“Matrix effects” in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy are the spectroscopic changes induced by intermolecular interactions, providing sensitivity to local structure and order in solids and liquids. This project aims to identify the effect of intermolecular interactions caused by different n-alkane solid state structures on their NEXAFS spectra. Changes to the carbon 1s NEXAFS spectra are studied as a function of their solid state structure and organization. Two experimental approaches were proposed in this project. In the first approach, different n-alkane crystal structures (orthorhombic, monoclinic, etc.) are examined which arise as a function of n-alkane chain length. In the second approach, changes observed through the pre-melting point order-disorder phase transition found in n-alkanes are examined. This work will explore the characteristic spectroscopic differences observed between n-alkanes in different crystalline forms as well as in the disordered phase below the melting points. In this project, well-ordered diamond shape n-alkane single crystals were obtained by solution casting, using experimental conditions optimized for each n-alkane. As circularly polarized radiation will average the effect of molecular orientation, circularly polarized radiation was used to obtain the NEXAFS spectra of n-alkanes. However, in the analysis of the NEXAFS spectra of n-alkanes recorded with the left circularly polarized X-rays, a significant linear polarization contamination was found. Therefore, linearly polarized X-rays were used to acquire angle dependent NEXAFS spectra, where the X-ray polarization was deliberately aligned along the principal axes (X, Y) of the n-alkane crystal. It was observed that the room temperature carbon 1s NEXAFS spectrum of n-octacosane (C28H58) was different from that of the other n-alkanes, n-tetracosane (C24H50), n-tricosane (C23H48) and n-tetracontane (C40H82). This difference can be attributed due to the different crystal packing of n-octacosane (C28H58 - monoclinic) relative to the other n-alkanes (triclinic and orthorhombic), suggesting different intermolecular interactions (matrix effects) in n-octacosane (C28H58). The analysis of the temperature dependent NEXAFS spectra of n-alkanes reveals that samples of the short chain n-alkane crystals, specially n-tricosane (C23H48), n-tetracosane (C24H50) and n-octacosane (C28H58), sublimed in the STXM microscope. Changes observed in the carbon 1s NEXAFS spectra of n-tetracontane (C40H82) with temperature were attributed to the order-disorder transition. This further illustrates the existence of matrix effects in the NEXAFS spectra of n-alkanes.

In this thesis, two objectives related to Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been studied. The first objective was to develop surface sensitivity in Scanning Transmission X-ray Microscopy (STXM) at the Canadian Light Source (CLS) and the Advanced Light Source (ALS). The second objective was to study sulphur 1s NEXAFS spectra of organosulphur compounds relevant to petroleum by experimental and computational methods. Towards the first objective, Total Electron Yield (TEY) detection has been implemented in a STXM microscope, by conventional sample current and single electron counting detection modes. This provides improved surface-sensitive detection, simultaneous with existing bulk-sensitive transmission detection in the STXM microscopes. Both approaches provide improved surface sensitive imaging and spectroscopy, although channeltron-based detection is superior. TEY-STXM provides surface sensitive imaging of ultrathin films such as phase-separated Langmuir-Blodgett monolayer films, phase separated polymer thin films, as well as differentiation of surface and bulk oxides of patterned metal thin films. The challenge for TEY-STXM measurements is the poor vacuum environment in the STXM chamber at the CLS, which greatly impacts the function of the channeltron as well as the rate of the photodeposition. Although the effect of photodeposition can be minimal in bulk spectroscopy of organic samples, it is a challenge in spectroscopy of organic thin films, where the photodeposits can dominate the weak signal originating from the surface. Chapter 4 of this thesis discusses the details of this study along with the challenges encountered in the development of this new TEY-STXM technique. The second goal of my research was the detailed study of sulphur 1s NEXAFS spectra of organosulphur compounds by experimental and computational methods to obtain a complete database of sulphur 1s NEXAFS spectra. The speciation and quantification of sulphur compounds is of great interest in different areas such as fossil fuel studies, biology, geology, and archaeology. Sulphur 1s NEXAFS spectroscopy can be used for speciation and quantification of these compounds. For this purpose a firm understanding of NEXAFS spectra of sulphur compounds is required. Therefore, the sulphur 1s NEXAFS spectra of different sulphur functionalities have been studied including thiols, thioethers, disulphides, sulfoxides, sulfones, and thiophenic compounds in gas and condensed phases. These highly resolved spectra have been further analyzed with the aid of ab initio calculations. The highly resolved experimental spectra showed fine features predicted by calculations. The combination of experiment and calculation has been used to improve assignment of spectroscopic features relevant for the speciation and quantification of sulphur compounds.

One of the critical challenges in the Canadian oil sand industry is improving processes used to separate bitumen from oil sands and to remove clay particulates from produced oil. The fine clay particles are believed to play a significant role in the oil sands industry, from stabilizing process emulsions to fouling problems in water treatment. Addressing the problems caused by these fine clay particulates is limited by the ability to characterize the hydrocarbon-clay interactions. Scanning Transmission X-ray Microscopy (STXM) is used to study hydrocarbon-clay interactions in controlled model systems, where all components are known, and in process samples extracted from oil sands. To use STXM to study our desired systems, many experimental developments were required. Well developed sample preparation was needed to provide samples free from contaminants and experiments free of artifacts. Clean clays, free of extraneous carbon were required for model studies. A device to reduce photodeposition in the STXM chamber was also required to examine interactions of hydrocarbons on clay surfaces. <p>Using these developments, Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of model clays and model hydrocarbon mixtures were recorded using the STXM microscope on beamline 5.3.2 at the Advanced Light Source, in Berkeley CA. Using NEXAFS spectroscopy in conjunction with the STXM microscope, allowed us to explore preferential interactions between specific hydrocarbon and fine clay particles (smaller than 1 µm) in our model studies. We were also able to assess the chemistry of the hydrocarbons before association with the clay particles. <p>Process samples, consisting of a set of four bitumen froths extracted from the oil sands were investigated. The carbon chemistry of the froths was assessed and quantitatively analyzed. The findings were correlated with previous confocal microscopy results from our collaborators at CANMET Energy Technology Centre in Devon, Alberta.

Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

Linear dichroism in Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy has been used to determine molecular orientation at surfaces and in microscopic domains. However, the molecular orientation of n-alkanes cannot be derived unambiguously from their NEXAFS spectra due to the inadequate understanding of the character of the relevant spectroscopic features in the NEXAFS spectra of n-alkanes (i.e. C 1s to sigma*C-H, C 1s to sigma*C-C transitions).<p>We have studied the linear dichroism in the NEXAFS spectra of n-alkane thin films by using angular dependent NEXAFS spectroscopy to explore the molecular orientation of hexacontane (HC, n-C60H122). The HC thin films were epitaxially grown onto the cleaved NaCl (001) surfaces by physical vapor deposition. NEXAFS spectra of the HC thin film were acquired at different angles using STXM microscopy. A detailed analysis of the angular dependence of the NEXAFS spectra of the HC thin film helps to understand the relationship between the linear dichroism and the molecular orientation in n-alkane molecules. This linear dichroism in the NEXAFS spectroscopy of n-alkanes is relevant for quantitative measurements of molecular orientation, such as for the microanalysis of crystalline organic materials. <p>The linear dichroism of the NEXAFS resonances for n-alkanes has also been studied by ab initio calculations. These calculations were carried out on an isolated n-alkane molecule and a cluster of n-alkane molecules. The calculations on an isolated n-alkane molecule are used to study the linear dichroism for the NEXAFS resonances above the C 1s IP. The cluster calculations account for matrix effects in the NEXAFS features of condensed n-alkanes. A comparison of calculations on an isolated molecule and on a cluster of molecules provides information on how the NEXAFS spectra change from gas phase to condensed phase and determines the linear dichroism of each NEXAFS feature below the C 1s IP.<p>In the process of preparing n-alkane thin films for the study of linear dichroism, the morphology and molecular orientation of n-alkane thin films with different chain length (n-C36H74 and n-C60H122) have also been investigated by the NEXAFS spectroscopy and microscopy. These thin films were epitaxially grown onto cleaved NaCl (001) surfaces by physical vapor deposition. The results revealed that the morphology and molecular orientation of n-alkane thin films depend on the chain length and deposition parameters, such as substrate temperature. These observations have been rationalized by the thermodynamics of nucleation and the kinetics of growth.

One of the critical challenges in the Canadian oil sand industry is improving processes used to separate bitumen from oil sands and to remove clay particulates from produced oil. The fine clay particles are believed to play a significant role in the oil sands industry, from stabilizing process emulsions to fouling problems in water treatment. Addressing the problems caused by these fine clay particulates is limited by the ability to characterize the hydrocarbon-clay interactions. Scanning Transmission X-ray Microscopy (STXM) is used to study hydrocarbon-clay interactions in controlled model systems, where all components are known, and in process samples extracted from oil sands. To use STXM to study our desired systems, many experimental developments were required. Well developed sample preparation was needed to provide samples free from contaminants and experiments free of artifacts. Clean clays, free of extraneous carbon were required for model studies. A device to reduce photodeposition in the STXM chamber was also required to examine interactions of hydrocarbons on clay surfaces. <p>Using these developments, Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of model clays and model hydrocarbon mixtures were recorded using the STXM microscope on beamline 5.3.2 at the Advanced Light Source, in Berkeley CA. Using NEXAFS spectroscopy in conjunction with the STXM microscope, allowed us to explore preferential interactions between specific hydrocarbon and fine clay particles (smaller than 1 µm) in our model studies. We were also able to assess the chemistry of the hydrocarbons before association with the clay particles. <p>Process samples, consisting of a set of four bitumen froths extracted from the oil sands were investigated. The carbon chemistry of the froths was assessed and quantitatively analyzed. The findings were correlated with previous confocal microscopy results from our collaborators at CANMET Energy Technology Centre in Devon, Alberta.

Les particules de suie émises par les moteurs d'avion influencent le climat en absorbant/diffusant la lumière solaire. Elles agissent aussi comme noyaux glaciogènes dans l’atmosphère en participant à la formation des traînées de condensation et des cirrus artificiels, ce qui augmente la nébulosité et affecte l'équilibre radiatif de l'atmosphère. Dans les zones aéroportuaires, elles contribuent à la dégradation de la qualité de l’air et peuvent affecter la santé humaine. Connaître leurs propriétés physico-chimiques est donc primordial pour évaluer leurs impacts environnementaux, sanitaires et agir pour leur réglementation. Nous avons caractérisé les propriétés physiques et chimiques de suies émises par un turboréacteur SaM146-1S17 alimenté avec du kérosène JET A-1 et fonctionnant à différents régimes, dont le régime de croisière. Des informations précises sur leur morphologie, leur (nano)structure, leur composition/spéciation chimique ont été obtenues par microscopie électronique à transmission (TEM), spectroscopie infra-rouge (FTIR), spectroscopie d'absorption des rayons X (NEXAFS) et photoémission X (XPS). Ces techniques ont également permis de caractériser des suies de laboratoire produites par un générateur commercial (miniCAST, Jing Ltd.) et de montrer qu’il permet de générer de bons analogues des suies aéronautiques. La production de quantités importantes de ces analogues aux propriétés physico-chimiques contrôlées offre de nouvelles perspectives quant à l’étude en laboratoire de la réactivité des suies aéronautiques vis-à-vis des environnements atmosphériques et biologiques, permettant d’améliorer notre compréhension de leurs impacts environnementaux et sanitaires. / Soot particles emitted from aircraft engines influence climate by absorbing and scattering sunlight. They also act as ice condensation nuclei in the atmosphere by participating to the formation of condensation trails and artificial cirrus clouds that increase the cloudiness and affects the radiative balance of the Earth’s atmosphere. In airport areas, they contribute to the degradation of air quality and can affect human health. Knowing their physical and chemical properties is therefore of prime importance to assess their environmental and health impacts as well as acting for their regulation. We have characterized physical and chemical properties of soot emitted by a SaM146-1S17 turbofan engine fueled with kerosene JET A-1 and operated at different regimes, including the cruise regime. Accurate information about their morphology, (nano)structure, chemical composition/speciation have been obtained by transmission electron microscopy (TEM), infrared spectroscopy (FTIR), Near-Edge X-ray Absorption Fine Structure (NEXAFS) and X-Ray Photoelectron Spectroscopy (XPS). These techniques have also been used to characterize laboratory soot produced by a commercial generator (miniCAST, Jing Ltd.) and to show that it can generate relevant analogues of aeronautic soot. The production of large amounts of these analogues with controlled physico-chemical properties offers new prospects for laboratory studies of aeronautic soot’s reactivity with respect to atmospheric and biological environments aiming at improving our understanding of their environmental and health impacts.

No description available.

Controlling molecular orientation is of great importance in organic thin films due to the fact that the fundamental properties of functional nanomaterials depend on molecular orientation at the nanoscale. However, controlling molecular orientation cannot be achieved without having an extensive understanding about the controlling factors in the organic film growth processes. Most previous studies have been devoted to monolayer structures. The structure of multilayer films has not been well investigated. This study was performed using a phenomenological approach, in which the morphology and orientation of n-alkane thin films were studied as a function of substrate identity, interface treatment, substrate temperature and deposition rate. The experimental techniques that were used include IR-spectroscopy, polarized optical microscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray microscopy. The kinetic and thermodynamic factors that govern the orientation of organic thin films were extracted from the experimental results, and generalized to make a framework by which the morphology and orientation of organic films can be predicted. Epitaxial growth was specifically considered as a method to pattern organic thin films. In epitaxial growth, the oriented crystals of an organic film grow on a crystalline substrate such that the structure of the substrate is copied by the deposit crystals. For epitaxy it is required that the lattice planes of two crystals are parallel and similar in the lattice points spacing. A minor part of this dissertation is devoted to epitaxy in an inorganic system. One of the favorable consequences of epitaxial growth in inorganic systems is lattice strain that alters the electronic properties of semiconductor devices. A synchrotron based experimental method has been developed to quantitatively measure the degree of strain in Si1-xGex alloy films grown epitaxially on the Si(100) substrate.

Two of the main technological challenges of the century are the production of clean energy, on the one hand, and the development of new materials for electronic and spintronic applications that could increase the speed and the storage capacity of regular electronic devices, on the other hand. Organic materials, including fullerenes, organic polymers and organic molecules with metal centres are promising candidates for low-cost, flexible and clean technologies that can address these challenges. A thorough description of the electronic properties of such materials is, therefore, crucial. The interaction of electromagnetic radiation with the molecule can provide the needed insight into the electronic and vibrational levels and on possible chemical interactions. In order to explain and interpret experimentally measured spectra, a good theoretical description of the particular spectroscopy is necessary. Within density functional theory (DFT), the current thesis discusses the theoretical tools used to describe the spectroscopic properties of molecules with emphasis on two classes of organic materials for photovoltaics, molecular electronics and spintronics. Specifically, the stability of the fullerene derivative PC60BM is investigated in connection with its use as an electron acceptor in organic solar cells and the valence band electronic structure of several transition metal phthalocyanines is studied for their possible application in electronics and spintronics. The spectroscopies discussed in the current work are: the photoelectron spectroscopy of the valence band, X-ray photoelectron spectroscopy of the core levels, near-edge X-ray absorption fine structure, Infrared and Raman vibrational spectroscopies