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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate–ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

NASICON Li 1.2 Mg 0.1 Zr 1.9 (PO 4 ) 3 Solid Electrolyte for an All‐Solid‐State Li‐Metal Battery

Abstract A thin solid electrolyte with a high Li + conductivity is used to separate the metallic lithium anode and the cathode in an all‐solid‐state Li‐metal battery. However, most solid Li‐ion electrolytes have a small electrochemical stability window, large interfacial resistance, and cannot block lithium‐dendrite growth when lithium is plated on charging of the cell. Mg 2+ stabilizes a rhombohedral NASICON‐structured solid electrolyte of the formula Li 1.2 Mg 0.1 Zr 1.9 (PO 4 ) 3 (LMZP). This solid electrolyte has Li‐ion conductivity two orders of magnitude higher at 25 °C than that of the triclinic LiZr 2 (PO 4 ) 3 . 7 Li and 6 Li NMR confirm the Li‐ions in two different crystallographic sites of the NASICON framework with 85% of the Li‐ions having a relatively higher mobility than the other 15%. The anode–electrolyte interface is further investigated with symmetric Li/LMZP/Li cell testing, while the cathode–electrolyte interface is explored with an all‐solid‐state Li/LMZP/LiFePO 4 cell. The enhanced performance of these cells enabled by the Li 1.2 Mg 0.1 Zr 1.9 (PO 4 ) 3 solid electrolyte is stable upon repeated charge/discharge cycling.

Zhou, Qiongyu↗
DOE OSTI2023

Stepwise deprotonation of truxene: structures, metal complexation, and charge-dependent optical properties

As a planar subunit of C 60 -fullerene, truxene (C 27 H 18 ) represents a highly symmetrical rigid hydrocarbon with strong blue emission. Herein, we used truxene as a model to investigate the chemical reactivity of a fullerene fragment with alkali metals. Monoanion, dianion, and trianion products with different alkali metal counterions were crystallized and fully characterized, revealing the core curvature dependence on charge and alkali metal coordination. Moreover, a proton nuclear magnetic resonance study coupled with computational analysis demonstrated that deprotonation of the aliphatic CH 2 segments introduces aromaticity in the five-membered rings. Importantly, the UV-vis absorption and photoluminescence of truxenyl anions with different charges reveal intriguing charge-dependent optical properties, implying variation of the electronic structure based on the deprotonation process. An increase in aromaticity and π-conjugation yielded a red shift in the absorption and photoluminescent spectra; in particular, large Stokes shifts were observed in the truxenyl monoanion and dianion with high emission quantum yield and time of decay. Overall, stepwise deprotonation of truxene provides the first crystallographically characterized examples of truxenyl anions with three different charges and charge-dependent optical properties, pointing to their potential applications in carbon-based functional materials.

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

Growth and structure of alpha-Ta films for quantum circuit integration

Tantalum films incorporated into superconducting circuits have exhibited low surface losses, resulting in long-lived qubit states. The remaining loss pathways originate in microscopic defects that manifest as two level systems (TLSs) at low temperatures. These defects limit performance, so careful attention to tantalum film structures is critical for optimal use in quantum devices. In this work, we investigate the growth of tantalum using magnetron sputtering on sapphire, Si, and photoresist substrates. In the case of sapphire, we present procedures for the growth of fully-oriented films with α-Ta [1 1 1]//Al2O3 [0 0 0 1] and α-Ta [1 −1 0]//Al2O3 [1 0 −1 0] orientational relationships and having residual resistivity ratio (RRR) ∼ 60 for 220 nm thick films. On Si, we find a complex grain texturing with Ta [1 1 0] normal to the substrate and RRR ∼ 30. We further demonstrate airbridge fabrication using Nb to nucleate α-Ta on photoresist surfaces. For the films on sapphire, resonators show TLS-limited quality factors of 1.3 ± 0.3 × 106 at 10 mK (for a waveguide gap and conductor width of 3 and 6 μm, respectively). Structural characterization using scanning electron microscopy, x-ray diffraction, low temperature transport, secondary ion mass spectrometry, and transmission electron microscopy reveal the dependence of residual impurities and screw dislocation density on processing conditions. The results provide practical insights into the fabrication of advanced superconducting devices including qubit arrays and guide future works on crystallographically deterministic qubit fabrication.

42 ENGINEERING↗
NASA NTRS2004

Triphasic Tooling with Small Oriented Diamond Tip for Turning and Smoothing Lightweight Mirrors

We are developing a new method for the growth of small diamond crystals at very high temperatures and pressures directly from a carbon melt. A prototype "Supercell" has been developed for this purpose. This system is capable of high rate crystal growth in relatively large working volumes. The resulting high quality diamond crystals will be incorporated into a triphasic diamond/titanium carbide/titanium composite tool, with an oriented diamond crystal at its tip. High pressure is needed to prevent degradation of diamond at high temperature, and to ensure the formation of a crack & composite structure. After grinding and polishing, the composite material will be joined to a steel holder, thus forming a diamond-tipped tool for turning and smoothing of a mirror surface. A properly oriented single-crystal diamond cuts and smoothes much better than a conventional polycrystalline diamond crystal. This is because the hardness depends on crystallographic orientation-the difference corresponds to 60-100 GPa on the Knoop scale. Our goal is to achieve surface roughness of about 1 nm, which will be accomplished by precision cutting and smoothing. The hardness of the functionally-graded diamond/titanium carbide/titanium composite tool varies from 100 GPa at its tip to 15 GPa at its base. Previous work has shown that the mass of machined material using an oriented-diamond tool is much larger than that for a standard diamond-metal composite tool.

Voronov, O. A.↗
NASA NTRS1997

A Novel Silicon Micromachined Integrated MCM Thermal Management System

"Micromachining" is a chemical means of etching three-dimensional structures, typically in single- crystalline silicon. These techniques are leading toward what is coming to be referred to as MEMS (Micro Electro Mechanical Systems), where in addition to the ordinary two-dimensional (planar) microelectronics, it is possible to build three-dimensional n-ticromotors, electrically- actuated raicrovalves, hydraulic systems and much more on the same microchip. These techniques become possible because of differential etching rates of various crystallographic planes and materials used for semiconductor n-ticrofabfication. The University of Cincinnati group in collaboration with Karl Baker at NASA Lewis were the first to form micro heat pipes in silicon by the above techniques. Current work now in progress using MEMS technology is now directed towards the development of the next generation in MCM (Multi Chip Module) packaging. Here we propose to develop a complete electronic thermal management system which will allow densifica6on in chip stacking by perhaps two orders of magnitude. Furthermore the proposed technique will allow ordinary conu-nercial integrated chips to be utilized. Basically, the new technique involves etching square holes into a silicon substrate and then inserting and bonding commercially available integrated chips into these holes. For example, over a 100 1/4 in. by 1 /4 in. integrated chips can be placed on a 4 in. by 4 in. silicon substrate to form a Multi-Chip Module (MCM). Placing these MCM's in-line within an integrated rack then allows for three-diniensional stacking. Increased miniaturization of microelectronic circuits will lead to very high local heat fluxes. A high performance thermal management system will be specifically designed to remove the generated energy. More specifically, a compact heat exchanger with milli / microchannels will be developed and tested to remove the heat through the back side of this MCM assembly for moderate and high heat flux applications, respectively. The high heat load application of particular interest in mind is the motor controller developed by Martin Marietta for Nasa to control the thruster's directional actuators on space vechicles. Work is also proposed to develop highly advanced and improved porous wick structures for use in advanced heat loops. The porous wick will be micromachined from silicon using MEMS technology, thus permitting far superior control of pore size and pore distribution (over wicks made from sintered n-ietals), which in turn is expected to led to significantly improved heat loop performance.

Kazmierczak, M. J.↗
DOE OSTI2022

Boundary characterization using 3D mapping of geometrically necessary dislocations in AM Ta microstructure

Additive manufacturing (AM) of high strength metallic materials produces microstructures and defects that deviate substantially from those created through conventional manufacturing methods. It has recently been demonstrated that with application of extreme energy densities, a high-temperature refractory metal, tantalum (Ta), can be printed to a fully dense state with exceptionally low porosity. Here we employ a combination of three-dimensional electron backscattered diffraction (EBSD) TriBeam technology and crystallographic geometrically necessary dislocation (GND) theory to characterize the microstructure and defect boundaries of this unusual AM product. Two-dimensional (2D) EBSD and these three-dimensional (3D) measurements indicate that the microstructure of AM Ta is highly oriented <111> along the build direction, yet at the same time contains large crystallographic orientation gradients that span mm’s across the build. Crystallographic GND density analysis of the 3D microstructure reveals that highly misoriented subboundaries exist within this strongly textured microstructure that have large dislocation densities of 1×10 16 m –2 , just as large as those comprising the high-angle grain boundaries (HAGBs) in the same material. The 3D crystallographic GND density mapping reveals these subboundaries are part of a complex, finely spaced network that extends throughout the entire microstructure. Here, the orientation of these boundaries can be related to the scan strategy used during printing. TEM measurements corroborate an extremely high dislocation density at the microscale and indicate a cell-like dislocation network structure existing in the AM Ta at the sub-μm scale.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Unraveling Site Selective Magnetic Properties of Cobalt Sites in Critical Elements Lean RE(TM)5 Magnet Materials

We report here our discovery of crystallographic and interstitial sites and onsite electron correlation propelled intrinsic and derived permanent magnetic properties of critical elements lean RE(TM) 5 (RE = La, Ce and TM = Fe, Co) magnet materials. A full potential linearized augmented plane wave (FP-LAPW) method within the local density approximation (LDA) is used to investigate and analyze the electronic structure and magnetism of these RE(TM) 5 type structures. To better correlate the experimental results, the effective Coulomb (U) and exchange (J) interactions (Hubbard parameters) are crucial at the transition metal sites. Results show that the main propeller of magnetic anisotropy in these compounds is the cobalt atoms at the 2c sites not the 3g sites. This site-specific property and site preference energetics are used to replace 3g sites with non-critical elements such as iron that exhibits a larger magnetic moment. Based on this strategic replacement, we predict two new compounds that have a larger hardness parameter with a relatively large energy product due to the atomic dilution caused by interstitial addition of nitrogen in the compounds: CeCo 2 Fe 3 N 2 and LaCo 2 Fe 3 N 2 .

Rare-earths↗
DOE OSTI2022

Extracting information from X-ray diffraction patterns containing Laue oscillations

The presence of Laue oscillations in a film grown on a solid surface is broadly taken as indicating a high quality, crystallographically aligned film of the targeted compound. In this paper we briefly review the origins of both Laue oscillations and Kiessig fringes and show how they can be used together to determine if extra thickness exists above or below the coherently diffracting domains. The differences between experimental and “ideal” films are discussed and the effect of structural features (roughness, different thickness coherently diffracting domains and thickness in addition to the coherently diffracting domains) are illustrated with experimental and simulated data for metal and mixed-metal chalcogenide films of titanium, bismuth, vanadium/iron, and bismuth/molybdenum. Examples are given showing how quantitative information can be extracted from experimental diffraction patterns.

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

Anisotropic Properties of Epitaxial Ferroelectric Lead-Free 0.5[Ba(Ti 0.8 Zr 0.2 )O 3 ]-0.5(Ba 0.7 Ca 0.3 )TiO 3 Films

As the energy demand is expected to double over the next 30 years, there has been a major initiative towards advancing the technology of both energy harvesting and storage for renewable energy. In this work, we explore a subset class of dielectrics for energy storage since ferroelectrics offer a unique combination of characteristics needed for energy storage devices. We investigate ferroelectric lead-free 0.5[Ba(Ti 0.8 Zr 0.2 )O 3 ]-0.5(Ba 0.7 Ca 0.3 )TiO 3 epitaxial thin films with different crystallographic orientations grown by pulsed laser deposition. We focus our attention on the influence of the crystallographic orientation on the microstructure, ferroelectric, and dielectric properties. Our results indicate an enhancement of the polarization and strong anisotropy in the dielectric response for the (001)-oriented film. The enhanced ferroelectric, energy storage, and dielectric properties of the (001)-oriented film is explained by the coexistence of orthorhombic-tetragonal phase, where the disordered local structure is in its free energy minimum.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Defect Diffusion Graph Neural Networks for Materials Discovery in High-Temperature Energy Applications

Here, the migration of crystallographic defects dictates material properties and performance for a plethora of technological applications. Density functional theory (DFT)-based nudged elastic band (NEB) calculations are a powerful computational technique for predicting defect migration activation energy barriers, yet they become prohibitively expensive for high-throughput screening of defect diffusivities. Without introducing hand-crafted (i.e., chemistry- or structure-specific) descriptors, we propose a generalized deep learning approach to train surrogate models for NEB energies of vacancy migration by hybridizing graph neural networks with transformer encoders and simply using pristine host structures as input. With sufficient training data, computationally efficient and simultaneous inference of vacancy defect thermodynamics and migration activation energies can be obtained to compute temperature-dependent vacancy diffusivities and to down-select candidates for more thorough DFT analysis or experiments. Thus, as we specifically demonstrate for potential water-splitting materials, candidates with desired defect thermodynamics, kinetics, and host stability properties can be more rapidly targeted from open-source databases of experimentally validated or hypothetical materials.

14 SOLAR ENERGY↗
DOE OSTI2022

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography

Chemical and conformational changes underlie the functional cycles of proteins. Comparative crystallography can reveal these changes over time, over ligands, and over chemical and physical perturbations in atomic detail. A key difficulty, however, is that the resulting observations must be placed on the same scale by correcting for experimental factors. We recently introduced a Bayesian framework for correcting (scaling) X-ray diffraction data by combining deep learning with statistical priors informed by crystallographic theory. To scale comparative crystallography data, we here combine this framework with a multivariate statistical theory of comparative crystallography. By doing so, we find strong improvements in the detection of protein dynamics, element-specific anomalous signal, and the binding of drug fragments.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗
DOE OSTI2025

Effect of laser melt schedule on the microstructure of additively manufactured IN718 Superalloy

Laser powder bed fusion (L-PBF) has enabled the fabrication of geometrically complex metallic structures and components that are challenging to producing using conventional manufacturing approaches. The site-specific and far from equilibrium thermal conditions of L-PBF offer the potential to facilitate multi-length scale design of structure and properties across the atomic-through macro-levels. However, L-PBF systems face scalability challenges due to throughput constraints. Laser rotary powder bed fusion (L-RPBF) systems are being investigated as a solution to enhance the deposition rates compared to conventional L-PBF. Rotary systems also offer additional flexibility for controlling the time structure of melting through laser interleaving on alternating layers. Here, in this study, IN718 test samples were printed using single-laser or interleaved dual-laser configuration in a L-RPBF system to investigates the effect of process settings and melt-interleaving on as-fabricated microstructure. The microstructural evolution, such as grain size and crystallographic texture, was assessed by determining variations in the melt-pool shapes. Laser interleaving leads to a reduction in average grain size compared to single laser by ∼ 40 % at high power (400 W) and by ∼36 % at medium power (370 W). Results presented here identify key challenge for obtaining uniform microstructures and barriers for the broader adoption of high-deposition rate L-RPBF.

Dual-laser↗
NASA NTRS2005

Metallographic Cooling Rate of IVA Irons Revisited

There is long standing problem reconciling the chemical evidence that the IVA iron meteorites formed in a core with the diverse cooling rates reported by several researchers. This large inferred range of cooling rates suggests that the IVA irons were distributed at different depths in a parent body with a complex structure when the Widmanstatten pattern formed. On the other hand, some researchers argued that the diverse cooling rates in group IVA result from inaccurate model parameters such as phase diagram, interdiffusion coefficients, and kamacite nucleation and growth mechanisms. In addition, the measured cooling rates may not apply for the same cooling temperature ranges, and the variation in the crystallographic orientations of the Widmanstatten plates on the analysis surface may result in inaccurate measurements of widths needed for the computer simulation models. We have revaluated the major parameters in computer model developed by Hopfe and Goldstein and measured cooling rates for the IVA irons. Such data are useful in evaluating whether these meteorites were part of a single core of a parent body during the formation of the Widmanstatten pattern.

Yang, J.↗
DOE OSTI2023

Finite temperature properties of uranium mononitride

Uranium mononitride (UN) is a promising nuclear fuel that combines the advantageous properties of readily used UO 2 and uranium alloys, such as high melting temperature and high uranium density, and thermal conductivity, respectively. A better understanding of UN behavior at operating temperatures can be obtained from finite temperature data, such as elastic properties. To get this information, ab initio molecular dynamics (AIMD) simulations were performed at five different temperatures using constant volume (NVT) and constant pressure (NPT) ensembles. Initially, the performance of PBE functional in reproducing experimental crystallographic properties and magnetic ordering is assessed. The finite temperature phonon dispersions are calculated using NVT simulation results, which show a softening of the phonon modes with increasing temperature. The NPT results are used to obtain the thermal expansion of UN and finite temperature electronic properties. The calculated thermal expansion is compared with our measurements using neutron diffraction. Additionally, the temperature dependent elastic properties of UN are evaluated using the strain-stress method in AIMD simulations, indicating that UN becomes softer and more compressible with increasing temperature. Also, the calculated Young’s modulus slope is in very good agreement with the experiment. The finite temperature heat capacity and electronic thermal conductivity are calculated from AIMD simulations, which are in better agreement with the experiment than the heat capacity and thermal conductivity calculated using the structures relaxed at 0K. Finally, the thermal diffusivity from AIMD has opposite temperature dependence compared to experimental results, which we argued comes from the underestimated electronic thermal conductivity.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

A Single Small-Scale Plutonium Redox Reaction System Yields Three Crystallographically-Characterizable Organoplutonium Complexes

Here, an approach to obtaining substantial amounts of data from a hazardous starting material that can only be obtained and handled in small quantities is demonstrated by the investigation of a single small-scale reaction of cyclooctatetraene, C 8 H 8 , with a solution obtained from the reduction of Cp' 3 Pu (Cp' = C 5 H 4 SiMe 3 ) with potassium graphite. This one reaction coupled with oxidation of a product has provided single-crystal X-ray structural data on three organoplutonium compounds as well as information on redox chemistry thereby demonstrating an efficient route to new reactivity and structural information on this highly radioactive element. The crystal structures were obtained from the reduction of C 8 H 8 by a putative Pu(II) complex, (Cp' 3 Pu II ) 1– , generated in situ, to form the Pu(III) cyclooctatetraenide complex, [K(crypt)][(C 8 H 8 ) 2 Pu III ], 1-Pu , and the tetra(cyclopentadienyl) Pu(III) complex, [K(crypt)][Cp' 4 Pu III ], 2-Pu . Oxidation of the sample of 1-Pu with Ag(I) afforded a third organoplutonium complex that has been structurally characterized for the first time, (C 8 H 8 ) 2 Pu IV , 3-Pu . Complexes 1-Pu and 3-Pu contain Pu sandwiched between parallel (C 8 H 8 ) 2– rings. The (Cp' 4 Pu III ) – anion in 2-Pu features three η 5 -Cp' rings and one η 1 -Cp' ring, which is a rare example of a formal Pu–C η 1 -bond. In addition, this study addresses the challenge of small-scale synthesis imparted by radiological and material availability of transuranium isotopes, in particular that of pure metal samples. A route to an anhydrous Pu(III) starting material from the more readily available Pu IV O 2 was developed to facilitate reproducible syntheses and allow complete spectroscopic analysis of 1-Pu and 2-Pu . Pu IV O 2 was converted to Pu III Br 3 (DME) 2 (DME = CH 3 OCH 2 CH 2 OCH 3 ) and subsequently Pu III Br 3 (THF) x , which was used to independently synthesize 1-Pu , 2-Pu , and 3-Pu .

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2026

Hydride and Seek: Comparing Crystallographic Hydride Placement Techniques with an Open-Shell Cobalt Complex

Locating hydrides is crucial in organometallic chemistry but difficult to do accurately using X-ray diffraction. Electron diffraction has been proposed as a way to overcome this problem but has not been systematically compared to neutron diffraction and to quantum crystallography (Hirshfeld atom refinement, HAR) to test this hypothesis. Here, we present a comparative analysis of methods for a terminal cobalt hydride complex by comparing a single-crystal neutron diffraction reference structure to results from single-crystal X-ray diffraction with and without Hirshfeld atom refinement (HAR, NoSpherA2), density functional theory (DFT), and electron diffraction (3D-ED/MicroED) refined under kinematical and dynamical formalisms. Conventional X-ray diffraction gives lower precision than neutron diffraction as expected. Despite expected improvements, HAR gives systematic deviation from the neutron benchmark. Interestingly, optimized DFT equilibrium geometries are closer to the neutron value than the value from HAR. On the other hand, electron diffraction with a high-quality data set coupled with dynamical refinement localizes the hydride in difference maps and gives excellent agreement with the neutron data. Dynamical refinement is crucial, as kinematical refinement does not allow assignment of a hydride peak. This cross-modal comparison defines the conditions under which 3D-ED/MicroED delivers high-precision metal–hydride distances for this open-shell cobalt hydride.

anions↗