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  • Author: Michal Dušek x
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Abstract

State of the art is presented in the field of structure analysis of aperiodic crystals. Based on the superspace theory that recovers translation periodicity of aperiodic crystals in a (3 + d)-dimensional space, generalized crystallographic methods have been developed that work analogous to standard tools in the classical crystallography. After introducing the basic types of modulations their combination and possible discontinuity is discussed as well as the basic concepts of composite structures. The ways of solution of modulated structures are described with special emphasis to the heavy atom method as an instructive example. The potential of the refinement methods is perspicuous in the example of hexagonal perovskite structure with discontinuous modulation functions and modulated anharmonic ADP. Finally we describe the basic features of the computing system Jana2000 that is the most used program in the field.

Abstract

Numerical modelling is used to analyze the transport of cadmium in response to an extreme rainfall event. The cadmium transport through the soil profile was simulated by the one-dimensional dual-permeability model, which assumes the existence of two mutually communicating domains: the soil matrix domain and the preferential flow domain. The model is based on Richards’ equation for water flow and advection-dispersion equation for solute transport. A modified batch technique allowed us to consider domain specific sorption, i.e. each of the domains has its own distribution coefficient. The dual-permeability model predicts that the cadmium can be transported substantially below the root zone after the storm. On the other hand, classical single permeability approach predicted that almost all applied cadmium stays retained near the soil surface.

Abstract

JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

Abstract

Twinning is a phenomenon complicating structure analysis of single crystals of standard as well as modulated structures. Jana2006 as a software for advanced structure analysis contains tools for recognition and refinement of twins including most complicated cases of modulated and magnetic structures. In order to efficiently use the tools of Jana2006 related to twinning, we explain the basic terminology and the underlying theory, especially the symmetry of the diffraction patterns affected by twinning. We present typical diffraction patterns of twins and show how twinning can be recognized or detected by various tools and described with twinning matrices. Data processing of twins and ways of how they can be imported to Jana2006 are also discussed. Two examples demonstrate the solution of typical twins: twinning by metric merohedry and twinning by reticular merohedry, followed by the third example demonstrating twinning in a commensurately modulated structure. The relationship between the dimensionality of the structure and twinning is discussed, too.

Abstract

Ponded infiltration experiment is a simple test used for in-situ determination of soil hydraulic properties, particularly saturated hydraulic conductivity and sorptivity. It is known that infiltration process in natural soils is strongly affected by presence of macropores, soil layering, initial and experimental conditions etc. As a result, infiltration record encompasses a complex of mutually compensating effects that are difficult to separate from each other. Determination of sorptivity and saturated hydraulic conductivity from such infiltration data is complicated. In the present study we use numerical simulation to examine the impact of selected experimental conditions and soil profile properties on the ponded infiltration experiment results, specifically in terms of the hydraulic conductivity and sorptivity evaluation. The effect of following factors was considered: depth of ponding, ring insertion depth, initial soil water content, presence of preferential pathways, hydraulic conductivity anisotropy, soil layering, surface layer retention capacity and hydraulic conductivity, and presence of soil pipes or stones under the infiltration ring. Results were compared with a large database of infiltration curves measured at the experimental site Liz (Bohemian Forest, Czech Republic). Reasonably good agreement between simulated and observed infiltration curves was achieved by combining several of factors tested. Moreover, the ring insertion effect was recognized as one of the major causes of uncertainty in the determination of soil hydraulic parameters.

Abstract

Combined approaches to the treatment of acute radiation disease are preferred to single-agent therapies due to proven or anticipated better outcomes comprising increased therapeutic efficacy and decreased incidence of undesirable side effects. Our studies on post-exposure treatment of mice irradiated by sublethal or lethal doses of ionizing radiation included testing the effectiveness of meloxicam, a cyclooxygenase-2 inhibitor, and IB-MECA, an adenosine A3 receptor agonist. The efficacy of meloxicam and IB-MECA to positively influence the progress of the acute radiation disease has been tested in situations of their combined administration with granulocyte colony-stimulating factor (G-CSF) or with each other. The results of our studies revealed a significantly improved regeneration of hematopoietic cell populations ranging from the bone marrow progenitor cells to mature blood cells following combined treatments. Also, survival of mice exposed to lethal radiation doses was highest in the animals treated with a combination of the two drugs. It can be inferred from the results that if the drug combinations employed were used in humans, e.g. in the treatment of victims of radiation accidents, a better therapeutic outcome could be expected. Therefore, further studies directed at clinical applications of meloxicam and IB-MECA in radiation victims is recommended.

Abstract

Sejkoraite-(Y), the triclinic (Y1.98Dy0.24)Σ2.22H+ 0.34[(UO2)8O88O7OH(SO4)4](OH)(H2O)26, is a new member of the zippeite group from the Červená vein, Jáchymov (Street Joachimsthal) ore district, Western Bohemia, Czech Republic. It grows on altered surface of relics of primary minerals: uraninite, chalcopyrite, and tennantite, and is associated with pseudojohannite, rabejacite, uranopilite, zippeite, and gypsum. Sejkoraite-(Y) forms crystalline aggregates consisting of yellow-orange to orange crystals, rarely up to 1 mm in diameter. The crystals have a strong vitreous luster and a pale yellow-to-yellow streak. The crystals are very brittle with perfect {100} cleavage and uneven fracture. The Mohs hardness is about 2. The mineral is not fluorescent either in short- or long-wavelength UV radiation. Sejkoraite-(Y) is yellow, with no visible pleochroism, biaxial negative with α′ = 1.62(2), β′ = 1.662(3), γ′ = 1.73(1), 2Vcalc = 79°. The empirical chemical formula (mean of 8 electron microprobe point analyses) was calculated on the basis of 12 (S + U) atoms: (Y1.49Dy0.17Gd0.11Er0.07Yb0.05Sm0.02)Σ1.90H+ 0.54 [(UO2)8.19O7OH(SO4)3.81](H2O)26.00. Sejkoraite-(Y) is triclinic, space group P1̄, a = 14.0743(6), b = 17.4174(7), c = 17.7062(8) Å, α = 75.933(4), β = 128.001(5), γ = 74.419(4)°, V = 2777.00(19) Å3, Z = 2, Dcalc = 4.04 g/cm3. The seven strongest reflections in the X-ray powder diffraction pattern are [dobs in Å (I) (hkl)]: 9.28 (100) (100), 4.64 (39) (200), 3.631 (6) (1̄42), 3.451 (13) (1̄44), 3.385 (10) (2̅4̅2), 3.292 (9) (044), 3.904(7) (300), 2.984 (10) (1̄4̅2). The crystal structure of sejkoraite-(Y) has been solved by the charge flipping method from single-crystal X-ray diffraction data and refined to Robs = 0.060 with GOFobs = 2.38, based on 6511 observed reflections. The crystal structure consists of uranyl sulfate sheets of zippeite anion topology, which alternate with an interlayer containing Y3+(H2O)n polyhedra and uncoordinated H2O groups. Two yttrium atoms are linked to the sheet directly via uranyl oxygen atom, and the remaining one is bonded by hydrogen bonds only. In the Raman and infrared spectrum of sejkoraite-(Y) there are dominating stretching vibrations of SO4 tetrahedra (-1200-1100 cm-1), UO2 2+ stretching vibrations (-900-800 cm-1), and O-H stretching (-3500-3200 cm-1) and H-O-H bending modes (-1640 cm-1). The new mineral is named to honor Jiří Sejkora, a Czech mineralogist of the National Museum in Prague.

Abstract

The crystal structure of čejkaite, Na4(UO2)(CO3)3, from the type locality, was determined for the first time by single-crystal X-ray diffraction. In contrast to the previously reported pseudohexagonal triclinic symmetry, the current data indicate čejkaite is monoclinic, triply twinned, and belongs to the space group Cc. Refined unit-cell parameters are a = 9.2919(8), b = 16.0991(11), c = 6.4436(3) Å, β = 91.404(5)°, and V = 963.62(12) Å3. The monoclinic unit cell is also supported by the good fit to the powder diffraction data. The structure of čejkaite consists of uranyl tricarbonate clusters, forming sheets sub-parallel to (001) by sharing edges with (NaΦ) polyhedra. Sheets are interconnected through the uranyl O atoms and columns of (Na1Φ) polyhedra that share their trigonal faces. All Na atoms in the structure are in sixfold coordination . The structure refinement yielded Robs = 0.0424 for 1687 observed reflections [Iobs > 3σ(I)] and 0.0538 for all 2016 unique reflections. Refinement and bondvalence analysis of the structure confirmed the previously proposed formula Na4(UO2)(CO3)3, Z = 4.

Abstract

The previously published crystal structure study suggested that haiweeite is orthorhombic, Cmcm, with a = 7.125(1), b = 17.937(2), c = 18.342(2) Å, and V = 2344.3(7) Å3, and an ideal chemical formula Ca[(UO2)2Si5O12(OH)2]·3H2O, with Z = 4. Using single-crystal X-ray diffraction and electron microprobe analysis we re-examined haiweeite from the Teofilo Otoni, Minas Gerais, Brazil. Our diffraction experiment provided weak reflections responsible for doubling of the b cell parameter (for the current space-group settings), leading finally to the choice of a different space group. Haiweeite is thus orthorhombic, the space group Pbcn, with the unit-cell parameters a = 18.3000(5), b = 14.2331(3), c = 17.9192(5) Å, V = 4667.3(2) Å3, and an ideal formula Ca[(UO2)2(SiO3OH)2(Si3O6)]·6H2O (6.25 H2O inferred from the thermal analysis; 7.50 H2O from the structure model), with Z = 8. The structure refinement yielded R1 = 0.0512 for 2498 observed reflections [Iobs > 3σ(I)] and wR2 = 0.1286 for all 6117 unique reflections. Structure solution confirmed by subsequent refinement provided a structure model with full occupancies for U, Si, and Ca atoms, contrasting to previous average structure model. Although the general topology of our structure resembles that reported previously, all Si and O sites in our structure are fully occupied, in contrast to the previous structure determination.

Abstract

A new cyclotriphosphazene, 2,2,4,4,6,6-hexakis (o-tolylamono)-1,3,5,2λ 5,4λ 5,6λ 5-triazatriphosphinine (MPAP), was prepared using microwave irradiation and identified by elemental analysis, FT-IR, Raman, 31P NMR spectroscopy, and single-crystal X-ray diffraction. In the crystal, in addition to hydrogen bonds, the network is further stabilized by inter- and intramolecular π–π stacking interactions between aromatic rings.