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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Random forest prediction of crystal structure from electron diffraction patterns incorporating multiple scattering

Diffraction is the most common method to solve for unknown or partially known crystal structures. However, it remains a challenge to determine the crystal structure of a new material that may have nanoscale size or heterogeneities. Here, in this study, we train an architecture of hierarchical random forest models capable of predicting the crystal system, space group, and lattice parameters from one or more unknown two-dimensional electron diffraction patterns. Our initial model correctly identifies the crystal system of a simulated electron diffraction pattern from a 20-nm-thick specimen of arbitrary orientation 67% of the time. We achieve a topline accuracy of 79% when aggregating predictions from ten patterns of the same material but different zone axes. The space group and lattice predictions range from 70% to 90% accuracy and median errors of 0.01-0.5Å, respectively, for cubic, hexagonal, trigonal, and tetragonal crystal systems while being less reliable on orthorhombic and monoclinic systems. We apply this architecture to a four-dimensional scanning transmission electron microscopy scan of gold nanoparticles, where it accurately predicts the crystal structure and lattice constants. These random forest models can be used to significantly accelerate the analysis of electron diffraction patterns, particularly in the case of unknown crystal structures. Additionally, due to the speed of inference, these models could be integrated into live transmission electron microscopy experiments, allowing real-Time labeling of a specimen.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Random Forest Prediction of Crystal Structure from Electron Diffraction Patterns

Transmission electron microscopy (TEM) diffraction patterns are regularly used to determine the structure of crystalline materials. Electron diffraction is the most common method to solve for unknown or partially known crystal structures, as it provides direct and interpretable feedback on the orientation of crystal grains under the beam [1]. However, it remains a challenge to determine the crystal structure of a new material or even a new phase of an existing material. Analysis of such materials commonly requires manual exploration and comparison with simulated diffraction patterns. This is often a time consuming process with no obvious start point when many similar structures are possible, and this method cannot be used to determine crystal structure or orientation from structures not included in the diffraction libraries. Therefore, we have developed a machine learning model to determine the crystal structure of a material from its electron diffraction pattern.

36 MATERIALS SCIENCE↗
DOE OSTI2024

An idealized model for the crystal structure of intermetallic compounds isostructural with Mg 3 Cr 2 Al 18

Mg 3 Cr 2 Al 18 (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, $Fd\overline{3}m$. 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 $A^{8a}_{1}B^{16c}_{2}C^{16d}_{2}D^{48f}_{6}E^{96g}_{12}$, 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.

36 MATERIALS SCIENCE↗
DOE OSTI2023

IrGe 4 : A Predicted Weyl-Metal with a Chiral Crystal Structure

Polycrystalline IrGe4 was synthesized by annealing elements at 800 °C for 240 h, and the composition was confirmed by energy-dispersive X-ray spectroscopy. IrGe 4 adopts a chiral crystal structure (space group P3 1 21) instead of a polar crystal structure (P3 1 ), which was corroborated by the convergent-beam electron diffraction and Rietveld refinements using synchrotron powder X-ray diffraction data. The crystal structure features layers of IrGe 8 polyhedra along the b axis, and the layers are connected by edge- and corner-sharing. Each layer consists of corner-shared [Ir 3 Ge 20 ] trimers, which are formed by three IrGe 8 polyhedra connected by edge-sharing. Temperature-dependent resistivity indicates metallic behavior. The magnetoresistance increases with increasing applied magnetic field, and the nonsaturating magnetoresistance reaches 11.5% at 9 T and 10 K. The Hall resistivity suggests that holes are the majority carrier type, with a carrier concentration of 4.02 × 10 21 cm –3 at 300 K. In conclusion, electronic band structures calculated by density functional theory reveal a Weyl point with a chiral charge of +3 above the Fermi level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

The seventh blind test of crystal structure prediction: structure ranking methods

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

Chemistry↗
DOE OSTI2024

Crystal structure of anthraquinone-2-carboxylic acid, C 15 H 8 O 4

The crystal structure of anthraquinone-2-carboxylic acid has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Anthraquinone-2-carboxylic acid crystallizes in space groupP-1 (#2) witha= 3.7942(2),b= 13.266(5),c= 22.835(15) Å,α= 73.355(30),β= 89.486(6),γ= 86.061(1)°,V= 1098.50(7) Å 3 , andZ= 4. The crystal structure contains two independent molecules of anthraquinone-2-carboxylic acid. Although the expected hydrogen-bonded dimers are present, the dimers are not centrosymmetric. The dimer contains one molecule of each planar low-energy conformation. The crystal structure consists of a herringbone array of centrosymmetric pairs of molecules parallel to thebc-plane. The molecules stack along the shorta-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Materials Science↗
DOE OSTI2022

Crystal structure and magnetic properties in semiconducting Eu 3-δ Zn x Sn y As 3 with Eu-Eu dimers

Magnetic structure and crystal symmetry, which primarily determine the time-reversal and inversion symmetry, may give rise to numerous exotic quantum phenomena in magnetic semiconductors and semimetals when arranged in different patterns. Here, a new layered magnetic semiconductor, Eu 3-δ Zn x Sn y As 3 , was discovered and high-quality single crystals were grown using the Sn flux. According to structural characterization by x-ray diffraction and atomic-resolution scanning transmission electron microscopy, Eu 3-δ Zn x Sn y As 3 is found to crystallize in a hexagonal symmetry with the space group P6 3 /mmc (No. 194). After examining different specimens, we conclude that their stoichiometry is fixed at ~Eu 2.6 Zn 0.65 Sn 0.85 As 3 , which meets the chemical charge balance. Eu 3-δ Zn x Sn y As 3 is composed of septuple (Eu 1-δ Sn y As 2 )-Eu-(Zn x As)-Eu sequences. The shortest Eu–Eu distance in the system is between two Eu layers separated by Zn x As along the c-axis. Magnetization measurement shows an antiferromagnetic ordering in Eu 3-δ Zn x Sn y As 3 at T N ~ 12 K, where the magnetic easy-axis is along the c-axis, and Mössbauer spectroscopy observes magnetic hyperfine splitting on Eu and Sn at 6 K. Magnetic anisotropy is significantly different from the ones along the ab-plane in other layered Eu-based magnetic semimetals. Heat capacity measurements confirm the magnetic transition around 12 K. Electrical resistivity measurement indicates semiconductor behavior with a band gap of ~0.86 eV. Finally, various Eu-based magnetic semiconductors could provide a tunable platform to study potential topological and magnetic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structure of meglumine diatrizoate, (C 7 H 18 NO 5 )(C 11 H 8 I 3 N 2 O 4 )

The crystal structure of meglumine diatrizoate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Meglumine diatrizoate crystallizes in space group P2 1 (#4) with a = 10.74697(4), b = 6.49364(2), c = 18.52774(7) Å, β = 90.2263(3), V = 1292.985(5) Å 3 , and Z = 2. Two different crystal structures, which yielded essentially identical refinement residuals and positions of the non-H atoms, were obtained. The differences were in the H atom positions and the hydrogen bonding. One structure was 123.0 kJ/mol/cell lower in energy than the other and was adopted for the final description. The crystal structure consists of alternating double layers of cations and anions along the c-axis. The hydrogen bonds link the cations and anions into a three-dimensional framework. Each of the hydrogen atoms on the ammonium nitrogen of the cation acts as a donor in a strong N–H∙∙∙O hydrogen bond. One of these is to a hydroxyl group of another cation, and the other is to the carboxylate group of the anion. Each of the amide nitrogen atoms of the anion forms a strong N–H∙∙∙O intermolecular hydrogen bond, one to a carbonyl and the other to a carboxylate group. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2021

Crystal structure of the $τ_{11}$ Al 4 Fe 1.7 Si phase from neutron diffraction and ab initio calculations

The intermetallic τ 11 Al 4 Fe 1.7 Si phase is of interest for high-temperature structural application due to its combination of low density and high strength. We determine the crystal structure of the τ 11 phase through a combination of powder neutron diffraction and density functional theory calculations. Using Pawley and Rietveld refinements of the neutron diffraction data provides an initial crystal structure model. Since Al and Si have nearly identical neutron scattering lengths, we use density-functional calculations to determine their preferred site occupations. The τ 11 phase exhibits a hexagonal crystal structure with space group P6 3 /mmc and lattice parameters of a = 7.478 Å and c = 7.472 Å. The structure comprises five Wyckoff positions; Al occupies the 6h and 12k sites, Fe the 2a and 6h sites, and Si the 2a sites. Here we observe site disorder and partial occupancies on all sites with a large fraction of 80% Fe vacancies on the 2d sites, indicating an entropic stabilization of the τ 11 phase at high temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structure of encorafenib, C 22 H 27 ClFN 7 O 4 S

The crystal structure of encorafenib, C 22 H 27 ClFN 7 O 4 S, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Encorafenib crystallizes in space group P2 1 (#4) with a = 16.17355(25), b = 9.52334(11), c = 17.12368(19) Å, β = 89.9928(22)°, V = 2637.50(4) Å 3 , and Z = 4. The crystal structure consists of alternating layers of stacked halogenated phenyl rings and the other parts of the molecules perpendicular to the a-axis. One molecule participates in two strong N–H∙∙∙N hydrogen bonds (one intra- and the other intermolecular), which are not present for the other molecule. The intermolecular hydrogen bonds link molecule 2 into a spiral chain along the b-axis. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structure of nequinate, C 22 H 23 NO 4

The crystal structure of nequinate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Nequinate crystallizes in the space group P2 1 /c (#14) with a = 18.35662(20), b = 11.68784(6), c = 9.06122(4) Å, β = 99.3314(5)°, V = 1918.352(13) Å 3 , and Z = 4. The crystal structure is dominated by the stacking of the approximately planar molecules. N–H∙∙∙O hydrogen bonds link adjacent molecules into chains parallel to the b-axis. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal structure of butenafine hydrochloride, C 23 H 28 NCl

The crystal structure of butenafine hydrochloride has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Butenafine hydrochloride crystallizes in space group P2 1 (#4) with a = 13.94807(5), b = 9.10722(2), c = 16.46676(6) Å, β = 93.9663(5)°, V = 2086.733(8) Å 3 , and Z = 4. Butenafine hydrochloride occurs as a racemic co-crystal of R and S enantiomers of the cation. The crystal structure is characterized by parallel stacks of aromatic rings along the b-axis. Each cation forms a strong discrete N–H∙∙∙Cl hydrogen bond. The chloride anions also act as acceptors in several C–H∙∙∙Cl hydrogen bonds from methylene, methyl, and aromatic groups. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Crystal structure of vismodegib, C 19 H 14 Cl 2 N 2 O 3 S

The crystal structure of vismodegib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Vismodegib crystallizes in space group P2 1 /a (#14) with a = 16.92070(20), b = 10.20235(4), c = 12.16161(10) Å, β = 108.6802(3)°, V = 1988.873(9) Å 3 , and Z = 4. The crystal structure consists of corrugated layers of molecules parallel to the bc-plane. There is only one classical hydrogen bond in the structure, between the amide nitrogen atom and the N atom of the pyridine ring. Pairs of these hydrogen bonds link the molecules into dimers, with a graph set R2,2(14) > a > a. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

36 MATERIALS SCIENCE↗
DOE OSTI2023

CCDC 2233284: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

6-phenyl-6-azabicyclo[3.2.1]octan-3-one↗