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This thesis describes the preparation of halogen bonding and chalcogen bonding macrocyclic and mechanically interlocked systems for the recognition of anions and ion-pairs. Chapter 1 introduces the field of supramolecular host-guest chemistry, with particular focus on the recognition of anions and ion-pair species. The synthesis and applications of mechanically interlocked molecules are also reviewed. Chapter 2 details the fundamental charged guest recognition properties of a novel family of σ-hole [2]rotaxanes incorporated with multiple halogen bonding and chalcogen bonding triazole-based donor motifs. Chapter 3 investigates the anion sensing capability of halogen bonding receptors functionalised with photo- and redox-active reporter groups. This entails the construction of zinc(II) metalloporphyrin-BODIPY [2]rotaxanes for the dual optical- and electrochemical sensing of anions. Chapter 4 describes the exploitation of halogen bonding and chalcogen bonding interactions to mediate ion-pair recognition in heteroditopic/multitopic macrocyclic and catenane host systems. Chapter 5 summarises the conclusion of this thesis. Chapter 6 provides the experimental procedures employed in this work, including synthetic protocols and characterisation of novel compounds.

Molecular recognition at biomembranes is one of the more poorly understood aspects of fundamental research in physical organic chemistry. Our aim was to improve our understanding of the molecular recognition of polysaccharides at biomembranes, in particular developing synthetic lipids that will recognise and report on the presence of glycosaminoglycans (GAG polysaccharides), like heparin and hyaluronic acid. Elevated levels of hyaluronic acid have been implicated in bladder carcinoma and osteoarthritis, and the use of heparin for medical applications is well documented. We synthesised a boronic acid capped lipid that also bore a fluorinated fluorescent reporter group, which could report on multivalent recognition events at bilayer membranes by fluorescent quenching and changes in the lateral distribution of the reporter groups. These preliminary studies showed these boronic acid capped fluorinated lipids gave a fluorescent signal upon interaction with simple mono- and poly- saccharides, albeit with unexpectedly weak binding to these saccharides. To understand and quantify the weaker binding of saccharides to membrane bound boronic acids a series of novel fluorescent and chromogenic lipids were synthesised that bore the reporter group close to the boronic acid. These studies revealed several underlying factors that had important roles in the recognition of oligosaccharides by boronic acid capped lipids. For the first time the effect of the bilayer on saccharide/boronic acid recognition was quantified, with the membrane weakening the interaction 33-fold. We were able to propose a model for the interaction of saccharides for membrane bound boronic acids that explained many of these unexpected observations.We also devised a parallel approach using GAGs to open or close synthetic membrane channels. Using a GAG to switch on the release of an ion or dye would generate a fluorescent signal that amplifies the original recognition event and improves sensitivity for GAGs. Proof-of-principle studies using palladium ions to open dye-transporting channels were successful and these studies were followed by the synthesis of boronic acid-capped cholates. Incorporation of boronic acid-capped cholates into membranes caused changes in the rate of release of alkali metal ions, which caused an enclosed fluorescent dye to give a signal, in the presence or absence of saccharides. These compounds successfully gave a response to the simple saccharide D-fructose but gave no response to other saccharides tested, including various hyaluronic acids. Although we were not able to develop a selective sensor for GAGs, we have developed a model for saccharide/boronic acid interactions that is a valuable addition to the physical organic chemistry of membranes.

Molecular recognition is essential to all biological interactions and processes. Knowledge of the structural basis of recognition offers a powerful mechanism for understanding, predicting and controlling the behaviour of biological systems. In this thesis, we present, firstly a computational and crystallographic analysis of molecular recognition in protein-ligand systems; and secondly, progress towards the synthesis of a fluorescent probe for calcium ion recognition. Class I phosphoinositide 3-kinases (PI3Ks), in particular PI3Kγ, have long been considered promising drug targets for the treatment of inflammatory and autoimmune disorders. As a step towards improved understanding of PI3K binding preferences, we examine the basis on which PI3Kγ distinguishes γ-selective inhibitors AS-605240 and AS-604850, with a ~30-fold preference for the former. Interestingly, despite the chemical similarity of the two ligands, the X-ray structures for their PI3Kγ complexes exhibit the molecules in different conformers, s-cis for AS-604850 and s-trans for AS-605240. Here, we re-examine the PI3Kγ/AS-605240 crystallographic data and find that not only is a s-cis conformation possible but in fact it has a much higher occupancy (87%) than the originally modelled s-trans isomer (13%). Subsequently, to account for the isomeric complexities presented by the ligands, we perform 140 ns MD simulations of the four PI3Kγ complexes in explicit solvent: this reveals similar conformational flexibility at the active site for all systems. Yet, the conformations sampled by the s-cis isomers are more consistent with the conformations reported by the X-ray crystal structures. Subsequent energetic analysis was performed incorporating ensemble-averaging and desolvation effects via the Poisson-Boltzmann continuum solvent model. For both inhibitors the s-cis isomers are predicted to be the most favourable conformations. Additionally, the results indicate a preference for AS-605240, as observed experimentally. The molecular basis for this preference is discussed, together with a comparison of molecular mechanical and quantum chemical treatments of the key ligand-Val882 interaction. This study provides structural, dynamical and energetic insights into the subtle basis of molecular recognition by PI3Kγ.Fluorescent probes have evolved into an extremely useful tool for the detection of calcium in biological systems. Benzothiazole derivatives BTC, and its iminocoumarin analogue BTIC, are two low affinity calcium indicators featuring many desirable properties for cellular calcium measurement. In an effort to produce fluorophores that can be chemically conjugated with a screening protein, such as Green Fluorescent Protein (GFP), we aimed to derivatise BTC and BTIC. Two synthetic approaches towards the synthesis of these potential fluorescent probes are outlined.

The failure of the pharmaceutical industry to increase the delivery of new drugs into the market is driving a re-assessment of practices and methods in drug discovery and development. In particular alternative strategies are being pursued to find therapeutics that are more selective, including small molecules that target protein-protein interactions. However, success depends on improving our understanding of the recognition of small molecules by interfaces in order to develop better methods for maximising their affinity and selectivity, whilst trying to confer an appropriate therapeutic profile. This thesis starts with the description of the creation of TIMBAL, a database that holds small molecules disrupting protein-protein interactions. The thesis then focuses on the analysis of these molecules and their interactions in a medicinal chemistry and structural biology context. TIMBAL molecules are profiled against other sets of molecules (drugs, drug-like and screening compounds) in terms of molecular properties. Using the structural databases in the Blundell group, the atomic detail of the interaction patterns of TIMBAL molecules with their protein targets are compared with other molecules interacting with proteins, comprising natural molecules, small peptides, synthetic small molecules (including drug-like and drugs) and other proteins. The structural features and composition of the binding sites of these complexes are also analysed. Keeping in mind that current drug candidates are somewhat too lipophilic to succeed, these interaction profiles are defined in terms of polar and apolar contacts, with the aim of migrating natural patterns into the design of new therapeutics.

Dynamic combinatorial chemistry (DCC) is a powerful method for synthesising complex molecules and identifying unexpected receptors. Chapter 1 gives an overview of the concept of DCC and its applications, and discusses its evolution to date. Chapter 2 describes the discovery of a new generation of donor-acceptor [2]catenanes in aqueous dynamic combinatorial systems. The assembly of these [2]catenanes is promoted by a high salt concentration (1 M NaNO3), which raises the ionic strength and encourages hydrophobic association. More importantly, a mechanism that explains and predicts the structures formed is proposed, giving a fundamental insight into the role played by hydrophobic effect and donor-acceptor interactions in this process. Building on these results, Chapter 3 describes the assembly in high salt aqueous libraries of a larger structure: a [3]catenane. Remarkably, the [3]catenane exhibits strong binding interactions with a biologically relevant target - spermine - in water under near-physiological conditions. Its synthesis is improved if the salt is replaced by a sub-mM concentration of spermine, acting as a template. Chapter 4 explores in further detail how subtle variations in the building block design influence the selective formation of either [2] or [3]catenanes. This last section underlines both the advantages and the limitations of the method developed in Chapter 3. After a short conclusion (Chapter 5), Chapter 6 gives experimental details.

This thesis describes the synthesis and investigation of novel anion templated interlocked structures which incorporate the positively charged imidazolium and triazolium binding motifs for applications in anion recognition and sensing. Chapter One introduces the fields of anion supramolecular chemistry and mechanically interlocked structures, focusing on topics of particular relevance to this thesis, including anion recognition, anion sensing and the templated synthesis of interlocked architectures. Chapter Two details the incorporation of the imidazolium motif into the axle components of anion templated rotaxane hosts to achieve selective anion recognition by virtue of their interlocked binding cavities. The effects of exploiting imidazolium motifs with contrasting hydrogen bond donor arrangements and reducing the macrocycle size on the anion recognition properties of such systems were investigated using 1H NMR spectroscopy. Chapter Three reports the work undertaken to utilise fluorescent reporter groups as stoppers in the synthesis of anion sensing rotaxanes. Imidazolium- and triazolium based systems containing either luminescent ruthenium(II) bipyridyl complexes or the organic fluorophore anthracene were prepared and their anion sensing behaviours explored using fluorescence spectroscopy. Synthetic efforts to construct suitable photo-active rotaxanes are detailed. Chapter Four describes investigations of the novel naphthalimide triazolium motif both for use in interlocked molecular motion systems, and for fluorescence sensing applications. The preparation of a naphthalimide triazolium rotaxane, capable of selective, anion-induced, uni-directional shuttling which was investigated extensively using 1H NMR spectroscopy and optically signalled by perturbations in the UV/Vis spectrum, is detailed. Preliminary research studies into the potential to exploit this motif for surface based fluorescence sensing devices are also included. Chapter Five presents research into the utilisation of acyclic receptors displaying considerable binding induced conformational changes for fluorescence anion sensing. The recognition properties of a series of imidazolium-based receptors were studied, whilst the ability of a pyrene appended analogue to signal anion complexation via changes in excimer emission is reported. The control of interpenetrated assembly formation using anion-induced conformational changes within the threading component of a pseudorotaxane is also discussed. Chapter Six provides the experimental procedures and characterisation details for the compounds synthesised in this thesis. Chapter Seven is a summary of conclusions from Chapters Two, Three, Four and Five. Supplementary information relating to titration protocols, crystallographic data and surface studies is provided in the Appendices.

Molecularly imprinted polymers (MIPs) are a novel, promising family of porous materials with potential applications ranging from separations, chemical sensing and catalysis to drug delivery and artificial immunoassays. The unique feature of these materials is their biomimetic molecular recognition functionality. Molecular recognition is the biological phenomenon of specific, selective and strong association between a substrate and a ligand. In man made MIPs this functionality is implemented via templated synthesis protocol. MIPs are synthesized in the presence of additional template molecules which form complexes with functional monomers in the pre‐polymerization mixture. After polymerization, the template is removed, leaving cavities in the structure which are complementary in shape and interaction patterns to the template molecules. These cavities act as mimics of biological receptors and are able to recognize and rebind template molecules. Although the imprinting concept is simple in principle, synthesis of MIPs with precisely controlled characteristics and performance remains a challenging task. Composition, polymerization conditions, template removal process and application conditions all affect the properties of MIPs. The material is affected at different scales, but crucially at the microscopic level, the number, fidelity and accessibility of binding sites are dependent on all the factors mentioned. The full potential of these materials can only be achieved if researchers can control and optimize the properties of MIPs through detailed understanding of adsorption and molecular recognition processes in these materials. The objective of this work is to, using computer simulations and statistical mechanics; develop a fundamental description of MIP formation and function, and to link morphological features of the model materials to their molecular recognition capabilities. In general, molecular simulations employed in this study should allow easier and more efficient exploration of a vast number of factors influencing the behaviour of MIPs. At the heart of the approach developed in this thesis is a computational strategy that imitates all the stages of MIP formation and function. First, the model simulates the pre‐polymerization mixture, allowing the formation of template‐functional monomer complexes. (This stage is implemented via canonical Monte Carlo simulation). Complexes can have different structures, depending on the chemical nature of template and functional monomer; therefore complexes can have a range of association constants. The distribution of template‐functional monomer complexes also translates into a distribution of binding sites of different specificity after template removal. In the second stage of the process, adsorption simulations (grand canonical Monte Carlo) are performed for a variety of model MIPs prepared to assess the role of various processing conditions such as composition, density and binding sites degeneration. This strategy was first applied to a simplified description of MIP species in order to identify the minimal model capable of molecular recognition and thus shed the light on the very nature of this phenomenon. In the developed model, the molecular species are constructed from hard spheres, featuring small interaction sites on their surfaces. The bond between two interaction sites has the strength and topological features of a typical hydrogen bond. The model exhibits molecular recognition, being able to preferentially adsorb template molecules. The associations between template and functional monomers were analyzed and classified to describe the distribution of binding sites and their heterogeneity. Using this model, several experimental trends typically observed in MIP studies could be explained, such as maximum in the selectivity as a function of monomer concentration. Using this model, we were also able to explore hypothetical, alternative protocols for MIP synthesis in order to improve their performance. These include the use of alternative templates and the post‐synthetic surface modifications of MIPs. The general strategy to modelling MIP, employed in this thesis, was then applied to a more detailed description of MIPs with realistic force field potentials for all the species involved. This more elaborate model is simulated with a combination of molecular dynamics (MD) and Monte Carlo techniques. This detailed model provided a wealth of information on various types of complexes observed in the pre‐polymerization mixture. Specifically, it revealed the relative weight of different interactions in the complex and their role in the binding energy of adsorbates. These simulations also provided the comparison of the relative contribution of different types of interactions (van der Waals, Coulombic) involved in a molecular recognition process. We believe the insights gained in this work will contribute to the development of rational MIP design strategies. In the discussion of the results of the thesis we speculate on how these models can be further developed in order to generate quantitative predictions and what type of systems it would be interesting and important to investigate in the future.

This thesis is concerned with the synthesis and study of novel anion templated rotaxanes and catenanes for electrochemical anion sensing, as well as interlocked structures that possess different anion binding properties, higher-order topologies and the ability to undergo molecular motion. Chapter One provides an introduction to anion recognition and the preparation of interlocked structures. A short summary of fundamental aspects of supramolecular chemistry is followed by detailed surveys of current approaches to anion binding and sensing, as well as the templated synthesis of rotaxanes and catenanes. Chapter Two describes the preparation of rotaxanes and catenanes appended with ferrocene to allow for electrochemical anion sensing. The anion recognition properties of a [2]rotaxane and a [2]catenane, as investigated by ¹H NMR spectroscopy and electrochemical methods, are presented. The utilization of a ferrocene-appended macrocycle in the construction of surface confined anion templated rotaxanes and catenanes is also discussed. Chapter Three reports the work carried out to achieve electrochemical anion sensing by the incorporation of redox-active groups into the integral structures of interlocked structures. The syntheses of a bis-stoppered 1, 2, 3, 4, 5-pentaphenylferrocene [2]rotaxane and a ferrocene containing [3]rotaxane are presented, along with their subsequent anion recognition studies. In addition, attempts to incorporate ferrocene into the macrocyclic components of rotaxanes and catenanes are outlined. Chapter Four details further investigations into the use of interlocked structures to achieve anion recognition. Doubly-charged [2]catenanes able to bind anions in aqueous solvent media, as well as the incorporation of alternative anion binding motifs into interlocked architectures are reported. The exploitation of anion templated synthesis to allow for the construction of higher order structures (including [3]catenanes, a “handcuff” catenane and a Janus [2]rotaxane), as well as a [2]catenane system with anion controlled molecular motion is also described. Chapter Five presents the experimental procedures and characterization data relating to the compounds prepared in Chapters Two, Three and Four. Chapter Six summarizes the main conclusions of the work contained within this thesis. Supplementary experimental information relating to titration protocols, investigations into self-assembled monolayers (SAMs) and crystallographic data are provided in Appendices I, II and III.

Development of selective artificial metalloenzymes by combining the biological concepts for selective recognition with those of transition metal catalysis has received much attention during the last decade. Targeting covalent incorporation of organometallic catalysts into proteins, we explored site-selective covalent coupling of phosphane and N–containing ligands. The successful approach for incorporation of phosphane ligands we report herein consists of site-specific covalent coupling of a maleimide functionalized hydrazide into proteins, followed by coupling of aldehyde functionalized phosphanes via a hydrazone linkage. Site selective incorporation of N–containing ligands was obtained by coupling maleimide functionalized N–ligands to proteins via Michael addition to the maleimide double bond. These two methods can be easily applied to virtually any protein displaying a single reactive cysteine and allows a wide range of possibilities in terms of cofactor design. Site-specific covalent incorporation of transition metal complexes of phosphane ligands into proteins was successfully obtained. The success of the approach is influenced by several factors like the metal precursor, the phosphane type and the protein scaffold. Metal complexes of 5–maleimido–1,10–phenanthroline modified proteins were formed in situ, via addition of a metal precursor to the phenanthroline modified proteins or by coupling preformed metal complexes to proteins via Michael addition of the thiol group from a cysteine residue to the maleimide double bond of the N-ligand. These successful coupling methods enable the use of a wide range of protein structures as templates for the preparation of artificial transition metalloenzymes, which opens the way to full exploration of the power of selective molecular recognition of proteins in transition metal catalysis.

Until very recently, synthetic chemistry has focussed on the creation of chemical entities with desirable properties through the programmed application of isolated chemical reactions, either individually or in a cascade that afford a target compound selectively. By contrast, biological systems operate using a plethora of complex interconnected signaling and metabolic networks with multiple checkpoint controls and feedback loops allowing biological systems to adapt and respond rapidly to external stimuli. Systems chemistry attempts to capture the complexity and emergent phenomena prevalent in the life sciences within a wholly synthetic chemical framework. In this approach, complex phenomena are expressed by a group of synthetic chemical entities designed to interact and react with many partners within the ensemble in programmed ways. In this manner, it should be possible to create synthetic chemical systems whose properties are not simply the linear sum of the attributes of the individual components. Chapter 1 discusses the role of complex networks in various aspects of chemistry- related research from the origin of life to nanotechnology. Further, it introduces the concept of Systems chemistry, giving various examples of dynamic covalent networks, self-replicating systems and molecular logic gates, showing the applications of complex system research. Chapter 2 discusses the components of replicator design. Further, it introduces a network based on recognition mediated reactions that is implemented by length- segregation of the substrates and displays properties of self-sorting. Chapter 3 presents a fully addressable chemical system based on auto- and cross- catalytic properties of product templates. The system is described by Boolean logic operations with different template inputs giving different template outputs. Chapter 4 introduces a dynamic network which fate is determined by a single recognition event. The replicator is capable of exploiting and dominating the exchanging pool of reagents in order to amplify its own formation at the expense of other species through the non-linear kinetics inherent in minimal replication. Chapter 5 focuses on the development of complex dynamic systems from structurally simple molecules. The new approach allows creating multicomponent networks with many reaction pathways operating simultaneously from readily available substrates.

In the last twenty years, chemists have devised numerous synthetic chemical systems in which self-replication operates, demonstrating that molecules can replicate themselves without the aid of enzymes and that self-replication is not a prerogative of nucleic acids only. However, the coupling of replication to other recognition-mediated events and its exploitation in the amplification of large supramolecular assemblies, such as mechanically interlocked molecules, have remained unexplored areas. Among mechanically interlocked molecules, rotaxanes represent particularly attractive targets because of their application as molecular switches. This thesis describes how the recognition-mediated synthesis of a rotaxane can be combined to the amplification of its structure by replication. Kinetic models for the integration of self-replication with the formation of a rotaxane are presented. The logical steps required to convert these models into molecular structures through consideration of the design criteria highlighted by the models are discussed and executed. The macrocyclic component is an essential part of a rotaxane. The synthesis of several novel macrocycles is presented. Their ability to bind guests in their cavities through hydrogen bonds was probed. The best macrocycle/guest pairs were integrated in the formation of rotaxanes. Further investigations on the stoppering reaction and on the various recognition processes involved in the system lead ultimately to the construction of self-replicating rotaxanes.

In the last 20 years there has been a number of synthetic and natural product based molecular replicators published in the literature. The majority of these systems have focused on the minimal model with only a few examples of cross-catalytic or reciprocal replication. Of the cross-catalytic systems investigated the majority focus around the use of natural products, oligonucleotides, peptides etc. This thesis will investigate the design, synthesis and kinetic analysis of both synthetic minimal and reciprocal replicating systems, and how these two forms of replication interact in a complex hypercyclic network. Chapter 1 introduces key concepts such as molecular recognition, intramolecularity/ enzyme kinetic, bisubstrate systems and the work conducted into replication systems to date. Chapter 2 describes the design, synthesis and kinetic analysis of a reciprocal replicating system, based on Diels-Alder and 1,3-dipolar cycloadditions, before going on to discuss what we have learned and how this system can be improved. Chapter 3 focuses on the design, synthesis and kinetic analysis of a replicating network (minimal and reciprocal replication), based on 1,3-dipolar cycloadditions. Initial individual systems are examined in isolation to determine their behavior and nature. After which the systems are combined to observe how each species interacts in a potential complex hypercyclic network. Chapter 4 investigates the redesign of the replicating network in Chapter 3 in order to overcome the problems identified from its kinetic analysis. Chapter 5 introduces the shift in direction away from kinetically controlled replicating networks towards systems in thermodynamic equilibrium.