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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment

Claudins are a 27-member family of ~25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. As the backbone of tight junction structure and function, claudins are attractive targets for modulating tissue permeability to deliver drugs or treat disease. However, structures of claudins are limited due to their small sizes and physicochemical properties—these traits also make therapy development a challenge. Here we report the development of a synthetic antibody fragment (sFab) that binds human claudin-4 and the determination of a high-resolution structure of it bound to claudin-4/enterotoxin complexes using cryogenic electron microscopy. Structural and biophysical results reveal this sFabs mechanism of select binding to human claudin-4 over other homologous claudins and establish the ability of sFabs to bind hard-to-target claudins to probe tight junction structure and function. The findings provide a framework for tight junction modulation by sFabs for tissue-selective therapies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore–quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric “A”-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore–quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST–tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Solvation directed morphological control in metal oxide nanostructures

The development of structural hierarchy on various length scales during the crystallization process is ubiquitous in biological systems and minerals and is common in synthetic nanomaterials. The driving forces for the formation of complex architectures range from local interfacial interactions, that modify interfacial speciation, local supersaturation, and nucleation barriers, to macroscopic interparticle forces. Although it is enticing to interpret the formation of hierarchical architectures as the assembly of independently nucleated building blocks, crystallization pathways often follow monomer-by-monomer addition with structural complexity arising from interfacial chemical coupling and strongly correlated fluctuation dynamics in the electric double layers. Here, we show that the development of structural hierarchy through heterogeneous nucleation is driven by dipolar and solvation forces. Specifically, coupled simulations and experimental studies revealed that dipole build-up along the slow growth direction can trigger twinning and the development of branched architectures. Enthalpic solvation interactions were shown to either enhance or reduce the dipole moment of the nanoparticles and, thereby, control crystal morphology and architecture. The systematic studies of chemical coupling between different solvents and undercoordinated surface atoms of the growing nanocrystals revealed the mechanism of dimensionality control and the development of structural hierarchy without ligands or structure-directing agents.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Structural and Spectroscopic Trends in Alkali Tris(Acetato)Actinyl(VI) Complexes

A series of alkali tris(acetato)actinyl(VI) compounds M[AnO 2 (CH 3 COO) 3 ] (M=Na, K, Rb, Cs and An=U, Np, Pu) is reported, applying a combination of singlecrystal X-ray diffraction, solid-state Raman spectroscopy, and U(VI) luminescence spectroscopy for their structural and spectroscopic characterization. The results show that complexes formed from the same alkali metal but different actinyl ions are mostly isostructural. The symmetric actinyl stretch (ν 1 (An=O yl )) in these isostructural complexes undergoes a redshift within the actinide series despite the shortening of the actinyl bond due to the actinide contraction. Complexes formed from the same actinyl but co-crystallized with different alkali metals show a progression toward lower space group symmetry. While the actinyl bond length remains unmodulated within the alkali series, a small redshift of ν 1 (An=O yl ) is observed, indicating minor changes in the vibrational properties of the actinyl moiety caused by the structural progression towards lower symmetry. This subtle change is also evidenced by a redshift of the U(VI) luminescence spectra within the M[UO 2 (CH 3 COO) 3 ] series.

Raman↗
DOE OSTI2025

Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii

Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold cell envelope integrity, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo–electron microscopy reconstructions ofAcinetobacter baumanniiTolQ in apo and TolR-bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a transmembrane funnel leading toward a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton nonpermeable stance, characterized by the TolQ pentamer’s flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers’ interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.

Science & Technology - Other Topics↗
DOE OSTI2025

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

Trasviña-Arenas, Carlos H [University of Californi↗
DOE OSTI2025

Spectroscopic and Theoretical Studies of Ruthenium Complexes with a Noninnocent N 2 S 2 Ligand in Different Redox States

Herein we report an electronic structure investigation of neutral and oxidized Ru complexes containing a redox noninnocent N 2 S 2 ligand derived from o-phenylenediamide (L1). UV–vis spectroelectrochemistry (SEC) studies were conducted on the square pyramidal complex [Ru I I(L1)(PPh 3 )] (1) and the six-coordinate complexes [Ru I I(μ-BH 3 )(L1)(PPh 3 )] (2) – which has BH 3 bound in a metal–ligand cooperative (MLC) fashion across Ru and L1 – and [Ru II (L1)(PPh 3 )(MeCN)] (3). The SEC results yielded spectra assigned to singly and doubly oxidized 1 and 3, revealing electronic structure changes as a function of oxidation state and in response to the presence and absence of bound MeCN. By contrast, the SEC results of 2 showed that it rapidly loses MLC-bound BH 3 upon oxidation. The SEC results for 1 and 3 were compared to single-crystal XRD data and UV–vis, EPR, and P K-edge, S K-edge, and Ru L 3 -edge X-ray absorption spectroscopy (XAS) data collected on isolated samples of chemically oxidized 3. The data revealed that the first two oxidations are primarily localized on the ligand, which was supported by DFT and TDDFT calculations. DFT calculations for the doubly oxidized species revealed a singlet ground state with a singlet–triplet gap of 8.9 kcal/mol. CASPT2 calculations corroborated the DFT calculations and further revealed that the singlet ground state is multiconfigurational with 21% radical character. Collectively, the results establish redox formalisms and the underlying electronic structure of Ru complexes containing a noninnocent tetradentate ligand in different oxidation states.

electronic structure↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Ferromagnetism and structural phase transition in rhombohedral PrI r 3

The synthesis, structural, magnetic, thermal, and transport properties are reported for polycrystalline PrI⁢r 3 . At room temperature PrI⁢r 3 displays the rhombohedral space group R–3m and a PuNi 3 -type structure. At around 70 K a phase transition to a monoclinic C⁢2/m structure is observed and continued cooling reveals temperature independent behavior of the unit cell volume. Further, PrI⁢r 3 undergoes a paramagnetic to ferromagnetic transition with T c =7.5K. The temperature dependent magnetic susceptibility follows the Curie-Weiss law with a positive Curie-Weiss temperature, and an effective moment that is close to the theoretical effective moment for a free P⁢r +3 ion. Finally, the structural transition introduces further complexity into the behavior of PuNi 3 -type materials and highlights the importance of temperature-dependent structural studies to complement physical property measurements in intermetallic compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Alkali Counterion-Dependent Crystallization of Uranium(IV)–Chloro Structural Units

The synthesis, structural characterization, and spectroscopic properties of five tetravalent uranium (U) phases including Li 6 [U 4 (μ 3 -O) 2 Cl 18 (H 2 O) 2 ]·10H 2 O (1), [U(H 2 O) 4 Cl 4 ] (2), [U(H 2 O) 4 Cl 4 ]·KCl (3), Rb 2 UCl 6 (4), and Cs 2 UCl 6 (5) are reported. Notably, a change in the U 4+ solid-state structural unit was observed based on the identity of the alkali counterion used in the synthesis. Li 1+ yielded a tetranuclear oxo-bridged cluster, [U 4 (μ 3 -O) 2 Cl 18 (H 2 O) 2 ] 6– , Na 1+ and K 1+ yielded two structurally distinct [U(H 2 O) 4 Cl 4 ] complexes, and Rb 1+ and Cs 1+ resulted in [UCl 6 ] 2– as the dominant phases. The spectroscopic properties of the compounds were analyzed using Raman and UV–vis–NIR absorption spectroscopy. The UV–vis–NIR spectra of compounds 1–5 exhibited transitions consistent with uranium in the +4 oxidation state. Clear differences in the absorption band splitting were observed and are likely attributed to differences in metal ion coordination, crystal field effects, and outer sphere interactions Overall, this work demonstrates the utility of noncovalent interactions in tuning the crystallization of various metal complexes from otherwise identical reaction solutions and provides further evidence that counterions impact the composition and structure of actinide complexes isolated in the solid state. In this way, this work affords important insight into directing and controlling the structure of actinide complexes and clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Screening a knowledge‐based library of low molecular weight compounds against the proline biosynthetic enzyme 1‐pyrroline‐5‐carboxylate 1 ( PYCR1)

Abstract Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H‐dependent reduction of Δ 1 ‐pyrroline‐5‐carboxylate toL‐proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of thePYCR1gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X‐ray crystallography and kinetic assays to determine affinity parameters. The library was counter‐screened against human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)‐tetrahydro‐2H‐pyran‐2‐carboxylic acid (70 μM) has higher affinity than the current best tool compoundN‐formyl‐l‐proline, is 30 times more specific for PYCR1 over human Δ 1 ‐pyrroline‐5‐carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure‐affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1‐hydroxyethane‐1‐sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed withl‐pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Complex-Concentrated Anion Doping Enables Ultra-Stable Lattice Oxygen and Structural Integrity in Lithium-Rich Layered Oxide Cathodes

Lithium- and manganese-rich layered oxides (LMR) stand out as next-generation lithium-ion cathode chemistries, which harness both transition-metal and lattice-oxygen redox processes to deliver exceptional capacity and energy density. However, their full potential is hindered by intrinsic oxygen instability and structural degradation, resulting in pronounced voltage fade and capacity decay. Here, we present a complex-concentrated anion-doping paradigm in which multiple anions, F, Br, and S, are incorporated into the oxygen sublattice to enhance oxygen-redox and structural stability. X-ray absorption spectroscopy and aberration-corrected scanning transmission electron microscopy confirm ultra-stable local oxygen coordination environments during long-term cycling, with detrimental phase transformations and oxygen-loss-induced cavitation dramatically inhibited. Notably, we show that the characteristic LiTM6 transition metal (TM) honeycomb ordering is preserved even after electrochemical cycling. Concurrently, this strategy yields an unprecedented volume change of only 0.63% upon charging to 4.8 V vs. Li+/Li, achieving the first zero-strain LMR cathode. The resulting LMR cathode delivers ultralow voltage fade (1 mV per cycle during the first 100 cycles and becomes negligible in subsequent cycles) and outstanding energy retention (93% after 200 cycles) in a pouch cell configuration. Our complex-concentrated anion-doping concept establishes a broadly applicable strategy for resolving chemo-mechanical failure mechanisms in ceramic intercalation electrodes for next-generation energy storage.

Li-ion batteries↗
DOE OSTI2024

Anti-idiotype isolation of a broad and potent influenza A virus-neutralizing human antibody

The VH6-1 class of antibodies includes some of the broadest and most potent antibodies that neutralize influenza A virus. Here, we elicit and isolate anti-idiotype antibodies against germline versions of VH6-1 antibodies, use these to sort human leukocytes, and isolate a new VH6-1-class member, antibody L5A7, which potently neutralized diverse group 1 and group 2 influenza A strains. While its heavy chain derived from the canonical IGHV6-1 heavy chain gene used by the class, L5A7 utilized a light chain gene, IGKV1-9, which had not been previously observed in other VH6-1-class antibodies. The cryo-EM structure of L5A7 in complex with Indonesia 2005 hemagglutinin revealed a nearly identical binding mode to other VH6-1-class members. The structure of L5A7 bound to the isolating anti-idiotype antibody, 28H6E11, revealed a shared surface for binding anti-idiotype and hemagglutinin that included two critical L5A7 regions: an FG motif in the third heavy chain-complementary determining region (CDR H3) and the CDR L1 loop. Surprisingly, the chemistries of L5A7 interactions with hemagglutinin and with anti-idiotype were substantially different. Overall, we demonstrate anti-idiotype-based isolation of a broad and potent influenza A virus-neutralizing antibody, revealing that anti-idiotypic selection of antibodies can involve features other than chemical mimicry of the target antigen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Isolation of a new polyoxometalate complex of plutonium

We report the synthesis, plus structural and spectroscopic characterization, of a plutonium(IV) complex with the polyoxometalate W 5 O 18 6− . The complex was isolated as Cs 8 [Pu(W 5 O 18 ) 2 ]·CsCl·6.5H 2 O, with the tetravalent actinide cation sandwiched between two lacunary polyoxotungstate anions. It represents a rare case of a POM compound with plutonium and also the first Peacock–Weakley type complex of plutonium.

Colliard, Ian [Lawrence Livermore National Laborat↗
DOE OSTI2024

Multiconfigurational Electronic Structure of Nickel Cross-Coupling Catalysts Revealed by X-ray Absorption Spectroscopy

Ni II 2,2'-bipyridine complexes are commonly invoked intermediates in metallaphotoredox cross-coupling reactions. Despite their ubiquity, design principles targeting improved catalytic performance remain underdetermined. A series of Ni( R bpy)( R 'Ar)Cl (R = MeOOC, t-Bu, R' = CH 3 , CF 3 ) complexes were proposed to have multiconfigurational electronic structures on the basis of multiconfigurational/multireference calculations, with significant mixing of Ni → bpy metal-to-ligand charge transfer (MLCT) configurations into the ground-state wave function. Here, Ni K-edge and L 2,3 -edge X-ray absorption spectroscopies provide experimental support for the highly covalent and multiconfigurational electronic structures of these complexes. The pre-edge intensity in the K-edge spectrum reflects highly covalent Ni–aryl bonding. The L 3 -edge spectral shape is dependent on ligand functionalization, and a feature reflecting the MLCT character is assigned using prior ab initio and new semiempirical calculations. The results suggest the push/pull effects of the aryl/bpy ligands moderate the changes in electron density on Ni during the multiredox cross-coupling reaction cycle.

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

Heterogeneous Multilayer Nanopores via Chemically Tuned Dielectric Breakdown for Single‐Molecule Sensing

Solid-state nanopores are powerful platforms for single-molecule sensing, yet their performance is often constrained by fabrication complexity, noise, and limited control over surface properties. Here we report a direct method to fabricate heterogeneous multilayer nanopores using chemically tuned controlled dielectric breakdown (CT-CDB). We integrate hBN, MoS 2 , or graphene atop a silicon nitride membrane to form five distinct bilayer and tri-layer architectures, with bare SiN x nanopore as a control. CT-CDB achieves pore formation reproducibly through material-stacks with high efficiency, good pore size control, and strong yield, validated by various characterizations. Transferrin protein translocation experiments, supported by simulations, reveal that multilayer configurations modulate protein conformations, ionic current blockade and dwell time distributions, reflecting combined effects of membrane type, interfacial chemistry, and local electric field gradients. A supervised machine learning framework is implemented to assist identifying multilayer structure effects embedded in signal signatures, with over 96% accuracy. This work presents a modular and scalable framework for functional nanopore engineering with complex structural integration, thereby expanding the potential of 2D materials in single-molecule sensing applications.

2D materials↗
DOE OSTI2024

Improved deep learning prediction of antigen–antibody interactions

Identifying antibodies that neutralize specific antigens is crucial for developing effective immunotherapies, but this task remains challenging for many target antigens. The rise of deep learning–based computational approaches presents a promising avenue to address this challenge. Here, we assess the performance of a deep learning approach through two benchmark tests aimed at predicting antibodies for the receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Three different strategies for constructing input sequence alignments are employed for predicting structural models of antigen–antibody complexes. In our initial testing set, which comprises known experimental structures, these strategies collectively yield a significant top-ranked prediction for 61% of cases and a success rate of 47%. Notably, one strategy that utilizes the sequences of known antigen binders outperforms the other two, achieving a precision of 90% in a subsequent test set of ~1,000 antibodies, balanced between true and control antibodies for the antigen, albeit with a lower recall of 25%. Our results underscore the potential of integrating deep learning methods with single B cell sequencing techniques to enhance the prediction accuracy of antigen–antibody interactions.

Science & Technology - Other Topics↗