Crystal Structure Refinement Research Articles

The OH-stretching region in infrared spectra of the apatite OH-Cl binary system

Abstract Polarized Fourier transform infrared (FTIR) microspectroscopy of the OH-stretching region of hydroxylapatite-chlorapatite solid solutions presents novel problems for the assignment of peaks to specific OH-Cl pairs. Crystal structure refinements of Hughes et al. (2016) identified new positions for column anions in synthetic mixed Cl-OH apatites, with three different column anion arrangements depending on composition. These structural refinements, combined with bond-valence calculations, allow for interpretation of the OH-stretching region. A peak at 3574 cm–1 is identified as that from end-member hydroxylapatite. A second major peak at 3548 cm–1 is only found in mixed chlorapatite-hydroxylapatite solid solutions, as is a third peak at 3592 cm–1. Both represent perturbations of the OH-stretching vibration as compared to hydroxylapatite, to lower and higher frequency, respectively. Both of the new peaks are the result of a Clb-OH sequence, with adjacent anions in crystallographically similar positions, both above or both below adjacent mirror planes. One configuration has the hydrogen atom pointed toward the chlorine atom. The second has the hydrogen of the OH group pointed away from the chlorine atom. Both configurations present novel problems. The shift to lower wavenumber at 3548 cm–1 is characteristic of hydrogen bonding in fluorapatite-hydroxylapatite mixtures, yet the distance between O(H) and Clb is too great to allow it. The shift of OH-stretching vibrations to lower wavenumber is produced through changes in polarization of intervening Cl-Ca2′ (or Ca2) and Ca2(′)-O3 bonds, which are affected by the presence of the large chlorine atom. Lowering the OH-stretching vibration mimics the expected effect of chlorine on a neighboring OH group in the apatite c-axis column, though without hydrogen bonding. The shift to higher wavenumbers, i.e., higher frequency at 3592 cm–1, is the opposite of that expected for hydrogen bonding between column anions in the apatite mineral group. It is ascribed to the interaction between an adjacent Clb and the oxygen end of an adjacent OH dipole. This pairing places an oxygen and a chlorine atom in close proximity. Possible means of accommodation are discussed. A ubiquitous peak at 3498 cm–1 represents hydrogen bonding between an OH and the OHa site, with an interoxygen distance of about 2.9 Å. Published modeling supports the hypothesis that the OHa site is occupied by an O rather than an OH. However, no clear counterpart to this pairing is observed in crystal structure refinements for specimens lacking OHa, although the infrared absorbance is present. The existence of oxyapatite is inferred from studies of plasma-sprayed biomaterials, but the crystal-lographic details of the substitution have remained elusive. A minor shoulder at 3517 cm–1 does not have a clear counterpart in the structural refinements. Sequences of three columnar anions (e.g., OH-Cl-OH or Cl-OH-OH) can be ruled out, but an unequivocal assignment awaits further research.

Refractive index of CdTe1-xSex thin films estimated by Swanepoel's method

CdTe1-xSex thin films were deposited on a quartz and silicon substrate using the method of high-frequency magnetron sputtering. The chemical composition analysis and crystal structure refinement were examined using X-ray fluorescence spectroscopy and X-ray diffraction data. CdTe1-xSex thin films with x < 0.7 are crystallized in hexagonal structure (structure type – ZnO, space group P63mc (No. 186)) and in cubic structure (structure type – ZnS, space group F-43m (No. 216)) with x < 0.35. Unit-cell parameters decrease with increasing Se content in CdTe1-xSex thin films. The values of the optical band gaps for CdTe1-xSex thin films were estimated using the Tauc plot and from the maximum position of the first derivative of the transmittance dT/dλ. The study of optical functions is performed on the basis of the transmission spectrum measured experimentally using the Swanepoel's method. The spectral behavior of the optical functions, such as refractive index and real part of dielectric function is established. The dispersion of the refractive index is discussed in terms of the Wemple and Di Domenico single oscillator model.

Towards expansion of the MATTS data bank with heavier elements: the influence of the wavefunction basis set on the multipole model derived from the wavefunction

The MATTS (multipolar atom types from theory and statistical clustering) data bank is an advanced tool for crystal structure refinement and properties analysis. It applies a multipole model (MM), which describes the asphericity of the atomic electron density and helps to interpret X-ray or electron diffraction data better than approaches based on the spherical atoms approximation. The generation of MATTS data involves density functional theory calculations, and until recently we used the B3LYP/6-31G** level of theory for this stage. However, it was not so clear how the wavefunction level of theory, especially the basis set used, influenced the resulting MM. This study investigates the influence of the wavefunction basis set on the resulting MM from a charge density point of view. For this purpose, we used charge density related properties, such as correlation of electrostatic potentials, atomic electron populations and average electrostatic potential values. The complex analysis reveals that, within the framework of MATTS data generation, the size of the basis set used has the most significant impact on the MM's charge density quality, and switching from double- to triple-zeta basis sets helps notably improve the charge density related properties. This research sets the foundation for the creation of a new version of the MATTS data bank, which will be expanded to include atom types for elements heavier than Kr and selected metal complexes important for biological systems.

An idealized model for the crystal structure of intermetallic compounds isostructural with Mg3Cr2Al18

ABSTRACT Mg3Cr2Al18 (abbreviated in this report as MCA) is the parent phase for a large class of intermetallic compounds that belong to the cubic crystal space group, Fd 3 ¯ m . The purpose of this paper is to introduce an ideal, unrelaxed crystal structure for compounds isostructural with MCA. There are five distinct atomic sublattices in MCA compounds, which can be denoted, A, B, C, D, and E. With this, a general description for MCA structures can be written as A 1 8 a B 2 16 c C 2 16 d D 6 48 f E 12 96 g , where the superscripts represent the Wyckoff special equipoints associated with the various sublattices in MCA, and the subscripts indicate the contributions of each sublattice to the stoichiometry of one formula unit in an any given MCA-structured compound. Sublattices D and E are where deviations from ideality occur in real, MCA-like compounds. This paper examines MCA bond lengths, nearest-neighbour polyhedral arrangements, 3-D sublattice crystal structures, 2-D atom tessellation patterns, and crystal chemical effects associated with atomic relaxations on the D and E sublattices. The ideal MCA crystal structure developed in this report provides an appropriate initial structure for use as input to crystal structure refinements of diffraction data for MCA-like phases being examined experimentally, or as input for computational, atomistic simulations of the structures of such compounds.

Development of ultrafast four-dimensional precession electron diffraction

Ultrafast electron diffraction/microscopy technique enables us to investigate the nonequilibrium dynamics of crystal structures in the femtosecond-nanosecond time domain. However, the electron diffraction intensities are in general extremely sensitive to the excitation errors (i.e., deviation from the Bragg condition) and the dynamical effects, which had prevented us from quantitatively discussing the crystal structure dynamics particularly in thick samples. Here, we develop a four-dimensional precession electron diffraction (4D-PED) system by which time (t) and electron-incident-angle (ϕ) dependences of electron diffraction patterns (qx,qy) are recorded. Nonequilibrium crystal structure refinement on VTe2 demonstrates that the ultrafast change in the crystal structure can be quantitatively determined from 4D-PED. We further perform the analysis of the ϕ dependence, from which we can qualitatively estimate the change in the reciprocal lattice vector parallel to the optical axis. These results show the capability of the 4D-PED method for the quantitative investigation of ultrafast crystal structural dynamics.

Mn2+ doped aluminum-rich spinel transparent ceramic phosphor with higher performance for wide color-gamut backlight display

Due to the great potential of narrow-band green-emitting phosphors for wide color-gamut white light-emitting diodes (WLED) backlight displays, there is great interest in finding host materials with the desired luminescent properties and high quantum efficiency. Herein, a series of Mg0.98-xAl2(1+x/3)O4: 0.02Mn2+ (x = 0, 0.125, 0.25) powders were synthesized using high-temperature solid-phase reactions, followed by a combination of pressureless sintering and hot isostatic pressure sintering to fabricate transparent ceramic phosphors. The crystal structure refinement, NMR spectroscopy, and photoluminescence results show tetrahedral coordination of Mn2+ ions and an increase in cation vacancies and disorder with increasing x. These transparent ceramics exhibit narrow-band green emission, which shifts from 523 to 520 nm with increasing x. The Mg0.855Al2.08O4: 0.02Mn2+ ceramic sample has an in-line transmittance of over 80 % above 500 nm and internal quantum efficiencies as high as 96.2 %. The luminous intensity of the Mg0.855Al2.08O4: 0.02Mn2+ ceramic remains above 88.6 % at 425 K compared to room temperature, with a thermal conductivity of 12.4 W·m−1·K−1. A WLED device fabricated using the Mg0.855Al2.08O4: 0.02Mn2+ ceramic, K2SiF6:Mn4+ phosphors, and a blue chip show a wide color gamut of 126 % National Television System Committee standard. The results show that Mn2+-doped aluminum-rich spinel transparent ceramics have great potential for application in wide color gamut WLED backlight devices.

Ca2.68Fe10.32Si1.00O20 - a strongly disordered SFCA-related phase in the system CaO-Fe2O3-SiO2

As part of a systematic investigation into the ternary system CaO-Fe2O3-SiO2, we discovered a phase with a general chemical composition of A14O20 (where A represents Ca, Fe, and Si) and previously unknown symmetry. Synthesis experiments were conducted at 1200 °C in air with an oxide ratio of CaO:Fe2O3:SiO2 = 3:5:1 in the starting mixture. In addition to β-Ca2SiO4, and hematite (Fe2O3), powder X-ray diffraction analysis indicated the presence of compounds related to the aluminum-free counterpart of a silico-ferrite of calcium and aluminum (SFCA), one of the major bonding phases in iron ore sinter. Single crystals of this so-called SFC phase, large enough for diffraction experiments, were found in the sintered pellet fragments under a digital microscope. The compound with composition Ca2.68Fe10.32Si1.00O20 crystallizes in space group I2/c and has the following basic crystallographic data: a = 10.4643(10) Å, b = 15.2740(11) Å, c = 5.3050(5) Å, β = 110.017(9)°, V = 796.69(13) Å3 and Z = 2. The final composition, as determined by crystal structure refinement, differs slightly from the weight-specified starting mixture of Ca3Fe10SiO20 and suggests the presence of both Fe(III) and small amounts of Fe(II) in the sample. The crystal structure is related to that of the triclinic polytype-1A of SFC, but exhibits a higher degree of disorder due to the partial occupation of additional octahedrally and tetrahedrally coordinated sites. This results in a smaller unit cell and an increased space-group symmetry. The described phase can be regarded as a basic or family structure, from which the two simplest polytypes (1A and hypothetical 2M) can be derived through ordering processes of cations among different possible vacancies. The chemical similarity to one of the phases of the SFCA-family suggests that such disordered compounds could also occur in industrial sinters.

Effect of phase composition on the crystal structure and microwave dielectric properties of ZnMg2TiO5 ceramics

Novel microwave dielectric ceramics ZnMg2TiO5 were synthesized by traditional solid-state method. Crystal structure refinement, transmission electron microscopy (TEM), and Raman spectroscopy reveal the coexistence of a secondary phase, MgO, with the predominant cubic spinel phase (Fd-3m) in ZnMg2TiO5 ceramics. The ceramics with dense microstructures exhibit excellent microwave dielectric properties at 1260 °C: εr = 15.6, Q×f = 92,899 GHz (at 10.8 GHz), and τf = −56.9 ppm/°C. The content of MgO, driven by thermodynamic factors, influences significantly impact the microstructure and microwave dielectric properties of the ceramics, particularly inducing the generation of localized lattice distortions and the formation of dislocations. The εr follows the same trend as the molecular polarizability of the actual individual crystal cells. Notably, a near-zero τf (−7.4 ppm/°C) was realized by two-phase composites and excellent comprehensive properties were obtained (εr = 17.9, Q×f = 57,546 GHz).

Analysis of magnetic structures in JANA2020.

JANA2020 is a program developed for the solution and refinement of regular, twinned, modulated, and composite crystal structures. In addition, JANA2020 also includes a magnetic option for solving magnetic structures from powder and single-crystal neutron diffraction data. This tool uses magnetic space and superspace symmetry to describe commensurate and incommensurate magnetic structures. The basics of the underlying formulation of magnetic structure factors and the use of magnetic symmetry for handling modulated and non-modulated magnetic structures are presented here, together with the general features of the magnetic tool. Examples of structures solved in the magnetic option of JANA2020 are given to illustrate the operation and capabilities of the program.

Nature of Scapolite Color: Ab Initio Calculations, Spectroscopy, and Structural Study

The article describes the results of a comprehensive study of the extra-framework components of scapolites using quantum–chemical calculations, electronic and vibrational spectroscopy, and single-crystal X-ray diffraction and crystal structure refinement. The ab initio calculations were performed using an embedded-cluster approach of extra-framework components in various cation surroundings. As a result, through comparing the experimental and ab initio calculation results, the energies of the electronic and vibrational transitions of various extra-framework components (CO3)2−, (CO3)·−, S3·−, S2·−—as well as the role of these components in the process of the lowering of the symmetry—were determined for scapolites belonging to the marialite–meionite solid–solution series. The nature of the various colors of the scapolites has also been established. Colors from purple to blue are a result of the presence of radiation-induced pairs of defects: carbonate radical anions (CO3)·− and F-centers. However, polysulfide S3·− radical anions are found in some violet scapolites.

The crystal structure of olanzapine form III.

The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.

Structural Features of Hydrated Representatives of the Labuntsovite Group: Refinement of Crystal Structures of Intermediate Members of the Tsepinite-Na–“Tsepinite-Ba”–Tsepinite-K Solid Solution

Structural Features of Hydrated Representatives of the Labuntsovite Group: Refinement of Crystal Structures of Intermediate Members of the Tsepinite-Na–“Tsepinite-Ba”–Tsepinite-K Solid Solution

Mn4+-activated NaSr10Y5W4O30 far-red emitting luminescent material for plant growth lighting

A series of Mn4+-doped NaSr10Y5W4O30 (NSYWO) phosphors have been successfully synthesized and further characterized to estimate their potentials for application as a far-red emitting component of pc-LED. An XRD analysis and crystal structure refinement have been carried out to characterize its quality. The doping concentration and temperature (80–500 K) dependent luminescence properties as well as decay kinetics have been studied and analyzed. It has been found that Mn4+ substitutes for W6+ sites resulting in far-red emission at 688 nm. The temperature quenching is attributed to thermal activation of an electron from Mn4+ 2Eg to 4A2g state via crossover, yielding an activation energy of 0.35 eV. Furthermore, to assess practical application of the novel phosphor, a blue-emitting LED chip combined with NSYWO: 0.8 mol% Mn4+has been packaged. The light from both the blue-emitting LED chip and NSYWO: Mn4+ phosphor was shown to be effectively utilized, revealing a good promise for application of the phosphor in the field of plant growth lighting.

Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure.

A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV-Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of -55.8 (57) MK-1 in the direction of C-H...O interactions.

Redetermination of germacrone type II based on single-crystal X-ray data.

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022 ▸). Powder Diffr. 37, 98-104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the inter-molecular inter-actions of germacrone type II.

Enhancement of superconductivity and phase diagram of Ta-doped Kagome superconductor CsV3Sb5

Kagome superconductors AV3Sb5 (A = K, Rb, and Cs) have attracted enormous interest due to the coexistence of charge density wave (CDW) order, unconventional superconductivity (SC) and anomalous Hall effect (AHE). In this paper, we reported an intensive investigation on Cs(V1−xTax)3Sb5 single crystals with systematic Ta doping. Ta was confirmed to be doped into V-site in the Kagome layer from both single crystal X-ray diffraction structural refinement and scanning transmission electron microscopy observation. The highest Ta doping level was found to be about 16%, which is more than twice as much as 7% in Nb-doped CsV3Sb5. With the increase of Ta doping, CDW order was gradually suppressed and finally vanished when the doping level reached to more than 8%. Meanwhile, superconductivity was enhanced with a maximum critical temperature (Tc) of 5.3 K, which is the highest Tc in the bulk crystal of this Kagome system at ambient pressure so far. The μ0Hc2(T) behavior demonstrates that the system is still a two-band superconductor after Ta doping. Based on the electrical transport measurement, a phase diagram was set up to exhibit the evolution of CDW and SC in the Cs(V1−xTax)3Sb5 system. These findings pave a new way to search for new superconductors with higher Tc in the AV3Sb5 family and establish a new platform for tuning and controlling the multiple orders and superconducting states.

Nanostructured Niobium and Titanium Carbonitrides as Electrocatalyst Supports.

Nanostructured niobium-titanium carbonitrides, (Nb,Ti)C1-xNx, with the cubic-rock salt structure are prepared without the use of reactive gases via thermal treatment (700-1200 °C) under nitrogen of mixtures of guanidine carbonate and ammonium niobate (V) oxalate hydrate, with addition of ammonium titanyl oxalate monohydrate as a titanium source. The bulk structure and chemical composition of the materials are characterized using powder X-ray diffraction (XRD) and powder neutron diffraction, elemental homogeneity is studied using energy dispersive spectroscopy (EDS) mapping using transmission electron microscopy (TEM), and surface chemical analysis is examined using X-ray photoelectron spectroscopy (XPS). Nanoscale crystallites of between 10 and 50 nm are observed by TEM, where EDS reveals the homogeneity of metal distribution for the mixed-metal materials. Titanium carbonitrides are found to be air sensitive, reacting with air under ambient conditions, while titanium-niobium carbonitrides are found to degrade in aqueous sulfuric acid. The niobium carbonitrides, however, show some stability toward acidic solutions. Materials are produced with composition NbC1-xNx with x between 0.35 and 0.45, and more carbon-rich materials (x ≈ 0.35) are found as the synthesis temperature is increased, as proven by Rietveld refinement of crystal structure against powder neutron diffraction data. Despite phase purity seen by diffraction and negligible bulk carbon content, XPS shows a complex surface chemistry for the NbC1-xNx materials, with evidence for Nb2O5-like oxide species in a carbon-rich environment. The NbC1-xNx prepared at 900 °C has a surface area around 50 m2 g-1, making it suitable as a catalyst support. Loading with iridium provides a material active for the oxygen evolution reaction in 0.1 M sulfuric acid, with minimal leaching of either Nb or Ir after 1000 cycles.

Evaluation of self-cleaning performance of TiO2-intermixed and TiO2-coated cement mortars under natural sunlight

Self-cleaning cementitious materials have gained significant attention due to urban environmental pollution. In this study, nano-TiO2 (NT) was first mixed with cement mortar. Second, NTs were coated on fresh cast mortars and on hardened surfaces. Photocatalytic efficiency was evaluated using Rhodamine B under natural sunlight with three types of cement: white Portland (WPC), ordinary Portland (OPC), and Portland pozzolana cement (PPC). Among them, PPC cement mortars exhibited superior photocatalytic performance compared to WPC and OPC even with lower dosages of NT. The order of photocatalytic efficiency was highest for the hard-coat followed by fresh-coat and then intermix sample. Furthermore, Rietveld analysis for crystal structure refinement was used, and crystallography analysis (VESTA software) confirmed the presence of specific atoms and bonds in the crystal structure of PPC with NT. Microstructural analysis using XRD, SEM, and EDAX revealed underlying structural changes and thus quantified the hydration products.

Crystal chemistry, Raman and FTIR spectroscopy, optical absorption, and luminescence study of Fe-dominant sogdianite

Abstract Fe-dominant sogdianite, a cyclosilicate compound with the chemical formula (Fe3+ 0.74Zr0.64Ti0.46 Al0.15)(□1.02Na0.98)K[Li3Si12O30], was studied. The investigation involved a comprehensive analysis of the mineral sample, including crystal-chemical analysis, Raman and FTIR spectroscopy, optical absorption, and luminescence study. Crystallographic site populations were determined through single crystal structure refinement and electron probe microanalysis. The thermoelastic behavior of a powder was studied using in situ high-temperature X-ray diffraction (30–750 °C). Notably, no phase transition was detected; sogdianite exhibited anisotropic thermal expansion. The first time study of vibrational spectra and spectral bands assigning were performed. The electronic transitions in d 5-ion impurities of sogdianite were studied using optical absorption and luminescence spectroscopy. The origin of pink color and luminescence of sogdianite was clarified. The broad spectral bands in the visible UV spectral region are responsible for the pink color exhibited by sogdianite and could be attributed to d–d transitions occurring in Fe3+ ions.

Crystal structures and crystallographic classification of titanium silicophosphates – with a note on structure and composition of silicophosphates “M 3P5SiO19”

Abstract The crystal structures of TiIII 4[Si2O(PO4)6] ( P 3 ‾ $P\overline{3}$ , Z = 3, a = 14.733(1), c = 7.363(1) Å, R1 = 0.040, wR2 = 0.098, 7649 ind. refl., 170 variables), FeII 0.79TiIII 2.42TiIV 0.79[Si2O(PO4)6] ( P 3 ‾ $P\overline{3}$ , Z = 3, a = 14.6534(2), c = 7.3829(1) Å, R1 = 0.036, wR2 = 0.088, 4026 ind. refl., 171 variables), and TiIII 2TiIV 6(PO4)6[Si2O(PO4)6] ( R 3 ‾ $R\overline{3}$ , Z = 1, a = 8.446(2), c = 44.21(2) Å, R1 = 0.047, wR2 = 0.120, 1373 ind. refl., 109 variables) have been refined from single-crystal data. The structures show hexagonal closest packing of phosphate groups with metal cations and [Si2O] groups occupying octahedral voids [□(PO4)6]. The close relationship of these and other silicophosphate structures to the NiAs and β-Fe2(SO4)3 (see also NaZr2(PO4)3 “NASICON”) structure types is rationalized by group/subgroup considerations. This symmetry approach shows that systematic twinning is highly likely in silicophosphates, thus possibly leading to faulty crystal structure refinements. Our investigation strongly suggests that the proper composition of silicophosphates “M III 3P5SiO19” (M = Cr, V, Fe, Mo) reported in literature is actually M III 4-[Si2O(PO4)6]. In the mixed-valent compounds oxidation states were assigned to the cation sites by comparison to Ti2O3, TiP2O7 and FeTiO3. The powder reflectance spectrum of dark-blue FeII 0.79TiIII 2.42TiIV 0.79[Si2O(PO4)6] shows a strong IVCT transition at ν ˜ $\widetilde{\nu }$ = 17,500 cm−1, and magnetic susceptibility data agree very well with the proposed oxidation states.