Search NASA⌕ Search

SEARCH · Search NASA

Results for “structure”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales

Organic C has many benefits for soil, but it is depleted by tillage and crop harvest, and especially so for biofuel crops. Accordingly, strategies such as partially retaining stover or planting a cover crop can help ameliorate the negative effect of C removal. We used a long-term field experiment to study the impacts of stover retention and planting cover crop on soil organic matter (SOM), its extractable components and the soil microbial community. SOM chemical composition characterization was determined by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sequential water, methanol (MeOH), and chloroform (CHCl3) extracts. The characteristics of the soil bacterial community were measured by phospholipid fatty acid (PLFA), real-time quantitative PCR, and 16S rRNA gene sequence. The variations in total SOM content, total microbial biomass, and bacterial population were slight among treatments, but SOM chemical compounds, arbuscular mycorrhizal fungi (AMF) biomass, and bacterial structure changed significantly, and especially so in the coupled application of stover retention and cover crop. Specifically, stover retention enriched more lignin-like compounds in soil, whereas cover crop enriched more condensed hydrocarbons, and had more compounds with an aromaticity index (AI) >0.5. The bacterial community was not altered by the cover crop, but the corn stover retention increased the relative abundances of Myxococcales (Deltaproteobacteria) and decreased that of Actinobacteria. Redundancy analysis (RDA) further unveiled that the bacterial community in the stover treatments had significantly positive association with CHCl3-extracted chemical classes, i.e. unsaturated hydrocarbon and lipid with the coupled application (stover and cover crop), and lignin and protein with the single corn stover treatment. Taken together, our study shows how different C addition practices influence the molecular composition of SOM and the structure of soil microbial communities.

Xu, Jiangbin↗
DOE OSTI2019

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structure determination of two structural analogs, named 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C23H16F2N4S) and 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-chlorophenyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazole (C23H16ClFN4S) by synchrotron X-ray powder diffraction

Two novel compounds, 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-fluorophenyl)-1,2,4-triazolo[3,4- b ]-1,3,4-thiadiazole (C 23 H 16 F 2 N 4 S) ( 1 ) and 3-[1-(2-fluoro-4-biphenyl)ethyl]-6-(4-chlorophenyl)-1,2,4-triazolo[3,4- b ]-1,3,4-thiadiazole (C 23 H 16 ClFN 4 S) ( 2 ), have been designed and synthesized as cytotoxic agents. The compounds were characterized by infrared, proton nuclear magnetic resonance, mass spectral data, elemental analysis and X-ray powder diffraction. The present study comprises spectral data and crystal structures of these novel compounds determined from synchrotron X-ray powder diffraction data. The structure solutions were obtained by simulated annealing. The final structures were achieved by Rietveld refinement using soft restraints for all bond lengths, bond angles, and planar groups. Both compounds crystallize in space group $P\bar 1$ , Z = 2, with the unit-cell parameters a = 6.37433(9), b = 11.3641(2), c = 14.09115(19) Å, α = 80.1740(8)°, β = 85.1164(8)°, γ = 80.9831(10)°, V = 991.55(3) Å 3 of compound ( 1 ) and a = 6.53736(6), b = 11.55725(15), c = 14.01373(13) Å, α = 80.3323(7)°, β = 84.8939(6)°, γ = 79.3954(8)°, V = 1024.08(2) Å 3 of compound ( 2 ). Structural analyses reveal that the title compounds are isostructural.

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

β-Hydroxyacyl-acyl Carrier Protein Dehydratase (FabZ) from Francisella tularensis and Yersinia pestis : Structure Determination, Enzymatic Characterization, and Cross-Inhibition Studies

The bacterial system for fatty acid biosynthesis (FAS) contains several enzymes whose sequence and structure are highly conserved across a vast array of pathogens. This, coupled with their low homology and difference in organization compared to the equivalent system in humans, makes the FAS pathway an excellent target for antimicrobial drug development. To this end, we have cloned, expressed, and purified the β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from both Francisella tularensis (FtFabZ) and Yersinia pestis (YpFabZ). We also solved the crystal structures and performed an enzymatic characterization of both enzymes and several mutant forms of YpFabZ. Additionally, we have discovered two novel inhibitors of FabZ, mangostin and stictic acid, which show similar potencies against both YpFabZ and FtFabZ. Lastly, we selected several compounds from the literature that have been shown to be active against single homologues of FabZ and tested them against both YpFabZ and FtFabZ. These results have revealed clues as to which scaffolds are likely to lead to broad-spectrum antimicrobials targeted against FabZ as well as modifications to existing FabZ inhibitors that may improve potency.

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

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2 Ru 0.5 Mn 0.5 O 3 Investigated in a Wide Voltage Window

Li 2 Ru 0.5 Mn 0.5 O 3 , a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of the structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.

25 ENERGY STORAGE↗
DOE OSTI2017

Structural, Electronic, and Optical Properties of K 2 Sn 3 O 7 with an Offset Hollandite Structure

Here, we present the compound K 2 Sn 3 O 7 , a Sn 4 +-containing oxide with a unique structure type among oxides. The compound is orthorhombic and reminiscent of an offset hollandite, where open channels hold a row of four K + per channel per cell. UV–visible spectroscopy indicates a wide band gap semiconductor, which is confirmed by first-principles electronic-structure calculations of band structures, densities of states, and optical properties. Thus, the continued discovery of new structure types in ternary tin oxides should remain a priority for the identification of prospective ion conductors and transparent conducting compounds.

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

Electronic and Structural Study of Zn x S x [ x = 12, 16, 24, 28, 36, 48, 96, and 108] Cage Structures

We present a density functional study on the structural and electronic properties of ZnS bubble clusters, specifically, hollow cages whose spontaneous formation was previously observed in classical molecular dynamics simulations by Spano et al. [J. Phys. Chem. B 2003, 107, 10337]. The hollow ZnS cages in our study were modeled as ZnxSx [x = 12, 16, 24, 28, 36, 48, 108], and an onionlike structure was modeled as Zn96S96. The study of energetics and stability, performed using large polarized Gaussian basis sets, indicated all structures to be energetically stable with similar binding energy of 5.5–5.6 eV per ZnS pair. Further computation of electronic properties showed that these cages have large vertical ionization energies and relatively low electron affinities in the ranges of 6.8–8.1 and 1.7–3.0 eV, respectively. They have large highest occupied molecular orbital–lowest unoccupied molecular orbital gaps between 2.5 and 3.3 eV, and quasi-particle gaps vary from 6.2 eV for Zn12S12 to 4.19 for Zn108S108. The computed vibrational frequencies for selected cages, that is, Zn12S12, Zn16S16, Zn28S28 (O, S4, and S8 point groups), and Zn36S36 indicate that these cage structures correspond to local minima on the potential energy surface. Finally, the infrared spectra calculated using large basis sets are also reported.

Bhusal, S.↗
DOE OSTI2016

Structure and Conductivity of Semiconducting Polymer Hydrogels

Poly(fluorene-alt-thiophene) (PFT) is a conjugated polyelectrolyte that self-assembles into rod-like micelles in water, with the conjugated polymer backbone running along the length of the micelle. At modest concentrations (-10 mg/mL in aqueous solutions), PFT forms hydrogels, and this work focuses on understanding the structure and intermolecular interactions in those gel networks. The network structure can be directly visualized using cryo electron microscopy. Oscillatory rheology studies further tell us about connectivity within the gel network, and the data are consistent with a picture where polymer chains bridge between micelles to hold the network together. Addition of tetrahydrofuran (THF) to the gels breaks those connections, but once the THF is removed, the gel becomes stronger than it was before, presumably due to the creation of a more interconnected nanoscale architecture. Small polymer oligomers can also passivate the bridging polymer chains, breaking connections between micelles and dramatically weakening the hydrogel network. Fits to solution-phase small-angle X-ray scattering data using a Dammin bead model support the hypothesis of a bridging connection between PFT micelles, even in dilute aqueous solutions. Finally, time-resolved microwave conductivity measurements on dried samples show an increase in carrier mobility after THF annealing of the PFT gel, likely due to increased connectivity within the polymer network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structural Tunability of Multicompartment Micelles as a Function of Lipophilic–Fluorophilic Block Length Ratio

Structural variation in multicompartment micelles consisting of lipophilic–hydrophilic–fluorophilic (hereafter referred to as BAC) triblock copolymers is investigated using the dissipative particle dynamics simulation method. It is demonstrated from our results that the structure of BAC multicompartment micelles is effectively tuned as a function of the lipophilic–fluorophilic ratio parameter, here termed $R_1$, of the constituent linear triblock copolymers. In particular, a morphological deviation from onion-like ABC micelles arises in BAC micelle systems as $R_1$ increases. The morphologies of BAC micelles with $R_1\ll$1 or $R_1\gg$1 display striking similarities, with the only notable difference being an inversion of the lipophilic and fluorophilic regions. When $R\approx$ 1, segmented worm-like structures with multiple cores are favored in BAC micelle systems. Through this study, it is confirmed that the block length ratio is an effective control parameter to tune the structure of multicompartment micelles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Understanding Structure, Metal Distribution, and Water Adsorption in Mixed-Metal MOF-74

We present a joint computational and experimental study of Mg–Ni-MOF-74 and Mg–Cd-MOF-74 to gain insight into the mixing of metals and understand how metal mixing affects the structure of the undercoordinated open-metal sites. Our calcula tions predict that metal mixing is energetically preferred in these materials. Recent experimental work has demonstrated that Mg–Ni-MOF-74 shows a much greater surface area retention in the presence of water than Mg-MOF-74. To probe this effect, we study H2O adsorption in Mg–Ni-MOF-74, finding that the adsorption en ergetics and electronic structure do not change significantly at the metal sites when compared to Mg-MOF-74 and Ni-MOF-74, respectively. We conclude that the in creased stability of Mg–Ni-MOF-74 is a result of a M–O bond length distortion in mixed-metal MOF-74, consistent with recent work on the stability of MOF-74 under water exposure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Beyond Badger’s Rule: The Origins and Generality of the Structure–Spectra Relationship of Aqueous Hydrogen Bonds

The structure of hydrogen bonded networks is intimately intertwined with their dynamics. Despite the incredibly wide range of hydrogen bond strengths encountered in water clusters, ion-water clusters and liquid water, we demonstrate that the previously reported correlation between the change in the equilibrium bond length of the hydrogen bonded OH covalent bond and the corresponding shift in its harmonic frequency in water clusters is much more broadly applicable. Surprisingly, this correlation describes the ratios for both the equilibrium OH bond length/harmonic frequency, and the vibrationally averaged bond length/anharmonic frequency in water, hydronium water and halide water clusters. Consideration of harmonic and anaharmonic data leads to a correlation of -19 ± 1 cm -1 /0.001 Å. The basic nature of this correlation is further confirmed through the analysis of ab initio Molecular Dynamics (AIMD) trajectories for liquid water. We show that this simple correlation for both harmonic and anharmonic systems can be modeled by the response of an OH bond to an external field. Treating the OH bond as a Morse oscillator, we develop analytic expressions, which relate the ratio of the shift in the vibrational frequency of the hydrogen-bonded OH bond to the shift in OH bond length, to parameters in the Morse potential and the ratio of the first and second derivatives of the field-dependent projection of the dipole moment of water onto the hydrogen-bonded OH bond. Based on our analysis, we develop a protocol for reconstructing the AIMD spectra of liquid water from the sampled distribution of the OH bond lengths. Our conclusions elucidate the origins of the relationship between the molecular structure of the fleeting hydrogen-bonded network and the ensuing dynamics, which can be probed by vibrational spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structure of Diisobutylene Maleic Acid Copolymer (DIBMA) and Its Lipid Particle as a “Stealth” Membrane-Mimetic for Membrane Protein Research

The study of membrane proteins remains challenging, especially in a native membrane environment. Recently, major progress has been made using maleic acid copolymers, such as styrene maleic acid, to purify membrane proteins and study them directly with native lipids associated with the membrane. Additional maleic acid copolymers, such as diisobutylene maleic acid (DIBMA) membrane-mimetic systems, are being developed and found to have improved spectroscopic properties and pH stability. We studied DIBMA and its lipid particles in solution to better understand its assembly, without and with the lipids, to provide an insight regarding how to use it in solution for better membrane extraction. Using small-angle neutron and X-ray scattering (SANS/SAXS), we show that DIBMA organizes into structures of different size scales at various concentrations and ionic strengths. The polymer performed reasonably well under most solvent conditions except in very low concentrations and high-salt conditions that could result in limited interaction with lipids. To explore DIBMA lipid particles as a suitable membrane-mimetic system for neutron scattering studies of membrane proteins, we measured and determined the contrast-matching point of DIBMA to be ~12% (v/v) D 2 O — similar to that of most protiated lipid molecules but distinct from that of regular protiated proteins — providing a natural contrast for separating their neutron scattering signals. Using SANS contrast variation, we demonstrated that the scattering from the whole lipid particle can be annihilated. Further, we determined that a well-defined lipid nanodisc structure with DIBMA was contrast-matched. These results demonstrate that the DIBMA lipid particle is an outstanding “stealth” membrane-mimetic for membrane proteins. The results provide a structural framework for understanding the organization and assembly process of the polymer itself and the lipid molecules. Such an understanding is imperative for structural techniques such as cryo-electron microscopy, nuclear magnetic resonance, small-angle scattering, and other biophysical techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity

Ergothioneine is a thiohistidine derivative with potential benefits on many aging-related diseases. The central step of aerobic ergothioneine biosynthesis is the oxidative C–S bond formation reaction catalyzed by mononuclear nonheme iron sulfoxide synthases (EgtB and Egt1). Thus far, only the Mycobacterium thermoresistibile EgtB (EgtB Mth ) crystal structure is available, while the structural information for the more industrially attractive Egt1 enzyme is not. In this paper, we reported the crystal structure of the ergothioneine sulfoxide synthase (EgtB Cth ) from Candidatus Chloracidobacterium thermophilum . EgtB Cth has both EgtB- and Egt1-type of activities. Guided by the structural information, we conducted Rosetta Enzyme Design calculations, and we biochemically demonstrated that EgtB Cth can be engineered more toward Egt1-type of activity. This study provides information regarding the factors governing the substrate selectivity in Egt1- and EgtB-catalysis and lays the groundwork for future sulfoxide synthase engineering toward the development of an effective ergothioneine process through a synthetic biology approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗