Dans ce travail, nous étudions l’adsorption de protéines sur des surfaces chimiquement contrôlées. Le but est d’établir le lien entre les propriétés physico-chimiques de la surface (hydrophobicité /charge) et la structure physique de protéines. Des couches auto-assemblées de thiols ayant des groupements terminaux différents sont formées sur des surfaces d’or (SAM) et servent de support à l’adsorption ou du greffage de protéines. Les SAM sont caractérisés, avant ou après l’adsorption de protéines, avec une combinaison de techniques. Des analyses ex situ sont réalisées, dans l’air, en spectroscopie infrarouge en lumière polarisée (PM-IRRAS) ou, sous ultra-vide, en spectroscopie des photoelectrons X (XPS) et en spectrométrie de masse d’ions secondaires (ToF-SIMS). L’analyse en composante principale (PCA) des résultats ToF-SIMS aide à révéler l’orientation des protéines adsorbées grâce à la répartition des fragments d’acides aminés. En microbalance à quartz avec mesure de la dissipation (QCM-D), l’adsorption des protéines est suivie in situ (i.e. en phase liquide). Deux protéines globulaires ayant des propriétés structurales différentes sont d’abord étudiées, la β-Lactoglobuline (βLG) est dite dure quand l’albumine de sérum bovin (BSA) est dite souple. Des orientations différentes sont proposées après adsorption sur les SAM. Un cas plus complexe est ensuite étudié avec l’adsorption ou le greffage d’un anticorps sur les surfaces. De nouveau, différentes orientations sont proposées et elles sont corrélées à des mesures de bio-reconnaissances. En conclusion, cette thèse établie une méthodologie de détermination directe et sans marquage de l’orientation de protéines adsorbées. / In this work we studied protein adsorption on chemically well-controlled surfaces. The focus is put on linking physico-chemical properties of surfaces (hydrophobicity/charge) to the structural properties of the adsorbed proteins. To this end, alkyl thiols differing by their end group were used to build self-assembled monolayers on gold substrates (SAM) that serve as templates for protein adsorption or covalent grafting. SAM surfaces before and after protein adsorption were characterized with a combination of techniques. Ex situ analysis were carried out, in air with polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS), or in vacuum using X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). ToF-SIMS results were analyzed statistically in principal component analysis (PCA) to reveal preferential orientations based on amino acids fragments distributions. Protein adsorption was also followed directly in situ (i.e. in the liquid phase) with quartz crystal microbalance with dissipation monitoring (QCM-D). Two model proteins – β-Lactoglobulin (βLG) and bovine serum albumin (BSA) – were first studied. They are both model globular proteins with different structural properties (βLG is hard while BSA is soft). Different orientations were proposed for both proteins on each SAM surface. A more complex case was then studied with the adsorption and grafting of a monoclonal antibody on the SAM. Again differences in orientations were determined and correlated to biorecognition measurements. In conclusion, this thesis establishes a methodology for the direct label free determination of protein orientation on surfaces.

My dissertation focuses on (i) the development of new analysis tools and methodologies for analyzing X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) data, and (ii) the comprehensive characterization of materials (nanodiamonds) using a multi-instrument approach. Chapter 1 contains (i) a discussion of the two techniques I focused on most in my work: XPS and ToF-SIMS, (ii) a discussion of the common chemometrics techniques used to analyze data from these methods, and (iii) the advantages/rationale behind the multi-instrument characterization of materials. Chapter 2 describes various good practices for obtaining reasonable peak fits in XPS, which can also be applied to peak fitting data from different techniques. To address the issue of user subjectivity/bias in XPS peak fitting, I introduce two less biased mathematical functions for characterizing XPS narrow scans, namely the equivalent width (EW) and the autocorrelation width (AW). These functions are discussed in Chapters 3 and 4. In Chapter 5, I then introduce uniqueness plots as simple and straightforward graphical tools for assessing the quality of XPS peak fits and for determining whether fit parameters are correlated. This tool is extensively used in spectroscopic ellipsometry, and the mathematics behind it is known in XPS. However, to the best of my knowledge, this graphical tool has never been applied to XPS. ToF-SIMS data analysis is somewhat challenging due to the enormous amounts of data that are collected, and also the matrix effect in SIMS. This amount of information is significantly increased when depth profiles are performed on samples. Chapter 6 discusses a new chemometrics tool that I introduce for analysis of complex data sets, with emphasis on XPS and ToF-SIMS depth profiling data. The new approach is called the Information Content (IC) or entropy, which is adapted from Claude Shannon's work on Information Theory. Chapter 7 then contains a presentation of the comprehensive characterization of five nanodiamond samples used to manufacture particles for liquid chromatography. The advantages of a multi-instrument approach for material characterization and the lack of comprehensive material characterization in the literature are emphasized. To the best of my knowledge this is the most comprehensive characterization of nanodiamonds that has been reported in the literature. Chapter 8 presents conclusions of my work and future work. This thesis also contains six appendices. Appendix 1 contains an article from a scientific magazine that I wrote to highlight the importance and applications of the EW and AW to characterize XPS narrow scans. Appendices 2-5 are application notes I wrote on separations I performed on a nanodiamond based HPLC column. Finally, Appendix 6 describes the ToF-SIMS analysis of the tungsten species in the nanodiamond samples characterized in Chapter 7.

<p>This work focuses on the surface and interfacial characterisation of silane films of a non-organofunctional silane, 1,2-bis(triethoxysilyl)ethane (BTSE), and an organofunctional silane, γ-mercaptopropyltrimethoxysilane (γ-MPS), deposited on Al, Zn and Al-43.4Zn-1.6Si (AlZn) alloy coated steel. Furthermore, a tribological study of a vegetable oil coupled to an aluminium surface pre-treated with γ-MPS is presented and, finally, the tribological response of thin organic coatings exposed to a sliding contact as evaluated by surface analysis is discussed. The main analyses techniques used were time-of-flight secondary ion mass spectrometry (ToF-SIMS), Auger electron spectroscopy (AES) and x-ray photoelectron spectroscopy (XPS). </p><p>The results presented in this thesis show that the combination of ToF-SIMS, AES and XPS analysis can be used in order to obtain useful and complementary information regarding the surface and interface characteristics of silane films and organic coatings deposited on metal substrates.</p><p>The major result regarding the silane films is that the silane film composition/structure is not dependent of pH-value during deposition or type of metal substrate. The presence of Si-O-Me ion fragments in the ToF-SIMS spectra is a strong indication that a chemical interaction between the silane film and the metal substrate exists. Furthermore, it has been shown that it is possible to bond a vegetable oil to a thiol functionalised aluminium surface and to produce a coating thick enough to obtain desired friction and wear characteristics. Finally, the use of ToF-SIMS analysis makes it possible to distinguish between mechanical and tribochemical wear mechanisms.</p>

Le but de ce travail est d’étudier l’effet de la vapeur d’eau contenue dans le plasma sur la composition et la vitesse de dépôt des couches minces d’oxynitrures de chrome déposées par pulvérisation cathodique magnétron réactive avec l’air contenant différentes teneurs en vapeur d’eau (humidité relative). Les techniques d’analyses par faisceau d’ions énergétiques : RBS et réactions nucléaires nous ont permis de déterminer les concentrations relatives des éléments déposés. Les profils d’hydrogène et d’azote ont été déterminés par RNRA et Tof- SIMS. La liaison chimique a été identifiée par LEEIXS et XPS. Les mesures XPS ont dévoilé la présence d’une phase autre que Cr, CrN, Cr2O3 et CrO2 ; cette nouvelle phase possède une stoechiométrie (CrO2)3-N. La teneur en Cr et ses composés varie en fonction du flux et de l’humidité relative de l’air. En mode métallique de la pulvérisation cathodique, la stoechiométrie Cr2O3 est majoritaire en coexistence avec de faibles teneurs et CrN, CrO2 et (CrO2)3-N alors qu’en mode composé, c’est la stoechiométrie CrO2 qui prédomine./ The aim of this work is to study the stoichiometry of chromium oxynitride thin films deposited by reactive magnetron sputtering in presence of air with various relative humidities. Ion Beam Analysis methods: RBS (Rutherford Backscattering Spectroscopy) and resonant nuclear reaction (RNRA) were used to determine the thickness and the composition of the films. Hydrogen and nitrogen profiles were obtained by RNRA and Tof-SIMS. The chemical bonds were investigated by XPS and LEEIXS. The chromium metallic and chromium compounds concentrations were measured versus the flow and relative humidity of the air. During sputtering in metallic mode, Cr2O3 stoichiometry is observed with low contents of CrN, CrO2 and (CrO2)3-N whereas in compound mode the CrO2 stoichiometry predominates.

This work focuses on the surface and interfacial characterisation of silane films of a non-organofunctional silane, 1,2-bis(triethoxysilyl)ethane (BTSE), and an organofunctional silane, γ-mercaptopropyltrimethoxysilane (γ-MPS), deposited on Al, Zn and Al-43.4Zn-1.6Si (AlZn) alloy coated steel. Furthermore, a tribological study of a vegetable oil coupled to an aluminium surface pre-treated with γ-MPS is presented and, finally, the tribological response of thin organic coatings exposed to a sliding contact as evaluated by surface analysis is discussed. The main analyses techniques used were time-of-flight secondary ion mass spectrometry (ToF-SIMS), Auger electron spectroscopy (AES) and x-ray photoelectron spectroscopy (XPS). The results presented in this thesis show that the combination of ToF-SIMS, AES and XPS analysis can be used in order to obtain useful and complementary information regarding the surface and interface characteristics of silane films and organic coatings deposited on metal substrates. The major result regarding the silane films is that the silane film composition/structure is not dependent of pH-value during deposition or type of metal substrate. The presence of Si-O-Me ion fragments in the ToF-SIMS spectra is a strong indication that a chemical interaction between the silane film and the metal substrate exists. Furthermore, it has been shown that it is possible to bond a vegetable oil to a thiol functionalised aluminium surface and to produce a coating thick enough to obtain desired friction and wear characteristics. Finally, the use of ToF-SIMS analysis makes it possible to distinguish between mechanical and tribochemical wear mechanisms.

Cluster ToF-SIMS (time-of-flight secondary ion mass spectrometry) operated in the event-by-event bombardment/detection mode has been applied to: 1) evaluate and screen the manufacturing quality of step-wise prepared micropatterned biointerfaces; 2) quantify the binding density of Au nanoparticles (AuNPs)-antiCD4 conjugates selectively attached on the cell surface; 3) elucidate the biological interaction of proteins and molecules by quantifying the fractional coverage of immobilized biomolecules; 4) enhance the accuracy of secondary ion identification of specific molecules. Briefly, our method consists of recording the secondary ions, SIs, individually emitted from a single projectile impact (C60 1,2+, Au400 +4). From the set of individual mass data, we select events where a specific SI was detected. The selected records reveal the SIs co-ejected from the nanovolume impacted by an individual cluster projectile from an emission area of 10-20 nm in diameter and an emission depth of 5-10 nm. The approach for quantifying the number of AuNPs or that of specific nanodomains is via the concept of the fractional coverage. The latter is the ratio of the effective number of projectile impacts on a specified sampling area (Ne) to the total number of impacts (No). The methodology has been validated with the determination of the number of antibody-AuNP conjugates on a cell, i.e. the number of disease related antigens on a cell via their specific binding sites with the AuNP-labeled antibodies. The number of AuNP-antibodies measured, ~42000 per cell, is in good agreement with literature results. The fractional coverage concept was also used to quantify several variants of biointerfaces. An example is the quantification of biotin and avidin immobilization as a function of the composition of silane substrates. The data collected in the event-by-event bombardment/detection mode expands the scope and quality of analytical information. One can identify SIs co-emitted with two specified SIs (double coincidence mass spectrometry) to inspect a specific stratum of a biointerface. A further refinement is the selection of events meeting a double coincidence emission condition. This mode enables the identification of nano-object of a few nm in size, which eliminates (anticoincidence) interferences from substrates.

In this work the methodology is developed to study spreading and penetration of a custom ink-jet ink formulation, containing hydrophobic cationic crystal violet dye, ethoxylated surfactant, and ink solvent marked by lithium salt. With a new technique utilizing Time-of-Flight Secondary Ion Mass Spectrometry imaging, the ink component distribution and its effect on print quality of uncoated and coated papers are evaluated. High spatially resolved images obtained by ToF-SIMS illustrate differentiation of individual ink components, with ink solvent spreading more than the dye in all paper samples. Uncoated papers show greater and more irregular spreading leading to poor edge definition and poor print quality. Large separation of the dye from the solvent in the vertical direction of multipurpose and photo glossy ink-jet paper suggests a step-wise progression of ink penetration: ink flows through a more porous structure in the x-direction before advancing to the next sublayer in the z-direction of paper.

In this work the methodology is developed to study spreading and penetration of a custom ink-jet ink formulation, containing hydrophobic cationic crystal violet dye, ethoxylated surfactant, and ink solvent marked by lithium salt. With a new technique utilizing Time-of-Flight Secondary Ion Mass Spectrometry imaging, the ink component distribution and its effect on print quality of uncoated and coated papers are evaluated. High spatially resolved images obtained by ToF-SIMS illustrate differentiation of individual ink components, with ink solvent spreading more than the dye in all paper samples. Uncoated papers show greater and more irregular spreading leading to poor edge definition and poor print quality. Large separation of the dye from the solvent in the vertical direction of multipurpose and photo glossy ink-jet paper suggests a step-wise progression of ink penetration: ink flows through a more porous structure in the x-direction before advancing to the next sublayer in the z-direction of paper.

Biocatalysts are important tools for harnessing the potential of wood fibres since they can perform specific reactions with low environmental impact. Challenges to bioconversion technologies as applied to wood fibres include low accessibility of plant cell wall polymers and the heterogeneity of plant cell walls, which makes it difficult to predict conversion efficiencies. White-rot fungi are among the most efficient degraders of plant fibre (lignocellulose), capable of degrading cellulose, hemicellulose and lignin. Phanerochaete carnosa is a white-rot fungus that, in contrast to many white-rot fungi that have been studied to date, was isolated almost exclusively from fallen coniferous trees (softwood). While several studies describe the lignocellulolytic activity of the hardwood-degrading, model white-rot fungus Phanerochaete chrysosporium, the lignocellulolytic activity of P. carnosa has not been investigated. An underlying hypothesis of this thesis is that P. carnosa encodes enzymes that are particularly well suited for processing softwood fibre, which is an especially recalcitrant feedstock, though a major resource for Canada. Moreover, given the phylogenetic similarity of P. carnosa and P. chrysosporium, it is anticipated that the identification of pertinent enzymes for softwood degradation can be more easily conducted. In particular, this project describes the characterization of P. carnosa in terms of the growth conditions that support lignocellulolytic activity, the effect of enzymes secreted by P. carnosa on the chemistry of softwood feedstocks, and the characterization of the corresponding secretome using proteomic techniques. Through this study, cultivation methods for P. carnosa were established and biochemical assays for protein activity and quantification were developed. Analytical methods, including FTIR and ToF-SIMS were used to characterize wood samples at advancing stages of decay, and revealed preferential degradation of lignin in the early stages of growth on all softwoods analyzed. Finally, an in depth proteomic analysis of the proteins secreted by P. carnosa on spruce and cellulose established that similar sets of enzyme activities are elicited by P. carnosa grown on different lignocellulosic substrates, albeit to different expression levels.

Biocatalysts are important tools for harnessing the potential of wood fibres since they can perform specific reactions with low environmental impact. Challenges to bioconversion technologies as applied to wood fibres include low accessibility of plant cell wall polymers and the heterogeneity of plant cell walls, which makes it difficult to predict conversion efficiencies. White-rot fungi are among the most efficient degraders of plant fibre (lignocellulose), capable of degrading cellulose, hemicellulose and lignin. Phanerochaete carnosa is a white-rot fungus that, in contrast to many white-rot fungi that have been studied to date, was isolated almost exclusively from fallen coniferous trees (softwood). While several studies describe the lignocellulolytic activity of the hardwood-degrading, model white-rot fungus Phanerochaete chrysosporium, the lignocellulolytic activity of P. carnosa has not been investigated. An underlying hypothesis of this thesis is that P. carnosa encodes enzymes that are particularly well suited for processing softwood fibre, which is an especially recalcitrant feedstock, though a major resource for Canada. Moreover, given the phylogenetic similarity of P. carnosa and P. chrysosporium, it is anticipated that the identification of pertinent enzymes for softwood degradation can be more easily conducted. In particular, this project describes the characterization of P. carnosa in terms of the growth conditions that support lignocellulolytic activity, the effect of enzymes secreted by P. carnosa on the chemistry of softwood feedstocks, and the characterization of the corresponding secretome using proteomic techniques. Through this study, cultivation methods for P. carnosa were established and biochemical assays for protein activity and quantification were developed. Analytical methods, including FTIR and ToF-SIMS were used to characterize wood samples at advancing stages of decay, and revealed preferential degradation of lignin in the early stages of growth on all softwoods analyzed. Finally, an in depth proteomic analysis of the proteins secreted by P. carnosa on spruce and cellulose established that similar sets of enzyme activities are elicited by P. carnosa grown on different lignocellulosic substrates, albeit to different expression levels.