The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of different interesting phenomena of biological relevance, ranging from enzyme specificity to allosteric communication, from selection of fold to structural organization / states of oligomerization, from half-sites-reactivity to reshuffling of the conformational free energy landscape, encompassing the dogma of sequence-structure dynamics-function of macromolecules. The role of striking an optimal balance between rigidity and flexibility in macromolecular 3D structural organisation is yet another concept that needs attention from the functional perspective. Needless to say that the variety of protein structures and conformations naturally leads to the diversity of their function and consequently many other biological functions in general. Classical models of allostery like the ‘MWC model’ or the ‘KNF model’ and the more recently proposed ‘population shift model’ have advanced our understanding of the underlying principles of long range signal transfer in macromolecules. Extensive studies have also reported the importance of the fold selection and 3D structural organisation in the context of macromolecular function. Also ligand induced conformational changes in macromolecules, both subtle and drastic, forms the basis for controlling several biological processes in an ordered manner by re-organizing the free energy landscape. The above mentioned biological phenomena have been observed from several different biochemical and biophysical approaches. Although these processes may often seem independent of each other and are associated with regulation of specialized functions in macromolecules, it is worthwhile to investigate if they share any commonality or interdependence at the detailed atomic level of the 3D structural organisation. So the nagging question is, do these diverse biological processes have a unifying theme, when probed at a level that takes into account even subtle re-orchestrations of the interactions and energetics at the protein/nucleic acid side-chain level. This is a complex problem to address and here we have made attempts to examine this problem using computational tools. Two methods have been extensively applied: Molecular Dynamics (MD) simulations and network theory and related parameters. Network theory has been extensively used in the past in several studies, ranging from analysis of social networks to systems level networks in biology (e.g., metabolic networks) and have also found applications in the varied fields of physics, economics, cartography and psychology. More recently, this concept has been applied to study the intricate details of the structural organisation in proteins, providing a local view of molecular interactions from a global perspective. On the other hand, MD simulations capture the dynamics of interactions and the conformational space associated with a given state (e.g., different ligand-bound states) of the macromolecule. The unison of these two methods enables the detection and investigation of the energetic and geometric re-arrangements of the 3D structural organisation of macromolecule/macromolecular complexes from a dynamical or ensemble perspective and this has been one of the thrust areas of the current study. So we not only correlate structure and functions in terms of subtle changes in interactions but also bring in conformational dynamics into the picture by studying such changes along the MD ensemble. The focus was to identify the subtle rearrangements of interactions between non-covalently interacting partners in proteins and the interacting nucleic acids. We propose that these rearrangements in interactions between residues (amino acids in proteins, nucleic acids in RNA/DNA) form the common basis for different biological phenomena which regulates several apparently unrelated processes in biology. Broadly, the major goal of this work is to elucidate the physico-chemical principles underlying some of the important biological phenomena, such as allosteric communication, ligand induced modulation of rigidity/flexibility, half-sites-reactivity and so on, in molecular details. We have investigated several proteins, protein-RNA/DNA complexes to formulate general methodologies to address these questions from a molecular perspective. In the process we have also specifically illuminated upon the mechanistic aspects of the aminoacylation reaction by aminoacyl-tRNA synthetases like tryptophanyl and pyrrolysyl tRNA synthetase, structural details related to an enzyme catalyzed reaction that influences the process of quorum sensing in bacteria. Further, we have also examined the ‘dynamic allosterism’ that manipulates the activity of MutS, a prominent component of the DNA bp ‘mismatch repair’ machinery. Additionally, our protein structure network (PSN) based studies on a dataset of Rossmann fold containing proteins have provided insights into the structural signatures that drive the adoption of a fold from a repertoire of diverse sequences. Ligand induced percolations distant from the active sites, which may be of functional relevance have also been probed, in the context of the S1A family of serine proteases. In the course of our investigation, we have borrowed several concepts of network parameters from social network analysis and have developed new concepts. The Introduction (Chapter-1) summarizes the relevant literature and lays down a suitable background for the subsequent chapters in the thesis. The major questions addressed and the main goal of this thesis are described to set an appropriate stage for the detailed discussions. The methodologies involved are discussed in Chapter-2. Chapter-3 deals with a protein, LuxS that is involved in the bacterial quorum sensing; the first part of the chapter describes the application of network analysis on the static structures of several LuxS proteins from different organisms and the second part of this chapter describes the application of a dynamic network approach to analyze the MD trajectories of H.pylori LuxS. Chapter-4 focuses on the investigation of human tryptophanyl-tRNA synthetase (hTrpRS), with an emphasis to identify ligand induced subtle conformational changes in terms of the alternation of rigidity/flexibility at different sites and the re-organisation of the free energy landscape. Chapter-5 presents a novel application of a quantum clustering (QC) technique, popular in the fields of pattern recognition, to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. The protein structure network (PSN) in the earlier studies were constituted on the basis of geometric interactions. In Chapters 6 and 7, we describe the networks (proteins+nucleic acids) using interaction energy as edges, thus incorporating the detailed chemistry in terms of an energy-weighted complex network. Chapter-6 describes an application of the energy weighted network formalism to probe allosteric communication in D.hafniense pyrrolysyl-tRNA synthetase. The methodology developed for in-depth study of ligand induced changes in DhPylRS has been adopted to the protein MutS, the first ‘check-point protein’ for DNA base pair (bp) mismatch repair. In Chapter-7, we describe the network analysis and the biological insights derived from this study (the work is done in collaboration with Prof. David Beveridge and Dr. Susan Pieniazek). Chapter-8 describes the application of a network approach to capture the ligand-induced subtle global changes in protein structures, using a dataset of high resolution structures from the S1A family of serine proteases. Chapter-9 deals with probing the structural rationale behind diverse sequences adopting the same fold with the NAD(P)-binding Rossmann fold as a case study. Future directions are discussed in the final chapter of the thesis (Chapter-10).

Suite à la première thèse sur le greffage et l’adsorption physique successives de sélecteurs chiraux dans des tubes ouverts en électrochromatographie capillaire (ECC ou CEC) chirale, menée par le Dr Guillaume Pédéhontaa-Hiaa au sein de l’équipe du laboratoire COBRA (IUT d’Evreux), nous avons développé des phases stationnaires chirales covalentes (CSPs) à base de cyclodextrines (CDs) en tubes ouverts et des CSPs sur supports monolithiques pour l’emploi en CEC. Nous avons ainsi évalué les paramètres électrochromatographiques et la stabilité de ces CSPs en séparant une variété de racémiques neutres et chargés. L’influence de la température d’analyse, le potentiel appliqué ainsi que la nature et le pH des électrolytes sur la qualité des électrochromatogrammes ont été étudié en CEC chirale. Cette étude se divise en deux grandes parties. La première concerne les CSPs élaborées sur colonnes à tubes ouverts pour l’OT-CEC. Il s’agit initialement de graver la surface interne d’un capillaire de silice de 50 μm de diamètre interne à l’aide d’une solution de bifluorure d’ammonium dans le but premier d’augmenter considérablement sa surface spécifique et d’immobiliser en surface une grande quantité de sélecteurs chiraux à base de β-CD. Nous avons alors décrit des greffages covalents de CDs anioniques (Scc-β-CD et CM-β-CD) et d’un polymère anionique de CDs (p-CM-β-CD-) en surface de capillaire de gel de silice gravée et modifiée chimiquement par l’aminopropyltriéthoxysilane (APTEOS). Les greffages des sélecteurs ont été reproduits dans les mêmes conditions que dans la thèse rapportée précédemment en électrophorèse. L’originalité de la construction de ces CSPs réside dans la rapidité et la simplicité du couplage dit péptidique à température ambiante, des sélecteurs carboxylés sur des colonnes préalablement gravées. Ce greffage nécessite des agents de couplage peptidique solubles dans l’eau tels que 1-Ethyl-3-(diméthylaminopropyl)carbodiimide (EDC) et le N-Hydroxysuccinimide (NHS). Il peut aussi être obtenu de manière moins efficace avec d’autres agents solubles en milieu organique tels que le O-(Benzotriazol-1-yl)-N,N,N’,N’-tétraméthyluronium tétrafluoroborate et la triéthylamine (TBTU/TEA). Chaque étape menant aux CSPs a été caractérisée par une étude de flux électroosmotique (FEO) en OT-CEC. Des analyses en AFM et en MEB nous renseignent d’avantage sur le succès du procédé « etching » de nos capillaires. La deuxième grande partie de cette étude traite de la synthèse in-situ de CSPs sur des colonnes de type polymères monolithes organiques et un monolithe hybride à base de sol gel. Des post modifications de surface de ces supports monolithiques nous ont permis d’immobiliser de façon covalente et non covalente des sélecteurs de β-CD en surface des volumes macroporeux. Deux collaborations ont vu le jour pour atteindre ces objectifs. La première eut lieu avec le Dr Thuy Tran et le Pr Myriam Taverna de la Faculté de Pharmacie de Chatenay Malabry (UMR 8612), durant laquelle nous avons reproduit une colonne monolithe organique de type méthacrylate, porteuse de groupements phosphate dans l’optique d’adsorber physiquement en surface le polymère cationique de CDs (p-CD+) que nous a transféré le Pr Benjamin Carbonnier et d’évaluer les capacités de discrimination chirale de cette nouvelle CSP en m-CEC. La seconde collaboration a eu lieu avec le Dr Mohamed Guerrouache et le Pr Benjamin Carbonnier au sein du laboratoire ICMPE de Thiais, où nous avons synthétisé des colonnes monolithiques organiques à base d’acrylates dans le but de greffer en surface de façon covalente et non covalente les CDs et polymères de CDs et d’évaluer ces nouvelles CSPs en m-CEC. La troisième phase stationnaire monolithique employée est celle décrite par le Dr Huihui Yang qui décrit un monolithe hybride porteur de groupements sulfonates nous permettant par la suite d’immobiliser électrostatiquement le p-CD+ sur le réseau poreux et d’évaluer cette nouvelle CSP en m-CEC. / New chiral stationary phases have been prepared for Open Tubular and monolithic columns used in electrochromatography capillary. In order to separate racemic mixtures such as flavonoïd, Hidantoïn derivatives, Binaphtalene-2, 2-hydrogenophosphate and others chiral solutes, we use the β-cyclodextrin forms as chiral selector. Besides, β-cyclodextrin seems to be the most efficient chiral selector in chromatography since it is able to complex and dissolve optical organic isomers in an aqueous media, this chiral selector is able to dissolve even lipophilic molecule with high weight. The complexation is based on interactions with β-cyclodextrin. This study aims to elaborate new chiral stationary phase for CEC using β-cyclodextrin polymers and β-cyclodextrin derivatives. Two approaches were used: Firstly, covalent stationary phases coating with carboxymethyl-β-cyclodextrin polymers and oligomers containing carboxyl’s group had been experimented for open tubular and monolithic column in CEC. Then a non-covalent coating cationic polymer of β-cyclodextrin’s derivatives was immobilized (polytrimethyl ammonium β-CD) on continuous organic monoliths bearing anionic’s group. Prior to the covalent coating of the CD’s chiral selector for OT-CEC and m-CEC, we needed to modify the silicate surface and the monolithic surface with a primary amine silicate1,2 (aminopropyltriethoxysilane) and EDA, an amino-organic moiety (Ethylene diamine). The stability of the bonded organic moiety (APTEOS, EDA) were studied by CEC at different pH with constant ionic strength’s buffer. In this way, graft of carboxymethyl-β-cyclodextrin polymer on silica inner surface modified by APTEOS and on NAS-co-EDMA surface modified by EDA succeeded in activating and covalently coupling reagent as EDC and NHS (1-ethyl-3(-3-dimethtylaminopropyl) carbodiimide and N-hydroxysuccinimide, respectively3) with carboxymethyl’s group of carboxymethyl-β-cyclodextrin . The resultant stationary phase lead to stable chiral stationary phases, easier to prepare starting by coupling the selector to the amine’s group using EDC and NHS. In order to optimize enantio-separations by increasing the specific surface of open tubular columns, we reproduce the etching process to bared capillaries with ammonium bifluoride solution, referred to Pesek’s process4. By this mean, we increase dramatically the specific surface of bared capillaries before anchoring CDs polymers to silicate surfaces modified by APTEOS. Finally due to etching process, we obtain a covalent bonded Chiral Stationary Phase (CSP) which led to more efficient and resolvent enantio-separations by CEC. To describe, in another way, the non-covalent coating of CSP, we immobilised a cationic polymer (polytrimethyl ammonium β-CD+) on two kind of continuous organic and silica hybrid monoliths bearing sulfonate5 and phosphate’s groups. Based on precedent results for OT-CEC enantio-separation with LbL stationary phase7, using successive layers charged polymers to separate racemic mixture in CEC, we decided to adsorb a polycationic polymer hydrosoluble onto the silica hybrid monolith column to form chiral stationary phase (CSP) polytrimethyl ammonium β-cyclodextrin. This way of modification for monolithic surface by chiral selectors is nowadays highly efficient and attractive for CEC. The effect of the matrix and the coating’s nature are discussed by comparing the chromatographic parameters.

Understanding the supramolecular interactions governing the self-assembly of molecular building blocks upon surfaces is fundamental to the design of new devices such as sensors or catalysts. Successful heterogeneous enantioselective catalysts have relied upon the adsorption of ‘chiral modifiers’, usually chiral amino acids, onto reactive metal surfaces. One of the most researched examples is the hydrogenation of β-ketoesters using nickel-based catalysts. The stability of the chiral modifiers upon catalyst surfaces is a major obstacle to the industrial scale-up of this reaction. In this study, the replacement of conventional modifiers with porous, chiral and functionalised self-assembled networks is investigated. Perylene-3,4,9,10-tetracarboxylic diimide (PTCDI) and melamine (1,3,5-triazine,-2,4,6-triamine) have been shown to form hydrogen bonded networks on Ag-Si(111)√3x√3R30° in ultra-high vacuum (UHV) and Au(111) substrates in UHV and ambient conditions, these networks are capable of hosting guest molecules. These networks are investigated further in this study. In UHV, the behaviour of the components and network formation on Ni(111) is probed using scanning tunnelling microscopy (STM) and temperature-programmed desorption (TPD). The stability of the PTCDI-melamine network on Au(111) was analysed using TPD. Metal coordination interactions between each of the network components and nickel upon the Au(111) surface were examined by STM before testing the ability of the network to act as a template for metal growth. Finally, a number of polymerisation reactions are investigated with a view to replacing chiral modifiers with porous, chiral, functionalised covalent networks. Periodic covalent networks should possess the greater chemical and thermal stability required for more widespread use. In UHV and ambient conditions, STM is used to monitor the progress of surface-confined reactions on Au(111) and characterise the resultant covalent structures.

La conception de nouveaux matériaux fonctionnels a une longue histoire. Durant les deux dernières décennies, le domaine des polymères organiques et inorganiques a attiré l'attention des chercheurs. Plus important encore, les matériaux poreux tels que les Metal Organic Frameworks (MOFs), en anglais, Covalent Organic Frameworks (COFs), en anglais, ainsi que des polymères de coordination poreux sont maintenant étudiés de manière intensive en raison de leurs applications potentielles, comprenant le stockage de gaz, la séparation de gaz, la catalyse et la détection. D'un autre côté, les polymères contenant du Pt ont montré l'application potentielle dans les cellules solaires et les diodes électroluminescentes. Le mémoire est divisé en trois sections principales présentant des résultats nouveaux. Dans la première section, le chapitre 2 traite essentiellement de la formation de polymères de coordination (CP) avec des sels CuX (X = Cl, Br, I) et trans-[p-MeSC6H4C≡C-Pt(PMe3)2-C≡CC6H4SMe] (L1), soit dans le PrCN ou PhCN. Les polymères résultants sont soit 2D (bidimensionel) ou 1D (unidimensionel). Cependant, en presence de PrCN ou de PhCN, le CP 2D obtenu avec le CuBr n'a pas incorporé de solvant dans ses espaces vides. D'autre part, le CP 2D et le reste des CP 1D obtenus avaient soit des molécules de solvant de cristallisation dans leurs cavités ou coordonnés au cuivre sur la chaîne. Les unités cuivre-halogénures étaient soit des rhomboïdes Cu2X2 ou le cubane Cu4I4. Leurs mesures photophysiques en présence et en l'absence de molécules de solvant de cristallisation ont été effectuées. En outre, la porosité du CP a été évaluée par BET (N2 à 77 K). Le vapochromisme du CP 2D sans solvant et des CP 1D ont été étudiés, ainsi que les mesures de sorption du CO2 ont été effectuées. De plus, nous avons utilisé CuCN et L1 dans MeCN pour former de nouveaux CP’s. Ceci est rapporté dans la deuxième section, le chapitre 3. Le CP obtenu était inattendu : L1 s’est rompu et du cyanure CN‾ s’est coordonné sur le Pt. Ceci a conduit à la formation d’un CP 1D zigzag. Généralement, les CP sont formés avec L1 via des liens Cu-S ou/et Cu([éta]2-C≡C), mais pas dans le cas du CuCN qui lui forme une chaîne 1D (CuCN)n où le L1 rompu se lie avec cette chaîne via un lien Cu-N. Les propriétés photophysiques et de stabilité thermique ont été étudiées. La troisième section (Chapitre 4) traite d'une exploration des CP formés par la reaction des sels CuX (X = Cl, Br, I) et le trans-[p-MeSC6H4C≡C-Pt(PMe3)2-C≡CC6H4SMe] (L1) ou le trans-[p-MeSC6H4C≡C-Pt(PEt3)2-C≡CC6H4SMe] (L2) dans du MeCN afin de trouver des tendances. L'utilisation de L1 a donné lieu à un CP 2D ou 1D CPs avec le MeCN piégé à l'intérieur des cavités, il y a de l’espace vide. L2 a conduit uniquement à des CP 1D sans molecules de solvant de cristallisation. Des analyses thermogravimétriques, photophysique et des mesures d’adsorption de gaz (uniquement pour ceux avec du solvant) ont été étudiées. / Abstract: The design of new functional materials has a long history. For the past two decades, the field of organic and inorganic polymers has attracted attention of researchers. More importantly, porous materials such as Metal Organic Frameworks (MOFs), Covalent Organic Frameworks (COFs) as well as porous coordination polymers are now being intensively studied due to their potential applications including gas storage, gas separations, catalyst and sensing. On another hand, Pt-containing polymers have shown potential applications in solar cells and light emitting diodes. The masters’ thesis is mainly divided into three main sections presenting new results. In the first section; Chapter 2 mainly discusses the formation of coordination polymers with CuX salts (X= Cl, Br, I) and trans-[p-MeSC6H4C≡C-Pt(PMe3)2-C≡CC6H4SMe] (L1), in either PrCN or PhCN. The resulting polymers obtained were 2D (bidimensional) CPs or 1D (unidimensional) CPs in all cases. However, 2D CPs obtained when CuBr salt is used by either using PrCN or PhCN did not incorporate the solvents in their cavities. On the other hand, the 2D CP and the rest of 1D CPs obtained had either the crystallization molecules in the cavities or coordinated to the copper cluster. The copper-halide clusters were either the rhomboids Cu2X2 fragments or the step cubane Cu4I4. The photophysical measurements in the presence and absence of solvent crystallization molecules were performed. In addition, the porosity of the CPs was evaluated by adsorption isotherms. The vapochromism of the solvent-free 2D and 1D CPs were investigated as well as CO2 sorption measurements were perfomed. Furthermore, we then attempted to use CuCN and L1 in MeCN which is reported in the second section as Chapter 3. The obtained CP was unexpected as L1 broke and a cyanide (CN‾) ion coordinated to the Pt atom leading to the formation of zigzag 1D CP. The coordination bonds Cu-S or/and Cu([eta]2-C≡C) were generally observed with L1, but not in the CuCN case. Instead a 1D chain of (CuCN)n was made and the broken L1 now binds the chain via a Cu-N bond. The photophysical and thermal stability properties were studied. Lastly, the third section, Chapter 4 deals with a potential predictability of CP formation by using CuX salts (X= Cl, Br, I) and either trans-[p-MeSC6H4C≡C-Pt(PMe3)2-C≡CC6H4SMe] (L1) or trans-[p-MeSC6H4C≡C-Pt(PEt3)2-C≡CC6H4SMe] (L2) in MeCN as the solvent. The use of L1 resulted in either 2D or 1D CPs with the MeCN trapped inside of the cavities while L2 resulted in 1D CPs without MeCN being present in their cavities. The thermogravimetric, photophysical as well as gas sorption measurements (only for those with crystalisation molecules) were perfomed.

Le sujet général de cette thèse est l’étude de la fonctionnalisation covalente des nanotubes de carbone (CNT) et son application en électronique. Premièrement, une introduction au sujet est présentée. Elle discute des propriétés des CNT, des différentes sortes de fonctionnalisation covalente ainsi que des principales techniques de caractérisation utilisées au cours de la thèse. Deuxièmement, les répercussions de la fonctionnalisation covalente sur les propriétés des nanotubes de carbone monoparoi (SWNT) sont étudiées. Deux types de fonctionnalisation sont regardés, soit le greffage de groupements phényles et le greffage de groupements dichlorométhylènes. Une diminution de l’absorption optique des SWNT dans le domaine du visible-proche infrarouge est observée ainsi qu’une modification de leur spectre Raman. De plus, pour les dérivés phényles, une importante diminution de la conductance des nanotubes est enregistrée. Troisièmement, la réversibilité de ces deux fonctionnalisations est examinée. Il est montré qu’un recuit permet de résorber les modifications structurales et retrouver, en majorité, les propriétés originales des SWNT. La température de défonctionnalisation varie selon le type de greffons, mais ne semble pas affectée par le diamètre des nanotubes (diamètre examinés : dérivés phényles, Ømoyen= 0,81 nm, 0,93 nm et 1,3 nm; dérivés dichlorométhylènes, Ømoyen = 0,81 nm et 0,93 nm). Quatrièmement, la polyvalence et la réversibilité de la fonctionnalisation covalente par des unités phényles sont exploitées afin de développer une méthode d’assemblage de réseaux de SWNT. Celle-ci, basée sur l’établissement de forces électrostatiques entre les greffons des SWNT et le substrat, est à la fois efficace et sélective quant à l’emplacement des SWNT sur le substrat. Son application à la fabrication de dispositifs électroniques est réalisée. Finalement, la fonctionnalisation covalente par des groupements phényles est appliquée aux nanotubes de carbone à double paroi (DWNT). Une étude spectroscopique montre que cette dernière s’effectue exclusivement sur la paroi externe. De plus, il est démontré que la signature électrique des DWNT avant et après la fonctionnalisation par des groupements phényles est caractéristique de l’agencement nanotube interne@ nanotube externe. / The general subject of this thesis is the covalent functionalization of carbon nanotubes and its applications in electronics. First, the properties of the carbon nanotubes, their functionalization, and the principal techniques used to characterize them are presented. Second, the repercussions of the grafting of phenyl addends and dichloromethylene addends on the properties of single-wall carbon nanotubes (SWNT) are investigated. A decrease of light absorption and a modification of the Raman spectra of the nanotubes are observed as well as, for the phenyl derivatives, an important loss of their electrical conductivity. Third, the reversibility of the functionalization is examined. The study shows that the addends are detached from the sidewall upon annealing, leading to the reconstruction of the graphene structure. Most of the original properties of the SWNT are then recovered. In addition, it is observed that the temperature of defunctionalization depends on the nature of the addends, but it is not influenced by the diameter of the SWNT (Range studied: phenyl derivatives, Ømoyen= 0,81 nm, 0,93 nm et 1,3 nm; dichlorométhylènes derivatives, Ømoyen = 0,81 nm et 0,93 nm). Fourth, a new method to reliably self-assemble networks of dense SWNT onto patterned substrates is presented. The method is based on covalent functionalization and electrostatic interactions. Its suitability for making electronic devices is demonstrated. Last, this thesis investigated the covalent functionalization of double-wall carbon nanotubes (DWNT). A spectroscopic study revealed that the grafting of the phenyl addends occurs exclusively on the outer wall. Furthermore, the identification of the metallic or semiconductor character of each wall of the DWNT is realized using electrical measurements taken before and after the functionalization.

Les nanotubes de carbone et le graphène sont des nanostructures de carbone hybridé en sp2 dont les propriétés électriques et optiques soulèvent un intérêt considérable pour la conception d’une nouvelle génération de dispositifs électroniques et de matériaux actifs optiquement. Or, de nombreux défis demeurent avant leur mise en œuvre dans des procédés industriels à grande échelle. La chimie des matériaux, et spécialement la fonctionnalisation covalente, est une avenue privilégiée afin de résoudre les difficultés reliées à la mise en œuvre de ces nanostructures. La fonctionnalisation covalente a néanmoins pour effet de perturber la structure cristalline des nanostructures de carbone sp2 et, par conséquent, d’affecter non seulement lesdites propriétés électriques, mais aussi les propriétés optiques en émanant. Il est donc primordial de caractériser les effets des défauts et du désordre dans le but d’en comprendre les conséquences, mais aussi potentiellement d’en exploiter les retombées. Cette thèse traite des propriétés optiques dans l’infrarouge des nanotubes de carbone et du graphène, avec pour but de comprendre et d’expliquer les mécanismes fondamentaux à l’origine de la réponse optique dans l’infrarouge des nanostructures de carbone sp2. Soumise à des règles de sélection strictes, la spectroscopie infrarouge permet de mesurer la conductivité en courant alternatif à haute fréquence des matériaux, dans une gamme d’énergie correspondant aux vibrations moléculaires, aux modes de phonons et aux excitations électroniques de faible énergie. Notre méthode expérimentale consiste donc à explorer un espace de paramètres défini par les trois axes que sont i. la dimensionnalité du matériau, ii. le potentiel chimique et iii. le niveau de désordre, ce qui nous permet de dégager les diverses contributions aux propriétés optiques dans l’infrarouge des nanostructures de carbone sp2. Dans un premier temps, nous nous intéressons à la spectroscopie infrarouge des nanotubes de carbone monoparois sous l’effet tout d’abord du dopage et ensuite du niveau de désordre. Premièrement, nous amendons l’origine couramment acceptée du spectre vibrationnel des nanotubes de carbone monoparois. Par des expériences de dopage chimique contrôlé, nous démontrons en effet que les anomalies dans lespectre apparaissent grâce à des interactions électron-phonon. Le modèle de la résonance de Fano procure une explication phénoménologique aux observations. Ensuite, nous établissons l’existence d’états localisés induits par la fonctionnalisation covalente, ce qui se traduit optiquement par l’apparition d’une bande de résonance de polaritons plasmons de surface (nanoantenne) participant au pic de conductivité dans le térahertz. Le dosage du désordre dans des films de nanotubes de carbone permet d’observer l’évolution de la résonance des nanoantennes. Nous concluons donc à une segmentation effective des nanotubes par les greffons. Enfin, nous montrons que le désordre active des modes de phonons normalement interdits par les règles de sélection de la spectroscopie infrarouge. Les collisions élastiques sur les défauts donnent ainsi accès à des modes ayant des vecteurs d’onde non nuls. Dans une deuxième partie, nous focalisons sur les propriétés du graphène. Tout d’abord, nous démontrons une méthode d’électrogreffage qui permet de fonctionnaliser rapidement et à haute densité le graphène sans égard au substrat. Par la suite, nous utilisons l’électrogreffage pour faire la preuve que le désordre active aussi des anomalies dépendantes du potentiel chimique dans le spectre vibrationnel du graphène monocouche, des attributs absents du spectre d’un échantillon non fonctionnalisé. Afin d’expliquer le phénomène, nous présentons une théorie basée sur l’interaction de transitions optiques intrabandes, de modes de phonons et de collisions élastiques. Nous terminons par l’étude du spectre infrarouge du graphène comportant des îlots de bicouches, pour lequel nous proposons de revoir la nature du mécanisme de couplage à l’œuvre à la lumière de nos découvertes concernant le graphène monocouche. / Carbon nanotubes and graphene are sp2 hybridized carbon nanostructures which electrical and optical properties raise considerable interest for the design of a new generation of electronic devices and optically active materials. However, many challenges remain before their implementation in industrial processes on a large scale. Materials chemistry, especially covalent functionalization, is a privileged avenue to resolve the difficulties related to the processing of these nanostructures. Covalent functionalization, however, disrupts the sp2 carbon nanostructures’ crystalline structure, and pertubs not only said electrical properties, but also the deriving optical properties. It is therefore essential to characterize the effects of defects and disorder in order to understand their consequences, but also to potentially exploit the benefits. This thesis deals with the optical properties in the infrared of carbon nanotubes and graphene, with the aim to understand and explain the fundamental mechanisms at the origin of the optical response in the infrared of sp2 carbon nanostructures. Subject to strict selection rules, infrared spectroscopy measures the high frequency AC conductivity of materials in an energy range corresponding to molecular vibrations, phonon modes and low energy electronic excitations. Our experimental method is therefore to explore a parameter space defined by the three axes that are i. the dimensionality of the material, ii. the chemical potential, and iii. the disorder level, which allows us to identify the various contributions to optical properties in the infrared of sp2 carbon nanostructures. At first, we focus on the infrared spectroscopy of single-walled carbon nanotubes as a function of doping and disorder level. We start by amending the commonly accepted origin of single-walled carbon nanotubes vibrational spectra. Using controlled chemical doping experiments, we show that the anomalies in the carbon nanotube spectra appear through electron-phonon interactions. The Fano resonance model provides a phenomenological explanation for the observations. Then, we establish the existence of localized states induced by covalent functionalization, which appear as a surface plasmon polariton resonance (nanoantenna) contributing to the terahertz conductivity peak. Control of the disorder level in carbon nanotube films allows us to observe the evolution of the nanoantenna resonance. We therefore conclude to an effective segmentation of the nanotubes by the grafts. Finally, we show that disorder activates phonon modes that are usually forbidden by infrared spectroscopy’s selection rules. Disorder-induced infrared activity originates from elastic collisions on defects that give access to phonon modes with non-zero wave vectors. In a second part, we focus on the properties of graphene. First, we demonstrate an electrografting method to rapidly functionalize graphene with high-density, regardless of the substrate. Subsequently, we use electrografting to show that disorder activates chemical potential dependent anomalies in the vibrational spectra of single-layer graphene. These anomalies are absent in the spectra of pristine samples. In order to explain this phenomenon, we present a theory based on the interaction of intraband optical transitions, phonon modes and elastic collisions. We conclude by studying the infrared spectra of graphene with bilayer islands, for which we propose to review the nature of the coupling mechanism in the light of our findings on single-layer graphene.

Le graphène est une nanostructure de carbone hybridé sp2 dont les propriétés électroniques et optiques en font un matériau novateur avec un très large potentiel d’application. Cependant, la production à large échelle de ce matériau reste encore un défi et de nombreuses propriétés physiques et chimiques doivent être étudiées plus en profondeur pour mieux les exploiter. La fonctionnalisation covalente est une réaction chimique qui a un impact important dans l’étude de ces propriétés, car celle-ci a pour conséquence une perte de la structure cristalline des carbones sp2. Néanmoins, la réaction a été très peu explorée pour ce qui est du graphène déposé sur des surfaces, car la réactivité chimique de ce dernier est grandement dépendante de l’environnement chimique. Il est donc important d’étudier la fonctionnalisation de ce type de graphène pour bien comprendre à la fois la réactivité chimique et la modification des propriétés électroniques et optiques pour pouvoir exploiter les retombées. D’un autre côté, les bicouches de graphène sont connues pour avoir des propriétés très différentes comparées à la monocouche à cause d’un empilement des structures électroniques, mais la croissance contrôlée de ceux-ci est encore très difficile, car la cinétique de croissance n’est pas encore maîtrisée. Ainsi, ce mémoire de maîtrise va porter sur l’étude de la réactivité chimique du graphène à la fonctionnalisation covalente et de l’étude des propriétés optiques du graphène. Dans un premier temps, nous avons effectué des croissances de graphène en utilisant la technique de dépôt chimique en phase vapeur. Après avoir réussi à obtenir du graphène monocouche, nous faisons varier les paramètres de croissance et nous nous rendons compte que les bicouches apparaissent lorsque le gaz carboné nécessaire à la croissance reste présent durant l’étape de refroidissement. À partir de cette observation, nous proposons un modèle cinétique de croissance des bicouches. Ensuite, nous effectuons une étude approfondie de la fonctionnalisation du graphène monocouche et bicouche. Tout d’abord, nous démontrons qu’il y a une interaction avec le substrat qui inhibe grandement le greffage covalent sur la surface du graphène. Cet effet peut cependant être contré de plusieurs façons différentes : 1) en dopant chimiquement le graphène avec des molécules réductrices, il est possible de modifier le potentiel électrochimique afin de favoriser la réaction; 2) en utilisant un substrat affectant peu les propriétés électroniques du graphène; 3) en utilisant la méthode d’électrogreffage avec une cellule électrochimique, car elle permet une modulation contrôlée du potentiel électrochimique du graphène. De plus, nous nous rendons compte que la réactivité chimique des bicouches est moindre dû à la rigidité de structure due à l’interaction entre les couches. En dernier lieu, nous démontrons la pertinence de la spectroscopie infrarouge pour étudier l’effet de la fonctionnalisation et l’effet des bicouches sur les propriétés optiques du graphène. Nous réussissons à observer des bandes du graphène bicouche dans la région du moyen infrarouge qui dépendent du dopage. Normalement interdites selon les règles de sélection pour la monocouche, ces bandes apparaissent néanmoins lorsque fonctionnalisée et changent grandement en amplitude dépendamment des niveaux de dopage et de fonctionnalisation. / Graphene is a sp2 hybridized carbon nanostructure with incredible electronical and optical properties that make it interesting for various applications. Its large scale production is still a challenge and there is still some physical and chemical properties that need further studies to better exploit them. Covalent functionalization is a chemical reaction that can be used as a tool to study those properties because it breaks the sp2 crystalline structure, so it modulates the properties of graphene. There are not many studies of that reaction on graphene deposited on a surface because the chemical reactivity depends greatly on the chemical environment. That is why it is important to study the functionalization of graphene on surfaces to understand chemical reactivity and the modification of electronical and optical properties in order to potentially exploit the benefits. This master thesis is focusing on the chemical reactivity of graphene to covalent functionalization and the study of its optical properties. First, we grow graphene using the chemical vapour deposition method. After the growth of monolayer, we change the parameters and we observe the formation of bilayers if the carbonated gas is present during the cooling step of the growth. From that observation, we propose a kinetic model of bilayer growth. Then we proceed to a detailed study of monolayer and bilayer graphene functionalization. First, we demonstrate that there is a substrate effect that inhibits greatly the grafting of organic molecules on the graphene surface. However it is possible to overcome this substrate effect by different ways: 1) chemical doping of the graphene with reducing molecules can modify the electrochemical potential to enhance the reaction; 2) transferring graphene on a substrate that doesn’t affect the electronical properties of graphene; 3) the use of an electrografting method with an electrochemical cell can also modulate the potential so the efficiency of the reaction is enhanced. Also, we observe that the chemical reactivity of bilayer graphene is lower compared to the monolayer because of structural rigidity caused by interlayer interaction. Finally, we demonstrate that the infrared spectroscopy is a powerful tool to study the effect of functionalization and the effect of bilayers on the optical properties of graphene. We observe some bands in the region of the mid-IR, while the infrared selection rules don’t predict any. Also, the shape of those bands change greatly depending on the doping level when there is bilayers or when the graphene is functionalized.

L’étude de la structure de complexes non-covalents présente un intérêt fondamental dans la recherche en chimie des protéines. Le premier objectif est de caractériser les interactions physico-chimiques sur lesquelles repose l’adoption d’une structure tridimensionnelle fonctionnelle par un édifice multimoléculaire. Le second objectif est de mettre en évidence les changements structuraux induits par le phénomène de complexation, et leur influence sur la fonction du système. Le couplage entre la spectrométrie de masse et la mobilité ionique (IM/MS) est une technique d’étude structurale en phase gazeuse, dont le principe repose sur la séparation d’ions selon leur forme et leur rapport masse sur charge, et qui permet en outre de mesurer leurs sections efficaces de diffusion. Grâce à cette technique, nous avons réalisé l’étude structurale de trois complexes non-covalents : l’agrégation de molécules de tanin sur la protéine salivaire humaine IB5, la fixation du ligand Ac2KAA sur la vancomycine, et la complexation de cations métalliques sur des polymères poly-lactide. L’évolution des sections efficaces en fonction de la taille du système ou de l’état de complexation met en évidence la présence de transitions structurales. De plus, utilisé avec de la modélisation moléculaire ou de la spectroscopie laser, le couplage IM/MS s’avère pertinent pour caractériser les interactions responsables de la stabilisation de tels complexes. Ces travaux de thèse montrent que cette technique , au-delà du simple aspect analytique (séparation d’isomères), peut également être utilisée au sein d’études plus globales, mettant en jeu plusieurs techniques afin de résoudre la structure de systèmes complexes / Knowing the structure of non-covalent complexes is essential to understand many biological processes. The first step is the characterization of the interactions leading to the adoption of a functional tridimensional structure by a multimeric assembly. The second step consists of underlining the structural modifications induced by the complexation, and their influence on the system’s function. The Ion Mobility/Mass Spectrometry (IM/MS) is a gas-phase method that is used to separate ions according to their geometry and their masse-to-charge ratio. IM/MS also provides insights on their intrinsic properties, by measuring their collision cross sections. Using this method, we have studied the structure of three different non-covalent complexes: the aggregation of tannins on the human salivary protein IB-5, the fixation of a small ligand (Ac2KAA) on vancomycin, and the complexation between metallic cations and poly-lactid polymers. The evolution of the collision cross-sections as a function of the size of the system or the complexation state clearly shows structural transitions. Moreover, combined with molecular modeling or laser spectroscopy, the IM/MS technique reveals to be a powerful tool to characterize the relevant interactions in such systems. This work proves that IM/MS, besides a powerful analytical aspect, can also be used in global studies that involve several structural methods to resolve the structure of large multimeric assemblies

Cerca de 20 % dos casos familiares de esclerose lateral amiotrófica (ELAf) são causados por mutações na enzima Cu,Zn-superóxido dismutase (SOD1). Inicialmente se supôs que as enzimas mutantes teriam a atividade SOD comprometida, entretanto isto não foi comprovado. Atualmente, considera-se que as enzimas mutantes adquiram propriedades tóxicas. Quais seriam estas propriedades e como levariam à degeneração do neurônio motor são questões ainda não respondidas. Neste trabalho, comparamos neuroblastomas humanos transfectados com SOD1 G93A associada à ELAf (SH-SY5YG93A), e SOD1 selvagem (SH-SY5YWT) com células parentais (SH-SY5Y) em relação ao crescimento, viabilidade, produção basal de oxidantes, atividades SOD e peroxidásica e modificações estruturais da SOD. As células transfectadas apresentaram aumento na taxa de crescimento e na produção basal de oxidantes. As células SH-SY5YWT e SH-SY5YG93A mantiveram a expressão de SOD1 e atividade consistente com o aumento esperado de duas vezes, em estágios iniciais de cultura. A atividade peroxidásica do homogenato da célula SH-SY5YG93A foi maior. Após quatro semanas, a linhagem SH-SY5YG93A manteve a expressão de SOD1, mas as atividades dismutásica e peroxidásica diminuíram. A expressão de SOD1 aumentou a proporção de formas alteradas de SOD1, como enzima reduzida, multímeros formados por ponte dissulfeto e formas insolúveis em detergente, particularmente na linhagem SH-SY5YG93A. Entre estas formas insolúveis, identificamos um dímero covalente de SOD. Estas formas alteradas provavelmente são responsáveis pela ativação do proteassomo e estresse do retículo endoplasmático, verificados nas células transfectadas. Concluindo, a superexpressão da SOD1 foi suficiente para elevar as formas imaturas e oligomerizadas de SOD1 e a oxidação basal, e a mutação G93A ressaltou estes processos. / Some familial ALS (fALS) are caused by mutations in the Cu,Zn-superoxide dismutase enzyme (SOD1). It was thought that the mutated enzymes would have impaired SOD activity, but this has not been corroborated so far. Presently, it is more accepted that the mutated enzymes acquire a new toxic function. What this new toxic function is and how it relates to the degeneration of motor neurons remains debatable. Here, we compared human neuroblastoma cells transfected with fALS mutant G93A (SH-SY5YG93A) or wild-type SOD1 (SH-SY5YWT) with parent cells (SH-SY5Y) in regard to growth, viability, basal oxidant production, SOD and peroxidase activities, and SOD forms. Transfected cells presented increased growth rate and basal oxidant production. SH-SY5YWT and SH-SY5YG93A cells in early culture stage showed SOD expression and activity consistent with the expected two-fold increase; SH-SY5YWT homogenates showed increased peroxidase activity. After four weeks, SH-SY5YG93A maintained SOD1 expression levels but peroxidase and dismutase activities were lower. SOD1 expression increased the levels of altered SOD1 forms such as the reduced enzyme, disulfide multimers and detergent-insoluble forms, particularly in SH-SY5YG93A cells. Among the insoluble forms a covalent SOD dimer was identified. These altered SOD forms are probably responsible for proteasome activation and endoplasmatic reticulum stress response verified in transfected cells. In conclusion, SOD1 over-expression was sufficient to increase intracellular immature and oligomerized SOD1 forms and basal oxidation and the G93A mutation enhanced these processes.

A atividade de cisteíno proteases (CP) tem sido relacionada a diferentes patologias, como no caso da leishmaniose, doença de Chagas de alguns tipos de câncer. Devido a homologia entre as cisteíno proteases presentes em altos níveis nesses sistemas celulares, foi investigada aqui a importância dessas enzimas para o desenvolvimento e estabelecimento dessas doenças a partir da atividade biológica in vitro de novos inibidores reversíveis de cisteíno proteases. De maneira geral, as substâncias apresentaram relevante atividade inibitória de cisteíno proteases expressas pelos diferentes sistemas celulares, com máximo de inibição de 42% para o Neq0554 em relação à atividade de CP expressas por Leishmania spp. e 76% em relação a atividade de CP expressas por células de câncer de pâncreas. Diferentes níveis de atividade biológica foram observados entre os sistemas celulares, porém todos apresentaram supressão em relação aos parâmetros citostáticos após a inibição da atividade de CP. Quando testados em Leishmania spp. o crescimento celular foi suprimido em pelo menos 67%, com máximo de inibição de 95% para o Neq0551 a 10 μM. Da mesma maneira, em células de câncer de pâncreas, alterações no ciclo celular e supressão dos processos de migração e formação de colônias foram os resultados mais evidentes, comretenção de 50% da capacidade de formação de colônias das células Mia-Paca2 pelo Neq0554 a 10 μM. Já em relação aos protozoários da capa Y de Trypanosoma cruzi os inibidores testados apresentaram interessante seletividade contra os parasitos, em relação à célula hospedeira LLC-MK2, além de promoverem a supressão de cerca de 80% do processo de invasão celular in vitro quando a célula hospedeira foi previamente tratada com 10 μM do inibidor Neq0662 por 2 h antes do processo de infecção. Por fim, a encapsulação do Neq0554 em apoferritina promoveu um incremento na atividade anticancerígena para células de câncer de pâncreas, com IC50 de 79 μM contra > 200 μM em relação às células de fibroblasto, aumentando sua seletividade. De maneira geral, os resultados corroboram a hipótese de a inibição de cisteíno proteases nos sistemas celulares é eficiente para promover efeitos citostáticos, podendo ser utilizada com controle e supressão do desenvolvimento das patologias. Além disso, a atividade de CP nas células de protozoários e câncer de pâncreas apresentou perfil semelhante de ação, no qual inibidores de CP não promoveram a morte em nível significativo das células, mas ressaltaram os efeitos citostáticos em relação ao crescimento celular. / Cysteine proteases (CP) activity has been related to different pathologies, such as leishmaniasis, Chagas disease and some types of cancer. Due to the homology between cysteine proteases expressed by these cellular systems, it was investigated here the importance of these enzymes for the development and establishment of these diseases based on the in vitro biological activity of novel reversible cysteine protease inhibitors. In general, the inhibitor showed a significant inhibitory activity of cysteine proteases expressed by the different cellular systems, with a maximum inhibition of 42% for Neq0554 concerning the CP activity expressed by Leishmania spp. and 76% to CP activity expressed by pancreatic cancer cells. Different profiles of biological activity were observed between the cellular systems, but all substances had significant CP activity suppression, in cytostatic levels after the inhibition of CPA. When the inhibitors were tested against Leishmania spp., the cell growth was suppressed by at least 67%, with maximum inhibition of 95% for Neq0551 at 10 μM. Similarly in pancreatic cancer cells, changes in the cell cycle profile were the most evident results, as well as the suppression of migration and colony formation ability, with 50% retention of the colony development of Mia-Paca2 cells by Neq0554 at 10 μM. In contrast, to protozoa from Trypanosoma cruzi Y strain, the inhibitors tested showed an interesting selectivity against the parasites concerning the host cell LLC-MK2, also promoting the in vitro cell invasion suppression in about 80% when the host cell was pre-treated with Neq0662 10 μM for 2 h. Finally, the encapsulation of Neq0554 promoted an increase in its anticancer activity against pancreatic cancer cells, with IC50 of 79 μM alongside > 200 μM to fibroblast cells, besides increasing its selectivity. In general, the results corroborate the hypothesis that the inhibition of cysteine proteases in the cellular systems is efficient to promote cytostatic effects, being an interesting tool to be used as control and development suppression of some pathologies. Also, CP activity in protozoa cells and pancreatic cancer showed a similar profile of action, in which cysteine protease inhibitors did not promote death at a significant level for the cells, but emphasized cytostatic effects about cell growth.