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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

New Class of 3D Topological Insulator in Double Perovskite

In this work, we predict a new class of 3D topological insulators (TIs) in which the spin–orbit coupling (SOC) can more effectively generate band gap. Band gap of conventional TI is mainly limited by two factors, the strength of SOC and, from electronic structure perspective, the band gap when SOC is absent. While the former is an atomic property, the latter can be minimized in a generic rock-salt lattice model in which a stable crossing of bands at the Fermi level along with band character inversion occurs in the absence of SOC. Thus large-gap TIs or TIs composed of lighter elements can be expected. In fact, we find by performing first-principles calculations that the model applies to a class of double perovskites A 2 BiXO 6 (A = Ca, Sr, Ba; X = Br, I) and the band gap is predicted up to 0.55 eV. Besides, surface Dirac cones are robust against the presence of dangling bond at boundary.

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

Partitioning of Seven Different Classes of Antibiotics into LPS Monolayers Supports Three Different Permeation Mechanisms through the Outer Bacterial Membrane

The outer membrane (OM) of Gram-negative (G-) bacteria presents a barrier for x classes of antibacterial agents. Lipopolysaccharide (LPS), present in the outer leaflet of the OM, is stabilized by divalent cations and is considered to be the major impediment for antibacterial agent permeation. However, the actual affinities of major antibiotic classes toward LPS have not yet been determined. In the present work, we use Langmuir monolayers formed from E. coli Re and Rd types of LPS to record pressure-area isotherms in the presence of antimicrobial agents. Our observations suggest three general types of interactions. Firstly, some antimicrobials demonstrated no measurable interactions with LPS. This lack of interaction in the case of cefsulodin, a third-generation cephalosporin antibiotic, correlates with its low efficacy against G- bacteria. Ampicillin and ciprofloxacin also show no interactions with LPS, but in contrast to cefsulodin, both exhibit good efficacy against G- bacteria, indicating permeation through common porins. Secondly, we observe substantial intercalation of the more hydrophobic antibiotics novobiocin, rifampicin, azithromycin, and telithromycin into relaxed LPS monolayers. These largely re-partition back to the subphase with monolayer compression. We find that the hydrophobic area, charge, and dipole all show correlations with both the mole fraction of antibiotic retained in the monolayer at the monolayer-bilayer equivalence pressure and the efficacies of these antibiotics against G- bacteria. Thirdly, amine-rich gentamicin and the cationic antimicrobial peptides polymyxin B and colistin show no hydrophobic insertion but are instead strongly driven into the polar LPS layer by electrostatic interactions in a pressure-independent manner. Their intercalation stably increases the area per molecule (by up to 20%), which indicates massive formation of defects in the LPS layer. These defects support a self-promoted permeation mechanism of these antibiotics through the OM, which explains the high efficacy and specificity of these antimicrobials against G- bacteria.

lateral pressure↗
DOE OSTI2016

Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata

Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases in which a catalytic distal aspartate is involved in H 2 O 2 activation to catalyze oxidations under acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds. On the basis of the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of the surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the cross-linking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal, possibly due to its extremely small solvent-accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding the DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter -Derived Cephalosporinase-7, a Unique Class C β-Lactamase

Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. K i values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase–inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest K i (0.45 nM) and greatest ΔT m (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. Here, the ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase

Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn{sub 2}{sup III}-Y{sm_bullet}, in their homodimeric NrdF ({beta}2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn{sub 2}{sup II} form of NrdF is an important component in understanding O{sub 2}-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is that of Escherichia coli Mn{sub 2}{sup II}-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 {angstrom} resolution crystal structure of Bacillus subtilis Mn{sub 2}{sup II}-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the {beta}2 dimer are distinct from those observed in E. coli Mn{sub 2}{sup II}-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn{sub 2}{sup II} cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn{sub 2}{sup III}-Y{sm_bullet} cofactor assembly in class Ib RNRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii

The carbapenem-hydrolyzing class D β-lactamases OXA-23 and OXA-24/40 have emerged world-wide as causative agents for β-lactam antibiotic resistance in Acinetobacter species. Many variants of these enzymes have appeared clinically, including OXA-160 and OXA-225, which both contain a P→S substitution at homologous positions in the OXA-24/40 and OXA-23 backgrounds respectively. We purified OXA-160 and OXA-225 and used steady-state kinetic analysis to compare the substrate profiles of these variants to their parental enzymes, OXA-24/40 and OXA-23. OXA-160 and OXA-225 possess greatly enhanced hydrolytic activities against aztreonam, ceftazidime, cefotaxime and ceftriaxone when compared to OXA-24/40 and OXA-23. These enhanced activities are the result of much lower Km values, suggesting that the P→S substitution enhances the binding affinity of these drugs. We have determined the structures of the acylated forms of OXA-160 (with ceftazidime and aztreonam) and OXA-225 (ceftazidime). These structures show that the R1 oxyimino side-chain of these drugs occupies a space near the β5-β6 loop and the omega loop of the enzymes. The P→S substitution found in OXA-160 and OXA-225 results in a deviation of the β5-β6 loop, relieving the steric clash with the R1 side-chain carboxypropyl group of aztreonam and ceftazidime. We found that these results reveal worrying trends in the enhancement of substrate spectrum of class D β-lactamases, but may also provide a map for β-lactam improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Speciation of Selenium, Arsenic, and Zinc in Class C Fly Ash

A major environmental concern associated with coal fly ash is the mobilization of trace elements that may contaminate water. To better evaluate proper use of fly ash, determine appropriate disposal methods, and monitor postdisposal conditions, it is important to understand the speciation of trace elements in fly ash and their possible environmental impact. The speciation of selenium, arsenic, and zinc was determined in five representative Class C fly ash samples from combustion of sub-bituminous Powder River Basin coal using synchrotron-based X-ray absorption spectroscopy to provide an improved understanding of the mechanisms of trace element association with the fly ash. Selenium in all fly ash samples occurs predominantly as Se(IV), with the exception of one sample, in which there was a minor amount of Se(0). Se(0) is likely associated with the high content of unburned coal in the sample. Arsenic exists in the fly ash as a single phase most consistent with calcium pyroarsenate. In contrast, zinc occurs as two distinct species in the silicate glass matrix of the fly ash. This work demonstrates that residual carbon in fly ash may reduce potential Se mobility in the environment by retaining it as less soluble elemental Se instead of Se(IV). Further, this work suggests that As and Zn in Class C fly ash will display substantially different release and mobilization behaviors in aquatic environments. While As release will primarily depend upon the dissolution and hydrolysis of calcium pyroarsenate, Zn release will be controlled by the dissolution of alkaline aluminosilicate glass in the ash.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2020

A New Class of Ionically Conducting Fluorinated Ether Electrolytes with High Electrochemical Stability

Increasing battery energy density is greatly desired for applications such as portable electronics and transportation. However, many next-generation batteries are limited by electrolyte selection because high ionic conductivity and poor electrochemical stability are typically observed in most electrolytes. For example, ether-based electrolytes have high ionic conductivity but are oxidatively unstable above 4 V, which prevents the use of high-voltage cathodes that promise higher energy densities. In contrast, hydrofluoroethers (HFEs) have high oxidative stability but do not dissolve lithium salt. Here, we synthesize a new class of fluorinated ether electrolytes that combine the oxidative stability of HFEs with the ionic conductivity of ethers in a single compound. We show that conductivities of up to 2.7 × 10 –4 S/cm (at 30 °C) can be obtained with oxidative stability up to 5.6 V. The compounds also show higher lithium transference numbers compared to typical ethers. Furthermore, we use nuclear magnetic resonance (NMR) and molecular dynamics (MD) to study their ionic transport behavior and ion solvation environment, respectively. Finally, we demonstrate that this new class of electrolytes can be used with a Ni-rich layered cathode (NMC 811) to obtain over 100 cycles at a C/5 rate. The design of new molecules with high ionic conductivity and high electrochemical stability is a novel approach for the rational design of next-generation batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Structure-Based Design of a Novel Series of Potent, Selective Inhibitors of the Class I Phosphatidylinositol 3-Kinases

A highly selective series of inhibitors of the class I phosphatidylinositol 3-kinases (PI3Ks) has been designed and synthesized. Starting from the dual PI3K/mTOR inhibitor 5, a structure-based approach was used to improve potency and selectivity, resulting in the identification of 54 as a potent inhibitor of the class I PI3Ks with excellent selectivity over mTOR, related phosphatidylinositol kinases, and a broad panel of protein kinases. Compound 54 demonstrated a robust PD-PK relationship inhibiting the PI3K/Akt pathway in vivo in a mouse model, and it potently inhibited tumor growth in a U-87 MG xenograft model with an activated PI3K/Akt pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Characterization of Two Distinct Structural Classes of Selective Aldehyde Dehydrogenase 1A1 Inhibitors

Aldehyde dehydrogenases (ALDH) catalyze the irreversible oxidation of aldehydes to their corresponding carboxylic acid. Alterations in ALDH1A1 activity are associated with such diverse diseases as cancer, Parkinson’s disease, obesity, and cataracts. Inhibitors of ALDH1A1 could aid in illuminating the role of this enzyme in disease processes. However, there are no commercially available selective inhibitors for ALDH1A1. Here we characterize two distinct chemical classes of inhibitors that are selective for human ALDH1A1 compared to eight other ALDH isoenzymes. The prototypical members of each structural class, CM026 and CM037, exhibit sub-micromolar inhibition constants, but have different mechanisms of inhibition. The crystal structures of these compounds bound to ALDH1A1 demonstrate that they bind within the aldehyde binding pocket of ALDH1A1 and exploit the presence of a unique Glycine residue to achieve their selectivity. Lastly, these two novel and selective ALDH1A1 inhibitors may serve as chemical tools to better understand the contributions of ALDH1A1 to normal biology and to disease states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structural signatures in EPR3 define a unique class of plant carbohydrate receptors

Abstract Receptor-mediated perception of surface-exposed carbohydrates like lipo- and exo-polysaccharides (EPS) is important for non-self recognition and responses to microbial associated molecular patterns in mammals and plants. In legumes, EPS are monitored and can either block or promote symbiosis with rhizobia depending on their molecular composition. To establish a deeper understanding of receptors involved in EPS recognition, we determined the structure of the Lotus japonicus ( Lotus ) exopolysaccharide receptor 3 (EPR3) ectodomain. EPR3 forms a compact structure built of three putative carbohydrate-binding modules (M1, M2 and LysM3). M1 and M2 have unique βαββ and βαβ folds that have not previously been observed in carbohydrate binding proteins, while LysM3 has a canonical βααβ fold. We demonstrate that this configuration is a structural signature for a ubiquitous class of receptors in the plant kingdom. We show that EPR3 is promiscuous, suggesting that plants can monitor complex microbial communities though this class of receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Revealing multiple classes of stable quantum emitters in hexagonal boron nitride with correlated optical and electron microscopy

Defects in hexagonal boron nitride (hBN) exhibit high-brightness, room-temperature quantum emission, but their large spectral variability and unknown local structure challenge their technological utility. Here, we directly correlate hBN quantum emission with local strain using a combination of photoluminescence (PL), cathodoluminescence (CL) and nanobeam electron diffraction. Across 40 emitters, we observe zero phonon lines (ZPLs) in PL and CL ranging from 540 to 720 nm. CL mapping reveals that multiple defects and distinct defect species located within an optically diffraction-limited region can each contribute to the observed PL spectra. Local strain maps indicate that strain is not required to activate the emitters and is not solely responsible for the observed ZPL spectral range. Instead, at least four distinct defect classes are responsible for the observed emission range, and all four classes are stable upon both optical and electron illumination. Our findings offer a foundation for future atomic-scale optical characterization of colour centres.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Evolution of neuronal cell classes and types in the vertebrate retina

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An infrared spectral biomarker accurately predicts neurodegenerative disease class in the absence of overt symptoms

Although some neurodegenerative diseases can be identified by behavioral characteristics relatively late in disease progression, we currently lack methods to predict who has developed disease before the onset of symptoms, when onset will occur, or the outcome of therapeutics. New biomarkers are needed. Here we describe spectral phenotyping, a new kind of biomarker that makes disease predictions based on chemical rather than biological endpoints in cells. Spectral phenotyping uses Fourier Transform Infrared (FTIR) spectromicroscopy to produce an absorbance signature as a rapid physiological indicator of disease state. FTIR spectromicroscopy has over the past been used in differential diagnoses of manifest disease. Here, we report that the unique FTIR chemical signature accurately predicts disease class in mouse with high probability in the absence of brain pathology. In human cells, the FTIR biomarker accurately predicts neurodegenerative disease class using fibroblasts as surrogate cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Functionalized nona-silicide [Si 9 R 3 ] Zintl clusters: a new class of superhalogens

Superatoms, due to their various applications in redox and materials chemistry, have been a major topic of study in cluster science. Superhalogens constitute a special class of superatoms that mimic the chemistry of halogens and serve as building blocks of novel materials such as super and hyper salts, perovskite-based solar cells, solid-state electrolytes, and ferroelectric materials. These applications have led to a constant search for new class of superhalogens. Here, in this study, using density functional theory, we show that recently synthesized [Si 9 {Si ( t Bu) 2 H} 3 ] and [Si 9 {Si (TMS) 3 } 3 ] Zintl clusters not only behave like halogens but also when functionalized with suitable ligands exhibit superhalogen characteristics. Frontier molecular orbital (FMO) analyses give insights into the electron-accepting nature of the Zintl clusters. Additional bonding techniques such as energy density at the bond critical point (BCP) and adaptive natural density partitioning (AdNDP) gives complementary information about the nature of bonding in Si 9 -based Zintl clusters. The potential of these Zintl clusters in the synthesis of new electrolytes in Li-ion batteries is also investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Phosphatidic acid: an emerging versatile class of cellular mediators

Abstract Lipids function not only as the major structural components of cell membranes, but also as molecular messengers that transduce signals to trigger downstream signaling events in the cell. Phosphatidic acid (PA), the simplest and a minor class of glycerophospholipids, is a key intermediate for the synthesis of membrane and storage lipids, and also plays important roles in mediating diverse cellular and physiological processes in eukaryotes ranging from microbes to mammals and higher plants. PA comprises different molecular species that can act differently, and is found in virtually all organisms, tissues, and organellar membranes, with variations in total content and molecular species composition. The cellular levels of PA are highly dynamic in response to stimuli and multiple enzymatic reactions can mediate its production and degradation. Moreover, its unique physicochemical properties compared with other glycerophospholipids allow PA to influence membrane structure and dynamics, and interact with various proteins. PA has emerged as a class of new lipid mediators modulating various signaling and cellular processes via its versatile effects, such as membrane tethering, conformational changes, and enzymatic activities of target proteins, and vesicular trafficking.

Biochemistry & Molecular Biology↗
DOE OSTI2013

Solutions to position-dependent mass quantum mechanics for a new class of hyperbolic potentials

We analytically solve the position-dependent mass (PDM) 1D Schrödinger equation for a new class of hyperbolic potentials V{sub q}{sup p}(x)=−V{sub 0}(sinh{sup p}x/cosh{sup q}x), p=−2,0,⋯q [see C. A. Downing, J. Math. Phys. 54, 072101 (2013)] among several hyperbolic single- and double-wells. For a solitonic mass distribution, m(x)=m{sub 0} sech{sup 2}(x), we obtain exact analytic solutions to the resulting differential equations. For several members of the class, the quantum mechanical problems map into confluent Heun differential equations. The PDM Poschl-Teller potential is considered and exactly solved as a particular case.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Hirota equations associated with simply laced affine Lie algebras: The cuspidal class E{sub 6} of e{sub 6}{sup (1)}

In this paper we derive Hirota equations associated with the simply laced affine Lie algebras g{sup (1)}, where g is one of the simply laced complex Lie algebras a{sub n},d{sub n},e{sub 6},e{sub 7} or e{sub 8}, defined by finite order automorphisms of g which we call Lepowsky automorphisms. In particular, we investigate the Hirota equations for Lepowsky automorphisms of e{sub 6} defined by the cuspidal class E{sub 6} of the Weyl group W(E{sub 6}) of e{sub 6}. We also investigate the relationship between the Lepowsky automorphisms of the simply laced complex Lie algebras g and the conjugate canonical automorphisms defined by Kac. This analysis is applied to identify the canonical automorphisms for the cuspidal class E{sub 6} of e{sub 6}.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗