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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Relationship Between Hydrogen-Bonding Motifs and the 1b1 Splitting in the X-ray Emission Spectrum of Liquid Water

The split of the 1??! peak observed in the X-ray emission (XE) spectrum of liquid water has been the focus of intense research over the last two decades. Although several hypotheses have been proposed to explain the origin of the 1??! splitting, a general consensus has not yet been reached. In this study, we introduce a novel theoretical/computational approach which, combining pathintegral molecular dynamics (PIMD) simulations carried out with the MB-pol potential energy function and time-dependent density functional theory (TD-DFT) calculations, correctly predicts the split of the 1??! peak in liquid water and not in crystalline ice. A systematic analysis in terms of the underlying local structure of liquid water at ambient conditions indicates that several different hydrogen-bonding motifs contribute to the overall XE lineshape in the energy range corresponding to emissions from the 1??! orbitals, which suggests that it is not possible to unambiguously attribute the split of the 1??! peak to only two specific structural arrangements of the underlying hydrogen-bonding network.

Cruzeiro, Vinicius↗
DOE OSTI2020

Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A structured RNA motif locks Argonaute2:miR-122 onto the 5’ end of the HCV genome

microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Au-activated N motifs in non-coherent cupric porphyrin metal organic frameworks for promoting and stabilizing ethylene production

Direct implementation of metal-organic frameworks as the catalyst for CO 2 electroreduction has been challenging due to issues such as poor conductivity, stability, and limited > 2e - products. In this study, Au nanoneedles are impregnated into a cupric porphyrin-based metal-organic framework by exploiting ligand carboxylates as the Au 3+ -reducing agent, simultaneously cleaving the ligand-node linkage. Surprisingly, despite the lack of a coherent structure, the Au-inserted framework affords a superb ethylene selectivity up to 52.5% in Faradaic efficiency, ranking among the best for metal-organic frameworks reported in the literature. Through operando X-ray, infrared spectroscopies and density functional theory calculations, the enhanced ethylene selectivity is attributed to Au-activated nitrogen motifs in coordination with the Cu centers for C-C coupling at the metalloporphyrin sites. Furthermore, the Au-inserted catalyst demonstrates both improved structural and catalytic stability, ascribed to the altered charge conduction path that bypasses the incoherent framework. This study underlines the modulation of reticular metalloporphyrin structure by metal impregnation for steering the CO 2 reduction reaction pathway.

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

Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals

Despite recent success in hepatitis C virus (HCV) treatment using antivirals, an HCV vaccine is still needed to prevent reinfections in treated patients, to avert the emergence of drug-resistant strains, and to provide protection for people with no access to the antiviral therapeutics. The early production of broadly neutralizing antibodies (bNAbs) associates with HCV clearance. Several potent bNAbs bind a conserved HCV glycoprotein E2 epitope using an unusual heavy chain complementarity determining region 3 (HCDR3) containing an intra-loop disulfide bond. Isolation of additional structurally-homologous bNAbs would facilitate the recognition of key determinants of such bNAbs and guide rational vaccine design. Here we report the identification of new antibodies containing an HCDR3 disulfide bond motif using computational screening with the Rosetta software. Using the newly-discovered and already-known members of this antibody family, we review the required HCDR3 amino acid composition and propose determinants for the bent versus straight HCDR3 loop conformation observed in these antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif

Abstract The mechanochemical GTPase dynamin-related protein 1 (Drp1) catalyzes mitochondrial and peroxisomal fission, but the regulatory mechanisms remain ambiguous. Here we find that a conserved, intrinsically disordered, six-residue Short Linear Motif at the extreme Drp1 C-terminus, named CT-SLiM, constitutes a critical allosteric site that controls Drp1 structure and function in vitro and in vivo. Extension of the CT-SLiM by non-native residues, or its interaction with the protein partner GIPC-1, constrains Drp1 subunit conformational dynamics, alters self-assembly properties, and limits cooperative GTP hydrolysis, surprisingly leading to the fission of model membranes in vitro. In vivo, the involvement of the native CT-SLiM is critical for productive mitochondrial and peroxisomal fission, as both deletion and non-native extension of the CT-SLiM severely impair their progression. Thus, contrary to prevailing models, Drp1-catalyzed membrane fission relies on allosteric communication mediated by the CT-SLiM, deceleration of GTPase activity, and coupled changes in subunit architecture and assembly-disassembly dynamics.

Science & Technology - Other Topics↗
DOE OSTI2022

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif

Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Highly soluble copper(ι) iodide-based hybrid luminescent semiconductors containing molecular and one-dimensional coordinated anionic inorganic motifs

Copper(I) iodide-based inorganic–organic hybrid semiconductors are considered promising materials for various optoelectronic applications. Here, using imidazolium bridged benzotriazoles as multidentate ligands, we designed and synthesized a series of all-in-one (AIO)-type CuI hybrid materials that hold both ionic and coordinate bonds at the interface of organic and inorganic modules. Their structures range from 0D clusters to 2D extended networks built on various molecular (0D) and chain-like (1D) anionic inorganic motifs that are interconnected through cationic ligands via multiple Cu–N bonds. Benefiting from their unique bonding nature, these compounds exhibit high stability towards heat and moisture and can be well dissolved in polar aprotic solvents. They emit low-energy light spanning from yellow to red color (550–625 nm). Finally, the electronic structure, emission mechanism, and effect of different coordination modes on their photophysical properties were studied using both experimental and theoretical methods, which has provided insight into the structure–property relationship of these inorganic–organic semiconductors.

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

Hierarchical supramolecular assembly of a single peptoid polymer into a planar nanobrush with two distinct molecular packing motifs

Significance The preparation of hierarchical biomimetic nanostructures remains a challenging task. Bioinspired peptoid polymers offer a promising opportunity to encode assembly information within the component chains. Here, we report a one-pot preparation of planar nanobrush structures from poly(ethyleneglycol)- block -poly( N -octylglycine) based on tuning the interplay of crystallization and solvophobicity. Each nanobrush assembly is composed of two distinct structural domains, which form sequentially by control of the solution temperature, and contain distinct molecular packing motifs. Micellar intermediates first assemble into linear arrays at elevated temperature in a mesophase state, followed by lateral, crystallization-driven growth in a living manner upon cooling. Precise control over the nanobrush dimensions could be achieved. The structural tunability and excellent biocompatibility of polypeptoids offer great potential for nanomaterials inaccessible previously.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Microwave-assisted synthesis of iron sulfide motifs for electrochemical applications

Abstract The syntheses of FeS 2 and Fe 3 S 4 nanomaterials were optimized using a novel facile, surfactant-free, and microwave-assisted, one-pot synthesis method, run under ambient and reasonably mild reaction conditions. Synthetic parameters, such as metal precursor salt identity, reaction time, reaction temperature, metal:sulfur molar ratios, and solvent combinations, were all systematically investigated and optimized. A series of FeS 2 (pyrite) samples was initially fabricated using thioacetamide (TAA) as the sulfur precursor to generate a distinctive, uniform octahedra-based morphology. Switching the sulfur precursor from TAA to L-cysteine resulted in a corresponding transformation in not only chemical composition from FeS 2 to an iron thiospinel structure, Fe 3 S 4 (otherwise known as greigite), but also an associated morphological evolution from octahedra to nanosheet aggregates. The study of these materials has enabled crucial insights into the formation mechanisms of these materials under a relatively non-conventional microwave-assisted setting. Furthermore, in separate experiments, multi-walled carbon nanotubes (MWNTs) and graphene were added in with underlying metal sulfide species to create conductive Fe–S/MWNT composites and Fe–S/graphene composites, respectively. The method of addition of either MWNTs or graphene was also explored, wherein an ‘ ex-situ ’ synthetic procedure was found to be the least disruptive means of attachment and immobilization onto iron sulfide co-reagents as a means of preserving the latter’s inherent composition and morphology. The redox acidity for the parent material and associated composites demonstrates the utility of our as-developed synthetic methods for creating motifs relevant for electrochemical applications, such as energy storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Motif magnetism and quantum many-body scars

In this work, we generally expect quantum systems to thermalize and satisfy the eigenstate thermalization hypothesis (ETH), which states that finite-energy-density eigenstates are thermal. However, some systems, such as many-body localized systems and systems with quantum many-body scars, violate ETH and have high-energy athermal eigenstates. In systems with scars, most eigenstates thermalize, but a few atypical scar states do not. Scar states can give rise to a periodic revival when time-evolving particular initial product states, which can be detected experimentally. Recently, a family of spin Hamiltonians was found with magnetically ordered three-colored eigenstates that are quantum many-body scars [Lee et al., Phys. Rev. B 101, 241111(R) (2020)]. These models can be realized in any lattice that can be tiled by triangles, such as the triangular or kagome lattices, and have been shown to have close connections to the physics of quantum spin liquids in the Heisenberg kagome antiferromagnet. In this paper, we introduce a generalized family of n-colored Hamiltonians with “spiral colored” eigenstates made from n-spin motifs such as polygons or polyhedra. We show how these models can be realized in many different lattice geometries and provide numerical evidence that they can exhibit quantum many-body scars with periodic revivals that can be observed by time-evolving simple product states. The simple structure of these Hamiltonians makes them promising candidates for future experimental studies of quantum many-body scars.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural motifs and bonding in two families of boron structures predicted at megabar pressures

The complex crystal chemistry of elemental boron has led to numerous proposed structures with distinctive motifs as well as contradictory findings. Herein, evolutionary structure searches performed at 100 GPa have uncovered a series of metastable phases of boron, and bonding analyses were carried out to elucidate their electronic structure. These polymorphs, dynamically stable at 100 GPa, were grouped into two families. Here, the first was derived from the thermodynamic minimum at these conditions, α-Ga, whereas channels comprised the second. Two additional intergrowth structures were uncovered, and it was shown they could be constructed by stacking layers of α-Ga-like and channel-like allotropes on top of each other. A detailed bonding analysis revealed networks of four-center σ-bonding functions linked by two-center B-B bonds in the α-Ga based structures, and networks that were largely composed of three-center σ-bonding functions in the channel-based structures. Seven of these high-pressure phases were found to be metastable at atmospheric conditions, and their Vickers hardnesses were estimated to ≈ 36 GPa.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Asymmetric photoenzymatic incorporation of fluorinated motifs into olefins

Enzymes capable of assimilating fluorinated feedstocks are scarce. This situation poses a challenge for the biosynthesis of fluorinated compounds used in pharmaceuticals, agrochemicals, and materials. We developed a photoenzymatic hydrofluoroalkylation that integrates fluorinated motifs into olefins. The photoinduced promiscuity of flavin-dependent ene-reductases enables the generation of carbon-centered radicals from iodinated fluoroalkanes, which are directed by the photoenzyme to engage enantioselectively with olefins. This approach facilitates stereocontrol through interaction between a singular fluorinated unit and the enzyme, securing high enantioselectivity at β, γ, or δ positions of fluorinated groups through enzymatic hydrogen atom transfer—a process that is notably challenging with conventional chemocatalysis. Furthermore, this work advances enzymatic strategies for integrating fluorinated chemical feedstocks and opens avenues for asymmetric synthesis of fluorinated compounds.

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

Identification of short-range ordering motifs in semiconductors

Chemical short-range ordering is expected to be a key factor for tuning the electronic structure of semiconductors. However, experimental evidence of short-range ordering is still lacking due to the challenge of characterizing atomic-scale ordering motifs. Here, we determined the presence of short-range order in a ternary GeSiSn semiconductor system using advanced energy-filtered four-dimensional scanning transmission electron microscopy and large-scale atomistic models generated by a machine learning neuroevolution potential of first-principles accuracy. This approach revealed preferred ordering of different atomic species with the dominant occurrence of Si–Ge–Sn triplets. Our findings not only confirmed the presence of short-range order but also directly revealed the actual atomic structure, demonstrating the potential for informed atomic order–based band engineering as a third degree of freedom beyond composition and strain tuning.

Vogl, Lilian M. [University of California Berkeley↗
DOE OSTI2022

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses

The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)–directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.

59 BASIC BIOLOGICAL SCIENCES↗