Volume 213, Issue 7-8

The density of proteins is an important quantity. For ab initio phasing in X-ray crystallography, such as low resolution envelope techniques [1, 2], an accurate protein density is essential to get a correct prediction of the protein volume from the amino acid sequence. An accurate value will also facilitate the determination of the number of protein subunits in the unit cell. There has long been a general consensus that the mean density of a protein is 1.35 g/cm 3 [3], but this value should be revised. The present study, based on X-ray crystallographic coordinates of 28 different proteins, shows that the mean density of proteins is 1.22 ± 0.02 g/cm 3 . The protein density was calculated using the Voronoi construction with over 80% of the total number of atoms in the protein molecules taken into account.

The 4-connected net derived by placing vertices in the tetrahedral holes of the β -Sn structure is described in its maximum volume conformation with equal edge lengths. The vertices correspond to the vertices of a space filling packing of simple polyhedra with 18 faces (32 vertices). The net is less dense than that of the least dense of known zeolites.

The new quaternary compounds KBi 6 O 9 X (X = Cl, Br, I) were synthesized with yields of about 90% by reaction of BiX 3 with >10 N KOH (X = Br, I) and by reaction of a H[BiCl 4 ] solution with solid KOH. Single crystals of the three compounds were grown by addition of diluted H[BiX 4 ] solutions to >10 N KOH. The crystal structures were solved and refined to R 1 = 0.0214, 0.0199, and 0.0205, respectively. The three compounds are isotypic; they crystallize with space group Ia [unk] d and Z = 16. K, Bi, X positions correspond to a distorted bcc lattice. The (K, X) substructure consists of arrays of non-intersecting linear “chains” parallel to 〈111〉.

The intermetallic compound Cu 9.1(1) TeSb 3 prepared at 973 K is an ordered member of the solid solution Cu 64 Te 31 Sb 5 –Cu 70 Te 8 Sb 22 which also exists, for more limited composition ranges, between 673 K and 1173 K. It is a stuffed derivative of the structure type A15 (Cr 3 Si). Te is surrounded by twelve 3/4-occupied Cu-positions in the vertices of a cubically-deformed icosahedron (Cu – Te = 2.614 Å) which itself is nested in an Sb-icosahedron (Cu–Sb = 2.777 Å (×2) and 2.603 Å). The Sb array corresponds to the Cr array in Cr 3 Si.

The title compound was prepared by heating an aqueous solution of sodiumhydroxide, zincchloride and arsenic acid at 350 K until a dry crystalline residue remained. The crystal structure of NaZnAsO 4 · 2H 2 O was determined from single crystal diffractometer data: P [unk], a = 561.08(3) pm, b = 608.75(4) pm, c = 795.15(5) pm, α = 86.64(1)°, β = 88.74(1)°, γ = 89.19(1)°, V = 0.2710 nm 3 , Z = 2, R = 0.042, wR 2 = 0.097 for 2650 structure factors and 99 variable parameters. The structure is built up from two-dimensional-infinite layers formed by ZnO 4 - and AsO 4 -tetrahedra which are separated by water molecules and sodium cations. Magnetic susceptibility measurements are compatible with diamagnetism with a susceptibility of χ mol = −0.929 · 10 −9 m 3 /mol. Infrared spectroscopy measurements indicate the existence of two crystallographic different water molecules in the structure. The thermogravimetric analysis and differential scanning calometry show a total loss of 13.4(1)wt-% water up to 1000 K (theoretical 13.7 wt-% in total) in five steps where the first four occur in the temperature range of 360 K – 430 K followed by a fifth step up to 450 K. Temperature depending X-ray powder diffractometer investigations confirm this behaviour which resulted in the formation of the structure of NaZnAsO 4 (I).

The crystal structure of the monoclinic low tridymite MC, a polymorph of SiO 2 , has been re-refined using the unpublished as-measured intensities of a twinned crystal collected by Kato and Nukui [Acta Crystallogr. B 32 (1976) 2486–2491]. Crystal data: space group Cc , a = 18.494(8) Å, b = 4.991(2) Å, c = 25.832(8) Å, β = 117.75(2)°, Z = 48. R = 0.071, R w = 0.071 based on 6453 F o 's for 325 variable parameters. The Si–O distances are between 1.575(6) Å and 1.620(7) Å; mean 1.598 Å. Except for an extreme value of 178.8(6)°, the Si–O–Si angles range from 142.9(4)° to 156.3(6)°; mean 148.6°. The structure was refined also as a commensurate modulated structure based on the high-tridymite structure.

The title compound has been considered to be isotypic with Ag 0.68 V 2 O 5 , a typical δ vanadium bronze crystallizing in space group C 2/ m . Through hydrothermal synthesis, however, crystals were obtained showing superlattice reflections. Triclinic, C [unk] (No. 2), a = 23.536(2) Å, b = 7.3985(3) Å, c = 8.801(1) Å, a = 90°, β = 88.28(1)°, γ = 90°, Z = 16. The structure was determined based on 2160 reflections of a specimen twinned about [010] | (010); R ( F ) = 0.032, R w ( F ) = 0.024. Twinning about [100] or (001) was also observed. The structure includes V 2 O 5 layers with Sr atoms sandwiched between them. The perfectly ordered arrangement of the Sr atoms leads to the superstructure. The V(V) and V(IV) positions can be distinguished. The structure has an idealized symmetry of a Brandt groupoid C 2/ m { t (1/4, 3/4, 0)}. An interpretation as OD structure is given to explain the mechanism of twinning.

The series of cuprates [M 2 CU 2 O 3 ] m [CuO 2 ] n (where M are alkaline earth or trivalent metals) consisting of two sublattices was studied. The first members [M 2 Cu 2 O 3 ][Cu 1+ δ O 2+ γ ] of the series were synthesized. The structural investigations of the obtained single crystals have shown that the latter structure can be interpreted as the commensurate version of two fragments due to the reconstruction of the Cu–O ribbons. Depending on the chemical composition, the crystals studied were either superconducting ( T c = 85 K) or non-superconducting.

The structures of three polymorphic forms of 4-hydroxy-3-methoxy-4′-nitro-trans-stilbene (HMONS; C 15 H 13 NO 4 , M r = 271.27) are reported. Crystal growth experiments of HMONS from different solvents and varying conditions showed the existence of three crystalline phases, red crystals with symmetry of the orthorhombic space group Pbca , with a = 7.811(2) Å, b = 13.410(4) Å, c = 24.597(5) Å ( 1 ), yellow crystals belonging to the monoclinic space group C 2/ c with lattice parameters a = 18.788(2) Å, b = 6.6945(5) Å, c = 21.013(2) Å, β = 90.761(6)° ( 2 ), and yellowish-orange crystals with space group symmetry P 2 1 , and a = 6.9302(12) Å, b = 13.493(4) Å, c = 7.247(2) Å, β = 102.08(2)° ( 3 ). The latter exhibits a powder second harmonic generation (SHG) efficiency 70 times as large as that of urea.

The title compound crystallizes in the monoclinic system with the space group P 2 1 / n (No. 14). Crystal data: a = 9.794(3) Å, b = 8.765(2) Å, c = 15.280(3) Å, β = 98.38(2)°, V = 1298(4) Å 3 , Z = 4, d calc = 1.89 g · cm −3 . The structure was solved from 1689 reflections with ( F o ) 2 > 2 σ ( F o ) 2 . The refinement converged to final indexes R and R w , respectively equal to 0.0289 and 0.0309. The compound has a layered structure. The asymmetric unit contains a binuclear complex built up from two zinc atoms linked together through one acetate and one ethane-1,2-olato(−1) ions. The bidimensional character results from the linking of the dimeric complexes through acetate groups. Each complex is bonded to four other ones in a plane parallel to (001). Cohesion between nets is week since it is allowed by van der Waals forces only.

C 11 H 10 N 2 O 2 crystallizes triclinically, space group P [unk], Z = 2; a = 8.261(1) Å, b = 8.478(1) Å, c = 8.470(1) Å, α = 72.49(1)°, β = 89.58(1)°, γ = 67.56(1)°, R = 0.068 for 549 observed reflections [ I ≥ 2 σ ( I )]. The molecule of the title compound is nearly planar. The dihedral angle between the weighted least-squares plane through the non-H atoms of the pyridine ring (maximum deviation from planarity 0.012(2) Å) and the weighted least squares plane through the remaining non-H atoms of the molecule (maximum deviation from planarity 0.027(2) Å) is 3.91(5)°.

Bis[aquadibutyl(4-hydroxy-2,6-pyridinedicarboxylato)tin] · 2[bis(dicyclohexylammonium) 2,6-pyridinedicarboxylate] crystallizes with the seven-coordinate tin atom in a trans -C 2 SnNO 4 pentagonal bipyramidal [C–Sn–C 164.5(2)°] coordination environment. The tin atom is O , N , O -chelated by the 4-hydroxy-2,6-pyridinedicarboxylato dianion, and is datively bonded to a carboxyl oxygen end of the other half of the centrosymmetric bis[aquadibutyl(4-hydroxy-2,6-pyridinedicarboxylato)tin] moiety. The neutral moiety is hydrogen bonded to two bis(dicyclohexylammonium) 2,6-pyridinedicarboxylate ionpairs, and adjacent bis[aquadibutyl(4-hydroxy-2,6-pyridinedicarboxylato)tin] · 2[bis(dicyclohexylammonium) 2,6-pyridinedicarboxylate] entities are linked by a short hydrogen bond [O hydmxyi … O carbonyl 2.474(5) Å] to form a ribbon running parallel to the a -axis. Dibutyl(4-hydroxy-2,6-pyridinedicarboxylato)tin is also O , N , O -chelated; the trans -C 2 SnNO 4 pentagonal bipyramidal [C–Sn–C 152.0(1)°] coordination arises from O , O -bridging by the carboxyl –CO 2 fragment of a neighboring molecule, the carboxylate bridge [Sn–O 2.733(2) Å, 2.983(2) Å] resulting in a three-dimensional network structure for the compound. The geometry is distorted towards a hexagonal bipyramid owing to a weak intermolecular [Sn … O 3.652(1) Å] contact.

Dibutytlin oxide condenses with diisopropylammonium hydrogen 2,6-pyridinedicarboxylate to form bis(diisopropylammonium) tris(2,6-pyridinedicarboxylato)bis(dibutylstannate) trihydrate, whose crystal structure consists of a three-dimensional hydrogen-bonded framework of ammonium cations, stannate anions and water molecules. In the dianion, the carboxyl –CO 2 groups of the central 2,6-pyridinedicarboxylato member are each chelating an O , N , O -dibutyl(2,6-pyridinedicarboxylato)tin molecule flanking it; one molecule has its C 2 Sn skeleton in an almost linear alignment [C–Sn–C 173.8(6)°; Sn–O 2.423(8) Å, 2.457(9) Å] whereas the other has a bent C 2 Sn skeleton [C–Sn–C 158.0(7)°] arising from anisobidentate chelation [Sn–0 2.303(7) Å, 2.785(8) Å]. Their tin atoms are seven-coordinate in trans -C 2 SnNO 4 pentagonal bipyramidal geometries. Dibutyltin oxide reacts with diisopropylammonium hydrogen 4-hydroxy-2,6-pyridinedicarboxylate to yield centrosymmetric bis(diisopropylammonium) bis[aquadibutylstanny(2,6-pyridinedicarboxylato-4-olate)]. The water-coordinated tin atom [Sn–O water 2.409(3) Å] in the bis[aquadibutylstanny(2,6-pyridinedicarboxylato-4-olate)] dianion, whose negative charges reside on the 4-substituent oxygen atoms, is also seven coordinate [C–Sn–C C 159.6(2)°]. The dianions are linked to adjacent dianions through the diisopropylammonium counterions [N … O esteryl 2.954(4) Å, N … O hydroxyl 2.719(5) Å)] to result in a one-dimensional hydrogenbonded chain structure.

The structure of the ripple phase in hydrated lecithin (DMPC) was determined by direct methods using data collected in an earlier synchrotron X-ray study. When the Sayre-Hughes equation or maximum entropy and like-lihood were used to determine phases of a basis set, recognizable features of the bilayer profile could be identified. The subsequent refinement, based on permutation of successive phase clusters, allowed a correct structural model to be visualized directly, by imposing the continuity of the directly-identified bilayer as a basis of accepting new phase terms.

The crystal and molecular structure of cis -bis(monothiodibenzoylmethanato)dioxomolybdenum(VI), [MoO 2 (SC(Ph)CHC(Ph)O) 2 ], C 30 H 22 MoO 4 S 2 , has been determined at room temperature. The orange crystals are monoclinic, space group P 2 1 / n with unit cell dimensions a = 11.573(2) Å, b = 12.073(8) Å, c = 18.958(2) Å, β = 104.05(1)°, Z = 4 and D x = 1.568 Mg m −3 . The structure was refined by a full-matrix least-squares procedure on F to final R = 0.045 using 2968 reflections with I ≥ 3.0 σ ( I ). The Mo atom exists in a distorted octahedral geometry defined by a O 4 S 2 donor set which features a cis -Mo(=O) 2 and a trans -MoS 2 arrangement. The coordination geometry is compared with related species.