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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Pressure‐Suppressed Carrier Trapping Leads to Enhanced Emission in Two‐Dimensional Perovskite (HA) 2 (GA)Pb 2 I 7

Abstract A remarkable PL enhancement by 12 fold is achieved using pressure to modulate the structure of a recently developed 2D perovskite (HA) 2 (GA)Pb 2 I 7 (HA= n ‐hexylammonium, GA=guanidinium). This structure features a previously unattainable, extremely large cage. In situ structural, spectroscopic, and theoretical analyses reveal that lattice compression under a mild pressure within 1.6 GPa considerably suppresses the carrier trapping, leading to significantly enhanced emission. Further pressurization induces a non‐luminescent amorphous yellow phase, which is retained and exhibits a continuously increasing band gap during decompression. When the pressure is released to 1.5 GPa, emission can be triggered by above‐band gap laser irradiation, accompanied by a color change from yellow to orange. The obtained orange phase could be retained at ambient conditions and exhibits two‐fold higher PL emission compared with the pristine (HA) 2 (GA)Pb 2 I 7 .

Guo, Songhao↗
DOE OSTI2016

Structural and Rotational Dynamics of Carbon Dioxide in 1-Alkyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquids: The Effect of Chain Length

Ionic liquids (ILs) have been proposed as possible carbon dioxide (CO 2 ) carbon capture media, and so it is useful to understand the dynamics of both the dissolved gas and its IL environment as well as how altering the IL affects these dynamics. With increasing alkyl chain length, it is well established that ILs obtain a mesoscopic structural feature assigned to polarapolar segregation, and the change in structure with chain length affects dynamics. In this work, the dynamics of CO 2 in a series of 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids (ILs), where alkyl is ethyl, butyl, hexyl, or decyl, were investigated using ultrafast infrared spectroscopy by measuring the reorientation and spectral diffusion of carbon dioxide in the ILs. It was found that reorientation of the carbon dioxide occurs on 3 timescales, which correspond to 2 different timescales of restricted wobbling-in-a-cone motions and a long time complete diffusive reorientation. The complete reorientation slows with increasing chain length but less than the increases in viscosity of the bulk liquids. Spectral diffusion, measured with 2D IR spectroscopy, is caused by a combination of the liquids’ structural fluctuations and reorientation of the CO 2 . The data were analyzed using recent theory that takes into account both contributions to spectral diffusion and extracts the structural spectral diffusion. Different components of the structural fluctuations have distinct dependences on the alkyl chain length. All of the dynamics are fast compared to the complete orientational randomization of the bulk ILs, as measured with optical heterodyne detected optical Kerr effect measurements. The results indicate a hierarchy of constraint releases in the liquids that give rise to increasingly slower dynamics.

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

Observation of a mixed close-packed structure in superionic water

The study of superionic (SI) water has been a highly active research area since its theoretical prediction. Despite significant experimental and computational efforts, its melting curve and the stability of different oxygen lattices remain debated, impacting our understanding of SI ice’s peculiar transport properties. Experimental results at lower pressures show disagreement, whereas data at higher pressures are scarce due to the extreme challenges of such experiments. In this work, we present ultrafast X-ray diffraction results of water compressed by multiple shocks to pressures up to ~ 180 GPa. At pressures exceeding 150 GPa and temperatures around 2500 K, our diffraction patterns challenge the pure FCC-SI phase model, providing experimental evidence of the mixed close-packed superionic phase predicted by advanced ab initio calculations. At lower pressures, we observe simultaneous signatures of BCC and FCC structures within a pressure-temperature range consistent with some static-compression experiments, helping to resolve contradictory results in literature. These insights offer new constraints on the stability domains of SI phases and reveal detailed structural features, such as stacking faults. Our results advance the structural understanding of high-pressure SI ice to a level approaching that of ice I polymorphs, with potential implications for water-rich interiors of giant planets.

Andriambariarijaona, Leon [Centre National de la R↗
DOE OSTI2016

Measurement and modeling of short and medium range order in amorphous Ta 2 O 5 thin films

Here, amorphous films and coatings are rapidly growing in importance. Yet, there is a dearth of high-quality structural data on sub-micron films. Not understanding how these materials assemble at atomic scale limits fundamental insights needed to improve their performance. Here, we use grazing-incidence x-ray total scattering measurements to examine the atomic structure of the top 50–100 nm of Ta 2 O 5 films; mirror coatings that show high promise to significantly improve the sensitivity of the next generation of gravitational-wave detectors. Our measurements show noticeable changes well into medium range, not only between crystalline and amorphous, but also between as-deposited, annealed and doped amorphous films. It is a further challenge to quickly translate the structural information into insights into mechanisms of packing and disorder. Here, we illustrate a modeling approach that allows translation of observed structural features to a physically intuitive packing of a primary structural unit based on a kinked Ta-O-Ta backbone. Our modeling illustrates how Ta-O-Ta units link to form longer 1D chains and even 2D ribbons, and how doping and annealing influences formation of 2D order. We also find that all the amorphousTa 2 O 5 films studied in here are not just poorly crystalline but appear to lack true 3D order.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A global view of structure–function relationships in the tautomerase superfamily

The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure–function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis-3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase–like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies.

Biochemistry & Molecular Biology↗
DOE OSTI2019

Multi-scale structural analysis of proteins by deep semantic segmentation

Abstract Motivation Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation—a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structure quality assessment. Results We train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model achieves a high per-residue accuracy of 90.8% on the test set (95.0% average per-class accuracy; 87.8% average per-structure accuracy). We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design. Availability and implementation The trained classifier network, parser network, and entropy calculation scripts are available for download at https://git.io/fp6bd, with detailed usage instructions provided at the download page. A step-by-step tutorial for setup is provided at https://goo.gl/e8GB2S. All Rosetta commands, RosettaRemodel blueprints, and predictions for all datasets used in the study are available in the Supplementary Information. Supplementary information Supplementary data are available at Bioinformatics online.

Eguchi, Raphael R.↗
DOE OSTI2018

Deep clustering of protein folding simulations

Background: We investigate the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensional representations that can be used to extract quantitative insights into the atomistic mechanisms that underlie complex biological processes. Results: We use a convolutional variational autoencoder (CVAE) to learn low dimensional, biophysically relevant latent features from long time-scale protein folding simulations in an unsupervised manner. We demonstrate our approach on three model protein folding systems, namely Fs-peptide (14 μs aggregate sampling), villin head piece (single trajectory of 125 μs) and β- β- α (BBA) protein (223 + 102 μs sampling across two independent trajectories). In these systems, we show that the CVAE latent features learned correspond to distinct conformational substates along the protein folding pathways. The CVAE model predicts, on average, nearly 89% of all contacts within the folding trajectories correctly, while being able to extract folded, unfolded and potentially misfolded states in an unsupervised manner. Further, the CVAE model can be used to learn latent features of protein folding that can be applied to other independent trajectories, making it particularly attractive for identifying intrinsic features that correspond to conformational substates that share similar structural features. Conclusions: Together, we demonstrate that the CVAE model can quantitatively describe complex biophysical processes such as protein folding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Robocrystallographer: automated crystal structure text descriptions and analysis

Our ability to describe crystal structure features is of crucial importance when attempting to understand structure–property relationships in the solid state. Here, the authors introduce robocrystallographer, an open-source toolkit for analyzing crystal structures. This package combines new and existing open-source analysis tools to provide structural information, including the local coordination and polyhedral type, polyhedral connectivity, octahedral tilt angles, component-dimensionality, and molecule-within-crystal and fuzzy prototype identification. Using this information, robocrystallographer can generate text-based descriptions of crystal structures that resemble descriptions written by human crystallographers. The authors use robocrystallographer to investigate the dimensionalities of all compounds in the Materials Project database and highlight its potential in machine learning studies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2019

Shining a light on amorphous U 2 O 7 : A computational approach to understanding amorphous uranium materials

Mixed-phase and low-symmetry systems are widely observed among uranium oxide materials. Amorphous-U 2 O 7 forms during the calcination of studtite, a uranyl peroxide mineral. Using a genetic algorithm search for stable crystalline phases, we have identified a potentially stable phase of U2O7 that shares structural features with experimentally observed amorphous U2O7 samples. The crystalline structure is expected to undergo a solid–solid phase change around 12 GPa.

Shields, Ashley E.↗
DOE OSTI2013

Structural investigation of the new Ca{sub 3}Ln{sub 2}Ge{sub 3}O{sub 12} (Ln=Pr, Nd, Sm, Gd and Dy) compounds and luminescence spectroscopy of Ca{sub 3}Gd{sub 2}Ge{sub 3}O{sub 12} doped with the Eu{sup 3+} ion

The crystal structures of new rare earth-based germanate compounds (Ca{sub 3}Pr{sub 2}Ge{sub 3}O{sub 12}, Ca{sub 3}Nd{sub 2}Ge{sub 3}O{sub 12}, Ca{sub 3}Sm{sub 2}Ge{sub 3}O{sub 12}, Ca{sub 3}Gd{sub 2}Ge{sub 3}O{sub 12} and Ca{sub 3}Dy{sub 2}Ge{sub 3}O{sub 12}) have been determined by Rietveld refinement calculations on the collected synchrotron X-ray diffraction powder patterns. A different distribution of the rare earth ions in the three available crystal sites was observed, as the main structural feature. The reasons of the instability of the silico-carnotite structure for lanthanide ions out of the range Pr–Dy have been proposed. Finally, the luminescence spectroscopy of the Eu{sup 3+} dopant ion in Ca{sub 3}Gd{sub 2}Ge{sub 3}O{sub 12} was presented and analyzed taking into account the observed structural characteristics. The Eu{sup 3+} luminescence spectroscopy was also compared with the one of Eu{sup 3+} doped Ca{sub 3}Gd{sub 2}Si{sub 3}O{sub 12} and Ca{sub 3}Lu{sub 2}Si{sub 3}O{sub 12} isostructural materials. - Graphical abstract: The structural study on Ca{sub 3}Ln{sub 2}Ge{sub 3}O{sub 12} exploiting synchrotron X-ray diffraction, allows us to determine the detailed geometry of the coordination polyhedra of the metals and their distribution in the crystal sites. These features are, in the case of Ca{sub 3}Gd{sub 2}Ge{sub 3}O{sub 12} host, closely related to the luminescence spectroscopy of the Eu{sup 3+} dopant ion. Display Omitted - Highlights: • The structure of the Ca{sub 3}Ln{sub 2}Ge{sub 3}O{sub 12} (Ln=Pr, Nd, Sm, Gd and Dy) was determined. • Different distribution of Ln{sup 3+} ions on the three available crystal sites was observed. • A detailed structural study focused on the metal coordination polyhedra was performed. • The instability of the silico-carnotite structure out of the range Pr–Dy was discussed. • The luminescence of the dopant Eu{sup 3+} ion in Ca{sub 3}Gd{sub 2}Ge{sub 3}O{sub 12} was presented and analyzed.

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

Local Atomic Structure in Photo-isomerized Ruthenium Sulfur Dioxide Complexes Revealed by Pair Distribution Function Analysis

SO 2 linkage photoisomerization in crystalline ruthenium-based complexes has demonstrated nanophotonic phenomena such as optical switching and nano-optomechanical transduction. Molecular insights into these materials have been explored largely via the characterization of their photoinduced crystal structures via in situ single-crystal X-ray diffraction, known as photocrystallography. Photoinduced molecular disorder is present, which photocrystallography can model to the extent that it is confined within the periodic boundary of a unit cell. However, non-periodic molecular disorder is suspected to exist as well. In situ total scattering experiments were therefore carried out on finely powdered crystals of four ruthenium-sulfur dioxide complexes. Data were modeled using light-minus-dark' difference pair distribution function analysis, which afforded photoinduced structural changes exclusively. This revealed structural features that were first compared against models of photoinduced crystal structures known a priori from photocrystallography. Furthermore, statistical inference was then employed, which evidenced generally good agreement between the total scattering data and the photocrystallographic models, while revealing real differences that are indicative of a structure with only a short-range order. Overall, our findings demonstrate that in situ light-induced total scattering experiments on finely powdered crystals are able to reveal the photoinduced structure. Overall, the evidence suggests that such structure could include a short-range order as well as photocrystallographic content. Our demonstration experiment offers a pathway to develop studies that capture the short-range order in linkage photoisomers, while we have outlined the procedure for testing the validity of associated structural models.

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

Structural architecture of prothrombin in solution revealed by single molecule spectroscopy

The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr 93 in kringle-1 onto Trp 547 in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. As a result, the open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.

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

Hydration and reaction mechanisms on sodium silicate glass surfaces from molecular dynamics simulations with reactive force fields

Recent development of reactive force fields have enabled molecular dynamics simulations of interactions between silicate glasses and water at the atomistic scale. While multicomponent silicate glasses encompass a wide variety of compositions and properties, one common structural feature in these glasses is the combination of the network structure that is made up of silica tetrahedra linked through corner sharing interspersed with network modifiers like alkali and alkaline-earth ions that break up the Si–O–Si linkages by forming nonbridging oxygen. In reactions with water, ion exchange between alkali ions in the glass and proton or hydronium in the solution, as well as hydrolysis reaction of the Si–O–Si linkages and subsequent silanol formation, is observed and well documented. Furthermore, we have used a set of recently developed reactive force field to investigate the reactions between water and the surfaces of silica and sodium silicate glasses of different compositions for reactions up to 8 nanoseconds. Our results indicate sodium leaching into water and diffusion of water molecules up to 25 Å into the glass surface. We examined the structural and compositional changes inside the glass and around the diffused ions and use these to explain the rates of silanol formation at the surface. We also observed proton transport in the glass which has an indirect influence on the silanol formation rates. While the surface of the glass was rough to start with, it undergoes further modification into a hydrated gel-like structure in the glass for up to 5 Å in the higher alkali containing glasses. It was found that the leached sodium ions remain close to the interface and that fragments of silicate network from the surface is capable of dislodging from the bulk glass and enter the aqueous solution. These simulations thus provide insights into the formation and structure of an alteration layers commonly observed in multicomponent silicate glasses corroded in aqueous solutions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties

Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180°C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be β-ether > phenylcoumaran (β−5′) > resinol (β−β′) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150°C temperature reaction, CELF lignin had higher molecular weight and retained more β-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

The Dimerization of H 2 NO

H 2 NO is the prototype of aminoxyls, kinetically persistent free radicals. The potential dimerization and reaction modes of H 2 NO are examined. The dimer potential energy surface features a barely metastable O–O bound species and several locally bound dimeric structures. One of these, a rectangular or rhomboid O–N–O-N ring, is a characteristic structural feature of more stable aminoxyls in the solid state. Its electronic structure is related to other four-center six-electron systems. A general picture of the weak dimer binding is constructed for these and other H 2 NO dimers from a balance of four-electron repulsions between NO π electrons, and two-electron attractive interaction between the singly occupied π* orbitals of the diradical. The most stable diradical structure is a surprisingly strongly hydrogen bonded dimer diradical. Lastly, the barriers separating the other isomers from this global minimum are calculated to be small.

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

Controlling the intermediate structure of an ionic liquid for f-block element separations

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregate structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.

36 MATERIALS SCIENCE↗