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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 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Unravelling surface and interfacial structures of a metal–organic framework by transmission electron microscopy

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. We use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. Our observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Surface charge dynamics in photosynthetic membranes and the structural consequences

The strict stacking of plant photosynthetic membranes into granal structures plays a vital role in energy conversion. The molecular forces that lead to grana stacking, however, are poorly understood. Here we evaluate the interplay between repulsive electrostatic (F el ) and attractive van der Waals (F vdWaals ) forces in grana stacking. In contrast to previous reports, we find that the physicochemical balance between attractive and repulsive forces fully explains grana stacking. Extending the force balance analysis to lateral interactions within the oxygen-evolving photosystem II (PSII)–light harvesting complex II (LHCII) supercomplex reveals that supercomplex stability is very sensitive to F el changes. F el is highly dynamic, increasing up to 1.7-fold on addition of negative charges by phosphorylation of grana-hosted proteins. We show that this leads to specific destabilization of the supercomplex, and that changes in F el have contrasting effects on vertical stacking and lateral intramembrane organization. Lastly, this enables discrete biological control of these central structural features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Deciphering minimal antigenic epitopes associated with Burkholderia pseudomallei and Burkholderia mallei lipopolysaccharide O-antigens

Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm), the etiologic agents of melioidosis and glanders, respectively, cause severe disease in both humans and animals. Studies have highlighted the importance of Bp and Bm lipopolysaccharides (LPS) as vaccine candidates. Here we describe the synthesis of seven oligosaccharides as the minimal structures featuring all of the reported acetylation/methylation patterns associated with Bp and Bm LPS O-antigens (OAgs). Our approach is based on the conversion of an L-rhamnose into a 6-deoxy-L-talose residue at a late stage of the synthetic sequence. Using biochemical and biophysical methods, we demonstrate the binding of several Bp and Bm LPS-specific monoclonal antibodies with terminal OAg residues. Mice immunized with terminal disaccharide–CRM197 constructs produced high-titer antibody responses that crossreacted with Bm-like OAgs. Collectively, these studies serve as foundation for the development of novel therapeutics, diagnostics, and vaccine candidates to combat diseases caused by Bp and Bm.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A diuranium carbide cluster stabilized inside a C 80 fullerene cage

Unsupported non-bridged uranium–carbon double bonds have long been sought after in actinide chemistry as fundamental synthetic targets in the study of actinide-ligand multiple bonding. Here we report that, utilizing I h (7)-C 80 fullerenes as nanocontainers, a diuranium carbide cluster, U=C=U, has been encapsulated and stabilized in the form of UCU@I h (7)-C 80 . This endohedral fullerene was prepared utilizing the Krätschmer–Huffman arc discharge method, and was then co-crystallized with nickel(II) octaethylporphyrin (Ni II -OEP) to produce UCU@I h (7)-C 80 ·[Ni II -OEP] as single crystals. X-ray diffraction analysis reveals a cage-stabilized, carbide-bridged, bent UCU cluster with unexpectedly short uranium–carbon distances (2.03 Å) indicative of covalent U=C double-bond character. The quantum-chemical results suggest that both U atoms in the UCU unit have formal oxidation state of +5. The structural features of UCU@I h (7)-C 80 and the covalent nature of the U(f 1 )=C double bonds were further affirmed through various spectroscopic and theoretical analyses.

36 MATERIALS SCIENCE↗
DOE OSTI2021

ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Abstract Machine learning has been increasingly used for protein engineering. However, because the general sequence contexts they capture are not specific to the protein being engineered, the accuracy of existing machine learning algorithms is rather limited. Here, we report ECNet (evolutionary context-integrated neural network), a deep-learning algorithm that exploits evolutionary contexts to predict functional fitness for protein engineering. This algorithm integrates local evolutionary context from homologous sequences that explicitly model residue-residue epistasis for the protein of interest with the global evolutionary context that encodes rich semantic and structural features from the enormous protein sequence universe. As such, it enables accurate mapping from sequence to function and provides generalization from low-order mutants to higher-order mutants. We show that ECNet predicts the sequence-function relationship more accurately as compared to existing machine learning algorithms by using ~50 deep mutational scanning and random mutagenesis datasets. Moreover, we used ECNet to guide the engineering of TEM-1 β-lactamase and identified variants with improved ampicillin resistance with high success rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Analysis of diverse double-strand break synapsis with Polλ reveals basis for unique substrate specificity in nonhomologous end-joining

DNA double-strand breaks (DSBs) threaten genomic stability, since their persistence can lead to loss of critical genetic information, chromosomal translocations or rearrangements, and cell death. DSBs can be repaired through the nonhomologous end-joining pathway (NHEJ), which processes and ligates DNA ends efficiently to prevent or minimize sequence loss. Polymerase λ (Polλ), one of the Family X polymerases, fills sequence gaps of DSB substrates with a strict specificity for a base-paired primer terminus. There is little information regarding Polλ’s approach to engaging such substrates. We used in vitro polymerization and cell-based NHEJ assays to explore the contributions of conserved loop regions toward DSB substrate specificity and utilization. In addition, we present multiple crystal structures of Polλ in synapsis with varying biologically relevant DSB end configurations, revealing how key structural features and hydrogen bonding networks work in concert to stabilize these tenuous, potentially cytotoxic DNA lesions during NHEJ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Emergence of high piezoelectricity from competing local polar order-disorder in relaxor ferroelectrics

Relaxor ferroelectrics are known for outstanding piezoelectric properties, finding a broad range of applications in advanced electromechanical devices. Decoding the origins of the enhanced properties, however, have long been complicated by the heterogeneous local structures. Here, we employ the advanced big-box refinement method by fitting neutron-, X-ray-based total scattering, and X-ray absorption spectrum simultaneously, to extract local atomic polar displacements and construct 3D polar configurations in the classical relaxor ferroelectric Pb(Mg 1/3 Nb 2/3 )O 3 –PbTiO 3 . Our results demonstrate that prevailing order-disorder character accompanied by the continuous rotation of local polar displacements commands the composition-driven global structure evolution. The omnidirectional local polar disordering appears as an indication of macroscopic relaxor characteristics. Combined with phase-field simulations, it demonstrates that the competing local polar order-disorder between different states with balanced local polar length and direction randomness leads to a flattening free-energy profile over a wide polar length, thus giving rise to high piezoelectricity. Our work clarifies that the critical structural feature required for high piezoelectricity is the competition states of local polar rather than relaxor.

42 ENGINEERING↗
DOE OSTI2023

Custom tuning of Rieske oxygenase reactivity

Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Evolution of dislocations during the rapid solidification in additive manufacturing

Materials processed by fusion-based additive manufacturing (AM) typically exhibit relatively high dislocation densities, along with cellular structures and elemental segregation. This representative structural feature significantly influences material performance; however, post-mortem microstructure characterizations of AM materials cannot capture the dynamic evolution of dislocations during the manufacturing process, thereby offering limited mechanism-based guidance for further advancing AM techniques and facilitating the qualification and certification of AM products. In this study, we conduct operando high-energy synchrotron X-ray diffraction experiments on wire-laser directed energy deposition of 316 L stainless steel. Through a unique configuration, our operando synchrotron experiments semi-quantitatively probe the dislocation density in solid phases and their dynamic changes during solidification and subsequent cooling. By integrating this advanced synchrotron technique with multi-physics simulation, in-situ neutron diffraction, and multi-scale electron microscopy characterization, our mechanistic study aims to elucidate the effects of rapid cooling and subsequent thermal cycling on the dislocation generation and evolution.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Nanoporous silica gel structures and evolution from reactive force field-based molecular dynamics simulations

Nanoporous silica-rich gel formed on silicate glass surfaces during dissolution in aqueous environment is critical in elucidating the corrosion mechanisms and the long-term residual dissolution behaviors. Silica gel models were created using two types of methods with reactive force field-based molecular dynamics simulations. The results show that the remnant silica gels created from the ISG bulk structure have a more isolated and closed pore morphology and slightly higher glass network connectivity. This contrasts with the gel structures created by hydrogarnet defect formation that exhibit more connected pore morphologies. The remnant gel structures show lower water diffusivity which was explained by the nano-confinement effect of water molecules due to frequent interactions of water molecules with adjacent silica walls and the more isolated pore morphology in the remnant gel structures. These results reveal the complexity in terms of micro and atomic structures of these silica gels, and both structure features have impact on water transport in the gel layer hence the passivating effect that controls the long-term dissolution behavior of these glasses.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Structural evolution of titanium dioxide during reduction in high-pressure hydrogen

The excellent photocatalytic properties of titanium oxide (TiO 2 ) under ultraviolet light have long motivated the search for doping strategies capable of extending its photoactivity to the visible part of the spectrum. One approach is high-pressure and high-temperature hydrogenation, which results in reduced ‘black TiO 2 ’ nanoparticles with a crystalline core and a disordered shell that absorbs visible light. Here we elucidate the formation mechanism and structural features of black TiO 2 using first-principles-validated reactive force field molecular dynamics simulations of anatase TiO 2 surfaces and nanoparticles at high temperature and under high hydrogen pressures. Simulations reveal that surface oxygen vacancies created upon reaction of H 2 with surface oxygen atoms diffuse towards the bulk material but encounter a high barrier for subsurface migration on {001} facets of the nanoparticles, which initiates surface disordering. Besides confirming that the hydrogenated amorphous shell has a key role in the photoactivity of black TiO 2 , our results provide insight into the properties of the disordered surface layers that are observed on regular anatase nanocrystals under photocatalytic water-splitting conditions.

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

Identification of LiH and nanocrystalline LiF in the solid–electrolyte interphase of lithium metal anodes

A comprehensive understanding of the solid–electrolyte interphase (SEI) composition is crucial to developing high-energy batteries based on lithium metal anodes. A particularly contentious issue concerns the presence of LiH in the SEI. In this work, we report on the use of synchrotron-based X-ray diffraction and pair distribution function analysis to identify and differentiate two elusive components, LiH and LiF, in the SEI of lithium metal anodes. LiH is identified as a component of the SEI in high abundance, and the possibility of its misidentification as LiF in the literature is discussed. LiF in the SEI is found to have different structural features from LiF in the bulk phase, including a larger lattice parameter and a smaller grain size (<3 nm). These characteristics favour Li + transport and explain why an ionic insulator, like LiF, has been found to be a favoured component for the SEI. Finally, pair distribution function analysis reveals key amorphous components in the SEI.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Short-range order and its impact on the CrCoNi medium-entropy alloy

Traditional metallic alloys are mixtures of elements in which the atoms of minority species tend to be distributed randomly if they are below their solubility limit, or to form secondary phases if they are above it. The concept of multiple-principal-element alloys has recently expanded this view, as these materials are single-phase solid solutions of generally equiatomic mixtures of metallic elements. This group of materials has received much interest owing to their enhanced mechanical properties 1,2,3,4,5 . They are usually called medium-entropy alloys in ternary systems and high-entropy alloys in quaternary or quinary systems, alluding to their high degree of configurational entropy. However, the question has remained as to how random these solid solutions actually are, with the influence of short-range order being suggested in computational simulations but not seen experimentally 6,7 . In this paper we report the observation, using energy-filtered transmission electron microscopy, of structural features attributable to short-range order in the CrCoNi medium-entropy alloy. Increasing amounts of such order give rise to both higher stacking-fault energy and hardness. These findings suggest that the degree of local ordering at the nanometre scale can be tailored through thermomechanical processing, providing a new avenue for tuning the mechanical properties of medium- and high-entropy alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Unlocking saponin biosynthesis in soapwort

Abstract Soapwort ( Saponaria officinalis ) is a flowering plant from the Caryophyllaceae family with a long history of human use as a traditional source of soap. Its detergent properties are because of the production of polar compounds (saponins), of which the oleanane-based triterpenoid saponins, saponariosides A and B, are the major components. Soapwort saponins have anticancer properties and are also of interest as endosomal escape enhancers for targeted tumor therapies. Intriguingly, these saponins share common structural features with the vaccine adjuvant QS-21 and, thus, represent a potential alternative supply of saponin adjuvant precursors. Here, we sequence the S . officinalis genome and, through genome mining and combinatorial expression, identify 14 enzymes that complete the biosynthetic pathway to saponarioside B. These enzymes include a noncanonical cytosolic GH1 (glycoside hydrolase family 1) transglycosidase required for the addition of d- quinovose. Our results open avenues for accessing and engineering natural and new-to-nature pharmaceuticals, drug delivery agents and potential immunostimulants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Interaction of the Antimicrobial Peptide Aurein 1.2 and Charged Lipid Bilayer

Aurein 1.2 is a potent antimicrobial peptide secreted by frog Litoria aurea. As a short membrane-active peptide with only 13 amino acids in sequence, it has been found to be residing on the surface of lipid bilayer and permeabilizing bacterial membranes at high concentration. However, the detail at the molecular level is largely unknown. Here in this study, we investigated the action of Aurein 1.2 in charged lipid bilayers composed of DMPC/DMPG. Oriented Circular Dichroism results showed that the peptide was on the surface of lipid bilayer regardless of the charged lipid ratio. Only at a very high peptide-to-lipid ratio (~1/10), the peptide became perpendicular to the bilayer, however no pore was detected by neutron in-plane scattering. To further understand how it interacted with charged lipid bilayers, we employed Small Angle Neutron Scattering to probe lipid distribution across bilayer leaflets in lipid vesicles. The results showed that Aurein 1.2 interacted strongly with negatively charged DMPG, causing strong asymmetry in lipid bilayer. At high concentration, while the vesicles were intact, we found additional structure feature on the bilayer. Finally, our study provides a glimpse into how Aurein 1.2 disturbs anionic lipid-containing membranes without pore formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Atomistic scale investigation of cation ordering and phase stability in Cs-substituted Ba 1.33 Zn 1.33 Ti 6.67 O 16 , Ba 1.33 Ga 2.66 Ti 5.67 O 16 and Ba 1.33 Al 2.66 Ti 5.33 O 16 hollandite

The titanate-based hollandite structure is proposed as an effective ceramic waste form for Cs-immobilization. In this study, quantum-mechanical calculations were used to quantify the impact of A-site and B-site ordering on the structural stability of hollandite with compositions Ba x Cs y (M z Ti 8-z )O16, where M = Zn 2+ , Ga 3+ , and Al 3+ . The calculated enthalpy of formation agrees with experimental measurements of related hollandite phases from melt solution calorimetry. Ground state geometry optimizations show that, for intermediate compositions (e.g., CsBaGa 6 Ti 18 O 48 ), the presence of both Cs and Ba in the A-site tunnels is not energetically favored. However, the decay heat generated during storage of the Cs-containing waste form may overcome the energetics of Ba and Cs mixing in the tunnel structure of hollandite. The ability of the hollandite structure to accommodate the radioparagenesis of Cs to Ba is critical for long term performance of the waste. For the first time, B-site ordering was observed along the tunnel direction ([001] zone axis) for the Ga-hollandite compositions, as well as the intermediate Al-hollandite composition. These compositionally dependent structural features, and associated formation enthalpies, are of importance to the stability and radiation damage tolerance of ceramic waste forms.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases

Bacterial β-glucuronidase (GUS) enzymes cause drug toxicity by reversing Phase II glucuronidation in the gastrointestinal tract. While many human gut microbial GUS enzymes have been examined with model glucuronide substrates like p-nitrophenol-β-D-glucuronide (pNPG), the GUS orthologs that are most efficient at processing drug-glucuronides remain unclear. Here we present the crystal structures of GUS enzymes from human gut commensals Lactobacillus rhamnosus, Ruminococcus gnavus , and Faecalibacterium prausnitzii that possess an active site loop (Loop 1; L1) analogous to that found in E. coli GUS, which processes drug substrates. We also resolve the structure of the No Loop GUS from Bacteroides dorei. We then compare the pNPG and diclofenac glucuronide processing abilities of a panel of twelve structurally diverse GUS proteins, and find that the new L1 GUS enzymes presented here process small glucuronide substrates inefficiently compared to previously characterized L1 GUS enzymes like E. coli GUS. We further demonstrate that our GUS inhibitors, which are effective against some L1 enzymes, are not potent towards all. Our findings pinpoint active site structural features necessary for the processing of drug-glucuronide substrates and the inhibition of such processing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Bonding and reactivity of isostructural uranyl and neptunyl peroxide phases

Understanding the reactivity of actinide peroxides is critical for predicting the behavior of spent nuclear fuel in radiolytic environments. Herein, we report the synthesis and characterization of a lithium neptunyl(VI) hydroxo peroxo compound (LiNp), which is isostructural to the uranyl analogue (LiU). Single-crystal X-ray diffraction reveals that LiNp contains both [NpO 2 (O 2 ) 3 ] 4- and [NpO 2 (OH) 4 ] 2- units stabilized by Li + and hydrogen bonding and Raman spectroscopy shows systematic redshifts in neptunyl vibrational modes relative to uranyl. DFT calculations highlight the importance of secondary coordination in reproducing vibrational and structural features, but challenges remain with correctly modeling strong sigma donors. Solid-state EPR spectroscopy and DFT confirm superoxide stabilization within LiU and calculations suggest favorability of the analogous radical species in LiNp. Solution state EPR spectroscopy with the radical spin trap 5-tert-butoxycarbonyl-5-methyl-1-pyrroline N-oxide (BMPO) reveal evidence of superoxide in the LiU and LiNp phases and suggests stabilization of superoxide within actinyl triperoxide complexes, forming [AnO 2 (O 2 ) 2 (O) 2 • ] 3- .

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗