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Structural Formation of Huntingtin Exon 1 Aggregates Probed by Small-Angle Neutron Scattering
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Structure–reactivity relationships in the removal efficiency of catechol and hydroquinone by structurally diverse Mn-oxides
Catechol and hydroquinone are widely present hydroxybenzene isomers in the natural environment that induce environmental toxicities. These hydroxybenzene compounds can be effectively removed by manganese (Mn)-oxides via sorption and oxidative degradation processes. In the present study, we investigated the structure–reactivity relationships in the sorption and oxidation of catechol and hydroquinone on Mn-oxide surfaces. Two widely present Mn-oxides, including hydrous Mn oxide (HMO) and cryptomelane, comprised of layer and tunnel structures, respectively, are specifically studied. Effects of Mn-oxide structures and environmental pH conditions on the removal efficiency of these hydroxybenzene compounds, via sorption and oxidative degradation, are investigated. Cryptomelane, which has a higher specific surface area than HMO, possesses a higher sorption and oxidation capacity. The complexation mechanisms of catechol and hydroquinone vary due to their structure-induced difference in reactivity. Catechol reduced and dissolved more Mn from Mn-oxides than hydroquinone, accompanied by a higher C loss of catechol-C, suggesting a higher reactivity of catechol. Structural changes occurred in the Mn-oxides resulting from reaction with catechol and hydroquinone: reduction of Mn(IV), corresponding formation of Mn(III) and Mn(II) in the mineral, and free Mn 2+ ions released into the suspension. Finally, these insights could help us better understand and predict the fate of hydroxybenzene compounds in Mn-oxide-rich soils and wastewater treatment systems that generate Mn-oxides via Mn removal and the associated environmental toxicity.
Stochastic generation of explicit pore structures by thresholding Gaussian random fields
We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone. -- Graphical abstract: -- Highlights: •An efficient method to stochastically generate realistic pore structures is provided. •Samples are generated by applying a level threshold to a Gaussian field realization. •Two user prescribed quantities determine the topology and geometry of the pore space. •Multiple pore structures and preferential flow directions can be produced. •A pore space based on Berea sandstone is generated.
Crystal structure of Na{sub 2}MMgP{sub 2}O{sub 8} (M: Ba, Sr, Ca) orthophosphates and their luminescence properties activated by Eu{sup 2+}; analogous structural behaviors of glaserite-type phosphates and silicates
Rietveld refinements of X-ray powder diffraction data and vibrational spectroscopy have confirmed the crystal structure of Na{sub 2}MMgP{sub 2}O{sub 8} (M: Ba, Sr, Ca) prepared by a standard solid state reaction. They have glaserite-type layered structure. Na{sub 2}MMgP{sub 2}O{sub 8} has a trigonal P3-bar form for M=Ba, and monoclinic P2{sub 1}/c forms for M=Sr and Ca. The observed structural transition is analogous to the corresponding layered orthosilicate M{sub 3}MgSi{sub 2}O{sub 8}. Eu{sup 2+}-doped Na{sub 2}MMgP{sub 2}O{sub 8} exhibits an intense blue to violet emission under ultraviolet excitation, based on 5d-4f electron transition of Eu{sup 2+} ions. The emission character is very sensitive to the structural transition induced by M{sup 2+} and the subsequent site symmetry changes. - Graphical abstract: Emission properties of Na{sub 2}MMgP{sub 2}O{sub 8} (M: Ba, Sr, Ca) are discussed from the viewpoint of the crystal structure solved by X-ray powder diffraction technique. Highlights: Black-Right-Pointing-Pointer Glaserite-type Na{sub 2}MMgP{sub 2}O{sub 8} (M: Ba, Sr, Ca) has been prepared by a solid state reaction. Black-Right-Pointing-Pointer Crystal system of Na{sub 2}MMgP{sub 2}O{sub 8} changes, depending on M{sup 2+} size. Black-Right-Pointing-Pointer Eu{sup 2+}-doped Na{sub 2}MMgP{sub 2}O{sub 8} exhibits blue to violet emission under ultraviolet irradiation.
Factors governing Yb magnetism in Yb{sub 0.95}PtIn{sub 2} and other MgCuAl{sub 2}-type structures
The ternary compound 'YbPtIn{sub 2}' has been synthesized and its crystal structure determined using single crystal X-ray diffraction techniques. The compound crystallizes in the MgCuAl{sub 2} structure, a ternary structure type often formed when rare earth metals, Group 10 transition metals, and indium are present in a 1:1:2 ratio. The unit cell is C-centered orthorhombic, space group Cmcm (no. 63) with lattice parameters of a=4.3410(1) A, b=10.3230(2) A, and c=7.8510(2) A. Evidence is found for a substantial non-stoichiometry on the Yb site, in contrast to the Pt and In sites which behave as expected, and it is believed that the stoichiometry of this compound is more properly described as Yb{sub 0.95}PtIn{sub 2}. Magnetic and resistivity measurements reveal that 'YbPtIn{sub 2}' is a weakly interacting, non-magnetic metal exclusively containing Yb{sup 2+}, and with a resistivity ({rho}) varying from 34 {mu}{Omega} cm at room temperature to a residual resistivity {rho}{sub 0} of 23 {mu}{Omega} cm at 1.8 K. Density functional theory calculations suggest that the observed diamagnetic Yb behavior is expected for this compound, but that certain substitutions on the Pt or In site could help stabilize magnetic Yb{sup 3+} and potentially induce heavy fermion behavior. - Graphical abstract: The crystal structure, magnetic behavior, and temperature-dependent resistivity of the new ternary compound Yb{sub 0.95}PtIn{sub 2.} Highlights: Black-Right-Pointing-Pointer Flux growth method used to produce Yb{sub 0.95}PtIn{sub 2} single crystals. Black-Right-Pointing-Pointer Found rare example of non-stoichiometry in a MgCuAl{sub 2}-type structure. Black-Right-Pointing-Pointer The resistivity and diamagnetic response of Yb{sub 0.95}PtIn{sub 2} were modeled. Black-Right-Pointing-Pointer DFT correctly predicts presence of Yb{sup 2+} in Yb{sub 0.95}PtIn{sub 2}. Black-Right-Pointing-Pointer COHP results suggest other MgCuAl{sub 2}-type indides that may contain paramagnetic Yb{sup 3+}.
Crystal structure study of new lanthanide silicates with silico-carnotite structure
The crystal structures of new rare earth-based silicate compounds (Ca{sub 3}Eu{sub 2}Si{sub 3}O{sub 12}, Ca{sub 3}Gd{sub 2}Si{sub 3}O{sub 12}, Ca{sub 3}Dy{sub 2}Si{sub 3}O{sub 12}, Ca{sub 3}Er{sub 2}Si{sub 3}O{sub 12} and Ca{sub 3}Lu{sub 2}Si{sub 3}O{sub 12}) have been determined using powder X-ray diffraction. From Rietveld refinement calculations on the collected powder patterns we observe a different distribution of the rare earth ions on the three available crystal sites characterized by different coordination numbers, depending on the ionic radius of the rare earth ion. The reasons of the instability of the silico-carnotite structure for lanthanide ions larger than Eu{sup 3+} have been deduced. In addition, in order to detect crystal phase transitions, the powder patterns of Ca{sub 3}Eu{sub 2}Si{sub 3}O{sub 12} and Ca{sub 3}Sm{sub 2}Si{sub 3}O{sub 12} samples have been collected as a function of the temperature (RT-1000 Degree-Sign C range), but no phase transitions have been observed. - Graphical abstract: Synchrotron X-ray diffraction allows us the accurate determination of the RE{sup 3+} ions distribution on the three available crystal sites of the silico-carnotite structure. Highlights: Black-Right-Pointing-Pointer The structure of the Ca{sub 3}M{sub 2}Si{sub 3}O{sub 12} (M=Eu, Gd, Dy, Er and Lu) was determined. Black-Right-Pointing-Pointer Different distribution of RE{sup 3+} ions on the three available crystal sites was observed. Black-Right-Pointing-Pointer The instability of the silico-carnotite structure for RE=La{yields}Sm was discussed.
Intermetallic solid solution Fe{sub 1-x}Co{sub x}Ga{sub 3}: Synthesis, structure, NQR study and electronic band structure calculations
Unlimited solid solution Fe{sub 1-x}Co{sub x}Ga{sub 3} was prepared from Ga flux. Its crystal structure was refined for Fe{sub 0.5}Co{sub 0.5}Ga{sub 3} (P4{sub 2}/mnm, a=6.2436(9), c=6.4654(13), Z=4) and showed no ordering of the metal atoms. A combination of the electronic band structure calculations within the density functional theory (DFT) approach and {sup 69,71}Ga nuclear quadrupole resonance (NQR) spectroscopy clearly shows that the Fe-Fe and Co-Co dumbbells are preferred to the Fe-Co dumbbells in the crystals structure. The band structure features a band gap of about 0.4 eV, with the Fermi level crossing peaks of a substantial density of electronic states above the gap for x>0. The solid solution is metallic for x>0.025. The study of the nuclear spin-lattice relaxation shows that the rate of the relaxation, 1/T{sub 1}, is very sensitive to the Co concentration and correlates well with the square of the density of states at the Fermi level, N{sup 2}(E{sub F}). - Graphical abstract: Rate of the nuclear spin-lattice relaxation, 1/T{sub 1}, observed in the {sup 69}Ga NQR experiments for the intermetallic solid solution Fe{sub 1-x}Co{sub x}Ga{sub 3} is the highest for x=0.25 with the highest calculated density of electronic states at the Fermi level, N(E{sub F}); in general, 1/T{sub 1} correlates with N{sup 2}(E{sub F}). Highlights: Black-Right-Pointing-Pointer Fe{sub 1-x}Co{sub x}Ga{sub 3} solid solution is prepared in single crystalline form from Ga flux. Black-Right-Pointing-Pointer In the crystal structure Fe-Fe and Co-Co dumbbells are preferred to Fe-Co dumbbells. Black-Right-Pointing-Pointer Metal-to-semiconductor transition occurs at 0<x<0.025. Black-Right-Pointing-Pointer {sup 69,71}Ga NQR spectra efficiently probe local environment of two independent Ga atoms. Black-Right-Pointing-Pointer Rate of nuclear spin-lattice relaxation follows squared DOS at the Fermi level.
Synthesis, crystal structure, and properties of KSbO{sub 3}-type Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11}
Single crystals of Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} were prepared from NaCl+KCl flux. This compound adopts KSbO{sub 3}-type crystal structure as evidenced by electron and single crystal X-ray diffraction analysis. The three-dimensional channel structure is formed by corner-sharing octahedral (Mn{sub 0.63}Te{sub 0.37}){sub 2}O{sub 10} dimers and two identical (Bi1){sub 4}(Bi2){sub 2} interpenetrating lattices. The intra-dimer Mn/Te-Mn/Te distances in Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} are short and are consistent with weak metal-metal interactions. The mixed oxidation state of manganese and the edge-sharing octahedral features are confirmed by X-ray near edge absorption spectroscopy measurements, which indicate Bi{sub 3}(Mn{sup III}{sub 1.1}Mn{sup IV}{sub 0.8})Te{sup VI}{sub 1.1}O{sub 11} with 57.7% Mn{sup 3+} and 42.3% Mn{sup 4+}. The partial substitution of Te for Mn perturbs long-range magnetic interactions, thereby destroying the ferromagnetic ordering found in Bi{sub 3}Mn{sub 3}O{sub 11} (T{sub C}=150 K). - Graphical abstract: Single crystal of Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} was grown from NaCl+KCl binary flux, suggesting that the high pressure Bi{sub 3}Mn{sub 3}O{sub 11} phase can be stabilized by partial substitution of Mn by Te at ambient pressure. Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} adopts a typical three dimensional KSbO{sub 3}-type crystal structure with three interpenetrating lattices and weak intra-dimmer metal-metal interaction caused by the d electrons of Mn. The edge-shared (Mn{sub 0.63}Te{sub 0.37}){sub 2}O{sub 10} octahedral dimer and mixed oxidation state of manganese (Bi{sub 3}(Mn{sup III}{sub 1.1}Mn{sup IV}{sub 0.8})Te{sup VI}{sub 1.1}O{sub 11} with 57.7% Mn{sup 3+} and 42.3% Mn{sup 4+}) features were evidenced by X-ray absorption near edge spectroscopy. Compared with Bi{sub 3}Mn{sub 3}O{sub 11}, the Te substituted Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} relaxes the crystal structure, but destroys the long-range magnetic ordering and gives short-range magnetic ordering below 5 K. Highlights: Black-Right-Pointing-Pointer High pressure Bi{sub 3}Mn{sub 3}O{sub 11} is stabilized by partial Te substitution at ambient pressure. Black-Right-Pointing-Pointer New KSbO{sub 3}-type Bi{sub 3}Mn{sub 1.9}Te{sub 1.1}O{sub 11} single crystal was grown from binary flux. Black-Right-Pointing-Pointer The presence of mixed oxidation state of manganese is evidenced by XANES study. Black-Right-Pointing-Pointer The Te-substitution destroys the long-range magnetic ordering and relaxes the structure.
Synthesis, crystal growth, structural and magnetic characterization of NH{sub 4}MCl{sub 2}(HCOO), M=(Fe, Co, Ni)
An ambient-pressure solution route and an improved solvothermal synthetic method have been developed to produce polycrystalline powders and large single crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni). The magnetic structure of the 1D linear chain compound NH{sub 4}FeCl{sub 2}(HCOO) has been determined by low-temperature neutron powder diffraction, revealing ferromagnetic intra-chain interactions and antiferromagnetic inter-chain interactions. The newly-reported Co and Ni analogs are isostructural with NH{sub 4}FeCl{sub 2}(HCOO), but there are significant differences in the magnetic properties of each compound; the Ni analog behaves similarly to the Fe compound but with stronger magnetic coupling, exhibiting antiferromagnetic ordering (T{sub N}=8.5 K) and a broad metamagnetic transition between 2 and 5 T, while the Co analog does not order magnetically above 2 K, despite strong antiferromagnetic nearest-neighbor interactions. - Graphical abstract: Large single crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni), which adopt a 1D zig-zag chain structure, can be grown via a solvothermal method. Neutron diffraction experiments revealed that the magnetic structure of the iron compound exhibits ferromagnetic intra-chain coupling and antiferromagnetic inter-chain coupling. - Highlights: • Large crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni) have been grown solvothermally. • The magnetic structure of M=Fe was solved by low-temperature neutron diffraction. • NH{sub 4}FeCl{sub 2}(HCOO) exhibits FM intra-chain and AFM inter-chain interactions. • NH{sub 4}CoCl{sub 2}(HCOO) exhibits no 3D magnetic ordering above 2 K. • NH{sub 4}NiCl{sub 2}(HCOO) exhibits AFM ordering (T{sub N}=8.5 K) and FM intra-chain interactions.
A phase width for CaGaSn. Crystal structure of mixed intermetallic Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} and SmGa{sub x}Sn{sub 3−x}, stability, geometry and electronic structure
X-ray single-crystal structure has been established for new compositions in intermetallic systems of tin and gallium. Crystals were successfully obtained in alloys prepared from elements. The structure of SmGaSn{sub 2} (cubic Pm3̄m, a=4.5778(8) Å, Z=1, R1=0.012) is described with atomic disorder at all Sn/Ga positions and the structure of Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} (hexagonal, P6{sub 3}/mmc, a=4.2233(9), c=17.601(7) Å, Z=1, R1=0.062) raises an interesting question about existence of a composition domain for CaGaSn. Finally, Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} should be considered as a particular composition of Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}, a compound assumed to exist in the range x ~ 0−1. Partial atomic ordering characterizes the Sn/Ga puckered layers of hexagons whose geometries are analyzed and discussed comparatively with analogous arrangements in AlB{sub 2} related hexagonal compounds. The study is supported by rigid band model and DFT calculations performed for different experimental and hypothetic arrangements. - Graphical abstract: A phase width for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} belonging to the hexagonal YPtAs structure-type. - Highlights: • Single crystals of mixed tin gallium ternary intermetallics were obtained. • Partial ordering at metal sites and phase width are evidenced for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}. • Layer deviation to flatness is studied comparatively with related structures. • Geometry and stability analyses based on DFT calculations are provided.
Pore- and micro-structural characterization of a novel structural binder based on iron carbonation
The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.
Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene
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Improved Fitting of Solution X-ray Scattering Data to Macromolecular Structures and Structural Ensembles by Explicit Water Modeling
A new procedure, AXES, is introduced for fitting small-angle X-ray scattering (SAXS) data to macromolecular structures and ensembles of structures. By using explicit water models to account for the effect of solvent, and by restricting the adjustable fitting parameters to those that dominate experimental uncertainties, including sample/buffer rescaling, detector dark current, and, within a narrow range, hydration layer density, superior fits between experimental high resolution structures and SAXS data are obtained. AXES results are found to be more discriminating than standard Crysol fitting of SAXS data when evaluating poorly or incorrectly modeled protein structures. AXES results for ensembles of structures previously generated for ubiquitin show improved fits over fitting of the individual members of these ensembles, indicating these ensembles capture the dynamic behavior of proteins in solution.
Supramolecular Exchange among Assemblies of Opposite Charge Leads to Hierarchical Structures
Abstract not provided