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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
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

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

Structure and Synthesizability of Iron–Sulfur Metal–Organic Frameworks

Sulfur-based metal–organic frameworks (MOFs) and coordination polymers (CPs) are an emerging class of hybrid materials that have received growing attention due to their magnetic, conductive, and catalytic properties with potential applications in electrocatalysis and energy storage. In this work, we report a high-throughput virtual screening protocol to predict the synthesizability of candidate metal–sulfur MOFs/CPs by computing the thermodynamically stable structures resulting from a particular combination of metal cluster, linker, cation, and synthetic conditions. Free energies are computed by using all-atom classical mechanical thermodynamic integration. Low-free-energy structures are refined using ab initio density functional theory, and pair distribution functions and powder X-ray diffraction patterns are calculated to complement and guide experimental structure determination. We validate the computational approach by retrospective predictions of the stable structure produced by experimental syntheses, and a subsequent screen predicts Fe 4 S 4 -BDT–TPP as a new thermodynamically stable one-dimensional (1D) CP comprising a redox-active Fe 4 S 4 cluster, a 1,4-benzenedithiolate (BDT) linker, and a tetraphenylphosphonium (TPP) countercation. Furthermore, this material is experimentally synthesized, and the 1D chain structure of the crystal is confirmed using microcrystal electron diffraction. The computational screening pipeline is generically transferable to neutral and ionic MOFs/CPs comprising arbitrary metal clusters, linkers, cations, and synthetic conditions, and we make it freely available as an open source tool to guide and accelerate the discovery and engineering of novel porous materials.

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

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Probing subwavelength in-plane anisotropy with antenna-assisted infrared nano-spectroscopy

Infrared nano-spectroscopy based on scattering-type scanning near-field optical microscopy (s-SNOM) is commonly employed to probe the vibrational fingerprints of materials at the nanometer length scale. However, due to the elongated and axisymmetric tip shank, s-SNOM is less sensitive to the in-plane sample anisotropy in general. In this article, we report an easy-to-implement method to probe the in-plane dielectric responses of materials with the assistance of a metallic disk micro-antenna. As a proof-of-concept demonstration, we investigate here the in-plane phonon responses of two prototypical samples, i.e. in (100) sapphire and x-cut lithium niobate (LiNbO 3 ). In particular, the sapphire in-plane vibrations between 350 cm–1 to 800 cm–1 that correspond to LO phonon modes along the crystal b- and c-axis are determined with a spatial resolution of < λ/10, without needing any fitting parameters. In LiNbO 3 , we identify the in-plane orientation of its optical axis via the phonon modes, demonstrating that our method can be applied without prior knowledge of the crystal orientation. Furthermore, our method can be elegantly adapted to retrieve the in-plane anisotropic response of a broad range of materials, i.e. subwavelength microcrystals, van-der-Waals materials, or topological insulators.

36 MATERIALS SCIENCE↗
DOE OSTI2021

DNA origami single crystals with Wulff shapes

DNA origami technology has proven to be an excellent tool for precisely manipulating molecules and colloidal elements in a three-dimensional manner. However, fabrication of single crystals with well-defined facets from highly programmable, complex DNA origami units is a great challenge. Here, we report the successful fabrication of DNA origami single crystals with Wulff shapes and high yield. By regulating the symmetries and binding modes of the DNA origami building blocks, the crystalline shapes can be designed and well-controlled. The single crystals are then used to induce precise growth of an ultrathin layer of silica on the edges, resulting in mechanically reinforced silica-DNA hybrid structures that preserve the details of the single crystals without distortion. The silica-infused microcrystals can be directly observed in the dry state, which allows meticulous analysis of the crystal facets and tomographic 3D reconstruction of the single crystals by high-resolution electron microscopy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Terahertz response of monolayer and few-layer WTe2 at the nanoscale

Abstract Tungsten ditelluride (WTe 2 ) is an atomically layered transition metal dichalcogenide whose physical properties change systematically from monolayer to bilayer and few-layer versions. In this report, we use apertureless scattering-type near-field optical microscopy operating at Terahertz (THz) frequencies and cryogenic temperatures to study the distinct THz range electromagnetic responses of mono-, bi- and trilayer WTe 2 in the same multi-terraced micro-crystal. THz nano-images of monolayer terraces uncovered weakly insulating behavior that is consistent with transport measurements. The near-field signal on bilayer regions shows moderate metallicity with negligible temperature dependence. Subdiffractional THz imaging data together with theoretical calculations involving thermally activated carriers favor the semimetal scenario with $$\Delta \approx -10\,{{{\rm{meV}}}}$$ Δ ≈ − 10 meV over the semiconductor scenario for bilayer WTe 2 . Also, we observed clear metallic behavior of the near-field signal on trilayer regions. Our data are consistent with the existence of surface plasmon polaritons in the THz range confined to trilayer terraces in our specimens. Finally, data for microcrystals up to 12 layers thick reveal how the response of a few-layer WTe 2 asymptotically approaches the bulk limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography

Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Solution-processable and functionalizable ultra-high molecular weight polymers via topochemical synthesis

Abstract Topochemical polymerization reactions hold the promise of producing ultra-high molecular weight crystalline polymers. However, the totality of topochemical polymerization reactions has failed to produce ultra-high molecular weight polymers that are both soluble and display variable functionality, which are restrained by the crystal-packing and reactivity requirements on their respective monomers in the solid state. Herein, we demonstrate the topochemical polymerization reaction of a family of para -azaquinodimethane compounds that undergo facile visible light and thermally initiated polymerization in the solid state, allowing for the first determination of a topochemical polymer crystal structure resolved via the cryoelectron microscopy technique of microcrystal electron diffraction. The topochemical polymerization reaction also displays excellent functional group tolerance, accommodating both solubilizing side chains and reactive groups that allow for post-polymerization functionalization. The thus-produced soluble ultra-high molecular weight polymers display superior capacitive energy storage properties. This study overcomes several synthetic and characterization challenges amongst topochemical polymerization reactions, representing a critical step toward their broader application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nano-spectroscopy of excitons in atomically thin transition metal dichalcogenides

Abstract Excitons play a dominant role in the optoelectronic properties of atomically thin van der Waals (vdW) semiconductors. These excitons are amenable to on-demand engineering with diverse control knobs, including dielectric screening, interlayer hybridization, and moiré potentials. However, external stimuli frequently yield heterogeneous excitonic responses at the nano- and meso-scales, making their spatial characterization with conventional diffraction-limited optics a formidable task. Here, we use a scattering-type scanning near-field optical microscope (s-SNOM) to acquire exciton spectra in atomically thin transition metal dichalcogenide microcrystals with previously unattainable 20 nm resolution. Our nano-optical data revealed material- and stacking-dependent exciton spectra of MoSe 2 , WSe 2 , and their heterostructures. Furthermore, we extracted the complex dielectric function of these prototypical vdW semiconductors. s-SNOM hyperspectral images uncovered how the dielectric screening modifies excitons at length scales as short as few nanometers. This work paves the way towards understanding and manipulation of excitons in atomically thin layers at the nanoscale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Heterogeneity in M. tuberculosis β-lactamase inhibition by Sulbactam

Abstract For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans- enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

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↗
DOE OSTI2026

Structural basis of the promiscuity of the unusual Fe(II) and 2-oxoglutarate dependent human aspartate/asparagine-β-hydroxylase

Protein-hydroxylation catalysed by Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases is an important regulatory mechanism in human biology. Such oxygenases typically coordinate their Fe(II) cofactor via a conserved triad of an aspartate- or glutamate- and two histidine-residues. By contrast, aspartate/asparagine β-hydroxylase (AspH), which catalyses asparagine/aspartate-residue oxidation in epidermal growth factor-like domains (EGFDs), has only two histidine-residues (H679, H725), with a water occupying the site normally occupied by an aspartate- or glutamate-residue. We describe mechanistic studies with catalytically active AspH crystals. Turnover studies with single crystals under cryogenic conditions give (3 R)-hydroxylated EGFDs with the product alcohol coordinating Fe(II) trans to H725. Time-resolved serial crystallography of microcrystals using an acoustic droplet ejection system, coupled to X-ray emission analyses, demonstrate turnover within 1.5 s, giving a product complex in which Fe(II) is regenerated. Solution and crystallographic studies with the O 2 surrogate nitric oxide imply O 2 binds to Fe(II) trans to H725. The additional Fe-chelating water is maintained throughout AspH catalysis and is not directly involved in substrate hydroxylation, because O 2 is the sole oxygen source in alcohol products, as shown by 18 O labelling studies. The results reveal how AspH accommodates both aspartate- and asparagine-substrates and will assist in efforts targeting AspH for cancer treatment.

de Munnik, Mariska↗
DOE OSTI2022

Materials synthesis at terapascal static pressures

Theoretical modelling predicts very unusual structures and properties of materials at extreme pressure and temperature conditions. Hitherto, their synthesis and investigation above 200 gigapascals have been hindered both by the technical complexity of ultrahigh-pressure experiments and by the absence of relevant in situ methods of materials analysis. Here we report on a methodology developed to enable experiments at static compression in the terapascal regime with laser heating. We apply this method to realize pressures of about 600 and 900 gigapascals in a laser-heated double-stage diamond anvil cell, producing a rhenium–nitrogen alloy and achieving the synthesis of rhenium nitride Re 7 N 3 —which, as our theoretical analysis shows, is only stable under extreme compression. Full chemical and structural characterization of the materials, realized using synchrotron single-crystal X-ray diffraction on microcrystals in situ, demonstrates the capabilities of the methodology to extend high-pressure crystallography to the terapascal regime.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography

Myxobacteria are non-photosynthetic, soil-dwelling bacteria distinguished by a multicellular stage in their life cycle known as fruiting bodies that are stimulated by light. Myxobacterial phytochromes are candidates for the perception of red-light. The mechanism how light is perceived and converted to a physiological response is unknown. Here, time-resolved serial femtosecond crystallographic (TR-SFX) experiments were conducted on microcrystals of the photosensory core module of the Stigmatella aurantiaca bacteriophytochrome 2 (SaBphP2). Initial events of the Z to E isomerization reaction of the covalently bound, open-chain tetrapyrrole biliverdin (BV) chromophore were determined. At 3 ps after light activation, the BV ring-D assumes a configuration needed for the isomerization. At 100 ps, a mixture of BV in the Z or E configuration is observed in subunit A, while in the other subunit the chromophore remains in the Z configuration. In conjunction with prior results, these structures reveal the molecular mechanism of phytochrome activation in the photomorphogenesis of the myxobacteria and provide the molecular foundation for physiological responses to red light in other bacteria.

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

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

3D printed water-stable Cd-doped Cs 4 MnBi 2 Cl 12 /polylactic acid perovskite/polymer composites for high-flux X-ray scintillation

Stable and efficient X-ray scintillators are crucial for medical diagnostics, industrial, and defense applications. However, conventional scintillator technologies face a trade-off between stability, optimal performance, and sustainability. Herein, we introduce 3D-printed Cs 4 MnBi 2 Cl 12 (Pero1) and Cs 4 Cd 0.68 Mn 0.32 Bi 2 Cl 12 (Pero2) perovskite microcrystals embedded within a polylactic acid (PLA) polymer composite as X-ray scintillators, combining efficiency, stability, and sustainability. The orange luminescent perovskite powder phosphors exhibited poor water stability, which was successfully addressed through incorporation into PLA via filament extrusion and fused deposition modeling (FDM) 3D printing. The resulting composite films demonstrated remarkable water stability while maintaining uniform orange emission throughout the polymer matrix, as confirmed by 3D topography scanning and X-ray fluorescence mapping. Structural characterization revealed minimal chemical interaction between the perovskite and PLA matrix, with the composites retaining their crystalline properties. The PLA-Pero2 composite exhibited superior optical properties, with a photoluminescence quantum yield of 47%, nearly 17 times higher than that of PLA-Pero1 (2.8%), attributed to the effective suppression of non-radiative decay pathways through Cd 2+ doping. Under hard X-ray irradiation at synchrotron beamlines, both composites exhibited excellent radioluminescence, with emission peaks at 605 nm, a linear response across a wide X-ray flux range, and remarkable radiation stability, showing less than 3% intensity degradation after 600 seconds of continuous high-dose exposure. The PLA-Pero2 composite achieved a spatial resolution of 5 line pairs per millimeter and a contrast ratio of 0.255. These performance metrics, combined with the polymer's biodegradability and scalability through additive manufacturing, position PLA-based composites as a more sustainable alternative to conventional petroleum-based polymer scintillators for next-generation medical imaging, radiation monitoring, and industrial radiography applications.

3D Printing↗
DOE OSTI2024

Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers

Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals and solutions at microscales. Microfluidics are the obvious approach for any high-throughput, nano-to-microliter sample handling, that also requires design flexibility and rapid prototyping to deal with the variable shapes, sizes, and density of crystals. Here, we discuss recent advances in polymer 3D printing for microfluidics-based serial crystallography research and present a demonstration of emerging, large-scale, nano-3D printing approaches leading into the future of 3D sample environment and delivery device fabrication from liquid jet gas-dynamic virtual nozzles devices to fixed-target sample environment technology.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Structural and mechanical properties of magnesium aluminate nanoceramics under high pressure

Nanoceramics may have different structural and physical properties compared to their coarse-grained counterparts. Here, we report the high-pressure study of micro- and nano-crystalline MgAl2O4 in order to examine the effect of particle size on the structural stability. A reversible pressure-induced phase transition (cubic to tetragonal) is observed in MgAl2O4 nanocrystals under non-hydrostatic pressure at room temperature, in contrast to the previously reported structural transition of MgAl2O4 at high pressure and high temperature. It is also found that the compressed MgAl2O4 microcrystals do not fracture further below 60 nm, suggesting a plastic deformation mechanism transition. MgAl2O4 with a grain size above ∼60 nm exhibits normal cracking behaviors, but shows metal-like plastic deformation behaviors below this critical size. It is implied that combined ductility and strength can be achieved in nanoceramic MgAl2O4.

Xu, Jianing (ORCID:0000000325474344)↗