No / Violacein is a bisindole pigment occurring as a biosynthetic product of Chromobacterium violaceum and Janthinobacterium lividum. It has some structural similarities to the cyanobacterial UV-protective pigment scytonemin, which has been the subject of comprehensive spectroscopic and structural studies. A detailed experimental Raman spectroscopic study with visible and near-infrared excitation of violacein produced by C. violaceum has been undertaken and supported using theoretical DFT calculations. Raman spectra with 514 and 785 nm excitation of cultivated cells as well as extracts and Gaussian (B3LYP/6-311++G(d,p)) calculations with proposed molecular vibrational assignments are reported here.

<p>This thesis describes the use of 2H-azirines as reactivesubstrates in Lewis acid catalysed nucleophilic additions andin the Diels-Alder reaction.A number of carbon nucleophiles have been added to aseries of 2H-azirines in the presence and absence ofBF3·Et2O. 3-(2-Naphthyl)-2H-azirine has been used as amodel substrate in the enantioselective addition oforganolithium reagents to an 2H-azirine.A selection of Lewis acids has been screened for theirpossible use in the normal electron demand Diels-Alder reactionbetween 3-alkyl-, 3-aryl-, and 3- carboxyl-2H-azirines and avariety of dienes. Lewis acid activation was found to shortenreaction times and facilitate lower reaction temperatures.These cycloadditions proceeded with endo selectivity providinga single diastereoisomeric product.DFT calculations of Lewis acid activated 2H-azirineshave been carried out.</p><p><b>Keywords:</b>2H-azirines, Lewis acid activation, chiralligands, organolithium reagents, Diels-Alder reactions,DFT-calculations</p>

Lucie Ducháčková Bipyridine N,N'-dioxides are organocatalysts, which are used as a chiral Lewis bases in enantioselective catalysis. The aim of this diploma thesis was systematic investigation of the proton affinities of bipyridine N,N'-dioxide derivatives. Further, the complexation properties and chiral recognition in the gas phase of bipyridine N,N'-dioxide derivatives were examined. Mass spectrometry complemented with infrared multiphoton dissociation spectroscopy and quantum-chemistry calculations using the density functional theory (DFT) were used as the main experimental methods. Bipyridine N,N'-dioxides are a new class of oxygen superbases with proton affinities larger than 1030 kJ/mol. Complexation properties and reactivities of their metal complexes are comparable to 2,2'-bipyridine.

The knowledge on the conformations of amino acids is essential to understand the biochemical behaviors and physical properties of proteins. Comprehensive computational study is focused to understand the conformational landscape of three aromatic amino acids (AAAs): tryptophan, tyrosine, and phenylalanine. Three different density functionals (B3LYP, M06-2X and wB97X-D) were used with two basis sets of 6-31G(d) and 6-31+G(d,p) for geometry optimizations of the conformers of AAAs followed by the vibrational frequencies. The goal was to identify the right choice of density functional theory (DFT) level for conformational analysis of amino acids by comparing the computational data against the available experimental results. Calculated infrared (IR) frequency values indicated that wB97X-D/6-31+G(d,p) level is less favorable than other DFT levels in case of O-H and N-H stretching frequencies for the conformers of AAAs. The C=O stretching frequencies at different computational levels were in good agreement with the experimental results. Interactions of AAAs (tryptophan, tyrosine, and phenylalanine) and two cyclic amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36) were explored using M06-2X/6-31G(d) level. Computational investigations of the binding of amino acids with graphene provide knowledge for designing of new graphene-based biological/biocompatible materials. Selected conformers for each amino acid with different orientations on the surface of graphene were examined. The purpose of computational study on graphene-amino acids interactions was to identify the preferred conformer of amino acid to bind on graphene as well as to find the influence of amino acid binding on the band gap of graphene. Different conformers of AAAs generally prefer parallel orientation through π-π interactions to bind with graphene. However, bent orientation is more preferred over parallel to bind on the surface of graphene in case of conformer having relative energy approximately equal to 5 kcal/mol for all three AAAs. Histidine generally exhibits higher binding affinity than proline to form complex with graphene. The binding energies in the aqueous medium were slightly lower than those obtained in the gas phase with some exceptions. The adsorption of amino acids did not affect the band gap of graphene.

Le présent travail de thèse porte sur la synthèse et la caractérisation de nouvelles molécules et matériaux à base de polyoxométallates (POMs) pour des applications dans les domaines de l’énergie et l’environnement. Dans le domaine de l’environnement, notre choix s’est porté sur la transformation électro-catalytique et photo-catalytique des espèces polluantes comme les oxydes d’azote et les colorants azoïques toxiques comme l’Acide Orange 7. Pour ce qui concerne le domaine de l’énergie, nous nous sommes focalisés sur des systèmes électro- catalytiques pour la production de l’hydrogène (combustible à fort pouvoir calorifique) et pour la réduction du di-oxygène (intérêt dans le fonctionnement des piles à combustibles). Ces réactions nécessitent généralement plusieurs électrons pour se produire, c’est pour cette raison que notre choix s’est porté sur les catalyseurs à base de POMs. En effet, les POMs sont capables de stocker, puis de restituer, un grand nombre d’électrons sans changer de structure.Dans la première partie, divers POMs qui prennent en sandwich plusieurs métaux de transition sont synthétisés et caractérisés par des méthodes expérimentales (voltamétrie cyclique, coulométrie, microbalance) et théoriques (calculs DFT). Ces composés montrent une très bonne activité électro-catalytique pour la réduction des substrats tels que les oxydes d’azote, le di-oxygène et le peroxyde d’hydrogène.Dans la seconde partie, des matériaux aux propriétés améliorées sont synthétisés par incorporation de POMs dans des matrices tels que les réseaux moléculaires de type MOF (Metal Organic Framework) et dans les polymères liquides ioniques. L’association avec un semi-conducteur comme le TiO₂ est aussi considérée. Les matériaux obtenus sont caractérisés par diverses techniques : infrarouge à transformée de fourrier, électrochimie, spectroscopie en réflectance diffuse, analyse thermogravimétrique, diffraction de rayons X, spectroscopie de photo-électrons X, microscopie électronique à transmission. Les matériaux à base de POMs et de MOFs sont très performants pour la réduction électro-catalytique des protons, avec des potentiels de début effectif de la réaction, meilleurs que ceux des électrodes de platine. Les hybrides à base de POMs, de polymères liquides ioniques et du TiO₂ sont photo-sensibles sous lumière visible, contrairement à leurs composants. Ils démontrent une bonne activité vis-à-vis de la dégradation de l’Acide Orange 7. De plus, le composite obtenu par photo-déposition de nanoparticules d’argent sur ces matériaux présente de bonnes performances électro-catalytiques comme cathode pour la réduction du O₂ et du NO‾₃. / The present work concerns the synthesis and characterisation of new polyoxometalate (POMs) based molecules and materials for applications in energy and environment matters. As far as the environment is concerned, our efforts involved the electro-catalytic and photo-catalytic transformation of pollutants such as nitrogen oxides and recalcitrant azo dyes like Acid Orange 7. As for the domain of energy, we focused on electro-catalytic systems aimed at producing dihydrogen (a high calorific power fuel) and at reducing dioxygen (an important reagent in fuel cells). These reactions usually require several electrons in order to take place, which led us to choose POM-based catalysts. In fact, POMs are capable of stocking and returning an important number of electrons without changing their structure.In the first part, several POMs in which different transition metals are sandwiched in the equatorial plane of the molecular scaffold are synthesised and characterised by experimental (cyclic voltammetry, coulometry, microbalance) et theoretical (DFT calculations) methods. These compounds have shown a very good electro-catalytic activity towards the reduction of substrates such as nitrogen oxides, dioxygen and hydrogen peroxide.In the second part, some materials exhibiting improved properties are synthesised through the incorporation of POMs in matrices like Metal Organic Framework (MOF)-type molecular networks and ionic liquid polymers. The association with a semi-conductor such as TiO₂ has also been considered. The materials obtained were characterised by several techniques: Fourier transform infrared spectroscopy, electrochemistry, diffuse reflectance spectroscopy, thermogravimetric analysis, X ray diffraction, X ray photoelectron spectroscopy, transmission electron microscopy. The POM and MOFs based materials are very performing for the electro-catalytic reduction of protons, having onset potentials better than those exhibited by platinum electrodes. The hybrids consisting of POMs, ionic liquid polymers and TiO₂ are photo-sensitive under visible light, unlike each component taken individually. They have shown a good activity towards the degradation of Acid Orange 7. In addition, the composite obtained by photo-deposition of silver nanoparticles on these materials exhibits a good electro-catalytic performance as a cathode for the reduction of O₂ and NO‾₃.

L'objectif de ce travail est de contribuer, par le biais d'approches expérimentales (XPS/chimisorption de sondes gazeuses) et théoriques (approches type DFT), à une meilleure compréhension fondamentale de la réactivité de surface de matériaux d'électrode positive et plus spécifiquement d'oxydes lamellaires lithiés LiMO2. La réactivité de surface du matériau LiCoO2 et l’influence d’une substitution de l’atome de cobalt par l’atome d’aluminium a été étudiée pour avancer dans la compréhension de l’effet bénéfique des « coatings » à base d’alumine. L’étude expérimentale a été centrée sur l’adsorption de SO2 et montre que la présence d’atomes d’aluminium induit une diminution de réactivité : elle génère des espèces de type sulfite, différentes des sulfates seuls identifiés pour LiCoO2. La modélisation de cette adsorption permet la mise en évidence de deux modes d’adsorption distincts : passage d’un contrôle rédox pour LiCoO2 à un contrôle acido-basique pour des matériaux contenant des atomes d’aluminium (LiAlO2), thermodynamiquement moins favorable. L’influence de la nature du métal de transition a été analysée sur la base d’études théoriques également menées sur LiMnO2 et LiNiO2. La modélisation de l’adsorption de SO2 sur les surfaces des matériaux LiMO2 révèle la présence des deux processus de chimisorption (formation de sulfites et sulfates), avec mise en évidence du rôle important des cations de sous-surface dans les processus de réduction conduisant aux sulfates. Cette étude théorique a permis d’interpréter les résultats expérimentaux obtenus pour Li(Ni1/3Mn1/3Co1/3)O2, l’identification de sulfites résulterait de la présence des ions Ni2+ alors que celle de sulfates serait liée à la présence des ions Mn4+ et Co3+. / This work is devoted to a better fundamental understanding of the surface reactivity of positive electrode materials, and specifically lamellar lithiated oxides LiMO2 through experimental (XPS/chemisorption of gaseous probes) and theoretical (DFT calculations) approaches. The beneficial effect of aluminum-based coatings on electrochemical performances is well known but the exact mechanisms are not totally understood. A detailed study of the surface reactivity of LiCoO2 and of the influence of Al/Co substitution is carried out. The experimental approach is focused on SO2 adsorption and shows that Al/Co substitution induces a decrease of the surface reactivity and a change in the nature of adsorbed species (identification of sulfite species whereas only sulfate species are characterized for LiCoO2). Theoretical calculations highlighs two different adsorption modes controlled by redox properties for LiCoO2 and by acid-base properties for -LiAlO2 (less energetically favorable). The theoretical study is extended to LiMnO2 and LiNiO2 in order to analyse the influence of the nature of the transition metal atom. The modelization of SO2 adsorption reveals two chemisorption processes (sulfite and sulfate formation), and highligths the key role of subsurface cations in the reduction process which leads to sulfates. Thus theoretical approach allows on interpretation of the experimental data obtained for Li(Ni1/3Mn1/3Co1/3)O2. The identification of sulfites may be explained by the presence of Ni2+ ions whereas sulfate species may result from the presence Mn4+ and Co3+ ions.

Um estudo teórico detalhado das estruturas e energias do ligante 1, 7, 11, 17-tetraoxa-2, 6, 12, 16-trazaocicloocsano ([20]aneN4O4) coordenado com íons metálicos de transição Fe2+, Co2+, Ni2+, Ru2+, Rh2+ e Pd2+ foi realizado em nível de teoria B3LYP/Lanl2DZ. As geometrias dos complexos foram totalmente otimizados em simetria Cs com os íons metálicos coordenados com quatro átomos de nitrogênio (complexos 1a e 1aq) ou quatro átomos de oxigênios (complexos 1b e 1bq) e duas moléculas de água. Os arranjos octaédricos (1a e 1b) e quadrado-planares (1aq e 1bq) foram consideremos neste trabalho. A estrutura teórica está em excelente acordo com a estrutura de difração de raio-x experimental determinada para o complexo octaédrico de Ni2+ de [20]AneN4O4. Os cátions M2+ ligam-se preferencialmente aos átomos de nitrogênios com energia de ligação que aumenta na ordem Fe2+ &lt; Ru2+ &lt; Co2+ &lt; Ni2+ &lt; Rh2+ &lt; Pd2+. Para os metais de transição da primeira fila, os complexos de spin alto são mais estáveis que os complexos de spin baixo. Em contraste, para os metais de transição da segunda fila, os estados de spin baixo mostraram-se mais estáveis que os estados de spin alto. As ligações metal-ligante nos complexos foram analisadas em termo das interações covalentes e iônicas e ajudaram a entender porque os complexos (1a e 1aq) são mais estáveis que os complexos (1b e 1bq). Os complexos poliaminas [20]aneN4 e poliéteres [20]aneO4 foram obtidos substituindo os átomos de nitrogênio e oxigênio da posição alfa dos macrociclos [20]aneN4O4 e [20]aneO4N4, respectivamente. O macrociclo [20]aneO4 tem preferência em complexar íons metálicos da primeira fila, enquanto o macrociclo [20]aneN4 prefere complexar os íons metálicos da segunda fila. / A detailed theoretical study of structures and energies of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN4O4) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+ and Pd2+ transition metals ions was carried out with the B3LYP/Lanl2DZ method. The geometries of the complexes were fully optimized in Cs symmetry with the metal ions coordinated either to four atoms nitrogen (complexes 1a e 1b) or to the four atoms oxygen (complexes 1aq e 1bq). The octahedral and square planar arrangements were considered in this work. The theoretical structure is in excellent agreement with the experimental X-ray diffraction structure determination for the [20]AneN4O4 octahedral Ni2+ complex. The M2+ cations bind preferentially to the nitrogen atoms with binding energies that increase in the order Fe2+ &lt; Ru2+ &lt; Co2+ &lt; Ni2+ &lt; Rh2+ &lt; Pd2+. For the first-row transition metals, the highspin complexes are more stable than the low-spin complexes. In contrast, for the second-row of transition metals, the low-spin states were found more stable than the high spin states. The metal-ligand bonds in the complexes were analyzed in terms of the covalent and ionic interactions and helped to understand why complexes (1a e 1aq) are more stable than complexes (1b e 1bq). The polyamines [20]aneN4 and polyethers [20]aneO4 complexes were obtained substituting the atoms N or O of the alfa position of the macrocycles [20]aneN4O4 and [20]aneO4N4, respectively. The macrocycle [20]aneO4 prefers to complex first-row transition metals; however, the macrocycle [20]aneN4 prefers to complex second-row transition metals.

<p>Oscillator strengths and transition energies are calculated for several mono-substitutes of benzene and naphthalene molecules. The substituents investigated are chlorine, bromine and iodine. Calculations for these molecules are presented, at the Hartree-Fock and DFT level of theory. The functional used in DFT is CAM-B3LYP.</p>

This thesis describes the development and study of catalysts for redox reactions, which either utilize oxygen or hydrogen peroxide for the purpose of selectively oxidizing organic substrates, or produce oxygen as the necessary byproduct in the production of hydrogen by artificial photosynthesis. The first chapter gives a general introduction about the use of environmentally friendly oxidants in the field of organic synthesis, and about the field of artificial photosynthesis. The second chapter describes a computational study of the mechanism of palladium-catalyzed oxidative carbohydroxylation of allene-substituted conjugated dienes. The proposed mechanism, which was supported by DFT calculations, involves an unusual water attack on a (π-allyl)palladium complex. The third chapter describes a computational study of the oxidation of unfunctionalized hydrocarbons, ethers and alcohols with hydrogen peroxide, catalyzed by methyltrioxorhenium (MTO). The mechanism was found to proceed via rate-limiting hydride abstraction followed by hydroxide transfer in a single concerted, but highly asynchronous, step as shown by intrinsic reaction coordinate (IRC) scans. The fourth chapter describes the use of a new hybrid (hydroquinone-Schiff base)cobalt catalyst as electron transfer mediator (ETM) in the palladium-catalyzed aerobic carbocyclization of enallenes. Covalently linking the two ETMs gave a fivefold rate increase compared to the use of separate components. The fifth chapter describes an improved synthetic route to the (hydroquinone-Schiff base)cobalt catalysts. Preparation of the key intermediate 5-(2,5-hydroxyphenyl)salicylaldehyde was improved by optimization of the key Suzuki coupling and change of protecting groups from methyl ethers to easily cleaved THP groups. The catalysts could thus be prepared in good overall yield from inexpensive starting materials. Finally, the sixth chapter describes the preparation and study of two catalysts for water oxidation, both based on ligands containing imidazole groups, analogous to the histidine residues present in the oxygen evolving complex (OEC) and in many other metalloenzymes. The first, ruthenium-based, catalyst was found to catalyze highly efficient water oxidation induced by visible light. The second catalyst is, to the best of our knowledge, the first homogeneous manganese complex to catalyze light-driven water oxidation. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 5: Accepted. Paper 6: Submitted.</p>

Synchrotron-based spectroscopic techniques enable investigations of the many important biological and environmental functions of the ubiquitous element sulfur. In this thesis the methods for interpreting sulfur K-edge X-ray absorption near edge structure (XANES) spectra are developed and applied for analyses of functional sulfur groups. The influence of coordination, pH, hydrogen bonding, etc., on the sulfur 1s electronic excitations is evaluated by transition potential density functional theory. Analyses have been performed of reduced sulfur compounds in marine-archaeological wood from historical shipwrecks, including the Vasa, Stockholm, Sweden and the Mary Rose, Portsmouth, U.K.. The accumulation of sulfur as thiols in lignin-rich parts of the wood on the seabed is also a probable pathway in the natural sulfur cycle for how reduced sulfur enters fossil fuels via humic matter in anaerobic marine sediments. Sulfur K-edge XANES spectra for several biochemical model compounds and for coexisting isomeric sulfur species in cysteine and sulfite(IV) aqueous solutions have been analyzed with the aid of theoretical calculations. Cysteine derivatives are important for biochemical detoxification, and mercury(II) cysteine complexes in solution have been structurally characterized by means of Extended X-ray Absorption Fine Structure (EXAFS), Raman and 199Hg NMR spectroscopy. Lanthanoid(III) ions were found to coordinate eight dimethyl sulfoxide oxygen atoms in a distorted square antiprism in the solid state and in solution, by combining crystallography, EXAFS, XANES and vibrational spectroscopy. The mean M-O bond distances for the disordered crystal structures are in good agreement with those from the lattice-independent EXAFS studies. The different sulfur K-edge XANES spectra for the dimethyl sulfoxide ligands in the hexasolvated complexes of the trivalent group 13 metal ions, Tl(III), In(III), Ga(III) and Al(III), were interpreted by theoretical calculations.