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Results for “Structure elucidation”

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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and inhibitory activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Mesoscale shock structure in particulate composites

Multiscale experiments in heterogeneous materials and the knowledge of their physics under shock compression are limited. Here, this study examines the multiscale shock response of particulate composites comprised of soda-lime glass particles in a PMMA matrix using full-field high speed digital image correlation (DIC) for the first time. Normal plate impact experiments, and complementary numerical simulations, are conducted at stresses ranging from 1.1 - 3.1 GPa to elucidate the mesoscale mechanisms responsible for the distinct shock structure observed in particulate composites. The particle velocity from the macroscopic measurement at continuum scale shows a relatively smooth velocity profile, with shock thickness decreasing with an increase in shock stress, and the composite exhibits strain rate scaling as the second power of the shock stress. In contrast, the mesoscopic response was highly heterogeneous, which led to a rough shock front and the formation of a train of weak shocks traveling at different velocities. Additionally, the normal shock was seen to diffuse the momentum in the transverse direction, affecting the shock rise and the rounding-off observed at the continuum scale measurements. The numerical simulations indicate that the reflections at the interfaces, wave scattering, and interference of these reflected waves are the primary mechanisms for the observed rough shock fronts.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Enhancing elastic properties of single element amorphous solids through long-range interactions

Elastic properties of amorphous solids remain a topic of intense interest due to their important roles in a wide range of applications. Prior works have focused on short-range, local structural features, such as number density and coordination number, to elucidate the underlying mechanism of elastic moduli in glasses. Here, we report strong correlations among the spatial extension of the interatomic potential, elastic moduli, and the coherence lengths of the medium-range structural order through molecular dynamics simulations for single element glasses. Our findings demonstrate an unconventional design principle to engineer elastic properties by extending the medium-range order and provide insights into the microscopic origin of elastic properties in amorphous solids.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure-Property Relationships of Hydrogel-Salt Composites for Extreme Sorption Performance

Hydrogel-salt composites have emerged as a promising low-cost material for a wide range of sorption applications including thermal energy storage, atmospheric water harvesting, and dehumidification. Despite significant efforts devoted to the synthesis of novel hydrogels and their implementation in sorption devices, very little is known about the fundamental connection between the hydrogel structure and composition with their material-level properties. This knowledge, however, is critical to enable the rational design of high-performance hydrogels targeted at the various applications. In this work, we elucidate via experiments and modeling the link between the hydrogel structure, including its salt content and polymer nanostructure, and its sorption properties. Using lithium chloride-embedded polyacrylamide hydrogels as model systems, we demonstrate that the hydrogel uptake and its kinetics are dominated by the content and properties of the salt. In fact, the polymer nanostructure has no a minor effect in its sorption performance. Based on our experimental insights, we develop a model for the simultaneous diffusion of water and salts in hydrogels, which helps to explain the observed relationship between hydrogel structure and its sorption properties. Furthermore, we leverage these insights to synthesize hydrogels with record-high water vapor uptakes of 1.79 g/g, 2.58 g/g, 3.86 g/g, and 8.51 g/g at 30%, 50%, 70%, and 90% relative humidity, respectively, owing to the use of large amounts of highly hygroscopic salts. By demonstrating the structure-property relationships, this work enables the rational design of salt-embedded hydrogels for low-cost and high-performance thermal energy storage, atmospheric freshwater production, and space conditioning.

Díaz-Marín, Carlos D↗
NASA NTRS1996

Microgravity Foam Structure and Rheology

The objective of this research was to exploit rheological and multiple-light scattering techniques, and ultimately microgravity conditions, in order to quantify and elucidate the unusual elastic character of foams in terms of their underlying microscopic structure and dynamics. Special interest was in determining how this elastic character vanishes, i.e. how the foam melts into a simple viscous liquid, as a function of both increasing liquid content and shear strain rate.

Durian, Douglas J.↗
DOE OSTI2025

Understanding the optoelectronic properties of doped 2D organic-inorganic halide perovskite quantum wells: towards efficient quantum well IR photodetectors

Metal halide perovskite (MHP) multiple quantum wells which consist of multilayers of alternate organic and inorganic layers exhibit large exciton binding energies due to the dielectric confinement between the inorganic and organic layers. These naturally formed multiple quantum wells have strong spin-orbit coupling (SOC) due to the presence of heavy elements in their crystal structures. Although the fundamental properties of 2D MHPs are far from being entirely understood, it is widely accepted that their band edge absorption coefficient results from strong exciton interactions. However, studies demonstrating how different exciton interactions and doping effects influence electronic traps and disorder on the band edge absorption coefficient of 2D MHPs have not been demonstrated. Understanding these interactions in MHPs will allow us to access low energy optical transitions for the fabrication of solution processable short-to-mid-wavelength IR photodetectors (1 – 8 μm). Moreover, upon doping, it is possible to move the Fermi energy into the conduction band (CB) to favorably promote the transport of charges in a working device. Herein, we study the development of 2D MHPs having strong SOC, high carrier mobility, and tunable quantum well structures. Our studies shed light on the design and modulation of fundamental physical phenomena by carefully elucidating the role of dopants (n-type and p-type), exciton heterogeneity, orientation, structure, and bias stress effects on the performance of MHPs as potential IR photodetectors.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Unraveling the structure and bonding evolution of the newly discovered iron oxide FeO 2

Recently reported synthesis of FeO 2 at high pressure has stimulated great interest in exploring this new iron oxide and elucidating its properties. Here, we present a systematic computational study of crystal structure, chemical bonding, and sound velocity of FeO 2 in a wide range of pressure. Our results establish thermodynamic stability of the experimentally observed pyrite phase (P-phase) of FeO 2 at pressures above 74 GPa and unveil two metastable FeO 2 phases in Pbcn and P4 2 /mnm symmetry at lower pressures. Simulated x-ray diffraction (XRD) spectra of Pbcn and P4 2 /mnm FeO 2 match well with measured XRD data of the decompression products of P-phase FeO 2 , providing compelling evidence for the presence of these metastable phases. Energetic calculations reveal unusually soft O-O bonds in P-phase FeO 2 stemming from a low-frequency libration mode of FeO 6 octahedra, rendering the O-O bond length highly sensitive to computational and physical environments. Calculated sound-velocity profiles of P-phase FeO 2 are markedly different from those of the Pbcn and P4 2 /mnm phases, underscoring their distinct seismic signatures. Here our findings offer insights for understanding the rich structural, bonding, and elastic behaviors of this newly discovered iron oxide.

36 MATERIALS SCIENCE↗
NASA NTRS2013

Biological Effects of Particles with Very High Energy Deposition on Mammalian Cells Utilizing the Brookhaven Tandem Van de Graaff Accelerator

High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of high charge and energy (HZE) nuclei and secondary protons and neutrons, and secondaries from protons in SPE (Solar Particle Event) pose a major health risk to astronauts due to induction of DNA damage and oxidative stress. Experiments with high energy particles mimicking the space environment for estimation of radiation risk are being performed at NASA Space Radiation Laboratory at BNL. Experiments with low energy particles comparing to high energy particles of similar LET are of interest for investigation of the role of track structure on biological effects. For this purpose, we report results utilizing the Tandem Van de Graaff accelerator at BNL. The primary objective of our studies is to elucidate the influence of high vs low energy deposition on track structure, delta ray contribution and resulting biological responses. These low energy ions are of special relevance as these energies may occur following absorption through the spacecraft and shielding materials in human tissues and nuclear fragments produced in tissues by high energy protons and neutrons. This study will help to verify the efficiency of these low energy particles and better understand how various cell types respond to them.

Saha, Janapriya↗
DOE OSTI2020

Engineering Atomically Dispersed FeN 4 Active Sites for CO 2 Electroreduction

Atomically dispersed FeN 4 active sites have exhibited exceptional catalytic activity and selectivity for the electrochemical CO 2 reduction reaction (CO2RR) to CO. However, the understanding behind the intrinsic and morphological factors contributing to the catalytic properties of FeN 4 sites is still lacking. By using a Fe-N-C model catalyst derived from the ZIF-8, we deconvoluted three key morphological and structural elements of FeN 4 sites, including particle sizes of catalysts, Fe content, and Fe-N bond structures. Furthermore, their respective impacts on the CO2RR were comprehensively elucidated. Engineering the particle size and Fe doping is critical to control extrinsic morphological factors of FeN 4 sites for optimal porosity, electrochemically active surface areas, and the graphitization of the carbon support. In contrast, the intrinsic activity of FeN 4 sites was only tunable by varying thermal activation temperatures during the formation of FeN 4 sites, which impacted the length of the Fe-N bonds and the local strains. The structural evolution of Fe-N bonds was examined at the atomic level. First-principles calculations further elucidated the origin of intrinsic activity improvement associated with the optimal local strain of the Fe-N bond.

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

Effect of Ni particle size on the production of renewable methane from CO 2 over Ni/CeO 2 catalyst

Production of ‘renewable Methane’ has attracted renewed research interest as a fundamental probe reaction and process for CO 2 utilization through potential use in C1 fuel production and even for future space exploration technologies. CO 2 methanation is a structure sensitive reaction on Ni/CeO 2 catalysts. To precisely elucidate the size effect of the Ni metal center on the CO 2 methanation performance, we prepared 2%Ni/CeO 2 catalysts with pre-synthesized uniform Ni particles (2, 4 and 8 nm) on a high surface area CeO 2 support. Transmission electron microscopy (TEM) and ambient pressure X-ray photo spectroscopy (AP-XPS) characterization have confirmed that the catalyst structure and chemical state was uniform and stable under reaction conditions. The 8 nm sized catalyst showed superior methanation selectivity over the 4 and 2 nm counterparts, and the methanation activity in term of TOF is 10 times and 70 times higher than for the 4 and 2 nm counterparts, respectively. Here, the DRIFTS studies revealed that the larger Ni (8 nm particles) over CeO 2 efficiently facilitated the hydrogenation of the surface formate intermediates, which is proposed as the rate determining step accounting for the excellent CO 2 methanation performance.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Crystal structure of hypothetical protein PA4202 from Pseudomonas aeruginosa PAO1 in complex with nitroethane as a nitroalkane substrate

Highlights: • Crystal structure of PA4202 protein in complex with FMN and NE was determined. • A kinetic study reveals that the PA4202 enzyme may catalyze a neutral nitroalkane. • Our results provide the first structure-based substrate binding property of PA4202. Nitroalkane oxidase (NAO) and nitronate monooxygenase (NMO) are two different types of nitroalkane oxidizing flavoenzymes identified in nature. A previous study suggested that the hypothetical protein PA4202 from Pseudomonas aeruginosa PAO1 is NMO and utilizes only anionic nitronates. However, the structural similarity between the PA4202 protein and Streptomyces ansochromogenes NAO has motivated investigation for what features of the two enzymes differentiate between the NAO and NMO activities. Herein, we report the crystal structure of PA4202 in a ternary complex with a neutral nitroethane (NE) and flavin mononucleotide (FMN) cofactor to elucidate the substrate recognition mechanism using a site-directed mutagenesis. The ternary complex structure indicates that the NE is bound with an orientation, which is poised for the proton transfer to H183 (which is the essential first catalytic step with nitroalkanes), and subsequent reactions with FMN. Moreover, a kinetic study reveals that the catalytic reactions of the wild type and H183 mutants PA4202s with nitroalkane substrates may yield the products of hydrogen peroxide and nitrite that are specified to NAO, although they show a low catalytic efficiency. Our results provide the first structure-based molecular insight into the substrate binding property of the hypothetical protein PA4202, including the interactions with neutral nitroalkanes as the substrate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Nanoscopic structure of borosilicate glass with additives for nuclear waste vitrification

In this report we investigated the nanoscopic structure of borosilicate glasses as a host for high-level radioactive liquid waste (HLLW) in the presence of the additives Na 2 O and CaO/ZnO with and without Li 2 O. These additives have been used to lower the glass melting point, suppress the macroscopic phase separation, and increase the chemical durability of glasses. Small-angle neutron scattering was used to elucidate the effect of the additives on the nanoscopic structure along with macro- and atomic-scale observations obtained using neutron imaging and X-ray diffraction, respectively. The borosilicate glass made without Na 2 O formed a microphase-separated structure of SiO 2 - and B 2 O 3 -rich domains approximately 100 nm in size, and the material was homogeneous at length scales up to millimeters. With the addition of increasing amounts of Na 2 O, the domain spacing decreased. Introducing CaO/ZnO additives induced inhomogeneities in the glass, such as void structures several nanometers in size, although the inhomogeneity was suppressed by the coaddition of Li 2 O. These results provide insights into the performance of host glasses for HLLW vitrification. Incorporating HLLW into glasses is likely to cause changes in the nanoscopic structure of host glasses similar to those revealed here.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

Analysis of Strand-Specific RNA-Seq Data Using Machine Learning Reveals the Structures of Transcription Units in Clostridium thermocellum

The identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets. Moreover, among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available athttps://code.google.com/p/seqtu/. We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.

09 BIOMASS FUELS↗
DOE OSTI2025

From Electronic Structure to Ion Transport: Photoelectron Spectroscopy and Molecular Dynamics Simulations Reveal the Role of Anions in Lithium Battery Electrolytes

Electrolyte anions are pivotal for lithium battery performance, yet their fundamental electronic structural properties are not well understood. In this work, we employ a combination of negative-ion photoelectron spectroscopy (NIPES), ab initio calculations, and molecular dynamics (MD) simulations to investigate the electronic structures of three representative electrolyte anions. This multiscale approach enables us to elucidate how their intrinsic electronic properties govern anion–solvent interactions in gas-phase clusters, as well as lithium-ion (Li + ) solvation structures and ion transport behavior in the condensed phase. NIPES reveals that difluoro(oxalato)borate (DFOB – ), bis(fluorosulfonyl)imide (FSI – ), and bis(oxalato)borate (BOB – ) all exhibit high electron binding energies, with vertical/adiabatic detachment energies increasing from DFOB – (6.09/5.70 eV) to FSI – (6.80/6.10 eV) to BOB – (6.82/6.40 eV), correlating with enhanced oxidation stability. Ab initio calculations reveal that DFOB – /FSI – –solvent complexes bind Li + ∼ 10 kcal/mol stronger than BOB – series, aligning with the strength of a Li + –anion model. DFOB – exhibits pronounced charge localization on both oxygen and fluorine atoms, enabling their involvement in Li + coordination. In contrast, fluorine atoms in FSI – are largely electron-depleted and remain excluded from direct Li + binding. MD simulations further demonstrate that LiDFOB and LiFSI systems exhibit Li + diffusion coefficients three and five times higher than those of LiBOB across four common solvents. Notably, LiFSI salt in acetonitrile (AN) exhibits the fastest Li + diffusion among 12 electrolyte systems, highlighting the synergistic effect of FSI – and AN in promoting ion mobility. In conclusion, these findings provide a molecular-level understanding of the critical roles of anion and its microsolvation in optimizing Li + diffusion dynamics, once again emphasizing the positioning of FSI – and DFOB – as prime candidates for next-generation electrolytes.

25 ENERGY STORAGE↗
DOE OSTI2019

Aza-proline effectively mimics L -proline stereochemistry in triple helical collagen

The prevalence of L -amino acids in biomolecules has been shown to have teleological importance in biomolecular structure and self-assembly. Recently, biophysical studies have demonstrated that natural L -amino acids can be replaced with non-natural achiral aza-amino acids in folded protein structures such as triple helical collagen. However, the structural consequences of achiral aza-amino acid incorporation has not been elucidated in the context of any relevant folded biomolecule. Herein, we use X-ray crystallography to provide the first atomic resolution crystal structure of an achiral aza-amino acid residue embedded within a folded protein structure, definitively illustrating that achiral aza-proline has the capacity to effectively mimic the stereochemistry of natural amino acids within the context of triple helical collagen. We further corroborate this finding with density functional theory computational analysis showing that the natural L -amino acid stereochemistry for aza-proline is energetically favored when arranged in the aza-proline-hydroxyproline-glycine motif. In addition to providing fundamental insight into peptide and protein structure, the incorporation of achiral stereochemical mimics such as aza-amino acids could have far reaching impacts in areas ranging from synthetic materials to drug design.

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

Solvation vs. surface charge transfer: an interfacial chemistry game drives cation motion

Electrolyte structure and ion solvation dynamics determine ionic conductivities, and ion (de)solvation processes dominate interfacial chemistry and electrodeposition barriers. In this work, we elucidate electrolyte effects facilitating or impeding Li + diffusion and deposition, and evaluate structural and energetic changes during the solvation complex pathway from the bulk to the anode surface.

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

Probing Supercritical Phase Transition using Ultrafast X-ray Diagnostics (Final Technical Report)

Over recent years, several hypotheses have been put forward to elucidate supercritical transition states. Despite significant progress on the fundamental understanding of fluids at these supercritical conditions, important questions concerning the microstructure and dynamical processes remain. A particular research issue is hereby the fundamental understanding of the morphology of the molecular microstructure and its effect on the macroscopic behaviour and thermodynamic response functions. It is widely believed that the supercritical state is homogeneous without structural and dynamic observables to distinguish between a liquid and a vapor. However, recent investigations have identified regions of distinct liquid-like or vapor-like properties even under supercritical conditions. Specifically, it was shown that the transition between liquid-like and vapor-like states occurs across an extension to the coexistence line, marked by almost discontinuous changes in fluid properties. This transition was first identified experimentally by Nishikawa and Tanaka and stands in contrast to the classical presentation of the supercritical state space as a featureless, homogeneous domain. Structurally, the most important properties of supercritical fluids are the dynamic heterogeneities and local density fluctuations that are present within the fluid state at the microscopic level. These inhomogeneities are associated with the formation of molecular clusters of various sizes with liquid-like properties separated by voids of unbound gas-phase molecules which continuously restructure itself at picosecond timescales. By utilizing ultrafast X-ray Photon Correlation Spectroscopy (XPCS) at the Linac Coherent Light Source (LCLS) and X-ray synchrotron measurements as an experimental probe of these structural changes at the molecular level we seek to elucidate the higher-order phase transition from a liquid-like to a vapor-like state in the region extending the critical point. Open questions we seek to address particularly with XPCS are: (i) the underlying mechanisms responsible for the density fluctuations at supercritical conditions and how these dynamical processes at the molecular level affect the thermodynamic response functions and (ii) on what timescales do dynamical processes evolve that are associated with thermalization, molecular diffusion, and intermolecular cluster transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗