Adsorption of monolayers and multilayers of metal-free and metal phthalocyanines molecules on metal surfaces has been investigated using complementary microscopic and synchrotron-based spectroscopic techniques. It was observed by STM measurements that at monolayer coverage the adsorption direction of the metal-free phthalocyanine molecules with respect to the gold surface vary as a function of temperature, i.e. at room temperature (RT) and low temperature (LT). It was explained by the difference in strength of intermolecular and adsorbate-substrate interactions at room and low temperatures. Nature of the interaction between adsorbed species and the surfaces as a function of coverage has been further characterized by XPS measurements. Binding energy shifts as a function of coverage have been attributed to initial- and final-state effects, the latter being due to different core-hole screening for the different molecular coverage. The alignment of molecular films at both monolayer and multilayer coverages, which has been determined by XAS measurements in several cases, is also dependent upon the relative strength of molecule-molecule versus molecule-substrate interaction. Parallel alignment of the molecular film with respect to the surface is the result of significant interaction between the adsorbate and the substrate, whilst standing geometry of the molecular film is due to more significant intermolecular interactions. DFT simulations have provided further information on the nature of the adsorbate-substrate interaction as well as contribution of different molecular orbitals in XPS and XAS spectra. Moreover, investigation of alkali interaction with the phthalocyanine films revealed a significant modification in their geometric and electronic structures due to charge transfer from the alkali metal to the molecular film. However, no sign of metallization of the molecules has been observed by spectroscopic and microscopic studies.

<p>The electronic structures of the nucleobases, 5-fluorouracil compounds, DNA, metallic DNA, and samples of boron nitride are investigated. Soft X-ray absorption (XAS) and emission (XES) spectroscopy using synchrotron radiation are used to probe the unoccupied and occupied partial densities of electronic states, respectively. Hartree-Fock and density functional theory calculations have been included to compare with experimental results.</p> <p>A systematic approach to understanding the complicated electronic structure of DNA and metallic DNA systems is to initially examine smaller components. Detailed experiment and theory for both absorption and emission spectroscopy was. performed for the nucleobases and 5-fluorouracil compounds. Main transitions in the XAS and XES spectra are identified. X-ray spectroscopy has proven to be extremely sensitive to changes in the environment of various DNA samples. The local chemical environment plays an important role in determining the electronic structure of DNA. In agreement with previous results indicating metallic DNA is more efficient at the transfer of electrons than DNA, XES measurements reveal that there are a higher number of charge carriers in the metallic system. Both liquid and powder samples of (Ni)·M-DNA are found to have a high spin Ni(II) configuration. The drying process significantly alters the electronic structure of the metallic DNA sample. A comparison of high quality single crystals and thin films of boron nitride found that differences between the electronic structures of the nanocrystalline films and the single crystal samples exist, and the surface roughness of the substrate plays an important role in determining the structure of the resulting deposited film.</p>

<p>The electronic structures of the nucleobases, 5-fluorouracil compounds, DNA, metallic DNA, and samples of boron nitride are investigated. Soft X-ray absorption (XAS) and emission (XES) spectroscopy using synchrotron radiation are used to probe the unoccupied and occupied partial densities of electronic states, respectively. Hartree-Fock and density functional theory calculations have been included to compare with experimental results.</p> <p>A systematic approach to understanding the complicated electronic structure of DNA and metallic DNA systems is to initially examine smaller components. Detailed experiment and theory for both absorption and emission spectroscopy was. performed for the nucleobases and 5-fluorouracil compounds. Main transitions in the XAS and XES spectra are identified. X-ray spectroscopy has proven to be extremely sensitive to changes in the environment of various DNA samples. The local chemical environment plays an important role in determining the electronic structure of DNA. In agreement with previous results indicating metallic DNA is more efficient at the transfer of electrons than DNA, XES measurements reveal that there are a higher number of charge carriers in the metallic system. Both liquid and powder samples of (Ni)·M-DNA are found to have a high spin Ni(II) configuration. The drying process significantly alters the electronic structure of the metallic DNA sample. A comparison of high quality single crystals and thin films of boron nitride found that differences between the electronic structures of the nanocrystalline films and the single crystal samples exist, and the surface roughness of the substrate plays an important role in determining the structure of the resulting deposited film.</p>

The groundwater bacterium Pseudomonas fluorescens (CCUG 32456) isolated at a depth of 70 m in the Äspö Hard Rock Laboratory secretes a pyoverdin-mixture with four main components (two pyoverdins and two ferribactins). The dominant influence of the pyoverdins of this mixture could be demonstrated by an absorption spectroscopy study. The comparison of the stability constants of U(VI), Cm(III), and Np(V) species with ligands simulating the functional groups of the pyoverdins results in the following order of complex strength: pyoverdins (PYO) > trihydroxamate (DFO) > catecholates (NAP, 6­HQ) > simple hydroxamates (SHA, BHA). The pyoverdin chromophore functionality shows a large affinity to bind actinides. As a result, pyoverdins are also able to complex and to mobilize elements other than Fe(III) at a considerably high efficiency. It is known that EDTA may form the strongest actinide complexes among the various organic components in nuclear wastes. The stability constants of 1:1 species formed between Cm(III) and U(VI) and pyoverdins are by a factor of 1.05 and 1.3, respectively, larger compared to the corresponding EDTA stability constants. The Np(V)-PYO stability constant is even by a factor of 1.83 greater than the EDTA stability constant. The identified Np(V)-PYO species belong to the strongest Np(V) species with organic material reported so far. All identified species influence the actinide speciation within the biologically relevant pH range. The metal binding properties of microbes are mainly determined by functional groups of their cell wall (LPS: Gram-negative bacteria and PG: Gram-positive bacteria). On the basis of the determined stability constants raw estimates are possible, if actinides prefer to interact with the microbial cell wall components or with the secreted pyoverdin bioligands. By taking pH 5 as an example, U(VI)-PYO interactions are slightly stronger than those observed with LPS and PG. For Cm(III) we found a much stronger affinity to aqueous pyoverdin species than to functional groups of the cell wall compartments. A similar behavior was observed for Np(V). This shows the importance of indirect interaction processes between actinides and bioligands secreted by resident microbes.

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

This thesis concerns studies of aqueous soft matter systems, especially surfactant micelle systems. The aim has been to study the molecular arrangement and electronic structure of the constituents of, as well as transport properties in such a system. The molecular arrangement and electronic structure has been studied by means of X-ray absorption spectroscopy (XAS) and resonant inelastic X-ray spectroscopy (RIXS). The transport properties have been investigated by low-frequency dielectric spectroscopy (LFDS) and small angle X-ray scattering (SAXS) as well as a theoretical modelling. The latter was based on Fick’s laws of the release from binary surfactant system and was validated by experiments. The RIXS and XAS measurements show the electronic structure in bulk water and the influence of the chemical surrounding of the water molecule in bulk water and of the water molecules confined in a micelle lattice. The spectra are highly dependent on the molecular arrangement in such systems. For glycine and sodium polyacrylate RIXS and XAS spectra show features which are unique for carboxyl and carboxylate groups and such measurements can thus be used for fingerprinting. The LFDS and SAXS measurements show a strong correlation between structure in a surfactant/poly-ion system and apparent mobility of surfactants. This conclusion is in line with earlier observations. By the theoretical modelling a predictive model for the surfactant release from a binary surfactant micelle system has been obtained and the importance of different factors for surfactant release has been further clarified.

Iron (Fe) speciation is important for many biogeochemical processes. The high abundance and limited solubility of Fe(III) are responsible for the widespread occurrence of Fe(III) minerals in the environment. Co-precipitation and adsorption onto mineral surfaces limits the free concentrations of compounds such as arsenate (As(V)), Fe(III) and, phosphate (P(V)). Mineral dissolution, on the other hand, might lead to elevated concentrations of these compounds. Fe speciation is strongly affected by natural organic matter (NOM), which suppresses hydrolysis of Fe(III) via complexation. It limits the formation of Fe(III) minerals and Fe(III) co-precipitation. This thesis is focused on interactions between Fe(III) and NOM as well as their impact on other elements (i.e. As(V) and P(V)). X-ray absorption spectroscopy (XAS) was used to obtain molecular scale information on Fe and As speciation. This was complemented with infrared spectroscopy, as well as traditional wet-chemical analysis, such as pH and total concentration determinations. Natural stream waters, soil solutions, ground water and soil samples from the Krycklan Catchment, in northern Sweden, were analyzed together with model compounds with different types of NOM. A protocol based on ion exchange resins was developed to concentrate Fe from dilute natural waters prior to XAS measurements. Iron speciation varied between the stream waters and was strongly affected by the surrounding landscape. Stream waters originating from forested or mixed sites contained both Fe(II, III)-NOM complexes and precipitated Fe(III) (hydr)oxides. The distribution between these two pools was influenced by pH, total concentrations and, properties of NOM. In contrast, stream waters from wetland sites and soil solutions from a forested site only contained organically complexed Fe. Furthermore, the soil solutions contained a significant fraction Fe(II)-NOM complexes. The soil samples were dominated by organically complexed Fe and a biotite-like phase. Two pools of Fe were also identified in the ternary systems with As(V) or P(V) mixed with Fe(III) and NOM: all Fe(III) was complexed with NOM at low total concentrations of Fe(III), As(V) and/or P(V). Hence, Fe(III) complexation by NOM reduced Fe(III)-As(V)/P(V) interactions at low Fe(III) concentrations, which led to higher bioavailability. Exceeding the Fe(III)-NOM complex equilibrium resulted in the occurrence of Fe(III)-As(V)/P(V) (co-)-precipitates.

Les microscopes en champ proche permettent d'obtenir la topographie d'un échantillon avec une résolution pouvant atteindre la résolution atomique. Ces techniques permettent également d'accéder à certaines propriétés locales de la surface telles que le potentiel, l'élasticité, la densité d'états... Ces spectroscopies locales sont de type 'contraste' et ne permettent pas de dresser la cartographie chimique de la surface sans connaissance a priori des éléments qui la composent. Les spectroscopies de rayons-X sont des méthodes de caractérisation puissantes qui permettent de déterminer la composition et la structure élémentaire de l'échantillon avec une précision inférieure à l'Ångström. La résolution latérale est essentiellement limitée par la taille du faisceau primaire, couramment de plusieurs μm². Deux voies sont possibles pour l'améliorer: - réduire l'étendue du faisceau primaire excitateur; - limiter la collecte du rayonnement émis à une portion du volume excité, tout en approchant le détecteur au maximum pour garder un rapport signal/bruit suffisant. C'est cette deuxième option que nous avons choisi de développer. Pour cela nous avons collecté localement la luminescence visible issue de l'échantillon par la pointe-sonde d'un microscope à force de cisaillement, constituée d'une fibre optique effilée de faible ouverture. Cette technique a été utilisée pour caractériser des échantillons semiconducteurs micro- et nano-structurés afin d'en obtenir simultanément la topographie et la cartographie de luminescence locale. Ces résultats ont été obtenus non seulement sur une ligne synchrotron mais également à l'aide d'une microsource de laboratoire équipée d'une lentille polycapillaire. Afin de pouvoir étendre ce concept à d'autres types de matériaux, la faisabilité de la collecte de la fluorescence X locale a été évaluée avec la microsource. Pour cela la fluorescence X émise par un échantillon de cobalt a été collectée par un capillaire cylindrique équipant un détecteur EDX. L'influence du diamètre du capillaire sur le niveau de signal a été mesurée. Une simulation numérique a été développée afin d'estimer le niveau de signal obtenu en utilisant un capillaire de 1 μm de diamètre et d'optimiser la géométrie du système. En couplant la microscopie en champ proche et l'analyse XRF, à la lumière de ces résultats, il sera possible d'atteindre 100 nm de résolution latérale en environnement synchrotron et moins de 1 μm à l'aide d'une source de laboratoire. Il serait alors possible de sélectionner un objet particulier sur une surface et d'en faire l'analyse élémentaire.

Based on a previously completed design for a soft X-ray (50-1100 eV) emission spectrometer, an endstation was constructed for the Resonant Elastic and Inelastic X-ray Scattering (REIXS) beamline at the CLS. The optical design employed techniques and software tools developed in-house using ray-tracing and diffraction grating efficiency calculations to analyze and compare existing designs and to propose a new design with superior performance. This design employs Rowland circle geometry to achieve a theoretical resolving power in excess of 2,500 in our range of interest. In addition, a novel optical design for a larger extremely high resolution spectrometer has been completed to provide theoretical resolving powers exceeding 10,000 throughout the higher end of the spectrum. To accommodate this optical design a completely new mechanical design was required, involving significant mechanical, electrical, vacuum and software engineering. Countless custom fabricated parts were required along with numerous o -the-shelf secondary instruments and systems. All told, this entirely student-managed project has cost over $1.5M and taken over 5 years. Construction is finally complete and the endstation is currently being commissioned. Necessary design changes made during the mechanical design process resulting in the selection of a more suitable, but lower resolution, detector. This reduced the theoretical maximum resolving power to 1,800 for the first order gratings and roughly 5,000 for the third order gratings. Commissioning is still underway, but first order resolutions in the range of 1,000 - 2,000 have been recorded as have third order resolutions exceeding 4,000. Publication quality data has been collecting by members of this research group and invited external users have successfully grown and measured samples here. Two of the optical elements required rework and upon their delivery the system commissioning will be completed and peer-reviewed access will begin.

Ce projet s'inscrit dans le cadre d'une étude fondamentale sur la spéciation du technétium en milieu fortement acide. Le comportement de Tc(VII) en milieu HTFMS a été étudié en absence et en présence d'irradiation α. Dans ces deux conditions différentes, les résultats spectrophotométriques de réduction de Tc (VII) obtenus pour les mélanges HTFMS-xH₂O sont similaires. L'analyse par SAX indique la formation d'un dimère cyclique de Tc(IV) complexé aux ligands triflates et formulé Tc₂O₂(CF₃SO₃)₄(H₂O)₄. Ce composé est linéarisé en TcIV-O-TcIV quand la concentration de HTFMS augmente. Dans HTFMS à +98% (CHTFMS=11,15 M), le Tc(VII) protoné, de formule TcO₃(OH)(H₂O)₂, stabilisé en absence de rayonnements ionisants externes est réduit en Tc(V) sous irradiation α. La caractérisation structurale par la spectroscopie EXAFS sur la base des calculs DFT suggère la formation d'un complexe monomère de Tc(V) avec les ligands triflates. Les deux composés [OTc(F₃CSO₃)₂(H₂O)₂]⁺ et [OTc(F₃CSO₃)₂(OH)₂]⁻ ont été proposées. En milieu H₂SO₄ concentré (CH₂SO₄ ≥ 12 M), des expériences de radiolyse α de Tc(VII) ont été menées afin de pouvoir comparer le comportement radiolytique de Tc(VII) dans les deux milieux apparentés HTFMS et H₂SO₄. Les études XANES montrent que la réduction radiolytique de Tc(VII) contribue à la formation d'un mélange de Tc(V) et Tc(VII) dans H₂SO₄ 13 M et à Tc(V) à 18 M en H₂SO₄. L'analyse des spectres EXAFS indique la formation de complexes monomères [TcO(HSO₄)₃(H₂O)₂] et [TcO(HSO₄)₃(H₂O)(OH)]⁻ en milieu H₂SO₄ 13 M et des espèces [Tc(HSO₄)₃(SO₄)(H₂O)] et [Tc(HSO₄)₃(SO₄)(OH)]⁻.