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L'héparine (Hp) est un polysaccharide sulfaté appartenant à la famille des glycosaminoglycanes (GAGs), et est constitué d'unités de répétition disaccharidiques composées d’un acide hexauronique lié par une liaison α1→4 à un résidu hexosamine. La sulfatation de ce polysaccharide peut avoir lieu sur les positions 6-O ou N du glucosamine, mais également sur la position 2-O de l'acide hexauronique. En général, les GAGs sont O-liés aux chaînes latérales des protéoglycanes, et sont associés à un nombre important d'activités physiologiques, généralement reliées à leur interaction avec diverses protéines. Dans certains cas, cette interaction peut-être influencée par la liaison à ces complexes Hp/protéine d'ions métalliques naturels. Ceux-ci influencent l'affinité, la spécificité et la stabilité de ces complexes. En dépit de sa pertinence, le mécanisme par lequel un cation métallique module l'activité de l'héparine au sein des complexes Hp-protéine, reste largement méconnu.Un éventail de stratégies et d'outils ont été développés afin de faciliter la détermination des structures primaires des biomolécules par spectrométrie de masse en tandem (MS/MS). En effet, la caractérisation structurale de l'héparine sulfatée et de ses complexes métalliques a été soutenue par le développement de techniques de spectrométrie de masse. Dans certains cas, il a été observé que lors de l'activation par dissociation induite par collision (CID), certains de ces isomères d'héparine partageaient à peu près les mêmes schémas de fragmentation, compliquant de ce fait le processus d'identification de ces composés. Néanmoins, des études réalisées au LAMBE ont montré que la réactivité en phase gazeuse des ions métalliques pouvait aider à la différenciation d'isomères saccharidiques. Ces études peuvent être utiles non seulement du point de vue purement analytique, mais également parce que le comportement différent des isomères envers un métal donnée conduit à informations sur le processus d'interaction Hp/Métal mis en jeu. Cela peut s’avérer important pour interpréter les mécanismes biologiques mentionnées auparavant.Dugourd et al ont récemment rapporté les spectres optiques et les motifs de photodissociation de différents oligosaccharides sous irradiation UV. En terme de chemins de fragmentation, il a été observé que les spectres de photodissociation Ultraviolet (UVPD) apparaissaient être plus informatifs que la CID en raison de clivages à travers les cycles supplémentaires, qui fournissent une information sur la position du groupe sulfate. Le spectre optique des disaccharides sulfatés est caractérisé par une bande large et intense centrée vers 240 nm. Suite à ces résultats, nous nous sommes intéressés au couplage de la spectroscopie optique et des calculs théoriques pour les disaccharides d'héparine, et avons employé la spectroscopie UVPD afin d’obtenir des informations complémentaires sur les interactions de ces sucres avec les métaux.Comme décrit auparavant, les processus CID représentent un outil très précieux pour la caractérisation structurale des biomolécules. Motivés par des travaux antérieurs publiés par W. Hase et K. Song, nous avons collaboré avec les groupe de R. Spezia et T. Riera afin de parvenir à une meilleure compréhension du processus MS/MS des sucres et des peptides protonés. Les mécanismes CID de modèles simples, N-Formylalanylamide (HCO-Ala-NH2) et Galactose-6-Sulfate, ont été étudiés par des simulations de dynamique moléculaire QM+MM et des expériences MS/MS. Les objectifs de cette thèse étaient les suivants: i) explorer la possibilité d'utiliser le calcium métallique à des fins analytiques ii) fournir de nouvelles données sur la nature de l’interaction Hp/Ca2+ en utilisant une stratégie multi-approches combinant plusieurs techniques expérimentales et de calculs quantiques iii) étudier le processus CID de différents systèmes par des simulations de dynamique moléculaire. / Heparin (Hp) is a sulfated polysaccharide composed of repeating dissacharide units of hexauronic acid linked (α1→4) to an hexosamine residue that belongs to the family of glycosaminoglycans (GAGs). Sulfation can occur at the 6-O and/or N-positions of the gluscosamine, as well as the 2-O position of the hexauronic acid. GAGs usually exist as the O-linked side-chains of proteoglycans, associated with numerous important physiological activities, generally related to their interaction with diverse proteins. In some cases, this interaction can be influenced by the binding of natural metal ions to these Hp/protein complexes. Their role is usually pertained to the affinity, specificity and stability of these complexes. Despite its relevance, the mechanism by which the cation modulates heparin activity in Hp-protein complexes is largely unknown. A range of strategies and tools has been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). In fact, structural characterization of heparin sulfated and its metal complexes has been sustained by the development of mass spectrometry techniques. In some cases, it was observed that upon collision-induced dissociation (CID) activation, some of these heparin-like isomers share nearly the same fragmentation patterns, turning the identification process into a complicated step. Nevertheless, a few years ago, our group showed that the gas-phase reactivity of metal ions can shed light into differentiating isomeric saccharides. These studies can be useful for two reasons: just for purely analytical purposes and also because the different behavior of the isomers towards the metal gives information about the Hp/Metal interaction. This might be important to explain the biological considerations mentioned before. Moreover, Dugourd et al recently reported the optical spectra and photodissociation patterns of different Hp oligosaccharides under UV irradiation. In terms of fragmentation pathways, it was observed that Ultraviolet photodissociation (UVPD) spectra appear to be more informative than CID due to additional cross-ring cleavages that provide information about the sulfate group location. Remarkably, the optical spectrum is characterized by an intense broad band centered at 240 nm for sulfated disaccharides. Following these findings, we became interested in coupling optical spectroscopy and theoretical calculations in heparin disaccharides and developing an alternative strategy to characterize these metal interactions. As described before, CID processes are commonly used in several fields and represent a very valuable tool in protein or carbohydrate characterization. Motivated by previous work published by W. Hase and K. Song, we collaborated with R.Spezia and T. Riera’s group in order to achieve a better understanding of the MS/MS process of protonated peptides and sugars. CID mechanisms of simple models, N-Formylalanylamide (HCO-Ala-NH2) and Galactose-6-Sulfate, were studied by QM+MM chemical dynamics simulations and MS/MS experiments.

The goal of the thesis is to evaluate if developed phase chemical process models for cement clinker and lime production processes are reliable to use as predictive tools in understanding the changes when introducing sustainability measures. The thesis describes the development of process simulation models in the application of sustainability measures as well as the evaluation of these models. The motivation for developing these types of models arises from the need to predict the chemical and the process changes in the production process, the impact on the product quality and the emissions from the flue gas. The main chemical reactions involving the major elements (calcium, silicon, aluminium and iron) are relatively well known. As for the minor elements, such as sodium and potassium metals, sulphur, chlorine, phosphorus and other trace elements, their influence on the main reactions and the formation of clinker minerals is not entirely known. When the concentrations of minor and trace elements increase due to the use of alternative materials and fuels, a model that can accurately predict their chemistry is invaluable. For example, the shift towards using less carbon intensive fuels and more biomass fuels often leads to an increased phosphorus concentration in the products. One way to commit to sustainable development methods in cement clinker and lime production is to use new combustion technologies, which increase the ability to capture carbon dioxide. Introducing oxy-fuel combustion achieves this, but at the same time, the overall process changes in many other ways. Some of these changes are evaluated by the models in this work. In this thesis, a combination of the software programs Aspen Plus™ and ChemApp™ constitutes the simulation model. Thermodynamic data from FACT are evaluated and adjusted to suit the chemistry of cement clinker and lime. The resulting model has been verified for one lime and two cement industrial processes. Simulated scenarios of co-combustion involving different fuels and different oxy-fuel combustion cases in both cement clinker and lime rotary kiln production are described as well as the influence of greater amounts of phosphorus on the cement clinker quality.

Introduction of soft ionization techniques, such as electrospray ionization (ESI), has resulted in extensive use of mass spectrometry based techniques to study biomolecules in the gas phase. Despite thorough studies of the gas-phase chemistry of even-electron biomolecules, the examination of their odd-electron counterparts has to this point been much less extensive due to the inefficiency of ESI in generating such species. Among various methods that could be employed to generate and study odd-electron biomolecules in the gas phase, redox processes involving metal ions and homolytic cleavage of metallated amino acid or peptide derivatives would be attractive from a chemical perspective since, in principle, a wide range of metals and biomolecules or biomolecule derivatives could be explored. An important aspect of these approaches is that they can be carried out on a wide range of tandem mass spectrometers equipped with electrospray ionization and collision induced dissociation capabilities. (For complete abstract open document)

<div>Heightened awareness regarding the implication of disturbances in lipid metabolism with respect to prevalent human-related pathologies demands analytical techniques that provide unambiguous structural characterization and accurate quantitation of lipids in complex biological samples. The diversity in molecular structures of lipids along with their wide range of concentrations in biological matrices present formidable analytical challenges. Modern mass spectrometry (MS) offers an unprecedented level of analytical power in lipid analysis, as many advancements in the field of lipidomics have been facilitated through novel applications of and developments in electrospray ionization tandem mass spectrometry (ESI-MS/MS). ESI allows for the formation of intact lipid ions with little to no fragmentation and has become widely used in contemporary lipidomics experiments due to its sensitivity, reproducibility, and compatibility with condensed-phase modes of separation, such as liquid chromatography (LC). Owing to variations in lipid functional groups, ESI enables partial chemical separation of the lipidome, yet the preferred ion-type is not always formed, impacting lipid detection, characterization, and quantitation. Moreover, conventional ESI-MS/MS approaches often fail to expose diverse subtle structural features like the sites of unsaturation in fatty acyl constituents or acyl chain regiochemistry along the glycerol backbone, representing a significant challenge for ESI-MS/MS. To overcome these shortcomings, various charge manipulation strategies, including charge-switching, have been developed to transform ion-type and charge state, with aims of increasing sensitivity and selectivity of ESI-MS/MS approaches. Importantly, charge manipulation approaches afford enhanced ionization efficiency, improved mixture analysis performance, and access to informative fragmentation channels.</div><div><br></div><div>Here, gas-phase ion/ion chemistry was developed to transform conventional lipid ion types formed upon direct ESI into structurally informative ion types entirely within the mass spectrometer. Explicitly, gas-phase anionic to cationic charge switching chemistries were first developed for fatty acid profiling, as unambiguous structural elucidation and relative quantitation were achieved. Extensions of this gas-phase charge switch derivatization strategy to glycerophospholipids (GPLs), including ether GPLs, and fatty acid esters of hydroxy fatty acids demonstrates the versatility and flexibility of the ion/ion platforms. In an alternate approach, gas-phase proton transfer ion/ion reactions were employed for the gas-phase separation, concentration, and identification of cardiolipins (CLs) from total lipid extract. In total, benefits for lipid structure elucidation and enhanced detection efficiencies have been demonstrated utilizing the reported gas-phase ion/ion platforms.</div>

Title: Study of C-C coupling of dienes catalyzed by ruthenium (II) complexes. Author: Bc. Eva Hanikýřová Department: Department of Organic Chemistry Supervisor: Mgr. Jana Roithová, Ph.D. Abstract Transition metal catalyzed cycloadditions have contributed extensively to organic synthesis. The use of ruthenium complexes in those reactions gain importance due to their demonstrated ability in the catalytic carbon-carbon bond formations via ruthenacycle intermediates. In our studies, we have concentrated on the interaction between ruthenium (II) and alkenes using mass spectrometry with electrospray ionization. This technique allows to investigate ruthenium complexes in the ionized states, and allows to investigate these structures by using MS/MS analyse. Our experimental research was complemented by quantum chemical calculations using Density functional theory. The research leads to a more detailed understanding to Ruthenium complexes with unsaturated hydrocarbons reaction mechanism. Key words Gas-phase chemistry, Reaction mechanisms, Electrospray Ionization, Catalyst, [CpRu(CH3CN)3]PF6, Mass Spectrometry

Presently, much research has been completed focusing on metal coordination complexes in the liquid phase but very little in terms of the gas phase. The purpose of this research is to further investigate these conditions and learn more about the reactions that can occur using Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry (ESI QToF MS). This research focuses on Nickel (II) and Iron (III) Nitrate solutions in combination with five ligands: 2,2’-Bipyridine, 4,4’-Bipyridine, 2,2’-Bipyridine-4,4’-Dicarboxylic Acid, 1,10-Phenanthroline and the Baker Group’s SNS Ligand. Observations of these complexes were restricted to the monocations. Those combinations that successfully coordinated in the gas phase were subjected to further analysis to determine their fragmentation pathways under specific conditions. To investigate their interactions, studies were conducted using three different mixing techniques. These techniques included a pre-mixed single-spray solution, a dual-spray injection method, and the TRESI (time-resolved electrospray ionization) method. By using all three methods, the compounds’ ability to react in solution over time can be compared to real-time mixing in both the gas and liquid phases, via dual-spray and TRESI techniques respectively. Further experimentation took place on target complexes, created by each of the ten combinations of starting compounds, to further investigate the gas phase properties and fragmentation patterns that exist. It was observed that most experiments with the Nickel (II) Nitrate solution were successful with all three methods, while the Iron (III) Nitrate however created some problems. In general, single-spray analysis gave the best results compared to dual-spray, which was ineffective for some combinations, particularly the 2,2’-Bipyridine-4,4’-Dicarboxylic Acid and SNS ligands. It was found that both the 2,2’-Bipyridine and 4,4’-Bipyrdine combinations produced very similar results despite their respective bidentate and bridging coordination tendencies. The TRESI method provided limited information due to the delayed reaction times with some combinations. Overall, this work proved useful in its ability to compare metal coordination complex formation in solution and gas phases.