The impact of crystal phase transition on the hardness and structure of kidney stones.

Calcium oxalate kidney stones, the most prevalent type of kidney stones, undergo a multi-step process of crystal nucleation, growth, aggregation, and secondary transition. The secondary transition has been rather overlooked, and thus, the effects on the disease and the underlying mechanism remain unclear. Here, we show, by periodic micro-CT images of human kidney stones in an ex vivo incubation experiment, that the growth of porous aggregates of calcium oxalate dihydrate (COD) crystals triggers the hardening of the kidney stones that causes difficulty in lithotripsy of kidney stone disease in the secondary transition. This hardening was caused by the internal nucleation and growth of precise calcium oxalate monohydrate (COM) crystals from isolated urine in which the calcium oxalate concentrations decreased by the growth of COD in closed grain boundaries of COD aggregate kidney stones. Reducing the calcium oxalate concentrations in urine is regarded as a typical approach for avoiding the recurrence. However, our results revealed that the decrease of the concentrations in closed microenvironments conversely promotes the transition of the COD aggregates into hard COM aggregates. We anticipate that the suppression of the secondary transition has the potential to manage the deterioration of kidney stone disease.

Oil Inclusions Found in Skeleton Crystals of Quartz Indicated the Existence of Organic Matter Surrounding Ancient Growth Environments.

In nature, minerals record various origins and information for geology and geobiochemistry. Here, we investigated the origin of organic matter and growth mechanism of quartz with oil inclusion revealing fluorescence under short ultraviolet (UV) light, obtained from the clay vein at Shimanto-cho, Kochi, Shikoku Island, Japan. Geological investigation indicated that the oil-quartz was formed in hydrothermal metamorphic veins found in the late Cretaceous interbedded sandstone and mudstone. The obtained oil-quartz crystals are mostly double-terminated. Micro-X-ray computed tomography (microCT) indicated that oil-quartz crystals have various veins originating as skeleton structures along the quartz crystal {111} and {1-11} faces. Spectroscopic and chromatographic studies indicated that aromatic ester and tetraterpene (lycopene) molecules, which revealed fluorescence, were detected. Large molecular weight sterol molecules, such as C40, were also detected in the vein of oil-quartz. This investigation indicated that organic inclusions in mineral crystals would form with ancient microorganism culture environments.

Quantitative analysis of calcium oxalate monohydrate and dihydrate for elucidating the formation mechanism of calcium oxalate kidney stones.

We sought to identify and quantitatively analyze calcium oxalate (CaOx) kidney stones on the order of micrometers, with a focus on the quantitative identification of calcium oxalate monohydrate (COM) and dihydrate (COD). We performed Fourier transform infrared (FTIR) spectroscopy, powder X-ray diffraction (PXRD), and microfocus X-ray computed tomography measurements (microfocus X-ray CT) and compared their results. An extended analysis of the FTIR spectrum focusing on the 780 cm-1 peak made it possible to achieve a reliable analysis of the COM/COD ratio. We succeeded in the quantitative analysis of COM/COD in 50-µm2 areas by applying microscopic FTIR for thin sections of kidney stones, and by applying microfocus X-ray CT system for bulk samples. The analysis results based on the PXRD measurements with micro-sampling, the microscopic FTIR analysis of thin sections, and the microfocus X-ray CT system observation of a bulk kidney stone sample showed roughly consistent results, indicating that all three methods can be used complementarily. This quantitative analysis method evaluates the detailed CaOx composition on the preserved stone surface and provides information on the stone formation processes. This information clarifies where and which crystal phase nucleates, how the crystals grow, and how the transition from the metastable phase to the stable phase proceeds. The phase transition affects the growth rate and hardness of kidney stones and thus provides crucial clues to the kidney stone formation process.

Crystal structure, XANES and charge distribution investigation of krennerite and sylvanite: analysis of Au-Te and Te-Te bonds in Au1-xAgxTe2 group minerals.

The structure refinement and XANES study of two gold-silver-tellurides [Au1+xAgxTe2, krennerite (x = 0.11-0.13) and sylvanite (x = 0.29-0.31)] are presented and the structures are compared with the prototype structure of calaverite (x = 0.08-0.10). Whereas the latter is well known for being incommensurately modulated at ambient conditions, neither krennerite nor sylvanite present any modulation. This is attributed to the presence of relatively strong Te-Te bonds (bond distances < 2.9 Å) in the two minerals, which are absent in calaverite (bond distances > 3.2 Å). In both tellurides, trivalent gold occurs in slightly distorted square planar coordination, whereas monovalent gold, partly substituted by monovalent silver, presents a 2+2+2 coordination, corresponding to distorted rhombic bipyramids. The differentiation between bonding and non-bonding contacts is obtained by computation of the Effective Coordination Number (ECoN). The CHARge DIstribution (CHARDI) analysis is satisfactory for both tellurides but suggests that the Te-Te bond in the [Te3]2- anion is not entirely homopolar. Both tellurides can therefore be described as Madelung-type compounds, despite the presence of Te-Te in both structures.

π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis.

A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.

Polytypism in mcalpineite: a study of natural and synthetic Cu3TeO6.

Synthetic and naturally occurring forms of tricopper orthotellurate, CuII3TeVIO6 (the mineral mcalpineite) have been investigated by 3D electron diffraction (3D ED), X-ray powder diffraction (XRPD), Raman and infrared (IR) spectroscopic measurements. As a result of the diffraction analyses, CuII3TeVIO6 is shown to occur in two polytypes. The higher-symmetric CuII3TeVIO6-1C polytype is cubic, space group Ia3, with a = 9.537 (1) Šand V = 867.4 (3) Å3 as reported in previous studies. The 1C polytype is a well characterized structure consisting of alternating layers of CuIIO6 octahedra and both CuIIO6 and TeVIO6 octahedra in a patchwork arrangement. The structure of the lower-symmetric orthorhombic CuII3TeVIO6-2O polytype was determined for the first time in this study by 3D ED and verified by Rietveld refinement. The 2O polytype crystallizes in space group Pcca, with a = 9.745 (3) Å, b = 9.749 (2) Å, c = 9.771 (2) Šand V = 928.3 (4) Å3. High-precision XRPD data were also collected on CuII3TeVIO6-2O to verify the lower-symmetric structure by performing a Rietveld refinement. The resultant structure is identical to that determined by 3D ED, with unit-cell parameters a = 9.56157 (19) Å, b = 9.55853 (11) Å, c = 9.62891 (15) Šand V = 880.03 (2) Å3. The lower symmetry of the 2O polytype is a consequence of a different cation ordering arrangement, which involves the movement of every second CuIIO6 and TeVIO6 octahedral layer by (1/4, 1/4, 0), leading to an offset of TeVIO6 and CuIIO6 octahedra in every second layer giving an ABAB* stacking arrangement. Syntheses of CuII3TeVIO6 showed that low-temperature (473 K) hydrothermal conditions generally produce the 2O polytype. XRPD measurements in combination with Raman spectroscopic analysis showed that most natural mcalpineite is the orthorhombic 2O polytype. Both XRPD and Raman spectroscopy measurements may be used to differentiate between the two polytypes of CuII3TeVIO6. In Raman spectroscopy, CuII3TeVIO6-1C has a single strong band around 730 cm-1, whereas CuII3TeVIO6-2O shows a broad double maximum with bands centred around 692 and 742 cm-1.

Multicolor imaging of calcium-binding proteins in human kidney stones for elucidating the effects of proteins on crystal growth.

The pathogenesis of kidney stone formation includes multi-step processes involving complex interactions between mineral components and protein matrix. Calcium-binding proteins in kidney stones have great influences on the stone formation. The spatial distributions of these proteins in kidney stones are essential for evaluating the in vivo effects of proteins on the stone formation, although the actual distribution of these proteins is still unclear. We reveal micro-scale distributions of three different proteins, namely osteopontin (OPN), renal prothrombin fragment 1 (RPTF-1), and calgranulin A (Cal-A), in human kidney stones retaining original mineral phases and textures: calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD). OPN and RPTF-1 were distributed inside of both COM and COD crystals, whereas Cal-A was distributed outside of crystals. OPN and RPTF-1 showed homogeneous distributions in COM crystals with mosaic texture, and periodically distributions parallel to specific crystal faces in COD crystals. The unique distributions of these proteins enable us to interpret the different in vivo effects of each protein on CaOx crystal growth based on their physico-chemical properties and the complex physical environment changes of each protein. This method will further allow us to elucidate in vivo effects of different proteins on kidney stone formation.

Coherent surface structure induces unique epitaxial overgrowth of metastable octacalcium phosphate on stable hydroxyapatite at critical fluoride concentration.

The phase transformation from soluble calcium phosphates to less-soluble hydroxyapatite (HAP) is a thermodynamically natural route. This process is irreversible, and effective use of poorly reactive HAP to repair teeth that have no cellular metabolism remains challenging. However, this thermodynamically controlled transformation may apparently be reversed through the fast nucleation and growth of metastable phases, leading to a reactive HAP surface. Here, the assembled HAP-nanorod phase is demonstrated to change into the metastable octacalcium phosphate (OCP) phase in a calcium phosphate solution containing 0.8 ppm fluoride. Grown OCPs display parallel surface streaks and their 11¯0 and 00l (l: odd) electron-diffraction spots are often not visible. The streaked, elongated OCP gradually grows into large plates with flat surfaces that exhibit an intense11¯0 spot. Crystal-structure models reveal that the unique epitaxial overgrowth of OCP on HAP occurs since both materials share coherent {100} faces, resulting in the distinctive disappearance of 11¯0 and 00l OCP spots. A polysynthetic twin model that reliably explains this disappearance is proposed for the growth of OCP. This apparent reverse phase transformation produces hybrid calcium phosphates consisting of HAP cores and highly reactive outer OCP layers that are promising for the repair of dentin caries. STATEMENT OF SIGNIFICANCE: This paper demonstrates important and interesting finding regarding formation of calcium phosphates in relation to their crystal structures. We first show that hydroxyapatite (HAP), the major constituent of human teeth and bone, can reversely change to its precursor, octacalcium phosphate (OCP), contrary to thermodynamic-stability rule. This apparent reverse phase transformation occurs through sharing the coherent {100} faces of both materials under controlled fluoride concentration. Nanoscale similarity of two crystal surfaces enables structurally shared epitaxial overgrowth of OCP on HAP aided by faster growth rate of OCP than that of HAP. This reaction produces hybrid crystal consisting of outer OCP and core HAP, that has not been known before and is able to be applied to dentin caries repair.

Isotherms of individual pores by gas adsorption crystallography.

Accurate measurements and assessments of gas adsorption isotherms are important to characterize porous materials and develop their applications. Although these isotherms provide knowledge of the overall gas uptake within a material, they do not directly give critical information concerning the adsorption behaviour of adsorbates in each individual pore, especially in porous materials in which multiple types of pore are present. Here we show how gas adsorption isotherms can be accurately decomposed into multiple sub-isotherms that correspond to each type of pore within a material. Specifically, two metal-organic frameworks, PCN-224 and ZIF-412, which contain two and three different types of pore, respectively, were used to generate isotherms of individual pores by combining gas adsorption measurements with in situ X-ray diffraction. This isotherm decomposition approach gives access to information about the gas uptake capacity, surface area and accessible pore volume of each individual pore, as well as the impact of pore geometry on the uptake and distribution of different adsorbates within the pores.

Natural arsenic with a unique order structure: potential for new quantum materials.

Study of arsenic (As) provides guidelines for the development of next-generation materials. We clarify the unique structure of the third crystalline polymorph of natural As (Pnm21-As) by crystallographical experiment and the electronic structure by first-principles computational method. The crystal structure of Pnm21-As is a novel structure in which the basic portions of semi-metalic grey-As and semi-conductor black-As are alternately arranged at the atomic level. For both covalent and van der Waals bonding, the contributions of sd and pd hybridizations are important. Van der Waals bonding characteristics and d orbital contributions can be varied by control of layer stacking. Total charges are clearly divided into positive and negative in the same elements for the grey-As and black-As portions, respectively, is of importance. The sequence in which one-dimensional electron donor and acceptor portions alternate in the layer will be the first description.

Encapsulation kinetics and dynamics of carbon monoxide in clathrate hydrate.

Carbon monoxide clathrate hydrate is a potentially important constituent in the solar system. In contrast to the well-established relation between the size of gaseous molecule and hydrate structure, previous work showed that carbon monoxide molecules preferentially form structure-I rather than structure-II gas hydrate. Resolving this discrepancy is fundamentally important to understanding clathrate formation, structure stabilization and the role the dipole moment/molecular polarizability plays in these processes. Here we report the synthesis of structure-II carbon monoxide hydrate under moderate high-pressure/low-temperature conditions. We demonstrate that the relative stability between structure-I and structure-II hydrates is primarily determined by kinetically controlled cage filling and associated binding energies. Within hexakaidecahedral cage, molecular dynamic simulations of density distributions reveal eight low-energy wells forming a cubic geometry in favour of the occupancy of carbon monoxide molecules, suggesting that the carbon monoxide-water and carbon monoxide-carbon monoxide interactions with adjacent cages provide a significant source of stability for the structure-II clathrate framework.

Clathrate compounds of silica.

A review on silica clathrate compounds, which are variants of pure silica zeolites with relatively small voids, is presented. Zeolites have found many uses in industrial and domestic settings as materials for catalysis, separations, adsorption, ion exchange, drug delivery, and other applications. Zeolites with pure silica frameworks have attracted particular interest because of their high thermal stability, well-characterized framework structures, and simple chemical compositions. Recent advances in new synthetic routes have extended the structural diversity of pure silica zeolite frameworks. Thermochemical analyses and computational simulations have provided a basis for applications of these materials and the syntheses of new types of pure silica zeolites. High-pressure and high-temperature experiments have also revealed diverse responses of these framework structures to pressure, temperature, and various guest species. This paper summarizes the framework topologies, synthetic processes, energetics, physical properties, and some applications of silica clathrate compounds.

Experimental visualization of lithium conduction pathways in garnet-type Li7La3Zr2O12.

The evolution of the Li-ion displacements in the 3D interstitial pathways of the cubic garnet-type Li(7)La(3)Zr(2)O(12), cubic Li(7)La(3)Zr(2)O(12), was investigated with high-temperature neutron diffraction (HTND) from RT to 600 °C; the maximum-entropy method (MEM) was applied to estimate the Li nuclear-density distribution. Temperature-driven Li displacements were observed; the displacements indicate that the conduction pathways in the garnet framework are restricted to diffusion through the tetrahedral sites of the interstitial space.

New silica clathrate minerals that are isostructural with natural gas hydrates.

Silica clathrate compounds (clathrasils) and clathrate hydrates are structurally analogous because both materials have framework structures with cage-like voids occupied by guest species. The following three structural types of clathrate hydrates are recognized in nature: cubic structure I (sI); cubic structure II (sII); and hexagonal structure H (sH). In contrast, only one naturally occurring silica clathrate mineral, melanophlogite (sI-type framework), has been found to date. Here, we report the discovery of two new silica clathrate minerals that are isostructural with sII and sH hydrates and contain hydrocarbon gases. Geological and mineralogical observations show that these silica clathrate minerals are traces of low-temperature hydrothermal systems at convergent plate margins, which are the sources of thermogenic natural gas hydrates. Given the widespread occurrence of submarine hydrocarbon seeps, silica clathrate minerals are likely to be found in a wide range of marine sediments.

Synthesis and crystal structure of a layered silicate HUS-1 with a halved sodalite-cage topology.

A new layered silicate, HUS-1, was synthesized by hydrothermal synthesis using decomposed FAU- and *BEA-type zeolites as nanosized silica parts. Structural analyses by X-ray powder diffractometry and solid-state magic-angle-spinning (MAS) NMR spectroscopy revealed that HUS-1 has a layered structure containing a silicate layer per unit cell along a stacking direction. Its framework topology is similar to that of SOD-type zeolites and consists of a halved sodalite cage, which includes four- and six-membered Si rings. Structure refinement by the Rietveld method showed that tetramethylammonium (TMA) ions used as a structure-directing agent (SDA) were incorporated into the interlayer. The four methyl groups of the TMA molecule were located orderly in a hemispherical cage in the silicate layer, which suggests restraint of molecular motion. The interlayer distance is estimated at about 0.15 nm, which is unusually short in comparison with that in other layered silicates (e.g., ß-HLS or RUB-15) with similar framework topologies. The presence of hydrogen bonding between adjacent terminal O atoms was clearly revealed by the (1)H MAS NMR spectroscopy and by electron-density distribution obtained by the maximum entropy method.