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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Heterometallic UO 2 2+ /Ag + Complexes: Structural Design and Luminescence Properties

Reported here are the synthesis, structural characterization, and luminescence properties of 11 novel UO 2 2+ /Ag + heterometallic complexes. Halogenated benzoic acids (2,6-dihalobenzoic acid (halo = F, Br), 3,5-dichlorobenzoic acid, and 3-halobenzoic acid (halo = Br, I)) and N-donor polycyclic ligands (2,2′-bipyridine, 2,2’;6′,2″-terpyridine, 1,10-phenanthroline, 2,2′-bipyrimidine) were employed to synthesize a set of compounds and induce structural diversity. The primary mode of coordination with the uranyl cation is hexagonal bipyramidal monomeric units with three halobenzoate ligands in the equatorial plane, though 1-D chains with pentagonal bipyramidal uranyl centers also form. The Ag + cations coordinate preferentially to the N-donor ligands and serve as counter-cations for the anionic uranyl motifs. The soft ligand character of the N-donor molecules is found to be a requirement for the inclusion of the Ag + cation into the structures. Anionic uranyl units and cationic silver units assemble via noncovalent interactions between π systems on adjacent rings and between halogens (when Br and I are present). Solid-state emission spectra display the usual uranyl band with superimposed vibronic fine structure, except for that of compound 1 , which shows emission from the 2,2′-bipyridine center. This family of compounds represents a substantial contribution to the already rich library of UO 2 2+ /Ag + compounds, and the synthetic parameters discussed within reveal a platform for the design of new heterometallic uranyl-containing materials.

anions↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2024

The seventh blind test of crystal structure prediction: structure ranking methods

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol −1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

Chemistry↗
DOE OSTI2025

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study

The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structural modulation, physical properties, and electronic band structure of the kagome metal UCr 6 ⁢Ge 6

The chemical flexibility of the 𝑅⁢𝑀 6 ⁢𝑋 6 stoichiometry, where an 𝑓-block element is intercalated in the CoSn structure type, allows for the tuning of flatbands associated with kagome lattices to the Fermi level and for emergent phenomena due to interactions between the 𝑓- and 𝑑-electron lattices. Yet, 5⁢𝑓 members of the “166” compounds are underrepresented compared with 4⁢𝑓 members. In this work, we report single-crystal growth of UCr 6 ⁢Ge 6 , which crystallizes in a monoclinically distorted Y 0.5⁢ Co 3 ⁢Ge 3 -type structure. The real-space character of the modulation, which is unique within the 𝑅⁢𝑀 6 ⁢𝑋 6 family, is approximated by a 3×1×2 supercell of the average monoclinic cell. The compound has kagome-lattice flatbands near the Fermi level and a moderately enhanced electronic heat capacity, as evidenced by its low-temperature Sommerfeld coefficient (𝛾=86.5 mJ mol −1 K −2 ) paired with band structure calculations. The small, isotropic magnetization and featureless resistivity of UCr 6 ⁢Ge 6 suggest itinerant uranium 5⁢𝑓 electrons and Pauli paramagnetism. Angle-resolved photoemission spectroscopy results provide evidence for uranium 5⁢𝑓 weight at the Fermi level and for a flatband near the Fermi level associated with the chromium 3⁢𝑑 kagome lattice. The isotropic magnetic behavior of the uranium 5⁢𝑓 electrons starkly contrasts with localized behavior in other uranium 166 compounds, highlighting the high tunability of the magnetic ground state across the material family.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features

Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.

Bio-based polymer↗
DOE OSTI2024

Adsorption Properties of Au−Ni Surface Alloys with a Nonstoichiometric Moiré Structure: A Density Functional Theory Study

Due to the large lattice mismatch between gold and nickel, gold–nickel surface alloys can form unique nonstoichiometric overlayer structures characterized by a moiré pattern and subsurface defects. For this work, we performed density functional theory (DFT) calculations to study the adsorption of molecular oxygen, atomic hydrogen, and atomic carbon on a gold–nickel(111) surface alloy with 0.46 monolayer gold randomly distributed in the surface layer. We observed six distinct adsorption structures for molecular oxygen characterized by intramolecular stretching frequencies of <700, 729, 795, 857, 929, and 1004 cm –1 , which describe well the experimentally observed high-resolution electron energy-loss spectra. Surface atomic hydrogen adsorption is associated with adsorbate–surface modes in the ∼1000 cm –1 range, while subsurface hydrogen can have features as low as ∼400 cm –1 . We observed a unique adsorption structure for atomic carbon inside the surface dislocation loop defect, which explains the experimentally observed low carbon-surface mode at ∼340 cm –1 . Our study sheds light on the unique adsorption properties of the gold–nickel surface alloys and helps with rationalizing vibrational frequency experimental studies for this system.

adsorption↗
DOE OSTI2024

Revealing the hidden structure of disordered materials by parameterizing their local structural manifold

Abstract Durable interest in developing a framework for the detailed structure of glassy materials has produced numerous structural descriptors that trade off between general applicability and interpretability. However, none approach the combination of simplicity and wide-ranging predictive power of the lattice-grain-defect framework for crystalline materials. Working from the hypothesis that the local atomic environments of a glassy material are constrained by enthalpy minimization to a low-dimensional manifold in atomic coordinate space, we develop a generalized distance function, the Gaussian Integral Inner Product (GIIP) distance, in connection with agglomerative clustering and diffusion maps, to parameterize that manifold. Applying this approach to a two-dimensional model crystal and a three-dimensional binary model metallic glass results in parameters interpretable as coordination number, composition, volumetric strain, and local symmetry. In particular, we show that a more slowly quenched glass has a higher degree of local tetrahedral symmetry at the expense of cyclic symmetry. While these descriptors require post-hoc interpretation, they minimize bias rooted in crystalline materials science and illuminate a range of structural trends that might otherwise be missed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2025

Impact of structural distortions on the correlated electronic structure of orbital-selective Mott insulating Na 3 ⁢Co 2 ⁢SbO 6 under strain

Na 3 Co 2 SbO 6 is a promising candidate to realize the Kitaev spin liquid phase since the large Kitaev spin exchange interaction is tunable via the change in electronic structure, such as the trigonal crystal field splitting (Δ TCF ). Here, in this study, we show that the uncorrelated electronic structure of Na 3 Co 2 SbO 6 is rather insensitive to the strain effect due to the low crystal symmetry accompanied by oxygen displacements and the presence of Sb s orbitals. Using density functional theory plus dynamical mean field theory, we find that the correlated electronic structure of Na 3 Co 2 SbO 6 is an orbital-selective Mott insulating state where the trigonal a 1g orbital is insulating due to the nearly full occupation, while other d orbitals behave as typical Mott insulators, resulting in the effective tunability of Δ TCF under the strain effect. The sign change of Δ TCF can occur as the in-plane tensile strain is applied, and the Kitaev spin liquid phase could possibly be realized due to the strongly suppressed Δ TCF under tensile strain. Our results show that the local Co-site symmetry and dynamical correlation effects will play an important role in engineering the novel magnetic phase in this and related materials.

Nguyen, Nam [Univ. of Illinois, Chicago, IL (Unite↗
DOE OSTI2025

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

PDB↗
DOE OSTI2025

Pentaerythritol structure-directing agents bias aluminum siting in MFI zeolites to increase para -xylene selectivity during toluene methylation

MFI zeolites contain ten-membered ring channels (∼0.55 nm diameter) that intersect to form larger voids (∼0.70 nm diameter). The distribution of framework Al sites dictates the void environments that confine active H + sites. MFI synthesized with pentaerythritol (PET) and Na + as structure-directing agents are interrogated using kinetically controlled toluene methylation rates and xylene isomer selectivities. High para-xylene selectivity and low toluene methylation rates indicate that MFI-PET samples contain H + sites predominantly in smaller channels. As-synthesized samples contain more framework Al than Na + , indicating that some charge compensation is provided by protonated PET-solvent complexes that bias Al siting towards these smaller channels.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Symmetric-asymmetric collision comparison: Disentangling nuclear structure and subnucleonic structure effects for small system flow

Previous flow measurements in small collision systems were mostly based on highly asymmetric collisions (p+Pb, p+Au, d+Au, 3 He+Au), where both nuclear structure and subnucleonic fluctuations are important. Comparing these asymmetric systems with the newly available symmetric 16 O+ 16 O collisions at RHIC and LHC provides a unique opportunity to disentangle these two contributions. Using Glauber models incorporating both nucleon and quark-level substructure, we analyze multiplicity distributions and initial-state estimators: eccentricities ε n for anisotropic flow ν n and inverse transverse size d ⟂ for radial flow. We find that subnucleonic fluctuations impact O+O collisions differently from asymmetric systems, creating specific patterns in flow observables that enable disentangling the competing contributions. Such experimental comparisons will reduce uncertainties in the initial conditions and improve our understanding of the properties of the QGP-like medium produced in small systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Sequence-Structure–Property Relationships in Short-Chain Polyesters: How Primary Structure Governs Macroscopic Performance

While polymer properties are fundamentally linked to their nanostructure, the influence of monomer sequence remains less understood than stereochemical factors like tacticity. This study examines how sequence distribution affects the thermal behavior and morphology of homo- and copolyesters, specifically comparing polymers derived from constitutionally identical monomers but with varying degrees of sequence regularity depending on monomer structure or polymerization selectivity. Our findings show that increasing sequence defects progressively diminish thermal stability, crystallinity, melting temperatures, and morphological order. As new materials become more compositionally complex, this work underscores the importance of sequence control in the design of advanced polymers for emerging applications.

Bocharova, Vera [Oak Ridge National Laboratory (OR↗
DOE OSTI2026

Exploring the Origins of Anti-Ambipolarity in BBL Polymer: Links to Redox Chemistry, Electronic Structure, and Structural Dynamics

We examine the intrinsic physical-chemical properties of the conjugated ladder-type polymer poly(benzimidazobenzophenanthroline) (BBL) in response to electron transfer. We aim at explaining the origin of the anti-ambipolar behavior behind the observed BBL nonlinear response associated with specific device architectures. To elucidate this point, we use theory and computation based on first principles, including density functional theory optimizations, ab initio molecular dynamics, time-dependent DFT, and Marcus-theory analysis. Our results reveal that this redox response is not simply monotonic but follows an alternating odd/even pattern in which gap narrowing and reopening occur sequentially before near-gapless behavior emerges at high charging. Converging theoretical evidence in this work demonstrates that bell shaped conductivity in BBL originates in its fundamental electronic structure and supramolecular organization.

FOS: Physical sciences↗