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Non-covalent interactions including nucleobase hydrogen bonding and phosphonium/ammonium ionic aggregation were studied in block and random polymers synthesized using controlled radical polymerization techniques such as nitroxide mediated polymerization (NMP) and reversible addition-fragmentation chain transfer polymerization (RAFT). Non-covalent interactions were expected to increase the effective molecular weight of the polymeric precursors through intermolecular associations and to induce microphase separation. The influence of non-covalent association on the structure/property relationships of these materials were studied in terms of physical properties (tensile, DMA, rheology) as well as morphological studies (AFM, SAXS). Ionic interactions, which possess stronger interaction energies than hydrogen bonds (~150 kJ/mol) were studied in the context of phosphonium-containing acrylate triblock (ABA) copolymers and random copolymers. Phosphonium-containing ionic liquid monomers with different alkyl substituent lengths and counterions enabled an investigation of the effects of ionic aggregation of phosphonium cations on the polymer physical properties. The polymerization of styrenic phosphonium-containing ionic liquid monomers using a difunctional alkoxyamine initiator, DEPN2, afforded an ABA triblock copolymer with an n-butyl acrylate soft center block and symmetric phosphonium-containing external reinforcing blocks. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) of triblock copolymers revealed pronounced microphase separation at the nanoscale. Phosphonium aggregation governed block copolymer flow activation energies. In random copolymers, the phosphonium cations only weakly aggregated, which strongly depended on the length of alkyl substituents and the type of counterions. Acrylate random copolymers consisting of quaternary ammonium functionalities were synthesized using reversible addition-fragmentation chain transfer polymerization (RAFT). The obtained copolymers possessed controlled compositions and narrow molecular weight distributions with molecular weights ranging from Mn =50,000 to 170,000 g/mol. DMA evidenced the weak aggregation of ammonium cations in the solid state. Additionally, this ionomer was salt-responsive in NaCl aqueous solutions. Hydrogen bonding, a dynamic interaction with intermediate enthalpies (10-40 kJ/mol) was introduced through complementary heterocyclic DNA nucleobases such as adenine, thymine and uracil. Our investigations in this field have focused on the use of DNA nucleobase pair interactions to control polymer self-assembly and rheological behavior. Novel acrylic adenine- and thymine-containing monomers were synthesized from aza-Michael addition reaction. The long alkyl spacers between nucleobase and polymer backbone afforded structural flexibility in self-assembly process. Adenine-containing polyacrylates exhibited unique morphologies due to adenine-adenine π-π interactions. The complementary hydrogen bonding of adenine and thymine resulted in disruption of adenine-adenine π-π interactions, leading to lower plateau modulus and lower softening temperatures. Moreover, hydrogen bonding interactions enabled the compatibilization of complementary hydrogen bonding guest molecules such as uracil phosphonium chloride. / Ph. D.

La synthèse de molécules possédant une cavité présente un grand intérêt car ces dernières peuvent agir comme récepteurs moléculaires ou comme catalyseurs supramoléculaires et ainsi mimer l'activité des enzymes. Les hémicryptophanes possèdent ainsi des cavités dissymétriques complexes formées à partir d'une unité cyclotrivératrylène et d'une seconde unité de symétrie C3 et présentent des propriétés catalytiques et de reconnaissance particulièrement intéressantes.Les travaux effectués au cours de cette thèse reposent donc sur la synthèse de nouveaux hémicryptophanes et sur leur utilisation pour la reconnaissance moléculaire de composés biologiquement actifs et pour la catalyse supramoléculaire. A ce titre, différentes voies de synthèse ont été abordées et ont permis d'obtenir un panel de nouveaux récepteurs. Ces composés ont alors été appliqués dans un premier temps à la reconnaissance sélective de paires d'ions et de neurotransmetteurs zwitterioniques puis à la reconnaissance stéréosélective de sucres. Les propriétés complexantes de ces composés ont principalement été étudiées par spectroscopie RMN et à l'aide de calculs quantiques. Enfin, la synthèse de complexes supramoléculaires cuivre-hémicryptophane nous a permis de développer l'utilisation de ces composés pour la catalyse biomimétique d'oxydation des alcanes. / Molecular containers are very attractive as they can act as molecular receptors or supramolecular catalysts and so mimic biological entities such as enzymes. Hemicryptophanes are heteroditopic host molecules created from the association of a cyclotriveratrylene unit with another C3-symmetric moiety and which present interesting catalytic and recognition properties. During this thesis, we based our work on the synthesis of new hemicryptophanes and their application, first in molecular recognition of bioactive molecules and then in supramolecular catalysis. Different synthetic paths have been developed to obtain several new receptors. Their binding abilities have then been studied in selective recognition of ion pairs and neurotransmitters and in stereoselective recognition of carbohydrates. These works have been performed mainly thanks to NMR spectroscopy and quantum calculations. Finally, copper-hemicryptophane complexes have been synthesized and used as supramolecular catalysts in C-H oxidation of alkanes.

La reconnaissance moléculaire est un phénomène omniprésent dans les systèmes vivants et intervient dans de nombreux processus biologiques comme la reconnaissance cellulaire ou encore la transmission de signaux par les neurotransmetteurs. L’élaboration de molécules synthétiques capables de mimer l’action des récepteurs naturels en complexant sélectivement un substrat cible est, à l’heure actuelle, très recherchée pour la détection ou le diagnostic en biologie et médecine. Parmi l’ensemble des récepteurs synthétiques, les hémicryptophanes sont des molécules cages composées d’un cyclotribenzylène connecté à une autre unité moléculaire par trois bras espaceurs. Les travaux de cette thèse reposent sur l’élaboration de nouveaux hémicryptophanes et l’étude de leurs propriétés de complexation vis-à-vis de molécules d’intérêt biologique. Dans un premier temps, la chiralité de ces récepteurs a été utilisée pour étudier leurs propriétés de reconnaissance stéréosélective face à différents sucres et analogues de neurotransmetteurs. De bonnes diastéréosélectivités et énantiosélectivités ont ainsi pu être observées en milieu organique pour les substrats étudiés. En parallèle, plusieurs hémicryptophanes hydrosolubles ont été synthétisés et ont permis de reconnaitre sélectivement des neurotransmetteurs comme la choline dans l’eau. Enfin, une dernière partie de cette thèse à été consacrée à la mise en place d’une voie de synthèse pour rendre ces récepteurs fluorescents, dans le but d’élaborer par la suite des sondes moléculaires capables de détecter et de suivre spatio-temporellement des molécules d’intérêt biologique dans les systèmes vivants par fluorescence. / Molecular recognition is a very important phenomenon for living systems as it occurs in many biological processes like cell-cell recognition or transmission of signals by neurotransmitters. Nowadays, the design of synthetic host molecules able to mimic natural receptors by complexing selectively a target substrate, is much sought-after for detection or diagnostic in biology and medicine. Among all the different synthetic receptors, hemicryptophanes are cage-shape molecules which are composed of a cyclotribenzylene moiety connected to another molecular unit by three spacer arms. This thesis is about the synthesis of new hemicryptophanes and the study of their complexation properties toward biologically important molecules. First, the stereoselective recognition of carbohydrates and neurotransmitter analogues by these chiral receptors was investigated in organic solvents and revealed good enantioselectivities and diastereoselectivities. In parallel, several water-soluble hemicryptophanes were synthesized and showed an aptitude for recognizing selectively ammonium substrates like choline in water. The last part was devoted to the development of a synthetic pathway to make hemicryptophanes fluorescent, in order to design molecular probes able to track biologically important molecules in living systems by fluorescence.

L’objectif de ces travaux de thèse était l’étude des interactions de petites molécules avec les multiples structures de l’ADN quadruplex via i) le développement et l’utilisation d’un test haut-débit pour l’analyse des interactions ligand-ADN quadruplex et le criblage de chimiothèques/ciblothèques et ii) la préparation de composés aux modes d’interactions multiples (empilement/sillon, covalent/non-covalent, etc.), sélectifs (quadruplex vs. duplex et intra-quadruplex) et éventuellement fonctionnalisés (biotine, fluorophore, etc.). La première partie des travaux a été centrée sur le développement du test G4-FID (G-quadruplex Fluorescent Intercalator Displacement) qui est une méthode semi-quantitative permettant l’évaluation de l’affinité et de la sélectivité de petites molécules pour l’ADN quadruplex par déplacement d’une sonde off/on, le Thiazole Orange (TO). Le test a notamment été transposé avec succès de la cuve vers la microplaque (HT-G4-FID). D’autre part, nous avons montré l’intérêt de fluorophores alternatifs, TO-PRO-3 et Hoechst 33258, aux caractéristiques spectrales complémentaires à TO. Cette méthode d’analyse a également été utilisée avec succès pour l’identification de nouveaux ligands sélectifs d’ADN quadruplex et la mise en évidence des relations structure-activité ainsi que des sélectivités structurales. La deuxième partie des travaux a été consacrée à la préparation et à l’étude de nouveaux ligands d’ADN quadruplex. Ces ligands possèdent des particularités, soit dans leur mode d’interaction (sillons, coordination) soit par leur bifonctionnalité (biotinylés, fluorescents). Nous avons ainsi préparé un ligand de quadruplex polyhétéroaryle acyclique (TOxaPy) possédant une sélectivité inattendue pour certaines structures de l’ADN quadruplex. D’autre part, nous avons montré que les complexes de dérivés de terpyridine peuvent être adaptés, en changeant le ligand organique et/ou la nature du métal, de façon à interagir avec l’ADN quadruplex par interaction covalentes et/ou non covalentes. / The aim of this thesis work was to study the interactions of small molecules with multiple structures of quadruplex DNA via i) the development and use of a high-throughput test for the analysis of ligand-quadruplex DNA interactions and screening of chemical libraries and ii) the preparation of compounds with multiple binding modes (stacking/groove, covalent/non-covalent, etc..) selective (quadruplex vs. duplex and intra-quadruplex) and possibly functionalized (biotin, fluorophore, etc.). The first part of the work was focused on the development of the G4-FID (G-quadruplex Intercalator Fluorescent Displacement) assay, which is a semi-quantitative method for evaluating the affinity and selectivity of small molecules for quadruplex DNA by displacing an off/on probe, the Thiazole Orange (TO). The test has been implemented successfully with microplate (HT-G4-FID). On the other hand, we have shown the importance of alternative fluorophores, TO-PRO-3 and Hoechst 33258, with complementary spectral characteristics. This method of analysis has also been successfully used for the identification of new selective ligands of quadruplex DNA and the identification of structure-activity relationships and structural selectivities. The second part of the work was devoted to the preparation and study of new DNA quadruplex ligands. These ligands possess particular characteristics either in their mode of interaction (grooves, coordination) or by their bifunctionality (biotinylated, fluorescent). We have prepared an acyclic polyheteroaryle quadruplex ligand (TOxaPy) with an unexpected selectivity for certain structures of quadruplex DNA. Furthermore, we showed that complexes of terpyridine derivatives can be tailored by changing the organic ligand and / or the metal in order to interact with quadruplex DNA by covalent and / or non-covalent interaction.

Dans ce manuscrit est décrite l'utilisation d'interactions supramoléculaires pour diriger l'auto-assemblage de composés donneurs et accepteurs d'électrons au sein de dispositifs photovoltaïques organiques. Dans ce but, des matériaux de type oligo-3-hexylthiophène et fullerène ont été fonctionnalisés avec des groupements de reconnaissance complémentaires mélamine – acide barbiturique. La présence de élements solubilisants confère à ces composés une bonne mise en oeuvre permettant la fabrication de dispositifs photovoltaïques à hétérojonction volumique. L'effet de la composition et du post-traitement de la couche active sur la performance de ces dispositifs ont été explorés. Les études de mobilité de charge et des mécanismes de recombinaison au sein de ces matériaux indiquent que l'équilibre entre auto-association et séparation de phases est crucial pour l'efficacité en conversion photovoltaïque. / This research aims to elucidate the use of supramolecular interaction to guide the formation of well-defined nanoscale self-assembled architecture in photovoltaic solar cells as a means to improve device efficiency. Complementary molecular recognition sites based on melamine and barbituric acid were used to obtain functionalized fullerene and oligothiophene materials with superior processibility thanks to the presence of specific solubilizing groups. The efficiency of solid-state devices fabricated using the bulk heterojunction design was studied with respect to device morphology and composition. Experiments on recombination mechanism and field effect mobilities suggest that the balance between hydrogen-bonding interactions induce self-assembly and p-p interactions to promote phase segregation is crucial to the micro-structure of the active layer. The investigated of the relationship between the oligothiophene chain size and various complementary hydrogen-bonding motifs is envisaged.

Les proazaphosphatranes sont des entités phosphorées bicycliques superbasiques également connues sous le nom de superbases de Verkade et les azaphosphatranes constituent leurs acides conjugués. Les travaux de cette thèse porte sur l’étude des propriétés de ces molécules en milieu confiné. Premièrement, le confinement des superbases a été étudié au sein de structure de type hémicryptophane (molécules possédant des cavités dissymétriques formées à partir d’une unité cyclotrivératrylène et d’une seconde unité de symétrie C3). Une modulation de la basicité a pu être notamment observée dans les différentes structures étudiées possédant des tailles de cavité différentes par comparaison avec les superbases modèles dépourvues de cavité. L’activité catalytique d’une superbase encagée a pu être testée dans deux réactions de catalyse nucléophile et basique. Puis les azaphosphatranes, acides faibles aux stuctures robustes, jusque-là peu utilisés en organocatalyse ont été valorisés pour la synthèse de carbonates cycliques à partir d’époxydes et de dioxyde de carbone (CO2). Un effet sur la stabilité des catalyseurs encagés a pu être démontré. Enfin un catalyseur hétérogène a pu être mis au point par immobilisation d’un azaphosphatrane sur silice mésoporeuse de type SBA-15. / Proazaphosphatranes are highly reactive phosphorous bicyclic compounds also called Verkade’s superbases and the azaphosphatranes are their acidic counterparts. The goal of the work is to investigate the modifications of the properties of these compounds when they are in confined space. Firstly, the superbases were encapsulated into hemicryptophane host compounds (molecular containers created from the association of a cyclotriveratrylene unit with another C3-symmetric moiety). Modifications in the basicity of the supramolecular superbases depending on the substitution pattern around the phosphorous were evidenced compare to the molecules lacking the cavity. The catalytic activity of a superbase was investigated on a nucleophilic and a basic reaction. The azaphosphatranes were then used to catalyze the cycloaddition of carbon dioxide (CO2) to epoxides to form a cyclic carbonate. Enhancements of the stability of encaged catalyst were demonstrated. Finally, an azaphophatrane was immobilized on mesoporous silica leading to a heterogeneous catalyst.

La reconnaissance moléculaire énantiosélective est un processus fondamental et universel qui est au cœur de tous les systèmes biologiques. Ce travail a pour but de contribuer à la compréhension des phénomènes, mis en jeu lors de cette reconnaissance, par l’utilisation de récepteurs artificiels, capables de complexer et discriminer des acides aminés. De par leurs rigidités et leurs modularités fonctionnelles, les calix[4]arènes constituent des plateformes de choix pour la conception de ces récepteurs organisés. Une série de 12 ligands calixarèniques et thiacalixarèniques chiraux homo et hétéroditopiques, portant des groupements fonctionnels dérivés d’acides aminés, a donc été synthétisée. La synthèse de ces ligands a nécessité la mise au point d’une méthode originale et sélective, qui a permis d’obtenir une série de calix[4]arènes mono-O-fonctionnalisés par des groupements fonctionnels variés. Une étude mécanistique a permis de mettre en évidence les intermédiaires réactionnels. Après caractérisation de tous les composés synthétisés, des études de complexation des ligands avec des dérivés tosylés d’acides aminés neutres ont été effectuées. Les investigations, menées par spectrométrie de masse, par microcalorimétrie et par RMN 1H, nous ont permis de mettre en évidence la capacité de certains ligands à complexer et discriminer des acides aminés. La stœchiométrie et les constantes d’association des complexes formés ont ainsi pu être déterminées. Des études par RMN 2D ont permis de déterminer les liaisons impliquées dans la formation des complexes et ont révélé un réarrangement spatial des ligands, au sein des complexes, afin d’améliorer la stabilité de ceux-ci / Molecular recognition is a fundamental and universal process in biological systems. This work aims to contribute to the understanding of phenomena involved in this recognition by the use of artificial receptors able to complex and discriminate amino acids. Because of their rigidity and their functional modularity, calix[4]arenes and thiacalix[4]arenes are good starting materials for the design of these receptors. A series of 12 chiral homo and heteroditopic calix[4]arenes and thiacalix[4]arenes bearing amino acids derivatives has been synthesized. In order to improve the synthesis of heteroditopic receptors, an original and selective method for the preparation of mono-O-functionalized calix[4]arenes was developed. This procedure, based on the de-O-functionalization of 1,3 di-O-substituted calix[4]arenes by titanium tetrachloride (TiCl4), yielded a series of calix[4]arenes, mono-O-substituted by various functional groups (alcohol, halogen, nitrile, ester, alkyne ...). A mechanistic study revealed the formation of two titanium calixarene complexes during the reaction. After characterization of all these compounds, complexation studies of chiral receptors with neutral N-tosyl amino acids derivatives (valine, leucine, and phenylalanine) were done. Various investigations carried out by mass spectrometry, microcalorimetry and 1 H NMR allowed us to establish the ability of some ligands to complex and discriminate amino acids. Stoichiometry and association constants of the complexes were determined. 2D NMR (NOESY, COSY) studies were used to specify the bonds implied in complex formation

The vast and growing volume of 3D protein structural data stored in the PDB contains abundant information about macromolecular complexes, and hence, data about protein interfaces. Non-covalent contacts between amino acids are the basis of protein interactions, and they are responsible for binding afinity and specificity in biological processes. In addition, water networks in protein interfaces can also complement direct interactions contributing significantly to molecular recognition, although their exact role is still not well understood. It is estimated that protein complexes in the PDB are substantially underrepresented due to their crystallization dificulties. Methods for automatic classifification and description of the protein complexes are essential to study protein interfaces, and to propose putative binding regions. Due to this strong need, several protein-protein interaction databases have been developed. However, most of them do not take into account either protein-peptide complexes, solvent information or a proper classification of the binding regions, which are fundamental components to provide an accurate description of protein interfaces. In the firest stage of my thesis, I developed the SCOWLP platform, a database and web application that structurally classifies protein binding regions at family level and defines accurately protein interfaces at atomic detail. The analysis of the results showed that protein-peptide complexes are substantially represented in the PDB, and are the only source of interacting information for several families. By clustering the family binding regions, I could identify 9,334 binding regions and 79,803 protein interfaces in the PDB. Interestingly, I observed that 65% of protein families interact to other molecules through more than one region and in 22% of the cases the same region recognizes different protein families. The database and web application are open to the research community (www.scowlp.org) and can tremendously facilitate high-throughput comparative analysis of protein binding regions, as well as, individual analysis of protein interfaces. SCOWLP and the other databases collect and classify the protein binding regions at family level, where sequence and structure homology exist. Interestingly, it has been observed that many protein families also present structural resemblances within each other, mostly across folds. Likewise, structurally similar interacting motifs (binding regions) have been identified among proteins with different folds and functions. For these reasons, I decided to explore the possibility to infer protein binding regions independently of their fold classification. Thus, I performed the firest systematic analysis of binding region conservation within all protein families that are structurally similar, calculated using non-sequential structural alignment methods. My results indicate there is a substantial molecular recognition information that could be potentially inferred among proteins beyond family level. I obtained a 6 to 8 fold enrichment of binding regions, and identified putative binding regions for 728 protein families that lack binding information. Within the results, I found out protein complexes from different folds that present similar interfaces, confirming the predictive usage of the methodology. The data obtained with my approach may complement the SCOWLP family binding regions suggesting alternative binding regions, and can be used to assist protein-protein docking experiments and facilitate rational ligand design. In the last part of my thesis, I used the interacting information contained in the SCOWLP database to help understand the role that water plays in protein interactions in terms of affinity and specificity. I carried out one of the firest high-throughput analysis of solvent in protein interfaces for a curated dataset of transient and obligate protein complexes. Surprisingly, the results highlight the abundance of water-bridged residues in protein interfaces (40.1% of the interfacial residues) that reinforces the importance of including solvent in protein interaction studies (14.5% extra residues interacting only water- mediated). Interestingly, I also observed that obligate and transient interfaces present a comparable amount of solvent, which contrasts the old thoughts saying that obligate protein complexes are expected to exhibit similarities to protein cores having a dry and hydrophobic interfaces. I characterized novel features of water-bridged residues in terms of secondary structure, temperature factors, residue composition, and pairing preferences that differed from direct residue-residue interactions. The results also showed relevant aspects in the mobility and energetics of water-bridged interfacial residues. Collectively, my doctoral thesis work can be summarized in the following points: 1. I developed SCOWLP, an improved framework that identiffies protein interfaces and classifies protein binding regions at family level. 2. I developed a novel methodology to predict alternative binding regions among structurally similar protein families independently of the fold they belong to. 3. I performed a high-throughput analysis of water-bridged interactions contained in SCOWLP to study the role of solvent in protein interfaces. These three components of my thesis represent novel methods for exploiting existing structural information to gain insights into protein- protein interactions, key mechanisms to understand biological processes.

Membrane transport processes underlie many purification technologies. The efficiency of a membrane separation process depends upon material throughput (flux), and the degree to which the membrane discriminates amongst species in the feed stock (selectivity). In a supported liquid membrane, flux may be enhanced by carrier molecules, which act as catalysts of translocation. Carrier molecules also confer selectivity, via differential molecular recognition of the substances in the feed stock. The effect of electrical potential on the flux and selectivity of carrier-containing supported liquid membranes is not well documented. We elected to study the effect of electrical potential on supported liquid membranes containing valinomycin, a potassium ionophore, and a calixarene ester, a sodium ionophore. In these systems, the open circuit membrane potential could be made positive or negative by the choice of anion. With both of these carriers, we observed that selectivity for potassium or sodium salts was dependent on the open circuit membrane potential. To confirm that electrical potential was responsible for the observed selectivity variance, we applied a potential across the membrane using a potentiostat. The applied potential created conditions for carrier-mediated electrodialysis, where oxidation and reduction reactions on either side of the membrane act as the driving force for transmembrane flux of charged species. In chronoamperometry experiments, we found that selectivity for potassium or sodium ion was dependent on the applied electrical potential. Subject to some constraints, selectivity and flux could be controlled by the application of positive or negative electrical potentials. Linear sweep voltammetry experiments allowed for the rapid prediction of the potential that must be applied to achieve optimal selectivity. We also found that membrane potential measurements, as well as the magnitude of current that flows in chronoamperometry experiments, could be interpreted to predict Eisenman and Hofmeister sequences. These results are novel, and await a convincing theoretical justification. The results also suggest that a separation technology could be developed around the idea of modulating selectivity with electrical potential. In this regard, carrier-mediated electrodialysis may be suitable for the sequestration of toxic or radioactive heavy metals, and a large number of carrier molecules for metal ions are currently known. The technique may also be suitable for separating organic molecules, such as high-value chiral pharmaceuticals. Supported liquid membranes are a useful research tool, but industrial applications may require a more stable membrane architecture. / Graduate