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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Passive Oxide Film Growth Observed On the Atomic Scale

Despite of the ubiquitous presence of passivation on most metal surfaces, the microscopic-level picture of how surface passivation occurs has been hitherto unclear. Using the canonical example of the surface passivation of aluminum, here we employ in situ atomistic transmission electron microscopy observations and computational modeling to disentangle entangled microscopic processes and identify the atomic processes leading to the surface passivation. Based on atomic-scale observations of the layer-by-layer expansion of the metal lattice and its subsequent transformation into the amorphous oxide, it is shown that the surface passivation occurs via a two-stage oxidation process, in which the first stage is dominated by intralayer atomic shuffling whereas the second stage is governed by interlayer atomic disordering upon the progressive oxygen uptake. The first stage can be bypassed by increasing surface defects to promote the interlayer atomic migration that results in direct amorphization of multiple atomic layers of the metal lattice. The identified two-stage reaction mechanism and the effect of surface defects in promoting interlayer atomic shuffling can find broader applicability in utilizing surface defects to tune the mass transport and passivation kinetics, as well as the composition, structure and transport properties of the passivation films.

25 ENERGY STORAGE↗
DOE OSTI2020

Sulfonyl PIM–1: A diverse separation membrane with dilation resistance

A sulfone modified variant (soPIM–1) of the first polymer of intrinsic microporosity has been studied through molecular simulations to analyze its applicability for adsorption–based separations of diverse nonpolar, quadrupolar, and dipolar adsorbate species. Single component gas phase adsorption isotherms of each adsorbate are provided. Here, the adsorptive properties of soPIM–1 are reported from the application of two methods: (a) traditional grand canonical Monte Carlo (GCMC) simulations and (b) a combination of Monte Carlo and molecular dynamics (GCMC/MD) techniques, which accounts for sorption–induced polymer dynamics. The calculated isosteric heats of adsorption are compared to those from the parent PIM–1 structure and reveals increased CO2 affinity with relatively no change in hydrocarbon affinity. Moreover, to quantify soPIM–1's resistance to dilation the evolution of the microporous structure across the adsorption isotherm loading pressures has been evaluated. Relatedly, nonequilibrium MD simulations have been utilized to determine that soPIM–1 is approximately twice as stiff as PIM–1.

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

Water Catalysis of the Reaction of Methanol with OH Radical in the Atmosphere is Negligible

Abstract Faced with the contradictory results of two recent experimental studies [Jara‐Toro et al., Angew. Chem. Int. Ed . 2017 , 56 , 2166 and Chao et al., Angew. Chem. Int. Ed . 2019 , 58 , 5013] of the possible catalytic effect of water vapor on CH 3 OH + OH reaction, we report calculations that corroborate the conclusion made by Chao et al. and extend the rate constant evaluation down to 200 K. The rate constants of the CH 3 OH + OH reaction catalyzed by a water molecule are computed as functions of temperature and relative humidity using high‐level electronic structure and kinetics calculations. The Wuhan–Minnesota Scaling (WMS) method is used to provide accurate energetics to benchmark a density functional for direct dynamics. Both high‐frequency and low‐frequency anharmonicities are included. Variational and tunneling effects are treated by canonical variational transition state theory with multidimensional small‐curvature tunneling. And, most significantly, we include multistructural effects in the rate constant calculations. Our calculations show that the catalytic effect of water vapor is not observable at 200–400 K.

Wu, Junjun↗
DOE OSTI2024

Biosynthesis of Strained Amino Acids by a PLP‐Dependent Enzyme through Cryptic Halogenation

Abstract Amino acids (AAs) are modular building blocks which nature uses to synthesize both macromolecules, such as proteins, and small molecule natural products, such as alkaloids and non‐ribosomal peptides. While the 20 main proteinogenic AAs display relatively limited side chain diversity, a wide range of non‐canonical amino acids (ncAAs) exist that are not used by the ribosome for protein synthesis, but contain a broad array of structural features and functional groups. In this communication, we report the discovery of the biosynthetic pathway for a new ncAA, pazamine, which contains a cyclopropane ring formed in two steps. In the first step, a chlorine is added onto the C 4 position of lysine by a radical halogenase, PazA. The cyclopropane ring is then formed in the next step by a pyridoxal‐5′‐phosphate‐dependent enzyme, PazB, via an S N 2‐like attack at C 4 to eliminate chloride. Genetic studies of this pathway in the native host, Pseudomonas azotoformans , show that pazamine potentially inhibits ethylene biosynthesis in growing plants based on alterations in the root phenotype of Arabidopsis thaliana seedlings. We further show that PazB can be utilized to make an alternative cyclobutane‐containing AA. These discoveries may lead to advances in biocatalytic production of specialty chemicals and agricultural biotechnology.

Sosa, Max B.↗
DOE OSTI2024

Rationalizing Acidic Oxygen Evolution Reaction over IrO 2 : Essential Role of Hydronium Cation

Abstract The development of active, stable, and more affordable electrocatalysts for acidic oxygen evolution reaction (OER) is of great importance for the practical application of electrolyzers and the advancement of renewable energy conversion technologies. Currently, IrO 2 is the only catalyst with high stability and activity, but a high cost. Further optimization of the catalyst is limited by the lack of understanding of catalytic behaviors at the acid‐IrO 2 interface. Here, in strong interaction with the experiment, we develop an explicit model based on grand‐canonical density function theory (GC‐DFT) calculations to describe acidic OER over IrO 2 . Compared to the explicit models reported previously, hydronium cations (H 3 O + ) are introduced at the electrochemical interface in the current model. As a result, a variation in stable IrO 2 surface configuration under the OER operating condition from previously proposed complete *O‐coverage to a mixture coverage of *OH and *O is revealed, which is well supported by in situ Raman measurements. In addition, the accuracy of predicted overpotential is increased in comparison with the experimentally measured. More importantly, an alteration of the potential limiting step from previously identified *O→*OOH to *OH→*O is observed, which opens new opportunities to advance the IrO 2 ‐based catalysts for acidic OER.

Mou, Tianyou↗
DOE OSTI2024

Rationalizing Acidic Oxygen Evolution Reaction over IrO 2 : Essential Role of Hydronium Cation

The development of active, stable, and more affordable electrocatalysts for acidic oxygen evolution reaction (OER) is of great importance for the practical application of electrolyzers and the advancement of renewable energy conversion technologies. Currently, IrO 2 is the only catalyst with high stability and activity, but a high cost. Further optimization of the catalyst is limited by the lack of understanding of catalytic behaviors at the acid-IrO 2 interface. Here, in strong interaction with the experiment, we develop an explicit model based on grand-canonical density function theory (GC-DFT) calculations to describe acidic OER over IrO 2 . Compared to the explicit models reported previously, hydronium cations (H 3 O + ) are introduced at the electrochemical interface in the current model. As a result, a variation in stable IrO 2 surface configuration under the OER operating condition from previously proposed complete *O-coverage to a mixture coverage of *OH and *O is revealed, which is well supported by in situ Raman measurements. In addition, the accuracy of predicted overpotential is increased in comparison with the experimentally measured. More importantly, in this study, an alteration of the potential limiting step from previously identified *O→*OOH to *OH→*O is observed, which opens new opportunities to advance the IrO 2 -based catalysts for acidic OER.

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

Conformational Change in a Four‐Tetrad DNA G‐Quadruplex upon Intercalation of a Small‐Molecule Ligand PyDH2

Abstract G‐quadruplexes (G4s) are non‐canonical DNA structures implicated in a number of biological processes. Small‐molecule ligands can alter stability and folding of G4s, which can potentially be exploited for therapeutic purposes. In this work, we investigate the interaction of telomeric DNA fragment fromTetrahymena thermophila(TET25, 5′‐G(TTGGGG) 4‐ 3′) with a G4 ligand PyDH2 belonging to the bisquinolinium family. When alone, TET25 adopts a mixture of three conformations, with the most abundant being a four‐tetrad hybrid G4. In the presence of PyDH2, surprisingly, TET25 folds into an antiparallel chair G4, with PyDH2 intercalated between G‐tetrads 2 and 3, according to our crystal structure. The structure represents the second example, and the first crystallographic evidence, of ligand intercalation into a G4. In solution, the interaction of PyDH2 and TET25 leads to a number of complexes differing by G4 topology and binding stoichiometry, strong stabilization of G4 (∆T m = 12.4 °C in the presence of one equiv. of PyDH2) and large hysteresis of ∼10 °C, suggesting that ligand binding and G4 folding processes are complex.

Chemistry↗
DOE OSTI2025

Structural Basis of Sequential Enantioselective Epoxidation by a Flavin‐Dependent Monooxygenase in Lasalocid A Biosynthesis

Abstract Polyether polyketides are a structurally diverse group of natural products known for their antimicrobial and antiproliferative activities. Lasalocid A is a canonical natural polyether produced by the soil bacteriumStreptomyces lasalocidi. In lasalocid A biosynthesis, a polyene polyketide intermediate is converted into a bisepoxide by the flavin‐dependent monooxygenase enzyme Lsd18. Remarkably, Lsd18 acts on two distinct C═C groups in the substrate molecule, forming two (R,R) epoxides. We have determined the X‐ray crystal structures of Lsd18 in the substrate‐free, substrate‐bound, and product‐bound forms. Our work has revealed that Lsd18 has an extra‐large substrate‐binding pocket that allows the polyene to adopt different conformations within the enzyme pocket. This feature enables Lsd18 to epoxidate both of the C═C groups. Additionally, a subpocket located near the Lsd18 active site controls stereoselectivity by dictating which face of the C═C group is placed next to the flavin. Molecular understanding of how Lsd18 transforms a polyene into a bisepoxide during lasalocid A biosynthesis lays the foundation for the production of designer polyethers for drug development.

Chemistry↗
DOE OSTI2021

The tree of life describes a tripartite cellular world

The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ‘‘gaps.’’ In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo -7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA

Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Crystallography Reveals Metal‐Triggered Restructuring of β‐Hairpins

Abstract Metal binding to β‐sheets occurs in many metalloproteins and is also implicated in the pathology of Alzheimer's disease. De novo designed metallo‐β‐sheets have been pursued as models and mimics of these proteins. However, no crystal structures of canonical β‐sheet metallopeptides have yet been obtained, in stark contrast to many examples for ɑ‐helical metallopeptides, leading to a poor understanding for their chemistry. To address this, we have engineered tryptophan zippers, stable 12‐residue β‐sheet peptides, to bind Cu(II) ions and obtained crystal structures through single crystal X‐ray diffraction (SC‐XRD). We find that metal binding triggers several unexpected supramolecular assemblies that demonstrate the range of higher‐order structures available to metallo‐β‐sheets. Overall, these findings underscore the importance of crystallography in elucidating the rich structural landscape of metallo‐β‐sheet peptides.

Thuc Dang, Viet↗
DOE OSTI2024

Molecular‐Level Insight into the Chlorofluorocarbons Adsorption by Defective Covalent Organic Polymers

Abstract Halocarbons have important industrial applications, but because of their contribution to global warming and the fact that they can cause ozone depletion, they are considered highly toxic. Hence, the techniques that can capture and recover the used halocarbons with energy‐efficient methods have been recently received greater attention. In this contribution, we report the capture of dichlorodifluoromethane (R12), which has high global warming and ozone depletion potential, using covalent organic polymers (COPs). The defect‐engineered COPs were synthesized and demonstrated outstanding sorption capacities, ~226 wt % of R12 combined with linear‐shaped adsorption isotherms. We further identified the plausible microscopic adsorption mechanism of the investigated COPs via grand canonical Monte Carlo simulations applied to non‐defective and a collection of atomistic models of the defective COPs. The modeling work suggests that significant R12 adsorption performance is attributed to a gradual increment of porosities due to isolated/interconnected micro‐/meso‐pore channels and the change of the long‐range ordering of both COPs. The successive hierarchical‐pore‐filling mechanism promotes R12 molecular adsorption via moderate van der Waals adsorbate‐adsorbent interactions in the micropores of both COPs at low pressure followed by adsorbate‐adsorbate interactions in the extra‐voids created at moderate to high pressure ranges. This continuous pore‐filling mechanism makes defective COPs as promising sorbents for halocarbon adsorption.

Shen, Jian↗
DOE OSTI2019

Expression of a Degradation-Resistant β-Catenin Mutant in Osteocytes Protects the Skeleton From Mechanodeprivation-Induced Bone Wasting

ABSTRACT Mechanical stimulation is a key regulator of bone mass, maintenance, and turnover. Wnt signaling is a key regulator of mechanotransduction in bone, but the role of β-catenin—an intracellular signaling node in the canonical Wnt pathway—in disuse mechanotransduction is not defined. Using the β-catenin exon 3 flox (constitutively active [CA]) mouse model, in conjunction with a tamoxifen-inducible, osteocyte-selective Cre driver, we evaluated the effects of degradation-resistant β-catenin on bone properties during disuse. We hypothesized that if β-catenin plays an important role in Wnt-mediated osteoprotection, then artificial stabilization of β-catenin in osteocytes would protect the limbs from disuse-induced bone wasting. Two disuse models were tested: tail suspension, which models fluid shift, and botulinum-toxin (botox)-induced muscle paralysis, which models loss of muscle force. Tail suspension was associated with a significant loss of tibial bone mass and density, reduced architectural properties, and decreased bone formation indices in uninduced (control) mice, as assessed by dual-energy X-ray absorptiometry (DXA), micro-computed tomography (µCT), and histomorphometry. Activation of the βcatCA allele in tail-suspended mice resulted in little to no change in those properties; ie, these mice were protected from bone loss. Similar protective effects were observed among botox-treated mice when the βcatCA was activated. RNAseq analysis of altered gene regulation in tail-suspended mice yielded 35 genes, including Wnt11, Gli1, Nell1, Gdf5, and Pgf, which were significantly differentially regulated between tail-suspended β-catenin stabilized mice and tail-suspended nonstabilized mice. Our findings indicate that selectively targeting/blocking of β-catenin degradation in bone cells could have therapeutic implications in mechanically induced bone disease. © 2019 American Society for Bone and Mineral Research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Sostdc1 Suppression in the Absence of Sclerostin Potentiates Anabolic Action of Cortical Bone in Mice

ABSTRACT The development of Wnt-based osteoanabolic agents has progressed rapidly in recent years, given the potent effects of Wnt modulation on bone homeostasis. Simultaneous pharmacologic inhibition of the Wnt antagonists sclerostin and Dkk1 can be optimized to create potentiated effects in the cancellous bone compartment. We looked for other candidates that might be co-inhibited along with sclerostin to potentiate the effects in the cortical compartment. Sostdc1 (Wise), like sclerostin and Dkk1, also binds and inhibits Lrp5/6 coreceptors to impair canonical Wnt signaling, but Sostdc1 has greater effects in the cortical bone. To test this concept, we deleted Sostdc1 and Sost from mice and measured the skeletal effects in cortical and cancellous compartments individually. Sost deletion alone produced high bone mass in all compartments, whereas Sostdc1 deletion alone had no measurable effects on either envelope. Mice with codeletion of Sostdc1 and Sost had high bone mass and increased cortical properties (bone mass, formation rates, mechanical properties), but only among males. Combined administration of sclerostin antibody and Sostdc1 antibody in wild-type female mice produced potentiation of cortical bone gain despite no effect of Sostdc1 antibody alone. In conclusion, Sostdc1 inhibition/deletion can work in concert with sclerostin deficiency to improve cortical bone properties. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fractional occupation numbers and self-interaction correction-scaling methods with the Fermi-Löwdin orbital self-interaction correction approach

In this work, we present a new assessment of the Fermi-Löwdin orbital self-interaction correction (FLO-SIC) approach with an emphasis on its performance for predicting energies as a function of fractional occupation numbers (FONs) for various multielectron systems. Our approach is implemented in the massively parallelized NWChem quantum chemistry software package and has been benchmarked on the prediction of total energies, atomization energies, and ionization potentials of small molecules and relatively large aromatic systems. Within our study, we also derive an alternate expression for the FLO-SIC energy gradient expressed in terms of gradients of the Fermi-orbital eigenvalues and revisit how the FLO-SIC methodology can be seen as a constrained unitary transformation of the canonical Kohn–Sham orbitals. Finally, we conclude with calculations of energies as a function of FONs using various SIC-scaling methods to test the limits of the FLO-SIC formalism on a variety of multielectron systems. We find that these relatively simple scaling methods do improve the prediction of total energies of atomic systems as well as enhance the accuracy of energies as a function of FONs for other multielectron chemical species.

fractional occupation number↗
DOE OSTI2024

Range‐separated density functional theory using multiresolution analysis and quantum computing

Quantum computers are expected to outperform classical computers for specific problems in quantum chemistry. Such calculations remain expensive, but costs can be lowered through the partition of the molecular system. In the present study, partition was achieved with range-separated density functional theory (RS-DFT). The use of RS-DFT reduces both the basis set size and the active space size dependence of the ground state energy in comparison with the use of wave function theory (WFT) alone. The utilization of pair natural orbitals (PNOs) in place of canonical molecular orbitals (MOs) results in more compact qubit Hamiltonians. To test this strategy, a basis-set independent framework, known as multiresolution analysis (MRA), was employed to generate PNOs. Tests were conducted with the variational quantum eigensolver for a number of molecules. The results show that the proposed approach reduces the number of qubits needed to reach a target energy accuracy.

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

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗