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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structure Activity Relationship Approach toward the Improved Separation of Rare-Earth Elements Using Diglycolamides

The separation of adjacent lanthanides continues to be a challenge worldwide because of the similar physical and chemical properties of these elements and a necessity to advance the use of clean-energy applications. In this paper, a systematic structure–performance relationship approach toward understanding the effect of N-alkyl group characteristics in diglycolamides (DGAs) on the separation of lanthanides(III) from a hydrochloric acid medium is presented. In addition to the three most extensively studied DGA complexants [N,N,N',N'-tetra(n-octyl)diglycolamide, TODGA; N,N,N',N'-tetra(2-ethylhexyl)diglycolamide, TEHDGA; N,N'-dimethyl-N,N'-di(n-octyl)diglycolamide, DMDODGA], 12 new extracting agents with varying substitution patterns were designed to study the interplay of steric and electronic effects that control rare-earth element extraction. Subtle changes in the structure around diglycolamide carbonyl oxygen atoms result in dramatic shifts in the lanthanide extraction strength and selectivity. The effects of the chain length and branching position of N-alkyl substituents in DGAs are elaborated on with the use of experimental, computational, and solution-structure characterization techniques.

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

Unraveling the Surface Termination and Evolution of Surface States for Electrocatalyst PtSn 4 in Alkaline HER

Semimetal PtSn 4 has been experimentally demonstrated as a promising topological electrocatalyst for the hydrogen evolution reaction (HER) under both acidic and alkaline conditions. While two possible mechanisms have been proposed to explain its activity, the role of its surface states in HER remains unclear. It is indeed in question how the surface states of this alloy evolve as HER proceeds. In this study, we investigate the surface termination that sustains conducting surface states on PtSn 4 , and we track their evolution during HER catalysis. We show that a reconstructed surface with a Sn-poor termination reproduces the scanning tunneling microscopy pattern observed in experiments and sustains a conducting surface. Through phase diagram and geometric structure analysis, we outline the HER profile following the Volmer–Heyrovsky mechanism. As hydrogen atoms adsorb onto the surface, the structure undergoes further reconstruction to an equilibrium phase with a coverage of two hydrides per unit cell. Meanwhile, the surface electronic bands evolve in response to interactions with the adsorbed hydrogen atoms. A hybridization diagram is further proposed for understanding the surface state evolution based on wave function and chemical bonding analyses. While the Pt atoms serve as conventional sites for hydrogen binding, the surface states of PtSn 4 are essential for stabilizing the hydrogen antibonding states via in-phase electronic interactions with the Sn components. This stabilization results in frontier surface bands that are responsible for driving the HER catalysis. Here, our findings provide a detailed description for the direct involvement of surface states on PtSn4 when employed as a catalyst for HER.

catalysts↗
DOE OSTI2025

Structure and Synthesizability of Iron–Sulfur Metal–Organic Frameworks

Sulfur-based metal–organic frameworks (MOFs) and coordination polymers (CPs) are an emerging class of hybrid materials that have received growing attention due to their magnetic, conductive, and catalytic properties with potential applications in electrocatalysis and energy storage. In this work, we report a high-throughput virtual screening protocol to predict the synthesizability of candidate metal–sulfur MOFs/CPs by computing the thermodynamically stable structures resulting from a particular combination of metal cluster, linker, cation, and synthetic conditions. Free energies are computed by using all-atom classical mechanical thermodynamic integration. Low-free-energy structures are refined using ab initio density functional theory, and pair distribution functions and powder X-ray diffraction patterns are calculated to complement and guide experimental structure determination. We validate the computational approach by retrospective predictions of the stable structure produced by experimental syntheses, and a subsequent screen predicts Fe 4 S 4 -BDT–TPP as a new thermodynamically stable one-dimensional (1D) CP comprising a redox-active Fe 4 S 4 cluster, a 1,4-benzenedithiolate (BDT) linker, and a tetraphenylphosphonium (TPP) countercation. Furthermore, this material is experimentally synthesized, and the 1D chain structure of the crystal is confirmed using microcrystal electron diffraction. The computational screening pipeline is generically transferable to neutral and ionic MOFs/CPs comprising arbitrary metal clusters, linkers, cations, and synthetic conditions, and we make it freely available as an open source tool to guide and accelerate the discovery and engineering of novel porous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Orientation-tunable local crystallization of Si films enabled by atomic imprint crystallization

Here, in this paper, we demonstrate area-selective crystallization of amorphous Si into tunable crystal orientations enabled by atomic imprint crystallization (AIC), where an amorphous Si layer is crystallized by solid phase epitaxy (SPE) from an externally impressed single-crystalline Si template. Using micro-patterned single-crystalline Si templates, a limited area of an amorphous Si film, where the film surface and patterned template surface are in contact, is crystallized via SPE to create an array of crystallographically aligned dots embedded in amorphous matrix. Combining AIC from the top surface and conventional SPE from the substrate, we demonstrate the fabrication of an array of crystalline dots embedded in single-crystalline matrix with tunable in-plane rotation angle. The results indicate the high tunability of the crystallization process enabled by AIC, allowing precise control of crystallographic properties of thin films with area-selectivity; such capability opens opportunities for the design of new materials for a wide range of applications in materials science.

Amorphous↗
DOE OSTI2021

Atomistic Mechanism Underlying the Si ( 111 ) - ( 7 × 7 ) Surface Reconstruction Revealed by Artificial Neural-Network Potential

The 7×7 reconstruction of the Si(111) surface represents arguably the most fascinating surface reconstruction so far observed in nature. Yet, the atomistic mechanism underpinning its formation remains unclear after it was discovered sixty years ago. Experimentally, it is observed post priori so that analysis of its formation mechanism can only be carried out in analogy with archaeology. Theoretically, density-functional theory (DFT) correctly predicts the Si(111)-(7×7) ground state but is impractical to simulate its formation process; while empirical potentials failed to produce it as the ground state. Developing an artificial neural-network potential of DFT quality, we carried out accurate large-scale simulations to unravel the formation of the Si(111)-(7×7) surface. We reveal a possible step-mediated atom-pop rate-limiting process that triggers massive nonconserved atomic rearrangements, most remarkably, a critical process of collective vacancy diffusion that mediates a sequence of selective dimer, corner-hole, stacking-fault, and dimer-line pattern formation, to fulfill the 7×7 reconstruction. Our findings may not only solve the long-standing mystery of this famous surface reconstruction but they also illustrate the power of machine learning in studying complex structures.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2020

Determination of excited state molecular structures from time-resolved gas-phase X-ray scattering

We present a comprehensive investigation of a recently introduced method to determine transient structures of molecules in excited electronic states with sub-ångstrom resolution from time-resolved gas-phase scattering signals. The method, which is examined using time-resolved X-ray scattering data measured on the molecule N-methylmorpholine (NMM) at the Linac Coherent Light Source (LCLS), compares the experimentally measured scattering patterns against the simulated patterns corresponding to a large pool of molecular structures to determine the full set of structural parameters. In addition, we examine the influence of vibrational state distributions and find the effect negligible within the current experimental detection limits, despite that the molecules have a comparatively high internal vibrational energy. Here, the excited state structures determined using three structure pools generated using three different computational methods are in good agreement, demonstrating that the procedure is largely independent of the computational chemistry method employed as long as the pool is sufficiently expansive in the vicinity of the sought structure and dense enough to yield good matches to the experimental patterns.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Computational approaches to model X-ray photon correlation spectroscopy from molecular dynamics

X-ray photon correlation spectroscopy (XPCS) allows for the resolution of dynamic processes within a material across a wide range of length and time scales. X-ray speckle visibility spectroscopy (XSVS) is a related method that uses a single diffraction pattern to probe ultrafast dynamics. Interpretation of the XPCS and XSVS data in terms of underlying physical processes is necessary to establish the connection between the macroscopic responses and the microstructural dynamics. To aid the interpretation of the XPCS and XSVS data, we present a computational framework to model these experiments by computing the X-ray scattering intensity directly from the atomic positions obtained from molecular dynamics simulations. We compare the efficiency and accuracy of two alternative computational methods: the direct method computing the intensity at each diffraction vector separately, and a method based on fast Fourier transform that computes the intensities at all diffraction vectors at once. Furthermore, the computed X-ray speckle patterns capture the density fluctuations over a range of length and time scales and are shown to reproduce the known properties and relations of experimental XPCS and XSVS for liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Synthesis and characterization of 5,15-bis(hydroxymethyl)porphyrins – simple compounds distantly inspired by the chlorosomal bacteriochlorophylls

A self-assembly paradigm is provided in green photosynthetic bacteria by the chlorin macrocycle bacteriochlorophyll (BChl) c, which contains a 3-(1-hydroxyethyl) substituent, central magnesium ion, and 13-keto group. The assembled BChl c structure is a powerful light-harvesting apparatus that can support life even under extreme low-light conditions. Here, inspired by the work of Balaban, two far simpler porphyrins have been synthesized, 5,15-bis(hydroxymethyl)-10,20-diphenylporphinatozinc(II) (Ph/CH 2 OH) and 5,15-bis(hydroxymethyl)porphinatozinc(II) (H/CH 2 OH), and analogues wherein ethyl replaces hydroxymethyl (Ph/Et and H/Et). Examination of Ph/CH 2 OH and H/CH 2 OH by time-resolved spectroscopy showed an ∼2-fold enhancement in the singlet excited-state lifetime compared to meso-tetraphenylporphinatozinc(II) (ZnTPP). The single-crystal X-ray diffraction revealed distinct packing patterns. Porphyrin Ph/CH 2 OH exhibited double staircases wherein (1) each zinc is pentacoordinate (by apical coordination of one hydroxymethyl group of a porphyrin in the same staircase), (2) the second hydroxymethyl group is hydrogen-bonded to an apically coordinated hydroxymethyl oxygen atom in the adjacent staircase, (3) the porphyrins in a given staircase are coplanar but cofacially offset with each other, and (4) the adjacent staircases are oriented approximately 72° relative to each other. Porphyrin H/CH 2 OH assembled wherein (1) each zinc is hexacoordinate by ligation of hydroxymethyl moieties, (2) each hydroxymethyl –OH is hydrogen-bonded with an acetonitrile solvent molecule in the lattice, and (3) the planes of the four nearest neighbor porphyrins are essentially perpendicular to a given porphyrin. Study of the solid-state packing patterns of sparsely substituted porphyrins enables insights into how the structural design of tetrapyrroles can guide their aggregate self-assembly.

Tran, Vy-Phuong [North Carolina State University, ↗
DOE OSTI2022

Electron-Beam Induced Emergence of Mesoscopic Ordering in Layered MnPS 3

Ordered mesoscale structures in 2D materials induced by small misorientations have allowed for a wide variety of electronic, ferroelectric, and quantum phenomena to be explored. Until now, the only mechanism to induce this periodic ordering was via mechanical rotations between the layers, with the periodicity of the resulting moiré pattern being directly related to twist angle. Here we report a fundamentally distinct mechanism for emergence of mesoscopic periodic patterns in multilayer sulfur-containing metal phosphorus trichalcogenide, MnPS3, induced by the electron beam. The formation under the beam of periodic hexagonal patterns with several characteristic length scales, nucleation and transitions between the phases, and local dynamics are demonstrated. The associated mechanisms are attributed to the relative contraction of the layers caused by beam-induced sulfur vacancy formation with subsequent ordering and lattice parameter change. As a result, the plasmonic response of the system is locally altered, suggesting an element of control over plasmon resonances by electron beam patterning. To conclude, we pose that harnessing this phenomenon provides both insight into fundamental physics of quantum materials and enables device applications by enabling controlled periodic potentials on the atomic scale.

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

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Continuous wave room temperature operation of the 2 $μ$m GaSb-based photonic crystal surface emitting diode lasers

Continuous wave room temperature operation of 2 μm GaSb-based photonic-crystal surface-emitting diode lasers has been realized. The deep etched square mesa devices showed threshold current densities of 500 A/cm 2 at 20 °C. The epi-side down mounted lasers generated above 10 mW of output power in the continuous wave regime and tens of milliwatts in pulses from the 200 × 200 μm 2 aperture. Here, the breakthrough in the device performance parameters was achieved thanks to a highly homogeneous air-pocket retaining epitaxial regrowth process optimized for a specifically designed antimonide diode laser heterostructure. The nanofabrication method utilizing low temperature atomic hydrogen surface cleaning yielded low disorder square lattice of droplet-shaped voids covered by uniform p-cladding layer. The laser emission spectrum as well as near/far field patterns demonstrated peculiar features presumably linked to deformation of the void shape during regrowth and formation of the array of filaments.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Coexistence of vitreous and crystalline phases of H 2 O at ambient temperature

Formation of vitreous ice during rapid compression of water at room temperature is important for biology and the study of biological systems. Here, we show that Raman spectra of rapidly compressed water at greater than 1 GPa at room temperature exhibits the signature of high-density amorphous ice, whereas the X-ray diffraction (XRD) pattern is dominated by crystalline ice VI. To resolve this apparent contradiction, we used molecular dynamics simulations to calculate full vibrational spectra and diffraction patterns of mixtures of vitreous ice and ice VI, including embedded interfaces between the two phases. We show quantitatively that Raman spectra, which probe the local polarizability with respect to atomic displacements, are dominated by the vitreous phase, whereas a small amount of the crystalline component is readily apparent by XRD. The results of our combined experimental and theoretical studies have implications for detecting vitreous phases of water, survival of biological systems under extreme conditions, and biological imaging. The results provide additional insight into the stable and metastable phases of H 2 O as a function of pressure and temperature, as well as of other materials undergoing pressure-induced amorphization and other metastable transitions.

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

Approaching Angstrom-Scale Resolution in Lithography Using Low-Molecular-Mass Resists (<500 Da)

Resists that enable high-throughput and high-resolution patterning are essential in driving the semiconductor technology forward. The ultimate patterning performance of a resist in lithography is limited because of the trade-off between resolution, line-width roughness, and sensitivity; improving one or two of these parameters typically leads to a loss in the third. As the patterned feature sizes approach angstrom scale, the trade-off between these three metrics becomes increasingly hard to resolve and calls for a fundamental rethinking of the resist chemistry. Low-molecular-mass monodispersed metal-containing resists of high atom economy can provide not only very high resolution but also very low line-width roughness without sacrificing sensitivity. Here we describe a modular metal-containing resist platform (molecular mass <500 Da) where a molecular resist consists of just two components: a metal and a radical initiator bonded to it. This simple system not only is amenable to high-resolution electron beam lithography (EBL) and extreme ultraviolet lithography (EUVL) but also unites them mechanistically, giving a consolidated perspective of molecular and chemical processes happening during exposure. Irradiation of the resist leads to the production of secondary electrons that generate radicals in the initiator bonded to metal. This brings about an intramolecular rearrangement and causes solubility switch in the exposed resist. We demonstrate record 1.9–2.0 nm isolated patterns and 7 nm half-pitch dense line-space features over a large area using EBL. With EUVL, 12 nm half-pitch line-space features are shown at a dose of 68 mJ/cm 2 . In both of these patterning techniques, the line-width roughness was found to be ≤2 nm, a record low value for any resist platform, also leading to a low-performance trade-off metric, Z factor, of 0.6 × 10 –8 mJ·nm 3 . With the ultimate resolution limited by instrumental factors, potential patterning at the level of a unit cell can be envisaged, making low-molecular-mass resists best poised for angstrom-scale lithography.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Effects of warming on bacterial growth rates in a peat soil under ambient and elevated CO 2

Boreal peatlands are important global carbon reservoirs that are particularly vulnerable to predicted climate changes such as increasing CO 2 and temperature. Since microbial activities regulate the balance of carbon sequestered into soil organic matter or remineralized to CO 2 , characterizing their response to these environmental factors is critical to predicting how peatland ecosystems will affect climate-carbon cycle feedbacks. Here we examined in-situ taxon-specific variation in microbial growth under long-term elevated CO 2 and across a gradient of warming treatments in a northern Minnesota peat bog using quantitative stable isotope probing with 18 O-water. Across temperatures, bacterial taxa were grouped according to the excess atom fraction 18 O (EAF) of their genomes, a proxy for DNA replication and hence, growth. Taxon-specific growth across CO 2 and temperature treatments clustered into relatively few response patterns. While a large portion of taxa showed little to no growth under ambient CO 2 , many of the same taxa grew rapidly under elevated CO 2 . We found support for phylogenetic conservation of response patterns among Acidobacteria and Proteobacteria, the two most abundant phyla in our data. Our results suggest certain taxa may be primed for new climate conditions and have a greater influence on carbon cycling with implications for future climate mitigation strategies.

16S amplicon sequencing, Carbon Dioxide (CO2), pea↗
DOE OSTI2025

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗
DOE OSTI2024

Observation of a single protein by ultrafast X-ray diffraction

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗