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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Probing Molecular Packing of Amorphous Pharmaceutical Solids Using X-ray Atomic Pair Distribution Function and Solid-State NMR

The structural investigation of amorphous pharmaceuticals is of paramount importance in comprehending their physicochemical stability. However, it has remained a relatively underexplored realm primarily due to the limited availability of high-resolution analytical tools. Here in this study, we utilized the combined power of X-ray pair distribution functions (PDFs) and solid-state nuclear magnetic resonance (ssNMR) techniques to probe the molecular packing of amorphous posaconazole and its amorphous solid dispersion at the molecular level. Leveraging synchrotron X-ray PDF data and employing the empirical potential structure refinement (EPSR) methodology, we unraveled the existence of a rigid conformation and discerned short-range intermolecular C–F contacts within amorphous posaconazole. Encouragingly, our ssNMR 19 F– 13 C distance measurements offered corroborative evidence supporting these findings. Furthermore, employing principal component analysis on the X-ray PDF and ssNMR data sets enabled us to gain invaluable insights into the chemical nature of the intermolecular interactions governing the drug–polymer interplay. These outcomes not only furnish crucial structural insights facilitating the comprehension of the underlying mechanisms governing the physicochemical stability but also underscore the efficacy of synergistically harnessing X-ray PDF and ssNMR techniques, complemented by robust modeling strategies, to achieve a high-resolution exploration of amorphous structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The Signature C=C=O Stretch of Propenylketenes and Ketene Clusters [Book Chapter]

A combined experimental and theoretical approach has been used to examine the signature antisymmetric C=C=O stretch of prop-1-enylketene and prop-2-enylketene, as well as a series of ketene multimers and hydrates. Optimization and frequency calculations executed at the B3LYP/6-311G++(d,p) level of theory reveal four conformers of prop-1-enylketene and three conformers of prop-2-enylketene. These ketenes were generated via the pyrolysis of 3-pentenoic anhydride and 4-pentenoic anhydride, respectively, and isolated in low-temperature argon matrices prior to FTIR analysis. The resultant spectra display several bands consistent with B3LYP predictions. A similar computational and experimental survey of ketene multimers and hydrates, generated by the pyrolysis of acetic anhydride, has generated a list of frequencies for the antisymmetric C=C=O stretching mode. Furthermore, the results provide useful benchmarks for identification of propenylketenes in future experiments as well as insight for assigning other substituted ketenes in infrared spectra.

02 PETROLEUM↗
DOE OSTI2024

Unveiling the Multielectron Acceptor Properties of π-Expanded Pyracylene: Reversible Boat to Chair Conversion

In this work, the chemical reduction of a hybrid pyracylene-hexa-peri-hexabenzocoronene (HPH) nanographene was investigated with different alkali metals (Na, K, Rb) to reveal its remarkable multielectron acceptor abilities. The UV–vis and 1 H NMR spectroscopy monitoring of the stepwise reduction reactions supports the existence of all intermediate reduction states up to the hexaanion for HPH. Tuning the experimental conditions enabled the synthesis of the HPH anions with gradually increasing reduction states (up to –5) isolated with different alkali metal ions as crystalline materials. The single-crystal X-ray diffraction structure analysis demonstrates that the highly negatively charged HPH anions (–4 and –5) exhibit a drastic geometry change from boat-shaped (observed in the neutral parent, mono- and dianions) to a chair conformation, which was proved to be fully reversible by NMR spectroscopy. DFT calculations show that this geometry change is induced by an enhanced interaction between the coordinated metal ions and negatively charged HPH core in the chair conformation.

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

Conformational space exploration of cryo-EM structures by variability refinement

Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. Here, in order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SENTRA: A Modular Computational Graph Framework for Critical Mineral and Materials Supply Chains: Part I: Network Construction Latent-Quantity Estimation, and Temporal Graph Forecasting

Global supply chains for critical minerals and materials are complex, evolving networks of countries, products, production stages, and trade relationships. Existing analytical approaches are limited by fragmented data and static network representations that do not capture the dynamic production dependencies linking raw materials, intermediate products, and final goods across multiple countries. Trade and production statistics provide only a partial view of domestic production, inventories, and material flows, making it difficult to identify indirect sourcing pathways, hidden dependencies, and embedded foreign exposures. This paper introduces the Supply Chain Exposure Network Tracking and Risk Assessment (SENTRA) framework, a modular graph-based computational framework for constructing, analyzing, and forecasting dynamic supply chain networks. As the first paper in a three-part methodological series, it establishes the computational foundation of SENTRA by constructing a temporal attributed multi-relational graph whose nodes represent product–country pairs and whose edges encode observed trade and within-country value-chain relationships. Statistical estimation and constrained optimization recover latent production, final demand, and product input dependency coefficients while enforcing economic accounting constraints. Graph-derived exposure measures quantify direct, transshipment, value-chain, and multi-hop supply chain dependencies independently of the forecasting model. A temporal graph forecasting architecture based on a relational graph neural network then forecasts the evolution of the graph under mass-balance constraints with distribution-free conformal uncertainty quantification. Validation on the global aluminum supply chain shows that the learned graph representations recover economically meaningful supply chain structure, accurately forecast out-of-sample trade relationships, and produce well-calibrated prediction intervals. Subsequent papers apply this computational foundation to exposure assessment, disruption analysis, and scenario-based policy analysis, and extend the framework to multimaterial supply chain modeling and decision support.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the hot surface ignition of a wall-stagnating spray flame

The ignition of fuel sprays due to interaction with hot surfaces is an important phenomenon in the safety analysis of many engineering systems. We perform a parametric study of the hot surface ignition (HSI) of a fuel spray approaching a heated surface caused by the accidental leakage of a fuel line. Here, to this end, we employ a one-dimensional Eulerian-Eulerian formulation with a non-equilibrium evaporation model and a realistic chemical mechanism to describe $n$-dodecane fuel chemistry. We first describe and analyze the phenomenology of the unsteady processes leading to ignition using non-dimensionalized quantities. Through consideration of the temporal development of the most reactive mixture, we demonstrate that ignition occurs at a fuel-lean composition in a premixed region near the hot surface. Using non-dimensional parameters identified from the governing equations, we perform a parametric study of the time, location and local mixture composition at ignition and determine the ignition limits. We then identify the most important parametric sensitivities for physical analysis using a data-driven classification method. Our analysis demonstrates a contraction of the ignition limits with increased Stokes number and a regime of parametric insensitivity of igniting mixture composition. We also show that at high Damköhler numbers, the ignition location conforms to the parametric behavior of the thermal boundary layer, whereas at low Damköhler numbers approaching the ignition limit it reaches a near-unity value of the quenching Peclet number. We then compare the demonstrated parametric dependencies to the results of the quasi-steady asymptotic ignition literature, showing that our results are consistent with those obtained analytically within the limitations imposed by the simplified formulation of the latter.

42 ENGINEERING↗
DOE OSTI2021

Electrostatics, Charge Transfer, and the Nature of the Halide–Water Hydrogen Bond

Binary halide–water complexes X – (H 2 O) are examined by means of symmetry-adapted perturbation theory, using charge-constrained promolecular reference densities to extract a meaningful charge-transfer component from the induction energy. As is known, the X – (H 2 O) potential energy surface (for X = F, Cl, Br, or I) is characterized by symmetric left and right hydrogen bonds separated by a C 2v -symmetric saddle point, with a tunneling barrier height that is <2 kcal/mol except in the case of F – (H 2 O). Our analysis demonstrates that the charge-transfer energy is correspondingly small (<2 kcal/mol except for X = F), considerably smaller than the electrostatic interaction energy. Nevertheless, charge transfer plays a crucial role determining the conformational preferences of X – (H 2 O) and provides a driving force for the formation of quasi-linear X··· H–O hydrogen bonds. Here, charge-transfer energies correlate well with measured O–H vibrational redshifts for the halide–water complexes and also for OH – (H 2 O) and NO 2 – (H 2 O), providing some indication of a general mechanism.

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

A pyridoxal 5'-phosphate-dependent Mannich cyclase

Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyse a diverse range of chemical transformations. Despite their extraordinary functional diversity, no PLP-dependent enzyme is known to catalyse Mannich-type reactions, an important carbon–carbon bond-forming reaction in synthetic organic chemistry. Here we report the discovery of a biosynthetic enzyme LolT, a PLP-dependent enzyme catalysing a stereoselective intramolecular Mannich reaction to construct the pyrrolizidine core scaffold in loline alkaloids. Importantly, its versatile catalytic activity is harnessed for stereoselective synthesis of a variety of conformationally constrained α,α-disubstituted α-amino acids, which bear vicinal quaternary–tertiary stereocentres and various aza(bi)cyclic backbones, such as indolizidine, quinolizidine, pyrrolidine and piperidine. Furthermore, crystallographic and mutagenesis analysis and computational studies together provided mechanistic insights and structural basis for understanding LolT’s catalytic activity and stereoselectivity. As a whole, this work expands the biocatalytic repertoire of carbon–carbon bond-forming enzymes and increases our knowledge of the catalytic versatility of PLP-dependent enzymes.

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

Multipole-based Cable Braid Magnetic Penetration Model for Conducting Wires

In this report, we investigate the effects of conductor losses in a multipole-based cable braid magnetic penetration model. Our multipole model uses a mesh of the actual cable geometry, which enables us to model more complicated structures. After summarizing the first principles model formulation, we consider a one-dimensional array of wires, for which an analytical solution is known in the lossless case. We extend this solution to the lossy case by using a complex-valued radius. We also model this structure analytically using a conformal-mapping solution. We then compare both the self-impedance and the transfer impedance results from our first principles cable braid electromagnetic penetration model to those obtained using the analytical solutions. An analysis for various frequencies (and skin depths) usually encountered in cable modeling is reported. These results are found in good agreement up to a radius to half spacing ratio of about 0.7, demonstrating a robustness needed for many commercial and non-commercial cables.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Wire Arc Additive Manufacturing of Lightweight High Pressure Die Casting Tooling

Oak Ridge National Laboratory (ORNL) and Mercury Marine partnered to develop and test methods for additively manufactured tooling for aluminum die casting applications under CRADA agreement NFE-20-08193. Tooling is the largest capital expense for high production casting projects. The lead time for tooling is often measured in months with a typical project taking 9-12 months to realize Production Part Approval Process (PPAP) ready die cast samples. This project demonstrated the technical viability of rapidly produced steel components for high pressure die casting tooling via Wire Arc Additive Manufacturing (WAAM). A 410 stainless steel tool was redesigned and optimized with conformal cooling channels and additively manufactured. The finished tool was tested and used to produce over 4000 parts, which well surpassed expectations. A secondary objective was to evaluate the durability of multi-material additively manufactured (AM) components with conformal cooling. A large multi-material tool (H13 and 410SSNiMo) was manufactured using the same methods showing potential reductions in used material and cost. However, the H13 section sustained material cracking. Further analysis showed that the potential cause was the CTE mismatch of the two materials at higher temperatures. It is also suggested that the material mix can be used if the steel processing temperature does not exceed 600 ̊C.This project has shown high potential for using the WAAM technology for creating AM parts for aluminum dies casting. However, the multi-material approach requires extended study and tests.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Wire Arc Additive Manufacturing of Lightweight High Pressure Die Casting Tooling

Oak Ridge National Laboratory (ORNL) and Mercury Marine partnered to develop and test methods for additively manufactured tooling for aluminum die casting applications under CRADA agreement NFE- 20-08193. Tooling is the largest capital expense for high production casting projects. The lead time for tooling is often measured in months with a typical project taking 9-12 months to realize Production Part Approval Process (PPAP) ready die cast samples. This project demonstrated the technical viability of rapidly produced steel components for high pressure die casting tooling via Wire Arc Additive Manufacturing (WAAM). A 410 stainless steel tool was redesigned and optimized with conformal cooling channels and additively manufactured. The finished tool was tested and used to produce over 4000 parts, which well surpassed expectations. A secondary objective was to evaluate the durability of multi-material additively manufactured (AM) components with conformal cooling. A large multi-material tool (H13 and 410SSNiMo) was manufactured using the same methods showing potential reductions in used material and cost. However, the H13 section sustained material cracking. Further analysis showed that the potential cause was the CTE mismatch of the two materials at higher temperatures. It is also suggested that the material mix can be used if the steel processing temperature does not exceed 600 ˚C. This project has shown high potential for using the WAAM technology for creating AM parts for aluminum dies casting. However, the multi-material approach requires extended study and tests.

36 MATERIALS SCIENCE↗
DOE OSTI2022

ECP SOLLVE: Validation and Verification Testsuite Status Update and Compiler Insight for OpenMP

The OpenMP language continues to evolve with every new specification release, as does the need to validate and verify the new features that have been implemented by the different vendors. With the release of OpenMP 5.0 and OpenMP 5.1, new target offload and host-based features have been introduced to the programming model. While OpenMP continues to grow in maturity, there is an observable growth in the number of compiler and hardware vendors that support OpenMP. In this manuscript, the main focus is on evaluating the conformity and OpenMP implementation progress of various compiler vendors such as Cray, IBM, GNU, Clang/LLVM, NVIDIA, and Intel. More specifically, the 4.5, 5.0, and 5.1 versions of the OpenMP specification are analyzed. For our experimental setup, the Crusher and Summit computing systems hosted by Oak Ridge National Lab’s Computing Facilities are utilized. The effort of vendor agnostic analysis of these implementations is especially valuable for application developers who are using new OpenMP features to accelerate their scientific codes. Insights are presented into the current implementation status of various vendors, the progression of specific compiler’s support for OpenMP overtime, the subset of OpenMP 4.5, 5.0, and 5.1 that is supported by all compilers, and examples of how our test suite has influenced discussion regarding the correct interpretation of the OpenMP specification. By evaluating OpenMP conformity of pre-Exascale computing systems, the aim is to detail progress and status of AMD + Cray ecosystem before the system and their OpenMP implementation is used for mission critical applications when the first Exascale Computer Frontier is made available to applications.

Huber, Thomas↗
DOE OSTI2020

Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A unifying Bayesian framework for merging X-ray diffraction data

Novel X-ray methods are transforming the study of the functional dynamics of biomolecules. Key to this revolution is detection of often subtle conformational changes from diffraction data. Diffraction data contain patterns of bright spots known as reflections. To compute the electron density of a molecule, the intensity of each reflection must be estimated, and redundant observations reduced to consensus intensities. Systematic effects, however, lead to the measurement of equivalent reflections on different scales, corrupting observation of changes in electron density. Here, we present a modern Bayesian solution to this problem, which uses deep learning and variational inference to simultaneously rescale and merge reflection observations. We successfully apply this method to monochromatic and polychromatic single-crystal diffraction data, as well as serial femtosecond crystallography data. We find that this approach is applicable to the analysis of many types of diffraction experiments, while accurately and sensitively detecting subtle dynamics and anomalous scattering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of a scalar-based geometric parameterization approach for the crystal structure landscape of dithienylethene-based crystalline solids

Dithienylethenes (DTEs) are a promising class of organic photoswitches that can be used to create crystalline solids with properties controlled by light. However, the ability of DTEs to adopt multiple conformations, only one of which is photoactive, complicates the rational design of these materials. Herein, the synthesis and structural characterization of 19 crystalline solids containing a single DTE molecule are described. A novel D – D analysis of the molecular geometries obtained from rotational potential energy surface calculations and the ensemble of experimental structures were used to construct a crystal landscape for DTE. Of the 19 crystal structures, 17 contained photoinactive DTE rotamers and only 2 were photoactive. These results highlight the challenges associated with the design of these materials. Overall, the D – D analysis described herein provides rapid, effective and intuitive means of linking the molecular structure to photoactivity that could be applied more broadly to afford a general strategy for producing photoactive diarylethene-based crystalline solids.

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

Rapid High-Resolution Analysis of Polysaccharide-Lignin Interactions in Secondary Plant Cell Walls Using Proton-Detected Solid-State NMR

The plant secondary cell wall, a complex matrix composed of cellulose, hemicellulose, and lignin, is crucial for the mechanical strength and water-proofing properties of plant tissues, and serves as a primary source of biomass for biorenewable energy and biomaterials. Structural analysis of these polymers and their interactions within the secondary cell wall has been heavily relying on 13 C-based solid-state NMR techniques. In this study, we explore the application of 1 H-detected solid-state NMR techniques for rapid, high-resolution structural characterization of polysaccharides and lignin, demonstrated on the stems of hardwood eucalyptus. We explored the use of synthesized 2D spectra to resolve central 1 H resonances and the combined application of 3D hCCH and hCHH experiments for complete resonance assignment and unambiguous identification of lignin-carbohydrate interactions. Our findings emphasize the central role of acetylated three-fold xylan conformers, rather than two-fold, in stabilizing the carbohydrate-lignin interface, with glucuronic acid sidechains in eucalyptus glucuronoxylan colocalizing with lignin, revised cellulose-lignin interactions involving uncoated microfibril surfaces, and pectin-lignin interactions indicative of early-stage lignification. These results present a novel approach for rapid structural analysis of lignocellulosic biomaterials without the need for solubilization or extraction.

09 BIOMASS FUELS↗