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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Denoising Autoencoder for Improved Kikuchi Pattern Quality and Indexing in Electron Backscatter Diffraction

The rapid collection and indexing of electron diffraction patterns as produced via electron backscatter diffraction (EBSD) has enabled crystallographic orientation and structural determination, as well as additional property-determining strain and dislocation density information with increasing speed, resolution, and efficiency. Pattern indexing quality is reliant on the noise of the collected electron diffraction patterns, which is often convoluted by sample preparation and data collection parameters. EBSD acquisition is sensitive to many factors and thus can result in low confidence index (CI), poor image quality (IQ), and improper minimization of fit, which can result in noisy datasets and misrepresent the microstructure. In an attempt to enable both higher speed EBSD data collection and enable greater orientation fit accuracy with noisy datasets, an image denoising autoencoder was implemented to improve pattern quality. Here, we show that EBSD data processed through the autoencoder results in a higher CI, IQ, and a more accurate degree of fit. In addition, using denoised datasets in HR-EBSD cross correlative strain analysis can result in reduced phantom strain from erroneous calculations due to the increased indexing accuracy and improved correspondence between collected and simulated patterns.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Advancing Heteroanionicity in Zintl Phases: Crystal Structures, Thermoelectric and Magnetic Properties of Two Quaternary Semiconducting Arsenide Oxides, Eu 8 Zn 2 As 6 O and Eu 14 Zn 5 As 12 O

Two novel quaternary oxyarsenides, Eu 8 Zn 2 As 6 O and Eu 14 Zn 5 As 12 O, were synthesized through metal flux reactions, and their crystal structures were established by single-crystal X-ray diffraction methods. Eu 8 Zn 2 As 6 O crystallizes in the orthorhombic space group Pbca, featuring polyanionic ribbons composed of corner-shared triangular [ZnAs 3 ] units, running along the [100] direction. The structure of Eu 14 Zn 5 As 12 O crystallizes in the monoclinic space group P2/m and its anionic substructure can be described as an infinite “ribbonlike” chain comprised of [ZnAs 3 ] trigonal-planar units, although the structural complexity here is greater and also amplified by disorder on multiple crystallographic positions. In both structures, the O 2– anion occupies an octahedral void with six neighboring Eu 2+ cations. Formal electron counting, electronic structure calculations, and transport properties reveal the charge-balanced semiconducting nature of these heteroanionic Zintl phases. High-temperature thermoelectric transport properties measurements on Eu 14 Zn 5 As 12 O reveal relatively high resistivity (ρ 500K = 8 Ω·cm) and Seebeck coefficient values (S 500K = 220 μV K –1 ), along with a low concentration and mobility of holes as the dominant charge-carriers (n 500K = 8.0 × 10 17 cm –3 , μ 500K = 6.4 cm 2 /V s). Magnetic studies indicate the presence of divalent Eu 2+ species in Eu 14 Zn 5 As 12 O and complex magnetic ordering, with two transitions observed at T 1 = 21.6 K and T 2 = 9 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Unconventional Superlattice Ordering in Intercalated Transition Metal Dichalcogenide V1/3NbS2

The interplay between symmetry and topology in magnetic materials makes it possible to engineer exotic phases and technologically useful properties. A key requirement for these pursuits is achieving control over local crystallographic and magnetic structure, usually through sample morphology (such as synthesis of bulk crystals versus thin films) and application of magnetic or electric fields. Here we show that V1/3NbS2 can be crystallized in two ordered superlattices, distinguished by the periodicity of out-of-plane magnetic intercalants. Whereas one of these structures is metallic and displays the hallmarks of altermagnetism, the other superlattice, which has not been isolated before in this family of intercalation compounds, is a semimetallic noncollinear antiferromagnet that may enable access to topologically nontrivial properties. This observation of an unconventional superlattice structure establishes a powerful route for tailoring the tremendous array of magnetic and electronic behaviors hosted in related materials and may expand their use in low-power spintronic or topological quantum devices.

Fender, Shannon S↗
DOE OSTI2022

Crystallographic dependence of CO 2 hydrogenation pathways over HCP-Co and FCC-Co catalysts

We report efficient conversion of CO 2 is of great significance for sustainable supply of chemicals and fuels. While Co-based catalysts are known to be effective for CO hydrogenation in Fischer-Tropsch synthesis, they work very differently in CO 2 hydrogenation. This study reveals a crystallographic dependence of reaction pathways for CO 2 hydrogenation on Co catalyst showing a new type of structure sensitivity and structure-activity-selectivity relationship for CO 2 conversion to chemicals and fuels. The experimental work on CO 2 conversion including steady-state isotopic transient kinetic analysis (SSITKA) using 13 C-labeled CO 2 shows a preferential CH 4 formation over HCP-Co but dominant CO formation over FCC-Co. The density functional theory calculations indicate that CO 2 does dissociate directly into chemisorbed CO * and O * on both HCP-Co and FCC-Co, but the CO * intermediates on HCP-Co prefer to be hydrogenated to form CH 4 whereas the CO* on FCC-Co preferentially desorb to form CO. The significantly altered adsorption strength of CO * due to the presence of chemisorbed O * and CO 2 * species on the catalyst surface is responsible for the mechanistic disconnection in product selectivity between the CO 2 and CO hydrogenation over Co catalysts. This study also shows that the addition of K to Co diminishes the direct impact of Co crystal structure, but improves the selectivity to C 2 + hydrocarbons along with higher CO 2 conversion. This seems to result from another pathway originating from HCOO* intermediate from bonding interaction of surface Co atoms with carbon in CO 2 , leading to the formation of CH x * whose coupling subsequently give rises to C 2 + products. The present study sheds new light into the crystallographic structural sensitivity of CO 2 hydrogenation towards the rational design of more selective catalysts for CO 2 conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Trivalent f-Element Squarates, Squarate-Oxalates, and Cationic Materials, and the Determination of the Nine-Coordinate Ionic Radius of Cf(III)

The synthesis, structure, and solid-state UV–vis–NIR spectroscopy of four new f-element squarates, M 2 (C 4 O 4 ) 3 (H 2 O) 4 (M = Eu, Am, Cf) and Sm(C 4 O 4 )(C 4 O 3 OH)(H 2 O) 2 ·0.5H 2 O, four new cationic lanthanide squarate chlorides, [M 4 (C 4 O 4 ) 5 (H 2 O) 12 ]Cl 2 ·5H 2 O (M = Eu, Dy, Ho Er), and two new actinide squarate oxalates, M 2 (C 4 O 4 ) 2 (C 2 O 4 )(H 2 O) 4 (M = Am, Cf), are presented. All of the metal centers are trivalent. Single-crystal X-ray diffraction analysis reveals that M 2 (C 4 O 4 ) 3 (H 2 O) 4 and Sm(C 4 O 4 )(C 4 O 3 OH)(H 2 O) 2 ·0.5H 2 O have a two-dimensional sheet structure constructed from MO 7 (H 2 O) 2 monocapped square-antiprismatic (coordination number (CN) = 9) metal centers and SmO 6 (H 2 O) 2 square-antiprismatic (CN = 8) metal centers, respectively, whereas M 2 (C 4 O 4 ) 2 (C 2 O 4 )(H 2 O) 4 have a three-dimensional (3D) structure constructed from MO 7 (H 2 O) 2 monocapped square-antiprismatic (CN = 9) metal centers. Additionally, the cationic framework materials [M 4 (C 4 O 4 ) 5 (H 2 O) 12 ]Cl 2 ·5H 2 O have a 3D structure constructed from two crystallographically unique MO 5 (H 2 O) 3 square-antiprismatic (CN = 8) metal centers. In these structures, the squarate ligands bind to the metal centers with varying coordination modes and denticities. The results of this study provide another example of the nonparallel chemistry between the lanthanides and transplutonium elements. From the crystallographic data for the isotypic series M 2 (C 4 O 4 ) 3 (H 2 O) 4 (M = La–Nd, Sm, Eu) and the linear regression fit to a plot of the unit cell volume as a function of the cube of the ionic radius, the nine-coordinate ionic radius of Cf 3+ was determined to be 1.127 ± 0.003 Å. Lastly, computational analysis of the americium and californium complexes M 2 (C 4 O 4 ) 3 (H 2 O) 4 and M 2 (C 4 O 4 ) 2 (C 2 O 4 )(H 2 O) 4 reveals three important attributes: (i) the 5f orbitals are nonbonding in all cases, with the bonding differences occurring with the empty 6d orbitals; (ii) the Cf complexes exhibit more covalent character than their Am counterparts; and (iii) there is more covalent character in the squarate-oxalate complexes than in the squarate complexes.

Crystallography↗
DOE OSTI2026

The high-valent vanadium chemistry of isoindoline chelates

Isoindoline-based chelates, in particular bis(arylimino)isoindolines, have shown extensive metal binding chemistry. Although this chemistry has been explored for the middle and late transition metal ions, little work has been carried out on early transition metal complexes. In this article, we present the first examples of vanadium coordinated using four bis(arylimino)isoindolines, in which the aryl groups are pyrazole, indazole, benzimidazole, and pyridine (ligands 1–4 , respectively). We isolated five complexes using vanadyl sulfate or vanadyl acetylacetonate as the vanadium source. In all cases, the ligands bound in a meridional mode, and for four of the complexes, the vanadium ion was observed in the V(v) oxidation state. Three of the ligands ( 1–3 ) formed VO 2 complexes with vanadyl sulfate and vanadyl acetylacetonate, but the bis(pyridylimino)isoindoline (ligand 4 ) formed a V(v) oxosulfonato complex with the former starting material and a vanadyl V(iv) acetylacetonate with the latter starting material. All metal compounds were structurally elucidated by X-ray crystallographic methods, and we probed their electronic structures using DFT methods.

Bore, Joan C. [Univ. of Akron, OH (United States)]↗
DOE OSTI2020

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10 4 -10 6 ) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb 3+ L -III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Machine learning magnetism classifiers from atomic coordinates

The determination of magnetic structure poses a long-standing challenge in condensed matter physics and materials science. Experimental techniques such as neutron diffraction are resource-limited and require complex structure refinement protocols, while computational approaches such as first-principles density functional theory (DFT) need additional semi-empirical correction, and reliable prediction is still largely limited to collinear magnetism. Here, we present a machine learning model that aims to classify the magnetic structure by inputting atomic coordinates containing transition metal and rare earth elements. By building a Euclidean equivariant neural network that preserves the crystallographic symmetry, the magnetic structure (ferromagnetic, antiferromagnetic, and nonmagnetic) and magnetic propagation vector (zero or non-zero) can be predicted with an average accuracy of 77.8% and 73.6%. In particular, a 91% accuracy is reached when predicting no magnetic ordering even if the structure contains magneticelement(s). Ourworkrepresents onestepforwardtosolvingthegrand challenge of full magnetic structure determination.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Direct observation of defect-aided structural evolution in Ni-rich layered cathode

Ni-rich LiNi 1-x-y Mn x Co y O 2 (NMC) layered compounds have become the dominated cathode for lithium ion batteries. The role of crystallographic defects on their structure evolution and consequent performance degradation during electrochemical cycling is not yet fully understood. In this work, we investigated the structural evolution of Ni-rich NMC cathode in a solid-state cell via in-situ transmission electron microscopy. We identified antiphase boundary (APB) and twin boundary (TB) separating layered phases played an important role on phase change. Upon the lithium depletion, the APB extends across the layered structure, while Li/transition metal (TM) ion mixing in the layered phases is detected to induce the rock-salt phase formation along the coherent TB. According to DFT calculations, Li/TM mixing and phase transition are aided by the low diffusion barriers of TM ions at planar defects. Finally, this work reveals the dynamical scenario of secondary phase evolution, which helps to unveil the origin of performance fading in Ni-rich NMC.

25 ENERGY STORAGE↗
DOE OSTI2023

Structural modulation and spin glassiness upon oxidation in oxygen storage material LnFeMnO 4+x for Ln = Y, Lu, and Yb

The mixed valence multiferroic LnFe 2+ Fe 3+ O 4 (where Ln = Y, Lu, and Yb) can reversibly uptake oxygen into its lattice, which is evidenced by a crystallographic phase transition along with the appearance of structural modulations. In this study, we show that the Mn-substituted version of this multiferroic can also be readily oxidized to LnFe 3+ Mn 3+ O 4.5 revealing similar oxygen storage behavior. Through neutron, electron, and synchrotron x-ray diffraction studies, we observe a structural modulation that we attribute to a displacement wave in the fully oxidized compound. This wave exhibits commensurability with a wavevector q = (-2/7, 1/7, 0). Bond valence summation analysis of plausible interstitial oxygen positions suggests that oxygen insertion likely occurs at the middle of the Fe/Mn–O bipyramid layers. The structural modulation of LnFeMnO 4.5 is two-dimensional, propagates along the ab-plane, and is highly symmetric as 12 identical modulation vectors are observed in the diffraction patterns. The nature of the lanthanide, Ln 3+ , does not seem to influence such modulations since we observe identical satellite reflections for all three samples of Ln = Y, Lu, and Yb. Both LnFeMnO 4 and LnFeMnO 4.5 display spin glassy behavior with 2D short-range magnetic ordering being observed in LnFeMnO 4 . Analysis of the neutron diffraction data reveals a correlation length of ~10 nm. Upon oxidation to LnFeMnO 4.5 , the short-range magnetic order is significantly suppressed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Uniaxial Strain Control of Bulk Ferromagnetism in Rare-Earth Titanates

The perovskite rare-earth titanates are model Mott insulators with magnetic ground states that are very sensitive to structural distortions. These distortions couple strongly to the orbital degrees of freedom and, in principle, it should be possible to tune the superexchange and the magnetic transition with strain. We investigate the representative system (Y,La,Ca)TiO 3 , which exhibits low crystallographic symmetry and no structural instabilities. From magnetic susceptibility measurements of the Curie temperature, we demonstrate direct, reversible, and continuous control of ferromagnetism by influencing the TiO 6 octahedral tilts and rotations with uniaxial strain. The relative change in T C as a function of strain is well described by ab initio calculations, which provides detailed understanding of the complex interactions among structural, orbital, and magnetic properties in rare-earth titanates. The demonstrated manipulation of octahedral distortions opens up far-reaching possibilities for investigations of electron-lattice coupling, competing ground states, and magnetic quantum phase transitions in a wide range of quantum materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Review of honeycomb-based Kitaev materials with zigzag magnetic ordering

The search for a Kitaev quantum spin liquid in crystalline magnetic materials has fueled intense interest in the two-dimensional honeycomb systems. Many promising candidate Kitaev systems are characterized by a long-range-ordered magnetic structure with an antiferromagnetic zigzag-type order, where the static moments form alternating ferromagnetic chains. Recent experiments on high-quality single crystals uncovered the existence of intriguing multi-k magnetic structures, which evolved from zigzag structures. Those discoveries have sparked new theoretical developments and amplified interest in these materials. We present an overview of the honeycomb materials known to display this type of magnetic structure and provide detailed crystallographic information for the possible single- and multi-k variants.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2020

Atomic structure and grain shape evolution of nanodiamond during annealing in oxidizing atmosphere from neutron diffraction and MD simulations

In this work, real space pair-distribution function (PDF) analysis in conjunction with molecular dynamics (MD) simulations was applied to characterize crystal structure, shape and surface structure of diamond nanoparticles annealed in air up to 880 °C. MD simulated models of individual nanodiamond particles of various shapes and sizes were used to calculate theoretical radial distribution functions G(r) for powders with different grain size distributions. The calculated curves, showing distinct differences for the explored parameter space, were compared to the experimental G(r) functions obtained from neutron scattering for annealed detonated nanodiamond samples in a search for a model best describing the actual powders. It was found that as-synthesized nanodiamond grains are terminated by equally abundant (100), (110) and (111) crystallographic faces and their structure does not change upon annealing in air up to 280 °C. The shape and size of grains annealed above 480 °C changes due to surface etching. The etching rate differs between crystals faces and depends on temperature, resulting in the observed differences in grain shape. Below 680 °C the share of the (110) facets gradually increases and at 680 °C the grains become rhombic dodecahedra terminated solely by (110) surfaces. Further increase of the annealing temperature promotes formation of (111) surfaces and at 880 °C the preferred grain shape becomes an octahedron terminated by a variant of (111) surfaces possessing three dangling sp3 bonds per atom. At lower temperatures all grains become smaller and the size distribution moves towards the lower values. Furthermore, as the annealing temperature increases, the smallest grains disappear entirely and the average grain size grows back.

36 MATERIALS SCIENCE↗
DOE OSTI2021

AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

59 BASIC BIOLOGICAL SCIENCES↗