Nuclear magnetic resonance (NMR) is a powerful experimental technique for probing the local environment of nuclei in materials. However, it can be difficult to separate the large number of interactions that are recorded in the resulting spectra. First-principles calculations based on quantum mechanics therefore provide much-needed support for interpreting experimental spectra. In this way, the underlying mechanisms recorded in experimental spectra can be investigated on an atomic level, and trends can be noted with which to guide the direction of future experiments. This thesis presents two cases in which first-principles calculations do just that. The first is an investigation of the perovskite structures of NaNbO₃, KNbO₃, LiNbO₃ and the related solid solutions of Na_xK_1-xNbO₃, K_xNa_1-xNbO₃ and Li_xNa_1-xNbO₃ in order to study how structural disorder affects their NMR parameters. The second investigation involves the calculation of the Knight shift in platinum, palladium and rhodium---in their elemental bulk forms and in a set of surface structures. The Knight shift is a systematic shift in the NMR frequencies of metallic systems. It arises from the hyperfine interaction between the nuclear spins and the spins of the unpaired conduction electrons. When calculating the Knight shift, it is found that the Brillouin zone must be very finely sampled. A discussion of core polarisation is also presented. This is the polarisation of core electrons as a result of their interaction with valence electrons. In the case of Curie paramagnets, core polarisation can have a significant effect on the calculation of hyperfine parameters.

This thesis describes the development of several spectroscopic methods based on impulsive vibrational spectroscopy as well as of the technique itself. The first chapter describes the ultrafast time domain Raman spectrometer including the development of two noncollinear optical parametric amplifiers for sub-10 fs pulse generation with 343 or 515 nm pumping. In the first spectroscopic study we demonstrate, for the first time, that impulsive vibrational spectroscopy can be used for recording transient Raman spectra of molecules in excited electronic states. We obtain spectra of beta-carotene with comparable, or better, quality than established frequency domain based nonlinear Raman techniques. The following two chapters address the questions on the fate of vibrational coherences when generated on a reactive potential energy surface. We photoexcite bacteriorhodopsin and observe anharmonic coupling mediated vibrational coherence transfer to initially silent vibrational modes. Additionally, we are able to correlate the vibrational coherence activation with the efficiency of the isomerisation reaction in bR. Upon generation of vibrational coherence in the second excited electronic state of beta-carotene, by excitation from the ground electronic state, we are able to follow the wavepacket motion out of the Franck-Condon region. We observe vibrationally coherent internal conversion, through a conical intersection, into the first excited electronic state and are hence able to demonstrate that electronic surface crossings can occur in a vibrationally coherent fashion. Additionally, we find strong evidence for vibronic coupling mediated back and forth crossing between the two electronic states. As a combination of this work we develop a IVS based technique that allows for the direct recording of background and baseline free Raman spectra in the time domain. Several proof of principle experiments highlight the capabilities of this technique for time resolved Raman spectroscopy. In the final chapter we present work on weak-field coherent control. Here, we address the question of whether a photochemical reaction can be controlled by the phase term of an electric excitation field, in the one photon excitation limit. We study the systems rhodamine 101, bacteriorhodopsin, rhodopsin and isorhodopsin and, contrary to previous reports, find no evidence for one photon control.

This thesis presents an experimental and theoretical study of the collision dynamics of OH(A²Σ⁺) with Kr and Xe. These two systems both exhibit a significant degree of electronically non-adiabatic behaviour, and a particular emphasis of the work presented here is to characterise the competition and interplay between electronic quenching on the one hand, and electronically adiabatic collisional processes on the other. Quenching takes place close to the bottom of the deepest potential well for both systems. In collisions that remain in the excited electronic state, this same region of the potential is also largely responsible for rotational energy transfer (RET) and the collisional depolarisation of angular momentum. Therefore, the direct competition between these processes suppresses the cross-sections for RET and collisional depolarisation from their expected value in the absence of quenching. To investigate this, experiments were carried out to measure cross-sections for the collisional transfer of electronic, vibrational and rotational energy in OH(A, v=0,1) + Kr and OH(A, v=0) + Xe. In addition, measurements were made of the j-j' correlation -- that is, the relationship between the angular momentum of the OH radical before and after a collision -- in collisions with Kr and Xe, using the experimental technique of Zeeman quantum beat spectroscopy. Collisions with both Kr and Xe tend to effectively depolarise the angular momentum of the OH radical, due to the very anisotropic character of the potential on which the process occurs. Electronic quenching, which plays an essential role in both systems, is more prevalent with xenon as the crossing to the ground state potential is located in a more accessible location. These experimental results were compared with single surface quasi-classical trajectory (QCT) calculations, where the overestimate of rotational energy transfer or collisional depolarisation helps to elucidate the degree to which the presence of quenching suppresses these processes. Surface hopping QCT was then used to account for non-adiabatic transitions in the theory, which led to an improvement in agreement with experiment. However, standard surface hopping QCT theory failed to account for the full extent of quenching in these two systems. A major focus of this work is therefore on the development of an extension to standard surface hopping QCT theory to incorporate rovibronic couplings. In non-linear configurations, the excited state of the OH + Kr, Xe systems has A' symmetry, while the ground state is split into symmetric (A') and antisymmetric (A'') components. For these symmetry reasons, coupling is restricted to the two states of the same symmetry, however a rotation of the correct (A'') symmetry can induce transitions to the A'' state too. Inclusion of all three electronic states, and the relevant couplings between them, is found to be crucial for a proper description of experimental reality.

Few experimental techniques have found such a diverse range of applications as has ion imaging. The field of chemical dynamics is constantly advancing, and new applications of ion imaging are being realised with increasing frequency. This thesis is concerned with the application of a fast pixelated imaging sensor, the Pixel Imaging Mass Spectrometry (PImMS) camera, to ion imaging applications. The experimental possibilities of such a marriage are exceptionally broad in scope, and this thesis is concerned with the development of a selection of velocity-map imaging applications within the field of photoinduced molecular dynamics. The capabilities of the PImMS camera in three-dimensional and slice imaging applications are investigated, in which the product fragment Newton-sphere is temporally stretched along the time-of-flight axis, and time-resolved slices through the product fragment distribution are acquired. Through experimental results following the photodissociation of ethyl iodide (CH₃CH₂I) at around 230 nm, the PImMS camera is demonstrated to be capable of recording well-resolved time slices through the product fragment Newton-sphere in a single experiment, without the requirement to time-gate the acquisition. The various multi-hit capabilities of the device represent a unique and significant advantage over alternative technologies. The details of a new experiment that allows the simultaneous imaging of both photoelectrons and photoions on a single detector for each experimental acquisition cycle using pulsed ion extraction are presented. It is demonstrated that it is possible to maintain a high velocity resolution using this approach through the simultaneous imaging of the photoelectrons and photoions that result from the (3 + 2) resonantly enhanced multi-photon ionisation of Br atoms produced following the photodissociation of Br₂ at 446.41 nm. Pulsed ion extraction represents a substantial simplification in experimental design over conventional photoelectron-photoion coincidence (PEPICO) imaging spectrometers and is an important step towards performing coincidence experiments using a conventional ion imaging apparatus coupled with a fast imaging detector. The performance of the PImMS camera in this application is investigated, and a new method for the determination of the photofragment detection efficiencies based on a statistical fitting of the coincident photoelectron and photoion data is presented. The PImMS camera is applied to laser-induced Coulomb explosion imaging (CEI) of an axially chiral substituted biphenyl molecule. The multi-hit capabilities of the device allow the concurrent detection of individual 2D momentum images of all ionic fragments resulting from the Coulomb explosion of multiple molecules in each acquisition cycle. Correlations between the recoil directions of the fragment ions are determined through a covariance analysis. In combination with the ability to align the molecules in space prior to the Coulomb explosion event, the experimental results demonstrate that it is possible to extract extensive information pertaining to the parent molecular structure and fragmentation dynamics following strong field ionisation. Preliminary simulations of the Coulomb explosion dynamics suggest that such an approach may hold promise for determining elements of molecular structure on a femtosecond timescale, bringing the concept of the `molecular movie' closer to realisation. Finally, the PImMS camera is applied to the imaging of laser-induced torsional motion of axially chiral biphenyl molecules through femtosecond Coulomb explosion imaging. The target molecules are initially aligned in space using a nanosecond laser pulse, and torsional motion induced using a femtosecond 'kick' pulse. Instantaneous measurements of the dihedral angle of the molecules are inferred from the correlated F+ and Br+ ion trajectories following photoinitiated Coulomb explosion at various time delays after the initial kick pulse. The technique is extended to include a second kick pulse, in order to achieve either an increase in the amplitude of the oscillations or to damp the motion, representing a substantial degree of control of the system. Measurements out to long kick-probe delays (200 ps) reveal that the initially prepared torsional wave packet periodically dephases and rephases, in accordance with the predictions of recent theoretical work.

The work presented in this thesis examines the electrochemical behaviour of a number of species, both surface-bound and in the solution phase, in various room-temperature ionic liquids (RTILs), in order to identify systems which show altered reactivities in room-temperature ionic liquids, compared to that in conventional, molecular, aprotic solvents. The fundamentals of electrochemistry are outlined and an introduction to room-temperature ionic liquids is given, after which the results of six original investigations are presented, as follows; The electrochemical response of surface-bound anthraquinonyl films was investigated as a function of RTIL cation size. The reduction of oxygen to superoxide in the [C₂mim][NTf₂] RTIL was studied at different carbon electrodes. The mechanisms of electrodeposition and stripping of Zn(II) onto bulk zinc deposits, on glassy carbon electrodes, in the [C₄mPyrr][NTf₂] RTIL were investigated. A novel and successful method for the fabrication of zinc microdisk electrodes was developed and the electrochemical behaviour of these electrodes was investigated. The mechanisms for the electrochemical reductions of some bromo- and nitrobenzenes at platinum microelectrodes were determined in the [C₄mPyrr][NTf₂] ionic liquid, in order to identify systems which displayed changed reactivities in RTILs compared to those in molecular aprotic solvents. The altered reactivity of 1-bromo-4-nitrobenzene in the [C₄mPyrr][NTf₂] ionic liquid was utilised via electrochemical reduction at zinc microelectrodes in order to form arylzinc compounds. The work presented in this thesis shows that the oft-taken view that the reactivity of a given species in an ionic liquid will mimic that in conventional aprotic solvents is not always the case. Reactivities can be markedly different between RTILs and aprotic solvents and can also be highly dependent on the specific ionic liquid employed.

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase. Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes. A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.

Protein tertiary structure is more conserved than amino acid sequence, leading to a diverse range of functions observed in the same fold. Despite < 20 % overall sequence identity, cytochromes P450 all have the same fold. Bacterial Class I P450s receive electrons from a highly specific, often unidentified, ferredoxin, in which case the hemoprotein is termed “orphaned”. CYP199A2, a Class I P450, accepts electrons from ferredoxins Pux and HaPux. Five orientation-dependent and one orientation-independent DEER measurements on paramagnetic HaPux and spin-labelled CYP199A2 yielded vector restraints, which were applied to building a model of the CYP199A2:HaPux complex in silico. A different binding mode was observed compared to P450cam:Pdx and P450scc:Adx, both recently elucidated by X-ray crystallography. This protocol was also applied to the CYP101D1:Arx complex. The first three measurements indicate that this heterodimer does not have a similar orientation to CYP199A2:HaPux, P450cam:Pdx, or P450scc:Adx. P450cam was fused to putidatredoxin reductase (PdR) to explore the kinetic effects with a view to improving electron transfer to orphan P450s. Heme incorporation of this enzyme depends on linker length. In whole cells, the fusion was more active after longer incubations. In vitro kinetics of the fusion exhibited some co-operativity and enhanced kinetics over the unfused system under steady-state conditions. The putative iron-sulfur biosynthesis ferredoxin PuxB had been engineered by rational mutagenesis to support catalysis by CYP199A2. It was confirmed this arose from improved protein-protein recognition. Engineering of E. coli ferredoxin based on these findings was carried out, resulting in electron-transfer to CYP199A4 from a novel engineered alien ferredoxin.

The development of interatomic potentials for magnetic transition metals, and particularly for iron, is difficult, yet it is also necessary for large-scale atomistic simulations of industrially important iron and steel alloys. The magnetism of iron is especially important as it is responsible for many of the element's unique physical properties -- its bcc ground state structure, its high-temperature phase transitions, and the mobility of its self-interstitial atom (SIA) defects. Yet an accurate description of itinerant magnetism within a real-space formalism is particularly challenging and existing interatomic potentials based on the Embedded Atom Method are suited only for studies of near-equilibrium ferritic iron, due to their restricted functional forms. For this work, the magnetic analytic Bond-Order Potential (BOP) method has been implemented in full to test the convergence properties in both collinear and non-collinear magnetic iron. The known problems with negative densities of states (DOS) are addressed by assessing various possible definitions for the bandwidth and by including the damping factors adapted from the Kernel Polynomial Method. A 9-moment approximation is found to be sufficient to reproduce the major structural energy differences observed in Density Functional Theory (DFT) and Tight Binding (TB) reference calculations, as well as the volume dependence of the atomic magnetic moments. The Bain path connecting bcc and fcc structures and the formation energy of mono- and divacancies are also described well at this level of approximation. Other quantities such as the high-spin/low-spin transition in fcc iron, the bcc elastic constants and the SIA formation energies converge more slowly towards the TB reference data. The theory of non-collinear magnetism within analytic BOP is extended as required for a practical implementation. The spin-rotational behaviour of the energy is shown to converge more slowly than the collinear bulk energy differences, and there are specific problems at low angles of rotation where the magnitude of the magnetic moment depends sensitively on the detailed structure of the local DOS. Issues of charge transfer in relation to magnetic defects are discussed, as well as inadequacies in the underlying d-electron TB model.

Electrolytic solutions contain mobile ions that can pass current, and are essential components of any solution-phase electrochemical system. The Nernst–Planck–Poisson equations describe the electrodynamics and transport dynamics of electrolytic solutions. This thesis applies modern numerical and mathematical techniques in order to solve these equations, and hence determine the behaviour of electrochemical systems involving charge transport. The following systems are studied: a liquid junction where a concentration gradient causes charge transport; an ideally polarisable electrode where an applied potential difference causes charge transport; and an electrochemical cell where electrolysis causes charge transport. The nanometre Debye length and nanosecond Debye time scales are shown to control charge separation in electrolytic solutions. At equilibrium, charge separation is confined to within a Debye length scale of a charged electrode surface. Non-equilibrium charge separation is compensated in solution on a Debye time scale following a perturbation, whereafter electroneutrality dictates charge transport. The mechanism for the recovery of electroneutrality involves both migration and diffusion, and is non-linear for larger electrical potentials. Charge separation is an extremely important consideration on length scales comparable to the Debye length. The predicted features of capacitive charging and electrolysis at nanoelectrodes are shown to differ qualitatively from the behaviour of larger electrodes. Nanoscale charge separation can influence the behaviour of a larger system if it limits the overall rate of mass transport or electron transfer. This thesis advocates the use of numerical methods to solve the Nernst–Planck–Poisson equations, in order to avoid the simplifying approximations required by traditional analytical methods. As this thesis demonstrates, this methodology can reveal the behaviour of increasingly elaborate electrochemical systems, while illustrating the self-consistency and generality of fundamental theories concerning charge transport.

Droplet Interface Bilayers (DIBs) have a number of attributes that distinguish them from conventional artificial lipid bilayers. In particular, the ability to manipulate bilayers mechanically is explored in this thesis. Directed bilayer area changes are used to make precise measurements of the specific capacitance of DIBs and to control the two dimensional concentration of a membrane protein reconstituted in the bilayer. Chapter 1 provides a general introduction to the role of the lipid membrane en- vironment in the function of biological membranes and their integral proteins. An overview of model lipid bilayer systems is given. Chapter 2 introduces work carried out in this laboratory previously and illustrates the experimental setup of DIBs. Some important bilayer biophysical concepts are covered to provide the theoretical background to experiments in this and in later chapters. Results from the characterisation of DIBs are reported, and an account of the development of methods to manipulate the bilayer by mechanical means is given. Chapter 3 describes experiments that apply bilayer area manipulation in DIBs to achieve precise measurement of specific capacitance in a range of lipid systems. Chapter 4 reports results from experiments investigating the response of bilayer specific capacitance to an applied potential. Chapter 5 covers the background and experimental setup for total internal fluo- rescence microscopy experiments in DIBs and describes the expression, purification and characterisation of the bacterial β-barrel membrane protein pore α-Hemolysin. Chapter 6 describes experiments that apply the mechanical manipulation of bilayer area in DIBs to the corralling and control of the surface density of α-Hemolysin.