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Exploring the potential of sodium‐based materials is of utmost importance, especially for next‐generation solid‐state batteries. Herein, Na3PS4 thiophosphate solid electrolyte is focused on. While its tetragonal α phase is initially studied for Na solid‐state batteries, the impact of heat treatment and the phase transitions of amorphous and semicrystalline polymorphs obtained by mechanochemical synthesis remains poorly understood. The structural evolution is evaluated as function of the temperature of amorphous and semicrystalline Na3PS4 polymorphs obtained by mechanochemical processes. Both samples are heat‐treated during an in situ synchrotron X‐ray diffraction measurement, and multiple phase transitions are detected, some of them being irreversible. A novel and abundant orthorhombic intermediary phase is observed when the heat treatment is performed on the amorphous sample. The ionic conductivity of both amorphous and semicrystalline samples undergoes significant enhancement after heat treatment, reaching 0.09 and 0.16 × 10−3 S cm−1, respectively. This research sheds light on the thermal dynamics of Na3PS4 polymorphs, providing valuable insights into their crystallization processes, especially in the amorphous‐to‐cubic transition. The discovered intermediate phases underscore the potential for further advancements in sodium‐based solid‐state battery technologies. [ABSTRACT FROM AUTHOR]

The present study investigates the structure-property relationship of gravity die-cast and rheocast in situ processed 1wt%TiB2/Al-3.5Mg-0.15Sc-0.075Zr composites. The reinforcement was synthesized via the reaction of fluoride salts (K2TiF6 and KBF4) in the melt at 750 °C for an hour. The cooling slope technique was used for rheocasting, wherein the melt (pouring temperature of 700 °C) was allowed to flow over the cooling slope at an angle of 60°. Thereafter, all samples (gravity die cast and rheocast) were aged at 300 °C for 5 h. Microstructural characterization, hardness measurements, tensile tests, and fractography were necessary supplements to this investigation. The results obtained from this investigation infer: (a) The presence of nano-TiB2 particles increases the ductility (15%) of the gravity die-cast specimens; (b) rheocasting increases the strength of the specimen due to transformation from dendritic to equiaxed dendritic morphology and uniform particle distribution (reduced agglomeration). (c) Rheocast and aged specimens show maximum strength and adequate ductility due to the combined effects of structure refinement, reduced agglomeration, and the formation of fine precipitates. [ABSTRACT FROM AUTHOR]

Scandio-winchite, the first natural Sc-dominant amphibole-supergroup mineral, has been discovered in a granitic pegmatite that crops out in close association with rodingite-like calc-silicate rocks and metasomatized granitic bodies in a serpentinite quarry at a Jordanów Śląski village near Sobótka, ~30 km south of Wrocław, Lower Silesia, SW Poland. It occurs as an isolated subhedral crystal, with the size of ~20 × 8 μm in planar section, and as three polycrystalline aggregates, up to 50 μm across, composed of needle-shaped crystals dominated by {110}. It is present within chlorite aggregates that supposedly represent remnants of partly recrystallized xenoliths of the blackwall chlorite schists and is in quartz-feldspar portions of the pegmatite adjoining such xenolithic assemblages. Owing to the scarcity of the material and the exceptionally small size of the crystals, the color, streak, and optical properties could not be measured. By analogy with other amphiboles, scandio-winchite has a vitreous luster, brittle tenacity, and a Mohs hardness of ~5½. The mineral shows an uneven fracture and {110} perfect cleavage, with an angle of ~56° between cleavage planes. The density calculated from the empirical formula and refined unit-cell parameters is 3.026 g/cm3. The holotype crystal is composed of (in wt%): 55.88 SiO2, 0.11 TiO2, 0.53 Al2O3, 9.22 Sc2O3, 0.44 MnO, 8.89 FeO, 12.77 MgO, 5.71 CaO, 4.12 Na2O, 0.17 K2O, and 2.09 H 2 O c a l c (+) ; total 99.93. The composition normalized on the basis of 22 O2− + 2 (OH)− ions corresponds to the empirical formula A(□0.966K0.031Na0.003)Σ1B(Na1.132Ca0.868)Σ2 C (M g 2.704 F e 1.055 2 + M n 0.053 S c 1.140 A l 0.023 T i 0.012 ) Σ 4.987 T (S i 7.935 A l 0.065 ) Σ 8.000 O 22 (O H) 2 , simplified formula (□,K)(Na,Ca)2[(Mg,Fe)4Sc](Si8O22)(OH)2, and the ideal formula □(NaCa)(Mg4Sc)(Si8O22)(OH)2. The crystal structure was refined in the monoclinic system, space-group symmetry C2/m, with R1 index of 6.57%. Its unit-cell parameters are: a = 9.864(2) Å, b = 18.163(3) Å, c = 5.3053(16) Å, β = 104.41(3)°, V = 920.6(4) Å3; Z = 2, and the a:b:c ratio is 0.5431:1:0.2921. The crystal-structure refinement indicates almost exclusively Si-occupied T sites, the M4 sites occupied by nearly equal amounts of Na and Ca, M1 and M3 sites by divalent Mg + Fe cations, and M2 filled in equal proportions by divalent cations and Sc. These results, along with the dominant vacancy at the A site, univocally indicate that the mineral corresponds to a M2Sc-analog of winchite. Scandio-winchite is most likely a secondary phase of metasomatic origin related to the evolution of the country rocks and partial alteration of the blackwall chlorite schists xenolith induced by the pegmatitic melt and associated fluids. [ABSTRACT FROM AUTHOR]

The binary Cd5.7Yb phase representing the Tsai‐type category of the icosahedral quasicrystals is solved by the assignment of a unique atomic decoration to rhombohedral units in the Ammann–Kramer–Neri tiling. The unique decoration is found for units with an edge length of 24.1 Å and 3m internal point symmetry. The structural refinement was carried out for two underlying tilings generated by the projection method for 6D space. The difference lies in the location of the origin point which for one tiling is in the vertex and for the second one in the center of the 6D unit cell. The two tilings exhibit mutual duality. The choice of the tiling has a minor effect on the final structural model as both converge to an R factor of ∼11.5%. The main difference is related to the treatment of the Cd4 tetrahedral motif which is either orientationally ordered and aligned with the threefold axis or disordered and modeled as a partially occupied icosahedron. Both models can be presented as a covering by rhombic triacontahedral clusters with identical positions of clusters within rhombohedral units. The shell structure is Tsai‐type in the case of the first tiling and Bergman‐type for the other. [ABSTRACT FROM AUTHOR]

Being the professional visual software for the refinement of small molecular crystal structure, ShelXle has a large number of users among college groups. Due to the lack of literature reports on the using and research of ShelXle at home and abroad nowadays, many teachers and students were puzzled on how to deal with the problems encountered in the process of refinement using ShelXle. In this paper, the development backgrounds, the basic and special functions and the using method of ShelXle are presented in detail. Combined with several cases and compared with other visual software, its technical superiorities in the refinement of small molecular crystal structures were analyzed, and some suggestions about enhancing its refinement effect were also illustrated. [ABSTRACT FROM AUTHOR]

This study investigates the effects of Al–5Ti–B master alloy addition on the electrochemical properties and discharge performance of commercial pure aluminum (1060Al) in 4 M NaOH solution. The results show that the coarse branch-like α-Al grains are transformed into finer and smaller equiaxed grains, and the iron-rich phase are changed from long rod-like to small spherical grains. TiB2 particles introduce more heterogeneous nucleation sites in the α-Al crystals, resulting in an increased amount of grain boundaries in the aluminum matrix. There are more crystal defects at the grain boundaries than in the interior of α-Al grains, which provids more channels and energy for the reactions. This significantly increases the electrochemical activity of the aluminum alloy, causing the negative shifts for both the open circuit potential and the corrosion potential. The reduction in the size and change in the morphology of the iron-rich phase decreased the contact area between the iron-rich phase and the aluminum matrix, weakening the galvanic action between them. Meanwhile, the refinement of the α-Al grains decreased the potential difference between the interior and exterior of the grains, resulting in a reduction in the material corrosion current and an improvement in its corrosion resistance. Therefore, compared to the method of adding high hydrogen evolution potential elements to suppress hydrogen evolution reaction, the refinement of α-Al grains and the changes in the size and morphology of iron-rich phases due to the presence of TiB2 particles are the main reasons for improving the corrosion resistance and discharge performance of aluminum-air batteries in NaOH solution.

Hinckley index (Hi) can be used to characterize the crystallinity of kaolinite. Stacking order-disorder in kaolinite can considerably affect its crystallinity. However, the correlation between Hi and stacking order-disorder in kaolinite has not been reported thus far. Herein, the correlation between stacking order-disorder in kaolinite and Hi was investigated via experiments (XRD, IR spectroscopy, TG-DSC), molecular simulation, and structure refinement. First, we experimentally discovered that the stacking order-disorder in kaolinite changed the relative position between two adjacent structural layers, mainly afecting the interlayer forces. When the kaolinite layers are orderly stacked, the interlayer force is higher and the stacking lattice energy is lower. The lattice energy of kaolinite in diferent stacking states was simulated and analyzed using first-principles calculation. It was determined that the kaolinite layers are orderly stacked when two kaolinite layers have zero shift and disorderly stacked otherwise. Finally, through structural refinements, we proposed a new crystallinity index based on stacking order-disorder in kaolinite (crystallinity index based on stacking, CIS). CIS was well fitted to Hi (R2 = 0.986), indicating that kaolinite crystallinity, characterized by Hi, is essentially the ratio of orderly stacking to total stacking (the sum of ordered and disordered stacks). Furthermore, measuring Hi is difficult when kaolinite crystallinity is poor; however, CIS can be used alternatively. This study of the crystallinity of kaolinite will have important significance for its industrial application. [ABSTRACT FROM AUTHOR]

Scandian actinolite evolving to scandio-winchite (up to 5.45 wt% Sc2O3) has been found in chloritedominant xenoliths incorporated into marginal portion of a granitic pegmatite. The pegmatite intruded a blackwall schist zone developed around rodingite-type rocks exposed in a serpentinite quarry at Jordanów Śląski near Sobótka, ~30 km south of Wrocław, Lower Silesia, Poland. The amphiboles form irregular overgrowths around cascandite and represent a complex solid-solution series among actinolite and scandio-winchite end-members, with a trace contribution of "scandio-magnesio-hornblende." Structural studies of a scandian actinolite crystal with composition A[□0.995(2)K0.005(2)]Σ1B[Na0.24(5)Ca1.73(4)]Σ1.98(1) C M g 3.74 (7) F e 0.90 (3) 2 + M n 0.04 (1) S c 0.26 (3) A l 0.05 (1) Σ 4.99 (1) T S i 7.98 (2) A l 0.02 (2) Σ 8.00 O 22 (O H) 2 revealed monoclinic C2/m structure with unit-cell parameters a = 9.8517(3), b = 18.0881(6), c = 5.28501(18) Å, β = 104.809(4)°, in which scandium is located solely at the CM2 site. Scandian amphiboles are uncommon in geological environments, and invite comments on the origin of the observed Sc enrichment in the amphibole structure. Textural appearance of the chlorite-cascandite-amphibole clusters suggests that the formation of the amphiboles is related to the evolution of the country rocks followed by partial alteration of blackwall schist xenoliths by pegmatite-forming melt. [ABSTRACT FROM AUTHOR]

The chemistry and the crystal structure of the recently described mineral argentopolybasite are critically discussed based on the study of two new occurrences of the mineral: Gowganda, Timiskaming District, Ontario, Canada and IXL Mine, Silver Mountain mining district, Alpine County, California. The crystal structure of argentopolybasite can be described as the sequence, along the c axis, of two alternating layers: a [Ag6Sb2S7]2– A layer and a [Ag10S4]2+ B layer. In the B layer there are linearly-coordinated metal positions (B sites), which are usually occupied by copper in all members of the pearceite–polybasite group, resulting in a B -layer composition [Ag9CuS4]2+. In argentopolybasite, however, Ag fills all the metal sites in both A and B layers. By means of a multi-regression analysis on 67 samples of the pearceite–polybasite group, which were studied by electron microprobe and single-crystal X-ray diffraction, the effect of Ag, Sb and Se on the B sites of the B layer was modelled. Although the nomenclature rules for these minerals are based on chemical data only, we think this approach is useful to evaluate the goodness of the refinement of the structure (Ag/Cu disorder) and thus fundamental to discriminate different members of the pearceite–polybasite group. [ABSTRACT FROM AUTHOR]

Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structure prediction has been paid much attention in the last two decades. Some computational models have been developed to predict RNA three-dimensional (3D) structures in silico, and these models are generally composed of predicting RNA 3D structure ensemble, evaluating near-native RNAs from the structure ensemble, and refining the identified RNAs. In this review, we will make a comprehensive overview of the recent advances in RNA 3D structure modeling, including structure ensemble prediction, evaluation, and refinement. Finally, we will emphasize some insights and perspectives in modeling RNA 3D structures. [ABSTRACT FROM AUTHOR]

Nine new crystal structures of CG‐rich DNA 18‐mers with the sequence 5′‐GGTGGGGGC‐XZ‐GCCCCACC‐3′, which are related to the bacterial repetitive extragenic palindromes, are reported. 18‐mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18‐mers crystallized as A‐form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC‐driven protocol significantly helped to stabilize the structure refinement. The NtC‐driven refinement protocol can be adapted to other low‐resolution data such as cryo‐EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed. [ABSTRACT FROM AUTHOR]

The crystal structure of uralolite, Ca2Be4(PO4)3(OH)3·5H2O, from the spodumene deposit of Weinebene, Carinthia, Austria, has been refined with X-ray single crystal data gathered on a CCD diffractometer. Uralolite is monoclinic, space group P21/n, a = 6.553(1), b = 16.005(3), c = 15.979(3) Å, β = 101.63(1)°, V = 1641.5(5) Å3. While previously only isotropic displacement parameters and no hydrogen atom positions were reported for uralolite, now anisotropic displacement parameters were used for non-hydrogen atoms and hydrogen atoms were located and refined yielding R1 = 0.038 for 3909 observed reflections. Uralolite is built up from corrugated layers [Be4(PO4)3(OH)3]4- parallel to (010), which contain Z-shaped groups of four BeO4 tetrahedra sharing corners via three OH groups and are further crosslinked by PO4 tetrahedra. Two Ca atoms in Ca(Ophosphate)5(H2O)2 coordination and an interstitial water molecule link these layers along [010]. The OH groups and the Ca-bonded H2O molecules are all involved in hydrogen bonds with O···O distances of 2.780(2) − 3.063(2) Å and O-H···O angles of 150(1) − 179(1)° excluding a bifurcated bond. The interstitial water molecule displays a distorted tetrahedral environment of O atoms and accepts and donates each two hydrogen bonds. The crystal structure exhibits a C2/c pseudosymmetry for the [Be4(PO4)3(OH)3]4- layers and the Ca atoms. However, the disposition of the water molecules and an asymmetric hydrogen bond pattern involving OH groups as well as H2O molecules are decisive for the lowering of the symmetry of the structure to the true space group P21/n. [ABSTRACT FROM AUTHOR]

Structural modelling of octahedral tilts in perovskites is typically carried out using the symmetry constraints of the resulting space group. In most cases, this introduces more degrees of freedom than those strictly necessary to describe only the octahedral tilts. It can therefore be a challenge to disentangle the octahedral tilts from other structural distortions such as cation displacements and octahedral distortions. This paper reports the development of constraints for modelling pure octahedral tilts and implementation of the constraints in diffpy-CMI, a powerful package to analyse pair distribution function (PDF) data. The model in the program allows features in the PDF that come from rigid tilts to be separated from non-rigid relaxations, providing an intuitive picture of the tilting. The model has many fewer refinable variables than the unconstrained space group fits and provides robust and stable refinements of the tilt components. It further demonstrates the use of the model on the canonical tilted perovskite CaTiO3 which has the known Glazer tilt system α+β−β−. The Glazer model fits comparably to the corresponding space-group model Pnma below r = 14 Å and becomes progressively worse than the space-group model at higher r due to non-rigid distortions in the real material.

Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen‐bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non‐spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X‐ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non‐hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen‐bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal–organic compounds and network structures such as covalent organic frameworks and metal–organic frameworks is now possible in a hybrid mode such as IAM–TAAM or HAR–TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid‐mode refinement. [ABSTRACT FROM AUTHOR]

Two tourmaline samples occurring in quartz veinlets, which cross-cut an amphibolite body at the Budniki camp near the Kowary town in the south-west part of the Karkonosze Mountains, SW Poland, were studied through microprobe and single crystal X-ray diffraction. Samples were extracted from core and rim regions of crystals with concentric zoning. Chemical and structural data revealed that the core tourmaline is characterised by a dravite–oxy-dravite composition, with the formula: X(Na0.82Ca0.07K0.01Sr0.01□0.09)Σ1Y(Mg1.73Fe2+0.81Fe3+0.41Ti0.04V0.01)Σ3Z(Al5.85Fe3+0.15)Σ6(TSi6O18)(BO3)3(OH)3W(OH0.50O0.50)Σ1 and unit cell parameters a = 15.97377(14) Å and c = 7.22644(7) Å. The rim part of the crystals has a magnesio-lucchesiite composition, described by the formula: X(Ca0.49Na0.41K0.04Sr0.02□0.04)Σ1Y(Mg1.87Fe2+0.95Ti0.15Fe3+0.02V0.02)Σ3Z(Al5.49Fe3+0.51)Σ6(BO3)3(TSi6O18)(OH)3W(O0.81F0.18OH0.01)Σ1 with unit cell parameters a = 15.9863(3) Å and c = 7.22426(15) Å. Both tourmalines show similar refined populations at the Y and Z sites: Y[(Fe2+0.810Mg0.680)Σ1.490(Al1.044Fe3+0.413V0.009)Σ1.465Ti0.045]Σ3Z(Al4.806Mg1.042Fe3+0.152)Σ6 (dravite–oxy-dravite), and Y[(Fe2+0.945Mg0.750)Σ1.695(Al0.737Fe3+0.404V0.018)Σ1.159Ti0.146]Σ3Z(Al4.749Mg1.115Fe3+0.137)Σ6 (magnesio-lucchesiite), with a comparable Mg/(Mg + Fe) ratio of ~0.54–0.56, oxidation of Fe expressed as Fe3+/Fetotal ratio ~0.36–0.41, and trace components such as Ti, Sr, V, Cr, Ni and Co. The geological history of the eastern Karkonosze region in the Kowary vicinity indicates that both tourmalines crystallised from B-bearing metamorphic fluids mobilised by Variscan prograde metamorphism from the protoliths of the Velká Upá mica schists that host the Budniki amphibolite. The fluids migrated into the tectonised amphibolite enriched in Ti, V, Cr, Ni and Co, and mineralised the fractures within it through deposition of soluble species in the form of quartz–tourmaline veinlets. Magnesio-lucchesiite crystallised in an early retrogression stage, probably from Ca- and F-bearing fluids secondary enriched in B by the dissolution of dravite–oxy-dravite. The Budniki camp is, in addition to the type and co-type magnesio-lucchesiite localities, the third documented occurrence of the species worldwide. [ABSTRACT FROM AUTHOR]

• 3DED can successfully solve structures using beam energies ranging 30 to 300 kV. • Dynamical scattering increases R INT as the acceleration voltage decreases. • Kinematical refinement is comparable for all energies, albeit with some deficiencies. • Extinction correction improves structure refinement at low acceleration voltages. • Dynamical refinement works better for higher acceleration voltages. Nowadays, 3D Electron Diffraction (3DED) is widely used for the structure determination of sub-micron-sized particles. In this work, we investigate the influence of the acceleration voltage on the quality of 3DED datasets acquired on BaTiO 3 nanoparticles. Datasets were acquired using a wide range of beam energies, from common, high acceleration voltages (300 kV and 200 kV) to medium (120 kV and 80 kV) and low acceleration voltages (60 kV and 30 kV). It was observed that, in the integration process, R int increases as the beam energy is reduced, which is mainly due to the increased dynamical scattering. Nevertheless, the structure was solved successfully in all cases. The structure refinement was comparable for all beam energies with small deficiencies such as negative atomic displacements for the heaviest atom in the structure, barium. Including extinction correction in the refinement noticeably improved the model for low acceleration voltages, probably due to higher beam absorption in these cases. Dynamical refinement, however, shows superior results for higher acceleration voltages, since the dynamical refinement calculations currently ignore inelastic scattering effects. [ABSTRACT FROM AUTHOR]

Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate in catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature in macromolecules can make them difficult to model and refine, and a substantial portion of metal ions in the PDB are misidentified or poorly refined. CheckMyMetal (CMM) is a validation tool that has gained widespread acceptance as an essential tool for researchers working on metal‐macromolecule complexes. CMM can be used during structure determination or to validate metal binding sites in structural models within the PDB. The functionalities of CMM have recently been greatly enhanced and provide researchers with additional information that can guide modeling decisions. The new version of CMM shows metals in the context of electron density maps and allows for on‐the‐fly refinement of metal binding sites. The improvements should increase the reproducibility of biomedical research. The web server is available at https://cmm.minorlab.org. [ABSTRACT FROM AUTHOR]

We performed an analysis by single‐crystal X‐ray diffraction and scanning electron microscopy (SEM), aiming to solve and refine the structure of an ilmenite single crystal [(Fe0.5832Mg04168)TiO3] from the city of Ouvidor (Goiás, Brazil). Hirshfeld partition was used to explore the values of w(r), dnorm and curvedness that achieve complementary surfaces for neighbouring atoms in this ionic system, and the subsequent impact on the charge distribution, allowing the ionic radius and the charges of the ilmenite sample to be modelled. [ABSTRACT FROM AUTHOR]

We performed an analysis by single‐crystal X‐ray diffraction and scanning electron microscopy (SEM), aiming to solve and refine the structure of an ilmenite single crystal [(Fe0.5832Mg04168)TiO3] from the city of Ouvidor (Goiás, Brazil). Hirshfeld partition was used to explore the values of w(r), dnorm and curvedness that achieve complementary surfaces for neighbouring atoms in this ionic system, and the subsequent impact on the charge distribution, allowing the ionic radius and the charges of the ilmenite sample to be modelled. [ABSTRACT FROM AUTHOR]

To achieve high‐quality WLED (White light emitting diodes) lighting, it is essential to accurately control the emission color of phosphor materials. The LiCa3ZnV3O12 : Bi3+/Eu3+ phosphors were synthesized by a traditional high‐temperature sintering reaction and characterized using XRD, SEM, Fluorescence Spectrophotometer. This paper firstly reported the luminescence properties of Bi3+ single‐doped garnet phosphors LiCa3ZnV3O12. Based on local lattice distortion and the energy transfer of VO43−→Bi3+, the luminescence color of LiCa3ZnV3O12 : Bi3+ could be adjusted from blue‐green (490 nm) to yellow‐green (517 nm) under NUV excitation. In addition, Bi3+→Eu3+ energy transfer was designed by Bi3+ and Eu3+ double doping, and full color emission tuning from blue to blue‐green and then to pink and white was successfully realized. The energy transfer mechanism, luminescence chromaticity coordinates and thermal stability are studied in detail. More significantly, by constructing efficient energy transfer between Eu3+ and Bi3+, the thermal stability of as‐synthesized samples are gradually improved. This paper proposes a new direction for the color tuning of phosphors through multiple energy transfers and local lattice distortion. [ABSTRACT FROM AUTHOR]

Six Al- and Li-bearing tourmaline crystals from pegmatites were structurally and chemically characterized. These samples can be assigned to elbaite, fluor-elbaite and rossmanite. Quantitative analyses of light elements such as Li, B and H are not always easily accessible. Therefore a method for the calculation of Li and OH would be of a general interest for the Geosciences. In the present work we test whether relatively accurate Li and OH estimations are possible based on the deconvolution of the O–H stretching vibration modes in a Raman spectrum on common (Al, Li)-rich tourmalines. We use the short-range arrangement model in our band interpretation as this model, in contrast to other models, provides the ability to evaluate an additional parameter by analyzing the OH stretching modes that can be used in the formula calculation process, which ultimately leads to the estimation of Li and OH with high accuracy. We also compare microprobe and Raman spectroscopy results, which we combine, with optimized data derived from microprobe and single-crystal structure refinement by using the same crystals. Based on our investigations, where the Raman spectra were recorded on non-oriented crystal sections, we conclude that we produce more accurate estimations, when the effects of the section orientation are considered. Therefore, we also propose a new method to correct the influence of the orientation of the crystal section. [ABSTRACT FROM AUTHOR]

In the present study, we solidified JIS A7204 and A6022 (7204 and 6022 in short hereafter) aluminum alloys using an electromagnetic vibration (EMV) technique as a function of vibration frequency. The solidified structures were qualitatively observed, and then average grain size was quantitatively measured using the Image-Pro Plusµ software by a centroid method. Similarly to our previous observations of other alloy systems, the average grain size versus vibration frequency in both alloys exhibits a "V-shaped" relation; it reaches minimum of approximately 50µm at the frequency of f = 1000 Hz in 7204 alloys and around 61µm from the frequency of f = 500 Hz to f = 750 Hz in 6022 alloys. The microstructure formation was discussed when considering the substantial difference in electrical resistivity between the primary aluminum solid solution and the remaining liquid, which resulted in an uncoupled movement between the primary mobile solid and remaining sluggish liquid. Possible influences of different solute elements on solidification structures were briefly presented. [ABSTRACT FROM AUTHOR]

At high pressures, autoionization – along with polymerization and metallization – is one of the responses of simple molecular systems to a rise in electron density. Nitrosonium nitrate (NO+NO3−), known for this property, has attracted a large interest in recent decades and was reported to be synthesized at high pressure and high temperature from a variety of nitrogen–oxygen precursors, such as N2O4, N2O and N2–O2 mixtures. However, its structure has not been determined unambiguously. Here, we present the first structure solution and refinement for nitrosonium nitrate on the basis of single-crystal X-ray diffraction at 7.0 and 37.0 GPa. The structure model (P21/m space group) contains the triple-bonded NO+ cation and the NO3− sp2-trigonal planar anion. Remarkably, crystal-chemical considerations and accompanying density-functional-theory calculations show that the oxygen atom of the NO+ unit is positively charged – a rare occurrence when in the presence of a less-electronegative element.

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may be explicitly treated, omitted, or represented by a potential of mean-solvation-force term, depending on protein coordinates only, in the force field used. These three approaches are compared for hen egg white lysozyme (HEWL). This 129-residue non-spherical protein contains a variety of secondary-structure elements, and ample experimental data are available: 1630 atom–atom Nuclear Overhauser Enhancement (NOE) upper distance bounds, 213 3 J-couplings and 200 S2 order parameters. These data are used to compare the performance of the three approaches. It is found that a molecular dynamics (MD) simulation in explicit water approximates the experimental data much better than stochastic dynamics (SD) simulation in vacuo without or with a solvent-accessible-surface-area (SASA) implicit-solvation term added to the force field. This is due to the missing energetic and entropic contributions and hydrogen-bonding capacities of the water molecules and the missing dielectric screening effect of this high-permittivity solvent. Omission of explicit water molecules leads to compaction of the protein, an increased internal strain, distortion of exposed loop and turn regions and excessive intra-protein hydrogen bonding. As a consequence, the conformation and dynamics of groups on the surface of the protein, which may play a key role in protein–protein interactions or ligand or substrate binding, may be incorrectly modelled. It is thus recommended to include water molecules explicitly in structure refinement of proteins in aqueous solution based on nuclear magnetic resonance (NMR) or other experimentally measured data. [ABSTRACT FROM AUTHOR]

We report the crystal structure of allanite-(Ce), with composition (Ca1.0REE0.9□0.1)Σ2.0(Al1.46Fe3+0.52Fe2+0.76Mg0.12Ti0.15)Σ3.01Si3O12(OH) from the Xinfeng rare earth element (REE)-bearing granite in Guangdong Province, China. It has the unit cell a = 8.9550(4) Å, b = 5.77875(16) Å, c = 10.2053(4) Å, β = 114.929(5)° and Z = 2 in space group P21/m and is characterised by site splitting at M3 into M3a and M3b, at a distance of 0.38(3) Å, which are occupied partially by Fe0.764Mg0.12 and Ti0.15, respectively. The structure was determined by single-crystal X-ray diffraction and refined with anisotropic full-matrix least-squares refinement on F2 to R1 = 2.82%, wR2 = 7.77% for 1856 independent reflections (8772 collected reflections). However, M3 splitting is not present in either ferriallanite-(Ce) or epidote, in which M3 is almost fully occupied either by Fe2+ or by Fe3+. Comparisons of bond lengths and volumes in cation polyhedra among allanite-(Ce), ferriallanite-(Ce) and epidote tend to indicate that the essential factor that facilitates site splitting of M3 in allanite-(Ce) is heterovalent substitution and occupation of a crystallographic site between Fe2+(Mg2+/Mn2+)–Al3+(Ti4+), a common phenomenon in minerals, such as the plagioclase series. Fine structure analysis of the M3 split model revealed that deformation of A2 is related closely to distorted M3, which is consistent with Fe2+ incorporation following REE substitution. [ABSTRACT FROM AUTHOR]

Alumino-oxy-rossmanite, ideally □Al3Al6(Si5AlO18)(BO3)3(OH)3O, is here described as a new member of the tourmaline supergroup. It is an early magmatic Al-rich oxy-tourmaline from a small pegmatitic body embedded in amphibolite and biotite-rich paragneiss. This new pink tourmaline was found in a Moldanubian pegmatite (of the Drosendorf Unit) that occurs in a large quarry near the village of Eibenstein an der Thaya, Waidhofen an der Thaya district, Lower Austria, Austria. The empirical formula of the holotype was determined on the basis of electron microprobe analysis (EMPA), secondary ion mass spectrometry (SIMS), spectroscopical methods (optical absorption and infrared spectroscopy), and crystal-structure refinement (SREF) as X(□0.53Na0.46Ca0.01) Y(Al2.37Mn30.21+ Li0.16□0.14 Mn20.07+ Fe30.03+ Fe20.01+ Ti40.01+) ZAl6(Si5.37Al0.41B0.22O18)(BO3)3V[(OH)2.77O0.23] W[O0.80(OH)0.15F0.05]. Chemical composition (wt%) is: SiO2 33.96, TiO2 0.10, Al2O3 47.08, B2O3 11.77, FeO 0.08, Fe2O3 0.23, MnO 0.52, Mn2O3 1.70, CaO 0.04, Li2O 0.25, ZnO 0.03, Na2O 1.51, H2O 2.79, F 0.09, total 100.11. The presence of relatively high amounts of trivalent Mn in alumino-oxy-rossmanite is in agreement with the observation that the OH groups are present at a lower concentration than commonly found in other Al-rich and Li-bearing tourmalines. The crystal structure of alumino-oxy-rossmanite [space group R3m; a = 15.803(1), c = 7.088(1) Å; V = 1532.9(3) Å3] was refined to an R1(F) value of 1.68%. The eight strongest X‑ray diffraction lines in the (calculated) powder pattern [d in Å (I) hkl] are: 2.5534 (100) 051, 3.9508 (85) 220, 2.9236 (78) 122, 4.1783 (61) 211, 2.4307 (55) 012, 2.0198 (39) 152, 1.8995 (30) 342, 6.294 (28) 101. The most common associated minerals are quartz, albite, microcline, and apatite. Beryl and, in places, schorl are also found as primary pegmatitic phases. Because of the low mode of associated mica (muscovite), we assume that the silica melt, which formed this pegmatite, crystallized under relatively dry conditions, in agreement with the observation that alumino-oxy-rossmanite contains a lower amount of OH than most other tourmalines. This new member of the tourmaline supergroup exhibits the most Al-rich end-member composition of the tourmaline supergroup (theoretical content: ~54 wt% Al2O3). The significant content of tetrahedrally coordinated Al could reflect the relatively high-temperature conditions (~700 °C) inferred for crystallization of the pegmatite. Alumino-oxy-rossmanite was named for its chemical relationship to rossmanite, □(LiAl2)Al6(Si6O18) (BO3)3(OH)3(OH), which in turn was named after George R. Rossman, Professor of Mineralogy at the California Institute of Technology (Pasadena, California, U.S.A.). [ABSTRACT FROM AUTHOR]

Kaliophilite is a feldspathoid mineral found in two Italian magmatic provinces and represents one of the 12 known phases with composition close to KAlSiO4. Despite its apparently simple formula, the structure of this mineral revealed extremely complex and resisted structure solution for more than a century. Samples from the Vesuvius–Monte Somma and Alban Hills volcanic areas were analyzed through a multi-technique approach, and finally the crystal structure of kaliophilite was solved using 3D electron diffraction and refined against X-ray diffraction data of a twinned crystal. Results were also ascertained by the Rietveld method using synchrotron powder intensities. It was found that kaliophilite crystallizes in space group P3 with unit-cell parameters a = 27.0597 (16), c = 8.5587 (6) Å, V = 5427.3 (7) Å3 and Z = 54. The kaliophilite framework is a variant of the tridymite topology, with alternating SiO4 and AlO4 tetrahedra forming sheets of six-membered rings (63 nets), which are connected along [001] by sharing the apical oxygen atoms. Considering the up (U) and down (D) orientations of the linking vertex, kaliophilite is the first framework that contains three different ring topologies: nine (1-3-5) (UDUDUD) rings, six (1-2-3) (UUUDDD) rings and twelve (1-2-4) (UUDUDD) rings. This results in a relatively open (19.9 tetrahedra nm−3) channel system with multiple connections between the double six-ring cavities. Such a framework requires a surprisingly large unit cell, 27 times larger than the cell of kalsilite, the simplest phase with the same composition. The occurrence of some Na for K substitution (3–10%) may be related to the characteristic structural features of kaliophilite. Micro-twinning, pseudo-symmetries and anisotropic hkl-dependent peak broadening were also detected, and they may account for the elusive character of the kaliophilite crystal structure.

Isomorphous bismuth substitution for neodymium in the Nd5Mo3O16 + δ compound has been studied by X-ray diffraction. The crystal structure of a single-phase solid solution with the composition Nd4.95Bi0.05Mo3O16 + δ has been refined by the Rietveld method, and the electrical conductivity of the modified molybdate has been measured in the temperature range 300–700°C. [ABSTRACT FROM AUTHOR]

Protein structure refinement is the last step in protein structure prediction pipelines. Physics‐based refinement via molecular dynamics (MD) simulations has made significant progress during recent years. During CASP14, we tested a new refinement protocol based on an improved sampling strategy via MD simulations. MD simulations were carried out at an elevated temperature (360 K). An optimized use of biasing restraints and the use of multiple starting models led to enhanced sampling. The new protocol generally improved the model quality. In comparison with our previous protocols, the CASP14 protocol showed clear improvements. Our approach was successful with most initial models, many based on deep learning methods. However, we found that our approach was not able to refine machine‐learning models from the AlphaFold2 group, often decreasing already high initial qualities. To better understand the role of refinement given new types of models based on machine‐learning, a detailed analysis via MD simulations and Markov state modeling is presented here. We continue to find that MD‐based refinement has the potential to improve AI predictions. We also identified several practical issues that make it difficult to realize that potential. Increasingly important is the consideration of inter‐domain and oligomeric contacts in simulations; the presence of large kinetic barriers in refinement pathways also continues to present challenges. Finally, we provide a perspective on how physics‐based refinement could continue to play a role in the future for improving initial predictions based on machine learning‐based methods. [ABSTRACT FROM AUTHOR]

The structural parameters of a second low-temperature form of KZnPO4 have been refined using Rietveld analysis of X-ray powder diffraction (XRPD) data. This form of KZnPO4 is isostructural with NH4ZnPO4I and has previously been denoted as KZnPO4II. This article uses the notation δ-KZnPO4, to be consistent with the α, β, and γ notation commonly used for other KZnPO4 phases. [ABSTRACT FROM AUTHOR]

[Display omitted] Phase transformation changes numerous properties of materials. Ti–Pt alloys have received much interest because of high martensitic transformation temperature. However, the intrinsic brittleness of these intermetallic compounds with low crystal symmetry and complicated phase structure limit their applications, especially when composition deviates from stoichiometry ratio. By performing in situ heating high-resolution scanning transmission electron microscopy experiment and micro-mechanical testing on Ti-35 at% Pt that contained majorly Ti 3 Pt and αTiPt phases, it was found that precipitating herringbone twinned αTiPt islands within Ti 3 Pt could occur upon heating, significantly refining mixed-phase structure. The refinement of multi-intermetallic mixed-phase structure endowed brittle material with remarkable capacity for plastic deformation and strain hardening. The plastic deformation mechanisms include phase transformation upon yielding and dislocation slips during hardening, which rarely occurs in intermetallic compounds with low symmetry. The strong interaction between different deformation modes even caused nano-crystallization along slip bands. The results demonstrate that brittle-to-ductile transition in intermetallic compounds can be achieved by tuning mixed-phase structure through phase transformations. [ABSTRACT FROM AUTHOR]

Ensemble refinement, the application of molecular dynamics to crystallographic refinement, explicitly models the disorder inherent in macromolecular structures. These ensemble models have been shown to produce more accurate structures than traditional single‐model structures. However, suboptimal sampling of the molecular‐dynamics simulation and modelling of crystallographic disorder has limited the utility of the method, and can lead to unphysical and strained models. Here, two improvements to the ensemble refinement method implemented within Phenix are presented: DEN restraints, which guide the local sampling of conformations and allow a more robust exploration of local conformational landscapes, and ECHT disorder models, which allow the selection of more physically meaningful and effective disorder models for parameterizing the continuous disorder components within a crystal. These improvements lead to more consistent and physically interpretable simulations of macromolecules in crystals, and allow structural heterogeneity and disorder to be systematically explored on different scales. The new approach is demonstrated on several case studies and the SARS‐CoV‐2 main protease, and demonstrates how the choice of disorder model affects the type of disorder that is sampled by the restrained molecular‐dynamics simulation. [ABSTRACT FROM AUTHOR]

Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution of crystalline atoms with imperfect precision, the resulting electron density can be compatible with multiple models of motion. Diffuse X-ray scattering can reduce this degeneracy by reporting on correlated atomic displacements. Although recent technological advances are increasing the potential to accurately measure diffuse scattering, computational modeling and validation tools are still needed to quantify the agreement between experimental data and different parameterizations of crystalline disorder. A new tool, phenix.diffuse, addresses this need by employing Guinier's equation to calculate diffuse scattering from Protein Data Bank (PDB)-formatted structural ensembles. As an example case, phenix.diffuse is applied to translation-libration-screw (TLS) refinement, which models rigid-body displacement for segments of the macromolecule. To enable the calculation of diffuse scattering from TLS-refined structures, phenix.tls_as_xyz builds multi-model PDB files that sample the underlying T, L and S tensors. In the glycerophosphodiesterase GpdQ, alternative TLS-group partitioning and different motional correlations between groups yield markedly dissimilar diffuse scattering maps with distinct implications for molecular mechanism and allostery. These methods demonstrate how, in principle, X-ray diffuse scattering could extend macromolecular structural refinement, validation and analysis.

NMR structures of membrane proteins are often hampered by poor chemical shift dispersion and internal dynamics which limit resolved distance restraints. However, the ordering and topology of these systems can be defined with site-specific water or lipid proximity. Membrane protein water accessibility surface area is often investigated as a topological function via solid-state NMR. Here we leverage water-edited solid-state NMR measurements in simulated annealing calculations to refine a membrane protein structure. This is demonstrated on the inward rectifier K+ channel KirBac1.1 found in Burkholderia pseudomallei. KirBac1.1 is homologous to human Kir channels, sharing a nearly identical fold. Like many existing Kir channel crystal structures, the 1p7b crystal structure is incomplete, missing 85 out of 333 residues, including the N-terminus and C-terminus. We measure solid-state NMR water proximity information and use this for refinement of KirBac1.1 using the Xplor-NIH structure determination program. Along with predicted dihedral angles and sparse intra- and inter-subunit distances, we refined the residues 1–300 to atomic resolution. All structural quality metrics indicate these restraints are a powerful way forward to solve high quality structures of membrane proteins using NMR.

In 2020, cryo‐EM single‐particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high‐resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo − Fc difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo − Fc map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron‐density maps produced by X‐ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point‐group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints. [ABSTRACT FROM AUTHOR]

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing. [ABSTRACT FROM AUTHOR]

The advancement in 3D electron diffraction (3D ED) techniques that lead to a revolution in molecular structure determination using nano‐sized crystals is now achieving atomic resolution. The structures can be obtained from 3D ED data with tools similar to those used for X‐ray structure determination. In this context, the MoPro software, originally designed for structure and charge density refinements using X‐ray diffraction data, has been adapted. Structure refinement on 3D ED data was achieved via implementation of electron scattering factors available in the literature and by application of the Mott–Bethe equation to X‐ray scattering factors computed from the multipolar atom model. The multipolar model was parametrized using the transferable pseudoatom databanks ELMAM2 and UBDB. Applying the independent atom model (IAM), i.e. spherical neutral atom refinement, to 3D ED data on β‐glycine in MoPro resulted in structure and refinement statistics comparable to those obtained from other well known software. Use of the transferred aspherical atom model (TAAM) led to improvement of the refinement statistics and a better fit of the model to the 3D ED data as compared with the spherical atom refinement. The anisotropic displacement parameters of non‐H atoms appear underestimated by typically 0.003 Å2 for the non‐H atoms in IAM refinement compared with TAAM. Thus, MoPro is shown to be an effective tool for crystal structure refinement on 3D ED data and allows use of a spherical or a multipolar atom model. Electron density databases can be readily transferred with no further modification needed when the Mott–Bethe equation is applied. [ABSTRACT FROM AUTHOR]

A detailed description of the structure of the amphibole‐supergroup minerals is very challenging owing to their complex chemical composition that renders the process of cation partition extremely difficult, particularly because of the occurrence of multivalent elements. Since amphiboles naturally occur under a fibrous morphology and have largely been used to produce asbestos, there is a growing demand for detailed and accurate structural data in order to study the relationships between structure, composition and toxicity. The present study proposes a recommended refinement procedure for both X‐ray single‐crystal structure refinement (SREF) and Rietveld analysis for tremolite, selected as a test case. The corresponding structural results are compared to estimate the 'degree of confidence' of the Rietveld refinement with regard to SREF. In particular, it is shown that the interpretation of the electron density of the tremolite structure by SREF is model dependent. By assuming that the site‐scattering values from SREF should be as close as possible to those from electron microprobe analysis, as a crucial constraint for the correct description of the final crystal‐chemical model, it is found that it is best satisfied by using partially ionized scattering curves (SCs) for O and Si, and neutral SCs (neutral oxygen curves or NOCs) for other atoms. This combination leads to the best fit to the diffraction data. Moreover, it is found that Rietveld refinement using NOCs produces the best structural results, in excellent agreement with SREF. It is worth noting that, due to the complexity of the diffraction pattern and the fairly large number of freely refinable parameters, refinements with different combinations of SCs produce results almost indistinguishable from a statistical point of view, albeit showing significant differences from a structural point of view. [ABSTRACT FROM AUTHOR]

The microstructure of 7A85 aluminum alloy forgings often contains coarse second-phase particles and grains. To improve the microstructures and balance the properties, we used an enhanced thermomechanical treatment process that included multiaxial hot forging, multiaxial cryoforging (MACF), and three-step aging treatment. We thoroughly investigated the effects of MACF with 1–3 passes on the evolution of microstructure, three-dimensional (3D) mechanical properties at the center and edge, fracture toughness, and corrosion resistance of the alloy. Our findings revealed that multiaxial hot forging had a limited ability to crush the coarse second-phase particles. However, the higher flow stress and compound brittleness of MACF resulted in a significant increase in particle fragmentation and driving force for precipitation. Additionally, under MACF, massive dislocations proliferated due to the inhibition of dynamic recovery, forming large orientation gradient regions, which promote static recrystallization and grain refinement during solution treatment. As the number of MACF passes increased from one to three, the effect of particle crushing initially increased and then plateaued, the 3D grain sizes first decreased and then slightly increased, and the spacing of grain boundary precipitates (GBPs) increased. The dense and uniform precipitates, finest equiaxed grains, a low fraction of coarse particles, and large GBP spacing in MACF2 resulted in the higher strength, highest elongation with minimal anisotropy, superior fracture toughness, and enhanced corrosion resistance. Ultimately, MACF2 demonstrated the best overall performance and good homogeneity, with an average 3D ultimate tensile strength, average 3D yield strength, average 3D elongation, and fracture toughness at the center of 548 MPa, 476 MPa, 13.4%, and 42.5 MPa m1/2, respectively. These values were respectively 4.2%, 1.9%, 50.6%, and 13.9% higher than those of the uncompressed sample. [ABSTRACT FROM AUTHOR]

This article presents a comprehensive investigation of dual-phase nano (BaTiO 3) - (ZnFe 2 O 4) ceramic composites prepared via a physical mixing route. The qualitative charge density analysis was conducted using Fullprof refinement data, and the results were visualized in 2D and 3D using VESTA software. The atomic bonding of the composite was examined through charge density analysis, focusing on the 1D electron density profile. This analysis was compared with the molecular elastic parameters obtained from previous research using FTIR data on the same composite. The optical properties of the composite were characterized to determine optical conductivity, refractive index, Urbach energy, surface optical effect (SELF, VELF), and optical dielectric constants. The P-E hysteresis loop analysis is conducted to understand the deviations from the expected ferroelectric loop, indicating the presence of lossy capacitance due to field discharge by the conductive ferrite phase, underscoring the dynamic nature of the material's electrical properties. Comprehensive magnetic characterization revealed soft ferromagnetic behavior with intricate magnetic interactions. Correlations between observed physical properties were explored to gain insights into the theoretical changes in charge density, which are responsible for the optical behavior of the composite. The unique approach employed in this study provides valuable information on the charge density distribution and atomic bonding of the composites, highlighting their potential applications in magneto-electric and photonic devices. • Identified atomic bonding for structural integrity using Fullprof refinement and VESTA. • Key optical properties include tunable bandgap, refractive index, energy loss, and dielectric response. • Observed ferroelectric transition from lossy to resistive capacitance. • Quantified magnetic moment contributions and interfacial couplings. • Composite dictates flux density-mediated mechanisms due to changes in electron density. [ABSTRACT FROM AUTHOR]

Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.