The non-destructive study and characterisation of thin films and their interfaces, on an atomic scale, is a crucially important area of study in many areas of science and technology. In this thesis both high angle and grazing incidence x-ray scattering techniques have been used to study the effect of depositing thin films on surfaces with a periodic roughness, as well as studying the structure of laterally modulated surfaces themselves. High angle diffraction measurements of the out-of-plane size of Co crystallites and the crystalline texture of the Ag lattice, in a series of CoAg granular fihns, has allowed a consistent growth mechanism for the Co grains to be deduced. In grazing incidence scattering studies of this series of thin, granular films it was observed that the diffuse scatter was offset from the specular condition and the position of this offset was seen to vary, sinusoidally, upon rotation of the sample. This led to the conclusion that the growth techniques employed had caused a regular step-bunching of the Si (111) substrate. As step-bunching of surfaces can affect greatly the properties of thin films deposited on them, the ability to characterise the substrate after growth is extremely important. In spin-valves deposited on rough, tiled, silicon oxide substrates, the presence of strong interference fringes in the off-specular scatter demonstrated that vertically conformal roughness dominated the system and this was seen to result in the degradation of the magnetic sensitivity of the samples. Conversely, an enhancement in the photoluminescence from thin polymer films deposited on laterally modulated substrates led to a series of studies being made on such structures. In order to obtain information on the lateral period of such structures, as well as their roughness and thickness, existing scattering theories have been modified and a semi-kinematical code of the coherent scatter has been developed.

The scattering mechanisms responsible for Giant Magneto-Resistance (OMR) in magnetic multilayers are believed to be related to many aspects of the multilayer structure. X-ray scattering techniques provide a powerful method with which to study the bulk and interface morphology in these systems, and are therefore crucial in developing an understanding of the dominant factors influencing the magnitude of the OMR. Reflectivity measurements performed on a series of Co/Cu multilayers, sputter deposited onto etched silicon, reveal no variation in the interface roughness with etching voltage, the thickness of the individual layers also remaining constant. The observed decrease in the OMR cannot, therefore, be attributed to variations in spacer thickness or interfacial spin-independent scattering. Electron and X-ray Diffraction measurements suggest the reduction in GMR is due to a loss of antiferromagnetic coupling associated with a transformation of the texture from a randomly oriented to well oriented (111) polycrystalline texture, and subsequent reduction in the volume fraction of (100) oriented grains. Interfaces within Co/Cu are found to propagate with a high degree of conformality with increasing bilayer number, with an out-of-plane correlation length well in excess of 300Å. In contrast, the Co/Pt system exhibits a limiting out-of-plane correlation length of the order of 350Å arising from a columnar growth mode. X-ray Reflectivity and Diffraction measurements provide no structural interpretation for the 3-fold enhancement in the rate of increase of the saturation conductivity, as a function of spacer thickness, in Fe/Au (100) compared to Fe/Au (111), or why large oscillations in the GMR occur for the (100) orientation only. Such observations are, however, consistent with the existence of a channelling mechanism in Fe/Au (100). Grazing Incidence Fluorescence data indicates that Nb acts as a surfactant in Fe/Au (111) growth on sapphire. The influence of different defect types within multilayers has also been observed.

Nucleic acids, as one of the most important macromolecules in living systems, play critical roles in storing, transferring, regulating genetic information, directing proteins synthesis, and catalysis. Understanding the structure of nucleic acid can bring us valuable information for mechanistic study and for drug discovery as well. Among all experimental methods, X-ray crystallography is the most powerful tool in structural biology study to reveal the 3D structure of macromolecules, which has provided over 80% of the highly detailed structural information to date. However, this great technology comes with two disturbing features, crystallization and phasing. The covalent selenium modification of nucleic acids has been proven to be a powerful tool to address both issues in nucleic acid crystallography. First part of this dissertation focuses on the development of novel selenium-modified nucleic acids (SeNA) for crystallization and phasing of B-form DNA containing structures. The novel 2’-SeMeANA modification is the first and currently the only selenium modification, which is fully compatible with X-ray crystallographic study of B-form DNA. Since selenium derivatization at 2’-arabino position dose not affect the B-type 2’-endo sugar conformation, this strategy is suitable for incorporating selenium into DNA for structural studies of B-DNA, DNA-protein complexes, and DNA-drug complexes. Specific base pairing is essential to many biological processes, including replication, transcription, and translation. It is crucial to NA (nucleic acid) sequence-based diagnostic and therapeutic applications as well. By utilizing the unique steric and electronic property of selenium, we designed, synthesized the novel 2-Se-U RNA modification, and demonstrated its highly specific base-pairing property by both biophysical and crystallographic methods. Our studies of 2-Se-U-containing RNAs suggest that this single-atom replacement can largely improve base pairing fidelity against U/G wobble pair, without significant impact on U/A pair.

The structural chemistry and magnetic properties of a number of manganese containing hexagonal perovskites have been studied by X-ray diffraction, neutron diffraction and magnetometry. Trends in the magnetic properties are investigated as a function of the hexagonal stacking sequence and manganese oxidation state. The synthesis of the series of BaMnO_3-x hexagonal perovskites is discussed. By varying both the partial pressure of oxygen and the firing temperature, stacking sequences with a range of hexagonal to cubic layer ratios can be synthesised. Factors which increase the structural tolerance factor are found to increase the proportion of hexagonal layers in the stacking sequence. The crystallographic properties of the BaMnO_3-x compounds are discussed, and the oxide vacancies are found to be exclusively located in the face-sharing hexagonal (h) layers, particularly those which are adjacent to two apex-sharing cubic (c) layers. The preferential localisation of oxide vacancies in chc sites can be used to rationalise the observed stacking sequences, as well as the limiting stoichiometries of BaMnO_3-x structures. The magnetic behaviour of the BaMnO_3-x phases is investigated, both individually and as a function of the stacking sequence. A strong direct exchange interaction between face-sharing cations couples all magnetic moments antiferromagnetically above ambient temperature. A slightly weaker interaction (utilising the 180° superexchange pathways between apex-sharing MnOe octahedra) results in three-dimensional antiferromagnetic order at a temperature in the range 230 ≤ T (K) ≤ 280. The strength of this interaction is found to be dependent on the length of the face-sharing chains. A third interaction occurs at T ~ 45K, believed to represent a canting transition. Low temperature neutron diffraction data reveal that the magnetic moments order in a simple antiferromagnetic manner. The magnitude of the ordered moment shows a dependence on the length of the face sharing chains, where phases with shorter chains have a larger ordered moment. Long-range magnetic order is disrupted by charge disorder in the mixed Mn(III)/Mn(IV) system 4H-BaMnO_{2.6 5(1)}. The hexagonal BaMn_1-zTi_z O_{3- x} and BaMn_1-zZr_z0_3-x systems were also studied. Synthesis under argon atmospheres allows a range of new phases to be accessed. These include a novel manganese-zirconium phase, 6H-BaMn_0.8Zr_0.2O_2.81(1), and BaMn_o.55Ti<sub>0.45,/sub>O_3-x, which adopts the rare 15R' stacking sequence. The BaMn_1-z Ti_zO_3-x system confirms that although the tolerance factor controls the proportion of cubic layers, it does not control the arrangement of these layers. This is controlled by the size of the B cations and the proportion of oxide vacancies. Partial cation order occurs in 6H-BaMn_o.8Zr_0.2O_2.81(1), which can be rationalised on the basis of the size difference between manganese and zirconium ions. Topotactic reductions using binary hydrides are carried out in order to decouple the manganese oxidation state from the adopted stacking sequence. Using hydride reductions, 4H-Ba_o.5Sr_o.5MnO_3-x can be topotactically reduced to 4H-Ba_o.5Sr_o.5MnO_2.o2(1). This increases the strength of the 180° superexchange interaction, and antiferromagnetic order is achieved above ambient temperature. Using the same techniques, 4H-BaMnO_3-x can be reduced to 4H-BaMnO_2.47(1) or 4H-BaMnO_2.o6(1). These phases undergo a distortion to an orthorhombic unit cell.

The structure of rabbit muscle glycogen phosphorylase b, an important regulatory enzyme in glycogen metabolism, has been studied by X-ray crystallographic techniques. This work was carried out as part of a group project, and the crystal structure of the enzyme had already been solved to 3 Å resolution, using the technique of Multiple Isomorphous Replacement. A search for additional heavy atom isomorphous derivatives was carried out, and photographic data to 3 Å resolution were collected for a further ethylmercurythiosalicylate derivative, using a screenless oscillation camera. The collection and reduction of this data, and the refinement of the heavy atom positions is described. The inclusion of this data allowed a new electron density map (with figure of merit = O.63) to be calculated, which enabled previously ambiguous areas in the electron density to be interpreted. Data to 2 Å resolution have been collected on an oscillation camera, using a synchrotron radiation source and cylindrical film cassettes. An intensity gain of up to 13O times, compared to a GX6 rotating anode source, was obtained with the synchrotron radiation source. A reduction in radiation damage, was also observed. The collection and reduction of the 2 Å data is described. The final overall merging R-factor was 15%. Some systematic errors remain in the data, and possible sources of these errors are discussed, and improvements to the data processing procedure suggested. The 2 Å data were empirically scaled to the 3 Å data and have been used in the first stages of the refinement of the phosphorylase b structure. The contribution of the crystallographic results towards an understanding of phosphorylase b as an allosteric protein is discussed.

In this thesis I study the inner-most regions of Active Galactic Nuclei (AGN) using the reverberation mapping technique, and neutron star low-mass X-ray binaries in quiescence using X-ray observations. Using the 13-year optical monitoring data for the AGN NGC 5548, the luminosity dependence of the Hβ emitting radius was modelled using a delay map, finding that the radius scales with luminosity as predicted by recent theoretical models. Time-delays between the continuum at different wavelengths in AGN can be used to probe the accretion disc. Here, continuum time-delays in a sample of 14 AGN were used to measure the radial temperature profile of the accretion discs, determine the nuclear extinction, and measure distances to the objects. However, the distances measured correspond to a value for Hubble's constant that is a factor of ~2 lower than the accepted value. The implications of this on the thermal disc reprocessing model are discussed. I present two Chandra observations of the neutron star transient in the globular cluster NGC 6440 in quiescence, where the power-law component to the spectrum is seen to be variable between the observations, suggesting that there is ongoing residual accretion. From a Chandra observation of the globular cluster Terzan 1, I have identifed the likely quiescent counterpart to a transient previously observed in outburst, and discuss the other sources within the cluster. Using Chandra and XMM-Newton monitoring observations of two neutron star transients (KS 1731-260 and MXB 1659-29) in quiescence I have found that the neutron star crusts in both sources have now returned to thermal equilibrium with the core. These observations also indicate that the crusts in both sources may have a high thermal conductivity and that enhanced neutrino emission may be occurring in the core. Finally, the discovery of an X-ray transient with XMM-Newton is presented, and the other sources in this observation discussed.

Type I X-ray bursts (XRB) are highly energetic and explosive astrophysical events, observed as very sudden and intense emissions of X-rays. X-ray bursts are believed to be powered by a thermonuclear runaway on the surface of a neutron star in a binary system. XRB models are dependent on the accurate information of the nuclear reactions involved. The 18Ne(α,p)21Na reaction is considered to be of great importance as a possible breakout route from the Hot-CNO cycle preceding the thermonuclear runaway. In this thesis work, the 18Ne(α,p)21Na reaction cross-section was indirectly measured at Ecm(α,p) = 2568, 1970, 1758, 1683, 1379 and 1194 keV, using the time-reverse 21Na(p,α)18Ne reaction. Since the time-reverse approach only connects the ground states of 21Na and 18Ne, the cross sections measured here represent lower limits of the 18Ne(α,p)21Na cross-section. An experiment was performed using the the ISAC-II facility at TRIUMF, Vancouver, Canada. A beam of 21Na ions was delivered to a polyethylene (CH2)n target placed within the TUDA scattering chamber. The reaction 18Ne and 4He ions were detected using silicon strip detectors, with time-of-flight and ΔE/E particle identification techniques used to distinguish the ions from background. The measurement at Ecm = 1194 keV is the lowest energy measurement to date of the 18Ne(α,p)21Na cross section. The measured cross sections presented in this thesis were compared to the NON-SMOKER Hauser-Feshbach statistical calculations of the cross section and to the unpublished results of another time-reverse investigation performed by a collaboration at the Argonne National Laboratory. A 18Ne(α,p)21Na reaction rate calculation based on the measured cross sections was performed. In comparison with previous reaction rate estimates, our results indicate a rate that is about a factor 2-3 lower than Hauser-Feshbach calculations, suggesting that a statistical approach may not be appropriate for cross section calculations for nuclei in this mass region. The astrophysical consequences of our new results appear to remain nevertheless negligible. These are also presented in this thesis.

The study of the magnetic and structural properties of matter under extreme conditions is a fast developing field. With the emergence of new techniques and innovative instruments for measuring physical properties, the need for compatible pressure generating devices is constantly growing. The work described in this thesis is focused on development, construction and testing of several high pressure (HP) cells of novel design. One of the cells is intended for single crystal X-ray diffraction (SXD) studies at low temperature (LT) and the other three HP devices are designed for a Magnetic Property Measurement System (MPMS), two of which are suitable for dc susceptibility studies and the other one is aimed at high frequency ac susceptibility measurements. HP crystallographic studies are routinely carried out in diamond anvil cells (DAC) at room temperature while ambient pressure SXD studies are often conducted at LT to reduce atomic vibrations and obtain more precise structural data as well as to study LT phases. Combining HP with LT gives access to a whole new area on the phase diagrams but due to the size of the existing DACs this is generally achieved by cooling down the cells inside a cryostat and it is mainly possible at synchrotrons where dedicated facilities exist. A miniature DAC which can be used with commercially available laboratory cry-flow cooling systems and achieves pressures in excess of 10 GPa has been developed. The design of the pressure cell is based on the turnbuckle principle and therefore it was called TX-DAC. Its dimensions have been minimised using Finite Element Analysis (FEA) and the final version of the cell weighs only 2.4 g. The cell is built around a pair of 600 μm culet Boehler-Almax anvils which have large conical openings for the diffracted beam. The TX-DAC is made of beryllium copper (BeCu) alloy which has good thermal conductivity and allows quick thermal equilibration of the cell. The MPMS from Quantum Design is the most popular instrument for studies of magnetic properties of materials. It is designed to measure ac and dc magnetic susceptibility of sample with detectable signals as low as 10-8 emu. The MPMS has a sample chamber bore of 9 mm in diameter and this puts a constraint on the dimensions of the pressure cells. However, several types of clamp piston-cylinder cells and DACs have been designed for the MPMS. The former are used for measurements at pressure up to 2 GPa and the later can be used for studies at higher pressure. Taking advantage of the turnbuckle principle, a DAC (TM-DAC) and a piston-cylinder cell (TM-PCC) for dc magnetic studies were built. They allow HP measurements to be performed at the full sensitivity of MPMS. Both pressure cells are made of BeCu and their small dimensions combined with symmetrical design is the key to an ideal background signal correction. The TM-DAC is 7 mm long and 7 mm in diameter, it weighs 1.5 g and with 800 μm culet anvils it can generate a sample pressure of 10 GPa. Inherently the sample volume is limited to approximately 10-3 mm3 and the signal corresponding to this volume of some weakly magnetic material remains below the sensitivity of the MPMS. This constraint led us to the development of the TM-PCC – a piston-cylinder variant of the turnbuckle design. With a 4 mm3 sample volume it allows the study of weakly magnetic samples in the range 0-1.9 GPa. The TM-PCC uses two zirconia pistons of 2.5 mm in diameter; it is 10 mm long, 7 mm in diameter and weights 2.7 g. Conventional metallic pressure cells perform well in dc mode however in ac susceptibility measurements, the Eddy currents set in the cells’ body lead to a screening effect which can significantly obscure the signal from the sample. This problem was solved by designing a composite piston-cylinder cell made with Zylon fibre and epoxy resin. The sample is located in the middle of the cell in the 2.5 mm bore and the pressure is transmitted through zirconia pistons. Keeping the metallic parts away from the sample resolves any interference issue. The composite cell performs well in a pressure range of 0-1 GPa. The performance of the pressure cells developed within this project is illustrated by studies of various systems at high pressure.

The effect of pressure on a number of magnetically interesting compounds such as single-molecule magnets and dimeric copper and manganese molecules has been investigated to probe the validity of ambient magneto-structural correlations. The first chapter is an introduction to the equipment and methodologies that have been adopted to carry out the experimental high-pressure work. The second chapter reports the first combined high-pressure single crystal X-ray diffraction and high pressure magnetism study of four single-molecule magnets (SMMs). At 1.5 GPa the structures [Mn6O2(Et-sao)6(O2CPh(Me)2)2(EtOH)6] (1) – an SMM with a record effective anisotropy barrier of ~86 K – and [Mn6O2(Etsao) 6(O2C-naphth)2(EtOH)4(H2O)2] (2) both undergo significant structural distortions of their metallic skeletons which has a direct effect upon the observed magnetic response. Up to 1.5 GPa pressure the effect is to flatten the Mn-N-O-Mn torsion angles weakening the magnetic exchange between the metal centres. In both compounds one pairwise interaction switches from ferro- to antiferromagnetic, with the Jahn-Teller (JT) axes compressing (on average) and re-aligning differently with respect to the plane of the three metal centres. High pressure dc χMT plots display a gradual decrease in the low temperature peak value and slope, simulations showing a decrease in |J| with increasing pressure with a second antiferromagnetic J value required to simulate the data. The “ground states” change from S = 12 to S = 11 for 1 and to S = 10 for 2. Magnetisation data for both 1 and 2 suggest a small decrease in |D|, while out-of-phase (χM //) ac data show a large decrease in the effective energy barrier for magnetisation reversal. The third SMM is the complex [Mn3(Hcht)2(bpy)4](ClO4)3·Et2O·2MeCN (3·Et2O·2MeCN) that at 0.16 GPa loses all associated solvent in the crystal lattice, becoming 3. At higher pressures structural distortions occur changing the distances between the metal centres and the bridging oxygen atoms making |J| between the manganese ions weaker. No significant variations are observed in the JT axis of the only MnIII present in the structure. Highpressure dc χMT plots display a gradual decrease in the low temperature peak value and slope. Simulations show a decrease in J with increasing pressure although the ground state is preserved. Magnetisation data do not show any change in |D|. The fourth SMM, [(tacn)6Fe8O2(OH)12](ClO4)3.9Br4.1⋅6H2O, (4) is the largest inorganic compound ever studied at high-pressure. Up to 2.0 GPa the conformation of the complex remains largely unaffected, with the counter ions and water molecules moving around to accommodate a compression of the unit cell volume. High pressure magnetic susceptibility data collected up to 0.93 GPa confirm minimal changes in the intra-molecular exchange interactions. The third chapter focuses on three hydroxo-bridged CuII dimers: [Cu2(OH)2(H2O)2(tmen)2](ClO4)2 (5), [Cu2(OH)2(tben)2](ClO4)2 (6) and [Cu2(OH)2(bpy)2](BF4)2 (7) have been structurally determined up to 2.5, 0.9 and 4.7 GPa, respectively. 6 and 7 have never been reported before. Pressure imposes important distortions in the structures of all three complexes, particularly on the bond distances and angles between the metal centres and the bridging hydroxo groups. 5 undergoes a phase transition between 1.2 and 2.5 GPa caused by the loss of a coordinated water molecule. This leads to a loss of symmetry and dramatic changes in the molecular structure of the complex. The structural changes are manifested in different magnetic behaviours of the complexes as seen in dc susceptibility measurements up to ~0.9 GPa: J becomes less antiferromagnetic in 5 and 6 and more ferromagnetic in 7. The fourth chapter shows the compression of two oxo-bridged MnII/MnIII mixed valence dimers: [Mn2O2(bpy)4](ClO4)3⋅3CH3CN, (8) has been squeezed up to 2.0 GPa whilst [Mn2O2(bpy)4](PF6)3⋅2CH3CN⋅1H2O, (9) could be measured crystallographically up to 4.55 GPa. 9 has never been reported before, while 8 has been reported in a different crystallographic space group. The application of pressure imposes significant alterations in the structures of both complexes. In particular, in 8 the Mn-Mn separation is reduced by the contraction of some of the Mn-O bond distances, 9 shows essentially analogous behaviour: the Mn-Mn distance and nearly all the Mn-N bonds shrink significantly. The magnetic behaviour of the complexes has been measured up to 0.87 GPa for 8 and 0.84 GPa for 9, but neither display any significant differences with respect to their ambient data.

Nanomaterials (NMs) are materials in which the size of at least one dimension is less than 100 nm. Examples include quantum dots, nanoparticles, “Buckminsterfullerene (C60)”, carbon nanotubes, graphene and TiO2 thin films. Many research groups have investigated the properties of NMs, and they have reported that some of them are clearly different to those of the bulk materials, and depend on the size of the NMs. Examples include melting temperatures, phase transition pressures, fluorescence spectra, catalytic properties and magnetic properties. Recently, a high-pressure study of Te nano-cylinders revealed compressibility effects that are different to those observed in bulk-Te. Although this study reported an elevation of phase transition pressure compared to the bulk, the authors did not investigate the structures of the high-pressure phases, and it is unclear whether the incommensurate phase found at high pressures in bulk-Te was observed or not. Indeed, it is completely unknown whether the incommensurate phases observed in a number of elements at high pressure also exist in nanoparticle samples of the same materials. The search for, and study of, such phases forms the subject of this thesis. Initial studies of commercial selenium nanoparticles (nano-Se) revealed that the incommensurate phase of bulk selenium (Se-IV) is also found in nano-Se. The transition pressures in nano-Se are slightly higher than those of bulk-Se. However, the nano-Se samples were subsequently found not to have the sizes, shapes, and properties claimed by the vendor, which was confirmed by transmission and scanning electron microscopy. Further commercial samples of nano-Se and nano-Bi were also found to be of extremely poor quality. It was clear, therefore, that a detailed study of incommensurate phases in NMs would require us to make our own samples. Bismuth nanoparticles (nano-Bi) with dimensions 51(6), 52(15), 92(13), 128(45), and 138(27) nm have been successfully synthesised by the author in collaboration with the Hybrid Nano Collods group at the University of St. Andrews. On compression, the nano-Bi samples were found to have the same order of phases Bi-I, Bi-II, Bi-III, and Bi-V and phase transitions as found in bulk-Bi, but were found to exhibit larger phase coexistence. The phase transition pressures on pressure increase were higher than those of the bulk materials, and the smaller the diameter of nano-Bi, the higher the phase-transition pressure. This behaviour is similar to, but more extreme than, that found in CdSe nanoparticles. The incommensurate Bi-III structure has been found in nano-Bi under increases in pressure. However, the di↵raction patterns from Bi-III contain additional unaccounted-for peaks, and this phase is referred to as complex Bi-III. The Debye- Scherrer rings from complex Bi-III are smooth, and do not exhibit the spottiness observed in the diffraction patterns of Bi-III obtained from bulk-Bi. This enables full Rietveld refinement of Bi-III in the nano-samples. Complex Bi-III exists from 3 GPa up to 30 GPa, compared to the stable range of only 2.7 to 7.7 GPa of Bi-III in the bulk material. While such a large range of pressure enables the structure of nano-Bi-III to be studied over a much wider pressure range than bulk-Bi-III, such studies were hampered by the existence of the unaccounted-for peaks. In order to get clean, single-phase patterns of Bi-III, samples of this phase were first prepared on pressure decrease from the higher-pressure Bi-V phase, before recompressing them. Single-phase samples of Bi-III were obtained and were found to be stable up to 14-18 GPa. However, because of phase coexistence, diffraction peaks from Bi-III were still visible at pressures as high as ~30 GPa, which is ~3 times larger than the upper limit pressure of existence of bulk-Bi-III. On pressure re-increase, nano-Bi-III has a higher bulk modulus than bulk-Bi-III. The bulk modulus was found to be size-dependent as it is higher when size decreases. Moreover, nano-Bi has a smaller value of the incommensurate wave vector, which is almost pressure independent, but is found to be particles size dependent. The incommensurate wave vector thus becomes another of the structural and physical properties of nanomaterials that is found to be sample-size dependent.