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At least 433 records · Page 24

Synthesis, structure, and electrochemical properties of [LNi(R f )(C 4 F 8 )] - and [LNi(R f ) 3 ] - complexes

The new anionic nickelate complexes [(MeCN)Ni(C 4 F 8 )(CF 3 )] -, [(MeCN)Ni(C 4 F 8 )(C 2 F 5 )] - , [(IMes)Ni(C 4 F 8 )(CF 3 )] - , [(IMes)Ni(CF 3 ) 3 ] - (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene), and [(F-NHC)Ni(Rf) 3 ] - (F-NHC = 1,3-bis(2,4-F2Ph), 2,4,6-F 3 Ph- or 3,4,5-F 3 Ph)imidazol-2-ylidene; (R f = CF 3 or C 2 F 5 ) were synthesized and structurally characterized. The electrochemical properties of all new compounds were revealed by cyclic voltammetry studies and compared to the known CF 3 analogue [(MeCN)Ni(CF 3 ) 3 ] -. The IMes-coordinated complexes exhibited initial oxidation events that were well-separated from a second oxidation process in the cyclic voltammograms. The complexes containing F-substituted NHC ligands [(F-NHC)Ni(CF 3 ) 3 ] - are structurally quite similar to the IMes derivative and reveal also two separated oxidation waves in their cyclic voltammograms. The absolute potentials as well as the separation between the two waves vary with the substitution pattern, suggesting that the NHC ligand environment (NHC = N-heterocyclic carbene) is an interesting platform for the development of new redox-triggered reactions that release trifluoromethyl and perfluoroalkyl radicals upon oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermally driven phase transitions in freestanding low-buckled silicene, germanene, and stanene

Low-buckled silicene, germanene, and stanene are group-IV graphene allotropes. They form a honeycomb lattice out of two interpenetrating (A and B) triangular sublattices that are vertically separated by a small distance Δ z . The atomic numbers Z of silicon, germanium, and tin are larger than that of carbon (Z C = 6), making them the first experimentally viable two-dimensional topological insulators. Those materials have a twice-energy-degenerate atomistic structure characterized by the buckling direction of the B sublattice with respect to the A sublattice [whereby the B atom either protrudes above (Δ z > 0) or below (Δ z < 0) the A atoms], and the consequences of that energy degeneracy on their elastic and electronic properties have not been reported thus far. Here, we uncover ferroelastic, bistable behavior on silicene, which turns into an average planar structure at about 600 K. Furthermore, the creation of electron and hole puddles obfuscates the zero-temperature spin-orbit coupling (SOC)-induced band gaps at temperatures as low as 200 K, which may discard silicene as a viable two-dimensional topological insulator for room-temperature applications. Germanene, on the other hand, never undergoes a low-buckled-to-planar two-dimensional transformation, becoming amorphous at around 675 K instead, and preserving its SOC-induced band gap despite band broadening. Stanene undergoes a transition onto a crystalline three-dimensional structure at about 300 K, preserving its SOC-induced electronic band gap up to that temperature. Unlike what is observed in silicene and germanene, stanene readily develops a higher-coordinated structure with a high degree of structural order. Furthermore, the structural phenomena are shown to have far-reaching consequences for the electronic and vibrational properties of those two-dimensional topological insulators.

36 MATERIALS SCIENCE↗

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗

The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding

Phosphatidylinositol (3,4,5)-trisphosphate (PIP 3 )-dependent Rac exchanger 1 (P-Rex1) catalyzes the exchange of GDP for GTP on Rac GTPases, thereby triggering changes in the actin cytoskeleton and in transcription. Its overexpression is highly correlated with the metastasis of certain cancers. P-Rex1 recruitment to the plasma membrane and its activity are regulated via interactions with heterotrimeric Gβγ subunits, PIP 3 , and protein kinase A (PKA). Deletion analysis has further shown that domains C-terminal to its catalytic Dbl homology (DH) domain confer autoinhibition. Among these, the first dishevelled, Egl-10, and pleckstrin domain (DEP1) remains to be structurally characterized. DEP1 also harbors the primary PKA phosphorylation site, suggesting that an improved understanding of this region could substantially increase our knowledge of P-Rex1 signaling and open the door to new selective chemotherapeutics. Here we show that the DEP1 domain alone can autoinhibit activity in context of the DH/PH-DEP1 fragment of P-Rex1 and interacts with the DH/PH domains in solution. The 3.1 Å crystal structure of DEP1 features a domain swap, similar to that observed previously in the Dvl2 DEP domain, involving an exposed basic loop that contains the PKA site. Using purified proteins, we show that although DEP1 phosphorylation has no effect on the activity or solution conformation of the DH/PH-DEP1 fragment, it inhibits binding of the DEP1 domain to liposomes containing phosphatidic acid. Thus, we propose that PKA phosphorylation of the DEP1 domain hampers P-Rex1 binding to negatively charged membranes in cells, freeing the DEP1 domain to associate with and inhibit the DH/PH module.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Lead‐Free Ferroelectric 2D Dion–Jacobson Tin Iodide Perovskite

2D hybrid organic–inorganic halide perovskites emerge as a new class of 2D semiconductors with the potential to combine excellent optoelectronic properties with symmetry-enabled properties such as ferroelectricity. Although many lead-based ferroelectric 2D halide perovskites are reported, there is yet to be a conclusive report of ferroelectricity in tin-based 2D perovskites. Here, the structures and properties of a new series of 2D Dion–Jacobson (DJ) Sn perovskites: (4AMP)SnI 4 , (4AMP)(MA)Sn 2 I 7 , and (4AMP)(FA)Sn 2 I 7 (4AMP = 4-(aminomethyl)piperidinium, MA = methylammonium, and FA = formamidinium), are reported. Structural characterization reveals that (4AMP)SnI 4 is polar with in-plane spontaneous polarization whereas (4AMP)(MA)Sn 2 I 7 and (4AMP)(FA)Sn 2 I 7 are centrosymmetric. Further, (4AMP)SnI 4 displays second harmonic generation (SHG) and polarization-electric field hysteresis measurements confirm it is ferroelectric with a spontaneous polarization of 10.0 µC cm −2 at room temperature. (4AMP)SnI 4 transitions into a centrosymmetric structure above 367 K. As the first direct experimental observation of the spontaneous ferroelectric polarization of a Sn-based 2D hybrid perovskite, this work opens up environmentally friendly 2D tin halide perovskites for ferroelectricity and other physical property studies.

2D↗

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↗

Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability

Mammalian cytochrome P450 enzymes often metabolize many pharmaceuticals and other xenobiotics, a feature that is valuable in a biotechnology setting. However, extant P450 enzymes are typically relatively unstable, with T 50 values of ~30–40 °C. Reconstructed ancestral cytochrome P450 enzymes tend to have variable substrate selectivity compared with related extant forms, but they also have higher thermostability and therefore may be excellent tools for commercial biosynthesis of important intermediates, final drug molecules, or drug metabolites. In this work, the mammalian ancestor of the cytochrome P450 1B subfamily was characterized structurally and functionally, revealing differences from the extant human CYP1B1 in ligand binding, metabolism, and potential molecular contributors to its thermostability. Whereas extant human CYP1B1 has one molecule of α-naphthoflavone in a closed active site, we observed that subtle amino acid substitutions outside the active site in the ancestor CYP1B enzyme yielded an open active site with four ligand copies. A structure of the ancestor with 17β-estradiol revealed only one molecule in the active site, which still had the same open conformation. Detailed comparisons between the extant and ancestor forms revealed increases in electrostatic and aromatic interactions between distinct secondary structure elements in the ancestral forms that may contribute to their thermostability. To the best of our knowledge, this represents the first structural evaluation of a reconstructed ancestral cytochrome P450, revealing key features that appear to contribute to its thermostability.

16beta-estradiol↗

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ A 4 ) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ A 4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σ A 4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σ A 4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σ A 4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

59 BASIC BIOLOGICAL SCIENCES↗

Rietveld Refinement for Macromolecular Powder Diffraction

Powder X-ray diffraction (PXRD) has been employed extensively for the structural characterization of materials, quantitative analysis of multicomponent mixtures, phase identification, texture, and microstructural analysis. At the heart of all those lies the Rietveld method, which has revolutionized the use of powder diffraction for materials studies. Initially applied to minerals and inorganics, the Rietveld method has progressively been used for more complex materials, for instance, zeolites and pharmaceuticals. A major advance of the method came some 20 years ago, when the first protein structure was successfully refined. Because of the sheer complexity of macromolecules, several new approaches and algorithms had to be pioneered or adapted from macromolecular single-crystal diffraction experiments, thus constituting macromolecular PXRD a quite unique field of study. This review aims to provide necessary elements of theory and application of structure solution and refinement via the Rietveld method for macromolecular PXRD data. Here, practical explanations and highlighted case studies are also presented.

36 MATERIALS SCIENCE↗

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗

Critical length scales for chemical heterogeneity at Cu/Nb 3D interfaces by atom probe tomography

Cu/Nb nanocomposites containing sharp, two-dimensional (2D) interfaces have outstanding strength but limited deformability. In contrast, Cu/Nb with three dimensional (3D) biphase interfaces exhibiting crystallographic, topological, and chemical variations in all spatial dimensions overcomes this limitation by simultaneously enhancing material strength and deformability. Here, while structural characterization of 3D interfaces has been performed to understand their mechanical behavior, three dimensional chemical characterization of such interfaces is lacking. In this work we quantify the local chemistry of 3D interfaces in Cu/Nb nanocomposites using atom probe tomography (APT). Our analysis demonstrates chemical heterogeneities along all spatial dimensions in 3D interfaces, establishes the length scale of such features, and quantifies the morphology of 3D interfaces. 3D interface heterogeneities form by surface diffusion during physical vapor deposition (PVD), suggesting that deposition parameters can be used to control interface structure and provide unique ways to explore processing-structure-property relationships in interface-dominated nanocomposites.

36 MATERIALS SCIENCE↗

Developing cathode infiltration processes for all-solid-state bilayer LLZO cells

To realize the bilayer architecture of lithium lanthanum zirconate (LLZO) for application in solid-state batteries (SSBs), the scaffold structure must be optimized, and effective cathode infiltration strategies must be established. In this study, we fabricate a modified bilayer LLZO using a sacrificial layer to enhance surface porosity, and systematically investigate various cathode infiltration techniques to fill the scaffold with oxide cathode active materials (CAM). Structural characterizations showed that the sacrificial layer significantly increased open surface porosity, enabling the surface of the scaffold to be filled with CAM. To further increase infiltration depth, applying vacuum or vibration was compared, with the full-depth infiltration achieved using a sonicator-based vibration. Full cells prepared using the modified bilayer LLZO and vibration-assisted technique demonstrated successful operation. This work demonstrates a practical and scalable approach for engineering bilayer LLZO structures and integrating oxide cathodes into porous scaffolds, offering a promising pathway toward high-performance solid-state batteries.

Bilayer↗

Identification of the glassy state in nanoparticles by transmission electron microscopy

Identification of amorphous phases in nanoparticles by atomic-resolution transmission electron microscopy (TEM) requires analyses such as tilt-angle-dependent TEM imaging and single-nanoparticle electron diffraction, rather than relying on a single TEM image. Here, the disordered structures of amorphous nanoparticles offer unique atomic configurations and properties that differ from the properties of their crystalline counterparts. These characteristics have motivated the exploration of such materials for mechanical, sensing and catalytic applications. In addition, the formation of amorphous metal nanoparticles is an important endeavour to understand the process of vitrification and the nature of the glassy state. Atomic-resolution transmission electron microscopy (TEM) is increasingly being used as a tool for characterizing structures of nanoparticles produced by vitrification. In this Comment, we discuss the pitfalls of using TEM for ascertaining whether nanoparticles are amorphous. We also make recommendations of best practices.

Alcorn, Francis M. [Sandia National Laboratories (↗

Graph Identification of Proteins in Tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have difficulty interpreting density associated with small proteins/complexes. To explore alternate approaches for identifying proteins in cryo-ET data we pursued a Graph Network and topologically invariant approach. Here, we report on a fast algorithm that classifies particles by searching for nuances of evolutionarily conversed motifs and the geometrical characteristics of protein structure. GRIP-Tomo 2.0 is a machine-learning pipeline that extracts interpretable topological features of protein structures within noisy experimental backgrounds. Compared to version 1.0, the new pipeline includes three upgrades that significantly improve performance including synthetic tomogram generation simulating realistic noise, graph-based persistent feature extraction as protein fingerprints, and high-performance computing acceleration. GRIP-Tomo 2.0 achieves over 90% accuracy in classifying between proteins and noise using both real and synthetic datasets which represents a foundational step toward advancing cryo-ET workflows and empowering automated visual proteomics.

Li, Chengxuan↗

Polyurethanes Based on Unmodified and Refined Technical Lignins: Correlation between Molecular Structure and Material Properties

The structural complexity and robust intermolecular interactions have challenged the incorporation of technical lignin into value-added polymeric materials for decades. To study the correlation between lignin molecular structure and material properties of lignin-based polyurethanes, we applied co-solvent enhanced lignocellulosic fractionation pretreatment followed by sequential precipitation to produce three distinct lignin preparations with narrowly distributed (molecular weight dispersity <2) and comparatively low molecular weight (<1500 g/mol) from poplar biomass. Structural characterization indicated that these lignin preparations differed in average molecular chain length and stiffness as well as hydroxyl group distribution. Secondary hydroxyl group providers such as aliphatic diols and polyethers were incorporated as building blocks into the lignin-based polyurethanes to provide additional hydrogen capacity to improve the dispersion of lignin in the polyurethane network. The selected aliphatic diols and polyethers interacted with lignin molecules at different levels of strength depending on their molecular structure, and their impacts were ultimately reflected in the mechanical and thermal properties of the resulting lignin-based polyurethanes. The copolymerization of technical lignin with tailored structure and secondary hydroxyl providers could provide new strategies in formulating lignin-based/containing polyurethanes for various functional applications.

36 MATERIALS SCIENCE↗

Grain‐Boundary‐Rich Noble Metal Nanoparticle Assemblies: Synthesis, Characterization, and Reactivity

Abstract Here, a comprehensive study on the synthesis, characterization, and reactivity of grain‐boundary (GB)‐rich noble metal nanoparticle (NP) assemblies is presented. A facile and scalable synthesis of Pt, Pd, Au, Ag, and Rh NP assemblies is developed, in which NPs are predominantly connected via Σ3 (111) twin GBs, forming a network. Driven by water electrolysis, the random collisions and oriented attachment of colloidal NPs in solution lead to the formation of Σ3 (111) twin boundaries and some highly mismatched GBs. This synthetic method also provides convenient control over the GB density without altering the crystallite size or GB type by varying the NP collision frequency. The structural characterization reveals the presence of localized tensile strain at the GB sites. The ultrahigh activity of GB‐rich Pt NP assembly toward catalytic hydrogen oxidation in air is demonstrated, enabling room‐temperature catalytic hydrogen sensing for the first time. Finally, density functional theory calculations reveal that the strained Σ3(111) twin boundary facilitates oxygen dissociation, drastically enhancing the hydrogen oxidation rate via the dissociative pathway. This reported large‐scale synthesis of the Σ3 (111) twin GB‐rich structures enables the development of a broad range of high‐performance GB‐rich catalysts.

Geng, Xin↗

Identifying Dense NiSe 2 /CoSe 2 Heterointerfaces Coupled with Surface High-Valence Bimetallic Sites for Synergistically Enhanced Oxygen Electrocatalysis

Constructing heterostructures with abundant interfaces is essential for integrating the multiple functionalities in single entities. Herein, the synthesis of NiSe 2 /CoSe 2 heterostructures with different interfacial densities via an innovative strategy of successive ion injection is reported. The resulting hybrid electrocatalyst with dense heterointerfaces exhibits superior electrocatalytic properties in an alkaline electrolyte, superior to other benchmarks and precious metal catalysts. Advanced synchrotron techniques, post structural characterizations, and density functional theory (DFT) simulations reveal that the introduction of atomic-level interfaces can lower the oxidation overpotential of bimetallic Ni and Co active sites (whereas Ni$^{2+}$ can be more easily activated than Co$^{2+}$) and induce the electronic interaction between the core selenides and surface in situ generated oxides/hydroxides, which play a critical role in synergistically reducing energetic barriers and accelerating reaction kinetics for catalyzing the oxygen evolution. Hence, the heterointerface structure facilitates the catalytic performance enhancement via increasing the intrinsic reactivity of metallic atoms and enhancing the synergistic effect between the inner selenides and surface oxidation species. This work not only complements the understanding on the origins of the activity of electrocatalysts based on metal selenides, but also sheds light on further surface and interfacial engineering of advanced hybrid materials.

36 MATERIALS SCIENCE↗

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗