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Results for “covalent functionalization”

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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module

Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A rigorous non-empirical theoretical analysis of the 2p XPS of NiO: Is it necessary to invoke nonlocal screening?

The role of ligand field effects and many-body effects arising from angular momentum coupling and shake effects for the XPS of NiO, as a representative transition metal oxide, have been investigated using rigorous, non-empirical wave functions for single site cluster models. Here it is shown that important features of the XPS arise from proper treatment of angular momentum coupling and it is unnecessary to invoke non-local screening to explain the experimental XPS. Contrary to the usual understanding, it is shown that inclusion of shake excitations in the many body wavefunctions is responsible for the high BE satellites that are observed. The contribution of covalent mixing of metal and ligand orbitals in the closed shells to screening of core-holes is demonstrated.

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

Electronic density of states as the descriptor of elastic bond strength, ductility, and local lattice distortion in BCC refractory alloys

Although electronic density of states (DOS) is fundamental to materials properties, its general relationship to mechanical properties of alloys is not well established. In this paper, using density functional theory (DFT) calculations, we show that the electronic occupancy at the Fermi level, N(E f ), obtained from DOS is a key descriptor of alloy strength and ductility. Our comprehensive analysis of numerous body centered cubic (BCC) refractory high entropy alloys (RHEAs) shows an overwhelming correlation that low N(E f ) indicates strong bonds that have high stiffness resulting in high elastic constants. High bond stiffness indicates presence of covalent nature of bonds that are directional in nature resulting in resistance to deformation leading to high bulk (B) and shear (G) moduli. Consequently, N(E f ) provides a direct correlation to the tendency of alloy ductility evidenced in the Pugh ratio (G/B). As stiffer bonds result in lower local lattice distortion (LLD), N(E f ) are LLD are also found to be corelated which opens up a correlation to solid solution strengthening and yield strength. Thus, this work unveils fundamental correlations between N(E f ) and (1) elastic bond strength, (2) ductility, and (3) LLD. These correlations open opportunities for the design of high strength high ductile RHEAs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Ceramic cation exchange materials

Cation exchange membranes and materials including silica-based ceramics, and associated methods, are provided. In some aspects, cation exchange membranes that include a silica-based ceramic that forms a coating on and/or within a porous support membrane are described. The cation exchange membranes and materials may have certain structural or chemical attributes (e.g., pore size/distribution, chemical functionalization) that, alone or in combination, can result in advantageous performance characteristics in any of a variety of applications for which selective transport of positively charged ions through membranes/materials is desired. In some embodiments, the silica-based ceramic contains relatively small pores (e.g., substantially spherical nanopores) that may contribute to some such advantageous properties. In some embodiments, the cation exchange membrane or material includes sulfonate and/or sulfonic acid groups covalently bound to the silica-based ceramic.

Newbloom, Gregory Matthew↗
DOE OSTI2023

Chemically Fueled Reinforcement of Polymer Hydrogels

Carbodiimide-fueled anhydride bond formation has been used to enhance the mechanical properties of permanently crosslinked polymer networks, giving materials that exhibit transitions from soft gels to covalently reinforced gels, eventually returning to the original soft gels. Temporary changes in mechanical properties result from a transient network of anhydride crosslinks, which eventually dissipate by hydrolysis. Over an order of magnitude increase in the storage modulus is possible through carbodiimide fueling. Here, the time-dependent mechanical properties can be modulated by the concentration of carbodiimide, temperature, and primary chain architecture. Because the materials remain rheological solids, new material functions such as temporally controlled adhesion and rewritable spatial patterns of mechanical properties have been realized.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions

Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Polymer / single-walled carbon nanotube composite for gas detection

A sensor can include a conductive region in electrical communication with at least two electrodes, the conductive region can include a composite of a polymer and SWCNTs immobilized onto a substrate. In certain embodiment, a linker can be grafted on the substrate. The linker can connect the substrate and the composite of the polymer and SWCNTs. In certain embodiments, the linker can covalently bond the polymer to the substrate. In certain embodiments, metal nanoparticles or ions can be incorporated as a metal sensitizer to confer further selectivity or sensitivity to the device. In certain embodiments, the polymer can act as a ligand for a variety of metal ions. By incorporating a specific metal ion, the sensor can selectively detect a specific analyte. In certain embodiments, the composite of the polymer and SWCNTs can be functionalized. In certain embodiments, the composite can further include a sensing element.

Swager, Timothy Manning↗
DOE OSTI2020

Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids

The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of beta-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Finally, our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.

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

Large Exciton Diffusion Coefficients in Two Dimensional Covalent Organic Frameworks with Different Domain Sizes Revealed by Ultrafast Exciton Dynamics

Large singlet exciton diffusion lengths are a hallmark of high performance in organic-based devices such as photovoltaics, chemical sensors, and photodetectors. In this study, exciton dynamics of a two-dimensional covalent organic framework, 2D COF-S, is investigated using ultrafast spectroscopic techniques. After photoexcitation, the COF-S exciton decays via three pathways: (1) excimer formation (4 +/- 2 ps), (2) excimer relaxation (160 +/- 40 ps), and (3) excimer decay (>3 ns). Excitation fluence-dependent transient absorption studies suggest that COF-5 has a relatively large diffusion coefficient (0.08 cm(2)/s). Furthermore, exciton-exciton annihilation processes are characterized as a function of COF-S crystallite domain size in four different samples, which reveal domain-size-dependent exciton diffusion kinetics. These results reveal that exciton diffusion in COF-S is constrained by its crystalline domain size. These insights indicate the outstanding promise of delocalized excitonic processes available in 2D COFs, which motivate their continued design and implementation into optoelectronic devices.

Flanders, Nathan C.↗
DOE OSTI2022

Mass spectrometry-based technologies for probing the 3D world of plant proteins

Abstract Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions—which are more difficult to study—dynamically regulate the proteome’s 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based “structural” proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.

Plant Sciences↗
DOE OSTI2023

Magnetic Properties of Tetravalent Pu in the Perovskites BaPuO 3 and SrPuO 3

BaPuO 3 and SrPuO 3 were synthesized, and their structures were refined in the orthorhombic space group Pbnm , a common distortion from the classic $Pm\bar{3}$m over barm cubic perovskite. Magnetic-susceptibility measurements, obtained as a function of temperature over the range of 1.8-320 K, exhibit temperature-dependent behavior, with evidence of long-range magnetic order at temperatures higher than their lanthanide and actinide analogues: BaPuO 3 below 164(1) K and SrPuO 3 below 76(1) K. Effective moments of 1.66(10)μ B for BaPuO 3 and 1.84(8)μ B for SrPuO 3 were obtained by fitting their paramagnetic susceptibilities using the Curie-Weiss law. Further, both are below the free-ion value of 2.68 μ B expected for a Pu 4+ 5 $\mid$ 4 ground level. Ab initio wave function calculations, performed at the relativistic complete active space level including spin-orbit coupling and with an embedded cluster approach that neglects interactions between Pu centers, were used to generate embedded-cluster Pu 4+ magnetic susceptibilities. The calculations agree well with experimental data at higher temperatures, providing evidence that a single-ion representation is sufficient to account for the observed paramagnetic behavior without the need to invoke charge transfer, disproportionation, strong covalent bonding, or other more complex electronic behavior.

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

CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid

hnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

In Vitro Encapsulation of Functionally Active Abiotic Photosensitizers Inside a Bacterial Microcompartment Shell

Bacterial microcompartments (BMCs) are self-assembling, selectively permeable protein shells that encapsulate enzymes to enhance catalytic efficiency of segments of metabolic pathways through means of confinement. The modular nature of BMC shells' structure and assembly enables programming of shell permeability and underscores their promise in biotechnology engineering efforts for applications in industry, medicine, and clean energy. Realizing this potential requires methods for encapsulation of abiotic molecules, which have been developed here for the first time. We report in vitro cargo loading of BMC shells with ruthenium photosensitizers (RuPS) by two approaches-one involving site-specific covalent labeling and the other driven by diffusion, requiring no specific interactions between cargo molecules and shell proteins. The highly stable shells retain encapsulated cargo over 1 week without egress and preserve RuPS photophysical activity. Finally, this study is an important foundation for further work that will converge biological BMC architecture with synthetic chemistry to facilitate biohybrid photocatalysis.

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

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds

We report a quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

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

Computational Investigation of the Chemical Bond between An(III) Ions and Soft-Donor Ligands

The chemical bonding of actinide ions with arene and borohydride ligands is explored via quantum chemical methods to understand how the transuranium elements interact with softdonor ligands. Specifically, the [An(C 6 Me 6 )(BH 4 ) 3 ] complexes (An = U, Np, and Pu) and their reduced congeners are studied. Density functional theory (DFT) shows that the metal–ligand interactions in the neutral complexes are governed by electrostatic interactions. Both DFT and complete active space (CASSCF) results show that as one moves from U to Pu, the 5f-orbitals are stabilized leading to a poorer energy match with the ligand orbitals. This contributes to progressively weaker metal-arene and metal-borohydride interactions across the series due to a decrease in energy-driven covalency. A reduction in orbital contributions to bonding is obtained for the transuranium-arene interactions as well. Upon reduction, the arene is reduced, forming a δ-bond. This causes the An–arene distances to contract by 0.1–0.2 Å compared to the neutral complexes. The ground state is assigned as the intermediate-spin state where the arene radical is antiferromagnetically coupled to the metal-centered f-electrons in Np and Pu. On the other hand, the ferromagnetically and antiferromagnetically coupled states are close in energy in the uranium complex, but do not mix when spin– orbit coupling is included using a state-interaction approach (SO-CASPT2). The population of the CASSCF δ*-antibonding natural orbital increases from U to Pu consistent with the increased An–arene distances, weaker interactions, and decreasing covalency across the series. Although the An–B distance increases by ca. 0.06 Å upon reduction, both the neutral and reduced species involve an An(III)–borohydride bond and as such are qualitatively similar. The Np complexes can be assigned to have slightly weaker bonding than the uranium analogs but are overall “uranium-like”. The Pu complexes are predicted to have less covalent contributions to bonding in both the Pu–arene and Pu–borohydride interactions; however, the Pu–arene interaction is predicted to be particularly weak.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Helical Complex Ladder Polymer with Amplification of Asymmetry

Here, we report a Cu–salen helical complex ladder polymer (HLP-Cu) built from covalently fused Cu(Salen) units. Point chirality from enantiopure diamines directs the formation of a rigid, π-conjugated helix. Compared with a planar analogue (LLP-Cu) and the Cu(Salen) monomer, HLP-Cu exhibits up to 5-fold stronger circular dichroism and a maximum dissymmetry factor of 7.4 × 10 –3 . Titration experiments suggest a cooperative amplification of asymmetry arising from extended conjugation and helical geometry during helix formation. Time-dependent density functional theory calculations are employed to support this hypothesis, showing that increasing conjugation length and helical order enhance the rotational strength of contributing excited states via elevated magnetic transition moments and improved alignment of electric and magnetic transition moments. Our findings provide a new polymer platform for designing functional chiral materials with tunable chiroptical and spin-dependent properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Design principles and physical properties of two-dimensional heterostructured borides

Principles of design to create dynamically stable transition metal-, lanthanide-, and actinide-based low-dimensional borides are presented. A charge transfer analysis of donor metal atoms to electron deficient honeycombed B lattices allows to predict complex covalent heterostructures hosting Dirac states. The applicable guidelines are supported with the analysis of phonon spectra computed with first-principles calculations to demonstrate the physical stability of nanometer-thick heterostructures. Similar or dissimilar layered borides can be stacked on top of each other in a layer-by-layer fashion creating compounds that can be fundamentally different from the individual layers, opening a rich playground to explore novel physical properties and new materials. Functionalities such as multiple Dirac states, highly dispersive electronic bands, and decoupled acoustic-optical phonon branches are studied. The combination of appealing electronic properties and physical realization makes of predicted layered borides promising materials to integrate a new generation of two-dimensional materials.

2-dimensional systems↗
DOE OSTI2026

Li + /H + Exchange in Solid-State Oxide Li-Ion Conductors

Understanding the moisture stability of oxide Li-ion conductors is important for their practical applications in solid-state batteries. Unlike sulfide or halide conductors, oxide conductors generally better resist degradation when in contact with water but can still undergo topotactic Li + /H + exchange (LHX). Here, we combine density functional theory (DFT) calculations with a machine-learning interatomic potential model to investigate the thermodynamic driving force of the LHX reaction for two representative oxide Li-ion conductor families: garnets and NASICONs. Li-stuffed garnets exhibit a strong driving force for proton exchange due to their high Li chemical potential. In contrast, NASICONs demonstrate a higher resistance against proton exchange due to the lower Li chemical potential and the lower O–H bond covalency for polyanion-bonded oxygens. Our findings reveal a critical trade-off: Li stuffing enhances conductivity but increases moisture susceptibility. This study underscores the importance of designing Li-ion conductors that possess both high conductivity and high stability in practical environments.

Li, Zhuohan [Lawrence Berkeley National Laboratory↗