Search NASA⌕ Search

SEARCH · Search NASA

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Superconductivity in a topological lattice model with strong repulsion

The highly tunable nature of synthetic quantum materials-both in the solid-state and cold atom contexts-invites examining which microscopic ingredients aid in the realization of correlated phases of matter such as superconductors. Recent experimental advances in moiré materials suggest that unifying the features of the Fermi-Hubbard model and quantum Hall systems creates a fertile ground for the emergence of such phases. Here, we introduce the "double Hofstadter"model, a minimal 2D lattice model that incorporates exactly these features: Time-reversal symmetry, band topology, and strong repulsive interactions. By using infinite cylinder density matrix renormalization group methods (cylinder iDMRG), we investigate the ground state phase diagram of this model. We find that it hosts an interaction-induced quantum spin Hall insulator and demonstrate that weakly hole-doping this state gives rise to a superconductor at a finite circumference, with indications that this behavior persists on larger cylinders. Further, at the aforementioned circumference, the superconducting phase is surprisingly robust to perturbations including additional repulsive interactions in the pairing channel. By developing a technique to probe the superconducting gap function in iDMRG, we phenomenologically characterize the superconductor. Namely, we demonstrate that it is formed from the weak pairing of holes atop the quantum spin Hall insulator. Furthermore, we determine the pairing symmetry of the superconductor, finding it to be p-wave-reminiscent of the unconventional superconductivity reported in experiments on twisted bilayer graphene (TBG). Motivated by this, we elucidate structural similarities and differences between our model and those of TBG in its chiral limit. Finally, to provide a more direct experimental realization, we detail an implementation of our Hamiltonian in a system of cold fermionic alkaline-earth atoms in an optical lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2024

Structural, electronic, and optical-absorption properties of 2D Si thin films

Recent experimental studies highlighted the potential of thin-film crystalline silicon (Si) for high-efficiency solar cells. Using density functional theory, we investigated 2D Si thin films across various orientations, thicknesses, and surface structures to elucidate their structure–property relationships. Through surface-energy calculations and Wulff construction, we determined the crystal habit of Si, which aligns with available experimental observations. Electronic-structure calculations underscored the critical role of valence saturation on surfaces in enabling semiconducting behavior in Si thin films, essential for optical applications. From optical-absorption calculations, we identified the surface index exhibiting the highest absorption coefficients for thin films Si solar cell applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Leisingera sp. ANG59 & Pseudoalteromonas sp. JC28 Genomes Overview

The Hawaiian bobtail squid, Euprymna scolopes, has a symbiotic bacterial consortium in the accessory nidamental gland (ANG), a female reproductive organ that protects eggs against fouling microorganisms. To test the antibacterial activity of ANG community members, 19 bacterial isolates were screened for their ability to inhibit Gram-negative and Gram-positive bacteria, of which two strains were inhibitory. These two antibacterial isolates, Leisingera sp. ANG59 and Pseudoalteromonas sp. JC28, were subjected to further genomic characterization. Genomic analysis of Leisingera sp. ANG59 revealed a biosynthetic gene cluster encoding the antimicrobial compound indigoidine. The genome of Pseudoalteromonas sp. JC28 had a 14-gene cluster with >95% amino acid identity to a known bromoalterochromide (BAC) cluster. Chemical analysis confirmed production of known BACs, BAC-A/A′ (compounds 1a/1b), as well as two new derivatives, BAC-D/D′ (compounds 2a/2b). Extensive nuclear magnetic resonance (NMR) analyses allowed complete structural elucidation of compounds 2a/2b, and the absolute stereochemistry was unambiguously determined using an optimized Marfey’s method. The BACs were then investigated for in vitro antibacterial, antifungal, and nitric oxide (NO) inhibitory activity. Compounds 1a/1b were active against the marine bacteria Bacillus algicola and Vibrio fischeri, while compounds 2a/2b were active only against B. algicola. Compounds 1a/1b inhibited NO production via lipopolysaccharide (LPS)-induced inflammation in RAW264.7 macrophage cells and also inhibited the pathogenic fungus Fusarium keratoplasticum, which, coupled with their antibacterial activity, suggests that these polyketide-nonribosomal peptides may be used for squid egg defense against potential pathogens and/or fouling microorganisms. These results indicate that BACs may provide Pseudoalteromonas sp. JC28 an ecological niche, facilitating competition against nonsymbiotic microorganisms in the host’s environment.​

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural mechanisms for VMAT2 inhibition by tetrabenazine

The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson’s disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2’s importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington’s chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Recent advances in nano-scale spatial resolution x-ray microscopy instrumentation at NSLS-II

X-ray microscopy is an invaluable and powerful characterization tool applied in many scientific fields, such as materials science, biology, environmental science, and energy research. In recent years it has been driven by rapid developments of novel technologies and systems resulting in imaging experiments elucidating structural inhomogeneities and chemical reactions at the nanometer scale. To obtain high spatial resolution comprehensive chemical and structural information, an X-ray microscope must be equipped with adequate capabilities and allow for simultaneous acquisition of multiple datasets. In recent years, a number of X-ray microscopes have been designed, constructed, and commissioned at NSLS-II. Here we provide an overview of the microscopy instrumentation development program at NSLS-II and specifically focus on the multilayer Laue lens-based hard X-ray nanoprobe optimized for ~10 nm spatial resolution imaging, its current status, and future upgrades along with recently constructed Kirkpatrick-Baez based scanning microscope designed for ~100 nm spatial resolution experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Resolving Atomic-Scale Structure and Chemical Coordination in High-Entropy Alloy Electrocatalysts for Structure–Function Relationship Elucidation

The recent breakthrough in confining five or more atomic species in nanocatalysts, referred to as high-entropy alloy nanocatalysts (HEAs), has revealed the possibilities of multielemental interactions that can surpass the limitations of binary and ternary electrocatalysts. The wide range of potential surface configurations in HEAs, however, presents a significant challenge in resolving active structural motifs, preventing the establishment of structure-function relationships for rational catalyst design and optimization. Here, we present a methodology for creating sub-5 nm HEAs using an aqueous-based peptide-directed route. Using a combination of pair distribution function and X-ray absorption spectroscopy, HEA structure models are constructed from reverse Monte Carlo modeling of experimental data sets and showcase a clear peptide-induced influence on atomic-structure and chemical miscibility. Coordination analysis of our structure models facilitated the construction of structure-function correlations applied to electrochemical methanol oxidation reactions, revealing the complex interplay between multiple metals that leads to improved catalytic properties. Our results showcase a viable strategy for elucidating structure-function relationships in HEAs, prospectively providing a pathway for future materials design.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Novel Amorphous Carbons for the Adsorption of Phosphate: Part I. Elucidation of Chemical Structure of N-Metal-Doped Chars

Due to phosphate’s necessity in agriculture and its danger to the environment, the development of adsorbents for its removal has been the subject of intensive research activity. Although the introduction of nitrogen functionality to chars and modification of biochar with metals have proven to change the character of the char structure, making it more active toward nutrients, there is no study regarding the doping of biochar with metals and nitrogen simultaneously for the adsorption of phosphates. This paper is the first of two in which we report the production, characterization, and evaluation of N-metal-doped biochars from cellulose for phosphate removal from liquid effluents. In this part, we describe the production and characterization of N-Ca-, N-Fe-, and N-Mg-doped biochars. The elemental composition and surface area of each of the materials produced is reported. Elemental and surface characterization of the chars are reported with the largest N content appearing at a temperature of 800 °C (12.5 wt %) and a maximum surface area for biochar produced at 900 °C (1314 m2/g). All of the adsorbents were visualized by scanning electron microscope (SEM), confirming that although there are some crystals on the surface of the biochar produced, most of the N, Mg, and Ca are part of the polyaromatic ring structure. Transmission electron microscope (TEM) images clearly show the formation of nanoclusters with the metals in the case of N-Fe and N-Ca biochars. The N-Mg biochars show a uniform distribution of the Mg through the carbon surface. X-ray photoelectron spectroscopy (XPS) studies of the biochars produced with metals and varying nitrogen levels clearly show Mg and Ca peaks shifting their position in the presence of N, suggesting the formation of stable structures between metals and N in the carbon polyaromatic ring system. To elucidate the nature of these structures, we conducted DFT-based calculations on different configurations of the nitrogenated structures. The calculated binding energy shifts were found to closely match the XPS experimental binding energy, confirming the likelihood of these structures in biochar. Finally, based on our experimental and modeling results, we hypothesize that an important fraction of the Mg and Ca is introduced to these biochars at the edges. Another fraction of Mg and Ca is in the form of phthalocyanine-like internal structures. More experimental studies are needed to confirm the formation of these very interesting structures and their potential use as adsorbents or catalysts.

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

Elucidating the Solvation Structures and Dynamics in Iron-Based TFSI – Aqueous Systems

This study investigates the solvation structures and dynamics of bis(trifluoromethanesulfonyl)imide (TFSI – )-based aqueous electrolytes, focusing on Fe(TFSI) 2 and Fe(TFSI) 3 . Using advanced characterization techniques, including small-angle X-ray scattering, molecular dynamics simulations, Raman spectroscopy, Fourier-transform infrared spectroscopy, and nuclear magnetic resonance, we elucidate how the electrolyte concentration influences ion association, solvation structures, and transport properties. Furthermore, our findings show that higher electrolyte concentrations promote the formation of contact ion pairs and anion networks, leading to reduced ion mobility and altered hydrogen-bonding dynamics. These insights provide a deeper understanding of solvation phenomena in TFSI-based electrolytes and contribute to the development of efficient and environmentally friendly iron electrodeposition processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Elucidating the Atomic Structures of the Gel Layer Formed during Aluminoborosilicate Glass Dissolution: An Integrated Experimental and Simulation Study

The altered glasses produced during aqueous dissolution of silicate and borosilicate glasses are among the most complex structures to understand at the atomic level due to their amorphous nature, random porosity and various levels of hydration. In this study, we gained insights of the complex atomic structures of altered aluminoborosilicate glasses by combining a range of experimental and computational approaches. The altered glasses were prepared by dissolution of three glasses with varying level of alumina in acid for 7 days. A comprehensive set of experimental [elemental analysis, high-energy X-ray diffraction, 29 Si and 27 Al solid-state nuclear magnetic resonance (NMR), and O 1s X-ray photoelectron spectroscopy (XPS)] and modeling (molecular dynamics (MD) simulations using non-reactive and reactive force fields) were used to study the atomic structures of these altered glasses. Elemental analysis showed that most of the B in the pristine glasses was leached into the solution and was not contained in the altered glass. The 29 Si and 27 Al solid-state NMR spectra revealed that the altered glasses have more polymerized silicate network as compared to those in the pristine glasses due to the reformation of linkages among Si and Al oxygen polyhedral in the altered glasses. The bridging and non-bridging (or hydroxyl O) atoms in the altered glasses were also quantified from their O 1s XPS spectra. Atomic structure models of the altered glasses were constructed by using MD simulations using the reactive force field based on the compositional information obtained from experiments. Various pore structures were generated using the charge-scaling (CS) method by using different initial densities and CS temperatures; the best CS parameters of each alternated glass were then determined by comparing with the experimental structure factors obtained from high energy X-ray diffraction. Pore and the atomic structures and vibrational properties around these pore surfaces were analyzed. Furthermore, these results from this comprehensive study thus provides a realistic insight into the pore morphology, atomic structure, and vibrational properties of altered glasses.

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

Interplay Between Metastability and Mechanically Induced Structural Instability in CsPbBr 3 Photovoltaic Perovskite

An atomic-level understanding of the underlying structural metastability is still absent in halide perovskite photovoltaic systems. Focusing on the model material CsPbBr 3 , the impact of mechanically induced atomic structure alteration is elucidated through structural modeling and X-ray diffraction measurements. Sudden Cs–Br bond breaking drives the system metastability, where the first-order transition arises from cation-halide bond strain relief by severing the corner connectivity of the PbBr 6 units. The pressure–volume and entropy terms govern the Gibbs free-energy landscape in halide perovskites. In conclusion, metastability is revealed as a critical factor limiting the performance of lead halide perovskites under extreme but natural environments.

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

Catalytic Water Electrolysis by Co–Cu–W Mixed Metal Oxides: Insights from X-ray Absorption Spectroelectrochemistry

Mixed metal oxides (MMOs) are a promising class of electrocatalysts for the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). Despite their importance for sustainable energy schemes, our understanding of relevant reaction pathways, catalytically active sites, and synergistic effects is rather limited. Here, we applied synchrotron-based X-ray absorption spectroscopy (XAS) to explore the evolution of the amorphous Co–Cu–W MMO electrocatalyst, shown previously to be an efficient bifunctional OER and HER catalyst for water splitting. Ex situ XAS measurements provided structural environments and the oxidation state of the metals involved, revealing Co 2+ (octahedral), Cu + / 2+ (tetrahedral/square-planar), and W 6+ (octahedral) centers. Operando XAS investigations, including X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), elucidated the dynamic structural transformations of Co, Cu, and W metal centers during the OER and HER. The experimental results indicate that Co 3+ and Cu 0 are the active catalytic sites involved in the OER and HER, respectively, while Cu 2+ and W 6+ play crucial roles as structure stabilizers, suggesting strong synergistic interactions within the Co–Cu–W MMO system. In conclusion, these results, combined with the Tafel slope analysis, revealed that the bottleneck intermediate during the OER is Co 3+ hydroperoxide, whose formation is accompanied by changes in the Cu–O bond lengths, pointing to a possible synergistic effect between Co and Cu ions. Our study reveals important structural effects taking place during MMO-driven OER/HER electrocatalysis and provides essential experimental insights into the complex catalytic mechanism of emerging noble-metal-free MMO electrocatalysts for full water splitting.

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

Elucidating the local structure of Li 1+ x Al x Ti 2– x (PO 4 ) 3 and Li 3 Al x Ti 2– x (PO 4 ) 3 ( x = 0, 0.3) via total scattering

Li 1+x Al x Ti 2–x (PO 4 ) 3 (LATP) and Li 3 Al x Ti 2–x (PO 4 ) 3 (x = 0, 0.3) are promising candidates in all-solid-state batteries due to their high room temperature conductivity of 10 –3 S cm –1 and air- and moisture-stability. They also exhibit unusual thermal expansion properties, with Li 1+x Al x Ti 2–x (PO 4 ) 3 showing near-zero thermal expansion along the a axis while Li 3 Al x Ti 2–x (PO 4 ) 3 exhibits polynomial positive thermal expansion along the a axis and polynomial negative thermal expansion along the c axis. A crucial component to understanding these properties is understanding the local structure. Total scattering is a powerful analytical technique as it provides information on the long-range, average structure as well as the local structure. Here, we report the first X-ray and neutron total scattering experiments performed on Li 1+x Al x Ti 2–x (PO 4 ) 3 and Li 3 Al x Ti 2–x (PO 4 ) 3 (x = 0, 0.3). We show that the PO 4 and TiO 6 polyhedra experience very little expansion of the P/Ti–O bonds up to 800 °C, nor is there much expansion when the Li content increases significantly. The minor thermal expansion of the nearest-neighbor bonds of the polyhedra is revealed to be the reason behind the unusual thermal expansion properties, causing the near-zero thermal expansion along a in Li 1+x Al x Ti 2–x (PO 4 ) 3 and moving as whole units in Li 3 Al x Ti 2–x (PO 4 ) 3 . The structural robustness of the framework is also the reason for the increased conductivity as Li content increases, as the framework remains undistorted as Li content increases, permitting Li-ion mobility as the number of charge carriers increases. Finally, this suggests that phosphate-based framework materials beyond LATP would also be a good material space to explore for new Li-ion (and other ion-) conducting materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗