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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception

KAI2 proteins are plant α/β hydrolase receptors which perceive smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). The number of functional KAI2 receptors varies among species and KAI2 gene duplication and sub-functionalization likely plays an adaptative role by altering specificity towards different KLs. Legumes represent one of the largest families of flowering plants and contain many agronomic crops. Prior to their diversification, KAI2 underwent duplication resulting in KAI2A and KAI2B. Here we demonstrate that Pisum sativum KAI2A and KAI2B are active receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a higher affinity for and hydrolyses a broader range of substrates including strigolactone-like stereoisomers. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical, structural, and mass spectra analyses of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, confirming its role as a bona fide enzyme. Our work uncovers the stereoselectivity of ligand perception and catalysis by diverged KAI2 receptors and proposes adaptive sensitivity to KAR/KL and strigolactones by KAI2B.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An Experimental and Theoretical Study of the High Temperature Reactions of the Four Butyl Radical Isomers

The high temperature gas phase chemistry of the four butyl radical isomers (n-butyl,sec-butyl, iso-butyl, andtert-butyl) was investigated in a combined experimental and theoretical study. Organic nitrites were used as convenient and clean sources of each of the butyl radical isomers. Rate coefficients for dissociation of each nitrite were obtained experimentally and are at, or close to, the high pressure limit. Low pressure experiments were performed in a diaphragmless shock tube with laser schlieren densitometry at post-shock pressures of 65, 130, and 260 Torr and post-shock temperatures of 700-1000 K. Additional experiments were conducted with iso-butyl radicals at 805 K and 8.7 bar to elucidate changes in mechanism at higher pressures. These experiments were performed in a miniature shock tube with synchrotron-based photoionization mass spectrometry. The mass spectra confirmed that scission of the O-NO bond is the primary channel by which the precursors dissociate, but they also provided evidence of a minor channel (<7.7%) through HNO loss and formation of an aldehyde. These high pressure experiments were also used to determine the disproportionation/recombination ratio for iso-butyl radicals as 0.3. Reanalysis of the lower-temperature literature and the present data yielded rate constants for the disproportionation reaction, iso-butyl + iso-butyl = iso-butene + iso-butane. A chemical kinetics model was developed for the reactions of the butyl isomers that included new paths for highly energized adducts. These adducts are formed by the addition of H, CH 3 or C 2 H 5 to the butyl radicals. Accompanying theoretical investigations show that chemically activated pathways are competitive with stabilization of the adduct by collision under the conditions of the laser schlieren experiments. These calculations also show that at 10 bar and T< 1000 K stabilization is the only important reaction, but at higher temperatures, even at 10 bar, chemically activated product channels should also be considered. Branching fractions and rate coefficients are presented for these reactions. Furthermore, this study also highlights the importance of the radical structure for determining branching ratios for disproportionation and recombination of alkyl radicals, and these were facilitated by theoretical calculations of recombination rate coefficients for the four butyl radical isomers. Overall, the results reveal previously unknown features of butyl radical chemistry under conditions that are relevant to a wide range of applications and reaction mechanisms are presented that incorporate pressure dependent rate coefficients for the key steps.

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

The electronic structure and deexcitation pathways of an isolated metalloporphyrin ion resolved by metal L-edge spectroscopy

The local electronic structure of the metal-active site and the deexcitation pathways of metalloporphyrins are crucial for numerous applications but difficult to access by commonly employed techniques. Here, we applied near-edge X-ray absorption mass spectrometry and quantum-mechanical restricted active space calculations to investigate the electronic structure of the metal-active site of the isolated cobalt(III) protoporphyrin IX cation (CoPPIX+) and its deexcitation pathways upon resonant absorption at the cobalt L-edge. The experiments were carried out in the gas phase, thus allowing for control over the chemical state and molecular environment of the metalloporphyrin. The obtained mass spectra reveal that resonant excitations of CoPPIX+ at the cobalt L3-edge lead predominantly to the formation of the intact radical dication and doubly charged fragments through losses of charged and neutral side chains from the macrocycle. The comparison between experiment and theory shows that CoPPIX + is in a 3 A 2g triplet ground state and that competing excitations to metal-centred non-bonding and antibonding σ* molecular orbitals lead to distinct deexcitation pathways.

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

Gas-phase pyrolysis of trans 3-pentenenitrile: competition between direct and isomerization-mediated dissociation

The flash pyrolysis of trans 3-pentenenitrile (3-PN, CH 3 –$CH=CH$–CH 2 –CN) was studied by combining the results of VUV photoionization mass spectra with broadband microwave spectra recorded as a function of the temperature of the pyrolysis tube. The two separated functional groups (vinyl and nitrile) open up isomerization as an initial step in competition with unimolecular dissociation. Primary products were detected by keeping the 3-PN concentration low and limiting reaction times to the traversal time of the gas in the pyrolysis tube (~100 μs). The reaction is quenched and products are cooled by expansion into vacuum before interrogation over the 8–18 GHz region using chirped-pulse broadband methods. 118 nm VUV photoionization of the same reaction mixture provides a means of detecting all products with ionization potentials below 10.5 eV with minimal fragmentation. These results are combined with a detailed computational investigation of the C 5 H 7 N and related potential energy surfaces, leading to a consistent picture of the unimolecular decomposition of 3-PN. Loss of two H-atoms to form a 79 amu product is proven from its microwave transitions to contain trans-Z-2,4-pentadienenitrile, while no pyridine is observed. Methyl loss, HCN loss, and breaking the central C(2)–C(3) bond all occur following isomerization of the position of the double bond, thereby opening up low-energy pathways to these decomposition channels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Size-dependent femtosecond proton transfer in protonated methanol clusters

Methanol clusters (CH 3 OH) n are prototypical hydrogen-bonded systems that bridge isolated molecules and bulk liquid methanol. Strong-field ionization of these clusters can trigger ultrafast charge migration, proton transfer, and isomerization; however, the onset timescales of these pathways remain largely unexplored despite extensive steady-state mass-spectrometric evidence for protonation and chemical rearrangement. Here we use femtosecond time-resolved strong-field ionization and disruptive probing to directly track the early-time dynamics of methanol clusters. Transient mass spectra yield size-dependent timescales for the formation of protonated clusters H + (CH 3 OH) n (n = 1–3) and an associated CHO˙ + radical cation. We find that both proton-transfer and subsequent stabilization become markedly faster with increasing cluster size. These measurements establish methanol clusters as a complementary benchmark to water for understanding ionization-initiated proton motion and chemical reorganization in hydrogen-bonded liquids.

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

Electron and ion spectroscopy of azobenzene in the valence and core shells

Azobenzene is a prototype and a building block of a class of molecules of extreme technological interest as molecular photo-switches. We present a joint experimental and theoretical study of its response to irradiation with light across the UV to x-ray spectrum. The study of valence and inner shell photo-ionization and excitation processes combined with measurement of valence photoelectron-photoion coincidence and mass spectra across the core thresholds provides a detailed insight into the site- and state-selected photo-induced processes. Photo-ionization and excitation measurements are interpreted via the multi-configurational restricted active space self-consistent field method corrected by second order perturbation theory. Using static modeling, we demonstrate that the carbon and nitrogen K edges of azobenzene are suitable candidates for exploring its photoinduced dynamics thanks to the transient signals appearing in background-free regions of the NEXAFS and XPS.

Chemistry↗
DOE OSTI2024

An experimental and computational view of the photoionization of diol–water clusters

In the interstellar medium, diols and other prebiotic molecules adsorb onto icy mantles surrounding dust grains. Water in the ice may affect the reactivity and photoionization of these diols. Ethylene glycol (EG), 1,2-propylene glycol, and 1,3-propylene glycol clusters with water clusters were used as a proxy to study these interactions. The diol–water clusters were generated in a continuous supersonic molecular beam, photoionized by synchrotron-based vacuum ultraviolet light from the Advanced Light Source, and subsequently detected by reflectron time-of-flight mass spectrometry. The appearance energies for the detected clusters were determined from the mass spectra, collected at increasing photon energy. Clusters of both diol fragments and unfragmented diols with water were detected. The lowest energy geometry optimized conformers for the observed EG–water clusters and EG fragment–water clusters have been visualized using density functional theory (DFT), providing insight into hydrogen bonding networks and how these affect fragmentation and appearance energy. As the number of water molecules clustered around EG fragments (m/z 31 and 32) increased, the appearance energy for the cluster decreased, indicating a stabilization by water. This trend was supported by DFT calculations. Fragment clusters from 1,2-propylene glycol exhibited a similar trend, but with a smaller energy decrease, and no trend was observed from 1,3-propylene glycol. In conclusion, we discuss and suggest that the reactivity and photoionization of diols in the presence of water depend on the size of the diol, the location of the hydroxyl group, and the number of waters clustered around the diol.

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

Systematic characterization of unknown compounds via dimensionality reduction of time series

Analysis of ambient aerosols provides valuable insight into particle sources and formation chemistry. However, due to the complexity of atmospheric data and the dynamic nature of aerosol composition, a substantial fraction of data often become discarded by conventional analysis methods. Furthermore, a large fraction of chemical species within those data are unidentifiable due to a lack of matching spectral information, resulting in suboptimal characterization of chemical composition. Previous work has demonstrated techniques for cataloging analytes in a chromatographic dataset by deconvolution of mass spectra, but integration of these analytes throughout a large dataset remains time consuming. Here, we present a method to automatically identify an ion for quantitation for single-ion chromatogram based peak fitting and integration, enabling comprehensive integration of analytes with minimal user interaction. The resulting time series are clustered with a machine-learning based dimensionality reduction technique to systematically investigate the underlying characteristics of the categorized analytes and gain new insights into the chemical composition and physicochemical properties of the unidentifiable analytes. We apply these methods to existing atmospheric datasets collected in Manacapuru, Brazil during the GoAmazon2014/5 campaign to identify new analytes and interpret their variability and transformations in the atmosphere. The analysis results generate 408 time series from cataloged analytes of interest, and the clustering of those time series with spherical k-means results in 8 distinct clusters. We find the analytes form clusters based on their distinct physicochemical properties, demonstrating the method’s ability to systematically identify and selectively filter contaminants and instrumental analytes and characterize the unidentifiable analytes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Observation of e⁺e⁻ → pp$\bar{p}\bar{n}\pi^-$ + c. c.

Using data taken at 29 center-of-mass energies between 4.16 and 4.70 GeV with the BESIII detector at the Beijing Electron Positron Collider corresponding to a total integrated luminosity of approximately 18.8 fb -1 , the process e⁺e⁻ → pp$\overline{p}\overline{n}\pi^-$ + c. c. is observed for the first time with a statistical significance of 11.5σ. The average Born cross sections in the energy ranges of (4.160, 4.380) GeV, (4.400, 4.600) GeV and (4.610, 4.700) GeV are measured to be (21.5 ± 5.7 ± 1.2) fb, (46.3 ± 10.6 ± 2.5) fb and (59.0 ± 9.4 ± 3.2) fb, respectively, where the first uncertainties are statistical and the second are systematic. The line shapes of the $\overline{p}\overline{n}$ and ppπ⁻ invariant mass spectra are consistent with phase space distributions, indicating that no hexaquark or di-baryon state is observed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Using spin alignment of inelastically excited nuclei in fast beams to assign spins: The spectroscopy of 13 O as a test case

Excited states in O 13 were investigated using inelastic scattering of an E / A = 69.5 MeV O 13 beam off of a Be 9 target. The excited states were identified in the invariant-mass spectra of the decay products. Both single-proton and sequential two-proton decays of the excited states were examined. Furthermore, for a number of the excited states, the protons were emitted with strong anisotropy where emissions transverse to the beam axis are favored. The measured proton-decay angular distributions were compared to predictions from distorted-wave Born-approximation calculations of the spin alignment which was shown to be largely independent of the excitation mechanism. The deduced O 13 level scheme is compared to ab initio no-core shell model with continuum predictions. The lowest-energy excited states decay isotropically consistent with predictions of strong proton 1 s 1 / 2 structure. Above these states in the level scheme, we observed a number of higher-spin states not predicted within the model. Possibly these are associated with rotational bands built on deformed cluster configurations predicted by antisymmetrized molecular dynamics calculations. The spin alignment mechanism is shown to be useful for making spin assignments and may have widespread use.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Search for an exotic S = – 2 , Q = – 2 baryon resonance in proton-proton interactions at s N N = 17.3 GeV

Pentaquark states have been extensively investigated theoretically in the context of the constituent quark model. In this paper results of an experimental search for pentaquarks in the Ξ – π – , Ξ – π + , Ξ ¯ + π – and Ξ ¯ + π + invariant mass spectra in proton-proton interactions at s = 17.3 GeV are presented. Previous possible evidence from the NA49 collaboration of the existence of a narrow Ξ – π – baryon resonance in p + p interactions is not confirmed with almost 10 times greater event statistics. The search was performed using the NA61/SHINE detector which reuses the main components of the NA49 apparatus. No signal was observed with either the selection cuts of NA49 or newly optimized cuts.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Twist-3 generalized parton distribution for the proton from basis light-front quantization

We investigate the twist-3 generalized parton distributions (GPDs) for the valence quarks of the proton within the basis light-front quantization (BLFQ) framework. We first solve for the mass spectra and light-front waved functions (LFWFs) in the leading Fock sector using an effective Hamiltonian. Using the LFWFs we then calculate the twist-3 GPDs via the overlap representation. By taking the forward limit, we also get the twist-3 parton distribution functions (PDFs), and discuss their properties. Our prediction for the twist-3 scalar PDF agrees well with the CLAS experimental extractions.

Astronomy & Astrophysics↗
DOE OSTI2024

Observation of ψ ( 3686 ) → 3 ϕ

Using ( 2.712 ± 0.014 ) × 10 9 ψ ( 3686 ) events collected by the BESIII detector operating at the BEPCII collider, we report the first observation of ψ ( 3686 ) → 3 ϕ decay with a significance larger than 10 σ . The branching fraction of this decay is determined to be ( 1.46 ± 0.05 ± 0.17 ) × 10 − 5 , where the first uncertainty is statistical and the second is systematic. No significant structure is observed in the ϕ ϕ invariant mass spectra. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2022

Balancing Trade-Offs Imposed by Growth Media and Mass Spectrometry for Bacterial Exometabolomics

The bacterial exometabolome consists of a vast array of specialized metabolites, many of which are only produced in response to specific environmental stimuli. For this reason, it is desirable to control the extracellular environment with a defined growth medium composed of pure ingredients. However, complex (undefined) media are expected to support the robust growth of a greater variety of microorganisms than defined media. Here, we investigate the trade-offs inherent to a range of complex and defined solid media for the growth of soil microorganisms, production of specialized metabolites, and detection of these compounds using direct infusion mass spectrometry. We find that complex media support growth of more soil microorganisms, as well as allowing for the detection of more previously discovered natural products as a fraction of total m/z features detected in each sample. However, the use of complex media often caused mass spectrometer injection failures and poor-quality mass spectra, which in some cases resulted in over a quarter of samples being removed from analysis. Defined media, while more limiting in growth, generated higher quality spectra and yielded more m/z features after background subtraction. These results inform future exometabolomic experiments requiring a medium that supports the robust growth of many soil microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Measurement of $\phi $ meson production in $p + p$ interactions at 40, 80 and $158 \, \hbox {GeV}/c$ with the NA61/SHINE spectrometer at the CERN SPS

Results on $\phi$ meson production in inelastic p+p collisions at CERN SPS energies are presented. They are derived from data collected by the NA61/SHINE fixed target experiment, by means of invariant mass spectra fits in the $\phi \to K^+K^-$ decay channel. They include the first ever measured double differential spectra of $\phi$ mesons as a function of rapidity $y$ and transverse momentum $p_T$ for proton beam momenta of 80 GeV/c and 158 GeV/c, as well as single differential spectra of $y$ or $p_T$ for beam momentum of 40 GeV/c. The corresponding total $\phi$ yields per inelastic p+p event are obtained. These results are compared with existing data on $\phi$ meson production in p+p collisions. The comparison shows consistency but superior accuracy of the present measurements. The emission of $\phi$ mesons in p+p reactions is confronted with that occurring in Pb+Pb collisions, and the experimental results are compared with model predictions. It appears that none of the considered models can properly describe all the experimental observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Heavy-light mesons on the light front

Abstract We study the heavy-light mesons within basis light-front quantization. The resulting mass spectra of D , $$D_s$$ D s , B , and $$B_s$$ B s agree reasonably well with experiments. We also predict states which could be measured in the near future. In the light-front formalism, we calculate the light-front wave functions and additional experimental observables, such as parton distribution functions, distribution amplitudes, and decay constants by means of integrations over light-front wave functions. We also provide ratios of decay constants for selected pseudoscalar meson decays ( $$D_s$$ D s to D and $$B_s$$ B s to B ) as they may prove to be theoretically more robust and more reliably determined in experiments. We find that our ratios are systematically smaller than existing experiments and other approaches by 5–18%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗