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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 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Selecting Suitable Near-Native Lignins for Research

There are several methods to isolate near-native lignins, including milled-wood lignin, enzymatic lignin, cellulolytic enzyme lignin, and enzymatic mild-acidolysis lignin. Which one is the most representative of the native lignin? Herein, near-native lignins were isolated from different plant groups and structurally analyzed to determine how well these lignins represented their native lignin counterparts. Analytical methods were applied to understand the molecular weight, monomer composition, and distribution of interunit linkages in the structure of the lignins. The results indicated that either enzymatic lignin or cellulolytic enzyme lignin may be used to represent native lignin in softwoods and hardwoods. None of the lignins, however, appeared to represent native lignins in grasses (monocot plants) because of substantial syringyl/guaiacyl differences. Furthermore, complicating the understanding of grass lignin structure, large amounts of hydroxycinnamates acylate their polysaccharides and, when released, are often conflated with actual lignin monomers.

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

Extracting the partonic structure of colorless exchanges at the Electron Ion Collider

We investigate the determination of the partonic structure of colorless exchanges in deep inelastic diffractive e p scattering at the Electron Ion Collider (EIC), using the standard decomposition into Pomeron and Reggeon contributions. We perform fits to simulated diffractive cross section pseudodata in four variables, including the momentum transfer t , to estimate the achievable precision on the Pomeron and Reggeon quark and gluon distributions. We analyze the influence of different cuts in the kinematic variables, beam energy configurations, and luminosities, including a “first year” scenario. We conclude that the EIC will be able to constrain the partonic structure of the subleading Reggeon exchange with a precision comparable to that of the leading Pomeron exchange. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2024

The seventh blind test of crystal structure prediction: structure generation methods

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Chemistry↗
DOE OSTI2020

Glycosidic linkage, N -acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β- D -glucopyranosyl-(1→4)-β- D -mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C 15 H 27 NO 11 ·H 2 O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N -acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N -acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis – trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O -glycosidic linkages on linkage torsion angles φ and ψ. Hypersurfaces correlating φ and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.

Chemistry↗
DOE OSTI2020

High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme that catalyzes the conversion of methane to methanol at ambient temperature using a nonheme, oxygen-bridged dinuclear iron cluster in the active site. Structural changes in the hydroxylase component (sMMOH) containing the diiron cluster caused by complex formation with a regulatory component (MMOB) and by iron reduction are important for the regulation of O 2 activation and substrate hydroxylation. Structural studies of metalloenzymes using traditional synchrotron-based X-ray crystallography are often complicated by partial X-ray-induced photoreduction of the metal center, thereby obviating determination of the structure of the enzyme in pure oxidation states. Here, microcrystals of the sMMOH:MMOB complex from Methylosinus trichosporium OB3b were serially exposed to X-ray free electron laser (XFEL) pulses, where the ≤35 fs duration of exposure of an individual crystal yields diffraction data before photoreduction-induced structural changes can manifest. Merging diffraction patterns obtained from thousands of crystals generates radiation damage-free, 1.95 Å resolution crystal structures for the fully oxidized and fully reduced states of the sMMOH:MMOB complex for the first time. The results provide new insight into the manner by which the diiron cluster and the active site environment are reorganized by the regulatory protein component in order to enhance the steps of oxygen activation and methane oxidation. Furthermore, this study also emphasizes the value of XFEL and serial femtosecond crystallography (SFX) methods for investigating the structures of metalloenzymes with radiation sensitive metal active sites.

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

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. Here, we observe and discuss systematic map quality deterioration as result of data incompleteness.

Hydrogen bond↗
DOE OSTI2022

Synthesis and structure of carbon-doped H 3 S compounds at high pressure

Understanding of recently reported putative close-to-room-temperature superconductivity in C-S-H compounds at 267 GPa demands a reproducible synthesis protocol as well as knowledge of the compounds' structure and composition. Here, we synthesized C-S-H compounds with various carbon compositions at high pressures from elemental carbon C and methane CH 4 , sulfur S, and molecular hydrogen H 2 . Here, we focus on compounds synthesized using methane as these allow a straightforward determination of their structure and composition by combining single-crystal x-ray diffraction and Raman spectroscopy. We applied a two-stage synthesis of [(CH 4 ) x (H 2 S) (1-x) ] 2 H 2 compounds with various compositions by first reacting sulfur and mixed methane-hydrogen fluids and forming CH 4 -doped H 2 S crystals at 0.5-3 GPa and then by growing single crystals of the desired hydrogen-rich compound. Raman spectroscopy applied to this material shows the presence of CH 4 molecules incorporated into the lattice and allows the determination of the CH 4 content, while single-crystal x-ray diffraction results suggest that the methane molecules substitute H 2 S molecules. The structural behavior of these compounds is very similar to the previously investigated methane-free crystals demonstrating a transition from Al 2 Cu type I4/mcm molecular crystal to a modulated molecular structure at 20-30 GPa and back to the same basic I4/mcm structure in an extended modification with greatly modified Raman spectra. This latter phase demonstrates a distortion into a Pnma structure at 132-159 GPa and then transforms into a common Im$\bar{3}$m H 3 S phase at higher pressures; however, no structural anomaly is detected near 220 GPa, where a sharp upturn in T c has been reported.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Crystal structure of vancomycin bound to the resistance determinant D -alanine- D -serine

Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to D-alanine-D-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the D-alanine-D-serine ligand is bound in essentially the same position and same pose as the native D-alanine-D-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups – one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic – are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site

Mycobacterium tuberculosis is the cause of the world’s most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts L-homoserine to O-acetyl-L-homoserine at the committed step of this pathway. In order to facilitate structure-based drug design, we determined the high-resolution crystal structures of three MetX proteins, including M. tuberculosis (MtMetX), Mycolicibacterium abscessus (MaMetX), and Mycolicibacterium hassiacum (MhMetX). A comparison of homoserine transacetylases from other bacterial and fungal species reveals a high degree of structural conservation amongst the enzymes. Utilizing homologous structures with bound cofactors, we analyzed the potential ligandability of MetX. The deep active-site tunnel surrounding the catalytic serine yielded many consensus clusters during mapping, suggesting that MtMetX is highly druggable.

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

gC1qR/C1qBP/HABP-1: Structural Analysis of the Trimeric Core Region, Interactions With a Novel Panel of Monoclonal Antibodies, and Their Influence on Binding to FXII

The protein gC1qR/C1qBP/HABP-1 plays an essential role in mitochondrial biogenesis, but becomes localized at the cellular surface in numerous pathophysiological states. When this occurs on endothelial cells, surface-exposed gC1qR activates the classical pathway of complement. It also promotes assembly of a multi-protein complex comprised of coagulation factor XII (FXII), pre-kallikrein (PK), and high-molecular weight kininogen (HMWK) that activates the contact system and the kinin-generating system. Since surface-exposed gC1qR triggers intravascular inflammatory pathways, there is interest in identifying molecules that block gC1qR function. Here we further that objective by reporting the outcome of a structure/function investigation of gC1qR, its interactions with FXII, and the impact of a panel of monoclonal anti-gC1qR antibodies on FXII binding to gC1qR. Although deletion mutants have been used extensively to assess gC1qR function, none of these proteins have been characterized structurally. To that end, we determined a 2.2 Å resolution crystal structure of a gC1qR mutant lacking both of its acidic loops, but which retained nanomolar-affinity binding to FXII and FXIIa. This structure revealed that the trimeric gC1qR assembly was maintained despite loss of roughly thirty residues. Characterization of a novel panel of anti-gC1qR monoclonal antibodies identified several with biochemical properties distinct from previously described antibodies, as well as one which bound to the first acidic loop of gC1qR. Intriguingly, we found that each of these antibodies could partly inhibit binding of FXII and FXIIa to gC1qR. Based on these results and previously published studies, we offer new perspectives for developing gC1qR inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Detailed Method for the Purification of Rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana

The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana . Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species.

25 ENERGY STORAGE↗
DOE OSTI2022

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes (zrg) have recently been shown to transport zinc with putative SBPs (zrgA) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa, illustrating diversity within this little-studied protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

New determination of the branching ratio of the structure dependent radiative K + → e + ν e γ

The branching ratio of the structure dependent (SD) radiative K + → e + ν e γ decay relative to that of the K + → e + ν e (γ) decay including the internal bremsstrahlung (IB) process (K e2 (γ) ) has been measured in the J-PARC E36 experiment using plastic scintillator/lead sandwich detectors, in contrast to the previous E36 measurement, which used a CsI(Tl) calorimeter. In the analysis, the effect of IB was also taken into account in the SD radiative decay as $K$$^{SD}_{e2γ(γ)}$. By combining the new data with the previous E36 result after revision for the IB correction for $K$$^{SD}_{e2γ(γ)}$, a new value Br($K$$^{SD}_{e2γ(γ)}$)/Br(Ke 2(γ) ) = 1.20 ± 0.07 has e2γ(γ) e2γ(γ) been determined. This is consistent with a recent lattice QCD calculation, but larger than the expectation of Chiral Perturbation Theory (ChPT) at order O(p 4 ) and the previous KLOE value. Using the method to relate form factor and branching ratio described in the KLOE paper, the present result is also consistent with the form factor prediction based on a gauged nonlocal chiral quark model, but larger than that from ChPT at order O(p 6 ).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Probing extreme states of matter using ultra-intense x-ray radiation

Extreme states of matter, that is, matter at extremes of density (pressure) and temperature, can be created in the laboratory either statically or dynamically. In the former, the pressure–temperature state can be maintained for relatively long periods of time, but the sample volume is necessarily extremely small. When the extreme states are generated dynamically, the sample volumes can be larger, but the pressure–temperature conditions are maintained for only short periods of time (ps to μs). In either case, structural information can be obtained from the extreme states by the use of x-ray scattering techniques, but the x-ray beam must be extremely intense in order to obtain sufficient signal from the extremely-small or short-lived sample. In this article I describe the use of x-ray diffraction at synchrotrons and XFELs to investigate how crystal structures evolve as a function of density and temperature. After a brief historical introduction, I describe the developments made at the Synchrotron Radiation Source in the 1990s which enabled the almost routine determination of crystal structure at high pressures, while also revealing that the structural behaviour of materials was much more complex than previously believed. I will then describe how these techniques are used at the current generation of synchrotron and XFEL sources, and then discuss how they might develop further in the future at the next generation of x-ray lightsources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Escape Ratio Contributes More Than Fluorescence Yield to SIF-GPP Relationship Over Crops and Rainforest

Solar-induced chlorophyll fluorescence (SIF) is an effective indicator to track the gross primary productivity (GPP). However, there is still a lack of a clear understanding for the contribution of physiological and structural factors to the SIF–GPP relationship at the canopy scale. To quantify the influence of different SIF components, particularly the photon escape ratio ($f$ esc ) and fluorescence yield (Φ F ), on the SIF–GPP relationship, this study evaluated the performance of various vegetation indices (VIs), SIF components, light use efficiency (LUE), and GPP over two typical biomes (crops and rainforest), using a range of satellite remote sensing products. In August of each year from 2018 to 2020, both SIF and GPP over United States (U.S.) Corn Belt are higher than those over the Amazon rainforest, attributed to the consistent pattern of higher $f$ esc and LUE over crops than over rainforest, as well as Φ F . Furthermore, the structural signals represented by $f$ esc (R = 0.41–0.64) can better capture the LUE variations than Φ F (R = 0.10–0.30) for each biome. In conclusion, this study highlights that $f$ esc , determined by canopy structure, has great potential to capture LUE and GPP changes within and across biomes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Polaron and Exciton Delocalization in Oligomers of High-Performance Polymer PTB7

A key characteristic of organic photovoltaic cells is the efficient charge separation in the active layer. Sufficient delocalization of the positive polaron in organic photovoltaics is considered essential for the effective separation of the opposite charges and the suppression of recombination. Here we use light-induced EPR and ENDOR spectroscopy combined with DFT calculations to determine the electronic structure of the positive polaron in PTB7-type oligomers. Utilizing the superior spectral resolution of high-frequency (130 GHz) D-band EPR, the principal components of the g tensors were determined. Pulsed ENDOR spectroscopy at X-band allowed the measurement of H-1 hyperfine coupling constants. A comparison of g tensors and H-1 hyperfine coupling constants of the PTB7-type oligomers with the high-performance PTB7 polymer revealed a delocalization of the positive polaron in the polymer over about four monomeric units, corresponding to about 45 angstrom in length. Our current study thus not only determines the polaron delocalization length in PTB7 but also validates the approach combining EPR/ENDOR spectroscopy with DFT-calculated magnetic resonance parameters. This is of importance in those cases where oligomers of defined length are not easily obtained. In addition, the delocalization of the neutral triplet exciton was also determined in the oligomers and compared with polymer PTB7. The analysis revealed that the neutral triplet exciton is substantially more delocalized than the positive polaron, exceeding 10 monomeric units.

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

Low-dimensional metal–organic frameworks: a pathway to design, explore and tune magnetic structures

Here, the magnetic structure adopted by a material relies on symmetry, the hierarchy of exchange interactions between magnetic ions and local anisotropy. A direct pathway to control the magnetic interactions is to enforce dimensionality within the material, from zero-dimensional isolated magnetic ions, one-dimensional (1D) spin-chains, two-dimensional (2D) layers to three-dimensional (3D) order. Being able to design a material with a specific dimensionality for the phenomena of interest is non-trivial. While many advances have been made in the area of inorganic magnetic materials, organic compounds offer distinct and potentially more fertile ground for material design. In particular magnetic metal–organic frameworks (mMOFs) combine magnetism with non-magnetic property functionality on the organic linkers within the structural framework, which can further be tuned with mild perturbations of pressure and field to induce phase transitions. Here, it is examined how neutron scattering measurements on mMOFs can be used to directly determine the magnetic structure when the magnetic ions are in a 2D layered environment within the wider 3D crystalline framework. The hydrated formate, in deuterated form, Co(DCOO) 2 ·2D 2 O, which was one of the first magnetic MOFs to be investigated with neutron diffraction, is reinvestigated as an exemplar case.

magnetism↗
DOE OSTI2026

Locating the atoms at the hard-soft interface of gold nanoparticles

Surface structure affects the growth, shape and properties of nanoparticles. In wet chemical syntheses, metal additives and surfactants are used to modify surfaces and guide nanocrystal growth. To understand this process, it is critical to understand how the surface structure, and hence its energy, is modified. However, measuring the type and arrangement of atoms at hard-soft interfaces on nanoscale surfaces, especially in the presence of surfactants, is extremely challenging. Here, we determine the atomic structure of the hard-soft interface in a metallic nanoparticle by developing low-dose imaging conditions in four-dimensional scanning transmission electron microscopy that are preferentially sensitive to surface adatoms. By revealing experimentally the copper additives and bromide surfactant counterion at the surface of a gold nanocuboid and quantifying their interatomic distances, our direct, low-dose imaging method provides atomic-level understanding of chemically sophisticated nanomaterial surface structures. These measurements of the atomic structure of the hard-soft interface provide the information necessary to understand and quantify surface chemistries and energies and their pivotal role in nanocrystal growth.

Li, Weilun [Monash University, Melbourne, VIC (Aus↗