The question posed in this work is how one would model and predict the rotational spectrum of open-shell open-shell van der Waals complexes. There are two secondary questions that arise: the nature of radical-radical interactions in such systems and the modelling of the large amplitude motion of the constituent molecules. Four different systems were studied in this work, each providing part of the answer to the main question. Starting with the large amplitude motion, there are two theoretical approaches that may be adopted: to either model the whole complex as a semi-rigid molecule, or to perform quantum dynamical calculations. We recorded and analysed the rotational spectrum (using Fourier transform microwave spectroscopy) of the molecule of tertiary butyl acetate (TBAc) which exhibits a high degree of internal rotation; and of the weakly-bound complex between a neon atom and a nitrogen dioxide molecule (Ne-NO2). We used the semi-rigid approach for TBAc and the quantum dynamical approach for Ne-NO2. We also explored the compatibility of these two approaches. Moreover, we were able to predict and analyse the fine and hyperfine structure of the Ne-NO2 spectrum using spherical tensor operator algebra and the results of our dynamics calculations. To explore the nature of the interactions in an radical-radical van der Waals complex we calculated the PESs of the possible states that the complex may be formed in, when an oxygen and a nitrogen monoxide molecule meet on a plane using a number of high level ab initio methods. Finally, our conclusions were tested and applied when we performed the angular quantum dynamics to predict the rotational spectrum of the complex between an oxygen and a nitrogen dioxide molecule, and account for the effect of nuclear spin statistics in that system.

The main aim of the work reported is the design of proof-of-concept of at point-of-use hydrogen peroxide electrogeneration from air. The experimental work discussed within this thesis explores five major areas: the kinetics of electrocatalysis, ion-pairing, change of solvent media, the electrode surface modication by a redox mediator, and the electrochemical reduction of oxygen within enhanced mass transport systems. The electrocatalytic rates and mass transport of two oxygen reduction redox meditors, viz. anthraquinone and methyl viologen, are studied in aqueous solutions. The investigation is facilitated through the use of a boron-doped diamond electrode, allowing the catalytic response to be clearly delineated from that of the direct oxygen reduction process. The use of simulation software is highlighted in combination with experimental voltammograms to extract kinetic data. Specifically, the voltammetric features, such as the `reverse' peak and the `split waves', are given particular attention. Consequently, it is possible to deconvolute the electrocatalytic reaction mechanisms. The reactivity of the viologen radical cation is comparable to the semiquinone radical anion in aqueous solution ((4.8~6)x10^9 M^-1 s^-1), but over a far wider pH range (pH 2.5 - pH 8.5). The change of local proton concentration, and sequential electron transfers play key roles here. Moreover, the reduced reactivity of semiquinone is observed upon formation of ion-pairs with tetrabutylammonium cations in alkaline solutions. The electro-reduction of oxygen and its mediated pathways are also investigated in non-aqueous media; in particular the thermodynamics, the kinetics, and mass transport involved in these processes. Through a variable temperature study in electrolytic acetonitrile solution, the oxygen dissolution is quantitatively shown to be an endothermic process. Moreover, the diffusion coeficients and concentration of oxygen upon change of acetonitrile mole fraction is also explored in water-acetonitrile mixtures. The rates of bimolecular reactions are extracted from simulation programs, involving semiquinone in anhydrous acetonitrile and viologen radical cation in ethanol, and show a 3 - 4 orders of magnitude reduction compared to that in aqueous solution. Although the solubility of oxygen is ca. 6 - 8 times larger in non-aqueous solvents, the much reduced homogeneous rates limit the electrogeneration of hydrogen peroxide in pure organic media. Novel surface modification methodologies for graphitic surfaces with covalently attached anthraquinonyl groups are studied and characterised. The anthraquinonyl-modified carbon surfaces show much reduced overpotentials required for oxygen reduction. In the final chapter, utilising the new surface modification methodology and novel designs, two gravity-feed flow cells for electrochemical reduction of oxygen in aqueous solutions are proposed and characterised, one based upon the tubular electrode geometry. The other exhibits much enhanced current conversion by using a porous reticulated vitreous carbon electrode. The latter may provide a prototype hydrodynamic system to produce dilute hydrogen peroxide solution at point-of-use.

Spin dynamics simulations are used to gain insight into important magnetic resonance experiments in the fields of chemistry, biochemistry, and physics. Presented in this thesis are investigations into how to accelerate these simulations by making them more efficient. Chapter 1 gives a brief introduction to the methods of spin dynamics simulation used in the rest of the thesis. The `exponential scaling problem' that formally limits the size of spin system that can be simulated is described. Chapter 2 provides a summary of methods that have been developed to overcome the exponential scaling problem in liquid state magnetic resonance. The possibility of utilizing the multiple processors prevalent in modern computers to accelerate spin dynamics simulations provides the impetus for the investigation found in Chapter 3. A number of different methods of parallelization leading to acceleration of spin dynamics simulations are derived and discussed. It is often the case that the parameters defining a spin system are time-dependent. This complicates the simulation of the spin dynamics of the system. Chapter 4 presents a method of simplifying such simulations by mapping the spin dynamics into a larger state space. This method is applied to simulations incorporating mechanical spinning of the sample with powder averaging. In Chapter 5, implementations of several magnetic resonance experiments are detailed. In so doing, use of techniques developed in Chapters 2 and 3 are exemplified. Further, specific details of these experiments are utilized to increase the efficiency of their simulation.

This thesis describes the study of a range of ion-molecule reactions at very low collision energies using a newly developed experimental technique which involves the reaction of velocity-selected beams of translationally cold neutral molecules with very low kinetic energy ion ensembles. These studies have been enabled by the construction of a new apparatus for trapping and laser-cooling gas phase atomic ions (⁴⁰Ca⁺). The laser-cooling process results in the formation of ordered, low kinetic energy, lattice-like ion structures, also known as "Coulomb crystals". The properties of single and multicomponent Coulomb crystals (which may also involve molecular ions), and their manipulation via modulation of the applied fields, are explored experimentally and with the use of molecular dynamics simulations. Variations in the laser-cooling parameters are shown to result in different steady-state populations of the electronic states of ⁴⁰Ca⁺ involved with the laser cooling cycle, and these are modelled within an appropriate theoretical framework. The imaging of ⁴⁰Ca⁺ fluorescence as a function of time allows the study of various ion-molecule reactions at collision energies around 300 K, with single ion sensitivity. These reaction studies are extended to low-temperature (collision energies close to 1 K), by combination of the ion trap apparatus with a bent quadrupole guide velocity-selector. Ion-molecule collision energies are shown to be variable over a short range through a change in the quadrupole guide voltage, or the ion trapping parameters; the effect of these modulations on the rate constant is explored for Ca⁺ + CH₃F. Bimolecular rate constants for the reactions of ⁴⁰Ca⁺ with CH₃F, CH₂F₂ and CH₃Cl have been determined for a range of ⁴⁰Ca⁺ state populations, allowing resolution of the global rate contributions from the ground and combined excited states. These results are analysed in the context of capture theories and ab initio electronic structure calculations. In each case, suppression of the ground state rate constant is explained by the presence of either a submerged or real barrier on the ground state potential surface. Rates of reaction from the combined excited states are generally found to be in line with capture theories, and in some cases variation is found between the high and low collision energy regimes. Molecular product ions generated in these experiments have been shown to be sympathetically-cooled into the crystal structure, and subsequently identified through resonance-excitation mass spectrometry. Molecular ions were also produced by multiphoton laser ionisation of a thermal background gas of OCS molecules. An ion-molecule reaction involving a molecular ion, that of charge transfer between OCS⁺ and ND₃, has been studied at a collision energy near 1 K for the first time using sympathetically-cooled OCS⁺ and velocity-selected ND₃. These experiments illustrate the generality of the techniques described herein, and should lead to many possibilities for future studies.

The past two decades have witnessed tremendous advances in the field of high accuracy, high mass resolution data acquisition of complex samples such as crude oils and the human proteome. With the development of Fourier transform ion cyclotron resonance mass spectrometry, the rapidly growing field of petroleomics has emerged, whose goal is to process and analyse the large volumes of complex and often poorly understood data on crude oils generated by mass spectrometry. As global oil resources deplete, oil companies are increasingly moving towards the extraction and refining of the still plentiful reserves of heavy, carbon rich and highly contaminated crude oil. It is essential that the oil industry gather the maximum possible amount of information about the crude oil prior to setting up the drilling infrastructure, in order to reduce processing costs. This project describes how machine learning can be used as a novel way to extract critical information from complex mass spectra which will aid in the processing of crude oils. The thesis discusses the experimental methods involved in acquiring high accuracy mass spectral data for a large and key industry-standard set of crude oil samples. These data are subsequently analysed to identify possible links between the raw mass spectra and certain physical properties of the oils, such as pour point and sulphur content. Methods including artificial neural networks and self organising maps are described and the use of spectral clustering and pattern recognition to classify crude oils is investigated. The main focus of the research, the creation of an original simulated annealing genetic algorithm hybrid technique (SAGA), is discussed in detail and the successes of modelling a number of different datasets using all described methods are outlined. Despite the complexity of the underlying mass spectrometry data, which reflects the considerable chemical diversity of the samples themselves, the results show that physical properties can be modelled with varying degrees of success. When modelling pour point temperatures, the artificial neural network achieved an average prediction error of less than 10% while SAGA predicted the same values with an average accuracy of more than 85%. It did not prove possible to model any of the other properties with such statistical significance; however improvements to feature extraction and pre-processing of the spectral data as well as enhancement of the modelling techniques should yield more consistent and statistically reliable results. These should in due course lead to a comprehensive model which the oil industry can use to process crude oil data using rapid and cost effective analytical methods.

Molecular dynamics (MD) simulations are used to compute the equilibrium dynamics of a single component fluid with Yukawa interaction potential v(r) = (Ze)^2 exp(−r/λs )/4π eps_0 r. This system, which is known as the Yukawa one-component plasma (YOCP), represents a simplified description of a non-ideal plasma consisting of ions, charge Ze, and electrons. For finite screening lengths λs, the MD results are used to investigate the domain of validity of the hydrodynamic description, i.e., the description given by the Navier-Stokes equations. The way in which this domain depends on the thermodynamic conditions of the YOCP, as well as the strength and range of the interactions, is determined. Remarkably, it is found that the domain of validity is completely determined by the range of the interactions (i.e., λs); this alone determines the maximum wave number k_max at which the hydrodynamic description is applicable. The dynamics of the YOCP at wavevectors beyond k_max are then investigated; these are shown to be in striking agreement with a simple and well known generalisation of the Navier-Stokes equations. In the extreme case of the Coulomb interaction potential (λs = ∞), the very existence of a hydrodynamic description is a known but unsolved problem [Baus & Hansen, 1980]. For this important special case, known as the one-component plasma (OCP), it is shown that the ordinary hydrodynamic description is never valid. Since the OCP is the prototypical system representing a non-ideal plasma, a number of different approaches for modelling its dynamics have been formulated previously. By computing the relevant quantities with MD, the applicability of a number of models proposed in the literature is examined for the first time.

This thesis describes the development of a relatively novel technique for the gen- eration and subsequent trapping of cold species. Molecules in a pulsed supersonic expansion are photolysed, such that the centre-of-mass velocity vector of one of the fragments is equal in magnitude but opposed in orientation to the lab-frame velocity of the precursor molecule. This technique, known as ‘Photostop’, leaves a fraction of the fragments with a narrow velocity distribution, centered around zero velocity in the lab-frame. They can be shown to have zero velocity by changing the time between photodissociation and ionisation; fragments with a high kinetic energy will leave the ionisation volume prior to interrogation. The underlying velocity distribu- tion is uncovered by using the velocity-map imaging technique, and the temperature of the fragments can be determined. The method was originally optimised for the molecular case. Cold NO has been produced from the dissociation of NO₂ molecules, and a single rotational state has been shown to remain in the ionisation volume 10 μs after dissociation, implying a sample temperature of 1.17 K. Using the optimised experimental conditions de- rived from the velocity cancellation of NO, the atomic case is demonstrated for the dissociation of Br₂ to give zero-velocity Br fragments. The Br atoms are seen for delay times in excess of 100 μs, showing the greater applicability of the method to the atomic case. The temperature of the residual atoms is shown to be in the milliKelvin regime, as determined through detailed Monte Carlo simulation of the motion of the stopped atoms. The possibility of trapping the ultracold Br atoms in a magnetic field is explored, and a quadrupolar trap created between two per- manent bar magnets is demonstrated to confine the atoms spatially, within the ion extraction optics, for delays in excess of 1 ms. The Photostop technique is intended to be a stepping stone on the way to widening the number of chemical species available for study in the ultracold regime. The possibility of improvements to the experiment is considered, in order to increase the efficiency of the experiment such that the number density becomes high enough to be viable as a source of atoms for use in cold chemical reactive studies. The possibility of extending the method so as to be used as a tunable velocity source of atoms is also discussed.

This thesis presents the study of a selection of gas phase chemical processes using time-resolved Fourier transform infrared (FTIR) emission spectroscopy. Such processes include molecular energy transfer, chemical reaction and photodissociation. The major focus of this thesis was the investigation of collisional energy transfer from the electronically excited states of NO and OH, with particular attention paid to the fate of the electronic energy. NO A²&Sigma;⁺(v = 0) is prepared by laser excitation, pumping the overlapped Q₁ and P₂₁ band heads of the NO A-X (0,0) transition at 226.257 nm. The quenching of this state by O₂ and CO₂ was studied. Experiments were performed to investigate what channels contribute to the quenching process, the branching ratio of these different channels and the partitioning of energy among the various products. Quenching by O₂ was found to proceed mostly through non-reactive channels. High vibrational excitation of NO X ²&Pi; was observed, with population detected in v = 22, representing 79% of the available energy. The O₂ product was found to be formed in more than one electronic state: the ground state, X ³&Sigma;^-<sub style='position: relative; left: -.3em;'>g</sub>, and a high-lying electronically excited state, such as the A ³&Sigma;⁺<sub style='position: relative; left: -.5em;'>u</sub>, A' ³&Delta;_u or c ¹&Sigma;^-<sub style='position: relative; left: -.5em;'>u</sub> states. A reactive channel producing vibrationally excited NO₂ was observed, but was found to be a minor process with an upper limit of 18% for the branching ratio. In contrast the quenching of NO A ²&Sigma;⁺(v = 0) by CO₂ was found to proceed predominately by reaction, with a branching ratio of 76 %. While emission from NO₂ was observed, it was weak, and therefore it was concluded that the main reaction products were CO, O(³P) and NO X ²&Pi;(v = 0). The nascent strong CO₂ v3 emission band from the non-reactive channel exhibited a large red-shift from its fundamental position. This indicates that the CO₂ vibrational distribution is significantly hotter than statistical. Investigations were then performed studying the quenching of NO A ²&Sigma;⁺(v = 1) by NO and CO₂, with both systems exhibiting similar characteristics to the quenching of the ground vibrational level of NO A ²&Sigma;⁺. From comparison of the emission intensity of the CO fundamental and CO₂ v3 mode following quenching of the v = 0 and 1 levels of the NO A ²&Sigma;⁺ state, it was concluded that the branching ratio for reactive quenching was larger in the latter case. Secondly, experiments were performed to measure the rate constants for the quenching of NO A ²&Sigma;⁺(v = 0) by the noble gases. The noble gases are inefficient quenchers of electronically excited NO and therefore careful experimental design was required to minimise the influence of impurities on the results. All the rate constants were found to be of the order of 10^-14 cm³ molecule^-1 s^-1. The value for Xe was 50 times smaller than reported previously in the literature. In light of this new measurement, a re-analysis of experiments, performed previously in the group, on the electronic quenching of NO A ²&Sigma;⁺(v = 0) by Xe was performed. A very hot vibrational distribution of NO X ²&Pi; was obtained. Next, the collisional quenching of OH A ²&Sigma;⁺(v = 0) by H₂ was investigated. OH radicals were generated in situ by the photolysis of HNO₃ at 193 nm, which were excited to the A ²&Sigma;⁺(v = 0) state on the overlapped Q₁(1) and P₂₁(1) rotational lines at 307.935 nm. Reactive quenching was found to be the major pathway, in agreement with the literature. Copious emission from vibrationally excited water was observed. Comparison of this emission with theoretical calculations revealed a hotter distribution than predicted. It was concluded that the energy channelled into the vibrational modes of H₂O is in excess of 60% of the available energy. Experiments performed with D₂ allowed the non-reactive channel to be studied; a cold vibrational distribution of the OH X ²&Pi; was observed. Finally the reaction between CN radicals and cyclohexane was studied. CN was generated by the photolysis of ICN at 266 nm. Prompt emission from HCN in the C-H stretching region was observed meaning the new bond was formed in a vibrationally excited state. Analysis of the emission revealed HCN was populated up to v3 = 2. Excellent agreement with the results of a theoretical study of the system was found.

The outcome of chemical reactions proceeding via radical pair (RP) intermediates can be influenced by the magnitude and direction of applied magnetic fields, even for interaction strengths far smaller than the thermal energy. Sensitivity to Earth-strength magnetic fields has been suggested as a biophysical mechanism of animal magnetoreception and this thesis is concerned with simulations of the effects of such weak magnetic fields on RP reaction yields. State-space restriction techniques previously used in the simulation of NMR spectra are here applied to RPs. Methods for improving the efficiency of Liouville-space spin dynamics calculations are presented along with a procedure to form operators directly into a reduced state-space. These are implemented in the spin dynamics software Spinach. Entanglement is shown to be a crucial ingredient for the observation of a low field effect on RP reaction yields in some cases. It is also observed that many chemically plausible initial states possess an inherent directionality which may be a useful source of anisotropy in RP reactions. The nature of the radical species involved in magnetoreception is investigated theoretically. It has been shown that European Robins are disorientated by weak radio-frequency (RF) fields at the frequency corresponding to the Zeeman splitting of a free electron. The potential role of superoxide and dioxygen is investigated and the anisotropic reaction yield in the presence of a RF-field, without a static field, is calculated. Magnetic field effect data for Escherichia coli photolyase and Arabidopsis thaliana cryptochrome 1, both expected to be magnetically sensitive, are satisfactorily modelled only when singlet-triplet dephasing is included. With a view to increasing the reaction yield anisotropy of a RP magnetoreceptor, a brief study of the amplification of the magnetic field experienced by a RP from nearby magnetite particles is presented. Finally in a digression from RPs, Spinach is used to determine the states expected to be immune from relaxation and therefore long-lived in NMR experiments on multi-spin systems.

This thesis studies the monohydrate, dihydrate and in some cases, trihydrate of five carboxylic acids, namely acetic acid, propanoic acid, T-difluoroacetic acid, Gdifluoroacetic acid and trifluoacetic acid using the technique of Fourier tranform microwave spectroscopy. The rotational and centrifugal distortion constants of these hydrates were determined with high accuracy. Ab initio calculations were also performed to locate the different conformational minima of the hydrates and to optimize their structures. Comparison of the ab initio predicted rotational and centrifugal distortion constants with the experimentally observed values allows us to determine the structures of the global minimum conformations of the various hydrates without ambiguity. Hydrogen-bonded ring structures are found to be the predominant feature in all observed hydrates. In this structural arrangement, all the hydrogen bonds formed are located in the same ring, and the cooperativity effect between them significantly strengthens each hydrogen bond, as suggested by the sharp increase of their binding energies in the larger hydrates. The fine and hyperfine splittings observed in the specrum were also successfully analyzed, which allows information on the dynamics of the intramolecular large amplitude tunnelling motions to be extracted explicitly. In the final part of this thesis, the equilibrium constants for the formation of monohydrates of the different carboxylic acids involved in this thesis, together with that of formic acid whose microwave spectrum has been analyzed elsewhere, were calculated to approximately derive their abundances under typical atmospheric conditions. It was found that about 2% of FMA, ACA and PPA will complex with one H2O molecule to form monohydrates in the low troposphere, while for TFA, the value increases to about 15%, mainly as a result of the larger binding energy of TFA–(H2O) due to fluorination on the end group.