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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Effect of Initial Structure on Performance of High-Entropy Oxide Anodes for Li-Ion Batteries

Two different high-entropy oxide materials were synthesized and studied as Li-ion battery anodes. The two materials have the same active metal constituents but different inactive elements which result in different initial crystalline structures: rock salt for (MgFeCoNiZn)O and spinel for (TiFeCoNiZn)3O4. Local structural studies of the metal elements in these two materials over extended electrochemical cycling reveal that the redox processes responsible for the electrode capacity are independent of the initial crystallographic structure and that the capacity is solely dependent on the initial random distribution of the metal atoms and the amount of active metals in the starting material.

25 ENERGY STORAGE↗
NASA NTRS2022

Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution

Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfde minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infnite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are fnite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a fnite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere

Kenneth N. McGuinness↗
DOE OSTI2022

Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina

Abstract Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the ‘docking power’. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein‐ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.

Agarwal, Rupesh↗
NASA NTRSDate not supplied

Twinned magnetite in granitic samples from the Siljan impact structure, Sweden

Impact cratering is a ubiquitous process throughout the solar system and has played a key role for the geologic evolution of Earth and other planets [1]. Magnetic anomalies are common characteristics of impact craters [2], so understanding how magnetite (Fe23+Fe2+O42-), an important magnetic carrier in both terrestrial and extraterrestrial rocks, is affected by shock waves, especially structurally and magnetically, is crucial. Magnetic minerals have been studied to gain insight into the geologic evolution of Mars, with specific focus including understanding the Martian crustal structure and the oxidization state of Martian rocks (e.g., [3,4,5]). Shock waves permanently alter the intrinsic magnetic properties of rocks (e.g., [6]), as do twinning in natural environments with less extreme P/T conditions [7]. In fact, pressure conditions induced by impacts have been suggested to explain demagnetization signatures observed around Martian impact basins [8]. It is still poorly understood what effects shock has on the crystallographic structure of magnetite and thus it’s intrinsic magnetic properties, and , how that affects the bulk magnetic properties of rocks (e.g., [9]). Limited experimental studies have investigated the effects of shock compression on magnetite, especially with the aim of describing crystallographic deformation (e.g., [9] and references therein). In this work we report preliminary results of an investigation of microstructures in magnetite, an “unconventional” mineral in shock studies, in granitic samples from the ca. 380 Ma ~52 km-in-diameter Siljan impact structure, located in south-central Sweden.

shock metamorphism↗
DOE OSTI2021

Characterization and structural analysis of a thermophilic GH11 xylanase from compost metatranscriptome

Xylanase is efficient for xylan degradation and widely applied in industries. We found a GH11 family xylanase (Xyn11A) with high thermostability and catalytic activity from compost metatranscriptome. This xylanase has the optimal reaction temperature at 80 °C with the activity of 2907.3 U/mg. The X-ray crystallographic structure shows a typical “right hand” architecture, which is the characteristics of the GH11 family enzymes. Comparing it with the mesophilic XYN II, a well-studied GH11 xylanase from Trichoderma reesei, Xyn11A is more compact with more H-bonds. Our mutagenic results show that the electrostatic interactions in the thumb and palm region of Xyn11A could result in its high thermostability and activity. Introducing a disulfide bond at the N-terminus further increased its optimal reaction temperature to 90 °C with augmented activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study

The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

Modeling of Ternary Element Site Substitution in NiAl

It is well recognized that ternary alloying additions can have a dramatic impact on the behavior of ordered intermetallic alloys such as nickel aluminides. Properties as diverse as yield strength, fracture strength, fracture mode, cyclic oxidation resistance, creep strength, and thermal and electrical diffusivity can change by orders of magnitude when a few percent or less of a ternary element is added. Yet our understanding of the resulting point defect structures and the simple site preferences of ternary alloying additions is poor because these are extremely difficult characteristics to determine. This disconnection between the understanding of the structure and properties in ordered alloys is at least in part responsible for the limited development and commercialization of these materials. Theoretical methods have provided useful but limited insight in this area, since most techniques suffer from constraints in the type of elements and the crystallographic structures that can be modeled. In an effort to overcome these limitations, the Bozzolo-Ferrante-Smith (BFS) method for alloys was designed. After a brief description of this approximate quantum mechanical approach, we use BFS to investigate the energetics of Si, Ti, V, Cr, Fe, Co, Cu, Zr, Nb, Mo, Ru, Hf, Ta and W additions to B2-ordered, stoichiometric NiAl. In addition to determining the site preference for these alloying additions over a range of compositions, we include results for the concentration dependence of the lattice parameter. In this introductory paper, we performed our analyses in the absence of constitutional and thermal vacancies for alloys of the form Ni50(Al,X)50. Where data exist, a comparison between experimental, theoretical, and BFS results is also included.

Bozzolo, Guillermo↗
NASA NTRS1973

Low-temperature epitaxy of Ge films by sputter deposition.

It is shown experimentally that isoepitaxial growth of Ge films on Ge substrates can be obtained by dc sputtering at substrate temperatures as low as 100 C. The crystallographic structure and orientation of the films are strongly influenced by such deposition parameters as substrate temperature, growth rate, surface contamination, and sputtering-gas purity. The amorphous-polycrystalline transition occurs between 110 and 115 C, while the polycrystalline-single crystalline transition occurs at roughly 140 C. The crystallographic order increases with increasing substrate temperature.

Khan, I. H.↗
NASA NTRS1995

Oxide perovskite crystals for HTSC film substrates microwave applications

The research focused upon generating new substrate materials for the deposition of superconducting yttrium barium cuprate (YBCO) has yielded several new hosts in complex perovskites, modified perovskites, and other structure families. New substrate candidates such as Sr(Al(1/2)Ta(1/2))O3 and Sr(Al(1/2)Nb(1/2))O3, Ba(Mg(1/3)Ta(2/3))O3 in complex oxide perovskite structure family and their solid solutions with ternary perovskite LaAlO3 and NdGaO3 are reported. Conventional ceramic processing techniques were used to fabricate dense ceramic samples. A laser heated molten zone growth system was utilized for the test-growth of these candidate materials in single crystal fiber form to determine crystallographic structure, melting point, thermal, and dielectric properties as well as to make positive identification of twin free systems. Some of those candidate materials present an excellent combination of properties suitable for microwave HTSC substrate applications.

Bhalla, A. S.↗
DOE OSTI2021

Anomalous Behavior in the Atomic Structure of Nb$^{3}$Sn under High Pressure

In the present study, the local atomic structure of a Nb3Sn superconductor sample has been probed by X-ray absorption fine structure (XAFS) as a function of hydrostatic pressure (from ambient up to 26 GPa) using a diamond anvil cell set-up. The analysis of the Nb-K edge extended X-ray absorption fine structure (EXAFS) data was carried out combining standard multi shell structural refinement and reverse Monte Carlo method to provide detailed in situ characterization of the pressure-induced evolution of the Nb local structure in Nb3Sn. The results highlight a complex evolution of Nb chains at the local atomic scale, with a peculiar correlated displacement of Nb–Nb and Nb–Nb–Nb configurations. Such a local effect appears related to anomalies evidenced by X-ray diffraction in other superconductors belonging to the same A15 crystallographic structure.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural and biochemical characterisation of Co 2+ -binding sites on serum albumins and their interplay with fatty acids

Serum albumin–Co 2+ interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and are central to the albumin cobalt binding (ACB) assay for diagnosis of myocardial ischemia. To further understand these processes, a deeper understanding of albumin–Co 2+ interactions is required. Here, we present the first crystallographic structures of human serum albumin (HSA; three structures) and equine serum albumin (ESA; one structure) in complex with Co 2+ . Amongst a total of sixteen sites bearing a cobalt ion across the structures, two locations were prominent, and they relate to metal-binding sites A and B. Site-directed mutagenesis and isothermal titration calorimetry (ITC) were employed to characterise sites on HSA. The results indicate that His9 and His67 contribute to the primary (putatively corresponding to site B) and secondary Co 2+ -binding sites (site A), respectively. The presence of additional multiple weak-affinity Co 2+ binding sites on HSA was also supported by ITC studies. Furthermore, addition of 5 molar equivalents of the non-esterified fatty acid palmitate (C16:0) reduced the Co 2+ -binding affinity at both sites A and B. The presence of bound myristate (C14:0) in the HSA crystal structures provided insight into the fatty acid-mediated structural changes that diminish the affinity of the protein toward Co 2+ . Together, these data provide further support for the idea that ischemia-modified albumin corresponds to albumin with excessive fatty-acid loading. Collectively, our findings provide a comprehensive understanding of the molecular underpinnings governing Co 2+ binding to serum albumin.

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

Cyclic versus Linear Alkylammonium Cations: Preventing Phase Transitions at Operational Temperatures in 2D Perovskites

Two-dimensional lead halide perovskites offer numerous attractive features for optoelectronics owing to their soft, deformable lattices and high degree of chemical tunability. While alteration of the metal and halide ions gives rise to significant modification of the bandgap energy, the organic spacer cations offer in-roads to tuning phase behavior and more subtle functionalities in ways that remain to be understood. Here, we study six variations of 2D perovskites changing only the organic spacer cations and demonstrate that these components intrinsically impact material response in important ways such as altering crystallographic structure, temperature-induced phase transitions, and photoluminescence emission. Two-dimensional perovskites containing commonly utilized aliphatic linear spacers, such as butylammonium, undergo phase transitions near room temperature. These transitions and temperature changes induce spacer-dependent variations in the emission spectra. Conversely, 2D perovskites comprising cyclic aliphatic spacers, such as cyclobutylammonium, are found to lack first-order phase transitions. These cyclic molecules are more sterically hindered within the crystal lattice, leading to temperature-induced contraction or expansion along certain crystallographic planes but no other significant thermal effects; additionally, they undergo changes in their emission spectra that cannot be explained by simple thermal expansion. Finally, given the similarities in the dielectric and chemical makeup of this set of six alkylammonium molecules, these results are unexpected and suggest a large structural and thermal phase space via spacer manipulation that could lead to improved 2D perovskite functionalization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

TPSAS-NF1676L-13664-DND

The safety of aerospace vehicles is largely dependent on the ability of modern non-destructive evaluation (NDE) tools to accurately detect structural damage before a critical flaw size is reached. However, existing NDE technologies are inherently limited by the physical response of the materials being inspected making the detection of small cracks or pre-crack damage difficult. One innovative solution to this problem is to create a multifunctional metallic material that can be used in structural applications and contains second phase sensory particles that significantly enhance the ability of conventional NDE techniques to detect incipient damage during use and at regularly scheduled inspections. Ferromagnetic shape-memory alloys (FSMAs) are an ideal material for use as this second phase material as they undergo a uniform and repeatable change in both magnetic properties and crystallographic structure when strained. These changes are more readily detected than small cracks, thereby, allowing for enhanced detection of damage by conventional NDE techniques. In this study, a multifunctional metallic material was produced by embedding the sensory material particles within an aluminum alloy to form a sensory alloy. The NDE response of the FSMA and the sensory alloy during tension/compression and fatigue loading have been investigated. These results suggest that sensory alloys can be utilized for improved on-board structural health monitoring and to improve the accuracy and reduce time for ground-based inspection.

T. A. Wallace↗
NASA NTRS1991

Molecular dynamics investigation of radiation damage in semiconductors

Results of a molecular dynamics investigation of the effects of radiation damage on the crystallographic structure of semiconductors are reported. Particular cosiderastion is given to the formation of point defects and small defect complexes in silicon at the end of a radiation-damage cascade. The calculations described make use of the equivalent crystal theory of Smith and Banerjea (1988). Results on the existence of an atomic displacement threshold, the defect formation energy, and some crystallographic information on the defects observed are reported.

Good, Brian S.↗
NASA NTRS2010

Development of Metallic Sensory Alloys

Existing nondestructive evaluation (NDE) technologies are inherently limited by the physical response of the structural material being inspected and are therefore not generally effective at the identification of small discontinuities, making the detection of incipient damage extremely difficult. One innovative solution to this problem is to enhance or complement the NDE signature of structural materials to dramatically improve the ability of existing NDE tools to detect damage. To address this need, a multifunctional metallic material has been developed that can be used in structural applications. The material is processed to contain second phase sensory particles that significantly improve the NDE response, enhancing the ability of conventional NDE techniques to detect incipient damage both during and after flight. Ferromagnetic shape-memory alloys (FSMAs) are an ideal material for these sensory particles as they undergo a uniform and repeatable change in both magnetic properties and crystallographic structure (martensitic transformation) when subjected to strain and/or temperature changes which can be detected using conventional NDE techniques. In this study, the use of a ferromagnetic shape memory alloy (FSMA) as the sensory particles was investigated.

Wallace Terryl A.↗
NASA NTRS1989

X-ray diffraction studies of model compounds of thermoplastic polyimides

Several model compounds which represent aspects of the chemical structure of the Langley Research Center thermoplastic (LARC-TPI) have been synthesized for comparison studies using wide angle X-ray scattering (WAXS) as the discriminatory tool. The model compounds included N-phenylphthalimide, 3,3',4,4'-benzophenonetetracarboxylic diphthalimide, and N,N'-diphenyl-3,3',4,4'-benzophenonetetracarboxylic diphthalimide. X-ray diffraction studies of appropriate model compounds can yield information to aid in the understanding of polymeric crystallographic structure. Crystallinity and physical property changes can thus be induced into materials having complicated structures by chemical and thermal processes.

Wakelyn, N. T.↗
DOE OSTI2022

Enzyme kinetics by GH7 cellobiohydrolases on chromogenic substrates is dictated by non‐productive binding: insights from crystal structures and MD simulation

Cellobiohydrolases (CBHs) in the glycoside hydrolase family 7 (GH7) ( EC3.2.1.176 ) are the major cellulose degrading enzymes both in industrial settings and in the context of carbon cycling in nature. Small carbohydrate conjugates such as p‐ nitrophenyl‐β‐ d ‐cellobioside (pNPC), p‐ nitrophenyl‐β‐ d ‐lactoside (pNPL) and methylumbelliferyl‐β‐ d ‐cellobioside have commonly been used in colorimetric and fluorometric assays for analysing activity of these enzymes. Despite the similar nature of these compounds the kinetics of their enzymatic hydrolysis vary greatly between the different compounds as well as among different enzymes within the GH7 family. Through enzyme kinetics, crystallographic structure determination, molecular dynamics simulations, and fluorometric binding studies using the closely related compound o‐nitrophenyl‐β‐ d ‐cellobioside (oNPC), in this work we examine the different hydrolysis characteristics of these compounds on two model enzymes of this class, TrCel7A from Trichoderma reesei and PcCel7D from Phanerochaete chrysosporium . Protein crystal structures of the E212Q mutant of TrCel7A with pNPC and pNPL, and the wildtype TrCel7A with oNPC, reveal that non‐productive binding at the product site is the dominating binding mode for these compounds. Enzyme kinetics results suggest the strength of non‐productive binding is a key determinant for the activity characteristics on these substrates, with PcCel7D consistently showing higher turnover rates ( k cat ) than TrCel7A, but higher Michaelis–Menten ( K M ) constants as well. Furthermore, oNPC turned out to be useful as an active‐site probe for fluorometric determination of the dissociation constant for cellobiose on TrCel7A but could not be utilized for the same purpose on PcCel7D, likely due to strong binding to an unknown site outside the active site.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗