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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

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

Conformational diversity of 1-phenylpiperidin-4-one in the gas phase

Conformational preferences of substituted, saturated cyclic ketones may deviate from those of their parent analogues. 1-Phenylpiperidin-4-one was found to exist in several forms differing by not only position (axial or equatorial) of the aryl-substituent but also by a configuration of the piperidine cycle itself: chair-Eq, chair-Ax and twist-Tw. Here, the ratios of the co-existing species contributions in gas phase predicted by various quantum chemical calculations were confirmed by synchronous gas-phase electron diffraction and mass spectrometric experiments carried out for the vapor at 337 K demonstrating a best fit with the B3LYP-D3/cc-pVTZ combination: Eq:Ax:Tw=55(13):22(9):23(10) vs. 40:35:25.

1-phenylpiperidin-4-one↗
DOE OSTI2020

Synthesis and spectroscopic characterization of actinyl(VI) tetrahalide coordination compounds containing 2, 2'-bipyridine

A series of three new actinide tetrahalide coordination compounds containing 2,2'-bipyridinium (H 2 bpy) have been synthesized by room temperature evaporation and characterized via single crystal X-ray diffraction, Raman spectroscopy, and infrared spectroscopy. The solid-state compounds (Np1, U1, and U2) contain the AnO 2 2+ cation coordinated to four halide (chloride or bromide) atoms to form the anionic tetrahalide molecular unit [AnO 2 X 4 ] 2– (X = Cl, Br) and are charge balanced by the 2,2'-bipyridinium cations that engage in electrostatic interactions with the actinyl complex. Np1 (N 2 C 10 H 10 )[NpO 2 Cl 4 ] contains 2,2'-bipyridine in the cis conformation where both the nitrogen atoms are directed towards the [NpO 2 Cl 4 ] 2– monomer. Within U1 (N 2 C 10 H 9 )[UO 2 Cl 4 ], the 2,2'-bipyridine is in a trans conformation, and found in the same orientation in the isomorphous structure U2 (N 2 C 10 H 9 )[UO 2 Br 4 ]. The compounds were further characterized by vibrational spectroscopy with specific interest in the actinyl cation. Raman spectroscopy provided information on the actinyl symmetric stretch (ν 1 ) whereas IR spectroscopy is used to determine the location of the asymmetric stretch (ν 3 ). Here, spectral similarities are observed between the two isomorphous structures, but slight variations across the series of structures are found to be associated with bipyridine bands in the various conformations. Additional analysis of these vibrational features in U1 and U2 provided information on the actinyl force constants, allowing insight into the relative uranyl bond strength that was compared to similar tetrahalide compounds.

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

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations

Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.

Biochemistry & Molecular Biology↗
DOE OSTI2022

A Combined DFT, Energy Decomposition, and Data Analysis Approach to Investigate the Relationship Between Noncovalent Interactions and Selectivity in a Flexible DABCOnium/Chiral Anion Catalyst System

Developing strategies to study reactivity and selectivity in flexible catalyst systems has become an important topic of research. Herein, we report a combined experimental and computational study aimed at understanding the mechanistic role of an achiral DABCOnium cofactor in a regio- and enantiodivergent bromocyclization reaction. In this study, it was found that electron-deficient aryl substituents enable rigidified transition states via an anion–π interaction with the catalyst, which drives the selectivity of the reaction. In contrast, electron-rich aryl groups on the DABCOnium result in significantly more flexible transition states, where interactions between the catalyst and substrate are more important. An analysis of not only the lowest-energy transition state structures but also an ensemble of low-energy transition state conformers via energy decomposition analysis and machine learning was crucial to revealing the dominant noncovalent interactions responsible for observed changes in selectivity in this flexible system.

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

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗
DOE OSTI2020

Influence of Added Salt on Chain Conformations in Poly(ethylene oxide) Melts: SANS Analysis with Complications

Poly(ethylene oxide) (PEO)-based electrolytes have gained increasing attention in both the rechargeable battery industry and fundamental research, but any influence of the ions on the polymer conformation is not fully understood. Small-angle neutron scattering (SANS) is a powerful means to determine single-polymer chain conformations. We conducted SANS experiments on 50:50 blends of perdeuterated PEO (dPEO) and hydrogenous PEO (hPEO) of two different molecular weights (20 and 40 kDa) doped with two different salts (LiTFSI and LiClO 4 ) at various concentrations. An additional measurement with LiI is also reported. The scattering profiles of salt-doped dPEO/hPEO blends were measured, and the incoherent scattering from dPEO and hPEO doped with salt was measured separately. A strong low q upturn was observed in some of the blends and in the pure dPEO homopolymers. The statistical segment lengths of PEO–salt mixtures were derived using a Kratky analysis. The segment length decreases modestly with increasing amounts of LiTFSI but apparently first increases then decreases with added LiClO 4 . At the highest salt concentration examined (r = [Li+]/[EO] = 0.125), a roughly 10% decrease in the statistical segment length was observed in both LiTFSI and LiClO 4 -doped PEOs, for both molecular weights. This work confirms that added salt causes a contraction of the PEO chain dimensions, but the effect appears slightly weaker than reported recently. Certain difficulties in data analysis are also discussed, including the unexplained low q scattering even in pure deuterated polymers, uncertainties in background subtraction, and inappropriate application of the Debye function.

36 MATERIALS SCIENCE↗
DOE OSTI2020

The arbitrary-order virtual element method for linear elastodynamics models. Convergence, stability and dispersion-dissipation analysis.

We design the conforming virtual element method for the numerical approximation of the two dimensional elastodynamics problem. We prove stability and convergence of the semi-discrete approximation and derive optimal error estimates under $\textit{h}$-refinement in both the energy and the $L^2$ norms, and optimal error estimates under $\textit{p}$-refinement in the energy norm. The performance of the proposed virtual element method is assessed on a set of different computational meshes, including non-convex cells up to order four in the h-refinement setting. Exponential convergence is also experimentally observed under p-refinement. Finally, we present a dispersion-dissipation analysis for both the semi-discrete and fully-discrete schemes, showing that polygonal meshes behave as classical simplicial/quadrilateral grids in terms of dispersion-dissipation properties.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Enantioselective Hydrodifluoroalkylation of Alkenes with Conformationally Tuned Peptidyl Hydrogen Atom Transfer Catalysts

Here, we report the enantioselective hydrodifluoroalkylation of alkenes proceeding via an asymmetric hydrogen atom transfer (HAT) event catalyzed by thiol-containing tetrapeptides. Photocatalytic generation of a difluoroacetyl radical followed by carbon–carbon bond formation results in a prochiral carbon-centered radical that engages with the chiral catalyst. A trialkylamine reductant is proposed to turn over the catalyst in this net-reductive transformation. Notably, incorporating an (S)-β-methyl-substituted cysteine as the N-terminal residue improved selectivity relative to that of the native N-terminal cysteine (Cys) residue, and X-ray crystallographic analysis supports the conformational underpinning of this effect. A range of enantioenriched γ-substituted amides were synthesized in up to a 96:4 enantiomeric ratio, demonstrating the broad functional group tolerance of this method. Models accounting for asymmetric induction are proposed with supporting DFT calculations.

08 HYDROGEN↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗
DOE OSTI2020

The arbitrary‐order virtual element method for linear elastodynamics models: convergence, stability and dispersion‐dissipation analysis

Abstract We design the conforming virtual element method for the numerical approximation of the two‐dimensional elastodynamics problem. We prove stability and convergence of the semidiscrete approximation and derive optimal error estimates under h ‐ and p ‐refinement in both the energy and the L 2 norms. The performance of the proposed virtual element method is assessed on a set of different computational meshes, including nonconvex cells up to order four in the h ‐refinement setting. Exponential convergence is also experimentally observed under p ‐refinement. Finally, we present a dispersion‐dissipation analysis for both the semidiscrete and fully discrete schemes, showing that polygonal meshes behave as classical simplicial/quadrilateral grids in terms of dispersion‐dissipation properties.

Antonietti, Paola F.↗
DOE OSTI2020

The inversion formula and 6j symbol for 3d fermions

In this work we study the 6 j symbol of the 3 d conformal group for fermionic operators. In particular, we study 4-point functions containing two fermions and two scalars and also those with four fermions. By using weight-shifting operators and harmonic analysis for the Euclidean conformal group, we relate these spinning 6 j symbols to the simpler 6 j symbol for four scalar operators. As one application we use these techniques to compute 3 d mean field theory (MFT) OPE coefficients for fermionic operators. We then compute corrections to the MFT spectrum and couplings due to the inversion of a single operator, such as the stress tensor or a low-dimension scalar. These results are valid at finite spin and extend the perturbative large spin analysis to include non-perturbative effects in spin.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗