Volume 214, Issue 8

Methanoihermus fervidus belongs to the group of hyperthermophilic Archaea. The Archaea comprise organisms that live under environmental extremes, like high temperature, low p H value or high salt concentration. The outer surface of the pseudomurein sacculi of the cells of Methanothermus fervidus is covered by glycoprotein subunits ( S -layer) directly exposed to the extreme environment. The elucidation of the crystal structure of this surface glycoprotein may provide important information on the survival strategies of these unusual micro-organisms. Before our investigations neither three-dimensional crystals have been obtained nor X-ray analyses were performed. Only electron microscopic and computer image enhancement techniques have been applied to obtain structural information from crystalline two-dimensional S -layer sheets. We describe here the successful crystallization of this surface glycoprotein under microgravity conditions.

Crystal structures of highly ordered triclinic kaolinite, cubic hexamethylentetramine and a part of the structure of monoclinic rare sugar were refined by Rietveld method using wavelet compressed sets of intensities. Compression of intensities sets was accomplished by a discrete wavelet transform (DWT). It was found that accuracy of refined positional parameters did not change significantly even if the compression ratio reached 8:1. Similarly, quantitative phase analysis done by Rietveld method provided very close estimates of phase composition for compression ratios 2:1 and 4:1. Application of DWT compressed data led to time savings approaching 50–60% without significant loss of information. This procedure may accelerate molecular modelling based on powder data, or speed up introductory steps of Rietveld refinements with extensive data/parameters sets.

The 4-connected nets derived from packings of non-convex parallelohedra, whose topology was previously described by Ferro and Fortes, with 16, 18, 20 (four cases) and 26 faces are described. A related net formed by a packing of polyhedra with 16 faces is also described.

The one-dimensional Ising model can explain the different stackings of close-packed alloys by attractive ( h 2 c 2 ) or repulsive ( ch ) interactions between metal atoms. A similar analysis explains the ordering in the hexagonal planes. The three-dimensional analysis of ordered hcp and ccp alloys shows the existence of different families of structures and the construction from structural units e.g. to long-range ordered alloys with antiphase boundaries or shearing.

This paper deals with the application of full group theoretical methods to the elucidation of the symmetry and structure of an incommensurate phase. The analysis shows that the full symmetry and structure of the incommensurate phase can be determined unequivocably where certain minimal symmetry data are available. The theory is compared with existing methods used in the study of incommensurate structures, and is applied to the elucidation of the incommensurate structure of melilite. The analysis demonstrates that there are two symmetrically distinct distortions of the Z tetrahedral site in melilite which, when it contains Fe, is responsible for two quite independent MÖssbauer signatures.

The crystal structure of kastningite, a new mineral from Waidhaus, Bavaria, Germany, has been determined. Ideal formula from X-ray structure analysis is Mn(H 2 O) 4 [Al 2 (OH) 2 (H 2 O) 2 (PO 4 ) 2 ] · 2 H 2 O. Lattice parameters are a = 10.205(1) Å, b = 10.504(1) Å, c = 7.010(1) Å, α = 90.38(1)°, β = 110.10(1)°, γ = 71.82(1)° (space group P [unk], Z = 2). Kastningite is isostructural to stewartite Mn(H 2 O) 4 · [Fe 2 3+ (OH) 2 (H 2 O) 2 (PO 4 ) 2 ] · 2H 2 O. Chains of corner sharing octahedra run in the [102] direction. Within the chain, octahedra of composition [Al(OH) 2 (O P ) 2 (H 2 O) 2 ] 3− alternate with others of composition [Al(OH) 2 (O P ) 4 ] 7− (with O P designating oxygen atoms which form part of a phosphate group). The resulting chain composition is [Al(O P ) 3 (OH)(H 2 O)] 4− . Symmetry equivalent chains are bridged by [PO 4 ] 3− tetrahedra and sheets parallel to {010} of composition [Al 2 (OH) 2 (H 2 O) 2 (PO 4 ) 2 ] 2− are formed. [Mn(H 2 O) 4 (O P ) 2 ] 2− octahedra link these sheets in the direction of [010] thus resulting in a three dimensional structure. The structure is further held together by a complex system of hydrogen bonds. Chains of corner-sharing octahedra which are further connected to [PO 4 ] 3− tetrahedra are a common feature within other aquated orthophosphate hydrate minerals. Yet there are differences with respect to the number of symmetrically equivalent octahedra within the chain, their composition as well as to the way they are connected to the tetrahedra. A brief comparison of kastningite to these other minerals is given.

The crystal structures of 4-(hydroxyl-phenyl)-acetonitrile (A) 4-(nitro-phenyl)-acetonitrile (B) and 2-(4-methoxy-phenoxy)-ethanol (C), I-bromomethyl-4-nitro-benzene (D) and I,4-dichloro-2-nitro-benzene (E) have been determined from X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine the structure. The crystals of (A) and (B) are monoclinic, space group P 2 1 / c , Z = 4 with cell parameters a = 6.771 Å, b = 8.568 Å, c = 11.766 Å and β = 93.47° for (A) and a = 8.444 Å, b = 5.942 Å, c = 15.780 Å and β = 100.06° for (B); the crystals of (C) and (D) are orthorhombic, space group Pbcn , Z = 8, a = 38.00 Å, b = 7.158 Å and c = 6.493 Å for (C) and space group P 2 1 2 1 2 1 , Z = 4, a = 6.506 Å, b = 25.49 Å and c = 4.735 Å for (D). The crystals for (E) are triclinic, space group P [unk], Z = 2, a = 7.404 Å, b = 8.273 Å, c = 7.234 Å, α = 109.6°, β = 112.9° and γ = 73.2°. Chemical diagrams of all five compounds are depicted in Fig. 1. Soft constraints have been applied to the molecules during Rietveld refinement. The final R p values obtained were 4.3 (A, Alpha1), 8.8 (A), 5.0 (B), 8.7 (C), 6.6 (D) and 5.7% (E), respectively. Compound (A) was measured both on a Bragg-Brentano Alpha1 diffractometer and on a Guinier camera. The other the structures were only measured with the Guinier camera.

The crystal structure of hexa(phenylthio)-l,3-butadiene, C 40 H 30 S 6 , was studied by X-ray diffraction at 87 K. The space group is monoclinic, Ia , a = 13.947(2) Å, b = 22.254(4) Å, c = 11.610(2) Å, β = 106.54(1)° and Z = 4. Intensity data were collected with Mo K α radiation to (sin θ )/ λ < 0.705 Å −1 . The structure was solved by direct methods. Refinement based on 4920 | F o | converged at R w = 0.032. The central bond of the butadienyl core, 1.472(4) Å, is comparable to the single bond of unconjugated 1,3-butadiene, whereas the two double bonds, 1.353(5) Å and 1.371(5) Å, are longer than expected for a C( sp 2 ) = C( sp 2 ) bond. This may be attributed in part to hybridization changes caused by the S atoms. The large torsion angle over the central bond C1–C2–C3–C4 = −66.8(4)°, reflects the accommodation of this fragment to a highly crowded intramolecular environment. All phenyl rings have intramolecular contacts within van der Waals radii with at least one other ring and one of the butadiene carbon atoms. The sulfur atoms are engaged in an inner loop of short 1, n S···S contacts in the range 3.070(3) Å −3.429(4) Å for n ≥ 3. Averaged deviations from 120° in the ipso , 0.5(1)°, and ortho , −0.5(1)°, positions of the six phenyl rings show that the S atoms serve as electronegative substituents attracting electron density from the rings.

The ordered, low-temperature structures of two globular bicyclic organic compounds have been solved by direct methods and refined at 100 K from powder synchrotron X-ray diffraction data. Bicyclo[3.3.1]nonan-9-one, C 9 H 14 O, space group P 2 1 / n , Z = 4, a = 10.4097(3) Å, b = 11.4187(3) Å, c = 6.4964(2) Å, β = 90.992(1)°, V = 772.1 Å 3 . 3-Azabicyclo[3.2.2]nonane, C 8 H 15 N, space group Aba 2, Z = 8, a = 21.1318(5) Å, b = 11.2357(3) Å, c = 6.0863(1) Å, V = 1445 Å 3 . Both structures display an efficient packing of molecules held together by intermolecular contacts between hydrogens and the oxygen or nitrogen atom, thus preventing the reorientation of the molecules.

The crystal and molecular structures of four compounds of the general formula Hg(S 2 COR) 2 are reported. The colorless crystals of [Hg(S 2 CO n Bu) 2 ] are orthorhombic, space group Pbcn with unit cell dimensions a = 7.418(5) Å, b = 25.66(5) Å, c = 8.61(3) Å, Z = 4 and D x = 2.022Mg m −3 . The colorless crystals of [Hg(S 2 COCH 2 CH 2 C(H)Me 2 ) 2 ] are monoclinic, space group Cc with unit cell dimensions a = 28.72(2) Å, b = 5.828(9) Å, c = 11.41(2) Å, β = 99.7(1)°, Z = 4 and D x = 1.859 Mg m −3 . Crystals of pale-yellow [Hg(S 2 COCH 2 CH 2 CMe 3 ) 2 ] are monoclinic, space group P 2 1 / c with unit cell dimensions a = 30.045(4) Å, b = 5.955(8) Å, c = 11.712(2) Å, β = 97.07(2)°, Z = 4 and D x = 1.773 Mg m −3 . The pale-yellow crystals of [Hg(S 2 CO n Pent) 2 ] are monoclinic, space group Cc with unit cell dimensions a = 27.32(1) Å, b = 5.854(7) Å, c = 11.384(7) Å, β = 95.35(5)°, Z = 4 and D x = 1.931 Mg m −3 . The structures were solved by direct methods and each refined by a full-matrix least-squares procedure to final R = 0.064 using 908 reflections for [Hg(S 2 CO n Bu) 2 ]; to R = 0.054 using 1336 reflections for [Hg(S 2 COCH 2 CH 2 C(H)Me 2 ) 2 ]; to R = 0.041 for 2365 reflections for [Hg(S 2 COCH 2 CH 2 CMe 3 ) 2 ]; and to R = 0.029 for 1094 reflections for [Hg(S 2 CO n Pent) 2 ]. The new structures reported herein feature interconnected 16-membered rings that arise as a result of bidentate bridging xanthate ligands. The overall structure in each case is best described as being comprised of layers separated by hydrophobic interactions. A qualitative model, based on the requirements of crystal packing, is proposed to explain the appearance of the three distinct structural motifs for the Hg(S 2 COR) 2 compounds.

The crystal and molecular structure of [Ba(dnp) 2 (OH 2 ) 5 ], where dnp is 2,4-dinitrophenoxide, has been determined at room temperature. The coordination number of the barium atom is nine with two phenoxide atoms, one nitro oxygen atom and six water molecules providing a O 9 donor set that defines a distorted capped square antiprismatic geometry. The presence of bridging water molecules leads to the formation of dinuclear barium entities that are further linked to each other via hydrogen bonds (involving the water molecules) which in turn results in the construction of two-dimensional networks. Successive layers are linked by the dnp molecules via weak Ba…O interactions (>3.2 Å) as well as hydrogen bonds. Evidence is found for both intra- and inter-molecular base stacking.

In the solid-state structure of K(dioxane) 2 PPh 2 ( 1 ), prepared from potassium and PPh 3 in dioxane, each K ion is surrounded by four bridging dioxane molecules in a plane, and the P atom of the PPh 2 anion occupies an axial position. A π interaction between the K ion and an aryl ring of a PPh 2 anion of a neighbouring plane generates a three-dimensional network. 1 crystallises in the monoclinic space group P 2 1 / n (no. 14), T = 200(2) K, with a = 8.854(1) Å, b = 15.904(2) Å, c = 15.740(2) Å, β = 99.16(1)°, V = 2188.1(5) Å 3 and Z = 4. The refinement converged to R 1 = 0.0372, wR 2 = 0.0949 (for reflections with I > 2 σ ( I )), R 1 = 0.0871, wR 2 = 0.1125 (all data).