bluuebunny/crossref_metadata_2025 huggingface dataset:
Multivalency
Authors: Cloninger Mary J. , Bilgiçer Başar , Li Lingyin , Mangold Shane L. , Phillips Scott T. , Wolfenden Mark L.
Published: February 2012

Multivalent interactions, in which multiple ligands on one entity bind simultaneously to multiple receptors on another, are ubiquitous in nature. The use of multivalent agents will undoubtedly transform existing methods that target important disease processes including infection, immune system regulation, cancer, and neurological pathways. The employment of multivalent systems as tools to study biological recognition processes and for therapeutic development is unique in that multivalency can address many problems that traditional monovalent materials cannot. Here, mechanisms of multivalent ligand binding as well as the thermodynamic principals of multivalency including the chelation effect, cooperativity, avidity enhancement, avidity entropy, and effective molarity are described. Experimental techniques that are currently used to study multivalent interactions are briefly compared. Key examples of systems that have been used to study multivalent interactions are highlighted and range from small molecules and carbohydrate‐functionalized macromolecules to antibodies and polymers. Overall, this chapter focuses on strategic approaches and enabling technologies that are advancing the development of multivalent therapeutic agents.
Supramolecular Information/Programming from a Boolean Perspective
Authors: de Silva A. Prasanna
Published: February 2012

Supramolecular interactions naturally involve information handling so that recognition takes place between two molecules. The gathering and processing (and to some extent, storing) components of information handling can be conveniently analyzed according to Boolean logic. Single‐input YES and NOT logic can be discerned within information gathering operations, that is, sensing. A fluorescent case that is useful for monitoring blood electrolytes illustrates some of the concepts and mechanistic considerations involved. Double‐input AND logic lies within some sensors with improved selectivity toward bifunctional molecular targets. Extension to triple‐input AND logic gives rise to “lab‐on‐a‐molecule” systems. These combine sensing with a rudimentary algorithm to allow a degree of decision‐making regarding the gathered information. The unique ability of molecular information processors to succeed in small spaces barred to semiconductor devices is illustrated by molecular computational identification (MCID) tags. Molecular systems that display aspects of random access memory illustrate progress in sequential logic.
Self‐Assembly and Self‐Organization
Authors: Geer Michael F. , Shimizu Linda S.
Published: February 2012

From the child making rock candy with his parents to the physicist studying the cosmic dust in deep space, the process of self‐assembly organizes smaller building blocks into larger discrete structures without outside influence. In this chapter, we identify and examine some of the factors that guide, limit, and define these supramolecular structures from the atomic up to the centimeter scale with a focus on molecular building blocks. The concepts herein provide the reader with an introduction to this fast developing field and highlight its important applications.
Reversible Covalent Bond Toolbox
Authors: Cheng Yunfeng , Peng Hanjing , Wang Binghe
Published: February 2012

In supramolecular chemistry, functional group interactions play a critical role. The use of covalent interactions, however, is not as common as noncovalent interactions mostly because of their irreversible nature. This chapter covers those covalent interactions that are readily reversible and are often used in the construction of supramolecular assemblies and sensor design. Especially important in such work are boronic acid interactions with diols and other nucleophiles/Lewis bases, anion–metal interactions, and aldehyde–amine/alcohol interactions because of their ready reversibility.
Binding Constants and Their Measurement
Authors: Thordarson Pall
Published: February 2012

This chapter is concerned with how binding constants in supramolecular chemistry are determined. It is divided into three main sections. The first and largest section of this chapter details the key mathematical equations used to describe supramolecular equilibria, including common ones such as 1:1, 1:2, and dimerization as well as less frequently encountered 2:1, 2:2, and linear aggregation models. Details are also provided on how these equations are used with commonly used experimental techniques such as NMR, UV–vis, and fluorescence spectroscopy as well as calorimetry. The next section then discusses methods used for the determination of stoichiometry, including Job's method. The final section is concerned with data analysis, including model selection and comparison, global analysis, estimation of uncertainties, software consideration, and a brief review of selected software packages available for analyzing data from supramolecular titrations. Representative examples from the literature are also included to highlight the topics covered in this chapter.
NMR
Spectroscopy in Solution
Authors: García Jesús , Martins Lucas G. , Pons Miquel
Published: February 2012

Solution NMR provides valuable structural information on supramolecular complexes, the dynamics of their formation, and possible rearrangement between isomeric forms or the interplay between hosts and guests in supramolecular cavities. The atomic resolution of NMR provides direct access to the symmetry properties of supramolecular species. Line shapes in NMR spectra are sensitive to the time scale of dynamic processes. NOESY and ROESY experiments are among the most powerful tools to characterize supramolecular structures, although the dynamics of supramolecular complexes is inextricably mixed in these experiments.

Transient supramolecular interactions between low‐molecular‐weight‐guests and macromolecular hosts detected by solution NMR enable the use of low‐molecular‐weight spies to report on large, NMR invisible, structures. This concept extends the interfaces between supramolecular chemistry, biomolecular structure, and material sciences.
Computational Techniques (DFT,MM,TD‐DFT,PCM)
Authors: Sheehan Rosemary , Cragg Peter J.
Published: February 2012

Computational techniques can be used to simulate molecular and atomic behavior based on fundamental descriptions of atomic and molecular orbitals (ab initioquantum mechanics), experimental data (a priorimolecular mechanics), or a combination of both (semiempirical methods). The choice of method depends on the task in hand and the computational resources available. Low‐level molecular mechanics, molecular dynamics, conformational analysis, and periodic boundary simulations are described along with quantum mechanical approaches (Hartree‐Fock, density functional theory, and other post‐Hartree‐Fock methods) and intermediate semiempirical methods. Keys to the success of any computational method are the adoption of an appropriate model and the methods used to generate that model. By constructing models that reflect both the correct structures of the complex and its components together with changes in experimental parameters, supramolecular phenomena, such as host–guest binding, can be studied in detail using theoretical models. Applications of these methods in the field of supramolecular chemistry are illustrated with examples drawn from crown ether, cyclodextrin, and calixarene complexes.
Diffusion Ordered
NMR
Spectroscopy (
DOSY
)
Authors: Macchioni Alceo , Ciancaleoni Gianluca , Zuccaccia Cristiano , Zuccaccia Daniele
Published: February 2012

This chapter deals with the applications of diffusion NMR spectroscopy to investigate supramolecular compounds in solution. It is organized in three main sections: (i) brief description of the basic concepts underlying self‐diffusion in solution and measurement of the self‐diffusion translational coefficient (
D
t
) by NMR experiments; (ii) critical discussion on the determination of accurate hydrodynamic dimensions (molecular weights) of supramolecular compounds by
D
t
through the Stokes–Einstein equation; (iii) deduction of thermodynamic self‐aggregation parameters using models of indefinite association. Emphasis is given to applications of diffusion NMR spectroscopy to supramolecular chemistry rather than to technical and theoretical aspects. Efforts are made to introduce new, potentially difficult concepts with suitable practical examples in order to facilitate the understanding to nonspecialist readers.
Mass Spectrometry and Gas‐Phase Chemistry of Supermolecules: A Primer
Authors: Dzyuba Egor V. , Poppenberg Johannes , Richter Sebastian , Troff Ralf W. , Schalley Christoph A.
Published: February 2012

Mass spectrometry offers unique tools to examine supermolecules in the gas phase. In this chapter, gas‐phase experiments that aim at determining the structures of supermolecules in solution and the gas phase, their reactivity in condensed phase and under environment‐free conditions, and their thermochemistry in the gas phase are discussed. A comparison of the gas‐phase properties with solution properties provides insight into the effects of solvation.
Supramolecular Electrochemistry
Authors: Flood Amar H. , Kaifer Angel E.
Published: February 2012

Electron transfer reactions afford a very powerful method to introduce controlled changes in supramolecular structures. This chapter provides a brief introduction to electrochemical parameters and voltammetric techniques that are commonly used to investigate supramolecular systems containing redox‐active groups. A discussion of redox‐active host–guest complexes is presented, alongside their corresponding diagnostic cyclic voltammetry titrations. Then we move on to describe the electrochemistry of redox‐switchable, mechanically interlocked molecules, such as rotaxanes and catenanes. The discussion includes thermodynamic considerations, as well as kinetic effects. We have strived to provide a number of selected examples that illustrate the power of electrochemical techniques, not only for characterization purposes but also as a versatile methodology to stimulate supramolecular systems and to control their structure and other chemical and physical properties.
Transport Experiments in Membranes
Authors: Matile Stefan , Sakai Naomi , Hennig Andreas
Published: February 2012

In this chapter, we describe methods to characterize the activity of synthetic transport systems in translocating molecules across otherwise impermeable membranes. The first two sections introduce methods with bulk membranes (U‐tube experiments) and planar or “black” lipid membranes (BLMs), and close with a more comprehensive overview of methods involving liposomes, in particular, large unilamellar vesicles (LUVs). The fourth section focuses on the application of these methods to the elucidation of the functional characteristics of synthetic transport systems. This includes sensitivity toward membrane composition, membrane potential, pH, anions, cations, molecular recognition (sensing), molecular transformation (catalysis), or light (photosynthesis).
Vesicles in Supramolecular Chemistry
Authors: Ravoo Bart Jan
Published: February 2012

Vesicles are self‐assembled nanoscale capsules consisting of a molecular layer enclosing an inner solvent compartment. Vesicles have been a versatile topic in supramolecular chemistry ever since the discovery that, besides phospholipids, also synthetic amphiphiles can form vesicles in aqueous solution. Vesicles are highly dynamic supramolecular structures that have been subject of investigation by many chemists over the last three decades. In particular, the range of building blocks for vesicles has expanded from “conventional” (i.e., phospholipid‐like) amphiphiles to block copolymers, giant amphiphiles, and supramolecular amphiphiles. Increasingly, vesicles are also assembled from nonconventional (i.e., non‐amphiphilic) components in aqueous as well as organic solvents. Vesicles can be tailor‐made to respond to external stimuli. Vesicles are also highly interesting biomimetic structures: molecular recognition of vesicles is a powerful model system for molecular recognition of biological membranes.
Hetero‐Crown Ethers—Synthesis and Metal‐Binding Properties of Macrocyclic Ligands Bearing Group 16 (S,Se,Te) Donor Atoms
Authors: Levason William , Reid Gillian
Published: February 2012

The development of hetero‐crown ethers containing neutral thio‐, seleno‐ and/or telluro‐ether donor atoms over the past 10 years is reviewed with the aim of providing a survey of the most significant advances in their preparations and metal‐binding properties (especially toward d‐block and p‐block acceptors).
Cryptands and Spherands
Authors: Lindoy Leonard F. , Park Ki‐Min , Sung Lee Shim
Published: February 2012

The cryptands and spherand are both categories of ligands exhibiting significant degrees of preorganization of their donor atom sets. The design, synthesis, and host–guest binding properties of representative examples of each ligand category are discussed, with emphasis on structure‐function relationships. A characteristic feature of both of these categories is their tendency to exhibit selective complexation behavior toward individual metal cations, especially alkali metal cations. Individual species from each category that bind ammonium and/or alkylammonium cations are also presented. Examples of spherand and cryptand derivatives, including “intermediate” ligand species of the hemispherand and cryptaspherands type, as well as chromoionophoric derivatives of each category, are also discussed. Spherand derivatives in which some or all of the anisyl groups of the “classical” spherands have been replaced by fluoro, cyano, or urea functions are described. Examples of both bicyclic and tricyclic cryptands and their cryptate derivatives, including anion‐binding systems and ones that yield binuclear metal complexes, are also discussed.
Calixarenes in Molecular Recognition
Authors: Baldini Laura , Sansone Francesco , Casnati Alessandro , Ungaro Rocco
Published: February 2012

This chapter summarizes the most important aspects of the chemistry of calixarenes and their applications in supramolecular chemistry. The first section gives a short summary of the synthesis and conformational properties of calixarenes and of their functionalization at the phenolic OH groups (lower rim) and at the para‐position of the aromatic nuclei (upper rim). The second section covers the properties of native and functionalized calixarenes (including chiral compounds) as receptors for the selective recognition of neutral molecules, cations, anions, and ion‐pairs in the solid state, organic media, and water solution. In the third section, the calixarenes are viewed as scaffolds for the construction of multivalent ligands able to target biomacromolecules eliciting or inhibiting a biological process. Calixarene glycoclusters, operating as efficient and selective multivalent inhibitors of vegetal and mammalian lectins; peptidocalixarenes, capable of disrupting protein–protein interactions; and guanidino‐calixarenes, able to target proteins or to condense DNA, acting, in this case, as efficient nonviral vectors for cell transfection, are discussed. When relevant, the use of calixarene receptors and multivalent ligands as active components of sensor devices for the detection of various analytes is also reported. Perspectives for future developments of calixarenes in supramolecular chemistry and bionanotechnology are indicated.
Cyclotriveratrylene and Cryptophanes
Authors: Hardie Michaele J.
Published: February 2012

A review of the chemistry and applications of cyclotriveratrylenes (CTVs) and cryptophanes is given. Synthetic approaches to CTVs and cryptophanes are discussed, including the recently reported mild cyclization conditions and strategies for the synthesis of lower symmetry cryptophanes. Host– guest and inclusion chemistry is surveyed, including binding of neutral and organic cations by cryptophanes in solution, clathrate structures of CTVs, the anion‐binding abilities of metalled CTVs and cryptophanes, the fullerene‐binding abilities of CTVs, and xenon binding by cryptophanes and their potential applications in xenon biosensors for imaging applications. The uses of CTVs and crytophanes as molecular platforms for other supramolecular chemistry applications are also discussed. These include development of coordination polymers with CTVs and cryptophanes; organic and metallo‐supramolecular prism‐like assemblies, some of which show unusual molecular topologies; and self‐organized systems such as liquid crystals and gels.
Carcerands and Hemicarcerands
Authors: Warmuth Ralf
Published: February 2012

Carcerands and hemicarcerands are spherical, hollow host molecules with inner cavities that are large enough to accommodate smaller organic guest molecules. Since the first synthesis of a carcerand in the mid‐1980s, a large variety of different hemicarcerands and carcerands have been prepared and their properties investigated. In this review, mechanism and scope of (hemi)carcerand synthesis, which is a templated reaction, is discussed. This includes recent work on dynamic hemicarcerands, in which building blocks are connected via dynamic covalent bonds, and gated hemicarcerands, which open and/or close in response to an external trigger such as irradiation or the addition of acid, base, or thiols. In the second part of this chapter, the molecular recognition properties of hemicarcerands are reviewed. As part of this, binding properties of chiral hemicarcerands and water‐soluble hosts are discussed. In the last part, applications of hemicarcerands as molecular reaction flasks are reviewed. Through‐shell reactions between an encapsulated reactant and a bulk‐phase reactant include amine protonation, oxidation/reduction, H/D exchange, and nucleophilic substitutions and additions. In most of these reactions, bond formation/breaking takes place in a size‐restricted portal in the host shell. Thus, scope and reaction rate depend on guest orientation in the inner phase as well as size and shape of the bulk‐phase reactant relative to those of the hemicarcerand's portal. Hemicarcerands have also been used extensively for the inner‐phase stabilization of reactive intermediates. If a reactive intermediate is generated photochemically or thermally in the inner phase of the hemicarcerand, the surrounding host prevents dimerization of the intermediate or reactions with bulk‐phase reactants that cannot pass through an opening in the host shell. Many otherwise fleeting intermediates gain longevity through this extrinsic stabilization, making possible their observation, for example, by NMR spectroscopy. Examples that are discussed include cyclobutadiene, benzyne,
anti
‐Bredt olefins, cyclic allenes and ketenimines, carbenes, and nitrenes. Furthermore, investigations of photoelectron transfer and energy transfer across the shell of hemicarcerands have improved our understanding of these important photophysical processes. Recent advances in this area are discussed.
Cucurbituril Receptors and Drug Delivery
Authors: Day Anthony Ivan , Collins J. Grant
Published: February 2012

The relatively new family of molecular host–guest macrocycles known as cucurbit[n]uril is discussed in the context of a drug delivery system. In less than a decade, cucurbit[n]uril and cucurbit[n]uril‐based supramolecular structures have emerged as promising vehicles for drug delivery. For the first time, this review brings together the results of cucurbit[n]uril‐drug studies and provides a general understanding of the relationship between drugs and this new type of molecular host.

Numerous examples are discussed that highlight the advantages and disadvantages that cucurbit[n]uril can offer, these include improvements in bioavailability and protection, increased stability, reduction in toxicity, and targeted delivery. The current knowledge of toxicology and pharmokinetics of cucurbit[n]uril is also evaluated. Finally, as a drug delivery vehicle, a number of mechanisms are discussed as to the release of the drug. Drug activity results are presented that indicate that there are generally minimal negative effects and there are significant advantages to drug encapsulation involving cucurbit[n]uril. General methods for the preparation of encapsulated drugs are provided, together with a convenient method of characterization using1H NMR.
Anion Receptors Containing Heterocyclic Rings
Authors: Gale Philip A. , Haynes Cally J. E.
Published: February 2012

Heterocyclic groups can play key roles as hydrogen bond donors and charged components in a wide range of anion receptors. This chapter reviews the roles the heterocycles play in anion recognition, covering pyrrole‐based systems (both macrocyclic and acyclic, including synthetic systems and natural products such as prodigiosin), indole‐based receptors, and foldamers‐ and charged‐imidazolium‐based hosts. The chemistry of pyridine‐ and quinoline‐based receptors, including metal‐templated systems that employ transition metals to assemble simple organic components, and the role of bipyridinium in anion complexation and sensing are also reviewed. Finally, the chemistry of 1,2,3‐triazoles as components of hosts that use CH· · ·anion hydrogen bonds to complex anionic guests is examined.
Amide and Urea‐Based Receptors
Authors: Hossain Md. Alamgir , Begum Rowshan A. , Day Victor W. , Bowman‐James Kristin
Published: February 2012

The chemistry, binding, and structure of amide‐ and urea‐based receptors, as well as its thioamide‐ and thiourea‐based corollaries are described. The chapter begins with a short historical introduction of these hosts as ligands for anions, followed by a description of their chemical properties, including similarities and differences in bonding. The remainder of the chapter provides examples of the two types of receptors, the monodentate amides/thioamides, and the chelating ureas/thioureas, in order of increasing dimensionality, that is, acyclic, monocyclic, and bicyclic and higher order hosts. Features such as common (and different) structural motifs, preorganization, and the unique chemistry of some of these hosts and their guests are described.
Receptors for Nucleotides
Authors: García‐España Enrique , Belda Raquel , González Jorge , Pitarch Javier , Bianchi Antonio
Published: February 2012

Recognition and activation of nucleotides by polyammonium receptors constitute an important target in supramolecular chemistry since the very beginning of this field. Nucleotides have three components: (i) the polyphosphate chain, (ii) the sugar moiety, and (iii) the nucleobase, which permit their multipoint binding through attractions between opposite charges, hydrogen bonding, π‐stacking, CH–π interactions, and so on. In this chapter, different receptors for nucleotides, most but not all of them consisting polyamines, are examined, focusing on their molecular structure that enables different binding modes to be operated. Also, a number of examples of nucleotide binding through metal complex formation are presented and discussed. The ATPase and/or kinase activity of abiotic molecules, in particular, of the macrocycle O‐BISDIEN, is briefly introduced. In the last part of the chapter, examples of receptors that are able to selectively sense nucleotides through different operational mechanisms are presented.
Metal Complexes as Receptors
Authors: Loeb Stephen J.
Published: February 2012

The incorporation of hydrogen‐bond donor or acceptor groups into ligands followed by their coordination to inert transition metals has proven to be a successful methodology for creating unique metal complex receptors for a wide variety of anions, some neutral molecules, and a limited number of cations. The metal ion can participate in binding a guest indirectly via second‐sphere coordination or directly via simultaneous first‐ and second‐sphere coordination. This chapter contains two major sections that outline the design strategies and describe a variety of metal complexes that function as receptors for (i) neutral molecules, (ii) cations, and (iii) anions. Under the heading of receptors for neutral molecules, the focus is on increasing complexity with respect to the targeted guest beginning with simple species such as H
2
O and NH
3
and featuring biologically important molecules such as DNA nucleobases. The section on metal complexes as anion receptors is structured to shed light on the different avenues used to design receptors and the structural features of these systems. A common theme is the idea that host–guest assemblies may have complicated structures, but the ligands themselves do not require tedious synthetic routes to prepare and coordination to the metal center is facile. Thus, the combination of coordination chemistry and noncovalent interactions such as hydrogen bonding and π‐stacking can be viewed as a powerful tool for molecular and ion recognition. The state of the art is advanced enough to allow targeting of specific guests by tailoring both the metal–ligand and host–guest interactions.
Hydrogen‐Bonding Receptors for Molecular Guests
Authors: Wilson Andrew J.
Published: February 2012

Hydrogen bonding is considered by many to be the “masterkey” of molecular recognition — owing to its strength and directionality — playing a key role in the assembly of biological supramolecular ensembles and architectures. Consequently, its study and exploitation within the context of host–guest chemistry has been a cornerstone of modern supramolecular chemistry, resulting in implementation within numerous applied settings such as catalysis and materials assembly. This chapter outlines the core concepts used to elaborate receptors that employ hydrogen bonding through modern efforts to recognize challenging targets in competitive media alongside a brief introduction covering the areas where such receptors are exploited.
Synthesis of Supramolecular Nanotubes
Authors: García‐Fandiño Rebeca , Amorín Manuel , Granja Juan R.
Published: February 2012

In the last few years, interest on nanotubes have induced the development of programs for the preparation of noncovalently bonded self‐organizing nanotubes from a variety of different methods, in most cases inspired by nature. These strategies include helically folded linear species, hollow bundles of rod‐like units, rolled‐up sheets, helically juxtapositioned truncated wedges, and stacked rings.
Self‐Assembly of Macromolecular Threaded Systems
Authors: Tachibana Yuya , Nakazono Kazuko , Takata Toshikazu
Published: February 2012

Recently, a polyrotaxane network material has been practically used, for the first time, as a coating material for mobile phones in Japan. This is an epoch‐making event in the science and technology of interlocked molecules, macromolecules, and related materials. Polymers possessing interlocked structures as key skeletons are, therefore, the most promising and intriguing materials, especially in the application fields. Polyrotaxanes and polycatenanes are characterized by the specific features based on the unique mobility of the noncovalently bonded components in their special polymer structures, such as molecular rotaxanes and catenanes, leading to the construction of a variety of sophisticated systems. In particular, when wheel components and a chain polymer form a macromolecular threaded system (i.e., polyrotaxane), combining the wheel components of different molecules results in producing the cross‐linked points that can move on the chain. Such a type of “topological cross‐linking” of polyrotaxane network can provide special mobility to the polymer chains, as de Gennes suggested in his paper entitled “Sliding Gels.” The topological cross‐linking is clearly distinguished from both physical and chemical cross‐linkings with little mobility of polymer chains. Thus, the research area of interlocked polymer systems has collected much attention from the fields of both supramolecular and polymer sciences, and the active investigation on them must be continued in the future, judging from the enthusiastic activity in materials science fields today.

In a whole research trend of interlocked polymers, being parallel to the development of the synthetic methods of interlocked polymers, various applications of them have been studied simultaneously. This chapter overviews the development of synthetic methods and applications of interlocked polymers such as polyrotaxane, polycatenane, and their networks that have been reported in these two decades. The works introduced are mainly the original ones. Owing to the limited space for this chapter, the authors cannot refer to the details of each work, although most works are very interesting. The detailed explanation of the important works published up to 2009 can be found in many reviews, including two comprehensive articles of Gibson and Stoddart on polyrotaxanes and polycatenanes in addition to a lot of review articles and books on the rotaxanes and catenanes that devote a small space for the polymers.
Self‐Assembled Links: Catenanes
Authors: Evans Nicholas H. , Beer Paul D.
Published: February 2012

Catenanes are molecules consisting of two or more rings that are mechanically interlocked requiring the cleavage of a chemical bond to separate the macrocyclic components. Initial attempts to synthesize these aesthetically pleasing molecules via nontemplated methods were blighted by low yields and lengthy syntheses, and it took Sauvage's use of the copper(I) cation as a template for the synthesis of a [2]catenane to ignite intense research activity in this field. This chapter summarizes this groundbreaking work and the array of template interactions such as metal cation, charge transfer π‐π stacking, hydrogen bonding, and anion coordination that have since been utilized to produce catenanes. Attention is then turned toward the progress that has been made in the practical applications of these mechanically chain linked structures, such as the control of their molecular motion, immobilization onto surfaces, and efforts to incorporate them into extended structures such as polymers and metal organic frameworks.
Viruses as Self‐Assembled Templates
Authors: Rego Jennifer M. , Yi Hyunmin
Published: February 2012

Research endeavors in employing viruses and virus‐like protein assemblies as biologically derived nanotemplates for nanomaterials synthesis and device fabrication have recently experienced significant growth. Materials and applications arising from this novel bottom‐up assembly approach vary widely from metal and metal oxide nanoparticles and nanowires for catalysis and nanoelectronics, high surface area electrodes for energy applications, to sensing or tissue engineering scaffolds for biomedical applications. By harnessing and manipulating the exquisite control that Nature has provided, the overarching goal for this emerging field of nanobiotechnology has been to achieve features and performances that transcend what is possible from inorganic, man‐made methods. In this review, we describe the chemical aspects from a selected number of exciting studies based on three viral shape categories: rod, icosahedral, and filamentous. Increasing the understanding and better manipulation of the unique advantages that each category of viruses offers has led to distinct nanomaterials and applications; polymeric conducting nanofibers from rod‐shaped tobacco mosaic virus (TMV), catalytically active nanoparticles with highly controlled sizes from cowpea chlorotic mosaic virus (CCMV), and biopanning‐based affinity selection from M13 bacteriophage libraries, to name a few. Such novel materials from these bottom‐up assembly approaches are starting to show performances and capabilities beyond or impossible to be achieved via traditional materials, top‐down approaches, and inorganic devices.
Molecular Devices: Molecular Machinery
Authors: Zhang Mingming , Zhu Kelong , Huang Feihe
Published: February 2012

According to the driving forces, molecular machines can be easily divided into chemically driven molecular machines, electrochemically driven molecular machines, photo‐driven molecular machines and molecular machines driven by combination of two or more of them. In this chapter, we will demonstrate these four types of molecular machines in detail.
Photoswitching Materials
Authors: Ko Chi‐Chiu , Wing‐Wah Yam Vivian
Published: February 2012

Photoswitchable materials are mainly engineered from molecules that are capable of undergoing reversible changes in their intrinsic properties through the use of light as an external stimulus. As the absorption properties of most of these molecules change reversibly with photoexcitation, most of them are also photochromic materials. Many of these photoswitching processes operate through reversible chemical transformations, such as trans‐cis isomerization, ionization, pericyclic ring‐opening and ring‐closing reaction, and intramolecular group transfer reaction. Through systematic investigations and subsequent rational designs on the photochromic frameworks using the state‐of‐the‐art organic synthetic methodologies, the photochromic properties could be modified, tuned, and tailored for molecular switching. In this chapter, different photochromic families and selected recent works dealing with the functionalization of different families of photochromic molecules for the photoswitching of luminescent behavior, electronic communication, optical properties, molecular shuttling, and host‐guest interaction are described.
Magnetic Resonance Imaging Contrast Agents
Authors: Bonnet Célia S. , Tóth Éva
Published: February 2012

Magnetic resonance imaging is one of the most efficient diagnostic modalities in clinical radiology and biomedical research. To enhance image contrast, paramagnetic complexes, mainly Gd3+chelates, are used. In recent years, molecular imaging has emerged as a new area aiming at noninvasive visualization of expression and function of bioactive molecules at the cellular level. This chapter is devoted to the description of supramolecular approaches in the development of highly efficient and smart contrast agents. We demonstrate via representative examples (micellar systems, liposomes, protein‐bound chelates, etc.) how supramolecular approaches are applied to increase the efficacy of Gd3+‐based contrast agents. We also include an introduction to chemical exchange saturation transfer (CEST) agents and show how supramolecular systems, such as liposomes, can be beneficial to decrease the sensitivity limit of CEST detection. Supramolecular assemblies offer an important advantage regarding the metabolic fate. While covalent polymers are excreted slowly from the body, supramolecular systems facilitate the body elimination via the excretion pathway of the small constituents. Finally, we discuss molecular imaging probes that provide an MRI response mainly through the modulation of supramolecular interactions to various biochemical variables, such as pH, temperature, metal ions, and enzymes.
Concepts and Nomenclature in Chemical Crystallography
Authors: Barbour Leonard J. , Das Dinabandhu , Jacobs Tia , Lloyd Gareth O. , Smith Vincent J.
Published: February 2012

The concepts relating to the structures and properties of crystals involve numerous terms that might be especially bewildering to the nonspecialist. Many of these terms have been borrowed and/or adapted from mineralogy, a much older branch of crystallography and involving a different community of researchers, while others have been coined at will to describe either new concepts or concepts for which suitable terms did not exist before. As a result, crystallographic nomenclature is far from systematic and the lexicon of modern crystallography has evolved as a haphazard collection of terms. This contribution presents a survey of the concepts that arise during the crystallographic studies of crystals, with the rather ambitious goal of achieving disambiguation regarding nomenclature. The authors specifically discuss terms that they have identified as being highly relevant to modern chemical crystallography.
Crystal Structure Prediction
Authors: Day Graeme M.
Published: February 2012

This review will overview current computational approaches to predicting crystal structures of organic molecules from first principles. The global lattice energy minimization approach to crystal structure prediction is described, along with the use of knowledge‐based methods, providing a perspective on current predictive capabilities, as well as the current areas of development in crystal structure prediction.
The Cambridge Structural Database System and Its Applications in Supramolecular Chemistry and Materials Design
Authors: Pidcock Elna , Chisholm James A. , Wood Peter A. , Galek Peter T.A. , Fábián László , Korb Oliver , Cruz‐Cabeza Aurora J. , Liebeschuetz John W. , Groom Colin R. , Allen Frank H.
Published: February 2012

The Cambridge Structural Database (CSD) now records data from more than half a million small‐molecule organic and metal‐organic crystal structures. Together with the database, the complete CSD System comprises (i) software for interrogating all information fields, including 2D and 3D substructure searching, (ii) structure visualization, (iii) analysis of retrieved geometrical information, and (iv) knowledge‐based libraries of intramolecular and intermolecular information. An Internet portal to the CSD is also available. The Mercury structure visualizer is now being onwardly developed with functionality that will aid crystal engineers, supramolecular chemists, and drug development and formulation scientists. The Materials module of Mercury incorporates tools for motif topology searches and crystal packing feature searches, as well as for evaluating crystal packing similarity and for H‐bond propensity analysis, all of which are described and illustrated. It is also shown that CSD‐related software developed for drug discovery has important applications in supramolecular chemistry and crystal engineering and, conversely, that the materials development tools can benefit drug designers. Two final sections illustrate how the CSD can be used to derive predictive descriptors of cocrystal formation, and stress the importance of CSD information in the various stages of computational crystal structure prediction.
Synthetic Clathrate Systems
Authors: Bishop Roger
Published: February 2012

Clathrate compounds traditionally were discovered by happy accident because of the considerable difficulty in predicting and controlling weak intermolecular forces in crystal engineering. This chapter surveys and analyzes the various approaches taken to obtain synthetic organic clathrates, ranging from modification of a known lead compound to the design of an entirely new host from first principles. The clathrate literature has been categorized into a series of recognizable families. The individual members of these families have certain structural characteristics that define their membership. These common features are described and their functions are analyzed in supramolecular terms. Once identified, these key characteristics can then be retained during the synthesis of new family members. A number of clathrand hosts are known that contain structural features associated with two or more of the basic clathrate families. These compounds are described and their relationship with multiple host families is delineated. Finally, the chapter examines the current state of play in this research area. Recent advances and current difficulties are highlighted.
Network and Graph Set Analysis
Authors: Öhrström Lars R.
Published: February 2012

In this chapter, it is first shown how a number of steps in the scientific process in this field of chemistry can be improved by naming and understanding the topology of three‐dimensional networks and can be the coordination polymers, metal–organic frameworks, or hydrogen bonded systems. Specifically, the discussion is centered on the use of network analysis and graph set analysis to (i) understand the products we get, (ii) compare these materials to what others have made, (iii) communicate our results to colleagues, and (iv) truly make something new by design. The topology symbols by O'Keeffe, Wells, and others are introduced, and the reader is given a step‐by‐step guide on how to obtain the topology of a 3D net. Finally, graph set analysis is introduced, and its utility in supramolecular chemistry and network analysis discussed.
Zeolitelike Metal–Organic Frameworks (
ZMOFs
): Design, Structure, and Properties
Authors: Alkordi Mohamed H. , Eddaoudi Mohamed
Published: February 2012

The quest for functional materials targeted at specific applications is ever increasing as societal needs and demands mount with advancing technology. One class of inorganic‐organic hybrid materials, metal‐organic materials (MOMs), has burgeoned in recent years due, in part, to effective design strategies (e.g., reticular chemistry) for their synthesis and their inherent (and readily interchangeable) hybrid, highly functional character. The molecular building block (MBB) approach introduces the ability to generate rigid and directional building blocks, mostly
in situ
, for the construction of MOMs having specific underlying networks and/or targeted functions/properties. Various MBBs can be targeted and utilized in the assembly of functional MOMs: (i) single‐metal‐ion‐based MBBs, which promote rational construction, by forcing rigidity and directionality through control of the metal coordination sphere and judicious selection of suitable heterofunctional (N‐, O‐coordination) organic ligands, of porous MOMs with extralarge cavities, including zeolitelike metal‐organic frameworks (ZMOFs); (ii) multinuclear metal‐cluster‐based MBBs, where, for example, simple metal‐carboxylate clusters possess multiple metal‐oxygen coordination bonds that result in the generation of rigid nodes with fixed geometry that, when combined with organic ligands of specific geometry, lead to the construction of desired MOMs; and (iii) supermolecular building blocks (SBBs), which involve enhanced built‐in directional and structural information (e.g., high degree of symmetry and connectivity) compared to simple MBBs and allow the construction of high‐connectivity nets (e.g., rht‐MOFs). The MBB approach and associated strategies, as well as physical properties of some corresponding MOMs, are presented.
Supramolecular Isomerism
Authors: Bourne Susan A.
Published: February 2012

Supramolecular isomers comprise network structures that have identical chemical compositions but differ from one another in their structure. In some instances, the term is also used to describe identical frameworks that contain different counterions, solvent, or guest molecules. Supramolecular isomerism can be observed in both molecular and coordination compounds. Like polymorphism, it results when different, but energetically similar, packing interactions can operate during crystallization.

Gaining control on crystallization of a particular isomer remains challenging as both thermodynamic and kinetic factors play a role, and as understanding the full energy profile of a self‐assembly process is extremely difficult. Some important variables within the crystallization system have been identified, including chemical and physical factors, which are described in this chapter.

Supramolecular isomers may be considered in four categories: structural, conformational, interpenetrated, and chiral networks. Examples of each are provided. A number of topological approaches have been described over the years, which aid in the description of extended structures. Both graph set and network analyses are useful for this purpose.

Crystal engineering aims to control structural characteristics of crystalline materials, with the aim of having greater control over their physical properties. Although hydrogen‐bonded supramolecular synthons have been studied in depth for more than a decade and although coordination bonds are stronger and more directional than other supramolecular interactions, structural uncertainty is still a characteristic of self‐assembled systems. Some structure‐property relationships are emerging, including luminescence and porosity.
Interpenetration
Authors: Batten Stuart R.
Published: February 2012

Interpenetration of multiple polymeric networks is an important and widespread phenomenon in crystal engineering. A thorough understanding of not just network topology but also interpenetration topology (i.e., the way networks interpenetrate) is therefore vital. 1D and 2D networks can interpenetrate in either a parallel or an inclined manner, leading to overall entanglements of the same or higher dimensions. This can be summarized using the notation
m
D(/
n
D) → 
p
D parallel/inclined interpenetration. For example, parallel interpenetration of 2D nets leading to an overall 3D entanglement is 2D → 3D parallel interpenetration. Within each of these subclasses, there are also many different possible interpenetration topologies, as there are for the interpenetration of 3D networks. Interpenetration of networks that are chemically, topologically, and even dimensionally different is rare but possible. Self‐penetration occurs when the smallest topological rings of a network are penetrated by rods from the same network.
Crystal Growth and Molecular Crystal Growth Modification
Authors: Jones Franca , Ogden Mark I.
Published: February 2012

Crystals have been described as the supermolecule
par excellence
, and hence it is important to have an understanding of how crystals grow and how to control the growth processes. The fundamentals of crystal growth are discussed, including recent developments such as two‐step nucleation theory and the concept of mesocrystals. The mesocrystals are formed by the aligned assembly of nanoparticles, and lead to products that are difficult, in some cases, to differentiate from genuine single crystals. The many different mechanisms by which impurities and additives can influence crystal growth are given, with an emphasis on the complexity associated with studying these systems. The control of crystal growth using tailor‐made additives is described, with particular application to molecular crystal systems. Examples focus on glycine, and include morphology control, determination of absolute configuration of a molecule, determination of crystal polarity, and polymorph control.
Multicomponent Self‐Assembled Polymers Based on π‐Conjugated Systems
Authors: Kaeser Adrien , Wolffs Martin , Schenning Albertus P. H. J.
Published: February 2012

The present chapter focuses on the most significant developments in the organization of multicomponent π‐conjugated molecules into supramolecular polymers. The different approaches to prepare these structures are presented and classified into the different types of supramolecular organizations that are obtained by simple mixing or by using a multistep methodology.
Self‐Healing and Mendable Supramolecular Polymers
Authors: Burattini Stefano , Colquhoun Howard M. , Greenland Barnaby W. , Hayes Wayne
Published: February 2012

This chapter reviews the recent development of self‐healing and easily mendable polymeric materials in which designed supramolecular interactions—notably hydrogen bonding, metal–ligand coordination, and complementary aromatic π−π‐stacking—play key roles. Factors such as molecular weight, association constants for key binding motifs, kinetic lability of binding interactions, compatibility of blended materials, extent of microphase separation, and degree of crystallinity are discussed with reference to the balance of polymer properties and achievement of healable characteristics. Supramolecular polymer systems that undergo spontaneous healing under specific damage conditions (e.g., projectile‐impact) are described, as are those which require some form of stimulus to initiate the healing process.