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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Materials Data on V(HO)2 by Materials Project

V(OH)2 crystallizes in the orthorhombic Pnnm space group. The structure is three-dimensional. V2+ is bonded to six equivalent O2- atoms to form a mixture of corner and edge-sharing VO6 octahedra. The corner-sharing octahedral tilt angles are 51°. There are four shorter (2.22 Å) and two longer (2.23 Å) V–O bond lengths. H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.98 Å. O2- is bonded in a distorted single-bond geometry to three equivalent V2+ and one H1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Insights into the Mechanism of Neptunium Oxidation to the Heptavalent State

Abstract Neptunium can exist in multiple oxidation states, including the rare and poorly understood heptavalent form. In this work, we monitored the formation of heptavalent neptunium [Np(VII)O 4 (OH) 2 ] 3− during ozonolysis of aqueous M OH ( M =Li, Na, K) solutions using a combined experimental and theoretical approach. All experimental reactions were closely monitored via absorption and vibrational spectroscopy to follow both the oxidation state and the speciation of neptunium guided by the calculated vibrational frequencies for various neptunium species. The mechanism of the reaction partly involves oxidative dissolution of transient Np(VI) oxide/hydroxide solid phases, the identity of which are dependent on the co‐precipitating counter‐cation Li + /Na + /K + . Additional calculations suggest that the most favorable energetic pathway occurs through the reaction of a [Np(V)O 2 (OH) 4 ] 3− with the hydroxide radical to form [Np(VI)O 2 (OH) 4 ] 2− , followed by an additional oxidation with HO⋅ to create [Np(VII)O 4 (OH) 2 ] 3− .

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

Materials Data on K2RbHoV2O8 by Materials Project

RbK2HoV2O8 crystallizes in the trigonal P-3m1 space group. The structure is three-dimensional. Rb1+ is bonded to twelve O2- atoms to form RbO12 cuboctahedra that share edges with six equivalent RbO12 cuboctahedra, edges with six equivalent VO4 tetrahedra, and faces with two equivalent HoO6 octahedra. There are six shorter (3.15 Å) and six longer (3.48 Å) Rb–O bond lengths. K1+ is bonded in a 1-coordinate geometry to ten O2- atoms. There are a spread of K–O bond distances ranging from 2.60–3.35 Å. Ho3+ is bonded to six equivalent O2- atoms to form HoO6 octahedra that share corners with six equivalent VO4 tetrahedra and faces with two equivalent RbO12 cuboctahedra. All Ho–O bond lengths are 2.25 Å. V5+ is bonded to four O2- atoms to form VO4 tetrahedra that share corners with three equivalent HoO6 octahedra and edges with three equivalent RbO12 cuboctahedra. The corner-sharing octahedral tilt angles are 16°. There is one shorter (1.69 Å) and three longer (1.77 Å) V–O bond length. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted linear geometry to three equivalent Rb1+, one K1+, and one V5+ atom. In the second O2- site, O2- is bonded in a 2-coordinate geometry to one Rb1+, three equivalent K1+, one Ho3+, and one V5+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Conversion of Formic Acid on Single- and Nano-Crystalline Anatase TiO 2 (101)

Understanding thermochemical transformations of formic acid (FA) on metal oxide surfaces is important for many catalytical reactions. Here we study thermally induced reactions of FA on a single-crystalline and nanocrystalline anatase TiO 2 (101). We employ a combination of scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and density functional theory (DFT) to follow the FA surface intermediates and reaction products above room temperature. We find that the primary reaction products desorbing at about 300, 480, and 515 K are molecular water, carbon monoxide, and formaldehyde, respectively. Bidentate (BD) formate and bridging hydroxyl (HO b ) are identified as central intermediates in the FA transformations. Bridging oxygen vacancies (V O ) are also likely participants despite their low stability at the surface. In conclusion, the parallel studies on single crystals and faceted TiO 2 (101) nanoparticles reveal the spectroscopic commonalities of surface species and of the thermal conversion of molecular and deprotonated forms of FA.

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

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗
DOE OSTI2025

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

SUMMARY: We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e. DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C2LR) strategy. Empirical results on 28 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. AVAILABILITY AND IMPLEMENTATION: Model, codes, and data are publically available at https://github.com/MAGICS-LAB/DNABERT_S.

Zhou, Zhihan↗
DOE OSTI2022

Stability and Activity of Cobalt Antimonate for Oxygen Reduction in Strong Acid

Guided by computational Pourbaix screening and high-throughput experiments aimed at the development of precious-metal-free fuel cells, we investigate rutile CoSb 2 O 6 as an electrocatalyst for oxygen reduction in 1 M sulfuric acid. Following 4 h of catalyst conditioning at 0.7 V vs RHE, operation at this potential for 20 h yielded an average current density of –0.17 mA cm –2 with corrosion at a rate of 0.04 nm hour –1 that is stoichiometric with catalyst composition. Surface Pourbaix analysis of the (111) surface identified partial H coverage under operating conditions. The Sb active site has an HO* binding free energy of 0.49 eV, which is near the peak of the kinetic 4e – ORR volcano for transition-metal oxides in acidic conditions. Furthermore, the experimental demonstration of operational stability and computational identification of a reaction pathway with favorable energetics place rutile CoSb 2 O 6 among the most promising precious-metal-free electrocatalysts for oxygen reduction in acidic media.

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

Effects of drive pulse shape on graded metal pushered single shell capsule implosions on the National Ignition Facility

Graded metal pushered single shells (PSS) are a viable alternative to low-Z capsules (Z is the atomic number) for indirect drive inertial confinement fusion implosions due to enhanced core tamping and radiation trapping, but they can be compromised by the pusher mixing with the fuel. We compare 2-shock and 3-shock laser pulses for Be/Cr PSS capsules filled with deuterium–tritium gas fuel at 6 mg/cc density. 1D radiation-hydrodynamic simulations predict higher core compression and, hence, ∼2× higher fusion yield for the 3-shock drive than for 2-shock. Nevertheless, we observe similar core ion temperatures and fusion yields for both drives. The implosion burn duration is 25% shorter and the core volume is ∼2.5× smaller for the 3-shock drive than for 2-shock, consistent with a higher compression. 1D LASNEX mix simulations using a buoyancy-drag model matching the measured yields also agree with the observed core sizes and burn durations and suggest ∼40% and ∼70% yield degradations for 2-shock and 3-shock drives due to hydrodynamic instabilities and atomic mix at the pusher–fuel interface. At the same time, 2D HYDRA simulations show that mid-mode (2–250) instability degradations are negligible for the 2-shock implosion (9%) and significant (45%) for 3-shock. Subtracting these from the 1D mix simulations, we infer similar degradations from high-mode instabilities and atomic mix for both drives. Due to its robustness to mid-mode instabilities, future pusher–gas mix studies will use the 2-shock drive.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Role of Pr-Vacancies and O-Interstitials on the Activity and Stability of (Pr 1−x Ln x ) 2 NiO 4 (Ln = La, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) towards Oxygen Reduction Reactions: A DFT Study

Praseodymium nickelate, Pr 2 NiO 4 (PNO), is a promising electrode to promote oxygen reduction reaction (ORR) in a solid oxide fuel cell, but it exhibits phase transformation during electrochemical operation. The origin of the simultaneous phase transformation and high electrochemical performance remains obscure. We carried out a systematic density functional theory study to elucidate the mechanism for this conjugated phenomenon. Charge, electronic structure, and normal-mode analysis suggest the presence of peroxide. Our study shows that the formation of peroxide (O 2 2– ) is attributed to both oxygen interstitials and Pr vacancies. The peroxide species limits the oxygen ion migration due to the additional energy required to break its O–O bond, which leads to a decrease in ORR activity. Subsequently, we investigate the diffusion paths of Pr-ions while comparing them with those of other Ln 3+ ions (La, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) in PNO. The formation energies for various Ln 3+ cation occupancies are calculated, as well as segregation energies in CeO 2 (111) surfaces. Lastly, criteria for effective Ln 3+ dopants are developed. La, Nd, and Pm are proposed as potential substituents in PNO to obtain a stable structure.

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

Synthesis and characterization of the rare-earth chloride complexes with N,N,N',N' -tetramethylmalonamide

Exploration of the solid-state chemistry of the f-elements and their coordination chemistry can assist in understanding the speciation of these elements in solution, which, in turn, can aid in the interpretation of their chemical behavior in complex liquid-liquid separations. Within these separation processes, malonamides are common organic extractants that are used for complexing both lanthanides and actinides, thus it is relevant to understand the malonamide ligand complexation under various conditions. In this work, we investigate solid-state complexes of the rare-earth chlorides with N,N,N',N' -tetramethylmalonamide (TMMA) across the entire lanthanide series. Here, we isolated two structural families of compounds Ln(TMMA) 2 Cl 3 Ln = La–Dy and [Ln(TMMA) 2 (H 2 O) 4 ]Cl 3 • x H 2 O x = 0,4 Ln = Ho–Lu, showing differences in chloride coordination from the inner-sphere complex for early lanthanides to outer-sphere for the late lanthanides. Both structural series were additionally analyzed by both IR and Raman spectroscopy confirming similarities in malonamide ligand coordination modes, while showing differences in vibrational features associated with chloride and aqua ligand coordination.

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

Reversible Electrochemical Lithium Cycling in a Vanadium(IV)- and Niobium(V)-Based Wadsley–Roth Phase

Fast charging remains one of the greatest safety challenges in Li-ion batteries due to Li-dendrite growth occurring on graphite anodes if they are lithiated too quickly. The search for high-rate anodes has highlighted materials in the Wadsley–Roth (WR) shear phase family. The relative abundance of V compared with traditional WR compositions of Nb and W makes V-based phases attractive. However, the high voltage and poor reversibility typically associated with V redox have made V-rich WR phases less studied than Nb- and W-rich phases. Here, we show that a new V-rich Wadsley–Roth phase, V 7 Nb 6 O 29 , achieves excellent rate capability and 80% capacity retention after 228 cycles with a relatively low average voltage of 1.76 V vs Li/Li + compared with other V-rich WR phases. Single-crystal X-ray diffraction reveals a P4/m space group with repeating 2 × 2 × ∞ and 3 × 3 × ∞ blocks of V 4+ and Nb 5+ octahedra. Finally, combined neutron pair distribution function analysis, X-ray absorption spectroscopy, and density functional theory calculations show that V redox is the primary source of capacity and that cycling stability is provided by the stable octahedral coordination adopted by V 4+ in the material.

25 ENERGY STORAGE↗
DOE OSTI2022

Experimental and modeling studies of the plasma chemistry in a humid Ar radiofrequency atmospheric pressure plasma jet

Abstract While humid atmospheric pressure plasmas are extensively modeled, reaction set validation for these conditions remains limited. We present a detailed comparison of a modelling and experimental study with a goal to elucidate the plasma chemistry in a humid Ar radiofrequency-driven atmospheric pressure plasma jet. A large group of species including radicals (H, OH, O, HO 2 ) and long-lived species (H 2 , O 2 and H 2 O 2 ) in the jet effluent was experimentally quantified by molecular beam mass spectroscopy (MBMS). MBMS measurements of H 2 O 2 , OH and H were validated by direct comparison with a liquid phase colorimetric measurement, laser-induced fluorescence (LIF) and two-photon absorption LIF respectively. While an excellent agreement was found for OH and H 2 O 2 by both techniques, a significant difference was found for H and shown to be due to boundary layer effects at the MBMS sampling substrate. The measured O, OH, HO 2 and H 2 are in good agreement with the plug model while H and O 2 were underestimated and H 2 O 2 was overestimated by the model. The accuracy of both the used reaction set and the diagnostics, as well as the observed discrepancies between the modeling and experimental results, are critically assessed. The results presented in this work enable us to identify further data needs for describing H 2 O vapor chemistry in low-temperature plasmas.

Physics↗
DOE OSTI2021

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Capturing CO 2 in Quadrupolar Binding Pockets: Broadband Microwave Spectroscopy of Pyrimidine-(CO 2 ) n , n = 1,2

Pyrimidine has two in-plane CH(δ+)/N̈(δ–)/CH(δ+) binding sites that are complementary to the (δ–/2δ+/δ–) quadrupole moment of CO 2 . For this study, we recorded broadband microwave spectra over the 7.5–17.5 GHz range for pyrimidine-(CO 2 ) n with n = 1 and 2 formed in a supersonic expansion. Based on fits of the rotational transitions, including nuclear hyperfine splitting due to the two 14 N nuclei, we have assigned 313 hyperfine components across 105 rotational transitions for the n = 1 complex and 208 hyperfine components across 105 rotational transitions for the n = 2 complex. The pyrimidine-CO 2 complex is planar, with CO 2 occupying one of the quadrupolar binding sites, forming a structure in which the CO 2 is stabilized in the plane by interactions with the C–H hydrogens adjacent to the nitrogen atom. This structure is closely analogous to that of the pyridine-CO 2 complex studied previously by (Doran, J. L. J. Mol. Struct. 2012, 1019, 191–195). The fit to the n = 2 cluster gives rotational constants consistent with a planar cluster of C 2v symmetry in which the second CO 2 molecule binds in the second quadrupolar binding pocket on the opposite side of the ring. The calculated total binding energy in pyrimidine-CO 2 is –13.7 kJ mol –1 , including corrections for basis set superposition error and zero-point energy, at the CCSD(T)/ 6-311++G(3df,2p) level, while that in pyrimidine-(CO 2 ) 2 is almost exactly double that size, indicating little interaction between the two CO 2 molecules in the two binding sites. The enthalpy, entropy, and free energy of binding are also calculated at 300 K within the harmonic oscillator/rigid-rotor model. This model is shown to lack quantitative accuracy when it is applied to the formation of weakly bound complexes.

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

Defect Engineering of WO 3 by Rapid Flame Reduction for Efficient Photoelectrochemical Conversion of Methane into Liquid Oxygenates

Photoelectrochemical (PEC) conversion is a promising way to use methane (CH 4 ) as a chemical building block without harsh conditions. However, the PEC conversion of CH 4 to value-added chemicals remains challenging due to the thermodynamically favorable overoxidation of CH 4 . Here, we report WO 3 nanotube (NT) photoelectrocatalysts for PEC CH 4 conversion with high liquid product selectivity through defect engineering. By tuning the flame reduction treatment, we carefully controlled the oxygen vacancies of WO 3 NTs. The optimally reduced WO 3 NTs suppressed overoxidation of CH4 showing a high total C1 liquid selectivity of 69.4% and a production rate of 0.174 μmol cm –2 h –1 . Scanning electrochemical microscopy revealed that oxygen vacancies can restrain the production of hydroxyl radicals, which, in excess, could further oxidize C1 intermediates to CO 2 . Additionally, band diagram analysis and computational studies elucidated that oxygen vacancies thermodynamically suppress overoxidation. In conclusion, this work introduces a strategy for understanding and controlling the selectivity of photoelectrocatalysts for direct conversion of CH 4 to liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Time-resolved measurements of HO 2 radical in a heated plasma flow reactor

Time-resolved, absolute HO 2 number density in diluted H 2 –O 2 –Ar, CH 4 –O 2 -Ar, and C 2 H 4 –O 2 –Ar mixtures excited by a repetitive ns pulse discharge in a heated plasma flow reactor is measured by Cavity Ringdown Spectroscopy (CRDS). The experimental results are obtained at $\textit{T}$ = 300-600 K and $\textit{P}$ = 130 Torr, both during the discharge pulse burst and in the afterglow. In this work, the HO 2 number density is inferred from the CRDS data using a spectral model exhibiting good agreement with previous measurements of absolute HO 2 absorption cross sections. In the room-temperature H 2 –O 2 mixture, as well as in CH 4 –O 2 and C 2 H 4 –O 2 mixtures over the entire temperature range studied, HO2 is generated only during the discharge burst and decays in the afterglow. However, in the H 2 –O 2 mixture at elevated temperatures, $\textit{T}$ = 400-600 K, HO 2 persists in the afterglow up to 10 ms after the discharge burst, comparable with the flow residence time in the reactor. Comparison with kinetic modeling shows that the sustained reactivity after the source of radicals is turned off is due to a chain propagation / hydrogen oxidation process, which dominates the radical recombination reactions. The kinetic modeling predictions are in good agreement with the relative HO 2 number density measured in all three mixtures, although the model underpredicts the absolute number densities in H 2 –O 2 at $\textit{T}$ = 400-600 K by up to a factor of two. Detection of the sustained low-temperature reactivity in H 2 –O 2 , initiated by the radical generation in the plasma, suggests that the plasma excitation may also affect kinetics of oxidation and reforming of fuels exhibiting low-temperature chemistry below hot ignition point.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Lasing characteristics of ZrO{sub 2} − Y{sub 2}O{sub 3} − Ho{sub 2}O{sub 3} crystals pumped by a Tm : LiYF{sub 4} laser

Two-micron lasing is obtained on the {sup 5}I{sub 7} → {sup 5}I{sub 8} transition of Ho{sup 3+} ions in ZrO{sub 2} − Y{sub 2}O{sub 3} −Ho{sub 2}O{sub 3} crystals upon resonance pumping into the {sup 5}I{sub 7} level of these ions by a pulsed laser based on a Tm : LiYF{sub 4} crystal. The efficiency of conversion of pump radiation incident on the crystal to laser radiation and the slope lasing efficiency at a pulse duration of 8 ms and a pulse repetition rate of 10 Hz were 25% and 28%, respectively. (paper)

36 MATERIALS SCIENCE↗