X-ray Intensity Data Research Articles

Isolation and Crystal Structure of 6α,7α-Epoxy-5α,17α,27-trihydroxy-1-oxo-22R-witha-2,24-dienolide monohydrate-A Withasteroid from Withania somnifera Leaves

(5R,6S,7S,8S,9S,10R,13S,14S,17S,20R,22R)-6α,7α-epoxy-5α,17α,27-trihydroxy-1-oxo-22R-witha-2,24-dienolide has been isolated from Withania somnifera leaves. Three-dimensional X-ray intensity data were collected at 293 K on Bruker CCD area-detector diffractometer equipped with graphite-monochromated MoKα radiation (λ = 0.71073 A). The compound crystallizes in monoclinic space group P21 with unit cell parameters: a = 6.4540(2), b = 11.3656(4), c = 17.4982(5) A, β = 90.730 o(2), Z = 2. The crystal structure was refined to a final R-value of 0.0419 for 6122 observed reflections. One water solvent molecule was observed. All the rings of the steroid skeleton are trans connected. Rings A and B exists in a half-chair conformation, ring C a chair, and five membered ring D is intermediate between half-chair and envelope. The δ-lactone ring E adopts a distorted sofa conformation. The characteristic pattern observed in the packing diagram is the appearance of twisted chains of molecules. The packing of the molecules in the crystal is stabilized by intra- and intermolecular O–H···O and C–H···O interactions. The isolation and crystal structure analysis of a withasteroid isolated from Withania somnifera leaves

Oscillatory zoned liddicoatite from Anjanabonoina, central Madagascar. I. Crystal chemistry and structure by SREF and 11B and 27Al MAS NMR spectroscopy

The crystal structures of 23 samples extracted from a large slice oriented along (001) of a single crystal of liddicoatite from the Anjanabonoina granitic pegmatite in Madagascar (showing pronounced, visually discontinuous oscillatory zones and anomalous biaxiality) were refined to R 1 indices of 1.5–2.9% ( R 1 > = 1.78%). Cell parameters are in the range a ≈ 15.82–15.87, c ≈ 7.10–7.12 A. Spindle-stage measurement of 2 V gave values of 0.0° for a fragment from the (001) zone and 8(3) and 18.9(5)° for fragments from the pyramidal zone of the crystal. However, single-crystal X-ray intensity data show no deviation from 3 m Laue symmetry, indicating that there is no information in the diffraction data on any deviation from R 3 m symmetry. The T –O> distances are in the range 1.616–1.619 A, with a grand mean value of 1.6175(7) A. The occupancy of the T site was expressed as x Si + (1− x )B, and x was treated as variable in the refinement procedure. The effect of using different scattering factors ( i.e ., ionized versus neutral) on the refined site-occupancies was investigated in detail. The grand mean refined [4] B content of the T site varies from −0.04 apfu for ionized scattering-curves for O and Si to 0.25 apfu for neutral scattering-curves for O and Si, illustrating the effect of the use of different scattering curves on refined [4] B site-populations. Examination of T –O> distances as a function of aggregate cation radius for tourmalines containing [4] B and [4] Al shows a large amount of scatter, emphasizing the need for more accurate data. The limits of detection for 11 B and 27 Al in tourmaline by Magic-Angle-Spinning Nuclear Magnetic Resonance (MAS NMR) spectroscopy were investigated by simulation. For minimum ( apfu ) and maximum (0.12 apfu ) contents of (paramagnetic) transition metals, the limits of detection of [4] B are~0.02 and 0.08 apfu , and of [4] Al are~0.01 and 0.01 apfu , respectively. 11 B and 27 Al MAS NMR spectroscopy gave no evidence of the presence of tetrahedrally coordinated B or Al at the T site above these detection limits in any sample. This result is in accord with our refinement results using an ionized scattering-curve for O and a neutral scattering-curve for Si, suggesting that use of these curves is giving more accurate results than refinement with neutral scattering factors. The Z –O> distances are in the range 1.904–1.907 A, with a grand mean value of 1.9047(8) A, and structure refinement indicates site-scattering values in accord with complete occupancy of the Z site by Al. Hence throughout this complexly zoned crystal, Si = 6.00 apfu and Z Al = 6.00 apfu .

Synthesis and Electron Density Analysis of SnO2 Nano Particles

Tin oxide material (SnO2) is synthesized in nano scale range and is characterized. The refined X-ray intensity data was obtained from the Reitveld method. The electron density of nano SnO2 is determined using MEM (Maximum Entropy Method). Using one, two and three dimensional MEM maps, the bonding within the atoms is clearly understood. The particle size of SnO2 is also analyzed using XRD and SEM.

Eirikite, a new mineral species of the leifite group from the Langesundsfjord district, Norway

Eirikite, ideally, KNa 6 [Be 2 (Si 15 Al 3 ) ∑= 18 O 39 F 2 ], is a new mineral species from the Vesle Aroya island in the Langesundsfjord district, Larvik, Vestfold, Norway. It is the potassium analogue of leifite, NaNa 6 [Be 2 (Si 15 Al 3 ) ∑=18 O 39 F 2 ], and telyushenkoite, CsNa 6 [Be 2 (Si 15 Al 3 ) ∑= 18 O 39 F 2 ]. An average of five electron microprobe analyses gave Na 2 O 13.38, K 2 O 3.13, Al 2 O 3 11.08, SiO 2 66.03, F 2.70, BeO 3.65 (calc.), O = F −1.14, total 98.83 wt. %, resulting in the empirical formula K 0.91 Na 5.92 [Be 2 (Si 15.07 Al 2.98 ) ∑=18.05 ]O 39 (F 1.95 O 0.05 ); infrared spectroscopy indicates the absence of OH and H 2 O. Eirikite occurs as both finely or coarsely fibrous, monomineralic aggregates and bundles up to 3 cm across, wholly or partly filling voids between larger microcline crystals. Individual acicular-prismatic crystals show the forms {1010}and {0001}. Eirikite also occurs as aggregates up to 100 cm 3 in volume, built of interlocking, radiating fibrous groups, each up to 5 mm across, intergrown with large amounts of small zircon crystals and penetrated by aegirine crystals. Polylithionite, albite, eudialyte, catapleiite and pyrochlore can be found within these aggregates. Eirikite is white to colourless with a white streak, a vitreous to silky lustre, Mohs hardness of 6; it is brittle with an uneven to conchoidal fracture, and with a good {1010} cleavage. The mineral is uniaxial positive, ω =1.517(1) and e = 1.521(1), and nonpleochroic; D meas = 2.59(1) g/cm 3 , D calc = 2.577 g/cm 3 (from the empirical chemical formula) and 2.584 g/cm 3 (from the crystal structure determination). Eirikite is trigonal, P 3 m 1 (no. 164), with a = 14.3865(9) A, c = 4.8733(4) A, V = 873.5(1) A 3 , and Z = 1, refined from X-ray powder diffraction data. The five strongest lines in the X-ray powder pattern are [d (in A) (I/I 0 )(hkl)]: 4.710(29)(120), 4.153(21)(030), 3.386(70)(211), 3.161(100)(031), and 2.466(31)(231). The crystal structure, which was determined from single-crystal X-ray intensity data and refined to R 1( F ) = 1.99 %, is a framework of corner-sharing (Si,Al)O 4 and BeO 3 F tetrahedra ( = 1.610 A), leading to chain and ring units. Voids in the framework are occupied by K ( = 3.105 A), and seven-coordinated Na atoms ( = 2.542 A). The B site, which is vacant in telyushenkoite and partly occupied by water molecules in leifite, is nearly vacant in eirikite.

K2.9Rb0.1ErSi3O9: a novel, non-centrosymmetric chain silicate and its crystal structure

AbstractThe new, non-centrosymmetric chain silicate, K2.9Rb0.1ErSi3O9, was prepared by a high-temperature flux-growth technique, and its crystal structure was determined from single-crystal X-ray intensity data (Mo-Kα, 293 K) in space P1, with a = 6.672(1), b = 6.719(1), c = 6.725(1) Å, α = 108.87(3), β = 106.72(3), γ = 107.61(3)°, V = 245.82(6) Å3, Z = 1, R(F) = 2.81%. The compound represents a novel structure type. K2.9Rb0.1ErSi3O9 is characterized by a mixed octahedral-tetrahedral framework, in which each corner of the isolated ErO6 octahedron (<Er—O> = 2.26 Å) is linked to infinite [Si3O9] chains extending approximately along [111]. This connectivity results in a microporous character with two different, narrow channels that extend parallel to [111] and [100] and host K+ cations. The atomic arrangement is strongly pseudorhombohedral. A single-crystal Raman spectrum of K2.9Rb0.1ErSi3O9 is in agreement with the low space-group symmetry. Relations to minerals and synthetic compounds based on [Si3O9] chains are discussed, revealing that the geometry of the chain in K2.9Rb0.1ErSi3O9 is similar to that in pectolite, NaCa2[HSi3O9].

Crystallization of the plant hormone receptors PYL9/RCAR1, PYL5/RCAR8 and PYR1/RCAR11 in the presence of (+)-abscisic acid.

Abscisic acid (ABA) is a plant hormone that plays key regulatory roles in physiological pathways for the adaptation of vegetative tissues to abiotic stresses such as water stress in addition to events pertaining to plant growth and development. The Arabidopsis ABA receptor proteins PYR/PYLs/RCARs form a START family that contains 14 members which are classified into three subfamilies (I-III). Here, purification, crystallization and X-ray data collection are reported for a member of each of the subfamilies, PYL9/RCAR1 from subfamily I, PYL5/RCAR8 from subfamily II and PYR1/RCAR11 from subfamily III, in the presence of (+)-abscisic acid. The three proteins crystallize in space groups P3(1)21/P3(2)21, P2 and P1, respectively. X-ray intensity data were collected to 1.9-2.6 A resolution.

THE CRYSTAL STRUCTURES OF NIOBOPHYLLITE, KUPLETSKITE-(Cs) AND Sn-RICH ASTROPHYLLITE: REVISIONS TO THE CRYSTAL CHEMISTRY OF THE ASTROPHYLLITE-GROUP MINERALS

The crystal structures of niobophyllite, K 2 Na Fe 2+ 7 (NbTi) (Si 4 O 12 ) 2 O 2 (OH) 4 O, kupletskite-(Cs), Cs 2 Na Mn 7 Ti 2 (Si 4 O 12 ) 2 O 2 (OH) 4 F, and Sn-rich astrophyllite, K 2 Na Fe 2+ 7 Ti 2 (Si 4 O 12 ) 2 O 2 (OH) 4 F, all members of the astrophyllite group, have been refined in space group P 1 to R 1 values 5.96, 3.33 and 3.53% for 3576, 3490 and 3791 observed [ F o > 4σ F ] unique reflections measured with Mo K α radiation on a Bruker AXS diffractometer with a CCD SMART APEX detector. The crystal structures of all three minerals are topologically identical to that of triclinic astrophyllite. The crystals used in the collection of the X-ray intensity data were analyzed by electron microprobe, Fe 3+ : (Fe 2+ + Fe 3+ ) ratios were measured by Mossbauer spectroscopy, and Li was determined by laser-ablation – inductively coupled plasma – mass spectrometry (LA–ICP–MS). The empirical formulae were calculated on an anion basis, (O + OH + F) = 31 apfu : niobophyllite, (K 1.79 Cs 0.03 ) ∑1.82 Na 1.01 (Fe 2+ 4.02 Mn 1.98 Fe 3+ 0.55 ) ∑6.55 (Nb 1.46 Ti 0.55 Ta 0.01 ) ∑2.02 [(Si 7.77 Al 0.20 ) ∑7.97 O 24 ] O 2.73 [(OH) 4.13 F 0.13 ] ∑4.26 ; kupletskite-(Cs), (Cs 1.42 K 0.36 Ca 0.08 Pb 0.06 Na 0.05 Sr 0.02 ) ∑1.99 (Na 0.73 Ca 0.27 ) ∑1 (Mn 3.74 Fe 2+ 1.82 Li 0.68 Zn 0.50 Fe 3+ 0.13 Mg 0.11 ) ∑6.99 (Ti 1.54 Nb 0.45 Zr 0.02 ) ∑2.01 [(Si 7.90 Al 0.05 ) ∑7.95 O 24 ] O 2.03 [(OH) 4.26 F 0.71 ] ∑4.97 ; Sn-rich astrophyllite, (K 1.70 Ca 0.04 Cs 0.03 Pb 0.01 ) ∑1.78 (Na 0.96 Ca 0.04 ) ∑1 (Fe 2+ 6.18 Mn 0.45 Fe 3+ 0.26 Ca 0.09 Zn 0.02 ) ∑7 (Ti 0.74 Sn 0.62 Nb 0.44 Zr 0.16 Ta 0.02 Mg 0.02 ) ∑2.00 [(Si 7.75 Al 0.16 ) ∑7.91 O 24 ] O 2 [(OH) 4.356 F 0.65 ] ∑5.00 ; Z = 1. In Sn-rich astrophyllite, Sn 4+ replaces Ti 4+ at the D site, and there is a corresponding expansion of the D octahedron: = 1.979 A, where φ represents O, F, OH. The discovery of Sn-rich astrophyllite indicates that there is potential for a new species in the astrophyllite group with Sn 4+ as the dominant cation at the D site. We have identified three distinct A sites, A (1), A (2) and A (3) with coordinations [13], [5] and [13], respectively, that are separated by ≤1.2 A such that locally adjacent sites cannot both be occupied. We suggest the possibility of Ca occupying the B site via the substitution B Ca 2+ + A □ → B Na + + A K + and producing a potential new mineral of the astrophyllite group. The general formula of the astrophyllite-group minerals should be written as A 2 B C 7 D 2 (T 4 O 12 ) 2 O 2 (OH) 4 X 0–1 as this (i) preserves the correct formula of the silicate radical in the structure, and (ii) identifies the O 2 anion component of the structure as not bonded to Si.

Purification and preliminary X-ray crystallographic studies of β-microseminoprotein from human seminal plasma

beta-Microseminoprotein (beta-MSP) is a small cysteine-rich protein with a molecular mass of 10 kDa. It was first isolated from human seminal plasma and has subsequently been identified from several species. Comparison of the amino-acid sequences of beta-MSP proteins suggests that the protein is a rapidly evolving protein. The function of beta-MSP is poorly understood. Furthermore, no crystal structure has been reported of any beta-MSP; therefore, determination of the crystal structure of beta-MSP is the foremost task in order to understand the function of this protein completely. Here, the purification, crystallization and preliminary X-ray diffraction analysis of beta-MSP from human seminal plasma are described. The protein was purified using anion-exchange and size-exclusion chromatography and the purified protein was crystallized using 0.1 M ammonium sulfate, 0.1 M HEPES buffer pH 7.0 and 20%(w/v) PEG 3350. The crystals belonged to the tetragonal space group P4(3)22 and contained three beta-MSP molecules in the asymmetric unit. X-ray intensity data were collected to 2.4 A resolution.

Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric β-lactamase

beta-Lactam antibiotics such as penicillins and cephalosporins have a four-atom ring as a common element in their structure. The beta-lactamases, which catalyze the inactivation of these antibiotics, are of great interest because of their high incidence in pathogenic bacteria. A novel oligomeric class C beta-lactamase (Est-Y29) from a metagenomic library was expressed, purified and crystallized. The recombinant protein was expressed in Escherichia coli with an N-terminal 6xHis tag and purified to homogeneity. EstY-29 was crystallized and X-ray intensity data were collected to 1.49 A resolution using synchrotron radiation.

COMPRESSIBILITY AND HIGH-PRESSURE BEHAVIOR OF Ab63Or27An10 ANORTHOCLASE

A natural sample of anorthoclase of composition Na 0.63 K 0.27 Ca 0.10 Al 1.10 Si 2.90 O 8 (Ab 63 Or 27 An 10 ) was treated at T = 950°C for one week, and then investigated by single-crystal X-ray diffraction in situ at high pressure using a diamond-anvil cell. After the thermal treatment, the unit-cell parameters at room pressure and temperature are a 8.2523(3), b 12.9363(5), c 7.1416(3) A, α 92.046(5), β 116.294(3), γ 90.206(4)°, V 682.91(5) A 3 , and indicate nearly complete Al–Si disorder. Unit-cell parameters were measured at room temperature as a function of pressure to 8.48 GPa. The P – V data are described by a fourth-order Birch–Murnaghan equation of state with the following coefficients: V 0 = 682.92(5) A 3 , K T0 = 54.4(4) GPa, K ′ = 6.4(3), K ″ = −1.16(12) GPa −1 . The unit-cell compression is anisotropic, as indicated by the unit strain tensors, with 53% of the total compression over the entire range in pressure accommodated along a direction close to a *. The axial linear compressibilities (β a = 6.92, β b = 2.83 and β c = 3.91 × 10 −3 GPa −1 ) reflect a compressibility pattern similar to that of other alkali feldspars. The X-ray intensity data were collected at a pressure of 0.0001, 4.7 and 6 GPa. The results of the refinements indicate that the symmetry of this anorthoclase remains triclinic, C 1, over the entire range in pressure; no phase transitions were observed. The pressure causes a strong deformation of the extra-framework M site, with a contraction of the volume by 16% at P = 6 GPa. The compression is accompanied by a decrease of the M –O distances and a possible increase in the coordination number of the non-tetrahedrally coordinated cations from “5+1” to “5+2”, related to the significant decrease of the M –OC(m) distance. The increase of the coordination number is not associated with any phase transition. Together with the deformation of the M site, the inter-tetrahedron tilting of essentially rigid tetrahedra (detectable by the changes in the T –O– T angles) is the main mechanism of compression of the structure of anorthoclase.

THE CRYSTAL CHEMISTRY OF THE SCAPOLITE-GROUP MINERALS. I. CRYSTAL STRUCTURE AND LONG-RANGE ORDER

Scapolite-group minerals are a group of rock-forming framework aluminosilicates common in a wide variety of igneous and metamorphic rocks. They have the general formula M 4 [ T 12 O 24 ] A , where M represents Na, K, Ca, Sr, Ba and Fe 2+ , T stands for Si, Al, (Fe 3+ ), and A represents Cl, (CO 3 ), (SO 4 ). They constitute a non-binary solid-solution series involving the end members marialite (Na 4 [Al 3 Si 9 O 24 ] Cl, Ma ) and meionite (Ca 4 [Al 6 Si 6 O 24 ] CO 3 , Me ). The crystal structures of eighteen scapolite-group minerals from Me 4.9 to Me 92.8 [ Me = 100 ∑ M 2+ /∑( M 2+ + M + )] have been refined with Mo K α X-radiation. The crystals, a 12.045–12.208, c 7.564–7.586 A, V 1099.7–1130.1 A 3 , I 4/ m or P 4 2 / n , Z = 2, were analyzed with an electron microprobe subsequently to collection of the X-ray intensity data. There are subtle differences between the behavior of the distinct T tetrahedra in the I 4/ m and P 4 2 / n structures. For Si and Al, determinative curves for the assignment of site populations from T –O> distances were developed for each T site in each structure type, and T -site populations were assigned from these curves. In I 4/ m marialite, there is no Al at the T (1) site. In P 4 2 / n scapolite, Al is strongly ordered at T (2), and Si is strongly ordered at T (3), but this order is never complete. The A -site cation (Na, Ca, K) is [8]-coordinated in end-member marialite and is (on average) [8.5]-coordinated in end-member meionite. Each ( M ϕ n ) polyhedron shares two edges with adjacent ( M ϕ n ) polyhedra, forming a three-dimensional framework that interpenetrates the [ T 12 O 24 ] silicate framework. In (CO 3 )-bearing structures, the model proposed by previous workers, four (CO 3 ) groups arranged about the 4 axis ( I 4/ m ) or 4 axis ( P 4 2 / m ), is consistent across the series from marialite to meionite. Any (SO 4 ) present is disordered by rotation of 90° about the central 4-fold axis; in I 4/ m structures, each arrangement is 50% occupied, whereas in P 4 2 / n structures, the occupancies of the two arrangements are not required to be equal.

Relationship between Guinier-Preston zones and the kinetics of the intracrystalline Fe2+, Mg exchange reaction in Johnstown meteoritic orthopyroxene

The Fe2+, Mg order/disorder process in orthopyroxenes from the Johnstown meteoritic diogenite is extremely slow. It is controlled by an activation energy of ≈ 100 kcal/mol, whereas in other orthopyroxenes with similar compositions the activation energy is only 60 and 65 kcal/mol. The microstructure of the orthopyroxenes is characterized by the exsolution of abundant coherently intergrown Guinier Preston (GP) zones that have been suggested to be responsible for the slow exchange kinetics. In order to test this hypothesis, orthopyroxene crystals were homogenized by dry heating at 1075 °C for 4 days at Fe/FeO buffer conditions. The variation of the distribution of Fe2+ and Mg on the M1 and M2 was followed by site refinements employing conventional X-ray intensity data. The kinetic behaviour of the homogenized crystals was studied in six controlled continuous cooling experiments in which the crystals were cooled from 850 °C to 250 °C at various rates. The quenched ordering states could be best reproduced by the Arrhenius relation \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \[ln \mathit{k}_{\mathit{dis}}[d^{{-}1}] = 34.0 {-}71.1 [kcal/mol] /\mathit{RT},\] \end{document}(1) where k dis is the rate constant for the microscopic disordering step. It appears that homogenization of the GP zones has in fact lowered the activation energy from ≈ 100 kcal/mol to 71 kcal/mol. Equilibrium experiments were performed at three different temperatures. Comparing the refined Fe2+, Mg distribution coefficients, K D , with data previously obtained on non-homogenized Johnstown orthopyroxenes (Heinemann et al ., 2000) shows that the presence or absence of GP zones has no effect on the equilibrium distribution. Regression analysis of the combined ln K D data yielded \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \[ln \mathit{K}_{\mathit{D}} = 0.467(77) {-}2535(87)/\mathit{T}.\] \end{document}(2) Using the derived k dis and K D relations, the cooling rate of the original Johnstown orthopyroxenes was calculated from the Mueller (1967, 1969) rate law yielding dT / dt ≈ −0.4 K/My near the temperature of apparent equilibrium T ae ≈ 325 °C. This rate is the maximum rate at which the orthopyroxenes have cooled, and T ae , albeit low, is the maximum temperature at which the GP zones have nucleated.

The crystal chemistry of the gedrite-group amphiboles. I. Crystal structure and site populations

AbstractThe crystal structures of twenty-five orthorhombic Fe-Mg-Mn amphiboles, a = 18.525 – 18.620, b = 17.806-18.034, c = 5.264-5.303 Å, V = 1737.6-1776.7, space group = Pnma, Z = 4, have been refined to R indices in the range 2.1–7.8% using 790–1804 unique observed reflections measured with Mo-Kα X-radiation on a Bruker P4 automated four-circle diffractometer equipped with a 1K CCD detector. The quality of the refinements is strongly a function of the [4]Al content of the crystals because of unmixing in the central part of the series due to the presence of a low-temperature solvus. The amphibole crystals were analysed by electron microprobe subsequent to collection of the X-ray intensity data and span the anthophyllite-gedrite series from 0.17–1.82 [4]Al a.p.f.u. Mössbauer spectroscopy shows that the amphiboles of this series commonly contain small but significant amounts of Fe3+ . The amount of [4]Al is linearly related to the grand <T-O> distance by the equation <T-O> = 1.6214 + 0.171 [4]Al, R = 0.980; the slope of this relation is not significantly different from that characteristic of a hard-sphere model. The <T-O> distances indicate the following site preference for [4]Al: T1B > T2B > T1A » T2A. The <M2-O> distances are compatible with all [6]Al and Fe3+ ordered at the M2 site. The grand <M1,2,3 '3 –O> distance is related to the mean radius of the constituent cations, <rM1,2,3>, by the equation ≪M1,2,3-O≫ = 1.4684 + 0.8553(7) <rM1,2,3>.

Dingdaohengite-(Ce) from the Bayan Obo REE-Nb-Fe Mine, China: Both a true polymorph of perrierite-(Ce) and a titanic analog at the C1 site of chevkinite subgroup

Dingdaohengite-(Ce), ideally Ce 4 Fe 2+ Ti 2 Ti 2 (Si 2 O 7 ) 2 O 8 , is a new member of the chevkinite group minerals from the world-famous Bayan Obo REE-Nb-Fe Mine near Baotou city, Inner Mongolian Autonomous Region, North China. It occurs in the magnesian skarn in the excontact of granite within dolomitic marble. Most individual crystals vary from 0.2 to 1.0 cm in length. Associated minerals are diopside, tremolite, richterite, allanite-(Ce), magnetite, ilmenite, spinel, titanite, pyrochlore, F-rich phlogopite, fluorapatite, quartz, and fluorite, etc. Dingdaohengite-(Ce) is probably of bimetasomatic origin among Ca-Mg-carbonate rock and/or carbonatite, and REE-, F-rich postmagmatic hydrothermal solutions. The mineral is black and becoming brown black in thin fragments. It is translucent to opaque with a submetallic-metallic luster, and a brown streak. It is brittle with conchoidal fracture. No cleavage or parting is observed. Its hardness is VHN 25g 606.0–717.4 kg/mm 2 (Mohs hardness near 5.9). The measured density is 4.83(7) g/cm 3 and the calculated density is 4.88(0) g/cm 3 . Its reflectance values (for λ = 589 nm) are 11.4–12.5%. It is biaxial negative. The strongest six X-ray diffraction lines in the powder pattern [ d in A ( I ) ( hkl )] are 2.7524(100)(121), 2.7263(98)(313), 3.1978(68)(212), 2.5460(54)(304), 2.8702(52)(020), and 3.1622(46)(312). An electron-microprobe analysis on the crystal used to collect X-ray intensity data for crystal-structure refinement gives SiO 2 19.29, TiO 2 18.26, Al 2 O 3 0.04, FeO 8.49, Fe 2 O 3 1.67, ThO 2 0.16, MgO 1.32, CaO 2.17, Nb 2 O 5 0.47, Ta 2 O 5 0.00, La 2 O 3 19.53, Ce 2 O 3 28.08, Nd 2 O 3 n.d., Y 2 O 3 0.00, Na 2 O 0.00, sum 99.48 wt%; the Fe 3+ /Fe 2+ ratio was converted by Mossbauer spectroscopy. The empirical formula is (Ce 2.13 La 1.49 Ca 0.48 Th 0.01 ) Σ4.11 Fe 2+ (Ti 0.88 Fe 2+ 0.47 Mg 0.41 Fe 3+ 0.26 Al 0.01 ) Σ2.03 (Ti 1.96 Nb 0.04 ) Σ2.00 (Si 2 O 7 ) 2 O 8 , based on 22 O atoms with prevalence of Ti in the C 1 site of the structure. Dingdaohengite-(Ce) is monoclinic, a = 13.4656(15) A, b = 5.7356(6) A, c = 11.0977(12) A, β = 100.636(2)°, V = 842.39(46) A 3 , and Z = 2. The crystal structure of dingdaohengite-(Ce) was refined with space groups P 2 1 / a and C 2/ m . Pseudo-extinction was found, i.e., reflections with h + k = 2n are systematically strong, while those with h + k = 2n + 1 are weak, which show that the true space group of dingdaohengite-(Ce) is P 2 1 / a (pseudo- C 2/ m) .

Crystal chemistry of hydration in aluminous orthopyroxene

Hydrogen incorporation in aluminous orthopyroxene may control the generation of melt and dominate the seismic properties at the base of the Earth.s lithosphere. To clarify the substitution mechanism of H, we have synthesized, characterized, and refined the crystal structure of this potentially significant variant of orthopyroxene. The experimentally produced crystals are small needles up to approximately 20 × 20 × 100 μm in size. Electron microprobe chemical analysis indicates about 11.7 wt% Al 2 O 3 . FTIR spectra indicate 7500 ppmw H 2 O with absorbance features qualitatively similar to natural mantle orthopyroxenes. TEM imagery indicates that the phase is pure orthopyroxene with low concentrations of defects and inclusions. Cell-parameter refinement from single-crystal X-ray diffraction gives a = 18.1876(7) Å; b = 8.7352(7) Å; c = 5.1789 (5) Å, V = 822.79(11) Å 3 , which is 1.2% smaller than pure Mg anhydrous orthoenstatite. The crystal structure has been refined from single-crystal X-ray intensity data measured using a rotating anode X-ray generator, micro-focused X-ray beam, and CCD detector system. The refined structure indicates about 5% vacancy in M2 and significant Al occupancy in both M1 and T2, consistent with its composition, (Mg 0.95,0.05 ) M2 , (Mg 0.79 Al 0.21 ) M1 , (Al 0.25 Si 0.75 ) T2 Si T1 O 6 . The existence of hydrous orthopyroxene in the mantle could absorb water released from olivine on decompression to delay the onset of melting in the spinel stability region in mantle peridotite compositions.

Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 Å resolution

The structure of the complex formed between bovine beta-trypsin and the highly potent synthetic inhibitor 2-{3'-[5'-methoxy-2'-(N-p-diaminomethylphenyl)amido]-1'-pyrido}-5-(N-2''-t-butylethanol)amidobenzoic acid (C(28)H(32)N(5)O(6)) has been determined at 0.97 A resolution. X-ray intensity data were collected to 0.97 A under cryocooled conditions. The structure was refined anisotropically using REFMAC5 and SHELX-97 to R(cryst) factors of 13.4 and 12.6% and R(free) factors of 15.7 and 16.3%, respectively. Several regions of the main chain and side chains that have not been previously observed were clearly defined in the present structure. H atoms are indicated as significant peaks in an |F(o) - F(c)| difference map, which accounts for an estimated 35% of all H atoms at the 2.5sigma level. The C, N and O atoms are definitively differentiated in the electron-density maps. The amido part of the inhibitor occupies the specificity pocket and the remainder fills the remaining part of the ligand-binding cleft and interacts with the enzyme through an extensive network of hydrogen bonds. The inhibitor distorts the stereochemistry of the catalytic triad, Ser195-His57-Asp102, thereby blocking the proton-relay process of the active site by preventing the formation of the crucial hydrogen bond between His57 N(delta1) and Asp102 O(delta1).

Preparation and preliminary X-ray diffraction analysis of crystals of bacterial flagellar sigma factor sigma 28 in complex with the sigma 28-binding region of its antisigma factor, FlgM.

The sigma 28 kDa (sigma28) factor is a transcription factor specific for the expression of bacterial flagellar and chemotaxis genes. Its antisigma factor, FlgM, binds sigma28 factor and inhibits its activity as a transcription factor. In this study, crystals of the complex between Escherichia coli sigma28 and the C-terminal sigma28-binding region of FlgM were obtained. The crystals belong to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 106.7 (2), c = 51.74 (3) A, containing one complex in the crystallographic asymmetric unit. An X-ray intensity data set was collected to a resolution of 2.7 A.

Distribution of chromium among the octahedral sites in chromian epidote from Iratsu, central Shikoku, Japan

The crystal structures of chromian epidotes from the Sambagawa metamorphic rocks, central Shikoku, Japan, were refined using single-crystal data to investigate the distribution of chromium among the three independent octahedral sites. On the basis of the electron probe microanalysis of the chromian epidotes on the polished surface of thin sections, three chromian epidote grains in a thin section were selected for X-ray intensity data collection, and their Cr2O3 values were as much as 1.79, 4.99, and 4.74 wt%, respectively, which led to values of 0.113, 0.315, and 0.299 Cr apfu, respectively. Nevertheless, their Fe2O3 contents were nearly constant (8.1-8.7 wt%, 0.49-0.52 Fe apfu) and their SrO contents were not significant (1.8-3.2 wt%, 0.08-0.15 Sr apfu). The selected chromian epidote grains were picked out using a binocular optical microscope from the thin sections, and were labeled as CrEp1, CrEp2, and CrEp3, respectively. The oxidation state of chromium was found to be trivalent by the optical spectrum. 57Fe Mossbauer doublets with isomer shift of 0.28-0.53 mm/sec and quadrupole splitting of 1.77-2.24 mm/sec indicate an exclusive distribution of Fe3+ at the M3 site. The crystal structure of CrEp1 [a = 8.8815(6), b = 5.5956(5), c = 10.1532(5) A, β = 115.159(2)], CrEp2 [a = 8.9165(4), b = 5.6226(2), c = 10.1728(5) A, β = 115.2365(9)], and CrEp3 [a = 8.895(2), b = 5.610(1), c = 10.146(2) A, β = 115.177(2)] were refined using 1145, 1853 and 1438 unique reflections, respectively, and the calculations converged at R factors of 5.8%, 6.6%, and 3.2%, respectively. The resulting structural formula were: [Ca]A1[Ca0.86Sr0.14]A2[Al]M1[Al]M2[Al0.43Cr3+0.09Fe3+0.48]M3Si3O12(OH) for CrEp1, [Ca]A1[Ca0.90Sr0.10]A2[Al0.86Cr3+0.14]M1[Al]M2[Al0.34Cr3+0.17Fe3+0.49]M3Si3O12(OH) for CrEp2, and [Ca]A1[Ca0.88Sr0.12]A2[Al0.90Cr3+0.10]M1[Al]M2[Al0.37Cr3+0.12Fe3+0.51]M3Si3O12(OH) for CrEp3. The selective distribution of Cr3+ at the M3 site in CrEp1, and the KD values (KD = (Cr3+/Al)M1/(Cr3+/Al)M3) of 0.35(3) for CrEp2 and 0.41(3) for CrEp3 show that the preference of Cr3+ in the octahedral sites is M3 > M1 » M2. The variations in the M1-Oi and M3-Oi distances indicate an equidimensional expansion of the M1O6 and M3O6 octahedra by the substitution of Cr3+(+ Fe3+) for Al3+.

Hydrothermal synthesis and crystal structure of Na(Na,Mn)7Mn22(PO4)180.5H2O, a new compound of fillowite structure type

The chemical compound Na(Na,Mn) 7 Mn 22 (PO 4 ) 18 ·0.5H 2 O was synthesized with a Tuttle pressure vessel at 800°C and 1 kbar during experimental investigations on the conditions of fillowite formation. The crystal structure of a single-crystal, space group R 3 (No. 148), a = 15.2741(9), c = 43.334(3) A, Z = 6, was determined from X-ray intensity data and refined up to R 1 = 0.0728 and R 1{FO>4σ(FO)} = 0.0546. The crystal structure of Na(Na,Mn) 7 Mn 22 (PO 4 ) 18 ·0.5H 2 O is similar to the structure of fillowite, Na 6 Ca 3 (Mn,Fe) 21 (PO 4 ) 18. , but a significant difference between the synthetic H 2 O containing compound and fillowite is the replacement of (Na12)O 8 - by Mn(H 2 O) 2 O 5 - polyhedra, which form characteristic six-member rings. The coordination polyhedra around Na12 and Mn12 are so different that simple isomorphous substitution of Na12 by Mn12 is very unlikely, but whole six-member rings either of (Na12)O 8 - or (Mn12)(H 2 O) 2 O 5 polyhedra seem to be distributed statistically over the crystal structure. No indication for ordering, e.g. sheet by sheet, has been observed. Na(Na,Mn) 7 Mn 22 (PO 4 ) 18 ·0.5H 2 O is the first fillowite-like compound for which water is located in the structure from single-crystal study. This result is proved by infrared spectral data and indicates that water can play an essential role in the fillowite structure-type. Structural features of the synthetic compounds Na(Na,Mn) 7 Mn 22 (PO 4 ) 18 ·0.5H 2 O, Na 4 Ca 4 Mg 21 (PO 4 ) 18 and fillowite are compared.

SHORT-RANGE ORDER IN AMPHIBOLES FROM THE BEAR LAKE DIGGINGS, ONTARIO

The crystal structures of four amphiboles from the Bear Lake diggings, in the Bancroft area of Ontario, fluorotremolite, fluororichterite and two samples of potassian fluor-magnesiokatophorite, have been refined to R indices in the range 1.5–2.2% using ~1380 unique reflections measured with Mo K α X-radiation. The crystals used in the collection of the X-ray intensity data were subsequently analyzed by electron and ion microprobes, and formulae were calculated using the Fe3+ and Fe2+ contents established by crystal-structure refinement. Site populations were assigned from the results of site-scattering refinement and stereochemical analysis, taking into account the unit formula determined for each crystal. Difference-Fourier maps through the A (2/ m ) site show that the A ( m ) site is occupied and the A (2) site is vacant in all crystals. Occupancy of the A ( m ) site, and not the A (2) site, by Na imposes strong constraints on the possible patterns of short-range order in these amphiboles. The site populations of the A ( m ), M (4) and O(3) sites are in accord with the local arrangement A ( m )(Na + K)–O(3)F– M (4)Na, with lesser amounts of A ( m )(Na + K)–O(3)OH– M (4)Na and major to minor amounts of A □–O(3)OH– M (4)Ca. The coupling of elements to specific short-range-ordered arrangements in these crystals suggests that the overall chemical variability of amphiboles is strongly constrained by local bond-valence restraints in addition to overall electroneutrality.