The refinement of the structures of 17 weddellite crystals [Ca(C₂O₄)·(2+x)H₂O, I4/m, a = 12.329–12.378 Å, c = 7.345–7.366 Å, V = 1117.8–1128.6 ų], which were taken from the oxalic renal stones of the St. Petersburg (Russian Federation) citizens of both sexes aged from 24 to 65 years, has been carried out by the means of single-crystal X-ray diffraction (R₁ = 0.024–0.057). According to the results of the study, the amount of “zeolitic” water molecules (x) in the structure of weddellite varies from 0.13 to 0.37 pfu. A significant positive correlation between the amount of “zeolitic” water in the structure of weddellite and the closest interatomic distance between coordination water molecules in the large channels (OW1-OW1) was found as well as positive correlation between the value of the a parameter and the average distance of in Ca polyhedron. Obtained linear regression equation: x = 5.43a – 66.80, can be used for determination of the “zeolitic” water amount using the known unit-cell a parameter with mean-root-square error ±0.03 pfu. It was found that the x value for the crystals selected from the “mono-weddellite” stones (x = 0.13–0.24) are at the bottom of the range, thus we can assume that weddellite crystals with fewer “zeolitic” water amounts would be relatively stable. This work expands the knowledge of pathogenic crystal growth processes in living organisms and the development of the theory of oxalate stone formation in humans and animals, and may provide a building block for biomolecular technologies that approach the prevention and treatment of diseases associated with lithiasis.

The present work contributes to the essential questions on calcium oxalate formation under the influence of lithobiont community organisms. We have discovered calcium oxalates in lichen thalli on surfaces of apatite-nepheline rocks of southeastern and southwestern titanite-apatite ore fields of the Khibiny peralkaline massif (Kola Peninsula, NW Russia) for the first time; investigated biofilm calcium oxalates with different methods (X-ray powder diffraction, scanning electron microscopy, and EDX analysis) and discussed morphogenetic patterns of its formation using results of model experiments. The influence of inorganic and organic components of the crystallization medium on the phase composition and morphology of oxalates has been analyzed. It was shown that, among the complex of factors controlling the patterns of biogenic oxalate formation, one of the main roles belongs to the metabolic activity of the lithobiont community organisms, which differs significantly from the activity of its individuals.

Single crystals and powder samples of uric acid and uric acid dihydrate, known as uricite and tinnunculite biominerals, were extracted from renal stones and studied using single-crystal and powder X-ray diffraction (SC and PXRD) at various temperatures, as well as IR spectroscopy. The results of high-temperature PXRD experiments revealed that the structure of uricite is stable up to 380 °C, and then it loses crystallinity. The crystal structure of tinnunculite is relatively stable up to 40 °C, whereas above this temperature, rapid release of H₂O molecules occurs followed by the direct transition to uricite phase without intermediate hydration states. SCXRD studies and IR spectroscopy data confirmed the similarity of uricite and tinnunculite crystal structures. SCXRD at low temperatures allowed us to determine the dynamics of the unit cells induced by temperature variations. The thermal behavior of uricite and tinnunculite is essentially anisotropic; the structures not only expand, but also contract with temperature increase. The maximal expansion occurs along the unit cell parameter of 7 Å (b in uricite and a in tinnunculite) as a result of the shifts of chains of H-bonded uric acid molecules and relaxation of the π-stacking forces, the weakest intermolecular interactions in these structures. The strongest contraction in the structure of uricite occurs perpendicular to the (101) plane, which is due to the orthogonalization of the monoclinic angle. The structure of tinnunculite also contracts along the [010] direction, which is mostly due to the stretching mechanism of the uric acid chains. These phase transitions that occur within the range of physiological temperatures emphasize the particular importance of the structural studies within the urate system, due to their importance in terms of human health. The removal of supersaturation in uric acid in urine at the initial stages of stone formation can occur due to the formation of metastable uric acid dihydrate in accordance with the Ostwald rule, which would serve as a nucleus for the subsequent growth of the stone at further formation stages; afterward, it irreversibly dehydrates into anhydrous uric acid.

The protein composition of the organic component of kidney stones and the effect of major amino acids of the physiological solution on the crystallization process of calcium oxalate is studied in the work. By means of a complex technique the protein compounds are analyzed in 40 samples of kidney stones obtained by both direct surgical operations and distant lithotripsy. A strong and selective concentration of amino acids in different stones in comparison with the physiological fluids forming them is established. Nucleation processes and the crystallization kinetics of calcium oxalate monohydrate are studied in the model solutions without impurities and with additions of 13 amino acids. Different amino acids can both inhibit and promote these processes depending on the acid structure.

Microfungi were able to alternate solid substrate in various environments and play a noticeable role in the formation of insoluble calcium oxalate crystals in subaerial biofilms on rock surfaces. The present work describes how iron oxalate dihydrate humboldtine is acquired under the influence of the acid-producing microscopic fungus Aspergillus niger on the surface of two iron- bearing mineral substrates in vitro. Pyrrhotite and siderite rocks, as well as the products of their alteration, were investigated using a complex of analytical methods, including powder X-ray diffraction, optical microscopy, scanning electron microscopy and EDX spectroscopy. The effect of the underlying rocks with different composition and solubility and different oxidation states of iron on Fe-oxalate crystallization and on the morphology of humboldtine crystals was shown. The mechanisms of humboldtine formation were discussed. The results obtained in vitro seem promising for using fungi in bioleaching iron and other metals from processed ores and for the development of environmentally friendly biotechnologies.