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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Nucleic acid mediated activation of a short prokaryotic Argonaute immune system

A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) + hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15–3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Modulating physicochemical interfaces enables li-rich oxides based ceramic solid-state li batteries under ambient conditions

Li-rich layered oxides exhibit promising potential applications in high-energy-density solid-state lithium metal batteries. Nevertheless, the strong oxidative oxygen species generate at high voltage, which poses great challenges to positive electrode-side interface stability. Herein, a robust in-situ polymerization gel polymer electrolyte with bifunctional additives is designed for interface modification. These additives, include lithium difluoro(oxalate) borate and LiPO 2 F 2 , regulate the Li + chemical environment in gel polymer electrolyte to enhance crosslink density without residual oligomer, which reduce gas generation and suppress contact loss, thus avoiding interfacial impedance divergence. Concurrently, the designed gel polymer electrolyte enables a wide electrochemical stability window (up to 4.7 V) and a high Li + transference number (0.82). Additionally, the additives induced F- and B-rich inorganic cathode-electrolyte interphase inhibits side reactions and oxygen/transition metal loss effectively, stabilizing the chemical interface. The as-constructed Li-rich layered oxides-based ceramic solid-state lithium metal batteries with gel polymer electrolyte interface modification exert a high discharge capacity of 276.5 mAh g -1 at 30 °C without external pressure, delivering a retention of 81.7% after 100 cycles at 25 mA g -1 during 2.0-4.7 V. This work provides a guideline for developing high-voltage solid-state lithium metal batteries via interfacial design.

Hu, Xinchao [Xiamen University (China)]↗
DOE OSTI2026

Discovery of tunable and soluble organic emitters for solid-state lasers with a self-driving laboratory

We have recently demonstrated the ability of using self-driving laboratories for AI-driven searches of organic emitters for solid-state lasing devices. Our past workflow featured solubility challenges for such large molecular moieties. In this next-generation study, we return to the drawing board to explore a family of com-pounds that are much solution processable and composed of a set of electronic cores that provide a broader color response. Out of 252 potential candidates,and with guidance from DFT calculations, we selectively perform a compre-hensive study exploring 51 fluorene-based A-B-A type organic laser oligomers, armed with our self-driving lab. The candidates range from simple hydrocarbon molecules to complex hetero atom-mixed molecules. As a result of this study, we highlight diketopyrrolopyrrole and benzodiazole derivatives for their largely red-shifted emissions. Furthermore, we investigate the effect of color change aris-ing from hetero atom permutation, fluorine addition, thiophene coupling, and a combination of fluorine addition and thiophene coupling. Amplified spontaneous emission (ASE) measurements in the solid state further corroborate the lasing potential of selected candidates, reinforcing their suitability for future device applications. The computational study with density functional theory confirms the experimental results.

fluorescence↗
DOE OSTI2023

Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-$α$-amino acids in vitro and in vivo

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Precisely patterned nanofibres made from extendable protein multiplexes

Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C 2 to C 8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Accurate computational design of three-dimensional protein crystals

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here, in this study, we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗
DOE OSTI2024

Blueprinting extendable nanomaterials with standardized protein blocks

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.

36 MATERIALS SCIENCE↗
DOE OSTI2022

De novo design of obligate ABC-type heterotrimeric proteins

The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Halogenation as a tool to tune antimicrobial activity of peptoids

Antimicrobial peptides have attracted considerable interest as potential new class of antibiotics against multi-drug resistant bacteria. However, their therapeutic potential is limited, in part due to susceptibility towards enzymatic degradation and low bioavailability. Peptoids (oligomers of N-substituted glycines) demonstrate proteolytic stability and better bioavailability than corresponding peptides while in many cases retaining antibacterial activity. In this study, we synthesized a library of 36 peptoids containing fluorine, chlorine, bromine and iodine atoms, which vary by length and level of halogen substitution in position 4 of the phenyl rings. As we observed a clear correlation between halogenation of an inactive model peptoid and its increased antimicrobial activity, we designed chlorinated and brominated analogues of a known peptoid and its shorter counterpart. Short brominated analogues displayed up to 32-fold increase of the activity against S. aureus and 16- to 64-fold against E. coli and P. aeruginosa alongside reduced cytotoxicity. The biological effect of halogens seems to be linked to the relative hydrophobicity and self-assembly properties of the compounds. By small angle X-ray scattering (SAXS) we have demontrated how the self-assembled structures are dependent on the size of the halogen, degree of substitution and length of the peptoid, and correlated these features to their activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural characterization of a GNAT family acetyltransferase from Elizabethkingia anophelis bound to acetyl-CoA reveals a new dimeric interface

General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNATs) catalyse the acetylation of a diverse range of substrates, thereby orchestrating a variety of biological processes within prokaryotes and eukaryotes. GNAT enzymes can catalyze the transfer of an acetyl group from acetyl coenzyme A to substrates such as aminoglycoside antibiotics, amino acids, polyamines, peptides, vitamins, catecholamines, and large macromolecules including proteins. Although GNATs generally exhibit low to moderate sequence identity, they share a conserved catalytic fold and conserved structural motifs. In this current study we characterize the high-resolution X-ray crystallographic structure of a GNAT enzyme bound with acetyl-CoA from Elizabethkingia anophelis , an important multi-drug resistant bacterium. The tertiary structure is comprised of six α-helices and nine β-strands, and is similar with other GNATs. We identify a new and uncharacterized GNAT dimer interface, which is conserved in at least two other unpublished GNAT structures. This suggests that GNAT enzymes can form at least five different types of dimers, in addition to a range of other oligomers including trimer, tetramer, hexamer, and dodecamer assemblies. The high-resolution structure presented in this study is suitable for future in-silico docking and structure–activity relationship studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Recent experimental explorations of non-classical nucleation

Nucleation, the early stage of crystallization, is a key step in producing functional materials, but nucleation processes have yet to be understood in detail. Recent advanced characterization techniques, especially atomic force microscopy, liquid-cell transmission electron microscopy (TEM) and cryo-TEM, enable scientists to observe previously inaccessible nucleation details at the nanoscale. In this review, we summarize newly suggested non-classical nucleation models with respect to mechanistic understanding from experimental views, which highlight multi-step nucleation mechanisms. Different intermediated phases such as clusters at the pre-nucleation stage, liquid-like precursors, amorphous phases and even oligomers have been revealed, which play vital roles in nucleation and structure control. Moreover, these intermediated phases practically contribute in general to the structural variances of materials for nanoscience and nanotechnology. Overall, these studies ultimately enable us to control nucleation processes for materials synthesis.

Jin, Biao↗
DOE OSTI2021

Exchange-biased quantum tunnelling of magnetization in a [Mn 3 ] 2 dimer of single-molecule magnets with rare ferromagnetic inter-Mn 3 coupling

A covalently-linked dimer of two single-molecule magnets (SMMs), [Mn 6 O(O 2 CMe) 6 (1,3-ppmd) 3 ](ClO 4 ) 2 , has been synthesized from the reaction of [Mn 3 O(O 2 CMe) 6 (py) 3 ](ClO 4 ) with 1,3-phenylene-bis(pyridin-2-ylmethanone) dioxime (1,3-ppmdH 2 ). It contains two [Mn III 3 O] +7 triangular units linked by three 1,3-ppmd 2 - groups into an [Mn 3 ] 2 dimer with D 3 symmetry. Solid-state dc and ac magnetic susceptibility measurements showed that each Mn 3 subunit retains its properties as an SMM with an S = 6 ground state. Magnetization vs. dc field sweeps on a single crystal reveal hysteresis loops below 1.3 K exhibiting exchange-biased quantum tunnelling of magnetization (QTM) steps with a bias field of +0.06 T. This is the first example of a dimer of SMMs showing a positive exchange bias of the QTM steps in the hysteresis loops, and it has therefore been subjected to a detailed analysis. Simulation of the loops determines that each Mn3 unit is exchange-coupled with its neighbour primarily through the 1,3-ppmd 2 - linkers, confirming a weak ferromagnetic inter-Mn 3 interaction of J 12 ≈ +6.5 mK ($\hat{H}= -2J\hat{S}_i·\hat{S}_j$ convention). High-frequency EPR studies of a microcrystalline powder sample enable accurate determination of the zero-field splitting parameters of the uncoupled Mn3 SMMs, while also confirming the weak exchange interaction between the two SMMs within each [Mn 3 ] 2 dimer. The combined results emphasize the ability of designed covalent linkers to generate inter-SMM coupling of a particular sign and relative magnitude, and thus the ability of such linkers to modulate the quantum physics. As such, this article supports the feasibility of using designed covalent linkers to develop molecular oligomers of SMMs, or other magnetic molecules, as multi-qubit systems and/or other components of new quantum technologies.

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

The interplay between spatial and heliconical orientational order in twist-bend nematic materials

The helical pitch formed by organic molecules, such as the α-helix of proteins, usually requires hydrogen bonding between chiral units and long-range positional order. It was recently found that certain liquid crystal oligomers can have a twist-bend nematic (NTB) phase with nanoscale heliconical structure without hydrogen bonding, molecular chirality or positional order. To understand the nature of this unique structure, here we present hard and resonant tender X-ray scattering studies of two novel sulfur containing dimer materials. We simultaneously measure the temperature dependences of the helical pitch and the correlation length of both the helical and positional order. In addition to an unexpected strong variation of the pitch with the length of the spacer connecting the monomer units, we find that at the transition to the NTB phase the positional correlation length drops. Additionally, the helical structure was found not only in the NTB phase but observed even in the upper range of a smectic phase that forms just below the NTB state. The coexistence of smectic layering and the heliconical order indicates a layered (SmATB) phase wherein the rigid units of the dimers are tilted with respect to the smectic layer normal in order to accommodate the bent conformation of the dimers and the tilt direction rotates along the heliconical axis.

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

Non-catalytic oxidative depolymerization of lignin in perfluorodecalin to produce phenolic monomers

We demonstrate for the first time non-catalytic, oxidative cracking with molecular oxygen (O 2 ) to depolymerize native lignin into oxygenated phenolic monomers. Maximum monomer yield of 10.5 wt% was achieved at 250 °C after only 10 min of reaction and included vanillin, syringaldehyde, vanillic acid, and syringic acid. High rates of oxidation are attributed to the use of perfluorodecalin as solvent. Perfluorodecalin is a perfluorocarbon (PFC), characterized by their chemical stability and exceptionally high solubility for O 2 . Monomer yields were typically five-fold higher in perfluorodecalin compared to solvents more commonly employed in lignin conversion, such as methanol, butanol, acetonitrile, and ethyl acetate. Phenolic monomer production in perfluorodecalin favors high temperatures and short reaction times to prevent further oxidation of the produced monomers. Lignin oil obtained under oxidative conditions in perfluorodecalin showed lower molecular weight and smaller polydispersity compared to other solvents. Increasing the reaction time further decreased the molecular weight, while increasing reaction time in an inert atmosphere increased the molecular weight of the lignin oil. High concentrations of O 2 in perfluorodecalin not only increased lignin depolymerization but suppressed undesirable condensation reactions. Depolymerization is likely initiated by thermally induced homolytic cleavage of ether linkages in lignin to form phenoxy and carbon-based radicals. These radicals bind with O 2 as a radical scavenger and further react to form phenolic monomeric products rather than repolymerizing to large oligomers. The PFC process was scaled from 5 mL to 250 mL without any loss of yield. Because most organic compounds are not soluble in perfluorodecalin, recycling is easily achieved via liquid–liquid separation.

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

Reductive catalytic fractionation of agricultural residue and energy crop lignin and application of lignin oil as antimicrobials

Cheap and abundant waste from bioethanol and agricultural processing industries are an alluring alternative feedstock for biorefineries. In this work, we employ reductive catalytic fractionation (RCF) to depolymerize, over Ru/C powder and Ru/Al 2 O 3 pellets, five herbaceous biomass feedstocks, namely corn stover, miscanthus, switchgrass, sugarcane bagasse, and wheat straw into phenolic monomers with high yields (~40 wt.% based on total (Klason + acid soluble) lignin and > 50 wt.% when stabilized using aldehydes), leaving behind a carbohydrate pulp residue. Interestingly, a polar solvent is sufficient to solubilize and fragment the lignin polymer into monomers without any catalyst. Here, contrary to woody biomass, where the monomer yields are positively correlated with the S-content of lignin, principal component analysis indicates that the monomer yields from herbaceous biomass depend on the content of lignin crosslinker – ferulate. Using NMR, we further identify α – 6 C-C linked oligomers formed from condensation reactions, explaining the unexpected low monomer yields of high β-O-4 herbaceous biomass. Recyclability experiments indicate that catalyst deactivation occurs through sintering, leaching, and fouling. Lignin oil from herbaceous biomass exhibits bacteriostatic effects against Staphylococcus aureus, highlighting a potential application in functional food development and as food or feed preservative.

09 BIOMASS FUELS↗
DOE OSTI2021

Compositional analysis of organosolv poplar lignin by using high-performance liquid chromatography/high-resolution multi-stage tandem mass spectrometry

Organosolv treatment is an efficient and environmentally friendly process to degrade lignin into small compounds. The capability of characterizing the individual compounds in the complex mixtures formed upon organosolv treatment is essential for the optimization of the further lignin conversion processes and for the rational genetic engineering of plants used to produce lignin in order to improve lignin properties. In this study, an organosolv poplar lignin sample was initially analyzed by high-resolution mass spectrometry coupled with negative-ion mode electrospray ionization ((-)ESI HRMS). Lignin monomers and dimers were found to constitute the majority of the compounds in the organosolv lignin sample. Larger lignin oligomers, such as trimers and tetramers, and some not lignin-related compounds, were also detected. A high-performance liquid chromatograph/linear quadrupole ion trap/orbitrap mass spectrometer capable of multi-stage high-resolution tandem mass spectrometry experiments (HRMS n ), equipped with an (-)ESI source (HPLC/(-)ESI HRMS n ), was employed to separate the unknown compounds in the organosolv mixture and to obtain structural information for the deprotonated compounds via collision-activated dissociation (CAD) HRMS n experiments. To improve the understanding of the CAD behavior of deprotonated lignin-related compounds, 16 deprotonated model compounds with different functionalities and linkage types were examined. This approach enabled the assignment of likely structures for several lignin monomers, dimers, trimers, and tetramers, and some not lignin-related compounds, most likely fatty acids. Based on the proposed structures, compounds in the organosolv lignin sample contain β-O-4, 5–5, β-5, and possibly also 4-O-5 linkages. Most compounds contain G- and S-monomeric units although a small amount of H-units were also detected.

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

Temperature-mediated molecular ladder self-assembly employing Diels–Alder cycloaddition

Dynamic covalent self-assembly processes often exhibit poor capacities for error-correction owing to the relatively low connectivity rearrangement rates of dynamic covalent interactions and the common use of reaction conditions where the equilibrium state remains fixed. Here, we report a dynamic covalent self-assembly technique employing temperature, a conventional, externally-applied stimulus, to mediate the hybridization of peptoid oligomers bearing maleimide- and furan-based pendant groups to afford molecular ladders incorporating Diels–Alder adduct-based rungs. By raising or lowing the reaction temperature, this system enables the equilibrium state to be readily varied without altering reagent concentrations. Both triethylamine and the Lewis acidic scandium triflate were examined as candidate reaction catalysts; however, only scandium triflate increased the rate of single strand conversion. Additionally, as the Diels–Alder cycloaddition reaction does not liberate a small molecule, a registry-dependent mass change was effected by employing a base-catalyzed thiol-Michael addition reaction between any un-reacted maleimide pendant groups and a low molecular weight thiol to enable the number of Diels–Alder adduct rungs to be readily determined by mass spectrometry. Finally, by employing a slow temperature ramp from high to low temperature, approximating the thermal cycle employed for nucleic acid hybridization, sequence-selective hybridization between model, tetra-functional precursor strands was demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗