Refinement of the twinned structure of cymrite from the Ruby Creek deposit (Alaska)

The mineral cymrite from the Ruby Creek deposit (Alaska) was reinvestigated by X-ray diffraction in a pseudo-orthorhombic unit cell with a = 5.3350(1) Å, b = 36.9258(8) Å, c = 7.6934(1) Å, β = 90.00(1)°. A twin law corresponding to a sixfold axis was revealed for the first time. The structure was refined in the monoclinic space group P12₁1 to the R factor of 5.4%. The Al and Si atoms are assumed to be ordered within a double layer. The rotation of the cation sublattice by 60° around the c axis leads to the disorder of the T sites in the crystal structure (T = Al, Si).     

Crystal structure analysis of two terpene derivatives

The crystal structures of two terpene derivatives, 2,4,5,6,7,7a-hexahydro-7a-hydroxy-3,6-dimethyl-2-benzofuranone (compound I) and β-cyclolavandulic acid (compound II), were determined by single-crystal diffractometry. Compound I, C₁₀H₁₄O₃, crystallizes in the orthorhombic space group P2₁2₁2₁ with the unit cell parameters a = 6.715(1) Å, b = 7.043(1) Å, c = 20.292(3) Å, and Z = 4. The six-membered ring has an ideal chair conformation. The five-membered ring is planar. Compound II, C₁₀H₁₆O₂, crystallizes in the monoclinic space group P2₁/n with the unit cell parameters a = 8.446(1) Å, b = 12.156(1) Å, c = 9.901(1) Å, β = 106.29(1)°, and Z = 4. The cyclohexene ring exhibits a half-chair conformation. Both the crystal structures are stabilized by intermolecular O-H?O hydrogen bonds.     

Crystal structure and microtwinning of monoclinic La<Subscript>3</Subscript>SbZn<Subscript>3</Subscript>Ge<Subscript>2</Subscript>O<Subscript>14</Subscript> crystals of the langasite family

The crystal structure of monoclinic La₃SbZn₃Ge₂O₁₄ crystals from the langasite family is determined by X-ray diffraction analysis [a = 5.202(1) Å, b = 8.312(1) Å, c = 14.394(2) Å, β = 90.02(1)°, sp. gr. A2, Z = 2, and R/R _w = (5.2/4.6)%]. The structure is a derivative of the Ca₃Ga₂Ge₄O₁₄-type structure (a = 8.069 Å, c = 4.967 Å, sp. gr. P321, Z = 1). The crystal studied is a polysynthetic twin with the twin index n = 2, whose monoclinic components are related by pseudomerohedry by a threefold rotation axis of the supergroup P321.     

Stereoselective Synthesis and X-Ray Structure Determination of Labeled [1, 2, 3-<Superscript>13</Superscript>C<Subscript>3</Subscript>]-1-(Phenylsulfinyl)-3-Benzyloxyacetone

[1,2,3-¹³C₃]-1-(Phenylsulfinyl)-3-benzyloxyacetone, C₁₆H₁₆O₃S, (3) has been synthesized and its crystal structure has been determined by a single-crystal X-ray diffraction analysis. The X-ray diffraction study revealed that compound 3 crystallizes in the monoclinic crystal system in the acentric space group Pc, with cell constants at T = 100 K: a = 16.073(5), b = 5.5079(16), c = 7.949(2) Å, β = 100.221(4)^°, V = 692.6(3) ų, Z = 2, d _calc = 1.383 g/cm³. Compound 3 contains the chiral tetravalent three-coordinated sulfur atom, which has a distorted tetrahedral configuration with a lone electron pair occupying one of the tetrahedron vertices. In the crystal, the molecules are packed in stacks along the b axis; the stacks consist of the molecules of the same chirality. Furthermore, the stacks of the molecules of the opposite chirality alternate along the c axis. The molecules in neighboring stacks are arranged by head-to-tail orientations. There are no short intermolecular contacts in the crystal of 3.     

Single-crystal structures of high-pressure phases FeOOH,FeOOD, and GaOOH

The structures of the ?-FeOOH, ?-FeOOD, and β-GaOOH phases, which belong to the InOOH structure type (the distorted TiO₂ structure type), are determined using single-crystal X-ray diffraction analysis. The measurements are performed on Xcalibur CCD and CAD-4F diffractometers. The calculations are carried out in space group P2_1nm with the JANA2000 program. The crystals are twinned and form aggregates related by the rotation around the b axis through an angle close to 62°. In the same crystals, the merohedral twinning is characterized by the rotation around the c axis through an angle of 180°. The alternation of these twin domains in the bulk of the crystal determines the corresponding disordering of the hydrogen positions.     

Recombinant formate dehydrogenase from <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: Preparation,crystal growth in microgravity,and preliminary X-ray diffraction study

Crystals of high-purity recombinant NAD⁺-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul’-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 Å using an X-ray synchrotron source. The crystals belong to sp. gr. P4₃2₁2; the unit-cell parameters are a = b = 107.865 Å, c = 71.180 Å, α = β = γ = 90°.     

X-ray structure analysis of 4-cyano-4′-<Emphasis Type="Italic">n</Emphasis>-undecyloxybiphenyl

The structure of a liquid crystal of 4-cyano-4′-n-undecyloxybiphenyl (C₂₄H₃₁NO) is determined by X-ray diffraction. The compound crystallizes in the monoclinic crystal system (space group C2/c) with the unit cell parameters a = 84.108(7) Å, b = 7.159(2) Å, c = 6.922(2) Å, and β = 91.6(4)°. The structure has been solved by direct methods and refined to the residual index R₁ = 0.067. Both phenyl rings are almost planar, and the dihedral angle between these rings is 31.5(6)°.     

Crystal structure and spectral characteristics of 2,4,7-trinitro-9-fluorenone

The crystal structure of 2,4,7-trinitro-9-fluorenone C₁₃H₅N₃O₇ is determined by X-ray diffraction analysis. The crystals are monoclinic, a = 4.024(1) Å, b = 16.763(3) Å, c = 18.250(4) Å, β = 96.32(3)°, V = 1223.6(5) ų, Z = 4, space group P2₁/c, and R = 0.0640 for 605 reflections with I > 2σ(I). The crystal is built of planar isolated molecules. The compound is characterized using IR and electronic absorption spectroscopy.     

Crystal structures of oxalate-bearing cancrinite with an unusual arrangement of CO<Subscript>3</Subscript> groups and sulfate-rich davyne

The crystal structures of two unusual varieties of cancrinite-group minerals—oxalate-bearing cancrinite from the Kovdor massif (Kola Peninsula) and the sulfate end member of the davyne series from the Sar-e Sang mine (Badakhshan, Afghanistan)—were studied by single-crystal X-ray diffraction. The unit-cell parameters of the hexagonal cells are a = 12.688(4) Å, c = 5.189(1) Å and a = 12.773(1) Å, c = 5.334(1) Å, sp. gr. P6₃; the R factors are 0.034 and 0.035, respectively. The presence of oxalate groups in cancrinite as admixtures is one of the factors responsible for the shift of CO₃ groups in wide channels.     

New data on vlasovite: Refinement of the crystal structure and the radiation damage of the crystal during the x-ray diffraction experiment

The crystal structure of vlasovite obtained from the Kipawa alkaline complex in Quebec is refined to R _F = 0.053 for 1515 unique reflections with |F| > 4σ(F). The parameters of the monoclinic unit are as follows: a = 11.063(8) Å, b = 10.15(1) Å, c = 8.60(1) Å, β = 100.3(1)°, space group C2/c, and Z = 4. The X-ray diffraction, electron microprobe, and IR spectroscopic data indicate that, under X-ray radiation, the specimen suffers radiation damage, which is accompanied by a partial removal of Na atoms, incorporation of H₂O molecules into the structure, and, possibly, a change in the configuration of the (Si,O) framework.     

Synthesis and Crystal Structure of a Four-coordinated Cobalt Complex with 1-Methylbenzimidazole

A four-coordinated complex, L₂Co(NCO)₂, (L = 1-methylbenzimidazole) has been synthesized and characterized by IR spectroscopy, elemental analyses, and single crystal X-ray diffraction. The crystal is monoclinic, a = 14.522(2) Å, b = 14.610(2) Å, c = 8.6850(13) Å, β = 92.037(3)°, Z = 4, sp. gr. P2₁/c. Bond lengths Co–N(L) are equal to 2.0165(16) and 2.0174(15) Å, Co–O(NCO) are 1.944(2) and 1.945(2) Å. Intermolecular C–H···O, C–H···N, and C–H···π interactions link the molecules into three-dimensional networks in the crystal.     

Crystal structure of a new representative of the cancrinite group with a 12-layer stacking sequence of tetrahedral rings

The crystal structure of a 12-layer tounkite-like mineral of the cancrinite group was determined for the first time by single-crystal X-ray diffraction analysis (the unit-cell parameters are a = 12.757 Å, c = 32.211 Å). The structure was refined in the space group P3 to R = 0.035 using 3834 reflections with | F| > 2σ(F). Si and Al atoms occupy tetrahedral framework positions in an ordered fashion. The average distances in the tetrahedra are 〈Si-O〉 = 1.611 Å and 〈Al-O〉 = 1.723 Å. The stacking sequence of the layers is described as CACACBCBCACB, where A, B, and C are six-membered rings arranged around the [2/3 1/3 z], [1/3 2/3 z], and [0 0 z] axes, respectively. In the structure of the mineral, the columns along the [0 0 z] axis are composed of cancrinite cages. The columns along the [2/3 1/3 z] and [1/3 2/3 z] axes contain alternating cancrinite, bystrite, and liottite cages.     

Defect structure of TiS<Subscript>3</Subscript> single crystals of the <Emphasis Type="Italic">A</Emphasis>-ZrSe<Subscript>3</Subscript> type

The defect structure of TiS₃ single crystals of the A-ZrSe₃ type has been determined based on X-ray diffraction data. Shear defects manifest themselves as displacements of ab layers (which can imitate a twin) by ～0.5a. Regular shears facilitate the formation of a superstructure along the c axis. A model of defect in the layer structure is proposed to explain the atomic displacements at an angle to the layer plane.     

Refinement of the crystal structure of rhombohedral KU<Subscript>2</Subscript>(PO<Subscript>4</Subscript>)<Subscript>3</Subscript> as a representative of orthophosphates with the NaZr<Subscript>2</Subscript>(PO<Subscript>4</Subscript>)<Subscript>3</Subscript> structure

The crystal structure of the high-temperature β modification of synthetic orthophosphate KU₂(PO₄)₃ was refined from powder X-ray diffraction data by the Rietveld method: sp. gr. \(R\bar 3c\), the unit-cell parameters a= 9.113(1) Å and c= 24.997(1) Å. The isotropic refinement converged to R _wp = 6.15, R _B = 2.14, R _F = 3.52, and S = 0.42. It was confirmed that β-KU₂(PO₄)₃ belongs to the structure type of sodium zirconium phosphate containing an actinide atom in a sixfold (octahedral) coordination formed by oxygen atoms, which is unusual for orthophosphates. The principal interatomic distances and bond angles in the structure are reported.     

Crystal structure of surkhobite: New mineral from the family of titanosilicate micas

The crystal structure of surkhobite, a new mineral from Tajikistan, was determined by methods of X-ray diffraction analysis (a = 10.723 Å, b = 13.826 Å, c = 20.791 Å, β = 95°, sp. gr. C2, R = 0.047). The structure is a derivative of the bafertisite structure but differs from it and other representatives of the titanosilicate micas: three-layered slabs are connected to form isolated channels orderly filled with Ca, Na, Ba, and K atoms.     

The crystal structure of vyuntspakhite: A redetermination

The crystal structure of the mineral vyuntspakhite (Y, TR)₆{Al₂(OH)₃[H_1.48Si_1.88O₇][SiO₄][SiO₃(OH)]}₂(a = 5.7551(11) Å, b = 14.752(3) Å, c = 15.906(4) Å, β = 96.046(4)°, sp. gr. P2₁/n, Z = 2), which had been established earlier in the pseudo-unit cell, is redetermined by X-ray diffraction (R = 0.040, T = 100 K). The redetermination of the structure shows that pronounced pseudotranslation along the axis c′ = c/3 is associated with the fact that Y(TR) atoms are related by a 1/3 translation along the [001] direction. Most of the hydrogen atoms are located. The crystal-chemical function of hydrogen bonds is analyzed. In the unit cell of vyuntspakhite, the cationic layers consisting of edge-sharing (Y,TR) eight-vertex polyhedra alternate along the b axis with mixed anionic layers composed of isolated Si tetrahedra (orthotetrahedra), Si₂O₇ double-tetrahedra (diortho) groups, Al five-vertex polyhedra, and Al₂O₈ double-tetrahedra groups linked by shared vertices and through hydrogen bonding.     

Synthesis and structural characterization of 2,5-dihalo-3,4-dinitrothiophenes

Using new nitration protocols, we have been able to efficiently dinitrate 2,5-dihalothiophenes with yields of ～80–95%. The resulting products 2,5-dibromo-3,4-dinitrothiophene (1), 2,5-dichloro-3,4-dinitrothiophene (2), 2-bromo-5-chloro-3,4-dinitrothiophene (3), as well as the analogous 2-bromo-3,4-dinitrothiophene (4), all crystallize easily allowing their characterization via X-ray crystallography. Crystallization of 1 occurs in the monoclinic space group C2/c with a = 14.547(3) Å, b = 7.3534(15) Å, c = 10.775(2) Å, β = 128.89(3)°, and Z = 4. Crystallization of 2 occurs in the tetragonal space group I-42d with a = 9.9398(14) Å, b = 9.9398(14) Å, c = 16.866(3) Å, and Z = 8. Crystallization of 3 occurs as a pseudo-merohedral twin in the triclinic space group P-1 with a = 7.340(5) Å, b = 8.094(5) Å, c = 9.112(5) Å, α = 82.059(5)°, β = 66.232(5)°, γ = 63.021(5)°, and Z = 2. Crystallization of 4 occurs in the triclinic space group P-1 with a = 7.1787(14) Å, b = 7.4092(15) Å, c = 8.3151(17) Å, α = 101.67(3)°, β = 96.00(3)°, γ = 116.13(3)°, and Z = 2. The structures of all compounds exhibit the formation of interesting solid-state assemblies due to halogen-bonding interactions between the halogen and nitro groups.     

Synthesis,Crystal Structure,Electrochemical Properties,and Biological Activity of 2-((1H-Benzimidazol-2-yl)methylamino)acetic Acid

A water soluble compound, (2-((1H-benzimidazol-2-yl)methylamino)acetic acid, BIGH, has been synthesized and structurally characterized by elemental analysis, IR and UV spectroscopies, ¹H-NMR, thermogravimetric and differential thermal analyses, and single crystal and powder X-ray diffraction. BIGH can act as a flexible planar ligand with three potential coordination sites. It crystallizes in a monoclinic system with the sp. gr. P2₁/c with the unit cell parameters, a = 9.3764(7) Å, b = 11.5031(8) Å, c = 10.0543(6) Å, and Z = 4. The crystal structure was stabilized through inter-molecular hydrogen bonds. The anti-microbial activity of the compound has been studied against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, and Staphylococcus aureus, which showed a good activity against Bacillus subtilis. Cyclic voltammogram of the compound shows that it is a redox-active molecule.     

X-ray mapping in heterocyclic design: XV. Tricyclic heterocycles based on 2-oxo-2,5,6,7-tetrahydro-1<Emphasis Type="Italic">H</Emphasis>-cyclopenta[<Emphasis Type="Italic">b</Emphasis>]pyridine-3-carbonitrile

The structures of five compounds are studied using single-crystal X-ray diffraction: 2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 15.641(8) Å, b = 9.373(5) Å, c = 7.387(4) Å, β = 92.91(5)°, Z = 4, space group P2₁/c]; 1-[2-(4-chlorophenyl)-2-oxoethyl]-2-oxo-2,5,6,7-tetrahydro-1H-cyclopenta[b]pyridine-3-carbonitrile [a = 4.728(4) Å, b = 28.035(11) Å, c = 11.184(3) Å, Z = 4, space group P2₁2₁2₁]; 2-[2-(4-chlorophenyl)-2-oxoethoxy]-6,7-dihydro-5H-cyclopenta[b]pyridine-3-carbonitrile [a = 10.1202(13) Å, b = 11.2484(18) Å, c = 13.4323(19) Å, β = 102.05(1)°, Z = 4, space group P2₁/c]; 2-(4-chlorophenyl)-3a, 6,7,8-tetrahydrocyclopenta[e][1.3]oxazolo[3.2-a]pyridine-4-carboxamide perchlorate [a = 7.702(2) Å, b = 9.599(3) Å, c = 23.798(5) Å, β = 93.44(2)°, Z = 4, space group P2₁/c]; and (3-amino-6,7-dihydro-5H-cyclopenta[b]furo[3.2-e]pyridin-2-yl)(4-chlorophenyl)methanone [a = 7.3273(2) Å, b = 13.390(3) Å, c = 28.792(8) Å, Z = 8, space group Pbca]. The structures are solved using direct methods and refined by the full-matrix least-squares procedure in the anisotropic approximation to R = 0.0580, 0.0724, 0.0469, 0.0477, and 0.0418, respectively.     

Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from <Emphasis Type="Italic">Thermus Species</Emphasis> 2.9

Ribokinase from a thermophilic strain of Thermus species 2.9 belonging to the carbohydrate ribokinase family (EC 2.7.1.15) was isolated, purified, and crystallized. The crystallization conditions were found by the vapor-diffusion technique and were then optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals, which were grown by the counter-diffusion technique, at the SPring-8 synchrotron radiation facility to 2.87 Å resolution. The crystals belong to sp. gr. P12₁1 and have the following unit-cell parameters: a = 81.613 Å, b = 156.132 Å, c = 87.714 Å, α = γ = 90°, β = 103.819°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the protein by the molecular-replacement method.