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Results for “Structure elucidation”

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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Local Atomic Configuration in Pristine and A-Site Doped Silver Niobate Perovskite Antiferroelectrics

Antiferroelectrics have attracted increasing research interests in recent years due to both their great potential in energy storage applications and intriguing structural characteristics. However, the links between the electrical properties and structural characteristics of distorted perovskite antiferroelectrics are yet to be fully deciphered. Here, we adopt local-structure methods to elucidate the nanoscale atomic structure of AgNbO3-based antiferroelectrics and their structural evolution upon La doping. The local structural features including interatomic distance distributions and atomic displacements have been analyzed using neutron small-box pair distribution function (PDF) refinement in conjunction with large-box Reverse Monte Carlo modelling. Our results highlight the correlation of cation displacements in AgNbO 3 and its disruption by the incorporation of La, apparently in corroboration with the observed anomalous dielectric properties. Spatial ordering of cation vacancies is observed in La-doped AgNbO 3 samples, which coordinates with oxygen octahedral tilting to relieve lattice strain. These results provide renewed insights into the atomic structure and antiferroelectric phase instabilities of AgNbO 3 and relevant perovskite materials, further lending versatile opportunities for enhancing their functionalities.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Impedance-Based Detection of NO 2 Using Ni-MOF-74: Influence of Competitive Gas Adsorption

Chemically robust, low-power sensors are needed for the direct electrical detection of toxic gases. Metal–organic frameworks (MOFs) offer exceptional chemical and structural tunability to meet this challenge, though further understanding is needed regarding how coadsorbed gases influence or interfere with the electrical response. To probe the influence of competitive gases on trace NO 2 detection in a simulated flue gas stream, a combined structure–property study integrating synchrotron powder diffraction and pair distribution function analyses was undertaken, to elucidate how structural changes associated with gas binding inside Ni-MOF-74 pores correlate with the electrical response from Ni-MOF-74-based sensors. Data were evaluated for 16 gas combinations of N 2 , NO 2 , SO 2 , CO 2 , and H 2 O at 50 °C. Fourier difference maps from a rigid-body Rietveld analysis showed that additional electron density localized around the Ni-MOF-74 lattice correlated with large decreases in Ni-MOF-74 film resistance of up to a factor of 6 × 10 3 , observed only when NO 2 was present. These changes in resistance were significantly amplified by the presence of competing gases, except for CO 2 . Without NO 2 , H 2 O rapidly (<120 s) produced small (1–3×) decreases in resistance, though this effect could be differentiated from the slower adsorption of NO 2 by the evaluation of the MOF’s capacitance. Furthermore, samples exposed to H 2 O displayed a significant shift in lattice parameters toward a larger lattice and more diffuse charge density in the MOF pore. Evaluating the Ni-MOF-74 impedance in real time, NO 2 adsorption was associated with two electrically distinct processes, the faster of which was inhibited by competitive adsorption of CO 2 . Together, this work points to the unique interaction of NO 2 and other specific gases (e.g., H 2 O, SO 2 ) with the MOF’s surface, leading to orders of magnitude decrease in MOF resistance and enhanced NO2 detection. Finally, understanding and leveraging these coadsorbed gases will further improve the gas detection properties of MOF materials.

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

Nanoscale Ion Transport Enhances Conductivity in Solid Polymer-Ceramic Lithium Electrolytes

The predictive design of flexible and solvent-free polymer electrolytes for solid-state batteries requires an understanding of the fundamental principles governing the ion transport. In this work, we establish a correlation among the composite structures, polymer segmental dynamics, and lithium ion (Li + ) transport in a ceramic-polymer composite. Elucidating this structure–property relationship will allow tailoring of the Li + conductivity by optimizing the macroscopic electrochemical stability of the electrolyte. The ion dissociation from the slow polymer segmental dynamics was found to be enhanced by controlling the morphology and functionality of the polymer/ceramic interface. The chemical structure of the Li + salt in the composite electrolyte was correlated with the size of the ionic cluster domains, the conductivity mechanism, and the electrochemical stability of the electrolyte. Polyethylene oxide (PEO) filled with lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) or lithium bis(fluorosulfonyl) imide (LiFSI) salts was used as a matrix. A garnet electrolyte, aluminum substituted lithium lanthanum zirconium oxide (Al-LLZO) with a planar geometry, was used for the ceramic nanoparticle moieties. Further, the dynamics of the strongly bound and highly mobile Li + were investigated using dielectric relaxation spectroscopy. The incorporation of the Al-LLZO platelets increased the number density of more mobile Li + . The structure of the nanoscale ion-agglomeration was investigated by small-angle X-ray scattering, while molecular dynamics (MD) simulation studies were conducted to obtain the fundamental mechanism of the decorrelation of the Li + in the LiTFSI and LiFSI salts from the long PEO chain.

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

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Hydrothermal Liquefaction of Structurally Diverse Lignins: Insights into Biocrude Yield, Fuel Properties, and Reaction Mechanisms

Lignin holds significant promise as a feedstock for biocrude production via hydrothermal liquefaction (HTL). Although lignin HTL has been widely studied, the specific depolymerization pathways associated with distinct lignin structures remain largely unexplored. This study investigates the HTL of four structurally diverse lignins: alkaline (AL), dealkaline (DAL), organosolv (OL), and lignosulfonate (LS) across 270–310 °C to elucidate structure-specific mechanisms governing biocrude yield and composition. AL and OL achieved the highest yields (16.8 ± 0.3% and 16.8 ± 2.5%), with AL-derived biocrude showing the highest carbon content (70.2 ± 0.0%) and HHV (31.0 ± 0.2 MJ/kg). In contrast, DAL and LS produced lower yields and inferior fuel quality due to higher sulfur content and lower carbon enrichment. The structures of AL and DAL, containing fewer methoxy groups, produced guaiacol-rich biocrudes (46.6% and 69.5%). Methylation in AL formed alkyl guaiacols and veratroles, while DAL favored side-chain oxidation. OL retained complex structures, forming syringols and desaspidinol, which contributed to heavier biocrude compounds. Sulfonate groups in LS were stabilized mostly as sulfides, leading to elevated sulfur content. These findings provide mechanistic insight into how lignin structure governs HTL behavior, enabling targeted control of biocrude yield and quality for renewable fuel production.

biocrude↗
DOE OSTI2021

Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail

Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each RNP incorporates multiple copies of nucleoprotein (NP), a fragment of the viral genome (vRNA), and a viral RNA-dependent RNA polymerase (POL), and is responsible for packaging the viral genome and performing critical functions including replication and transcription. A complete model of an Influenza RNP in atomic detail can elucidate the structural basis for viral genome functions, and identify potential targets for viral therapeutics. In this work we construct a model of a complete Influenza A RNP complex in atomic detail using multiple sources of structural and sequence information and a series of homology-modeling techniques, including a motif-matching fragment assembly method. Our final model provides a rationale for experimentally-observed changes to viral polymerase activity in numerous mutational assays. Further, our model reveals specific interactions between the three primary structural components of the RNP, including potential targets for blocking POL-binding to the NP-vRNA complex. The methods developed in this work open the possibility of elucidating other functionally-relevant atomic-scale interactions in additional RNP structures and other biomolecular complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Retrieving functional pathways of biomolecules from single-particle snapshots

Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thiol-promoted catalytic synthesis of high-performance furan-containing lubricant base oils from biomass derived 2-alkylfurans and ketones

About 97% of lubricant base oils are currently sourced from petroleum and the majority of the rest is produced from vegetable oils. We demonstrate a promising catalytic route to produce base oils from lignocellulosic biomass-derived 2-alkylfurans and ketones via carbon–carbon coupling in neat conditions. Among several homogeneous and heterogeneous acid catalysts tested, a perfluorinated sulfonic acid (Aquivion PW79S) exhibits the best catalytic performance and yields up to 90% renewable furan-containing base oils with the use of a thiol promotor. The effects of the acid strength of the catalysts, molecular size and structure of thiols and ketones, and fraction of thiols are studied. Electronic structure calculations elucidate the reaction pathway and indicate that the thiol reduces the barrier of the rate-determining dehydration step. The structure and properties of base oils can be tuned by using different synthons. Here, these base oils have excellent properties and can be competitive with or surpass the commercial synthetic alkylnaphthalene and furan-containing bio-ester base oils.

09 BIOMASS FUELS↗
DOE OSTI2025

Li 21 Ge 8 P 3 S 34 : New Lithium Superionic Conductor with Unprecedented Structural Type

Abstract Lithium superionic conductors are pivotal for enabling all‐solid‐state batteries, which aim to replace liquid electrolytes and enhance safety. Herein, we report the discovery of an unprecedented lithium superionic conductor, Li 21 Ge 8 P 3 S 34 , featuring a novel structural type and a new composition in the Li–Ge–P–S system. This material exhibits high lithium ionic conductivity of approximately 1.0 mS cm −1 at 303 K with a low activation energy of 0.20(1) eV. It's unique crystal structure was elucidated using three‐dimensional electron diffraction (3D ED) and further refined through combined powder X‐ray and neutron diffraction analyses. The structure consists of alternating two‐dimensional slabs: one of corner‐sharing GeS 4 tetrahedra and the other of isolated PS 4 tetrahedra, enabling efficient lithium‐ion transport through a tetrahedrally interconnected network of 1D, 2D, and 3D diffusion pathways. This distinctive structural motif provides a novel design strategy for next‐generation solid electrolytes, broadening the structural landscape of lithium superionic conductors. With further advancements in compositional tuning and interfacial engineering, Li 21 Ge 8 P 3 S 34 could contribute to the development of high‐performance all‐solid‐state batteries.

Chemistry↗
DOE OSTI2020

NELL2-Robo3 complex structure reveals mechanisms of receptor activation for axon guidance

Axon pathfinding is critical for nervous system development, and it is orchestrated by molecular cues that activate receptors on the axonal growth cone. Robo family receptors bind Slit guidance cues to mediate axon repulsion. In mammals, the divergent family member Robo3 does not bind Slits, but instead signals axon repulsion from its own ligand, NELL2. Conversely, canonical Robos do not mediate NELL2 signaling. Here, we present the structures of NELL-Robo3 complexes, identifying a mode of ligand engagement for Robos that is orthogonal to Slit binding. We elucidate the structural basis for differential binding between NELL and Robo family members and show that NELL2 repulsive activity is a function of its Robo3 affinity and is enhanced by ligand trimerization. Our results reveal a mechanism of oligomerization-induced Robo activation for axon guidance and shed light on Robo family member ligand binding specificity, conformational variability, divergent modes of signaling, and evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Direct structural retrieval from gas-phase ultrafast diffraction data using a genetic algorithm

Ultrafast scattering techniques such as ultrafast electron diffraction and ultrafast x-ray diffraction have been utilized to elucidate the structural dynamics, reaction intermediates, and final products in molecular reactions following photoexcitation. The time-dependent structures are typically not directly retrieved from the experimental data, but they rely on comparison with calculations. The genetic algorithm (GA), a global optimization strategy, can be used to retrieve the molecular structures directly from diffraction patterns without any theoretical input. However, the robustness of the GA with respect to real experimental conditions such as a limited momentum transfer range, noise, and artifacts has not been studied in detail. In this work, we characterize the performance of the GA with simulated data that mimic realistic experimental conditions. We have developed and implemented a variant of the GA specific to diffraction measurements which performs better in the presence of imperfect data compared to the standard implementation of the GA. We demonstrate this method with both synthetic data and experimental ultrafast electron diffraction data on the UV-induced photodissociation of trifluoroiodomethane (C⁢F 3⁡ I) molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Structure and composition of blueberry fiber pectin and xyloglucan that bind anthocyanins during fruit puree processing

Blueberry is a well-known source of antioxidants and prebiotic dietary fiber yet the fate of these health-beneficial ingredients during fruit processing it is not understood. Detailed composition and structure of blueberry pomace (PF) remaining after commercial blueberry fruit puree processing, as well as the water soluble and water insoluble fractions, were determined. The PF was comprised of dietary fiber (60.8%) that was largely insoluble (46.2% vs. 14.6% soluble dietary fiber) pectin, xyloglucan, arabinoxylan and mannan polysaccharides, fructose (11.22%) and glucose (10.37%) free sugars, protein (9%), fat (5%), and anthocyanins (6444.5 μg/g). The most abundant anthocyanins detected in PF were malvidin 3-arabinoside and peonidin 3-glucoside and the pectin was determined to be methyl-esterified and acetylated rhamnogalacturonan I with a 4,5-unsaturated function at the non-reducing end based on oligosaccharide structural analysis. Blueberry PF xyloglucan oligosaccharide side chain structures included xylose, arabinose and galactose consistent with arabino-xyloglucan structure. Additionally, microwave-assisted extraction of blueberry PF (pH 2 for 10 min at 80 °C) was performed to more clearly elucidate pectin structure, and revealed a pectin polymer with high molar mass (1072 kDa) and viscosity that was dependent upon the molar mass. A random coil shape was confirmed for both the blueberry PF and microwave extracted blueberry pectin, which agreed with previous reports that flexible blueberry pectin contributes to strong anthocyanin binding. In summary, the blueberry pomace anthocyanin content was slightly higher than that reported for fresh whole blueberry fruit, which suggests that most blueberry anthocyanins adhered to the pomace fiber, and most likely the insoluble pectin, during and after processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Cryo-EM structures reveal native GABA A receptor assemblies and pharmacology

Type A γ-aminobutyric acid receptors (GABA A Rs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants. However, our understanding of GABA A R pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABA A R assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABA A Rs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABA A R assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Controlling protein adsorption modes electrostatically

Protein adsorption on surfaces is ubiquitous in biology and in biotechnology. There are various forces required for controlling protein adsorption. Here, we introduce an explicit ion coarse-grained molecular dynamics simulation approach for studying the effects of electrostatics on protein adsorption, and 2D protein assembly on charged surfaces. Our model accounts for the spatial distribution of protein charges. We use catalase as our model protein. We find that the preferential adsorption mode of proteins at low protein concentration on a charged surface is “standing up”. When the protein concentration in a solution increases to reach a critical density on the surface, the adsorption mode switches from “standing up” to a mixed state “flat on” and “standing up”, which increases the lateral correlations among the adsorbed proteins. As such, the changes in the adsorption mode arise from the protein adsorption that cancel the surface charge and the protein–protein repulsion. This correlated surface structure melts as the salt concentration increases because the charged surface is cancelled by the salt ions and the proteins de-adsorb. For the case of strongly charged surfaces the “standing up” conformation remains more favorable even at high protein adsorption at low salt concentrations since in that conformation the surface charge is cancelled more effectively, generating an even more laterally correlated structure. We elucidate the effects of parameters such as surface charge density, salt concentration, and protein charges on the different adsorption modes and the structure and organization of proteins on the charged surfaces. Finally, this study provides a guide for controlling protein assembly on surfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure sensitivity in adsorbate-induced adatom formation on FCC transition-metal surfaces

Recent surface science discoveries reveal that adsorbates may induce in situ sub-nanometer cluster formation on transition-metal surfaces. To elucidate the structure sensitivity behind this phenomenon, we performed density functional theory calculations to construct an adatom formation energy database for eight fcc metals and 26 adsorbates commonly involved in catalytic reactions. We show that the adatom formation on (100) surfaces is generally easier than that on (111) surfaces. Many adsorbate/metal pairs exist, mostly on Pd, Ni, Rh, Pt, and Ir, for which adsorbates might induce adatom formation under near-ambient conditions on the (100) facet, but not on (111), highlighting the role of more open facets in adatom formation on metals intrinsically harder than Ag, Au, and Cu. Furthermore, our study offers a new perspective towards understanding structure sensitivity in heterogeneous thermal- and electro-catalytic systems such as methane steam reforming, Fischer-Tropsch synthesis, and ammonia decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Cation Site Occupancy in Natural Ferroan Double Carbonates via Mössbauer and Fe K-Edge X-ray Absorption Spectroscopy

Double carbonates are minerals with a calcite type structure with alternating cation layers composed of Ca and Mg/Fe coordinated by carbonate groups. While the perfectly ordered AB-stacked crystal is the thermodynamically most stable configuration, natural mineral formation pathways can leave signatures through kinetically trapped disorder such as AB antisite cation substitutions. This study probes the degree of cation ordering in naturally occurring double carbonate samples.in particular, the distribution of Fe A and B crystallographic sites (A site is Ca layer and B site is Mg/Fe layer). Mössbauer, X-ray diffraction, X-ray absorption fine structure (both X-ray absorption near edge structure, XANES, and extended x-ray absorption fine structure, EXAFS), and energy dispersive X-ray spectroscopies were used to collect a comprehensive experimental data set, which we interpret using density functional theory to elucidate the structural effects of cation disorder. Our results show that the A (nominally Ca) site can host a relatively high Fe fraction. We discuss the implications in terms of mineral formation.

Boglaienko, Daria (ORCID:0000000160943877)↗
DOE OSTI2023

Antibodies Raised Against an Aβ Oligomer Mimic Recognize Pathological Features in Alzheimer’s Disease and Associated Amyloid-Disease Brain Tissue

Antibodies that target the β-amyloid peptide (Aβ) and its associated assemblies are important tools in Alzheimer’s disease research and have emerged as promising Alzheimer’s disease therapies. This paper reports the creation and characterization of a triangular Aβ trimer mimic composed of Aβ 17–36 β-hairpins and the generation and study of polyclonal antibodies raised against the Aβ trimer mimic. The Aβ trimer mimic is covalently stabilized by three disulfide bonds at the corners of the triangular trimer to create a homogeneous oligomer. Structural, biophysical, and cell-based studies demonstrate that the Aβ trimer mimic shares characteristics with oligomers of full-length Aβ. X-ray crystallography elucidates the structure of the trimer and reveals that four copies of the trimer assemble to form a dodecamer. SDS-PAGE, size exclusion chromatography, and dynamic light scattering reveal that the trimer also forms higher-order assemblies in solution. Cell-based toxicity assays show that the trimer elicits LDH release, decreases ATP levels, and activates caspase-3/7 mediated apoptosis. Immunostaining studies on brain slices from people who lived with Alzheimer’s disease and people who lived with Down syndrome reveal that the polyclonal antibodies raised against the Aβ trimer mimic recognize pathological features including different types of Aβ plaques and cerebral amyloid angiopathy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗