As ligações de hidrogênio (LH), fundamentais na determinação da estrutura da água, proteínas, etc., são muito importantes no reconhecimento molecular e nos mecanismos de reações enzimáticas. A determinação da energia das LHs intramoleculares em proteínas e intermoleculares entre uma proteína e o solvente água, porque fornece informações sobre a estrutura secundária, terciária e quaternária das proteínas. Um método para quantificar e qualificar as LHs foi desenvolvido utilizando critérios de distância, geométricos e energéticos a partir das trajetórias obtidas por simulações de dinâmica molecular. O método foi testado com o monômero de uma fosfolipase A2 homodimérica, sem atividade catalítica, isolada do veneno da Bothrops asper(BaspMT-II). No dímero, a análise das LHs mostrou que elas são também essenciais na manutenção da estrutura quaternária. Essa análise permitiu identificar movimentos do tipo dobradiça acompanhados da formação transitória, na interface dimérica, de LHs controladas pelo triptofano na posição 77. Esses movimentos podem estar associados à ação danosa às membranas, uma vez que podem promover a inserção da região C-terminal na membrana. Estudos prévios mostraram que o peptídeo sintético (3Y codificado pelos aminoácidos 115-129 da BaspMT-II) apresenta atividade bactericida e citolítica. Um outro peptídeo (3W), mutante de 3Y, no qual três resíduos tirosina são substituidos por triptofano, apresenta um aumento do dano às membranas e do efeito miotóxico. Os mecanismos de ação desses peptídeos e as suas estruturas foram estudados por dinâmica molecular, dicroísmo circular (DC), microscopia de fluorescência e monocamadas de Langmuir (Mlang). As adsorções dos peptídeos em monocamadas de ácido dimiristoil fosfatídico (DMPA) e dimiristoilfosfatidilcolina (DMPC) se processam por mecanismos diferentes ocasionados pelas diferentes naturezas físico-químicas dos resíduos tirosina e triptofano. A microscopia de fluorescência acoplada a Mlang de DMPA com 3W adsorvido mostra um aumento da fluidez da monocamada, enquanto que o 3Y modifica os domínios do DMPA para pequenas estruturas circulares. Foram realizadas simulações dos peptídeos 3Y e 3W em meio aquoso e nas regiões interfaciais água/n-hexano e água/bicamadas de DMPC. Os resultados confirmam os obtidos por Mlang, demonstrando que os peptídeos interagem diferentemente com as membranas por adotar conformações alternativas definidas previamente. Essas conformações, diferentes das observadas em meio aquoso, dependem da natureza da interface. As estruturas encontradas no final das simulaçoes corroboram o mecanismo proposto por Mlang, assim como as estruturas sugeridas por DC. Isso sugere que a atividade biológica reduzida do peptídeo 3Y ocorre porque os seus dois resíduos Leu se adsorvem na interface sem penetrá-la. Ao contrário de 3W, os resíduos carregados do peptídeo 3Y não estão localizados corretamente para promover uma interação suficientemente atrativa para permitir a sua inserção na membrana celular. / Hydrogen bonds (HB) are highly important in the determination of the structure of the water and proteins. They also play a important role in molecular recognition and in enzyme reaction mechanisms. The determination of protein/water intermolecular and protein intramolecular HB energies provide information with respect to the formation and stabilization of secondary, tertiary and quaternary protein structure. A method that quantifies and qualifies the properties of HB was developed using distance, geometric and energy criteria as applied to data obtained from the atomic trajectories generated by molecular dynamics simulations. The method was tested with a monomer of a catalytically inactive homodimeric phospholipase A2 from Bothrops asper(BaspMT-II) venom. HBs at dimmer interface are essential for maintaining the quaternary structure, and are highly conserved during hinge-like movements of the dimmer. HB formed by tryptophan residue at position 77 controls this movement. These motions can be associated to the membrane damaging action since they facilitate the insertion of the C-terminus into the cellular membrane. Previous studies have shown that synthetic peptide (3Y, coding the amino acids 115-129 of BaspMT-II ) presents bactericidal and cytolitic activities. A peptide variant ( 3W ), in which tyrosine residues were substituted by tryptophan residues, presents an enhanced membrane damaging activity increased miotoxic effect. The mechanism of action of the peptides and their structures were studied by molecular dynamics simulations, circular dichroism (CD), fluorescence microscopy and Langmuir monolayers (Mlang). The adsorption of the peptides on a monolayer composed of dimiristoyl phosphatidic acid (DMPA) and dimiristoylphosphatidyl choline (DMPC) occurs through different processes due to the differences in the physic-chemical nature of the tyrosine and tryptophan residues. Fluorescence microscopy together with Mlang of DMPA with adsorbed 3W indicates an increase of the membrane fluidity while small circular domains are formed with DMPA. Simulations were conducted with the 3Y and 3W peptides in aqueous media, is a water/n-hexane and water/DMPC bilayers. The results confirm the Mlang results, showing that the peptides interact differently with the membranes by adopting alternative previously defined conformations. These two conformations, both of which are different to those observed in water, are dependent of the nature of the interfaces. The final simulated configurations confirm the mechanism proposed by Mlang and the structures proposed by CD. It is suggest that the reduced biological activity of the 3Y peptide is due to the two Leu residues that only adsorb to the cellular membrane without penetrating the bilayer. In contrast to the 3W peptide, no charged residue is correctly located to promote the interaction and insertion of the 3Y peptide into the membrane.

Muitas espécies do gênero Aristolochia (Familia Aristolochiaceae) têm sido usadas na medicina tradicional e folclórica como medicamentos e tônicos, as quais demonstravam atividades farmacológicas de interesse clínica e medica como anti-hemorrágica, anti-parasita, antibacteriano, antifúngico, analgésico, antitumoral entre outras. Visando a obtenção de mais informações sobre essas plantas e na procura por substâncias com efeitos antiofídicos, neste trabalho avaliou-se à ação de extratos aquoso, metanólico e de acetato de etila de folhas e caule contra as ações tóxicas da peçonha de Bothrops asper, ambos procedentes do Panamá e contra o efeito miotóxico da peçonha de Bothrops jararacussu e das miotoxinas BthTX-I (isolada de B. jararacussu) e Mtx-II (isolada de B. asper). O extrato das folhas em acetato de etila apresentou a melhor inibição da atividade fosfolipásica da peçonha de B. asper, demonstrando inibição de 45%, 35% e 33% nas proporções de 1:5, 1:10 e 1:30 (m/m), respectivamente. Enquanto que, o extrato de caule em acetato de etila demonstrou maior eficácia na neutralização da atividade coagulante, e, além disso, inibiu 96%, 92% e 87% do edema, da miotoxicidade e hemorragia induzidas pela peçonha de B. asper, respectivamente. Os percentuais diferenciados na neutralização das ações tóxicas da peçonha de Bothrops asper, revelam diferentes perfis do potencial antiofídico de Aristolochia sprucei. Um dos componentes bioativos foi isolado do extrato de caule desta planta por CLAE, e a caracterização química, por ressonância magnética nuclear, demonstrou ser o ácido aristolóquio que inibiu a atividade miotóxica das peçonhas de B. jararacussu e de B. asper em 80% e 85% e assim como a atividade miotóxica da BthTX-I e Mtx-II em 64% e 60%, respectivamente. A atividade hemolítica indireta da peçonha de B. asper foi inibida em 43% pelo o ácido aristolóquio. A análise dos espectros de dicroísmo circular e os estudos de interação por modelagem molecular sugerem que o ácido aristolóquio forma um complexo com a Mtx-II de B. asper inibindo sua atividade. A ligação do ácido aristoloquio com as miotoxinas (MjTX-1, BthTX-II) modificou a forma e a intensidade dos espectros de dicroísmo circular da miotoxina e induziu alterações na porcentagem dos diversos domínios que constituem a estrutura secundária desta miotoxina. Os resultados obtidos confirmam que os extratos de A. sprucei possuem propriedades antiofídicas e sugerem a necessidade de aprofundar estudos que permitam utilizar com segurança os extratos e o principio ativo isolado como suplementos dos antisoros para aumentar a eficácia na neutralização dos efeitos tóxicos locais da peçonha das serpentes. / A lot of species of genus Aristolochia (Familia Aristolochiacheae) have been used in traditional medicine and folk, such as medicaments and tonics, which show pharmacological activities of clinic and medical interest, like antihemorragic, antiparasitic, antibacterial, antifungic, analgesic, antitumoral between others. Expecting to get more information about these plants and in the search by substances with antiophidic effects, in this work was evaluated the action of aqueous, metanolic and ethyl acetate extracts from leaves and stems of Aristolochia sprucei against the toxic action of Bothrops asper venom, both native from Panamá and against the myotoxic effect of Bothrops jararacussu venom and BthTX1 (isolated from B. jararacussu) and Mtx-II (isolated from Bothorps asper). The leaves extracts in ethyl acetate showed the best inhibition registered of PLA2 activity of venom de B. asper showing inhibition of 45 %, 35 % and 33 %, in proportion (m/m) of 1:5, 1:10 and 1:30 respectively. As regards to stem extract in ethyl acetate, it showed high efficacy in neutralization of coagulant activity, besides It inhibited 96 %, 92 % and 87 % of edema, myotoxicity and hemorrhage induced by B. asper venom, respectively. One of bioactives components was isolated from stem extract of this plant by CLAE and the chemical characterization by nuclear magnetic resonance, this showed that the compound is the aristolochic acid. This compound inhibited the myotoxic activity of B. jararacussu and B. asper venom in 80 % and 85 %, so like myotoxic activity of BthTx-I and MTx-II in 64 % and 60 % respectively. The indirect hemolytic activity of B. asper venom was inhibited in 43 % by the aristolochic acid. The analyze of spectrum of circular dichroism and the studies of interaction by molecular modelagem suggest that the aristolochic acid forms a complex 1:1 with the miotoxin inhibiting their activity. The joint of aristolochic acid with the miotoxins (MjTX-1, BthTx-II) changes the way and the intensity of spectra from dichroism circular of miotoxin and It induced alteration in percentage of several domains that constitute a secondary structure from this toxin. The results obtained confirm that the extracts of A. sprucei have antiophidic properties and it suggest the necessity of deepen studies that allow to use with safety the extracts and the isolated active principle, like antiserum supplements to increase the efficacy in the neutralization of local toxics effects of snakes venoms.

Cette thèse porte sur l'étude des interactions faibles et de la spectroscopie vibrationnelle en phase condensée à partir d'un développement théorique basé sur la théorie de la perturbation de la fonctionnelle de densité. D'une part des corrections de la fonction d'onde Born-Oppenheimer ont été calculées pour déterminer le moment magnétique induit par les vibrations et ainsi calculer des spectres de dichroïsme circulaire vibrationnel. D'autre part, une modélisation des effets de polarisation est réalisée à l'aide d'une nouvelle représentation de la susceptibilité électronique non-locale. / This thesis deals with the development and application of computational methods for the efficient and accurate calculation of spectroscopic parameters and non-covalent inter-molecular interactions in condensed-phase systems from quantum chemical methods. Specifically, electronic current densities and polarizability effects are computed using density functional perturbation theory. The nuclear velocity perturbation theory is rigorously derived from the exact factorization of the electron-nuclear wave function. Its implementation within a large-scale electronic structure program package is reported and the calculation of dynamical vibrational circular dichroism in the condensed phase is demonstrated. A position-dependent mass of nuclei in molecules is derived, addressing the fundamental questions as to how masses move in a molecule. First steps towards a density-based modeling of inter-molecular interactions using a compact representation of the electronic susceptibility are devised.

Le but de cette thèse est de montrer la réponse de la membrane mitochondriale au cours la régulation de l’apoptose en étudiant l’effet de domaines clés sur la dynamique membranaire et l’importance de la composition phospholipidiques des modèles utilisés. Le domaine BH4 est la partie spécifique anti-apoptotique de la famille Bcl-2. La première étape a été de synthétiser le peptide par voie chimique en utilisant la synthèse peptidique en phase solide. Un protocole décrivant les étapes de purification par chromatographie liquide et de caractérisation par spectroscopie de masse, garantissant une pureté indispensable pour des études biophysiques, a été établi. La modification de la structure secondaire du peptide interagissant avec des vésicules a été étudiée par spectroscopie infrarouge ainsi que par dichroïsme circulaire. Le peptide s’agrège à la surface et s’insère peu profondément dans la partie hydrophobe de la membrane. En utilisant la résonance magnétique nucléaire (RMN) et la calorimétrie, il a été montré que le peptide BH4 modifie l’organisation et la dynamique des liposomes mimant la surface mitochondriale. La deuxième étude a porté sur la première hélice de la protéine pro-apoptotique Bax (Bax-a1) qui a la propriété de diriger la protéine cytosolique vers la mitochondrie. Un protocole de synthèse et purification a été à nouveau établi. Le but de cette étude est de démontrer le rôle de l’interaction spécifique entre la cardiolipine, un phospholipide uniquement présent dans la mitochondrie et le peptide Bax-a1. Les études RMN ont montré que Bax-a1 n’interagissait uniquement que si la cardiolipine était présente, produisant un fort effet électrostatique piégeant le peptide à la surface de la membrane. Enfin, un nouveau protocole permettant d’étudier la réponse des lipides de mitochondries isolées toujours actives par RMN est présenté. Le but est de pouvoir directement observer les modifications subies par chaque phospholipide de la mitochondrie. . / The aim of this thesis was the investigation of the mitochondrial response mechanisms upon apoptotic stimuli. The specific objectives were the biophysical characterization of membrane dynamics and the specific roles of lipids in the context of apoptotic regulation occurring at the mitochondrion and its complex membrane systems. The BH4 domain is an anti-apoptotic specific domain of the Bcl-2 protein. Solid phase peptide synthesis was used to produce large amount of the peptide for biophysical studies. A protocol has been established and optimized, guarantying the required purity for biophysical studies. In detail the purification by high performance liquid chromatography and the characterisation via mass spectroscopy are described. The secondary structure of BH4 changes significantly in the presence of lipid vesicles as observed by infrared spectroscopy and circular dichroism. The BH4 peptide aggregates at the membrane surface and inserts slightly into the hydrophobic part of the membrane. Using nuclear magnetic resonance (NMR) and calorimetry techniques, it could even be shown that the BH4 domain modifies the dynamic and organization of the liposomes which mimic a mitochondrial surface. The second study was on the first helix of the pro-apoptotic protein Bax. This sequence called Bax-a1 has the function to address the cytosolic Bax protein to the mitochondrial membrane upon activation. Once again a protocol has been established for the synthesis and purification of this peptide. The aim was to elucidate the key role of cardiolipin, a mitochondria-specific phospholipid, in the interaction of Bax-a1 with the mitochondrial membrane system. The NMR and circular dichroism studies showed that Bax-a1 interacts with the membrane models only if they contain the cardiolipin, producing a strong electrostatic lock effect which is located at the membrane surface. Finally, a new NMR approach was developed which allows the investigation of the lipid response of isolated active mitochondria upon the presence of apoptotic stimuli. The goal was there to directly monitor lipid specific the occurring changes during these physiological activities.

This thesis explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant-inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. On top of that, detailed information is given for the derivation and program implementation of damped cubic response functions. Complex-valued cubic response functions have been implemented in the quantum chemistry package DALTON, based on working equations formulated for an approximate-state wave function. An assessment of the implementation, such that for small frequencies the second-order hyperpolarizability should behave according to an analytic function that depends quadratically on the optical frequencies. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or via the damped cubic response function. A few calculated TPA profiles are produced for a set of smaller molecules, in order to display the capability of the cubic response function in the x-ray frequency region. Resonance-inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown how the second-order hyperpolarizability can represent RIXS in the limit of intermediate-state and final-state resonances. Complications emerging from the complex dispersion of the hyperpolarizability are discussed. Moreover, linear birefringences, with focus on the Jones birefringence, are investigated for noble gases, monosubstituted benzenes, furan homologues, and a pure acetonitrile liquid. A linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. Estimations of three linear birefringences --- Kerr, Cotton--Mouton, and Jones ---are obtained by averaging over a set of liquid snapshots. The Jones effect for acetonitrile turns out to be unusually large inmparison to the other two investigated linear birefringences. The final chapter of the thesis investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra is explored. The effect on uracil MCD spectrum due to thionation is studied, for which the degree of redshifting for systems 2-thiouracil and 4-thiouracil can be seen to be addative as compared to the 2,4-dithiouracil system. / <p>QC 20171129</p>

Ce travail décrit la synthèse et les propriétés gélifiantes de nouveaux dérivés d’acides aminés de faible poids moléculaire dans des solvants organiques ainsi que l’élaboration d’aérogels correspondants par séchage au CO2 supercritique. Nous avons pu montrer, dans notre cas, que seuls les dérivés de la leucine et de la phénylalanine étaient nécessaires au phénomène de gélation. L’étude des paramètres des solvants a permis de montrer que les paramètres de Hansen h des solvants gélifiés s’inscrivaient dans un domaine étroit de valeurs faibles ; il inclut des solvants aromatiques et des solvants chlorés. L’usage de spectroscopies diverses (IR, RMN, dichroïsme circulaire et fluorescence) a permis de mettre en évidence les interactions responsables du phénomène de gélation. Les liaisons hydrogène permettent l’empilement unidimensionnel des molécules gélatrices, ces empilements s’associent ensuite grâce à des interactions de - stacking intercolonnaires. Des aérogels monolithiques ont pu être obtenus. Ils présentent des propriétés remarquables parmi lesquelles une conductivité thermique sous vide extrêmement faible / This work describes the synthesis and the gelation properties of new amino-acid-based low-molecular-weight derivatives in organic solvents as well as the development of the corresponding aerogels by supercritical CO2 drying. We have proved that in our case the presence of phenylalanine or leucine lateral chains were necessary for gelation. A solvent parameters study led us to define a favourable narrow h Hansen parameter domain for gelation including aromatic and chlorinated solvents. The use of several spectroscopy methods (IR, NMR, circular dihroism and fluorescence) allowed to settle the interactions accountable for gelation phenomenon. Hydrogen bonds enable the unidimensional stacking-up of gelator molecules; next, the stacking-up are associated through intercolumnar - stacking interactions. Monolithic aerogels were obtained. They display noteworthy properties among them an extremely low thermal conductivity under vacuum

Orientadores: Narcizo Marques de Souza Neto, Flávio Cesar Guimarães Gandra / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin / Made available in DSpace on 2018-08-27T10:57:14Z (GMT). No. of bitstreams: 1 Veiga_LarissaSayuriIshibe_D.pdf: 10330689 bytes, checksum: 72bdd1a8fad1f82f880bb2c86fcd6a9e (MD5) Previous issue date: 2015 / Resumo: Este trabalho teve como objetivo a investigação de diversos mecanismos físicos provenientes das estruturas eletrônicas, magnéticas e cristalinas de sistemas ternários de terras raras e metais de transição 3d-5d através do uso das técnicas de espectroscopia de absorção de raios X e difração de raios X sob altas pressões. Dentre os fenômenos físicos estudados em função da compressão da rede cristalina induzida pela aplicação da pressão estão o magnetismo proveniente dos orbitais 4f e 5d nos sistemas ternários RERh4B4 (com RE = Dy e Er), os efeitos do campo elétrico cristalino e as interações de troca magnéticas nas perovskitas duplas 3d-5d (AFeOsO6, com A = Ca e Sr) e o acoplamento spin-órbita nos metais de transição 5d. As propriedades eletrônicas e magnéticas dos orbitais 4f e 5d das terras raras nos compostos da família RERh4B4 (RE = Dy e Er) foram investigadas através de experimentos de XANES e XMCD sob altas pressões na borda L3 do Dy e Er . Os sinais magnéticos das contribuições quadrupolar (2p3/2-> 4f) e dipolar (2p3/2->5d) presentes nos espectros de XMCD, em ambos os compostos, diminuem progressivamente em função da pressão. Este comportamento foi explicado em termos das interações de troca magnéticas entre os íons de terras raras, que são enfraquecidas pelas alterações locais da estrutura atômica induzidas pela compressão da rede cristalina. Já no sistema de perovskitas duplas, foi demonstrado que a compressão da estrutura Sr2FeOsO6, com um arranjo cristalino ordenado dos íons de Fe (3d) e Os (5d), permite o controle contínuo e reversível da coercividade e magnetização de saturação. Este efeito foi explicado em termos do aumento do campo elétrico cristalino em função da pressão, que altera as interações de troca magnéticas Fe-O-Os e transforma o material com magnetização remanente e coercividade praticamente nulas a pressão ambiente em outro com uma coercividade robusta (~0.5 T) e magnetização de saturação expressiva a pressões acima de ~10 GPa. Por fim, a última parte desta tese de doutorado foi dedicada ao uso da seletividade química e orbital da técnica de XANES na investigação do acoplamento spin-órbita nos elementos Pt (Pt0, 5d9) e Hf (Hf0, 5d2) sob altas pressões. Ao contrário do observado para a Pt, o cálculo do branching ratio a partir dos espectros de absorção nas bordas L2,3 do Hf revelaram que o acoplamento spin-órbita aumenta monotonicamente em função da pressão aplicada. Esse comportamento foi relacionado às propriedades supercondutoras e estruturais presentes nesse elemento sob altas pressões / Abstract: The scientific goal of this work has been the investigation of several physical mechanisms derived from the electronic, magnetic and structural properties of ternary rare earth and transition metal systems by means of X-ray absorption spectroscopy and X-ray diffraction techniques in a diamond anvil cell. Among the physical properties studied as a function of lattice compression induced by applied pressure are the magnetism of the 4f and 5d orbitals in tetragonal rare earth rhodium borides RERh4B4 (with RE = Dy e Er), the crystal electric field effects and magnetic exchange interactions in 3d-5d double perovskite systems (A2FeOsO6, with A = Ca e Sr) and the spin-orbit coupling in 5d transition metals. The electronic and magnetic properties of the rare earth 4f and 5d orbitals in the RERh4B4 (RE = Dy e Er) systems were investigated through high pressure XANES and XMCD experiments at Dy and Er L3 edges. For both compounds, the magnetic signals of the quadrupole (2p3/2->4f) and dipole (2p3/2->5d) contributions to the XMCD spectra progressively decrease as a function of pressure. This behavior was explained in terms of the magnetic exchange interactions between the rare earth ions, which are weakened by changes in the local atomic structure induced by compression of the crystal lattice. In the double perovskite system, it has been shown that compression of Sr2FeOsO6 structure with an ordered crystalline arrangement of iron (3d) and osmium (5d) transition metal ions, allows for continuous and reversible control of magnetic coercivity and saturation magnetization. This effect was explained in terms of enhanced crystal electric fields under high pressure, which alter the Fe-O-Os magnetic exchange interactions and transform the material with an otherwise mute response to magnetic fields into one with a strong coercivity (~0.5 T) and substantial saturation magnetization at pressures above ~10 GPa. Finally, the last part of this thesis is dedicated to the use of chemical and orbital selectivity of XANES technique as a tool to investigate the spin-orbit coupling in Pt (Pt0, 5d9) and Hf (Hf0, 5d2) elements under high pressures. Unlike observed for Pt, the calculated branching ratio determined from the integrated intensities of the Hf L2,3 white lines shows that the spin-orbit coupling increases monotonically as a function of applied pressure. This behavior was related to the superconducting and structural properties displayed by this element at high pressures / Doutorado / Física / Doutora em Ciências

Le principal objectif de cette thèse, au caractère interdisciplinaire, concernait l'étude de l'éponge Biemna laboutei de Madagascar, connue pour sa toxicité (causant notamment des dermatites). Les travaux entrepris comprenaient en premier lieu, l'étude chimique de cette éponge incluant l'extraction, l'isolement et l'identification des métabolites secondaires par différentes techniques chromatographiques (CLMP, CLHP…) et spectroscopiques (UV-visible, HRMS, RMN 1D et 2D…). Dix-huit alcaloïdes appartenant à la classe rare des hétérocycles tricycliques (5,6,8b)-triazaperhydroacénaphtylène (i.e. ptilocaulines, mirabilines, nétamines) ont été isolés et identifiés. Douze de ces alcaloïdes tricycliques guanidiniques, de structures nouvelles, ont été nommées nétamines H-S. Ces composés ont été classés en fonction des insaturations de leur noyau tricyclique : type pyrimidine, insaturés en Δ8,8a et insaturés en Δ8a,8b. Pour deux des composés isolés, les nétamines I (58) et J (59), une étude configurationnelle reposant sur la comparaison de spectres UV et DCE, expérimentaux et théoriques (théorie de la fonctionnelle et de la densité), a permis la détermination de leurs configurations absolues : 5aS, 7R, 8R pour la nétamine I et 5aS, 7R, 8S pour la nétamine J. La valorisation des molécules isolées a ensuite été envisagée via d'une part la réalisation d'une étude chimiotaxonomique et d'autre part, l'évaluation de leurs activités biologiques (cytotoxicité, activité antipaludique, …). La nétamine M (62) a présenté une activité cytotoxique sur les cellules cancéreuses KB (CI50 = 1,0 μg/mL) et les nétamines O (64), Q (66) et K (60) se sont montrées actives contre le parasite Plasmodium falciparum, responsable du paludisme avec respectivement une CI50 de 4,66 ; 2,53 et 0,62 μg/mL. Enfin, au cours de ces travaux de thèse, ont été explorées trois nouvelles stratégies de synthèse conduisant au squelette des alcaloïdes guanidiniques tricycliques, suivant une approche biomimétique. / The main purpose of this interdisciplinary thesis was to study Biemna laboutei, a sponge from Madagascar, known to have toxic properties (dermatitis-producing). The chemical investigation of this sponge including extraction, isolation and identification of secondary metabolites was first undertaken using several chromatographic (HPLC, MPLC…) and spectroscopic (UV-visible, HRMS, NMR 1D et 2D…) techniques. Eighteen alkaloids belonging to the rare class of tricyclic (5,6,8b)-triazaperhydroacenaphtylene heterocycles (i.e. ptilocaulins, mirabilins, netamines) were isolated and identified. Twelve new alkaloids from this group of guanidine derivatives were named netamine H-S. These compounds were grouped on the basis of unsaturation and double bond regiochemistry, with pyrimidine, Δ8,8a and Δ8a,8b heterocycles. For two compounds, netamine I (58) and J (59), a joint theoretical (Density functional theory) and experimental study of UV and ECD spectra allowed the determination of their absolute configuration: 5aS, 7R, 8R for netamine I and 5aS, 7R, 8S for netamine J. The chemotaxonomic meaning of these alkaloids was discussed. Their biological activities were also evaluated. Netamine M (62) exhibited a cytotoxic activity towards KB cells (IC50 = 1,0 μg/mL) while netamine O (64), Q (66) and K (60) were active against the malaria parasite Plasmodium falciparum with IC50 value of 4,66; 2,53 and 0,62 μg/mL respectively. Finally, this work was also dedicated to the biomimetic synthesis of the tricyclic guanidine skeleton. Three new synthesis routes were explored.

Dans ce travail de thèse, nous illustrons la pertinence de la technique de photoémission pour l'étude des propriétés électroniques des matériaux. Dans la première partie, nous détaillons le développement et la phase de tests d'un nouveau bâti expérimental composé d'une chambre d'épitaxie par jets moléculaires (MBE) ainsi que d'une chambre de photoémission résolue en angle et en spin (SR-ARPES), connecté au tube Daum à l'Institut Jean Lamour. Les hautes performances de ce nouveau dispositif sont d'une part évaluées par une série de mesures expérimentales sur un système connu de la littérature (état de Shockley à la surface de l'Au(111)), et d'autre part illustrées par l'analyse de matériaux originaux (isolants topologiques, effet Kondo moléculaire …). Les valeurs de résolution en énergie sont inférieures à 2 meV et 300 meV pour la photoémission utilisant les rayonnements UV (UPS) et X (XPS) respectivement. La résolution angulaire est quant à elle meilleure que 0,2° et la température minimale atteignable est de 8,7 K. Finalement, des premières mesures de SR-ARPES ont démontré la capacité de ce nouveau bâti à mesurer les détails les plus fins de la structure de bandes polarisée en spin, se rapprochant ainsi de l'état de l'art dans le domaine. Ce nouveau dispositif est donc pleinement opérationnel. La seconde partie est consacrée à l'étude d'un oxyde de silicium ultra-mince bidimensionnel (2D) à la surface d'un substrat monocristallin de Ru(0001). Nous étudions tous les stades de croissance en partant du substrat nu de Ru(0001) jusqu'à une bicouche cristalline de cet oxyde, par XPS haute résolution (rayonnement synchrotron) et photoémission résolue en angle (ARPES). Nous confirmons la structure atomique établie dans la littérature pour ce système à la monocouche, avec en particulier l'existence de deux types de liaisons inéquivalentes Si-O-Ru révélées par des mesures inédites d’XPS haute résolution au niveau de la raie de cœur de l'O1s. En outre, nos mesures ARPES mettent en évidence l'existence d'états dispersifs bidimensionnels propres à ce matériau 2D. Alors que la monocouche est fortement connectée au substrat de ruthénium (liaisons covalentes), la bicouche en est déconnectée (liaisons de van der Waals). Notre étude confirme l'existence d’une telle transition avec des signatures claires à la fois en XPS et en ARPES, démontrant notamment la disparition des liaisons Si-O-Ru. Nous démontrons également la robustesse de ce système, qui une fois cristallisé peut être remis à l'air sans modifications majeures de ses propriétés électroniques, lui donnant ainsi un fort potentiel de fonctionnalisation (par exemple au sein d'hétérostructures 2D complexes comme couche isolante). Finalement, dans une troisième partie nous nous intéressons aux aspects théoriques de la photoémission résolue en angle. Alors que la structure de bandes est périodique dans l'espace réciproque, ce n'est pas le cas de l'intensité de photoémission, qui peut présenter des variations complexes dépendant de nombreux paramètres. Ces aspects sont généralement mal compris par les expérimentateurs. Nous présentons ici un modèle simple récemment proposé qui s'inscrit dans une description en trois étapes du processus de photoémission, et qui permet d'évaluer les éléments de matrice à un électron. Ces éléments de matrice représentent l'ingrédient essentiel permettant de comprendre la répartition du poids spectral en photoémission. Nous démontrons que dans ce modèle ils sont proportionnels à la transformée de Fourier de l'état de Wannier du système considéré, ainsi qu'à un terme de polarisation contenant les effets géométriques inhérents à toute expérience de photoémission. Nous appliquons alors cette approche à des systèmes physiques comme le graphène, ou encore au cas de mesures de dichroïsme circulaire réalisées au niveau des états d et de l'état de Shockley d'un monocristal de Cu(111), mettant ainsi en évidence ses succès et ses limitations / In this work, we highlight the relevance of photoemission spectroscopy for investigating the electronic properties of materials. In the first part, we tackle the development and the test phase of a new experimental setup which is composed of a molecular beam epitaxy (MBE) and a spin and angle resolved photoemission (SR-ARPES) chambers, connected to the tube at the Institut Jean Lamour. The high performances of this new setup are evaluated. On one hand by measuring well known system from the litterature (Shockley state at the Au(111) surface) and on the other hand by studying materials with novel properties (topological insulators, molecular Kondo effect …). Energy resolution is better than 2 meV for UV photoemission (UPS) and 300 meV for X-ray photoemission (XPS). We also have an angular resolution better than 0.2° and a lowest sample temperature of 8.7 K. Finally, first SR-ARPES measurements demonstrate the ability of this new installation to measure finest details of the spin polarized band structure. In short, this new setup is fully operationnal. The second part is dedicated to the study of a two dimensionnal (2D) ultra thin silicon oxide at the surface of a cristalline Ru(0001) substrate. Both growth and electronic properties are studied by high resolution XPS and ARPES. We confirm the structural model accepted for the system in the litterature for the monolayer case. In particular we confirm the existence of two inequivalent Si-O-Ru bonds with unprecedented high resolution XPS measurements on the O1s core level. In addition, our ARPES measurements highlight new dispersives states with 2D character which are unambiguously attributed to this oxide. While the monolayer is strongly connected to the ruthenium substrate (covalent bonds), the bilayer is disconnected from this latter one (van der Waals). Our work confirms the existence of such a transition with unambiguous signatures both in XPS and ARPES, in particular with the breaking of Si-O-Ru bonds. We also demonstrate the robustness of this system which, after being cristallised, can go to atmosphere without fundamental modification of his electronic properties. That gives a lot of potential applications to this 2D cristalline oxide, which could play in the futur the role of a wide band gap insulator in 2D heterostructures. In the last part, we focus on the theoretical aspects of photoemission. While band structure is periodic in the reciprocal space, it is not the case of photoemission intensity which can depend on a lot of parameters. We are motivated by the fact that these considerations are generally not well understood by experimentalists. Here, we present a simple model recently proposed in the three step approach of the photoemission process. With this model we can evaluate the one-electron matrix elements which play a key role to understand the variations of spectral weight in photoemission. In this approach, one-electron matrix elements are proportionnal to both Fourier transform of the Wannier state of the system and to a polarization term. We apply this model to « real » systems, in particular to graphene and to circular dichroism measurements on Cu(111) sample, highlighting sucess and limitations of this model

Hfq est une protéine bactérienne qui a un rôle pleiotropique. La principale fonction de la protéine Hfq bactérienne consiste à répondre aux stress que peut rencontrer la bactérie lors d’un changement environnemental, en utilisant essentiellement un contrôle post-transcriptionnel. La protéine, par sa capacité à interagir avec les ARN et notamment les petits ARN non codant, permet ainsi une régulation rapide de l’expression génétique. En outre la protéine interagit aussi avec l’ADN qu’elle aide à se structurer. Les mutations dans le gène qui code pour Hfq ont des effets pleïotropes (déterminant plusieurs caractères phénotypiques).D’un point de vue structural, la protéine adopte un repliement de type Sm, caractérisé par un oligomère toroïdal reposant sur la formation d’un feuillet β continu à 30 brins. Cependant, outre cette région Sm N-terminale, Hfq possède également une région C-terminale (CTR) de taille et de séquence variables selon les bactéries. Mon travail de thèse a porté sur l’analyse de cette région CTR chez la bactérie Escherichia coli. Cette région a en effet la capacité de former une structure de type amyloïde : structures auto-assemblées in vivo, à proximité de la membrane interne et dans le nucléoïde.Par l’utilisation de diverses techniques physico-chimiques (microscopie moléculaire, spectroscopie et microscopie infrarouge, dichroïsme circulaire et diffusion aux petits angles), mon travail a consisté à caractériser l’assemblage de cette région de Hfq ainsi que les facteurs l’influençant en particulier la présence d’acide nucléique. Une partie de mon travail de thèse a aussi consisté à mettre en place une méthode d’imagerie corrélative innovante permettant d’analyser la signature chimique et morphologique d’une fibre amyloïde unique. Mon travail a enfin porté sur l’analyse de l’effet de composés inhibant l’agrégation de la structure amyloïde, ce qui pourrait constituer une piste pour développer une nouvelle classe d’antibiotiques. / Hfq is a pleiotropic bacterial protein that determines several phenotypic characteristics. Its main function is to facilitate responses to stresses that bacteria may encounter during environmental changes, mainly by using post-transcriptional genetic control. The protein, by its capacity to interact with RNA, in particular small non-coding RNA, enables a rapid regulation of gene expression. In addition, the protein also interacts with DNA and compacts it. From a structural point of view, the protein adopts an Sm-like fold, characterized by a toroidal oligomer formed by a continuous 30-stranded β-sheet. Besides its conserved N-terminal Sm domain, Hfq also possesses a C-terminal region (CTR) that can vary in size and sequence between bacteria. My PhD work focused on the analysis of this CTR region in Escherichia coli bacteria. Indeed, this region has the capacity to form an amyloid structure. This structural dynamic is related to the formation of self-assembled structures in vivo, in the proximity of the inner membrane and in the nucleoid.Using various physicochemical techniques (molecular microscopy, spectroscopy and infrared microscopy, circular dichroism and small angle X-ray scattering), my work consisted in characterizing the assembly of this region of Hfq, as well as the factors influencing its assembly (in particular, the presence of nucleic acids). A part of my work consisted in setting up an innovative correlative–imaging method to analyze the chemical and morphological signature of a single amyloid fibre. Finally, my work focused on the analysis of the effect of compounds that inhibit the aggregation of the amyloid structure, which could constitute a new way to develop a novel class of antibiotics.