The study of topologically complex molecules is necessary to better understand the knotted architectures that abound within Nature and are vital in the functioning of DNA and proteins. Metal based template strategies have played a key role in the successful synthesis of a number of interwoven structures constructed from small molecule building blocks, however novel methodology is crucial for the expansion of this fascinating field of chemistry. The strategy of linking the ends of a cyclic helicate has been developed within the Leigh group and applied with great success to the synthesis of the first molecular pentafoil knot. This thesis presents the application of this strategy to the high yielding synthesis of a molecular Solomon link. In depth studies of the self-assembly of a pentafoil knot and self-sorting reactions are also presented, offering insights into the nontrivial self-assembly of these topologically complex molecules.

The use of a chemical template to control the spatial arrangement of reactants revolutionized the synthesis of mechanically interlocked molecules. The recently developed ‘active metal template’ strategy, in which transition metal ions act as both the template to guide interlocking and as the catalyst for the covalent bond forming reaction that captures the interlocked structure, has several advantages in comparison with traditional ‘passive template’ approaches. In contrast with passive template approaches the active template strategy is more efficient, completing the assembly of the interlocked structure in one step instead of two and in some cases requiring only a substoichiometric amount of metal template. In addition, fewer permanent recognition sites are required and in certain cases the active template reaction can shed light on mechanistic details of related metalcatalyzed processes and act as a conduit for reaction discovery. This Thesis will discuss the expansion of this new methodology in two main directions: firstly, exploration of new active metal template reactions, specifically the application of a novel Ni catalyzed sp3–sp3 C–C bond forming reaction, and secondly, the application of previously developed active template reactions to the synthesis of agrochemical-based [2]rotaxanes and other architectures, macrobicyclic [3]rotaxanes, [2]catenanes and a trefoil knot.

This thesis describes the synthesis of acyclic, macrocyclic and, in particular, interlocked anion and ion-pair receptors and sensors. <strong>Chapter One</strong> will introduce the field of supramolecular chemistry with particular emphasis on areas which are pertinent to this thesis, including anion receptor design and templated synthesis of interlocked structures. <strong>Chapter Two</strong> focuses on the synthesis of new heteroditopic macrocycles functionalised with both cation and anion recognition sites and their incorporation into interlocked architectures. The affinity for a range of anions and ion-pairs is explored via ¹H NMR and UV-visible spectroscopy as well as by X-ray crystallography. <strong>Chapter Three</strong> details the incorporation of d- and f-metal luminescent reporter groups into an isophthalamide motif in order to construct acyclic, macrocyclic and [2]rotaxane receptors. <strong>Chapter Four</strong> investigates the synthesis of complex higher-order interlocked structures through post-synthetic modification of lower-order interlocked structures. <strong>Chapter Five</strong> explores the potential for fluorescent gold nanoparticle conjugates to act as luminescent and colourimetric sensors for chemical warfare agents (CWAs) by employing a fluorescent displacement assay technique.

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.

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.

Polyrotaxanes are molecular composites consisting of three components: linear polymers, bulky stoppers at the ends of polymer chains and macrocycles threaded by the polymers. A series of tetraarylmethyl derivatives as blocking groups were synthesized. Using tris(p-ten-butylphenyl)( 4-hydroxyphenyl)methane a new blocking groupfmitiator (BO(mit) was synthesized. The BG(mit's ability of blockingfmitiation in free radical polymerizations was established by polymerization of styrene. As cyclic components, aliphatic crown ethers (30-crown-lO, "42-crown-14" and "6O-crown-20") were synthesized by multi-piece combination methods. The purification of the crown ethers was achieved by treatment with poly(methacryloyl chloride), column chromatography and recrystallization; by NMR in DMSO-<i>d₆</i> the purity of the products was demonstrated. The 42-crown-based [2]catenane was isolated while synthesizing "42- crown-14" and characterized in terms of its physically interlocked structure. Two new hydrocarbon-based macrocycles were prepared by two-piece combination method. / Ph. D.

This thesis explores the use of anions in the design and construction of interlocked architectures for applications in anion recognition and sensing, and to function as molecular machines upon a given stimulus. Chapter One introduces the field of anionic supramolecular chemistry focusing on host-guest chemistry and directed self-assembly. A review of the recognition and sensing of anionic guest species is given before strategies for the construction of interlocked architectures are discussed, and the potential functions of these structures considered. Chapter Two details the development of a novel anion-templation route for the synthesis of macrocycles and rotaxanes. The versatility of this route in constructing new [2]rotaxanes is explored by varying several features of the macrocyclic component, with emphasis on creating the most powerful anion complexant. Proton NMR spectroscopy is used to probe the anion binding properties of the rotaxanes, and X-ray crystallography and MD simulations are used to rationalize anion binding trends. The possibility of synthesizing catenanes for anion recognition via this new synthetic route is also investigated. Chapter Three investigates the appendage of transition metal complexes to rotaxanes to create interlocked host architectures capable of sensing anions via luminescence spectroscopy. The incorporation of rhenium(I) and ruthenium(II) polypyridyl complexes into the macrocyclic and axle component of [2]rotaxanes are described, before the anion binding studies of these structures using ¹H NMR and luminescence spectroscopy are reported. Chapter Four describes the strategic synthesis of [2]rotaxanes designed to undergo molecular motion upon a given stimulus. Initially, the possibility of exploiting anions to stimulate the macrocyclic component of the [2]rotaxanes to translocate to a second station on the axle is investigated. The use of pyridine N-oxide as an integrated template for rotaxane formation is reported before the ability of these rotaxanes to undergo anion and pH driven molecular motion is explored. This chapter concludes with the construction of a calix[4]diquinone N-oxide containing [2]rotaxane capable of undergoing sodium- and barium-induced molecular pirouetting. Chapter Five provides synthetic procedures and characterisation details for compounds listed in this thesis. Chapter Six reports supplementary experimental information including titration protocols, X-ray crystal structures and MD simulations.

Supramolecular chemistry is an emerging field of chemistry which has attracted much attention in recent years as a result of its broad applicability in many areas. Thus, the design of functional supramolecular systems is strongly in demand in this field. For this purpose, we have developed ratiometric fluorescent chemosensors for ion sensing and mechanically interlocked structures for their application in molecular logic. In the first part, we report a novel dimeric boradiazaindacene dye which can be converted in one step to an efficient resonance energy transfer (RET) dyad. In addition, if this modification is done with appropriate ligands, RET can be coupled to ion sensing. The utility of this approach is demonstrated in a highly selective, emission ratiometric chemosensor for Ag(I). In the second part, boradiazaindacene dyads designed as energy transfer casettes were modified to signal cation concentrations ratiometrically. If the energy transfer efficiency is increased by changing spectral overlap on cation binding, an enhancement of emission signal ratios can be obtained. A larger range of ratios results in highly improved sensitivity to analyte concentrations. We demonstrate this approach in a de novo design of a novel and highly selective ratiometric chemosensor for Hg(II) ions. In the last part, we synthesized a two-station [2]catenane composed of an &amp / #960 / -electron rich bis-1,5-dihydroxynapthalene[38]-crown-10 (1/5DNPC10) ring interlocked with a second macrocycle containing two &amp / #960 / -electron deficient unit, namely, napthodiimide (NpI) and bipyridinium (BIPY)2+ unit using the Cu(I)-catalyzed Huisgen 1,3-cycloaddition reaction. The resulting bistable [2]catenane is isolated as a single co-conformation which is comprised of the 1/5DNP[38]C10 ring around the NpI unit. Thermal activation of the pure NpI-isomer at 70&amp / #730 / C for 60 h leads to the formation of the BIPY2+-isomer by virtue of the circumrotation of the crown-ether ring along the backbone of the other macrocycle over the steric barrier of the tetra-aryl methane units. The energy barrier for the circumrotation is 28.5&plusmn / 0.3 kcal/mol. Electrochemistry of a 1:1 mixture of the two possible isomers shows that the [2]catenane cannot be switched mechanically on account of the large steric barriers presented by the tetra-aryl methane groups on the electron-accepting ring.

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This thesis explores the surface assembly of mechanically interlocked molecular architectures at gold surfaces for potential applications in molecular switches, anion sensing and stimuli (redox and optical) responsive molecular films. <b>Chapter One</b> introduces the field of mechanically interlocked molecules focusing on rotaxane and catenane surface assemblies in the form of single molecule thick self-assembled monolayers. A review of the surface-attached characteristics of mechanically interlocked molecules is given before exploring specific anion template directed strategies for their construction. The potential to incorporate both redox-active and optically-active functional groups within these mechanically interlocked molecules is also discussed. <b>Chapter Two</b> provides the experimental details and procedures employed in this thesis to characterise the molecular systems under investigation. <b>Chapter Three</b> introduces several surface characterisation techniques such as; ellipsometry, contact angle, X-ray reflectivity and X-ray photoelectron spectroscopy, with a particular focus of applying these tools to probe the surface co-conformation of switchable and interlocked molecules at surfaces. Electroanalytical techniques such as cyclic voltammetry, chronoamperometry and electrical impedance spectroscopy are also introduced. <b>Chapter Four</b> details the surface assembly of a series of ferrocene containing anion templated catenane self-assembled monolayers on gold. Detailed electrochemical and angle resolved X- ray photoelectron spectroscopy characterisation elucidates the co-conformation upon surface attachment. <b>Chapter Five</b> details the anion templated surface assembly of a redox-active rotaxane self- assembled monolayer on gold. Subsequent electroanalysis and X-ray photoelectron spectroscopy characterisation confirms the structural integrity of the film and a possible co- conformation at the surface is discussed. <b>Chapter Six</b> describes efforts towards constructing optically responsive hybrid d-f lanthanide containing mechanically interlocked molecules. Initial work focuses on switching characteristics of a redox switchable antennae and its ability to modulate the luminescence of a series of lanthanide complexes in solution. Subsequent surface attachment of the lanthanide complexes in the form of emissive self-assembled monolayers is also investigated.