically in the region 310 for microporous solids In Section 7.9 we identified the various categories of micro- meso- and macroporous solids and the size ranges of the pores they possess Note however that pore size, particularly in microporous solids, is somewhat dependent on how it is measured The usual method involves choosing a probe of arbitrary radius (e.g 1.1 the radius of a hydrogen atom) and computationally rolling the probe around the van der Waals surface of the void space and measuring the volume swept out using software such as MSROLL The result is clearly dependent on the choice of probe radius! Conventional porosity is exhibited by compounds such as zeolites and is of tremendous academic and industrial interest The third category, virtual porosity, is not a category of porosity at all according to the definitions given above, but rather a warning to researchers to beware misleading pitfalls Virtual porosity can come about by the appearance of a pore or cavity if a crystal structure is viewed in ball-and-stick mode but disappears if viewed in van der Waals space-filling mode Virtual pores can also be created by artificially not showing a component that the naùve user designates as a guest even if that guest is necessary for the maintenance of the structure, e.g counter anions Thankfully publications exhibiting this false, virtual kind of porosity are rare! 9.2 Zeolites Web site of the International Zeolite Association: http://www.iza-online.org/ This resource contains a comprehensive database of manipulable 3D zeolite structures 9.2.1 Composition and Structure Cejka, J., Zeolites: structures and inclusion properties, in Encyclopedia of Supramolecular Chemistry, Atwood, J L., Steed, J W., eds Marcel Dekker: New York, 2004; Vol 2, pp 16231630 Zeolites are naturally occurring and artificial porous aluminosilicates in which a generally anionic framework is balanced by cations, usually located within the solid cavities or channels, although by no means filling them The global annual market for zeolites is several million tons and they have been phenomenally successful over a wide range of applications particularly in catalysis and separation science problems, especially in the petrochemicals industry Key areas include adsorptive separation of hydrocarbons, purification of gases and liquids, and catalytic cracking of long-chain hydrocarbons to form more valuable short-chain homologues Zeolites also have applications in ion exchange, particularly as a detergent additive (water softening), and the separation and extraction of gases and solvents, e.g as molecular sieves for dehydration of organic solvents The general formula defined by the International Union of Pure and Applied Chemistry (IUPAC) for a zeolite takes the form: [ A a Bb Cc ] {(Ald M e Sif )Og } (xH O, yN) Cations A, B, C Framework composition Occluded guests Each species is also denoted by a three-letter structure code that describes the framework topology (connectivity, channel dimensionality etc.) Examples are given in Table 9.1; common structures of some representative zeolites are shown in Figure 9.6 Network Solids 544 Table 9.1 Characteristics of some common zeolite framework topologies Structure type code Name Type of material Formula AFI AlPO4-5 FAU Faujasite M29[Al58Si134O384] ã 240H2O Al12P12O48 Framework composition Channel Pore system opening AlPO4-based High silica 1D 12-rings 7.3 None Aluminosilicate 3D 12-rings fau 7.4 sod (M Na2, Ca, Mg) High silica AlPO4-based LTA Cage Comments Linde {Na12 [Al12Si12O48] ã Aluminosilicate 27H2O}8 type A ABC stacking of puckered sodalite cage layers d6R 3D High silica Eightrings sod 4.1 Elliptical None Straight channels AlPO4-based GaPO4-based MEL ZSM-11 Nan [AlnSi96nO192] ã High silica 16H2O 3D (n 16) MFI ZSM-5 10-rings 5.5 (mean) Nan [AlnSi96nO192] ã High silica 16H2O 3D (n 27) SOD Sodalite Na6 [Al6Si6O24] ã 2NaCl Elliptical None One straight and one zigzag channel 10-rings 5.5 (mean) Many combinations of Al, Si, P, Ga, Be, As and Zn None 6-rings only sod 2.8 ABC stacking of six rings Zeolites are generally regular crystalline materials, although defects such as non-bridging oxygen atoms, vacant sites or large pores are common, and often contribute to the reactivity of the materials Silicon is the key element in the zeolite framework, with aluminium, as the AlO anionic fragment, most easily substituted within the neutral SiO4 sites In every case the oxygen atoms are bridging A wide range of other TO4 species (termed the primary building units) may also be included (T tetrahedral centre such as Ge, Ga, P, As etc.) In zeolites, Al/Si ratios are known from one to infinity, which corresponds to a minimum requirement that there should be no AlOAl bonds anywhere in the structure; only AlOSi and SiOSi are stable Based on their aluminium to silicon ratio, zeolites are usually divided into two broad categories: Zeolites with low or medium Si/Al ratio (Si/Al 5) Zeolites with high Si/Al ratio (5 Si/Al) Materials with very high Si/Al ratios (tending to infinity) are called all-silica molecular sieves, zeosils or porosils If any aluminium is present, non-framework cations such as alkaline or alkaline earth metals Zeolites 545 Figure 9.6 Topologies of zeolite structure types (a) Sodalite; (b) Linde type A; (c) faujasite (zeolite X and Y); (d) AlPO4-5; and (e) ZSM-5 The vertices represent the positions of AlO4 or SiO4 tetrahedra while straight lines represent SiOSi or SiOAl linkages (Reproduced with permission from [5]) or organic tetraalkyl or tetraarylammonium ions are incorporated within the pores Neutral organic molecules or solvent molecules and water may also be present depending on the synthesis method The smaller cations may be exchanged in ion-exchange processes, while the organic species may be transformed into protons by calcination (heat treatment at about 500 C) About 60 naturally occurring zeolites are known, of which bikitaite, Li2[Al2Si4O12] ã 2H2O, heulandite, Ca4[Al8Si28O72] ã 24H2O and faujasite, (Na2, Ca, Mg)29 [Al58Si134O384] ã 240H2O, are examples The first naturally occurring zeolite, stilbite (NaCa2Al5Si13O36 ã 14H2O), was discovered by the Swedish mineralologist Crứnsted about 250 years ago who found that the new mineral released water on heating, hence its name from the Greek zeo (to boil) and lithos (stone) Many of the more important zeolites, such as ZSM-5 used in the petrochemicals industry for gasoline production, are synthetic, however Recent template syntheses using surfactants have given access to very interesting mesoporous (intermediate pore size) materials such as MCM-41 and MCM-48, which have much larger cavities than the traditional microporous materials ZSM and MCM stand for Zeolite Socony Mobil and Mobil Catalytic Material respectively They form part of a large series of three-letter code descriptions for particular series of materials, particularly those of industrial importance, which have a historical basis, but are still in common usage A full listing is given on the web site of the International Zeolite Association cited at the beginning of this section Much of the usefulness and chemistry of zeolites arises as a consequence of the presence of channels and cavities in the structures, which include metal cations (which counterbalance the charge of the anionic framework), water and a vast range of other guests The beauty of zeolites is that the aluminosilicate cages are sufficiently robust that guest species may enter and leave the channels with no disruption of the host structure As a result, zeolites are used as molecular sieves, separating catioic and molecular guests on a size or adsorption-selective basis, and as reaction vessels for high selective intrachannel and intracavity reactions Network Solids 546 Figure 9.7 Zeolite cage structures incorporated as secondary building units In general the tetrahedral primary building units form common structural features termed secondary building units (SBU some examples are shown in Figure 9.7) that are linked together in different ways to give the overall zeolite structure The inclusion chemistry of zeolites depends very much on the channel and pore size and on the size of the windows giving access to those solid state cavities In the case of sodalite, the -cages (Figure 9.7) are accessible only through four- and six-membered rings (that is comprising four or six tetrahedral atoms with their associated oxygen linkers) that are not large enough to admit the vast majority of guest species In contrast, the Linde type A (LTA) topology, while still based on sodalite cages, contains additional double four-ring spacers This results in -cages accessible by eight-rings and giving the material an overall three-dimensional channel structure Extending the structure still further, in the faujasite type, sodalite cages are arranged in a tetrahedral fashion, exactly like the carbon atoms in diamond, joined by double six-rings The result is the faujasite cage (fau), which comprises a three-dimensional 12-ring channel system The framework is highly porous and ideal for a number of inclusion catalytic purposes In contrast to the SOD, LTA and FAU topologies, ZSM-5 and ZSM-11 are not based on the sodalite motif They are complex structures with 10-ring aperture channels based on the six-ring wrap motif in which the channel walls are made of a sheath of fused six-rings The only difference between the two substances is the occurrence of an inversion centre in ZSM-5 and a mirror plane in ZSM-11 This results in one straight and one zigzag channel in ZSM-5 (Figure 9.8) and entirely linear channels for ZSM-11 The AFI type, typified by AlPO4-5, is also based on channels In pure aluminophosphate zeolites, the Al3 and PO43components strictly alternate to give a neutral cage framework and so there are only even-membered rings The pore system is based on a one-dimensional channel with 12-ring openings Figure 9.8 Linear and zigzag channels in ZSM-5 Index 956 ionophores 53, 54, 57, 2078, 809 binding constants 57 iridescent colours 905, 906 iridium(III)-based antenna array 7234 iridium(III) dihydride, bonding in 516 IRMOF-6 57980 iron, biochemical role 213 iron maidens 180, 3456 iron(III) porphyrin compound 806 iron(IV) tetramethylcyclam oxo complex 8067 irreversible self-assembly 596 2-(4-isobutyryl-phenyl)-propionic acid 817 isochratic (chromatographic) technique 257n isocyanato surfactant 804, 805 isocyanide-based polymers 878 isoleucine 89 isomeric constellations 645, 646 isomorphous crystals 467n isophthalamide, effect of attaching Cr(CO)3 groups 263 isophthalic acid hydrogen bonding interactions, dendrimer assembly by 872 p-isopropylcalix[4]arene 31213 isoreticular expansion 561 isoreticular metal-organic frameworks (IRMOFs) 561, 562, 57980 isosbestic point 15 isoskeletal structures 402 IsoStar scatterplots 485 isostructural crystals 467n isothermal titration calorimetry (ITC) 15, 16, 233 isotopic structures 654 IUPAC see International Union of Pure and Applied Chemistry jam/jelly doughnut molecule jasmine oil 86 Job plots 1213, 14 Johnson solid 648 junk DNA 99 644, 645 Kagans ether, molecular tweezers containing 339 katapinands 224, 225 as anion hosts 233 conformational change on anion binding 233 Kemps triacid 311, 338 molecular clips derived from 3389 Kemps triacid derivative, in self-replicating system 821, 822 kinesin 763 kinetic effects, chelate effect and 18 kinetic selectivity 26, 227 kinetic stability, coordination complexes 636 kinetic template effect 121, 1556, 604, 626 kinetic template synthesis approach 155, 604, 626, 672 knots DNA knots 692, 6967, 698 molecular knots 596, 692700 as topological isomers 692 prime knots 692 topology 6912 kohnkene 3267 X-ray structure 327 Kohnkene precursor 311, 326 koilands 313 koilates 313 Kondo resonance 761 Koopmans theorem 717 Kroto, Harold W 423, 424, 425 Kryptofixđ products 122, 146, 147 labile complexes, meaning of term 636 labile coordination compounds, as anion hosts 260, 299303 -lactamase 892 functional model for 797 lactase 76 ladder structures 494, 565, 637, 638, 639 ladderanes 473, 474 lamellar liquid crystal phases 846 LangmuirBlodgett technique 831, 8334 Langmuir isotherm 833 Langmuir monolayer films 831, 833 nonlinear optical materials in 768, 769 Langmuir trough 8323 lantern structures 575, 577, 579 lanthanide-based networks 567 lanthanide cations binding of 108 dendrimers as ligands for 872, 873 lanthanide(III) complexes in logic gates 7589 in sensors 7345 lanthanide cryptates, in light-conversion devices 7256 lanthanide helicates 61415 lanthanides/lanthanoids see europium; gadolinium; terbium lanthanum complexes of fullerenes 929 lariat ethers 1201, 128 ammonium binding to 141, 142 bibracchial lariat ethers 121, 128, 1412 binding constants for alkali metal complexes 25, 120, 1401 binding free energies for alkali-metal picrates 146 cation binding by 1402 cation interactions 20910 lateral discrimination 182, 183 lateral pressure (monolayer films) 833 lattice energy minimisation procedures 5023 layer-type cyclodextrin complexes 334 layered solids characteristics 5503 classes 551 controlling 5546 Le Chateliers Principle 605 LedenChatt triangle 110 Lehn, Jean-Marie 2, 4, 5, 122, 594 leucine 89 Index Lewis acid chelates 26871 Lewis bases 107, 235 librational shortening of covalent bonds 449 life definitions 820, 823 emergence of 8235 ligand bite angle 137 ligand-exchange reactions 6367 ligand field activation energy (LFAE) 637 ligand field stabilisation energy (LFSE) 636 ligands 107 ligase ribozymes, in self-replicating system 823, 824 light-conversion devices 7256 light-harvesting antenna arrays and pigments 63, 65, 721, 7234 light-harvesting devices 71824 light-harvesting pigments 61, 63, 65 light-powered molecular shuttle 763, 764 Linde type A (LTA) zeolites 544, 545, 546 linear dichroism (LD) spectroscopy 747 & n linear molecular recognition 1845 lipid bilayers 825, 836 lipid-world theory 825 lipids, self-assembly into complex structures 825, 834 liposomes 811 liquid aerosol 922 liquid clathrates 8548 A/A number 855 factors affecting 856 advantages over solid-state separations 857 key properties 854 solution-behaviour model 8556 term first coined 854 liquid crystal displays (LCDs) 830, 8512 liquid crystalline materials, design of 8468 liquid crystals 83952 applications 8512 polymeric 8934 supramolecular 84851 liquid ordering 8301 lithium greases 891 lithography 901, 907 see also soft lithography living system, definition 823 localised molecular orbital approximation 712 lock-and-key interactions enzymesubstrate binding 78, 778 in ferritin molecule 101 modifications 89 logic gates 756, 758 London dispersion forces 35 low-molecular-weight gelators (LMWGs) 889, 890 properties 891 lucigenin (dye), quenching of fluorescence 280, 281 luminescence 710 see also fluorescence; phosphorescence Lycurgus cup (Roman chalice) 922 957 lyotropic liquid crystal phases lyotropic series 2267 lysine 89 835, 841, 846 à2:2 bridging mode of peroxide ligand 794 machine(s) definition 708 molecular analogues 7625 MacKinnon, Roderick 5, 58, 227 macrobicycles contact ion pair receptors 2878 tin-containing 2745 see also cryptands; katapinands macrobicyclic amides 255 macrobicyclic effect 23 chelate effect and 24 macrocyclic amides 254 macrocyclic effect 22, 135 chelate effect and 24 macroporous materials 430 macrotricycles 41 Maddox, J., on crystal structure prediction 500 magnesium tetrapyrrole macrocycles, in photosynthesis 61, 637 magnetic resonance imaging (MRI) 876 magnetic spin crossover 56970 magnetic tweezers 913 magnetism, coordination polymers 56870 manganese, suitability as oxidation catalyst 6970 manganese catalase enzyme 290 manganese-catalysed oxidation of water to oxygen 6870 manganese cubane 527, 528 Mannich reaction 294 Markov growth model 405 mass spectrometry catenands 675 catenanes 669, 671 Maxwells Demon 764 MCM zeolites 545, 547 MECAM 215 mechanical machines, molecular analogues 7625 mechanochemistry 460, 4703, 577 melamineãcyanuric acid derivatives 6512, 653 rosette motifs 651, 652 tape motifs 651, 652 melamineãtetracarboxylic acid diimide network 915, 916 membrane ionophores, in CHEMFETs 7456 membrane potentials 503 membrane transport 5360 menaquinone 66, 67, 81 [9]mercuracarborand-3 273 [12]mercuracarborand-4 273 chloride inclusion within 273, 274 mercury crown compounds 2723 mesogenic polymers 893, 894 mesogens 839 Index 958 mesomorphic behaviour 839 see also liquid crystalline behaviour mesophases, characterisation of 8434 mesoporous materials 430, 545, 547 mesoporous silica structures, templating of 9034 [mesotetrakis(sulfonatomesityl)porphyrinato]iron(III) 806 metacyclophanes in-[34,10][7]metacyclophane 180, 345 [1.1.1]metacyclophanes, substituted see calixarenes metalacetylide polymers 749 metal-atom ligand-vapour synthesis 213 metal-backbone catenanes 6256 metal extraction processes 2978 metal hydrides, hydrogen bonds to 51516 metal-ion-templated synthesis 604 catenanes 672-6 metal-organic frameworks (MOFs) 538, 561, 562, 57883 catalysis by 583 hydrogen storage by 5836 MOF-5 579, 585, 586 MOF-9 5801 MOF-177 584, 585 pyrazene-based 582 see also isorecticular metal-organic frameworks metal interactions 5234 metal salt symport 2978 metal-to-ligand charge transfer (MLCT) 712, 713 metallobiosites 7928 metallocene derivatives in electrochemical sensors 7424 nonlinear optical properties 770 see also cobaltocinium; ferrocene metallogels 888 metallohemicarcerands 6345 metallomesogens 848 metallophilic interactions 36, 37, 525 metalloporphyrin O2 complexes 799800 metalloproteins 704, 792 metallotropic materials 850 metals, hydrogen bonds to 51415 metastable polymorphs 488, 4912 methane absorption by IRMOF-6 57980 encapsulation by tennis ball hosts 642 environmental impacts 392 steam reforming reaction 429, 430 methane hydrate 392 methionine 89 methyl jasmonate 86 p-methylcalix[4]arene, synthesis 199 methylene blue (dye) 8, 805 methylmalonyl-CoA mutase 83 model for 808 5-methyl-2-[(nitrophenyl)amino]-3-thiophenecarbonitrile 488 micelles 8345 self-replication of 825 Michael addition 293, 294 Michaelis constant 77 MichaelisMenten model 77 exceptions 78 microcontact moulding, solvent-assisted 911 microcontact printing 910 microfabrication 9079 micromoulding in capillaries 910 microporous materials 430 microscale machines 708 microtransfer moulding 910 Miller indices 456 minimal self-replicating model 820 examples 820, 821 factors affecting success 821 MIP sensor arrays 87980 Mitsonobu reaction 342, 343 mixed Cheteroatom hosts 20911 mixed cryptates 168 mixed-valence devices 71516 Mn12-acetate 562, 563 models 778, 779 see also biological models; corroborative models; functional models; speculative models; structural models MOFs see metal-organic frameworks molecular baskets 323 molecular beam epitaxy (MBE) technique 921 molecular biology 50 molecular chaperones 596, 598 molecular chemistry, compared with supramolecular chemistry molecular clips 323, 3389 molecular containers 61719, 62035 molecular devices and machines 70775 principles 708 molecular electronics 746, 892 molecular elevator 7623 molecular extension cable 729 molecular graph 654 molecular guests, in solution 30784 molecular imprinted polymers (MIPs) 87980 molecular imprinting in dendrimers 8702 molecular iron maidens 180, 3456 molecular knots 596, 691700 molecular lock method, platinum catenane synthesis by 626 molecular logic 75660 molecular loops 635 molecular machines 7625 molecular memory devices 7601 molecular motors 763, 886, 887 molecular muscles 762 molecular necklaces 325, 6778 molecular orbital (MO) diagram, octahedral transition metal complex 712 molecular panelling 61718, 62933 Index molecular ratchets 7645 molecular reaction vessels hemicarcerands as 3767 softball and tennis ball hosts as 6434 molecular recognition between host and guest 8, 709 molecular recognition strategy (in catalysis) 815, 816 example of application 816, 817 potential problems 81516, 817 molecular rectifiers 7502 molecular rosettes 6512 molecular scaffolding 6249 molecular self-assembly, compared with supramolecular self-assembly 594 molecular sensors basis 730 construction criteria 731 molecular sieves, zeolites as 545 molecular squares and boxes 62435 coordination capsules 6345 molecular panelling approach 62933 molecular scaffolding approach 619, 619, 6249 molecular surgery approach to guest-encapsulation in fullerenes 9301 molecular switch tunnel junction (MSTJ) 760 molecular switches 7526 molecular symmetry operations 460 molecular syringe 208 molecular transistor 761 molecular tweezers 3368, 33940 chiral 33940 progression to cyclophanes 3467 molecular wires 713, 7469, 750, 892 molecular zippers 616, 617 molybdenum blues 563 molybdenum carbide complex, formation using macrocycles 1523 monodisperse latex spheres 906 monolayers, formation of 832, 833 monotropic polymorphism 489 montmorillonite 551 montmorillonite clay particles, condensation of nucleotides catalysed by 469, 824 Mo(O)Cl2 (PMe2Ph)3 466 Moores law 901 & n morpholine 48 inclusion by Dianins compound 409 morphosynthesis 9025 motif 477 Mukaiyama-aldol reaction 583 Mỹlliken correlation 33 Mullis, Kary B 91, 594 multi-component molecular crystals 493 see also co-crystals multimediated multiple interaction self-assembly 597 multiple interaction self-assembly 597 multistorey self-assembled structures 639, 640 multi-walled carbon nanotubes (MWCNTs) 933, 936 959 murexide indicator 112, 739 muscle contraction 886 muscle mimics 7623 mycobactin 213, 214 myoglobin, oxygen saturation curve myosin 763, 886, 887 74 NaCl lattice 27, 233 Na /K-ATPase enzyme 50, 51, 76, 785 crystal structure 5960 see also ATPase naked anion effect 1501, 286 example 1523 NAND gate, molecular logic 7589 nanobelts 927 nanobiology 9012 nanochemistry 445, 899938 nanoclusters 922 nanocomposites 9045 nanocrystals 44, 922 see also quantum dots nanofabrication 90911 nanomaterials 44 nanoparticle-based sensors 9245 nanoparticles 44, 9217 definition 9212 gold nanoparticles 44, 9225 non-spherical nanoparticles 927 nanorings 927 nanorods 927 nanoscale containers 909, 915, 916 nanoscale machines 708 nanoscale photonics 905-6 nanoscience, meaning of term 900 nanoscratching 4723 nanosphere templated materials 906 nanostar dendrimer 874, 875 nanotechnology 44, 9002 bottom-up/synthesising up approach 593, 901, 909 top-down/engineering-down approach 593, 901, 907 nanotubes 553, 8813, 927 see also carbon nanotubes; peptide nanotubes napalm 891 naphthalene, crystal structure calculation for 5034 naphthalene-2-sulfonate, binding in diphenylene-based host 352 natural gas hydrates 392 NbO framework 541, 567 negative cooperativity 17, 610 negative thermal expansion (NTE), coordination polymers 5701 nematic liquid crystal phase 840, 8412 degree of order 842, 843 in LCD applications 8512 nerve cells, signal transduction in 52 nerve gas agents, colorimetric detection of 738 nesting complexes 148, 183 Index 960 nests 2301 netropsin, binding to DNA 97 network solids 53789 classification 5389 concepts 538 network topology 53941 (6,3) net 540 (10,3)-a nets 541, 542 notation 5401 neurodegenerative diseases 885 neurotransmitters 834 neutral anion receptors 2519 neutron diffraction 175, 448 nicotinamide adenine dinucleotide 797 reduced form (NADH) 80, 803 nicotine 84 nicotinic acetylcholine receptor protein 845 nitro/iodo supramolecular sython 445, 446 nitroanilines, Etters rules for hydrogen bonding 479 nitrocefin, hydrolysis of 797 nitrogen analogues crown ethers 25, 120, 143, 1602 cryptands 1634 nitrogen dioxide, calixarene binding 314 NMR spectroscopy see nuclear magnetic resonance (NMR) spectroscopy noble metal nanoparticles 923 see also gold nanoparticles nomenclature cation-binding macrocycles 1279 coordination complexes 1089 enzymes 76 nonactin 53, 57 binding to DNA 97 non-covalent anion coordination chemistry 224 non-covalent interactions 2737, 4456 nonlinear optical (NLO) effects 765 origins 7658 nonlinear optical (NLO) materials 76571 crystal engineering 445, 446, 526, 765 data for metallocene derivatives 770 second-order 76871 third harmonic generation materials 771 non-spherical nanoparticles 927 non-vitamin coenzymes 81 NOT gate 758 nuclear fuel industry applications 225, 292, 297, 299 nuclear magnetic resonance (NMR) spectroscopy 1869 aromatic ring current effects 186 azacyclophanes 179 chiral shift agents 681 complexation-induced shifts (CIS) 352 crystal nucleation analysed by 4556 guest exchange dynamics 1878 solution structures analysed by 3523 spinspin coupling 187 nuclear magnetic resonance (NMR) titration 12, 13, 186 examples 252 nuclear Overhauser enhancement (NOE) effects 1867, 352 calix[4]arenes 2012 nucleobases 87, 88 hydrogen bonding interactions between 901 nucleotide base co-crystals, Etters rules for hydrogen bonding 480 nucleotides 87, 88 octahedral iridium(III) compounds, energy-transfer processes in 7234 octahedron, self-assembly of 6302, 631 octaphyrin, diprotonated, SO4 binding by 245, 246 octaporphyrin nanocyle 632, 634 octazacryptand 238, 247 office block structures 639 oil and gas industry hydrate-formation problems and ways of addressing 3912 see also petroleum industry Okazaki fragments 98, 99 olympiadane 665 one-dimensional chains/ladders/strands 529, 538, 539, 565 opal 9056 optical isomerism 11012 optical lithography 9079 photochemistry 908 optical tweezers, nanomanipulation using 913, 914 OR gate, molecular logic 759 order in liquids 8301 organic cations, complexation of 18095 organic zeolites 4345, 52830, 558, 575 organocatalysis 814 organogels 888 organometallic materials, nonlinear optical properties 770 organometallic receptors 2616 Ostwalds step rule 488 oxidation states 107 oxonium ion crown ether complexes 1746 oxygen-evolving complex (OEC) 68 oxygen uptake and transport by haemoglobin 704, 798 by mimics/models 798803 oxyhaemocyanin, X-ray crystal structure 794 -acid ligands, complexes stabilised by 169, 20813 interactions 335, 310, 51922 edge-to-face interactions 34, 310, 519, 616, 617 face-to-face interactions 34, 310, 519, 5202 in molecular tweezers 337 in photochemical devices 728 synthesis of catenanes involving 6606 synthesis of pseudorotaxanes involving 6567 synthesis of rotaxanes involving 65760 P-loop 231 31 P NMR spectroscopy, ATP hydrolysis by azacorand 786 paddle structures 575, 577, 579 Index paracetamol, crystallisation of 4534 paracyclophanes [2.2]paracyclophane 211, 212 Cr complex 213 [3.3]paracyclophane 211, 212 Cr complex 212, 213 [2.2.2]paracyclophane 211, 212 paraquat 194, 195, 656, 657 charge-transfer complexes 195, 357 Pauling, Linus, on enzymes 78 Pauling model (for binding of oxygen to haemoglobin) 71, 72, 78 Pd(en) moiety 617, 619 in molecular panels 632, 633 in molecular squares 619, 625, 626 peak selectivity (of cryptands) 1423 Pedersen, Charles 5, 114, 195, 224 pencillin-resistant bacteria, sensor for 8923 pentaethyleneglycoldimethylether 25 pentafoil knots 696 pentagon-based topology 566 peptide-based anion receptors 2589 peptide links 889 peptide nanotubes 881 perching complexes 148, 181 perching geometry 241, 257, 273 perhydrotriphenylene (PHTP) inclusion compounds 4036 3-periodic network topologies 541 peripheral crowding, rosette formation by 651, 652 pernicious anaemia, treatment of 82 persistence length (of polymers) 878 pertechnetate anion, binding of 292 perylenyl chromphore 729, 730, 874 petroleum industry separation of hydrocarbons 3945 zeolites in 54850 see also oil and gas industry pH-activated molecular elevator 7623 pH measurements 177 pH sensors 734, 745 pharmaceutical industry applications co-crystallising agents 496 cyclodextrins 336, 493 effects of hydrate formation 497 polymorphism 4878 phase problem (in X-ray crystallography) 55 phase transfer catalysis 14950, 151, 204 phenanthroline and derivatives in catenate synthesis 6734, 676 in helicate synthesis 679, 693 in photochemical devices 717 phenylacetic acid, retrosynthetic analysis 4445 phenylalanine 89, 250 m-phenylene diamide anion binding group 2878 o-phenylenedimercurial receptor adducts/complexes with chloride anion 271 oxo-bridged analogue 272 961 pheromones 85, 778 phloroglucinol see 1,3,5-trihydroxybenzene phosphate binding protein (PBP) 228, 235 phosphodiesterase, cyclodextrins as mimics 782, 783 phospholipid biomembrane 53 ion transport across 54 molecular conductivity through 747, 748 phosphorescence 710, 711 phosphorus-containing macrocycles 1678 photochemistry see supramolecular photochemistry photo-excitation, radiative events following 71011 photo-induced electron collection and storage system 720 photo-induced electron transfer 714, 715, 720 mediation by -stacking interactions 728 photo-induced electron transfer (PET) sensors 732, 733 photolithography 907 photonic crystals 9056 photonic devices, in biological systems 601 photophysical fundamentals of supramolecular photochemical 71013 photophysical sensing and imaging 7318 photoresist 907 photoswitchable systems 753, 755 photosynthesis 6370, 720 photosynthetic systems key components 65, 726 mimics 7204, 726 photosystems PSI and PSII 68 phthalocyanines 172 picket fence porphyrins 73, 801 picnic basket porphyrins 801, 802 picrates, alkali-metal 144, 1456, 150, 151 piedfort unit 409, 410 pillared clays 5523 mimics 555 PIXEL method 503 plastic materials 865 plateau selectivity (of crown ethers) 135, 136, 137 platinum anticancer drugs 934 platinum(II) ethylenediamine complexes 6256 in molecular necklaces 6778 see also Pt(en) moiety platinum(II) polyalkyne molecular wire 747 Platonic solids 427, 648, 649 occurrence in natural forms 444 plug-and-socket system 728, 729 molecular extension cable as part of 729 Pockels surface balance 831 pocket porphyrins 801, 802 podands 19, 22, 24, 11820, 127 ammonium-based 23940 binding constant of K complex 25, 120, 135 binding free energies for alkali-metal picrates 146 rigid end group concept 11920, 346 podates 129 polar flattening effect 486, 487 polar superlattices 876, 877 Index 962 polarisability 766 factors affecting 767 polarised optical hot-stage microscopy, liquid crystals viewed in 83940, 843 poliovirus, assembly of protein capsid 593 -polonium (-Po) network 541, 568 polyacetylene 424, 425 polyamides, in protein backbones 230 poly(amido amine) (PAMAM) dendrimers 863 rheology 865 polyamines basicity 177, 178 location of protonation site 179 polycatenanes 8834 polymer surfaces, crystal nucleation affected by 492 polymerase chain reaction (PCR) 923, 94, 594 polymeric liquid crystals 8934 polymersomes 878 polymorph screening 492 polymorphism 48792 controlling 492 first described 487 importance 4878 types 48992 polyoxomolybdate nanoclusters 5623 polypeptide-based materials, electron-transfer characteristics 748 polypeptide chains 75 poly(propylene imine) dendrimers divergent approach to synthesis 867 ESI-MS spectra 869 polyrotaxanes 883, 885 nets 678 poly(styrene)-b-poly(butadiene)-b-poly(t-butyl methacrylate) triblock co-polymer 876, 877 polytopic receptors 184 porosity of solids, factors affecting 5423 porous materials classification by pore size 430, 543 coordination polymers 5758 without pores 436, 5423 porphobilinogen deaminase 231 dipyrromethane-based cofactor in 232 porphyrin-based molecular wire 749 porphyrin chromophores magnesium-containing 63, 64, 65 zinc-containing 7267, 728 porphyrin-imprinted covalent dendrimer 871, 872 porphyrins 612 doming in 71, 72, 799, 800, 803 expanded 2445 iron-containing 806 zinc-containing 60610, 646, 726 see also expanded porphyrins; picket fence porphyrins; picnic basket porphyrins; pocket porphyrins positive cooperativity 17, 610 in helicate formation 685, 686 postmodification, self-assembly with 596, 6023, 604, 632, 634 potassium channels 58, 227 potassium dihydrogen phosphate (KDP) 454, 526 diamondoid networks 526, 527 uses 527, 765, 767 potassium hydrogen phthalate crystals 469 potassium ion (K), biochemical distribution 51 potassium permanganate, oxidation of organic substrates by 151, 152 potassium sulfate, hourglass inclusion compounds 465 potentiometric titration 1112, 240 powder X-ray diffraction (PXRD) 471, 4746 compared with single-crystal method 474 structure solution model 475 Powell, H M 6, 386 prebiotic chemistry 823 precursor preprocessing 602, 603 precursors, modification followed by self-assembly 596 preinsulin 603, 604 preorganisation 225 anion hosts 2323 combined with complementarity 256 for herbicide receptors 195 kinetic and dynamic effects 1479 rosette formation by 651, 652 thermodynamic effects 1447, 604 preprogramming 592 pretzelane 666, 667 primary charge separation 66, 67, 710 primary hydrogen-bond interactions 30 principal component analysis (PCA) 742 prion-based diseases 885 prions 598, 886 processive catalysis 99 prodigiosins 232 mimics 257, 258, 296 proinsulin 603, 604 proline 89 O-propyl-p-t-butylcalix[4]arene, NO complex 314 propylene diamine, donor group orientation for 133 protein amino acids 8890 protein self-assembly 10010 protein tyrosine phosphatases (PTPases) 229 proteins diffusion into 432 folding of 596 main-chain anion binding sites 2301 quaternary structures 75, 598 secondary structures 75, 598 self-assembly of 598 tertiary structures 75, 598 X-ray crystallography 56 protocells 825, 836 proton binding hosts 17380 Index proton complexes solution chemistry 17780 see also pH proton NMR spectroscopy cryptophanes binding to halocarbons 361 crystal nucleation studied by 4556 solution structures analysed by 3523 proton sponge 268, 269 complexes 449 protoporphyrin IX 62, 231 Prussian blue 56871 bridging cyanides in 5689, 624 PS-PIAT block co-polymer 878 vesicles formed by 878, 879 pseudopolymorphism 489, 490 pseudorotaxane-based chromophoric switch 756, 757 pseudorotaxane-based XOR gate 75960 pseudorotaxanes 641, 6534 polyrotaxanes synthesised from 885 synthesis directed approach 6567 statistical approach 656 Pt(en) moiety, in molecular squares 6256 PtS network 541 pulsed laser deposition (PLD) technique 920, 921 pump storage model 512 purines (in DNA) 87, 88 pushpull polyenes 768, 769 pyrazene carceplex relative stability 374 X-ray crystal structure 375 pyrazole ligands 301 pyrene butyric acid 650, 651 pyrene excimer 711, 712 pyridoxamine cofactor 785 pyridyl/terpyridyl tecton, coordination polymers based on 915, 917 pyridylpyrazne-based assemblies 627 pyrimidines (in DNA) 87, 88 pyrogallo[4]arene 647 hexameric assembly 650 pyrrole-based anion receptors 2578 pyrrole-based biomolecules 62, 2312 pyrrole-based macrocycles 2456 quantum corrals 9001 quantum dots 922, 9256 quaterpyridine, in helicates 680, 6812, 6823 quencher 726 quinone receptors 3556, 507 quinquepyridine, in helicates 682 racemic crystals 4934 rack structures, self-assembled 637, 640, 641 radiolaria, structural mimics 9023 ranitidine hydrochloride 488 ratchet movement 764 963 ravels 697, 698 reaction vessels see molecular reaction vessels receptorsubstrate binding, enzymes 78 receptors term first introduced see also anion receptors; cation receptors; ion pair receptors; neutral receptors rectifiers 750 redox potential environmental factors affecting 267 estimation by cyclic voltammetry 266 redox sensors 254, 354, 7423, 928 redox-switchable rotaxanes 755 reflection high-energy electron diffraction (RHEED) 921 replica moulding 910 reporter dye(s) 650 repulsive gauche effect 131 resorcarene-based carcerands 3705 [5]resorcarene-based carcerand 379, 380 resorcarene-based ion pair receptors 294, 295 [4]resorcarenecalix[4]arene hybrid carcerands 3756 resorcarene hexamers 635 [4]resorcarene tetracarboxylic acid, in hydrogen-bonded capsules 648 resorcarene trimers 635 resorcarenes conformations 312 dithiocarbamate-functionalised 635 [4]resorcarenes dimethylsilyl derivative 316, 317 dodecyl phosphocholine complex 318 hexamers, fluorescence detection by 72930 intramolecular hydrogen-bonding interactions 312 in molecular containers 6478 multiply bridged 316, 317 with rigid upper rim 322 structure 311, 312, 647 sulfonated derivatives 31516 synthesis 311, 312 tetrametallic complexes 276 reticular synthesis 561 retina (of human eye) cone cells 61 rod cells 601 retrosynthesis 443 example 4445 retroviruses 824 reverse micelles 834, 835 rheniumalkyne oligomers 7489 rheology 8645 dendrimers 8656 rhinovirus 101 topology 650 Rhodopseudomonas viridis photosynthetic reaction centre 656 charge separation at 67 rhodopsin 601 Index 964 rhombicubeoctahedron 427 ribbon structures 445, 446, 511, 517, 525 ribonuclease 100 ribonucleic acid (RNA) 90, 824 ribozymes 823, 824 RichmanAtkins cyclisation reaction 158, 159, 344 Rietveld refinement method 471, 476 rigid end group concept, in podands 11920, 346 rigid group principle 345 ring-opening metathesis polymerisation (ROMP) 748 ritonavir 488 RNA-world hypothesis 824 rod-coil co-polymers 8778 rose Bengal (dye) 870 rosettes 6512 rotavirus 1012 [2]rotaxane-based switchable molecular shuttle 7545 rotaxanes 325, 605, 606, 65378 hydrogen-bonded 6679 in molecular necklaces 678 nomenclature 6534, 654 [2]rotaxane 658 [3]rotaxane 658, 659 [4]rotaxane 658, 659 synthesis 6534 alkene metathesis approach 658 auxiliary linkage approach 676, 677 clipping procedure 658 directed approaches 65760 slipping procedure 658 statistical approach 656, 672, 673 threading procedure 657, 658 see also polyrotaxanes ROY 488 [Ru([9]ane-S3)(4,4-bipyridyl)3]21 (supramolecular cube) 622, 6234 [Ru(bpy)3] electrochemical properties 717 phosphorescence spectrum 717 RuddlesdenPopper (RP) series 921 Russian doll complex 335 ruthenium(II) biimidazole complexes, hydrogen bonding from 51112 ruthenium(II) calix[4]arene host 252, 264 ruthenium(II) chelate complexes 25960 ruthenium(II) complexes in nonlinear optical devices 7701 in photochemical devices 717 ruthenium(II)/iridium(III) photochemical device 720, 721 rutile network 541, 568, 569 saccharin co-crystal with carbamazepine crystallisation of 4624 salen-based receptor 292 salicylaldoxime 298 Salmonella typhimurium 4967 binding-protein/sulfate interactons 228 chloride channel 58 enterobactin 214 sandic nematic liquid crystal phase 893, 894 sandwich polymers 272, 273 sapphyrin diprotonated 244 complex with fluoride 245 sarcophagenes 1234, 128 saturated hydrogen-bonded (SHB) co-crystals 494 scaffolds 27681 cholapods 27881 trialkylbenzene-based 251, 2778 scanning probe microscopies carbon nanotubes as probes 933 see also atomic force microscopy; scanning tunnelling microscopy scanning tunnelling microscopy (STM) 45, 91112 high-resolution 91718, 919 nanomanipulation using 45, 913, 914, 915 visualisation by 914, 916, 917, 919 scanning tunnelling spectroscopy (STS) 918 Scatchard equation/plot 21, 22, 610 Schiff base condensation reactions 4, 1701, 342 Schiff base macrocycles in cascade complexes 28990 example of use 1712 first to be synthesised 170 Schiff bases 1702 Schlọfli symbols 540 second-generation dendrimers 862, 863 second harmonic generation (SHG) 767 second harmonic generation (SHG) nonlinear optical materials 765, 76871 secondary bonding 37, 525 secondary building units (SBUs) 540, 546, 561, 562 secondary charge separation 66, 67 secondary hydrogen-bond interactions 301 Seebeck effect 761 selectivity 16, 26, 740, 7789 selenium-containing macrocycles 163 self-assembled monolayers (SAMs) 8379 cyclodextrins 320, 321 on silicon surface 8389 thiol-based 8378 self-assembled supramolecular polymers 8803 self-assembled viruses 101 self-assembling catalysis 815, 819 self-assembling coordination compounds 62041 design 620, 621 grid/ladder/rack arrays 63741 molecular squares and boxes 62435 notation 621, 622 supramolecular cubes 6214 self-assembly 3, 7, 42, 43, 591706 anion templating 3003 assisted 596 Index biochemical 99102, 6004 catenanes and rotaxanes 65577 classification 5957 closed complexes 64153 concepts 5945 cooperativity in 61015 with covalent modification 596, 6023, 632, 634 crystallisation as 442 definition 592 directed 596, 626 DNA 91, 99100 extended-site binding model 611, 61315 helicates 68191 hydrogen bonding in 64153 with intermittent processing 596 irreversible 596 labile complexes 300, 3012 ligands with anion and cation binding functionality 260 metal arrays 63741 panelling approach 61718, 62936 with postmodification 596, 6023, 604, 632, 634 precursor modification followed by 596, 602, 603 probability 61619 scope and goals 5924 strict 5956, 6002 on surfaces 91418 template effects 6046 thermodynamic model 60610 time-resolved 594 self-complementary assemblies 6416 self-complementary building blocks 527, 528, 606 self-organisation 43, 595 self-recognition, helicates 6845 self-replicating peptides/proteins 824 self-replicating systems 606, 81923 self-poisoning in 8212, 823 see also minimal self-replicating model self-replication 5934 and Darwinian evolution 823 minimal model for 820 semiconductor nanocrystals 926 see also quantum dots semiochemistry biological 856 meaning of term 85, 730 supramolecular 7301 sensing arrays 740, 741 sensing and signalling 85, 730 sensitised lanthanide(III) complexes, as sensors 7345 sephulchrates 123, 124, 128 serine 89, 228 serine proteases, oxyanion hole in 231 seven bridges of Kửnisberg problem, Euler solution 53940 sexipyridine 683, 684, 716 sheathed rack structures 640, 641 ship-in-a-bottle structure, in octahedral capsule 630, 632 965 siderands 217 siderophores 21317 naturally occurring 21315 synthetic 21517, 604 silicon-containing Lewis acid chelates 270 silicon surfaces, self-assembled monolayers on 8389 silk inverse opal 906 simultaneous anion and cation binding 28699 single cell patch clamp method 811 single-crystal neutron diffraction 448 single-crystal X-ray crystallography 556 compared with powder X-ray diffraction 474 single-interaction self-assembly 597 single-molecule chemistry 91314, 915, 91820 single-molecule magnet 562, 563 single-molecule wire 749, 750 single-walled carbon nanotubes (SWCNTs) 933 buckminsterfullerence molecules as inclusions 933, 934 carborane derivative confined in 933, 934, 935 single crystals encapsulated in 933, 934 site binding model 610 Ercolanis model 61113 extended 611, 61315 site-directed mutagenesis 912, 93 sixfold aryl embrace (6AE) 446, 522, 523 small-angle X-ray scattering, liquid crystals studied by 844 Smalley, Richard E 423, 425 smectic liquid crystal phases 841, 8423 degree of order 842 Smith, Michael 91 snub cube, [4]resorcarene-based 64950 soaps 832, 834 soccer ball cryptand 123, 129, 236, 237 tetrahedral recognition of NH4 by 180, 181 soccer ball cryptates 237 social isomerism 644, 645, 646 sodalite (SOD) zeolites 544, 545, 546 sodium chlorate, magnetically stirred crystallisation of 459 sodium chloride (NaCl) lattice 27 sodium dodecyl sulfate (SDS) 318 sodium ion (Na), biochemical distribution 51 sodium ion channel 54 soft ions and ligands 110 soft ligands for soft metal ions 16073 soft lithography 90911 advantages and disadvantages 911 softball-shaped hosts 6423, 814, 815 sol 890, 922 solgel process 88990, 922 solid aerosol 922 solid solutions 493 solid-state cyclodextrin hydrates 3301 solid-state cyclodextrin inclusion complexes 3335 solid-state hostguest compounds 6, 3867 see also clathrates Index 966 solid-state inclusion complexes calix[4]arene-based 313 [4]resorcarene-based 313 solid-state inclusion compounds 385440 solid-state inclusion polymer(s), silicon-containing 313 solid-state separation, liquid clathrate based separation compared with 857 Solomon knot 699 solution, molecular guests in 30784 solution self-assembly 442 solvating reagents, in metals extraction processes 297 solvation effects 3941 in anion binding 234 solvation free energies, listed for various anions and cations 226 solvation shell 830 solvatomorphism 489 solvent-assisted micromoulding 911 solvent-separated ion pairs 286 solvophobic effects, guest encapsulation affected by 643 sonic spray ionisation mass spectrometry (SSI-MS) 635 sorption, compared with clathration 538 spatiotemporal theory 79 speciation maps, Pd(en) /4,4-dipyridine mixtures 619, 620 specific rotation 369 speculative models 793 speleands 193 speleates 193 spherands 4, 1256, 127 binding constants 25 binding free energies for alkali-metal picrates 145 binding of NH4 by 183 conformational rearrangement in Li spheraplex 147 hybrid hosts 126, 127 synthesis 126 spheraplexes 126, 129, 144, 147 spillover (hydrogen molecule splitting) 585, 923 square brackets 9n, 106, 197, 341 square grid topology 539, 566 square planar Pd(II) and Pt(II) complexes 95, 112, 162 in metallomesogen 848, 849 transformation to square pyramidal adduct 4367 squarine-based siderophore 216, 217 SrAl2 framework 541 SrSi2 framework 541 stannacycles 2745 starch 331 steel swords 9356 stepwise binding constants 10 formation of supercomplexes 242, 243 steric compression, in cyclophanes 3456 sterically directed synthesis of catenanes 669, 670, 671 Stern layer 834, 835 steroids, binding in dendrophanes 351 sterol framework, in cholapods 278, 279 stilbite 545 Streptomyces lividans, potassium channel 58 strict self-assembly 5956 examples 6002 structural isomerism, bipyridyl and terpyridyl complexes 717, 718 structural models 792 structure correlation principle 484 sulfamerizine 4556 sulfate binding protein (SBP) 228 sulfonated [4]resorcarenes 31516 binding constants with various alcohol guests 316 p-sulfonatocalix[4]arene 4269 in heterodimeric capsules 646 spherical assemblies 427, 428, 429 structure compared with vermiculite 426 tubular assemblies 427, 428, 429 p-sulfonatocalix[n]arenes 315, 426 sulfur analogues crown ethers 161, 1623 cryptands 163 sulfur dioxide, absorption by coordination compounds 4367 sulfur extrusion reactions, cyclophanes synthesised by 342, 343 superanion complexes 427 superatoms 927 supercomplexes 241 superexchange mechanism 715 superlubricity of graphite 34, 520, 5512 supersaturated solutions, crystal growth in 454 supersecondary structure 598 superstring theory 691 super-wurtzite structure 495 supported liquid membrane (SLM) 297 supramolecular catalysis 81323 supramolecular chemistry compared with molecular chemistry definitions 23, 708 development 46 supramolecular chemistry of life 49104 supramolecular cubes 6214, 648 supramolecular dendrimer assemblies 8724 supramolecular design 415 supramolecular devices, definition 70910 supramolecular gels 88893 applications 8913 rheological properties 865, 866 supramolecular grid-type assemblies 63741, 919, 920 supramolecular interactions 27, 308 types 2737, 30910 anion interactions 33 cation interactions 32 closed shell interactions 367 crystal close packing 36 dipoledipole interactions 28, 308 electrostatic interactions 310 hydrogen bonding 2832, 308, 310 Index hydrophobic binding 389, 309 induced dipolar interactions 310 iondipole interactions 278, 308 ionion interactions 27 interactions 335, 310 van der Waals interactions 35, 235 supramolecular isomerism 492, 555, 562 supramolecular liquid crystals 84851 supramolecular photochemistry 71030 energy/electron-transfer mechanisms 71315 light-conversion devices 7256 light-harvesting devices 71824 mixed-valence devices 71516 non-covalently bonded systems 72630 photophysical fundamentals 71013 pyridyls as device components 71618 supramolecular plug-and-socket system 728, 729 supramolecular polymers, self-assembled 8803 supramolecular self-assembly 3, 7, 42, 43, 591706 compared with molecular self-assembly 5945 supramolecular semiochemistry 7301 supramolecular synthons 4434, 445, 446 supramolecular tectons 42, 445, 594 surface adhesives 887 surface interactions 309 surface plasmon resonance (SPR) absorption 44, 922 surface tension 833 surfaces, self-assembly on 91418 surfactants 8312 types 832 SuzukiMiyaura cross-coupling reaction 344 switchable molecular devices 7526 switchable nonlinear optical devices 7701 symport 59, 286, 2956 examples 245, 246, 258, 2968 synergic effect 16970 synthesising up approach 593 synthons 4434, 446 syringe action of calixarenes 208 tailbiter foldamer 600 tape structures 445, 446, 511, 517, 525, 651, 652, 749, 8901 tartaric acid derivatives, in hydrogen-bonded helices 6889 Taube, Henry 286n, 636 tectons 42, 445, 594 tellurium-containing macrocycles 163 template effect 122, 1537, 594 in self-assembly 6046 template patterning mechanism for biomimetic structures 903 template positioning, for solid-state topochemical photocyclisation 473 template ratios, carcerand synthesis 373, 374 template reactions/synthesis 43, 109, 1537 benzo[18]crown-6 1556 carcerands 373 catenanes 660 967 clathrate hydrates 3889 enterobactin 214 metal-ion-templated 604, 6726 metalloid-templated 6045 phthalocyanines 172 tetraazamacrocycles 156, 166 triphosphine macrocycle 168 zeolites 547, 548 templation, self-assembly based on 43, 594, 8912 tennis ball-shaped hosts 6412, 648 terbium complexes in logic gates 7589 in sensors 734 terephthalic acid 529 termite mound 43 terpyridine, in photochemical devices 716, 71718 testosterone 351 binding in dendrophanes 351 1,4,7,10-tetraazacyclododecane, synthesis 159 1,4,8,11-tetraazacyclotetradecane synthesis 165, 166 see also cyclam 1,6,20,25-tetraaza[6.1.6.1]paracyclophane 347, 348 durene complex 347, 348 1,1,2,2-tetrachloroethane, effect on binding constant of host 39, 40 tetra-N-cyclam basicity 178 binding with transition metals 165 tetrahedral receptors 2367 tetrahedral tetrametallic self-assembled clusters 6289 tetra(hydroxypropyl)cyclam 2934 tetra-1-naphthoid 412, 413 tetranuclear complexes, energy-transfer processes in 723 tetrapyrrole macrocycles 612, 801, 244 in photosynthesis 61, 637 tetrathiafulvalene (TTF) 358 cyclophane based on 358 redox chemistry 358 tetrathiafulvalene (TTF) derivatives in addressable molecular electronic devices 7601 in electrochemical sensors 745 tetrathiafulvalene-derived dipyridophenazine (TTF-dppz) ligands, in photochemical devices 724 tetrazamacrocycles, synthesis 156 thermal conductivity, inclusion compounds 390, 408 thermal expansion, negative 5701 thermodynamic anion templating 3002 thermodynamic effects, chelate effect and 18 thermodynamic selectivity 26, 227 thermodynamic stability, coordination complexes 636 thermodynamic template effect 156, 605 thermodynamic template synthesis of Schiff base macrocycles 1701 of tetrazamacrocycles 156 thermoelectric effect 7612 Index 968 thermogravimetric analysis (TGA) 55960 examples 3667, 558, 559, 561 thermometers, liquid crystalline 851 thermotropic liquid crystal phases 8413, 8445 thiacalixarenes, water binding in 434 thiacrowns 131 thiohydantoin, nanoscratching of 472, 473 thiols, functionalised 837, 923, 924 thiourea-based receptors 2567 thiourea clathrates 2556, 393 1-bromoadamantane-based 398 thiourea derivatives, organocatalysis with 814 third-generation dendrimers 862, 863 third harmonic generation 767 third harmonic generation nonlinear optical materials 771 thixotropy 889 threaded rotaxane-type compounds 669 three-dimensional hosts, binding of ammonium cations by 1834 three-dimensional networks 52630, 539, 567 see also diamondoid networks three point rule (in chiral recognition) 18990 threonine 89 ThSi2 framework 541 time-resolved self-assembly 594 timeline, supramolecular chemistry development tissue engineering 891 titanium dioxide nanoparticle, in photon acceptor 727, 728 tobacco mosaic virus (TMV) 101, 6001 6(p-toluidino)naphthalene-2-sulfonate 352 top-down approach 593, 901, 907 topochemistry 443, 470, 4734, 917, 918 topoisomerase 98 topological isomers catenanes as 654, 655, 691 knots as 692 topological trapping by dendrimers 870 topology 53940 knots 6913 torands 173 trace products, amplification of 818, 819 trans/anti conformation 130, 319 transacylases cation-binding hosts as mimics 78892 functional mimics 78890 structural mimics 7902 see also chymotrypsin transamination, -amino acid synthesis by 785 transduction between receptor and signalling units 731 transesterification reactions, catalysts for 249 transition metal ion pair receptors 2934 transition state selectivity in zeolites 550 transition state stabilisation, in enzymatic catalysis 78 translational isomerism, catenanes 671, 756, 757 translational symmetry operators 461 transmembrane current flow 512 transmembrane enzymes 51 trefoil knots DNA knots 697, 698 synthesis 671, 672, 6935 as topological enantiomers 655, 698 tren (2,2,2-tris(aminoethyl)amine) and derivatives 239, 254 trialkylbenzene-based cores/scaffolds 251, 254, 255, 2778 1,5,9-triazacyclododecane, synthesis 156 tribenzo[21]crown-7 138, 139 tricatecholate mesitylene derivative 215 1,3,5-tricyanobenzene, co-crystal with hexamethylbenzene 451, 452 triethylbenzene-derived anion hosts 254, 255, 277 triethylbenzene pinwheel structure 277, 311, 740, 741 triflate (trifluoromethane sulfonate) anion 211 trigger mechanism 71 1,3,5-trihydroxybenzene (THB), hydrogen bonding to cyclophanes 3567 trilactone rings, in siderophores 214, 215 trimeric carcerand 379 trimesic acid (TMA) 399, 579 channel clathrates 399401 layered coordination polymer based on 578, 579 as two-dimensional sheet 529 4,4-trimethylenedipyridine, co-crystal with 4,4-sulfonyldiphenol 573 N,N,N-trimethyltriazacyclononane, copper(II) complexes 468 triphenylmethane and derivatives 311 triphosphine macrocycle, synthesis 1678 triple-helicate complexes 683, 684 triple helices 689, 690 triply interlocked structures synthesis 671, 672 see also trefoil knots tripyridyltriazine-based complex 541, 542 tripyridyltriazine-based molecular panels 617, 619 trischelate unit(s), in ammonium-based podands 240 tris(diazabicyclooctane) 27 tris(guanidinium) receptors 250 trislactams 412 tri-o-thymotide (TOT) 410 applications 413 conformations 41011 derivatives 41213 inclusion chemistry 41012 synthesis 412 tritopic receptors 184 Trửgers base 311 in cyclophanes 349 truth table, for Boolean operations 758 tryptophan 89, 250 TSQ 736 tubular mesophases 845 twisted nematic cells (TNCs) 8512 two-dimensional hosts 2406 Index two-dimensional nets/grids/honeycombs/sheets 538, 539, 566 tyrosine 89 969 529, U-tube model membranes, transport across 245, 246, 304 ubiquinone 66, 67 Ullman reaction, single-molecule analogue 914, 915 2,10-undecanedione, urea inclusion compound 3978 UNI atomatom potential method 5034 unimediated multiple interaction self-assembly 597 unitary graph set 477 unobstructed cross-sectional area (UCA), helical tubulands 402 unsaturated hydrocarbon macrocycle 211 uranyl cation extraction in nuclear industry 297 in Schiff base macrocycle 1712 uranyl-centred ditopic receptors 292 phosphate complexes 292, 293 uranyl complex, co-crystal with [15]crown-5 499500 urea-based gels 8901 urea-based receptors 256, 257 urea clathrates 255, 3938 applications 398 guest order and disorder in 3948 structure 3934, 435 ureases 7923 2-ureido-4[1H]pyrimidone-based polymers 8801 urotropin, ammonium tetrafluoroborate complex 495 US Department of Energy (DOE), hydrogen storage materials targets 430, 584 UV-Vis spectrophotometric titration 15 valine 89 valinomycin 53, 57 K complex 54 van der Waals interactions 34, 35, 235 in layered solids 550 van der Waals radii 448 van tHoff plots 340, 362 vancomycin, drugreceptor complex 19 Vaskas compound 70, 71 vermiculite 551 structure compared with p-sulfonatocalix[4]arene 426 Vernier mechanism for controlling supramolecular oligomerisation 883 vesicle-directed biomimetic mineralisation 596 vesicle walls with bilayer surfactant membranes 805 molecular conductivity through 747, 748 vesicles 834, 836 chloride efflux from 296 cholapods in 2801 viologens (N,N-disubstituted 4,4-bipyridyl derivatives) 194, 310, 357 ditopic receptors based on 277, 278 redox chemistry 358 see also paraquat viral capsids, self-assembly of 101, 593 virtual porosity 543 virtual products (in dynamic combinatorial chemistry) 817 viscoelastic materials 865 viscous materials 865 vitamin B12 61 X-ray crystal structure 82, 83 vitamin coenzymes 803, 808 voltage-gated chloride transport 813 water in co-crystals 4978 hydrogen bonding in 830 molecular structure 527 oxidation to oxygen 65, 6870 oxygenoxygen radial distribution function 830, 831 see also ice watergas shift reaction 429, 430 water molecules, structure in clathrate hydrates 389 water motifs, classification scheme 4978 WatsonCrick base pairs 901 Weiss model (for binding of oxygen to haemoglobin) 71, 72 Wells notation 540 Werner, Alfred 5, 8, 106 Werner clathrates 556, 5578 wheel-and-axle concept 4023 whisky tumbler shape, resorcarene derivative 322 Wilkinsons compound Williamson ether synthesis 116 Wurtz coupling 342, 343 X-ray crystallography 556, 112 X-ray dichroic filters 398 xenon, absorption in clathrates 430, 431 xerogels 889 XOR gate, molecular logic 75960 Yersinia protein tyrosine phosphatase 229 Zeises salt 32 zeolites 54350 applications 543, 54850 composition 543, 544 organic mimics 4345, 52830, 558, 575 primary building units 544 secondary building units 546 structure 5447, 544 synthesis 5478 see also aluminosilicate zeolites; organic zeolites zero-dimensional clusters/molecules/points 529, 538, 5624 zig-zag chains 565 zinc, biological roles 736, 795 Index 970 zinc(II) bis(porphyrin), pentagonic assembly 917, 919 zinc-containing enzymes 737, 7958 zinc porphyrin complexes in heterodimeric capsules 646 in photochemical devices 726 self-assembly of 60610 zinc(II) porphyrin-derived anion sensor 917, 924 zinc sensors 7368 Zinke reaction 198 Zinquin (fluorophore) 736 zipper complexes 616, 617 zipping up of double helices 602, 685 ZSM zeolites 545, 546 zwitterionic receptors 253 zwitterionic structure of amino acid 286, 287 zwitterions, receptors for 286, 287, 3034 ... bikitaite, Li2[Al2Si4O 12] ã 2H2O, heulandite, Ca4[Al8Si28O 72] ã 24 H2O and faujasite, (Na2, Ca, Mg )29 [Al58Si134O384] ã 24 0H2O, are examples The first naturally occurring zeolite, stilbite (NaCa2Al5Si13O36... [{Pd(en)(à-bpy)}4] 8 ,22 (b) [Zn(acac )2 (à-bpy)] n ,23 (c) [Co(bpy )2 (CF3CO2 )2] n ,24 and (d) the pyrazene complex {[Ag(pyrazene)3](SbF6)}n .25 Coordination Polymers 565 Figure 9 .26 (a) zig-zag and helical supramolecular. .. biological ion channels (cf Section 2. 2) The adaptation of the confined Figure 9 .24 The polyoxomolybdate nanocluster [P 12{ Mo2O4 (MeCO2)}30] 42 (P {(Mo)Mo5O21 (H2O) 6}6) that behaves as an artificial