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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Local atomic configurations in mechanically alloyed amorphous (FeCoNi) 70 Ti 10 B 20 powders

Here, the atomic structure of amorphous (FeCoNi) 70 Ti 10 B 20 alloy synthesized by mechanical alloying was investigated using high energy synchrotron X-ray diffraction and inverse Monte Carlo simulations of pair distribution functions. Empirical potential structure refinement indicates a chemical short-range order at the length scales of 2.1–2.5 Å via local atomic arrangements forming deformed bcc-like clusters. The structural model obtained was described by bond lengths, coordination numbers, and bond angle distribution functions determined for the first neighbor atoms by x-ray scattering supplemented with 3D Monte Carlo simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB

Iron is an essential element for nearly all organisms, and under anoxic and/or reducing conditions, Fe 2+ is the dominant form of iron available to bacteria. The ferrous iron transport (Feo) system is the primary prokaryotic Fe 2+ import machinery, and two constituent proteins (FeoA and FeoB) are conserved across most bacterial species. However, how FeoA and FeoB function relative to one another remains enigmatic. In this work, we explored the distribution of feoAB operons encoding a fusion of FeoA tethered to the N-terminal, G-protein domain of FeoB via a connecting linker region. We hypothesized that this fusion poises FeoA to interact with FeoB to affect function. To test this hypothesis, we characterized the soluble NFeoAB fusion protein from Bacteroides fragilis, a commensal organism implicated in drug-resistant infections. Using X-ray crystallography, we determined the 1.50-Å resolution structure of BfFeoA, which adopts an SH3-like fold implicated in protein–protein interactions. Using a combination of structural modeling, small-angle X-ray scattering, and hydrogen–deuterium exchange mass spectrometry, we show that FeoA and NFeoB interact in a nucleotide-dependent manner, and we mapped the protein–protein interaction interface. Finally, using guanosine triphosphate (GTP) hydrolysis assays, we demonstrate that BfNFeoAB exhibits one of the slowest known rates of Feo-mediated GTP hydrolysis that is not potassium-stimulated. Importantly, truncation of FeoA from this fusion demonstrates that FeoA–NFeoB interactions function to stabilize the GTP-bound form of FeoB. Taken together, our work reveals a role for FeoA function in the fused FeoAB system and suggests a function for FeoA among prokaryotes.

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

A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex

Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, “PAAR-like” DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG–PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.

DUF2169↗
DOE OSTI2023

Ab initio study of the structure and properties of amorphous silicon hydride from accelerated molecular dynamics simulations

This paper presents a large-scale ab initio simulation study of amorphous silicon hydride (a-Si 1-x H x ) with an emphasis on the structure and properties of the material across a range of hydrogen concentration by combining accelerated molecular dynamics (MD) simulations with first-principles density-functional calculations. The accelerated MD scheme relied on classical metadynamics, which enabled the development of 2500+ high-quality structural models of a-Si 1-x H x , with system sizes ranging from 150 to 6000 atoms and hydrogen concentrations vary from 6 to 20 at. %. The resulting amorphous networks were found to be completely free from any coordination defects and that they all exhibited a pristine band-gap in their electronic spectrum. The microstructural properties of hydrogen distributions were examined with an emphasis on the presence of isolated and clustered environments of hydrogen atoms. The results were compared with experimental data obtained from X-ray diffraction, infrared spectroscopy and nuclear magnetic resonance studies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structure of triple perovskite BaSr 2 MgTa 2 O 9 revisited

An experimental investigation of the structure and crystal-chemistry of the triple perovskite BaSr 2 MgTa 2 O 9 is reported. Polycrystalline BaSr 2 MgTa 2 O 9 was synthesized via solid-state reaction and its structure quantitatively probed at 10 and 300 ​K using neutron diffraction. Monoclinic (A2/m, a 0 $\bar{b}$ – $b$ – ) and trigonal structural models (P$\bar{3}$c1, a – a – a – ) were fit to diffraction data. The former was found to correctly reproduce experimental intensities, while the latter failed to do so. This difference is attributed to the ability of the monoclinic model to accurately reflect octahedral tilting. BaSr 2 MgTa 2 O 9 features corner-sharing MgO 6 and TaO 6 octahedra with barium and strontium cations occupying cubooctahedral holes. Barium and strontium are disordered over the A site, whereas B site cations magnesium and tantalum are ordered. Finally, chemical substitution of strontium for barium in Ba 3 MgTa 2 O 9 induces tilting of MgO 6 and TaO 6 octahedra in two directions and geometric distortions of MgO 6 octahedra.

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

Large Propagation-Direction-Dependent Circularly Polarized Emission and Scattering Anisotropies of a Chiral Organic-Inorganic Semiconductor

Chiral materials are important tools for transducing circularly polarized light within many emerging opto-electronic and spin-based technologies. Here, we demonstrate that thin films of a bismuth iodide-based 0D chiral hybrid organic-inorganic semiconductor (HOIS) exhibit large anisotropy values in circularly polarized light emission (CPLE) that approach 50%, with mirror-image responses from front- and back-side measurements. A comprehensive analysis of light-wave propagation, absorption, emission, and scattering is constructed on the basis of a symmetry-derived exciton fine structure model, which accurately describes the direction and polarization dependence of the observed excitonic circular dichroism and CPLE, including contributions from both photoluminescence and resonant Raman scattering. Our analysis indicates that molecular chirality drives preferential film alignment with respect to the out-of-plane lattice vector direction, producing the observed anisotropies. This first demonstration in an HOIS system provides a unique route for enhancing polarization-dependent emission, and circularly polarized light transduction more broadly, in self-assembled HOIS.

14 SOLAR ENERGY↗
DOE OSTI2023

Binding of radionuclides and surrogate to 18-crown-6 ether by density functional theory

For this work, we use density functional theory to investigate the interactions of cerium, americium, and curium cations with crown ethers. Our calculations reveal that the modeled structure of cerium integrated within the crown ether is in good agreement with experimental data, with the negative binding energy indicating that capturing the cerium nitrates is thermodynamically favorable. Our results demonstrate that crown ethers can also bind americium and curium, providing insights into the potential applications of crown ether in radionuclide sequestration. Finally, we explore the impact of the skeleton modification of different crown ethers through by substitution of nitrogen atoms in the core of the crown ether for oxygen atoms and find that this structural modification significantly increases the radionuclide binding energies. These findings provide insights on the potential for the use of organic linkers such as crown ethers to address the urgent needs in radionuclide sequestration, separation and sensing.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Investigating radioactive negative ion production via double electron capture

The relative cross sections for radioactive negative ion production via double electron capture have been measured for collisions between a 40 keV projectile beam of uranium-238 and potassium vapor. This was performed at the collinear resonance ionization spectroscopy (CRIS) experiment at CERN-ISOLDE and is a step towards measuring the electron affinities (EAs) of elements that cannot be efficiently produced in negative ion sources at radioactive ion beam (RIB) facilities. This includes short-lived radioactive isotopes that have low production quantities and heavy and superheavy elements that systematically have smaller EAs than work functions of available ion source materials. Negative ions are particularly sensitive to electron–electron correlation effects, which make such studies ideal for benchmarking atomic structure models that go beyond the independent particle model. While the EAs of most light elements have been measured, experimental investigations on heavier elements, namely the actinides, remain scarce due to their radioactive nature and production difficulty. By developing negative ion production by charge exchange, we aim to make these studies feasible at RIB facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

The role of dissolved pyrogenic carbon from biochar in the sorption of As(V) in biogenic iron (oxyhydr)oxides

Water contamination by arsenic (As) affects millions of people around the world, making techniques to immobilize or remove this contaminant a pressing societal need. Biochar and iron (oxyhydr)oxides [in particular, biogenic iron (oxyhydr)oxides (BIOS)] offer the possibility of stabilizing As in remediation systems. However, little is known about the potential antagonism in As sorption generated by the dissolved organic carbon (DOC) from biochar, or whether DOC affects how As(V) interacts with BIOS. For this reason, our objectives were to evaluate the i) As(V) sorption potential in BIOS when there is presence of DOC from pyrolyzed biochars at different temperatures; and ii) identify whether the presence of DOC alters the surface complexes formed by As(V) sorbed in the BIOS. We conducted As(V) sorption experiments with BIOS at circumneutral pH conditions and in the presence of DOC from sugarcane (Saccharum officinarum) straw biochar at pyrolyzed 350 (BC350) and 750 °C (BC750). The As(V) content was quantified by inductively coupled plasma mass spectrometry, and the BIOS structure and As(V) sorption mechanisms were investigated by X-ray absorption spectroscopy. In addition, the organic moieties comprising the DOC from biochars were investigated by attenuated total reflectance Fourier transform infrared spectroscopy. The addition of DOC did not change the biomineral structure or As(V) oxidation state. The presence of DOC, however, reduced by 25 % the sorption of As(V), with BC350 being responsible for the greatest reduction in As(V) sorption capacity. Structural modeling revealed As(V) predominantly formed binuclear bidentate surface complexes on BIOS. The presence of DOC did not change the binding mechanism of As(V) in BIOS, suggesting that the reduction of As(V) sorption to BIOS was due to site blocking. In conclusion, our results bring insights into the fate of As(V) in surface waters and provide a basis for understanding the competitive sorption of As(V) in environments with biochar application.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Selective acetate recognition and sensing using SWCNTs functionalized with croconamides

Croconamides are a new class of dual-hydrogen bond donors that have attracted interest in anion recognition and sensing applications due to their strong H-bond donation capability. In this work, we report chemiresistive sensors for the detection of anions based on poly(4-vinylpyridine) (P4VP)-wrapped single-walled carbon nanotubes (SWCNTs) functionalized with croconamide-based selectors. Model structures of asymmetric N,N-substituted croconamide selectors with N,N-substitutional groups of alkyl cationic pyridinium and electron-withdrawing moieties such as aniline (6) and 3,5-bis(trifluoromethyl)phenyl (7) groups were synthesized and their binding affinities for various anions were characterized using UV–vis and 1 H NMR titrations. Switchable binding of oxoanions was observed with selector 7, wherein HSO 4 – formed hydrogen bonding interactions and acetate (AcO – ) induced deprotonation of the NH- protons of the croconamide. Large sensitivity transitions were obtained toward AcO – for both P4VP-6-SWCNT (S = 95.68 ± 2.11 %) and P4VP-7-SWCNT (S = 140.91 ± 3.68 %) at 83.33 mM, which was attributed to deprotonation of the croconamide selectors upon addition of AcO – . In conclusion, three serial sensors were assembled in a sensor array that rapid and selective screening of AcO – was demonstrated against other oxoanions such as HSO 4 – and H 2 PO 4 – in real-time.

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

Electronic and thermal properties of the phase-change memory material, Ge 2 Sb 2 Te 5 , and results from spatially resolved transport calculations

Here, we report new insights into the electronic, structural, and transport (heat and charge) properties of the phase-change memory material amorphous Ge 2 Sb 2 Te 5 . Using realistic structural models of Konstantinou et al., (2019), we analyze the topology, electronic states, and lattice dynamics with density functional methods, including hybrid-functional calculations and machine-learned interatomic potentials. The Kohn–Sham orbitals near the Fermi level display a strong electron–phonon coupling, and exhibit large energy fluctuations at room temperature. The conduction tail states exhibit larger phonon-induced fluctuations than the valence tail states. To resolve transport at the atomic scale, we employ space-projected electronic conductivity and site-projected thermal conductivity methods. Local analysis of heat transport highlights the role of filamentary networks dominated by Te, with Sb and Ge making progressively smaller contributions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Direct observation of oxygen vacancy ordering evolution in cerium oxide at varying concentrations via high-resolution transmission electron microscopy

Under illumination by a 300 keV electron beam, oxygen vacancy ordering structures are induced within cerium oxide grains. Here, our high-resolution transmission electron microscopy (HRTEM) study, supported by image simulation, reveals the evolution of these structures as vacancy concentration increases. The observed fluorite-type superlattice structures are identified as CeO 1.825 , CeO 1.75 , Ce 2 O 3 , displaying a gradient in oxygen vacancy concentration moving away from the grain surface. Correspondingly, the structural sequence transitions from Ce 2 O 3 to CeO 1.75 and then to CeO 1.825 . Without the constraints of surrounding grains, fluorite-type Ce 2 O 3 nanocrystals show a preference for transformation into an A-type trigonal structure. Notably, at temperatures up to 200°C, only the perfect fluorite structure is observed. Structural models were validated through both [110] and [001] projections. Our findings further confirm lattice expansion associated with local oxygen vacancy enrichment, which can be compensated by the formation of stacking faults, where a {111} oxygen plane is lost at defect sites.

Cerium oxide↗
DOE OSTI2020

The Role of Surface Oxygen Vacancies in BiVO 4

Bismuth vanadate (BiVO 4 ) is a widely studied oxide in solar water splitting, known for its ease of synthesis, high charge extraction yields, and advantageous band alignment with water. We present a combined first-principles and experimental study of the electronic structure of the (010) surface of BiVO 4 aimed at disentangling the impact of the surface and bulk oxygen vacancies on the electronic structure and transport properties. We found that oxygen vacancies are deep donors at the surface as they are in the bulk; our calculations on defect and polaron formation energies suggest that, while polarons formed from oxygen vacancies in the bulk can contribute to conductivity, those at the surface likely do not. Our results also show that out-of-plane structural relaxations at the surface contribute to the relatively immobile nature of electron polarons derived from surface oxygen vacancies. The structural model derived from first-principles calculation was validated by comparing computed results with experimental measurements of single-crystal and epitaxially grown single-crystalline BiVO 4 samples. Finally, we also found a reasonably good agreement between our calculated and measured work functions for BiVO 4 samples with and without oxygen vacancies.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Stabilization of Dinuclear Rhodium and Iridium Clusters on Layered Titanate and Niobate Supports

Atomically dispersed organometallic clusters can provide well-defined nuclearity of active sites for both fundamental studies as well as new regimes of activity and selectivity in chemical transformations. More recently, dinuclear clusters adsorbed onto solid surfaces have shown novel catalytic properties resulting from the synergistic effect of two metal centers to anchor different reactant species. Difficulty in synthesizing, stabilizing, and characterizing isolated atoms and clusters without agglomeration challenges allocating catalytic performance to atomic structure. Here, we explore the stability of dinuclear rhodium and iridium clusters adsorbed onto layered titanate and niobate supports using molecular precursors. Both systems maintain their nuclearity when Statistical analysis of HAADF-STEM images revealed that rhodium and iridium dimers had mean cluster-to-cluster distances very similar to what is expected from a random distribution of atoms over a large area, indicating that they are dispersed without aggregation. The stability of dinuclear rhodium clusters supported on titanate nanosheets was also investigated by X-ray absorption fine structure (EXAFS), DRIFTS, and first-principles calculations. Both X-ray absorption spectroscopy and HAADF-STEM simulations, guided by density functional theory (DFT)-optimized structure models, suggested that rhodium dimers adsorb onto the nanosheets in an end-on binding mode that is stable up to 100 degrees C under reducing conditions. Finally, this study highlights that crystalline nanosheets derived from layered metal oxides can be used as model supports to selectively stabilize dinuclear clusters, which could have implications for heterogeneous catalysis.

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

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree–Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Furthermore, our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

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

Density Functional Theory Investigation of Oxidation Intermediates on Gold and Gold–Silver Surfaces

Gold and gold-silver alloys can be active and selective oxidation catalysts. Previous work has suggested that O 2 dissociation occurs at bimetallic step sites on gold-silver alloys, but the site responsible for the rest of the reaction steps has not been studied. As a first step in gaining insight into this issue, in this work we investigated the adsorption of oxygen and other oxidation intermediates on the (111) and (211) facets of gold-silver alloys using density functional theory. Oxygen and silver coverage effects were analyzed, and different model structures were compared. We also examined the energy barriers for the diffusion of atomic oxygen to gain insight into O migration and spillover. On (111) surfaces, O adsorption is much stronger at low O coverage (less than 0.22 ML), while on (211) surfaces O is strongly bound at both high and low O coverage. O diffusion across the step is faster than diffusion along the step. Ag stabilizes O, both when directly bound to it and when in an adjacent site. Ag also reduces repulsive O-O interactions at low O coverage. Our calculated reaction barriers for O-assisted CH 3 O dehydrogenation suggest that reaction is faster on steps than on terraces. Overall, our findings suggest that spillover of O from Ag-rich steps to Au-rich terraces does not occur, and that oxidation reactions on gold-silver alloys occurs on step sites. More specifically, oxidation likely occurs either on Ag-rich step sites or on Au-rich step sites that are adjacent to Ag-rich step sites.

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

Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases

Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.

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

Twisto-Electrochemical Activity Volcanoes in Trilayer Graphene

In this work, we develop a twist-dependent electrochemical activity map, combining a low-energy continuum electronic structure model with modified Marcus–Hush–Chidsey kinetics in trilayer graphene. We identify a counterintuitive rate enhancement region spanning the magic angle curve and incommensurate twists in the system geometry. We find a broad activity peak with a ruthenium hexamine redox couple in regions corresponding to both magic angles and incommensurate angles, a result qualitatively distinct from the twisted bilayer case. Flat bands and incommensurability offer new avenues for reaction rate enhancements in electrochemical transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗