X-ray Intensity Data Research Articles

Gallic acid-butyramide monohydrate cocrystal: Crystal growth, Structural insights, Theoretical calculations and Molecular docking studies against COVID-19 main protease

Single crystal X-ray diffraction is the only experimental technique available to elucidate the complete three-dimensional structure of the samples at molecular and atomic levels. But this technique demands defect-free single crystals. Growing good quality single crystals which are suitable to collect X-ray intensity data is an art rather than science. Among the various crystal growth methods, the most effective and commonly used is the slow evaporation method. Using this method, defect-free single crystals of the ground mixture of gallic acid (GA) and butyramide (BU) taken in a 1:1 molar ratio are obtained. The compound was subjected to experimental characterizations like; PXRD, FTIR, SCXRD, and TGA. Further, these results were utilized in the computational characterizations namely, Hirshfeld surface analysis, interaction energy calculations, DFT studies, and docking studies. Structural characterization revealed that the GA-BU compound was crystallized as a cocrystal hydrate with 2:1:1 stoichiometry in a monoclinic crystal system and P21/n space group. Structural studies exposed the presence of various inter and intramolecular hydrogen bond interactions, ring synthons, DDAA environment of the water molecule, and π ... π stacking interactions. The contribution of the several close contacts to the crystal structure, the influence of different interaction energies in the packing, the HOMO-LUMO energy gap, and the location of reactive sites were realized through computational studies. Further, a molecular docking study has been performed to check the antiviral activity of the title compound against COVID-19.

Incorporating previously neglected excess oxygen associated with ferric iron in matrix corrections of microprobe data from cubic and rhombohedral Fe-Ti oxides

Abstract Estimates of the oxidation states of magmas are important to current investigations of the geo-chemical characteristics of their source regions and of evolved magmatic series created during differentiation. One means of achieving such estimates is to capitalize on compositions of coexisting cubic and rhombohedral Fe-Ti oxides determined by electron microprobe. A combination of experimental calibration points and thermodynamic modeling provides a basis for translating such compositions into T-fO2 values. This has been done until recently by estimating Fe3+/ΣFe on the basis of charge balance and stoichiometry by the method of Droop (1987), after matrix corrections of X-ray intensity data have been performed, as EPMA cannot be used routinely to distinguish different elemental valence states, much less accurately quantify abundances of Fe3+ and Fe2+. The traditional approach of undertaking post-data-reduction calculations falls short of attaining the best possible quantitative results. The tactical choice of not accounting for light elements that have not been explicitly analyzed prior to matrix corrections of X-ray intensity data leads to systematic errors in reported oxide abundances for measured elements. This article addresses one such issue, the oxygen associated with Fe3+ (hereafter “excess oxygen”), on the basis of coexisting Fe-Ti oxides from Andean lavas. A new software routine in probe for EPMA (PFE) uses an iterative calculation scheme to calculate amounts of excess oxygen that would not be considered if all iron were assumed to be ferrous and then applies this excess oxygen during matrix corrections. The PFE approach reveals that Fe-concentrations have been underestimated, universally, in these minerals because O atoms absorb FeKα radiation: discrepancies increase as total Fe and Fe3+/Fe2+, hence excess oxygen, increase. Analyses of the most Fe-rich cubic oxide compositions in this data set have ~6 wt% excess oxygen and ~1 wt% more FeO+Fe2O3 than would be reported without incorporating the impact of excess oxygen in matrix corrections. Minor to negligible differences in other elements are also observed. These effects are not because excess oxygen is directly attributed to these elements, although some may be present in multiple valence states, as matrix corrections are undertaken on the basis of the conventional assumptions that they occur as Cr3+, V3+, Mn2+, Mg2+, Ca2+, and Si4+. Rather, variably small increases in total Fe propagate through the matrix corrections for other elements, and these differences may be recorded as minor increases or decreases in some concentrations, depending on the particular element and the amount of change in Fe-concentration. Fe3+/ΣFe in analyses produced with the PFE routine are essentially identical to those determined in the traditional mode, as cation proportions calculated on the basis of charge balance and stoichiometry, with the method of Droop (1987), is a necessary step. The new method: (1) provides more accurate concentrations, mainly for Fe and Ti; (2) is applicable to any mineral containing ferric iron (subject to stoichiometric constraints); (3) provides more accurate analytical totals, which can be advantageous for evaluating analytical quality; and (4) does not impact estimates of oxidation state. Oxygen fugacities and temperatures determined with the model of Ghiorso and Evans (2008) are essentially unchanged.

π-Pimer, π-Dimer, π-Trimer, and 1D π-Stacks in a Series of Benzene Triimide Radical Anions: Substituent-Modulated π Interactions and Physical Properties in Crystalline State

π-Pimer, π-Dimer, π-Trimer, and 1D π-Stacks in a Series of Benzene Triimide Radical Anions: Substituent-Modulated π Interactions and Physical Properties in Crystalline State

Local structure and electron density distribution analysis of tin(II) sulfide using pair distribution function and maximum entropy method

Abstract Tin(II) sulfide (SnS) is a low symmetric orthorhombic double-layered dual bandgap semiconductor. It is low cost, toxic-free and highly abundant on Earth, with multifunctional optical, electronic, magnetic and light conversion applications when doped adequately with impurity. These physical properties can be understood only by the complete understanding of microstructural properties like average structure, electron density distribution inside the unit cell, bonding nature and local structure. In this work, the average and local structure, along with the electron density distribution of a nano crystallite sized single-phase sample of tin(II) sulfide is elucidated with the help of precise X-ray intensity data. The average structural information was extracted using Rietveld refinement analysis and the visual mapping of 3D, 2D and 1D electron density distribution inside the unit cell and its numerical contribution using maximum entropy method (MEM). The bonding between the first inter and intra bonding between Sn and S atoms is 2.65,105 Å and 3.2689 Å with mid bond electron density 0.907 e/Å3 and 0.1688 e/Å3 respectively. The inter-atomic correlations of 1st, 2nd and 3rd nearest neighbour atoms, their bond length, and the crystallite size are reported from pair distribution function (PDF) analysis using low Q-XRD data (Q ∼ 6.5 Å−1). The PDF analysis shows that the first and second nearest Sn–S bonding distance is 2.6064 Å and 3.4402 Å, first is between the Sn and S atoms of the same layer and the other between the Sn and S atoms of the adjacent layers respectively.

Princivalleite, Na(Mn2Al)Al6(Si6O18)(BO3)3(OH)3O, a new mineral species of the tourmaline supergroup from Veddasca Valley, Varese, Italy

AbstractPrincivalleite, Na(Mn2Al)Al6(Si6O18)(BO3)3(OH)3O, is a new mineral (IMA2020-056) of the tourmaline supergroup. It occurs in the Veddasca Valley, Luino area, Varese, Lombardy, Italy (46°03’30.74’’N, 8°48’24.47’’E) at the centre of a narrow (2–3 cm wide) vertical pegmatitic vein, a few metres long, crosscutting a lens of flaser gneiss. Crystals are subhedral (up to 10 mm in size), azure with a vitreous lustre, conchoidal fracture and white streak. Princivalleite has a Mohs hardness of ~7, a calculated density of 3.168 g/cm3 and is uniaxial (–). Princivalleite has trigonal symmetry, space group R3m, a = 15.9155(2) Å, c = 7.11660(10) Å, V = 1561.15(4) Å3 and Z = 3. The crystal structure was refined to R1 = 1.36% using 1758 unique reflections collected with MoKα X-ray intensity data. Crystal-chemical analysis resulted in the empirical crystal-chemical formulaX(Na0.54Ca0.11□0.35)Σ1.00Y(Al1.82Mn2+0.84Fe2+0.19Zn0.07Li0.08)Σ3.00Z(Al5.85Fe2+0.13Mg0.02)Σ6.00[T(Si5.60Al0.40)Σ6.00O18](BO3)3O(3)[(OH)2.71O0.29]Σ3.00O(1)[O0.66F0.22(OH)0.12]Σ1.00 which recast in its ordered form for classification purposes is:X(Na0.54Ca0.11□0.35)Σ1.00Y(Al1.67Mn2+0.84Fe2+0.32Zn0.07Mg0.02Li0.08)Σ3.00ZAl6.00[T(Si5.60Al0.40)Σ6.00O18](BO3)3V[(OH)2.71O0.29]Σ3.00W[O0.66F0.22(OH)0.12]Σ1.00.Princivalleite is an oxy-species belonging to the alkali group of the tourmaline supergroup. The closest end-member compositions of valid tourmaline species are those of oxy-schorl and darrellhenryite, to which princivalleite is related by the substitutions Mn2+ ↔ Fe2+ and Mn2+ ↔ 0.5Al3+ + 0.5Li+, respectively. Princivalleite from Veddasca Valley is a geochemical anomaly, originated in a B-rich and peraluminous anatectic pegmatitic melt formed in situ, poor in Fe and characterised by reducing conditions in the late-stage metamorphic fluids derived by the flaser gneiss. The Mn-enrichment in this new tourmaline is due to absence of other minerals competing for Mn such as garnet.

Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase.

Lactoperoxidase (1.11.1.7, LPO) is a mammalian heme peroxidase found in the extracellular fluids of mammals including plasma, saliva, airway epithelial lining fluids, nasal lining fluid, milk, tears, gastric juices, and intestinal mucosa. To perform its innate immune action against invading microbes, LPO utilizes hydrogen peroxide (H2 O2 ) to convert thiocyanate (SCN- ) and iodide (I- ) ions into the oxidizing compounds hypothiocyanite (OSCN- ) and hypoiodite (IO- ). Previously determined structures of the complexes of LPO with SCN- , OSCN- , and I- show that SCN- and I- occupy appropriate positions in the distal heme cavity as substrates while OSCN- binds in the distal heme cavity as a product inhibitor. We report here the structure of the complex of LPO with IO- as the first structural evidence of the conversion of iodide into hypoiodite by LPO. To obtain this complex, a solution of LPO was first incubated with H2 O2 , then mixed with ammonium iodide solution and the complex crystallized by the addition of PEG-3350, 20% (wt/vol). These crystals were used for X-ray intensity data collection and structure analysis. The structure determination revealed the presence of four hypoiodite ions in the substrate binding channel of LPO. In addition to these, six other hypoiodite ions were observed at different exterior sites. We surmise that the presence of hypoiodite ions in the distal heme cavity blocks the substrate binding site and inhibits catalysis. This was confirmed by activity experiments with the colorimetric substrate, ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-sulfonic acid)), in the presence of hypoiodite and iodide ions.

Celleriite, ☐(Mn22+Al)Al6(Si6O18)(BO3)3(OH)3(OH), a new mineral species of the tourmaline supergroup

Abstract Celleriite, ☐(Mn22+Al)Al6(Si6O18)(BO3)3(OH)3(OH), is a new mineral of the tourmaline supergroup. It was discovered in the Rosina pegmatite, San Piero in Campo, Elba Island, Italy (holotype specimen), and in the Pikárec pegmatite, western Moravia, Czech Republic (co-type specimen). Celleriite in hand specimen is violet to gray-blue (holotype) and dark brownish-green (co-type) with a vitreous luster, conchoidal fracture, and white streak. Celleriite has a Mohs hardness of ~7 and a calculated density of 3.13 and 3.14 g/cm3 for holotype and its co-type, respectively. In plane-polarized light in thin section, celleriite is pleochroic (O = pale violet and E = light gray-blue in holotype; O = pale green and E = colorless in co-type) and uniaxial negative. Celleriite has trigonal symmetry: space group R3m, Z = 3, a = 15.9518(4) and 15.9332(3) Å, c = 7.1579(2) and 7.13086(15) Å, V = 1577.38(9) and 1567.76(6) Å3 for holotype and co-type, respectively (data from single-crystal X-ray diffraction). The crystal structure of the holotype specimen was refined to R1 = 2.89% using 1696 unique reflections collected with MoKα X-ray intensity data. Structural, chemical, and spectroscopic analyses resulted in the formulas: x ( ◻ 0.58 N a 0.42 ) Σ 1.00 Y ( M n 1.39 2 + F e 0.16 2 + M g 0.01 A l 1.14 F e 0.01 3 + L i 0.28 T i 0.01 ) Σ 3.00 Z A l 6 [ T ( S i 5.99 A l 0.01 ) Σ 6.00 O 18 ] ( B O 3 ) 3 ( O H ) 3 w [ ( O H ) 0.65 F 0.03 O 0.32 ] Σ 1.00 ( for holotype ) and x ( ◻ 0.51 N a 0.49 ) Σ 1.00 Y ( M n 0.90 2 + F e 0.50 2 + A l 1.36 F e 0.04 3 + L i 0.17 Zn 0.04 ) Σ 3.00 Z A l 6 [ T ( S i 5.75 B 0.25 ) Σ 6.00 O 18 ] ( B O 3 ) 3 ( O H ) 3 w [ ( O H ) 0.35 F 0.17 O 0.48 ] Σ 1.00 ( for co-type ) Celleriite is a hydroxy species belonging to the X-site vacant group of the tourmaline supergroup. The new mineral was approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, proposal no. 2019-089. In the Rosina pegmatite, celleriite formed an overgrowth at the analogous pole of elbaite–fluorelbaite–rossmanite crystals during the latest stage of evolution of pegmatite cavities after an event of a pocket rupture. In the Pikárec pegmatite, celleriite occurs as an intermediate growth sector of elbaite, princivalleite, and fluor-elbaite.

Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20Å resolution.

Lactoperoxidase, a heme-containing glycoprotein, catalyzes the oxidation of thiocyanate by hydrogen peroxide into hypothiocyanite which acts as an antibacterial agent. The prosthetic heme moiety is attached to the protein through two ester linkages via Glu258 and Asp108. In lactoperoxidase, the substrate-binding site is formed on the distal heme side. To study the effect of physiologically important potassium ion on the structure and function of lactoperoxidase, the fresh protein samples were isolated from yak (Bos grunniens) colostrum and purified to homogeneity. The biochemical studies with potassium fluoride showed a significant reduction in the catalytic activity. Lactoperoxidase was crystallized using 200mM ammonium nitrate and 20% PEG-3350 at pH 6.0. The crystals of LPO were soaked in the solution of potassium fluoride and used for the X-ray intensity data collection. Structure determination at 2.20Å resolution revealed the presence of a potassium ion in the distal heme cavity. Structure determination further revealed that the propionic chain attached to pyrrole ring C of the heme moiety, was disordered into two components each having an occupancy of 0.5. One component occupied a position similar to the normally observed position of propionic chain while the second component was found in the distal heme cavity. The potassium ion in the distal heme cavity formed five coordinate bonds with two oxygen atoms of propionic moiety, Nε2 atom of His109 and two oxygen atoms of water molecules. The presence of potassium ion in the distal heme cavity hampered the catalytic activity of lactoperoxidase.

Biophysical Characterization of Type III Pantothenate Kinase (PanK) from Acinetobacter baumannii

Type-III Pantothenate kinase from the multi drug resistant bacteria, Acinetobacter baumannii (AbPanK) catalyzes the first step of the essential Coenzyme A biosynthesis pathway. AbPanK is an attractive drug target against the bacteria since it is an essential enzyme and its structure is significantly different from the human PanK. AbPanK was cloned, expressed, purified and crystallized. A good quality single crystal was used for X-ray intensity data collection. Dynamic light scattering was done for calculating the hydrodynamic radii and its oligomeric nature in the solution. Binding studies of this protein with its two substrates, Pantothenate and ATP were done using spectrofluorometer. Our results indicated that AbPanK shows a strong affinity with pantothenate with dissociation constant of 1.2 x 10- 8 M and moderate affinity towards ATP of 3.7x 10-3 M. This fact was further substantiated by the calculations of Km of both substrates using kinase assay kit. Dynamic light scattering studies have shown that it exists as homogenous solution with hydrodynamic radii corresponding to the molecular weight of 29.55 kDa. A low-resolution X-ray intensity data set was collected, which shows that AbPank crystallizes in P2 space group with cell dimensions of a= 165 Å, b= 260 Å, and, c= 197 Å and α= 90.0, β= 113.60, γ= 90.0. Recombinant Pantothenate kinase from Acinetobacter baumannii was purified to homogeneity and crystallized. The enzyme exhibits very low sequence identity (28%) to other corresponding enzymes. The recombinant enzyme was active and its binding affinities with its substrates pantothenate and ATP have been studied. This information would be very useful while designing the inhibitors of this enzyme in order to fight bacterial infections associated to this pathogen.

Crystal chemistry of the variscite and metavariscite groups: Crystal structures of synthetic CrAsO4⋅2H2O, TlPO4⋅2H2O, MnSeO4⋅2H2O, CdSeO4⋅2H2O and natural bonacinaite, ScAsO4⋅2H2O

AbstractWe report the crystal structures of four synthetic members of the variscite group (space group typePbca) and of bonacinaite, the first naturally occurring scandium arsenate member of the metavariscite group. All structures were determined using single-crystal X-ray intensity data. The following members were all synthesised under either mild hydrothermal conditions or by wet-chemical methods (<90°C). CrAsO4⋅2H2O (deep green):a= 8.894(2),b= 9.946(2),c= 10.206(2) Å andV= 902.8(3) Å3;R1= 2.14%. Tl3+PO4⋅2H2O (colourless):a= 10.2848(7),b= 8.8578(6),c= 10.3637(7) Å andV= 944.14(11) Å3(data at –173°C);R1= 2.56%. MnSeO4⋅2H2O (pale pink):a= 10.441(2),b= 9.2410(18),c= 10.552(2) Å andV= 1018.1(3) Å3;R1= 2.19%. A different method of preparation of MnSeO4⋅2H2O yielded crystals with very similar unit-cell parameters,a= 10.4353(5),b= 9.2420(5) andc= 10.5349(6) Å;R1= 2.25%. CdSeO4⋅2H2O (colourless) hasa= 10.481(1),b= 9.416(1),c= 10.755(1) Å andV= 1061.4(2) Å3;R1= 1.53%. The thermal behaviour of the two selenate members was studied by a combination of DSC and TG, supplemented by PXRD. Bonacinaite (IMA2018-056), metavariscite-type natural (Sc,Al)(As,P)O4⋅2H2O (ideally ScAsO4⋅2H2O), crystallises in the space groupP21/n, witha= 5.533(1),b= 10.409(2),c= 9.036(2) Å, β = 91.94(3)° andV= 520.11(18) Å3;R1= 3.66%. The structural formula, supported by chemical analysis, is (Sc0.807(1)Al0.193)(As0.767(7)P0.233)O4⋅2H2O. All structures are based on frameworks built by corner-sharing of TO4tetrahedra (T = P5+, As5+or Se6+) with MO4(H2O)2(M = Mn2+, Cd2+, Cr3+, Sc3+or Tl3+) octahedra. The flexible frameworks are reinforced by partly bifurcated, strong to weak hydrogen bonds.The crystal chemistry of all known synthetic and natural members of the variscite and metavariscite groups is discussed and compared, and the relative stabilities are evaluated. With the aid of theCOMPSTRUprogram (Bilbao Crystallographic Server), a quantitative comparison of the crystal structures in both groups is given. Calculations of the structural and topological complexity reveal that the metavariscite structure type is structurally and topologically simpler than that of variscite. It is suggested that metavariscite and phosphosiderite are metastable kinetically stabilised phases, in contrast to thermodynamically stable variscite and strengite, respectively. The 3D frameworks of the members of both groups have been shown to be potential electrode materials for rechargeable Li ion batteries.

Revision of the crystal structure of `bis(glycine) squaric acid'

The crystal structure of `bis(glycine) squaric acid' [Tyagi et al. (2016). RSC Adv. 6, 24565–24576], is revised. Re-refinement of the structure against the original X-ray intensity data after correct placement of the donor H atoms proves that the compound is in fact the previously reported diglycinium squarate [systematic name: bis(carboxymethanaminium) 3,4-dioxocyclobut-1-ene-1,2-diolate; Anioła et al. (2014). New J. Chem. 38, 3556–3568]. The findings are consistent with the pKa rule.

Crystal structure and electrochemical hydrogenation of LaZn5-хMnx.solid solution

Systematic investigation of the interaction between the components in La–Mn–Zn ternary system revealed that binary intermetallic compound LaZn 5 (structure type CaCu 5 , space group P 6 /mmm ) dissolve some amount of Mn forming a solid solution of substitution LaZn 5– x Mn x with the homogeneity range of about 6 аt. %. Alloys for investigation have been synthesized by arc melting of pure metals, further annealing at 500 °С over a two-month period and quenching in cold water. Phase analysis of the samples has been performed on data obtained by powder X-ray diffraction, scanning electron microscopy and energy dispersive X-ray spectroscopy. The crystal structure of solid solution has been investigated using single crystal X-ray intensity data collected on Xcalibur Oxford Diffraction diffractometer with graphite-monocromated Mo K α–radiation using w scans. The space group P 6 /mmm was chosen and the initial atomic parameters were found by direct methods, confirming the expected CaCu 5 -type structure. The refinement of coordinates and displacement parameters of atoms has been carried out by least squares method in anisotropic approximation to R F = 0.0563 and wR = 0.1391. The atoms in structure occupy the same positions as in CaCu 5 structure, yet in 3 с position there is a statistic mixture M (12 % Mn + 88 % Zn). That is why the calculated composition of single crystal corresponds to the LaZn 4.64 Mn 0.36 formula. The effectiveness of electrochemical hydrogenation of the solid solution has been studied on LaZn 5– x Mn x alloy, x = 0.12, which served as anode material, in a prototype of nickel-metal hydride batteries. Ni(OH) 2 and graphite mixture served as cathode material and a 6 М solution of KOH served as electrolyte. Investigation of the alloy over 30 cycles of charge-discharge showed that it is electrochemically active and can reversibly absorb up to 0.044 Н/f.u. The crystal structure of obtained LaZn 4.88 Mn 0.12 H 0.044 hydride remained unchanged, though the unit cell volume naturally increased as compared to the initial sample. Keywords: solid solution, crystal structure, X-ray structure analysis, electrochemical hydrogenation, nickel-metalhydride battery.

Development of a Wood Computed Tomography Imaging System Using a Butterworth Filtered Back-Projection Algorithm

Abstract Aiming to provide economical equipment support for nondestructive wood testing, we developed a wood computed tomography (CT) imaging system to aid wood researchers in accurately understanding wood internal structures and defect characteristics. The wood CT system consists of an X-ray source, an X-ray detector, an electric rotational stage, and a computer. The X-ray source projects a fan-shaped X-ray beam to the wood, and the X-ray detector captures the penetrated X-ray intensity data when the wood is at different angles of rotation. The projection data were preprocessed before they were used for image reconstruction. An improved filtered back-projection (FBP) algorithm specialized for wood cross section CT image reconstruction was proposed. The traditional Ram-Lak (RL) filter and Shepp-Logan (SL) filter were replaced by a Butterworth filter. The Butterworth parameters were determined to achieve a desirable compromise between spatial resolution and image noise. Two pieces of cylindrical log (Thuja sp., Pinus sp.) and a block of laminated timber were scanned. The reconstructed images clearly revealed the internal structures of wood, and the fine features such as pith, annual growth rings, radial cracks, knots, and outer edge were enhanced, while the image noise and blurring effect were suppressed.

Fluor-elbaite, lepidolite and Ta–Nb oxides from a pegmatite of the 3000 Ma Sinceni Pluton, Swaziland: evidence for lithium–cesium–tantalum (LCT) pegmatites in the Mesoarchean

Mineral evolution is concerned with the timing of mineral occurrences, such as the earliest reported occurrences in the geologic record. Minerals containing essential Li have not been reported from rocks older than ca. 3000 Ma, thus the lithian tourmaline (fluor-elbaite) and mica (lepidolite) assemblage from a pegmatite near Zishineni associated with the ca. 3000 Ma Sinceni Pluton presents unusual interest. Fluor-elbaite (0.75–0.98 F per formula unit) forms green crystals up to 50 mm long. Spindle stage measurements give ω = 1.652(1), e = 1.627(1) (589.3 nm). Optical absorption spectroscopy shows Fe and Mn are divalent; infra-red spectroscopy demonstrates the presence of Li and indicates the presence of (OH) at both the (OH) sites. Electron microprobe analysis of 330 points on several prisms, the largest of which is zoned in Fe and Ca, gives the following average and standard deviations in wt%: SiO2 37.29 (0.26), TiO2 0.05 (0.05), Al2O3 38.14 (0.35), Cr2O3 0 (0.02), MgO 0.02 (0.01), MnO 3.57 (0.25), FeO 2.48 (0.60), Na2O 2.48 (0.09), K2O 0.03 (0.12), CaO 0.77 (0.21), F 1.80 (0.11) wt%; Cl 0 (0.01). Nuclear reaction analyses gave Li2O 0.91 (0.04) and B2O3 10.55 (0.45). The empirical formula of fluor-elbaite was determined by integrating crystal-chemical data from electron microprobe analysis, nuclear reaction analysis, crystal structure refinement using X-ray diffraction, infra-red and optical absorption spectroscopy: X(□0.09Na0.77K0.01Ca0.13)Σ1.00Y(□0.35Li0.59Mn 2+ 0.49 Fe 2+ 0.33 Mn0.492+Fe0.332+Al1.23Ti0.01)Σ3.00Al6(Si6O18)(BO3)3O3(OH)3O1[F0.92(OH)0.08]Σ1.00. The crystal structure of fluor-elbaite was refined to statistical indices R1 for 1454 reflections ∼2% using MoKα X-ray intensity data. Structural data confirm the presence of significant vacancies at the Y site. Micas include lepidolite in flakes several millimeters across that are veined and overgrown by fine-grained muscovite. Silica and (FeO + MnO) increase, and Al decreases with F, all giving tight linear fits for both micas taken together, suggesting both micas can be regarded as interstratified muscovite and lithium mica consisting of 35.2 wt% masutomilite containing nearly equal amounts of Mn and Fe, 52.8 wt% polylithionite and 11.9 wt% trilithionite. Muscovite and lepidolite contain Ta, hubnerite(?) and a possible Pb-bearing microlite (Ta > Nb). The oxides, together with the muscovite, are interpreted to be related to later hydrothermal reworking of the primary lepidolite–fluor-elbaite assemblage. Given the 2990 ± 43 Ma Rb–Sr isochron and 3074 ± 4 Ma evaporation Pb–Pb ages reported for the Sinceni Pluton and Rb/Sr mineral ages ranging from 2906 ± 31 Ma to 3072 ± 33 Ma reported for the pegmatites, the fluor-elbaite–cesian lepidolite–fluorcalciomicrolite-bearing pegmatite is the first reported occurrence of a lithian tourmaline and lepidolite in the geologic record, as well as one of the two earliest known examples of the lithium–cesium–tantalum (LCT) family of pegmatites. The Sinceni magma is most plausibly derived from a metasedimentary source by intrusion of hot mantle melts into the crust from below, thereby indicating that a “mature” continental crust existed in the Kaapvaal craton at ca. 3000 Ma. (Less)

Model and reconstruction of a K-edge contrast agent distribution with an X-ray photon-counting detector.

Contrast-enhanced computed tomography (CECT) helps enhance the visibility for tumor imaging. When a high-Z contrast agent interacts with X-rays across its K-edge, X-ray photoelectric absorption would experience a sudden increment, resulting in a significant difference of the X-ray transmission intensity between the left and right energy windows of the K-edge. Using photon-counting detectors, the X-ray intensity data in the left and right windows of the K-edge can be measured simultaneously. The differential information of the two kinds of intensity data reflects the contrast-agent concentration distribution. K-edge differences between various matters allow opportunities for the identification of contrast agents in biomedical applications. In this paper, a general radon transform is established to link the contrast-agent concentration to X-ray intensity measurement data. An iterative algorithm is proposed to reconstruct a contrast-agent distribution and tissue attenuation background simultaneously. Comprehensive numerical simulations are performed to demonstrate the merits of the proposed method over the existing K-edge imaging methods. Our results show that the proposed method accurately quantifies a distribution of a contrast agent, optimizing the contrast-to-noise ratio at a high dose efficiency.

Lucchesiite, CaFe2+3Al6(Si6O18)(BO3)3(OH)3O, a new mineral species of the tourmaline supergroup

AbstractLucchesiite, CaFe32+Al6(Si6O18)(BO3)3(OH)3O, is a new mineral of the tourmaline supergroup. It occurs in the Ratnapura District, Sri Lanka (6°35'N, 80°35'E), most probably from pegmatites and in Mirošov near Strážek, western Moravia, Czech Republic, (49°27'49.38"N, 16°9'54.34"E) in anatectic pegmatite contaminated by host calc-silicate rock. Crystals are black with a vitreous lustre, conchoidal fracture and grey streak. Lucchesiite has a Mohs hardnessof ∼7 and a calculated density of 3.209 g/cm3(Sri Lanka) to 3.243 g/cm3(Czech Republic). In plane-polarized light, lucchesiite is pleochroic (O = very dark brown and E = light brown) and uniaxial (–). Lucchesiite is rhombohedral, space groupR3m,a≈ 16.00 Å,c≈ 7.21 Å,V≈ 1599.9 Å3,Z= 3. The crystal structure of lucchesiite was refined toR1 ≈ 1.5% using ∼2000 unique reflections collected with MoKα X-ray intensity data. Crystal-chemical analysis for the Sri Lanka (holotype) and Czech Republic (cotype) samples resulted in the empirical formulae, respectively:X(Ca0.69Na0.30K0.02)∑1.01Y(Fe1.442+Mg0.72Al0.48Ti0.334+V0.023+Mn0.013+Zn0.01)∑3.00Z(Al4.74Mg1.01Fe0.253+)∑6.00[T(Si5.85Al0.15)∑6.00O18](BO3)3V(OH)3W[O0.69F0.24(OH)0.07]∑1.00andX(Ca0.49Na0.45□0.05K0.01)∑1.00Y(Fe1.142+Fe0.953+Mg0.42Al0.37Mn0.03Ti0.084+Zn0.01)∑3.00Z(Al5.11Fe0.383+Mg0.52)∑6.00[T(Si5.88Al0.12)∑6.00O18](BO3)3V[(OH)2.66O0.34]∑3.00W(O0.94F0.06)∑1.00.Lucchesiite is an oxy-species belonging to the calcic group of the tourmaline supergroup. The closest end-member composition of a valid tourmaline species is that of feruvite, to which lucchesiite is ideally related by the heterovalent coupled substitutionZAl3++O1O2–↔ZMg2++O1(OH)1–. The new mineral was approved by the International Mineralogical Association Commission on New Minerals, Nomenclature and Classification (IMA 2015-043).

Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii

Dehydroquinase (3-dehydroquinate dehydratase, DHQD, EC 4.2.1.10) catalyzes the conversion of dehydroquinate to dehydroshikimate. DHQD from Acinetobacter baumannii (AbDHQD) was cloned, expressed and purified to homogeneity. The binding studies showed that two compounds quinic acid and citrazinic acid bound to AbDHQD at micromolar concentrations. AbDHQD was crystallized using 30% PEG-3350, 50mM tris-HCl and 1.0M MgSO4 at pH 8.0. Crystals of AbDHQD were stabilized with 25% glycerol for data collection at 100K. The X-ray intensity data were collected to 2.0Å resolution. Crystals belonged to monoclinic space group P21 with cell dimensions, a=82.3, b=95.3, c=132.3Å and β=95.7°. The structure was solved with molecular replacement method and refined to values of 0.200 and 0.232 for Rcryst and Rfree factors. The structures of 12 crystallographically independent molecules in the asymmetry unit were identical with r.m.s shifts for the Cα atoms ranging from 0.3Å to 0.8Å. They formed a dodecamer with four trimers arranged in a tetrahedral manner. The classical lid adopted an open conformation although a sulfate ion was observed in the substrate binding site. As a result of which, the compounds quinic acid and citrazinic acid could not bind to AbDHQD.

Order of [6]Ti4+ in a Ti-rich calcium amphibole from Kaersut, Greenland: a combined X-ray and neutron diffraction study

In order to characterize the role of Ti in the crystal structure of calcium amphiboles with high or even dominant oxo-component, the crystal structure of a Ti-rich calcium amphibole from a gabbro at Kaersut, Greenland, has been refined with single-crystal MoKα X-ray intensity data to an R 1(F) index of ~0.025, and with single-crystal Laue neutron intensity data to an R 1(F) index of ~0.053. The crystal used for X-ray structure refinement was characterized by electron- and ion-microprobe analysis. The site populations of the C-group cations Mg, Fe and Ti were calculated from the refined site-scattering values for the M(1), M(2) and M(3) sites derived by both X-ray and neutron diffraction. Ti is distributed among all the three sixfold coordinated M sites, with a strong preference for the M(1) and M(3) sites, where its main role is maintaining electroneutrality at the deprotonated O(3) site. The pattern of distortion of the M(1), M(2) and M(3) octahedra differs from that in F-free deprotonated or partly deprotonated amphiboles, where Ti4+ does not occur at the M(3) site. The neutron structure refinement provides also a clear picture of the environment of the proton, anisotropic displacement behaviour and potential hydrogen-bonding arrangements. A trifurcated hydrogen-bonding configuration has been identified, with two O(6) and one O(7) oxygen atoms as acceptors of weak hydrogen-bonds.

Spectral CT Reconstruction with Image Sparsity and Spectral Mean.

Photon-counting detectors can acquire x-ray intensity data in different energy bins. The signal to noise ratio of resultant raw data in each energy bin is generally low due to the narrow bin width and quantum noise. To address this problem, here we propose an image reconstruction approach for spectral CT to simultaneously reconstructs x-ray attenuation coefficients in all the energy bins. Because the measured spectral data are highly correlated among the x-ray energy bins, the intra-image sparsity and inter-image similarity are important prior acknowledge for image reconstruction. Inspired by this observation, the total variation (TV) and spectral mean (SM) measures are combined to improve the quality of reconstructed images. For this purpose, a linear mapping function is used to minimalize image differences between energy bins. The split Bregman technique is applied to perform image reconstruction. Our numerical and experimental results show that the proposed algorithms outperform competing iterative algorithms in this context.

FLUORNATROPYROCHLORE, A NEW PYROCHLORE SUPERGROUP MINERAL FROM THE BOZIGUOER RARE EARTH ELEMENT DEPOSIT, BAICHENG COUNTY, AKESU, XINJIANG, CHINA

Fluornatropyrochlore is a new pyrochlore supergroup mineral species found in the intrusive alkali granite of the Boziguoer rare earth element deposit in Baicheng County, Akesu, Xinjiang Autonomous Region, China. This new mineral is found to be closely associated with microcline, albite, aegirine, a sodic amphibole, biotite, zircon, rutile, thorite, fluorite, fluocerite-(Ce), columbite-(Fe), xenotime-(Y), astrophyllite, chevkinite-(Ce), and fergusonite-(Y). Fluornatropyrochlore occurs mostly as anhedral crystals, rarely as subhedral grains, with a grain size of 0.02 to 0.25 mm. The color is brownish yellow to reddish orange. Other physical properties are: brittle, translucent to transparent, non-fluorescent, adamantine luster, light yellow streak, with Mohs hardness 4–4½, and calculated density 5.275 g cm−3. Fluornatropyrochlore is isotropic, n = 2.10(5) (589.9 nm). It has a cubic crystal structure, with unit-cell parameters determined using single-crystal X-ray diffraction as: a 10.5053(10) A, V 1159.4(2) A3, Z = 8, space group Fd 3 m . The strongest ten X-ray diffraction (XRD) peaks in the powder XRD pattern are [ d in A( I )( hkl )]: 6.0741(3)(111), 3.0416(100)(222), 2.6280(38)(004), 1.8568(34)(044), 1.5820(15)(226), 1.5148(4)(444), 1.3137(2)(008), 1.2045(3)(266), 1.1726(2)(048), and 1.0712(1)(448). Chemical analyses by a combination of electron microprobe, Fourier transform infrared spectroscopy (FTIR), and single crystal-structure refinement give its chemical composition as: Na2O 6.80, K2O 0.01, CaO 2.01, MgO 0.01, FeO 0.05, SrO 0.03, PbO 16.17, Ce2O3 4.29, La2O3 1.65, Nd2O3 0.41, Y2O3 0.42, SiO2 0.03, TiO2 1.36, UO2 5.81, Ta2O5 3.00, Nb2O5 53.42, F 3.19, Cl 0.02, ThO2, Sb2O5 0.01, ZrO2 0.01, MnO 0.04, SnO2 0.34, H2O not detected, with a sum of 98.21 wt.%. The empirical formula derived from its averaged composition is (Na1.03Pb0.34Ca0.17U0.10Th0.01Ce0.12La0.05Y0.02Nd0.01)Σ1.85(Nb1.88Ti0.08Ta0.06Sn0.01)Σ2.03O6.21F0.79 based on 7 anions per formula unit. The crystal structure was refined to an R index of 0.053 using Mo Ka X-ray intensity data. Site-scattering refinement analysis shows that the new mineral is characterized by F dominance at the Y site, Na dominance at the A site, and Nb dominance at the B site, based on the overall electroneutrality requirement of the structural formula.