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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 OSTI2022

The influence of molecular design on structure–property relationships of a supramolecular polymer prodrug

Supramolecular self-assemblies of hydrophilic macromolecules functionalized with hydrophobic, structure-directing components have long been used for drug delivery. In these systems, loading of poorly soluble compounds is typically achieved through physical encapsulation during or after formation of the supramolecular assembly, resulting in low encapsulation efficiencies and limited control over release kinetics, which are predominately governed by diffusion and carrier degradation. To overcome these limitations, amphiphilic prodrugs that leverage a hydrophobic drug as both the therapeutic and structure-directing component can be used to create supramolecular materials with higher loading and controlled-release kinetics using biodegradable or enzymatically cleavable linkers. Here, we report the design, synthesis, and characterization of a library of supramolecular polymer prodrugs based on poly(ethylene glycol) (PEG) and the proregenerative drug 1,4-dihydrophenonthrolin-4-one-3-carboxylic acid (DPCA). Structure–property relationships were elucidated through experimental characterization of prodrug behavior in both the wet and dry states using scattering techniques and electron microscopy and corroborated by coarse-grained modeling. Molecular architecture and the hydrophobic-to-hydrophilic ratio of PEG–DPCA conjugates strongly influenced their physical state in water, ranging from fully soluble to supramolecular spherical assemblies and nanofibers. Molecular design and supramolecular structure, in turn, were shown to dramatically alter hydrolytic and enzymatic release and cellular transport of DPCA. In addition to potentially expanding therapeutic options for DPCA through control of supramolecular assemblies, the design principles elaborated here may inform the development of other supramolecular prodrugs based on hydrophobic small-molecule compounds.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae . A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S . cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S . cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum . Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae . The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S . cerevisiae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bayesian optimization for chemical products and functional materials

The design of chemical-based products and functional materials is vital to modern technologies, yet remains expensive and slow. Artificial intelligence and machine learning offer new approaches to leverage data to overcome these challenges. Herein this review focuses on recent applications of Bayesian optimization (BO) to chemical products and materials including molecular design, drug discovery, molecular modeling, electrolyte design, and additive manufacturing. Numerous examples show how BO often requires an order of magnitude fewer experiments than Edisonian search. The essential equations for BO are introduced in a self-contained primer specifically written for chemical engineers and others new to the area. Finally, the review discusses four current research directions for BO and their relevance to product and materials design.

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

Atomistic Mechanics of Torn Back Folded Edges of Triangular Voids in Monolayer WS 2

Triangular nanovoids in 2D materials transition metal dichalcogenides have vertex points that cause stress concentration and lead to sharp crack propagation and failure. Here, the atomistic mechanics of back folding around triangular nanovoids in monolayer WS 2 sheets is examined. Combining atomic-resolution images from annular dark-field scanning transmission electron microscopy with reactive molecular modelling, it is revealed that the folding edge formation has statistical preferences under geometric conditions based on the orientation mismatch. It is further investigated how loading directions and strong interlayer friction, interplay with WS 2 lattice's crack preference, govern the deformation and fracture pattern around folding edges. Finally, these results provide fundamental insights into the combination of fracture and folding in flexible monolayer crystals and the resultant Moiré lattices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Polymorphism and Negative Linear Compressibility in Pyrazine-d4

Pyrazine (1,4-diazine) is a widely used linker in coordination polymers, molecular magnets, and metal–organic frameworks, yet its solid-state polymorphism is controlled by weak C–H···N interactions. Using variable-temperature and high-pressure neutron diffraction, a previously unrecognized low-temperature transition to phase IV is identified, showing that the form stabilized under pressure can also be accessed below ∼90 K at ambient pressure in the perdeuterated compound. The transition from phase III → IV involves a symmetry-breaking lattice distortion driven by the reorganization of C–H···N hydrogen bonds, accompanied by negative linear compressibility, which is primarily accommodated through the reduction in void-space within the structure. Structural analysis reveals that while the overall monoclinic framework of phase IV is preserved under both temperature and pressure routes, the evolution of hydrogen-bonded network is distinct depending on the pathway taken. These results establish pyrazine as a model molecular solid for studying pressure–temperature polymorphism and demonstrate how weak directional interactions can produce anomalous mechanical responses in organic crystals.

Ridley, Christopher J. [Oak Ridge National Laborat↗
DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

NASA Discipline Neuroscience↗
DOE OSTI2024

A structural underpinning of the lower critical solution temperature (LCST) behavior behind temperature-switchable liquids

In this work, we use state-of-the-art X-ray scattering and molecular dynamics to analyze amine-water mixtures that show the unusual lower critical solution temperature (LCST) behavior. The goal is to provide direct experimental evidence for the entropy-lowering molecular cluster formation hypothesized as necessary for LCST behavior. Differential wide-angle X-ray scattering and pair distribution analysis and small-angle X-ray scattering measurements were combined with molecular modeling and liquid-liquid equilibrium measurements, revealing direct experimental evidence for the hypothesis. However, the response of the amine phase to accommodating water is even more subtle than the simple hypothesis suggests, with the formation of robust nanoscale reverse micelles. The techniques developed in this paper can be expected to yield insights in the use of temperature-switchable liquids in solvent extraction and other separations, and the stabilization of organelles in living cells that do not have physical membranes but do require compositional gradients to operate.

36 MATERIALS SCIENCE↗
DOE OSTI2021

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ~8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation–π and anion–π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion–π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E int ) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent—these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)- based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation–π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E int values, and maximum errors of ±0.2–0.3 kcal/mol (i.e., ~±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

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

On the Finite Nuclear Effect and Gaussian Basis Sets for Four-Component Dirac Hartree-Fock Calculations

In this perspective we describe an overview of Dirac Hartree-Fock theory, which is the foundation of relativistic quantum chemistry methods vital in the molecular modeling of heavy element chemistry and physics. A special emphasis was placed upon the physical connection between the finite nuclear model and the kinetic-balance condition between the large and small components. Additionally, we review the consequences of basis set choices for Dirac Hartree-Fock calculations in the restricted kinetic balance formalism, and show that the basis set limit does not have a hard lower bound due to the nature of the Hamiltonian, referred to in the literature as prolapse. Standard Gaussian basis set contraction schemes can break down in Dirac Hartree-Fock calculations, and special care must be taken for the description of core orbitals near the nucleus. The phenomena described in this perspective are vital for theoreticians and practitioners to understand when selecting a basis set for heavy element quantum chemical calculations using Dirac Hartree-Fock theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

Positive selection moments identify potential functional residues in human olfactory receptors

Correlated mutation analysis and molecular models of olfactory receptors have provided evidence that residues in the transmembrane domains form a binding pocket for odor ligands. As an independent test of these results, we have calculated positive selection moments for the alpha-helical sixth transmembrane domain (TM6) of human olfactory receptors. The moments can be used to identify residues that have been preferentially affected by positive selection and are thus likely to interact with odor ligands. The results suggest that residue 622, which is commonly a serine or threonine, could form critical H-bonds. In some receptors a dual-serine subsite, formed by residues 622 and 625, could bind hydroxyl determinants on odor ligands. The potential importance of these residues is further supported by site-directed mutagenesis in the beta-adrenergic receptor. The findings should be of practical value for future physiological studies, binding assays, and site-directed mutagenesis.

Non-NASA Center↗
DOE OSTI2021

Molecular Origin of Strain-Induced Chain Alignment in PDPP-Based Semiconducting Polymeric Thin Films

Donor–acceptor (D–A) type semiconducting polymers have shown great potential for the application of deformable and stretchable electronics in recent decades. However, due to their heterogeneous structure with rigid backbones and long solubilizing side chains, the fundamental understanding of their molecular picture upon mechanical deformation still lacks investigation. Here, the molecular orientation of diketopyrrolopyrrole (DPP)-based D–A polymer thin films is probed under tensile deformation via both experimental measurements and molecular modeling. The detailed morphological analysis demonstrates highly aligned polymer crystallites upon deformation, while the degree of backbone alignment is limited within the crystalline domain. Besides, the aromatic ring on polymer backbones rotates parallel to the strain direction despite the relatively low overall chain anisotropy. Additionally, the effect of side-chain length on the DPP chain alignment is observed to be less noticeable. These observations are distinct from traditional linear-chain semicrystalline polymers like polyethylene due to distinct characteristics of backbone/side-chain combination and the crystallographic characteristics in DPP polymers. Furthermore, a stable and isotropic charge carrier mobility is obtained from fabricated organic field-effect transistors. This study deconvolutes the alignment of different components within the thin-film microstructure and highlights that crystallite rotation and chain slippage are the primary deformation mechanisms for semiconducting polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors

Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goal. Herein, we use molecular modeling approaches to identify and target potential novel pockets specific to Class IIA HDAC-HDAC4 at the interface between HDAC4 and the transcriptional corepressor component protein NCoR. These pockets were screened using an ensemble docking approach combined with consensus scoring to identify compounds with a different binding mechanism than the currently known HDAC modulators. Binding was compared in experimental assays between HDAC4 and HDAC3, which belong to a different family of HDACs. HDAC4 was significantly inhibited by compound 88402 but not HDAC3. Two other compounds (67436 and 134199) had IC50 values in the low micromolar range for both HDACs, which is comparable to the known inhibitor of HDAC4, SAHA (Vorinostat). However, both of these compounds were significantly weaker inhibitors of HDAC3 than SAHA and thus more selective, albeit to a limited extent. Five compounds exhibited activity on human breast carcinoma and/or urothelial carcinoma cell lines. The present result suggests potential mechanistic and chemical approaches for developing selective HDAC4 modulators.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

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

Dendrite Suppression by a Polymer Coating: A Coarse‐Grained Molecular Study

Abstract A major hurdle to the successful deployment of high‐energy‐density lithium metal based batteries is dendrite growth during battery cycling, which raises safety and cycle life concerns. Coating the Li metal anode with a soft polymer layer has been previously shown to be effective in suppressing dendrite growth, leading to uniform lithium deposition even at high current densities. A 3D coarse‐grained molecular model to study the mechanism of dendrite suppression is presented. It is found that the most effective coatings delay or even prevent dendrites from penetrating the polymer layer during deposition. The optimal deposition can be achieved by jointly tuning the polymer stiffness and relaxation time. Higher polymer dielectric permittivity and coating thickness are also effective, but the deposition rate and, therefore, the charging current density is reduced. These findings provide the basis for rational design of soft polymer coatings for stable lithium deposition.

Kong, Xian↗
DOE OSTI2023

Revealing the Anion–Solvent Interaction for Ultralow Temperature Lithium Metal Batteries

Anion solvation in electrolytes can largely change the electrochemical performance of the electrolytes, yet has been rarely investigated. Herein, three anions of bis(trifluoromethanesulfonyl)imide (TFSI), bis(fluorosulfonyl)imide (FSI), and derived asymmetric (fluorosulfonyl)(trifluoro-methanesulfonyl)imide (FTFSI) are systematically examined in a weakly Li + cation solvating solvent of bis(3-fluoropropyl)ether (BFPE). In-situ liquid secondary ion mass spectrometry demonstrates that FTFSI - and FSI - anions are associated with BFPE solvent, while weak TFSI - /BFPE cluster signals are detected. Molecular modeling further reveals that the anion–solvent interaction is accompanied by the formation of H-bonding-like interactions. Further, anion solvation enhances the Li + cation transfer number and reduces the organic component in solid electrolyte interphase, which enhances the Li plating/stripping Coulombic efficiency at a low temperature of -30 °C from 42.4% in TFSI-based electrolytes to 98.7% in 1.5 m LiFTFSI and 97.9% in LiFSI-BFPE electrolytes. The anion–solvent interactions, especially asymmetric anion solvation also accelerate the Li + desolvation kinetics. The 1.5 m LiFTFSI-BFPE electrolyte with strong anion–solvent interaction enables LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811)||Li (20 µm) full cell with stable cyclability even under -40 °C, retaining over 92% of initial capacity (115 mAh g -1 , after 100 cycles). The anion–solvent interactions insights allow to rational design the electrolyte for lithium metal batteries and beyond to achieve high performance.

25 ENERGY STORAGE↗
DOE OSTI2021

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

Abstract High‐energy X‐ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long‐range order, but is underutilized for molecular complexes in solution. We demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal⋅⋅⋅metal distances separated by over 12 Å. The metal⋅⋅⋅metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub‐Ångström conformational differences by direct comparison of solution phase and solid‐state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

Xie, Zhu‐Lin↗
DOE OSTI2021

Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis

High-energy X-ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long-range order, but is underutilized for molecular complexes in solution. Here we demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal...metal distances separated by over 12 Å. The metal…metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub-Ångström conformational differences by direct comparison of solution phase and solid-state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗