On appelle biominéraux l’ensemble des minéraux fabriqués par le vivant. Ce sont des matériaux essentiels, présents dans la quasi-totalitédes espèces vivantes. Néanmoins les caractéristiques structurales, chimiques ainsi que les mécanismes de formation, et l’évolution de cesmatériaux sont encore fortement débattus. Cela s’explique notamment par les difficultés à étudier expérimentalement des espèces chimiquesévoluant en milieux biologiques.Bien que tout aussi complexe, une approche théorique, à l’échelle moléculaire, peut aider à la caractérisation de ces matériaux biologiqueset notamment la caractérisation de leurs interfaces formées avec les milieux biologiques environnants. Cela étant essentiel pour une meilleurecompréhension de la formation et de l’évolution de ces minéraux.Les oxalates de calcium constituent une famille de biominéraux très importante dans le monde du vivant. Ils constituent notamment les principales espèces cristallinesrencontrées dans les calculs rénaux où ils peuvent exister sous trois phases possédant différents degrés d'hydratation. Au cours de cette thèse, nous avons effectuéles simulations des propriétés spectroscopique IR et RMN des ces trois phases, ce qui permet d'obtenir une signature propre à chacune d'entre elle, aidant ainsi àl'identification de ces phases à partir des spectres obtenus expérimentalement.Les phosphates de calcium font aussi partie des biominéraux. Ils composent la majeure partie du minéral osseux des mammifères. Ce minéral se trouvesous la forme de nanoparticules décrites comme possédant un cœur cristallin d’hydroxyapatite substituées entourée d'une couche hydratée et désordonnée en surface.Durant ce travail de thèse, nous nous sommes intéressés à ces deux composantes. Concernant le cœur cristallin des particules, nous avons étudié en particulierle cas des substitutions par des carbonates car il s'agit de la substitution prédominante dans les apatites biologiques. En couplant ce travail à des expériencesde RMN solide nous pouvons proposé une localisation précise de ces substituants au sein de la maille d’hydroxyapatite.La couche désordonnée de surface est encore très mal comprise à l'heure actuelle et de nombreux modèles structuraux sont proposés dans la littérature pour la décrire. Nous avonsconsidéré un certain nombre d'entre eux pour lesquels nous avons modélisé les propriétés RMN, qui confrontées à celle issues de l'expérience nous ontpermis d'identifier les points forts et faibles des différentes hypothèses. / Biominerals are all the minerals produced by living organisms. They are essential materials, present in almost all living species. Nevertheless,the structural, chemical properties and, formation mechanisms and the evolution of these materials are still heavily debated. This is due in particular to thedifficulties of experimentally studying chemical species evolving in biologicalenvironments. Although, equally complex, a theoretical approach at the molecular level can help in the characterization of these biological materialsand in particular the characterization of their interfaces formed with the surrounding biological media. This is essential for a better understandingof the formation and evolution of these minerals.Calcium oxalates are essential biominerals that are very common in the living world. They constitute the main crystalline speciesencountered in kidney stones where they can exist in three phases possessing different degrees of hydration. In this, thesis we carried outsimulations to predict the IR and NMR spectroscopic properties of these three phases. Thsi enabled us to obtain specificsignature of each polyhydrate, and thus makes it possible to obtain a signature specific to each of them, thus helpingthe identification of these phases from the experimentally spectra obtained.Calcium phosphates are part of the bio/biological minerals. They make up the major part of the bone mineral of mammals. This mineral is in the form of nanoparticles havinga crystalline core of hydroxyapatite and a hydrated and disordered surface layer.During this thesis we were interested in these two components. Concerning the crystalline core of the particles, we studied in particularthe case of carbonate substitutions because of its predominant substitution in biological apatites. By combining this work with solid state NMR experimentswe can propose a precise localization of these substituents within the hydroxyapatite crystalline cell.The disordered surface layer is still very poorly understood and many structural models are proposed in the literature to describe it. We haveconsidered a number of them for which we have modeled the NMR properties which were then confronted with experimental results. The comparaisonmade it possible to identify the strengths and weaknesses of the various hypotheses.

With respect to the principles of biomineralization, it is of interest to study the crystallization of calcium oxalates under various experimental conditions. Calcium oxalates play decisive roles as biominerals in plants and as pathological “urinary/kidney stones” in vertebrates. Calcium oxalate exists in three different hydration states; calcium oxalate monohydrate (COM, monoclinic, a = 6.290(1)Å, b = 14.583(1)Å, c = 10.116(1)Å, β = 109.46°, P21/c), calcium oxalate dihydrate (COD, tetragonal, a = b = 12.371(3)Å, c = 7.357(2)Å, α = β = γ = 90°, I4/m) and calcium oxalate trihydrate (COT, triclinic, a = 6.11(1)Å, b = 7.167(2)Å, c = 8.457(2)Å, α = 76.5(2)°, β = 70.35(2)°, γ = 70.62(2)°, P ). Monoclinic COM and tetragonal COD are the most common phyto-crystals and the main constituents of kidney and urinary stones. The occurrence of calcium oxalates in plants represents a useful biogenesis (protection against herbivores) unlike the devastating occurrence in renal tubules. Therefore, biomineralization can be physiological or pathological. A systematic investigation of the morphological evolution of calcium oxalates in the presence of organic components is essential for understanding the mechanism of “pathological biomineralization”. In order to understand the pathological biomineralization of uroliths, it is necessary grow calcium oxalates comparable in morphology under similar growth conditions. The formation of calcium oxalate stones within a gelatinous state of proteins, polysaccharides, lipids and other biomacromolecules under a flow of supersaturated urine supports the fact that an “organic” gel model can simulate the process of urinary stone formation under in vitro conditions. Furthermore, synthetic polymers with precisely known functions and solution behaviours are better choices to understand the interaction of acidic proteins with calcium oxalates. Therefore, as a first step to unravel the complex pathology of uro/nephro lithiasis, we started to examine the structure and morphology of calcium oxalates crystallized in the presence of organic additives such as the sodium salt of polyacrylic acid (PAA) as well as agar gel. The influence of initial calcium oxalate concentration, pH and concentration of the additives on the formation of hydration states of calcium oxalates have been investigated along with the stated general methods. Apart from the three hydrated forms, calcium oxalate exists also in the anhydrous form (COA). Although three modifications of COA (α, β and γ) are reported in the literatures, the crystal structures and phase transformations were controversially discussed. We have been able to reveal the crystal structure of the β-modification of the anhydrous calcium oxalate by a combination of atomistic simulations and Rietveld refinements on the basis of powder X-ray diffraction pattern. β-COA belongs to the monoclinic system with unit cell parameters, a = 6.1644(3)Å, b = 7.3623(2)Å, c = 9.5371(5)Å, β = 90.24(2)°, P2/m (No. 10). The dehydration of COM was mimicked in silico to receive an initial model of the crystal structure of anhydrous calcium oxalate. This general approach may also be accessible for other decomposition processes ending up with crystalline powders of unknown crystal structure. No evidence for transformations from or to the α- or γ- modifications was found during our investigations. The growth pattern of COD crystals precipitated from aqueous solutions in the presence of PAA is clearly dependent on the concentration of PAA. By increasing the concentration of PAA, the shape of COD has been found to change from tetragonal bi-pyramids with dominant (101) pyramidal faces to tetragonal prisms with dominant (100) prism faces and finally to dumbbells. At still higher PAA concentrations, the morphology is reverted back to rod-like tetragonal prisms. Apart from these experiments, the interaction of PAA with (100) and (101) crystal faces of COD was explored with the aid of atomistic simulations. The simulation confirmed that during the development of the aggregates, strong interactions of PAA with the (100) faces take over control of morphologies. Our investigations show that the inner architecture of all the morphological varieties of COD was found to be dominated by an inner “core” consisting of thin elongated crystallites together with incorporated PAA and an outer “shell” formed as a consequence of secondary nucleation processes. We propose that for all types of COD aggregates, relative proportion of calcium oxalate and PAA dictates the shape and formation of nanometer sized crystallites which then aggregate and align to form the core. Such cores enriched with PAA may act as the sites for secondary nucleation events of calcium oxalate crystallites which then cover the core like a shell. In vitro experimental models for the growth of calcium oxalates can give valuable information on the growth and aggregation of urinary stones. Therefore, the “double diffusion technique” in agar gel matrix has been used for the biomimetic growth of calcium oxalate (COM) stones. A great variety of morphological forms of COM are produced in agar gel matrices (2 wt.-% agar gel of pH 8.5) ranging from platy crystallites to dumbbells and spherulites. The COM dumbbells and spherulites are assumed to be formed by the aggregation of smaller crystallites as a consequence of increased supersaturation inside the gel. Moreover, an increase of the pH value of the agar gel has been found to suppress the growth of COM and favours the growth of COD. The morphology of COD crystals grown in 2 wt.-% agar gel of pH 11.5 includes tetragonal prisms and dumbbells. The system calcium oxalate/ PAA/ H2O is a suitable model system for the investigation of principles of biomineral growth (shape development) in general. Our results demonstrate that the double diffusion technique in agar gel is a convenient route to grow calcium oxalate aggregates showing close resemblance to biogenic calculi and to study their ontogeny.

With respect to the principles of biomineralization, it is of interest to study the crystallization of calcium oxalates under various experimental conditions. Calcium oxalates play decisive roles as biominerals in plants and as pathological “urinary/kidney stones” in vertebrates. Calcium oxalate exists in three different hydration states; calcium oxalate monohydrate (COM, monoclinic, a = 6.290(1)Å, b = 14.583(1)Å, c = 10.116(1)Å, β = 109.46°, P21/c), calcium oxalate dihydrate (COD, tetragonal, a = b = 12.371(3)Å, c = 7.357(2)Å, α = β = γ = 90°, I4/m) and calcium oxalate trihydrate (COT, triclinic, a = 6.11(1)Å, b = 7.167(2)Å, c = 8.457(2)Å, α = 76.5(2)°, β = 70.35(2)°, γ = 70.62(2)°, P ). Monoclinic COM and tetragonal COD are the most common phyto-crystals and the main constituents of kidney and urinary stones. The occurrence of calcium oxalates in plants represents a useful biogenesis (protection against herbivores) unlike the devastating occurrence in renal tubules. Therefore, biomineralization can be physiological or pathological. A systematic investigation of the morphological evolution of calcium oxalates in the presence of organic components is essential for understanding the mechanism of “pathological biomineralization”. In order to understand the pathological biomineralization of uroliths, it is necessary grow calcium oxalates comparable in morphology under similar growth conditions. The formation of calcium oxalate stones within a gelatinous state of proteins, polysaccharides, lipids and other biomacromolecules under a flow of supersaturated urine supports the fact that an “organic” gel model can simulate the process of urinary stone formation under in vitro conditions. Furthermore, synthetic polymers with precisely known functions and solution behaviours are better choices to understand the interaction of acidic proteins with calcium oxalates. Therefore, as a first step to unravel the complex pathology of uro/nephro lithiasis, we started to examine the structure and morphology of calcium oxalates crystallized in the presence of organic additives such as the sodium salt of polyacrylic acid (PAA) as well as agar gel. The influence of initial calcium oxalate concentration, pH and concentration of the additives on the formation of hydration states of calcium oxalates have been investigated along with the stated general methods. Apart from the three hydrated forms, calcium oxalate exists also in the anhydrous form (COA). Although three modifications of COA (α, β and γ) are reported in the literatures, the crystal structures and phase transformations were controversially discussed. We have been able to reveal the crystal structure of the β-modification of the anhydrous calcium oxalate by a combination of atomistic simulations and Rietveld refinements on the basis of powder X-ray diffraction pattern. β-COA belongs to the monoclinic system with unit cell parameters, a = 6.1644(3)Å, b = 7.3623(2)Å, c = 9.5371(5)Å, β = 90.24(2)°, P2/m (No. 10). The dehydration of COM was mimicked in silico to receive an initial model of the crystal structure of anhydrous calcium oxalate. This general approach may also be accessible for other decomposition processes ending up with crystalline powders of unknown crystal structure. No evidence for transformations from or to the α- or γ- modifications was found during our investigations. The growth pattern of COD crystals precipitated from aqueous solutions in the presence of PAA is clearly dependent on the concentration of PAA. By increasing the concentration of PAA, the shape of COD has been found to change from tetragonal bi-pyramids with dominant (101) pyramidal faces to tetragonal prisms with dominant (100) prism faces and finally to dumbbells. At still higher PAA concentrations, the morphology is reverted back to rod-like tetragonal prisms. Apart from these experiments, the interaction of PAA with (100) and (101) crystal faces of COD was explored with the aid of atomistic simulations. The simulation confirmed that during the development of the aggregates, strong interactions of PAA with the (100) faces take over control of morphologies. Our investigations show that the inner architecture of all the morphological varieties of COD was found to be dominated by an inner “core” consisting of thin elongated crystallites together with incorporated PAA and an outer “shell” formed as a consequence of secondary nucleation processes. We propose that for all types of COD aggregates, relative proportion of calcium oxalate and PAA dictates the shape and formation of nanometer sized crystallites which then aggregate and align to form the core. Such cores enriched with PAA may act as the sites for secondary nucleation events of calcium oxalate crystallites which then cover the core like a shell. In vitro experimental models for the growth of calcium oxalates can give valuable information on the growth and aggregation of urinary stones. Therefore, the “double diffusion technique” in agar gel matrix has been used for the biomimetic growth of calcium oxalate (COM) stones. A great variety of morphological forms of COM are produced in agar gel matrices (2 wt.-% agar gel of pH 8.5) ranging from platy crystallites to dumbbells and spherulites. The COM dumbbells and spherulites are assumed to be formed by the aggregation of smaller crystallites as a consequence of increased supersaturation inside the gel. Moreover, an increase of the pH value of the agar gel has been found to suppress the growth of COM and favours the growth of COD. The morphology of COD crystals grown in 2 wt.-% agar gel of pH 11.5 includes tetragonal prisms and dumbbells. The system calcium oxalate/ PAA/ H2O is a suitable model system for the investigation of principles of biomineral growth (shape development) in general. Our results demonstrate that the double diffusion technique in agar gel is a convenient route to grow calcium oxalate aggregates showing close resemblance to biogenic calculi and to study their ontogeny.

The work deals with evaluation of the incidence of individual types of urinary stones in dogs, and the effect of specialised clinical diets on the treatment of urolithiasis. The evaluted material consists of an aggregate of analytical results from extracted urinary stones from the Veterinary clinic Vltava, in the period from January 30, 2008 to September 12, 2011. The effect of administration of specialised clinical diets for urolithiasis was evaluated on the basis of case histories of sample patients with proven struvite urolithiasis and an occurence of calcium oxalates and urates. The analysed aggregate of laboratory results of tested urinary stones has shown that besides a high incidence of struvite, the frequency of occurence of calcium oxalates increases as well. In this analysis even up to an identical percentage with struvite occurence at 44,44 % (that is, 24) analysed concrements. A link has been established with overal greater proneness of males to the formation of urinary stones. In the patient group with analysed majority percentage of whewellite, only 12,5 % of the analysed aggregate were females. Considering the widely varied pedigrees of analysed patients, incidence of urolithiasis is expected with ever greater frequency even in dogs not predisposed by breed and crossbreeds. Specialised clinical diets are employed in the treatment and prevention of certain types of urinary stons with high success rate, which adjust the urine environment and thus reduce the risk of occurence of urinary stones. Given the possibility of recurrence of urinary stones, i tis necessary to perform regular urine testing, and eventual sonographic examinations of the bladder