Protein interactions are crucial for the survival of living organisms. The possibility of mapping the contact surfaces between proteins and their interacting partners is fundamental to understanding the mechanisms involved in the process. For these reasons techniques able to provide structural information on a short time scale and employing small amounts of material are sought after. The work reported in this thesis explores the use of carbene-based labelling in combination with mass spectrometry for protein footprinting and its applications in the study of protein structure and interactions. Studies on the efficiency and selectivity of a novel water-soluble photo-activated probe revealed its superior properties in comparison with diazirine-based reagents previously described for the same application. Using this methodology, the contact surface of the complex between lysozyme and NAG5, a carbohydrate substrate, was accurately mapped. The same technique was successfully employed to shed light on the structural change occurring to USP5, a large multi-domain deubiquitinating enzyme, upon its binding to diubiquitin. The use of carbene footprinting in combination with other biophysical techniques allowed to characterise the spatial arrangement of domains located at a module junction in the large multi-modular gladiolin polyketide synthase paving the way for future efforts by synthetic biologists to hijack the chemistry of this antibiotic-producing multiprotein enzyme to produce novel active compounds. The possibility of using carbene-based footprinting to gain insight into the structure of integral membrane proteins was also explored. The probe introduced in this work exhibited peculiar labelling properties when activated in the presence of a detergent-solubilised membrane protein. The reagent selectively reacted with portion of the protein in contact with detergent molecules showing potential to elucidate the quaternary structure of multimeric membrane proteins.

This work contains two main areas of research within the field of bonding and spectroscopy. The first is the interactions of metals and metal ions with rare gas atoms; the second concerns vibrational dynamics in para-fluorotoluene(pFT). The research has been carried out as part of a collaboration between the SOCAR and Reid groups at the University of Nottingham and also involved external research teams. The work combines the results from experiments employing several different spectroscopic techniques with theoretical calculations, which support the experimental data, assist in their interpretation and provide new information. Resonance enhanced multiphoton ionisation spectroscopy is employed to investigate the Au–Xe and Au–Ne neutral complexes in the region of the 62PJ ← 62S1/2 Au atomic transition. High-level ab initio calculations provide further insight, which is necessary to explain the unusual spectra obtained. A theoretical study of complexes containing Group 2 metal cations and rare gases also reveals some unexpected trends that are related to some of the effects seen in the Au–RG series. A combination of nanosecond zero electron kinetic energy spectroscopy and time-resolved picosecond photoelectron spectroscopy is employed to investigate the vibrational dynamics of pFT. Excitation via several different vibrational states allows the study of a Fermi resonance, statistical intramolecular vibrational energy redistribution and an intermediate case that shows evidence of so-called “doorway states”.

The work in this thesis looks at the spectroscopy and interactions of metals and metal cation complexes. There are two aspects of this vast subject that are considered: the electronic spectroscopy of Au-RG complexes and the ion-molecule chemistry of metals important in the mesosphere-lower thermosphere (MLT) region of the atmosphere. The spectroscopy of the molecular states in the vicinity of the strong Au 2P3/2, 1/2 ← 2S1/2 atomic transition, have been studied for the Au-RG (RG = Ne, Ar, Kr, Xe) series using resonance enhanced multiphoton ionization (REMPI). The spectroscopy of these systems was more involved than expected and high level ab initio calculations were required to complement and aid interpretation of the REMPI spectra obtained. Two main effects were seen to influence the spectroscopy in this energetic region — the mixing between D2Π1/2 and E2Σ1/2+ states through spin-orbit interactions and the interaction of lower lying states arising from the Au(2D) + RG (1S0) asymptote, resulting in predissociation being observed. The MLT is the only region of the Earth’s atmosphere in which metals exist in a free atomic state. It is known that their presence in this region occurs via the ablation of meteors entering the upper atmosphere, but certain aspects of their chemistry are still unclear. Using high level ab initio theory, spectroscopic constants were determined for metal cation complexes that can be formed in this region. These values are used by collaborators in conjunction with laboratory measurement to establish accurate rate coefficients that will allow the ion-molecule chemistry of calcium and magnesium in the MLT region to be modelled.

New solid-state NMR experiments for measuring internuclear distances are designed using symmetry principles. The “recoupling” sequences described here are intended to reintroduce the MAS-averaged heteronuclear dipole-dipole coupling between a spin-1/2 nucleus (e.g. 1H) and a half-integer quadrupolar nucleus (e.g. 17O, I = 5/2). The magnitude of the dipolar interaction depends on the separation between the coupled nuclei, so the evolution of the spin system under the recoupled Hamiltonian can be used to measure the internuclear distance. Simulations of the spin dynamics are used initially to select candidate sequences and these are subsequently employed to measure both long-range and direct O–H distances in powdered L-Tyrosine.HCl (isotopically enriched with 17O at 20%to 30% at the O$^\eta$ site). Improvements to existing methods for the data analysis for this type of NMR experiment are also discussed, including the restriction and/or removal of certain fit parameters and the explicit inclusion of inhomogeneous radio-frequency fields as part of the fitting procedure. The effects of processing on the uncertainty of experimentally determined distances are considered, and a new analysis method which circumvents several of these effects is presented. Similar recoupling sequences can be used to measure the anisotropy of proton chemical shifts, and some preliminary results are also presented for this application. A systematic method for the assignment of congested spin-1/2 spectra resulting from molecules with large numbers of chemically similar sites is also described. This makes use of a comparison between the chemical shift tensor measured as usual by the 2D-PASS experiment and its principal components calculated from first principles using the density functional theory package CASTEP. The initial peak assignment is generated randomly and then varied using a steepest-ascent hill climbing algorithm with the square sum of the difference between the experimental and calculated principal values of the chemical shift tensor as the target function. The new method is tested on the 13C spectrum of the anti-inflammatory drug flufenamic acid and found to be superior to simple assignments using only the isotropic chemical shift.

Two-dimensional correlation spectroscopy in solid-state NMR is an immensely important tool for the analysis of materials, such as technologically interesting nano-materials or bio-materials. After detailing one method that returns high-resolution one-dimensional solid-state proton NMR spectra, high-resolution proton-proton two-dimensional correlation experiments are described and demonstrated. Subsequently, a new two-dimensional NMR experiment is described which is suitable for obtaining a high-resolution proton dimension in heteronuclear dipolar correlation spectra of solids. This new experiment has been used to characterise the interface between the organic and inorganic components of "coreshell" colloidal nanocomposite particles. In addition, a new two-dimensional NMR experiment is described which is suitable for obtaining homonuclear scalar correlation spectra in solids. This new experiment has several advantages, including increased cross peak intensities coupled with good suppression of the diagonal. Its utility is demonstrated via carbon-13 spectra of natural abundance samples as well as the polymer phase of caesium fulleride.

An advanced Electron Energy Loss Spectrometer has been used to study the formation of 3,3,3-trifluoropropylidyne on Pt (111). This has been compared to the results from the same system using the complementary vibrational spectroscopic technique of Reflection Absorption Infrared Spectroscopy (RAIRS). This study demonstrates the improved resolution of the new spectrometer. The thermal decomposition products, CF3 and CF2 have been detected in the Electron Energy Loss (EEL) spectra. The RAIR spectra of carbon monoxide on Cu (111) have been recorded using synchrotron radiation. An optical accessory has been used to record the RAIR spectra at an incident angle of 20°. The results have been compared to an incident angle of 87°. At 20° no conventional absorption band at 339 cm-l was observed and an anti absorption band at 274 em-l of similar magnitude to that at 87° was seen. This has confirmed the involvement of the parallel electric field in the observation of antiabsorption bands. The EEL spectra of hydrogen and deuterium adsorbed on Pt (111) at 160 K have been recorded. The data has been interpreted using the Nearest Neighbour Central Force Constant (NNCFC) model in terms of 3- fold and 2-fold bridging sites. It is the 2-fold site which offers the more complete assignment of the vibrational bands observed.

High resolution (< 0.005 cm−1) electronic spectra of the diatomic molecular ions 70GeH+ and 74GeH+ have been recorded using a fast ion beam irradiated by a cw tunable dye laser. Over 150 transitions between the ground X1∑ + state and near-threshold levels of electronic states correlating to the lowest dissociation asymptotes Ge+(2P3/2) + H(2S) and Ge+(2P1/2) + H(2S) were observed in the range 16500 cm−1 to 18500 cm−1. The majority of the lines arise from a 1π-1∑ transition, where the predissociated excited state levels lie between the fine structure dissociation limits (Feshbach Resonances). The lifetimes of the rovibrational levels are found to increase, then decrease, with increasing rotational quantum number. Evidence for triplet (multichannel) mixing is revealed through the observation of additional lines and proton nuclear hyperfine splittings. Experimental results are compared with predictions of the vibrational and rotational energy levels obtained from a numerical solution of the Schrodinger equation. Least squares fitting yields molecular constants for the 1∑and the 1π states. A new apparatus used to create jet-cold molecular ions in a fast ion beam is detailed. Preliminary results have been obtained for the b4∑− g ← a4πu transition of O+ 2 which allow a rotational temperature for the source to be calculated.

The technique of electron spin resonance was used to study the magnetic properties of a number of complex salts of 7,7' ,8,8'-tetracyanoquinodimethane (TCNQ) in order to obtain a more complete understanding of the electronic states in these materials. All but one of the cations used in the preparation of these compounds were divalent and their TCNQ complex salts exhibit magnetic behaviour characteristic of thermally accessible triplet excitons. Three of these compounds, 1,2-di(N-p-cyanobenzyl-4-pyridinium)ethylene (DCBP)-(TCNQ)3' 1,2-di(N-methyl-4-pyridinium)ethane (DMPA)-(TCNQ)4 (I), and 1,4-di(N-pyridinium)butane (DPB)-(TCNQ)4' were available as single crystals and could be studied in detail. Four of these, however, were only available in polycrystalline form and these were DMPA(TCNQ)4(II) and 1,2-di(N-alkyl-4-pyridinium)ethylene (DRPE)-(TCNQ)S' in which R equals n-propyl (P), n-butyl (B), and cyclohexyl (H). The existence of two phases (I and II) of DMPA(TCNQ)4' first indicated by the electrical data, was supported by the different magnetic behaviour observed in this work. The absolute magnitudes of the signal intensity for DPPE(TCNQ)S' DHPE(TCNQ)S and DMPA(TCNQ)4 (II) ,were found to be well described by an approximate solution to the Heisenberg Hamiltonian, which indicates an exciton band is present in these compounds. The absence of dipolar splitting and the high d.c. conductivity supports this interpretation. However, DMPA(TCNQ)4(I), DPB(TCNQ)4' DBPE(TCNQ)S and DCBP(TCNQ)3 gave results indicative of localised triplet excitons. The latter compound exhibits dipolar splitting, and information concerning the exciton dynamics could be obtained. These results were consistent with the conductivity data and, where available, the crystal structure determinations. The complex salt TPT(TCNQ)4 was available in single crystal form and contained the only trivalent cation studied in this work. The temperature independent signal intensity indicated that triplet excitons were not present, and this behaviour was typical of Pauli paramagnetism. This observation was consistent with the semi-metallic d.c. conductivity observed and was explained in terms of the high degree of disorder present, as indicated by the crystal structure determination.

This may be interpreted as evidence that the profile of sub-structure of the lambda 6614 DIB is skewed towards the red in these three sightlines (Sk -68°135, Sk -69°223 and Sk -69°243) to a greater degree than that found in the Galactic ISM. Compared to Galactic trends, the LMC DIBs are found to be weak with respect to the reddening and neutral potassium column density towards Sk -67°2 and Sk -68°135. This may be attributable to a combination of the high UV flux and reduced shielding of interstellar clouds due to the low metallicity of the interstellar gas of the LMC, and results in the destruction of DIB carriers by photodissociation and/or photoionisation. Relative to N(H I) the lambda 6284 DIB observed in four LMC sightlines is shown to be approximately 1/5 to 1/2 of its average strength in the Milky Way. This supports the idea that the metallicity and/or dust-to-gas ratio of the ISM is closely linked with the chemistry that governs the abundance of DIB carriers relative to N(H I). Variations in the N(Ca II)/N(Ti II) ratio are found over at least an order of magnitude in the LMC ISM, and are taken as evidence for significant variation in the Ca n/Ca m ionisation balance. Derived logarithmic titanium depletions are found to be relatively low in the six LMC sightlines studied, with values between approximately -0.8 and -1.9, which are similar to the levels of depletion generally seen in the warm, shocked interstellar medium of the Galaxy.

The domain sizes of a range of diblock polymers have been measured using solid-state NMR spin diffusion experiments carried out under fast magic angle spinning (MAS). 1H-1H exchange spectra were acquired at a range of mixing times and the results displayed effects due to both intra-domain and inter-domain spin diffusion. By fitting the data to an initial rate approximation domain sizes and spin diffusion coefficients were calculated. Simulations were also carried out to determine the impact of T1 relaxation during the experimental mixing time. The spin diffusion coefficient of polystyrene has also been studied under a variety of different conditions. Increasing MAS rate caused a decrease in the spin diffusion coefficient and at the fastest spinning speeds the rate of spin diffusion was much reduced. Temperature changes were shown to have little effect on the spin diffusion coefficient. The incorporation of recoupling sequences into the experimental mixing time was also studied. Solid-state NMR was also used to study a selection of hydroxyapatite nanoparticle/organic dispersant molecule composite materials with potential biomedical applications. 1H-31P correlation experiments were used to investigate the interaction between the dispersant molecules and the surface of hydroxyapatite nanoparticles. The spectra suggested that the dispersant molecules containing polylactic acid interacted with the surface of the nanoparticle via the polymer chain. Whereas dispersant molecules with an aliphatic chain appeared to interact with the particle via their head group. The results from DNP spectra, which selectively enhanced the surface regions, also supported this conclusion.