Proteomic studies aim to identify, quantify and characterise the full complement of proteins in a cell or organism under a defined set of conditions, and are important to our understanding of cellular mechanisms. However, such studies represent a major analytical challenge. A typical proteome analysis involves enzyme-mediated digestion of complex protein mixtures to yield an even more complex mixture of peptides. Combined reverse-phase liquid chromatography and tandem mass spectrometry is then traditionally utilised to ascertain sequence information from the characteristic peptide sequences. Analytical data derived for the peptides are employed as search terms in database searching of protein sequences derived from gene sequences. The extreme complexity of the peptide mixtures analysed means that additional novel approaches are required to fully interrogate the vast number of tandem mass spectra generated, assigning peptide identity and thereby helping to address demanding biological questions. The research reported here aims to further our understanding of both gas phase peptide/peptide fragment ion structure and peptide fragmentation behaviour using a combination of tandem mass spectrometry and ion mobility measurement.To facilitate the determination of peptide ion collision cross section, a novel standard, QCAL-IM, produced using the QconCAT strategy, has been developed to enable calibration of drift time in Travelling Wave Ion Mobility instruments. The standard facilitates empirical determination of the rotationally averaged collision cross section of any peptide/peptide fragment ion that lies within the calibration range encompassed. QCAL-IM was subsequently utilised to determine the collision cross section of a range of peptide ions produced by Lys-C and Lys-N proteolysis of ‘standard’ proteins. Data produced allowed the effect upon gas phase ion conformation through changing the location of the basic residue lysine within a peptide sequence to be assessed.The fragmentation behaviour of peptide ions produced by a variety of digestion regimes during both collision-induced dissociation (CID) and electron transfer dissociation (ETD) has also been extensively studied. The proteases trypsin and Lys-C are those typically utilised during proteomic studies and peptides produced by each have either the basic residues arginine or lysine at their carboxy-terminus. Secondary enzymatic treatment with the exoprotease carboxypeptidase B cleaves these basic residues from the C-terminus. Tandem mass spectrometric analysis of both tryptic/Lys-C peptides and their CBPB truncated analogue highlights that the dominant fragment ion series observed during both CID and ETD is determined, at least in part, by the location of such basic residues.Finally, studies were undertaken to investigate the factors which may promote/inhibit scrambling of peptide fragment ion sequence, which has recently been shown to take place during CID. The effect of modifying the gas phase basicity of the N-terminal amino acid residue is studied through a combination of derivatisation and synthesis of alternative peptide sequences. Increasing the gas phase basicity is shown to inhibit the observed sequence scrambling while promoting concomitant rearrangement/retention of a carboxyl oxygen at the C-terminus to give enhanced formation of bn+H2O product ion species.

Depuis leur découverte dans les années 90, les molécules-aimants constituent une classe de matériaux magnétiques qui a attiré l'attention du fait de leur bistabilité magnétique. Ces systèmes donnent l’espoir formidable de pouvoir stocker un bit d’information à l’échelle moléculaire. Ainsi, leur organisation dans des réseaux est devenue un enjeu essentiel en vue de leur intégration dans des dispositifs. Lors de cette thèse, l’organisation contrôlée de ces molécules par chimie de coordination en utilisant différents connecteurs s’est révélée être une stratégie de choix. Le chapitre I présente une approche théorique de ce projet de recherche. Dans ce chapitre, les propriétés de molécules-aimants, chaînes-aimants, conversion de spin et transfert d'électron sont décrits et discutés. Le chapitre II contient la bibliographie pertinente sur les réseaux de coordination à base de molécules-aimants et les systèmes photoactifs bimétalliques conténant des groupements cyanures. Le chapitre III présente l'organisation de molécules aimants[Mn4] en réseaux 1D et 2D par des liens diamagnétiques (ions chlorures) ou des liens paramagnétiques contenant des ions métalliques (NiII, MnII et CuII). Les études physiques (cristallographie par rayons X, mesuresmagnétiques et de chaleurs spécifiques) et des analyses théoriques sur ces nouveaux réseaux ont montré des propriétés magnétiques améliorées par rapport à la molécule-aimant [Mn4] isolée. Dans le chapitre IV, nous avonspréparé de nouveaux connecteurs commutables pour in fine concevoir des réseaux de molécules-aimants photomagnétiques. Une approche « building-block » a été utilisée pour obtenir un composé binucléaire de Fe et Co.Des études spectroscopiques, électrochimiques et magnétiques ont été effectuées et ont révélé sans ambiguïté une conversion de spin thermo-induite à l'état solide, et un transfert d'électron intramoléculaire assisté par protonation contrôlée en solution, accompagnés de changements optiques et magnétiques. Pour la première fois, ce nouveaucomplexe montre deux processus de commutation distincts selon son état physique et le stimulus externe utilisé. / The beginning of the 1990’s marked the discovery of Single-Molecule Magnets (SMMs), which created the hope tostore information on a single molecule due to their magnetic bistability. However, it is becoming of strategicimportance to dedicate a part of our research to their organization in order to achieve devices for the potentialapplication. During this thesis work, our strategy was to exploit coordination chemistry to organize these moleculesin a controlled way by using different types of linkers.Chapter I covers theoretical backgrounds for this research project. In this chapter, Single-Molecule Magnets(SMMs), Single-Chain Magnets (SCMs), Spin Crossover (SC) and Electron Transfer (ET) systems are described anddiscussed. Chapter II contains relevant literature on SMM-based coordination networks and photoactive cyanidobasedbimetallic systems. Chapter III presents the organization of [Mn4] SMMs in 1D and 2D networks withdiamagnetic linkers (chlorido ions) or paramagnetic linkers containing NiII, MnII, and CuII ions. The extensivephysical studies (X-ray crystallography, magnetic and heat capacity measurements, and theoretical analysis) on thesenetworks demonstrated new magnetic behavior and enhanced energy barrier compared to the isolated [Mn4] SMMs.In Chapter IV, we prepared new switchable linkers based on the cyanido-bridged Fe/Co unit, to realizephotomagnetic networks of SMMs. A rational building-block approach has been used to design these dinuclearFe/Co complexes. Extensive spectroscopic, electrochemical and magnetic characterizations have been performed tounambiguously reveal in one of the synthesized complexes the presence of a spin crossover induced by temperaturein the solid-state, and an intramolecular electron transfer assisted by controlled protonation in solution, bothaccompanied by optical and magnetic changes. For the first time, this new complex shows two distinct switchingprocesses depending on its physical state and external stimuli.

Bile acid-based cation sensors involving through space photo-induced electron transfer (PET) processes have been synthesized. In this approach, appropriate known fluorophores and aza crown ether receptor units were attached on a suitable bile acid scaffold. A through space photo induced electron transfer from N-atom of the aza 18-crown-6 to the excited pyrene was responsible for quenching of the pyrene fluorescence. A fluorescence enhancement was observed with the addition of K+ due to the inhibition of fluorescence quenching by PET mechanism. In order check the relationship between the sensitivity and the molecular structure of the sensors, four different molecules with different geometries were synthesized. The changes in the fluorescence spectra for different sensors were recorded in MeOH. The binding constants calculated by curve fitting showed that while the binding constants did not significantly vary, the sensitivities were different depending on the structure of the sensors. The modular nature of the sensor design was verified by changing the receptor module from aza-18-crown-6 to aza-15-crown-5, keeping other parts of the sensor same, to prepare a sodium selective sensor using the same principle. Fluorescence titration in MeOH confirmed the Na+ selective sensing in the presence of K+. The modular design concept was further extended by replacing the fluorophore pyrene to a coumarin derivative. Coumarin sensors showed a behavior similar to that of the pyrene sensors. In order to check the possibility of sensing metal ions in water, non ionic surfactant, Triton X-100 was chosen to dissolve the sensor in water. Fluorescence titration of the sensors showed a desired selective fluorescence enhancement with the particular metal ions. Merrifield resin and water swellable Tentagel® was used to immobilize the sensor to fabricate reusable sensor beads for detecting the metal ions in non polar solvent and water respectively. Fluorescence enhancements of the sensor beads with the metal ions confirmed the process in the immobilized solid state. K+ and Na+ selective sensor beads successfully demonstrated the fluorescence enhancement with the respective cations. This general strategy can be extended to fabricate other sensors for practical uses.

No description available.

Dans cette thèse, nous avons développé la synthèse de nouveaux matériaux magnétiques hybrides afin d’améliorer la mise en forme de ces systèmes. Une partie de notre travail a consisté à fonctionnaliser la partie organique de matériaux moléculaires possédant des propriétés magnétiques remarquables, par des groupes fonctionnels connus pour induire des phases cristal-liquide ou pour augmenter la solubilité. Nous avons réalisé la fonctionnalisation rationnelle (i) de molécules aimants (Single-Molecule Magnets, SMM), (ii) de systèmes à conversion de spin et (iii) à transfert d'électrons, induisant ainsi des matériaux plus solubles et des phases cristal liquide.Le Chapitre I présente trois classes importantes de complexes magnétiques: les molécules-aimants, les systèmes à conversion de spin et de transfert d'électrons. Afin d’illustrer les motivations de notre travail une étude bibliographique dédiée aux matériaux hybrides magnétiques est ensuit présentée. La fonctionnalisation rationnelle des SMM et des systèmes à conversion de spin, respectivement, vers des phases cristallines liquides ont été discutés dans le Chapitre II et III. De nouveaux complexes fonctionnalisés à base de Mn12, FeII/triazole et [FeII(LN2O2)(LN)2] ont été obtenus. La conservation des propriétés magnétiques après fonctionnalisation du ligand a été confirmée, mais malheureusement, ces nouveaux composés ne montrent pas de comportement mésomorphe en dessous de la température de décomposition. Le Chapitre IV porte sur la fonctionnalisation des complexes à transfert d'électrons. La fonctionnalisation du ligand alkyle confère une bonne solubilité à ces complexes, et le comportement commutable activé thermiquement à l’état solide a ainsi pu être transféré à des solutions diluées. / In this thesis, we tried to develop hybrid magnetic material chemistry in order to get soft systems that can be easy-processable. This work deals with functionalization of the organic part of interesting molecule-based magnetic materials by groups known to induce liquid crystal phase or to increase the solubility. We achieved the rational functionalization of molecule-based magnetic materials, like (i) Single-Molecule Magnets (SMM), (ii) Spin Crossover (SC), and (iii) Electron Transfer (ET) systems, towards more soluble systems and liquid crystal phases.Chapter I contains general information about three important classes of magnetic complexes: SMMs, SC and ET systems. In order to illustrate the motivation of our work, a bibliographic study about hybrid magnetic materials is then presented. Rational ligand functionalization of SMMs and SC systems towards liquid crystalline phases are discussed in Chapter II and III, respectively. New functionalized Mn12 complexes, FeII/triazole-based and [FeII(LN2O2)(LN)2] systems were obtained. The conservation of magnetic properties after ligand functionalization was confirmed, but unfortunately, these new compounds do not show mesomorphic behaviour below the decomposition temperature. The Chapter IV is focused on ligand functionalization of ET complexes. Alkyl functionalization of the ligand provides a good solubility to these complexes, and the thermally-induced switchable behaviour observed in solid state has been successfully transferred to dilute solutions.

No description available.

Les maladies d’Alzheimer et de Parkinson (MA et MP) sont des maladies neurodégénératives entrainant une diminution des fonctions cognitives et locomotrices et toujours dépourvues de traitements curatifs. La consommation d’huile d’olive et des polyphénols qu’elle contient atténuerait la survenue des démences telles qu’observées dans la MA ou la MP. À ce jour, ces composés phénoliques ont été étudiés de manière isolée afin de caractériser leur réactivité vis à vis des radicaux et leurs effets biologiques, mais les concentrations utilisées (5–100 µM) sont supérieures aux concentrations retrouvées dans le plasma (0.5-2,8 ng/ml). Jusqu’à présent, aucune étude n’a observé les effets de ces composés combinés, alors que l’oleuropéine et le tyrosol, des composés phénoliques parmi les plus abondants dans l’huile d’olive et que l’acide p-coumarique, un dérivé d’acide hydroxycinnamique, sont connus pour leurs activités antioxydantes et leur biodisponibilité. Dans un contexte cellulaire, les composés phénoliques agissent à travers leurs capacités de donneurs d’atomes d’hydrogène et/ou d’électrons, et impactent la régulation des défenses antioxydante. En conditions oxydatives, ils peuvent subir des modifications structurelles et mener à de nouveaux composés. L’impact cellulaire de ces derniers est encore peu étudié, car leur devenir dans le contexte d’un métabolisme oxydatif reste obscur. L’étude des métabolites issus de l’oxydation des composés phénoliques est donc d’une réelle importance afin d’approfondir les connaissances sur leurs mécanismes d’actions au niveau biologique. Nous avons émis l’hypothèse que la combinaison de l’oleuropéine, du tyrosol et de l’acide p-coumarique potentialise leurs effets neuroprotecteurs à travers leurs capacités de donneurs d’électrons et en lien avec la production des métabolites associés. Ce propose une approche pluridisciplinaire intégrant des composantes biologiques et des questions relevant de la physico-chimie, en s’appuyant sur des outils électrochimiques. En premier lieu, nous avons démontré que l’association de ces trois composés (Mix 1) permettait de potentialiser leurs effets neuroprotecteurs avec concentrations efficaces à 0.1 et 1µM, contrairement aux concentrations neuroprotectrices lorsque ces composés sont utilisés individuellement (5 à 10 fois plus élevées). Le Mix1 augmente la réactivité des composés phénoliques vis-à-vis d’espèces réactives de l’oxygène et permet une diminution de leur génération intracellulaire. Cette neuroprotection semble en partie médiée par une régulation des facteurs de régulation rédox endogènes. Dans un second temps, nous avons comparé le comportement en conditions oxydatives acellulaires de l’oleuropéine, du tyrosol et de l’acide p-coumarique individuellement et dans le Mix1. L’analyse en LC-MS2 des composés stables issus de l’oxydation du Mix 1 a montré une diminution des taux d’oxydation relatifs de chacun des composés, ainsi que la détection de trois néocomposés spécifiques de l’oxydation du Mix1. De plus, un effet neuroprotecteur significatif du Mix1 oxydé a été observé dès 1 et 5 nM, ce qui soutient l’hypothèse que les produits issus de l’oxydation des composés phénoliques peuvent participer aux effets biologiques des composés natifs. Notre troisième objectif était d’évaluer si les composés issus de l’oxydation des composés phénoliques pouvaient être générés dans un système biologique. L’analyse en LC-HRMS des extraits de cellules neuronales traitées avec le Mix1 en conditions oxydatives a révélé que ces composés étaient toujours présents sous leurs formes natives dans les cellules après plusieurs heures de traitement. Ce projet multidisciplinaire a permis d’observer les effets des composés phénoliques sous plusieurs angles. Il confirme qu’un effet neuroprotecteur de composés issus de l’oxydation est possible et ouvre la voie à de nouvelles approches pour le développement de formulations efficaces pour limiter le stress oxydatif au niveau cérébral. / Alzheimer and Parkinson diseases (AD and PD) are neurodegenerative disorders leading to cognitive function decline and curative treatments are still missing. Olive oil and related phenolic compounds consumption could prevent or slow down cognitive decline through neuronal preservation. Indeed, they have direct antioxidant properties as electrons or H-atom donors, which are largely suspected of being responsible for their biological effects, but also of some indirect properties as modulators of endogenous antioxidant defenses. The secoiridoid oleuropein and the monophenols tyrosol and p-coumaric acid have shown abilities to counteract oxidative injuries and associated neuronal death in several cellular and in vivo models. However, the basic mechanisms of action of phenolic compounds remain to be elucidated. In fact, phenolic compounds are highly sensitive to oxidative modifications and could be transformed into new compounds in an oxidative context. Cellular impacts of these products are rarely considered, probably because their intracellular detection is a great challenge and remain an important field to explore. Moreover, oleuropein, tyrosol and p-coumaric were individually evaluated in order to characterize their own reactivity towards ROS and their biological properties. However, the concentration ranges used to observe neuroprotection in cellular models (5 – 100 µM) were far from the possibly recovered phenolic concentration in plasma (0.5 - 2,8 ng /ml of plasma). To observe an effect with concentration range closer to the physiological ones, several antioxidant combinations could be proposed. Nevertheless, despite the biological promises of phenolic compounds from olive oil, studies which combined some of the most abundant phenolic compounds in the neuroprotection field is still missing. We thus hypothesized that the combination of oleuropein, tyrosol and p-coumaric acid in equimolar proportion (Mix 1) could potentiated their ROS scavenging and neuroprotective properties to counteract oxidative stress-induced neuronal death. These effects could be in part due to their oxidized metabolites. First, we demonstrated that the association of these three phenolic compounds potentiated their neuroprotective effects with efficient concentrations at 0.1 and 1µM, contrary to concentration ranges when there are used individually (5 to 10 higher). The Mix1 increase the reactivity of phenolic compounds towards ROS and decreases their intracellular production. These neuroprotective properties seems, at least in part, lead by a regulation of the endogenous redox factors. Then, we compared the behavior of Oleuropein, tyrosol and p-coumaric acid individually and in the Mix1 under acellular oxidative conditions. The oxidized Mix1 LC-ESI-MS2 profiles showed a regeneration of oleuropein through a decrease of the phenolic compounds oxidation rate and highlight the presence of specific oxidized products in Mix 1. This study also showed a significant neuroprotection of oxidized Ole and oxidized Mix1 with very low concentrations (1 and 5 nM), suggesting the putative relevant role of oxidized Ole products to protect or delay neuronal death. Our third objective was to evaluate if these oxidized metabolites could be produced in a biological system. Even under oxidative conditions, we recovered these compounds in cellular extracts under their native forms after few hours of treatments, attesting their accumulation in neuronal cells. Taking together, our results pointed out the relevance to study the phenolic compounds from a chemical and a biological point of view, which should always be as cellular redox reactions are between biological and chemical fields. Lastly, we confirmed the significance to take into account the oxidized metabolites from phenolic compounds to deeper understand their biological properties.

No description available.

No description available.

<div>The first chapter reports a study of aryl nitrene intermediates. Although extensively studied over the past 30 years, phenyl nitrenes have a propensity to undergo rearrangement reactions and form polymeric tars. This is in stark contrast to the phenyl carbenes which are known to undergo several important reactions to produce a library of useful organic compounds. One such reaction is the insertion of phenyl carbenes into a double bond to produce a cyclopropane moiety. If aryl nitrenes can be exploited to conjure a similar reactivity, they would be an excellent synthetic route to produce aziridine rings which are a crucial component of many natural products. This review chapter is a collection of all the efforts that have been made in this regard.</div><div><br></div><div>In the next chapter, the electronic effect of the azide functional group on an aromatic system has been investigated by using Hammett-Taft parameters obtained from the effect of azide-substitution on the gas-phase acidity of phenol. Gas-phase acidities of 3- and 4-azidophenol have been measured by using mass spectrometry and the kinetic method and found to be 340.8 ± 2.2 and 340.3 ± 2.0 kcal/mol respectively. The relative electronic effects of the azide substituent on an aromatic system have been measured by using Hammett-Taft parameters. The σF and σR values are determined to be 0.38 and 0.02 respectively, consistent with predictions based on electronic structure calculations. The values of σF and σR demonstrate that azide acts an inductively withdrawing group but has negligible resonance contribution on the phenol. In contrast, acidity values calculated for substituted benzoic acids gives values of σF = 0.69 and σR = -0.39, indicating that the azide is a strong  donor, comparable to that of a hydroxyl group. The difference is explained as being the result of “chimeric” electronic behavior of the azide, similar to that observed previously for the n-oxide moiety, which can be more or less resonance donating depending on the electronic effects of other groups in the system.</div><div><br></div><div>Phenyl nitrenes undergo bimolecular chemistry under very specific circumstances. For example, having an oxide substituent at the para position of the phenyl ring enables the formation of an indophenol product from a photocatalyzed reaction of the nitrene. Although, this reaction has been reported before, the mechanism involved in this reaction has not been fully understood. A two-electron mechanism involving electrophilic aromatic substitution reaction has been proposed in the literature, however we found evidence that did not support this theory. Instead, we find this reaction analogous to the popular Gibbs’ reaction whose single electron transfer mechanism has been extensively studied. The following chapter encompasses a study of the mechanism of the photolysis reaction to look for evidence of a single electron transfer similar to the Gibbs’ reaction.</div><div><br></div><div>As mentioned earlier, phenyl nitrenes have a proclivity to undergo rearrangement reactions instead of exhibiting bimolecular reactivity that can lead to useful products. One of the strategies to overcome this challenge is to spatially separate the two electrons of an open-shell singlet nitrene so as to minimize electron-electron repulsion. This separation can be achieved by delocalizing the individual electrons over multiple aromatic rings and heteroatoms which can act as radical stabilizers. In this chapter, a short review of literature that sets precedence for developing a unique heteroatom containing aromatic backbone to achieve the necessary stabilization is presented. Our efforts in synthesizing the model azide precursor compound have also been discussed.</div>