Search NASA⌕ Search

SEARCH · Search NASA

Results for “neutron crystallography”

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.

85 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography

SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (M pro ) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of M pro , a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of M pro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH 2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free M pro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 M pro catalytic mechanism.

3CL protease↗
DOE OSTI2021

Powder Diffraction Crystallography : 98 Years as Plan B?

A historical essay written in 2014 to accompany a talk in the Transactions Symposium "100 Years of Crystallography" at the 2014 American Crystallographic Association Annual Meeting (talk at https://history.amercrystalassn.org/h-brian-toby-videos). Abstract: Powder diffraction patterns were used for structure solution almost contemporaneously with the Bragg’s initial single-crystal determinations. Structures have continued to be determined from powders, in the subsequent century. There has been a nearly explosive growth in this technique since the 1970’s. This was initially driven by neutron diffraction, which prompted the invention of Rietveld analysis, but synchrotrons have gone on to have at least as large an impact. There is no apparent upper limit to the scale of systems that can be structurally studied with powder diffraction; novel protein structures have been determined. When short-range ordering or disordered regions of a material are of interest, the Fourier transform of a powder diffraction pattern, the pair distribution function can be modeled.

Toby, Brian H.↗
DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗
DOE OSTI2020

Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data

An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving the phase problem and increasing the thicknesses of samples used in materials science, solid-state chemistry, and small molecule crystallography. For high-energy transmission electron diffraction, we show that the algorithm recovers accurate complex structure factors from a wide range of thicknesses, orientations, and relativistic beam energies, and does not require known thickness or atomic-resolution data if sufficient multiple scattering occurs. Furthermore, extensions to Cryo-electron microscopy and Micro-electron diffraction are suggested.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Crystal Plasticity Simulation of Magnesium and Its Alloys: A Review of Recent Advances

Slip and extension twinning are the dominant deformation mechanisms in Magnesium (Mg) and its alloys. Crystal plasticity is a powerful tool to study these deformation mechanisms. Different schemes have incorporated crystal plasticity models to capture different properties, which vary from the simple homogenization Taylor model to the full-scale crystal plasticity finite element model. In the current study, a review of works available in the literature that addresses different properties of Mg and its alloys using crystal plasticity modes is presented. In addition to slip and twinning, detwinning is another deformation mechanism that is activated in Mg and its alloys. The different models that capture detwinning will also be addressed here. Finally, the recent experimental frameworks, such as in-situ neutron diffraction, 3D high energy synchrotron X-ray techniques, and digital image correlation under scanning electron microscopy (SEM-DIC), which are incorporated along crystal plasticity models to investigate the properties of Mg and its alloys, are addressed. Future research directions towards improving the deformation response of Mg and its alloys are identified, which can lead to increased deployment of the lightest structural metal in engineering applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural and Dynamic Analysis of Sulphur Dioxide Adsorption in a Series of Zirconium-Based Metal–Organic Frameworks

We report reversible high capacity adsorption of SO 2 in robust Zr-based metal–organic framework (MOF) materials. Zr-bptc (H 4 bptc=biphenyl-3,3',5,5'-tetracarboxylic acid) shows a high SO 2 uptake of 6.2 mmol g -1 at 0.1 bar and 298 K, reflecting excellent capture capability and removal of SO 2 at low concentration (2500 ppm). Dynamic breakthrough experiments confirm that the introduction of amine, atomically-dispersed Cu II or heteroatomic sulphur sites into the pores enhance the capture of SO 2 at low concentrations. The captured SO 2 can be converted quantitatively to a pharmaceutical intermediate, aryl N-aminosulfonamide, thus converting waste to chemical values. In situ X-ray diffraction, infrared micro-spectroscopy and inelastic neutron scattering enable the visualisation of the binding domains of adsorbed SO 2 molecules and host–guest binding dynamics in these materials at the atomic level. Refinement of the pore environment plays a critical role in designing efficient sorbent materials.

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

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O 2 •– . The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn 3+ and Mn 2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pK a s, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn 3+ and Mn 2+ redox states.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microstructure analysis of laser beam weldments performed on neutron-irradiated 304L steel containing 3 and 8 appm helium

We report that AISI 304 L austenitic stainless steel is one of the major structural materials used in light water reactors (LWRs). In the future, 304 L components may require repair, and several welding techniques have been proposed as candidates. In this study, laser beam welding using the low-energy contribution approach was performed in ~2016 on neutron-irradiated AISI 304 L steel with nominal values of 3 and 8 appm helium (He). The goal was to investigate the impact of helium on the irradiated material weldability and evaluate helium-associated damage. The weld and heat-affected zone (HAZ) microstructure was studied using scanning electron microscopy, electron backscatter diffraction, and transmission electron microscopy (TEM). Analysis of the weldment cross-sections did not reveal severe cracking. Still, evidence of incipient helium-associated damage was observed in the HAZ, manifesting as degraded grain boundaries (GBs) “decorated” by pore chains and mostly small (i.e., ≤ 25-30 µm) scattered cracks. The largest observed crack was ~50 µm in length. Helium-associated damage was localized within ~200-300 µm of the weld pool boundary, and the fraction of the compromised GBs, as a rule, was below ~9-11% of the total GB network. TEM analysis showed significant annealing of the radiation-induced defects at distances up to ~300 µm from the weld pool boundary. Inside the HAZ, the cavities (likely, helium bubbles) tended to form at GBs and inclusions, such as manganese sulfide precipitates in the grain interior. Crystallography analysis of the HAZ damage showed that random high-angle boundaries were most susceptible to helium-associated damage. In contrast, low-angle random boundaries and twin boundaries appeared to be strongly resistant to degradation from the combined effects of helium and welding.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors

Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen–Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen–Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen–Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.

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

Revisiting the structures and phase transitions of Ba 2 NaNb 5 O 15

The room-temperature and low-temperature structure(s) of Ba 2 NaNb 5 O 15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.

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

The role of Tyr34 in proton coupled electron transfer and product inhibition of manganese superoxide dismutase

Human manganese superoxide dismutase (MnSOD) plays a crucial role in controlling levels of reactive oxygen species (ROS) by converting superoxide (O$^{•–}_{2}$) to molecular oxygen (O 2 ) and hydrogen peroxide (H 2 O 2 ) with proton-coupled electron transfers (PCETs). A key catalytic residue, Tyr34, determines the activity of human MnSOD and also becomes post-translationally inactivated by nitration in various diseases associated with mitochondrial dysfunction. Tyr34 has an unusual pK a due to its proximity to the Mn metal and undergoes cyclic deprotonation and protonation events to promote the electron transfers of MnSOD. Neutron diffraction, X-ray spectroscopy, and quantum chemistry calculations in oxidized, reduced and product inhibited enzymatic states shed light on the role of Tyr34 in MnSOD catalysis. The data identify the contributions of Tyr34 in MnSOD activity that support mitochondrial function and give a thorough characterization of how a single tyrosine modulates PCET catalysis. Product inhibition occurs by an associative displacement mechanism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Solving the “Coloring Problem” in InPd 3– x Ag x ( x = 0–0.7) by Phase Diagrams Modeling and Diffraction Experiments

Here, a series of InPd 3–x Ag x (x = 0–1) compositions were synthesized by conventional high-temperature synthesis, and as-synthesized samples were characterized by powder X-ray diffraction experiments. Up to x = 0.7, InPd 3–x Ag x adopts the ternary substitutional variant of the InPd 3 structure (TiAl 3 -type), when x > 0.7, elemental Ag starts to segregate along with the main phase. Accurate structural characterization in InPd 3–x Ag x faces a critical challenge due to the narrow X-ray scattering contrast among constituents In, Pd, and Ag and nearly identical neutron scattering lengths of Pd and Ag. To overcome this “coloring problem”, a combination of calculation of phase diagrams modeling (CALPHAD) and diffraction techniques (X-ray and neutron) was employed. In the compositional range 0 ≤ x ≤ 0.7, InPd 3–x Ag x presents a ternary variant of the TiAl 3 -type structure, where Ag atoms selectively substitute one (the 2b Wyckoff site) of the two Pd sites in InPd 3 . Notably, in contrast to the isologous InPd 3–x Cu x (x = 0–1) system, Ag substitution does not form an ordered VRh 2 Sn-type structure at the limiting composition. The distinct site preference in InPd 3–x Ag x is elucidated by charge population analysis, electronic structure calculations, and orbital-resolved chemical bonding investigations, and the extent of substitution is supported by formation free energy calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Exploring the Structural Behavior of Hydrophilic Diglycolamide Complexes with the Lanthanides and Actinides

In the ongoing effort to meet the anticipated rise in energy demand while maintaining the full-scale abandonment of natural gas and coal, a substantial shift in our considerations of green energy is required through the wider adoption of nuclear power. However, the advantages of nuclear power are hindered by the challenges of safely managing nuclear waste. Hydrophilic diglycolamides (DGA) ligands have been explored for use as stripping agents in various lanthanide and actinide partitioning processes. Additionally, the separation of lanthanide fission products and transplutonic actinides can serve multifaceted advantages in that the separation neutron poisoning rare earth element (REE) fission products from minor actinides from used nuclear fuel (UNF) can be mutually beneficial to the fundamental research behind REE separations and UNF separations. With this in mind, understanding the bonding differences between the Ln3+ and An3+ ions as a function of DGA structure, such as varying the alkyl groups on each of the amide functional groups, has an influence on the molecule’s selectivity and solubility and whose changes in molecular architecture also impact the radiolytic behavior of these molecules. As such, crystal structures of (Y3+, La-Lu3+, excl. Pm, Pu3+/4+, Am3+, Bk3+, and Cf3+) with hydrophilic diglycolamides show the systematic progression, and changes in coordination habits, as a function of a f-element ions. These coordination complexes see a consistent decrease in bond lengths and changes in the coordination environment while traversing across the f-elements, owing to the effects of the lanthanide contraction as well as local geometry around the metal centers. Direct comparisons of lanthanide with actinide DGA structures display both striking similarities in coordination with earlier actinides of Pu and Am, while later actinides of Bk and Cf display a complete breakdown of these observed trends. This work has also presented the rare opportunity to study homoleptic DGA compounds across multiple oxidation states have provided insight into their nuanced differences in structural chemistry.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗