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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Binding of Formic Acid on Anatase TiO2(101)

The adsorption of formic acid (FA) and the formation of formate species on metal oxide surfaces are of great interest in catalysis. Formic acid is used to probe the adsorption properties of surface sites and formates are common intermediates in many catalytic reactions. Here we focus on the interaction of FA with a prototypical anatase TiO2(101) surface by using a combination of scanning tunneling microscopy (STM), infrared reflection absorption spectroscopy (IRAS), electron stimulated desorption (ESD), and density functional theory (DFT) to assess the coverage dependent evolution of different FA-derived surface species at low temperatures (80–240 K). We find that isolated FA adsorbs at 80 K in both monodentate (MD) and bidentate (BD) configurations on top of undercoordinated Ti sites (Ti5c). The MD form is likely deprotonated and readily converts upon annealing to bridging BD on two neighboring Ti5c sites. DFT calculations show that molecularly-bound MD FA is metastable and readily converts into a deprotonated state in the proximity of subsurface oxygen vacancy. The stability of the MD species increases as the availability of the paired Ti5c sites for BD formation diminishes at high coverages. Upon surface saturation, a mixed configuration of alternating bidentate and monodentate species with coverage of 2/3 FA/Ti5c represents the most favorable configuration. This is in contrast with the adsorption of FA on rutile TiO2(110) and many other oxides, where bidentate formate species dominate. Y.W., A.D., G.A.K., R.R., N.G.P., and Z.D. were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences (CSGB) under FWP 47319. B.W. and A.S. acknowledge the support of DOE BES, CSGB Division under Award DESC0007347. The experimental studies were performed in EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated for DOE by Battelle. The authors also acknowledge computational resources from the TIGRESS high-performance computer center at Princeton University.

Wang, Yang↗
DOE OSTI2020

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗
DOE OSTI2020

Gas phase formation of phenalene via 10π-aromatic, resonantly stabilized free radical intermediates

For the last few decades, the Hydrogen-Abstraction/aCetylene-Addition (HACA) mechanism has been fundamental in aiding our understanding of the source of polycyclic aromatic hydrocarbons (PAHs) in combustion processes and in circumstellar envelopes of carbon rich stars. However, the reaction mechanisms driving high temperature molecular mass growth beyond triphenylene (C 18 H 12 ) along with the link between PAHs and graphene-type nanostructures as identified in carbonaceous meteorites such as in Murchison and Allende has remained elusive. By exploring the reaction of the 1-naphthyl radical (C 10 H 7 ˙) with methylacetylene (CH 3 CCH) and allene (H 2 CCCH 2 ) under conditions prevalent in carbon-rich circumstellar environments and combustion systems, we provide compelling evidence on a facile formation of 1H-phenalene (C 13 H 10 ) – the central molecular building block of graphene-type nanostructures. Beyond PAHs, molecular mass growth processes from 1H-phenalene via ring-annulation through C3 molecular building blocks may ultimately lead to two-dimensional structures such as graphene nano flakes and after condensation of multiple layers to graphitized carbon. Furthermore, these fundamental reaction mechanisms are of crucial significance to facilitate an understanding of the origin and chemical evolution of carbon in our Galaxy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Concentric core-shell tracks and spectroscopic properties of SrTiO 3 under intense electronic excitation

A deeper understanding of the intrinsic link between the irradiation-induced microstructures and the corresponding spectroscopic properties is becoming increasingly attractive for the research fields of materials science, physics, and information technology. In this work, the structural damage response, spectroscopic features, and associated physical mechanisms of SrTiO 3 single crystals under swift heavy ion irradiation were comparatively analyzed using a combination of experimental and theoretical approaches. Corresponding to 0.11–5.00 MeV/u ion irradiation with electronic energy loss ranging from 4.0 to 29.3 keV/nm, the inelastic thermal spike calculations combined with molecular dynamics simulations are compared with the experimental observations, revealing the track fine structures (individual spherical defects with a disordered region, and discontinuous and continuous tracks consisting of an amorphous core and a disordered outer shell) and demonstrating the dominant effects of the deposition energy and lattice temperature on track damage formation and evolution; thus, two essential thresholds for defect formation of ~0.60 eV/atom and amorphous region formation of ~1.81 eV/atom were identified to better describe the concentric core-shell track structure. The enhanced nanohillock formation in the surface region is attributed to the combined action of kinetic and potential energy depositions, and the fluence dependence in regulating the hillock dimensions is also presented. The measured refractive index profiles along different crystal axes further indicate the anisotropy of irradiation-induced lattice expansion. With increasing ion fluence and damage level, the intrinsic bandgap gradually decreased, and the concentration of additional radiative recombination centers (1.81 eV, 2.31 eV, and 2.42 eV) accordingly increased in the SrTiO 3 crystal, providing the possibility of regulating related defects to achieve tunable/selective photon emission for more critical technological applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ

Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.

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

Adapting enzymes to improve their functionality in plants: why and how

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context (‘plantized’) even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can — or cannot — be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Optical readout of singlet fission biexcitons in a heteroacene with photoluminescence detected magnetic resonance

Molecular spin systems based on photoexcited triplet pairs formed via singlet fission (SF) are attractive as carriers of quantum information because of their potentially pure and controllable spin polarization, but developing systems that offer optical routes to readout as well as initialization is challenging. Herein, we characterize the electron spin magnetic resonance change in the photoluminescence intensity for a tailored organic molecular crystal while sweeping a microwave drive up to 10 GHz in a broadband loop structure. We observe resonant transitions for both triplet and quintet spin sublevel populations showing their optical sensitivity and revealing the zero-field parameters for each. We map the evolution of these spectra in both microwave frequency and magnetic field, producing a pattern of optically detected magnetic resonance (ODMR) peaks. Fits to these data using a suitable model suggest significant spin polarization in this system with orientation selectivity. Unusual excitation intensity dependence is also observed, which inverts the sign of the ODMR signal for the triplet features, but not for the quintet. These observations demonstrate optical detection of the spin sublevel population dictated by SF and intermolecular geometry, and highlight anisotropic and multi-scale dynamics of triplet pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Origin of Plutonium-244 in the Early Solar System

We investigate the origin in the early Solar System of the short-lived radionuclide 244 Pu (with a half life of 80 Myr) produced by the rapid (r) neutron-capture process. We consider two large sets of r-process nucleosynthesis models and analyse if the origin of 244 Pu in the ESS is consistent with that of the other r and slow (s) neutron-capture process radioactive nuclei. Uncertainties on the r-process models come from both the nuclear physics input and the astrophysical site. The former strongly affects the ratios of isotopes of close mass ( 129 I/ 127 I, 244 Pu/ 238 U, and 247 Pu/ 235 U). The 129 I/ 247 Cm ratio, instead, which involves isotopes of a very different mass, is much more variable than those listed above and is more affected by the physics of the astrophysical site. We consider possible scenarios for the evolution of the abundances of these radioactive nuclei in the galactic interstellar medium and verify under which scenarios and conditions solutions can be found for the origin of 244 Pu that are consistent with the origin of the other isotopes. Solutions are generally found for all the possible different regimes controlled by the interval (δ) between additions from the source to the parcel of interstellar medium gas that ended up in the Solar System, relative to decay timescales. If r-process ejecta in interstellar medium are mixed within a relatively small area (leading to a long δ), we derive that the last event that explains the 129 I and 247 Cm abundances in the early Solar System can also account for the abundance of 244 Pu. Due to its longer half life, however, 244 Pu may have originated from a few events instead of one only. If r-process ejecta in interstellar medium are mixed within a relatively large area (leading to a short δ), we derive that the time elapsed from the formation of the molecular cloud to the formation of the Sun was 9-16 Myr.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Nanostructures evolution assessment and spectroscopic properties modification induced by electronic energy loss in KTaO 3 crystal

Modifications of micro/nanostructure and photoelectric properties under swift ion irradiation (645 MeV Xe 35+ ) of KTaO 3 crystal with varying electronic energy losses (7.2–31.4 keV/nm) and ion velocities (0.18–5.00 MeV/u) have been studied by combining experimental and calculated approaches. The i-TS calculations combined with molecular dynamics simulations are compared with the experimental observations, revealing the inner track fine structures from individual spherical defects to continuous ion tracks with core–shell morphologies, and a quantitative relationship, including the melting (0.42 eV/atom), damage (0.75 eV/atom), and amorphous (1.71 eV/atom) thresholds, is established to successfully predict the inner disorder/amorphous proportions and track damage morphologies. The surface nanostructures of nanohillocks (isolated or partial overlaps) and nanopits (serious overlaps) directly depend on the combined action of the deposited potential and kinetic energies of incident ions, which induce local melting and sublimation in the near-surface region. Owing to the decreased recombination and the increased separation efficiency between electrons and holes, the higher photogenerated charge carrier mobility enhanced the photocurrent effect, further optimizing the photoconductivity performance in Xe 35+ -irradiated KTaO 3 . Therefore, controlled defect engineering using the ion irradiation technique, as an effective strategy, could design tailored nanostructure systems and regulate photoelectric properties, further promoting the development of novel technological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An unexpected hydratase synthesizes the green light-absorbing pigment fucoxanthin

Abstract The ketocarotenoid fucoxanthin and its derivatives can absorb blue–green light enriched in marine environments. Fucoxanthin is widely adopted by phytoplankton species as a main light-harvesting pigment, in contrast to land plants that primarily employ chlorophylls. Despite its supreme abundance in the oceans, the last steps of fucoxanthin biosynthesis have remained elusive. Here, we identified the carotenoid isomerase-like protein CRTISO5 as the diatom fucoxanthin synthase that is related to the carotenoid cis–trans isomerase CRTISO from land plants but harbors unexpected enzymatic activity. A crtiso5 knockout mutant in the model diatom Phaeodactylum tricornutum completely lacked fucoxanthin and accumulated the acetylenic carotenoid phaneroxanthin. Recombinant CRTISO5 converted phaneroxanthin into fucoxanthin in vitro by hydrating its carbon–carbon triple bond, instead of functioning as an isomerase. Molecular docking and mutational analyses revealed residues essential for this activity. Furthermore, a photophysiological characterization of the crtiso5 mutant revealed a major structural and functional role of fucoxanthin in photosynthetic pigment–protein complexes of diatoms. As CRTISO5 hydrates an internal alkyne physiologically, the enzyme has unique potential for biocatalytic applications. The discovery of CRTISO5 illustrates how neofunctionalization leads to major diversification events in evolution of photosynthetic mechanisms and the prominent brown coloration of most marine photosynthetic eukaryotes.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Atomistic Mechanisms of Stress-Dependent Molten Salt Corrosion in NiCr Alloys

Ni-based structural alloys in molten salt environments often experience simultaneous mechanical loading and corrosive attack, yet the mechanisms governing stress-corrosion interactions remain unclear. Prior studies largely emphasize tensile stress, while the role of compressive stress has received limited attention. Here, reactive molecular dynamics simulations are used to investigate the coupled effects of applied strain and corrosion in Ni 0.75 Cr 0.25 exposed to molten FLiNaK at 800 °C. A Σ5(210) grain boundary model is subjected to tensile (+4%) to compressive (−4%) uniaxial strains, and corrosion behavior is evaluated through fluorine adsorption, charge redistribution, and grain boundary evolution. Tensile strain accelerates intergranular corrosion susceptibility by reducing local atomic packing through elastic dilation and increasing excess free volume at the grain boundary, which enhances atomic mobility and salt infiltration. In contrast, compressive strain can suppress corrosion by promoting the formation of a ridge-like surface layer along the grain boundary, limiting salt access to the underlying alloy. These results provide atomistic insight into how stress states influence grain boundary corrosion in molten salts.

36 - MATERIALS SCIENCE↗
DOE OSTI2021

Anomalous thermoelectricity at the two-dimensional structural transition of SnSe monolayers

The thermoelectric figure of merit ZT comprises electronic and vibrational contributions that drastically change across phase transitions, and the most common theoretical ab initio approach to thermoelectricity fails to describe the evolution of ZT across finite-temperature structural transitions in its entirety. Furthermore, while the thermoelectric behavior of bulk SnSe has been extensively studied, SnSe monolayers have been experimentally realized only recently, and the existent prediction of thermoelectricity on this two-dimensional material is unreliable because it misses its structural transition altogether. SnSe monolayers (and similar GeS, GeSe, GeTe, SnS, and SnTe monolayers) experience a temperature-induced two-dimensional Pnm2 1 → P4/nmm structural transition precipitated by the softening of vibrational modes, and we describe their thermoelectric properties across the phase transition, using molecular dynamics data to inform both electronic and vibrational coefficients directly and within the same footing. Similar to recent experimental observations pointing to an overestimated ZT past the transition temperature in bulk SnSe, we find a smaller ZT on SnSe monolayers when compared to its value predicted by the standard paradigm, due to the dramatic changes in the electrical conductivity and lattice thermal conductivity as the structural transition ensues. Here, the process described here lends a strong focus to both the vibrational and electronic evolutions throughout the structural transition, and it applies to thermoelectric materials undergoing thermally driven solid-to-solid structural phase transitions in one, two, and three dimensions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Plasma production and composition from hypervelocity impacts on solar cell cover glass

Satellites are subjected to detrimental effects from the space environment, including impacts by orbital debris and meteoroids that can cause mechanical or electrical damage. While mechanical damage is well studied, electrical effects resulting from hypervelocity impact (HVI) remain poorly understood. In HVIs, where the projectile speed exceeds the speed of sound in the target material, the impact energy ionizes the material near the surface, creating a plasma that can cause radio frequency emission. This emission is the main source of electrical anomalies in satellites, but the mechanism behind its creation is still unknown. Ground-based experiments have been used to characterize HVI plasma, including the empirical power law relations that describe the impact charge produced as a function of impactor mass and speed. Quantifying these power law relations gives us a better understanding of the species formed in the impact which can eventually lead to plasma evolution models and help us first, understand the mechanism behind radio frequency emission and second, ways to prevent its damage to the satellites. In this paper, we interpret the results of the HVI experiments on solar cell coverglass targets and identify the potential chemical or molecular reactions that form the impact ion species. This is done by looking simultaneously at multiple data sets for different species within the same impact configuration, and using a new technique for quantifying the power law relations for each emitted species. We use time of flight analysis (TOF) to detect the charged particle compositions and determine their initial speeds. The results suggest that the charge production power law is species specific, with different formation mechanisms involved in a single HVI event, some of which are associated with dissociation and some with ionization of a molecule. Furthermore, our results also show that electrons have different power laws that depend on the spacecraft surface charge. TOF measurements of ions from impact events on solar cell cover glass shows the presence of SiO + and SiO – 2 as the dominant species present in plasmas on positively and negatively charged targets, respectively, as well as the formation of FeO + .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Birth of the Hydrated Electron via Charge-Transfer-to-Solvent Excitation of Aqueous Iodide

A primary means to generate hydrated electrons in laboratory experiments is excitation to the charge-transfer-to-solvent (CTTS) state of a solute such as I – (aq), but this initial step in the genesis of e – (aq) has never been simulated directly using ab initio molecular dynamics. Here, we report the first such simulations, combining ground- and excited-state simulations of I – (aq) with a detailed analysis of fluctuations in the Coulomb potential experienced by the nascent solvated electron. What emerges is a two-step picture of the evolution of e – (aq) starting from the CTTS state: I – (aq) + hν → I –* (aq) → I • (aq) + e – (aq). Notably, the equilibrated ground state of e – (aq) evolves from I –* (aq) without any nonadiabatic transitions, simply as a result of solvent reorganization. The methodology used here should be applicable to other photochemical electron transfer processes in solution, an important class of problems directly relevant to photocatalysis and energy transfer.

Carter-Fenk, Kevin↗
DOE OSTI2021

Electrocatalytic Isoxazoline–Nanocarbon Metal Complexes

In this work, we report the synthesis of new carbon-nanomaterial-based metal chelates that enable effective electronic coupling to electrocatalytic transition metals. In particular, multiwalled carbon nanotubes (MWCNTs) and few-layered graphene (FLG) were covalently functionalized by a microwave-assisted cyclo-addition with nitrile oxides to form metal-binding isoxazoline functional groups with high densities. The covalent attachment was evidenced by Raman spectroscopy, and the chemical identity of the surface functional groups was confirmed by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). The functional carbon nanomaterials effectively chelate precious metals Ir(III), Pt(II), and Ru(III), as well as earth-abundant metals such as Ni(II), to afford materials with metal contents as high as 3.0 atom %. The molecularly dispersed nature of the catalysts was confirmed by X-ray absorption spectroscopy (XAS) and energy-dispersive X-ray spectroscopy (STEM-EDS) elemental mapping. The interplay between the chelate structure on the graphene surface and its metal binding ability has also been investigated by a combination of experimental and computational studies. The defined ligands on the graphene surfaces enable the formation of structurally precise heterogeneous molecular catalysts. The direct attachment of the isoxazoline functional group on the graphene surfaces provides strong electronic coupling between the chelated metal species and the conductive carbon nanomaterial support. We demonstrate that the metal-chelated carbon nanomaterials are effective heterogeneous catalysts in the oxygen evolution reaction with low overpotentials and tunable catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Using enzymes to tame nitrogen-centred radicals for enantioselective hydroamination

The formation of C–N bonds—of great importance to the pharmaceutical industry—can be facilitated enzymatically using nucleophilic and nitrene transfer mechanisms. However, neither natural nor engineered enzymes are known to generate and control nitrogen-centred radicals, which serve as valuable species for C–N bond formation. Here we use flavin-dependent ‘ene’-reductases with an exogenous photoredox catalyst to selectively generate amidyl radicals within the protein active site. These enzymes are engineered through directed evolution to catalyse 5-exo, 6-endo, 7-endo, 8-endo, and intermolecular hydroamination reactions with high levels of enantioselectivity. Mechanistic studies suggest that radical initiation occurs via an enzyme-gated mechanism, where the protein thermodynamically activates the substrate for reduction by the photocatalyst. Molecular dynamics studies indicate that the enzymes bind substrates using non-canonical binding interactions, which may serve as a handle to further manipulate reactivity. Furthermore, this approach demonstrates the versatility of these enzymes for controlling the reactivity of high-energy radical intermediates and highlights the opportunity for synergistic catalyst strategies to unlock previously inaccessible enzymatic functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗