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This thesis presents Electron Paramagnetic Resonance (EPR) studies of a series of molecules to assess the suitability of heterometallic rings for applications in Quantum Information Processing (QIP). Of particular interest here are complexes containing multiple paramagnetic centres, which have been proposed as multi-qubit gates - the quantum analogue of classical multi-input logic gates. Such gates are an essential component of any viable quantum computer, and so if electron spins contained in molecules are to be used as qubits it must be possible to use them to perform multi-qubit operations. To this end a novel method of manipulating and detecting the states of multi-spin Molecular Electron Spin Qubits (MESQs) is proposed. This method is experimentally tested on a model system and its efficacy is examined through numerical simulations. In addition to these methodological developments, the magnetic properties of a series of novel complexes are determined, a crucial first step towards assessing their suitability as qubit candidates. The inter-spin interactions in a family of heterometallic rings linked to metalloporphyrins are quantified using a combination of Continuous Wave (CW) and pulse EPR techniques. Further, the magnetic properties of single isomer {Cr6M2} heterometallic rings are able to provide insight into the isomeric structure of the clusters.

This thesis summarises attempts towards polyyne [n]rotaxanes and cyclocarbon [n]catenanes. Carbon allotropes built purely from sp carbon atoms have long fascinated chemists but have yet to be isolated or characterised due to their high reactivity. This thesis documents work towards isolating both linear and cyclic sp carbon chains. Chapter 1 reviews the history of carbon allotropes, focussing on cyclic and linear forms of sp carbon. Synthetic strategies towards preparing acetylene-rich molecules, rotaxanes and catenanes are discussed. Chapter 2 discusses development of a novel masked alkyne equivalent (MAE) with intrinsic metal binding abilities. A simple masked triyne can be synthesised in only three steps, but photochemical unmasking of this group could not be realised due to a competing dimerisation process. Chapter 3 details new strategies for synthesising polyyne [3]rotaxanes with two macrocycles on the same polyyne thread. An active metal template route using dicobalt-masked precursors was developed to prepare two polyyne [3]rotaxanes. The thermal stabilities of the two rotaxanes were evaluated relative to the naked polyyne dumbbell and were found to be significantly more stable in decalin at 80 °C. Chapter 4 presents a novel approach to cyclocarbon [n]catenanes and polyyne [n]rotaxanes. The coupling of a [2]rotaxane bearing two temporary bulky MAE stoppers provides access to precursors of cyclocarbon [n]catenanes and polyyne [n]rotaxanes. Early unmasking experiments have successfully afforded a polyyne bearing 24 contiguous acetylene units and indicate that larger polyynes should be viable using this route. Chapter 5 summarises.

Supramolecular chemistry deals with systems made of distinct chemical species which, when put together, have different properties than each individual component. These species are often not bonded in a covalent or ionic sense, but are based on host-guest chemistry. Mechanically interlocked molecules (MIMs) and handcuff rotaxanes in particular, which are systems containing multiple covalently bonded macrocycles, through which a rod is threaded then stoppered, are an example of such species. MIMs have wide ranging applications in nanoscale electronics, systems which mimic biology, and many others. Since its recent discovery, pillar[5]arene has been used extensively in MIMs due to its interesting host guest properties, and this work deals with handcuff rotaxanes containing it, as well as perylene diimide (PDI), tetrazine, and imidazole groups. The feasibility of the synthesis of a three-membered PDI cofacial stack or a 'triple decker handcuff rotaxane', using a templated, clipping method, utilising interactions between PDI cores and between pillar[5]arenes and imidazole groups, is investigated. The difficulty in this lies in the synthesis of a 'linker' that can connect two pillar[5]arene macrocycles and also the PDI core of the macrocycle based component of the handcuff rotaxane. Various methods of amine alkylation, amide coupling and ether synthesis were explored to connect the functionalised pillar[5]arenes together, but due to the difficulties with pillar[5]arene syntheses and purifications they were all unsuccessful in either of those steps. However, novel pillar[5]arene-based species were successfully synthesised in this part of the project and fully or partially characterised. Next, a simpler cofacial stack of a PDI and a tetrazine based on handcuff rotaxane topology was attempted but was unsuccessful due to the low solubility of pillar[5]arenebased species in solvents required for the tetrazine forming reaction. However, during this part of the project two new functionalised pillar[5]arenes were synthesised and characterised and attempts at optimising these syntheses were made. Finally, a handcuff rotaxane containing only one PDI species was successfully synthesised and characterised. Its properties were probed using cyclic voltammetry, spectroelectrochemistry and electron paramagnetic resonance spectroscopy and compared with similar handcuff rotaxanes previously synthesised in the group. The lack of stacking species in this handcuff proved a previously postulated hypothesis that the synthesis method here described only requires templating between the host's macrocycles and the threading guest. This does however, lower the yields relative to species with additional molecular recognition sites. The thus far described part of this work explored and celebrated the organic synthesis of supramolecular structures, while the second part focuses on spectroscopic analysis of supramolecular systems. The systems in question are the collagen-tannin matrices found in leather, and more specifically in deteriorated leather book bindings from the Natural History Museum. As such the two parts of this thesis are only related due to dealing with supramolecular structures and should be interpreted separately. This second project explored a leather acidic deterioration process known to conservators as red rot. Red rot affects leather book bindings from the late 19th and early 20th centuries and causes them to become dry and reddish, or in advanced stages crumble into a dark powder. This project set out to explore health and safety aspects of red rot dust using various spectroscopic techniques and suggest further necessary tests. This was evaluated using Inductively Coupled Plasma analysis (Optical Emission Spectroscopy and Mass Spectrometry), in comparison with permissible heavy metal content in samples as defined by a commercial certification body, OEKO TEX. For the tested samples, it was found that arsenic, cadmium and lead were not within the permissible limits and hence caution when handling these items is recommended. Furthermore, this work aimed to understand more about the red rot deterioration process by comparing undeteriorated and deteriorated leather samples with Fourier Transform Infrared spectroscopy and Scanning Electron Microscopy. No features present in red rot but absent in other types of deterioration were found, however, this work recommends gas chromatography as another technique that might achieve this. Finally, this work attempts to quantify the degree of deterioration of bindings suffering from red rot through an FTIR peak ratios. Such a ratio is explored and found to relate to visually assessed levels of degradation. However it is not certain that this is a red rot specific ratio and not a general degradation ratio. This work allowed for health and safety recommendations to be made to the museum, as well as for a deeper understanding of the red rot deterioration process to be obtained.

The work presented in this thesis centres on the synthesis and measurements of paramagnetic rotaxane molecules consisting of [Cr₇NiF₈(O₂C^tBu)₁₆]⁻ {Cr₇Ni} octametallic rings. The possibility of using {Cr₇Ni} rings as qubits has triggered interest from research chemists. The aim of the project is to synthesise molecules which connect {Cr₇Ni} rings and dissimilar qubits via an ammonium thread. Paramagnetic NMR is used to investigate the relative solution stabilities for a series of pseudorotaxanes by exchanging the ammonium thread. An understanding of the binding preferences of the octametallic macrocycles is important in the design of more complex molecular assemblies. This work begins by exploring the binding preferences between a [Cr₇CoF₈(O₂CCH₂^tBu)₁₆]⁻ macrocycle and dialkylammonium cations through equilibrium constants, quantified using paramagnetic NMR. The study concludes that the relative stability of a pseudorotaxane is dependent upon the structure of the ammonium cation and solvent used. Knowledge of the molecules' relative stabilities was used to synthesise new pseudorotaxanes via an indirect route in high yields (> 80 %). The observations are the first step in the design of more elaborate [n]rotaxane molecules and dynamic systems. A series of two- and three-spin [2]rotaxanes have been synthesised involving [Cr₇NiF₈(O₂C^tBu)₁₆]⁻ {Cr₇Ni} macrocycles, charge-balanced by ammonium threads terminated with metal salen groups (where M = Cu, Ni, VO). Each compound has been characterised using single crystal X-ray diffraction. One of the complexes synthesised includes a three-hetero-spin [2]rotaxane comprising three spin = ½ centres. Continuous wave and pulsed electron paramagnetic resonance (EPR) experiments were implemented to investigate the structure of the molecules in solution. The inter-spin distances obtained from pulsed EPR experiments are consistent with those observed in the crystal. A twelve-membered nickel cluster has been used to bring multiple {Cr₇Ni} rings together to form a series of [7]rotaxanes. The structure of each molecule differs in the crystal depending on the structure of the coordinated thread. Small angle X-ray scattering supported by molecular dynamic simulations were used to investigate the structure of the molecules in solution. The results indicate that the molecule is stable in solution but adopts conformations which differ to that in the crystal.

Molecular machines are ubiquitous in nature and drive almost all important biological processes. In the past couple of decades, chemists have become interested in mimicking the behaviour of biological machines with small molecule molecular machines. In this context, mechanically interlocked structures like [2]rotaxanes have played a significant role. Herein we explore the application and synthesis of novel [2]rotaxane architectures to solve different problems encountered in the field of molecular machines. Firstly, a molecular walker based on a [2]rotaxane architecture is explored. The mechanically interlocked structure renders each walking step highly directional, which was not the case for previously reported small molecule walkers. The herein reported system might serve as a platform to explore the application of molecular fuels to walkers. If successful, this could be the next step towards fully autonomous small molecule walkers. Secondly, [2]rotaxanes are explored for the sequence specific synthesis of peptides. In this context, the direct aminolysis of thioesters is explored as a new mode of operation. It was hypothesised that this type of reactivity could help to circumvent some of the limitations of previous designs. Thioester-based molecular machines were synthesised and operated, however initial operations with a 3-barrier machine remain unsuccessful. Further investigations will be necessary; however the synthesis of the machines is challenging and it remains to be seen whether large enough quantities can be synthesised to thoroughly investigate this system. Finally, a new C(sp3)-C(sp3) bond forming reaction reported by Baran and co-workers is explored for the synthesis of asymmetric traceless [2]rotaxanes where the axle does not contain any obvious retrosynthetic disconnection. The methodology successfully furnished the desired species; however a symmetric homo-coupling product was also obtained. Based on this unexpected observation, potential implications for the mechanism of the reaction are discussed.

Once merely a synthetic curiosity, mechanically interlocked molecules (MIMs) have become readily accessible structures thanks to the development of template approaches, and their properties are now being explored for applications in materials, catalysis, sensing, and molecular machines. This thesis describes work to expand the understanding and applications of MIMs prepared via an active template approach. In the first chapter, topics related to MIMs are discussed with the aim of introducing the work presented in chapters 2-4. These include the active template copper-mediated azide alkyne cycloaddition, emissive rotaxanes, and the stereogenic units that can arise from the mechanical bond. In the second, the synthesis of a selection of rotaxanes based on a thermally activated delayed fluorescence (TADF) emitter scaffold is reported. The effect of the mechanical bond on the TADF properties of three of these emitters was investigated and was shown to improve key photophysical properties. In the third, the synthesis of cycloplatinated rotaxanes is explored for potential applications in luminescent materials. A robust procedure could not be developed. However, the platination exhibited unexpected regioselectivity depending on the components used to prepare the rotaxanes, highlighting the ability of the mechanical bond to influence unexplored reactivities. Finally, in the fourth chapter, the concept of topological chirality in MIMs is discussed. Using a chiral auxiliary approach developed by the Goldup group, a chiral catenane is synthesised where an exocyclic double bond determines the orientation of one ring, challenging common terminology used to describe such stereogenic units.

Interlocked molecules contain two or more components that cannot be separated without breaking any covalent bonds, such as rotaxanes and catenanes. A rotaxane is a molecular structure that has an axle threaded through a macrocycle with two bulky stoppers on either side. The stoppers are physically larger than the internal diameter of the ring and prevent dissociation of the components. A catenane is a molecular architecture consisting of two or more interlocked macrocycles which cannot be separated without breaking one of the covalent bonds of the macrocycles. Interlocked molecules offer numerous potential applications in molecular machines, catalysis and drug delivery.

Mechanically interlocked molecules have been of interest to chemists since the 1960s. Recent synthetic advances have made the investigation of the mechanical bond more accessible, with most applications of interlocked molecules in molecular machines. The field of interlocked molecules was acknowledged by the Nobel committee in 2016, with the prestigeous prize being awarded to Sir J. Fraser Stoddart, Jean-Pierre Sauvage and Ben Feringa for their contribution to "the design and synthesis of molecular machines". This thesis discusses mechanical planar chirality, the challenging synthesis of interlocked molecules displaying this type of chirality, and the first application of this type of chirality in enantioselective catalysis. Finally this thesis presents a new, general approach to the synthesis of interlocked molecules displaying this type of chirality, allowing unprecedented access to enantiopure rotaxanes and a library of ligands for catalysis by application of this methodology.

Many biological processes require the intervention of sophisticated molecular machines to orchestrate complex actions. The last few decades have witnessed how the community of synthetic chemists has learnt the lessons from biology to create a wide variety of different artificial molecular machines able to perform all sorts of different tasks. The development of new artificial molecular machines has evolved hand in hand with the synthesis of new molecular structures and topologies. This thesis revolves around the use of [2]rotaxanes (a particular kind of mechanically interlocked structure with an axle threaded across a macrocycle) as privilege scaffolds for their use as molecular machines. In particular, the large amplitude motion of a macrocycle in a rotaxane with respect to its threaded axle can allow for the fine control in the outcome of a reaction. This feature has been explored in this thesis for two different applications. First a [2]rotaxane has been used to assemble a peptide in a sequence specific way via the direct aminolysis of thioesters. This is reminiscent of the way in which the ribosome operates to decode genetic material into proteins. Secondly, a structurally different [2]rotaxane architecture has been employed as a switchable organocatalyst to selectively flip the enantioselectivity in the conjugative addition of aldehydes to activated electrophiles. Finally, due to the importance of rotaxanes as molecular machines, a new method for the synthesis of non-symmetric alkyl [2]rotaxanes is described using a recently reported Ni-catalysed decarboxylative protocol.

Reports of mechanically interlocked molecules (MIMs) have grown in recent years, aided by the relative synthetic ease by which they can now be obtained in comparison to the challenging syntheses reported originally. With this influx of research into the area, boosted even more by the 2016 Nobel Prize in the field for ‘the design and production of molecular machines’ there have been a lot of recent developments, showing the potential of MIMs for different applications such as switches, sensors or in catalysis due to the unique environment of the mechanical bond. The introductory chapter provides a detailed overview of chirality in the context of MIMs. In addition to discussing the properties and applications of MIMs containing covalent stereogenic units, the different forms of chirality that arise as a consequence of the mechanical bond, and the influence this can have on the properties of molecules will be outlined. Chapter two details the design and synthesis of a dynamic co-conformationally mechanically planar chiral rotaxane which exists as a pair of rapidly exchanging enantiomers. This novel rotaxane binds diastereoselectively to chiral anions. The biasing of the coconformations of the rotaxane host through guest binding leads to an induced circular dichroism (CD) signal even when the chiral anionic guest does not display a CD signal on its own. Our results demonstrate the long-term potential of such stereodynamic rotaxanes in determining the enantiopurity of chiral analytes. Chapter three describes the unexpected discovery of a novel acrylamide rotaxane, formed as an unintended consequence of the mechanical bond stabilizing a CuI-triazolide intermediate. This novel reactivity was investigated in depth, firstly by exploring the scope of the reaction and then via experiments designed to gain insight into key reaction intermediates. Using our results, a possible a mechanism of the reaction was proposed.

Although known to chemists for nearly a century, interlocked structures have only been synthetically accessible since the 1980s when 'passive template' methods allowed the pre-complexation of components to increase yields. 'Active template' methods, initially developed by the Leigh group in 2006, have resulted in even higher yields of rotaxanes - "interlocked structures formed of at least one macrocycle penetrated by at least one impassably-stoppered axle" - and a phenomenal surge in interest in their properties as a result of this increased availability. This first method adapted highly efficient 'click' methodology to give the Active Template Copper-Mediated Alkyne-Azide Cycloaddition reaction (AT-CuAAC) and is still the most used rotaxane-forming method today. In this work, I provide the reader with an overview of these mechanically-interlocked architectures from synthesis to application. Later work by the Goldup group showed that a smaller macrocycle could make [2]rotaxanes (one macrocycle, one axle) with complete efficiency compared to their larger forebears, while intermediate sizes gave incomplete conversion, with unused macrocycle unrecovered. In this investigation, I then identify a series of novel doubly-interlocked [3]rotaxane products from this reaction that explain the absence of unused macrocycle. I then explore the variation of conditions and show how these novel products are favoured by high temperatures and high catalyst loading in a non-coordinating solvent, whereas their yields are suppressed in low temperatures and catalyst loading in a co-ordinating solvent with base, giving up to quantitative [2]rotaxane formation. To provide a mechanistic rationale for the formation of these products I then assess the effects of stopper length, macrocycle structure and lithiation experiments on the ratio of the [2]- to [3]rotaxane. The results of the above allow me to derive a new mechanistic hypothesis when I then test in a series of experiments to form [3]rotaxanes with two rings differing in either structure, size or both. Finally, the design, synthesis and testing of a stopper developed and used by myself for the AT-CuAAC reaction is described such that where two macrocycles differ in size, the larger can only be held in a novel heterocircuit [3]rotaxane, produced in synthetically useful yields.

Rotaxanes are a class of compounds composed of two or more mechanically interlocked molecules. Mechanically planar chiral rotaxanes are a novel class of compound in that their chirality is due to the isomerism of a mechanical bond, as opposed to the covalent bonding of the individual components. We know of no method to synthesise enantiomerically pure samples of the mechanical isomers of a mechanically planar chiral rotaxane without resorting to advanced purification techniques. The lack of ready availability of these materials has hampered the full investigation of their properties and applications. Of particular interest are their properties as chiral reaction-spaces, such as ligands, organo-catalysts, and chiral resolution agents. This thesis addresses these issues by developing a chiral-auxiliary approach toward the synthesis of mechanically planar chiral rotaxanes whereby an intermediate pair of diastereomeric rotaxanes are synthesised and separated using reliable and scalable standard laboratory techniques. Cleavage of the chiral auxiliary allows for the synthesis of enantiopure mechanically planar chiral rotaxanes. Tuning the structure of the mechanically interlocked components as well as the reaction conditions allows for control over the diastereoselectivity during the mechanical bond forming step.

Mechanically interlocked molecules (MIMs) have been attracting increasing interest since their emergence in the 1960s. The development of passive template and active template synthetic approaches facilitated the rapid growth in synthesis of various functionalised mechanically interlocked molecules (MIMs), allowing for a wide range of applications. In this thesis, Chapter 1 will discuss the synthetic methodologies from earliest statistical methods to passive templates and the latest active templates. Amongst the active template methodologies, the Cu catalysed alkyne azide cycloaddition (AT-CuAAC), together with its introduction, mechanistic studies as well as its application in syntheses of various functionalised rotaxanes will be presented. Chapter 2 will illustrate the discovery of an unexpected dinuclear Cu(I) complex during the investigation of an AT-CuAAC reaction and its selective demetallation. Chapter 3 highlights the important role of the mechanical geometry on stabilising a Pt(II) centre in ligand substitution reactions and oxidation reactions. Finally, Chapter 4 reports the synthesis of two Pt based chiral rotaxanes where the ultimate aim is to investigate these complexes as emitters of circularly polarized light (CPL) for OLED applications.

Molecular machines and motors play a key role in numerous biological processes. Nature has thrown down the gauntlet regarding complexity and function of these systems. Over the last decade advances in synthetic and supramolecular chemistry have enabled chemists all over the world to make significant progress towards conquering the realm of nanomachines. At the forefront of this are mechanically interlocked molecules (MIMs), which have also added an additional dimension to various fields of both experimental and theoretical chemistry. The potential applications of molecular machines is undoubtedly immense and bridging the gap between the current generation of molecular machines and state of the art systems found in nature bears great reward. MIMs commonly feature members of the key macrocycle families. One of the most prominent recently discovered families of macrocycles are pillar[n]arenes. Their potential in the synthesis of MIMs is of great interest and is currently subject to substantial investigation. Unlike in macroscopic machines where energy is typically converted to motion, in the realm of nanomachines Brownian motion results in continuous movement of the molecular components relative to each other. Therefore, one of the key challenges emerging in the field of molecular machines is controlling the motion of mechanically interlocked components relative to each other. A typical example of this are two station molecular shuttles, in which a macrocycle continuously moves back and forth between two identical stations. Metal coordination to a series of pillar[5]arene/bis-imidazolium [2]rotaxanes through the formation of metal-carbene bonds facilitates a new strategy to restrict the shuttling motion in two station molecular shuttles. Whilst pillar[5]arene exhibits fast shuttling along the entire bis-imidazolium axle in the parent [2]rotaxanes, Ag(I)- or Pd(II)-coordination to the imidazoliums through the formation of an N-heterocyclic carbene results in restricted motion. Ag(I)-coordination can be reversed to obtain the parent species and is a potential starting material for further transmetalation reactions with a range of other metals. The asymmetric Pd(II)-coordination to only one imidazolium is achieved through fine tuning of the spacer length, separating the two imidazolium units. In order to synthesise MIMs with specific functions for applications, it is necessary to develop a synthetic toolbox which allows the straightforward combination of different components to produce systems with desirable and predictable properties in high yields under mild conditions. Furthermore, it has to be possible to build up more complex [n]rotaxanes and include supramolecular building blocks such as porphyrins, carbazoles, NIs and BODIPYs. Such a toolbox approach is developed by demonstrating that the three constituents of a [n]rotaxane (the rod, the macrocycle and the stopper group) can all be functionalised to contain an array of desirable moieties. The complex interplay of components in MIMs and the significant impact threading can have on the overall properties of the system is demonstrated by fluorescence measurements, finding that regulation of the fluorescent response can be achieved through certain combinations of macrocycle and rod substitution. The toolbox developed herein is employed in the synthesis of [2]rotaxanes with handcuff topology, which allows molecules to be loosely connected whilst positioning them in close proximity. This strategy is demonstrated by the production of rylene diimide dimers, connected through pillar[5]arene/imidazole mechanical bonds. The spectroscopic and electrochemical investigation of these compounds enables a rare insight into the manner in which these compounds interact and demonstrates some intriguing new properties. In particular, the perylene diimide dimer handcuff displays fascinating characteristics such as excimer emission and an unusual visible absorption profile, showing the formation of a radical anion -dimer upon double reduction. Interesting interactions in a naphthalene diimide dimer and a mixed perylene/naphthalene diimide dimer are also observed, the second of which demonstrates the superior flexibility of this synthetic approach. The effect of Pd(II)-coordination to the imidazoliums of the handcuffs on the overall properties of the system is evaluated, showing small but important changes in the way the rylene cores interact. The synthetic strategy described within this thesis facilitates the creation of unusual dimeric structures and the adaptability of this approach is demonstrated through the introduction of 1,5-dialkoxynaphthalene (DAN) units. The unique arrangement of redox active moieties in this way allows intermolecular interactions to be investigated and their effect on each other's electronic and magnetic properties to be probed. Demonstrated herein is that the pillar[5]arene-imidazole interaction can be used as a versatile motif in the synthesis of mechanically interlocked molecules with new and enhanced properties.

This thesis reports upon investigations towards the synthesis and study of enantiopure interlocked molecules for the application of enantioselective recognition of chiral guest species. Chapter One introduces the field of enantioselective recognition of chiral guest species and the synthesis of interlocked molecules. The review focuses upon enantioselective recognition of chiral anions, before taking an overview of the strategies employed to synthesise rotaxanes. The chapter concludes with how chirality can be introduced into rotaxanes and applications where the chirality of such rotaxanes has been explored. Chapter Two charts the development and synthesis of a family of enantiopure chloride templated rotaxanes, incorporating enantiopure amino acid moieties as the chiral element. The enantioselective properties of these rotaxanes are then elucidated by NMR titrations using enantiopure chiral anions. Chapter Three details the synthesis of a racemic chloride templated chiral rotaxane and behaviour of the diastereomers formed when the templating chloride anion is replaced with various enantiopure chiral anions. The separation of the diastereomeric salts of the rotaxane is reported. Chapter Four investigates efforts towards a chiral sensing palladium (II) templated rotaxane. Both 3,5- and 2,6-substituted pyridine axle motifs are discussed. Chapter Five describes the synthesis of a hydrogen bond templated chiral rotaxane. Following observation of diastereotopic effects on the axle due to the influence of the rotationally directional macrocycle, the effect of solvent, pH and presence of alkali metal cations on this expression of chirality by the rotaxane are disclosed. Chapter Six further investigates the shuttling motion reported in Chapter Five. It commences with a short survey of developments to date regarding hydrogen bond templated rotaxanes demonstrating molecular motion and responding to changes in pH or addition of alkali metal cations. Chapter Seven details the synthetic procedures and characterisation of compounds reported in this thesis, as well as titration protocols and x-ray crystal structures.