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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS1991

The interaction of hydrogen with metal alloys

Hydrogen diffusion coefficients were measured for several alloys, and these were determined to be about the same at 25 C for all alloys investigated. The relation of structure, both metallurgical and crystallographic, to the observed hydrogen distribution on charging was investigated, as well as the role of hydride formation in the hydrogen resistance of metal alloys. An attempt was made to correlate the structures and compositions of metal alloys as well as other parameters with the ratios of their notched tensile strengths in hydrogen to that in helium, R(H2/He), which are believed to represent a measure of their hydrogen resistance. Evidence supports the belief that hydrogen permeability and hydrogen resistance are increased by smaller grain sizes for a given alloy composition.

Danford, M. D.↗
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↗
DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2010

A Compendium of Scale Surface Microstructures: Ni(pt)al Coatings Oxidized at 1150 C for 2000 1-h Cycles

The surface structure of scales formed on Ni(Pt)Al coatings was characterized by SEM/EDS/BSE in plan view. Two nominally identical {100} samples of aluminide coated CMSX4 single crystal were oxidized at 1150 C for 2000 1-h cycles and were found to produce somewhat disparate behavior. One sample, with less propensity for coating grain boundary ridge deformation, presented primarily alpha-Al2O3 scale structures, with minimal weight loss and spallation. The original scale structure, still retained over most of the sample, consisted of the classic theta-alpha transformation-induced ridge network structure, with approx. 25 nm crystallographic steps and terraces indicative of surface rearrangement to low energy alumina planes. The scale grain boundary ridges were often decorated with a fine, uniform distribution of (Hf,Ti)O2 particles. Another sample, producing steady state weight losses, exhibited much interfacial spallation and a complex assortment of different structures. Broad areas of interfacial spalling, crystallographically-faceted (Ni,Co)(Al,Cr)2O4 spinel, with an alpha-Al2O3 base scale, were the dominant features. Other regions exhibited nodular spinel grains, with fine or (Ta,Ti)-rich (rutile) particles decorating or interspersed with the spinel. While these features were consistent with a coating that presented more deformation at extruded grain boundaries, the root cause of the different behavior between the duplicate samples could not be conclusively identified.

Smialek, James L.↗
DOE OSTI2025

Structure refinement and anisotropic atomic displacement parameters of 1M Illite: Rietveld and pair distribution function analysis using synchrotron X-ray radiation

Illite, a widespread clay mineral, plays a pivotal role in geological processes, notably as an indicator in diagenetic and hydrothermal alteration environments, and possesses significant industrial relevance in applications including ceramics, construction and catalysis. However, challenges including its nanoscale crystallinity, structural disorder and frequent interstratification with other clay minerals have hindered detailed structural characterization using conventional X-ray diffraction (XRD) techniques. This study employs integrated synchrotron XRD and pair distribution function (PDF) analysis to elucidate the crystal structure of the 1M illite polytype, yielding the first determination of its anisotropic atomic displacement parameters (U aniso ). TheseU aniso parameters provide critical insights into atomic dynamics and static disorder within the structure, enabling a more refined understanding of structure–property relationships. This integrated approach, combining synchrotron XRD, Rietveld refinement and PDF analysis, yields a comprehensive structural characterization, capturing both average crystallographic and local atomic arrangements. Considering illite's widespread geological occurrence and industrial importance, this high-precision structural dataset, especially the determinedU aniso values, provides a crucial benchmark for future modeling and simulation efforts targeting accurate prediction of its physicochemical behavior.

Chemistry↗
DOE OSTI2021

Utilizing Oxygen Redox in Layered Cathode Materials from Multiscale Perspective

We report in high-capacity layered oxide cathode materials, utilization of lattice oxygen as a redox center is considered to be one of the most promising approaches to overcome the capacity limitation set by conventional transition metal redox centers. However, rapid material degradation is often associated with oxygen oxidation, leading to formidable challenges in utilizing oxygen redox. Further mechanistic understanding of the oxygen activities thus becomes critical to better control oxygen redox reactions. This review summarizes recent advances for investigating oxygen redox reactions in cathode materials from a multiscale perspective, i.e., from the atomistic level to the microstructure regime. First the mechanistic aspects of oxygen redox and the consequences of this reaction on various electrode degradation pathways during battery operation (e.g., oxygen loss, transition metal migration, irreversible phase transition), relating structural changes at the crystallographic scale to those at the macro scale, are discussed. Then recent developments based on atomic and microstructure modifications that are promising for improving the reversibility of oxygen redox reaction or mitigating the harmful processes arising from oxidation of the oxygen centers under high operating voltage are recounted. The analysis is concluded with a commentary on further research directions toward optimizing the oxygen activity for high-capacity charge storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Determining elastic anisotropy of textured polycrystals using resonant ultrasound spectroscopy

Abstract Polycrystalline materials can have complex anisotropic properties depending on their crystallographic texture and crystal structure. In this study, we use resonant ultrasound spectroscopy (RUS) to nondestructively quantify the elastic anisotropy in extruded aluminum alloy 1100-O, an inherently low-anisotropy material. Further, we show that RUS can be used to indirectly provide a description of the material’s texture, which in the present case is found to be transversely isotropic. By determining the entire elastic tensor, we can identify the level and orientation of the anisotropy originated during extrusion. The relative anisotropy of the compressive (c 11 /c 33 ) and shear (c 44 /c 66 ) elastic constants is 1.5% ± 0.5% and 5.7% ± 0.5%, respectively, where the elastic constants (five independent elastic constants for transversely isotropic) are those associated with the extrusion axis that defines the symmetry of the texture. These results indicate that the texture is expected to have transversely isotropic symmetry. This finding is confirmed by two additional approaches. First, we confirm elastic constants and the degree of elastic anisotropy by direct sound velocity measurements using ultrasonic pulse echo. Second, neutron diffraction (ND) data confirm the symmetry of the bulk texture consistent with extrusion-induced anisotropy, and polycrystal elasticity simulations using the elastic self-consistent model with input from ND textures and aluminum single-crystal elastic constants render similar levels of polycrystal elastic anisotropy to those measured by RUS. We demonstrate the ability of RUS to detect texture-induced anisotropy in inherently low-anisotropy materials. Therefore, as many other common materials have intrinsically higher elastic anisotropy, this technique should be applicable for similar levels of texture, providing an efficient general diagnostic and characterization tool.

36 MATERIALS SCIENCE↗