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At least 757 records · Page 42

Structural complexity of γ-Al 2 O 3 : The nature of vacancy ordering and the structure of complex antiphase boundaries

The structure of γ-Al2O3 remains largely undetermined despite decades of research. This is due to the high degree of disorder, which poses significant challenges for structural analysis using conventional crystallographic approaches. Herein, we study the structure of γ-Al2O3 with Scanning Transmission Electron Microscopy (STEM) and ab-initio calculations to provide a complete structural description. We show that the microstructure can be understood in terms of two key structural features of nanoscale spinel domains and finite thickness segments termed as complex antiphase boundaries (cAPB) that provide the domain interconnectivity. The spinel domains have a distinctive preference for vacancy ordering, which can be rationalized in terms of a structure with a stacking disorder. Tetragonal P4 1 2 1 2 or monoclinic P2 1 models, all based on the identical motif, can be considered as representative ordered forms. Individual spinel domains are interconnected via cAPBs, which adopt a distinct non-spinel bonding environment of δ-Al 2 O 3 . The most common cAPB consists of a single delta motif with thickness of just 0.6 nm on (001), with the resulting displacement a/4 [101]. Remarkably, the cAPBs are shown to energetically stabilize the spinel domains of γ-Al 2 O 3 explaining their high abundance. We demonstrate how the tetragonal distortions naturally arise in this intricate microstructure and place the proposed model in the context of phase transformations to high temperature transition aluminas.

36 MATERIALS SCIENCE↗

Isolation and structural characterization of sugarcane bagasse lignin after dilute phosphoric acid plus steam explosion pretreatment and its effect on cellulose hydrolysis

The structure of lignin after dilute phosphoric acid plus steam explosion pretreatment process of sugarcane bagasse in a pilot scale and the effect of the lignin extracted by ethanol on subsequent cellulose hydrolysis were investigated. Here, the lignin structural changes caused by pretreatment were identified using advanced nondestructive techniques such as gel permeation chromatography (GPC), quantitative 13 C, and 2-D nuclear magnetic resonance (NMR). The structural analysis revealed that ethanol extractable lignin preserved basic lignin structure, but had relatively lower amount of β-O-4 linkages, syringyl/guaiacyl units ratio (S/G), p-coumarate/ferulate ratio, and other ending structures. The results also indicated that approximately 8% of mass weight was extracted by pure ethanol. The bagasse after ethanol extraction had an approximate 22% higher glucose yield after enzyme hydrolysis compared to pretreated bagasse without extraction.

Cellulose hydrolysis↗

Understanding fluorine-free electrolytes via small-angle X-ray scattering

Fluorine-free electrolytes have attracted great attention because of its low-cost and environmental friendliness. However, so far, little is known about the solution structures of these electrolytes. Here, we compare the solvation phenomenon of sodium tetraphenylborate (NaBPh 4 ) salt dissolved in organic solvents of propylene carbonate (PC), 1,2-dimethoxyethane (DME), acetonitrile (ACN) and tetrahydrofuran (THF). Small-angle X-ray scattering (SAXS) reveals a unique two-peak structural feature in this salt concentrated PC electrolyte, while solutions using other solvents only have one scattering peak. Molecular dynamics (MD) simulations further reveal that there are anion-based clusters in addition to the short-range charge ordering in the concentrated NaBPh4/PC electrolyte. Raman spectroscopy confirms the existence of considerable contact ion pairs (CIPs). Here, this work emphasizes the importance of global and local structural analysis, which will provide valuable clues for understanding the structure performance relationship of electrolytes.

25 ENERGY STORAGE↗

Fe(III) and Cu(II) coordination polymers assembled from di/tris-phosphonic acid and auxiliary ligands: Structure, SOD-like activity and magnetic behavior

Hydrothermal reactions of (benzylazanediyl)bis(methylene)-diphosphonic acid (H{sub 4}L{sup 1}) or (benzene-1,3,5-triyltris(methylene))triphosphonic acid (H{sub 6}L{sup 2}) with Fe(III)/Cu(II) nitrate and 4, 4′-bipy or 2, 2′-bipy result in five new phosphonates, namely, [FeHL{sup 1}(H{sub 2}O)]{sub n} (1), {[Cu_2L"1(4, 4′-bipy)_0_._5(H_2O)]·0.25H_2O}{sub n} (2), [Cu{sub 2}H{sub 2}L{sup 2}(4, 4′-bipy)(H{sub 2}O){sub 2}]{sub n} (3), [CuH{sub 4}L{sup 2}(2, 2′-bipy)]{sub n} (4) and [Cu{sub 2}(H{sub 4}L{sup 2}){sub 2}(2, 2′-bipy){sub 2}(H{sub 2}O){sub 4}] (5), respectively. X-ray structural analysis indicates that 2 and 3 feature 3D framework structures with 3, 3, 3, 4-connected and 4, 5-connected topology; 1 and 4 display 1D chain structures, while 5 has a dimer structure. The di- or trisphosphonate ligands (H{sub 4}L{sup 1} and H{sub 6}L{sup 2}) in the five complexes adopt different coordination modes and auxiliary ligands (4, 4′-bipy and 2, 2′-bipy) control the dimensionality of the final complexes. The superoxide dismutase (SOD) activities of 2–5 were assessed by modified nitrobluetetrazolium (NBT) assay. The IC{sub 50} values required to yield 50% inhibition of the reduction of NBT are 1.84, 2.02, 6.95 and 1.70 μM for 2–5, respectively, demonstrating better SOD-like activity than most of the Cu-SOD mimic enzymes reported in literatures. Among them, 2 and 3 have good stability and reusability under the simulative physiological conditions. The dismutation of 4 and 5 toward superoxide anion radicals can be attributed to the synergistic effect of the decomposition products of 4 and 5 containing Cu(II) and [H{sub 4}L{sup 2}]{sup 2-} with or without 2, 2′-bipy or Cu(II) and 2, 2′-bipy, which were identified by liquid mass spectrometry (LC/MS). The magnetic properties of complexes 1–4 were also investigated, indicating the presence of magnetic exchange between metal ions. The results show that 1 and 3 exhibit antiferromagnetic interactions, while 2 and 4 show ferromagnetic interactions between metal centres.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Four different dimensional Zn(II) coordination polymers as fluorescent sensor for detecting Hg{sup 2+}, Cr{sub 2}O{sub 7}{sup 2-} in aqueous solution

Highlights: • Four Zn-based coordination polymers were solvethermally synthesized. • Compound 1 and 2 could mutual conversion between different solvent ratios. • Both 1 and 2 exhibit high selectivity for Cr{sub 2}O{sub 7}{sup 2-} and Hg{sup 2+} ions in aqueous solution. • The mechanism of sensing properties were discussed in details. - Abstract: Four Zn(II) coordination polymers (CPs), [Zn(4-pzpt){sub 2}(H{sub 2}O)]{sub n} (1), {[Zn(4-pzpt)_2]·CH_3OH}{sub n} (2), [Zn{sub 2}(4-pzpt){sub 2}(suc)(H{sub 2}O)]{sub n} (3) and [Zn{sub 2}(4-pzpt){sub 2}(ndc)]{sub n} (4) were obtained from 3-(pyridin-4-yl)-5-(pyrazin-2-yl)-1H-1,2,4-triazole (4-Hpzpt), 1,4-Naphthalenedicarboxylic acid (H{sub 2}ndc) and succinic acid (H{sub 2}suc) ligands. Structural analysis reveals that 1 represents a five coordinated 0D structure. 2 possess a network featuring 2D 4{sup 4} grid-like layers structure. 3 displays a network featuring 2D (6{sup 3})-hcb layered structure. 4 shows a rare 3D (4,4)-connected topology with a Schläfli symbol of (4.6{sup 4.}7){sub 2}(6{sup 4.}7{sup 2}). Complexes 1 and 2 can mutual conversion between different solvent ratios. Luminescence properties reveal that 1 and 2 exhibit excellent selectivity for Hg{sup 2+} and Cr{sub 2}O{sub 7}{sup 2-} ions in aqueous solution, in which suggests that 1 and 2 is a promising multifunctional sensing materials. The possible sensing mechanism is also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Peculiar Magnetic and Magneto-Transport Properties in a Noncentrosymmetric Self-Intercalated van der Waals Ferromagnet Cr 5 Te 8

Trigonal Cr 5 Te 8 , a self-intercalated van der Waals ferromagnet with an out-of-plane magnetic anisotropy, has long been known to crystallize in a centrosymmetric structure. However, optical second harmonic generation experiments, together with comprehensive structural analysis, indicate that this compound rather adopts a noncentrosymmetric structure. Lorentz transmission electron microscopy reveals the presence of Néel-type skyrmions, consistent with its noncentrosymmetric structure. A large anomalous Hall conductivity of 102 Ω –1 cm –1 at low temperature stems from intrinsic origin, which is larger than any previously reported values in the bulk Cr–Te system. Notably, spontaneous topological Hall resistivity arising from the skyrmionic phase has been observed. Here, our findings not only elucidate the unique magnetic and magneto-transport properties of noncentrosymmetric trigonal Cr 5 Te 8 , but also open new avenues for investigating the effects of broken inversion symmetry on material properties and their potential applications.

crystal structure↗

Multifunctional Polar 2D Lead Iodide Perovskites Exhibiting Persistent Spin Texture

Ferroelectric Rashba semiconductors are a rare class of multifunctional materials promising for spin–orbitronics due to the possibility of electrically switchable spin textures. Hybrid organic–inorganic metal halide perovskites offer exceptional tunability that can be harnessed to target noncentrosymmetry; however, the complex interactions between organic and inorganic components are not rationally understood. Here, we use an asymmetric spacer cation with a strong molecular dipole moment (2-fluorobenzylammonium, 2FBZ) and increase the intrinsic quantum well thickness to n > 1 to synthesize three new polar 2D lead iodide perovskites (2FBZ) 2 (A) n-1 Pb n I 3n+1 with A = methylammonium (MA) or formamidinium (FA) and n = 2, 3. Single-crystal structure analysis reveals the C 2v symmetry of these crystal structures and substantial structural distortions, which enable Rashba and Dresselhaus band splitting and persistent spin texture, confirmed by DFT calculations. Measurements of the resulting symmetry-dependent properties, such as second harmonic generation, switchable photovoltaic effect, ferroelectric polarization, and low temperature photoluminescence show switchable ferroelectric semiconducting properties. Furthermore, these results introduce a general chemical design strategy toward polar symmetry by exploiting the complex interplay between asymmetric spacer cations and A-site cations in quasi-2D (n > 1) halide perovskites to realize new classes of multifunctional materials for future spin–orbitronic applications.

Cations↗

Synthesis of highly efficient antibacterial agent Ag doped ZnO nanorods: Structural, Raman and optical properties

Here, synthesis, structural, morphological, Raman, optical properties and antibacterial activity of undoped and Ag doped ZnO nanorods by chemical co-precipitation technique have been reported. Structural analysis has revealed that Ag doping cannot deteriorate the structure of ZnO and wurtzite phase is maintained. Lattice constants are found to be decreased with the Ag doping. Fourier transform infrared and Raman spectroscopy also confirm the X-ray diffraction results. Scanning electron microscopy results have demonstrated the formation of ZnO nanorods with average diameter and length of 96 nm and 700 nm, respectively. Raman spectroscopy results suggest that the Ag doping enhances the number of defects in ZnO crystal. It has been found from optical study that Ag doping results in positional shift of band edge absorption peak. This is attributed to the successful incorporation of Ag dopant into ZnO host matrix. The antibacterial activity of prepared nanorods has been determined by two different methods and compared to that of undoped ZnO nanorods. Ag doped ZnO nanorods exhibit excellent antibacterial activity as compared to that of undoped ZnO nanorods. This excellent antibacterial activity may be attributed to the presence of oxygen vacancies and Zn{sup 2+} interstitial defects. Our preliminary findings suggest that Ag doped ZnO nanorods can be used externally to control the spreading of infections related with tested bacterial strains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells

NANOG (from Irish mythology Tír na nÓg) transcription factor plays a central role in maintaining pluripotency, cooperating with OCT4 (also known as POU5F1 or OCT3/4), SOX2, and other pluripotency factors. Although the physiological roles of the NANOG protein have been extensively explored, biochemical and biophysical properties in relation to its structural analysis are poorly understood. Here we determined the crystal structure of the human NANOG homeodomain (hNANOG HD) bound to an OCT4 promoter DNA, which revealed amino acid residues involved in DNA recognition that are likely to be functionally important. We generated a series of hNANOG HD alanine substitution mutants based on the protein–DNA interaction and evolutionary conservation and determined their biological activities. Some mutant proteins were less stable, resulting in loss or decreased affinity for DNA binding. Overexpression of the orthologous mouse NANOG (mNANOG) mutants failed to maintain self-renewal of mouse embryonic stem cells without leukemia inhibitory factor. These results suggest that these residues are critical for NANOG transcriptional activity. Interestingly, one mutant, hNANOG L122A, conversely enhanced protein stability and DNA-binding affinity. The mNANOG L122A, when overexpressed in mouse embryonic stem cells, maintained their expression of self-renewal markers even when retinoic acid was added to forcibly drive differentiation. When overexpressed in epiblast stem cells or human induced pluripotent stem cells, the L122A mutants enhanced reprogramming into ground-state pluripotency. These findings indicate that structural and biophysical information on key transcriptional factors provides insights into the manipulation of stem cell behaviors and a framework for rational protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗

The Influence of Cation Substitution on the Kinetics of Phase Transitions in Crystals of (K,NH{sub 4}){sub 3}H(SO{sub 4}){sub 2} Solid Solutions

The structure of (K{sub 0.967}(NH{sub 4}){sub 0.033}){sub 3}H(SO{sub 4}){sub 2} crystals, belonging to the K{sub 3}H(SO{sub 4}){sub 2}–(NH{sub 4}){sub 3}H(SO{sub 4}){sub 2}–H{sub 2}O salt system, has been investigated by X-ray structural analysis. The room-temperature characteristics of the atomic structure of these crystals are found to be as follows: sp. gr. C2/c, Z = 4, a = 14.7025(4) Å, b = 5.6859(2) Å, c = 9.7885(3) Å, and R/wR = 0.021/0.030%. The thermal and optical properties of (K,NH{sub 4}){sub 3}H(SO{sub 4}){sub 2} and K{sub 3}H(SO{sub 4}){sub 2} single crystals have been investigated and compared in a temperature range of 295–500 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pair distribution function analysis of discrete nanomaterials in PDFgui

Pair distribution functions (PDFs) are a leading tool for atomic structure analysis of nanomaterials. However, the most widely used programs for refining atomic structure against PDF data are based on extended crystallographic models, which cannot be applied to discrete, whole nanoparticles. Furthermore, this work describes a straightforward approach to simulate and refine atomistic models of discrete clusters and nanoparticles employing widely used PDF modelling programs such as PDFgui that utilize extended crystallographic models. In this approach, the whole particle to be modelled is contained within an expanded, and otherwise empty, unit cell that is sufficiently large to avoid correlations between atoms in neighbouring unit cells over the r range analyzed. The PDF of the particle is simulated as a composite using two conventional `phases': one that calculates the atom–atom correlations and one that approximates the local number density. This approach is first validated for large nanoparticles that are well modelled by a conventional shape factor model, and then applied to simulate the PDF of discrete particles and low-dimensional materials (graphene and MXene) and to model the experimental PDF data for single-layer FeS nanosheets. A comparison of this approach with the DiffPy-CMI program, which calculates the PDF of discrete species, shows that the composite modelling approach is equally or more accurate. Example input files for implementing this approach within PDFgui and TOPAS, and recommendations for selecting model parameters for reliable application of this refinement strategy, are provided.

36 MATERIALS SCIENCE↗

Melting Point Depression and Phase Identification of Sugar Alcohols Encapsulated in ZIF Nanopores

Sugar alcohols (SAs) have attractive characteristics as phase-change materials, but their relatively high melting temperature limits their application in the real world. Nanoconfinement can be a useful parameter to reduce the melting temperature to pragmatic ranges. Using molecular dynamics simulations, we investigate the phases and behaviors of encapsulated SA in ZIF-8 and ZIF-11, which cannot be experimentally observed. Based on reliable partial charges for the zeolitic imidazolate framework (ZIF) structures calculated by a density functional theory, structural analysis shows that the SA’s attractive interaction with the ZIF structure frustrates the SA crystallization and also elucidates the second-order phase transition between amorphous phases. A methodology is suggested to determine the phase transition temperature of confined materials and used to quantify the melting temperature depression of the ZIF-confined SAs. We also explored the thermal conductivity of SA-in-ZIF composites. Phonon frequency analysis verifies that the presence of SA molecules enhances the heat transfer by adding heat pathways between the nanoporous structure of ZIFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases

Abstract Engineered polyketide synthases (PKSs) are promising synthetic biology platforms for the production of chemicals with diverse applications. The dehydratase (DH) domain within modular type I PKSs generates an α,β-unsaturated bond in nascent polyketide intermediates through a dehydration reaction. Several crystal structures of DH domains have been solved, providing important structural insights into substrate selection and dehydration. Here, we present two DH domain structures from two chemically diverse PKSs. The first DH domain, isolated from the third module in the borrelidin PKS, is specific towards a trans-cyclopentane-carboxylate-containing polyketide substrate. The second DH domain, isolated from the first module in the fluvirucin B1 PKS, accepts an amide-containing polyketide intermediate. Sequence-structure analysis of these domains, in addition to previously published DH structures, display many significant similarities and key differences pertaining to substrate selection. The two major differences between BorA DH M3, FluA DH M1 and other DH domains are found in regions of unmodeled residues or residues containing high B-factors. These two regions are located between α3–β11 and β7–α2. From the catalytic Asp located in α3 to a conserved Pro in β11, the residues between them form part of the bottom of the substrate-binding cavity responsible for binding to acyl-ACP intermediates.

42 ENGINEERING↗

Structural Confinement Assisted a Robust Superparamagnetic State in MgNi{sub 2}O{sub 3} and MgNi{sub 1.5}Co{sub 0.5}O{sub 3} Nanoparticles at Room Temperature

In this study, ideal spherical-shaped cubic metal oxide nanoparticles of < 30 nm in size were prepared by a citric acid sol-gel combustion method. The detailed structural analysis and microscopic techniques clearly support the existing grade of structural confinement effect in MgNi{sub 2}O{sub 3} and MgNi{sub 1.5}Co{sub 0.5}O{sub 3}. Temperature-dependent magnetisation studies at various applied fields revealed a moderate change of T{sub B} near room temperature by distinct particle size. Magnetic crystalline anisotropy and energy barrier density theoretical model results suggested the importance of innermost magnetic particle stability-aided spin orientation with a fascinating magnetic moment in superparamagnetic region exerted by Ni and Co remarkably postured as a significant part of these nanoparticles.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Synthesis of CuO by Cu-CPPs with the determination of Cu(II) coordination modes from a novel complex of [Cu(terpyOH){sub 2}]·(HBTC)·2H{sub 2}O

In this study, we investigated the synthesis of CuO microrods by simple calcination of copper-based coordination polymer particles (Cu-CPPs) at high temperature in air. The photocatalytic activity of the CuO microrods was tested by the decomposition of aqueous solution of RhB, which was completely decomposed by irradiation with light. To analyze the relationship of metal ions and ligands in the Cu-CPPs, the single crystal of [Cu(terpyOH){sub 2}]∙(HBTC)∙2H{sub 2}O (1) (terpyOH=4′-hydroxy-2,2′:6′,2″-terpyridine, BTC=1,3,5-benzene tricarboxylate) was first prepared and characterized by X-ray single crystal structural analysis. A variety of hydrogen bonds constructing the 3D complex structure in [Cu(terpyOH){sub 2}]∙(HBTC)∙2H{sub 2}O (1) were observed. - Graphical abstract: Demonstrating a general method to synthesize CuO microrods via simple calcination of Cu-CPPs and Cu(II) coordination modes from a novel complex of [Cu(terpyOH){sub 2}]∙(HBTC)·2H{sub 2}O constructed by hydrogen bonding. Display Omitted - Highlights: • The formation of microrods CuO from thermal treatment of Cu-CPPs through an “escape-by-crafty-scheme” strategy has been studied. • Determination of Cu(II) coordination modes in Cu-CPPs from a novel complex of [Cu(terpyOH){sub 2}]∙(HBTC) 2H{sub 2}O. • Invested the behave of hydrogen bonding to construct the 3D complex structure. • Commendable photodegradation performance was observed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Configurational Disorder for Impurities in a Low-Entropy Phase

Hematite (α-Fe 2 O 3 ) exerts a strong control over the transport of minor but critical metals in the environment and is used in multiple industrial applications; the photocatalysis community has explored the properties of hematite nanoparticles over a wide range of transition metal dopants. Nonetheless, simplistic assumptions are used to rationalize the local coordination environment of impurities in hematite. Here, we use ab initio molecular dynamics (AIMD)-guided structural analysis to model the extended X-ray absorption fine structure (EXAFS) of Cu 2+ - and Zn 2+ -doped hematite nanoparticles. Specific defect–impurity associations were identified, and the local coordination environments of Cu and Zn both displayed considerable configurational disorder that, in aggregate, approached Jahn–Teller-like distortion for Cu but, in contrast, maintained hematite-like symmetry for Zn. This study highlights the role of defects in accommodating impurities in a nominally low-entropy phase and the limits to traditional shell-by-shell fitting of EXAFS for dopants/impurities in unprecedented bonding environments.

36 MATERIALS SCIENCE↗

Distinctive Klf4 mutants determine preference for DNA methylation status

Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.

59 BASIC BIOLOGICAL SCIENCES↗

Structural disorder-driven topological phase transition in noncentrosymmetric BiTeI

In this work, we investigate using local structural disorder to induce a topologically nontrivial phase in a solid state system. Using first-principles calculations, we introduce structural disorder in the trivial insulator BiTeI and observe the emergence of a topological insulating phase. By modifying the bonding environments, the crystal-field splitting is enhanced, with spin-orbit interactions producing a band inversion in the bulk electronic structure. Analysis of the Wannier charge centers and the surface electronic structure reveals a strong topological insulator with Dirac surface states. Finally, we propose a prescription for inducing topological states from disorder in crystalline materials. Understanding how local environments produce topological phases is a key step for predicting disordered and amorphous topological materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗