Simulated X-ray Powder Diffraction Research Articles

Crystallographic phase identifier of a convolutional self-attention neural network (CPICANN) on powder diffraction patterns.

Spectroscopic data, particularly diffraction data, are essential for materials characterization due to their comprehensive crystallographic information. The current crystallographic phase identification, however, is very time consuming. To address this challenge, we have developed a real-time crystallographic phase identifier based on a convolutional self-attention neural network (CPICANN). Trained on 692 190 simulated powder X-ray diffraction (XRD) patterns from 23 073 distinct inorganic crystallographic information files, CPICANN demonstrates superior phase-identification power. Single-phase identification on simulated XRD patterns yields 98.5 and 87.5% accuracies with and without elemental information, respectively, outperforming JADE software (68.2 and 38.7%, respectively). Bi-phase identification on simulated XRD patterns achieves 84.2 and 51.5% accuracies, respectively. In experimental settings, CPICANN achieves an 80% identification accuracy, surpassing JADE software (61%). Integration of CPICANN into XRD refinement software will significantly advance the cutting-edge technology in XRD materials characterization.

High Proton Conductivity of the UiO-66-NH2-SPES Composite Membrane Prepared by Covalent Cross-Linking.

A sulfonated poly(ethersulfone) (SPES)-metal-organic framework (MOF) film with excellent proton conductivity was synthesized by anchoring UiO-66-NH2 to the main chain of the aromatic polymer through the Hinsberg reaction. The chemical bond was formed between the amino group in MOFs and the -SO2Cl group in chlorosulfonated poly(ethersulfones) to conduct protons in the proton channel of the membrane, making the membrane have excellent proton conductivity. UiO-66-NH2 is successfully prepared as a result of the consistency of the experimental and simulated powder X-ray diffraction (PXRD) patterns of MOFs. The existence of absorption peaks of characteristic functional groups in Fourier transform infrared (FTIR) spectra proved the successful preparation of SPES, PES-SO2Cl, and a composite film. The results of the AC impedance test indicate that the composite film with a 3% mass fraction has the best proton conductivity of 0.215 S·cm-1, which is 6.2 times higher than that of the blended film without a chemical bond at 98% RH and 353 K. To our knowledge, there are rarely any reports on the preparation of a composite membrane by directly linking MOFs and the membrane matrix with chemical bonds. This work provides a good way to synthesize the highly conductive proton exchange film.

Pseudotetrahedral C2-symmetrical Co/Zn(II)-achiral Schiff base complexes with Δ/Λ-chirality induction at-metal as a racemic mixture

Reaction of achiral Schiff base ligands 1-((X-phenylimino)methyl)naphthalen-2-ol {X = 2-ethyl (HL1) or 4-methyl (HL2)} with cobalt(II) or zinc(II) acetate provided the corresponding bis[1-((X-phenylimino)methyl)naphthalen-2-olato-k2N,O]cobalt(II) or zinc(II) {X = 2-ethyl: M = Co (1) and Zn (2) or X = 4-methyl: M = Co (3) and Zn (4)} complexes. The molecules crystallize in the centrosymmetric space groups R–3 (1) and P–1 (3 or 4). Molecular structures determinations showed coordination of two molecules of the N,O-chelate ligands to the metal ion and formation of pseudotetrahedral complexes with C2-symmetry. Furthermore, coordination of two unsymmetrical achiral N,O-chelates induces Λ/Δ-chirality at the metal atom as a racemic mixture in the centrosymmetric space groups. Structural analyses further reveal that incorporation of 2-ethyl (1) or 4-methyl (3 or 4) group on the N-bound phenyl ring leads to an increase of both the O1-M-O2 and N1-M-N2 bond angles on going from 1 to 3 or 4, with the N1-M-N2 angle increasing to a much greater extent. The fair matching of the experimental and simulated powder X-ray diffraction patterns confirms the phase purity of bulk microcrystalline sample. Differential scanning calorimetry (DSC) results suggest an irreversible phase transformation from solid crystals to isotropic-liquids and subsequent thermal stability of the complexes. Cyclic voltammograms indicate a quasi-reversible two one electron charge transfer processes for 1 or 3 in N,N-dimethylformamide (DMF). Optimized geometry and excited state properties by density functional theory (DFT) and time dependent-density functional theory (TD-DFT) calculations correspond well to the experimental results.

CrystalMELA: a new crystallographic machine learning platform for crystal system determination.

Determination of the crystal system and space group is the first step of crystal structure analysis. Often this turns out to be a bottleneck in the material characterization workflow for polycrystalline compounds, thus requiring manual interventions. This work proposes a new machine-learning (ML)-based web platform, CrystalMELA (Crystallography MachinE LeArning), for crystal systems classification. Two different ML models, random forest and convolutional neural network, are available through the platform, as well as the extremely randomized trees algorithm, available from the literature. The ML models learned from simulated powder X-ray diffraction patterns of more than 280 000 published crystal structures from organic, inorganic and metal-organic compounds and minerals which were collected from the POW_COD database. A crystal system classification accuracy of 70%, which improved to more than 90% when considering the Top-2 classification accuracy, was obtained in tenfold cross-validation. The validity of the trained models has also been tested against independent experimental data of published compounds. The classification options in the CrystalMELA platform are powerful, easy to use and supported by a user-friendly graphic interface. They can be extended over time with contributions from the community. The tool is freely available at https://www.ba.ic.cnr.it/softwareic/crystalmela/ following registration.

Band-gap assessment from X-ray powder diffraction using artificial intelligence

X-ray diffraction is a phenomenon that stems from the interaction of the electron density of a crystalline material and the electric field of the X-ray waves. The product of this interaction, the diffraction pattern, provides a picture of the reciprocal space of the atomic distribution in terms of intensities of certain scattering wavevectors. In this manner, a correlation between those intensities seen in a diffraction pattern and the electronic properties of a material is suggested. This correlation, if it exists, may not be directly proposed using analytical expressions. This article shows for the first time the feasibility of assessing the band gap of metal–organic frameworks (MOFs) and organic and inorganic materials from their X-ray powder diffraction pattern. The band gaps were assessed with convolutional neural networks (CNNs). These CNNs were developed using simulated X-ray powder diffraction patterns and the band gaps calculated with density functional theory. The diffraction patterns were simulated with different crystal sizes, from 10 nm to the macrocrystalline size. In addition, the reported band gaps of MOFs and organic compounds in the Quantum MOF Database and the Organic Materials Database data sets were used, which were calculated with the PBE functional. Furthermore, the band gaps calculated by Kim et al. [Sci. Data (2020), 7, 387] for inorganic compounds with the HSE functional were used. The developed CNNs were tested with simulated diffraction patterns of compounds different from those used to train the CNNs, as well as with experimentally recorded diffraction patterns. The developed CNNs allowed the assessment of the band gap of the compounds with a root-mean-square error as low as 0.492 eV after training with over 64 000 diffraction patterns.

Theoretical Study on the Vapochromic Ni(II)-Quinonoid Complex: One-Dimensional Stacking Structure-Based Color Switching.

Vapochromic crystals of Ni(II)-quinonoid complexes were theoretically investigated using density functional theory (DFT) calculations. Kato et al. previously reported that the purple crystals of a four-coordinate Ni(II)-quinonoid complex (1P) exhibited vapochromic characteristics upon exposure to methanol gas, resulting in orange crystals of the six-coordinate methanol-bound complex (1O) [Angew. Chem., Int. Ed.2017, 56, 2345-2349]. However, the authors did not characterize the crystal structure of 1P. In the present study, we computationally predicted the crystal structure of 1P by performing a crystal structure search with classical force-field computations followed by optimization using DFT calculations. The simulated powder X-ray diffraction pattern of the DFT-optimized structure agreed with experimental observations, indicating that our predicted crystal structure is reliable. Investigation of the optimized crystal structure of 1P revealed that its color change arose from changes in its 1D-band structure, which consists of Ni 3d orbitals and quinonoid π-orbitals. Intermolecular interactions were weakened upon the binding of methanol to the Ni(II) center in 1O. Consequently, the intermolecular 3d-π interaction in 1P lowered the band gap and induced the red-shifting of the monomeric four-coordinate Ni(II)-quinonoid complex. Meanwhile, the obtained absorption spectrum of 1O closely corresponded to that of the monomeric six-coordinate Ni(II)-quinonoid complex. Our study provides a new strategy for accurately predicting molecular crystal structures and reveals a new insight into vapochromism based on band structure color switching.

Superior Iodine Uptake Capacity Enabled by an Open Metal-Sulfide Framework Composed of Three Types of Active Sites

Superior Iodine Uptake Capacity Enabled by an Open Metal-Sulfide Framework Composed of Three Types of Active Sites

Anchoring HFO nanoparticles on MWCNTs as high electron transfer composite adsorbent for the removal of H2S at low temperature

As a significant component in desulfurizers, iron-based desulfurizer has already been widely investigated in the past decades because of their convenience, low cost and high sulfur capacity. In this work, the highly active hydrated ferric oxide (HFO) nanoparticles anchored on multi-walled carbon nanotubes (MWCNTs) were synthesized via the co-precipitation method. The result of the H2S breakthrough capacity test indicated that the low-temperature desulfurization performance of HFO was significantly promoted by adding of MWCNTs. The best desulfurization performance (144.2 mg g−1) was obtained using the sample with 20 wt% MWCNTs. The structure of formation of HFO is equivalent to the predicted structure by generating simulated powder X-ray diffraction patterns using the Reflex module of Material Studio 2019. The calculation results from VASP show the highly dispersed HFO nanoparticles were anchored on MWCNTs surface, which means the Fe-O-C bond was formed. The improved desulfurization performance was attributed to the dispersion of HFO nanoparticles and more exposed adsorption sites due to the strong interaction between MWCNTs and HFO.

Influence of temperature and point defects on the X-ray diffraction pattern of graphite

The atomic structure of pure and defective graphite has been modelled using classical many body potentials from which simulated powder X-ray Diffraction (XRD) patterns were produced using the Debyer software. The changes in the XRD patterns due to both heating and the inclusion of defects were investigated. After heating, the results show a shift in the 004 Laue peak in qualitative agreement with experiment. The c parameter is shown to increase over the temperature range 0 – 1000 K but there is a slight reduction in the a parameter over this range. The scattering angle for the 004 peak reduces with the introduction of defects up to ≈5% defect concentration for both vacancies and interstitials with a larger reduction in the case of interstitials. The intensity of the scattering peak is reduced with increasing interstitials (25% reduction at 5% concentration), but remains relatively constant with increasing vacancies. The introduction of a small percentage of interstitials causes an increase in both the a and c parameters but vacancies cause a reduction in the a parameter.

α−β phase transition of zirconium predicted by on-the-fly machine-learned force field

The accurate prediction of solid-solid structural phase transitions at finite temperature is a challenging task, since the dynamics is so slow that direct simulations of the phase transitions by first-principles (FP) methods are typically not possible. Here, we study the $\ensuremath{\alpha}\text{\ensuremath{-}}\ensuremath{\beta}$ phase transition of Zr at ambient pressure by means of on-the-fly machine-learned force fields. These are automatically generated during FP molecular dynamics (MD) simulations without the need of human intervention, while retaining almost FP accuracy. Our MD simulations successfully reproduce the first-order displacive nature of the phase transition, which is manifested by an abrupt jump of the volume and a cooperative displacement of atoms at the phase transition temperature. The phase transition is further identified by the simulated x-ray powder diffraction, and the predicted phase transition temperature is in reasonable agreement with experiment. Furthermore, we show that using a singular value decomposition and pseudo inversion of the design matrix generally improves the machine-learned force field compared to the usual inversion of the squared matrix in the regularized Bayesian regression.

Electronic structure of cobalt/iron carbide from ab-initio calculations

This work presents theoretical study of structural and electronic properties of bulk cobalt and iron carbide by the first-principles calculations. Structural optimization has been performed and the ground state properties such as the equilibrium lattice constants, cohesive energy (Ecoh) and bulk modulus (B0) of Co2C/η-Fe2C have been calculated. Band structure, density of states (DOS) and 3D isosurface of valence charge density difference for Co2C and η-Fe2C has been reported. The experimental and simulated powder x-ray diffraction data were compared and the Miller indices which define the crystallographic planes in the crystal lattices were identified. Mechanical stability of these compounds was discussed in terms of their equilibrium Ecoh and B0 values. Our computed values were also compared with the available experimental and theoretical data.

Database Mining of Zeolite Structures

Zeolites are widely used in industrial applications such as ion exchange, gas separation and adsorption, and organic catalysis. In particular, in petroleum refining and petrochemical productions, zeolites are catalysts of utmost importance. In order to classify the known zeolites and correlate the structures with their unique properties, an online Database of Zeolite Structures was established in 1996 and continuously developed by Baerlocher and McCusker at ETH-Zurich. The database contains a lot of useful structural information such as unit cell dimensions, space group, atomic coordinates of tetrahedra (T) atoms, secondary building units (SBUs), composite building units (CBUs), natural tilings, simulated powder X-ray diffraction (PXRD), etc. It has served the zeolite community for more than 20 years and has made great contributions to the development of zeolites and zeolite-related fields. In this article, we take a further step to mine the intrinsic structural information on zeolites including character...

Structural characterization, spectroscopic signatures, nonlinear optical response, and antioxidant property of 4-benzyloxybenzaldehyde and its binding activity with microtubule-associated tau protein

In the proposed work, the non-linear optical response, spectroscopic signature and binding activity of 4-Benzyloxybenzaldehyde (4BB) has been investigated. In order to find the vibrational contribution of functional groups in mixed or coupled modes in the experimental FT-IR and FT-Raman spectra, the potential energy distribution (PED) based on the internal coordinates have been computed. Since the molecule exists in the form of dimer in solid state, the electronic structure of dimer has been proposed in order to explain the intermolecular hydrogen bonding interactions via aldehyde group. The experimental and simulated powder X-ray diffraction data was compared and the miller indices which define the crystallographic planes in the crystal lattices were identified. Optical transmittance and absorbance measurement were taken at ambient temperature in order to investigate the transparency and optical band gap. For screening the material for nonlinear applications, theoretical second order hyperpolarizability studies were performed and compared with the standard reference urea. To validate the theoretical results, powder second harmonic generation (SHG) studies were carried out using Kurtz and Perry technique. The results show that the molecule studied in this work exhibit considerable non-linear optical (NLO) response. In addition to the characterization and NLO studies, we also claimed based on the experimental and theoretical data that the molecule shows antioxidant property and inhibition capability. Since the title molecule shows significant binding with Tau protein that helps to stabilize microtubules in the nervous system, the molecular docking investigation was performed to find the inhibition constant, binding affinity and active binding residues.

Study on four polymorphs of bifendate based on X-ray crystallography

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C–C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

Ab initio investigations of dioctahedral interlayer-deficient mica: modelling 1 M polymorphs of illite found within gas shale

In this investigation we create a variety of dioctahedral, interlayer (cation)-deficient mica clay mineral models of the 1 M -illite series, using the ab initio method of density functional theory (DFT), employing plane waves, pseudo potentials, and super cells. The structures we create are modelled on an average formula of illite such as (Ca 0.059 , K 0.655 )(Si 3.597 , Al 0.403 )(Fe 0.628 , Al 0.969 ,Mg 0.428 )O 10 (OH) 2 , as well as existing crystal structures and experimental data. This study investigates the relative positions of both octahedral and tetrahedral cation substitutions ( e.g . Fe 3+ for Al 3+ and Al 3+ for Si 4+ ) in both trans- and cis-vacant structures. The purpose of this work is to create robust, representative models of single layers (I) and double layers (I-I) of illite found within gas shale, that can be used in future investigations. We examine lattice parameters, interatomic distances of tetrahedral and octahedral sheets, K–O distances, and K positions, and find reasonable agreement with experimental data, and excellent agreement with simulated data of similar structures. Finally, to enable experimental characterization of samples of illite with different compositions, we provide simulated X-ray powder diffraction (XRPD) patterns including up to the first ten ( h k l ) reflections, and find characteristic identifiers of trans- and cis-vacant micas in agreement with previous theoretical and experimental studies. We conclude that the models we create are feasible models of I and I-I layers of illite found within shale and are ready for use in future work.

Study of titanate nanotubes by X-ray and electron diffraction and electron microscopy

The structure of titanate nanotubes (Ti-NTs) was studied by a combination of powder X-ray diffraction (PXRD), electron diffraction and high resolution transmission electron microscopy (HRTEM). Ti-NTs are prepared by hydrothermal treatment of TiO2 powder. The structure is identified by powder X-ray diffraction as the one based on the structure of H2Ti2O5·H2O phase. The same structure is obtained by projected potential from HRTEM through-focus image series. The structure is verified by simulated PXRD pattern with the aid of the Debye formula. The validity of the model is tested by computing Fourier transformation of a single nanotube which is proportional to measured electron diffraction intensities. A good agreement of this calculation with measured precession electron diffraction data is achieved.

Tobelite and NH4+-rich muscovite single crystals from Ordovician Armorican sandstones (Brittany, France): Structure and crystal chemistry

The crystal structures of tobelite and NH 4 + -rich muscovite from the sedimentary rocks of the Armorican sandstones (Brittany, France) have been solved for the first time by single-crystal X-ray diffraction. The structural study was integrated by electron probe microanalyses, and X-ray photoelectron and micro-Fourier transform infrared spectroscopy. The crystals belong to the 2 M 2 polytype with the following unit-cell parameters: a = 9.024(1), b = 5.2055(6), c = 20.825(3) A, and β = 99.995(8)° for tobelite and a = 9.027(1), b = 5.1999(5), c = 20.616(3) A, and β = 100.113(8)° for NH 4 + -rich muscovite. Structure refinements in the space group C 2/ c converged at R 1 = 8.01%, wR 2 = 8.84% and R 1 = 5.59%, wR 2 = 5.63% for tobelite and NH 4 + -rich muscovite, respectively. X-ray photoelectron spectroscopy revealed nitrogen environments associated either with inorganic (B.E. 401.31 eV) or organic (B.E. 398.67 eV) compounds. Infrared spectra showed, in the OH − -stretching region (3700–3575 cm −1 ), two prominent bands, centered at ~3629 and ~3646 cm −1 , and two shoulders at ~3664 and ~3615 cm −1 that were assigned to Al 3+ Al 3+ □-OH − arrangements having OH − groups affected by different local configurations. In addition, a series of overlapping bands from about 3500 to 2700 cm −1 characteristic of the NH 4 + -stretching vibrations, a main band at ~1430 and a shoulder at ~1460 cm −1 that were associated to the NH 4 + -bending vibration (ν 4 ) were also present. The ammonium concentration was semi-quantitatively estimated in both crystals from the absorbance of the OH − -stretching and NH 4 + -bending vibrations in the infrared spectra. An additional estimate was obtained for the NH 4 + -rich muscovite by considering the normalized peak area between K2 p 3 / 2 and N1 s in the X-ray photoelectron spectrum. The obtained values are in agreement with those derived from the interlayer spacing in the simulated X-ray powder diffraction spectra. The results of this integrated approach converged to (K 0.18 Na 0.01 NH 4 + 0.62 ) ∑=0.81 (Al 1.98 Fe 2+ 0.02 ) ∑=2.00 (Si 3.19 Al 0.81 ) ∑=4.00 O 10.00 OH 2.00 for tobelite and to (K 0.46 Na 0.03 Ba 0.01 NH 4 + 0.36 ) ∑=0.86 (Al 1.98 Mg 0.01 Fe 2+ 0.01 V 3+ 0.01 ) ∑=2.01 (Si 3.13 Al 0.87 ) ∑=4.00 O 10.00 F 0.08 OH 1.92 for NH 4 + -rich muscovite.

Stacking structure in disordered talc: Interpretation of its X-ray diffraction pattern by using pattern simulation and high-resolution transmission electron microscopy

Stacking structure in disordered talc, Mg3Si4O10(OH)2, has been investigated by using highresolution transmission electron microscopy (HRTEM) and by comparison between experimental and simulated powder X-ray diffraction (XRD) patterns. The talc specimen investigated was massive aggregates of Þ ne platy crystals from the Shirakashi mine, Nagasaki-Prefecture, Japan, formed from regional metamorphism. HRTEM observations revealed that the orientation of the 2:1 layer, which is described by the direction of the lateral shift of a/3 from the lower tetrahedral sheet to the upper tetrahedral sheet within the 2:1 layer (intralayer shift), is almost completely disordered. In contrast, lateral displacement between the adjacent tetrahedral sheets across the interlayer region (interlayer displacement) is relatively ordered. The interlayer displacement parallel to the intralayer shift in lower or upper 2:1 layers tends to be avoided. A GandolÞ camera was used to record XRD patterns from a small fragment of the aggregates, to avoid preferred orientation and artifacts in stacking sequence by grinding. XRD patterns were simulated using the DIFFaX program and compared with experimental patterns. The experimental pattern from hk = 02, 11, and 1 –lattice rows is explained by a mixture of the stacking sequence with almost random directions of intralayer shift and a small amount of 1A dominant stacking sequence. The peak proÞ les for the res ections indexed with 20l, 13l, or 1 –l are reproduced by considering their

Large Cage Face-Centered-Cubic Fm3m Mesoporous Silica: Synthesis and Structure

The synthesis and precise structural characterization of highly ordered three-dimensional close-packed cage-type mesoporous silica is reported. The siliceous mesoporous material is proven to be commensurate with the face-centered-cubic Fm3m symmetry in high purity by a combination of experimental and simulated powder X-ray diffraction (XRD) and transmission electron microscopy (TEM) analyses. The cage-type calcined samples were additionally characterized by nitrogen physisorption. The aqueous synthesis method to prepare large cage mesoporous silica with cubic Fm3m structure is based on the use of EO106PO70EO106 triblock copolymer (F127) at low HCl concentrations, with no additional salts or organic additives. Here, emphasis is put on the low HCl concentration regime, allowing the facile thermodynamic control of the silica−triblock copolymer mesophase self-assembly. Further, simple application of hydrothermal treatments at various temperatures ranging from 45 to 150 °C enables the tailoring of the mesopore diameters and apertures. The combination of experimental and simulated XRD patterns and TEM images is confirmed to be a very powerful means for the accurate elucidation of the structure of new mesoporous materials.

Comment on ‘Order–disorder phase transition induced by swift ions in MgAl 2O 4 and ZnAl 2O 4 spinels’ by D. Simeone et al., J. Nucl. Mater. 300 (2002) 151–160

In this letter, structure factor calculations and computer simulated powder X-ray diffraction patterns are used to challenge conclusions reached in a recent study by D. Simeone et al. regarding radiation-induced phase transformations in MgAl 2O 4 spinel. Based on experimental results presented by D. Simeone et al. and previously by other researchers, and based on the structure factor results presented here, spinel most likely succumbs to a phase transformation under irradiation that involves a profound change in the arrangement of cations in the lattice. The space group is modified by the transformation and the new, metastable structure is most likely a defective rocksalt structure. These conclusions are at odds with the description of the spinel metastable phase offered by Simeone et al.