Water exhibits rich polymorphism, where more than 20 crystalline phases have been experimentally reported. Five of them are metastable and form at low temperatures by either heating amorphous ice or degassing clathrate hydrates. However, such metastable phases rarely crystallise directly from liquid water, making it challenging to study metastable phase relations at relatively high temperatures. Here, we report that high-pressure metastable phases of ice, including two unknown phases named ices XXI and XXII, crystallise directly from liquid water in a deeply supercooled region around the homogeneous nucleation temperature. The key is to use emulsified water to stabilise supercooled water in laboratory timescales. Ices XXI and XXII are obtained by isothermal compression of emulsified water at 295 K and 250 K, respectively. Our powder x-ray and neutron diffraction analyses combined with molecular dynamics (MD) simulations revealed the surprisingly complex structures of these new phases with Z = 152 (ice XXI) and 304 (ice XXII). Ice XXI is topologically identical to 'ice T2' previously predicted by MD simulations, and our experimental structural model can be used as a benchmark for its structures in simulations, which depend on the force fields. On cooling, ice XXI transforms into an orientationally ordered counterpart named ice XXIII. Our results revealed the "hidden" structural complexity of water underlying the phase diagram, as implied by previous computational works. Further efforts at unveiling such metastable phase relations will bridge the large gaps between computational and experimental phase diagrams of water.

Moss agate is a variety of agate characterized by the presence of black, green, or red filamentous fabrics that resemble vegetation such as moss, algae, ferns, and other plant-like forms. These fabrics occur within chalcedony, opal, or other silica minerals across various geologic periods. Traditionally, these filamentous fabrics have been regarded as the result of inorganic precipitates. In this study, we investigated filamentous fabrics within typical green-colored moss agates collected from Miocene rhyolitic pyroclastic rocks at Bodai (Komatsu, Ishikawa) and from Miocene andesites or andesitic pyroclastic rocks at Imakane (Kunnui, Hokkaido), Japan. Our analyses demonstrate that the filamentous fabrics in the green moss agates are of biogenic origin. The biogenic materials had been subjected to corrosion, after which the resulting voids were filled by celadonite precipitates. In certain portions of these filamentous fabrics, carbonaceous matter, representing the remnants that resisted corrosion, was detected. These findings suggest that some filamentous fabrics observed in green-colored moss agates worldwide should be reconsidered as being of biogenic origin. Consequently, such filamentous fabrics of biogenic derivation warrant investigation as potential "fossils" within the context of Earth's history.

Miyawakiite-(Y), a newly distovered mineral having the ideal formula square Y4Fe2(Si8O20)(CO3)(4)(H2O)(3) of a new structure type, was found in a granitic pegmatite from Suishoyama, Kawamata Town, Fukushima Prefecture, Japan. It is composed of tiny crystals of granular, plate-like, or columnar shape up to 0.8 mm with a pale-yellow color. It is transparent with a vitreous luster, occurring as a secondary mineral in a cavity in an aggregate composed of allanite-(Y) and britholite-(Y). The Mohs hardness is 3-4. Its tenacity is brittle, and its calculated density is 2.95 g center dot cm(-3). Under plane-polarized light, the mineral is pleochroic with O = colorless and E = pale yellow. It is uniaxial (+), with refractive indices of omega = 1.593(3) and epsilon = 1.654(2) (white light). Dispersion is weak. The empirical formula, calculated on the basis of 4 C and 8 Si atoms per formula unit, is (square K-0.70(0.30))(Sigma 1.00) (Y2.95Dy0.21Yb0.12Er0.10Gd0.08Sm0.02Tb0.01Ca0.33)(Sigma 3.82)(Fe1.142+Mg0.48Mn0.24)(Sigma 1.86)Si8C4O31.42[(H2O)(2.70)(OH)(0.30)] after electron microprobe, Raman spectroscopic, and crystal structure analyses. The refined unit-cell parameters determined by single-crystal X-ray diffraction are a = 17.53637(9), c = 9.55702(8) angstrom, V = 2939.02(4) angstrom(3), and Z = 4 in conjunction with the I4/mcm (#140) tetragonal space group. The structure is quite unique: the Y- and Fe-centered polyhedral arrangement with CO3 triangles forms a prismatic framework, with channels leading in the c-axis direction. The SiO4 tetrahedral networks are developed in this channel, forming a zeolite-like framework with K sites inside. The correlation between the OH/H2O and K contents results in a solid-solution series of square Y4Fe2(Si8O20)(CO3)(4)(H2O)(3)-KY4Fe2(Si8O20)(CO3)(4)[(H2O)(2)(OH)].

Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.

Kidney stone disease is a serious disease due to the severe pain it causes, high morbidity, and high recurrence rate. Notably, calcium oxalate stones are the most common type of kidney stone. Calcium oxalate appears in two forms in kidney stones: the stable phase, monohydrate (COM), and the metastable phase, dihydrate (COD). Particularly, COM stones with concentric structures are hard and difficult to treat. However, the factor determining the growth of either COM or COD crystals in the urine, which is supersaturated for both phases, remains unclear. This study shows that calcium phosphate ingredients preferentially induce COM crystal nucleation and growth, by observing and analyzing kidney stones containing both COM and COD crystals. The forms of calcium phosphate are not limited to Randall's plaques (1-2 mm size aggregates, which contain calcium phosphate nanoparticles and proteins, and form in the renal papilla). For example, aggregates of strip-shaped calcium phosphate crystals and fields of dispersed calcium phosphate microcrystals (nano to micrometer order) also promote the growth of concentric COM structures. This suggests that patients who excrete urine with a higher quantity of calcium phosphate crystals may be more prone to forming hard and troublesome COM stones.

The chemical composition of swedenborgite sample obtained from the type locality, L & aring;ngban, V & auml;rmland, Sweden, was determined using scanning electron microscopy and energy-dispersive X-ray spectroscopy. It was observed that swedenbolgite crystals possess both Ca-free and Ca-containing zones. The crystal structures of swedenborgite [space group P6(3)mc, a = 5.4402(10) & Aring; c = 8.8690(9) & Aring;, Z = 2] was refined to R1 = 0.012 using 1573 unique reflections. In addition, the threshold energy of the Sb K-edge XANES spectrum of swedenborgite was found to be higher than that of Sb2O3, but almost the same as that of Sb2O5. These results indicated that the oxidation state of Sb in swedenborgite was almost pentavalent, although the presence of a small amount of trivalent Sb is also suggested. It was therefore assumed that the following substitution relationship exists: 2Na(+) + Sb5+ -><- 2Ca(2+) + Sb3+, and that the charge balance of Ca occupation is achieved by reduction of some Sb5+ ions in the Ca-containing zone. The general formula of swedenborgite was therefore expressed as (Na1-xCax)Be4Sb1-0.5x5+Sb0.5x3+O7 (x = 0.0 or 0.05-0.07). The distortions of the Be-O distances along the c-axis and O-Be-O angles of BeO4 trigonal pyramid in swedenborgite were significantly larger than those in BeO bromellite. Opposite coordinate shifts between cations and anions along the c-axis occur because of the asymmetric arrangement around the NaO12 tetradecahedra with upper face sharing and lower edge sharing. The structure of swedenborgite therefore exhibits a biased arrangement of cations and anions parallel to the c-axis, which induces spontaneous polarization.

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.

The degree of anisotropy and the domain arrangement of crystal structures in ferroelectrics are affected by the grain boundaries and by the shape and size of the grains. To understand the grain boundary effects that occur in ferroelectric ceramics, we introduce a technique for nondestructively observing the internal lattice strain distribution of a submicrometer-sized ferroelectric grain in polycrystalline materials. The ferroelectric phase transition of a single grain in the polycrystalline materials was evaluated by tracking the changes in the Bragg coherent X-ray diffraction (CXD) patterns. The internal lattice strain distribution of the grains in the paraelectric phase was visualized via Bragg CXD imaging. A pair of 90° domains in the ferroelectric phase were also imaged in three dimensions, and showed a domain boundary correlated with the internal lattice strain caused by the stresses from the adjacent grains.

Abstract 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.

Katoite, ideally denoted as {Ca-3}[Al-2](square Si-x(3-x))(OH)(4x)O12-4x , where 1.5 < x <= 3, was found in skarn xenoliths from Tadano, Fukushima Prefecture, Japan, and investigated by electron microprobe analyses, X-ray single crystal structure refinement, and infrared (IR) spectroscopy. Katoite characteristically contains up to 0.18 atoms per formula unit (apfu) of S and has a range of compositions, wherein Si = 0.96-1.25 apfu, Al = 1.47-1.74 apfu, Fe = 0.13-0.28 apfu, and Mg = 0.01-0.10 apfu. A difference Fourier map revealed the residual electron density near the octahedral Y site (Wyckoff position = 16a), and we interpreted that S with three-fold coordination occurs at the position of the residual electron density, which is represented as the Y' site (Wyckoff position = 32e). The final refinement introduced the Y' site to yield R1 [F-2 > 2 sigma(F-2)] = 0.0353 with space group Ia (3) over bard and unit cell parameter a = 12.24095(8) angstrom. The IR spectrum in the range of 800-1200 cm(-1) shows a band at 1124 cm(-1) due to v(3)(SO4) and doublet bands at 879 and 931 cm(-1) with different absorbances interpreted as v(3)(SiO4) overlapping with v(3)(SO3). The combined results of IR spectroscopy and structure refinement imply that in the Tadano katoite, S4+ and S6+ , forming (SO3)(2-) and (SO4)(2-) coordinations, are placed at the Y' and tetrahedral Z sites, respectively. Assuming that S is preferentially allotted to the Y' site as S4+ to compensate for the deficiency of the octahedral cations Al, Fe, Mg, Mn, and Ti at the Y site, chemical formulae, including possible S4+ and S6+ contents, may be calculated. The average chemical formula for 14 different spots is as follows: {Ca-3}[(Al1.614Fe0.2083+Mg0.063Ti0.019)(Sigma 1.90)S-0.096(4+)](Sigma 2.00)(square 1.867Si1.120S0.0136+)(Sigma 3.00)[(OH)(7.192)O4.612F0.147Cl0.048](Sigma 12.00).

In nature, minerals record various origins and informationforgeology and geobiochemistry. Here, we investigated the origin of organicmatter and growth mechanism of quartz with oil inclusion revealingfluorescence under short ultraviolet (UV) light, obtained from theclay vein at Shimanto-cho, Kochi, Shikoku Island, Japan. Geologicalinvestigation indicated that the oil-quartz was formed in hydrothermalmetamorphic veins found in the late Cretaceous interbedded sandstoneand mudstone. The obtained oil-quartz crystals are mostly double-terminated.Micro-X-ray computed tomography (microCT) indicated that oil-quartzcrystals have various veins originating as skeleton structures alongthe quartz crystal {111} and {1-11} faces. Spectroscopic andchromatographic studies indicated that aromatic ester and tetraterpene(lycopene) molecules, which revealed fluorescence, were detected.Large molecular weight sterol molecules, such as C40, were also detectedin the vein of oil-quartz. This investigation indicated thatorganic inclusions in mineral crystals would form with ancient microorganismculture environments.

The cerite and merrillite groups belong to the cerite supergroup. Some nomenclature and classification changes have been made to the cerite group, whereas the merrillite group remains unchanged. Minerals of the cerite group have the general formula A9XM[T7O24Ø4]Z3, where T is Si. The cerite group, from now on, is subdivided into two subgroups, cerite and taipingite. The root name will be cerite and taipingite if the Z anions are dominated by (OH) and F, respectively. The prefix ferri- or alumino- will be added if the M cations are dominated by Fe3+ or Al, respectively. If the M cation is Mg, there will be no prefix. Taking into account the valency-imposed double site occupancy and the site total charge approach, a double suffix will be used to represent the essential A constituents in the general chemical formula. Cerite-(Ce), aluminocerite-(Ce), ferricerite-(La), and taipingite-(Ce) have been renamed cerite-(CeCa), aluminocerite-(CeCa), ferricerite-(LaCa), and taipingite-(CeCa), respectively. The newly approved mineral aluminotaipingite-(CeCa) also belongs to the taipingite subgroup.

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-μm 2 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.

In this study, we investigated calcium oxalate (CaOx) kidney stones and showed direct evidence of the solution-mediated phase transition of calcium oxalate dihydrate (COD; the metastable phase) to calcium oxalate monohydrate (COM; the stable phase). We examined the crystal phases, crystal textures, and protein distributions within thin sections of calcium oxalate kidney stones. Observation with a polarized-light microscope showed that the outline of the mosaic texture, in which COM crystals are assembled in a mosaic pattern, roughly coincides with COD's crystallographically stable face angles. Microfocus X-ray CT measurement captured the intermediate process of the phase transition, starting inside the COD single crystal and gradually transforming to COM crystals. In addition, the distribution of osteopontin and prothrombin fragment-1, common proteins contained in urine and visualized by multicolor fluorescence immunostaining, showed no apparent striations inside the COM single crystals with the mosaic texture, although the striation is apparent inside the COD single crystals. This is probably because the phase transition of mosaic-like COM occurred in a semiclosed system inside the COD single crystal, so the effect of periodic (day-night, seasonal, etc.) urinary protein concentration changes was small. On the other hand, striations were visible in concentrically laminated COM. This indicated that concentrically laminated COM formed in response to the changes in urinary protein concentrations. From the above, we conclude that the COD single crystals and the concentrically laminated COM seen in CaOx stones are primary structures, and the mosaic COM is a secondary structure that is a pseudomorph formed by the solution-mediated phase transition from COD single crystals.

The shapes and sizes of grains influence the anisotropy of crystal structures and the configuration of ferroelectric domains. In order to better understand these effects, we introduce a method to observe a ferroelectric phase transition in a single ferroelectric particle of sub-micrometer size. The phase transition was observed by cooling the sample through its Curie temperature, and studying the pattern variations of Bragg coherent X-ray diffraction from a single particle of 500 nm sized BaTiO 3 . A change from a single 200 peak (cubic phase) to both 200 and 002 peaks (tetragonal phase); was seen, with fringes connecting them like a bridge. The pattern from the BaTiO 3 particle in the cubic phase was also imaged using Bragg coherent diffraction imaging. The apparent strain distribution caused by dislocation internal to the BaTiO 3 crystal was visible in the reconstructed image.

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.

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) Å and 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) Å and 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) Å and 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.