In this thesis, two aspects of research in soft X-ray absorption spectroscopy chemistry are explored. The first objective was to measure the natural circular dichroism of small chiral organic molecules at soft X-ray wavelengths. The second objective was to characterize the electronic structure and spectra of a series of organometallic polymers. <p>The goal of the first part of this thesis was to enhance the sensitivity of Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy to the intrinsic handedness of chiral organic molecules. The phenomenon of X-ray natural circular dichroism (XNCD) has been well described by theoreticians; however, there have been few successful measurements reported, mainly due to the weakness of the effect and the difficulty of preparing suitable samples. The fourth chapter of this thesis outlines the requirements for XNCD experiments and the efforts made to prepare appropriate samples. <p>The goal of the second part was to use NEXAFS spectroscopy as an analytical technique for the elemental and chemical characterization of innovative materials based on organoiron compounds. The interpretation of transition metal compounds by NEXAFS spectroscopy is difficult due to complex interactions between the metal and its surroundings. Two approaches are commonly used; an atomic multiplet model and a covalent bonding model, which lead to conflicting spectral assignments. Earlier NEXAFS studies of metallocene complexes were found to be lacking as these two models were not adequately rationalized. Owing in part to greatly improved instrumental sensitivity and to efficient theoretical calculations, the interpretation of NEXAFS spectra for a series of metallocene and metal arene complexes was refined. Enhanced understanding of the spectroscopy of these compounds eventually contributed to the characterization of a series of organometallic polymeric materials.<p>Underlining these studies is the remarkable complementarity of NEXAFS spectroscopy and chemistry. A comprehensive understanding of the chemistry of the samples examined in the measurement of XNCD is shown to be crucial for a successful advancement of this spectroscopy. In return, optimization of soft X-ray spectroscopy of metallocenes is demonstrated to remarkably benefit the understanding of the organometallic polymers.

Living organisms constantly respond to changing environmental conditions, and some changes can be far from optimal for many organisms. Insects represent the majority of species in many ecosystems and play an important role in bioaccumulation and biotransformation of environmental contaminants such as selenium and arsenic. Some insectivorous predators feeding on these insects are highly sensitive to such elements resulting in reduced growth, reproductive failures and low population numbers. The mechanisms of selenium and arsenic uptake through the food chain are poorly understood. The determination of chemical speciation is a prerequisite for a mechanistic understanding of a contaminants bioavailability and toxicity to an organism. Synchrotron-based X-ray absorption spectroscopy was used to identify the chemical form of selenium and arsenic in insects in both the field and laboratory conditions. Insects living in streams near Hinton, Alberta affected by coal mine activities were examined for selenium speciation. Results showed higher percentages of inorganic selenium in primary consumers, detritivores and filter feeders than in predatory insects. Selenides and diselenides constitute a major fraction of selenium in these insects. In another field setting, speciation of selenium was studied in insects attacking selenium hyperaccumulating plant <i>Astragalus bisulcatus</i>. The effect of selenate and arsenate alone and the combined effects of selenate and arsenate on insects and parasitoids were monitored using a laboratory-reared moth (<i>Mamestra configurata</i>). Hosts receiving selenium biotransformed selenate to organic selenides and diselenides, which were transferred to the parasitoids in the third trophic level. Arsenic fed larvae biotransformed dietary arsenate to yield predominantly trivalent arsenic coordinated with three aliphatic sulfurs. Larvae receiving arsenate used a novel six-coordinated arsenic form as an excretory molecule in fecal matter and cast skin. X-ray absorption spectroscopy imaging with micro X-ray fluorescence imaging on selenate and arsenate fed larvae revealed highly localized selenium and arsenic species, zinc and copper within the gut. The results provide insights into how the insects cope with their toxic cargo, including how selenium and arsenic are biotransformed into other chemical forms and how they can be eliminated from the insects. The implication of selenium and arsenic species in the diet of predators and detritivores is discussed.

The Drosophila mutant fumble has a defect in mitochondrially targeted pantothenate kinase (PANK) and exhibits a movement disorder in the females. The human disease pantothenate kinase associated neurodegeneration (PKAN) has the same genetic defect and a neurodegenerative phenotype as well as iron accumulation in the brain. We have found that fumble females accumulate almost 2 fold more iron in the heads than wildtype. Dietary iron supplementation increases the iron accumulation in the heads further. The small isoform of malvolio (MVL), a homologue of mammalian NRAMP iron transporters, is expressed in the heads of flies. Its expression is upregulated in the fumble females, as well as in dietary iron supplemented wildtype flies. Unlike in the wildtype, dietary iron supplementation leads to a downregulation of MVL in the fumble flies. Although iron levels were elevated in fumble, ferritin expression was relatively unchanged and remained unchanged in the heads of fumble and wildtype with dietary iron supplementation. <p>The Drosophila mutant malvolio was used to determine how iron metabolism is affected when the MVL gene is defective. Iron levels were unchanged in malvolio relative to its parental strain (w1118) with or without dietary iron supplementation. Despite similar iron levels, a small decrease in ferritin expression was found in malvolio relative to w1118, and dietary iron increased ferritin expression in malvolio. However ferritin expression decreased in the parental strain of malvolio after iron supplementation. <p>Most of the iron in the Drosophila heads was in the form of goethite and ferrihydrite. The presence of iron oxides implies that this iron is in a mineralized storage form, likely ferritin. Dietary iron supplementation induced the appearance of ferric phosphates in fumble, malvolio, and wildtype. The subcellular location of this iron is unknown. It may be non-transferrin bound iron in the hemolymph, or a cytosolic intermediate in the labile iron pool. Also of note was the presence of transferrin-bound iron in wildtype heads on normal diet that was not seen after iron supplementation or in the heads of the fumble mutant. The presence in fumble of the kind of ferrihydrite characteristic of the mitochondrial protein frataxin may indicate that iron is accumulating in mitochondria.<p>The upregulation of MVL in the fumble mutant is of significant interest because it is the first protein involved in iron metabolism found to be altered with mitochondrial PANK deficiency. A disruption in MVL could be relevant to the brain iron accumulation in fumble and could be a treatment target for human PKAN.

X-ray absorption spectroscopy (XAS) is a powerful probe of electronic and spatial structure that has been at the heart of many advances in physics, biology, chemistry, engineering and the earth sciences. Unfortunately, the existing experimental techniques are subject to fundamental limitations that complicate the interpretation of x-ray absorption spectra in many important cases. These limitations have motivated an effort to develop an alternative measure of the absorption cross-section that is not subject to the same set of limitations. In this thesis, a technique known as inverse partial fluorescence yield (IPFY) is described which addresses this problem. IPFY differs from existing approaches in a significant way — by using an energy-discriminating photon detector, one gains access to fluorescence information from both resonant and non-resonant x-ray emission processes. We will show that the non-resonant emission is fundamentally related to the total absorption cross-section of a material through an inverse relation. This will be proven by extension of the general theory of fluorescence yield for the case of a thick, homogeneous specimen. We will also demonstrate the utility of IPFY with measurements of NiO, NdGaO₃, LNSCO, and stainless steel 304 at soft and intermediate x-ray energies. These experiments will highlight some essential features of IPFY spectroscopy and demonstrate how it can be an invaluable tool when the other experimental techniques fail to provide reliable spectra. We will also demonstrate how one can exploit the geometry dependence of IPFY to quantitatively determine the composition of a sample and the total x-ray absorption coefficient. Additionally, we will consider the special cases of multilayers and powder specimens, where the theory of fluorescence yield requires approximations and is not as well-behaved as in thick, homogenous specimens. Ultimately, these experiments and theoretical developments will be used to support the claim that IPFY is a bulk sensitive measure of the total x-ray absorption coefficient. Moreover, we will show that IPFY is not affected by saturation effects, is insensitive to surface contamination layers and provides reliable spectra even for strongly insulating materials. These properties make IPFY a suitable spectroscopic technique for studying XAS in a wide range of materials.

The Drosophila mutant fumble has a defect in mitochondrially targeted pantothenate kinase (PANK) and exhibits a movement disorder in the females. The human disease pantothenate kinase associated neurodegeneration (PKAN) has the same genetic defect and a neurodegenerative phenotype as well as iron accumulation in the brain. We have found that fumble females accumulate almost 2 fold more iron in the heads than wildtype. Dietary iron supplementation increases the iron accumulation in the heads further. The small isoform of malvolio (MVL), a homologue of mammalian NRAMP iron transporters, is expressed in the heads of flies. Its expression is upregulated in the fumble females, as well as in dietary iron supplemented wildtype flies. Unlike in the wildtype, dietary iron supplementation leads to a downregulation of MVL in the fumble flies. Although iron levels were elevated in fumble, ferritin expression was relatively unchanged and remained unchanged in the heads of fumble and wildtype with dietary iron supplementation. <p>The Drosophila mutant malvolio was used to determine how iron metabolism is affected when the MVL gene is defective. Iron levels were unchanged in malvolio relative to its parental strain (w1118) with or without dietary iron supplementation. Despite similar iron levels, a small decrease in ferritin expression was found in malvolio relative to w1118, and dietary iron increased ferritin expression in malvolio. However ferritin expression decreased in the parental strain of malvolio after iron supplementation. <p>Most of the iron in the Drosophila heads was in the form of goethite and ferrihydrite. The presence of iron oxides implies that this iron is in a mineralized storage form, likely ferritin. Dietary iron supplementation induced the appearance of ferric phosphates in fumble, malvolio, and wildtype. The subcellular location of this iron is unknown. It may be non-transferrin bound iron in the hemolymph, or a cytosolic intermediate in the labile iron pool. Also of note was the presence of transferrin-bound iron in wildtype heads on normal diet that was not seen after iron supplementation or in the heads of the fumble mutant. The presence in fumble of the kind of ferrihydrite characteristic of the mitochondrial protein frataxin may indicate that iron is accumulating in mitochondria.<p>The upregulation of MVL in the fumble mutant is of significant interest because it is the first protein involved in iron metabolism found to be altered with mitochondrial PANK deficiency. A disruption in MVL could be relevant to the brain iron accumulation in fumble and could be a treatment target for human PKAN.

In this thesis, two aspects of research in soft X-ray absorption spectroscopy chemistry are explored. The first objective was to measure the natural circular dichroism of small chiral organic molecules at soft X-ray wavelengths. The second objective was to characterize the electronic structure and spectra of a series of organometallic polymers. <p>The goal of the first part of this thesis was to enhance the sensitivity of Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy to the intrinsic handedness of chiral organic molecules. The phenomenon of X-ray natural circular dichroism (XNCD) has been well described by theoreticians; however, there have been few successful measurements reported, mainly due to the weakness of the effect and the difficulty of preparing suitable samples. The fourth chapter of this thesis outlines the requirements for XNCD experiments and the efforts made to prepare appropriate samples. <p>The goal of the second part was to use NEXAFS spectroscopy as an analytical technique for the elemental and chemical characterization of innovative materials based on organoiron compounds. The interpretation of transition metal compounds by NEXAFS spectroscopy is difficult due to complex interactions between the metal and its surroundings. Two approaches are commonly used; an atomic multiplet model and a covalent bonding model, which lead to conflicting spectral assignments. Earlier NEXAFS studies of metallocene complexes were found to be lacking as these two models were not adequately rationalized. Owing in part to greatly improved instrumental sensitivity and to efficient theoretical calculations, the interpretation of NEXAFS spectra for a series of metallocene and metal arene complexes was refined. Enhanced understanding of the spectroscopy of these compounds eventually contributed to the characterization of a series of organometallic polymeric materials.<p>Underlining these studies is the remarkable complementarity of NEXAFS spectroscopy and chemistry. A comprehensive understanding of the chemistry of the samples examined in the measurement of XNCD is shown to be crucial for a successful advancement of this spectroscopy. In return, optimization of soft X-ray spectroscopy of metallocenes is demonstrated to remarkably benefit the understanding of the organometallic polymers.

Living organisms constantly respond to changing environmental conditions, and some changes can be far from optimal for many organisms. Insects represent the majority of species in many ecosystems and play an important role in bioaccumulation and biotransformation of environmental contaminants such as selenium and arsenic. Some insectivorous predators feeding on these insects are highly sensitive to such elements resulting in reduced growth, reproductive failures and low population numbers. The mechanisms of selenium and arsenic uptake through the food chain are poorly understood. The determination of chemical speciation is a prerequisite for a mechanistic understanding of a contaminants bioavailability and toxicity to an organism. Synchrotron-based X-ray absorption spectroscopy was used to identify the chemical form of selenium and arsenic in insects in both the field and laboratory conditions. Insects living in streams near Hinton, Alberta affected by coal mine activities were examined for selenium speciation. Results showed higher percentages of inorganic selenium in primary consumers, detritivores and filter feeders than in predatory insects. Selenides and diselenides constitute a major fraction of selenium in these insects. In another field setting, speciation of selenium was studied in insects attacking selenium hyperaccumulating plant <i>Astragalus bisulcatus</i>. The effect of selenate and arsenate alone and the combined effects of selenate and arsenate on insects and parasitoids were monitored using a laboratory-reared moth (<i>Mamestra configurata</i>). Hosts receiving selenium biotransformed selenate to organic selenides and diselenides, which were transferred to the parasitoids in the third trophic level. Arsenic fed larvae biotransformed dietary arsenate to yield predominantly trivalent arsenic coordinated with three aliphatic sulfurs. Larvae receiving arsenate used a novel six-coordinated arsenic form as an excretory molecule in fecal matter and cast skin. X-ray absorption spectroscopy imaging with micro X-ray fluorescence imaging on selenate and arsenate fed larvae revealed highly localized selenium and arsenic species, zinc and copper within the gut. The results provide insights into how the insects cope with their toxic cargo, including how selenium and arsenic are biotransformed into other chemical forms and how they can be eliminated from the insects. The implication of selenium and arsenic species in the diet of predators and detritivores is discussed.

This thesis investigates the synthesis and activation of highly monodisperse Au25(SR)18 - clusters and bimetallic clusters (AuAg and AuPd) protected with various stabilizers for reduction and hydrogenation catalytic reactions. The first chapter is the introduction chapter, which summarizes the literature involving monolayer protected Au clusters, atomically precise Au clusters, bimetallic clusters, X-ray absorption spectroscopy, research objectives, and organization and scope. The second chapter describes the synthesis of Au25(SR)18 - clusters protected with various thiolate stabilizers for nitrophenol reduction catalysis using NaBH4 as a reducing agent. This chapter also describes the stability of these clusters under reaction conditions using UV-Vis spectroscopy and MALDI mass spectrometry. The third chapter details the synthesis of carboxylic acid-protected Au25 clusters using a NaBH4 purification strategy. Here, the knowledge obtained in the second chapter regarding the exceptional stability of Au25(SR)18 - clusters in the presence of NaBH4 was used to isolate carboxylic acid protected Au25 clusters from a polydisperse reaction mixture. The fourth chapter describes the synthesis and activation of mesoporous carbon supported Au25(SR)18 - clusters for nitrophenol reduction catalysis. Here, thermal removal of thiolate stabilizers led to the enhancement in the catalytic activity at low calcination temperatures; however, at higher calcination temperatures activity dropped as particle sintering was observed. Activation of these clusters on mesoporous carbon support was followed by TEM and X-ray absorption spectroscopy. The fifth chapter describes the thermal and chemical removal of thiolate stabilizers from supported Au25(SC8H9)18 - clusters. Here, the removal of thiolate stabilizers and subsequent growth of Au25 clusters was followed by TEM and EXAFS spectroscopy. The sixth and seventh chapters describe the synthesis of AuPd and AuAg bimetallic clusters using Au25(SR)18 - clusters as precursors and their characterization using UV-Vis spectroscopy, transmission electron microscopy, and X-ray absorption spectroscopy. Here, AuPd bimetallic clusters were thermally and chemically treated, which resulted in the formation of AuPd bimetallic nanoparticles with segregated Pd atoms on the surface. AuPd bimetallic nanoparticles were used for the selective hydrogenation catalysis of allyl alcohol. The last chapter of this thesis includes final conclusions and possible avenues for future work.

Thesis (MTech. degree in Chemistry)--Tshwane University of Technology, 2010. / Discusses an accurate and sensitive method for the determination of trace levels of mercury in environmental air samples may be established using cost effective technologies.

Thesis (MTech. degree in Chemistry)--Tshwane University of Technology, 2008. / This work is aimed at experimental verification of the theory about the advantages of the two-step sample vapour release in a fast-heated ballast furnace. The term “ballast” was introduced earlier in electrothermal atomic absorption spectrometry, as an alternative to a platform to describe a compact body of refractive material loosely located on the bottom of a tube furnace atomiser. The thermal behaviour of the ballast furnace is similar to that of the platform, but without restriction created by the platform area. Compared with the flat or concave platform, a compact ballast of similar mass to the platform should have less impact on gas temperature because of the smaller surface area. The theoretical predictions concerning atomisation efficiency in the fast-heated ballast furnace were examined by the determination of metals in organic and inorganic matrices using a Quantum Z.ETA atomic absorption spectrometer. The instrument provided fast heating of the tube atomizer, 10 K ms-1. It is shown that in the employed ballast furnace the vapour released into the gas phase occurs after interim condensation on the ballast. For the samples of tetraethyllead, base oil and aqueous solutions of various metals, analytical signals are observed after stabilisation of tube temperature, independent of volatility of the analyte and level of temperature setting. For those samples, a high gas phase temperature provides complete recovery of the analyte without involvement of chemical modifiers and the reduction of spectral interferences from chloride matrices.