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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Periodic trends in gas–phase oxidation and hydrogenation reactions of lanthanides and 5d transition metal cations

Of the many publications coming from the laboratory of Diethard K. Bohme, among the most valuable were the surveys of reactivity throughout the periodic table as studied using selected ion flow tube (SIFT) mass spectrometry. In all cases, quantitative rate constants at 295 K and 0.35 Torr of He were obtained for metal cations generated by an inductively coupled plasma (ICP). This source creates ions at a temperature characterized as 5500 K. Here, it was believed that radiative relaxation and interactions with the flow gases would rapidly deplete most excited electronic states of the metal cations, although this is unknown

transition metals↗
DOE OSTI2021

Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides

Microbial natural products are a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class of natural products that include antibiotics, immunosuppressants, and anticancer agents. Recent breakthroughs in natural product discovery have revealed the chemical structure of several thousand NRPs. However, biosynthetic gene clusters (BGCs) encoding them are known only for a few hundred compounds. Here, we developed Nerpa, a computational method for the high-throughput discovery of novel BGCs responsible for producing known NRPs. After searching 13,399 representative bacterial genomes from the RefSeq repository against 8368 known NRPs, Nerpa linked 117 BGCs to their products. We further experimentally validated the predicted BGC of ngercheumicin from Photobacterium galatheae via mass spectrometry. Nerpa supports searching new genomes against thousands of known NRP structures, and novel molecular structures against tens of thousands of bacterial genomes. The availability of these tools can enhance our understanding of NRP synthesis and the function of their biosynthetic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Study of the Synchrotron Photoionization Oxidation of Alpha-Angelica Lactone (AAL) Initiated by O( 3 P) at 298, 550, and 700 K

In recent years, biofuels have been receiving significant attention because of their potential for decreasing carbon emissions and providing a long-term renewable solution to unsustainable fossil fuels. Currently, lactones are some of the alternatives being produced. Many lactones occur in a range of natural substances and have many advantages over bioethanol. In this study, the oxidation of alpha-angelica lactone initiated by ground-state atomic oxygen, O( 3 P), was studied at 298, 550, and 700 K using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at the Lawrence Berkeley National Lab (LBNL). Photoionization spectra and kinetic time traces were measured to identify the primary products. Ketene, acetaldehyde, methyl vinyl ketone, methylglyoxal, dimethyl glyoxal, and 5-methyl-2,4-furandione were characterized as major reaction products, with ketene being the most abundant at all three temperatures. Possible reaction pathways for the formation of the observed primary products were computed using the CBS–QB3 composite method.

09 BIOMASS FUELS↗
DOE OSTI2024

Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis

Immunoprecipitation is one of the most effective methods for enrichment of lysine-acetylated peptides for comprehensive acetylome analysis using mass spectrometry. Manual acetyl peptide enrichment method using non-conjugated antibodies and agarose beads has been developed and applied in various studies. However, it is time consuming, and can introduce contaminants and variability that leads to potential sample loss and decreased sensitivity and robustness of the analysis. Here we describe a fast, automated enrichment protocol that enables reproducible and comprehensive acetylome analysis using a magnetic bead-based immunoprecipitation reagent.

Lysine acetylation, Acetylome, Acetyl peptide enri↗
DOE OSTI2024

Advancing the Prediction of MS/MS Spectra Using Machine Learning

Tandem mass spectrometry (MS/MS) is an important tool for the identification of small molecules and metabolites where resultant spectra are most commonly identified by matching them with spectra in MS/MS reference libraries. While popular, this strategy is limited by the contents of existing reference libraries. In response to this limitation, various methods are being developed for the in silico generation of spectra to augment existing libraries. Recently, machine learning and deep learning techniques have been applied to predict spectra with greater speed and accuracy. Here, in this work, we investigate the challenges these algorithms face in achieving fast and accurate predictions on a wide range of small molecules. The challenges are often amplified by the use of generic machine learning benchmarking tactics, which lead to misleading accuracy scores. Curating data sets, only predicting spectra for sufficiently high collision energies, and working more closely with experimental mass spectrometrists are recommended strategies to improve overall prediction accuracy in this nuanced field.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Scalable synthesis of supported catalysts using fluidized bed atomic layer deposition

Overcoating layers deposited on the surface of heterogeneous catalysts using atomic layer deposition (ALD) have been shown to increase catalyst activity, lifetime, and selectivity. In this study, we performed Al 2 O 3 ALD and Pd ALD in a commercial fluidized bed reactor on high surface area mesoporous powder supports to create overcoated catalysts with high precursor utilization. We investigated the reaction mechanism for both Al 2 O 3 ALD and Pd ALD using in situ mass spectrometry and developed a mathematical model to understand the precursor saturation behaviors. We characterized the catalyst samples using a variety of techniques to measure the surface area, porosity, composition, and surface chemistry of the overcoated catalysts. Finally, we used propane dehydrogenation as a probe reaction to evaluate the performance of the catalysts prepared by fluidized bed ALD.

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

Clean quartz matters for cosmogenic nuclide analyses: An exploration of the importance of sample purity using the CRONUS-N reference material

We report reference materials are key for assessing inter-laboratory variability and measurement quality, and for placing analytical uncertainty bounds on sample analyses. Here, we investigate four years of data resulting from repeated processing of the CRONUS-N reference material for cosmogenic 10 Be and 26 Al analyses. At University of Vermont, we prepared a CRONUS-N aliquot with most of our sample batches from 2013 to 2017; these reference material samples were then distributed to four different accelerator mass spectrometry facilities, yielding 73 10 Be analyses and 58 26 Al analyses. We determine CRONUS-N 10 Be concentrations of (2.26 ± 0.14) x 10 5 atoms g -1 (n = 73, mean, 1 SD) and 26 Al concentrations of (1.00 ± 0.08) x 10 6 atoms g -1 (n = 58, mean, 1 SD). We find a reproducibility of 6.3% for 10 Be and 7.7% for 26 Al (relative standard deviations). We also document highly variable 27 Al and Mg concentrations and a 10 Be dispersion twice as large as the mean AMS analytic uncertainty. Analyses of the CRONUS-N material with and without density separation demonstrate that non-quartz minerals are present in the material and have a large impact on measured concentrations of 27 Al, 10 Be, and impurities; these non-quartz minerals represent only a very small portion of the total mass (0.6–0.8%) but have a disproportionally large effect on the resulting data. Our results highlight the importance of completely removing all non-quartz mineral phases from samples prior to Be/Al extraction for the determination of in situ cosmogenic 10 Be and 26 Al concentrations.

58 GEOSCIENCES↗
DOE OSTI2023

Elucidating the molecular programming of a nonlinear non-ribosomal peptide synthetase responsible for fungal siderophore biosynthesis

Abstract Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) enzymes remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC reveals its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovers several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chemical and structural characterization of particulate fallout isolated from air-filters

We report particulate nuclear fallout is the radioactive byproduct of a nuclear event formed by the mixture of proximate environmental materials with vaporized bomb debris. The fallout debris can be transported into the atmosphere during cloud rise, raining out locally and dispersing globally constituting a radiation hazard and contributing to the distribution of anthropogenic radionuclides in the environment. Questions remain on how entrainment of environmental material in the fireball affects fallout formation processes and radionuclide incorporation and distribution during cooling. To inform the characterization of fallout including the development of fallout size distributions and how radionuclides are incorporated into fallout debris where entrainment plays a role, we analyzed an archived historic US air-filter collected by aircraft in the aftermath of ground interacting nuclear tests. Particulate fallout collected on the filter was isolated and analyzed using scanning electron microscopy (SEM), transmission electron microscopy (TEM) and NanoSIMS (Secondary Ion Mass Spectrometry) to determine chemistry, structure, morphology, and size of the particles. Results demonstrate that the particles isolated from the filter have spherical shape, display complex internal structures, and are mainly composed of Fe and Si oxides. In these spherical particles, Pu is preferentially associated with Fe-rich composition. The characterization of fallout particulate samples can provide information on nucleation and particle growth from the vapor phase to improve modeling and simulation of fallout hazards.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Quantitative Analysis of The High‐Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase

Abstract Kelp is an abundant, farmable biomass‐containing laminarin and alginate as major polysaccharides, providing an excellent model substrate to study their deconstruction by simple enzyme mixtures. Our previous study showed strong reactivity of the glycoside hydrolase family 55 during hydrolysis of purified laminarin, raising the question of its reactivity with intact kelp. In this study, we determined that a combination of a single glycoside hydrolase family 55 β‐1,3‐exoglucanase with a broad‐specificity alginate lyase from the polysaccharide lyase family 18 gives efficient hydrolysis of untreated kelp to a mixture of simple sugars, that is, glucose, gentiobiose, mannitol‐end glucose, and mannuronic and guluronic acids and their soluble oligomers. Quantitative assignments from nanostructure initiator mass spectrometry (NIMS) and 2D HSQC NMR spectroscopy and analysis of the reaction time‐course are provided. The data suggest that binary combinations of enzymes targeted to the unique polysaccharide composition of marine biomass are sufficient to deconstruct kelp into soluble sugars for microbial fermentation.

2D HSQC NMR↗
DOE OSTI2021

Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

The Ebola virus matrix protein VP40 forms distinct structures linked to distinct functions in the virus life cycle. Dimeric VP40 is a structural protein associated with virus assembly, while octameric, ring-shaped VP40 is associated with transcriptional control. In this study, we show that suitable nucleic acid is sufficient to trigger a dynamic transformation of VP40 dimer into the octameric ring. Deep sequencing reveals a binding preference of the VP40 ring for the 3' untranslated region of cellular mRNA and a guanine- and adenine-rich binding motif. Complementary analyses of the nucleic-acid-induced VP40 ring by native mass spectrometry, electron microscopy, and X-ray crystal structures at 1.8 and 1.4 Å resolution reveal the stoichiometry of RNA binding, as well as an interface involving a key guanine nucleotide. The host factor-induced structural transformation of protein structure in response to specific RNA triggers in the Ebola virus life cycle presents unique opportunities for therapeutic inhibition.

3′ UTR↗
DOE OSTI2020

A Phenotarget Approach for Identifying an Alkaloid Interacting with the Tuberculosis Protein Rv1466

In recent years, there has been a revival of interest in phenotypic-based drug discovery (PDD) due to target-based drug discovery (TDD) falling below expectations. Both PDD and TDD have their unique advantages and should be used as complementary methods in drug discovery. The PhenoTarget approach combines the strengths of the PDD and TDD approaches. Phenotypic screening is conducted initially to detect cellular active components and the hits are then screened against a panel of putative targets. This PhenoTarget protocol can be equally applied to pure compound libraries as well as natural product fractions. Here we described the use of the PhenoTarget approach to identify an anti-tuberculosis lead compound. Fractions from Polycarpa aurata were identified with activity against Mycobacterium tuberculosis H37Rv. Native magnetic resonance mass spectrometry (MRMS) against a panel of 37 proteins from Mycobacterium proteomes showed that a fraction from a 95% ethanol re-extraction specifically formed a protein-ligand complex with Rv1466, a putative uncharacterized Mycobacterium tuberculosis protein. The natural product responsible was isolated and characterized to be polycarpine. The molecular weight of the ligand bound to Rv1466, 233 Da, was half the molecular weight of polycarpine less one proton, indicating that polycarpine formed a covalent bond with Rv1466.

phenotarget approach, MRMS, polycarpine, drug disc↗
DOE OSTI2021

Pregnancy is accompanied by larger high density lipoprotein particles and compositionally distinct subspecies

Pregnancy is accompanied by significant physiological changes, which can impact the health and development of the fetus and mother. Pregnancy-induced changes in plasma lipoproteins are well documented, with modest to no impact observed on the generic measure of high density lipoprotein (HDL) cholesterol. However, the impact of pregnancy on the concentration and composition of HDL subspecies has not been examined in depth. In this prospective study, we collected plasma from 24 nonpregnant and 19 pregnant women in their second trimester. Using nuclear magnetic resonance (NMR), we quantified 11 different lipoprotein subspecies from plasma by size, including three in the HDL class. We observed an increase in the number of larger HDL particles in pregnant women, which were confirmed by tracking phospholipids across lipoproteins using high-resolution gel-filtration chromatography. Using liquid chromatography-mass spectrometry (LC-MS), we identified 87 lipid-associated proteins across size-speciated fractions. We report drastic shifts in multiple protein clusters across different HDL size fractions in pregnant females compared with nonpregnant controls that have major implications on HDL function. These findings significantly elevate our understanding of how changes in lipoprotein metabolism during pregnancy could impact the health of both the fetus and the mother.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evolution of solid electrolyte interphase and active material in the silicon wafer model system

Alloying anode materials for lithium-ion batteries, such as silicon (Si), are an important focus of materials research due to the demand for increased energy density for electric vehicles and stationary grid storage. However, progress towards next generation anode materials has been hindered by poor capacity retention due to the instability of the Si active material and the solid electrolyte interphase (SEI). Herein, the evolution of the active Si material and the SEI are simultaneously investigated from the perspective of chemical, structural, morphological, and electronic evolution in the Si wafer model system through its cycling life, using time-of-flight secondary ion mass spectrometry (TOF-SIMS), scanning transmission electron microscopy (STEM), atomic force microscopy (AFM), and scanning spreading resistance microscopy (SSRM). The results illustrate a dynamic evolution of the SEI and active Si material through cycling. Through an improved understanding of evolution of SEI and Si active material within the Si wafer model system, mitigation strategies may be designed to extend the lifetime of Si anodes.

25 ENERGY STORAGE↗
DOE OSTI2022

Gaussian mixture model clustering algorithms for the analysis of high-precision mass measurements

The development of the phase-imaging ion-cyclotron resonance (PI-ICR) technique for use in Penning trap mass spectrometry (PTMS) increased the speed and precision with which PTMS experiments can be carried out. In PI-ICR, data sets of the locations of individual ion hits on a detector are created showing how ions cluster together into spots according to their cyclotron frequency. Ideal data sets would consist of a single, 2D-spherical spot with no other noise, but in practice data sets typically contain multiple spots, non-spherical spots, or significant noise, all of which can make determining the locations of spot centers non-trivial. A method for assigning groups of ions to their respective spots and determining the spot centers is therefore essential for further improving precision and confidence in PI-ICR experiments. Here, we present the class of Gaussian mixture model (GMM) clustering algorithms as an optimal solution. We show that on simulated PI-ICR data, several types of GMM clustering algorithms perform better than other clustering algorithms over a variety of typical scenarios encountered in PI-ICR. The mass spectra of 163Gd, 163 mGd, 162 Tb, and 162 mTb measured using PI-ICR at the Canadian Penning trap mass spectrometer were checked using GMMs, producing results that were in close agreement with the previously published values.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

RF surface resistance tuning of superconducting niobium via thermal diffusion of native oxide

Recently, Nb superconducting radio frequency cavities vacuum heat treated between 300 and 400°C for a few hours have exhibited very high quality factors (~5 × 10 10 at 2.0 K). Secondary ion mass spectrometry measurements of O, N, and C show that this enhancement in RF surface conductivity is primarily associated with interstitial O alloying via dissolution and diffusion of the native oxide. We use a theory of oxide decomposition and O diffusion to quantify previously unknown parameters crucial in modeling this process. RF measurements of a vacuum heat-treated Nb superconducting radio frequency cavity confirm the minimized surface resistance (higher Q 0 ) previously expected only from 800 °C diffusive alloying with N.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Aluminum hydroxide, bayerite, boehmite, and gibbsite ToF-SIMS spectra in the positive ion mode. II

We report time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for boehmite (AOH-60) and its potential products of oxidation including pseudo-boehmite (AOH-180), α- and γ-Al 2 O 3 , and α- and γ-Al(OH) 3 . Since boehmite often forms on the cladding materials to prevent corrosion, surface analysis techniques are performed to determine the amount of oxidation present. This ToF-SIMS spectral library is of significance because it includes boehmite and its potential oxidation products (i.e., aluminum oxide and hydroxide), which can be used to compare to spectra obtained for real-world samples containing boehmite. Furthermore, ToF-SIMS is often used as a complementary technique to x-ray photoelectron spectroscopy (XPS) due to its surface sensitivity and ability to compare spectra via multivariate analysis, therefore establishing the molecular signatures of boehmite and relevant compounds are essential for peak identification. The SIMS spectra shown are acquired from commercially available powders, which were deposited onto a Si wafer substrate via liquid slurry drop casting. This library of SIMS mass spectra will serve as a comparison of boehmite [γ-AlO(OH)], pseudo-boehmite [AlOOH∙nH 2 O], α- and γ-Al 2 O 3 aluminum oxide, and α- and γ-Al 2 O 3 aluminum hydroxide in the positive ion mode, which compliments those reported in the negative ion mode (Part 1).

36 MATERIALS SCIENCE↗
DOE OSTI2022

Aluminum hydroxide, bayerite, boehmite, and gibbsite ToF-SIMS spectra in the negative ion mode. I

We report time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for boehmite (AOH-60) and its potential products of oxidation including pseudo-boehmite (AOH-180), α- and γ-Al 2 O 3 , and α- and γ-Al(OH) 3 . Since boehmite is often incorporated on cladding materials to prevent corrosion, surface analysis techniques are performed to determine the amount of oxidation present. This ToF-SIMS spectral library is of significance because it includes boehmite and its potential oxidation products (i.e., aluminum oxide and hydroxide), which can be used to compare to spectra obtained for real-world samples containing boehmite. Furthermore, ToF-SIMS is often used as a complementary technique to x-ray photoelectron spectroscopy due to its surface sensitivity and ability to compare spectra via a multivariate analysis, therefore establishing that the molecular signatures of boehmite and relevant compounds are essential for peak identification. The SIMS spectra shown are acquired from commercially available powders, which were deposited onto a silicon wafer substrate via liquid slurry drop casting. This library of SIMS mass spectra will serve as a comparison of boehmite [γ-AlO(OH)], pseudo-boehmite [AlOOH∙nH 2 O], α- and γ-Al 2 O 3 aluminum oxide, and α- and γ-Al 2 O 3 aluminum hydroxide in the negative ion mode, which compliments those reported in the positive ion mode.

36 MATERIALS SCIENCE↗