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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Remote Epitaxy of III-V Solar Cells via Hydride Vapor Phase Epitaxy

The promise of remote epitaxy, in which epitaxial registry of a film can still be maintained through two-dimensional layers, has emerged from an advanced understanding of the interactions between two dimensional materials and bulk semiconductors. A promising application of this technology is to facilitate substrate reuse in epitaxial III-V systems, which could significantly reduce material cost and improve commercial viability of this high-efficiency photovoltaic technology. In this process the weak van der Waal bonds between the 2D layer and the III-V substrate make separation of epitaxially-grown layers simple and leaves a smooth substrate that can be reused for cost reduction. Here we present a study of growth parameters of GaAs on AlGaAs through a low dimensional carbon interlayer via hydride vapor phase epitaxy (HVPE). We Investigate the effect of various GaAs nucleation conditions such as V/III ratio, temperature and growth rate on film roughness, crystallinity, and degree of epitaxial alignment. We demonstrate growth of single crystal GaAs layer on top of the low dimensional carbon that follow the crystal orientation of the substrate. Surface roughness measured via AFM found that lower V/III ratios result in smoother III-V films grown on the low dimensional carbon, with a lowest RMS of ~60 nm obtained at a V/III ratio of 5. Growth temperatures are optimized at 650 C, as temperatures below 550 C show non-crystalline growth and higher temperature samples display very rough surfaces. Additionally, we investigate HVPE growth on various forms of low-dimensional carbon including transferred graphene, CVD-grown graphene, and MOCVD-growth amorphous carbon and find the latter to be most well suited for III-V growth as this method results in cleaner interface and potential for direct, large-area coverage. We also identify techniques to mitigate surface degradation in carbon layers as a function of both exposure time and growth environment by analyzing surface changes via x-ray reflectivity. We show growth of heteroepitaxial III-V solar cells on carbon interlayers and preliminary cell results, which are currently limited to 4% efficiency under one sun.

AlGaAs↗
DOE OSTI2018

Metal-Semiconductor Nanoheterostructures with an AlGaN Quantum Well and In Situ Formed Surface Al Nanoislands

We report on fabrication and studies of composite heterostuctures consisting of an Al{sub 0.55}Ga{sub 0.45}N/A{sub l0.8}Ga{sub 0.2}N quantum well and surface Al nanoislands, grown by plasma-assisted molecularbeam epitaxy on c-sapphire substrates. The influence of a substrate temperature varied between 320 and 700ºC on the size and density of the deposited Al nanoislands is evaluated. The effect of Al nanoislands on decay kinetics of the quantum well middle-ultraviolet photoluminescence has been investigated by time resolved photoluminescence. The samples with the maximum density of Al nanoislands of 10{sup 8} cm{sup –2} and lateral dimensions in the range of 100–500 nm demonstrated shortening of the photoluminescence lifetime, induced by interaction of the emitting quantum well and the plasmonic metal particles.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Substrate-selective Inhibition of Cyclooxygeanse-2 by Fenamic Acid Derivatives Is Dependent on Peroxide Tone

Cyclooxygenase-2 (COX-2) catalyzes the oxygenation of arachidonic acid (AA) and endocannabinoid substrates, placing the enzyme at a unique junction between the eicosanoid and endocannabinoid signaling pathways. COX-2 is a sequence homodimer, but the enzyme displays half-of-site reactivity, such that only one monomer of the dimer is active at a given time. Certain rapid reversible, competitive nonsteroidal anti-inflammatory drugs (NSAIDs) have been shown to inhibit COX-2 in a substrate-selective manner, with the binding of inhibitor to a single monomer sufficient to inhibit the oxygenation of endocannabinoids but not arachidonic acid. The underlying mechanism responsible for substrate-selective inhibition has remained elusive. In this work, we utilized structural and biophysical methods to evaluate flufenamic acid, meclofenamic acid, mefenamic acid, and tolfenamic acid for their ability to act as substrate-selective inhibitors. Crystal structures of each drug in complex with human COX-2 revealed that the inhibitor binds within the cyclooxygenase channel in an inverted orientation, with the carboxylate group interacting with Tyr-385 and Ser-530 at the top of the channel. Tryptophan fluorescence quenching, continuous-wave electron spin resonance, and UV-visible spectroscopy demonstrate that flufenamic acid, mefenamic acid, and tolfenamic acid are substrate-selective inhibitors that bind rapidly to COX-2, quench tyrosyl radicals, and reduce higher oxidation states of the heme moiety. Substrate-selective inhibition was attenuated by the addition of the lipid peroxide 15-hydroperoxyeicosatertaenoic acid. Collectively, these studies implicate peroxide tone as an important mechanistic component of substrate-selective inhibition by flufenamic acid, mefenamic acid, and tolfenamic acid.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450 BM3 Variants

Cytochrome P450 BM3 is a heme-containing enzyme from Bacillus megaterium that displays high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450 BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450 BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Atomistic Insights into Nucleation and Formation of Hexagonal Boron Nitride on Nickel from First-Principles-Based Reactive Molecular Dynamics Simulations

Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni–B and Ni–N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.

Liu, Song↗
DOE OSTI2018

Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin

Viperin is a radical SAM enzyme that has been shown to possess antiviral activity against a broad spectrum of viruses; however, its molecular mechanism is unknown. We report here that recombinant fungal and archaeal viperin enzymes catalyze the addition of the 5'-deoxyadenosyl radical (5'-dA•) to the double bond of isopentenyl pyrophosphate (IPP), producing a new compound we named adenylated isopentyl pyrophosphate (AIPP). The reaction is specific for IPP, as other pyrophosphate compounds involved in the mevalonate biosynthetic pathway did not react with 5'-dA • . Enzymatic reactions employing IPP derivatives as substrates revealed that any chemical change in IPP diminishes its ability to be an effective substrate of fungal viperin. Mutational studies disclosed that the hydroxyl group on the side chain of Tyr-245 in fungal viperin is the likely source of hydrogen in the last step of the radical addition, providing mechanistic insight into the radical reaction catalyzed by fungal viperin. Structure-based molecular dynamics (MD) simulations of viperin interacting with IPP revealed a good fit of the isopentenyl motif of IPP to the active site cavity of viperin, unraveling the molecular basis of substrate specificity of viperin for IPP. Collectively, our findings indicate that IPP is an effective substrate of fungal and archaeal viperin enzymes and provide critical insights into the reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Catalytic Mechanism of Aryl-Ether Bond Cleavage in Lignin by LigF and LigG

Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the β-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione S-transferases (GSTs) has been reported in several sphingomonads. Here in this paper, we apply quantum mechanics/molecular mechanics simulations to study the mechanism of two glutathione-dependent enzymes in the β-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a β-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a SN2 reaction mechanism, with the monoaromatic leaving group being promptly neutralized upon release. Specific interactions with conserved residues are responsible for stereoselectivity and for activation of the cofactor as a nucleophile. A glutathione conjugate is also released by LigF and serves the substrate of LigG, undergoing a S N 2-like reaction, in which Cys15 acts as the nucleophile, to yield the second monoaromatic product. The simulations suggest that the electron-donating substituent at the para-position found in lignin-derived aromatics and the interaction with Tyr217 are essential for reactivity in LigG. Overall, this work deepens the understanding of the stereospecific enzymatic mechanisms in the β-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs.

09 BIOMASS FUELS↗
DOE OSTI2016

Exchange bias and bistable magneto-resistance states in amorphous TbFeCo thin films

Amorphous TbFeCo thin films sputter deposited at room temperature on thermally oxidized Si substrate are found to exhibit strong perpendicular magnetic anisotropy. Atom probe tomography, scanning transmission electron microscopy, and energy dispersive X-ray spectroscopy mapping have revealed two nanoscale amorphous phases with different Tb atomic percentages distributed within the amorphous film. Exchange bias accompanied by bistable magneto-resistance states has been uncovered near room temperature by magnetization and magneto-transport measurements. The exchange anisotropy originates from the exchange interaction between the ferrimagnetic and ferromagnetic components corresponding to the two amorphous phases. This study provides a platform for exchange bias and magneto-resistance switching using single-layer amorphous ferrimagnetic thin films that require no epitaxial growth.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Encoding of Promiscuity in an Aminoglycoside Acetyltransferase

Aminoglycoside antibiotics are a large family of antibiotics that can be divided into two distinct classes on the basis of the substitution pattern of the central deoxystreptamine ring. Although aminoglycosides are chemically, structurally, and topologically diverse, some aminoglycoside-modifying enzymes (AGMEs) are able to inactivate as many as 15 aminoglycosides from the two main classes, the kanamycin- and neomycin-based antibiotics. In this paper, we present the crystal structure of a promiscuous AGME, aminoglycoside-N3-acetyltransferase-IIIb (AAC-IIIb), in the apo form, in binary drug (sisomicin, neomycin, and paromomycin) and coenzyme A (CoASH) complexes, and in the ternary neomycin–CoASH complex. These data provide a structural framework for interpretation of the thermodynamics of enzyme–ligand interactions and the role of solvent in the recognition of ligands. In combination with the recent structure of an AGME that does not have broad substrate specificity, these structures allow for the direct determination of how antibiotic promiscuity is encoded in some AGMEs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Structure of the glucosyltransferase domain of TcdA in complex with RhoA provides insights into substrate recognition

Clostridioides difficile is one of the most common causes of antibiotic-associated diarrhea in developed countries. As key virulence factors of C. difficile, toxin A (TcdA) and toxin B (TcdB) act by glucosylating and inactivating Rho and Ras family small GTPases in host cells, which leads to actin cytoskeleton disruption, cell rounding, and ultimately cell death. Here we present the co-crystal structure of the glucosyltransferase domain (GTD) of TcdA in complex with its substrate human RhoA at 2.60-angstrom resolution. This structure reveals that TcdA GTD grips RhoA mainly through its switch I and switch II regions, which is complemented by interactions involving RhoA’s pre-switch I region. Comprehensive structural comparisons between the TcdA GTD–RhoA complex and the structures of TcdB GTD in complex with Cdc42 and R-Ras reveal both the conserved and divergent features of these two toxins in terms of substrate recognition. Taken together, these findings establish the structural basis for TcdA recognition of small GTPases and advance our understanding of the substrates selectivity of large clostridial toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

NDR1 modulates the UV-induced DNA-damage checkpoint and nucleotide excision repair

Nucleotide excision repair (NER) is the sole mechanism of UV-induced DNA lesion repair in mammals. A single round of NER requires multiple components including seven core NER factors, xeroderma pigmentosum A–G (XPA–XPG), and many auxiliary effector proteins including ATR serine/threonine kinase. The XPA protein helps to verify DNA damage and thus plays a rate-limiting role in NER. Hence, the regulation of XPA is important for the entire NER kinetic. We found that NDR1, a novel XPA-interacting protein, modulates NER by modulating the UV-induced DNA-damage checkpoint. In quiescent cells, NDR1 localized mainly in the cytoplasm. After UV irradiation, NDR1 accumulated in the nucleus. The siRNA knockdown of NDR1 delayed the repair of UV-induced cyclobutane pyrimidine dimers in both normal cells and cancer cells. It did not, however, alter the expression levels or the chromatin association levels of the core NER factors following UV irradiation. Instead, the NDR1-depleted cells displayed reduced activity of ATR for some set of its substrates including CHK1 and p53, suggesting that NDR1 modulates NER indirectly via the ATR pathway. - Highlights: • NDR1 is a novel XPA-interacting protein. • NDR1 accumulates in the nucleus in response to UV irradiation. • NDR1 modulates NER (nucleotide excision repair) by modulating the UV-induced DNA-damage checkpoint response.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2015

Calcium-magnesium Aluminosilicate (CMAS) Interactions with Advanced Environmental Barrier Coating Material

Particulates, like sand and volcanic ash, threaten the development of robust environmental barrier coatings (EBCs) that protect next-generation silicon-based ceramic matrix composite (CMC) turbine engine components from harsh combustion environments during service. The siliceous particulates transform into molten glassy deposits of calcium-magnesium aluminosilicate (CMAS) when ingested by an aircraft engine operating at temperatures above 1200C. In this study, a sample of desert sand was melted into CMAS glass to evaluate high-temperature interactions between the sand glass and an advanced EBC material. Desert sand glass was added to the surface of hot-pressed EBC substrates, which were then heated in air at temperatures ranging from 1200C to 1500C. Scanning electron microscopy and X-ray energy-dispersive spectroscopy were used to evaluate microstructure and phase compositions of specimens and the CMASEBC interface after heat treatments.

CMAS-coating interactions↗
DOE OSTI2019

Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly’s global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE–p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.

Biochemistry & Molecular Biology↗
DOE OSTI2016

Platinum-Coated Hollow Graphene Nanocages as Cathode Used in Lithium-Oxygen Batteries

One of the formidable challenges facing aprotic lithium-oxygen (Li-O-2) batteries is the high charge overpotential, which induces the formation of byproducts, loss in efficiency, and poor cycling performance. Herein, the synthesis of the ultrasmall Pt-coated hollow graphene nano cages as cathode in Li-O-2 batteries is reported. The charge voltage plateau can reduce to 3.2 V at the current density of 100 mA g(-1), even maintain below 3.5 V when the current density increased to 500 mA g(-1). The unique hollow graphene nanocages matrix can not only provide numerous nanoscale tri-phase regions as active sites for efficient oxygen reduction, but also offer sufficient amount of mesoscale pores for rapid oxygen diffusion. Furthermore, with strong atomic-level oxygen absorption into its subsurface, ultrasmall Pt catalytically serves as the nucleation site for Li2O2 growth. The Li2O2 is subsequently induced into a favorable form with small size and amorphous state, decomposed more easily during recharge. Meanwhile, the conductive hollow graphene substrate can enhance the catalytic activity of noble metal Pt catalysts due to the graphene-metal interfacial interaction. Benefiting from the above synergistic effects between the hollow graphene nanocages and the nanosized Pt catalysts, the ultrasmall Pt-decorated graphene nanocage cathode exhibits enhanced electrochemical performances.

Wu, Feng↗
DOE OSTI2022

Synthesizing Carbon‐Supported, High‐Loading, Ultra‐Small Pt 3 Ni Nanoparticles via Tuning the Surface Electrostatic Effect

Carbon‐supported nanoparticles (NPs) are widely used as catalysts in fuel cells and electrolyzers. While it is well known that NPs with smaller size and higher loading often lead to better catalytic activity, they remain challenging to synthesize due to the weak control over the surface properties of the support. Herein, a facile approach to synthesize carbon‐supported, high‐loading, and ultra‐small Pt 3 Ni NPs via applying thermal shock on strongly interacted carbon support with metal salt is reported. Specifically, sodium citrate is introduced into the precursor solution and substrate mixture, which induces strong electrostatic effect between metal salts and carbon particles that markedly improves precursor anchoring and dispersion, thereby achieving high particle loading as well as small size and distribution. As a proof‐of‐concept, the synthesis of Pt 3 Ni NPs supported on carbon black with particle size of 1.56 ± 0.36 nm at 30 wt% loading and 1.66 ± 0.56 nm at 40 wt% loading is reported, where the sizes are among the smallest while the loadings are among the highest in the literature. This approach can be readily extended to many compositions and substrates, with tunable particle size and loading, thereby substantially expanding the synthesis space for NP catalysts in various electrochemical applications.

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

Two-State Reactivity in Iron-Catalyzed Alkene Isomerization Confers σ-Base Resistance

A low-coordinate, high spin (S = 3/2) organometallic iron(I) complex is a catalyst for the isomerization of alkenes. A combination of experimental and computational mechanistic studies supports a mechanism in which alkene isomerization occurs by the allyl mechanism. Importantly, while substrate binding occurs on the S = 3/2 surface, oxidative addition to an η 1 -allyl intermediate only occurs on the S = 1/2 surface. In conclusion, since this spin state change is only possible when the alkene substrate is bound, the catalyst has high immunity to typical σ-base poisons due to the antibonding interactions of the high spin state.

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

Leveraging Triphenylphosphine-Containing Polymers to Explore Design Principles for Protein-Mimetic Catalysts

Complex interactions between noncoordinating residues are significant yet commonly overlooked components of macromolecular catalyst function. While these interactions have been demonstrated to impact binding affinities and catalytic rates in metalloenzymes, the roles of similar structural elements in synthetic polymeric catalysts remain underexplored. Using a model Suzuki–Miyuara cross-coupling reaction, we performed a series of systematic studies to probe the interconnected effects of metal–ligand cross-links, electrostatic interactions, and local rigidity in polymer catalysts. To achieve this, a novel bifunctional triphenylphosphine acrylamide (BisTPPAm) monomer was synthesized and evaluated alongside an analogous monofunctional triphenylphosphine acrylamide (TPPAm). In model copolymer catalysts, increased initial reaction rates were observed for copolymers untethered by Pd complexation (BisTPPAm-containing) compared to Pd-cross-linked catalysts (TPPAm-containing). Further, incorporating local rigidity through secondary structure-like and electrostatic interactions revealed nonmonotonic relationships between composition and the reaction rate, demonstrating the potential for tunable behavior through secondary-sphere interactions. Lastly, through rigorous cheminformatics featurization strategies and statistical modeling, we quantitated relationships between chemical descriptors of the substrate and reaction conditions on catalytic performance. Collectively, these results provide insights into relationships among the composition, structure, and function of protein-mimetic catalytic copolymers.

Catalysts↗