When approaching a metal surface, the electronic structure of Rydberg atoms or molecules is perturbed by the surface potential and at close enough distances resonant ionisation of the Rydberg electron into the conduction band of the surface can occur. It is possible to interfere in this process and steer the ionisation distance by making use of the polarisability of the Rydberg orbital in the presence of electric fields. The resulting ions from the surface can extracted via electric fields and subsequently detected via well established ion detection schemes. The question of how this charge-transfer process is affected by different properties of the surface (both electronic and structural) represents the main aspect of the work presented in this thesis. At first, the charge transfer of atomic hydrogen Rydberg atoms with a flat gold metal surface is investigated. While such a surface might appear homogeneous, stray fields are present in its vicinity due to local variations in the surface work function. The surface ionisation process as a function of applied electric field is therefore measured experimentally and the results are compared with classical Monte-Carlo simulations (which include stray field effects). This way the possibility to utilize Rydberg states as a probe of the magnitude of such stray fields is demonstrated. To investigate the effect the surface structure can have on the ionisation process, the interaction of Rydberg atoms with surfaces covered by nanoparticles is investigated. Surface ionisation is measured at a 5 nm nanoparticle monolayer surface and it is shown that population transfer between surface- and vacuum-oriented Rydberg states occurs. In addition, results are presented, which suggest a dependence of the ionisation process on the relative size of Rydberg orbital and nanoparticle. Furthermore, charge transfer between a Rydberg state and discrete electronic states at the surface vacuum interface are investigated by performing experiments with a Cu(100) band-gap semiconductor surface. By analysing surface ionisation as a function of collisional velocity ionisation rates can be determined and are subsequently compared with theoretical predictions. The potential of identifying resonant ionisation is thereby demonstrated. Last, a new method to produce 2s atomic hydrogen via mixing of the 2s and 2p state in an electric field is proposed and first experimental results are presented, thus demonstrating viability of the idea. The experiments presented in this thesis represent the most in depth analysis of the charge-transfer process between atomic hydrogen Rydberg states and a range of different surfaces to date. As such, they demonstrate the potential of utilizing the unique properties of Rydberg states and their applicability as surface probes. In addition, these results pave the way for further experiments involving thin films or the phenomenon of quantum reflectivity.

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.

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.

In this thesis H-bonded systems (natural gas hydrates, water clusters, and crystal ice) are studied by density functional theory (DFT) computations. Natural gas hydrates (NGHs) play an important role in energy and environmental fields: NGHs are considered as a promising backup energy resource in the near-future due to their tremendous carbon content; improper exploration of NGHs could induce geological disasters and aggravate the greenhouse effect. In addition, many technologies based on gas hydrates are being applied and developed. The thermodynamic stabilities of various water cavities in different clathrate crystalline phases occupied by hydrocarbon gas molecules are studied by dispersion-corrected hybrid functionals. The Raman spectra of C-C and C-H stretching vibrations of hydrocarbon molecules in various water cavities in the solid state are derived. The trends of C-H stretching vibrational frequencies are found to follow the prediction by the “loose cage ─| tight cage” model. In addition, the trends and origins of 13C NMR chemical shifts of hydrocarbon molecules in various NGHs are presented. These theoretical results will enlarge the database of C-C and C-H stretching vibrational frequencies and 13C NMR parameters of hydrocarbon molecules in NGHs, and provide valuable information to help identify the types of clathrate phases and varieties of guest molecules included in NGHs samples taken from natural sites. The behavior of water clusters may help to understand the properties of its liquid and solid states. The thermodynamic stabilities and IR spectra of a small-, medium-, and large-sized water cluster are studied in this work. After full optimization of (H2O)20,54,100 using the hybrid functional B3LYP, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters are computed. The OH stretching vibrational IR spectra of (H2O)20,54,100 are also presented and split into sub-spectra for different H-bond types based on the specific contributions from each group. It is found that the OH stretching vibrational frequencies of water are sensitive to the conformations of the H-bonds and the vibrations of the H-bonds belonging to different types are located in separated regions in the IR spectra. Thus, the spectroscopic fingerprints will reflect the H-bond topology of the water molecules in a water cluster. Ice XI has been suggested to be involved in the process of planetary formation as a considerable electric field might be formed from the ferroelectric ice XI in space. IR and Raman spectroscopic technology can be directly used to identify the occurrence of ferroelectric ice XI in laboratory or extraterrestrial settings. Due to the difficulty for DFT to describe non-covalent systems, the performance of 16 different DFT methods applied on the ice Ih, VIII, IX, and XI crystal phases are assessed. Based on the computational accuracy and cost, the IR and Raman spectra of ice Ih and XI are derived and compared. The librational vibrations are found to be the identifier which can be used to distinguish ice Ih and ice XI in the universe. In addition, the existence only one kind of H-bond in ice Ih is demonstrated from the overlapping sub-spectra for different types of H-bonded pair configurations in 16 isomers of ice Ih. The region of water under negative pressure is an exotic land in lack of exploitation. Guest free clathrate hydrate (clathrate ice) of sII type has been recently confirmed experimentally at negative pressure. Does any other clathrate ice phase exist at negative pressure region? Since clathrate hydrate are isostructural with silica clathrate minerals and semiconductor clathrates, and crystal structure prediction by analogy with known structures and first-principles computations is an effective way to find new crystalline phases of solid materials, we are motived to look for new clathrate ice phases from silica or semiconductor clathrate materials based on first-principles computations. Borrowing the idea new clathrate frameworks of ZnO and SiC can be constructed by connecting their bubble clusters in different ways, new clathrate ice phases (sL, sL_I, sL_II, and sL_III) are generated by connecting the water bubble clusters according to different rules. Using the non-local dispersion-corrected vdW-DF2 functional, clathrate ice sL with ultralow density (0.6 g/cm3) is predicted by first-principles phase diagram computations to be stable under larger negative pressures than the sII phase. The phase diagram of water is thus extended into the lower negative pressure region.

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.