Search

Moolooite, Cu(C2O4)·nH2O, is a typical biomineral which forms due to Cu-bearing minerals coming into contact with oxalic acid sources such as bird guano deposits or lichens, and no single crystals of moolooite of either natural or synthetic origin have been found yet. This paper reports, for the first time, on the preparation of single crystals of a synthetic analog of the copper-oxalate biomineral moolooite, and on the refinement of its crystal structure from the single-crystal X-ray diffraction (SCXRD) data. Along with the structural model, the SCXRD experiment showed the significant contribution of diffuse scattering to the overall diffraction data, which comes from the nanostructural disorder caused by stacking faults of Cu oxalate chains as they lengthen. This type of disorder should result in the chains breaking, at which point the H2O molecules may be arranged. The amount of water in the studied samples did not exceed 0.15 H2O molecules per formula unit. Apparently, the mechanism of incorporation of H2O molecules governs the absence of good-quality single crystals in nature and a lack of them in synthetic experiments: the more H2O content in the structure, the stronger the disorder will be. A description of the crystal structure indicates that the ideal structure of the Cu oxalate biomineral moolooite should not contain H2O molecules and should be described by the Cu(C2O4) formula. However, it was shown that natural and synthetic moolooite crystals contain a significant portion of “structural” water, which cannot be ignored. Considering the substantially variable amount of water, which can be incorporated into the crystal structure, the formula Cu(C2O4)·nH2O for moolooite is justified.

BACKGROUND: Bladder outlet obstruction is one of the main factors leading to the formation of stones in the urinary bladder. Understanding of the physico-biochemical processes in urine and blood, as well as the biomineralogy of urinary bladder stones, will make it possible to determine the pathogenetically justified treatment of such patients. AIM: The aim of the study was to identify and study the relationship between the physico-biochemical parameters of urine and blood and the biomineralogical composition of urinary bladder stones in patients with bladder outlet obstruction. MATERIALS AND METHODS: A comprehensive examination of 76 patients at the age of 37 to 89 years with urinary bladder stones occurred against the background of bladder outlet obstruction was carried out. A comprehensive diagnosis, including an assessment of the physico-biochemical parameters of urine and blood, bacteriological urine tests, radiological diagnostics, as well as biomineralogical studies of concretions, was carried out. RESULTS: The data obtained show that not all physicochemical parameters of blood and urine of the subjects are comparable with the data of patients with nephrolithiasis. In the vast majority of the studied kidney calculi were not detected, in addition, blood biochemical parameters, including the level of stone-forming substances were within the reference values. In urine tests an increase in some lithogenic substances is detected. Urinary stones in patients with bladder outlet obstruction had a mixed composition, more often phosphates and uric acid salts were detected (75 and 54% of cases, respectively). Considering the nature of metabolism and the increase in uric acid excretion with age, as well as the presence of residual urine in case of bladder outlet obstruction, it can be assumed that uric acid is the primary matrix in cystolithiasis. The data obtained indicate a connection between the infectious process in the bladder and the composition of urinary stones. Against this background, there is a more intensive process of cystolithogenesis. CONCLUSIONS: The algorithm for the diagnosis of urinary bladder stones secondary to bladder outlet obstruction should include not only the collection of anamnesis and the performance of routine blood and urine tests, but also specific physical and biochemical studies, as well as assess the biomineralogy of urinary stones, which will make it possible to choose an adequate tactics for the pathogenetic treatment of patients and effective metaphylaxis of stone formation.

To clarify the crystal chemical features of natural and synthetic oxalates Me2+(C2O4)∙2H2O (Me2+ = Fe, Mn, Mg, Zn), including minerals of the humboldtine group, solid solutions of lindbergite Mn(C2O4)∙2H2O–glushinskite Mg(C2O4)∙2H2O were precipitated under various conditions, close to those characteristic of mineralization in biofilms: at the stoichiometric ratios ((Mn + Mg)/C2O4 = 1) and non-stochiometric ratios ((Mn + Mg)/C2O4 < 1), in the presence and absence of citrate ions. Investigation of precipitates was carried out by powder X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Thermodynamic modelling was performed in order to evaluate the lindbergite–glushinskite equilibrium. It was shown that glushinskite belongs to the orthorhombic β-modification (sp. Gr. Fddd), while lindbergite has a monoclinic α-modification (sp. gr. C2/c). Mg ions incorporate lindbergite in much higher quantities than Mn ions incorporate glushinskite; moreover, Mn glushinskites are characterized by violations of long-range order in their crystal structure. Lindbergite–glushinskite transition occurs abruptly and can be classified as a first-order isodimorphic transition. The Me2+/C2O4 ratio and the presence of citric acid in the solution affect the isomorphic capacity of lindbergite and glushinskite, the width of the transition and the equilibrium Mg/Mn ratio. The transition is accompanied by continuous morphological changes in crystals and crystal intergrowths. Given the obtained results, it is necessary to take into account in biotechnologies aimed at the bioremediation/bioleaching of metals from media containing mixtures of cations (Mg, Mn, Fe, Zn).

Chemically induced polytypic phase transitions have been observed during experimental investigations of crystallization in the mixed uranyl sulfate-selenate Mg[(UO2)(TO4)2(H2O)](H2O)4 (T = S, Se) system. Three different structure types form in the system, depending upon the Se:S ratio in the initial aqueous solution. The phases with the Se/(Se + S) ratios (in mol %) in the ranges 0-9, 16-47, and 58-100 crystallize in the space groups P21, Pmn21, and P21/c, respectively. The structures of the phases are based upon the same type of uranyl-based sulfate/selenate chains that, through hydrogen bonds, are linked into pseudolayers of the same topological type. The layers are linked into three-dimensional structures via interlayer Mg-centered octahedra. The three structure types contain the same layers but with different stacking sequences that can be conveniently described as belonging to the 1M, 2O, and 2M polytypic modifications. The Se-for-S substitution demonstrates a strong selectivity with preferential incorporation of Se into less tightly bonded T1 site. The larger ionic radius of Se6+ relative to S6+ induces rotation of (T1O4) tetrahedra in the adjacent layers and reconstruction of the structure types. From the information-theoretic viewpoint, the intermediate Pmn21 structure type is more complex than the monoclinic end-member structure types.

Centimeter-sized crystals of orthorhombic calcium formate, α-Ca(HCO2)2 from Alkali Lake, Oregon, USA have been studied by means of powder and single-crystal X-ray diffraction analysis, infrared, and Raman spectroscopy. Based on the data on carbon isotope abundance in calcium formate and associated minerals, it was concluded that the formation of α-Ca(HCO2)2 may be a result of a combination of two factors: lake microbial metabolism and anthropogenic pollution with Agent Orange. Possible causes of stability of the low-density tetragonal β-Ca(HCO2)2 polymorph (formicaite) in boron ores are discussed.

The pattern of elements accumulation in biodeposits formed by living organisms and extracellular products of their metabolism (biofouling, primary soils) on different bedrocks (of the monuments of Historical necropoleis in Saint Petersburg) were studied by a complex of biological and mineralogical methods (optical microscopy, SEM, EDX, XRD, ICP MS, XRFS). The content of 46 elements in biodeposits with various communities of microorganisms is determined. The model recreating the picture of the input and selective accumulation of elements in biodeposits on the stone surface in outdoor conditions is assumed. It is shown that the main contribution to the elemental composition of biodeposits is made by the environment and the composition of the microbial community. The contribution of leaching under the action of microbial metabolites of mineral grains, entering biodeposits from the environment, is significantly greater than that of the underlying rock.

Thermal stability, structural evolution pathways, and phase transition mechanisms of the calcium oxalates whewellite (CaC2O4·H2O), weddellite (CaC2O4·(2+x)H2O), and caoxite (CaC2O4·3H2O) have been ...

To study strontium (Sr) incorporation into calcium oxalates (weddellite and whewellite), calcium-strontium oxalate solid solutions (Ca,Sr)[C2O4]∙nH2O (n = 1, 2) are synthesized and studied by a complex of methods: powder X-ray diffraction (PXRD), scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Two series of solid solutions, isomorphous (Ca,Sr)[C2O4]&middot, (2.5 &minus, x)H2O) (space group I4/m) and isodimorphous Ca[C2O4]&middot, H2O(sp.gr. P21/c)&ndash, Sr[C2O4]&middot, H2O(sp.gr. P 1 - ), are experimentally detected. The morphogenetic regularities of their crystallization are revealed. The factors controlling this process are discussed.

Chemically induced polytypic phase transitions have been observed during experimental investigations of crystallization in the mixed uranyl sulfate-selenate Mg[(UO

The crystallization of calcium oxalates (weddellite and whewellite) by interaction of natural and synthetic apatites and fossilized tooth tissue with fungus Aspergillus niger, one of most active acid producers, was studied in vitro. The morphology and the sequence of formation of growing oxalate hydrate crystals were revealed. It was shown that morphogenetic patterns of calcium oxalate crystallization on apatite substrates under the action of Aspergillus niger micromycete are determined by the chemical properties of the crystallization medium, which depends on the solubility of the underlying substrate and on its chemical composition and structural features (dispersity and porosity). The main difference between oxalate crystallization under the influence of Aspergillus niger micromycete on the surface of apatite substrates and on the surface of calcite marble is the predominance of whewellite over weddellite on all stages of growth.

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 &deg, C, and then it loses crystallinity. The crystal structure of tinnunculite is relatively stable up to 40 &deg, 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 &Aring, (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 &pi, 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 effect of bacteria that present in the human urine (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus) was studied under the conditions of biomimetic synthesis. It was shown that the addition of bacteria significantly affects both the phase composition of the synthesized material and the position of crystallization boundaries of the resulting phosphate phases, which can shift toward more acidic (struvite, apatite) or toward more alkaline (brushite) conditions. Under conditions of oxalate mineralization, bacteria accelerate the nucleation of calcium oxalates by almost two times and also increase the amount of oxalate precipitates along with phosphates and stabilize the calcium oxalate dihydrate (weddellite). The multidirectional changes in the pH values of the solutions, which are the result of the interaction of all system components and the crystallization process, were analyzed. The obtained results are the scientific basis for understanding the mechanisms of bacterial involvement in stone formation within the human body and the creation of biotechnological methods that inhibit this process.

The presence and study of the species composition of bacterial and fungal colonies in renal stones was determined. It was shown that the presence of microorganisms depends on the phase composition of the renal stone. No microbial colonies were detected in oxalate stones. Under the action of the acid-producing bacterial and fungal colonies, secondary crystallization of calcium oxalates (whewellite and weddellite) on phosphate aggregates can occur.

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.

The work considers the aggregation process of calcium oxalate monohydrate crystals (whewellite) during their crystallization from aqueous solutions. The intensive crystal aggregation during the precipitation is evidenced by a decrease in the bulk concentration against an increase in the crystal size. At the initial stages of crystallization fine particles are mainly captured by larger ones in the form of substance deposition on the initiating centers: organic blobs, dead cells, and so on. During the crystallization the effect of the dominant growth of large aggregates increases; the process develops autocatalytically; fine particles disappear more rapidly than large ones, and the crystal size distribution compresses simultaneously with an increase in the average particle size.

The single-crystal structures of four biomimetic weddellites CaC2O4 · (2 + x)H2O with different contents of zeolitic water (x = 0.10–0.24 formula units) produced by the microscopic fungus Aspergillus niger were refined from X-ray diffraction data (R = 0.029–0.038). The effect of zeolitic water content on the structural stability of weddellite was analyzed. The parameter a was shown to increase with increasing x due to the increase in the distance between water molecules along this direction. The water content and structural parameters of the synthesized weddellites are similar to those of weddellites from biofilms and kidney stones.

The refinement of the structures of 17 weddellite crystals [Ca(C 2 O 4 )·(2+ x )H 2 O, I 4/ m , a = 12.329–12.378 A, c = 7.345–7.366 A, V = 1117.8–1128.6 A 3 ], 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 ( R 1 = 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 = 5.43 a – 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.

A sample of uranyl carbonate mineral andersonite, Na2Ca[(UO2)(CO3)3]·5−6H2O, originating from the Cane Springs Canyon, San Juan Co., UT, USA was studied using single-crystal and powder X-ray diffraction at various temperatures. Andersonite is trigonal, R−3m, a = 17.8448(4), c = 23.6688(6) Å, V = 6527.3(3) Å3, Z = 18, R1 = 0.018. Low-temperature SCXRD determined the positions of H atoms and disordered H2O molecules, arranged within the zeolite-like channels. The results of high-temperature PXRD experiments revealed that the structure of andersonite is stable up to 100 °C, afterwards, it loses crystallinity due to release of H2O molecules. Taking into account the well-defined presence of H2O molecules forming channels’ walls that to the total of five molecules p.f.u., we suggest that the formula of andersonite is Na2Ca[(UO2)(CO3)3]·(5+x)H2O, where x ≤ 1. The thermal behavior of andersonite is essentially anisotropic with the lowest values of the main thermal expansion coefficients in the direction perpendicular to the channels (plane (001)), while the maximal expansion is observed along the c axis—in the direction of channels. The thermal expansion around 80 °C within the (001) plane becomes negative due to the total release of “zeolitic” H2O molecules. The information-based structural complexity parameters of andersonite were calculated after the removal of all the disordered atoms, leaving only the predominantly occupied sites, and show that the crystal structure of the mineral should be described as complex, possessing 4.535 bits/atom and 961.477 bits/cell, which is comparative to the values for another very common natural uranyl carbonate, liebigite.

The pattern of ion substitutions and non-stoichiometry of oxalate and phosphate human body minerals (weddellite, whewellite, hydroxyapatite, struvite, and brushite) and their synthetic analogs was investigated by complex X-ray diffraction, spectroscopic, and chemical methods. All the studied biological minerals are characterized by variable non-stoichiometry composition that reflects the non- stationarity of formation conditions. Non-stoichiometry of calcium oxalates results from variations in quantities of disorderly distributed water molecules. The water amount in weddellite significantly influences the crystal structure parameters. In particular, there is positive correlation between the value of a parameter and the occupancy of “zeolitic” water sites. Variations in composition of calcium and magnesium phosphates are caused by substitutions at all the crystallographic sites. Ion replacements in apatite and struvite are more prominent in comparison with those in brushite. Non-stoichiometry of apatite and brushite is due to the presence of vacancies at the Ca-sites, and that of struvite is due to the vacancies at the Mg-site. Two types of non-stoichiometry in carbonated apatites of B-type realize due to replacements PO4 3− ← CO3 2− or OH− ← H2O. Maximum concentrations of impurity ions in magnesium and calcium phosphates are mainly limited by the content of these ions in the physiological solution. In case of Mg replacement with Ca in struvite and Ca with K in brushite and apatite, it is also essentially limited by the size differences of the host and admixture ions.

Urolithiasis is rather widespread disease. However, till now there are no reliable methods of treatment and preventive maintenance for this illness, despite significant efforts. Moreover, it is completely not clear how renal stones are forming. The majority of renal stones consist of calcium oxalates – monohydrated whewellite CaC2O4·H2O and dihydrated weddellite CaC2O4·2H2O. Weddellite is a metastable phase under crystallizing conditions, and usually its crystals are substituted with small-grained whewellite. At the same time, about 38% of oxalate renal stones are made of weddellite. The purpose of this work is to examine the influence of crystallizing conditions on the calcium oxalates phase formation in the renal stones. Our modeling experiments were carried out with the variation of crystallizing conditions (temperature, pH, proportion of calcium and oxalate, organic and inorganic species in the physiological solution, amount of micromycetes and bacterial–viral associates, and time of crystallization). Experimental data show that the presence of peptides, bacteria, micromycetes and viruses, Mg2+, and CO3 2− ions in the solution stabilizes the calcium oxalate dehydrate crystallization.

Wide spread of oxalate mineralization in living organisms is a strong reason for its intense worldwide study during recent decades. Calcium oxalates can be found in human body (stones of urinary system, calcifications in lungs, crystals in a bone marrow etc.) (Socol et al. 2003; Zuzuk2005; Korago1992), in body of animals (stones of cats urinary system), and in plants (Korago 1992). Most often calcium oxalates occur as a part of pathogenic formations of the human urinary system (Korago 1992). The part of oxalate kidney stones ranges from50%to 75%depending of the geographical region. Our collection of kidney stones that were removed in Saint-Petersburg hospitals includes 263 samples, 81% of which consists of calcium oxalate minerals fully or as a part.