Lignin, one of main components in the woody cell walls, is a complex heterogeneous biopolymer, which provides structural support and transportation of water in plants. It is highly recalcitrant to degradation (both chemically and environmentally) and protects cellulose from being degraded/hydrolyzed. Due to the structural complexity of native lignin, complete characterization and elucidation of lignin’s structure remains very challenging. The overarching goal of this work is to develop mass spectrometry based analytical methods to contribute to a better understanding of lignin structures. This dissertation will focus on the development and application of High-Resolution Accurate-Mass (HRAM) Mass Spectrometry (MS) as main analytical technique for studying lignin model compounds, including understanding the ionization behavior, studying corresponding fragmentation patterns and extracting structural information for structural elucidation eventually. Analytical methods were also developed to study the post-pretreatment products of the synthetic trimeric model compound using High-Performance Liquid Chromatography (HPLC) coupled with High-Resolution Accurate Mass (HRAM) Mass Spectrometry (MS). The first project of this dissertation focuses on mass spectral the characterization of lignin models from the in vitro oxidative coupling reactions. Three specific trimeric compounds were isolated and their ionization behaviors were investigated using HRAMMS via electrospray ionization (ESI). The reaction parameters of the in vitro oxidative coupling reaction were critical in alternating the linkage profiles of resulting dehydrogenation polymers (DHPs). Reaction parameters were tuned to obtain desired DHP linkages profile. Upon the isolation of three different trimeric compounds, a systematic comparison of ionization efficiency of three trimeric compounds was carried out using ESI-HRAM-MS under different ionization conditions. The second project was aimed to design a synthetic route for a lignin model compound that will be a good representation for native lignin during the pretreatment process. The model compound of interest has not been obtained previously through chemical synthesis. Due to the reactivity of cinnamyl alcohol, which contains the unsaturated side chain, this new synthesis strategy was developed based on the known aldol-type reaction route. A versatile synthesis procedure for preparation of β-O-4 oligomeric compounds was designed and implemented to include the most important functional groups (phenolic alcohol, aryl glycerol β-aryl ether bond and unsaturated side chain) in the resulting model compound. This new synthesis route also allowed incorporation of different monolignols. In the third project, Fenton chemistry was applied to a synthetic lignin model compound. Due to the non-specificity in the post pretreatment product profile, nontargeted analytical strategy was developed and applied to study the post-pretreatment products of the model compound using HPLC-HRMS. The results from this dissertation showed a significant difference in ionization behavior between three structurally different model compounds and indicated that primary structures of lignin compounds can largely affect corresponding electrospray ionization properties as well as fragmentation pattern. The work in this dissertation provides analytical techniques for non-targeted analysis of complex lignin samples and an insightful understanding of Fenton’s reaction pretreatment upon lignin model compound.

The current work is part of the EPSRC MUZIC project, which established the collaboration among several universities to carry out a multidiscipline study on the breakaway oxidation of zirconium alloys. The overall goal of the project is to further understand the mechanisms of the oxidation and breakaway process of zirconium alloys. This thesis describes the nano/micro-structural study and nano-analysis of the corroded zirconium alloys using up-to-date TEM and 3D focused ion beam (FIB) slicing and reconstruction techniques. The work mainly focused on the characterization of ZIRLO. The oxide morphology in general comprises an inner columnar layer and an outer equiaxed layer, except for a post-second transition oxide grown on a Zr-Nb-Ti test alloy with a very poor corrosion resistance, which exhibits generally only equiaxed grains throughout the whole oxide scale. Detailed investigation reveals oxides in a slower oxidation stage exhibit better developed columnar grain structure. All the oxides, independent of different corrosion stages and alloy types, contain predominantly monoclinic oxide and a small amount of tetragonal oxide. Defects at different length scales were examined. In stead of a sudden burst of crack nucleation at the kinetic transition, a gradual introduction of cracks parallel to the metal/oxide interface throughout the pre-transition stage is found, suggesting no direction correlation between the formation of cracks and the transition. Besides cracks, the oxide also contains different forms of nano-porosity: isolated pores of 1-3 nm or interconnected pores at grain boundaries. The density of interconnected porosity, especially those along the oxide growth direction, increases towards the oxide surface, evolving over time. It is suggested that the kinetic transition is related to the development of an interconnected porosity down to the metal/oxide interface, providing easy pathways for the transportation of oxidation species. The metal-oxide interface has a wavy morphology both in the micrometer and nanometer scale. The roughness develops to a maximum just before the first kinetic transition. An intermediate suboxide layer with complex 3D morphology between the bulk oxide and the metal substrate is found. Quantitative EELS analysis shows the composition of this layer to be 40-50 at. % oxygen. The suboxide appears to develop in thickness with increasing oxidation time for the pre-transition oxides, while is very thin or absent in the post-, and post-second transition oxides. In the suboxide region, multiple phases including α-Zr, ω-Zr, tetragonal oxide and a phase with an unidentified structure were found, suggesting different structures can coexist in the suboxide layer. Second-phase particles (SSPs) of β-Nb and hexagonal Zr(Fe,Nb)₂ types were found in ZIRLO samples and FCC Zr(Fe,Cr)₂ was the predominant type in Zircaloy-4. The SPPs showed delayed oxidation compared to surrounding Zr. In ZIRLO, those containing high Fe contents were found to be oxidized and transform into an amorphous state much earlier than β-Nb. Hydrides of different types (γ, σ and ε) were observed in the metal and metal/oxide region for both Zircaloy-4 and ZIRLO samples. A higher density of hydrides was seen in post-transition oxides of ZIRLO than in pre-transition oxides.

This thesis considers the theory and calculations of image formation mechanisms for various modes of three-dimensional imaging in aberration-corrected scanning transmission electron microscopy. Discrete tomography is used to determine and refine the three-dimensional structure of molecular nanowire bundles. The structure determination is expedited by the use of annular dark-field imaging, an incoherent imaging mode which provides directly interpretable images. The development of spherical aberration correctors and the subsequent reduction in probe sizes, including the depth of field, has made optical depth sectioning a feasible technique. The localisation in three dimensions of substitutional impurity atoms in zone-axis imaging is discussed. Both the channelling of the probe and the pre-focussing effect of the atomic column play an important role in determining the depth response of the impurity atom. Interband scattering within a sample is shown to be influential in imaging crystals containing dislocations and optical depth sectioning is explored as a possible option for overcoming surface relaxation effects in the imaging of screw dislocations end-on. The possibility of extending the optical depth sectioning approach using aberration-corrected scanning confocal electron microscopy is discussed. The coherent and incoherent imaging modes, involving elastically and inelastically scattered electrons respectively, are investigated.

Understanding the plastic deformation mechanisms in polycrystals is a long-standing fundamental problem and its improvement has significant potential impact on the increase in materials resistance to typical failure modes such as fatigue cracking and stress corrosion cracking and hence the increase in the materials strength. However many deformation models are yet to be validated as quantitative experimental results at mesoscale to correlate dislocations and microstructure features are limited. This thesis furthers the High Resolution EBSD (HR-EBSD) technique in Geometrically Necessary Dislocation (GND) density measurement from qualitative analysis with a typical map size of 100 μm x100 μm to quantitative analysis with a map of 500 μm x500 μm by determining the optimised scanning step size (0.5 μm) and detector binning level (4x4 binning). This allows a statistically large number of grains to be sampled. Combining with obtained crystallographical information from a conventional EBSD system, systematic studies on GNDs behaviours with respect to a range of microstructure features such as grain boundaries and triple junctions were conducted on monotonically deformed polycrystal copper samples under tension. Relatively high GND density points were found near triple junctions and some grain boundaries whereas the low GND density points tend to appear near the grains’ interiors. These tendencies are particularly profound in low and moderately deformed samples. Hence more detailed analyses were performed to investigate the relations of GND density and the properties of grain boundaries and triple junctions. These quantitative analyses were complemented with direct visual assessment. The visual inspection provides interesting findings such as the strong GND structure dependence on grain orientations and GND structure development through increasing deformation; grain-grain interaction influences on GND structure development and GND structures near triple junctions. These GND density studies provide experimental results to validate some of the existing plastic deformation models for instance Ashby’s model of hardening and Hall-Petch relation. However, some of the new observations on GND structures at mesoscale cannot be fully rationalised by existing proposed mechanisms. Hence new models have been proposed that these GND structures might be generated from the intersections of different slip systems which occurred in various parts of a grain, or by the dislocation piling-up at some microstructural features e.g. triple junctions and twin boundaries.

This thesis studies quaternary chalcogenide nanocrystals and their photovoltaic applications. A temperature-dependent phase change between two distinct crystallographic phases of stoichiometric Cu₂ZnSnS₄ is investigated through the development of a one pot synthesis method. Characterisation of the Cu₂ZnSnS₄ nanocrystals was performed using absorption spectroscopy, transmission electron microscopy (TEM) and powder X-ray diffraction (XRD). An investigation was conducted into the effects of using hexamethyldisilathiane (a volatile sulphur precursor) in the nucleation of small (<7nm), mono-dispersed and solution-stable quaternary Cu₂ZnSnS₄ nanocrystals. A strategy to synthesize high quality thermodynamically stable kesterite Cu₂ZnSnS₄ nanocrystals is established, which subsequently enabled the systematic study of Cu₂ZnSnS₄ nanocrystal formation mechanisms, using optical characterization, XRD, TEM and Raman spectroscopy. Further studies employed scanning transmission electron microscopy (STEM) energy dispersive x-ray (EDX) mapping to examine the elemental spatial distributions of Cu₂ZnSnS₄ nanocrystals, in order to analyse their compositional uniformity. In addition, the stability of nanocrystals synthesised using alternative ligands is investigated using Fourier transform infrared spectroscopy, without solution based ligand substitution protocol is used to replace aliphatic reaction ligands with short, aromatic pyridine ligands in order to further improve Cu₂ZnSnS₄ colloid stability. A layer-by-layer spin coating method is developed to fabricate a semiconductor heterojunction, using CdS as an n-type window, which is utilised to investigate the photovoltaic properties of Cu₂ZnSnS₄ nanocrystals. Finally, three novel passivation techniques are investigated, in order to optimise the optoelectronic properties of the solar cells to the point where a power conversion efficiency (PCE) of 1.00±0.04% is achieved. Although seemingly modest when compared to the performance of leading devices (PCE>12%) this represents one of the highest obtained for a Cu₂ZnSnS₄ nanocrystal solar cell, fabricated completely under ambient conditions at low temperatures.

The RHEA Spectrograph is a single-mode echelle spectrograph designed to be a replicable and cost effective method of undertaking precision radial velocity measurements. Two versions of RHEA currently exist, one located at the Australian National University in Canberra, Australia (450 - 600nm wavelength range), and another located at the Subaru Telescope in Hawaii, USA (600 - 800 nm wavelength range). Both instruments have a novel fibre feed consisting of an integral field unit injecting light into a 2D grid of single mode fibres. This grid of fibres is then reformatted into a 1D array at the input of the spectrograph (consisting of the science fibres and a reference fibre capable of receiving a white-light or xenon reference source for simultaneous calibration). The use of single mode fibres frees RHEA from the issue of modal noise and significantly reduces the size of the optics used. In addition to increasing the overall light throughput of the system, the integral field unit allows for cutting edge science goals to be achieved when operating behind the 8.2 m Subaru Telescope and the SCExAO adaptive optics system. These include, but are not limited to: resolved stellar photospheres; resolved protoplanetary disk structures; resolved Mira shocks, dust and winds; and sub-arcsecond companions. We present details and results of early tests of RHEA Subaru and progress towards the stated science goals.

Mes travaux de thèse mettent en avant le développement de la stratégie métabonomique dans le cadre de deux thématiques d'actualité : le domaine du dopage sportif (Partie A) et celui de l'Exposome (Partie B). La première partie regroupe deux études et a pour objectif d'évaluer la contribution de la métabonomique au développement de nouveaux outils de criblage du dopage. Au cours de ces études, je me suis intéressée à l'analyse non-ciblée d'échantillons d'urine d'athlètes dopés et non- dopés, fournis par l'Agence Française de Lutte contre le Dopage et par des volontaires. L'originalité de cette démarche réside dans son caractère non-ciblé et plus particulièrement, dans sa capacité à mettre en évidence des perturbations au niveau métabolique grâce à (i) la spectrométrie de masse haute résolution (ToF) et très-haute résolution (FT-ICR) et (ii) l'analyse de données multivariées. Des potentiels biomarqueurs du dopage au tétrahydrocannabinol, salbutamol et budésonide ont ainsi pu être mis en évidence. La deuxième partie de ma thèse a pour objectif d'évaluer l'impact de la vinclozoline sur le système hormonal de rats et répond ainsi aux besoins de la nouvelle réglementation. Pour cette étude, je me suis donc intéressée aux échantillons de testicules de rats ayant subi un traitement à la vinclozoline. De par son caractère compréhensif, l'approche métabonomique m'a permis d'apporter des informations complémentaires aux études ciblées réalisées auparavant. Ces travaux me permettent alors de mettre en évidence les apports et les limites de la stratégie métabonomique par rapport : (1) au choix et à la préparation des échantillons d'origine biologique, (2) aux avantages et aux inconvénients des différentes techniques analytiques, (3) aux possibilités en termes de traitement des données, (4) aux exigences statistiques et (5) à la valeur biologique des résultats obtenus / My research work highlights the development of a metabonomic strategy through two topical issues: the doping in sport (Part A) and the Exposome (Part B). The first part includes two studies and aims to assess the contribution of metabonomics to the development of new screening tools. During these studies, I focused on the non-targeted analysis of clean and doped urine samples provided by the French Anti-Doping Agency and by volunteers. The originality of this approach lies in its non-targeted nature and, particularly, in its ability to highlight metabolic disruptions by (i) high-resolution (ToF) and very high-resolution (FT ICR) mass spectrometry and (ii) the analysis of multivariate data. The implemented strategy revealed several potential biomarkers for the use of tetrahydrocannabinol, budesonide and salbutamol. The second part of this thesis aims to evaluate the impact of vinclozolin on the hormonal system of rats and thus meets the requirements of the new regulations. For this study, I focused on testes extracts coming from rats treated with vinclozolin. Due to its comprehensive nature, the metabonomic study provided additional information to the previous targeted approach. All these results highlight the contributions and the limitations of metabonomics with regard to: (1) the choice and the preparation of biological samples, (2) the advantages and disadvantages of different analytical techniques, (3) the opportunities in terms of data processing, (4) the statistical requirements and (5) the biological value of the results

Este trabalho descreve técnicas de espectroscopia de alta resolução em sólidos por Ressonância Magnética Nuclear (RMN), o projeto de construção de um espectrômetro para este fim e sua avaliação experimental com a utilização deste equipamento na caracterização de amostras sólidas. O espectrômetro de alta resolução em sólidos por RMN desenvolvido, permite a utilização de técnicas de dupla ressonância, múltiplos pulsos e rotação da amostra em tomo do ângulo mágico e pode também ser utilizado para líquidos. A máxima freqüência de rotação para MAS é da ordem de 5KHz e as seqüências de dupla ressonância podem ser utilizadas pala quaisquer pares de núcleos atômicos. Os experimentos podem ser realizados com variação de temperatura de -120&#176C a + 160&#176C e o equipamento é totalmente controlado por um microcomputador Macintosh IIci. / This work describes the nuclear magnetic resonance (NMR) techniques for High Resolution Spectroscopy in Solids. Also, the construction project of a partially \"home made\" spectrometer and its applications in the characterization of solid samples are shown in detail. Our high resolution spectrometer is implemented with the double resonance multiple pulses sequences and magic angle spinning (MAS) and can be used with solid and liquid samples. The maximum spinning frequency for the MAS experiment is in excess of 5KHz, the double resonance sequences can be performed with any type of nucleus, in the variable temperature operating range with nitrogen gas: -120&#176C to +160&#176C, and is fully controlled by a Macintosh IIci microcomputer.

Objetivos: Investigar possíveis alterações citogenéticas, através da técnica de bandamento de alta resolução, em indivíduos com anomalias craniofaciais associadas ao atraso no desenvolvimento neuropsicomotor e sem diagnóstico clínico-genético definido, com cariótipo (com bandas) prévio normal e estabelecer possível correlação entre o fenótipo dos indivíduos e as regiões cromossômicas alteradas. Local de execução: Laboratório de Citogenética Humana e Serviço de Genética Clínica, HRAC-USP, Bauru-SP. Indivíduos estudados e Resultados: O cariótipo de alta resolução de 16 indivíduos com anomalias craniofaciais associadas ao atraso no desenvolvimento neuropsicomotor pertencentes ao HRAC-USP, Bauru permitiu detectar alterações citogenéticas estruturais em 4 (25%) dos 16 indivíduos. Em 3 indivíduos detectou-se deleções em regiões subteloméricas (cromossomos 4p, 9p e 18q) e, em 1 indivíduo detectou-se adição de segmento cromossômico de origem desconhecida na região telomérica do cromossomo 12p. Conclusões: A frequência alta (25%) de alterações cromossômicas estruturais em regiões cromossômicas terminais (teloméricas e subteloméricas) mostra que a técnica de alta resolução é útil na identificação de alterações nessas regiões, portanto, indivíduos com anomalias craniofaciais e atraso mental, sem diagnóstico genético-clínico definido, cujo cariótipo convencional foi normal, devem ser, submetidos à análise dos cromossomos por meio do cariótipo de alta resolução antes do procedimento de CGHarray. / Objective: To investigate possible cytogenetic abnormalities through high resolution banding technique in individuals with craniofacial anomalies presenting previous normal karyotype, associated to neuropsychological development delay, without clinic-genetic diagnoses, and establish possible correlation between phenotype and possible candidate chromosomal regions. Local: Human Cytogenetic Laboratory and Clinical Genetic Service, HRAC-USP, Bauru, SP. Individuals and Results: High resolution karyotype of 16 individuals with craniofacial anomalies associated to neuropsychological development delay in follow-up at the HRAC-USP, Bauru allowed the detection of structural chromosomal abnormalities in 4 (25%) of them. Three individuals presented deletion in the subtelomeric region (chromosomes 4p, 9p, and 18q), and one individual presented an addition of an unknown chromosomal fragment in the telomeric region of chromosome 12p. Conclusions: The high frequency (25%) of structural chromosomal abnormalities in terminal region (telomeric and subtelomeric) shows that the high resolution technique is useful for identification of structural anomalies in these regions. Therefore, individuals with craniofacial anomalies associated to neuropsychological development delay without a definitive clinic-genetic diagnoses presenting a normal conventional karyotype, should be submitted to chromosomal analysis through high resolution karyotype before CGH-array procedure.

O biodiesel é quimicamente definido como ésteres monoalquílicos de ácidos graxos derivados de óleos vegetais, gorduras animais ou matérias graxas de descarte. O processo mais comumente empregado para a sua produção é a transesterificação catalisada por base. O controle de qualidade do biodiesel produzido é essencial para o aproveitamento deste como combustível. A Agência Nacional de Petróleo (ANP) estabelece diferentes métodos e especificações para a análise de biodiesel. A cromatografia gasosa é a técnica utilizada para a determinação de glicerol livre e ligado. Esta dissertação apresenta os resultados de dois processos de transesterificação para o óleo de soja: reação catalisada por ácido e reação catalisada por base. Os resultados foram avaliados por cromatografia gasosa de alta resolução, tendo sido demonstrado que a reação catalisada por base apresenta melhores resultados. Desenvolveu-se também nesta dissertação uma metodologia para análise de mono, di e triacilglicerídeos, como uma extensão da resolução ANP 42. A metodologia desenvolvida apresentou excelentes resultados para análises de glicerol ligado em amostra de óleos e biodiesel. / Biodiesel is chemically defined as fatty acid mono-alkyl esters derived of vegetable oils, animal fats or discarded greases. The process more commonly employed for biodiesel production is transesterification catalyzed by base. The quality control of the produced biodiesel is essential for its use as fuel. The National Agency of Petroleum (ANP) establishes different methods and specifications for the analysis of biodiesel. The proposed technique for determination of free and bonded glycerol is gas chromatography. This study presents the results of two reactions of transesterification of the soy oil: catalyzed by acid and catalyzed by base. The results were evaluated by high resolution gas chromatography, which demonstrated better results when basic catalysis was employed. A methodology for mono, di and triacylglicerides was also developed in this dissertation, as an extension of the resolution ANP 42. The developed methodology presented excellent results for bonded glycerol analyses in samples of oils and biodiesel.