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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 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Structural and magnetic characterization of the one-dimensional S = 5/2 antiferromagnetic chain system SrMn(VO 4 )(OH)

The descloizite-type compound, SrMn(VO 4 )(OH), was synthesized as large single crystals (1-2mm) using a high-temperature high-pressure hydrothermal technique. X-ray single crystal structure analysis reveals that the material crystallizes in the acentric orthorhombic space group of P2 1 2 1 2 1 (no. 19), Z = 4. The structure exhibits a one-dimensional feature, with [MnO 4 ] chains propagating along the a-axis which are interconnected by VO 4 tetrahedra. Raman and infrared spectra were obtained to identify the fundamental vanadate and hydroxide vibrational modes. Magnetization data reveal a broad maximum at approximately 80 K, arising from one-dimensional magnetic correlations with intrachain exchange constant of J/k B = 9.97(3) K between nearest Mn neighbors and a canted antiferromagnetic behavior below T N = 30 K. Single crystal neutron diffraction at 4 K yielded a magnetic structure solution in the lower symmetry of the magnetic space group P2 1 with two unique chains displaying antiferromagnetically ordered Mn moments oriented nearly perpendicular to the chain axis. Lastly, the presence of the Dzyaloshinskii Moriya antisymmetric exchange interaction leads to a slight canting of the spins and gives rise to a weak ferromagnetic component along the chain direction.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Spinodal Decomposition of Ga{sub x}In{sub 1-x}As{sub y}P{sub 1-y}Quaternary Alloys

Using X-ray structural analysis, scanning electron microscopy, atomic force microscopy, and photoluminescent spectroscopy, it is shown that it is possible to obtain a small-scale domain structure on the surface of liquid-phase epitaxial heterostructures. The domain structure emerges as a result of spinodal decomposition of the Ga{sub x}In{sub 1-x}As{sub y}P{sub 1-y} quaternary alloy due to immiscibility of its components and relaxation of its lattice parameter to surrounding layers.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Formation of nickel magnetic nanoparticles and modification of nickel phthalocyanine matrix by sodium doping

Data for the vapor-phase doping (300°C) of nickel phthalocyanine (NiPc) by sodium taken in different concentrations (x), as well as structural analysis data for Na{sub x=0.2}NiPc, Na{sub x=1}NiPc, and Na{sub x=3}NiPc samples, have been reported. The structure of the samples and their atomic configuration versus the doping level have been studied by transmission electron microscopy, Raman scattering, X-ray diffraction, X-ray absorption spectroscopy, and extended X-ray absorption fine structure (EXAFS) spectroscopy. The structural parameters of Ni–N, Ni–C, and Ni–Ni bonds have been determined, and it has been found that, at a low level of doping by sodium, local structural distortions are observed in some molecules of the NiPc matrix near nickel atoms. The fraction of these molecules grows as the doping level rises from x = 0.2 to x = 1.0. It has been shown that doping changes the oscillation mode of light atoms, which indicates a rise in the electron concentration on five- and six-membered rings. At a high level of sodium doping (x = 3.0), nickel nanoparticles with a mean size of 20 nm and molecule decomposition products have been observed in the NiPc matrix. It has been found that the fraction of nickel atoms in the Na{sub x=3}NiPc nanoparticles as estimated from EXAFS data is sufficient for the room-temperature magnetic properties of the samples to persist for a long time.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2013

Laterally self-ordered silicon-germanium islands with optimized confinement properties

We present an analysis of the electronic confinement properties of self-assembled islands forming via silicon and germanium co-deposition in molecular beam epitaxy. This approach allows the fabrication of laterally self-ordered three dimensional islands in the Stranski-Krastanow growth mode. Using a systematic structural analysis, we derive a realistic fit-parameter free island model for band structure simulations. A comparison between these band structure simulations and photoluminescence spectroscopy shows that such islands have a significant three dimensional spatial electron-hole wave function overlap. In addition, we show that this spatial wave function overlap overcompensates a weak wave function spreading in k-space.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Phenol-soluble modulins PSMα3 and PSMβ2 form nanotubes that are cross-α amyloids

The formation of cross-α amyloids has been shown by crystallographic analysis of the highly cytolytic peptide PSMα3, a secreted virulence factor associated with the human pathogen Staphylococcus aureus . However, the relationship of the crystallographic cross-α structure to self-assembled filaments of PSMα3 and its relevance to other phenol-soluble modulin (PSM) peptides remained an open question. We report the cryo–electron microscopy structural analysis of three nanotubes derived from self-assembly of PSMα3 and PSMβ2 peptides in aqueous solution. In each case, the nanotubes are derived from self-association of cross-α amyloid protofilaments. The self-assembly behavior of S. aureus PSMα3 and PSMβ2 peptides provides strong evidence for the importance of the cross-α fold in self-assembled peptide and protein structures in general and for PSMs in particular.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity

Synonymous variants within coding regions may influence protein expression and function. We have previously reported increased protein expression levels ex vivo (~120% in comparison to wild-type) from a synonymous polymorphism variant, c.354G>A [p.P118P], of the ADAMTS13 gene, encoding a plasma protease responsible for von Willebrand Factor (VWF) degradation. In the current study, we investigated the potential mechanism(s) behind the increased protein expression levels from this variant and its effect on ADAMTS13 physico-chemical properties. Cell-free assays showed enhanced translation of the c.354G>A variant and the analysis of codon usage characteristics suggested that introduction of the frequently used codon/codon pair(s) may have been potentially responsible for this effect. Limited proteolysis, however, showed no substantial influence of altered translation on protein conformation. Analysis of post-translational modifications also showed no notable differences but identified three previously unreported glycosylation markers. Despite these similarities, p.P118P variant unexpectedly showed higher specific activity. Structural analysis using modeled interactions indicated that subtle conformational changes arising from altered translation kinetics could affect interactions between an exosite of ADAMTS13 and VWF resulting in altered specific activity. This report highlights how a single synonymous nucleotide variation can impact cellular expression and specific activity in the absence of measurable impact on protein structure.

Hunt, Ryan↗
DOE OSTI2018

Atomic Scale Account of the Surface Effect on Ionic Transport in Silver Hollandite

Here, nanosized electrodes for Li-ion batteries typically display improved electrochemical properties, which are generally attributed to the reduced dimensionality for lithiation. However, the intriguing roles of surface defects and disorder associated with the nanosized materials are often overlooked. Here, combining atomically resolved structural analysis with density functional theory calculations, we reveal that the formation of intrinsic oxygen vacancies near surface in silver hollandite nanorods modifies the local atomic structure and valence state. These surface reconstructions resulted from oxygen vacancies can significantly affect the diffusion pathways in what are otherwise one-dimensional (1D) tunneled structures. On the basis of energy barrier calculations, we demonstrate that the oxygen vacancies boost ionic transport through the edge sharing MnO 6 polyhedra in the a–b plane. Thus, within a single rod different from the inherent 1D tunnel diffusion in the interior, the ionic transport at oxygen vacancy decorated surfaces likely adopts a three-dimensional diffusion pathway including both tunnel and planar diffusion.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure–activity relationship (SAR) study of noncovalent compounds that bind in the enzyme’s substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor’s P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues

We report the structural analysis of highly drug-resistant human immunodeficiency virus protease (PR) variant PR S17 , rationally selected by machine learning, in complex with substrate analogues. Crystal structures were solved of inhibitor-free inactive PR S17 -D25N, wild-type PR/CA-p2 complex, and PR S17 in complex with substrate analogues, CA-p2 and p2-NC. Peptide analogues p2-NC and CA-p2 exhibit inhibition constants of 514 and 22 nM, respectively, for PR S17 or approximately 3-fold better than for PR. CA-p2 is a better inhibitor of PR S17 than are clinical inhibitors ( K i = 50–8390 nM) except for amprenavir ( K i = 11 nM). G48V resistance mutation induces curled flap tips in PR S17 -D25N structure. The inner P2–P2' residues of substrate analogues in PR S17 complexes maintain similar conformations to those of wild-type complex, while significant conformational changes are observed in the peripheral residues P3, P4' of CA-p2 and P3, P4, and P3' of p2-NC. The loss of β-branched side chain by V82S mutation initiates a shift in 80’s loop and reshapes the S3/S3' subsite, which enhances substrate binding with new hydrogen bonds and van der Waals interactions that are absent in the wild-type structures. The steric hindrance caused by G48V mutation in the flap of PR S17 contributes to altered binding interactions of P3 Arg, P4' norleucine of CA-p2, and P4 and P3' of p2-NC with the addition of new hydrogen bonds and van der Waals contacts. The enhanced interaction of PR S17 with substrate analogues agrees with their relative inhibition, suggesting that this mutant improves substrate binding while decreasing affinity for clinical inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Luminescence and Stimulated Emission of Polycrystalline Cu(In,Ga)Se{sub 2} Films Deposited by Magnetron-Assisted Sputtering

The stimulated emission of Cu(In,Ga)Se{sub 2} alloy thin films formed by magnetron-assisted sputtering onto a sodium-fluoride layer deposited onto a molybdenum layer on a glass substrate is observed. The structural and optical parameters of the films are determined by scanning electron microscopy, local X-ray spectral microanalysis, X-ray structural analysis, and low-temperature luminescence (T = 10 K) measurements in the range of excitation levels of 1.6–75 kW cm{sup –2} provided by nanosecond nitrogen-laser pulses. The stimulated emission threshold corresponds to ~25 kW cm{sup –2}. Comparative analysis of the emission of Cu(In,Ga)Se{sub 2} thin films suggests that the introduction of sodium results in significant improvement of the structural quality, specifically, in a decrease in the density of energy states in the band tails and in a decrease in the concentration of nonradiative-recombination centers.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics

We report structural analysis of HIV protease variant PR S17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PR S17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PR S17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PR S17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PR S17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PR S17 D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PR S17 , the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PR S17 /DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PR S17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PR S17 . PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Engineering a Cu‐Pd Paddle‐Wheel Metal–Organic Framework for Selective CO 2 Electroreduction

Optimizing the binding energy between the intermediate and the active site is a key factor for tuning catalytic product selectivity and activity in the electrochemical carbon dioxide reduction reaction. Copper active sites are known to reduce CO 2 to hydrocarbons and oxygenates, but suffer from poor product selectivity due to the moderate binding energies of several of the reaction intermediates. Here, we report an ion exchange strategy to construct Cu−Pd paddle wheel dimers within Cu-based metal–organic frameworks (MOFs), [Cu 3-x Pd x (BTC) 2 ] (BTC=benzentricarboxylate), without altering the overall MOF structural properties. Compared to the pristine Cu MOF ([Cu 3 (BTC) 2 ], HKUST-1), the Cu−Pd MOF shifts CO 2 electroreduction products from diverse chemical species to selective CO generation. In situ X-ray absorption fine structure analysis of the catalyst oxidation state and local geometry, combined with theoretical calculations, reveal that the incorporation of Pd within the Cu−Pd paddle wheel node structure of the MOF promotes adsorption of the key intermediate COOH* at the Cu site. This permits CO-selective catalytic mechanisms and thus advances our understanding of the interplay between structure and activity toward electrochemical CO 2 reduction using molecular catalysts.

CO2 electroreduction reaction↗
DOE OSTI2018

Structural and functional characterization of a missense mutant of human γS-crystallin associated with dominant infantile cataracts

Highlights: • We present structural analysis of γS-Y67N, a cataract-active mutant of human γS-crystallin. • Mutation alters the energetics and kinetics of γS-Y67N underlying structural changes. • Aggregation is enhanced and Ca{sup 2+} binding is compromised as a result of mutation. • We explore the structure-function relationship in human γS-crystallin in health and disease. Infantile cataracts constitute one of the most important causes of childhood blindness worldwide. Human γS-crystallin is the most abundant protein in the eye lens cortex. A missense mutant of human γS-crystallin, Y67N (abbreviated hereafter as γS-Y67N) is recently reported to be associated with dominant infantile cataracts. To understand the structural basis for γS-Y67N to cause lens opacification, we constructed, expressed and purified γS-Y67N and its wild-type (abbreviated hereafter as γS-WT) and studied the structural and functional differences between them in solution using circular dichroism (CD), differential scanning calorimetry (DSC), fluorescence spectroscopy and extrinsic spectral probes. Extensive equilibrium characterization indicate that replacement of the highly conserved Tyr at 67th position by Asn distorts the conserved Tyr corner at the second Greek key motif in the N-terminal domain (NTD) and leads to substantial loss of structural stability. Our intrinsic fluorescence quenching results reveal differential in-vitro refolding kinetics identifying partially folded kinetic intermediates for both proteins. Extrinsic fluorescence studies further reveal loosening up of the compact structure of γS-crystallin upon mutation associated with enhanced aggregation. As Ca{sup 2+} homeostasis is a crucial regulator of lens transparency, we further investigated the Ca{sup 2+}-binding properties of γS-WT and γS-Y67N by isothermal titration calorimetry (ITC) to identify lens Ca{sup 2+} distribution in health and in disease. Overall, our results highlight the vital role of conserved Tyr corners in stabilizing Greek key motifs and provide useful structural and functional insights into the mechanism of cataract formation in humans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structural and mechanistic basis for protein glutamylation by the kinase fold

The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here, in this work, we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.

59 BASIC BIOLOGICAL SCIENCES↗