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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microscopic Theory of Plasmons in Substrate-Supported Borophene

Here, we compute the dielectric properties of freestanding and metal-supported borophene from first-principles time-dependent density functional theory. We find that both the low- and high-energy plasmons of borophene are fully quenched by the presence of a metallic substrate at borophene–metal distances smaller than ≃9 Å. Based on these findings, we derive an electrodynamic model of the interacting, momentum-dependent polarizability for a two-dimensional metal on a model metallic substrate, which quantitatively captures the evolution of the dielectric properties of borophene as a function of metal–borophene distance. Applying this model to a series of metallic substrates, we show that maximizing the plasmon energy detuning between borophene and substrate is the key material descriptor for plasmonic performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Gate-Tunable Short-Wave Infrared Polycrystalline GeSn Phototransistors on Noncrystalline Substrates

GeSn is a group-IV alloy with immense potential to advance microelectronics technology due to its intrinsic compatibility with existing Si CMOS processes. With a sufficiently high Sn composition, GeSn is classified as a direct bandgap semiconductor. Polycrystalline GeSn holds several additional advantages, including its significantly lower synthesis cost compared to its epitaxial counterpart, as well as the versatility to grow these films on a variety of substrates. Here, in this work, we present a polycrystalline thin-film GeSn phototransistor on a fused silica substrate with a Sn composition of ~10%, showing a photoresponse in the short-wave infrared wavelength range, critical for emerging sensing applications. This device shows a gate-tunable response, with responsivities approaching up to 1.7 mA/W with only a 30 nm-thick GeSn layer. Furthermore, phototransistors offer additional adaptability through gating, which allows for the reduction of dark current. This not only enhances the signal-to-noise ratio but also offers more flexible integration with various image sensor readout implementations using different substrates. The specific detectivity of this phototransistor is within an order of magnitude of those of previously reported GeSn photodetectors grown by molecular beam epitaxy and chemical vapor deposition, even though the absorber is 3 to 20× thinner while the electrode spacing for photocarrier transport is approximately 15× longer than the carrier diffusion length in this work, showing great potential benefits of extending similar device structures to epitaxial GeSn layers. As these GeSn phototransistors utilize a noncrystalline substrate, our work establishes a fundamentally more versatile path toward monolithically integrated GeSn-based photodetectors for next-generation multimodal sensors.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Scalable Light-Printing of Substrate-Engraved Free-Form Metasurfaces

A key challenge for metasurface research is locally controlling at will the nanoscale geometric features on meter-scale apertures. Such a technology is expected to enable large aperture meta-optics and revolutionize fields such as long-range imaging, lasers, laser detection and ranging (LADAR), and optical communications. Furthermore, these applications are often more sensitive to light-induced and environmental degradation, which constrains the possible materials and fabrication process. Here, we present a relatively simple and scalable method to fabricate a substrate-engraved metasurface with locally printed index determined by induced illumination, which, therefore, addresses both the challenges of scalability and durability. In this process, a thin metal film is deposited onto a substrate and transformed into a mask via local laser-induced dewetting into nanoparticles. The substrate is then dry-etched through this mask, and selective mask removal finally reveals the metasurface. We show that masking by the local nanoparticle distribution, and, therefore, the local index, is dependent on the local light-induced dewetting temperature. Here, we demonstrate printing of a free-form pattern engraved into a fused silica glass substrate using a laser raster scan. Large-scale spatially controlled engraving of metasurfaces has implications on other technological fields beyond optics, such as surface fluidics, acoustics, and thermomechanics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Substrate–Support Interactions Mediate Hydrogenation of Phenolic Compounds by Pd/CeO 2 Nanorods

Ceria-supported palladium (Pd/CeO 2 ) has spawned significant attention in recent years due to its ability to catalyze selective hydrogenation of phenolic compounds to cyclohexanones and cyclohexanols at a mild temperature and pressure. However, the mechanistic basis by which ceria enhances catalytic conversion is still unclear. Here, we use the increase in the 13 C transverse relaxation rate upon the addition of nanoparticles (NPs) ( 13 C ΔR 2 ) to investigate the adsorption of phenolic compounds on the surface of the Pd/CeO 2 catalyst by solution NMR. We show that hydroxyphenols adsorb on the support more efficiently than underivatized phenol and methoxyphenols and that phenol derivatives with an oxygen atom at position 2 (i.e., 2-hydroxyphenol and 2-methoxyphenol) form very stable interactions with the Pd site of Pd/CeO 2 . An analysis of the kinetics of hydrogenation revealed that catalytic conversion is linearly correlated with the ability of the substrate to form interactions with the CeO 2 support and is inhibited by the formation of stable substrate–Pd adducts. Our data suggest that CeO 2 –substrate interactions mediate phenol hydrogenation more efficiently than Pd–substrate interactions and explain the exceptional catalytic performance reported for Pd/CeO 2 .

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

Identification of Surface-Exposed Protein Radicals and A Substrate Oxidation Site in A-Class Dye-Decolorizing Peroxidase from Thermomonospora curvata

Dye-decolorizing peroxidases (DyPs) are a family of heme peroxidases in which a catalytic distal aspartate is involved in H 2 O 2 activation to catalyze oxidations under acidic conditions. They have received much attention due to their potential applications in lignin compound degradation and biofuel production from biomass. However, the mode of oxidation in bacterial DyPs remains unknown. We have recently reported that the bacterial TcDyP from Thermomonospora curvata is among the most active DyPs and shows activity toward phenolic lignin model compounds. On the basis of the X-ray crystal structure solved at 1.75 Å, sigmoidal steady-state kinetics with Reactive Blue 19 (RB19), and formation of compound II like product in the absence of reducing substrates observed with stopped-flow spectroscopy and electron paramagnetic resonance (EPR), we hypothesized that the TcDyP catalyzes oxidation of large-size substrates via multiple surface-exposed protein radicals. Among 7 tryptophans and 3 tyrosines in TcDyP consisting of 376 residues for the matured protein, W263, W376, and Y332 were identified as surface-exposed protein radicals. Only the W263 was also characterized as one of the surface-exposed oxidation sites. SDS-PAGE and size-exclusion chromatography demonstrated that W376 represents an off-pathway destination for electron transfer, resulting in the cross-linking of proteins in the absence of substrates. Mutation of W376 improved compound I stability and overall catalytic efficiency toward RB19. While Y332 is highly conserved across all four classes of DyPs, its catalytic function in A-class TcDyP is minimal, possibly due to its extremely small solvent-accessible areas. Identification of surface-exposed protein radicals and substrate oxidation sites is important for understanding the DyP mechanism and modulating its catalytic functions for improved activity on phenolic lignin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Polyphosphate (polyP) kinases are widely conserved enzymes with importance in basic bacterial metabolism and virulence in many pathogens. However, the molecular mechanisms of their substrate specificity and catalysis remain unknown. Here, we present the results of comprehensive biochemical and structural studies of three polyP kinases from different bacteria, which belong to different clusters of the PPK2 class III family. Purified PPK2 proteins catalyzed polyP-dependent phosphorylation of AMP, ADP, GMP, and GDP to corresponding nucleoside di- and triphosphates. Crystal structures of these proteins in complex with substrates, products, Mg 2+ , and inhibitors revealed the binding sites for the nucleotide and polyP substrates overlapping at the Walker A and B loops. The Walker A loop is involved in the binding of polyP and the Mg 2+ ion, whereas the Walker B loop coordinates the nucleotide phosphate groups. Structure-based site-directed mutagenesis of CHU0107 from Cytophaga hutchinsonii demonstrated the critical role of several conserved residues from the PPK2 core and lid domains, involved in the coordination of both substrates and two Mg 2+ ions. Additionally, a two-times higher activity was observed following deletion of the C-terminal tail in the CHU0107 mutant protein L285Stop. Crystal structures of PPK2 in complex with three aryl phosphonate inhibitors indicated the presence of at least two binding pockets for inhibitors located close to the Walker A loop and the catalytic residues Lys81 and Arg208. Our findings provide a molecular framework for understanding the molecular mechanisms of PPK2 kinases and have implications for future drug design and biocatalytic applications

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides

Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB–TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.

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

Modifying Surface Fluctuations of Polymer Melt Films with Substrate Modification

Deposition of a plasma polymerized film on a silicon substrate substantially changes the fluctuations on the surface of a sufficiently thin, melt polystyrene (PS) film atop the substrate. Surface fluctuation relaxation times measured with X-ray photon correlation spectroscopy (XPCS) for ca. 4R g thick melt films of 131 kg/mol linear PS on silicon and on a plasma polymer modified silicon wafer can both be described using a hydrodynamic continuum theory (HCT) that assumes the film is characterized throughout its depth by the bulk viscosity. However, when the film thickness is reduced to ~3R g , confinement effects are evident. The surface fluctuations are slower than predicted using the HCT, and the confinement effect for the PS on silicon is larger than that for the PS on the plasma polymerized film. This deviation is thus due to a difference in the thicknesses of the strongly adsorbed layers at the substrate which are impacted by the substrate surface energy.

36 MATERIALS SCIENCE↗
DOE OSTI2013

The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family

Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH 3 and CO 2 . AH belongs to the amidase signature family, which is characterized by a conserved block of 130 amino acids rich in Gly and Ser and a Ser-cis-Ser-Lys catalytic triad. In this study, the first structures of AH fromGranulibacter bethesdensis were determined, with and without the substrate analogue malonate, to 2.2 and 2.8 Å, respectively. The structures confirm the identity of the catalytic triad residues and reveal an altered dimerization interface that is not conserved in the amidase signature family. The structures also provide insights into previously unrecognized substrate specificity determinants in AH. Two residues, Tyr 299 and Arg 307 , are within hydrogen bonding distance of a carboxylate moiety of malonate. Both Tyr 299 and Arg 307 were mutated, and the resulting modified enzymes revealed >3 order of magnitude reductions in both catalytic efficiency and substrate stringency. It is proposed that Tyr 299 and Arg 307 serve to anchor and orient the substrate for attack by the catalytic nucleophile, Ser 172 . The structure further suggests the presence of a unique C-terminal domain in AH. While this domain is conserved, it does not contribute to catalysis or to the structural integrity of the core domain, suggesting that it may play a role in mediating transient and specific interactions with the urea carboxylase component of urea amidolyase. Analysis of the AH active site architecture offers new insights into common determinants of catalysis and specificity among divergent members of the amidase signature family.

Lin, Yi↗
DOE OSTI2013

A Substrate-Assisted Mechanism of Nucleophile Activation in a Ser-His-Asp Containing C-C Bond Hydrolase

The meta-cleavage product (MCP) hydrolases utilize a Ser–His–Asp triad to hydrolyze a carbon–carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ES red , which possesses a remarkable bathochromically shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid to 2-hydroxy-2,4-pentadienoic acid and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ES red decay and product formation showed a solvent kinetic isotope effect of 2.5, indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pK a2 (β nuc ~ 1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His–Asp pair does not play an essential role. The data further suggest that ES red represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.

Ruzzini, Antonio C.↗
DOE OSTI2023

Enhancing Substrate–Metal Catalyst Affinity via Hydrogen Bonding: Pd(II)-Catalyzed β-C(sp 3 )–H Bromination of Free Carboxylic Acids

Achieving sufficient substrate-metal catalyst affinity is a fundamental challenge for developing synthetically useful C–H activation reactions of weakly coordinating native substrates. While hydrogen bonding has been harnessed to bias site selectivity in existing C(sp 2 )–H activation reactions, the potential for designing catalysts with hydrogen bond donors (HBDs) to enhance catalyst substrate affinity, and thereby facilitate otherwise unreactive C(sp 3 )–H activation, remains to be demonstrated. Herein, we report the discovery of a ligand scaffold containing a remote amide motif that can form a favorable meta-macrocyclic hydrogen bonding interaction with the aliphatic acid substrate. The utility of this ligand scaffold is demonstrated through the development of an unprecedented C(sp 3 )–H bromination of α-tertiary and α-quaternary free carboxylic acids, which proceeds in exceedingly high mono-selectivity. Furthermore, the geometric relationship of the NHAc hydrogen bond donor and the coordinating quinoline ligand is crucial for forming the meta-macrocyclophane-like hydrogen bonding interaction, providing a guideline for the future design of catalysts employing secondary interactions.

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

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

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

Direct growth of single-crystalline III–V semiconductors on amorphous substrates

The III–V compound semiconductors exhibit superb electronic and optoelectronic properties. Traditionally, closely lattice-matched epitaxial substrates have been required for the growth of high-quality single-crystal III–V thin films and patterned microstructures. To remove this materials constraint, here we introduce a growth mode that enables direct writing of single-crystalline III–V’s on amorphous substrates, thus further expanding their utility for various applications. The process utilizes templated liquid-phase crystal growth that results in user-tunable, patterned micro and nanostructures of single-crystalline III–V’s of up to tens of micrometres in lateral dimensions. InP is chosen as a model material system owing to its technological importance. The patterned InP single crystals are configured as high-performance transistors and photodetectors directly on amorphous SiO 2 growth substrates, with performance matching state-of-the-art epitaxially grown devices. In conclusion, the work presents an important advance towards universal integration of III–V’s on application-specific substrates by direct growth.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase

The O-linked β-N-acetyl glucosamine (O-GlcNAc) modification dynamically regulates the functions of numerous proteins. A single human enzyme O-linked β-N-acetyl glucosaminase (O-GlcNAcase or OGA) hydrolyzes this modification. To date, it remains largely unknown how OGA recognizes various substrates. Here we report the structures of OGA in complex with each of four distinct glycopeptide substrates that contain a single O-GlcNAc modification on a serine or threonine residue. Intriguingly, these glycopeptides bind in a bidirectional yet conserved conformation within the substrate-binding cleft of OGA. This study provides fundamental insights into a general principle that confers the substrate binding adaptability and specificity to OGA in O-GlcNAc regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis

Enzymes with high activity are readily produced through protein engineering, but intentionally and efficiently engineering enzymes for an expanded substrate scope is a contemporary challenge. One approach to address this challenge is Substrate Multiplexed Screening (SUMS), where enzyme activity is measured on competing substrates. SUMS has long been used to rigorously quantitate native enzyme specificity, primarily for in vivo settings. SUMS has more recently found sporadic use as a protein engineering approach but has not been widely adopted by the field, despite its potential utility. Here, we develop principles of how to design and interpret SUMS assays to guide protein engineering. This rich information enables improving activity with multiple substrates simultaneously, identifies enzyme variants with altered scope, and indicates potential mutational hot-spots as sites for further engineering. These advances leverage common laboratory equipment and represent a highly accessible and customizable method for enzyme engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis of promiscuous substrate transport by Organic Cation Transporter 1

Organic Cation Transporter 1 (OCT1) plays a crucial role in hepatic metabolism by mediating the uptake of a range of metabolites and drugs. Genetic variations can alter the efficacy and safety of compounds transported by OCT1, such as those used for cardiovascular, oncological, and psychological indications. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 remain poorly understood. Here, we present cryo-EM structures of full-length human OCT1 in the inward-open conformation, both ligand-free and drug-bound, indicating the basis for its broad substrate recognition. Comparison of our structures with those of outward-open OCTs provides molecular insight into the alternating access mechanism of OCTs. We observe that hydrophobic gates stabilize the inward-facing conformation, whereas charge neutralization in the binding pocket facilitates the release of cationic substrates. These findings provide a framework for understanding the structural basis of the promiscuity of drug binding and substrate translocation in OCT1.

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

Substrate effects on spin relaxation in two-dimensional Dirac materials with strong spin-orbit coupling

Understanding substrate effects on spin dynamics and relaxation is of key importance for spin-based information technologies. However, the key factors that determine such effects, in particular for materials with strong spin-orbit coupling (SOC), have not been well understood. Here we performed first-principles real-time density-matrix dynamics simulations with SOC and the electron phonon and electron-impurity scattering for spin lifetimes (τ s ) of supported/free-standing germanene, a prototypical strong SOC 2D Dirac material. We show that the effects of different substrates on τ s can surprisingly differ by two orders of magnitude. We find that substrate effects on τ s are closely related to substrate-induced modifications of the SOC-field anisotropy, which changes the spin flip scattering matrix elements. We propose a new electronic quantity, named spin-flip angle θ ↑↓ , to characterize spin relaxation through intervalley spin-flip scattering. We find that $τ^{-1}_s$ is approximately proportional to the averaged value of sin 2 (θ ↑↓ /2), which serves as a guiding parameter of controlling spin relaxation.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Different Behaviors of a Substrate in P450 Decarboxylase and Hydroxylase Reveal Reactivity-Enabling Actors

Biological routes to the production of fuels from renewable feedstocks hold significant promise in our efforts towards a sustainable future. The fatty acid decarboxylase enzyme (OleT JE ) is a cytochrome P450 enzyme that converts long and medium chain fatty acids to terminal alkenes and shares significant similarities in terms of structure, substrate scope and mechanism with the hydroxylase cytochrome P450 (P450 BSβ ). Recent reports have demonstrated that catalytic pathways in these enzymes bifurcate when the heme is in its iron-hydroxo (compound II) state. In spite of significant similarities, the fundamental underpinnings of their different characteristic wild-type reactivities remain ambiguous. In this work, we develop point charges, modified parameters and report molecular simulations of this crucial intermediate step. Water occupancies and substrate mobility at the active site are observed to be vital differentiating aspects between the two enzymes in the compound II state and corroborate recent experimental hypotheses. Apart from increased substrate mobility in the hydroxylase, which could have implications for enabling the rebound mechanism for hydroxylation, OleT JE is characterized by much stronger binding of the substrate carboxylate group to the active site arginine, implicating it as an important enabling actor for decarboxylation.

09 BIOMASS FUELS↗