The iron and manganese superoxide dismutases are a family of metallo-enzymes with highly conserved protein folds, active sites and dimer interfaces. They catalyse the elimination of the cytotoxic free radical superoxide to molecular oxygen and hydrogen peroxide by alternate reduction then oxidation of the activesite with the concomitant transfer of protons from the solvent. There are many key aspects of enzymatic function that lack a structural explanation. The focus of this study is on three crystal structures. The iron-substituted manganese superoxide dismutase from Escherichia coli complexed with azide, a substrate-mimicking inhibitor, was solved to 2.2 Å. This “wrong” metal form shows a binding pattern seen previously in the manganese superoxide dismutase from Thermus thermophilus. Wild-type manganese specific superoxide dismutase from the extremophile Deinococcus radiodurans was solved to 2.0 Å and has an active site reminiscent of other solved manganese superoxide dismutases despite a lack of product inhibition. The azide-inhibited manganese superoxide dismutase from Deinococcus radiodurans was determined to a resolution of 2.0 Å and showed binding of azide, and by inference superoxide, different to that seen in Thermus thermophilus, but reminiscent of that seen in azide-inhibited iron superoxide dismutases. These results indicate that the azide ion, and by inference superoxide, bind to the metal centre of manganese superoxide dismutases in two modes, and transition between the two modes may be entropy dependent. These structures, integrated with knowledge from other structures, known biochemistry and various spectra, provide insight into catalytic function. An outer-sphere mechanism of proton transfer that does not rely on through-peptide proton uptake is proposed and compared to a previously proposed inner-sphere mechanism. This is based on the observation that a water molecule moves into the active site of the manganese superoxide dismutase from Deinococcus radiodurans upon azide binding, providing a Grötthus pathway for rapid proton transfer to the active site from the bulk solvent. Also presented in this study are the partially refined structures of four point mutants (S82T, L83M, L133V, and M164L/L166V) of the manganese superoxide dismutase from Escherichia coli all solved to roughly 2 Å resolution, designed to investigate product inhibition which varies across species.

Structures as determined by single crystal X-ray methods for lanthanoid(III) compounds for series of simple homoleptic species with diverse ligands frequently display variations entailing a diminution in coordination number (‘C.N.’), a consequence of the variation in the size of the atoms/ions due to the ‘lanthanoid contraction’. A change from C.N. nine to eight is common, clearly separating compounds of the light/‘early’ or heavy/‘later’ metal atoms. Earlier work on the complexes of the lanthanoid(III) picrates arose out of the exploration of simple reagents which might usefully exploit lanthanoid ion properties for purposes such as solvent extraction. They are also of potential synthetic utility because of their relatively high solubility in apolar solvents. This thesis encompasses a systematic structural study of hydrated lanthanoid picrate complexes (including those of yttrium) with a selection of dipolar aprotic solvent ligands, namely trimethylphosphate (‘tmp’), dimethylsulfoxide (‘dmso’), hexamethylphosphoramide (‘hmpa’), N,N´-dimethylacetamide (‘dma’), N-methylpyrrolidinone (‘nmp’) and octamethylpyrophosphoramide (‘ompa’), all liquids at room temperature and all unidentate, with the exception of ompa which can be considered in some cases to behave as the equivalent of two unidentate ligands, in others as a chelate. Structures of adducts of these ligands with scandium picrate are also included in order to gain further insight into the coordination behavior of the totality of the group ‘3’ transition metals, and, for similar reasons, a study of the structures of complexes of Eu(dipivaloylmethanide)3 with the same (solvent) ligands as a ‘baseline’. In the course of these studies, hydrolysis of the aprotic solvent trimethylphosphate was found to lead to novel adducts of the dimethylphosphate (‘dmp’) ligand; the introduction of polycyclic aromatic nitrogen base ligand complexes resulted in further novel mixed ligand compounds, supplemented by a study of protonated base picrate salts. This work aims not only to establish structural ‘domains of existence’ with a concomitant consideration of the associated stereochemistry for these related series of rare earth complexes, but, also, to enhance our understanding of metal ion solvation and the interactions of aromatic groups within these types of crystal structures.

Ce travail est consacré à l’étude cristallographique et aux propriétés électrochimiques et optiques de phosphates et fluorophosphates de cadmium. L’exploration du système NaF – CdO – NaPO3 a mis en évidence un nouveau fluorophosphate de formule Na2CdPO4F et a permis de reconsidérer le polymorphisme du phosphate NaCdPO4. Les structures cristallines de ces deux phases ont été résolues grâce à des données de diffraction des rayons X, à partir de matériaux obtenus sous forme pulvérulente par voie céramique. La caractérisation du fluorophosphate Na2CdPO4F a également menée par spectroscopie infrarouge, diffusion Raman et Résonance Magnétique Nucléaire. L’étude électrochimique, menée sur des solutions solides de type Na2(Cd/Mn)PO4F, a révélé que la présence simultanée de deux cations divalents était bénéfique pour l’amélioration des taux de sodation/désodation. Les propriétés de luminescence des matériaux NaCdPO4 et Na2CdPO4F dopés en ions Eu3+, ion émetteur d’une fluorescence rouge, sont étroitement corrélées aux propriétés structurales. Certaines formulations de type NaCdPO4 : Eu3+ sont intéressantes en vue d’une application comme composante rouge dans des dispositifs d’émission de lumière. L’étude du système LiF – CdO – NaPO3 a révélé l’existence d’un fluorophosphate inédit de formule Li4Na41Cd30P30O117F20. Sa structure cristalline, déterminée sur monocristal, est caractérisée par la présence d’une entité inédite PO3F2, où le phosphore admet une coordinence 5. / This work is devoted to the crystallographic study and the electrochemical and optical properties of cadmium phosphates and fluorophosphates. The investigation of the NaF - CdO - NaPO3 system revealed a new fluorophosphate of formula Na2CdPO4F and the polymorphism of the phosphate NaCdPO4. The crystal structures of these two phases were solved using XRD powder diffraction data, from materials obtained by a ceramic route. The characterization of the fluorophosphate Na2CdPO4F was also carried out by infrared spectroscopy, Raman scattering and Nuclear Magnetic Resonance. The electrochemical study, carried out on solid solutions of the Na2(Cd/Mn)PO4F type, revealed that the simultaneous presence of two divalent cations was beneficial for the improvement of the sodation/desodation rates. The luminescence properties of the red emitters NaCdPO4: Eu3+ and Na2CdPO4F: Eu3+ are closely correlated with the structural properties. Some formulations of NaCdPO4: Eu3+ type are of interest for application as red components in light emitting devices. The study of the LiF - CdO - NaPO3 system revealed the existence of an original fluorophosphate of formula Li4Na41Cd30P30O117F20. Its crystal structure, determined on monocrystal, is characterized by the presence of a novel entity PO3F2, where the phosphorus admits a five-fold coordination.

The main goal of the present work was the synthesis of alkaline-earth nitridomanganates (AExMnyNz) with extended anionic structures and the characterization of their electronic and magnetic properties. Up to now, only compounds with isolated nitridomanganate anions have been reported in the discussed ternary systems. A systematic exploratory synthesis, employing high-temperature treatment of AE nitrides and Mn under controlled N2 pressure, yielded more than ten new nitridomanganates. Their crystal structures contain anionic building blocks of different dimensionalities, ranging from isolated species to three-dimensional frameworks. In general, the formation of Mn-rich compositions was found to be driven by the emergence of Mn-Mn interactions, which creates a link between nitridometalates and transition-metal-rich binary nitrides. The obtained nitridomanganates display a plethora of interesting phenomena, such as large spin-orbit coupling, magnetic frustration, quenching of magnetism due to Mn-Mn interactions, and metal-insulator transition.

<p> The crystal structures of Ca3(VO4)2, Ca3(asO4)2, alpha-Zn3(VO4)2, alpha-Zn2V2O7, Mg2V2O7, VPO5, and whitlockite (Room temperature and 1200 degree C) have determined by X-ray diffraction methods. Tests on the existing theories on the prediction of bond lengths have been made on the vanadate structures determined in this work as well as other reported structures. The range of validity of these theories have been brought out. The importance of the difference of the structure of whitlockite from that of BetaCa3(PO4)2, have also been discussed in detail. </p> / Thesis / Doctor of Philosophy (PhD)

A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-06-10T11:28:09Z No. of bitstreams: 1 robertodecarvalhoferreira.pdf: 4632819 bytes, checksum: e5bd9a607a629a54c4f57e8d4c95a5ed (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-07-13T13:47:43Z (GMT) No. of bitstreams: 1 robertodecarvalhoferreira.pdf: 4632819 bytes, checksum: e5bd9a607a629a54c4f57e8d4c95a5ed (MD5) / Made available in DSpace on 2016-07-13T13:47:43Z (GMT). No. of bitstreams: 1 robertodecarvalhoferreira.pdf: 4632819 bytes, checksum: e5bd9a607a629a54c4f57e8d4c95a5ed (MD5) Previous issue date: 2012-08-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A evolução dos computadores, mais especificamente no que diz respeito ao aumento de sua capacidade de armazenamento e de processamento de dados, possibilitou a construção de ferramentas computacionais destinadas à simulação de fenômenos físicos e químicos. Com isso, a realização de experimentos práticos vem, em alguns casos, sendo substituída pela utilização de experimentos computacionais, que simulam o comportamento de inúmeros elementos que compõem o experimento original. Neste contexto, podemos destacar os modelos utilizados para a simulação de fenômenos em escala atômica. A construção desses simuladores requer, por parte dos desenvolvedores, um amplo estudo e definição de modelos precisos e confiáveis. Tal complexidade se reflete, muitas vezes, em simuladores complexos, destinados a simulação de um grupo restrito de estruturas, expressos de maneira fixa, utilizando algumas formas geométricas padrões. Este trabalho propõe uma ferramenta computacional para a geração de um conjunto de estruturas cristalinas. Este conjunto é caracterizado pela organização espacial regular dos átomos que a compõe. A ferramenta é composta por a) uma linguagem de programação, que rege a criação das estruturas através da definição de um sistema cristalino e a construção de objetos a partir de funções características e operadores CSG (Construtive Solid Geometry), e b) um compilador/interpretador que analisa um código fonte escrito na linguagem, e gera a partir deste o objeto correspondente. A ferramenta oferece aos desenvolvedores um mecanismo simples que possibilita a geração de um número irrestrito de estruturas. Sua aplicabilidade é demonstrada através da incorporação de uma estrutura, gerada a partir de um código fonte, ao simulador Monte Carlo Spins Engine, criado pelo Grupo de Computação Gráfica da Universidade Federal de Juiz de Fora. / The evolution of computers, more specifically regarding the increased storage and data processing capacity, allowed the construction of computational tools for the simulation of physical and chemical phenomena. Thus, practical experiments are being replaced, in some cases, by computational experiments that simulate the behavior of many elements that compose the original one. In this context, we can highlight the models used to simulate phenomena at the atomic scale. The construction of these simulators requires, by developers, the study and definition of accurate and reliable models. This complexity is often reflected in the construction of complex simulators, which simulate a limited group of structures. Such structures are sometimes expressed in a fixed manner using a limited set of geometric shapes. This work proposes a computational tool that aims to generate a set crystal structures. Crystal structures are characterized by a set of atoms arranged in a regular way. The proposed tool consists of a) a programming language, which is used to describe the structures using for this purpose characteristic functions and CSG (Construtive Solid Geometry) operators, and b) a compiler/interpreter that examines the source code written in the proposed language, and generates the objects accordingly. This tool enables the generation of an unrestricted number of structures. Its applicability is demonstrated through the incorporation of a structure, generated from the source code, to the Monte Carlo Spins Engine, a spin simulator developed by the Group of Computer Graphics of the Federal University of Juiz de Fora.

Au cours des dernières années, le domaine de la cristallisation a pris de l'importance. Avec l'amélioration de techniques analytiques, la compréhension et la prédiction de structures cristallines deviennent plus précises. Ce travail porte sur l’un des cas limites répertoriés, qui défient la compréhension de la cristallographie, du polymorphisme, des théories de transition de phases et des mécanismes de discrimination chirale. La diprophylline est une molécule chirale d’intérêt pharmaceutique, et rentre dans cette catégorie de cas limites, au moins en ce qui concerne le comportement à la cristallisation. Les compositions énantiomérique et racémique de ce système à l'état amorphe ont été traitées, afin de soigneusement étudier les transitions cinétiques en lien avec la mobilité moléculaire globale. Un protocole robuste a été élaboré afin d’étudier la mobilité moléculaire par spectroscopie diélectrique, en couvrant une gamme de température de 200 °C. L’étude comparative des échantillons purifiés a démontré que le comportement dynamique d’un seul énantiomère et du mélange racémique était très similaire. Une autre relaxation secondaire γ a été trouvée pour les échantillons contenant de la théophylline, l’impureté majeure détectée par chromatographie. De plus, cette étude démontre que la cristallisation depuis l’état vitreux se déroule en plusieurs étapes complexes. Il s’agit d’abord de la nucléation homogène et croissance d’une première population de cristaux, dont les caractéristiques sont détaillées, et qui agit comme support pour le développement de populations secondaires constituées de solutions solides métastables ayant des cinétiques de croissance plus élevées. Ces études démontrent également que la présence d’interfaces favorise la nucléation hétérogène de formes plus stables, et ce à différents taux énantiomériques. / During the last few decades, the field of crystal engineering has gained prominence. Along with the improvement of analytical techniques, the understanding and prediction of crystal structures become more and more accurate. The present work is dedicated to one of the borderline cases encountered that challenge the general understanding of crystallography, polymorphism, phase transition theories and chiral discrimination mechanisms. The chiral pharmaceutical drug diprophylline is one of them, at least for crystallization aspects. Both racemic and enantiopure compositions of this system at the amorphous state have been considered, to carefully study the kinetic transitions with respect to the global molecular mobility. A robust protocol has been established to investigate the molecular mobility by broadband dielectric spectroscopy covering a temperature range of more than 200 °C. The comparative dielectric study of the purified samples proved that the dynamic behaviors of a single enantiomer and of the racemic mixture are very similar; but another secondary relaxation γ was found in samples containing theophylline, the main impurity identified by chromatographic measurements. Additionally, the present study demonstrated that the crystallization from the supercooled melt occurs as a complex multistep process. It involves the homogeneous nucleation and growth of a first population, whose characteristics are highlighted, and which acts as support for the development of secondary populations constituted of metastable solid solutions with higher growth rates. Moreover, the conducted studies demonstrated that at various enantiomeric compositions, the presence of interfaces favored the heterogeneous nucleation of a more stable form.

Due to the successful commercialization of lithium-ion batteries (LIBs), there is a growing interest in developing new battery materials with beneficial electrochemical properties. However, the uneven distribution of lithium resources and the low abundance of lithium in the earth crust are the main obstacles for further development and large-scale production of LIBs. Sodium-ion batteries (SIBs), an alternative that can partly meet the energy storage challenges, are getting attentions of researchers due to the wide availability and lower cost of sodium resources. Nevertheless, the conventional liquid electrolytes of either LIBs or SIBs composed of fluorinated salts dissolved in volatile organic solvents, posing serious safety issues due to the instability of the salts and flammability of the solvents. There is an urge to develop new fluorine-free electrolytes with improved physicochemical and electrochemical properties. In this context, the conventional fluorinated salts should be replaced with fluorine-free salts and the flammable solvents should be substituted with non-flammable solvents. There are a number of strategies to develop high-performant electrolytes including ambient-temperature ionic liquids (ILs), organic ionic plastic crystals (OIPCs) and highly concentrated electrolytes (HCEs) utilizing new salts and solvents. In this thesis, novel phosphorus-based ionic materials and electrolytes are introduced and their properties are thoroughly investigated. In the first part (Paper I), fluorine-free NaDEEP salt and TEOP solvent are employed to make “solvent-in-salt” (SIS) sodium electrolytes, also known as HCEs. Unexpectedly, the addition of TEOP solvent lead to an increase in the oxidation stability of the SIS electrolytes. In addition, an unusual ionic conductivity behavior is found – the ionic conductivities of Na electrolytes increase with increasing salt concentration. The “salt-rich” and “solvent-rich” phases formed within the electrolytes are investigated using multinuclear liquid-state NMR spectroscopy and NMR diffusometry. In the second part (Paper II), a series of orthoborate-based ionic materials, specifically OIPCs, containing phosphonium/ammonium cations are prepared to compare with the popular fluorine-free, bis(oxalato)borate (BOB) salts. The tetrabutyl phosphonium bis(glycolato)borate ([P4444][BGB]) OIPC displays much higher decomposition temperature than the structural analogous [P4444][BOB] IL. The crystal structures of LiBGB and NaBGB salts are resolved using single-crystal X-ray diffraction analysis. Unlike LiBOB, the BGB-based salts revealed excellent moisture stability over an extended time of up to 8-weeks air exposure. Multinuclear solid-state NMR spectroscopy indicates weaker cation-anion interactions in phosphonium-based salts than the ammonium-based ones. Finally, in the third part (Paper III), two-component and three-component eutectic electrolytes, composed of pyrrolidinium saccharin (PySc), lithium saccharin (LiSc) and/or [P4444][BGB] salt. The resulting mixtures showed significantly lower melting temperatures than the neat salts. The physicochemical and thermal properties of these salts are thoroughly investigated and discussed.

A molecule can crystallise in more than one crystal structure, a common phenomenon in organic compounds known as polymorphism. Different polymorphic forms may have significantly different physical properties, and a reliable prediction would be beneficial to the pharmaceutical industry. However, crystal structure prediction (CSP) based on the knowledge of the chemical structure had long been considered impossible. Previous failures of some CSP attempts led to speculation that the thermodynamic calculations in CSP methodologies failed to predict the kinetically favoured structures. Similarly, regarding the stabilities of co-crystals relative to their pure components, the results from lattice energy calculations and full CSP studies were inconclusive. In this thesis, these problems are addressed using the state-of-the-art CSP methodology implemented in the GRACE software. Firstly, it is shown that the low-energy predicted structures of four organic molecules, which have previously been considered difficult for CSP, correspond to their experimental structures. The possible outcomes of crystallisation can be reliably predicted by sufficiently accurate thermodynamic calculations. Then, the polymorphism of 5- chloroaspirin is investigated theoretically. The order of polymorph stability is predicted correctly and the isostructural relationships between a number of predicted structures and the experimental structures of other aspirin derivatives are established. Regarding the stabilities of co-crystals, 99 out of 102 co-crystals and salts of nicotinamide, isonicotinamide and picolinamide reported in the Cambridge Structural Database (CSD) are found to be more stable than their corresponding co-formers. Finally, full CSP studies of two co-crystal systems are conducted to explain why the co-crystals are not easily obtained experimentally. / University of Bradford