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DOE OSTI2022

Saccharomycopsis sp. isolate UFMG-CM-Y6632 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↗

DOE OSTI2023

Saccharomycopsis sp. KB-2023a isolate UFMG-CM-Y6991, whole genome shotgun sequencing project

Amazonian Forest↗

DOE OSTI2020

A quantitative phase-field model for gas bubble evolution in UO2

Due to the large formation energy of vacancies and noble gas atoms in the form of interstitials or substitutional atoms in nuclear fuel (UO2), the thermodynamic equilibrium concentrations of these species are very low in the nuclear fuel matrix even at very high temperatures, which imposes difficulties upon the quantitative study of bubble evolution via the phase-field method. In this study, a quantitative phase-field model is proposed to deal with this problem. The system’s free energy density is derived according to the principles of thermodynamics, with consideration of the elastic effect and with the use of real material parameters from experiments. The model is useful for the study of the kinetics of gas bubble growth with very dilute concentrations of vacancy and gas atoms in the matrix. This model is applied to study single bubble growth and multiple bubble growth under various concentrations of vacancy and gas atoms and at various temperatures. The elastic effect and the effects of the generation rate of vacancies and gas atoms on bubble growth are analyzed.

low defect concentration, nuclear fuel, gas bubble↗

DOE OSTI2025

Alloying multiple halide perovskites on the same sublattice in search of stability and target band gaps

Single-component halide perovskites (HPs) rarely satisfy all the necessary criteria for optoelectronic applications, such as achieving an optimal band gap while maintaining high chemical and structural stability. Alloying halide perovskites has emerged as a promising strategy, not only to enhance stability but also to fine-tune their electronic and optical properties. In this work, we explore multiple degrees of freedom in alloy design, considering different substitution sublattices sites (A, B, or X in ABX3 perovskites), various chemical species (isovalent and hetero-valent elements), and multi-component compositions on a given sublattice. Using first-principles calculations based on density functional theory (DFT), we investigate how compositional variations influence the electronic (band gap) and structural properties (mixing enthalpy) of HP alloys. Our approach employs the polymorphous cell model, allowing full local relaxation which breaks local symmetry while preserving global cubic symmetry—an essential framework for accurately modeling HPs. Our results reveal that X-site mixing (halogen substitution) primarily affects the valence band maximum, allowing target band gap engineering. Additionally, variations in halogen radii introduce internal strain through octahedral distortions, influencing the mixing enthalpy. A-site substitution, while not directly contributing to the band edge states, modifies structural stability via volume effects, indirectly impacting the band gap. B-site alloying plays a dominant role in band gap modulation, leading to either positive or negative band gap bowing. Specifically, isovalent B-site mixing (Sn–Pb) induces strong positive bowing, where the alloy band gap is smaller than the average gap of parent compounds, whereas hetero-valent mixing (Cd–Pb) results in pronounced negative bowing. As an aside, we investigate the competition between the excess energy of disordered alloys vs. that of long-range ordered double perovskites of the same compositions, seeking examples of ordered phases emerging from disordered alloys. Furthermore, our findings provide fundamental insights into the electronic and structural behavior of HP alloys, offering valuable design principles for the development of stable and efficient materials for next-generation photovoltaic and optoelectronic devices.

14 SOLAR ENERGY↗

DOE OSTI2026

Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly

How large, flexible enzymes assemble into defined oligomeric architectures remains a central question in biology. NADPH-dependent assimilatory sulfite reductase (SiR) forms a heterododecamer built on an octameric flavoprotein (SiRFP) core, yet the molecular basis for this assembly has been unresolved because of its disordered N-terminus. Here, we use ion mobility mass spectrometry, small-angle neutron scattering, and mutagenesis to define the mechanism of SiRFP oligomerization. We show that SiRFP forms a discrete, stable octamer in solution. We also report that its N-terminal 52-residue segment is necessary and sufficient to mediate assembly, also mediating oligomerization when fused to a heterologous protein. Structure-guided mutagenesis identifies four residues (Gln22, Tyr39, Phe40, and Gln47) whose substitution disrupts the octamer, producing concentration-dependent lower-order species while retaining catalytic activity. These findings define the determinants of SiRFP assembly with broader implications for engineering homomeric protein complexes.

Nagy, Gergely [ORNL] (ORCID:0000000327420198)↗

DOE OSTI2024

Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

The recognition of the 5′ splice site (5′ ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5′ ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5′ ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5′ ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7–Prp40–Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Enhanced Tritium Retention in LiAlO2 Pellets via Engineered Glazes: Tritium Science Project

This project investigated the impact of adding a thin (10 – 50 µm) layer of amorphous glaze to the surface of a TPBAR pellet on its retention of helium, hydrogen (as a surrogate for tritium), and water (as a surrogate for tritiated water). The hypothesis was that the glaze would significantly reduce permeation of hydrogen species with a lesser impact on hindering helium permeation. A non-crystallizing soda-lime-silicate glass, known as SCN-1, was selected for this proof-of-concept study. It was found that continuous glaze layers of the desired thickness could be applied to the pellets with two or more dip coats, depending on the targeted thickness. At 330°C, the glaze was found to have a permeability that was lower than that of the pellet by a factor of ~10 6 , implying that a thin 10 – 50 µm layer can significantly increase pellet retention of hydrogen. Meanwhile, the permeation rate of helium through the glaze was found to be ~20 times higher than that of hydrogen or water. An unanticipated outcome of the study was that unglazed pellets were measured to have hydrogen diffusivities that are a factor of ~105 greater than the diffusivity value used in the TPBAR COMSOL model to achieve observed tritium retention rates. When the higher measured diffusivity was substituted into the model and the model was run with all tritium species in the pellet in the form of T 2 O at a partial pressure of 20 Pa in equilibrium with LiOT, the resulting retention was 50% after 500 days.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Structural phase diagram for Sm-substituted BiFeO 3 multiferroics

The structural evolution of Sm substituted BiFe⁢O 3 is studied by total x-ray scattering and structure modeling. It is shown that the crystal structure changes from polar to antipolar and then to nonpolar when the Sm to Bi ratio in the material approaches 20% and 40%, respectively, with no intermixing between the structure types. The evolution is driven by lattice strain induced by the difference in the size of Sm and Bi atoms, leading to changes in the pattern of octahedral tilts and Bi off-centering, which, in turn, induce changes in the multiferroic properties. Furthermore, the substitution ratio at which the different structure types emerge appears to be tied up with the average radius of the atomic species occupying the Bi sites in the perovskite lattice and volume occupied by a formula unit, rendering both quantities useful predictor variables for guiding computational searches for substituted BiFe⁢O 3 multiferroics with improved functional properties.

Ferroelectricity↗

DOE OSTI2022

The presence and role of the intermediary CO reservoir in heterogeneous electroreduction of CO 2

Significance The electroconversion of CO 2 to value-added products is a promising path to sustainable fuels and chemicals. However, the microenvironment that is created during CO 2 electroreduction near the surface of heterogeneous Cu electrocatalysts remains unknown. Its understanding can lead to the development of ways to improve activity and selectivity toward multicarbon products. This work introduces a method called on-stream substitution of reactant isotope that provides quantitative information of the CO intermediate species present on Cu surfaces during electrolysis. An intermediary CO reservoir that contains more CO molecules than typically expected in a surface adsorbed configuration was identified. Its size was shown to be a factor closely associated with the formation of multicarbon products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Vacuum-ultraviolet absorption cross-sections of functionalized cyclic hydrocarbons: Five-membered rings

Cross-sections were measured at 50 °C and 800 Torr using differential absorption spectroscopy in the vacuum-ultraviolet from 5.17 – 9.92 eV for a series of five-membered cyclic hydrocarbons: cyclopentane, cyclopentene, methylcyclopentane, tetrahydrofuran, furan, 2-methyltetrahydrofuran, 2,3-dihydro-5-methylfuran, tetrahydrofuran-3-one, 2-methyl-1,3-dioxolane, cyclopentanol, 2-hydroxytetrahydrofuran, cyclopentanone, 2-cyclopenten-1-one, 3-cyclopenten-1-one, 2-methylcyclopentan-1-one, 2-methylcyclopent-2-en-1-one, 1,2-epoxycyclopentane, 2,3-epoxycyclopentanone, and 3,4-epoxycyclopentanone. The majority of the species are functionalized and are directly related to chain-reactions relevant to combustion, such as substituted cyclic ethers and cycloalkenes. Uncertainty calculations were conducted as a function of photon energy to quantify errors associated with experimental repeatability, signal-to-noise ratio, and gas-phase concentration, yielding an upper limit of 5% in spectral regions where absorption is >2%. Here, the primary objective of the present work is to provide quantitative absorption cross-sections of species commonly produced in combustion reactions. Comparing qualitative differences among the five-membered cyclic species, in order to analyze the effect of functional groups on absorption, is a secondary objective. The majority of the spectra are reported for the first time and enable quantitative isomer-resolved speciation measurements in combustion chemistry.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Kinetic Isotope Effects: Interpretation and Prediction Using Degrees of Rate Control

Kinetic isotope effects (KIEs) have been used for decades in catalysis research as a tool for clarifying reaction mechanisms. Significant primary kinetic isotope effects have usually been interpreted as being a result of isotope substitution at a site of bond breaking (or forming) in the rate-determining step in the reaction mechanism. However, quantitative analysis of the magnitude of the KIE in complex multistep reaction mechanisms is seldom reported. We prove here that the logarithm of the rate ratio for two isotopes is the weighted average over all species in the mechanism of their standard-state free energy difference between the two isotopes, divided by RT. The weighting factor is the degree of rate control (DRC) for that species (e.g., transition state, intermediate, reactant) when the rate is measured separately for each isotope. It is instead the degree of selectivity ratio control (DSRC) when the KIE is measured as the product selectivity in a parallel competition between two isotopes within the same reactant molecule. Since only a few species have non-zero DRCs (or DSRCs) for most reactions, only these few contribute to this weighted average and the KIE. We show that this provides a simple way to interpret and quantitatively predict kinetic isotope effects that is powerful in the insights it provides, allowing one to evaluate directly which species contribute most to the KIE. By applying it to H/D KIEs in several example mechanisms, we further show that the traditional way of interpreting KIEs that focuses only on the rate-determining step can easily lead to misunderstanding of KIE and the reaction mechanism. Finally, this highlights the importance to consider the effect of isotope substitution on the energies of all species with large DRCs (i.e, those whose energies are kinetically relevant). This method also offers opportunities for quantitative validation of mechanism-based microkinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Unimolecular and bimolecular formic acid decomposition routes on dispersed Cu nanoparticles

The elementary steps and site requirements in formic acid (HCOOH) dehydrogenation on Cu surfaces remain of keen interest because formate species act as intermediates or spectators in methanol synthesis and water–gas shift reactions. Steady-state and transient kinetic data, isotopic effects, infrared spectra during catalytic and stoichiometric reactions, and theoretical treatments based on density functional theory (DFT) provide evidence for bimolecular reactions, in which saturated bidentate formate (*HCOO*) adlayers, present at 0.25 ML (0.25 *HCOO* per surface Cu atom), react with undissociated species (HCOOH$^\square$) bound at interstices within formate adlayers ($^\square$) to form H-bonded bimolecular HCOOH$^\square$-*HCOO* adducts. The co-existence of vicinal HCOOH$^\square$ and *HCOO* moieties is evident from antisymmetric infrared bands for *HCOO* that become stronger as a result of their H-bonding that perturbs the induced dipole moment of *HCOO* upon vibration, consistent with DFT-derived vibrational frequencies and intensities for such perturbed species. The *HCOO* moiety in this complex undergoes C-H activation via a transition state that is preferentially stabilized through H-bonding with the vicinal HCOOH$^\square$ relative to its *HCOO* precursor. DFT-derived HCOOH dehydrogenation activation barriers and those determined from the evolution of CO 2 from pre-adsorbed *HCOO* species are about 10 kJ mol -1 smaller in the presence of gaseous HCOOH reactants (because of HCOOH$^\square$-*HCOO* interactions) than those for the unimolecular decomposition of bound *HCOO* species. Such bimolecular routes are consistent with measured effects of HCOOH, H 2 , and CO pressures and of H/D isotopic substitution on dehydrogenation turnover rates and represent the predominant channel for the formation of CO 2 and H 2 during catalytic HCOOH dehydrogenation on Cu nanoparticles. A saturated *HCOO* adlayer that retains binding interstices and the presence of HCOOH(g) enable a sequence of elementary steps unavailable for *HCOO* species, thus circumventing unassisted unimolecular routes that exhibit higher activation barriers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Suppressing CO formation in low-temperature methanol steam reforming via Ce-modified CuZnGa layered oxide catalysts

Cu-based layered double hydroxides (LDHs) are widely recognized as effective catalysts for low-temperature methanol steam reforming, yet achieving high hydrogen productivity together with near-complete suppression of CO formation remains challenging. Here, we report the synthesis and evaluation of a series of CuZnGa LDH-derived catalysts and Ce-modified analogues prepared via an aqueous miscible organic method, which enables high metal dispersion and precise structural control. The optimized CuZnGa catalyst exhibits a hydrogen production rate of 16.9 µmol H 2 ·g cat −1 ·s −1 at 180 °C with an H 2 /CO ratio exceeding 3500, outperforming many state-of-the-art low-temperature systems. Importantly, the incorporation of small amounts of Ce further suppresses CO formation while maintaining high hydrogen productivity. Combined spectroscopic characterization and density functional theory calculations reveal that Ce is incorporated into the LDH lattice by substituting Ga 3+ sites up to a critical threshold, beyond which highly dispersed CeO x species are formed. These species provide mobile lattice oxygen that participates in a Mars-van Krevelen-type pathway, selectively oxidizing CO and suppressing the reverse water-gas shift reaction. This study establishes a clear relationship between Ce speciation, oxygen mobility, and catalytic selectivity in LDH-derived systems. The resulting catalysts demonstrate the potential of interface-engineered Cu-based materials for efficient low-temperature hydrogen production with minimal CO contamination.

09 BIOMASS FUELS↗

DOE OSTI2022

Identification of xylan arabinosyl 2- O -xylosyltransferases catalyzing the addition of 2- O -xylosyl residue onto arabinosyl side chains of xylan in grass species

Grass xylan, the major hemicellulose in both primary and secondary cell walls, is heavily decorated with α-1,3-linked arabinofuranosyl (Araf) residues that may be further substituted at O-2 with xylosyl (Xyl) or Araf residues. Although xylan 3-O-arabinosyltransferases (XATs) catalyzing 3-O-Araf addition onto xylan have been characterized, glycosyltransferases responsible for the transfer of 2-O-Xyl or 2-O-Araf onto 3-O-Araf residues of xylan to produce the Xyl-Araf and Araf-Araf disaccharide side chains remain to be identified. In this report, we showed that a rice GT61 member, named OsXAXT1 (xylan arabinosyl 2-O-xylosyltransferase 1) herein, was able to mediate the addition of Xyl-Araf disaccharide side chains onto xylan when heterologously co-expressed with OsXAT2 in the Arabidopsis gux1/2/3 (glucuronic acid substitution of xylan 1/2/3) triple mutant that lacks any glycosyl substitutions. Recombinant OsXAXT1 protein expressed in human embryonic kidney 293 cells exhibited a xylosyltransferase activity catalyzing the addition of Xyl from UDP-Xyl onto arabinosylated xylooligomers. Further, consistent with its function as a xylan arabinosyl 2-O-xylosyltransferase, CRISPR-Cas9-mediated mutations of the OsXAXT1 gene in transgenic rice plants resulted in a reduction in the level of Xyl-Araf disaccharide side chains in xylan. Furthermore, we revealed that XAXT1 close homologs from several other grass species, including switchgrass, maize, and Brachypodium, possessed the same functions as OsXAXT1, indicating functional conservation of XAXTs in grass species. Together, our findings establish that grass XAXTs are xylosyltransferases catalyzing Xyl transfer onto O-2 of Araf residues of xylan to form the Xyl-Araf disaccharide side chains, which furthers our understanding of genes involved in xylan biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Tandem synthesis of tetrahydroquinolines and identification of the reaction network by operando NMR

The study of the reaction mechanism and complex network for heterogeneously catalyzed tandem reactions is challenging but can guide reaction design and optimization. Here, we describe a case study using bifunctional metal–organic framework supported Pd nanoparticles (Pd/UiO-66(HCl)) for the one-pot tandem synthesis of substituted tetrahydroquinolines via the Claisen–Schmidt condensation and reductive intramolecular cyclization. The directly observed evolution of intermediates and products, including reactive species containing hydroxylamine group and unstable intermediate 2-phenyl-3,4-dihydroquinoline, was enabled by operando magic angle spinning nuclear magnetic resonance studies under 50 bar H 2 . The reaction network of the tandem reaction is deduced based on reaction kinetic information obtained from the operando study. The optimized procedure was applied to various acetophenone and nitrobenzaldehyde derivatives carrying different functional groups, and eight valuable substituted tetrahydroquinolines were obtained in moderate to good yields. This work provides a molecular-level understanding of the catalytic system and brings up new opportunities for efficient and sustainable synthesis of medicinally relevant building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗

DOE OSTI2020

Static to inducibly dynamic stereocontrol: The convergent use of racemic β-substituted ketones

The synthesis of stereochemically complex molecules in the pharmaceutical and agrochemical industries requires precise control over each distinct stereocenter, a feat that can be challenging and time consuming using traditional asymmetric synthesis. Although stereoconvergent processes have the potential to streamline and simplify synthetic routes, they are currently limited by a narrow scope of inducibly dynamic stereocenters that can be readily epimerized. Furthermore, we report the use of photoredox catalysis to enable the racemization of traditionally static, unreactive stereocenters through the intermediacy of prochiral radical species. This technology was applied in conjunction with biocatalysts such as ketoreductases and aminotransferases to realize stereoconvergent syntheses of stereodefined γ-substituted alcohols and amines from β-substituted ketones.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Exciton-vibrational dynamics induces efficient self-trapping in a substituted nanoring

Cycloparaphenylenes, being the smallest segments of carbon nanotubes, have emerged as prototypes of the simplest carbon nanohoops. Their unique structure–dynamics–optical properties relationships have motivated a wide variety of synthesis of new related nanohoop species. Studies of how chemical changes, introduced in these new materials, lead to systems with new structural, dynamics and optical properties, expand their functionalities for optoelectronics applications. Herein, we study the effect that conjugation extension of a cycloparaphenylene through the introduction of a satellite tetraphenyl substitution has on its structural and dynamical properties. Our non-adiabatic excited state molecular dynamics simulations suggest that this substitution accelerates the electronic relaxation from the high-energy band to the lowest excited state. This is partially due to efficient conjugation achieved between specific phenyl units as introduced by the tetraphenyl substitution. We observe a particular exciton redistribution during relaxation, in which the tetraphenyl substitution plays a significant role. As a result, an efficient inter-band energy transfer takes place. Besides, the observed phonon-exciton interplay induces a significant exciton self-trapping. Finally, our results encourage and guide the future studies of new phenyl substitutions in carbon nanorings with desired optoelectronic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗