Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “crystallographic structures”

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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Impact of Structural Distortions on the Magnetism of Double Perovskites Containing 5d 1 Transition-Metal Ions

Five double perovskites, each containing a transition-metal ion with a 5d 1 configuration, have been studied to better understand the surprising diversity of magnetic ground states seen in these isoelectronic compounds. Ba 2 ZnReO 6 adopts the cubic double perovskite structure and magnetically orders below 16 K, with a canted ferromagnetic structure and a saturated magnetization of ~0.24 μ B /Re. X-ray magnetic circular dichroism indicates a substantial orbital moment of approximately 0.4 μ B /Re that opposes the spin moment. The structures of Ba 2 NaOsO 6 (canted ferromagnet, T C = 7 K) and Ba 2 LiOsO 6 (antiferromagnet, T N = 8 K) are reinvestigated using time-of-flight neutron powder diffraction and found to crystallize with the cubic double perovskite structure. No evidence for a structural distortion can be found in either compound down to 10 K. Ba 2 CdReO 6 is also cubic at room temperature but undergoes a structural transition upon cooling below ~180 K to a tetragonal structure with I4/m symmetry that involves compression of the Re–O bonds that are parallel to the c-axis. Sr 2 LiOsO 6 shows a similar tetragonal distortion at room temperature and maintains that structure down to 10 K. Surprisingly, the Os-centered octahedron in Sr 2 LiOsO 6 is distorted in the opposite direction, exhibiting an elongation of the Os–O bonds along the c-axis. Differences in the distortions of the octahedra lead to different magnetic ground states, antiferromagnetic (T N = 4 K) for Ba 2 CdReO 6 and spin glass (T g = 30 K) for Sr 2 LiOsO 6 . Theoretical modeling shows that the varied magnetic behaviors of double perovskites containing 5d 1 ions are closely tied to crystallographic distortions. Furthermore, these distortions remove the degeneracy of the 5d t 2g orbitals, leading to changes in orbital occupation that ultimately determine which of the several competing magnetic ground states is favored.

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

GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure

We propose GrainGNN, a surrogate model for the evolution of polycrystalline grain structure under rapid solidification conditions in metal additive manufacturing. High fidelity simulations of solidification microstructures are typically performed using multicomponent partial differential equations (PDEs) with moving interfaces. The inherent randomness of the PDE initial conditions (grain seeds) necessitates ensemble simulations to predict microstructure statistics, e.g., grain size, aspect ratio, and crystallographic orientation. Here, currently such ensemble simulations are prohibitively expensive and surrogates are necessary.In GrainGNN, we use a dynamic graph to represent interface motion and topological changes due to grain coarsening. We use a reduced representation of the microstructure using hand-crafted features; we combine pattern finding and altering graph algorithms with two neural networks, a classifier (for topological changes) and a regressor (for interface motion). Both networks have an encoder-decoder architecture; the encoder has a multi-layer transformer long-short-term-memory architecture; the decoder is a single layer perceptron.We evaluate GrainGNN by comparing it to high-fidelity phase field simulations for in-distribution and out-of-distribution grain configurations for solidification under laser power bed fusion conditions. GrainGNN results in 80%–90% pointwise accuracy; and nearly identical distributions of scalar quantities of interest (QoI) between phase field and GrainGNN simulations compared using Kolmogorov-Smirnov test. GrainGNN's inference speedup (PyTorch on single x86 CPU) over a high-fidelity phase field simulation (CUDA on a single NVIDIA A100 GPU) is 150×–2000× for 100-initial grain problem. Further, using GrainGNN, we model the formation of 11,600 grains in 220 seconds on a single CPU core.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Site-Selective Modification of Lanthanum Oxychloride to Modulate Halide-Ion Conduction

Design principles for solid-state halide-ion conduction remain poorly defined despite the increasing importance of halide ions as charge carriers in a variety of energy storage and electrochemical computing technologies. Here, we employ a siteselective modification strategy in which aliovalent cations are preferentially introduced at the La 3+ crystallographic site of LaOCl in the 2c Wyckoff position, enabling controlled generation of chloride vacancies and modification of lattice dynamics to enhance chloride-ion conductivity. Aliovalent substitution of La 3+ with Mg 2+ , Ca 2+ , and Sr 2+ generates charge-compensating Cl vacancies while preserving the matlockite crystal structure. X-ray excited optical luminescence measurements with Dy 3+ as a reporter chromophore evidence vacancy-derived midgap electronic states and an extended energy range of radiation-less Auger electron emission corresponding to substantial modification of electronic structure and local electrostatic potentials. Ca alloying at 8−10 at. % increases the chloride-ion conductivity by three- to 4 orders of magnitude as compared to unalloyed LaOCl, whereas comparable amounts of Sr- and Mg-alloying in LaOCl imbue less pronounced conductivity enhancements. Temperature-dependent Raman spectroscopy measurements reveal that Ca- and Sr-alloying substantially soften the La−Cl sublattice and yield a more compliant crystal lattice that can deform to accommodate Cl-ion migration. Structure solutions derived from Rietveld refinements to powder Xray diffraction reveal larger O−La−Cl bond-angle deviations and enhanced out-of-plane cation displacements for Ca- and Sr-alloyed compositions as compared to Mg-alloyed LaOCl. Such local distortions enhance chloride-ion mobility by reshaping and flattening vacancy migration energy landscapes and by modulating lattice dynamics governing anion conduction. We further illustrate that coalloying of Ca with Mg and Sr induces a nonmonotonic conductivity−defect stoichiometry relationship that can be rationalized based on cooperative interactions. Together, these results establish site-selective aliovalent alloying of LaOCl as an effective route to halide-ion solid electrolytes and provide broadly generalizable design principles for site-selective modification to induce vacancy formation and lattice softening to engender facile anion transport

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

From +I to +IV, Alkalis to Actinides: Capturing Cations across the Periodic Table with Keggin Polyoxometalate Ligands

Coordination chemistry trends across the periodic table are often difficult to probe experimentally due to limitations in finding a versatile but consistent chelating platform that can accommodate various elements without changing its coordination mode. Herein, we present new metal/ligand systems covering a wide range of ionic radii, charges, and elements. Five different ligands derived from the Keggin structure (HBW 11 O 39 8– , PW 11 O 39 7– , SiW 11 O 39 8– , GeW 11 O 39 8– , and GaW 11 O 39 9– ) were successfully crystallized with six different cations (Na + , Sr 2+ , Ba 2+ , La 3+ , Ce 4+ , and Th 4+ ) and characterized by single-crystal X-ray diffraction. Twenty-five new compounds were obtained by using Cs + as the counterion, yielding a consistent base formula of Cs x [M(XW 11 O 39 ) 2 ]·nH 2 O. Despite having a similar first-coordination sphere geometry (i.e., 8-coordinated), the nature of the central cation was found to impact the long-range geometry of the complexes. This unique crystallographic data set shows that, despite the traditional consensus, the local geometry of the cation (i.e., metal–oxygen bond distance) is not enough to depict the full impact of the complexed metal ion. The bending and twisting of the complexes, as well as ligand–ligand distances, were all impacted by the nature of the central cation. We also observed that counterions play a critical role by stabilizing the geometry of the M(XW 11 ) 2 complex and directing complex–complex interactions in the lattice. We also define certain structural limits for this type of complex, with the large Ba 2+ ion seemingly approaching those limits. Finally, this study thus lays the foundation for capturing the coordination chemistry of other rarer elements across the periodic table such as Ra 2+ , Ac 3+ , Bk 4+ , Cf 3+ , etc.

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

Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k cat /K M 146 M -1 s -1 ). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (k cat /K M 103,000 M -1 s -1 ) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Mycobacterium tuberculosis mycothiol S -transferase is divalent metal-dependent for mycothiol binding and transfer

Mycothiol S-transferase (MST) (encoded by the rv0443 gene) was previously identified as the enzyme responsible for the transfer of Mycothiol (MSH) to xenobiotic acceptors in Mycobacterium tuberculosis (M.tb) during xenobiotic stress. To further characterize the functionality of MST in vitro and the possible roles in vivo, X-ray crystallographic, metal-dependent enzyme kinetics, thermal denaturation studies, and antibiotic MIC determination in rv0433 knockout strain were performed. The binding of MSH and Zn 2+ increases the melting temperature by 12.9 °C as a consequence of the cooperative stabilization of MST by both MSH and metal. The co-crystal structure of MST in complex with MSH and Zn 2+ to 1.45 Å resolution supports the specific utilization of MSH as a substrate as well as affording insights into the structural requirements of MSH binding and the metal-assisted catalytic mechanism of MST. Further, contrary to the well-defined role of MSH in mycobacterial xenobiotic responses and the ability of MST to bind MSH, cell-based studies with an M.tb rv0443 knockout strain failed to provide evidence for a role of MST in processing of rifampicin or isoniazid. These studies suggest the necessity of a new direction to identify acceptors of the enzyme and better define the biological role of MST in mycobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Detection of translational noncrystallographic symmetry in Patterson functions

Detection of translational noncrystallographic symmetry (TNCS) can be critical for success in crystallographic phasing, particularly when molecular-replacement models are poor or anomalous phasing information is weak. If the correct TNCS is detected then expected intensity factors for each reflection can be refined, so that the maximum-likelihood functions underlying molecular replacement and single-wavelength anomalous dispersion use appropriate structure-factor normalization and variance terms. Here, an analysis of a curated database of protein structures from the Protein Data Bank to investigate how TNCS manifests in the Patterson function is described. These studies informed an algorithm for the detection of TNCS, which includes a method for detecting the number of vectors involved in any commensurate modulation (the TNCS order). The algorithm generates a ranked list of possible TNCS associations in the asymmetric unit for exploration during structure solution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Expanding the Boundaries of Transuranium Chemistry

During the last several Heavy Elements Chemistry grant cycles under award(s): DE-FG02-13ER16414, we have published nearly 90 research articles (see bibliography) in 25 peer-reviewed journals. Additionally, this funding has resulted in several review articles. Together, these publications have already reached well over 4500 citations. These research articles have introduced several hundreds of new crystallographically authenticated f-element compounds and materials and have greatly affected the field of Heavy Elements Chemistry. Concentrating on the heaviest elements that can be studied on the milligram scale, the transplutonium elements are the focus of nearly 30 of these manuscripts containing results such as the first single crystal structure of a berkelium compound and californium presenting itself as an additional transition point in the actinide series.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

1,8-Dihydroxy Naphthalene—A New Building Block for the Self-Assembly with Boronic Acids and 4,4′-Bipyridine to Stable Host–Guest Complexes with Aromatic Hydrocarbons

The new Lewis acid–base adducts of general formula X(nad)B←NC5H4-C5H4N→B(nad)X [nad = 1,8-O2C10H6, X = C6H5 (2c), 3,4,5-F3-C6H2 (2d)] were synthesized in high yields via reactions of 1,8-dihydroxy naphthalene [nadH2] and 4,4′-bipyridine with the aryl boronic acids C6H5B(OH)2 and 3,4,5-F3-C6H2B(OH)2, respectively, and structurally characterized by multi-nuclear NMR spectroscopy and SCXRD. Self-assembled H-shaped Lewis acid–base adduct 2d proved to be effective in forming thermally stable host–guest complexes, 2d × solvent, with aromatic hydrocarbon solvents such as benzene, toluene, mesitylene, aniline, and m-, p-, and o-xylene. Crystallographic analysis of these solvent adducts revealed host–guest interactions to primarily occur via π···π contacts between the 4,4′-bipyridyl linker and the aromatic solvents, resulting in the formation of 1:1 and 1:2 host–guest complexes. Thermogravimetric analysis of the isolated complexes 2d × solvent revealed their high thermal stability with peak temperatures associated with the loss of solvent ranging from 122 to 147 °C. 2d, when self-assembled in an equimolar mixture of m-, p-, and o-xylene (1:1:1), preferentially binds to o-xylene. Collectively, these results demonstrate the ability of 1,8-dihydroxy naphthalene to serve as an effective building block in the selective self-assembly to supramolecular aggregates through dative covalent N→B bonds.

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

Stress localization investigation of additively manufactured GRCop-42 thin-wall structure

A full-field crystal plasticity (CP) framework is presented for the GRCop-42 alloy to study microscopic mechanical behavior and local stress heterogeneities. The microstructures of additively manufactured (AM) materials are often unique relative to conventionally processed materials, and the local thermal histories drive these differences during the build process. These thermal histories depend on the process parameters (laser power, scan speed, and scan strategy) and the part geometry. Prior research has shown that the mechanical properties of thin-walled structures can vary significantly with wall thickness due to changes in the thermal boundary conditions during manufacturing. It is, therefore, desirable to perform CP simulations based on the phenomenological constitutive model to predict the local mechanical responses induced by microstructural heterogeneities. This work generates representative microstructures based on experimentally collected grain information (i.e., texture) for grain scale stress analysis, and the material constitutive parameters are calibrated using the experimental mechanical testing data. Here, we specifically investigated the effect of crystallographic texture and grain morphologies on the size-dependent mechanical properties of AM GRCop-42. The selection of appropriate material properties for implementing an effective free surface boundary condition and the influence of adjacent buffer layers are also discussed. Analysis of local field results reveals a strong correlation between stress localization and the initial grain orientation. However, no significant relationship between the misorientation of the individual adjacent grains and the average misorientation is observed.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A sensitivity analysis of twinning crystal plasticity finite element model using single crystal and poly crystal Zircaloy

The popularity of crystal plasticity finite element method (CPFEM) models is increasing due to their ability to predict the mechanical response of crystalline materials such as metals and metal alloys more accurately than traditional continuum mechanics models. This is since the crystal plasticity models consider the effect of atomic structure, microstructural morphology, and properties of individual grains. These CPFEM models use a large number of material parameters in order to capture the mesoscale physics which comes with the downside of the tedious calibration process. In this paper, a CPFEM code was developed to include the twinning induced grain reorientation and subsequent crystallographic slip for HPC material. The developed code is incorporated in a large-scale, parallelized nonlinear solver WARP3D. Further, a sensitivity analysis with respect to 22 material parameters was then conducted using single crystal and polycrystal representative volume element (RVE) of Zircaloy material. Loading was applied along five different crystallographic orientations for single crystal RVE and along three directions namely, rolling (RD), transverse (TD), and normal (ND) direction for polycrystal RVE. Results obtained from the sensitivity analysis were used for the calibration of material parameters for Zircaloy. Finally, developed code along with calibrated material parameters was used to investigate the effect of the hydride phase formation in Zircaloy which is a typical case observed for nuclear applications. It was found that the volume fraction of the hydride phase has a significant impact on the mechanical properties of Zircaloy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Diamagnetic mechanism of critical current non-reciprocity in multilayered superconductors

The suggestion that non-reciprocal critical current (NRC) may be an intrinsic property of non-centrosymmetric superconductors has generated renewed theoretical and experimental interest motivated by an analogy with the non-reciprocal resistivity due to the magnetochiral effect in uniform materials with broken spatial and time-reversal symmetry. Theoretically it has been understood that terms linear in the Cooper pair momentum do not contribute to NRC, although the role of higher-order terms remains unclear. In this work we show that critical current non-reciprocity is a generic property of multilayered superconductor structures in the presence of magnetic field-generated diamagnetic currents. In the regime of an intermediate coupling between the layers, the Josephson vortices are predicted to form at high fields and currents. Experimentally, we report the observation of NRC in nanowires fabricated from InAs/Al heterostructures. The effect is independent of the crystallographic orientation of the wire, ruling out an intrinsic origin of NRC. Non-monotonic NRC evolution with magnetic field is consistent with the generation of diamagnetic currents and formation of the Josephson vortices. This extrinsic NRC mechanism can be used to design novel devices for superconducting circuits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Behavior of strain stripe networks in barium titanate nanocrystals on crossing its ferroelectric phase transition

Nanoscale strain networks are reported in BaTi O 3 (BTO) crystals of 300 nm size using Bragg coherent diffractive imaging. BTO nanocrystals with clear facets were chosen to identify the crystallographic directions, allowing the strain field direction and periodicity to be studied in detail. Stripes of strain were observed, which were both stable and preserved in tetragonal and cubic phases at elevated temperatures, above the tetragonal-to-cubic phase transition. A finite element analysis approach was used to simulate the domain structures inside a BTO crystal and to understand the origins of the strain stripes as piezoelectric blocks. A 180 ∘ domain model gives a better qualitative match to the experimental images. Published by the American Physical Society 2024

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Crystallographic Insight of Reduced Lattice Volume Expansion in Mesoporous Cu 2+ -Doped TiNb 2 O 7 Microspheres during Li + Insertion

TiNb 2 O 7 represents a promising anode material for lithium-ion batteries (LIBs), but its practical applications are currently hampered by the non-negligible volumetric expansion and contraction during the charge/discharge process and the sluggish ion/electron kinetics. Here a combination technique is reported by systematically optimizing the porous and spherical morphology, crystal structure, and surface decoration of mesoporous Cu 2+ -doped TiNb 2 O 7 microspheres to enhance the electrochemical Li + storage performance and stability simultaneously. The Cu 2+ dopants preferentially replace Ti 4+ in crystal lattices, which decreases the Li + diffusion barrier and increases the electronic conductivity, as confirmed by density functional theory (DFT) calculation and demonstrated by diverse electrochemical characterizations. The successful Cu 2+ doping significantly reduces the lattice expansion coefficient from 7.26% to 4.61% after Li + insertion along the b-axis of TiNb 2 O 7 , as visualized from in situ and ex situ XRD analysis. The optimal 5% Cu 2+ -doped TiNb 2 O 7 with surface coating of N-doped carbon exhibits significantly enhanced specific capacity and rate and cyclic performances in both half- and full-cell configurations, demonstrating an excellent electrochemical behavior for fast-charging LIB applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural and optical properties of cubic GaN on U-grooved Si (100)

Cubic GaN epitaxy on large-area U-grooved silicon (100) dies is demonstrated by metalorganic chemical vapor deposition, and its structural and optical properties are reported. Scanning electron, atomic force, and transmission electron microscopy studies reveal that cubic GaN shows no discernible threading dislocations and a low stacking fault density of 3.27 ± 0.18 × 10 4 cm –1 . Temperature-dependent photoluminescence studies reveal as-grown cubic GaN band edge emission internal quantum efficiency as 25.6% ± 0.9%. Selective etching of the low-temperature AlN buffer layer, SiO 2 sidewalls, and hexagonal-phase GaN is demonstrated, which increases the cubic GaN band edge emission internal quantum efficiency to 31.6% ± 0.8%. This increase is attributed to the decrease in the radiative recombination lifetime via the removal of defective hexagonal-phase GaN. Altogether, cubic GaN on U-grooved silicon with high structural and optical quality is reported, promising its suitability for next-generation devices.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Three-dimensional atomic scale characterization of {11$\overline{2}$2} twin boundaries in titanium

The {11$\overline{2}$2}<11$\overline{23}$> compression twin can accommodate a considerable amount of strain under c-axis compression in Ti. However, unlike the tensile twin, the structure of the {10$\overline{1}$2}$\langle$$\overline{1}$011$\rangle$ compressive twins has not been completely characterized. In this study, we apply a combined technique of HR-TEM characterization, topological analysis, and atomistic simulations to explore the facets that bound the {11$\overline{2}$2}<11$\overline{23}$> twin in Ti. In addition to the currently known facets (CTB and B-Py), six new facets are observed and categorized for the first time from atomic-scale TEM observations along five crystallographic directions. The six new facets are (11$\overline{2}$0)//(11$\overline{2}$6), PrPr1, PyPy1, (2$\overline{11}$1)//($\overline{1}$2$\overline{1}$2), (1$\overline{1}$04)//(01$\overline{11}$), and (01$\overline{1}$0)//(2$\overline{11}$4). Results from the topological and computational analysis are in reasonable agreement with and support the HRTEM observations. Specifically, (1) the observed facets align with low-index interfaces in both twin and matrix domains, (2) the facets with lower surface energies are found to form extended interfaces, and (3) high-surface-energy facets are found at the twin tip region and explained by the fact that the energy of the combined facet and facet junction configuration is energetically preferred in the twin tip region. These results not only provide a comprehensive understanding of the 3D structure of the {11$\overline{2}$2}<11$\overline{23}$> compressive twins in Ti, but also validate the MD procedure and the Ti interatomic potential employed. This is extremely important for future study of the {11$\overline{2}$2} twin mobility and interactions with other defects, both features that remain extremely challenging to capture in experiments.

36 MATERIALS SCIENCE↗
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↗