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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Vanderwaltozyma urihicola sp. nov., a yeast species isolated from rotting wood and beetles in a Brazilian Amazonian rainforest biome

Five yeast isolates belonging to a candidate for novel species were obtained from rotting wood and the gut of a passalid beetle larva in a site of Amazonian rainforest biome in Brazil. Sequence analysis of the Internal Transcribed Spacer (ITS)-5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Vanderwaltozyma. The closest relative of the novel species is Vanderwaltozyma huisunica. These species differs due to 44 nt substitutions and 21 indels in the sequences of the ITS region, as well as by 15 substitutions and four indels in the sequences of the D1/D2 domains. A phylogenomic analysis of the Vanderwaltozyma species with genomes sequenced showed that this novel species is an outgroup to the other species of this genus. We propose the name Vanderwaltozyma urihicola sp. nov. (CBS 18107T, MycoBank MB 856975) to accommodate these isolates. Furthermore, the species is homothallic, producing one to two ascospores per ascus. The habitat of V. urihicola is rotting wood in the Brazilian Amazonian rainforest biome.

Amazonian Forest↗
DOE OSTI2022

From classical to quantum dynamics of atomic and ionic species interacting with graphene and its analogue

Graphene and its analogues offer a broad range of application opportunities for (opto)-electronics, sensing, catalysis, phase separation, energy conversion and storage, etc. Engineering graphene properties often relies on its controllable functionalization, defect formation and patterning, and reactive gas etching. In this chapter, we survey the dynamics of graphene using classical and quantum-classical dynamics methods. We discuss the reactivity, scattering, and transmission of atomic and ionic species including Ar cluster ion, H/D, and H+/D+ on graphene flakes of various sizes, focusing on the atomic-scale motion and energy dissipation pathways involved in forming and breaking covalent bonding. Discussions on the nuclear quantum effects of light species, the effects of isotopic substitution, and the methodologies for such modeling are also included.

Garashchuk, Sofiya V.↗
DOE OSTI2020

Experimental and theoretical study of the soot-forming tendencies of furans as potential biofuels

Sustainably-produced biofuels, including furans derived from lignocellulosic biomass, are being studied as potential next-generation fuels. Biofuels have unique structures that are absent in conventional fuels and they potentially emit fewer particulates than conventional fuels because of the presence of oxygen atoms. In this work, we focus on quantification and measurement of sooting tendency. A set of furans was selected and their sooting tendencies were characterized by Yield Sooting Index (YSI), which was obtained by measuring the line-of-sight spectral radiance (LSSR) of a coflow laminar diffusion flame doped with 1000 ppm of each test fuel. The measured YSIs are lower than traditional gasoline fuels and benzenoid aromatics (e.g., YSIbenzene = 100). We also performed numerical simulations with a detailed chemical kinetic mechanism to analyze the flame chemistry of 2-methylfuran (2MF). 4→5 H-atom migration in the furan ring causes 31.0% of the total decomposition and is the dominant fuel consumption pathway leading to soot. DFT calculations via the G4 composite method were carried out to obtain activation energies (Ea) and bond dissociation energies (BDE). The results showed that the 4→5 H-atom migration in the furan ring has the second lowest Ea and subsequently forms a 1,2-diene-substituted ketone derivative as a stable species. The ring-opening products of the 4→5 H-atom migration are propyne + a linear ketene for 2-n-alkylfurans, and 1-butyne + a methyl-substituted ketene for 2-t-butylfuran. These results can explain the trends of the measured YSIs of 2-alkylfurans.

09 BIOMASS FUELS↗
DOE OSTI2023

Spectra and characteristics of somatic mutations induced by ionizing radiation in hematopoietic stem cells

Spectra and frequencies of spontaneous and X-ray-induced somatic mutations were revealed with mouse long-term hematopoietic stem cells (LT-HSCs) by whole-genome sequencing of clonal cell populations propagated in vitro from single isolated LT-HSCs. SNVs and small indels were the most common types of somatic mutations, and increased up to twofold to threefold by whole-body X-irradiation. Base substitution patterns in the SNVs suggested a role of reactive oxygen species in radiation mutagenesis, and signature analysis of single base substitutions (SBS) revealed a dose-dependent increase of SBS40. Most of spontaneous small deletions were shrinkage of tandem repeats, and X-irradiation specifically induced small deletions out of tandem repeats (non-repeat deletions). Presence of microhomology sequences in non-repeat deletions suggested involvement of microhomology mediated end-joining repair mechanisms as well as nonhomologous end-joining in radiation-induced DNA damages. We also identified multisite mutations and structural variants (SV), i.e., large indels, inversions, reciprocal translocations, and complex variants. The radiation-specificity of each mutation type was evaluated from the spontaneous mutation rate and the per-Gy mutation rate estimated by linear regression, and was highest with non-repeat deletions without microhomology, followed by those with microhomology, SV except retroelement insertions, and multisite mutations; these types were thus revealed as mutational signatures of ionizing radiation. Further analysis of somatic mutations in multiple LT-HSCs indicated that large fractions of postirradiation LT-HSCs originated from single LT-HSCs that survived the irradiation and then expanded in vivo to confer marked clonality to the entire hematopoietic system, with varying clonal expansion and dynamics depending on radiation dose and fractionation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2022

Preparation and Characterization of Model Homotopic Catalysts: Rh Adatoms, Nanoparticles, and Mixed Oxide Surfaces on Fe 3 O 4 (001)

The atomic-level characterization of active sites is essential to understanding the mechanisms behind catalytic reactions. In this study, using scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS), we follow the morphological changes of a model Rh catalysts supported on Fe 3 O 4 (001) as a function of temperature and Rh coverage. Here, we identify the preparation conditions leading to model catalysts containing homotopic or nearly homotopic Rh species bound as adatoms, small clusters, substitutional within the Fe 3 O 4 (001), and nanoparticles. Adsorbates such as CO and CO 2 are further subsequently used to characterize the properties of different Rh sites. Using temperature programmed desorption (TPD), we demonstrate that adatoms, clusters, and nanoparticles exhibit high-temperature CO desorption (250-600 K). Strong binding on such sites further allows for CO oxidation to CO 2 via the Mars-van-Krevelen mechanism. In contrast, CO 2 was found to interact weakly with all Rh sites. Differences in desorption temperature enable the use of CO and CO 2 as titration methods for nanoparticles and Fe 3 O 4 (001), respectively. A small quantity of CO 2 was found to be reduced to CO on Rh adatoms and clusters.

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

Identification of efficient and stable solid-solid electrochemical interfaces for Li-S batteries. Final Report

The objective of this work is to develop a better understanding of the interactions between battery components that drive the observed battery performance. Using computational tools at the atomistic level, we elucidate molecular, crystal, and amorphous structures, interfacial structures and reactions, and electrochemical behavior. We focus on Li metal anodes, liquid electrolytes, solid electrolytes, S cathodes, and metal-oxide cathodes, and their corresponding interfaces. Within liquid electrolytes, we study their bulk structure and dynamics, as a function of salt concentration. The analysis allows to understand the formation of localized high concentrated regions as the solvent is substituted by a weakly interacting diluent species. Analysis of the electron distribution yields the reactive behavior at interfaces. Moreover, we employ tools that allow the characterization of ion and electron transport at interfaces, during the processes of solvation and desolvation occurring while cycling. For Sulfur cathodes we elucidate synthesis processes and the role of carbon-sulfur and nitrogen-sulfur interactions not only to provide electronic conductivity but also to define alternative reaction pathways during discharge of Li-S batteries. Full-cell simulations offer new insights regarding the integration of all the battery components. Our studies also include solid electrolytes and their interfaces with Li metal, S-C, and metal-oxide electrodes.

25 ENERGY STORAGE↗
DOE OSTI2021

Chemical compositions, pharmacological activities, quality control studies of Erycibes plants, and the development of their substitutes

Erycibes are members of the Convolvulaceae family, including more than 10 species worldwide that are distributed in tropical Asia. Some Erycibes species have long been used as traditional remedies for rheumatoid arthritis, fever, hepatitis, and liver injury in China and Thailand. A total of 152 compounds from Erycibes plants have been isolated and identified, categorized as flavonoids, coumarins, quinic acid derivatives, lignans, and alkaloids. Coumarins are the characteristic and active constituents of this species, including scopoletin and scopolin. Modern pharmacological studies have shown that the extracts and bioactive components of Erycibes plants exhibit several biological activities, including antiinflammatory, analgesic, hepatoprotective, anti‐gout, antitumor, antioxidation, and other therapeutic effects. However, in recent years, due to destructive exploitation and utilization, some Erycibes plants' natural resources have become rare or endangered. Developing substitutes is a strategy to alleviate the pressure on those endangered medicinal plant resources. To provide a scientific basis for the development and protection of those threatened Erycibes species, this review summarized the current status of the chemical compositions, pharmacological activities, quality control studies, and the development of substitutes for Erycibes plants. In particular, the rationale for use of Porana sinensis currently on the market is discussed.

Peng, Yu↗
DOE OSTI2022

Multigram Synthesis of a Combustion‐Relevant δ‐Ketohydroperoxide through Sulfonylhydrazine Substitution

Abstract A synthesis of a δ‐ketohydroperoxide is described, addressing potential functional‐group compatibilities in these elusive species relevant to combustion and atmospheric chemistries. The hydroperoxide is installed via sulfonylhydrazine substitution, which was found to be more effective than displacement of secondary halides. As part of this protocol, it was observed that 1,2‐dimethoxyethane is an advantageous medium for the reaction, avoiding the formation of a tetrahydrofuran hydroperoxide side product. This discovery facilitated the multigram synthesis (6 steps, 41 % yield overall) and discrete characterization of the target δ‐ketohydroperoxide.

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

Probing O 2 -dependence of tetrahydrofuranyl reactions via isomer-resolved speciation

Low-temperature oxidation of tetrahydrofuran involves competing reactions that depend on temperature, pressure, and oxygen concentration, including ring-opening and subsequent oxidation of initial radicals ($\dot{R}$), HOO-elimination yielding dihydrofuran isomers, and the formation of peroxy radicals ($RO\dot{O}$). Here, the latter species, upon isomerization, lead to hydroperoxy-substituted radicals ($\dot{Q}OOH$) that undergo reaction either via unimolecular decomposition or second-O 2 -addition. Quantitative measurements of partially oxidized intermediates formed from each type of reaction provide critical constraints that are required for accurate modeling of combustion. To examine the influence of temperature and oxygen concentration on intermediates from tetrahydrofuran, isomer-resolved speciation measurements were conducted at 810 Torr in a jet-stirred reactor (JSR) from 500 – 1000 K. Resulting from negative-temperature coefficient behavior, species concentrations peaked at two temperatures, 600 K and 800 K, which were then selected for separate experiments to quantify O 2 -dependence using concentrations of 0.37 • 10 18 – 7.40 • 10 18 molecules cm –3 .

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

A Model for Atomic Precision p-Type Doping with Diborane on Si(100)-2×1

Diborane (B 2 H 6 ) is a promising molecular precursor for atomic precision p-type doping of silicon that has recently been experimentally demonstrated. In this study, we use density functional theory (DFT) calculations to determine the reaction pathway for diborane dissociating into a species that will incorporate as electrically active substitutional boron after adsorbing onto the Si(100)-2×1 surface. Our calculations indicate that diborane must overcome an energy barrier to adsorb, explaining the experimentally observed low sticking coefficient (<1 × 10 –4 at room temperature) and suggesting that heating can be used to increase the adsorption rate. Upon sticking, diborane has an ≈50% chance of splitting into two BH 3 fragments versus merely losing hydrogen to form a dimer such as B 2 H 4 . As boron dimers are likely electrically inactive, whether this latter reaction occurs is shown to be predictive of the incorporation rate. The dissociation process proceeds with significant energy barriers, necessitating the use of high temperatures for incorporation. Using the barriers calculated from DFT, we parameterize a Kinetic Monte Carlo model that predicts the incorporation statistics of boron as a function of the initial depassivation geometry, dose, and anneal temperature. Our results suggest that the dimer nature of diborane inherently limits its doping density as an acceptor precursor and furthermore that heating the boron dimers to split before exposure to silicon can lead to poor selectivity on hydrogen and halogen resists. This suggests that, while diborane works as an atomic precision acceptor precursor, other non-dimerized acceptor precursors may lead to higher incorporation rates at lower temperatures.

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

Isomers and band assignments in the cryogenic vibrational spectrum of the binary complex between water and protonated formic acid using two color, IR–IR photobleaching and H/D isotopic substitution

Protonated formic acid (PFA) is purported to be the active species in the catalytic activation of condensation reactions at the acidic interface of microdroplets. Here, we investigate the fundamental interaction between PFA and water with cryogenic ion vibrational spectroscopy of the binary PFA–H 2 O complexes generated via electrospray ionization followed by buffer gas cooling to about 20 K. The patterns displayed by the isomer-specific IR spectra of D 2 -tagged PFA–H 2 O indicate that two distinct, non-interconverting rotamers are present at low temperatures based on the cis and trans structures of the HCO 2 $H$$^{+}_{2}$ core ion. Both of these occur with the water molecule attached to the OH that is in a cis-configuration relative to the CH group (denoted E), but differ in the E vs Z (cis vs trans relative to the CH group) orientation of the spectator OH. This assignment scheme corrects a previous theoretical analysis that invoked a scenario in which structures with E- and Z-bound water molecules interconvert at low (20 K) temperatures. Isomer-specific bands arising from the OH stretches and water bending modes are deconvoluted using isotopomer-specific spectroscopy of the complexes with partial H/D exchange. The dependence of the nominal shared proton OH stretch frequency on the deuteration of the tethered water confirms strong coupling between this mode and the water bending fundamental.

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

Effect of tert -Butyl Substitution on the Interactions of Cobalt Phthalocyanine with a Carbon Monoxide-Functionalized Tip

Supported cobalt phthalocyanines (CoPc) are promising catalysts for CO 2 reduction, a critical process for mitigating greenhouse gas emissions. Enhancing the catalytic performance of CoPc involves modifying the interaction between the cobalt center and intermediate species. This study focuses on the effects of tert-butyl substitution on CoPc using (tert-butyl) 4 CoPc, where the substitution can both directly alter the molecule’s intramolecular electronic structure and indirectly alter it by the bulky group weakening the interaction with the support. Toward this end, we investigated the structural and chemical properties of (tert-butyl) 4 CoPc on a Ag(111) surface at the single-molecule level using three-dimensional atomic force microscopy (AFM) with a CO-terminated tip and discussed them in comparison with data for unmodified CoPc and amino-substituted CoPc. Notably, distance-dependent force measurements revealed anomalies in the tert-butyl groups’ force curves, attributed to their rotational flexibility. The tert-butyl (t-butyl) groups were also observed to increase the attraction of the central Co atom to CO, but this effect was attributed largely to enhanced interactions of the back of the tip with the peripheral t-butyl groups. In conclusion, while this longer-range interaction would not be expected to impact the interaction of small molecules with the catalytic center, the results reveal the ability of AFM to characterize longer range environmental interactions that can enhance adsorption and subsequent reactions of larger molecules, as well as the role side chains that offer configurational adaptability may play in these interactions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Covalent Functionalization of Nickel Phosphide Nanocrystals with Aryl-Diazonium Salts

Covalent functionalization of Ni 2 P nanocrystals was demonstrated using aryl-diazonium salts. Spontaneous adsorption of aryl functional groups was observed, with surface coverages ranging from 20 to 96% depending on the native reactivity of the salt as determined by the aryl substitution pattern. Increased coverage was possible for low reactivity species using a sacrificial reductant. Functionalization was confirmed using thermogravimetric analysis, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The structure and energetics of this nanocrystal electrocatalyst system, as a function of ligand coverage, were explored with density functional theory calculations. The Hammett parameter of the surface functional group was found to linearly correlate with the change in Ni and P core-electron binding energies and the nanocrystal's experimentally and computationally determined work function. The electrocatalytic activity and stability of the functionalized nanocrystals for hydrogen evolution were also improved when compared to the unfunctionalized material, but a simple trend based on electrostatics was not evident. Density functional theory was used to understand this discrepancy, revealing that H adsorption energies on the covalently functionalized Ni 2 P also do not follow the electrostatic trend and are predictive descriptors of the experimental results.

14 SOLAR ENERGY↗
DOE OSTI2024

Ag Intercalation in Layered Cs 3 Bi 2 Br 9 Perovskite for Enhanced Light Emission with Bound Interlayer Excitons

Cesium bismuth bromide (CBB) has garnered considerable attention as a vacancy-ordered layered perovskite with notable optoelectronic applications. However, its use as a light source has been limited due to its weak photoluminescence (PL). Here, we demonstrate metal intercalation as a novel approach to engineer the room-temperature PL of CBB using experimental and computational methods. Ag, when introduced into CBB, occupies vacant sites in the spacer region, forming octahedral coordination with surrounding Br anions. First-principles density functional theory calculations reveal that intercalated Ag represents the most energetically stable Ag species compared to other potential forms, such as Ag substituting Bi. The intercalated Ag forms a strong polaronic trap state close to the conduction band minimum and quickly captures photoexcited electrons with holes remaining in CBB layers, leading to the formation of a bound interlayer exciton, or BIE. The radiative recombination of this BIE exhibits bright room-temperature PL at 600 nm and a decay time of 38.6 ns, 35 times greater than that of free excitons, originating from the spatial separation of photocarriers by half a unit cell separation distance. The BIE as a new form of interlayer exciton is expected to inspire new research directions for vacancy-ordered perovskites.

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

Isotopic and vibrational-level dependence of H 2 dissociation by electron impact

The low-energy electron-impact dissociation of molecular hydrogen has been a source of disagreement between various calculations and measurements for decades. Excitation of the ground state of H 2 into the dissociative b 3 $Σ$$$^{+}_{u}$ state is now well understood, with the most recent measurements being in excellent agreement with the molecular convergent close-coupling (MCCC) calculations of both integral and differential cross sections [Zawadzki et al., Phys. Rev. A 98, 062704 (2018)]. However, in the absence of similar measurements for vibrationally excited or isotopically substituted H 2 , cross sections for dissociation of these species must be determined by theory alone. We have identified large discrepancies between MCCC calculations and the recommended R-matrix cross sections for dissociation of vibrationally excited H 2 , D 2 , T 2 , HD, HT, and DT [Trevisan et al., Plasma Phys. Contr. Fusion 44 1263 (2002); Plasma Phys. Contr. Fusion 44, 2217 (2002)], with disagreement in both the isotope effect and dependence on initial vibrational level. Furthermore, we investigate the source of the discrepancies, and discuss the consequences for plasma models, which have incorporated the previously recommended data.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Franck-Condon Tuning of Optical Cycling Centers by Organic Functionalization

Laser induced electronic excitations that spontaneously emit photons and decay directly to the initial ground state (“optical cycling transitions”) are used in quantum information and precision measurement for state initialization and readout. To extend this primarily atomic technique to large, organic compounds, we theoretically investigate optical cycling of alkaline earth phenoxides and their functionalized derivatives. We find that optical cycle leakage due to wave function mismatch is low in these species, and can be further suppressed by using chemical substitution to boost the electron-withdrawing strength of the aromatic molecular ligand through resonance and induction effects. This provides a straightforward way to use chemical functional groups to construct optical cycling moieties for laser cooling, state preparation, and quantum measurement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Saccharomycopsis praedatoria sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589 T . The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Saccharomycopsis sp. strain UFMG-CM-Y6632 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗