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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 73 records · Page 4

Elucidating metal–organic framework structures using synchrotron serial crystallography

Metal organic frameworks (MOFs) are porous crystalline materials that display a wide variety of physical and chemical properties. Their single crystal structure determination is often challenging because in most cases micro- or nano-sized crystals spontaneously form upon MOF synthesis, which cannot be recrystallized. The production of larger single crystals for structure determination involves optimizing, and thus modifying, the conditions of synthesis, in which success cannot be guaranteed. Failure to produce crystals suitable for single-crystal X-ray diffraction leaves the 3D structure of the MOF compound unknown, and scientists must resort to more challenging structure solution methods based on X-ray powder or electron diffraction data. These laborious tasks can be avoided by using serial crystallography techniques which merge data collected on many micro-crystals. Here, we report the application of three synchrotron serial crystallography methods. We call these “mesh”, “grid” and “mesh&collect” scans. “Still” images (no rotation) are collected in the mesh scan approach, whereas small rotational wedges are collected in the grid scan method. The third protocol, mesh&collect, combines the acquisition of still images and rotational wedges. Using these means, we determine the ab initio structure of benchmark MOFs, MIL-100(Fe) and ZIF-8, that differ largely in unit cell size. These methods are expected to be widely applicable and facilitate structure determination of many MOF microcrystalline systems.

36 MATERIALS SCIENCE↗

ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science

ExaFEL is an HPC-capable X-ray Free Electron Laser (XFEL) data analysis software suite for both Serial Femtosecond Crystallography (SFX) and Single Particle Imaging (SPI) developed in collaboration with the Linac Coherent Lightsource (LCLS), Lawrence Berkeley National Laboratory (LBNL) and Los Alamos National Laboratory. ExaFEL supports real-time data analysis via a cross-facility workflow spanning LCLS and HPC centers such as NERSC and OLCF. Our work therefore constitutes initial path-finding for the US Department of Energy's (DOE) Integrated Research Infrastructure (IRI) program. We present the ExaFEL team's 7 years of experience in developing real-time XFEL data analysis software for the DOE's exascale supercomputers. We present our experiences and lessons learned with the Perlmutter and Frontier supercomputers. Furthermore we outline essential data center services (and the implications for institutional policy) required for real-time data analysis. Finally we summarize our software and performance engineering approaches and our experiences with NERSC's Perlmutter and OLCF's Frontier systems. This work is intended to be a practical blueprint for similar efforts in integrating exascale compute resources into other cross-facility workflows.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of heme scavenging by the ChtA and HtaA hemophores in Corynebacterium diphtheriae

Corynebacterium diphtheriae causes diphtheria, a potentially fatal infectious disease that damages tissues in the upper respiratory tract. In order to proliferate, this pathogen acquires the essential nutrient iron from heme (iron-protoporphyrin IX) primarily found in human hemoglobin (Hb). C. diphtheriae secretes ChtA and HtaA hemophore proteins that bind ferric heme (hemin) via conserved region (CR) domains. Here, we demonstrate that their CR domains scavenge hemin after it is spontaneously released from Hb, and define the structural basis of hemin binding to ChtA and the N-terminal CR domain from HtaA by determining X-ray crystal structures of their protein-hemin complexes. Resonance Raman and electron paramagnetic resonance experiments demonstrate that the CR domains from ChtA and HtaA engage in pentacoordinate hemin binding through a conserved iron-tyrosyl linkage, though variations in their hemin pockets alter the way they stabilize the axial tyrosine and mask hemin’s metal. The importance of these interactions is probed using isothermal titration calorimetry experiments, which represent the first quantitative assessment of CR-hemin affinity and reveal that ChtA binds hemin via an enthalpically driven process. Hemin partitioning experiments using native mass spectrometry demonstrate that the cohort of CR domains within C. diphtheriae ’s hemin-uptake system have dissociation constants for hemin between 0.8 and 22 nM, raising the possibility that affinity differences contribute to the directional flow of hemin into the cell. Collectively, the results of this work provide insight into how C. diphtheriae and other pathogenic and commensal corynebacterium species utilize CR domains to scavenge iron rich hemin from their environment.

Corynebacterium diphtheriae↗

Measurement bias in self-heating x-ray free electron laser experiments from diffraction studies of phase transformation in titanium

X-ray self-heating is a common by-product of X-ray Free Electron Laser (XFEL) techniques that can affect targets, optics, and other irradiated materials. Diagnosis of heating and induced changes in samples may be performed using the x-ray beam itself as a probe. However, the relationship between conditions created by and inferred from x-ray irradiation is unclear and may be highly dependent on the material system under consideration. Here, we report on a simple case study of a titanium foil irradiated, heated, and probed by a MHz XFEL pulse train at 18.1 keV delivered by the European XFEL using measured x-ray diffraction to determine temperature and finite element analysis to interpret the experimental data. We find a complex relationship between apparent temperatures and sample temperature distributions that must be accounted for to adequately interpret the data, including beam averaging effects, multivalued temperatures due to sample phase transitions, and jumps and gaps in the observable temperature near phase transformations. The results have implications for studies employing x-ray probing of systems with large temperature gradients, particularly where these gradients are produced by the beam itself. Finally, this study shows the potential complexity of studying nonlinear sample behavior, such as phase transformations, where biasing effects of temperature gradients can become paramount, precluding clear observation of true transformation conditions.

Crystallography↗

Preparing for successful protein crystallization experiments

Crystal-based structural methods, including X-ray crystallography, are frequently utilized for the determination of high-resolution structures of biomolecules. All crystal-based diffraction methods first require the preparation of biomolecular crystals, and careful sample preparation for crystallization experiments can increase the frequency of success. In this article, strategies to optimize factors that can impact crystallization are presented, from which buffers and reducing agents are most favorable to which crystallization techniques could be used.

36 MATERIALS SCIENCE↗

Materials Signatures of Metallic Phases (Final Report)

This report summarizes key accomplishments from a 2 year Laboratory Directed Research and Development (LDRD) project focused on advancing nanoscale characterization of metallic particulates and synthesis of laboratory-scale analogs. We successfully developed and refined nanoscale crystallography techniques with significantly improved spatial resolution and throughput compared to traditional transmission electron microscopy. We also established nanotomography capabilities for 3D particle reconstruction and began optimizing throughput for broader application. Additionally, we demonstrated the ability to relocate and characterize individual particles using atomic force microscopy (AFM), providing insights into hardness, conductivity, and magnetic behavior. On the synthesis front, we leveraged controlled and combustion-based methods to investigate annealing effects and rapid oxidation behavior of U–Fe–Ni compounds. These efforts collectively enhance our ability to characterize and interpret particulate formation and transformation under relevant conditions.

36 MATERIALS SCIENCE↗

Dose-dependent structural and electron-density features in the lytic polysaccharide monooxygenase NcAA9D

Structural studies of copper-containing lytic polysaccharide monooxygenases (LPMOs) by X-ray crystallography are often complicated by radiation damage. In this study, we analyze a series of 36 X-ray crystal structures of NcAA9D, a Neurospora crassa AA9-family LPMO, determined from data collected at cryogenic temperature from a single crystal to investigate the progressive effects of radiation damage at the active site of this enzyme. We report new insights into the dose-dependence of active-site geometry in LPMOs and utilize the unique pre-bound dioxygen site of NcAA9D to analyze the impact of X-ray dose on the electron density of this species. It is well established that photoreduction of the LPMO active-site copper(II) leads to expulsion of its water ligands. We further characterize this displacement and the corresponding electron-density smearing, a phenomenon that can lead to the erroneous modeling of copper-bound dioxygen species. These findings suggest that radiation-dose series collected from a single crystal provide invaluable data to support unambiguous assignment of radiation-sensitive intermediates at the active site of LPMOs and other radiation-sensitive redox enzymes.

Miller, Samuel [ORNL] (ORCID:0009000459491817)↗

LaFeSi–LaFe 13-x Si x composites: Modulating magnetic and magnetocaloric properties through inherent stress manipulation

We examine structural and magnetic properties of a series of La–Fe–Si alloys in the region of concentrations where they naturally form two-phase LaFeSi–LaFe 13-x Si x composites with variable content and connectivity of LaFe 13-x Si x grains distributed within the LaFeSi matrix. Theoretical calculations confirm that the LaFeSi constituent is magnetically and structurally inert below room temperature and at pressures between -10 and 10 GPa. The LaFe 13-x Si x constituent, on the other hand, is magnetically and structurally active: it exhibits first-order magnetostructural transformations that, in addition to x Si , can be controlled with temperature, magnetic field, and pressure. In composites where the concentration of the inactive constituent is ~70 wt. % or greater, the standard, single-step, LaFe 13-x Si x first-order phase transformation proceeds in two steps separated by over 30 K in a zero magnetic field. Increasing the magnetic field recouples the two steps and restores the single-step phase transformation pathway. We analyze the roles of stresses caused by both thermal expansion mismatch and the first-order magnetic phase transition in LaFe 13-x Si x to rationalize the observed physical behaviors that emerge as the temperature or/and magnetic field vary.

36 MATERIALS SCIENCE↗

Evaluation of ovostatin and ovostatin assay

Ovostatin is a 780,000 MW protein, originally isolated from chicken egg white, which is active as a protease inhibitor. Structural studies indicate that the protein is a tetramer of identical subunits of 165,000 MW which can be separated upon reduction with beta- mercaptoethanol. Chicken ovostatin is an inhibitor of metalloproteases such as collagenase and thermolysin, and of acid proteases such as pepsin and rennin. Ovostatin isolated from duck eggs and from crocodile eggs appears to be similar to chicken egg ovostatin, but with significant differences in structure and function. Duck ovostatin contains a reactive thiol ester which is not found in the chicken protein, and duck and crocodile ovostatin inhibit serine protease such as trypsin and chymotrypsin, while chicken ovostatin does not. Electron microscopy of ovostatin indicates that two subunits associated near the middle of each polypeptide to form a dimer with four arms. Two of these dimers then associate to produce a tetramer with eight arms, with the protease binding site near the center of the molecule. Upon binding of the protease, a conformational change causes all eight arms to curl toward the center of the molecule, effectively trapping the protease and sterically hindering access of the substrates to its active site. The structural organization and mechanism of action proposed for ovostatin are nearly identical to that proposed for alpha(sub 2)- macroglobulin, a serum protease inhibitor which may play an important role in regulation of proteases in animal tissues. Although the general arrangement of subunits appears to be the same for all ovostatins studied, some differences have been observed, with chicken ovostatin more closely resembling reptilian ovostatin than the duck protein. This is a surprising result, given the evolutionary relatedness of chickens and ducks. It is possible that the differences in structures may be due to deformed subunit arrangements which occur during the processing and fixing necessary for electron microscopy. Examination of the native structure of these proteins using X-ray crystallography would help clarify these discrepancies.

Moriarity, Debra M.↗

Outstanding Natural Occurrence of TiO2-II at the Chicxulub Crater - Anatomy of A Shock-Produced High-Pressure Polymorph

Scientific drilling of the end-Cretaceous, approximately 180 kilometers-diameter Chicxulub crater (Yucatan Peninsula, Mexico) during IODP–ICDP (Integrated Ocean Drilling Program - International Continental Scientific Drilling Program) Expedition 364 has provided new insights into the formation, shock metamorphism, structural evolution, and thermal history of peak rings in large complex impact craters. An outstanding feature in uplifted granitoid rocks of the Chicxulub peak ring is the preservation of TiO2-II, an orthorhombic high-pressure polymorph of TiO2 with an alpha-PbO2 structure, produced during the impact from rutile and/or anatase at shock pressures of approximately 12.5-17.5 gigapascals. Unlike other mostly micro- and cryptocrystalline occurrences of TiO2-II at terrestrial impact sites, ejecta deposits, and in rare ultra-high pressure metamorphic rocks, TiO2-II at Chicxulub occurs as abundant euhedral crystals greater than or equal to 70 microns in size within aggregates of altered magmatic titanite. This mode of occurrence provides an excellent opportunity to investigate the crystallography and transformation kinetics of the shock-produced high-pressure polymorph using scanning electron microscopic, micro-Raman, electron backscatter diffraction (EBSD), focused ion beam (FIB), as well as transmission-EBSD and transmission electron microscopic (TEM) techniques. Here we present refined microstructural and new crystallographic results for TiO2-II at the Chicxulub crater.

Schmieder, Martin↗

Crystallography of decahedral and icosahedral particles. II - High symmetry orientations

Based on the exact crystal structure of decahedral and icosahedral particles, high energy electron diffraction patterns and image profiles have been derived for various high symmetry orientations of the particles with respect to the incident beam. These results form a basis for the identification of small metal particle structures with advanced methods of transmission electron microscopy.

Yang, C. Y.↗

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↗

Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.

Williams, Lewis J. [University of Essex, Colcheste↗

Formation of distinctive nanostructured metastable polymorphs mediated by kinetic transition pathways in germanium

High-pressure β -Sn germanium may transform into diverse metastable allotropes with distinctive nanostructures and unique physical properties via multiple pathways under decompression. However, the mechanism and transition kinetics remain poorly understood. Here, we investigate the formation of metastable phases and nanostructures in germanium via controllable transition pathways of β -Sn Ge under rapid decompression at different rates. High-resolution transmission electron microscopy reveals three distinct metastable phases with the distinctive nanostructures: an almost perfect st12 Ge crystal, nanosized bc8/r8 structures with amorphous boundaries, and amorphous Ge with nanosized clusters (0.8–2.5 nm). Fast in situ x-ray diffraction and x-ray absorption measurements indicate that these nanostructured products form in certain pressure regions via distinct kinetic pathways and are strongly correlated with nucleation rates and electronic transitions mediated by compression rate, temperature, and stress. This work provides deep insight into the controllable synthesis of metastable materials with unique crystal symmetries and nanostructures for potential applications.

36 MATERIALS SCIENCE↗

A quantitative comparison of the fingerprint of twinned microstructures through surface and three-dimensional techniques

Assessing the fingerprint of a material’s microstructure is key for supporting materials design. With the emergence of a wide range of 3D characterization techniques, it is critical to understand the main differences in fingerprints reconstructed from 2D and 3D datasets. To this end, we introduce a graph-based microstructure reconstruction framework that enables structural comparisons of twin domain networks in high purity Ti using 3D and 2D electron backscatter diffraction. Insights into the structure of the twin networks are facilitated by combining statistical analysis of twin crystallography with visual and graphical analysis of the novel graph abstractions of the twins. We demonstrate that compared to 3D reconstructions, conventional 2D views of twinning miss key aspects of the microstructure including the high interconnectivity of domains into networks that span the full reconstruction volume. The reduced cross-grain and in-grain twin connectivity typically observed in 2D has notable implications on our understanding of how twinning mediates the plastic response of microstructures and how twin networks evolve. It is thus clear that 3D characterization is critical for accurately inferring both twin network morphologies as well as the key unit processes facilitating network formation.

36 MATERIALS SCIENCE↗

Dynamic nanodomains dictate macroscopic properties in lead halide perovskites

Lead halide perovskites have emerged as promising materials for solar energy conversion and X-ray detection owing to their remarkable optoelectronic properties. However, the microscopic origins of their superior performance remain unclear. Here we show that low-symmetry dynamic nanodomains present in the high-symmetry average cubic phases, whose characteristics are dictated by the A-site cation, govern the macroscopic behaviour. We combine X-ray diffuse scattering, inelastic neutron spectroscopy, hyperspectral photoluminescence microscopy and machine-learning-assisted molecular dynamics simulations to directly correlate local nanoscale dynamics with macroscopic optoelectronic response. Our approach reveals that methylammonium-based perovskites form densely packed, anisotropic dynamic nanodomains with out-of-phase octahedral tilting, whereas formamidinium-based systems develop sparse, isotropic, spherical nanodomains with in-phase tilting, even when crystallography reveals cubic symmetry on average. We demonstrate that these sparsely distributed isotropic nanodomains present in formamidinium-based systems reduce electronic dynamic disorder, resulting in a beneficial optoelectronic response, thereby enhancing the performance of formamidinium-based lead halide perovskite devices. By elucidating the influence of the A-site cation on local dynamic nanodomains, and consequently, on the macroscopic properties, we propose leveraging this relationship to engineer the optoelectronic response of these materials, propelling further advancements in perovskite-based photovoltaics, optoelectronics and X-ray imaging.

Materials Science↗

Crystallography of Magnetite Plaquettes and their Significance as Asymmetric Catalysts for the Synthesis of Chiral Organics in Carbonaceous Chondrites

We have previously observed the magnetite plaquettes in carbonaceous chondrites using scanning electron microscope (SEM) imaging, examined the crystal orientation of the polished surfaces of magnetite plaquettes in CI Orgueil using electron backscattered diffraction (EBSD) analysis, and concluded that these magnetite plaquettes are likely naturally asymmetric materials. In this study, we expanded our EBSD observation to other magnetite plaquettes in Orgueil, and further examined the internal structure of these remarkable crystals with the use of X-ray computed microtomography.

Chan, Q. H. S.↗

De novo design of proteins housing excitonically coupled chlorophyll special pairs

Natural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C 2 -symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.

59 BASIC BIOLOGICAL SCIENCES↗