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

No description available.

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.

Lactobacillus kunkeei is one of the most abundant bacteria within the honey crop of the honey bee. Genome sequencing of L. kunkeei isolated from honey bees all over the world showed several genes unique for L. kunkeei. Among these orphan genes, an array of four to five highly conserved genes coding for giant extracellular proteins were found. Cryogenic electron microscopy imaging of a giant-protein preparation from L. kunkeei A00901 showed an overall structure similar to a long string with a knot at the end. Further analysis showed high similarity between the different giants at the N-terminus, and secondary structure predictions showed that the same region was rich in β-sheets.  These results, combined with the knowledge of other large extracellular proteins, led to the hypothesis that the “knot” domain is located at the N-terminus and that these proteins are used by the cell to latch on to the intestine lining or other cells in the honey crop. In this study, predictions were made to locate the N-terminal domains of two of these giant proteins. Four different constructs were made for each protein, where three constructs were designed for expression and purification of the N-terminal domain with different end-positions, and one construct was for a predicted β-solenoid domain located downstream from the N-terminal domain. The protein constructs were recombinantly produced in E. coli, and three of the N-terminal constructs from both proteins were purified. Thermal stability was tested using nano differential scanning fluorimetry (nanoDSF), Thermofluor, and circular dichroism (CD), which all showed characteristic melting curves at low melting temperatures, ranging from 33 °C to 44 °C, for all three constructs. During CD measurements, all three constructs showed refolding after thermal denaturation and a higher abundance of antiparallel β-sheets over α-helices. Looking at the protein structure, small angle X-ray scattering data indicated that all three proteins formed elongated structures. These results indicate that a folded domain has been found for both proteins. Although, further analysis will be required to determine the boundaries of the N-terminal domains, and to elucidate if these domains have anything to do with ligand binding and the L. kunkeei ability to latch onto the honey crop.

This thesis is about the multicolored gradients seen when using certain dichroic color lters with artificial light. As of now, this phenomenon lacks a unambiguous descriptor, and “Goniochromatic Gradient” is proposed. With help of optical physics, the science of color vision and information about dichroic products, principles for the relationship between goniochromatic gradients and dichroic filters are formulated for anyone interested in exploring this visual phenomenon.

No description available.