<p>Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO₂ cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding.</p><p>This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified.</p><p>Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.</p>

Ordinary yet unique, water is the substance on which life is based. Water seems, at first sight, to be a very simple molecule, consisting of two hydrogen atoms attached to one oxygen. Its small size belies the complexity of its action and its numerous anomalies, central to a broad class of important phenomena, ranging from global current circulation, terrestrial water and CO2 cycles to corrosion and wetting. The explanation of this complex behavior comes from water's unique ability to form extensive three-dimensional networks of hydrogen-bonds, whose nature and structures, in spite of a great deal of efforts involving a plethora of experimental and theoretical techniques, still lacks a complete scientific understanding. This thesis is devoted to the study of the local structure of hydrogen-bonded liquids, with a particular emphasis on water, taking advantage of a combination of core-level spectroscopies and density functional theory spectra calculations. X-ray absorption, in particular, is found to be sensitive to the local hydrogen-bond environment, thus offering a very promising tool for spectroscopic identification of specific structural configurations in water, alcohols and aqueous solutions. More specifically, the characteristic spectroscopic signature of the broken hydrogen-bond at the hydrogen side is used to analyze the structure of bulk water, leading to the finding that most molecules are arranged in two hydrogen-bond configurations, in contrast to the picture provided by molecular dynamics simulations. At the liquid-vapor interface, an interplay of surface sensitive measurements and theoretical calculations enables us to distinguish a new interfacial species in equilibrium with the gas. In a similar approach the cluster form of the excess proton in highly concentrated acid solutions and the different coordination of methanol at the vacuum interface and in the bulk can also be clearly identified. Finally the ability of core-level spectroscopies, aided by sophisticated density functional theory calculations, to directly probe the valence electronic structure of a system is used to observe the nature of the interaction between water molecules and solvated ions in solution. Water around transition metal ions is found to interact with the solute via orbital mixing with the metal d-orbitals. The hydrogen-bond between water molecules is explained in terms of electrostatic interactions enhanced by charge rehybridization in which charge transfer between connecting molecules is shown to be fundamental.

There is a great need in the transportation industry for high strength, high stiffness and lightweight materials with excellent dimensional stability. The use of these materials reduces fuel consumption and greenhouse gas emission as well as malfunctioning of components when subjected to fluctuating temperatures. Metal matrix composites (MMCs) are designed to meet these needs of transportation and other industries. However, their use is limited by lack of information on their thermal behaviour. In addition, reactions that occur in MMCs alter their microstructure and properties. These reactions have been widely investigated using X-ray Diffractometry (XRD) and electron microscopy (EM). However, these techniques cannot provide information such as charge transfer and local elemental structures in materials. Synchrotron X-ray Absorption Spectroscopy (XAS) could be used to identify reaction products in MMCs as well as provide information which XRD and EM cannot provide.<p> The thermal behaviour of Al-Mg alloy A535 containing fly ash particles as well as charge transfer and reactivity in particulate aluminium alloy metal matrix composites (MMCs) were investigated in this work. The materials studied were (i) Al-Cu-Mg alloy AA2618 and its composites reinforced with 10 and 15 vol.% alumina (Al2O3) particles and (ii) Al-Mg alloy A535 and its composites reinforced with a mixture of 5 wt.% fly ash and 5 wt.% silicon carbide, 10 wt.% and 15 wt.% fly ash. The investigative techniques used included Differential Scanning Calorimetry (DSC), Thermomechanical Analysis (TMA), Optical Microscopy (OM), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDS), and synchrotron X-ray Absorption Spectroscopy (XAS).<p> The results obtained showed that the coefficient of thermal expansion (CTE) of A535 decreased with the addition of fly ash and silicon carbide. Also, the addition of these particles improved the dimensional stability of the alloy in that the residual strain, åp, cycling strain, åc, and CTE decreased. The results obtained from XAS measurements showed evidence of charge redistribution in the aluminium in AA2618 with the addition of alumina particles. The results obtained from XAS measurements showed evidence of charge redistribution in the aluminium in AA2618 with the addition of alumina particles. The addition of alumina particles into AA2618 increased the p-orbital population and also changed the surface chemistry of the matrix. It was also demonstrated that the XAS technique can be used to determine the presence of various oxides in industrial fly ash and spinel (MgAl2O4) in alumina and fly ash particles extracted from the MMCs.

X-ray absorption spectroscopy and computational chemistry have been used to probe the structure of biomolecules involved in cellular copper homeostasis. X-ray absorption spectroscopy shows that copper chaperones involved in cytochrome c oxidase assembly bind Cu(I) with trigonal coordination environments in poly-copper thiolate clusters, but the number of coppers in these clusters remains unclear. X-ray absorption spectroscopy of the metal-sensing transcription factor-1 from Drosophila melanogaster and metallothionein from Saccharomyces cerevisiae with stoichiometries of four or less shows a tetracopper cluster in an all-or-none manner in these molecules. These results suggest that cooperative binding of copper to form tetracopper clusters may be a common mechanism employed by copper control molecules. The active site structure of the novel copper-sensitive repressor CsoR in Mycobacterium tuberculosis binds copper in a trigonal coordination geometry with two sulfur and one nitrogen donors according to X-ray absorption spectroscopy results. Molecular dynamics simulations of both apo- and Cu-bound CsoR reveal local conformational changes in CsoR upon copper binding, which suggests multiple possible mechanisms of Cu-dependent transcriptional regulation by CsoR. Finally, X-ray absorption spectroscopy and X-ray fluorescence imaging have been used to understand the molecular basis of a promisng new treatment for Wilsons disease (a genetic disorder of Cu homeostasis) using tetrathiomolybdate. Overall, the results presented provide an essential structural basis for understanding copper homeostasis in living cells.

The general application of soft X-ray spectroscopy in the study of the electronic structure of materials is discussed, with particular emphasis on broad band materials. Several materials are studied using both soft X-ray spectroscopy and density functional theory to provide experimental and theoretical electronic structures, respectively. In particular, bonding, cation hybridization, and band gaps for several binary oxides (the alkali oxides: BeO, MgO, CaO, SrO, BaO; the post-transition metal oxides: ZnO, CdO, HgO; and the period 5 oxides In2O3, SnO, SnO2, Sb2O3, Sb2O5, and TeO2) are studied. The technique of using the peaks in the second derivatives of an X-ray emission and an X-ray absorption spectrum to estimate the band gap of a material is critically analyzed, and a more accurate ``semi-empirical'' method that involves both measured spectra and theoretical calculations is proposed. The techniques used in the study of binary oxides are then applied to a more interesting (and industrially relevant) group of ternary oxides based on TiO2 (PbTiO3, Sn2TiO4, Bi2Ti4O11, Bi4Ti3O12, and ZnTiO3), and a general rule for the band gaps of these materials is suggested based on empirical data. This research may help direct efforts in synthesizing a hydrogen-producing photocatalyst with a band gap that can efficiently harness the bulk of the solar spectrum. Finally, several layered pnictide superconductors and related compounds (CaFe2As2, Co-, Ni- and Cu-doped BaFe2As2, LiFeAs, LiMnAs, CaCu1.7As2, SrCu2As2, SrCu2(As0.84Sb0.16)2, SrCu2Sb2, and BaCu2Sb2) are studied. The X-ray spectra provide rather strong evidence that these materials lack strong on-site Hubbard-like correlations, and that their electronic structures are almost entirely like those of a broad band metal. In particular, it is shown that the notion that the transition metals are all divalent is completely wrong for copper in a layered pnictide, and that at best in these systems the copper is monovalent.

There is a great need in the transportation industry for high strength, high stiffness and lightweight materials with excellent dimensional stability. The use of these materials reduces fuel consumption and greenhouse gas emission as well as malfunctioning of components when subjected to fluctuating temperatures. Metal matrix composites (MMCs) are designed to meet these needs of transportation and other industries. However, their use is limited by lack of information on their thermal behaviour. In addition, reactions that occur in MMCs alter their microstructure and properties. These reactions have been widely investigated using X-ray Diffractometry (XRD) and electron microscopy (EM). However, these techniques cannot provide information such as charge transfer and local elemental structures in materials. Synchrotron X-ray Absorption Spectroscopy (XAS) could be used to identify reaction products in MMCs as well as provide information which XRD and EM cannot provide.<p> The thermal behaviour of Al-Mg alloy A535 containing fly ash particles as well as charge transfer and reactivity in particulate aluminium alloy metal matrix composites (MMCs) were investigated in this work. The materials studied were (i) Al-Cu-Mg alloy AA2618 and its composites reinforced with 10 and 15 vol.% alumina (Al2O3) particles and (ii) Al-Mg alloy A535 and its composites reinforced with a mixture of 5 wt.% fly ash and 5 wt.% silicon carbide, 10 wt.% and 15 wt.% fly ash. The investigative techniques used included Differential Scanning Calorimetry (DSC), Thermomechanical Analysis (TMA), Optical Microscopy (OM), Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDS), and synchrotron X-ray Absorption Spectroscopy (XAS).<p> The results obtained showed that the coefficient of thermal expansion (CTE) of A535 decreased with the addition of fly ash and silicon carbide. Also, the addition of these particles improved the dimensional stability of the alloy in that the residual strain, åp, cycling strain, åc, and CTE decreased. The results obtained from XAS measurements showed evidence of charge redistribution in the aluminium in AA2618 with the addition of alumina particles. The results obtained from XAS measurements showed evidence of charge redistribution in the aluminium in AA2618 with the addition of alumina particles. The addition of alumina particles into AA2618 increased the p-orbital population and also changed the surface chemistry of the matrix. It was also demonstrated that the XAS technique can be used to determine the presence of various oxides in industrial fly ash and spinel (MgAl2O4) in alumina and fly ash particles extracted from the MMCs.

X-ray absorption spectroscopy and computational chemistry have been used to probe the structure of biomolecules involved in cellular copper homeostasis. X-ray absorption spectroscopy shows that copper chaperones involved in cytochrome c oxidase assembly bind Cu(I) with trigonal coordination environments in poly-copper thiolate clusters, but the number of coppers in these clusters remains unclear. X-ray absorption spectroscopy of the metal-sensing transcription factor-1 from Drosophila melanogaster and metallothionein from Saccharomyces cerevisiae with stoichiometries of four or less shows a tetracopper cluster in an all-or-none manner in these molecules. These results suggest that cooperative binding of copper to form tetracopper clusters may be a common mechanism employed by copper control molecules. The active site structure of the novel copper-sensitive repressor CsoR in Mycobacterium tuberculosis binds copper in a trigonal coordination geometry with two sulfur and one nitrogen donors according to X-ray absorption spectroscopy results. Molecular dynamics simulations of both apo- and Cu-bound CsoR reveal local conformational changes in CsoR upon copper binding, which suggests multiple possible mechanisms of Cu-dependent transcriptional regulation by CsoR. Finally, X-ray absorption spectroscopy and X-ray fluorescence imaging have been used to understand the molecular basis of a promisng new treatment for Wilsons disease (a genetic disorder of Cu homeostasis) using tetrathiomolybdate. Overall, the results presented provide an essential structural basis for understanding copper homeostasis in living cells.

The memristor is a two-terminal semiconductor device that is able to mimic the conductance response of synapses and can be utilized in next-generation computing platforms that will compute similarly to the mammalian brain. The initial memristor implementation is operated by the digital formation and dissolution of a highly conductive filament. However, an analog memristor is necessary to mimic analog synapses in the mammalian brain. To understand the mechanisms of operation and impact of different device designs, analog memristors were fabricated, modeled, and characterized. To realize analog memristors, lithiated transition metal oxides were grown by molecular beam epitaxy, RF sputtering, and liquid phase electro-epitaxy. Analog memristors were modeled using a finite element model simulation and characterized with X-ray absorption spectroscopy, impedance spectroscopy, and other electrical methods. It was shown that lithium movement facilitates analog memristance and nanoscopic ionic-electronic memristors with ion-soluble electrodes can be key enabling devices for brain-inspired computing.

Water is an important substance. It is part of us, of our environment, and is a fundamental prerequisite for the existence of life as we know it. The structure of water is still, after over 100 years of research on the subject, however under debate. In this thesis x-ray absorption spectroscopy (XAS) and reverse Monte Carlo (RMC) modeling are used to search for structural solutions of water consistent with many different experimental data sets, with emphasis on the combination of different experimental techniques for a reliable structure determination. Neutron and x-ray diffraction are analyzed in combination with the more recent synchrotron radiation based XAS. Geometrical criteria for H-bonding are implemented in RMC to drive the fits and allow to evaluate differently H-bonded structure models against the data. It is shown that the available diffraction data put little constraints on the type of H-bond topology or O-O-O tetrahedrality for the structure of liquid water. It is also demonstrated that classical MD simulations, using some of the most common interaction potentials for water, give rise to O-O and O-H pair-correlation functions with too sharp first peaks at too short distances to be in agreement with diffraction, and furthermore that requiring a large fraction of broken H-bonds is not in itself enough for a structure model to reproduce the experimental XAS. A contribution to the theoretical description of XAS is made by an in-depth investigation of important technical aspects of the TP-DFT spectrum calculations. A novel approach to RMC, applicable also to data that require a significant amount of computer time to evaluate, is developed which makes use of pre-computed properties from a large set of local geometries allowing RMC simulations directly on data from core-level spectroscopies such as XAS. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4, 5 and 6: Submitted

Most urinary tract infections in humans and dogs are caused by uropathogenic strains of , and increasing antimicrobial resistance among these pathogens has created a need for a novel approach to therapy. Bacterial iron uptake and metabolism are potential targets for novel antimicrobial therapy, as iron is a limiting factor in . growth during infection. As a trivalent metal of similar atomic size to iron (III), gallium can interact with a wide variety of biomolecules that normally contain or interact with iron. Gallium compounds disrupt bacterial iron metabolism, are known to accumulate at sites of infection and inflammation in mammals, exert antimicrobial activity against multiple bacterial pathogens in vitro, and may be good candidates as novel antimicrobial drugs. We assessed the suitability of orally administered gallium maltolate as a potential new antimicrobial therapy for urinary tract infections by evaluating its distribution into the bladder, its activity against uropathogenic . in vitro, and its pharmacokinetics and efficacy in a mouse cystitis model. Using a novel application of synchrotron-based analytical methods, we confirmed the distribution of gallium to the bladder mucosa and characterized the relationship between iron and gallium distribution in the bladder. In vitro experiments with human and canine uropathogenic . isolates demonstrated that gallium maltolate exerts antimicrobial effects in a time-dependent, bacteriostatic manner. Minimum inhibitory concentrations ranged from 0.144 µmol/mL to >9.20 µmol/mL with a median of 1.15 µmol/mL. Isolates resistant to ampicillin, ciprofloxacin, or with decreased susceptibility to cephalothin were susceptible to the antimicrobial activity of gallium maltolate, suggesting that resistance to conventional antimicrobials does not predict resistance to gallium maltolate. Pharmacokinetic studies in healthy mice and in a mouse model of urinary tract infection confirmed that gallium is absorbed into systemic circulation after oral administration of gallium maltolate. Gallium is slowly eliminated from the body, with a trend toward longer terminal half-lives in blood and bladder for infected mice relative to healthy mice. This study did not reveal any statistically significant effect of infection status on maximum blood gallium concentrations (4.46 nmol/mL, 95% confidence interval 2.75 nmol/mL – 6.18 nmol/mL and 4.80 nmol/mL, 95% confidence interval 2.53 nmol/mL – 7.06 nmol/mL in healthy and infected mice, respectively) or total gallium exposure in blood and kidney as represented by area under the concentration vs. time curves. Gallium exposure in the bladder was significantly greater for mice with urinary tract infections than for healthy mice. The investigation of gallium distribution within tissues represented a novel application of synchrotron-based analytical techniques to antimicrobial pharmacokinetics. Prior to analysing tissue samples, a library of x-ray absorption spectra was assembled for gallium compounds in both the hard and soft x-ray ranges. The suitability of hard x-ray fluorescence imaging and scanning and transmission x-ray microscopy for localizing and speciating trace elements in tissues was subsequently assessed. Of these methods, only hard x-ray microprobe analysis was well-suited to the analysis and was successfully used for this application. This approach confirmed that gallium arrives at the bladder mucosa after oral administration of gallium maltolate. Furthermore, comparison of iron and gallium distribution within the bladder mucosa indicated that these elements are similarly but not identically distributed and that they do not significantly inhibit one another’s distribution. This finding suggests that gallium may be distributed in part via pathways that do not involve iron. Despite the favorable distribution characteristics of gallium and the persistence of gallium in target tissues following the oral administration of gallium maltolate, its efficacy in a mouse model of urinary tract infection was disappointing. In this study, no statistically significant difference was detected between gallium maltolate, ciprofloxacin and sham treatments in their ability to eliminate bacteria in the urinary tracts. The failure of ciprofloxacin treatment to render bladder tissue culture-negative for an organism that is classified as ciprofloxacin-susceptible in vitro is consistent with observations from other research groups. The similar lack of efficacy observed for gallium maltolate may be related to the large gap between minimum inhibitory concentrations observed in vitro and gallium concentrations observed in tissues from treated mice, but may also be related to the small study size if the effect size of gallium maltolate treatment is small. Given the magnitude of the difference between tissue concentrations and minimum inhibitory concentrations, it may not be possible to increase the dose sufficiently to achieve therapeutic concentrations without causing toxicity. While the results of these experiments suggest that orally administered gallium maltolate may not be a reasonable antimicrobial drug candidate for treating urinary tract infections caused by uropathogenic . , it may be useful for other applications. Other bacterial pathogens may be more susceptible to the antimicrobial effects of gallium maltolate, and local or topical administration could produce much higher concentrations than we observed following oral administration. Continued development of the synchrotron-based analytical techniques used in these experiments could provide new and important opportunities to investigate antimicrobial distribution and metabolism within cells and tissues, particularly for metal-based drugs.