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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

A Ni(II) Bis(diphosphine)-Hydride Complex Containing Proton Relays - Structural Characterization and Electrocatalytic Studies

The syntheses of the new 1,5-diphenyl-3,7-di(isopropyl)-1,5-diaza-3,7-diphosphacyclooctane ligand, PiPr2NPh2, is reported. The two equivalents of the ligand react with [Ni(CH3CN)6](BF4)2 to form the bis-diphosphine Ni(II)-complex [Ni(PiPr2NPh2)2](BF4)2, which acts as a proton reduction electrocatalyst. In addition to [Ni(PiPr2NPh2)2]2+, we report the syntheses and structural characterization of the Ni(0)-complex Ni(PiPr2NPh2)2, and the Ni(II)-hydride complex [HNi(PiPr2NPh2)2]BF4. The [HNi(PiPr2NPh2)2]BF4 complex represents the first Ni(II)-hydride in the [Ni(PR2NR'2)2]2+ family of compounds to be isolated and structurally characterized. In addition to the experimental data, the mechanism of electrocatalysis facilitated by [Ni(PiPr2NPh2)2]2+ is analyzed using linear free energy relationships recently established for the [Ni(PR2NR'2)2]2+ family. We thank Dr. Aaron Appel, Dr. Simone Raugei and Dr. Eric Wiedner for helpful discussions. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Mass spectrometry was provided at W. R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s office of Biological and Environmental Research located at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

diphosphine↗
DOE OSTI2016

The structure of a doripenem‐bound OXA‐51 class D β‐lactamase variant with enhanced carbapenemase activity

Abstract OXA‐51 is a class D β‐lactamase that is thought to be the native carbapenemase of Acinetobacter baumannii . Many variants of OXA‐51 containing active site substitutions have been identified from A. baumannii isolates, and some of these substitutions increase hydrolytic activity toward carbapenem antibiotics. We have determined the high‐resolution structures of apo OXA‐51 and OXA‐51 with one such substitution (I129L) with the carbapenem doripenem trapped in the active site as an acyl‐intermediate. The structure shows that acyl‐doripenem adopts an orientation very similar to carbapenem ligands observed in the active site of OXA‐24/40 (doripenem) and OXA‐23 (meropenem). In the OXA‐51 variant/doripenem complex, the indole ring of W222 is oriented away from the doripenem binding site, thereby eliminating a clash that is predicted to occur in wildtype OXA‐51. Similarly, in the OXA‐51 variant complex, L129 adopts a different rotamer compared to I129 in wildtype OXA‐51. This alternative position moves its side chain away from the hydroxyethyl moiety of doripenem and relieves another potential clash between the enzyme and carbapenem substrates. Molecular dynamics simulations of OXA‐51 and OXA‐51 I129L demonstrate that compared to isoleucine, a leucine at this position greatly favors a rotamer that accommodates the ligand. These results provide a molecular justification for how this substitution generates enhanced binding affinity for carbapenems, and therefore helps explain the prevalence of this substitution in clinical OXA‐51 variants.

June, Cynthia M.↗
DOE OSTI2018

4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae – structure and interactions with coenzymes and substrate analog

Highlights: • N. gonorrhoeae is an obligate human pathogen which is a leading cause of communicable diseases. • 4-Hydroxy-tetrahydrodipicolinate reductase from N. gonorrhoeae (NgDapB) is a new drug target, and its structure was determined. • ITC we have demonstrated and characterized binding of NADH, NADPH and an inhibitor (2,6-PDC) to NgDapB. • In the case of NgDapB, the ITC results suggest random sequential mechanism for substrate binding. • A large scale analysis of DapBs' sequences revealed that DapBs can be segregated into three distinct groups. Neisseria gonorrhoeae, an obligate human pathogen, is a leading cause of communicable diseases globally. Due to rapid development of drug resistance, the rate of successfully curing gonococcal infections is rapidly decreasing. Hence, research is being directed toward finding alternative drugs or drug targets to help eradicate these infections. 4-Hydroxy-tetrahydrodipicolinate reductase (DapB), an important enzyme in the meso-diaminopimelate pathway, is a promising target for the development of new antibiotics. This manuscript describes the first structure of DapB from N. gonorrhoeae determined at 1.85 Å. This enzyme uses NAD(P)H as cofactor. Details of the interactions of the enzyme with its cofactors and a substrate analog/inhibitor are discussed. A large scale bioinformatics analysis of DapBs' sequences is also described.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Non-Gaussian structure of B-mode polarization after delensing

The B-mode polarization of the cosmic microwave background on large scales has been considered as a probe of gravitational waves from the cosmic inflation. Ongoing and future experiments will, however, suffer from contamination due to the B-modes of non-primordial origins, one of which is the lensing induced B-mode polarization. Subtraction of the lensing B-modes, usually referred to as delensing, will be required for further improvement of detection sensitivity of the gravitational waves. In such experiments, knowledge of statistical properties of the B-modes after delensing is indispensable to likelihood analysis particularly because the lensing B-modes are known to be non-Gaussian. In this paper, we study non-Gaussian structure of the delensed B-modes on large scales, comparing it with that of the lensing B-modes. In particular, we investigate the power spectrum correlation matrix and the probability distribution function (PDF) of the power spectrum amplitude. Assuming an experiment in which the quadratic delensing is an almost optimal method, we find that delensing reduces correlations of the lensing B-mode power spectra between different multipoles, and that the PDF of the power spectrum amplitude is well described as a normal distribution function with a variance larger than that in the case of a Gaussian field. These features are well captured by an analytic model based on the 4th order Edgeworth expansion. As a consequence of the non-Gaussianity, the constraint on the tensor-to-scalar ratio after delensing is degraded within approximately a few percent, which depends on the multipole range included in the analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1993

AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference, 34th and AIAA/ASME Adaptive Structures Forum, La Jolla, CA, Apr. 19-22, 1993, Technical Papers. Pts. 1-6

Topics addressed include the prediction of helicopter component loads using neural networks, spacecraft on-orbit coupled loads analysis, hypersonic flutter of a curved shallow panel with aerodynamic heating, thermal-acoustic fatigue of ceramic matrix composite materials, transition elements based on transfinite interpolation, damage progression in stiffened composite panels, a direct treatment of min-max dynamic response optimization problems, and sources of helicopter rotor hub inplane shears. Also discussed are dynamics of a layered elastic system, confidence bounds on structural reliability, mixed triangular space-time finite elements, advanced transparency development for USAF aircraft, a low-velocity impact on a graphite/PEEK, an automated mode-tracking strategy, transonic flutter suppression by a passive flap, a nonlinear response of composite panels to random excitation, an optimal placement of elastic supports on a simply supported plate, a probabilistic assessment of composite structures, a model for mode I failure of laminated composites, a residual flexibility approach to multibody dynamics,and multilayer piezoelectric actuators.

Source record↗
DOE OSTI2024

The Interplay of Binary and Quantitative Structure on the Stability of Mutualistic Networks

Synopsis Understanding how the structure of biological systems impacts their resilience (broadly defined) is a recurring question across multiple levels of biological organization. In ecology, considerable effort has been devoted to understanding how the structure of interactions between species in ecological networks is linked to different broad resilience outcomes, especially local stability. Still, nearly all of that work has focused on interaction structure in presence-absence terms and has not investigated quantitative structure, i.e., the arrangement of interaction strengths in ecological networks. We investigated how the interplay between binary and quantitative structure impacts stability in mutualistic interaction networks (those in which species interactions are mutually beneficial), using community matrix approaches. We additionally examined the effects of network complexity and within-guild competition for context. In terms of structure, we focused on understanding the stability impacts of nestedness, a structure in which more-specialized species interact with smaller subsets of the same species that more-generalized species interact with. Most mutualistic networks in nature display binary nestedness, which is puzzling because both binary and quantitative nestedness are known to be destabilizing on their own. We found that quantitative network structure has important consequences for local stability. In more-complex networks, binary-nested structures were the most stable configurations, depending on the quantitative structures, but which quantitative structure was stabilizing depended on network complexity and competitive context. As complexity increases and in the absence of within-guild competition, the most stable configurations have a nested binary structure with a complementary (i.e., anti-nested) quantitative structure. In the presence of within-guild competition, however, the most stable networks are those with a nested binary structure and a nested quantitative structure. In other words, the impact of interaction overlap on community persistence is dependent on the competitive context. These results help to explain the prevalence of binary-nested structures in nature and underscore the need for future empirical work on quantitative structure.

Zoology↗
DOE OSTI2018

Crystal structure, electronic structure, optical and scintillation properties of self-activated Cs 4 YbI 6 [Crystal structure, optical and scintillation properties of self-activated Cs 4 YbI 6 ]

A self-activated Cs 4 YbI 6 single crystal was grown by the vertical Bridgman method. Crystal structure refinements verified the phase purity and the trigonal crystal system with a space group of $\bar{R}$ 3 c . By using differential scanning calorimetry, the melting and crystallization points were determined to be 550 and 510 °C, respectively. Luminescence and scintillation properties were systematically studied. Upon ultraviolet light (360 nm) excitation, the Cs 4 YbI 6 crystal exhibits bluish-green emission centered at 450 and 480 nm due to spin-allowed and spin-forbidden transitions of Yb 2+ activators. The lifetimes of the corresponding emission bands at room temperature are tens and hundreds of nanoseconds, respectively. X-ray excited radioluminescence spectrum is dominated by the spin-forbidden transition of Yb 2+ at 480 nm. The absolute light yield is 2700 ± 200 photons/MeV with a principal scintillation decay time of 33 ns. In conclusion, the physical explanation for the low light yield observed is proposed from experimental and theoretical insights.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm{sup −1}. At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm{sup −1} para-hydrogen provides a test case for improved approximations to quantum dynamics.

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

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗