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At least 865 records · Page 48

Dimensional Evolution Guides Property Control in the A n Cu 4– n TiS 4 Semiconductor Series

Through progressive reduction of the three-dimensional (3D) covalent network of Cu 4 TiS 4 , we isolate seven new members of the A n Cu 4–n TiS 4 family (A = alkali metal; n = 0–4), spanning 3D, 2D, 1D, and 0D structural fragments. The dimensional reduction is rational, as it preserves the edge-sharing connectivity between [CuS 4 ] 7– and [TiS 4 ] 4– tetrahedra across the series. This structural evolution is driven by the stepwise substitution of Cu with alkali metals, guiding the formation of fragments with reduced dimensionality. The effects of “n” and “A” on the crystal structures, stabilities, electronic structures, and optoelectronic properties are profound, demonstrating that the manipulation of alkali metal size and A n Cu 4–n TiS 4 stoichiometry enables predictable variations in structure and properties. For example, the n = 0 and n = 4 end members of the A n Cu 4–n TiS 4 family set the range of achievable band gaps with 2.00 eV for Cu 4 TiS 4 , 2.60 eV for Na 4 TiS 4 , and intermediate values for the n = 1–3 members. Notably, CsCu 3 TiS 4 exhibits exceptional air stability and congruent melting, with density functional theory (DFT) calculating moderate hole and electron effective masses in specific crystallographic directions (mh = 1.24m 0 , me = 0.87m 0 ). Additionally, A 3 CuTiS 4 (A = Na, K, Rb) displays direct band gap behavior and long photoluminescence lifetimes of 2.3–8.6 μs, and K 3 CuTiS 4 has a PLQY of 5.19%. These findings underscore the potential of the A n Cu 4–n TiS 4 family for applications in optoelectronics and demonstrate widely applicable design concepts that unveil rational stoichiometries within a given composition space to generate a series of crystal structures related through an evolving covalent dimensionality that corresponds to a predictable electronic structure and property progression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗

Allosteric inhibition of the IZUMO1–JUNO fertilization complex by the naturally occurring antisperm antibody OBF13

Sperm IZUMO1 binds to egg JUNO, and this interaction is essential for mammalian fertilization. Isolated from a female mouse immunized with syngeneic sperm, the antisperm antibody OBF13 recognizes IZUMO1 and inhibits murine fertilization. How OBF13 interferes with sperm–egg interactions was unknown. Here, we present the X-ray crystal structure of IZUMO1 in complex with OBF13. OBF13 binds to the apex of the four-helix domain of IZUMO1, distant from the JUNO-binding site. Our crystal structure of OBF13-bound IZUMO1 resembles apo-IZUMO1 and differs from the structure of IZUMO1 in complex with JUNO. We identify that OBF13 carries a low level of somatic hypermutation, and through deep mutational scanning, we engineer an affinity-enhanced OBF13 variant. This OBF13 variant single-chain fragment variable decreases the apparent affinity of IZUMO1 for membrane-bound murine JUNO and blocks the binding of acrosome-reacted sperm to eggs, thereby preventing fertilization. We propose allostery between the OBF13 epitope and the JUNO-binding site. OBF13 inhibits a conformational change in IZUMO1, preventing fusion-competent sperm from adhering to murine eggs during fertilization. Surprisingly, murine IZUMO1 binds to hamster JUNO with an affinity ~20-fold higher than to murine JUNO. The decreased affinity caused by OBF13 of murine IZUMO1 for hamster JUNO is sufficient for murine sperm to bind to and fuse with hamster eggs. Our studies provide a structural and mechanistic framework for species-specific, allosteric inhibition of IZUMO1 by a naturally occurring antisperm antibody and offer insights into the development of immunocontraceptives.

Science & Technology - Other Topics↗

Nitrogen in black phosphorus structure

Group V elements in crystal structure isostructural to black phosphorus with unique puckered two-dimensional layers exhibit exciting physical and chemical phenomena. However, as the first element of group V, nitrogen has never been found in the black phosphorus structure. Here, we report the synthesis of the black phosphorus–structured nitrogen at 146 GPa and 2200 K. Metastable black phosphorus–structured nitrogen was retained after quenching it to room temperature under compression and characterized in situ during decompression to 48 GPa, using synchrotron x-ray diffraction and Raman spectroscopy. We show that the original molecular nitrogen is transformed into extended single-bonded structure through gauche and trans conformations. Raman spectroscopy shows that black phosphorus–structured nitrogen is strongly anisotropic and exhibits high Raman intensities in two A g normal modes. Synthesis of black phosphorus–structured nitrogen provides a firm base for exploring new type of high-energy-density nitrogen and a new direction of two-dimensional nitrogen.

58 GEOSCIENCES↗

La 4 Co 4 X ( X = Pb , Bi , Sb ) : A demonstration of antagonistic pairs as a route to quasi-low-dimensional ternary compounds

We outline how pairs of strongly immiscible elements, referred to here as antagonistic pairs, can be used to synthesize ternary compounds with low or quasi-reduced-dimensional motifs intrinsically built into their crystal structures. By identifying third elements that are mutually compatible with a given antagonistic pair, ternary compounds can be formed in which the third element segregates the immiscible atoms into spatially separated substructures. Quasi-low-dimensional structural units, such as sheets, chains, or clusters are a natural consequence of the immiscible atoms seeking to avoid close contact in the solid state. Further, as proof of principle, we present the discovery, crystal growth, and basic physical properties of La 4 ⁢Co 4 ⁢$\mathrm{X}$ (X = Pb, Bi, Sb), a family of intermetallic compounds based on the antagonistic pairs Co-Pb and Co-Bi. La 4 ⁢Co 4 ⁢$\mathrm{X}$ adopts an orthorhombic crystal structure (space group Pbam) containing quasi-two-dimensional Co slabs and La-X polyhedra that stack in an alternating manner along the α axis. Consistent with our proposal, the La atoms separate the Co and X substructures, ensuring there are no direct contacts between the members of the immiscible (antagonistic) pair. Within the Co slabs, the atoms occupy the vertices of corner sharing tetrahedra and triangles, and this bonding motif produces narrow electronic bands near the Fermi level that favor magnetism. The Co is moment bearing in each La 4 ⁢Co 4 $\mathrm{X}$ compound studied, and we show that whereas La 4 ⁢Co 4 ⁢Pb behaves as a three-dimensional antiferromagnet with T N =220K, La 4 ⁢Co 4 ⁢Bi and La 4⁢ Co 4 ⁢Sb have behavior consistent with low-dimensional magnetic coupling and ordering, with T N =153K and 143 K, respectively. In addition to the Pb-, Bi-, and Sb-based La 4 ⁢Co 4 ⁢$\mathrm{X}$ compounds, we also were likely able to produce an analogous La 4 ⁢Co 4 ⁢Sn in polycrystalline form, although we were unable to isolate single crystals. We anticipate that identifying and using mutually compatible third elements together with an antagonistic pair represents a generalizable design principle for discovering new materials and new structure types containing low-dimensional substructures.

36 MATERIALS SCIENCE↗

Influence of Peripheral Substituents on Fe(II) Spin State in Complexes with Tridentate Schiff‐Base Ligands

Abstract Six Fe(II) complexes with substituted 6‐((quinoline‐8‐ylimino)methyl)phenolates (R 2 qsal) were synthesized. X‐ray crystal structure determination for [Fe(R 2 qsal) 2 ], where R=F ( 1 ), Cl ( 2 ), Br ( 3 ), I ( 4 ), CF 3 /H ( 5 ), or CN/H ( 6 ), revealed mononuclear complexes that crystallize either solvent‐free in case of 1 , 5 , and 6 or as CH 2 Cl 2 solvates in the case of 2 , 3 , and 4 . Complexes 1 – 4 , which contain π‐donating substituents, exhibit only high‐spin (HS) state, as shown by crystal structure analysis and magnetic measurements. In contrast, complexes 5 and 6 , which contain electron‐withdrawing substituents, exist in the low‐spin (LS) state at lower temperatures but exhibit crossover to the HS state above 300 K. Electronic structure calculations show a good correlation between the relative energies of the LS and HS states and the experimentally observed behavior.

Gakiya‐Teruya, Miguel↗

N-terminal domain swapping: A new paradigm for spermidine/spermine N -acetyltransferase (SSAT) protein structures?

Enterococcus faecalis is a multi-drug-resistant human pathogen that is found in a variety of environments and is challenging to treat. Under stress conditions, some bacteria regulate intracellular polyamine concentrations via polyamine acetyltransferases to reduce their toxicity. The E. faecalis genome encodes two polyamine acetyltransferases: PmvE and BltD. Both of these proteins belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily. It is unclear why there are two enzymes with similar substrate specificities in this organism. To better understand the structure/function relationship of the E. faecalis BltD enzyme, we determined its crystal structure and performed additional assays to explore its oligomeric state and enzymatic activity. The goal was to determine whether there were structural or catalytic differences between this enzyme and other polyamine acetyltransferases that could explain this redundancy and be exploited for future development of targeted inhibitors for this important human pathogen. We found the BltD enzyme was structurally unique due to its N-terminal domain swapped dimer. However, this enzyme adopts a catalytically active monomer rather than dimer in solution. This indicates the crystal structure we obtained may represent a state that forms at high protein and salt concentrations and at low pH used during crystallization. The BltD dimer found in the crystal may represent a unique view of how an inhibitory peptide or molecule could be designed to occupy its active site. Additionally, this structure shows the extensive flexibility of the N-terminal portion of the E. faecalis BltD enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

An in-situ 3D micro-XRD investigation of water uptake by alkali-silica-reaction (ASR) product

The ASR products in concrete have various chemical compositions. It is yet unclear whether and how these products develop micro-expansion upon moisture ingress. This paper presents a 3D in-situ observation of the crystallography and volume change of an ASR-product-filled vein under varying relative-humidity (R.H.). The vein was observed to contain two layered nano-crystalline phases with distinct basal spacings, and was distributed heterogeneously in space. When R.H. changed from 10% to >38%, the basal spacing increased from 7.43 Å to 8.89 Å for one phase, whereas it remained constant (~10.9 Å) for the other. This is the first time that an ASR product is observed in-situ to exhibit crystal structural expansion during wetting process. However, the product-filled vein exhibited no noticeable swelling when R.H. varied from 10% to 97%. Our findings provide the first direct evidence that the moisturization-induced crystal structural change of ASR product may not be a plausible explanation to the macroscale concrete expansion.

36 MATERIALS SCIENCE↗

Intercalation And High-Pressure Effects On Structural Phase Transitions In Layered As x P 1-x Alloys

This project was aimed at understanding the role of composition, intercalation, and high pressure on the structural evolution of black phosphorous (BP) and layered arsenic phosphorous alloys, As y P 1-y . Under normal conditions, BP is the most stable phase of phosphorous, known as the α-phase, characterized by an orthorhombic honeycomb puckered crystal structure with the Cmca space group. On the other hand, the most stable phase of arsenic is its β-phase, known as gray arsenic (g-As), which has a rhombohedral buckled layered crystal structure with the R3m space group. In a wide range of compositions (y < 0.83), the arsenic phosphorous alloys form the α-phase, known as black arsenic phosphorous (b-As y P 1-y ) with a similar structure to BP. The project was aimed at the synthesis of BP and b-As y P 1-y with different compositions and at studying the structural evolution of these materials during intercalation with alkali metal (especially Li), and under high-pressure conditions. The main goals were to gain a better understanding of these processes and structural changes taking place under these conditions. In particular, the project was aimed at addressing whether such conditions could induce a structural transition between the α- and β-phases. For this, a series of systematic in-situ studies were conducted, including electrochemical lithium intercalation in an in-situ electrochemical cell, and high-pressure experiments in a diamond anvil cell (DAC). Overall, both types of experiments have shown that above a certain composition-dependent threshold level of intercalation or high pressure, the system undergoes phase segregation rather than phase transition. Specifically, the segregation of the excess arsenic was observed, and a single-phase system of b-As y P 1-y transformed into a two-phase system consisting of b-As y P 1-y and g-As, through the following process: 1∗(b-As y P 1-y ) → 1∗(b As y-δ P 1-y ) + δ∗(g-As). Also, the study showed that intercalation and high-pressure are two competing rather than synergistic processes causing at least a partial cancelation of these two factors

36 MATERIALS SCIENCE↗

The impact of metastability on the high-pressure behavior of cerium

The structures adopted by solids under pressure are often assumed to reflect thermodynamic equilibrium, yet in many materials phase selection is strongly influenced by kinetic pathways and microstructural inheritance. Elemental cerium (Ce) exemplifies this challenge, with decades of conflicting reports describing different high-pressure crystal structures emerging under nominally identical conditions. Here we use neutron diffraction from large ( ~ 60 mm 3 ) sample volumes to follow the structural evolution in ultra-high-purity Ce during controlled pressure-temperature cycling between 85 and 295 K and up to 8 GPa. We find that the crystal structure formed at high pressure depends on the compression pathway: slow compression ( ~ 0.25 GPa hr −1 ) at room temperature favors an orthorhombic phase (α'), whereas slow ( ~ 0.25 GPa hr −1 ) and also moderately faster ( ~ 0.5 GPa hr −1 ) compression at low temperature stabilizes a pure monoclinic phase (α"). The low-temperature phase persists metastably over a wide temperature range but transforms irreversibly upon heating above ~ 280 K, or modest pressure cycling. Remarkably, the lower-pressure γ phase remains trapped far beyond the expected stability field, persisting to the highest pressures studied. These observations show that phase selection in Ce is governed by kinetics and microstructural memory rather than equilibrium thermodynamics or sample morphology alone, establishing path dependence as a defining feature of its high-pressure behavior.

Ridley, Christopher J. [Oak Ridge National Laborat↗

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal and magnetic structures of magnetic topological insulators MnBi 2 Te 4 and MnBi 4 Te 7

Using single-crystal neutron diffraction, we present a systematic investigation of the crystal structure and magnetism of the van der Waals topological insulators MnBi 2 Te 4 and MnBi 4 Te 7 , where rich topological quantum states have been recently predicted and observed. Structural refinements reveal that considerable Bi atoms occupied on the Mn sites in both materials, distinct from the previously reported antisite disorder. We show unambiguously that MnBi 2 Te 4 orders antiferromagnetically below 24 K, featured by a magnetic symmetry R I - 3 c , while MnBi 4 Te 7 is antiferromagnetic below 13 K with a magnetic space group P c - 3 c 1 . They both present antiferromagnetically coupled ferromagnetic layers with spins along the c axis. We put forward a stacking rule for the crystal structure of an infinitely adaptive series MnBi 2 n Te 3 n + 1 ( n ≥ 1 ) with a building unit of [ Bi 2 Te 3 ] . Overall, by comparing the magnetic properties between MnBi 2 Te 4 and MnBi 4 Te 7 , together with recent density-functional theory calculations, we concluded that a two-dimensional magnetism limit might be realized in the derivatives. Our work may promote theoretical studies of topological magnetic states in the series of MnBi 2 n Te 3 n + 1 .

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation

Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO 4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl–AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl•ATP•(Mn 2+ ) 2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn 2+ . The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.

59 BASIC BIOLOGICAL SCIENCES↗

B1-B2 transition in shock-compressed MgO

Magnesium oxide (MgO) is a major component of the Earth’s mantle and is expected to play a similar role in the mantles of large rocky exoplanets. At extreme pressures, MgO transitions from the NaCl B1 crystal structure to a CsCl B2 structure, which may have implications for exoplanetary deep mantle dynamics. In this study, we constrain the phase diagram of MgO with laser-compression along the shock Hugoniot, with simultaneous measurements of crystal structure, density, pressure, and temperature. We identify the B1 to B2 phase transition between 397 and 425 gigapascal (around 9700 kelvin), in agreement with recent theory that accounts for phonon anharmonicity. From 425 to 493 gigapascal, we observe a mixed-phase region of B1 and B2 coexistence. The transformation follows the Watanabe-Tokonami-Morimoto mechanism. Our data are consistent with B2-liquid coexistence above 500 gigapascal and complete melting at 634 gigapascal. This study bridges the gap between previous theoretical and experimental studies, providing insights into the timescale of this phase transition.

58 GEOSCIENCES↗

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are “dual-action” inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

Science & Technology - Other Topics↗

Enabling Real-time Scattering Data Analysis with Scalable Optimization [Slides]

Diffraction experiments produce datasets with rich multidimensional physics information such as microstructure, equations of state, crystal structure, elastoplastic properties, and other key inputs to LANL mission-essential multiphysics models. This information is typically extracted through a process called Rietveld refinement, which involves selecting appropriate models of the instrument, crystal structure, and microstructure, identifying suitable starting values, and then fitting often hundreds of model parameters using a sequence of empirical parameter turnon/off sequences within a non-global gradient-based optimization. Extensive user expertise is required to properly setup a refinement, identify appropriate models, and select initial parameter values close to truth, such that the refinement will yield parameter values that are optimally predictive. This is a very tedious manual process performed far after the beamline campaign has ended. As facilities have become capable of generating larger volumes of data, the limitation in throughput due to Rietveld refinement has led to a dramatic increase in unanalyzed data as opposed to an intended increase in new science. In our FY22 TED, we demonstrated an integrated toolset providing near real-time automated Rietveld analysis. If this toolset can be optimized to provide automated Rietveld analysis in real-time, this could alleviate the bottleneck in unanalyzed diffraction data, aid in decision-making during experiments, and increase efficiency of the facility.

74 ATOMIC AND MOLECULAR PHYSICS↗