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Gas phase studies of the secondary structure of peptides and proteins have become increasingly popular as they offer distinct advantages of small sample usage and experiment time. The mass spectrometer is key to performing these experiments as ions can be manipulated based on their mass to charge ratio. Combining mass spectroscopy with laser spectroscopy birthed a new method for determining gas phase structures, ion spectroscopy. This document begins with an overview of secondary structure analysis using several techniques in solid, liquid, and gas phases. It then describes how ion spectroscopy can also be utilized to obtain detailed fingerprint infrared spectra of ions which are then matched with density functional theory calculations to determine the 3D structure of an ion. After describing the instrumental apparatus, four examples of the use of ion spectroscopy to determine structure are presented. The first study looked to understand the effect of increased flexibility around a proline residue in the diastereomeric pair YAD/LPGA and how a simple switch to glycine can greatly affect beta turn formation in peptides. The next three studies describe an attempt to form a single turn alpha helix in the gas phase using a highly stable tethered peptide motif. Failure to form the single turn helix in the first study led to an interesting examination of the use of computational chemistry to lead the synthesis of peptides where a specific structure is required. After observing the single turn helix attention is then diverted to expanding and controlling its handedness via stereochemistry. In all, this document will guide the reader through the methods and experiments possible with ion spectroscopy. <br>

Thesis (MSc (Wine Biotechnology))--University of Stellenbosch, 2007. / The discrimination between wine yeast strains as well as between their fermented wines has been investigated in this pilot study. The study was divided in two parts, the first to investigate the discrimination between wines fermented with five different Saccharomyces cerevisiae yeast strains, analysed by gas chromatography (GC) and Fourier transform infrared spectroscopy (FTIR) and the second part to investigate discrimination between wine yeast strains in different liquid media and in dried form using FTIR in transmission and attenuated total reflectance (ATR) modes. Wines from three cultivars (Clairette Blanche, Pinotage and Cabernet Sauvignon) that were fermented by five Saccharomyces cerevisiae yeast strains (VIN13, WE372, VIN13-EXS, VIN13-PPK and ML01) were analysed by GC and FTIR. This analysis was done on individual sample sets that consisted of the wines of each of the mentioned cultivars and also on samples drawn throughout the ageing process of these wines. The data obtained were analysed by PLS-Discrimination (PLS-discrim), a chemometric method. Using the data from both the analytical methods, discrimination was observed between wines fermented with different yeast strains in each of the two vintages (2005 and 2006) for all the cultivars. When combining the data from the two vintages no discrimination could be observed between the fermented wines. The discrimination of the fermented wines was found to be similar when using data from GC and FTIR, respectively. Since analysis with FTIR is considerably faster than analysis by GC, it would be recommended that FTIR is used for future studies of similar nature. Combining the samples into one set consisting of wines fermented with commercial wine yeast strains and wines fermented from closely related wine yeast strains (the parental strain and two genetically modified versions thereof (VIN13, VIN13-EXS and VIN13- PPK), those fermented with closely related stains did not show good discrimination from each other. Discrimination was found between wines fermented with genetically modified (GM) wine yeast strains and those fermented with non-GM wine yeast strains. This was done on a limited number of yeast strains and a larger study is needed to confirm these results. As this is the first study of this nature and differences seen could be as result of the different phenotypes. It was shown that it is possible to use both FTIR-transmission and FTIR-ATR (attenuated total reflectance) to discriminate between different wine yeast strain phenotypes. It was shown that when using FTIR-transmission there is discrimination between yeast samples suspended in yeast-peptone-dextrose (YPD) and in water. Dried yeast samples could be discriminated when the yeast samples were in a granular, powder form or in a pellet form, using FTIR-ATR. It was possible to discriminate between the closely related yeast strain phenotypes using FTIR-ATR. In this pilot study it was shown that there can be discriminated between different wine yeast strains and also between the wines fermented with different wine yeast strains. It is recommended that further studies be conducted to refine and expand the study.

Ternary lipid mixtures composed of cholesterol, saturated (frequently with sphingosine backbone), and unsaturated phospholipids show stable phase separation and are often used as model systems of lipid rafts. Yet, their ability to reproduce raft properties and function is still debated. We investigated the properties and functional aspects of three lipid raft model systems of varying degrees of biological relevance – PSM/POPC/Chol, DPPC/POPC/Chol, and DPPC/DOPC/Chol – using 2H solidstate nuclear magnetic resonance (NMR) spectroscopy, fluorescence microscopy, and atomic force microscopy. While some minor differences were observed, the general behavior and properties of all three model mixtures were similar to previously investigated influenza envelope lipid membranes, which closely mimic the lipid composition of biological membranes. For the investigation of the functional aspects, we employed the human N-Ras protein, which is posttranslationally modified by two lipid modifications that anchor the protein to the membrane. It was previously shown that N-Ras preferentially resides in liquid-disordered domains and exhibits a time-dependent accumulation in the domain boundaries of influenza envelope lipid membranes. For all three model mixtures, we observed the same membrane partitioning behavior for N-Ras. Therefore, we conclude that even relatively simple models of raft membranes are able to reproduce many of their specific properties and functions.

Laser-Induced Breakdown Spectroscopy (LIBS) is an analytical technique that has the potential to detect all the elements present in the periodic table. The limit of detection can go below a few ppm and this regardless of the physical phase of the analyzed sample (solid, liquid or gas). Its simplicity of use, its rapidity to get results and its versatility provide this technique with attractive features. The technique is currently developed for applications in a large number of domains such as online control, spatial explorations and the environment. However the weakness of the LIBS technique, compared to other more conventional ones, is still its difficulty in providing reliable quantitative results, especially for inhomogeneous and complex matrix such as organic or biological materials. The work presented in this thesis includes a study of the properties of plasma induced from different organic materials. First, a study of the plasma induced on the surface of a Nylon sample at short time delays (~ns) was carried out using the time-resolved shadowgraph technique for different experimental parameters (laser energy, pulse duration, wavelength). Then, a complete diagnostics of the plasma was performed using the plasma emission spectroscopy. A detailed analysis of the emission spectra at different detection delays allowed us to determine the evolution of the temperatures of the different species in the plasma (atoms, ions and molecules). The homogeneity and the local thermodynamic equilibrium within the plasma was then experimentally checked and validated. We demonstrated that the optimisation of the signalto- noise ratio and a quantitative procedure, such as the calibration-free LIBS, can be put in place within a properly chosen detection window. In our experiments, such optimised detection configuration was further employed to record LIBS spectra from different families of polymer in order to identify and classify them. For this purpose, the chemometrics procedure of artificial neural networks (ANN) was used to process the recorded LIBS spectroscopic data. The promising results obtained in this thesis makes LIBS stand out as a potentially useful tool for real time identification of plastic materials. Finally, this work can also be considered as a base for the further studies of more complex materials such as biological tissues with LIBS.

La spectrométrie de plasma induit par laser, plus connue sous le nom de LIBS (l’acronyme du terme en anglais Laser-Induced Breakdown Spectroscopy) est une technique analytique qui permet la détection de l’ensemble des éléments du tableau périodique avec des limites de détection de l’ordre du ppm et ceci sur tous types d’échantillons qu’ils soient liquides, solides ou gazeux. Sa simplicité de mise en œuvre, sa rapidité et sa versatilité en font une technique très attractive avec un fort potentiel en termes d’applications que ce soit pour le contrôle en ligne, l’environnement ou l’exploration spatiale. Son point faible reste cependant son manque de fiabilité dans l’analyse quantitative, en particulier lors de l’étude d’échantillons hétérogènes ou de matrices complexes telles que les matrices organiques. Ce travail de thèse propose une étude des propriétés des plasmas induit par laser sur différentes familles de polymères. Une étude du plasma au temps court (~ns) par ombroscopie est tout d’abord présentée, ceci pour différents paramètres expérimentaux (énergie laser, durée d’impulsion, longueur d’onde). Un diagnostic complet du plasma par spectrométrie d’émission est ensuite détaillé pour différents délais de détection et montre que la mesure des températures des différentes espèces du plasma (atomique, ionique et moléculaire) permet de vérifier, dans certaines conditions, les hypothèses d’homogénéité et de l’équilibre thermodynamique local. Ceci permet alors la mise en place de procédures quantitatives telles que la méthode dite sans calibration (calibration free LIBS) tout en optimisant le rapport signal sur bruit de la mesure LIBS. Dans nos expériences cette optimisation est mise à profit pour l’identification de différentes familles de polymères en utilisant, pour le traitement des données de la spectroscopie LIBS, la méthode chimiométrique des réseaux de neurones artificiels. Les résultats obtenus, très prometteurs, permettent d’envisager l’utilisation de la LIBS pour l’identification en temps réel des matières plastiques sur chaine de tri. Par ailleurs et de manière plus générale, ce travail pourrait constituer une base solide pour aller étudier d’autres matériaux organiques plus complexes tels que des tissus biologiques. / Laser-Induced Breakdown Spectroscopy (LIBS) is an analytical technique that has the potential to detect all the elements present in the periodic table. The limit of detection can go below a few ppm and this regardless of the physical phase of the analyzed sample (solid, liquid or gas). Its simplicity of use, its rapidity to get results and its versatility provide this technique with attractive features. The technique is currently developed for applications in a large number of domains such as online control, spatial explorations and the environment. However the weakness of the LIBS technique, compared to other more conventional ones, is still its difficulty in providing reliable quantitative results, especially for inhomogeneous and complex matrix such as organic or biological materials. The work presented in this thesis includes a study of the properties of plasma induced from different organic materials. First, a study of the plasma induced on the surface of a Nylon sample at short time delays (~ns) was carried out using the time-resolved shadowgraph technique for different experimental parameters (laser energy, pulse duration, wavelength). Then, a complete diagnostics of the plasma was performed using the plasma emission spectroscopy. A detailed analysis of the emission spectra at different detection delays allowed us to determine the evolution of the temperatures of the different species in the plasma (atoms, ions and molecules). The homogeneity and the local thermodynamic equilibrium within the plasma was then experimentally checked and validated. We demonstrated that the optimisation of the signalto- noise ratio and a quantitative procedure, such as the calibration-free LIBS, can be put in place within a properly chosen detection window. In our experiments, such optimised detection configuration was further employed to record LIBS spectra from different families of polymer in order to identify and classify them. For this purpose, the chemometrics procedure of artificial neural networks (ANN) was used to process the recorded LIBS spectroscopic data. The promising results obtained in this thesis makes LIBS stand out as a potentially useful tool for real time identification of plastic materials. Finally, this work can also be considered as a base for the further studies of more complex materials such as biological tissues with LIBS.

Ternary lipid mixtures composed of cholesterol, saturated (frequently with sphingosine backbone), and unsaturated phospholipids show stable phase separation and are often used as model systems of lipid rafts. Yet, their ability to reproduce raft properties and function is still debated. We investigated the properties and functional aspects of three lipid raft model systems of varying degrees of biological relevance – PSM/POPC/Chol, DPPC/POPC/Chol, and DPPC/DOPC/Chol – using 2H solidstate nuclear magnetic resonance (NMR) spectroscopy, fluorescence microscopy, and atomic force microscopy. While some minor differences were observed, the general behavior and properties of all three model mixtures were similar to previously investigated influenza envelope lipid membranes, which closely mimic the lipid composition of biological membranes. For the investigation of the functional aspects, we employed the human N-Ras protein, which is posttranslationally modified by two lipid modifications that anchor the protein to the membrane. It was previously shown that N-Ras preferentially resides in liquid-disordered domains and exhibits a time-dependent accumulation in the domain boundaries of influenza envelope lipid membranes. For all three model mixtures, we observed the same membrane partitioning behavior for N-Ras. Therefore, we conclude that even relatively simple models of raft membranes are able to reproduce many of their specific properties and functions.

Ce travail s'inscrit dans le cadre d'études de structures nucléaires réalisées en utilisant des réactions de fission induites par neutrons froids. Il décrit successivement les résultats d'une étude sur des noyaux ayant un nombre de neutrons N=50-60, sur le développement d'un marqueur d'événements de fission et enfin sur la production de l'isomère Pt-195m. Chacun des différents sous-thèmes trouve son origine dans la campagne EXILL qui s'est déroulée en 2012-2013 et durant laquelle un spectromètre de grande efficacité pour la détection des rayonnements γ (EXOGAM) a été utilisé auprès du réacteur à haut flux de neutrons de l'Institut Laue-Langevin (ILL). Dans la première partie de cette thèse, les noyaux d'intérêt ont été produits par fission induites par des neutrons sur les cibles fissiles U-235 et Pu-241. Des méthodes de spectroscopie γ ont été appliquées pour l'identification des fragments de fission, l'attribution des transitions γ à un noyau et l'analyse des durées de vie moyenne des états excités. L'analyse des durées de vie moyenne des états excités dans la plage de quelques picosecondes à quelques nanosecondes a été réalisée en utilisant deux méthodes complémentaires. Dans les deux cas, il s'agit de réaliser un spectre en temps construit à partir de la coincidence entre une transition qui alimente le niveau mesuré et une transition qui le désexcite. Les durées de vie moyenne pour les noyaux Kr-92, Kr-93 et Zr-101 sont présentées. Dans la seconde partie, les premiers résultats du développement d'un nouveau détecteur pour la discrimination des fragments de fission sont présentés. Ce marqueur d'événements de fission est destiné à être utilisé sur le spectromètre FIssion Prompt Product γ-ray Spectrometer (FIPPS) de l'ILL. Dans le cadre de cette étude, deux conceptions de détecteurs différentes, basées sur un scintillateur en plastique solide et un scintillateur liquide organique, ont été testées. Dans la troisième partie, la possibilité de la population spécifique de l'isomère de spin dans Pt-195 est examinée au regard particulièrement de son utilisation en tant que radio-isotope en médecine nucléaire. Une telle activation spécifique pourrait être réalisée grâce à l'existence d'états excités dont la structure permettrait une population ciblée dans le cas de l'utilisation de réactions de photo-excitation. La recherche de tels états a été initiée lors d'une expérience de capture de neutrons à EXILL dans laquelle des états potentiels ont été identifiés. L'activation de l'isomère par ces états a ensuite été testée avec des réactions photonucléaires à l'aide du faisceau haute intensité disponible auprès de l'installation γ HIGS de TUNL (Triangle Universities Nuclear Laboratory, Duke, USA). / Within the scope of atomic nuclear structure studies with neutron-induced reactions, this work presents the results of a fission fragment study in the N=50-60 region, the development of a fission event tagger, and the production of the isomer Pt-195m. Each of the different sub-topics has its origin in the 2012/13 EXILL campaign, where nuclear structure studies were carried out with neutron-induced reactions, and explored with a γ-efficient detector array. In the first part of this thesis, the neutron-rich region around neutron number N=50-60 was investigated with neutron-induced fission reactions on the fissile targets U-235 and Pu-241. Gamma spectroscopy methods were applied for the identification of the respective fission fragments, the assignment of γ transitions, and the analysis of lifetimes of excited states. The slope fit method as well as the recently developed generalized centroid difference method were used for the analysis of lifetimes in the low picoseconds to sub-nanoseconds range. Lifetimes for the nuclei Kr-92, Kr-93 and Zr-101 are presented. In the second part, first results of the development of a new detector for the discrimination of fission fragments are presented. This fission event tagger is intended to be used at the FIssion Product Prompt γ-ray Spectrometer (FIPPS) at the Institut Laue-Langevin. Within the scope of this study, two different detector designs, based on a solid plastic scintillator and an organic liquid scintillator, respectively, were tested. In the third part the possibility of the specific population of the spin-isomer in Pt-195 is discussed with special regard to its use as radioisotope in nuclear medicine. Such a specific activation could be realized via certain “doorway states” in photo-excitation reactions. The search for these doorway states was initiated within a neutron capture experiment at EXILL where potential states were found. The activation of the isomer via these states was tested afterwards with photonuclear reactions using the high intense γ-beam HIGS of the TUNL facility.