A variety of mass spectrometers have been used to study four projects, involving three different applications of gas phase ion- molecule reactions. Firstly, the use of the vinyl methyl ether radical cation for the location of olefinic bonds (NEUTRAL STRUCTURE DETERMINATION) has been improved by altering the mode of production of the reagent ion. The scope and application of this technique have been reviewed. Secondly, the structures of various C3H6O† and C4H5N+ ions (ION STRUCTURE DETERMINATION) have been studied. Reactions specific for the structures (i) CH3-O-CH-CH2ר+ and (ii)CH2=O+-CH2-CH2 have been identified and employed to detect the presence of C3H6O+‘ ions of these structures formed from a variety of precursors. These results provide an insight into the mechanisms of sane gas phase elimination reactions and allow this method to be compared with those providing analogous information. Reactions have been sought to characterise the structure of C4H3N+ ions generated from five different neutral precursors. Such reactions proved not to be identifiable readily, with the exception of a reaction involving 1.3-butadiene which appears to be specific for the pyrrole molecular ion structure. Finally, the beginning of the application of the technique of Mass Spectrometry/Mass Spectrometry to the detection of gibberellins in mixtures (MIXTURE ANALYSIS) is described. The results of a survey of the chemical ionisation of the gibberellins are presented. The collision induced decomposition spectra of nine gibberellin/ammonium adduct ions are reported, showing that this method is capable of distinguishing readily all these gibberellins, some of which are isomers. Preliminary results involving crude grass extracts spiked with gibberellins are presented and methods of lowering the detection levels obtained have been suggested. Evidence concerning the pyrolysis of gibberellic acid is presented and discussed. These experiments and results serve to illustrate the varied use of gas phase ion-molecule reactions in structure determination.

Mullite stoichiometry powders have been produced using a "water-free" sol-gel approach. The powders are fabricated by mixing aluminium isopropoxide and tetraethyl silicate (TEOS) in butan-l-ol, under conditions where the amount of water allowed into the system from external sources is minimised. The powders are obtained from the solution by rapid removal of the alcohol and other volatile organics. The sols that are produced by the unidentified condensation reactions are then deposited. A homogeneity coefficient has been defined, and is dependant on the crystalline phases that are produced on heating the material to completion of the 980°C exotherm. Two crystalline phases are seen on such a heat treatment, spinel and mullite. This semi-quantitative coefficient is defined as the ratio of the peak height of the x-ray reflections from the (440) plane of spinel and the (331) plane of mullite. Using this definition there is a reproducible and regular variation in the homogeneities of the powders yielded when compared with the length of time the solution was stirred before the sols were deposited. With the concentration used, 0.25M for the t'sopropoxide and 0.083M for the TEOS, the sols deposited early in the reaction were relatively inhomogeous. At approximately 19 hours after stirring of both reactants had begun, the homogeneity increased. That is, the amount of mullite that was yielded after completion of the exotherm increased. Continued stirring of the solution gave less homogeneous materials. This behaviour is novel in terms of sol- gel fabrication. The amount of water present in the system, from contamination of the reactants is insignificant compared to the amount of water demanded by the traditional water consuming reactions of sol-gel. Aluminium alkoxides have been found to react directly with alcohols and this reaction has been proposed as being central to the condensation reactions that have been inferred as occurring by the production of Al-O-Si bonds. A phenomenological explanation of the homogeneity has been proposed based on the aluminium alkoxide being the active species after reaction with the alcohol. Linear polymeric species are formed increasing the overall homogeneity of the system, a point is reached in the reaction where the polymers cross-link via aluminium atoms rather than grow in length, the homogeneity of the sols then decreases. The crystallisation sequence of the materials has been explained in terms of the homogeneity In particular, the detailed structure of the materials has been related to the coordination of aluminium. At low levels of homogeneity, the material is grossly segregated in terms of the coordination polyhedra of aluminium and silicon. The alumina rich regions have aluminium preferentially in octahedral environments. These materials crystallise to predominantly spinel, an alumina polymorph that probably contains a small amount of silica. Increasing the homogeneity decreases the size of the alumina rich regions. These still exist however due to the stoichiometry of the system. As they decrease in size the interfacial surface area between these regions and the silica rich matrix increases. It is proposed that pentacoordinate aluminium is found in these interfacial areas. The pentacoordinate aluminium is metastable and transforms at 980°C to octahedral and tetrahedral coordinations. It is this transformation that initiates crystallisation of the material. The smaller the volume occupied by the inhomogeneities the more mullite is yielded since the aluminium and silicon are more intimately mixed. Heat treatments of the amorphous material below this temperature will yield spinel from the crystallisation of the unstable alumina rich regions, with some mullite being formed at the interface. Again the smaller the inhomogeneities the more mullite is produced by such a treatment.

This thesis describes the development of a Crossed Beam instrument for the study of ion-molecule reactions. A full investigation of some gross systematic errors, in apparatus which had been previously installed, is made. Where time has prevented the further development, then conclusions have been transformed into specifications, and practical solutions described. Experimental data is presented which is interpreted as evidence that the beams intersect and that low intensity of the scattered products and the forementioned systematic errors veil these data. The reduction of data, containing such errors, to useful chemical interpretation is extremely difficult, hence the need for further modification. Data are presented in chapter 3 consistent with the quadrupole acting as a linear particle accelerator. The effect on an initially monochromated beam is of causing an unacceptable energy spread. The spherical and chromatic aberrations of both source and detector are identified as the principal systematic errors using computer simulation (SIMION) for forward convolution. The development of a pulsed neutral beam source is described in chapter 4. The performance of the beam source is critically analysed and compared to alternative sources. A generally applicable model is derived to predict the shutter opening function of pulsed sources. Such a study has not previously been made. It is anticipated that this model will be of use to the solution of non-steady flow problems i.e. calculation of time dependent flow field properties, or in the deconvolution of TOF spectra from beam sources. Performance data for the beam source and some calculated properties are given. The subject of ion-molecule reactions is introduced by development from simple ideas. The subject matter covered is not intended to be exhaustive, but covers the examples of ion-molecule reactions of personal Interest. Recent crossed beam studies are examined and suggestions of possible new experiments made.

The kinetics of complexation of labile transition metal ions with three classes of macrocyclic N-donor ligands have been studied in dmso solution using pseudo-first- order conditions and employing the stopped-flow technique, with observation of U. V. / visible absorbance changes on reaction. All reactions studied displayed biphasic, consecutive first-order kinetics with an initial, rapid step which was first-order in both metal and ligand, followed by a second, slower step which was independent of the metal concentration. The unsubstituted macrocycles cyclam and [9]aneNj reacted via a dissociative interchange mechanism with the formation of an unstable intermediate which isomerises to the stable product. This intermediate is proposed to involve full co-ordination of the macrocycles to the metal ions with one or more N atoms co-ordinated in an unstable configuration. For the same macrocycles, each containing a single, pendent co-ordinating 2,2’-bipyri-dyl-6-yl-methyl arm, the complexation reactions occurred via an intermediate which involved co-ordination of the metal ions to the bipyridyl moiety, the ensuing slower reaction involving co-ordination of the macrocyclic moiety. This presents the most clear-cut evidence so far that pendent arm macrocycles react initially by coordination to the pendent arm. For N4 macrocycles, with a pyridine group substituted for a secondary amine, the reactions occur by initial attack at the secondary amines adjacent to the pyridine moiety. With the tri-methylated form of the macrocycle Ni2+ ions react more rapidly than do Co2 + ions, which is very unusual. This behaviour is explained by proposing a different reaction mechanism for each ion with Mej-PyNj as the final products are of different geometries. With Cu2+ an unstable intermediate is formed involving formation of only one Cu-N bond. The properties of silica gels modified with open-chain and macrocyclic polyamines were also studied. The less bulky and least sterically hindered polyamines were bound to the surfaces in greater quantities, although pretreatment involving heating at high temperatures significantly improved the binding of cyclam to the surfaces. An investigation of the uptake of transition metal ions from aqueous solutions illustrated the important role that the surface structure has to play on the activity of the binding sites. A gel modified with cyclam displayed a high degree of selectivity for Cu2+ over Co2+ and Ni2+ illustrating the potentially important application of such systems in ion selective waste water treatments.

During this study the effect of electrostatic analysers on the time-of-flight of ions was studied theoretically, and it was shown that small energy spreads in the ion packet do not affect seriously the time-of-flight of an ion. The initial angle of an ion upon entering the electrostatic analyser does affect the time-of- flight of the ion. A C-shape configuration with two electrostatic analysers has been proposed as a solution eliminating time broadening due to spread in initial angle. An energy resolved time-of-flight mass (ER-TOF) spectrometer was constructed. Metastable fragmentation and collision-induced dissociation experiments were carried out with different molecular-mass proteins and 3- nitrobenzyl alcohol as matrix. It has been shown that in matrix-assisted laser desorption/ionisation (MALDI) there is a substantial number of ions that decay after acceleration and prior to detection. The energy resolved time-of- flight spectra show that there is a peak broadening resulting from the lack of stability of the high-mass ions during their flight through a time-of-flight instrument. The effect of the electric field above the target on the kinetic energy of the ions when 3-nitrobenzyl alcohol was used as matrix has been studied, and the energy spreads explained as being predominately energy deficits arising from the combination of high electrostatic fields, the liquid nature of the matrix and the inherent characteristics of the desorption / ionisation process. Collision experiments with different molecular-mass proteins ranging from 34% Da to 18300 Da and different collision gases over a wide range of kinetic energies showed that there is a decrease in the analyte signal with respect to the matrix signal for specific collision gases and collision energies. The ions were collected with an off-axis post acceleration detector. The decrease in the analyte signal has been explained as loss of the charge possessed by the analyte ion through charge exchange with the collision gas.

Supramolecular chemistry, the domain of chemistry ‘beyond the molecule’, is finding increasing application in a diverse range of scientific fields. A key concept in this field, termed molecular self-assembly, has important applications ranging from nanotechnology to medicine, and refers to the intermolecular assembly of individual molecules via non-covalent forces, most importantly hydrogen bonding and π-π stacking interactions. Specifically, this thesis considers the self-assembling arrangements of synthetic pyrimidine-based heterocyclic systems, which present guanine/cytosine DDA/AAD hydrogen bonding motifs. Characterisation of such systems is well documented in the liquid phase, but there exists a general paucity of solid-state analytical data for such materials. Owing to the inherent difficulty in crystallising these systems, typically due to disordered alkyl and aryl sidechains, high-resolution 1H MAS NMR is uniquely placed to elucidate hydrogen bonding arrangements in these systems, given the sensitivity of the 1H chemical shift to its local atomic environment. For cases where single-crystal X-ray structures can be obtained, a so-called NMR crystallographic approach can be used to complement the existing single-crystal X-ray data. By comparison of GIPAW calculated 1H chemical shielding parameters to experimentally observed chemical shifts and, more specifically, through comparison of calculated shielding values for the full crystal versus the isolated molecule, an analysis of the strength of non-covalent phenomenon present in a given system can be presented. This thesis applies fast MAS 1H detected 2D NMR methods to a range of structural problems concerning pyrimidine-based synthetic organic molecules. Specifically,1H – 1H DQ/SQ MAS, 14N – 1H HMQC and 1H – 13C techniques, such as the refocused INEPT and well-known CP MAS methods, are used, where applicable, in conjunction with GIPAW calculated NMR parameters to provide a comprehensive study of the solid-state packing arrangements of a series of guanine/cytosine synthetic derivatives which exhibit a diverse range of self-assembling architectures, including helical and stacking trimeric motifs. It is shown that, for crystalline compounds, confirmation of chemical shift assignments via the GIPAW method can be used to infer the structure of related systems for which diffraction data is not available, through comparison of the observed experimental NMR data. In addition, it is demonstrated that, for a series of pyrimidine and pyridopyrimidine intermediates which form non-crystalline powdered solids, high-resolution 1H MAS NMR methods can be applied alone to elucidate likely hydrogen bonding motifs in the absence of crystallographic data, thereby allowing the observer to speculate on likely modes of self-assembly in the solid state. Interestingly, this study involves the relatively novel investigation (by means of solid-state NMR) of aldehyde and, in particular, oxime containing organic molecules, for which (in the case of the latter functional group) no published 1H MAS NMR studies have been presented at the time of writing. Finally, in collaboration with the spectrometer company JEOL, it is shown that a selective saturation pulse can be employed to supress excessive t1 noise in two-dimensional 1 H MAS NMR spectra, at fast MAS frequencies. To demonstrate this effect, the intense methyl resonance of a synthetic nucleoside derivative is suppressed, whilst reduced spin diffusion rates at higher MAS frequencies ensure that the effect on nearby spins is minimised.

Little is known about historic wood as it ages naturally. Instead, most studies focus on biological decay, as it is often assumed that wood remains otherwise stable with age. This PhD project was organised by Historic Scotland and the University of Glasgow to investigate the natural chemical and physical aging of wood. The natural aging of wood was a concern for Historic Scotland as traditional timber replacement is the standard form of repair used in wooden cultural heritage; replacing rotten timber with new timber of the same species. The project was set up to look at what differences could exist both chemically and physically between old and new wood, which could put unforeseen stress on the joint between them. Through Historic Scotland it was possible to work with genuine historic wood from two species, Oak and Scots pine, both from the 1500’s, rather than relying on artificial aging. Artificial aging of wood is still a debated topic, with consideration given to whether it is truly mimicking the aging process or just damaging the wood cells. The chemical stability of wood was investigated using Fourier-transform infrared (FTIR) microscopy, as well as wet chemistry methods including a test for soluble sugars from the possible breakdown of the wood polymers. The physical properties assessed included using a tensile testing machine to uncover possible differences in mechanical properties. An environmental chamber was used to test the reaction to moisture of wood of different ages, as moisture is the most damaging aspect of the environment to wooden cultural objects. The project uncovered several differences, both physical and chemical, between the modern and historic wood which could affect the success of traditional ‘like for like’ repairs. Both oak and pine lost acetyl groups, over historic time, from their hemicellulose polymers. This chemical reaction releases acetic acid, which had no effect on the historic oak but was associated with reduced stiffness in historic pine, probably due to degradation of the hemicellulose polymers by acid hydrolysis. The stiffness of historic oak and pine was also reduced by decay. Visible pest decay led to loss of wood density but there was evidence that fungal decay, extending beyond what was visible, degraded the S2 layer of the pine cell walls, reducing the stiffness of the wood by depleting the cellulose microfibrils most aligned with the grain. Fungal decay of polysaccharides in pine wood left behind sugars that attracted increased levels of moisture. The degradation of essential polymers in the wood structure due to age had different impacts on the two species of wood, and raised questions concerning both the mechanism of aging of wood and the ways in which traditional repairs are implemented, especially in Scots pine. These repairs need to be done with more care and precision, especially in choosing new timber to match the old. Within this project a quantitative method of measuring the microfibril angle (MFA) of wood using polarised Fourier transform infrared (FTIR) microscopy has been developed, allowing the MFA of both new and historic pine to be measured. This provides some of the information needed for a more specific match when selecting replacement timbers for historic buildings.

The overall goal of this thesis was to investigate the feasibility of a new route to anthropogenic nitrogen fixation based on the oxidation of nitrogen (to give primarily nitrite), and then electrocatalytic conversion of nitrite to other N-containing species of interest, such as nitrate and nitric oxide (NO). In pursuit of this goal, the synthesis of metal-ligand coordination complexes that could act as electrocatalysts for the oxidation of nitrite to nitrate was attempted, as was the synthesis of metal-ligand coordination complexes that could act as electrocatalysts for the reduction of nitrite to NO. As a corollary to this, routes for the initial fixation reaction were also investigated, of which the ultrasonic generation of nitrite from aerated aqueous solutions was found to be the most promising. The work detailed in this thesis is organized in the following manner: In Chapter 1 we discuss coordination complexes that mimic the enzymes promoting the redox reactions of the nitrogen cycle involving nitrite as a substrate or product. During this introduction we will also give an overview of topics that are relevant to the following chapters, such as proton-coupled-electron transfer and basic kinetic treatment of catalytic reactions. Chapter 2 is a description of the different techniques used throughout this thesis. Once having set the bases, we shall start with the actual research, which corresponds to Chapters 3 to 6. Chapter 3 deals with the synthesis, characterization and catalytic properties of a copper coordination compound mimicking the active site of the copper nitrite reductase (CuNiR) class of enzymes. This chapter includes a detailed study of the kinetics and electrocatalytic properties of this complex towards the mono-electronic reduction of nitrite to nitric oxide. Chapters 4 and 5 deal with the unusual structures and spectroscopic properties of a number of new cobalt complexes that we isolated whilst trying to develop Mo(bis-dithiolene) coordination complexes that might act as analogues of the molybdenum nitrite oxidoreductase (MoNiOR), which oxidises nitrite to nitrate in nature. Our original Mo-containing targets proved impossible to obtain and are not discussed in this thesis. However, we found that cobalt readily makes coordination complexes with these bis-dithiolene ligands, which allowed us to isolate the compounds we present in Chapters 4 and 5. Hence in Chapter 4 we show the synthesis and the solvatochromic properties of mixed-ligand mono-nuclear Co-diimine o-catecholato complexes and compare these complexes with the analogous compounds prepared with o-benzenedithiolato ligands. Chapter 5 then discusses the synthesis and redox properties of a mixed-ligand di-cobalt coordination complex in which the two cobalt centres have (unprecedented) inequivalent metal coordination environments. Finally, in Chapter 6 we describe a much-underexplored way to fix nitrogen based on a sonochemical reaction. After a brief introduction we describe the optimisation of the procedure and comparisons with previous reports.

This thesis focusses on two models (inactive and active) for fibre-reinforced viscous flows, examples of which may be found in numerous industrial and biological applications. In chapters 2-4 we consider Ericksen's model for a transversely isotropic fluid, which treats suspensions of nonmotile particles as a continuum with an evolving preferred direction; this model describes fibrous materials as diverse as extracellular matrix, textile tufts and cellulose microfibers. Linear stability analyses of transversely isotropic viscous fluid between two rotating co-axial cylinders and two horizontal boundaries of different temperatures are undertaken in chapters 3 and 4 respectively. In both cases, the inclusion of transversely isotropic effects delays the onset of instability. In chapter 5 we describe a framework commonly used to model active suspensions, which has been applied to suspensions of self-propelling bacteria, algae and sperm, and artificial swimmers. Through linking this model for an active suspension with that for a transversely isotropic fluid, we identify previously neglected components of the stress tensor that significantly alter the rheology. In chapter 6 we examine the linear stability of isotropic and nearly-aligned suspensions of elongated particles, before giving a summary of our findings in chapter 7.

Metallic nanoparticles (MNPs) are attracting increasing interest for many applications in photonics, ranging from optoelectronic devices to bioimaging and biosensing. An advantage of these systems is that their optical properties, governed by their localised surface plasmon resonance, are widely tunable via the nanoparticle shape and size, which can be controlled via e.g. colloid synthesis. In that context, it is important to develop accurate experimental methods able to correlate the size and shape of an individual single MNP, measured with nanometric precision, with its individual optical properties. In this thesis, three different MNP systems, namely i) commercially-available Ag nanocubes of 75 nm edge; ii) Ag tetrahedra, bi-tetrahedra and decahedra in the 25 - 50 nm size range which was fabricated in-house using a plasmon-mediated photochemistry method; iii) Ag nanodimers was fabricated in-house via controlled self-assembly of polymer linkers onto commercial nominally spherical Ag nanoparticles of 40 nm diameter. Beyond fabrication, a substantial part of the work reported in this thesis describes the experimental protocol for correlative optical and transmission electron microscopy, which was developed and optimised, comprising reproducible deposition of these silver nanoparticles onto TEM grids, their optical characterisation via polarisation-resolved high-resolution dark-field and extinction micro-spectroscopy, and subsequent high-resolution TEM of the same particle. As proof-of-concept, the same Ag nanocubes of 75 nm edge were characterised optically in different dielectric environments, using solvents of different refractive index n; specifically, anisole (n=1.52), water (n=1.33), and air (n=1). The MNP scattering and extinction cross-section was determined in absolute units using an in-house developed quantitative measurement protocol, and the results are compared with numerical simulations using the measured geometry. These studies pave the way toward an in depth understanding of the relationship between geometrical and optical properties of MNPs of non-trivial shapes, which in turn have the potential to be exploited in innovative bioimaging and biosensing platforms.