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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Flux-Assisted Boron Chalcogen Mixture (BCM) Method for Synthesizing Mixed Chalcogenide Semiconductors (AkRE 2 Si 2 Se x S 8– x and CaRE 2 Si 2 Se 8 ) ( Ak = Ca and Sr; RE = La, Ce, Pr, Nd, and Sm): Investigation of Their Magnetic and Optical Properties

We report a detailed structural analysis of a series of ten quaternary rare-earth-containing seleno-thiosilicates AkRE 2 Si 2 Se x S 8-x and selenosilicates, CaRE 2 Si 2 Se 8 (Ak = Ca and Sr; RE = La, Ce, Pr, Nd, and Sm). Single crystals were obtained by using the flux-assisted boron chalcogen mixture (BCM) method and single crystal X-ray diffraction was used to determine their structures. All members of the AkRE 2 Si 2 Se x S 8-x and CaRE 2 Si 2 Se 8 series crystallize in the space group R$\bar{3}$c (space group number 167) of the trigonal crystal system. The single-crystal X-ray diffraction analysis revealed a strong preference for Se/S atoms to occupy one vs. the other of the two available sites. Polycrystalline samples were used for magnetic susceptibility and UV–visible diffuse reflectance measurements. Magnetic measurements show that CaCe₂Si₂Se₁.₇₃S₆.₂₇ and CaNd₂Si₂Se₂.₅S₅.₅ are paramagnetic with negative Weiss constants (θ = –60.1 and –26.2). Diffuse reflectance analysis gives optical band gaps of 2.7(1) eV (CaLa₂Si₂Se₂.₃₈S₅.₆₂), 2.2(1) eV (CaCe₂Si₂Se₁.₇₃S₆.₂₇), 2.5(1) eV (CaNd₂Si₂Se₂.₅S₅.₅), and 2.0(1) eV (CaCe₂Si₂Se₈), consistent with density functional theory calculations. By partially or fully replacing S sites with Se it was possible to achieve band gap tuning. Photoluminescence behavior was also investigated for CaCe 2 Si 2 Se 1.73 S 6.27 via irradiation with 375 nm ultraviolet light.

BCM method↗
DOE OSTI2016

First principles prediction of amorphous phases using evolutionary algorithms

We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bond angle are within ∼2% of those reported by ab initio MD calculations and experimental studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c = 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.

peptidyl-tRNA↗
DOE OSTI2012

Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme

Ubiquitin carboxy-terminal hydrolase L5 (UCHL5) is a proteasome-associated deubiquitinating enzyme, which, along with RPN11 and USP14, is known to carry out deubiquitination on proteasome. As a member of the ubiquitin carboxy-terminal hydrolase (UCH) family, UCHL5 is unusual because, unlike UCHL1 and UCHL3, it can process polyubiquitin chain. However, it does so only when it is bound to the proteasome; in its free form, it is capable of releasing only relatively small leaving groups from the C-terminus of ubiquitin. Such a behavior might suggest at least two catalytically distinct forms of the enzyme, an apo form incapable of chain processing activity, and a proteasome-induced activated form capable of cleaving polyubiquitin chain. Through the crystal structure analysis of two truncated constructs representing the catalytic domain (UCH domain) of this enzyme, we were able to visualize a state of this enzyme that we interpret as its inactive form, because the catalytic cysteine appears to be in an unproductive orientation. While this work was in progress, the structure of a different construct representing the UCH domain was reported; however, in that work the structure reported was that of an inactive mutant [catalytic Cys to Ala; Nishio K et al. (2009) Biochem Biophys Res Commun390, 855-860], which precluded the observation that we are reporting here. Additionally, our structures reveal conformationally dynamic parts of the enzyme that may play a role in the structural transition to the more active form.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A model of lipid-free Apolipoprotein A-I revealed by iterative molecular dynamics simulation

Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state of apo A-I is the initial stage which binds to lipids forming high-density lipoprotein. Molecular models of lipid-free apo A-I have been reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current models had limited consistency with other experimental results, such as those from hydrogen exchange with mass spectrometry. Through molecular dynamics simulations, we also found those models could not reach a stable equilibrium state. Therefore, by integrating various experimental results, we proposed a new structural model for lipidfree apo A-I, which contains a bundled four-helix N-terminal domain (1–192) that forms a variable hydrophobic groove and a mobile short hairpin C-terminal domain (193–243). This model exhibits an equilibrium state through molecular dynamics simulation and is consistent with most of the experimental results known from CCL/MS on lysine pairs, fluorescence resonance energy transfer and hydrogen exchange. This solution-state lipid-free apo A-I model may elucidate the possible conformational transitions of apo A-I binding with lipids in high-density lipoprotein formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Energy Expenditure Upon the Formation of the Elastically Stressed State in the Layers of a Step-Graded Metamorphic Buffer in a Heterostructure Grown on a (001) GaAs Substrate

On the basis of data on X-ray structural analysis performed by the method of reciprocal-space mapping and investigations using secondary-ion mass spectrometry and transmission electron microscopy, it is shown that vertical compressive stresses also arise in a multilayer epitaxial heterostructure comprised of a step-graded metamorphic buffer along with lateral compressive stresses. The cause of the appearance of vertical stresses is the effect of interlayer hardening, which arises due to the deceleration of fragments of glide dislocations by interphase boundaries. Analysis performed within the framework of the linear theory of elasticity shows that the elastically stressed state of the buffer steps is similar to the state that can be achieved as a result of a two-stage deformation process: bulk and biaxial compression. Bulk compression leads to large energy expenditures in the formation of the structure of the buffer steps, which is reflected, in particular, in violation of the coherence between the dislocation-free and the underlying layers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Pro5 is not essential for the formation of ‘Ni-hook’ in nickel superoxide dismutase

The N-terminus of nickel-dependent superoxide dismutase (NiSOD) forms a structural motif known as the "Ni-hook," where the peptide wraps around the metal to bring cysteine-2 and cysteine-6 into spatial proximity, allowing these residues to coordinate in a cis-geometry. A highly conserved proline-5 residue in the Ni-hook adopts a cis-conformation that is widely considered important for its formation. Herein, we investigate this role by point mutation of Pro5 to alanine. The results obtained show that the variant exhibits wild-type-like redox catalysis and features a Ni(III) center very similar to that found in enzyme. Structural analysis using x-ray absorption spectroscopy of the nickel sites in as-isolated P5A-NiSOD reveals changes in the variant and are consistent with a six-coordinate Ni site with (N/O) 4 S 2 coordination. These changes are attributed to changes in the Ni(II) site structure. Nickel-binding studies using isothermal titration calorimetry reveal two binding events with K d = 25(20) nM, and 250(60) nM. These events are attributed to i) Ni(II) binding to a preformed Ni-hook containing cis-Pro5 and ii) the combination of trans- to cis- isomerization upon Ni(II) binding, respectively. Finally, the higher-affinity binding event is absent in P5A-NiSOD, an observation attributed to the low abundance of the cis-Ala5 isomer in the apo-protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations

Structure and properties of Cu-doped diamond-like carbon films (DLC) were investigated using ab initio calculations. The effect of Cu concentrations (1.56∼7.81 at.%) on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) encode multifunctional papain-like proteases (PLPs) that have the ability to process the viral polyprotein to facilitate RNA replication and antagonize the host innate immune response. The latter function involves reversing the post-translational modification of cellular proteins conjugated with either ubiquitin (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). Ub is known to be highly conserved among eukaryotes, but surprisingly, ISG15 is highly divergent among animals. The ramifications of this sequence divergence to the recognition of ISG15 by coronavirus PLPs at a structural and biochemical level are poorly understood. Therefore, the activity of PLPs from SARS-CoV, MERS–CoV, and mouse hepatitis virus was evaluated against seven ISG15s originating from an assortment of animal species susceptible, and not, to certain coronavirus infections. Excitingly, our kinetic, thermodynamic, and structural analysis revealed an array of different preferences among PLPs. Included in these studies is the first insight into a coronavirus PLP’s interface with ISG15 via SARS-CoV PLpro in complex with the principle binding domain of human ISG15 (hISG15) and mouse ISG15s (mISG15s). Here, the first X-ray structure of the full-length mISG15 protein is also reported and highlights a unique, twisted hinge region of ISG15 that is not conserved in hISG15, suggesting a potential role in differential recognition. Taken together, this new information provides a structural and biochemical understanding of the distinct specificities among coronavirus PLPs observed and addresses a critical gap of how PLPs can interact with ISG15s from a wide variety of species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Role of Dimer Formation in the Nucleation of Superlattice Transformations and Its Impact on Disorder

The formation of defect-free two-dimensional nanocrystal (NC) superstructures remains a challenge as persistent defects hinder charge delocalization and related device performance. Understanding defect formation is an important step toward developing strategies to mitigate their formation. However, specific mechanisms of defect formation are difficult to determine, as superlattice phase transformations that occur during fabrication are quite complex and there are a variety of factors influencing the disorder in the final structure. Here, we use Molecular Dynamics (MD) and electron microscopy in concert to investigate the nucleation of the epitaxial attachment of lead chalcogenide (PbX, where X = S, Se) NC assemblies. We use an updated implementation of an existing reactive force field in an MD framework to investigate how initial orientational (mis)alignment of the constituent building blocks impacts the final structure of the epitaxially connected superlattice. This Simple Molecular Reactive Force Field (SMRFF) captures both short-range covalent forces and long-range electrostatic forces and allows us to follow orientational and translational changes of NCs during superlattice transformation. Our simulations reveal how robust the oriented attachment is with regard to the initial configuration of the NCs, measuring its sensitivity to both in-plane and out-of-plane misorientation. We show that oriented attachment nucleates through the initial formation of dimers, which corroborate experimentally observed structures. We present high-resolution structural analysis of dimers at early stages of the superlattice transformation and rationalize their contribution to the formation of defects in the final superlattice. Collectively, the simulations and experiments presented in this paper provide insights into the nucleation of NC oriented attachment, the impact of the initial configuration of NCs on the structural fidelity of the final epitaxially connected superlattice, and the propensity to form commonly observed defects, such as missing bridges and atomic misalignment in the superlattice due to the formation of dimers. Here, we present potential strategies to mitigate the formation of superlattice defects.

36 MATERIALS SCIENCE↗
DOE OSTI2022

X-ray absorption spectroscopy insights on the structure anisotropy and charge transfer in Chevrel Phase chalcogenides

Here, the electronic structure and local coordination of binary (Mo 6 T 8 ) and ternary Chevrel Phases (M x Mo 6 T 8 ) are investigated for a range of metal intercalant and chalcogen compositions. We evaluate differences in the Mo L 3 -edge and K-edge X-ray absorption near edge structure across the suite of chalcogenides M x Mo 6 T 8 (M = Cu, Ni, x = 1–2, T = S, Se, Te), quantifying the effect of compositional and structural modification on electronic structure. Furthermore, we highlight the expansion, contraction, and anisotropy of Mo 6 clusters within these Chevrel Phase frameworks through extended X-ray absorption fine structure analysis. Our results show that metal-to-cluster charge transfer upon intercalation is dominated by the chalcogen acceptors, evidenced by significant changes in their respective X-ray absorption spectra in comparison to relatively unaffected Mo cations. These results explain the effects of metal intercalation on the electronic and local structure of Chevrel Phases across various chalcogen compositions, and aid in rationalizing electron distribution within the structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Local structure studies of Fe{sub 2}TeO{sub 6} using x-ray absorption spectroscopy

In the present study, we have performed EXAFS measurements on powder samples of Fe{sub 2}TeO{sub 6} (FTO) to probe the local structure surrounding at the Fe site. The structural parameters (atomic coordination and lattice parameters) of FTO used for simulation of theoretical EXAFS spectra of the samples have been obtained from Rietveld refined structure on synchrotron X-ray Diffraction (SXRD) data. Quite similar and satisfactory structural parameters have been obtained from both the study, indicating goodness of synchrotron structural analysis over EXAFS analysis. SXRD and EXAFS results shows absence of any secondary phase proves current synthesis superior over reported techniques.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2011

Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase

In all organisms, aminoacyl tRNA synthetases covalently attach amino acids to their cognate tRNAs. Many eukaryotic tRNA synthetases have acquired appended domains, whose origin, structure and function are poorly understood. The N-terminal appended domain (NTD) of glutaminyl-tRNA synthetase (GlnRS) is intriguing since GlnRS is primarily a eukaryotic enzyme, whereas in other kingdoms Gln-tRNA Gln is primarily synthesized by first forming Glu-tRNA Gln , followed by conversion to Gln-tRNA Gln by a tRNA-dependent amidotransferase. We report a functional and structural analysis of the NTD of Saccharomyces cerevisiae GlnRS, Gln4. Yeast mutants lacking the NTD exhibit growth defects, and Gln4 lacking the NTD has reduced complementarity for tRNA Gln and glutamine. The 187-amino acid Gln4 NTD, crystallized and solved at 2.3 Å resolution, consists of two subdomains, each exhibiting an extraordinary structural resemblance to adjacent tRNA specificity determining domains in the GatB subunit of the GatCAB amidotransferase, which forms Gln-tRNA Gln . These subdomains are connected by an apparent hinge comprised of conserved residues. Mutation of these amino acids produces Gln4 variants with reduced affinity for tRNA Gln , consistent with a hinge-closing mechanism proposed for GatB recognition of tRNA. Our results suggest a possible origin and function of the NTD that would link the phylogenetically diverse mechanisms of Gln-tRNA Gln synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanism-Guided Kinetic Analysis of Electrocatalytic Proton Reduction Mediated by a Cobalt Catalyst Bearing a Pendant Basic Site

Cobalt polypyridyl complexes stand out as efficient catalysts for electrochemical proton reduction, but investigations into their operating mechanisms, with broad-reaching implications in catalyst design, have been limited. Herein, we investigate the catalytic activity of a cobalt(II) polypyridyl complex bearing a pendant pyridyl base with a series of organic acids spanning 20 pKa units in acetonitrile. Structural analysis, as well as electrochemical studies, reveals that the Co(III) hydride intermediate is formed through reduction of the Co(II) catalyst followed by direct metal protonation in the initial EC step despite the presence of the pendant base, which is commonly thought of as a more kinetically accessible protonation site. Protonation of the pendant base occurs after the Co(III) hydride intermediate is further reduced in the overall ECEC pathway. Additionally, when the acid used is sufficiently strong, the Co(II) catalyst can be protonated, and the Co(III) hydride can react directly with acid to release H 2 . With thorough mechanistic understanding, the appropriate electroanalytical methods were identified to extract rate constants for the elementary steps over a range of conditions. Thermodynamic square schemes relating catalytic intermediates proposed in the three electrocatalytic HER mechanisms were constructed. Furthermore, these findings reveal a full description of the HER electrocatalysis mediated by this molecular system and provide insights into strategies to improve synthetic fuel-forming catalysts operative through metal hydride intermediates.

08 HYDROGEN↗
DOE OSTI2026

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗
DOE OSTI2013

Syntheses, structures and photoelectric properties of a series of Cd(II)/Zn(II) coordination polymers and coordination supramolecules

Five Cd(II)/Zn(II) complexes [Cd(1,2-bdc)(pz){sub 2}(H{sub 2}O)]{sub n} (1), [Cd1Cd2(btec)(H{sub 2}O){sub 6}]{sub n} (2), [Cd(3,4-pdc) (H{sub 2}O)]{sub n} (3), [Zn(2,5-pdc)(H{sub 2}O){sub 4}]{center_dot}2H{sub 2}O (4) and {l_brace} [Zn(2,5-pdc)(H{sub 2}O){sub 2}]{center_dot}H{sub 2}O{r_brace} {sub n} (5) (H{sub 2}bdc=1,2-benzenedicarboxylic acid, pz=pyrazole, H{sub 4}btec=1,2,4,5-benzenetetracarboxylic acid, H{sub 2}pdc=pyridine-dicarboxylic acid) were hydrothermally synthesized and characterized by single-crystal X-ray diffraction, surface photovoltage spectroscopy, XRD, TG analysis, IR and UV-vis spectra and elemental analysis. Structural analyses show that complexes 1-3 are 1D, 2D and 3D Cd(II) coordination polymers, respectively. Complex 4 is a mononuclear Zn(II) complex. Complex 5 is a 3D Zn(II) coordination polymer. The surface photoelectric properties of complexes were investigated by SPS. The results indicate that all complexes exhibit photoelectric responses in the range of 300-600 nm, which reveals that they all possess certain photoelectric conversion properties. By the comparative analyses, it can be found that the species and coordination micro-environment of central metal ion, the species and property of ligands affect the intensity and scope of photoelectric response. - Graphical abstract: Five Cd(II)/Zn(II) complexes have been hydrothermally synthesized and characterized. The photoelectric properties were studied with SPS. The species and coordination micro-environment of central metal ion, the species and property of ligands all affect the photoelectric responses. Highlights: Black-Right-Pointing-Pointer Five Cd/Zn complexes have been synthesized and characterized. Black-Right-Pointing-Pointer The SPS results indicate they possess obvious photoelectric conversion property. Black-Right-Pointing-Pointer The species and coordination environment of central metal ion affect SPS. Black-Right-Pointing-Pointer The species and property of ligands affect SPS. Black-Right-Pointing-Pointer By the energy-band theory and the crystal filed theory, the SPS are analyzed and assigned.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Radiation effects on stress evolution and dimensional stability of large fusion energy structures

Here we assess the effects of neutron irradiation on the deformation and stress evolution of large-scale fusion energy structures. This is accomplished through non-linear finite element structural analysis of the coupled thermal and mechanical fields at the Beginning-Of-Life (BOL), at 45 dpa, and at 90 dpa. Radiation effects include volumetric swelling and the influence of radiation on the mechanical properties. The system studied here is a large section of a full inboard module of an integrated structure comprising the First Wall and Blanket (FW/B) of a Dual Cooled Lithium-Lead (DCLL) energy conversion unit in the Fusion Nuclear Science Facility (FNSF). The structural material is the ferritic/martensitic steel F82H. We analyze several radiation effects phenomena that can lead to significant impact on the mechanical design and lifetime of the structure. These include volumetric swelling effects on the assembly and disassembly of modules and the impact of spatial gradients in neutron damage and helium generation on deformation, stress evolution, and plastic strain accumulation. We show that the stress state is strongly influenced by the accumulation of swelling strains, radiation hardening and softening, and by spatial gradients in displacement damage and helium gas generation. Several key regions in the FW/B structure are identified where severe plastic strains accumulate and may be potential sites for failure, especially during cyclic reactor operations. We finally show that minimum gaps between Inboard (IB) blanket sectors must be present during assembly so as to avoid excessive stress and strain in FW/B modules critical regions and raising chances of failure. A range of structural displacements are shown, from as low as 4 mm at BOL for free side walls to as high as 46 mm at 90 dpa for fully constrained side walls.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗