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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 OSTI2021

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. Here, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20 3 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

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

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes

Protein–protein interactions play a key role in mediating numerous biological functions, with more than half the proteins in living organisms existing as either homo- or hetero-oligomeric assemblies. Protein subunits that form oligomers minimize the free energy of the complex, but exhaustive computational search-based docking methods have not comprehensively addressed the challenge of distinguishing a natively bound complex from non-native forms. Current protein docking approaches address this problem by sampling multiple binding modes in proteins and scoring each mode, with the lowest-energy (or highest scoring) binding mode being regarded as a near-native complex. However, high-scoring modes often match poorly with the true bound form, suggesting a need for improvement of the scoring function. Here in this study, we propose a scoring function, KFC-E, that accounts for both conservation and coevolution of putative binding hotspot residues at protein–protein interfaces. We tested KFC-E on four benchmark sets of unbound examples and two benchmark sets of bound examples, with the results demonstrating a clear improvement over scores that examine conservation and coevolution across the entire interface.

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

Helical Organic and Inorganic Polymers

Despite being a staple of synthetic plastics and biomolecules, helical polymers are scarcely studied with Gaussian-basis-set ab initio electron-correlated methods on an equal footing with molecules. This article introduces an ab initio second-order many-body Green’s-function [MBGF(2)] method with nondiagonal, frequency-dependent Dyson self-energy for infinite helical polymers using screw-axis-symmetry-adapted Gaussian-spherical-harmonics basis functions. Together with the Gaussian-basis-set density-functional theory for energies, analytical atomic forces, translational-period force, and helical-angle force, it can compute correlated energy, quasiparticle energy bands, structures, and vibrational frequencies of an infinite helical polymer, which smoothly converge at the corresponding oligomer results. These methods can handle incommensurable structures, which have an infinite translational period and are hard to characterize by any other method, just as efficiently as commensurable structures. We apply them to polyethylene (2/1 helix), polyacetylene (Peierls’ system), and polytetrafluoroethylene (13/6 helix) to establish the quantitative accuracy of MBGF(2)/cc-pVDZ in simulating their (angle-resolved) ultraviolet photoelectron spectra, and of B3LYP/cc-pVDZ or 6-31G** in reproducing their structures, infrared and Raman band positions, phonon dispersions, and (coherent and incoherent) inelastic neutron scattering spectra. We then predict the same properties for infinitely catenated chains of nitrogen or oxygen and discuss their possible metastable existence under ambient conditions. They include planar zigzag polyazene (N2)x (Peierls’ system), 11/3-helical isotactic polyazane (NH)x, 9/4-helical isotactic polyfluoroazane (NF)x, and 7/2-helical polyoxane (O)x as potential high-energy-density materials.

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

Effect of Background Electrolyte Composition on the Interfacial Formation of Th(IV) Nanoparticles on the Muscovite (001) Basal Plane

Understanding the impact of actinide nanoparticle (NP) formation is important to assess radionuclide mobility in the environment. We combined surface X-ray diffraction (SXRD) and in situ AFM to investigate the previously reported unusual electrolyte effects on Th uptake on mica. At low [Th] (0.1 mM), interfacial structures show a broad Th electron density (~50 Å). A linear decrease of Th uptake with decreasing hydration enthalpy of the electrolyte cation (Li+, K+, NH4+, and Cs+) indicates a competitive effect between Th and the electrolyte cation. Na+ is a clear outlier from this trend. In situ AFM imaging confirms the results. Particles show a vertical size of ~1–2 nm and larger lateral dimensions of ~10–20 nm, which is typical for particles formed at interfaces (heterogeneous nucleation). At high [Th] = 1 and 3 mM, all investigated electrolytes (ACl, A = Li+, Na+, K+) show similar Th uptake, indicating a much smaller impact of electrolyte composition. The interfacial structures are dominated by a high Th loading at a distinct distance (~6.5 Å) from the surface. Therefore, the main retention mechanism at high [Th] is suggested to be the sorption of Th NPs aggregated from Th oligomers present in solution (homogeneous nucleation).

Neumann, J↗
DOE OSTI2021

Impact of Hydration on Supported V 2 O 5 /TiO 2 Catalysts as Explored by Magnetic Resonance Spectroscopy

Supported vanadium oxide catalysts are important industrial materials for a wide array of chemical transformations. The condition of surface hydration is of particular interest as a reflection of the state of a freshly manufactured catalysts prior to its activation in catalytic reactors or under conditions of photocatalysis where surface vandia are exposed to moisture. Under such conditions, the surface vanadia species undergo structural changes as evidenced by 51 V MAS NMR in this study. For low surface vanadia densities on titania, a modest trend towards the formation of dimeric and oligomeric vanadia species was observed under hydrated conditions when compared to the corresponding dehydrated catalyst, which contains a large abundance of monomeric vanadia species. The incorporation of tungsten oxide to the V 2 O 5 /TiO 2 catalyst with low surface vanadia density, however, is found to better stabilize the surface vanadia species on the titania support upon hydration than its tungsta-free counterpart. This stabilization is not an intrinsic property of more extensively oligomerized surface vanadia species in the presence of tungsten oxide, evidenced by conditions of high concentrations of surface vanadia oligomers on titania that exhibit dramatic structural changes upon hydration. At high surface vanadia coverage under hydrated environments, the simultaneous observation of crystalline V 2 O 5 nanoparticles and a mobile phase of surface vanadia species is apparent, where vanadia species are dissolved in the thin hydration layer on the titania support. These new findings have broad implications on the behavior of other metal oxide species on high surface oxide supports under hydrated conditions.

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

Phase Control of Nanocrystalline Inclusions in Bioprecipitated Titania with a Panel of Mutant Silica-Binding Proteins

The biomimetic route to inorganic synthesis presents an opportunity to produce complex materials with superior properties under ambient conditions and from nontoxic precursors. While there has been significant progress in using solid-binding peptides (SBPs), proteins, and organisms to produce a variety of inorganic and hybrid structures, it has been more challenging to understand the interplay of solution conditions and solid-binding peptide (SBP) sequence, structure, and self-association on synthetic outcomes. Here, we show that fusing the Car9 silica-binding peptide—but not the silaffin-derived R5 peptide—to superfolder green fluorescent protein (sfGFP) enhances the ability of micromolar concentrations of protein to induce rapid titania (TiO 2 ) precipitation from acidified solutions of tetrakis(di-lactato)-oxo-titanate (TiBALDH). TiO 2 is produced stoichiometrically and although predominantly amorphous, contains nanosized anatase and monoclinic TiO 2 (B) inclusions. Remarkably, the phase of these nanocrystallites can be tuned from about 80% TiO 2 (B) to about 65% anatase by using Car9 mutants impaired in their ability to drive the formation of higher-order sfGFP-Car9 oligomers. Our results suggest that the presentation of multiple basic side chains in an extended plane formed by SBP self-association is critical to template the formation of monoclinic crystallites and underscore the subtle influence that single or dual substitutions in dodecameric SBPs can exert on the yield and crystallinity of biomineralized inorganics.

mutagenesis↗
DOE OSTI2025

Molar-Mass-Dependent Partitioning of Polyethylene in Nanopores of Model Catalyst Supports from Small-Angle Neutron Scattering

Heterogeneous catalysis offers opportunities to enhance valorization of plastic waste via chemical recycling through control of the upcycled product distributions. Minimizing low-value light hydrocarbons is desired; however, fundamental insights into how to control selectivity are lacking. Here we use contrast variation with small-angle neutron scattering (SANS), model perdeuterated polyethylenes (dPEs), and a model liquid hydrocracking product (tetradecane) to quantify polymer partitioning within mesoporous silica (SBA-15). Polyethylene concentration within the mesopores is increased relative to the bulk solution, and this partitioning increases as the temperature increases. However, this polyethylene partitioning is maximized when the radius of gyration of the polymer chains is comparable to the SBA-15 pore size (10 nm). An increased partitioning at higher temperatures is attributed to entropically driven adsorption of PE within the mesopores. There is no observed preferential partitioning of hexatriacontane (a model oligomer) within the mesopores at the temperatures examined. Furthermore, these results suggest that pore size could promote the selective partitioning of polymer species into the mesopores by size. For plastic upcycling, pore-size-dependent partitioning should increase the probability for the reaction of long polymers over oligomeric and small-molecule polyolefin depolymerization products.

Adsorption↗
DOE OSTI2025

Chain Flexibility and Structure of a Polyimide Copolymer: Revisiting the Freely Rotating Chain Model

Poly(4–4′-oxydiphenylene-pyromellitimide)-based polyimides─trade name Kapton─have wide-ranging engineering applications owing to their thermal and mechanical stability, but little is known about underlying chain-level characteristics. While theoretical models have conceptualized Kapton as inflexible polycyclic rods separated by freely rotating diphenyl ether hinge groups, the model’s core predictions remain untested and subtleties of the relaxation behavior are missed, which atomistic modeling can resolve. To these ends, we examine all-atom Kapton structures in crystalline and glassy amorphous configurations using a DFT-validated class II force field. Constructing amorphous configurations is challenging, as the fused-ring-containing backbone has slow relaxation dynamics and scaling suggestive of entanglements even in oligomers. In conclusion, we find larger backbone rearrangements of the linear polycyclic segments about ether groups that are consistent with the rod-hinge picture on the monomer scale, whereas a ring rotation analysis suggests partially flexible rod-like segments and involves multiple facile rotational relaxation modes.

Liesen, Nicholas T. [Lawrence Livermore National L↗
DOE OSTI2025

Modulating Poly(oligocyclobutane) Properties Through Backbone Modifications

Poly(1,n′-divinyl)oligocyclobutane (pDVOCB) has emerged as a class of poly(cycloolefin) that is amenable to chemical recycling and demonstrates promising thermomechanical properties. However, their high melting temperatures coupled with insolubility makes melt processing challenging due to thermo-oxidation of internal alkenes. To address these issues, we describe a series of polymers incorporating modifications to the pDVOCB backbone and analyze the effects on material stability and processability. Intentional migration of the internal 1,2-disubstituted alkenes to an exocyclic trisubstituted position yields isomerized pDVOCB (IpDVOCB) which exhibits a depression of thermal transitions by up to 50 °C. Conversely, elimination of stereoirregularity between enchained DVOCB oligomers through alkene saturation yields hydrogenated pDVOCB (HpDVOCB), resulting in elevated thermal transitions by up to 30 °C. Furthermore, these shifts are attributed to changes in crystal defect density which is strongly influenced by chain stereoregularity. Understanding these behaviors guides future polymer design and expands the control and use of this new class of recyclable poly(cycloolefin)s.

Differential scanning calorimetry↗
DOE OSTI2019

Efficient Multiscale Optoelectronic Prediction for Conjugated Polymers

Conjugated polymers represent a high-potential material class due to the tunability of their optoelectronic properties via straightforward processing protocols. However, to in silico tailor these optoelectronic properties, one must compute the conformationally dependent electronic structure over mesoscopic length and time scales. This task represents a challenging multiscale computational problem in which quantum chemistry and atomistic or coarse-grained molecular dynamics must be integrated. Recently, we introduced a methodology, called electronic coarse graining (ECG), that utilizes artificial neural networks to compute ab initio quality electronic structures using only the reduced degrees of freedom of coarse-grained models. Here, we adapt ECG to variable-molecular weight conjugated oligomers by casting the problem in the framework of sequence detection. A machine-learning (ML) architecture employing one-dimensional convolutional neural networks and long short-term memory networks is utilized to compute ground-state orbital energies, charge density distributions, and optical spectra solely from the coarse-grained model's configurational degrees of freedom. Robust molecular weight transferability for ECG is established via a A-ML approach that leverages model electronic Hamiltonians for ground and excited-state property determination. The accuracy and transferability of the ECG methodology opens the door for scalable optoelectronic property prediction in conjugated polymers directly from coarse-grained degrees of freedom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Toughening by Nanodroplets: Polymer–Droplet Biocomposite with Anomalous Toughness

The development of new polymer composites is highly dependent on the design of novel fillers that can bring more benefits in the design and control of structure–property–function than conventional solid particles. Here, inspired by the unique coupling structures of tough mussel byssus, we employ nanodroplets of high-boiling-point oligomers as the liquid filler to fabricate a new class of polymer–droplet composites (PDCs). The combination of nanodroplets and chain end/tail modifier in PDCs finally generates soft-coupling structures with chain ends coupled by the nanodroplets. With this strategy, brittle poly(lactic acid) is successfully transformed into a tough bioplastic with toughness improved by over 2000% via a minimal amount of the modifiers (1.5 wt %). Moreover, the composites show unexpected speed-enhanced energy absorption capability. A soft-coupling toughening mechanism is further proposed for the first time to understand the PDCs’ mechanical properties. This work also indicates the potential of nanodroplets as a new tool for tuning the mechanical properties and even functions of polymer composites.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Nanoparticle-Mediated Assembly of Peptoid Nanosheets Functionalized with Solid-Binding Proteins: Designing Heterostructures for Hierarchy

The fabrication of ordered architectures that intimately integrate polymer, protein and inorganic components remains difficult. Two promising building blocks to tackle this challenge are peptoids, peptide mimics capable of self-assembly into well-defined structures, and solid-binding peptides, which offer a biological path to controlled inorganic assembly. Here, we report on the synthesis of 3.3 nm-thick, thiol-reactive peptoid nanosheets from equimolar mixtures of unmodified and maleimide-derivatized versions of the Nbpe 6 Nce 6 oligomer, optimize the location of engineered cysteine residues in silica-binding derivatives of superfolder green fluorescent protein for maleimide conjugation, and react the two components to form proteinpeptoid hybrids exhibiting partial or uniform protein coverage on both of their sides. Using 10 nm silica nanoparticles, we trigger the stacking of these 2D structures into a multi-layer material comprised of alternating peptoid, protein and organic layers. This simple and modular approach to hierarchical hybrid synthesis should prove useful in bioimaging and photocatalysis applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Six-Letter DNA Nanotechnology: Incorporation of Z-P Base Pairs into Self-Assembling 3D Crystals

Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for information storage and retrieval as well as useful for basic biotechnologies. In tandem, nucleic acid nanotechnology has seen the use of information-based “semantomorphic” encoding to drive the self-assembly of a vast array of supramolecular devices. To establish the effectiveness of AEGIS toward nanotechnological applications, we investigated the ability of a six-letter alphabet composed of A:T, G:C and synthetic Z:P (Z, 6-amino-3-(1'-β- D-2'-deoxy ribofuranosyl)-5-nitro-(1H)-pyridin-2-one; P, 2-amino-8-(1'- β-D-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8H)-4-one) base pairs to engage in 3D self-assembly. We found that crystals could be programmably assembled from AEGIS oligomers. We conclude that unnatural base pairs can be used for the topological self-assembly of crystals. We anticipate the expansion of AEGISbased nucleic acid nanotechnologies to enable the development of novel nanomaterials, high-fidelity signal cascades, and dynamic nanoscale devices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electrolyte Design for Silicon-Based Li-Ion Battery Guided by Chemical Reactivity of Solvents with a Model Silicon Anode

Here, the use of a model compound trimethylsilyllithium was demonstrated to study the chemical reactions of electrolyte with as a principal guide to design electrolyte for silicon-based Li-ion battery. Me 3 Si - anion initiates ring-opening polymerization of EC leading to the formation of poly(ethylene ether carbonate), which subsequently defragments into oligomers and dissolves in electrolyte. FEC was found to react differently, generating LiF and vinylene carbonate (VC). Further reaction of VC with Me 3 SiLi generated poly(hydroxymethylene), which is a nonsoluble polymer and the critical SEI component. The insights from this study have guided the new electrolyte design for the Si-based battery.

25 ENERGY STORAGE↗
DOE OSTI2024

Deep-Learning Interatomic Potential Connects Molecular Structural Ordering to the Macroscale Properties of Polyacrylonitrile

Polyacrylonitrile (PAN) is an important commercial polymer, bearing atactic stereochemistry resulting from nonselective radical polymerization. As such, an accurate, fundamental understanding of governing interactions among PAN molecular units is indispensable for advancing the design principles of final products at reduced processability costs. While ab initio molecular dynamics (AIMD) simulations can provide the necessary accuracy for treating key interactions in polar polymers, such as dipole–dipole interactions and hydrogen bonding, and analyzing their influence on the molecular orientation, their implementation is limited to small molecules only. Herein, we show that the neural network interatomic potentials (NNIPs) that are trained on the small-scale AIMD data (acquired for oligomers) can be efficiently employed to examine the structures and properties at large scales (polymers). NNIP provides critical insight into intra- and interchain hydrogen-bonding and dipolar correlations and accurately predicts the amorphous bulk PAN structure validated by modeling the experimental X-ray structure factor. Furthermore, the NNIP-predicted PAN properties, such as density and elastic modulus, are in good agreement with their experimental values. Overall, the trend in the elastic modulus is found to correlate strongly with the PAN structural orientations encoded in the Hermans orientation factor. In conclusion, this study enables the ability to predict the structure–property relations for PAN and analogues with sustainable ab initio accuracy across scales.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structure-Activity Relationships of Hydrothermally Aged Titania-Supported Vanadium-Tungsten Oxide Catalysts for SCR of NOx Emissions with NH3

Supported V2O5-WO3/TiO2 materials employed as selective catalytic reduction (SCR) catalysts for NOx emission control from power plants. Fresh SCR catalysts usually receive exposure to harsh treatments in industry to accelerate catalyst activation (calcination in air at 650oC) and catalyst aging (hydrothermal aging at 650oC) in a way that represents various points in the catalyst/product lifetime. The present study investigates the catalyst structural and chemical changes occurring during such harsh treatments. Three series of supported V2O5-WO3/TiO2 catalysts were prepared by incipient-wetness impregnation of aqueous ammonium metavanadate and metatungstate precursors. The catalysts were subsequently dried and calcined at 550oC in O2, 650oC in O2, and hydrothermal conditions (10% O2, 8% H2O, 7% CO2 and 75% N2) at 650oC. The resulting catalysts were physically characterized by numerous techniques (in situ Raman, in situ IR, in situ High Field-High Spinning solid-state 51V MAS NMR, in situ EPR, XRD, BET surface area and ICP) and chemically probed with adsorbed ammonia, SCR-TPSR, and the SCR reaction. The surface WOx sites on the TiO2 support behave as a textural promoter that stabilizes the TiO2 (anatase) phase from sintering and transforming to the undesirable crystalline TiO2 (rutile) phase that can lead to formation of a Ti1-xVxO2 (rutile) solid solution with reduced V4+ cations (~7-15%). The surface VOx sites are mostly oligomerized as surface V+5Ox sites (~50-85% oligomers) and the extent of oligomerization tends to increase with surface WOx coverage and calcination temperature. A major difference between the calcined and hydrothermally treated catalysts was the low concentration of surface NH3* species on Lewis acid sites for the hydrothermally treated catalysts, yet the SCR activity was almost comparable for both catalysts. This finding suggests that surface NH4+*, primarily associated with the surface VOx sites, are able to efficiently perform the SCR reaction. Given that multiple catalyst parameters were simultaneously varying during these treatments, it was difficult to correlate the SCR activity with any single catalyst parameter. A correlation, however, was found between the SCR TOF/activity and the sum of the surface NH3* and NH4+* species, which is dominated by the surface NH4+* species.

SCR, NO, NH3, catalyst, V2O5, WO3, TiO2, promotion↗
DOE OSTI2021

Inhibition of Amyloid β-Induced Lipid Membrane Permeation and Amyloid β Aggregation by K162

Alzheimer's disease (AD) is characterized by progressive neurodegeneration associated with amyloid β (Aβ) peptide aggregation. The aggregation of Aβ monomers (AβMs) leads to the formation of Aβ oligomers (AβOs), the neurotoxic Aβ form, capable of permeating the cell membrane. Here, we investigated the effect of a fluorene-based active drug candidate, named K162, on both Aβ aggregation and AβO toxicity toward the bilayer lipid membrane (BLM). Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and molecular dynamics (MD) were employed to show that K162 inhibits AβOs-induced BLM permeation, thus preserving BLM integrity. In the presence of K162, only shallow defects on the BLM surface were formed. Apparently, K162 modifies Aβ aggregation by bypassing the formation of toxic AβOs, and only nontoxic AβMs, dimers (AβDs), and fibrils (AβFs) are produced. Unlike other Aβ toxicity inhibitors, K162 preserves neurologically beneficial AβMs. This unique K162 inhibition mechanism provides an alternative AD therapeutic strategy that could be explored in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗