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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 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Does photoinduced structural change by β-rhombohedral boron occur at room temperature?

β-rhombohedral boron (β-B) is an intriguing solid among the elements. The crystal structure of β-B is widely accepted as a complex structure based on the B 12 clusters, and with a lot of intrinsic structural defects. In the last decade, β-B was proved to be the only elemental semiconductor that exhibits the self-compensation property accompanied by changing structural defects during atom doping. Moreover, it is reported that various physical properties of β-B change discontinuously around 550 K, which may originate from defect diffusion [S. Hoffmann and H. Werheit, Solid State Sciences 14, 1572 (2012)]. We previously reported that a volume expansion of about 1.5% takes place above this temperature (between 650 K and 850 K). On the other hand, this expanded structure is stable in dark conditions for more than 4.5 months. Finally, light irradiation at room temperature reverses the volume back to the initial state, and a possible scenario will be discussed in this paper.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS

Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An experimental and computational investigation of the structure and spectroscopic signatures of α -UO 3

α-UO 3 is a common intermediate compound found in the nuclear fuel cycle, yet the exact crystal structure of this material has long been debated. Inconsistent computational and experimental data in previous works has led to varying conclusions between authors. Furthermore, to ensure the validity of our results in this work, the structural and spectroscopic signatures of pure phase α-UO 3 are investigated using powder X-ray diffraction and optical vibrational spectroscopy (infrared and Raman). Rietveld refinement of powder X-ray diffraction data on pure phase α-UO 3 collected in this work allows us to propose an alteration to the currently accepted C2mm structure (a = 3.9705 Å, b = 6.8553 Å, c = 4.15955 Å, α = β = γ = 90°) for α-UO 3 with no uranyl [UO 2 2+ ] bonds. Raman spectra collected using two excitation wavelengths (two instruments using 532 nm and one 785 nm) are presented, and differences with recently published results are discussed. Infrared spectra from two instruments used here agree well with recently published results, but the spectral range encompassed in our data extends past what has been reported with modern techniques. Additionally, we provide tentative vibrational mode assignments based on density functional perturbation theory calculations and resulting phonon eigenvector visualizations. Unexpected features in the optical vibrational spectra of α-UO 3 are explained by unique features in the structure we present.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Chemical crystallography by serial femtosecond X-ray diffraction

Abstract Inorganic–organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties 1 . This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction 2,3 and electron microdiffraction 4–11 . Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals. We subjected microcrystalline suspensions to X-ray free-electron laser radiation 12,13 and obtained thousands of randomly oriented diffraction patterns. We determined unit cells by aggregating spot-finding results into high-resolution powder diffractograms. After indexing the sparse serial patterns by a graph theory approach 14 , the resulting datasets can be solved and refined using standard tools for single-crystal diffraction data 15–17 . We describe the ab initio structure solutions of mithrene (AgSePh) 18–20 , thiorene (AgSPh) and tethrene (AgTePh), of which the latter two were previously unknown structures. In thiorene, we identify a geometric change in the silver–silver bonding network that is linked to its divergent optoelectronic properties 20 . We demonstrate that smSFX can be applied as a general technique for structure determination of beam-sensitive microcrystalline materials at near-ambient temperature and pressure.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Regulation of Surface Defect Chemistry toward Stable Ni-Rich Cathodes

Surface reconstruction of Ni-rich layered oxides (NLO) degrades the cycling stability and safety of high-energy-density lithium-ion batteries (LIBs), which challenges typical surface-modification approaches to build a robust interface with electrochemical activity. Here, a strategy of leveraging the low-strain analogues of Li- and Mn-rich layered oxides (LMR) to reconstruct a stable surface on the Ni-rich layered cathodes is proposed. The new surface structure not only consists of a gradient chemical composition but also contains a defect-rich structure regarding the formation of oxygen vacancies and cationic ordering, which can simultaneously facilitate lithium diffusion and stabilize the crystal structure during the (de)lithiation. These features in the NLO lead to a dramatic improvement in electrochemical properties, especially the cyclability under high voltage cycling, exhibiting the 30% increase in capacity retention after 200 cycles at the current density of 1 C (3.0-4.6 V). We report the findings offer a facile and effective way to regulate defect chemistry and surface structure in parallel on Ni-rich layered structure cathodes to achieve high-energy density LIBs.

25 ENERGY STORAGE↗
DOE OSTI2025

Structure Prediction of Ionic Epitaxial Interfaces with Ogre Demonstrated for Colloidal Heterostructures of Lead Halide Perovskites

Colloidal epitaxial heterostructures are nanoparticles composed of two different materials connected at an interface, which can exhibit properties different from those of their individual components. Combining dissimilar materials offers exciting opportunities to create a wide variety of functional heterostructures. However, assessing structural compatibility–the main prerequisite for epitaxial growth–is challenging when pairing complex materials with different lattice parameters and crystal structures. This complicates both the selection of target heterostructures for synthesis and the assignment of interface models when new heterostructures are obtained. Here, we demonstrate Ogre as a powerful tool to accelerate the design and characterization of colloidal heterostructures. To this end, we implemented developments tailored for the high-efficiency prediction of epitaxial interfaces between ionic/polar materials, which encompass most colloidal semiconductors. These include the use of pre-screening candidate models based on charge balance at the interface and the use of a classical potential for fast energy evaluations, with parameters automatically calculated based on the input bulk structures. These developments are validated for perovskite-based CsPbBr 3 /Pb 4 S 3 Br 2 heterostructures, where Ogre produces interface models in excellent agreement with density functional theory and experiments. Furthermore, we use Ogre to rationalize the templating effect of CsPbCl 3 on the growth of lead sulfochlorides, where perovskite seeds induce the formation of Pb 4 S 3 Cl 2 rather than Pb 3 S 2 Cl 2 due to better epitaxial compatibility. Finally, combining Ogre simulations with experimental data enables us to unravel the structure and composition of the hitherto unsolved CsPbBr 3 /Bi x Pb y S z interface, and to assign a structure to several other reported metal halide- and oxide-based interfaces. The Ogre package is available on GitHub or via the OgreInterface desktop application, available for Windows, Linux, and Mac.

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

Machine-learning accelerated geometry optimization in molecular simulation

Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of thermodynamic and kinetic properties of molecular and crystal structures. This process is slow at the quantum level of theory because it involves an iterative calculation of forces using quantum chemical codes such as density functional theory (DFT), which are computationally expensive and which limit the speed of the optimization algorithms. It would be highly advantageous to accelerate this process because then one could do either the same amount of work in less time or more work in the same time. Here, we provide a neural network (NN) ensemble based active learning method to accelerate the local geometry optimization for multiple configurations simultaneously. We illustrate the acceleration on several case studies including bare metal surfaces, surfaces with adsorbates, and nudged elastic band for two reactions. In all cases, the accelerated method requires fewer DFT calculations than the standard method. In addition, we provide an Atomic Simulation Environment (ASE)-optimizer Python package to make the usage of the NN ensemble active learning for geometry optimization easier.

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

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗
DOE OSTI2024

Absence of magnetoelastic deformation in the spin-chain compound CuBr 2

Here, we investigate a spin-$\frac{1}{2}$ antiferromagnet, CuBr 2 , which has quasi-one-dimensional structural motifs. The system has previously been observed to exhibit unusual Raman modes possibly due to a locally deformed crystal structure driven by the low-dimensional magnetism. Using hard x-ray scattering and neutron total scattering, here we aim to verify a specific form of tetramerizing deformation proposed in the previous study. Apart from diffuse scattering signals, which we can reproduce by performing a thorough modeling of the lattice's thermal vibrations, we do not observe evidence for a tetramerized lattice structure within our detection sensitivity. Consequently, we consider it unlikely that the unusual Raman modes in CuBr 2 arise from quantum spin-singlet-driven lattice deformations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Dynamically tunable second-harmonic generation using hybrid nanostructures incorporating phase-change chalcogenides

Nonlinear metasurfaces with high conversion efficiencies have been vastly investigated. However, strong dynamic tunability of such devices is limited in conventional passive plasmonic and dielectric material platforms. Germanium antimony telluride (GST) is a promising phase-change chalcogenide for the reconfiguration of metamaterials due to strong nonvolatile changes of the real and imaginary parts of the refraction index through amorphous-crystalline phase change. The orderly structured GST has an even higher potential in tunable second-harmonic generation (SHG) with a non-centrosymmetric crystal structure at the crystalline phase, while the amorphous phase of GST does not exhibit bulk second-order nonlinearity. Here, we experimentally demonstrate SHG switches by actively controlling the crystalline phase of GST for a GST-based hybrid metasurface featuring a gap-surface plasmon resonance, and a quarter-wave asymmetric Fabry–Perot (F–P) cavity incorporating GST. We obtain SHG switches with modulation depths as high as ~ 20 dB for the wavelengths at the on-state resonance. We also demonstrate the feasibility of multi-level SHG modulation by leveraging three controlled GST phases, i.e., amorphous, semi-crystalline, and crystalline, for the gap-surface plasmon hybrid device, which features stronger light–matter interaction and has higher resonant SHG efficiencies than the asymmetric F–P cavity device at respective GST phases. This research reveals that GST-based dynamic SHG switches can be potentially employed in practical applications, such as microscopy, optical communication, and photonic computing in the nonlinear regime.

42 ENGINEERING↗
DOE OSTI2024

Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB

In the Firmicutes phylum, GpsB is a membrane associated protein that coordinates peptidoglycan synthesis with cell growth and division. Although GpsB has been studied in several bacteria, the structure, function, and interactome of Staphylococcus aureus GpsB is largely uncharacterized. To address this knowledge gap, we solved the crystal structure of the N-terminal domain of S. aureus GpsB, which adopts an atypical, asymmetric dimer, and demonstrates major conformational flexibility that can be mapped to a hinge region formed by a three-residue insertion exclusive to Staphylococci. When this three-residue insertion is excised, its thermal stability increases, and the mutant no longer produces a previously reported lethal phenotype when overexpressed in Bacillus subtilis. In S. aureus, we show that these hinge mutants are less functional and speculate that the conformational flexibility imparted by the hinge region may serve as a dynamic switch to fine-tune the function of the GpsB complex and/or to promote interaction with its various partners. Furthermore, we provide the first biochemical, biophysical, and crystallographic evidence that the N-terminal domain of GpsB binds not only PBP4, but also FtsZ, through a conserved recognition motif located on their C-termini, thus coupling peptidoglycan synthesis to cell division. Taken together, the unique structure of S. aureus GpsB and its direct interaction with FtsZ/PBP4 provide deeper insight into the central role of GpsB in S. aureus cell division.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure of the master regulator Rns reveals an inhibitor of enterotoxigenic Escherichia coli virulence regulons

Enteric infections caused by the gram-negative bacteria enterotoxigenic Escherichia coli (ETEC), Vibrio cholerae, Shigella flexneri, and Salmonella enterica are among the most common and affect billions of people each year. These bacteria control expression of virulence factors using a network of transcriptional regulators, some of which are modulated by small molecules as has been shown for ToxT, an AraC family member from V. cholerae. In ETEC the expression of many types of adhesive pili is dependent upon the AraC family member Rns. We present here the 3 Å crystal structure of Rns and show it closely resembles ToxT. Rns crystallized as a dimer via an interface similar to that observed in other dimeric AraC’s. Furthermore, the structure of Rns revealed the presence of a ligand, decanoic acid, that inhibits its activity in a manner similar to the fatty acid mediated inhibition observed for ToxT and the S. enterica homologue HilD. Together, these results support our hypothesis that fatty acids regulate virulence controlling AraC family members in a common manner across a number of enteric pathogens. Furthermore, for the first time this work identifies a small molecule capable of inhibiting the ETEC Rns regulon, providing a basis for development of therapeutics against this deadly human pathogen.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Investigating the Electronic Structure of Prospective Water-Splitting Oxide BaCe 0.25 Mn 0.75 O 3-δ before and after Thermal Reduction

BaCe 0.25 Mn 0.75 O 3-δ (BCM), a non-stoichiometric oxide with a layered perovskite-like crystal structure, has recently emerged as a prospective contender for application in renewable energy harvesting by solar thermochemical hydrogen generation. Using solar-thermal energy and a reducing environment, oxygen vacancies can be created in high-temperature BCM, and the reduced crystal so obtained can, in turn, produce H 2 by stripping oxygen from H 2 O. Therefore, a first step toward understanding the working mechanism and optimizing the performance of BCM is a thorough and comparative analysis of the electronic structure of the pristine and the reduced material. In this paper, we probe the electronic structure of BCM using the combined effort of first-principles calculations and experimental O K-edge X-ray absorption spectroscopy (XAS). The computed projected density of states (PDOS) and orbital plots are used to propose a simplified model for orbital mixing between the oxygen and metal atoms. With the help of state-of-the-art simulations, we are able to find the origins of the XAS peaks and categorize them on the basis of contribution from Ce and Mn. For the reduced crystal, the calculations show that the change in electron density resulting from the reduction is strongly localized around the oxygen vacancy. Experimental measurements reveal a marked lowering of the first O K-edge peak in the reduced crystal. Using theoretical analysis, this is shown to result from lifting of spin degeneracy in the absorption peaks as well as from a diminished O 2p contribution to the frontier unoccupied orbitals, in accordance with the tight binding scheme. The simulated results serve as a reference for the extent of spectral change as a function of the percentage of oxygen vacancies in the reduced crystal. Here, our study paves the way for the investigation of the working mechanism of BCM and for computational and experimental efforts aimed at design and discovery of efficient water-splitting oxides.

08 HYDROGEN↗
DOE OSTI2020

Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR

Biased agonists of G protein–coupled receptors (GPCRs) preferentially activate a subset of downstream signaling pathways. In this work, we present crystal structures of angiotensin II type 1 receptor (AT1R) (2.7 to 2.9 angstroms) bound to three ligands with divergent bias profiles: the balanced endogenous agonist angiotensin II (AngII) and two strongly β-arrestin–biased analogs. Compared with other ligands, AngII promotes more-substantial rearrangements not only at the bottom of the ligand-binding pocket but also in a key polar network in the receptor core, which forms a sodium-binding site in most GPCRs. Divergences from the family consensus in this region, which appears to act as a biased signaling switch, may predispose the AT1R and certain other GPCRs (such as chemokine receptors) to adopt conformations that are capable of activating β-arrestin but not heterotrimeric G q protein signaling.

Wingler, Laura M. (ORCID:0000000236885088)↗
DOE OSTI2022

Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer

Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo–electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.

Science & Technology - Other Topics↗
DOE OSTI2021

3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for Intermolecular Singlet Fission

Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri-condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion-inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P2 1 /a, arranging in a sandwich-herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many-body perturbation theory to evaluate the excited-state properties of terrylene in the solid-state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.

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

A High-Energy NASICON-Type Cathode Material for Na-Ion Batteries

Over the last decade, Na-ion batteries have been extensively studied as low-cost alternatives to Li-ion batteries for large-scale grid storage applications; however, the development of high-energy positive electrodes remains a major challenge. Materials with a polyanionic framework, such as Na superionic conductor (NASICON)-structured cathodes with formula Na x M 2 (PO 4 ) 3 , have attracted considerable attention because of their stable 3D crystal structure and high operating potential. Herein, a novel NASICON-type compound, Na 4 MnCr(PO 4 ) 3 , is reported as a promising cathode material for Na-ion batteries that deliver a high specific capacity of 130 mAh g –1 during discharge utilizing high-voltage Mn 2+/3+ (3.5 V), Mn 3+/4+ (4.0 V), and Cr 3+/4+ (4.35 V) transition metal redox. In addition, Na 4 MnCr(PO 4 ) 3 exhibits a high rate capability (97 mAh g –1 at 5 C) and excellent all-temperature performance. In situ X-ray diffraction and synchrotron X-ray diffraction analyses reveal reversible structural evolution for both charge and discharge.

25 ENERGY STORAGE↗