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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Synthesis and structural characterization of a hydrated sodium–caesium tetracosatungstate(VI), Na 5 Cs 19 [W 24 O 84 ]·21H 2 O

Crystal formation of penta­sodium nona­deca­cesium tetra­cosa­tungstate(VI) heneikosahydrate, Na 5 Cs 19 [W 24 O 84 ]·21H 2 O, was successfully achieved by the conversion of [H 2 W 12 O 42 ] 10– through the addition of excess Cs + . The crystal structure comprising the toroidal isopolyoxidometalate is presented, as well as its Raman spectrum. Na 5 Cs 19 (H 2 O) 21 W 24 O 84 crystallizes in the rhombohedral space group R$\overline{3}$ with an obverse centering. The title compound represents the addition of a new member to the isopolytungstate family with mixed alkali counter-ions and contains rarely observed five-coordinate tungsten(VI) atoms in the [W 24 O 84 ] 24– anion (site symmetry C 3i ) arising from the conversion mediated by Cs + counter-ions.

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

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure↗
DOE OSTI2023

A methodology to generate crystal-based molecular structures for atomistic simulations

Abstract We propose a systematic method to construct crystal-based molecular structures often needed as input for computational chemistry studies. These structures include crystal ‘slabs’ with periodic boundary conditions (PBCs) and non-periodic solids such as Wulff structures. We also introduce a method to build crystal slabs with orthogonal PBC vectors. These methods are integrated into our code, Los Alamos Crystal Cut ( LCC ), which is open source and thus fully available to the community. Examples showing the use of these methods are given throughout the manuscript.

42 ENGINEERING↗
DOE OSTI2023

Synthesis, structure and canted antiferromagnetism of layered cobalt hydroxide sorbate

Layered hybrid organic–inorganic compounds of the transition metal hydroxides, in which part of the hydroxide ions are exchanged for organic ligands that act as spacers of the 2-dimensional inorganic layers, elicit new or enhanced properties. The interlayer ligands enable fine-tuning of the physicochemical properties of the metal hydroxide layers, including their magnetism. Specifically, within the Co(OH) 2 family of transition ion hydroxides, this approach has been leveraged to stabilize antiferromagnetic and ferrimagnetic ground states for pillared and layered complexes, respectively. Here, in this work, we further investigate the effects of changing dimensionality, local Co coordination, and interlayer spacing on the magnetic ground state of brucite-like β-Co(OH) layered complexes. We report the hydrothermal synthesis of a new crystalline material, Co(OH)(sorb), where the inorganic layers are spaced by monotopic, doubly unsaturated sorbate ligands (sorb = [C 6 H 7 O 2 ] – ). The material was structurally characterized using powder X-ray and neutron diffraction measurements and the crystal structure was solved ab initio from powder diffraction data and refined using the Rietveld method. The magnetic susceptibility and magnetization measurements reveal canted antiferromagnetic ordering with T N = 41.7 K. This report augments our understanding of tuning magnetism through dimensionality in layered complexes and represents a step forward in the design of new 2D layered hybrid compounds.

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

Synthesis, structural, and magnetic properties of Heusler-type Mn 2-x Fe 1+x Ge (0.0 ≤ x ≤ 1.0) alloys

Bulk Mn 2-x Fe 1+x Ge (0.0 ≤ x ≤ 1.0) alloys have been synthesized by arc-melting followed by a low temperature homogenization thermal annealing, whereas for comparison purposes the Mn 2 FeGe alloy was also produced in ribbon form by rapid solidification. Here, a study of the structural and magnetic properties is presented. Contrary to theoretical predictions, Mn 2 FeGe crystallizes in a hexagonal DO 19 crystal structure (space group P63/mmc) and orders ferromagnetically with a saturation magnetization (M S ) value of ~1.7 µB/f.u. in the ground state. With the substitution of Fe for Mn in bulk Mn 2-x Fe 1+x Ge, we observed an increase in the FM interactions with a maximum MS value of 5.1 µ B /f.u. for x = 1.0, and a significant progressive increase in the Curie temperature (T C ) in a wide range spanning ~200 K to over 400 K.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Tunable Broad Light Emission from 3D “Hollow” Bromide Perovskites through Defect Engineering

We report hybrid halide perovskites consisting of corner-sharing metal halide octahedra and small cuboctahedral cages filled with counter cations have proven to be prominent candidates for many high-performance optoelectronic devices. The stability limits of their three-dimensional perovskite framework are defined by the size range of the cations present in the cages of the structure. In some cases, the stability of the perovskite-type structure can be extended even when the counterions violate the size and shape requirements, as is the case in the so-called "hollow" perovskites. In this work, we engineered a new family of 3D highly defective yet crystalline "hollow" bromide perovskites with general formula (FA) 1-x (en) x (Pb) 1-0.7x (Br) 3-0.4x (FA = formamidinium (FA + ), en = ethylenediammonium (en 2+ ), x = 0-0.44). Pair distribution function analysis shed light on the local structural coherence, revealing a wide distribution of Pb-Pb distances in the crystal structure as a consequence of the Pb/Br-deficient nature and en inclusion in the lattice. By manipulating the number of Pb/Br vacancies, we finely tune the optical properties of the pristine FAPbBr 3 by blue shifting the band gap from 2.20 to 2.60 eV for the x = 0.42 en sample. A most unexpected outcome was that at x > 0.33 en incorporation, the material exhibits strong broad light emission (1% photoluminescence quantum yield (PLQY)) that is maintained after exposure to air for more than a year. This is the first example of strong broad light emission from a 3D hybrid halide perovskite, demonstrating that meticulous defect engineering is an excellent tool for customizing the optical properties of these semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Plant metacaspase: A case study of microcrystal structure determination and analysis

Metacaspases are highly conserved in plants and play essential roles in mediating programmed cell death, biotic and abiotic stress responses, and damage-induced innate immunity. Ca 2+ signaling induced by plant damage leads to activation of metacaspase from Arabidopsis thaliana (AtMC4), which subsequently processes a plant elicitor peptide to trigger downstream immuno-response. To understand the structural basis of AtMC4 activation by Ca 2+ , we previously determined its crystal structure and performed in-crystal Ca 2+ treatment to probe activation-associated conformational changes. To enable structure determination and in-crystal Ca 2+ activation analysis, we used microcrystals and related methods which were essential for our successful approach. Here, in this paper, we describe in detail the methods that we used for determination of AtMC4 structure using single-wavelength isomorphous replacement with anomalous signals assembled from 22 microcrystals. We also describe the method for in-crystal Ca 2+ soaking, microcrystal data collection, data assembly and analysis to obtain the activated structure of AtMC4 from 91 micro-sized crystals. The described methods may be useful to study other plant metacaspases and more broadly other plant enzymes for their structure determination and in-crystal functional characterization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ferromagnetic MnBi 4 Te 7 obtained with low-concentration Sb doping: A promising platform for exploring topological quantum states

The tuning of the magnetic phase, chemical potential, and structure is crucial to observe diverse exotic topological quantum states in Mn Bi 2 Te 4 (Bi 2 Te 3 ) m (m = 0–3). Here we show a ferromagnetic (FM) phase with a chiral crystal structure in Mn (Bi 1–x Sb x ) 4 Te 7 , obtained via tuning the growth conditions and Sb concentration. Unlike previously reported Mn (Bi 1–x Sb x ) 4 Te 7 , which exhibits FM transitions only at high Sb doping levels, our samples show FM transitions (T C = 13.5 K) at 15%–27% doping levels. Furthermore, our single-crystal x-ray-diffraction structure refinements find Sb doping leads to a chiral structure with the space group of P3, contrasted with the centrosymmetric $P\bar{3}m1$ crystal structure of the parent compound MnBi 4 Te 7 . Through angle-resolved photoemission spectroscopy measurements, we also demonstrated that the nontrivial band topology is preserved in the Sb-doped FM samples. Given that the nontrivial band topology of this system remains robust for low Sb doping levels, our success in making FM Mn(Bi 1–x Sb x ) 4 Te 7 with x = 0.15, 0.175, 0.2, and 0.27 paves the way for realizing the predicted topological quantum states, such as the axion insulator and Weyl semimetals. Additionally, we also observed magnetic glassy behavior in both antiferromagnetic MnBi 4 Te 7 and FM Mn (Bi 1–x Sb x )4 Te 7 samples, which we believe originates from cluster spin-glass phases coexisting with long-range antiferromagnetic/FM orders. Further, we have also discussed how the antisite Mn ions impact the interlayer magnetic coupling and how FM interlayer coupling is stabilized in this system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Magnetic and structural properties of Mn X NiSn ( X = Mn, Fe, Co)

Crystal structure and magnetic properties of Heusler alloys MnXNiSn (X = Mn, Fe, Co) are investigated using density functional theory and compared with experimental results. The parent alloy Mn 2 NiSn, which crystallizes in the inverse Heusler structure, is found to be ferrimagnetic, in agreement with previous experimental and theoretical work. The Fe and Co substitutions cause the alloys to assume a fairly well-ordered Y structure and enhance the magnetization substantially. We find that the strong nearest neighbour Mn-X exchange changes from antiferromagnetic (X = Mn) to ferromagnetic (X = Fe, Co), which explains and actually overestimates the experimental changes. A striking feature of the system is that Fe and Co have opposite effects on the Curie temperature T c : they reduce and enhance T c , respectively. We qualitatively explain this behaviour in terms of two-sublattice model based on the nearest-neighbour exchange.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗
DOE OSTI2020

A stable and highly selective metalloporphyrin based framework for the catalytic oxidation of cyclohexene

A new metalloporphyrin framework of molybdenum Mo 2 O 4 (C 48 H 28 N 4 O 8 )·(CH 3 ) 2 NH·5H 2 O·2DMF (Mo 2 TCPP) was synthesized from tetrakis(4-carboxyphenyl)porphyrin (H 4 TCPP) and sodium molybdate dihydrate by a hydrothermal method. Mo 2 TCPP is a 3D network with two sub-units, in which both TCPP ligands and each Mo 2 dimer act as four connection nodes. The crystal structure was determined by single crystal analysis and further characterized by FTIR, SEM, EDX, PXRD, XPS and TGA. Here cumene hydrogen peroxide and hydrogen peroxide were used as oxidants to study the catalytic activity of new metalloporphyrins in the oxidation of cyclohexene at different temperatures. The conversion rate of cyclohexene and the selectivity of epoxycyclohexane were both higher than 99%, which was better than the previously published research results. The stability of the catalyst before and after the reaction was further tested for 10 runs without obvious degradation. The catalyst was stable in different solutions such as acidic, water and alkaline. These results shed light on the future development of new catalytic materials based on metalloporphyrin.

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

Structure and lithium insertion in oxides of molybdenum

Oxides of molybdenum, MoO x , have a rich structural chemistry arising from the accommodation of oxygen deficiency as MoO 3 is reduced and varied redox behavior arising from the ability of Mo to take on several different oxidation states. We review MoO 3 , MoO 2 , and all the reduced Mo oxides with intermediate compositions for their performance as Li-ion battery electrode materials. These reduced oxides are perhaps the most structurally diverse in the field of energy storage materials, taking on structures ranging from ones with crystallographic shear to bronze-like structures and distorted rutile. The crystal structure can have a significant impact on the performance of battery materials, which makes the reduced Mo oxides a promising domain of study. Electrochemical studies of these oxides from as early as 1971 to as recently as 2022 are compiled, and characteristics of capacity, capacity retention, and rate performance are compared. We find that certain oxides indeed display promising and highly reversible capacities for Li + storage. Typical redox voltages for Mo oxides lie in a regime that hinders maximizing energy density when they are paired with higher-voltage cathodes or lower-voltage anodes. The possibility of decreasing the redox voltage in the future will expand the promise of these materials while offering an alternative to more critical elements such as Nb.

25 ENERGY STORAGE↗
DOE OSTI2026

AlGaN/GaN Core-Shell Nanofin Diodes on Si Substrates for Vertical GaN Electronics

We demonstrate plasma-assisted MBE selective-area growth of GaN/AlGaN core-shell structures on Si(111) as a path to vertical GaN devices. The selective-area growth enables the full vertical and uniform core-shell fin structures to be realized in a continuous growth without breaking vacuum. TEM images and EDS mapping of the core-shell structures show well-aligned crystal structure and sharp heterointerfaces. Dislocation filtering was observed in STEM imaging of the fin structure. P-N junction diodes fabricated with GaN/AlGaN core-shell structures reveal ideality factors as low as 1.5, and the reverse-bias leakage is consistent with trap-assisted space-charge-limited conduction. While practical challenges exist, including material-related leakage, growth-related challenges and optimization, this demonstration of p-n junction by this method may provide a path to vertical Superjunction device concepts in GaN and related materials.

Xiong, Juncheng [University of Notre Dame, IN (Uni↗
DOE OSTI2020

rlmolecule: A library for general-purpose material and molecular optimization using AlphaZero-style reinforcement learning

This library includes in-progress code for the optimization of materials and molecules using reinforcement learning. This project seeks to develop a generalized machine learning approach for optimizing targeted, and often complex, functional properties over the space of possible material structures, allowing faster identification of promising candidates. Electronic and transport properties of materials are determined by their molecular structure (for molecules) or their crystal structure (for in-organic crystalline materials). The atomic composition, bonding, and 3-D-spatial arrangement in these systems therefore represent a vast, discontinuous search space for optimal candidates. This library implements AlphaZero style reinforcement learning applied to two worked examples: the optimization of stable organic radicals for redox flow batteries, and the determination of stable electrolyte species for solid state batteries. The current code contains proof-of-concept results run on the Eagle HPC system, while the completed package will be a flexible tool for material optimization across of number of energy-relevant fields, which leverages cloud compute resources for the majority of the computational heavy lifting.

Biagioni, David↗
DOE OSTI2023

Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5

Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation

Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α) 8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. Further, the noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structural Phase Transitions in the van der Waals Ferromagnets Fe x Pd y Te 2

Two-dimensional van der Waals (vdW) magnets are attracting significant attention, both as platforms for studying fundamental magnetic interactions and for the exciting possibility of utilizing them as building blocks in devices and heterostructures, which may lead to new physical phenomena and functionalities. Here, we provide a detailed study of the crystal structure and physical properties of the recently discovered vdW ferromagnet FePd 2 Te 2 . We find this compound has a relatively wide width of formation, and grow single crystals with compositions Fe x Pd y Te 2 where x ranges from 0.9 to 1.1 and y from 1.8 to 2.5, respectively. Temperature-dependent X-ray diffraction and transport measurements reveal that a first-order structural transition occurs in the range of T = 360–420 K, where the critical temperature, modulation wave vector, and corresponding room-temperature crystal structures all depend on chemical composition. Above the transition, the compounds with Pd fraction y > 2 adopt a disordered derivative of the tetragonal FeTe structure, with the Fe layer showing mixed Fe/Pd occupancy and the extra Pd atoms partially occupying interstitial sites. Below 370 K, the structure is incommensurately modulated, likely associated with the complex ordering of Pd/Fe atoms in the metal layers or the interstitial Pd in the vdW gaps. For y < 2, the composition Fe 1.1 Pd 1.8 Te 2 has monoclinic symmetry at room temperature that is consistent with the reported structure of FePd 2 Te 2 . This phase undergoes a structural transition at 420 K for which the high temperature structure is yet to be determined; however, based on the similarities with the y > 2 compounds, we speculate that its T > 420 K structure is also tetragonal. Importantly, the high temperature, symmetry-breaking structural transition observed here provides a likely explanation for the origin of the structural domains previously observed in FePd 2 Te 2 . All compounds investigated in the Fe x Pd y Te 2 series show metallic behavior, with magnetic characterization indicating that they are easy-plane, hard, ferromagnets with T C spanning 98–180 K. Both the critical temperature for the structural transition and the Curie temperature are moderately suppressed with increasing Pd fraction y and corresponding decreasing Fe fraction x, indicating that synthetic control over x and y paves way for the further exploration of these compounds.

crystal structure↗
DOE OSTI2020

Structural insights into the mechanism of rhodopsin phosphodiesterase

Crystal structures of TMD of Rhodopsin phosphodiesterase (Rh-PDE). 6160 small-wedge (10°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. Beam size was around 15×10 µm2 and oscillation step was 0.1°. The crystals belonged to space group P212121 with unit cell parameters a~66, b~74, c~117 Å. 864 datasets were indexed and integrated using XDS with KAMO pipeline. Finally 271 integrated results were merged at 2.6 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result.

BL32XU↗