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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 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Hydrophilic domain structure in polymer exchange membranes: Simulations of NMR spin diffusion experiments to address ability for model discrimination

Here, we detail the development of a flexible simulation program (NMR_DIFFSIM) that solves the nuclear magnetic resonance (NMR) spin diffusion equation for arbitrary polymer architectures. The program was used to explore the proton ( 1 H) NMR spin diffusion behavior predicted for a range of geometrical models describing polymer exchange membranes. These results were also directly compared with the NMR spin diffusion behavior predicted for more complex domain structures obtained from molecular dynamics (MD) simulations. The numerical implementation and capabilities of NMR_DIFFSIM were demonstrated by evaluating the experimental NMR spin diffusion behavior for the hydrophilic domain structure in sulfonated Diels-Alder Poly(Phenylene) (SDAPP) polymer membranes. The impact of morphology variations as a function of sulfonation and hydration level on the resulting NMR spin diffusion behavior were determined. These simulations allowed us to critically address the ability of NMR spin diffusion to discriminate between different structural models, and to highlight the extremely high fidelity experimental data required to accomplish this. A direct comparison of experimental double-quantum-filtered 1 H NMR spin diffusion in SDAPP membranes to the spin diffusion behavior predicted for MD-proposed morphologies revealed excellent agreement, providing experimental support for the MD structures at low to moderate hydration levels.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Syntheses and characterization of isotopically labeled 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)

Synthesis and characterization of chemical analogues of TATB, where specific atoms in the structure have been isotopically substituted, are reported. 15 N, 2 H, and 18 O have replaced the naturally occurring isotope distributions in the amino and/or the nitro attendant sites and 13 C has replaced the carbon in the ring structure. A modified wet-amination method was used to produce the analogues, and the isotopic replacements were performed by selective choice of labeled precursors. Four 15 N-labeled compounds (N replaced in the amino and nitro positions), two deuterium-labeled compounds (hydrogens replaced on the amino groups), and one 13 C-labeled compound (C in the ring substituted) were synthesized of high isotopic and chemical purity. One partially labeled 18 O-labeled compound (O in the nitro position) was a result of incomplete labeling due to exchange reactions during synthesis. The compounds were characterized by various spectroscopic methods – mass spectrometry (MS), solid-state nuclear magnetic resonance (SS-NMR), infrared (FTIR), powder x-ray diffraction (PXRD), and differential scanning calorimetry (DSC), depending upon the substitution. In conclusion, these compounds have been critical to the efforts in understanding the decomposition pathways of TATB when exposed to abnormal thermal environments.

36 MATERIALS SCIENCE↗
DOE OSTI2014

The dynamics of interleukin-8 and its interaction with human CXC receptor I peptide

Interleukin-8 (CXCL8, IL-8) is a pro-inflammatory chemokine important for the regulation of inflammatory and immune responses via its interaction with G-protein coupled receptors, including CXC receptor 1 (CXCR1). CXCL8 exists as both a monomer and as a dimer at physiological concentrations, yet the molecular basis of CXCL8 interaction with its receptor as well as the importance of CXCL8 dimer formation remain poorly characterized. Although several biological studies have indicated that both the CXCL8 monomer and dimer are active, biophysical studies have reported conflicting results regarding the binding of CXCL8 to CXCR1. To clarify this problem, we expressed and purified a peptide (hCXCR1pep) corresponding to the N-terminal region of human CXCR1 (hCXCR1) and utilized nuclear magnetic resonance (NMR) spectroscopy to interrogate the binding of wild-type CXCL8 and a previously reported mutant (CXCL8M) that stabilizes the monomeric form. Our data reveal that CXCL8M engages hCXCR1pep with a slightly higher affinity than CXCL8, and that CXCL8 does not dissociate upon binding hCXCR1pep. These investigations also indicate that CXCL8 exhibits inherent flexibility within its receptor-binding site on multiple timescales, which may help explain the versatility in this interleukin for engaging its target receptors.

dimer↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗
DOE OSTI2021

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Common functionally important motions of the nucleotide‐binding domain of H sp70

ABSTRACT The 70 kDa heat shock proteins (Hsp70) are a family of molecular chaperones involved in protein folding, aggregate prevention, and protein disaggregation. They consist of the substrate‐binding domain (SBD) that binds client substrates, and the nucleotide‐binding domain (NBD), whose cycles of nucleotide hydrolysis and exchange underpin the activity of the chaperone. To characterize the structure–function relationships that link the binding state of the NBD to its conformational behavior, we analyzed the dynamics of the NBD of the Hsp70 chaperone from Bos taurus (PDB 3C7N:B) by all‐atom canonical molecular dynamics simulations. It was found that essential motions within the NBD fall into three major classes: the mutual class, reflecting tendencies common to all binding states, and the ADP‐ and ATP‐unique classes, which reflect conformational trends that are unique to either the ADP‐ or ATP‐bound states, respectively. “Mutual” class motions generally describe “in‐plane” and/or “out‐of‐plane” (scissor‐like) rotation of the subdomains within the NBD. This result is consistent with experimental nuclear magnetic resonance data on the NBD. The “unique” class motions target specific regions on the NBD, usually surface loops or sites involved in nucleotide binding and are, therefore, expected to be involved in allostery and signal transmission. For all classes, and especially for those of the “unique” type, regions of enhanced mobility can be identified; these are termed “hot spots,” and their locations generally parallel those found by NMR spectroscopy. The presence of magnesium and potassium cations in the nucleotide‐binding pocket was also found to influence the dynamics of the NBD significantly. Proteins 2015; 83:282–299. © 2014 Wiley Periodicals, Inc.

Gołaś, Ewa I.↗
DOE OSTI2015

BCL::MP-fold: Membrane protein structure prediction guided by EPR restraints

For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold (BioChemical Library membrane protein fold) algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The RMSD100 value of the most accurate model is better than 8 Å for 27, better than 6 Å for 22, and better than 4 Å for 15 of the 29 proteins, demonstrating the algorithms' ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data. Proteins 2015; 83:1947–1962. © 2015 Wiley Periodicals, Inc

Biochemistry & Molecular Biology↗
DOE OSTI2021

The denatured state of HIV ‐1 protease under native conditions

Abstract The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Establishing the accuracy of position–specific carbon isotope analysis of propane by GC–pyrolysis–GC–IRMS

Rationale: Position-specific (PS) δ 13 C values of propane have proven their ability to provide valuable information on the evolution history of natural gases. Two major approaches to measure PS δ 13 C values of propane are isotopic 13 C nuclear magnetic resonance (NMR) and gas chromatography-pyrolysis-gas chromatography-isotope ratio mass spectrometry (GC-Py-GC-IRMS). Measurement accuracy of the isotopic 13 C NMR has been verified, but the requirements of large sample size and long experimental time limit its applications. GC-Py-GC-IRMS is a more versatile method with a small sample size, but its accuracy has not been demonstrated. Methods: We measured the PS δ 13 C values of propane from nine natural gases using both 13 C NMR and GC-Py-GC-IRMS, then evaluated the accuracy of the GC-Py-GC-IRMS method. Results: The results show that large carbon isotope fractionations occurred for both terminal and central carbons within propane during pyrolysis. The isotope fractionations during the pyrolysis are reproducible at optimum conditions, but vary between the two GC-Py-GC-IRMS systems tested, affected by experimental conditions (e.g., pyrolysis temperature, flow rate, and reactor conditions). Conclusions: It is necessary to evaluate and calibrate each GC-Py-GC-IRMS system using propane gases with accurately determined PS δ 13 C values. Finally, this study also highlights a need for PS isotope standards for propane and other molecules (e.g., butane and acetic acid).

03 NATURAL GAS↗
DOE OSTI2016

Production of Hydroxyl-rich Acids from Xylose and Glucose Using Sn-BEA Zeolite

Sn-BEA zeolite is known to catalyze the aldose-to-ketose isomerization of xylose and glucose; however, the selectivity to pentose and hexose isomers is not stoichiometric, suggesting the formation of other products. In the present study, we have observed near-complete conversion of all pentose and hexose isomers when xylose and glucose were reacted in the presence of Sn-BEA at 140 °C and 200 °C, respectively. The previously unidentified products were identified by nuclear magnetic resonance and mass spectrometry to be hydroxyalkanoic acids and their derivatives. Here, the hydroxyl-rich acids comprise a significant fraction of the converted sugars and are potential monomers for the synthesis of hyper-crosslinked, biodegradable polymers.

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

31 P NMR Characterization of Tricin and Its Structurally Similar Flavonoids

Tricin, a flavonoid metabolite, has been recently identified as a component of lignin in select monocot plants. This finding has initiated consideration on updating the lignin biosynthesis pathway. Here, we report a rapid method of determination of tricin in corn stover lignin, based on 31 P nuclear magnetic resonance (NMR) spectroscopy by phosphitylating with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (TMDP). Nine other flavonoids, with similar structure to tricin, have also been examined using the current method. The application of 31 P NMR enables rapid identification of tricin-like flavonoids in the heterogeneous lignin polymer. The well resolved spectroscopic peaks from these derivatized flavonoids and lignin functional groups provide important information for the determination of flavonoids individually or their association with lignin.

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

2D HSQC Chemical Shifts of Impurities from Biomass Pretreatment

Two dimensional (2D) heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) is a powerful analytical method which can be used to elucidate the structure of biomass. During processing, biomass is typically subjected to some form of chemical treatment which can be performed with a variety of compounds. The presence of these compounds, even in trace amounts, has the potential to contaminate the sample and lead to misinterpretation of the HSQC spectra. Here we report the chemical shifts of 29 compounds commonly used in biomass processing which have the potential to contaminate the biomass samples and lead to the misinterpretation of peaks associated with biomass (Populus trichocarpa ) pretreated via autohydrolysis. The identification of these chemical shifts could serve as a valuable tool in preventing errors in characterizing biomass via HSQC.

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

Ionic Pairs-Engineered Fluorinated Covalent Organic Frameworks Toward Direct Air Capture of CO 2

The covalent organic frameworks (COFs) possessing high crystallinity and capability to capture low-concentration CO 2 (400 ppm) from air are still underdeveloped. The challenge lies in simultaneously incorporating high-density active sites for CO 2 insertion and maintaining the ordered structure. Herein, a structure engineering approach is developed to afford an ionic pair-functionalized crystalline and stable fluorinated COF (F-COF) skeleton. The ordered structure of the F-COF is well maintained after the integration of abundant basic fluorinated alcoholate anions, as revealed by synchrotron X-ray scattering experiments. The breakthrough test demonstrates its attractive performance in capturing (400 ppm) CO 2 from gas mixtures via O$-$C bond formation, as indicated by the in situ spectroscopy and operando nuclear magnetic resonance spectroscopy using 13 C-labeled CO 2 sources. Both theoretical and experimental thermodynamic studies reveal the reaction enthalpy of ≈-40 kJ mol -1 between CO 2 and the COF scaffolds. This implies weaker interaction strength compared with state-of-the-art amine-derived sorbents, thus allowing complete CO 2 release with less energy input. The structure evolution study from synchrotron X-ray scattering and small-angle neutron scattering confirms the well-maintained crystalline patterns after CO 2 insertion. In conclusion, the as-developed proof-of-concept approach provides guidance on anchoring binding sites for direct air capture (DAC) of CO 2 in crystalline scaffolds.

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

Hierarchically Structured Vitrimer Biocomposites for Sustainable Manufacturing

Polymers containing dynamic covalent bonds (DCBs) exhibit thermoplastic-like flow above their topology freezing temperature (T v ) while maintaining thermoset-like properties below it, making them promising for sustainable manufacturing. However, their large-scale adoption remains limited due to challenges in accurately determining T v and achieving efficient fiber-matrix bonding in composite applications. Here, hierarchically structured epoxy-anhydride-based polyester vitrimer composites reinforced with cellulosic filaments is demonstrated, where hydroxyl groups on fiber surfaces participate directly in transesterification with the matrix. Further, this dynamic interfacial bonding delivers exceptional mechanical properties, including ≈70 MPa shear strength and >10% strain-to-failure, while enabling thermal malleability. Using a combination of nuclear magnetic resonance and nano-infrared spectroscopies, direct evidence is provided that chemical bond exchange begins well below the conventionally measured T v , supporting the hypothesis that rheologically determined T v reflects a combination of chemical exchange and frictional dynamics rather than a discrete transition. The composites demonstrate excellent processability through vacuum-assisted resin transfer molding and maintain >90% of their mechanical properties after multiple thermal reforming cycles. These findings advance both the fundamental understanding of vitrimeric transitions and the practical development of sustainable, high-performance composite materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Probing Interfacial Reaction Pathways in Atomic Layer Deposition on Sulfide Superionic Conductors

Sulfide superionic conductors (e.g., argyrodite Li 6 PS 5 Cl, LPSCl) are extremely promising for all solid-state batteries, but poor atmospheric stability and high interfacial reactivity limit widespread adoption. Coating LPSCl powders with ultrathin coatings using atomic layer deposition (ALD) mitigates these problems, protecting against atmospheric degradation and reducing reactivity with Li metal, yielding more stable cycling. Despite significant promise, the ALD mechanism is unknown, hampering the development of new coating chemistries. In this study, we elucidate the mechanism for Al 2 O 3 ALD on LPSCl using trimethyl aluminum (TMA) and H 2 O by combining in situ Fourier transform infrared spectroscopy, ex situ solid-state magic angle spinning nuclear magnetic resonance, UV Raman spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. We determine that ALD Al 2 O 3 nucleates promptly via TMA reaction with native —OH, —SH, and PS 3 -OH groups to form transient C–Al–O(S) species that are rapidly hydrolyzed during the subsequent H 2 O exposure. This reversible transformation maintains surface nucleophilicity and prevents sulfide decomposition. The resulting layer-by-layer growth leads to highly conformal Al 2 O 3 coatings on LPSCl that are readily scalable to ≥ 50 g quantities using a rotating drum fixture. This detailed understanding of ALD surface reactions provides critical insights guiding the selection of future ALD chemistries with improved performance.

atomic layer deposition↗
DOE OSTI2021

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Measuring Biomass-Derived Products in Biological Conversion and Metabolic Process

Biomass can be converted to various types of products in biological and metabolic processes. For an in-depth understanding of biomass conversion, quantitative and qualitative information of products in these conversion processes are essential. Here we introduce analytical techniques including high-performance liquid chromatography (HPLC), gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR) for biomass-based products characterization in biological and metabolic processes.

Yoo, Chang Geun↗