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At least 1,153 records · Page 64

Flat bands in the CoSn-type compounds

Quantum interference on the kagome lattice generates electronic bands with narrow bandwidth, called flat bands. Crystal structures incorporating this lattice can host strong electron correlations with nonstandard ingredients, but only if these bands lie at the Fermi level. In the six compounds with the CoSn structure type (FeGe, FeSn, CoSn, NiIn, RhPb, and PtTl) the transition metals form a kagome lattice. The two iron variants are robust antiferromagnets so we focus on the latter four and investigate their thermodynamic and transport properties. We consider these results and calculated band structures to locate and characterize the flat bands in these materials. Finally, we propose that CoSn and RhPb deserve the community's attention for exploring flat-band physics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Chaperone-tip adhesin complex is vital for synergistic activation of CFA/I fimbriae biogenesis

Colonization factor CFA/I defines the major adhesive fimbriae of enterotoxigenic Escherichia coli and mediates bacterial attachment to host intestinal epithelial cells. The CFA/I fimbria consists of a tip-localized minor adhesive subunit, CfaE, and thousands of copies of the major subunit CfaB polymerized into an ordered helical rod. Biosynthesis of CFA/I fimbriae requires the assistance of the periplasmic chaperone CfaA and outer membrane usher CfaC. Although the CfaE subunit is proposed to initiate the assembly of CFA/I fimbriae, how it performs this function remains elusive. Here, we report the establishment of an in vitro assay for CFA/I fimbria assembly and show that stabilized CfaA-CfaB and CfaA-CfaE binary complexes together with CfaC are sufficient to drive fimbria formation. The presence of both CfaA-CfaE and CfaC accelerates fimbria formation, while the absence of either component leads to linearized CfaB polymers in vitro. We further report the crystal structure of the stabilized CfaA-CfaE complex, revealing features unique for biogenesis of Class 5 fimbriae.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Impact of a Cancer-Related Variant in Human Δ 1 -Pyrroline-5-Carboxylate Reductase 1

Pyrroline-5-carboxylate reductase (PYCR) is a proline biosynthetic enzyme that catalyzes the NAD(P)H-dependent reduction of Δ 1 -pyrroline-5-carboxylate (P5C) to proline. Humans have three PYCR isoforms, with PYCR1 often upregulated in different types of cancers. Here, we studied the biochemical and structural properties of the Thr171Met variant of PYCR1, which is found in patients with malignant melanoma and lung adenocarcinoma. Although PYCR1 is strongly associated with cancer progression, characterization of a PYCR1 variant in cancer patients has not yet been reported. Thr171 is conserved in all three PYCR isozymes and is located near the P5C substrate binding site. We found that the amino acid replacement does not affect thermostability but has a profound effect on PYCR1 catalytic activity. The k cat of the PYCR1 variant T171M is 100- to 200-fold lower than wild-type PYCR1 when P5C is the variable substrate, and 10- to 25-fold lower when NAD(P)H is varied. A 1.84 Å resolution X-ray crystal structure of T171M reveals that the Met side chain invades the P5C substrate binding site, suggesting that the catalytic defect is due to steric clash preventing P5C from achieving the optimal pose for hydride transfer from NAD(P)H. These results suggest that any impact on PYCR1 function associated with T171M in cancer does not derive from increased catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Energy dispersive x-ray diffraction of luminescent powders: A complement to visible phosphor thermometry

Energy-dispersive x-ray diffraction of thermographic phosphors has been explored as a complementary temperature diagnostic to visible phosphor thermometry in environments where the temperature-dependent optical luminescence of the phosphors is occluded. Powder phosphor samples were heated from ambient to 300°C in incremental steps and probed with polychromatic synchrotron x rays; scattered photons were collected at a fixed diffraction angle of 3.9°. Crystal structure, lattice parameters, and coefficients of thermal expansion were calculated from the diffraction data. Finally, of the several phosphors surveyed, YAG:Dy, ZnO:Ga, and GOS:Tb were found to be excellent candidates for diffraction thermometry due to their strong, distinct diffraction peaks that shift in a repeatable and linear manner with temperature.

47 OTHER INSTRUMENTATION↗

Predictive Model of Charge Mobilities in Organic Semiconductor Small Molecules with Force-Matched Potentials

Charge mobility of crystalline organic semiconductors (OSC) is limited by local dynamic disorder. Recently, the charge mobility for several high mobility OSCs, including TIPS-pentacene, were accurately predicted from a density functional theory (DFT) simulation constrained by the crystal structure and the inelastic neutron scattering spectrum, which provide direct measures of the structure and the dynamic disorder in the length scale and energy range of interest. However, the computational expense required for calculating all of the atomic and molecular forces is prohibitive. In this work, we demonstrate the use of density functional tight binding (DFTB), a semiempirical quantum mechanical method that is 2 to 3 orders of magnitude more efficient than DFT. We show that force matching a many-body interaction potential to DFT derived forces yields highly accurate DFTB models capable of reproducing the low-frequency intricacies of experimental inelastic neutron scattering (INS) spectra and accurately predicting charge mobility. We subsequently predicted charge mobilities from our DFTB model of a number of previously unstudied structural analogues to TIPS-pentacene using dynamic disorder from DFTB and transient localization theory. The approach we establish here could provide a truly rapid simulation pathway for accurate materials properties prediction, in our vision applied to new OSCs with tailored properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing Phosphorus Solubility and Its Effect on Critical Temperature ( T c ) in the Helical Superconducting Magnet RbEuFe 4 As 4– x P x

RbEuFe 4 As 4 exhibits a rare combination of high-temperature superconductivity and noncollinear magnetism, originating from the FeAs and Eu layers, respectively. In order to fine-tune its superconducting and magnetic properties, we studied P-doped RbEuFe 4 As 4–x P x . To determine the value of x for which RbEuFe 4 As 4–x P x exists, members of the series have been synthesized in the form of relatively large-sized single crystals by a high-temperature flux growth technique using RbAs flux as well as polycrystalline powder by direct combination reactions between RbFe 2 As 2 and EuFe 2 As 2–x P x . The flux crystal growth reactions indicate that RbEuFe 4 As 4–x P x forms with the values of x ≤ 0.12, which is corroborated by the Rietveld refinement analysis on the products obtained from direct combination reactions. The solubility limit exists primarily due to the preferential site As(2) occupation by P in the RbEuFe 4 As 4 crystal structure. Finally, as x increases in RbEuFe 4 As 4–x P x , magnetization measurements reveal that the superconducting critical transition temperature (T c ) decreases, while the magnetic ordering temperature (T N ) remains almost unchanged in comparison to undoped RbEuFe 4 As 4 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the Structural Origin of Fast Li-Ion Cycling in Tetragonal Bronze-Type Nb 8 W 9 O 47

Bronze and bronze-derived, mixed metal oxides are materials of growing interest for lithium-ion battery anodes due to their high-rate capabilities and the potential for high energy densities via multielectron redox. We report on the synthesis and electrochemical properties of the tetragonal tungsten bronzetype phase Nb 8 W 9 O 47 and our investigation into the structural evolution of this phase upon lithium (de)intercalation, with particular attention to how it relates to the fast-cycling capabilities. Electrochemical cycling shows Nb 8 W 9 O 47 can achieve greater than one Li + per transition metal at rates of C/2 or slower and maintains a capacity equivalent to 0.65 Li + per transition metal at a rate of 20C. Sequential Rietveld analysis of operando X-ray diffraction data reveals anisotropic changes to the unit cell parameters during discharge, accompanied by an off-centering of the transition metals within their octahedral environments. While higher capacities can be accessed below 1.2 V, cells discharged to 1.0 V exhibit a significant expansion of the unit cell volume and reduced Coulombic efficiencies. This report suggests that rigid crystal structures incapable of undergoing polyhedral rotational deformations can instead exploit displacive distortions of the transition metal redox center to enable fast Li-ion cycling with minimal atomic rearrangements.

25 ENERGY STORAGE↗

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C . difficile , MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn 2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn 2+ , which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn 2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗

Electronic Structure and Spin Correlations in Novel Magnetic Structures

The research has advanced understanding of the interrelation between the crystal structure and magnetism in several materials which are or can be of interest for the development of improved, specialized or more cost-effective permanent magnets, as well as in selected materials for biomedical and catalytic applications. Fundamental aspects of ferromagnetism were investigated for Mn-Ge, Co-V and Co-Ge nanoclusters and for melt-spun Co-Sn alloys. New solution-chemistry synthesis methods were designed and tested for Fe-Pt, Fe3C and Fe3O4 nanoparticles. Off-stoichiometric Laves phases in the Fe-Si-Zr, Fe-Nb and Fe-Ta systems, as well as Fe5(Si,Ge)B2 compounds were assessed as new rare-earth-free permanent magnet materials; all except the Fe-Si-Zr Laves phases were found to be promising enough to merit a further exploration. A new method for manufacturing rare-earth-free magnets based on the MnBi compound was developed; by purposely avoiding oxidation-sensitive fine single-crystalline powders, the new method yields magnets with a 50% larger energy storage capacity. Studies of rare-earth-lean permanent-magnet materials (lean compared to the currently predominant Nd-Fe-B materials) were focused on the tetragonal compound of the ThMn12 structure type and included both discovery and characterization of new formulations and exploration of new fabrication/processing techniques. Among the most significant achievements were successful preparation of a vanadium-lean SmFe11V compound, the first observation of thermomechanically induced texture in nanocrystalline Sm(Fe,V)12 alloys, and a breakthrough reduction-diffusion synthesis of Sm1-xZrx(Fe0.8Co0.2)11.2Ti0.8 single-crystal particles with a coercivity as high as 12.6 kOe. Several experiments aimed at improvement of the Nd-Fe-B magnet have also been undertaken including a five-fold increase of the coercivity through a grain-boundary diffusion treatment of a Nd10Fe84B6 nanocrystalline alloy.

36 MATERIALS SCIENCE↗

Side Chain Regioisomers that Dictate Optical Properties and Mechanofluorochromism through Crystal Packing

Designing strong interactions into $π$-conjugated materials can direct their typically uncontrolled molecular packing and is an important strategy toward tuning their technologically relevant properties in the solid state. In this paper we demonstrate unconventional control over solid-state fluorescence and mechanofluorochromism (MFC) through regiochemical substitutions in side chains of 12 three-ring phenylene ethynylenes (PEs) that employ fluoroarene–arene (ArF–ArH) interactions between tetrafluoro ArF pendants and PE main chains to direct crystal packing, with single-atom variations of the lone proton in ArF pendants between 4-hydro, 5-hydro, and 6-hydro substitution yielding in two cases dramatically different fluorescence and MFC behavior. X-ray crystal structures reveal key intermolecular interactions of ArF rings, including their lone protons, which vary as a function of substitution pattern and contribute to optical properties in solids. Rarely reported, particularly with such dramatic results, this systematic study on regiochemical effects over solid-state properties demonstrates the versatility of using discrete, directional interactions of side chains for noncovalent control in conjugated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗

Surface Conversion of Single-Crystal Bi 2 Se 3 to β-In 2 Se 3

In this work, we demonstrate that the surface layers of single-crystal layered-2D Bi 2 Se 3 can be converted to layered-2D rhombohedral ß-In 2 Se 3 by annealing under a trimethylindium (TMIn) flux. Samples were prepared in a metalorganic chemical vapor deposition (MOCVD) chamber, then transferred under vacuum to a surface analysis chamber for analysis with low-energy electron diffraction (LEED) and Auger electron spectroscopy. Additional ex situ characterization included x-ray diffraction, transmission-electron microscopy (TEM), energy dispersive x-ray spectroscopy (EDS) elemental mapping, and Raman spectroscopy. The resulting single-crystal ß-In 2 Se 3 adopts the rhombohedral crystal structure (space group R-3m) and orientation of the underlying Bi 2 Se 3 , and the excess Bi atoms generated by this process create an underlying region of Bi-rich Bi x Se y . Due to the difference in bandgap between Bi 2 Se 3 and In 2 Se 3 , this conversion reaction presents a pathway to lateral heterojunctions if only selected regions are converted by masking the surface to spatially define the TMIn exposure. The conversion may also have implications for heteroepitaxy, because the in-plane lattice constants of Bi 2 Se 3 and In 2 Se 3 (0001) surfaces match those of InP and GaAs (111), respectively, and the natural cleavage planes of a layered-2D crystal facilitate substrate removal and reuse.

14 SOLAR ENERGY↗

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

1,3-Dimethyl-2,3-dihydrobenzo[ d ]imidazoles, 1H , and 1,1',3,3'-tetramethyl-2,2',3,3'-tetrahydro-2,2'-bibenzo[ d ]imidazoles, 1 2 , are of interest as n-dopants for organic electron-transport materials. Salts of 2-(4-(dimethylamino)phenyl)-4,7-dimethoxy-, 2-cyclohexyl-4,7-dimethoxy-, and 2-(5-(dimethylamino)thiophen-2-yl)benzo[ d ]imidazolium ( 1g–i + , respectively) have been synthesized and reduced with NaBH 4 to 1gH , 1hH , and 1iH , and with Na:Hg to 1g 2 and 1h 2 . Their electrochemistry and reactivity were compared to those derived from 2-(4-(dimethylamino)phenyl)- ( 1b + ) and 2-cyclohexylbenzo[ d ]imidazolium ( 1e + ) salts. E ( 1 + / 1 • ) values for 2-aryl species are less reducing than for 2-alkyl analogues, i.e., the radicals are stabilized more by aryl groups than the cations, while 4,7-dimethoxy substitution leads to more reducing E ( 1 + / 1 • ) values, as well as cathodic shifts in E ( 1 2 •+ / 1 2 ) and E ( 1H •+ / 1H ) values. Both the use of 3,4-dimethoxy and 2-aryl substituents accelerates the reaction of the 1H species with PC 61 BM. Because 2-aryl groups stabilize radicals, 1b 2 and 1g 2 exhibit weaker bonds than 1e 2 and 1h 2 and thus react with 6,13-bis(triisopropylsilylethynyl)pentacene ( VII ) via a “cleavage-first” pathway, while 1e 2 and 1h 2 react only via “electron-transfer-first”. 1h 2 exhibits the most cathodic E ( 1 2 •+ / 1 2 ) value of the dimers considered here and, therefore, reacts more rapidly than any of the other dimers with VII via “electron-transfer-first”. Crystal structures show rather long central C–C bonds for 1b 2 (1.5899(11) and 1.6194(8) Å) and 1h 2 (1.6299(13) Å).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers

The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.

carbohydrate-binding protein↗

Structural stability, elemental ordering, and transport properties of layered ScTaN 2

Ternary transition metal (TM) nitrides have gained significant attention in thin film research due to their promising properties for a broad range of applications. Particularly, some of the ternary TM nitrides have been predicted to adopt layered structures that make them interesting for thermoelectric conversion and quantum materials applications. Unfortunately, synthesis of TM ternary nitride films by physical vapor deposition often favors disordered 3D structures rather than the predicted 2D-like layered structure. In this study, we investigate the structural interplay in the Sc-Ta-N ternary system using a combinatorial approach. Combinatorial libraries S⁢c 𝑥 ⁢T⁢a 1−𝑥 ⁢N are synthesized following a two-step method: First, deposit film precursors by cosputtering and then process the resulting 3D-structured samples with rapid thermal annealing. Synchrotron grazing-incidence wide-angle x-ray scattering on films annealed at 1200 ⁢°⁢C for 20 min leads to the nucleation of ScTaN 2 layered structure (𝑃⁢6 3 /𝑚⁢𝑚⁢𝑐) near stoichiometry. We find that the layered structure can accommodate large off-stoichiometry in the Ta-rich region (𝑥 < 0.5), facilitated by the alloying with quasi-isostructural Ta 5 ⁢N 6 compound that exists on a composition tie line at 𝑥 = 0. While focusing on ScTaN 2 , we estimate the long-range order parameter in near-stoichiometric films to be 0.86, corresponding to a fraction of Sc/Ta antisites of 7%. Transport measurements on ScTaN 2 reveal a nearly temperature-independent high carrier density (10 21 c⁢m −3 ), suggesting a heavily doped semiconductor or semimetallic character, consistent with a small positive Seebeck coefficient of +19 µV/K. The carrier mobility at 2 K is relatively small (9.5c⁢m 2 V −1 s −1 ) and the residual-resistivity ratio is minor, suggesting that electrical conduction is dominated by defects or disorder. Measured magnetoresistance suggests possible weak antilocalization at 2 K. This paper highlights the interplay between ScTaN 2 and Ta 5 ⁢N 6 crystal structures in stabilizing layered materials, emphasizes the importance of cation order/disorder for potential tunable alloys, and suggests that ScTaN 2 is a promising platform for exploring electronic properties.

36 MATERIALS SCIENCE↗

Cation reordering instead of phase transitions: Origins and implications of contrasting lithiation mechanisms in 1D ζ- and 2D α-V 2 O 5

Substantial improvements in cycle life, rate performance, accessible voltage, and reversible capacity are required to realize the promise of Li-ion batteries in full measure. Here, we have examined insertion electrodes of the same composition (V 2 O 5 ) prepared according to the same electrode specifications and comprising particles with similar dimensions and geometries that differ only in terms of their atomic connectivity and crystal structure, specifically two-dimensional (2D) layered α-V 2 O 5 that crystallizes in an orthorhombic space group and one-dimensional (1D) tunnel-structured ζ-V 2 O 5 crystallized in a monoclinic space group. By using particles of similar dimensions, we have disentangled the role of specific structural motifs and atomistic diffusion pathways in affecting electrochemical performance by mapping the dynamical evolution of lithiation-induced structural modifications using ex situ scanning transmission X-ray microscopy, operando synchrotron X-ray diffraction measurements, and phase-field modeling. We find the operation of sharply divergent mechanisms to accommodate increasing concentrations of Li-ions: a series of distortive phase transformations that result in puckering and expansion of interlayer spacing in layered α-V 2 O 5 , as compared with cation reordering along interstitial sites in tunnel-structured ζ-V 2 O 5 . By alleviating distortive phase transformations, the ζ-V 2 O 5 cathode shows reduced voltage hysteresis, increased Li-ion diffusivity, alleviation of stress gradients, and improved capacity retention. The findings demonstrate that alternative lithiation mechanisms can be accessed in metastable compounds by dint of their reconfigured atomic connectivity and can unlock substantially improved electrochemical performance not accessible in the thermodynamically stable phase.

25 ENERGY STORAGE↗

Convergent Evolution in Breadth of Two V H 6-1-Encoded Influenza Antibody Clonotypes from a Single Donor

Understanding how broadly neutralizing antibodies (bnAbs) to influenza hemagglutinin (HA) naturally develop in humans is critical to the design of universal influenza vaccines. Several classes of bnAbs directed to the conserved HA stem were found in multiple individuals, including one encoded by heavy-chain variable domain V H 6-1. We describe two genetically similar V H 6-1 bnAb clonotypes from the same individual that exhibit different developmental paths toward broad neutralization activity. One clonotype evolved from a germline precursor recognizing influenza group 1 subtypes to gain breadth to group 2 subtypes. The other clonotype recognized group 2 subtypes and developed binding to group 1 subtypes through somatic hypermutation. Crystal structures reveal that the specificity differences are primarily mediated by complementarity-determining region H3 (CDR H3). Thus, while V H 6-1 provides a framework for development of HA stem-directed bnAbs, sequence differences in CDR H3 junctional regions during VDJ recombination can alter reactivity and evolutionary pathways toward increased breadth.

59 BASIC BIOLOGICAL SCIENCES↗

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗