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Results for “Crystal structure identification”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ 1 -pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15

Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg 2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg 2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg 2+ and Zn 2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

In cellulo crystallization of Trypanosoma brucei IMP dehydrogenase enables the identification of genuine co-factors

Sleeping sickness is a fatal disease caused by the protozoan parasite Trypanosoma brucei (Tb). Inosine-5’-monophosphate dehydrogenase (IMPDH) has been proposed as a potential drug target, since it maintains the balance between guanylate deoxynucleotide and ribonucleotide levels that is pivotal for the parasite. Here we report the structure of TbIMPDH at room temperature utilizing free-electron laser radiation on crystals grown in living insect cells. The 2.80 Å resolution structure reveals the presence of ATP and GMP at the canonical sites of the Bateman domains, the latter in a so far unknown coordination mode. Consistent with previously reported IMPDH complexes harboring guanosine nucleotides at the second canonical site, TbIMPDH forms a compact oligomer structure, supporting a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity. The oligomeric TbIMPDH structure we present here reveals the potential of in cellulo crystallization to identify genuine allosteric co-factors from a natural reservoir of specific compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2022

High entropy alloys with hexagonal close-packed structure derived from thin film combinatorial approach

A thin film combinatorial synthesis approach was utilized to develop a compositional and structural library for the OsRuWCo alloy system. The survey of this alloy space produced 24 unique compositions and their corresponding crystal structures, which represent a phase map where amorphous and single-phase hexagonal close-packed alloys were identified. Based on the identification of a promising candidate film region, a new high entropy alloy based on OsRuWCo, but with non-equiatomic composition, was synthesized in bulk form. The alloy exhibited a single-phase hexagonal close-packed structure in the as-cast state. Three derivatives from this system were also developed by considering the heat of mixing, atomic size, and binary solubility. These new alloys are based on OsRuWCoIr and OsRuWCoFe, both of which exhibit single-phase hexagonal close-packed as-cast structures, as determined by X-ray diffraction and electron microscopy. Additionally, this large compositional space was utilized to evaluate conventional parameters that describe high entropy alloys (ΔS mix , ΔH mix , Ω, δ, and VEC), and these were found to elucidate the criteria for solid solution formation in this system. Additionally, trends illustrating the evolution from amorphous to crystalline phases are demonstrated and discussed. It is concluded that in this particular case, the dominant factors promoting crystallinity are thermodynamic or electronic, rather than geometric.

36 MATERIALS SCIENCE↗
DOE OSTI2025

X-ray Diffraction Studies of Single-Crystal Materials for Broad Battery Applications

Single-crystal materials have attracted growing interest in battery research due to their well-defined crystallographic orientation, absence of grain boundaries, and enhanced mechanical and electrochemical stability. This Review provides a comprehensive overview of recent advances in the synthesis, structural evolution, and performance optimization of single-crystal electrodes and solid electrolytes. Particular focus is placed on the application of advanced X-ray diffraction (XRD) techniques, including operando synchrotron diffraction, reciprocal space mapping, and Bragg coherent diffraction imaging, which have enabled in-depth investigations of lattice strain, cation disorder, phase transitions, and defect formation. Representative case studies across Ni-rich layered oxides, spinel-type cathodes, and garnet-based electrolytes are examined to highlight the structural features unique to single crystals. Additionally, the synergistic integration of XRD with machine learning, tomography, and spectroscopy is discussed as a powerful direction for real-time analysis and predictive modeling. Furthermore, these insights provide critical guidance for the rational design of high-performance single-crystal materials in lithium, sodium, and solid-state battery systems.

25 ENERGY STORAGE↗
DOE OSTI2021

Defect detection in atomic-resolution images via unsupervised learning with translational invariance

Abstract Crystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Machine learning technique to identify grains in polycrystalline materials samples

A method of identifying grains in polycrystalline materials, the method including (a) identifying local crystal structure of the polycrystalline material based on neighbor coordination or pattern recognition machine learning, the local crystal structure including grains and grain boundaries, (b) pre-processing the grains and the grain boundaries using image processing techniques, (c) conducting grain identification using unsupervised machine learning; and (d) refining a resolution of the grain boundaries.

Sankaranarayanan, Subramanian↗
DOE OSTI2022

Cluster Analysis of Combined EDS and EBSD Data to Solve Ambiguous Phase Identifications

A common problem in analytical scanning electron microscopy (SEM) using electron backscatter diffraction (EBSD) is the differentiation of phases with distinct chemistry but the same or very similar crystal structure. X-ray energy dispersive spectroscopy (EDS) is useful to help differentiate these phases of similar crystal structures but different elemental makeups. However, open, automated, and unbiased methods of differentiating phases of similar EBSD responses based on their EDS response are lacking. This paper describes a simple data analytics-based method, using a combination of singular value decomposition and cluster analysis, to merge simultaneously acquired EDS + EBSD information and automatically determine phases from both their crystal and elemental data. I use hexagonal TiB 2 ceramic contaminated with multiple crystallographically ambiguous but chemically distinct cubic phases to illustrate the method. Code, in the form of a Python 3 Jupyter Notebook, and the necessary data to replicate the analysis are provided as Supplementary material.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Streptococcus mutans, found in the human oral cavity, is a significant contributor to the pathogenesis of dental caries. This bacterium expresses three genetically distinct types of glucosyltransferases named GtfB (GTF-I), GtfC (GTF-SI) and GtfD (GTF-S) that play critical roles in the development of dental plaque. The catalytic domains of GtfB, GtfC and GtfD contain conserved active-site residues for the overall enzymatic activity that relate to hydrolytic glycosidic cleavage of sucrose to glucose and fructose, release of fructose and generation of a glycosyl-enzyme intermediate in the reducing end. In a subsequent transglycosylation step, the glucosyl moiety is transferred to the nonreducing end of an acceptor to form a growing glucan polymer chain made up of glucose molecules. It has been proposed that both sucrose breakdown and glucan synthesis occur in the same active site of the catalytic domain, although the active site does not appear to be large enough to accommodate both functions. These three enzymes belong to glycoside hydrolase family 70 (GH70), which shows homology to glycoside hydrolase family 13 (GH13). GtfC synthesizes both soluble and insoluble glucans (α-1,3 and α-1,6 glycosidic linkages), while GtfB and GtfD synthesize only insoluble or soluble glucans, respectively. Here, crystal structures of the catalytic domains of GtfB and GtfD are reported. These structures are compared with previously determined structures of the catalytic domain of GtfC. With this work, apo structures and inhibitor-complex structures with acarbose are now available for the catalytic domains of GtfC and GtfB. The structure of GtfC with maltose allows further identification and comparison of active-site residues. A model of sucrose binding to GtfB is also included. The new structure of the catalytic domain of GtfD affords a structural comparison of the three S. mutans glycosyltransferases. Unfortunately, the catalytic domain of GtfD is not complete since crystallization resulted in the structure of a truncated protein lacking approximately 200 N-terminal residues of domain IV.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Tuning chemical precompression: Theoretical design and crystal chemistry of novel hydrides in the quest for warm and light superconductivity at ambient pressures

Over the past decade, a combination of crystal structure prediction techniques and experimental synthetic work has thoroughly explored the phase diagrams of binary hydrides under pressure. The fruitfulness of this dual approach is demonstrated in the recent identification of several superconducting hydrides with T c s approaching room temperature. We start with an overview of the computational procedures for predicting stable structures and estimating their propensity for superconductivity. A survey of phases with high T c reveals some common structural features that appear conducive to the strong coupling of the electronic structure with atomic vibrations that leads to superconductivity. We discuss the stability and superconducting properties of phases containing two of these—molecular H 2 units mixed with atomic H and hydrogenic clathrate-like cages—as well as more unique motifs. Lastly, we argue that ternary hydride phases, whose exploration is still in its infancy, are a promising route to achieve simultaneous superconductivity at high temperatures and stability at low pressures. Several ternary hydrides arise from the addition of a third element to a known binary hydride structure through site mixing or onto a new site, and several more are based on altogether new structural motifs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Fantastic n = 4: Ce5Co4+xGe13−ySny of the A n +1M n X3 n +1 homologous series

Ce-based intermetallics are of interest due to the potential to study the interplay of localized magnetic moments and conduction electrons. Our work on Ce-based germanides led to the identification of a new homologous series An+1MnX3n+1 (A = rare earth, M = transition metal, X = tetrels, and n = 1–6). This work presents the single-crystal growth, structure determination, and anisotropic magnetic properties of the n = 4 member of the Cen+1ConGe3n+1 homologous series. Ce5Co4+xGe13−ySny consists of three Ce sites, three Co sites, seven Ge sites, and two Sn sites, and the crystal structure is best modeled in the orthorhombic space group Cmmm where a = 4.3031(8) Å, b = 45.608(13) Å, and c = 4.3264(8) Å, which is in close agreement with the previously reported Sn-free analog where a = 4.265(1) Å, b = 45.175(9) Å, and c = 4.293(3) Å. Anisotropic magnetic measurements show Kondo-like behavior and three magnetic transitions at 6, 4.9, and 2.4 K for Ce5Co4+xGe13−ySny.

Weiland, Ashley (ORCID:0000000171983559)↗
DOE OSTI2020

Giant momentum-dependent spin splitting in centrosymmetric low-$\textit{Z}$ antiferromagnets

The energy vs crystal momentum $\textit{E(k)}$ diagram for a solid (band structure) constitutes the road map for navigating its optical, magnetic, and transport properties. By selecting crystals with specific atom types, composition, and symmetries, one could design a target band structure and thus desired properties. A particularly attractive outcome would be to design energy bands that are split into spin components with a momentum-dependent splitting, as envisioned by Pekar and Rashba, enabling spintronic application. The current paper provides “design principles” for wave-vector dependent spin splitting (SS) of energy bands that parallel the traditional Dresselhaus and Rashba spin-orbit coupling (SOC)–induced splitting, but originates from a fundamentally different source—antiferromagnetism. Here, we identify a few generic antiferromagnetic (AFM) prototypes with distinct SS patterns using magnetic symmetry design principles. These tools allow also the identification of specific AFM compounds with SS belonging to different prototypes. A specific compound—centrosymmetric tetragonal MnF 2 —is used via density functional band-structure calculations to quantitatively illustrate one type of AFM SS. Unlike the traditional SOC-induced effects restricted to noncentrosymmetric crystals, we show that antiferromagnetic-induced spin splitting broadens the playing field to include even centrosymmetric compounds, and gives SS comparable in magnitude to the best known (“giant’” SOC effects, even without traditional SOC, and consequently does not rely on the often-unstable high atomic number elements required for high SOC. We envision that use of the current design principles to identify an optimal antiferromagnet with spin-split energy bands would be beneficial for efficient spin-charge conversion and spin-orbit torque applications without the burden of requiring compounds containing heavy elements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. Further, the denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Accurate prediction of terahertz spectra of molecular crystals of fentanyl and its analogs

Fentanyl is a potent synthetic opioid pain reliever with a high bioavailability that can be used as prescription anesthetic. Rapid identification via non-contact methods of both known and emerging opioid substances in the fentanyl family help identify the substances and enable rapid medical attention. We apply PBEh-3c method to identify vibrational normal modes from 0.01 to 3 THz in solid fentanyl and its selected analogs. The molecular structure of each fentanyl analog and unique arrangement of H-bonds and dispersion interactions significantly change crystal packing and is subsequently reflected in the THz spectrum. Further, the study of THz spectra of a series of stereoisomers shows that small changes in molecular structure results in distinct crystal packing and significantly alters THz spectra as well. We discuss spectral features of synthetic opioids with higher potency than conventional fentanyl such as ohmefentanyl and sufentanil and discover the pattern of THz spectra of fentanyl analogs.

42 ENGINEERING↗
DOE OSTI2023

Atomistic‐Level Effects of Noncovalent Interactions and Crystalline Packing for Organic Material Structural Integrity upon Exposure to Gamma Radiation

Developing an atomistic understanding of ionizing radiation induced changes to organic materials is necessary for intentional design of greener and more sustainable materials for radiation shielding and detection. Cocrystals are promising for these purposes, but a detailed understanding of how the specific intermolecular interactions within the lattice upon exposure to radiation affect the structural stability of the organic crystalline material is unknown. This study evaluates atomistic-level effects of γ radiation on both single- and multicomponent organic crystalline materials and how specific noncovalent interactions and packing within the crystalline lattice enhance structural stability. Dose studies were performed on all crystalline systems and evaluated via experimental and computational methods. Changes in crystallinity were evaluated by p-XRD and free radical formation was analyzed via EPR spectroscopy. Type of intermolecular interactions and packing within the crystal lattice was delineated and related to the specific free radical species formed and the structural integrity of each material. Periodic DFT and HOMO-LUMO surface mapping calculations provided atomistic-level identifications of the most probable sites for the radicals formed upon exposure to γ radiation and relate intermolecular interactions and molecular packing within the crystalline lattice to experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Crystal Orientation and Defect Mapping in Electron-Beam-Sensitive Zeolites with Near-Axis Transmission Kikuchi Diffraction

Porous materials are vital in catalysis, energy conversion, and environmental remediation. Understanding structural heterogeneity in zeolites is key to linking synthesis, framework intergrowths, and catalytic performance, yet current methods for phase identification and spatial mapping lack sufficient resolution or throughput. We present a high-throughput approach using near-axis transmission Kikuchi diffraction in a scanning electron microscope, achieving high phase and spatial resolution for electron-beam-sensitive zeolites, including ZSM-5 and, for the first time, Zeolite A. Here, this method enables direct visualization of intergrowth features that critically affect catalytic and adsorption behavior, bridging the gap between ensemble-averaged X-ray diffraction and high-resolution but low-throughput transmission electron microscopy. Combining nanoscale mapping with statistical sampling is highly suited for machine-learning pipelines guiding new structure function understanding and could be extended to other beam-sensitive porous materials such as metal–organic or covalent–organic frameworks.

crystallography↗
DOE OSTI2022

Electrocatalysis in Alkaline Media and Alkaline Membrane-Based Energy Technologies

Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly alkaline fuel cells and water electrolyzers. Anion exchange (alkaline) membrane fuel cells (AEMFCs) enable the use of nonprecious electrocatalysts for the sluggish oxygen reduction reaction (ORR), relative to proton exchange membrane fuel cells (PEMFCs), which require Pt-based electrocatalysts. However, the hydrogen oxidation reaction (HOR) kinetics is significantly slower in alkaline media than in acidic media. Understanding these phenomena requires applying theoretical and experimental methods to unravel molecular-level thermodynamics and kinetics of hydrogen and oxygen electrocatalysis and, particularly, the proton-coupled electron transfer (PCET) process that takes place in a proton-deficient alkaline media. Extensive electrochemical and spectroscopic studies, on single-crystal Pt and metal oxides, have contributed to the development of activity descriptors, as well as the identification of the nature of active sites, and the rate-determining steps of the HOR and ORR. Among these, the structure and reactivity of interfacial water serve as key potential and pH-dependent kinetic factors that are helping elucidate the origins of the HOR and ORR activity differences in acids and bases. Additionally, deliberately modulating and controlling catalyst-support interactions have provided valuable insights for enhancing catalyst accessibility and durability during operation. The design and synthesis of highly conductive and durable alkaline membranes/ionomers have enabled AEMFCs to reach initial performance metrics equal to or higher than those of PEMFCs. We emphasize the importance of using membrane electrode assemblies (MEAs) to integrate the often separately pursued/optimized electrocatalyst/support and membranes/ionomer components. Operando/in situ methods, at multiscales, and ab initio simulations provide a mechanistic understanding of electron, ion, and mass transport at catalyst/ionomer/membrane interfaces and the necessary guidance to achieve fuel cell operation in air over thousands of hours. We hope that this Review will serve as a roadmap for advancing the scientific understanding of the fundamental factors governing electrochemical energy conversion in alkaline media with the ultimate goal of achieving ultralow Pt or precious-metal-free high-performance and durable alkaline fuel cells and related technologies.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Development and construction status of the Mu2e electromagnetic calorimeter mechanical structures

Abstract The Mu2e experiment at Fermilab will search for the CLFV neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the evidence of physics beyond the Standard Model. Mu2e comprises a straw-tracker, an electromagnetic calorimeter and an external veto for cosmic rays. The calorimeter provides electron identification, a fast trigger and aids track reconstruction. It is a state-of-the-art crystal calorimeter and employs 1340 pure CsI crystals readout by UV-extended SiPM and fast electronics. The design consists of two identical annular disks positioned at the relative distance of 70 cm downstream the target.The hostile Mu2e conditions (total ionizing dose of 12 krad and a neutron fluence of 5 × 10 10 n/cm 2 @ 1 MeVeq (Si)/y, 1 T magnetic field and vacuum level of 10 −4 Torr) posed tight constraints on the mechanical structures and materials choice. The support structure of the two crystal matrices employs two aluminum hollow rings and parts made of open-cell vacuum-compatible carbon fiber. SiPMs and front-end electronics for each crystal are assembled in one mechanical unit inserted in a machined copper holder. The units are supported by a plate made of vacuum-compatible material. The plate integrates the cooling system made of a network of copper lines flowing a low temperature fluid and placed in thermal contact with the copper holders. The DAQ is hosted in aluminum crates positioned on the lateral surface of the disks. The crates also integrate the DAQ electronics cooling system. We review the constraints on the calorimeter structures design, the development of all the structural components, including the simulations that have determined the materials and technological choices and the specifications of the cooling station, components production and quality assurance tests, the procedures for detector assembly, transportation and installation in the experimental area.

Instruments & Instrumentation↗