Unit Cell Edge Research Articles

Stirring Effects on Properties of Al Goethite Formed From Ferrihydrite

AbstractMinerals in surface environments form in both turbulent and non-turbulent systems. This study compares the properties of Al goethite formed from ferrihydrite at 60°C in 0.3 M KOH with and without mechanical stirring. Compared to the static system, stirring increased crystal order and needle thickness, decreased unit cell edge length a, but not b and c, reduced the separation between the 2 OH-bending vibrations, increased Al substitution and promoted hematite formation.

Crystallization and preliminary X-ray analysis of thiaminase I from Bacillus thiaminolyticus: space group change upon freezing of crystals.

Thiaminase I (Mr = 42 100) from B. thiaminolyticus, expressed in E. coli, has been crystallized by the vapor-diffusion method. Three crystal forms, two of which grew from 0.1 M sodium acetate (pH = 4.6), 0.2 M ammonium sulfate and 30%(w/v) PEG 2000, have been examined by X-ray analysis. One crystal form diffracted to 2.5 A at room temperature, was orthorhombic, and had unit-cell edges of a = 87.7, b = 120.5 and c = 76.7 A with space group P212121. A self-Patterson map showed a strong peak indicating noncrystallographic translational pseudosymmetry with (u, v, w) = (0.03, 0.0, 0.5). When these crystals were frozen at liquid-nitrogen temperatures, a second crystal form was observed which had unit-cell dimensions a = 85.5, b = 117.5 and c = 36.6 A with space group P21212. A third crystal form grew from 0.1 M Tris (pH = 8.5), 0.2 M sodium acetate trihydrate and 28%(w/v) PEG 6000 to produce orthorhombic crystals of space group P212121 with cell edges of a = 114.4, b = 123.1 and c = 92.5 A.

Synthesis, electrochemistry, structure, and magnetic susceptibility of 5-tert-butyl-1,3-bis- (1,2,3,5-dithiadiazolyl)benzene. Structural effect of the bulky substituent

The crystal structure of the title compound was determined at 250 K in space group I 4 bar 2m, a = 20.661(5) Å , c = 6.764(7) Å , Z = 8. The individual dithiadiazole rings form two sets of contrarotatory 4-member pinwheels clustered around a 4-fold rotation-inversion axis located halfway along the unit cell edges, describing an infinite channel lined with sulfur atoms but in which there are short intra-stack contacts through only one S atom of each CN2S2 group. The double-layer stacking occurs in order to accommodate the bulk of the tBu group, and the spacing between layers is very regular, with short and long S cdot cdot cdot S contacts of 3.48(2) and 3.61(2) Å and considerable thermal motion in the c direction. The title compound and its SbF6- salt are oxidized at + 0.81 V (in CH2Cl2) and at + 0.61 V (in CH3CN), while a reduction process is observed only in CH2Cl2 at -0.73 V vs. SCE. Magnetic susceptibility data between 5 and 400 K demonstrate at very low temperature that the sample follows the Curie-Weiss law, θ = 0 K, and χ 0= -156 ppm emu mol-1. The free-spin concentration at T = 0 K is approx 1.3%, due to paramagnetic defects in an essentially diamagnetic structure. The diamagnetism starts to lift above 210 K; above 260 K, a strong antiferromagnetic exchange is operative. These results are consistent with the lifting of the Peierls distortion in this structure, starting above approx 200 K. The crystal structure of the parent diamidine 5-tert-butyl-1,3-[(Me3Si)2NCNSiMe3]2C6H3 was determined in C2/c with a = 10.0788(3), b = 21.328(5), c = 20.876(5) Å , β = 99.41(2)°, Z = 4. The two amidine functional groups are equivalent by crystal symmetry.Key words: dithiadiazole, diradical, magnetic susceptibility, crystal structure, bulky substituent.

Two-dimensional small-angle X-ray scattering investigation of stretched borosilicate glasses. Erratum

Printer's errors in the paper by Polizzi, Riello, Fagherazzi, Bark & Borrelli [J. Appl. Cryst. (1997). 30, 487–494] are corrected. In the Abstract, the value of the average of the volumetric particle distribution was given incorrectly as 22 × 70 nm. The correct value is 22 × 370 nm. In §5.1 on p. 491, the size of the particles whose dimensions are very close to the volumetric average obtained by the fitting method was given incorrectly as 22 × 80 nm. The correct value is 22 × 380 nm. In §5.2 on p. 491, the unit-cell edge of Ag determined was given incorrectly as 4.709 (6) A. The correct value is 4.079 (6) A. The TEM micrographs of Figs. 2 and 6 were transposed. These figures are printed correctly below.

Formation of cubic phases on heating ferrihydrite

AbstractHeating experiments were carried out with ferrihydrite, in the presence of organics, to gain more insight into the intermediate formation of a ferrimagnetic cubic phase often observed in soils as the result of fire. Without an organic reductant, no intermediate cubic phase was formed when ferrihydrite was transformed into hematite, regardless of whether the ferrihydrite DTA curve showed one or two exothermic peaks. Addition of glucose or charcoal as reductant caused the initial formation of a cubic magnetite and/or magnetite/maghemite phase in samples heated above 300°C in both air and N2 atmospheres. Ferrihydrite reduction, as determined by increasing cubic unit-cell edge lengths between 0.832 and 0.840 nm, increased with reductant concentration and heating time, providing excess reductant remained. Following consumption of the reductant, FeII may be partially or completely reoxidized, forming maghemite and then hematite. The occurrence of maghemite, but not of magnetite, in soils where forest fires have occurred suggests that sufficient oxygen was available, while temperatures remained elevated, to oxidize magnetite to maghemite.

Powder neutron diffraction studies of the thermal expansion, compressibility and dehydration of deuterated gypsum

The unit cell parameters of deuterated gypsum have been extracted from Rietveld analysis of powder neutron diffraction data between the temperature limits 4.2–320 K and pressures up to 5.4 GPa at 293 K. The thermal expansion is highly anisotropic along the b-axis. The high-temperature limits of the expansion coefficients for the unit cell edges a, b and c are 3.98 × 10 −6, 4.36 × 10 −5 and 2.53 × 10 −5 K −1. That for the unit cell volume is 6.96 × 10 −5 K −1. The β angle shows oscillatory variation, and empirical analysis results in α β = 1.251 × 10 −6 sin(0.0116 T + 0.311) K −1. The principal axes of the thermal expansion tensor at 300 K are α 22, 3.7 × 10 −5 K −1, parallel to the b-axis with α 11, 2.5 × 10 −5 K −1, and α 33, 1.1 × 10 −6 K −1, both in the ac-plane. α 11 is rotated by 12.1° towards a from c at 300 K. The static compressibility has been measured at room temperature and up to 5.4 GPa. The unit cell of gypsum compresses anisotropically, with the largest compression along the b-axis. Using a third-order Birch-Murnaghan equation of state values of 45 GPa and 2.0 are calculated for the bulk modulus and its pressure derivative.

Pressure dependence of structural parameters of paragonite

The compressibility and structure of a 2M1 paragonite with composition [Na0.88K0.10Ca0.01Ba0.01] [Al1.97Ti0.007Fe0.01Mn0.002Mg0.006]Si3.01Al0.99O10OH2 were determined at pressures between 1 bar and 41 kbar, by single crystal X-ray diffraction using a Merrill-Bassett diamond anvil cell. Compressibility turned out to be largely anisotropic, linear compressibility coefficients parallel to the unit cell edges being βa=3.5(1)·10−4, βb=3.6(1)·10−4, βc=8.3(3)·10−4 kbar−1 (βa:βb·βc=1:1028:2.371). The isothermal bulk modulus, calculated as the reciprocal of the mean compressibility of the cell volume, was 650(20) kbar. The main features of the deformation mechanism resulting from structural refinements at pressures of 0.5, 25.4, 40.5 kbar were: – variation in sheet thickness, showing that compression of the c parameter was mainly due to the interlayer thickness reduction from 3.07 A at 0.5 kbar to 2.81 A at 40.5 kbar; – the compressibility of octahedra was greater than that of tetrahedra, the dimensional misfit between tetrahedral and octahedral sheets increased with P, so that tetrahedral rotation angel α increased from 15° at 0.5 kbar to 21.6° at 40.5 kbar; – the basal surface corrugation (Δz) of the tetrahedral layer, due to the different dimensions of M1 and M2 octahedra and to the octahedral distortion, decreased with P (Δz=0.19 and 0.12 A at 0.5 and 40.5 kbar respectively). Comparison of the new data on paragonite with those of a K-muscovite and a Na-rich muscovite (Comodi and Zanazzi 1995) revealed a clear trend toward decreasing of compressibility when Na substitutes for K atoms in the interlayer sites.

Magnetic properties of magnetite arrays produced by the method of electron beam lithography

Arrays of magnetite particles in the submicron range (0.1–4.0 µm) have been produced. A novel method involving the utilisation of Electron Beam Lithography techniques often employed in the engineering design of integrated circuits of microchips was used. The fabrication process involved first producing arrays of iron (Fe) particles and then converting them to magnetite (Fe3O4) by thermal treatment. The fabricated magnetite particles have well controlled parameters including inter‐particle spacing, an impossible task to achieve using artificially produced powders often employed in rockmagnetic studies. Two methods of converting Fe to Fe3O4 by annealing were used. One method led to Fe3O4 grains with high coercivities, typical of stressed grains and the other low coercivities in agreement with those for laboratory grown crystals. The crystal unit cell edge. Curie temperature, and saturation isothermal remanent magnetisation (SIRM) intensity observed at the Verwey transition are all consistent with stoichiometric magnetite.

Modelling of the thermal dependence of structural and elastic properties of calcite, CaCO3

A computational method, based on the quasiharmonic approximation, has been computer-coded to calculate the temperature dependence of elastic constants and structural features of crystals. The model is applied to calcite, CaCO3; an interatomic potential based on a C-O Morse function and Ca-O and O-O Borntype interactions, including a shell model for O, has been used. Equilibrations in the range 300–800 K reproduce the experimental unit-cell edges and bond lengths within 1%. The simulated thermal expansion coefficients are 22.3 (//c) and 2.6 (⊥ c), against 25.5 and-3.7×10−6K−1 experimental values, respectively. The thermal coefficients of elastic constants tend to be underestimated; for the bulk modulus, -2.3 against-3.7×10−4K−1 is obtained.

High Conductivity in Gallium-Doped Zinc Oxide Powders

Gallium-doped zinc oxide powders have been prepared with electrical conductivities at 25 {degrees}C as 300 {Omega}{sup -1} cm{sup -1}, more than 1000 higher than previously reported. All materials prepared can be represented an Zn{sub 1-x}Ga{sub x}O, Zn{sub 1-y}Ga{sub y}O{sub 1+(y/2)}, or a combination of these two. For Zn{sub 1-x}Ga{sub x}O, the room-temperature conductivity increases monotonically with increasing x up to 2.7%, which is the limit of Ga solubility for this formulation at our synthesis temperatures of 1000 to 1200 {degrees}C. Conductivities measured from 4.2 to 500 K showed only a very small temperature dependence. An ESR peak (g=1.96), attributed to the conduction electrons, broadens with increased doping level. The hexagonal unit-cell edges increase with increasing x over the entire range of x. For the low conductivity Zn{sub 1-y}Ga{sub y}O{sub 1+(y/2)} series, the level of Ga substitution can reach at least 4.0%. 16 refs., 19 figs., 1 tab.

Preliminary X-ray crystallographic analysis of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase.

Inosine-5'-monophosphate dehydrogenase (IMPDH) from the protozoan parasite Tritrichomonas foetus has been expressed in E. coli and crystallized. Crystals were grown to 0.1 mm in each dimension in 18 to 72 h using ammonium sulfate and low-molecular-weight polyethylene glycols. The crystals belong to the cubic space group P432 with unit cell edge = 157.25 A. The enzyme is a homotetramer with each monomer having a molecular weight of 55,534 Da. There is one monomer per asymmetric unit, based on a volume/mass ratio of 2.7 A3/Da and self-rotation analysis. The crystals are adequately stable to allow a complete data set to be collected from a single crystal. Complete native data sets have been collected to 2.3 A resolution at 4 degrees C using synchrotron radiation. High-quality complete data extending to 3.0 A resolution have been collected from crystals of four putative derivatives, and the data appear to be isomorphous with that of the native crystals in each case. Efforts to solve the derivatives for use in MIR phasing are underway.

Tl2Nb2O6+x (0 ≤ x ≤ 1): A Continuous Cubic Pyrochlore Type Solid Solution

Thallium metaniobate, Tl2Nb2O6, belongs to the cubic pyrochlore structural type (space group Fd3m). It is demonstrated by TGA, chemical analysis, and X-ray thermodiffractometry that it gives a continuous solid solution Tl2Nb2O6+x (0 ≤ x ≤ 1) under oxidation; the cubic pyrochlore structure is maintained with a continuous decreasing unit cell edge: x oxide ions being progressively incorporated into the network while x Tl3+ ions substitute to x Tl+ ones. Rietveld refinements of X-ray powder diffraction data reveal that, in the classical model of the pyrochlore structure, Tl+ and Tl3+ are disordered on half of the 32e positions for 0 ≤ x < 0.5 and on the 16d ones for 0.5 < x ≤ 1. Bond valence calculations are in good agreement with the decrease in the splitting of Tl cations from 32e to 16d positions when x increases, provided that a correlation exists between oxygen insertion and the Tl3+ distribution: each extra oxygen O' oxidizes one of its closest Tl neighbors to +3 while the three remaining monovalent Tl cations are repelled.

Electrochemical lithium insertion into magnesium titanate spinels

Electrochemical lithium insertion into magnesium titanate spinels of composition Mg 2− y Ti 1+ y O 4 ( y=0.33, 0.57) has been investigated. Insertion into the y=0.33 spinel appears to take place via a two-phase equilibrium reaction, as indicated by both cell potential and lattice parameter measurements. The insertion process for the y=0.57 spinel appears to be somewhat different, with a minimum in unit cell parameter and a marked drop in cell potential being observed at an Li content of about 0.2 per formula unit. This is thought to reflect a change in the dominant insertion mechanism as the reaction progresses. The magnetic properties of the spinel were found also to depend upon the degree of substitution, with some inserted samples exhibiting spin- glass type behaviour. The structure of the sample was found to change markedly on heating in an inert atmosphere, both a rocksalt type phase and a spinel phase, with a much decreased unit cell edge, were encountered after heating to about 500°C in an inert atmosphere.

RICICLE: A FORTRAN program to refine unit cell parameters of incommensurate structures

A FORTRAN 77 program to perform full matrix least-squares refinement of unit cell parameters from powder diffraction patterns showing incommensurate supercell reflections is described. The code is completely general, being applicable to any crystal system, and can refine all three unit cell edges and angles and, in the presence of an incommensurate supercell, can refine the components of the modulation vector along all three reciprocal axes. Estimated standard deviations on all the refined parameters are calculated analytically.

Crystallization and Preliminary Crystallographic Analysis of Recombinant Xenopus laevis Cu, Zn Superoxide Dismutase b

The recombinant Cu,Zn superoxide dismutase from the South African frog Xenopus laevis, expressed in E. coli, has been crystallized in a form suitable for high resolution crystallographic investigations. The crystals grow from polyethylene glycol solutions, at pH 6.0, 28° C, and belong to the orthorhombic space group P2 12 12 1 with unit cell edges a = 73.33, b = 68.86, c = 59.73 Å, one protein dimer (32,000 Mr) per asymmetric unit. Diffraction data have been collected to 3.0 Å resolution, and a molecular replacement solution found for Xenopus laevis superoxide dismutase using the bovine enzyme as search model. The crystallographic R-factor corresponding to this solution is 0.412, in the 15.0-3.0 Å resolution range.

XRD investigation of the crystallization process in Fe 40Ni 40B 20 metallic glass

X-ray diffraction analysis showed that two crystalline solid solutions simultaneously arise when Fe 40Ni 40B 20 glassy metallic ribbons, aged at room temperature for about 1 year, are heated in an inert atmosphere at 653 and at 663 K (first steps of the crystallization process). These two compounds are orthorhombic (Fe, Ni) 3B and fcc γ-(Fe, Ni). The first compound had larger unit cell parameters than those of both Ni 3B and Co 3B, while the second phase had a unit cell edge shorter than that of equiatomic γ-(Fe, Ni). These unit cell parameters indicate the formation of an orthorhombic solid solution richer in Fe than in Ni and, conversely, of a cubic solid solution richer in Ni than in Fe. The orthorhombic phase had the largest volume fraction and crystallites larger than those of the fcc phase (average sizes of 36 and 6 nm, respectively). The crystalline fraction of the metallic ribbons, partially crystallized after isothermal heating at the above temperatures, was determined as a function of the heating time. A modified Avrami kinetic analysis was carried out with computed values of the crystallized fraction. Dependence of the ‘local’ Avrami exponent on crystallized fraction is indicative of a crystal growth mechanism based on pre-existing nuclei (surface plus quenched-in nuclei). By applying the well known Arrhenius equation to the kinetic constants, as obtained by the ‘locally’ applied Avrami analysis, an initial activation energy of 250±50 kJ mol −1 was determined for the growth process.

Structural study and preliminary crystallographic data for the hemoglobin from reindeer ( Rangifer tarandus tarandus)

The ferric form of reindeer hemoglobin ( Rangifer tarandus tarandus) has been crystallized in an orthorhombic crystalline form from polyethylene glycol solutions, at pH 8.2. The crystals belong to the orthorhombic space group P2 12 12 1, with unit cell edges a = 84.2 A ̊ , b = 59.9 A ̊ , c = 119.5 A ̊ ; one hemoglobin tetramer is contained in the asymmetric unit. The crystals diffract X-rays to a limit spacing of 3.0 Å. Inspection of amino acid sequences in the N-terminal region of β-chains, and analysis of hemoglobin three-dimensional models, allows one to rationalize, on a molecular basis, the reduced O 2 affinity and the decreased effect of organic phosphates observed in ruminant hemoglobins. By analogy, the analysis is extended to birds and reptiles, whose hemoglobin β-chains display, as in ruminants, the deletion of the N-terminal residue and a methionine at the NA2 position.

Interatomic potentials for CaCO3 polymorphs (calcite and aragonite), fitted to elastic and vibrational data

Calcite and aragonite have been modeled using rigid-ion, two-body Born-type potentials, supplemented by O-C-O angular terms inside the CO3 groups. A shell model has also been developed for calcite. Atomic charges, repulsive parameters and force constants have been optimized to reproduce the equilibrium crystal structures, the elastic constants and the Raman and infrared vibrational frequencies. The rigid-ion potential RIM (atomic charges: z(O) = -0.995 e, z(C) = 0.985 e, z(Ca) = 2.0 e) fitted to calcite properties is able to account for those of aragonite as well. Experimental unit-cell edges, elastic constants, internal and lattice frequencies are reproduced with average relative errors of 2.1, 5.5, 2.4, 15.1 % for calcite and of 0.2, 19.4, 2.5, 11.8 % for aragonite, respectively. The RIM potential is suitable for thermodynamic and phase diagram simulations in the CaCO3 system, and is discussed and compared to other potentials.

Yttrium Substitution in CaS

Substitution of Y3+ in CaS results in the cubic rock-salt-type solid-solution Ca1−xY2x/3□x/3S, with x 0.37 and where □ denotes cation vacancies that form for charge compensation. The substitution range determined from polycrystalline samples prepared at 1025°C corresponds to a solubility limit of 16 mol% Y2S3 in CaS. Evolution of the unit cell edge with x indicates that the CaS lattice expands about the cation vacancies. Single-crystal X-ray diffraction studies of samples grown from a eutectic CaCl2–KCl flux revealed no indication of superstructure formation, indicating that Ca2+, Y3+, and vacancies are disordered across the cation sites. Thermogravimetric analysis curves for Ca0.7Y0.2S, CaS, and the ternary compound CaY2S4 indicate oxidative stability up to 430°, 410°, and 490°C, respectively.

Magnesiochloritoid: Compressibility and high pressure structure refinement

The response of magnesiochloritoid to pressure has been studied by single crystal X-ray diffraction in a diamond anvil cell, using crystals with composition Mg1.3Fe0.7Al4Si2O10(OH)4. The unit cell parameters decrease from a = 9.434 (3), b = 5.452 (2), c = 18.136 (5) A, β = 101.42° (2) (1 bar pressure) to a = 9.370 (7), b = 5.419 (5), c = 17.88 (1) A, β = 101.5° (1) (42 kbar pressure), following a slightly anisotropic compression pattern (linear compressibilities parallel to unit cell edges: β a = 1.85, β b = 1.74, βc = 3.05 × 10−4 kbar−1) with a bulk modulus of 1480 kbar. Perpendicular to c, the most compressible direction, the crystal structure (space group C2/c) consists of two kinds of alternating octahedral layers connected via isolated SiO4 tetrahedra. With increasing pressure the slightly wavy layer [Mg1.3Fe0.7AlO2(OH)4] tends to flatten. Furthermore, the octahedra in this layer, with all cations underbonded, are more compressible than the octahedra in the (A13O8) layer with slightly overbonded aluminum. Comparison between high-pressure and high-temperature data yields the following equations: $$\begin{gathered} a_{P,T} = 9.434{\text{ }}{\AA} - 174 \cdot 10^{ - 5} {\text{ }}{\AA}{\text{kb}}^{{\text{ - 1}}} \cdot P \hfill \\ {\text{ }} + 9 \cdot 10^{ - 5} {\text{ }}{\AA}^\circ C^{ - 1} \cdot (T - 25^\circ C) \hfill \\ b_{P,T} = 5.452{\text{ }}{\AA} - 95 \cdot 10^{ - 5} {\text{ }}{\AA}{\text{kb}}^{{\text{ - 1}}} \cdot P \hfill \\ {\text{ }} + 5 \cdot 65 \cdot 10^{ - 5} {\text{ }}{\AA}^\circ C^{ - 1} \cdot (T - 25^\circ C) \hfill \\ c_{P,T} = 18.136{\text{ }}{\AA} - 549 \cdot 10^{ - 5} {\text{ }}{\AA}{\text{kb}}^{{\text{ - 1}}} \cdot P \hfill \\ {\text{ }} + 16 \cdot 2^{ - 5} {\text{ }}{\AA}^\circ C^{ - 1} \cdot (T - 25^\circ C) \hfill \\ \end{gathered} $$ with P in kbar and T in °C. These equations indicate that the unit cell and bond geometry of magnesiochloritoid at formation conditions do not differ greatly from those at the outcrop conditions, e.g. the calculated unitcell volume is 917.3 A3 at P = 16 kbar and T=500 °C, whereas the observed volume at room conditions is 914.4 A3. In addition, they show that the specific gravity increases from formation at depth to outcrop at surface conditions.