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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

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

Inorganic Sulfur Species Formed upon Heterogeneous OH Oxidation of Organosulfates: A Case Study of Methyl Sulfate

In this report recent studies reveal that organosulfates at the particle surface can be oxidized by gas-phase OH radicals with significant rates. Inorganic sulfur species, such as the bisulfate ion (HSO 4 - ) and sulfate ion (SO 4 2- ), can be formed upon these heterogeneous oxidation processes through the formation and subsequent reactions of sulfate radical anions (SO 4 •- ) in the particle phase. However, the amount of inorganic sulfur species produced in these heterogeneous oxidation reactions is not known. We investigate the heterogeneous OH oxidation of sodium methyl sulfate (CH 3 SO 4 Na), the smallest organosulfate detected in atmospheric particles, using an oxidation flow reactor at a relative humidity of 75%. We quantify the kinetics by measuring the decay of CH 3 SO 4 Na and the amount of HSO 4 - and SO 4 2- formed upon oxidation using ion chromatography. Kinetic measurements determine the heterogeneous OH reaction rate to be (5.72 ± 0.14) x 10 -13 cm 3 molecule -1 s -1 , with an effective OH uptake coefficient, γ eff , of 0.31 ± 0.06. The molar yield of inorganic sulfur species, defined as the total number of moles of HSO 4 - and SO 4 2- formed per mole of CH 3 SO 4 Na consumed upon oxidation, is found to be significant and has an average value of 0.62 ± 0.18 upon oxidation. A kinetic model is developed to describe the kinetics and inorganic sulfur species formation upon oxidation. Model simulations suggest that CH 3 SO 4 Na tends to decompose rapidly into formaldehyde and SO 4 •- , and the reaction of SO 4 •- with CH 3 SO 4 Na plays a significant role in both governing the kinetics and the formation of inorganic sulfur species.

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

Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Abstract Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S 2 to S 3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural evidence for intermediates during O 2 formation in photosystem II

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn 4 CaO 5 cluster first stores four oxidizing equivalents, the S 0 to S 4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S 3 →[S 4 ]→S 0 transition where O 2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn 4 CaO 5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom O x , which was introduced as a bridging ligand between Ca and Mn1 during the S 2 →S 3 transition disappears or relocates in parallel with Y z reduction starting at approximately 700 μs after the third flash. The onset of O 2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A 1A and A 1B . The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A 1A . These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tree foliage as a net accumulator of highly toxic methylmercury

Tree canopies are known to elevate atmospheric inputs of both mercury (Hg) and methylmercury (MeHg). While foliar uptake of gaseous Hg is well documented, little is known regarding the temporal dynamics and origins of MeHg in tree foliage, which represents typically less than 1% of total Hg in foliage. In this work, we examined the foliar total Hg and MeHg content by following the growth of five individual trees of American Beech (Fagus grandifolia) for one growing season (April–November, 2017) in North Carolina, USA. We show that similar to other studies foliar Hg content increased almost linearly over time, with daily accumulation rates ranging from 0.123 to 0.161 ng/g/day. However, not all trees showed linear increases of foliar MeHg content along the growing season; we found that 2 out of 5 trees showed elevated foliar MeHg content at the initial phase of the growing season but their MeHg content declined through early summer. However, foliar MeHg content among all 5 trees showed eventual increases through the end of the growing season, proving that foliage is a net accumulator of MeHg while foliar gain of biomass did not “dilute” MeHg content.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quashing a suspected selection bias in galaxy samples having dynamically measured supermassive black holes

Local early-type galaxies (ETGs) with directly measured black hole masses, M bh , have been reported to represent a biased sample relative to the ETG population at large. Such galaxies with Spitzer Space Telescope imaging have been purported to possess velocity dispersions, σ, at least ∼0.1 dex larger for a given galaxy stellar mass, M * , gal , than is typically observed among thousands of ETGs imaged by the Sloan Digital Sky Survey (SDSS). This apparent offset led Shankar et al. to reduce the normalisation of the observed M bh ∝ σ 5 relation by at least ∼0.5 dex to give their ‘intrinsic relations’, including σ-based modifications to the observed M bh –M * , gal relation. These modifications were based on the untested assumption that the stellar masses had been derived consistently between the two samples. Here, we provide the necessary check using galaxies common to the Spitzer Survey of Stellar Structure in Galaxies (S 4 G) and the SDSS. We find that the stellar masses of galaxies with and without directly measured black hole masses had appeared offset from each other due to the use of inconsistent stellar mass-to-light ratios, Υ * , for the optical and infrared data. We briefly discuss the ‘intrinsic relations’ and why some of these will at times appear to have had partial success when applied to data based on similarly inconsistent values ofΥ * . Finally, we reiterate the importance of the υ (lower-case Υ) term, which we previously introduced into the M bh –M * relations to help avoid Υ * -related mismatches.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A prescription for the asteroseismic surface correction

In asteroseismology, the surface effect refers to a disparity between the observed and the modelled frequencies in stars with solar-like oscillations. It originates from improper modelling of the surface layers. Correcting the surface effect usually requires using functions with free parameters, which are conventionally fitted to the observed frequencies. On the basis that the correction should vary smoothly across the H–R diagram, we parameterize it as a simple function of surface gravity, effective temperature, and metallicity. We determine this function by fitting a wide range of stars. The absolute amount of the surface correction decreases with luminosity, but the ratio between it and νmax increases, suggesting the surface effect is more important for red giants than dwarfs. Applying the prescription can eliminate unrealistic surface correction, which improves parameter estimations with stellar modelling. Using two open clusters, we found a reduction of scatter in the model-derived ages for each star in the same cluster. As an important application, we provide a new revision for the Δν scaling relation that, for the first time, accounts for the surface correction. The values of the correction factor, f Δν , are up to 2 percent smaller than those determined without the surface effect considered, suggesting decreases of up to 4 percent in radii and up to 8 percent in masses when using the asteroseismic scaling relations. This revision brings the asteroseismic properties into an agreement with those determined from eclipsing binaries. The new correction factor and the stellar models with the corrected frequencies are available at https://www.github.com/parallelpro/surface.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A unified exploration of the chronology of the Galaxy

The Milky Way has distinct structural stellar components linked to its formation and subsequent evolution, but disentangling them is non-trivial. With the recent availability of high-quality data for a large numbers of stars in the Milky Way, it is a natural next step for research in the evolution of the Galaxy to perform automated explorations with unsupervised methods of the structures hidden in the combination of large-scale spectroscopic, astrometric, and asteroseismic data sets. We determine precise stellar properties for 21 076 red giants, mainly spanning 2–15 kpc in Galactocentric radii, making it the largest sample of red giants with measured asteroseismic ages available to date. We explore the nature of different stellar structures in the Galactic disc by using Gaussian mixture models as an unsupervised clustering method to find substructure in the combined chemical, kinematic, and age subspace. The best-fitting mixture model yields four distinct physical Galactic components in the stellar disc: the thin disc, the kinematically heated thin disc, the thick disc, and the stellar halo. We find hints of an age asymmetry between the Northern and Southern hemisphere, and we measure the vertical and radial age gradient of the Galactic disc using the asteroseismic ages extended to further distances than previous studies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Indirect determination of the astrophysical S factor for the Li 6 ( p , γ ) Be 7 reaction using the asymptotic normalization coefficient method

The 6 Li(p,γ) 7 Be cross section influences a variety of astrophysical scenarios, including big-bang and stellar nucleosynthesis. In recent years, conflicting results of direct measurements have been published, reporting contradictory low-energy trends. To shed light on the contradiction between the existing data sets, the reaction was studied using the asymptotic normalization coefficient (ANC) technique which was up-to-now never used for this reaction. To derive the ANC, the 6 Li( 3 He,d) 7 Be transfer reaction, studied at the Department of Physics and Astronomy of the University of Catania and at the John. D. Fox Superconducting Accelerator Laboratory at Florida State University, was re-analyzed, focusing on the proton transfer mechanism [the α transfer process is discussed by Kiss et al. [Phys. Lett. B 807, 135606 (2020)]. Here, the energy of the 3 He beam impinging on a 6 Li target was E lab = 3 MeV and E lab = 5 MeV. The yield of the emitted deuterons was measured with high precision by using silicon ΔE – E telescopes.

6 ≤ A ≤ 19↗
DOE OSTI2023

Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography

The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO 2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn 4 Ca complex (Mn 4 CaO 5 ) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of O X from a new water molecule, which disappears on completion of the reaction, implicating it in the O—O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn 4 Ca cluster.

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

Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in Clostridium thermocellum

Glycolysis is an ancient, widespread, and highly conserved metabolic pathway that converts glucose into pyruvate. In the canonical pathway, the phosphofructokinase (PFK) reaction plays an important role in controlling flux through the pathway. Clostridium thermocellum has an atypical glycolysis and uses pyrophosphate (PP i ) instead of ATP as the phosphate donor for the PFK reaction. The reduced thermodynamic driving force of the PP i -PFK reaction shifts the entire pathway closer to thermodynamic equilibrium, which has been predicted to limit product titers. Here, in this study, we replace the PP i -PFK reaction with an ATP-PFK reaction. We demonstrate that the local changes are consistent with thermodynamic predictions: the ratio of fructose 1,6-bisphosphate to fructose-6-phosphate increases, and the reverse flux through the reaction (determined by 13 C labeling) decreases. The final titer and distribution of fermentation products, however, do not change, demonstrating that the thermodynamic constraints of the PP i -PFK reaction are not the sole factor limiting product titer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in Escherichia coli but instead use a reversible membrane-bound proton-pumping enzyme. In such organisms, the charging of tRNA with amino acids may become more reversible. This may contribute to the observed excretion of amino acids during sugar fermentation by Clostridium thermocellum and Thermoanaerobacterium saccharolyticum . Calculation of the energetic advantage of reversible pyrophosphate-dependent glycolysis, as occurs in Clostridium thermocellum , could not be properly evaluated, as currently available genome-scale models neglect the anabolic generation of pyrophosphate in, for example, polymerization of amino acids to protein. This anabolic pyrophosphate replaces ATP and thus saves energy. Its amount is, however, too small to cover the pyrophosphate requirement of sugar catabolism in glycolysis. Consequently, pyrophosphate for catabolism is generated according to ATP + P i → ADP + PP i .

59 BASIC BIOLOGICAL SCIENCES↗