SciCombinator

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Concept: Crystallography

174

Crystallization of noble metal atoms usually leads to the highly symmetric face-centred cubic phase that represents the thermodynamically stable structure. Introducing defective microstructures into a metal crystal lattice may induce distortions to form non-face-centered cubic phases when the lateral dimensions of objects decrease down to nanometre scale. However, stable non-face-centered cubic phases have not been reported in noble metal nanoparticles. Here we report that a stable body-centred tetragonal phase is observed in silver nanoparticles with fivefold twinning even at ambient conditions. The body-centered tetragonal phase originates from the distortion of cubic silver lattices due to internal strains in the twinned nanoparticles. The lattice distortion in the centre of such a nanoparticle is larger than that in the surfaces, indicating that the nanoparticle is composed of a highly strained core encapsulated in a less-strained sheath that helps stabilize the strained core.

Concepts: Crystal, Crystallography, Nanomaterials, Gold, Crystal system, Atomic packing factor, Reciprocal lattice, Diamond cubic

164

We report a simple method to fabricate nano-porous tantalum oxide films via anodization with Ta foils as the anode at room temperature. A mixture of ethylene glycol, phosphoric acid, NH4F and H2O was used as the electrolyte where the nano-porous tantalum oxide could be synthesized by anodizing a tantalum foil for 1 h at 20 V in a two-electrode configuration. The as-prepared porous film exhibited a continuous, uniform and coral-like morphology. The diameters of pores ranged from 30 nm to 50 nm. The pores interlaced each other and the depth was about 150 nm. After calcination, the as-synthesized amorphous tantalum oxide could be crystallized to the orthorhombic crystal system. As observed in photocatalytic experiments, the coral-like tantalum oxide exhibited a higher photocatalytic activity for the degradation of phenol than that with a compact surface morphology, and the elimination rate of phenol increased by 66.7%.

Concepts: Crystallography, Crystal system, Ethylene glycol, Niobium, Electrolytic capacitor, Orthorhombic crystal system, Tantalum capacitor

163

CeB2O4F is the first cerium fluoride borate, which is exclusively built up of one-dimensional, infinite chains of condensed trigonal-planar [BO3](3-) groups. This new cerium fluoride borate was synthesized under high-pressure/high-temperature conditions of 0.9 GPa and 1450 °C in a Walker-type multianvil apparatus. The compound crystallizes in the orthorhombic space group Pbca (No. 61) with eight formula units and the lattice parameters a=821.63(5), b=1257.50(9), c=726.71(6) pm, V=750.84(9) Å(3), R 1=0.0698, and wR 2=0.0682 (all data). The structure exhibits a 9+1 coordinated cerium ion, one three-fold coordinated fluoride ion and a one-dimensional chain of [BO3](3-) groups. Furthermore, IR spectroscopy, Electron Micro Probe Analysis and temperature-dependent X-ray powder diffraction measurements were performed.

Concepts: Diffraction, Crystallography, Materials science, X-ray crystallography, Crystal system, Powder diffraction, Neutron diffraction, Crystallographic database

162

Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of “diffraction-before-destruction.” However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

Concepts: Diffraction, X-ray, Crystallography, Fundamental physics concepts, Laser, X-ray crystallography, Neutron diffraction, Free electron laser

160

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Concepts: DNA, Diffraction, X-ray, Crystallography, X-ray crystallography, Powder diffraction, Neutron diffraction, Bragg's law

150

A series of Fe(3+)-bearing Li7La3Zr2O12 (LLZO) garnets was synthesized using solid-state synthesis methods. The synthetic products were characterized compositionally using electron microprobe analysis and inductively coupled plasma optical emission spectroscopy (ICP-OES) and structurally using X-ray powder diffraction and (57)Fe Mössbauer spectroscopy. A maximum of about 0.25 Fe(3+) pfu could be incorporated in Li7-3x Fe x La3Zr2O12 garnet solid solutions. At Fe(3+) concentrations lower than about 0.16 pfu, both tetragonal and cubic garnets were obtained in the synthesis experiments. X-ray powder diffraction analysis showed only a garnet phase for syntheses with starting materials having intended Fe(3+) contents lower than 0.52 Fe(3+) pfu. Back-scattered electron images made with an electron microprobe also showed no phase other than garnet for these compositions. The lattice parameter, a 0, for all solid-solution garnets is similar with a value of a 0≈12.98 Å regardless of the amount of Fe(3+). (57)Fe Mössbauer spectroscopic measurements indicate the presence of poorly- or nano-crystalline FeLaO3 in syntheses with Fe(3+) contents greater than 0.16 Fe(3+) pfu. The composition of different phase pure Li7-3x Fe x La3Zr2O12 garnets, as determined by electron microprobe (Fe, La, Zr) and ICP-OES (Li) measurements, give Li6.89Fe0.03La3.05Zr2.01O12, Li6.66Fe0.06La3.06Zr2.01O12, Li6.54Fe0.12La3.01Zr1.98O12, and Li6.19Fe0.19La3.02Zr2.04O12. The (57)Fe Mössbauer spectrum of cubic Li6.54Fe0.12La3.01Zr1.98O12 garnet indicates that most Fe(3+) occurs at the special crystallographic 24d position, which is the standard tetrahedrally coordinated site in garnet. Fe(3+) in smaller amounts occurs at a general 96h site, which is only present for certain Li-oxide garnets, and in Li6.54Fe0.12La3.01Zr1.98O12 this Fe(3+) has a distorted 4-fold coordination.

Concepts: Spectroscopy, Diffraction, Crystallography, Chemical synthesis, X-ray crystallography, Powder diffraction, Neutron diffraction, Electron microprobe

143

Two new 16-nor limonoids, harperspinoids A and B (1 and 2), with a unique 7/5/5/6/5 ring system, have been isolated from the plant Harrisonia perforate together with a known one, Harperforin G (3). Their structures were elucidated by NMR spectroscopy, X-ray diffraction analysis and computational modelling. Compound 1 exists as polymorphic crystals. Conformations of 1 in solution were further discussed based on the computational results. These compounds exhibited notable inhibitory activity against the 11β-HSD1 enzyme. Compound 3 had potencies for the inhibition of human 11β-HSD1 with high selectivity against 11β-HSD2 (IC50 0.58 μM, SI > 174). Molecular docking and quantitative structure-activity relationship studies revealed a mixed regulatory mechanism.

Concepts: Protein structure, Diffraction, X-ray, Crystallography, Chemistry, Enzyme inhibitor, Medicinal chemistry, Protein nuclear magnetic resonance spectroscopy

142

In competitive thermoelectric devices for energy conversion and generation, high-efficiency materials of both n-type and p-type are required. For this, Bi2Te3-based alloys have the best thermoelectric properties in room temperature applications. Partial replacement of tellurium by selenium is expected to introduce new donor states in the band gap, which would alter electrical conductivity and thermopower. We report on the preparation of n-type Bi2(Te1-xSex)3 solid solutions by a straightforward arc-melting technique, yielding nanostructured polycrystalline pellets. X-ray and neutron powder diffraction was used to assess Se inclusion, also indicating that the interactions between quintuple layers constituting this material are weakened upon Se doping, while the covalency of intralayer bonds is augmented. Moreover, scanning electron microscopy shows large surfaces perpendicular to the c crystallographic axis assembled as stacked sheets. Grain boundaries related to this 2D nanostructuration affect the thermal conductivity reducing it below 0.8 Wm(-1)K(-1) at room temperature. Furthermore, Se doping increases the absolute Seebeck coefficient up to -140 μV K(-1) at 400 K, which is also beneficial for improved thermoelectric efficiency.

Concepts: Electron, Crystallography, Semiconductor, Solid, Bismuth telluride, Electrical conductivity, Selenium, Thermoelectric effect

139

We have produced a superconducting binary-elements intercalated graphite, CaxSr1-xCy, with the intercalation of Sr and Ca in highly-oriented pyrolytic graphite; the superconducting transition temperature, T c, was ~3 K. The superconducting CaxSr1-xCy sample was fabricated with the nominal x value of 0.8, i.e., Ca0.8Sr0.2Cy. Energy dispersive X-ray (EDX) spectroscopy provided the stoichiometry of Ca0.5(2)Sr0.5(2)Cy for this sample, and the X-ray powder diffraction (XRD) pattern showed that Ca0.5(2)Sr0.5(2)Cy took the SrC6-type hexagonal-structure rather than CaC6-type rhombohedral-structure. Consequently, the chemical formula of CaxSr1-xCy sample could be expressed as ‘Ca0.5(2)Sr0.5(2)C6’. The XRD pattern of Ca0.5(2)Sr0.5(2)C6 was measured at 0-31 GPa, showing that the lattice shrank monotonically with increasing pressure up to 8.6 GPa, with the structural phase transition occurring above 8.6 GPa. The pressure dependence of T c was determined from the DC magnetic susceptibility and resistance up to 15 GPa, which exhibited a positive pressure dependence of T c up to 8.3 GPa, as in YbC6, SrC6, KC8, CaC6 and Ca0.6K0.4C8. The further application of pressure caused the rapid decrease of T c. In this study, the fabrication and superconducting properties of new binary-elements intercalated graphite, CaxSr1-xCy, are fully investigated, and suitable combinations of elements are suggested for binary-elements intercalated graphite.

Concepts: Diffraction, Crystallography, Fundamental physics concepts, Graphite, X-ray crystallography, Phase transition, Superconductivity, X-ray scattering techniques

112

Tridymite, a low-pressure, high-temperature (>870 °C) SiO2 polymorph, was detected in a drill sample of laminated mudstone (Buckskin) at Marias Pass in Gale crater, Mars, by the Chemistry and Mineralogy X-ray diffraction instrument onboard the Mars Science Laboratory rover Curiosity The tridymitic mudstone has ∼40 wt.% crystalline and ∼60 wt.% X-ray amorphous material and a bulk composition with ∼74 wt.% SiO2 (Alpha Particle X-Ray Spectrometer analysis). Plagioclase (∼17 wt.% of bulk sample), tridymite (∼14 wt.%), sanidine (∼3 wt.%), cation-deficient magnetite (∼3 wt.%), cristobalite (∼2 wt.%), and anhydrite (∼1 wt.%) are the mudstone crystalline minerals. Amorphous material is silica-rich (∼39 wt.% opal-A and/or high-SiO2 glass and opal-CT), volatile-bearing (16 wt.% mixed cation sulfates, phosphates, and chlorides-perchlorates-chlorates), and has minor TiO2 and Fe2O3T oxides (∼5 wt.%). Rietveld refinement yielded a monoclinic structural model for a well-crystalline tridymite, consistent with high formation temperatures. Terrestrial tridymite is commonly associated with silicic volcanism, and detritus from such volcanism in a “Lake Gale” catchment environment can account for Buckskin’s tridymite, cristobalite, feldspar, and any residual high-SiO2 glass. These cogenetic detrital phases are possibly sourced from the Gale crater wall/rim/central peak. Opaline silica could form during diagenesis from high-SiO2 glass, as amorphous precipitated silica, or as a residue of acidic leaching in the sediment source region or at Marias Pass. The amorphous mixed-cation salts and oxides and possibly the crystalline magnetite (otherwise detrital) are primary precipitates and/or their diagenesis products derived from multiple infiltrations of aqueous solutions having variable compositions, temperatures, and acidities. Anhydrite is post lithification fracture/vein fill.

Concepts: Crystallography, Chemistry, Sedimentary rock, Mineral, Solid, Quartz, Silicon dioxide, Amorphous solid