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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Supramolecular and Hybrid Bonding Polymers

Staudinger established a century ago the existence of covalent macromolecules, work that led to the development of transformative materials of great benefit to society and a “quantum leap” in our understanding of biological systems. Over the past few decades the concept of supramolecular polymers has emerged–chemical systems in which structural units bond strongly to each other non-covalently. Herein, we discuss how these dynamic systems actually exist in the natural world and can create soft materials with structures, properties, and functions beyond the ones we know in Staudinger polymers. We reflect here on the potential of novel systems in which covalent and supramolecular polymers are chemically integrated and describe them as hybrid bonding polymers. This paper describes the concept with recent examples from the Stupp laboratory, and discusses their potential functions as robotic materials that mimic living matter and structures that offer new ideas on how to recycle and reuse soft materials.

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

Giant Dipole Moments: Remarkable Effects Mono‐, Di‐, and Tri‐ Hydrated 5,6‐Diaminobenzene‐1,2,3,4‐Tetracarbonnitrile

The molecule 5,6-diaminobenzene-1,2,3,4-tetracarbonnitrile (MOI) was first synthesized by Müllen and coworkers in 2016 and boasts an ultrastrong dipole moment of $14.1\pm 0.7$ Debye in THF. Gas phase DFT computations do not fully reflect this ultrastrong dipole moment, demonstrating the role of solvent in increasing this dipole moment. Here, we investigate the effect of solvent molecule position on the dipole moment of this species, computationally examining systems with giant dipole moments. These systems are optimized in the gas phase with the B3LYP functional, employing the aug-cc-pVTZ and def2-TZVP basis sets, as well as the B3LYP-D3BJ/aug-cc-pVTZ functional in Orca. Single point DLPNO-CCSD/aug-cc-pVDZ results were obtained from Orca and Psi4, as well as DLPNO-CCSD(T)/CBS information from Psi4. Additionally, these are compared to the dipole moments of di- and tri-hydrated systems, and the SMD models for THF and water at the B3LYP/aug-cc-pVTZ level of theory. The dissociation energies, HOMO-LUMO energy gaps, and dipole moments are presented. These metrics show the nh1nh1′ THF system boasts the largest dissociation energy and dipole moment of the singly solvated systems, due to its strong hydrogen bonding. The importance of solvent placement is highlighted and may guide the synthesis of macromolecules or organic frameworks incorporating the MOI or MOI-like subunits. Remarkably, a single solvent molecule provides a good model for the difference between the gas phase and solvated species. The predicted gas phase dipole moments computed with B3LYP/aug-cc-pVTZ for the MOI, its monohydrated complex, dihydrated complex, and its trihydrated complex are 9.6, 14.2, 16.0, and 16.8 Debye, respectively.

dipole↗
DOE OSTI2022

Anomalous structural recovery in the near glass transition range in a polymer glass: Data revisited in light of temperature variability in vacuum oven‐based experiments*

Abstract There is considerable interest in data reported by Cangialosi et al. [Cangialosi, D., Boucher, V. M., Alegría, A., & Colmenero, J. (2013). Physical Review Letters , 111 (9), 095701] that purportedly showed unusual irregular responses in the isothermal structural recovery behavior of glasses because the observation challenges the general view of the dynamics being smooth functions of time as observed in extensive dilatometric experiments by Kovacs [Kovacs, A. J. (1964). In Fortschritte der Hochpolymeren‐Forschung , 3 , 394–507. Springer, Berlin, Heidelberg.] in the 1960s. The reported data show an apparent two mechanism structural (enthalpy) recovery at aging temperatures ranging from 6 to 17 K below which is also controversial as it could not be reproduced in work from Koh and Simon [Koh, Y. P., & Simon, S. L. (2013). Macromolecules , 46(14), 5815–5821.] where a second plateau observed in the enthalpy loss curve was not reproduced in nearly 1‐year‐long experiments at 15 K below . Therefore, it is important to determine what might be possible reasons for the apparent non‐smooth relaxations. Here, we examine the possibility that the poor temperature control of a typical vacuum oven could explain the anomalous results. We used the Tool–Narayanaswamy–Moynihan (TNM) model of structural recovery to calculate the effect of typical vacuum oven temperature variation on the structural recovery of polystyrene and find that we can reproduce the reported experimental results. The issue of temperature control using a vacuum oven is discussed, and data from thermocouple measurements of temperature at various locations inside a vacuum oven are shown.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Chain trajectories, domain shapes, and terminal boundaries in block copolymers

The packing geometry of macromolecules in complex mesophases is of key importance to self-organization in synthetic and biological soft materials. While approximate or heuristic models rely on often-untested assumptions about how flexible molecules “fit in” to distinct locations of complex assemblies, physical assemblies derive from ensembles of fluctuating conformations, obscuring the connection between mesophase geometry and the underlying arrangements. Here, we present an approach to extract and analyze features of molecular packing in diblock block copolymer (BCP) melts, a prototypical soft matter system, based on the statistical description of chain conformations in self-consistent field (SCF) theory. We show how average BCP chain trajectories in ordered morphologies can be analyzed from the SCF-derived orientational order parameter of chain segments. We use these extracted trajectories to analyze the features of local packing geometry, including chain bending and tilt, as well as the terminal boundaries that delineate distinct domains in ordered BCP morphologies. In conclusion, we illustrate this analysis by focusing on measurable features of packing frustration in 2D (columnar) and 3D (spherical and bicontinuous) morphologies, notably establishing an explicit link between chain conformations in complex morphologies and their medial geometry.

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

Engineering highly stable variants of Corynactis californica green fluorescent proteins

Fluorescent proteins (FPs) are versatile biomarkers that facilitate effective detection and tracking of macromolecules of interest in real time. Engineered FPs such as superfolder green fluorescent protein (sfGFP) and superfolder Cherry (sfCherry) have exceptional refolding capability capable of delivering fluorescent readout in harsh environments where most proteins lose their native functions. Our recent work on the development of a split FP from a species of strawberry anemone, Corynactis californica, delivered pairs of fragments with up to threefold faster complementation than split GFP. We present the biophysical, biochemical, and structural characteristics of five full-length variants derived from these split C. californica GFP (ccGFP). These ccGFP variants are more tolerant under chemical denaturation with up to 8 kcal/mol lower unfolding free energy than that of the sfGFP. It is likely that some of these ccGFP variants could be suitable as biomarkers under more adverse environments where sfGFP fails to survive. A structural analysis suggests explanations of the variations in stabilities among the ccGFP variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗
DOE OSTI2021

Phase segregation mechanisms of small molecule-polymer blends unraveled by varying polymer chain architecture

As phase separation between the small-molecule semiconductor and the polymer binder is the key enabler of blend-based organic field-effect transistors (OFETs) fabricated by low-cost solution processing, it is crucial to understand the underlying phase separation mechanisms that determine the phase morphology, which significantly impacts device performance. Beyond the parameter space investigated in previous work, here we investigate the formation of blends by varying the branch architecture of the polymer binder and by shortening the solvent dry time using ultrasonic spray casting. The phase morphologies of the resulting blend films have been thoroughly characterized with a variety of techniques in three dimensions over multiple length scales, including AFM, energy-filtered transmission electron microscope, and neutron reflectivity, and have been correlated with electrical transport performance. From the results, we have inferred that the phase morphology is kinetically determined, limited by the inherent slow movement of polymer macromolecules. The kinetic picture, supported by molecular dynamics modeling, not only consistently explains our observations but also resolves inconsistencies in previous works. The achieved mechanistic understanding will guide further optimization of blend-based organic electronics, such as OFETs and organic photovoltaics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction

The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-reaching implications for a range of problems, including metabolomics. However, problems such as predicting the bound structure of a protein–ligand complex along with its affinity have proven to be an enormous challenge. In recent years, machine learning-based methods have proven to be more accurate than older methods, many based on simple linear regression. Nonetheless, there remains room for improvement, as these methods are often trained on a small set of features, with a single functional form for any given physical effect, and often with little mention of the rationale behind choosing one functional form over another. Moreover, it is not entirely clear why one machine learning method is favored over another. Here, we endeavor to undertake a comprehensive effort towards developing high-accuracy, machine-learned scoring functions, systematically investigating the effects of machine learning method and choice of features, and, when possible, providing insights into the relevant physics using methods that assess feature importance. Here, we show synergism among disparate features, yielding adjusted R 2 with experimental binding affinities of up to 0.871 on an independent test set and enrichment for native bound structures of up to 0.913. When purely physical terms that model enthalpic and entropic effects are used in the training, we use feature importance assessments to probe the relevant physics and hopefully guide future investigators working on this and other computational chemistry problems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Neutron scattering maps the higher-order assembly of NADPH-dependent assimilatory sulfite reductase

Precursor molecules for biomass incorporation must be imported into cells and made available to the molecular machines that build the cell. Sulfur-containing macromolecules require that sulfur be in its S2- oxidation state before assimilation into amino acids, cofactors, and vitamins that are essential to organisms throughout the biosphere. In α-proteobacteria, NADPH-dependent assimilatory sulfite reductase (SiR) performs the final six-electron reduction of sulfur. SiR is a dodecameric oxidoreductase composed of an octameric flavoprotein reductase (SiRFP) and four hemoprotein metalloenzyme oxidases (SiRHPs). SiR performs the electron transfer reduction reaction to produce sulfide from sulfite through coordinated domain movements and subunit interactions without release of partially reduced intermediates. Efforts to understand the electron transfer mechanism responsible for SiR’s efficiency are confounded by structural heterogeneity arising from intrinsically disordered regions throughout its complex, including the flexible linker joining SiRFP’s flavin-binding domains. As a result, high-resolution structures of SiR dodecamer and its subcomplexes are unknown, leaving a gap in the fundamental understanding of how SiR performs this uniquely large-volume electron transfer reaction. In this work, we use deuterium labeling, in vitro reconstitution, analytical ultracentrifugation (AUC), small-angle neutron scattering (SANS), and neutron contrast variation (NCV) to observe the relative subunit positions within SiR’s higher-order assembly. AUC and SANS reveal SiR to be a flexible dodecamer and confirm the mismatched SiRFP and SiRHP subunit stoichiometry. NCV shows that the complex is asymmetric, with SiRHP on the periphery of the complex and the centers of mass between SiRFP and SiRHP components over 100 Å apart. SiRFP undergoes compaction upon assembly into SiR’s dodecamer and SiRHP adopts multiple positions in the complex. The resulting map of SiR’s higher-order structure supports a cis/trans mechanism for electron transfer between domains of reductase subunits as well as between tightly bound or transiently interacting reductase and oxidase subunits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗
DOE OSTI2021

Multiple charging and chemical stability of tripodal catholyte redoxmers

Macromolecular catholyte materials store multiple positive charges in all-organic redox flow cells. Presently, little is known about the electronic structure and chemical stability of these macromolecules in different states of charge. Here we demonstrate that in propeller-like catholyte trimers (tripods), chemical stability increases when they become fully charged.

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

Are we modeling the properties of unconventional shales correctly?

Technological advancements have led to impressive growth in hydrocarbon (HC) production from unconventional shale reservoirs. However, major limiting factors in shale gas development are i) low recovery of gas in place (<20%), (ii) a rapid decline in well productivity, iii) release of contaminants, despite the use of advanced hydraulic fracturing fluids and multiple fracturing stages. This is mainly due to a lack of understanding of the nanoscale physicochemical properties of shales, especially that of kerogen, the macromolecule that is not only the source of the majority of the HC’s in shales but also holds most of the HC’s in adsorbed state. Over the last few years, a large number of studies have been published on simulating the physicochemical properties of shale utilizing molecular models of kerogen. However, the molecular models of kerogen input into these simulations are based on the kerogen “type” derived from a very limited number of shale samples. In this paper, we examine the variations that can exist in kerogen structure within a particular kerogen “type” across different shale basins and single shale basin at similar thermal maturity levels. We propose that using kerogen “type” based structural models for molecular simulations could lead to inaccurate estimation of HC reserves, HC recovery, HC production, frackability, and quantity and quality of produced water. Our study highlights the need for developing a better classification of kerogen based on its “molecular structure” instead of “type” for a more accurate prediction of physicochemical properties of shales.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2025

Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features

Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.

Bio-based polymer↗
DOE OSTI2020

Ionic complexation of endblock-sulfonated thermoplastic elastomers and their physical gels for improved thermomechanical performance

Thermoplastic elastomers (TPEs) composed of nonpolar triblock copolymers constitute a broadly important class of (re)processable network-forming macromolecules employed in ubiquitous commercial applications. Physical gelation of these materials in the presence of a low-volatility oil that is midblock-selective yields tunably soft TPE gels (TPEGs) that are suitable for emergent technologies ranging from electroactive, phase-change and shape-memory responsive media to patternable soft substrates for flexible electronics and microfluidics. Many of the high-volume TPEs used for these purposes possess styrenic endblocks that are inherently limited by a relatively low glass transition temperature. To mitigate this shortcoming, we sulfonate and subsequently complex (and physically crosslink) the endblocks with trivalent Al3+ ions. Doing so reduces the effective hydrophilicity of the sulfonated endblocks, as evidenced by water uptake measurements, while concurrently enhancing the thermomechanical stability of the corresponding TPEGs. Chemical modification results, as well as morphological and property development, are investigated as functions of the degree of sulfonation, complexation and TPEG composition. (C) 2020 Published by Elsevier Inc.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Infrared laser ablation of poly(vinylidene fluoride): The Loss of HF

The mechanism and kinetics of infrared laser ablation of poly(vinylidene fluoride) (PVDF) in vacuum have been investigated to understand how this can be used as a polymer processing technology. The laser heats the surface and initiates decomposition of macromolecules in the molten polymer layer which rapidly leads to production of an ablative flow of polymer decomposition products. There is only a short induction period of up to 2 s before ablation begins. After the initial period, the rate of mass loss increases linearly with the time of laser exposure. Spherical particles with an average diameter of about 100 nm are formed on the surface of the powder coating obtained by laser ablation. Here, the particle distribution ranges from 50 nm to 300 nm. The main gaseous product of ablation is HF from dehydrofluorination. A second important ablation process is the formation of gaseous carbenes generated during secondary reactions. Proposed ablation reactions due to laser-induced thermal dehydrofluorination occur in two stages. In the first stage, a double bond appears in PVDF due to direct loss of HF. Subsequent detachment of HF leads to the appearance of both triple bonds and cumulene bonds.

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

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Montage electron tomography of vitrified specimens

Cryo-electron tomography provides detailed views of macromolecules in situ. However, imaging a large field of view to provide more cellular context requires reducing magnification during data collection, which in turn restricts the resolution. To circumvent this trade-off between field of view and resolution, we have developed a montage data collection scheme that uniformly distributes the dose throughout the specimen. In this approach, sets of slightly overlapping circular tiles are collected at high magnification and stitched to form a composite projection image at each tilt angle. These montage tilt-series are then reconstructed into massive tomograms with a small pixel size but a large field of view. For proof-of-principle, we applied this method to the thin edge of HeLa cells. Thon rings to better than 10 Å were detected in the montaged tilt-series, and diverse cellular features were observed in the resulting tomograms. These results indicate that the additional dose required by this technique is not prohibitive to performing structural analysis to intermediate resolution across a large field of view. We anticipate that montage tomography will prove particularly useful for lamellae, increase the likelihood of imaging rare cellular events, and facilitate visual proteomics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Resolving protein-mineral interfacial interactions during in vitro mineralization by atom probe tomography

Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.

36 MATERIALS SCIENCE↗