京都大学 / 新制・課程博士 / 博士(人間・環境学) / 甲第23995号 / 人博第1047号 / 新制||人||245(附属図書館) / 2022||人博||1047(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 内本 喜晴, 教授 中村 敏浩, 教授 陰山 洋, 教授 雨澤 浩史 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

<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