Cluster self-organization of <Emphasis Type="Italic">TR</Emphasis>-containing germanate systems: Suprapolyhedral precursors and self-assembly of the crystal structures of the LiNdGeO<Subscript>4</Subscript> and CeGeO<Subscript>4</Subscript> compounds

A combinatorial-topological analysis of the orthogermanates LiNdGeO₄ (space group Pbcn) and CeGeO₄ (space group I 4₁/a, the scheelite structure type), which have MT frameworks composed of polyhedral structural units in the form of M dodecahedra (NdO₈ and CeO₈) and T tetrahedra (GeO₄), is performed using the method of coordination sequences with the TOPOS program package. It is established that the structures of both orthogermanates are characterized by equivalent crystal-forming nets 4444. The cluster precursors of the M ₂ T ₂ cyclic type are identified by the method of two-color decomposition. The local symmetry of four-polyhedral clusters corresponds to the point group 2. In the precursor of the LiNdGeO₄ orthogermanate, the Li atom is located above the M ₂ T ₂ ring. The number of Li-O bonds in this precursor is 4. The cluster precursors M ₂ T ₂ and LiM ₂ T ₂ are responsible for the formation of crystal-forming clusters of a higher level according to the mechanism of matrix self-assembly. The coordination numbers of the cluster precursors in two-dimensional nets for these structures are found to be equal to 4. The equivalent bilayer TR,Ge stacks that consist of eight cluster precursors are revealed in the structures under investigation. It is demonstrated that there exist three types of translational interlayer arrangements of cluster precursors upon the formation of macrostructures of the orthogermanates.     

Structure of Triammonium <Emphasis Type="Italic">fac</Emphasis>-Trichloridotrioxidorhenate(VII) Chloride with <Emphasis Type="Italic">C</Emphasis><Subscript>3<Emphasis Type="Italic">v</Emphasis></Subscript> Crystallographic Symmetry of the Complex Anion

Abstract  

The unstable crystals of triammonium fac-trichloridotrioxidorhenate(VII) chloride have been obtained from ammonium rhenate(VII) solution in concentrated hydrochloric acid. The crystal structure consists of fac-trichloridotrioxidorhenate(VII) anions, chloride anions and ammonium cations. Each fac-trichloridotrioxidorhenate(VII) anion and each chloride anion lies in special position of 3m site symmetry (cell parameters: a = 9.026(3) Å; c = 7.690(4) Å; space group: P6₃ mc). The ammonium cation lies in special position of m site symmetry. The following anion geometrical parameters of the fac-trichloridotrioxidorhenate(VII) anion have been obtained: Re–O bond length of 1.720(2) Å, Re–Cl bond length of 2.5428(9) Å, the bond angles: O–Re–O of 103.5(1)° and Cl–Re–Cl of 79.8(1)°.     

Lead (II) selenite halides Pb<Subscript>3</Subscript>(SeO<Subscript>3</Subscript>)<Subscript>2</Subscript><Emphasis Type="Italic">X</Emphasis><Subscript>2</Subscript> (<Emphasis Type="Italic">X</Emphasis> = Br,I): Synthesis and crystal structure

Two lead selenite halides, Pb₃(SeO₃)₂Br₂ and Pb₃(SeO₃)₂I₂, have been prepared by solid-phase synthesis and structurally characterized. These compounds are isotypic and can be considered 3D with a microporous framework composed of lead polyhedra (distorted Archimedean antiprisms formed by oxygen and halogen atoms). The framework contains channels oriented in the [010] direction. These channels contain selenium atoms, which are bound with framework oxygen atoms belonging to different lead polyhedra.     

Structure of octaheme cytochrome <Emphasis Type="Italic">c</Emphasis> nitrite reductase from <Emphasis Type="Italic">Thioalkalivibrio nitratireducens</Emphasis> in a complex with phosphate

Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of the oxidized complex of TvNiR with phosphate and of this complex reduced by europium(II) chloride (1.8- and 2.0-Å resolution, the R factors are 15.9 and 16.7%, respectively) and the structure of the enzyme in the complex with cyanide (1.76-Å resolution, the R factor is 16.5%), which was prepared by soaking a crystal of the oxidized phosphate complex of TvNiR. In the active site of the enzyme, the phosphate ion binds to the iron ion of the catalytic heme and to the side chains of the catalytic residues Arg131, Tyr303, and His361. The cyanide ion is coordinated to the heme-iron ion and is hydrogen bonded to the residue His361. In the structure of reduced TvNiR, the phosphate ion is bound in the same manner as in the structure of oxidized TvNiR, and the nine_coordinated europium ion is located on the surface of one of the crystallographically independent monomers of the enzyme.     

Synthesis,redox properties,and X-ray diffraction structure of 2,3-<Emphasis Type="Italic">bis</Emphasis>(ethylthio)-<Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">p</Emphasis>-MeOC<Subscript>6</Subscript>H<Subscript>4</Subscript>)maleimide

Refluxing 2,3-dichloromaleic anhydride with p-anisidine in benzene with water removal gives the condensation product 2,3-dichloro-N-(p-MeOC₆H₄)maleimide (1) 75% yield. This new maleimide compound reacts with added ethanethiol in the presence of Et₃N or DBU to furnish the bidentate sulfide ligand 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) in 85% yield. Each product has been characterized in solution by IR, NMR, and UV-vis spectroscopies, and the solid-state structure of 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide was unequivocally established by single-crystal X-ray diffraction analysis. 2,3-bis(Ethylthio)-N-(p-MeOC₆H₄)maleimide crystallizes in the monoclinic space group C2/c, a = 20.035(3)Å, b = 9.188(1)Å, c = 16.887(2)Å, = 93.696(2)°, V = 3102.3(8)ų, Z = 8, and D_calcd = 1.385 mg/m³; R = 0.0268, R_w = 0.0676 for 2025 reflections with I > 2 (I). The nature of the LUMO in 2,3-bis(ethylthio)-N-(p-MeOC₆H₄)maleimide (2) has been determined by extended Hückel molecular orbital calculations, and these data are discussed relative to the cyclic voltammetry results and other structurally relevant compounds prepared in our labs.     

Crystal structure of <Emphasis Type="Italic">L</Emphasis>-alanine phosphate

The crystal structure of L-alanine phosphate (C₃O₂NH₇ · H₃PO₄) is determined by the single-crystal diffraction technique; a = 11.918(1) Å, b = 9.117(1) Å, c = 7.285(1) Å, γ = 104.7(1)°, space group P2₁, and Z = 4. The amino group of the alanine is protonated by the hydrogen atom of the phosphoric acid. Pairs of H₂PO ₄ ^? hydrogen-bonded ions are packed into layers alternating with layers of alanine molecules in the crystal. No hydrogen bonds are formed immediately between the alanine molecules.     

Synthesis and structure of 7-methyl-5-phenyl-1<Emphasis Type="Italic">H</Emphasis>-pyrazolo[4,3-<Emphasis Type="Italic">e</Emphasis>]tetrazolo[4,5-<Emphasis Type="Italic">b</Emphasis>][1,2,4]triazine<Superscript>(1)</Superscript>

The synthesis of 5-azido-3-methyl-1-phenyl-1H-pyrazolo[4,3-e][1,2,4]triazine 2 and 7-methyl-5-phenyl-1H-pyrazolo[4,3-e]tetrazolo[4,5-b][1,2,4]triazine 3 is described and the crystal and molecular structure of the latter is reported. This compound crystallizes in the monoclinic system, space group P2₁/n, with cell constants a = 11.607(2) Å, b = 7.982(1) Å, c = 13.147(2) Å, = 110.60(1), Z = 4, T = 293 K and D_cal = 1.470 g cm^–3. The structure was solved by direct methods and refined to R value of 0.0368 for 1906 reflections. The X-ray analysis revealed that the linear form of the tetrazolo-fused ring system of 3 exists in the crystal. The molecule as a whole has an almost planar conformation stabilized by the short intramolecular NsH interaction. The molecular packing in the crystal is determined by the van der Waals forces only.Part 26 in 1,2,4-triazines in organic synthesis. For part 25 see Mojzych et al.¹     

Structure of 6,13-bis(<Emphasis Type="Italic">N</Emphasis>, <Emphasis Type="Italic">N</Emphasis>-dimethylcarbamoyl) thioquinanthrene

The crystal structure of 6,13-bis-(N,N-dimethylcarbamoyl)thioquinanthrene 3 has been determined as monoclinic, with space group P2(1)/c with lattice parameters a = 10.044(2) Å, b = 21.385(4) Å, c = 10.889(3) Å, = 102.92(3)°, Z = 4 and D_calc = 1.342 Mg/m³. The middle 1,4-dithiin ring in the title compound 3, C₂₄H₂₀N₄O₂S₂ is in a boat conformation with the dihedral angle between the planes of the aromatic rings 132.45(8)°.     

Crystal Structure of [Zn(2-Bromobenzoato)<Subscript>2</Subscript>]<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> and [Zn(2-Bromobenzoato)<Subscript>2</Subscript>(<Emphasis Type="Italic">N</Emphasis>-Methylnicotinamide)]<Subscript>2</Subscript>

Abstract  

The syntheses and structural characterizations of two novel 2-bromobenzoatozinc(II) complexes—[Zn(2-BrC₆H₄COO)₂] _n (I) and [Zn(2-BrC₆H₄COO)₂(mnad)]₂ (II), where mnad is N-methylnicotinamide are reported. Compound (I) crystallized with a monoclinic lattice (space group P2₁/c) and is polymeric in solid state. Its cell parameters are: a = 7.37220(10) Å, b = 19.9639(3) Å, c = 30.2756(5) Å, β = 94.7510(7)°, V = 4440.59(12) ų, Z = 4. The coordination environments of all zinc atoms are distorted tetrahedra built from four carboxylate oxygen atoms coming from four 2-bromobenzoato ligands. Compound (II) crystallized with a monoclinic lattice (space group P2₁/c) with a = 11.7488(2) Å, b = 20.3683(3) Å, c = 9.30130(10) Å, β = 100.3941(11)°, V = 2189.30(5) ų, Z = 2. This dimeric molecule features a paddle-wheel [Zn₂O₈] cage in solid state; the coordination environment of the central atom is square pyramidal consisting of four carboxylate oxygen atoms and the pyridine N atom of the mnad ligand.     

Synthesis and investigation of the new phosphates K<Subscript>2</Subscript><Emphasis Type="Italic">Ln</Emphasis>Zr(PO<Subscript>4</Subscript>)<Subscript>3</Subscript> (<Emphasis Type="Italic">Ln</Emphasis> = Ce-Yb,Y) with langbeinite Structure

New orthophosphates of potassium, zirconium, and rare earth elements K₂LnZr(PO₄)₃ (Ln = Ce-Yb, Y) that crystallize in a langbeinite structure (cubic system, sp. gr. P2₁3, Z = 4) were prepared and investigated by X-ray diffraction and IR spectroscopy. The structure of the K₂PrZr(PO₄)₃ phosphate was refined by the Rietveld method using neutron powder diffraction data (DN-2 time-of-flight diffractometer, Joint Institute for Nuclear Research, Dubna). This structure is characterized by a mixed framework [PrZr(PO₄)₃] with large cavities in which potassium cations are located. Pr³⁺ and Zr⁴⁺ cations are distributed in order over two independent crystallographic positions. The limits of the incorporation of lanthanide cations into the anionic framework in phosphates with sodium-zirconium phosphate and langbeinite structures are considered.     

A New <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethyl Purine from an Australian <Emphasis Type="Italic">Dictyoceratid Sponge</Emphasis>

Abstract  

N6-methyl mucronatine (C₈H₁₂N₅O) has been isolated from a dictyoceratid sponge collected in South East Queensland. The solid state structure of the new metabolite (I) was confirmed by X-ray crystallography, while an NMR study in d ₄-MeOH reveals the presence of a minor tautomer identified as (II).     

Structure and magnetic properties of a dinuclear complex [Cu<Subscript>2</Subscript>(TPA)<Subscript>2</Subscript>(<Emphasis Type="Italic">o-</Emphasis>phth)](ClO<Subscript>4</Subscript>)<Subscript>2</Subscript>

A new dinuclear complex, [Cu₂(TPA)₂(o-phth)](ClO₄)₂ (TPA = tris(2-pyridylmethyl) amine, o-phth = terephthalato dianion), was synthesized and characterized by X-ray crystallography. The unit of dinuclear Cu(II) was bridged by terephthalato dianion. The complex crystallizes in triclinic space group P1, with a = 8.287(3) Å, b = 10.623(4) Å, c = 13.818(5) Å; α = 92.077(7)^∘, β = 94.768(7)^∘, γ = 90.352(6)^∘; V = 1211.4(8) ų; Z = 2; R₁ = 0.0604, wR₂ = 0.1707. In the temperature range 4–300 K, magnetic measurement shows that the exchange interaction of the two metal ions is weak ferromagnetic with J = 1.20 cm⁻¹, g = 1.97.     

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.     

Synthesis and crystal chemical characteristics of the structure of <Emphasis Type="Italic">M</Emphasis><Subscript>0.5</Subscript>Zr<Subscript>2</Subscript>(PO<Subscript>4</Subscript>)<Subscript>3</Subscript> phosphates

Double phosphates of zirconium and metals with an oxidation degree of +2 of the composition M_0.5Zr₂(PO₄)₃ (M = Mg, Ca, Mn, Co, Ni, Cu, Zn, Sr, Cd, and Ba) are synthesized and characterized by X-ray diffraction methods and IR spectroscopy. The crystal structures of all the compounds are based on three-dimensional frameworks of corner-sharing PO₄-tetrahedra and ZrO₆-octahedra. Phosphates with large Cd²⁺, Ca²⁺, Sr²⁺, and Ba²⁺ cations octahedrally coordinated with oxygen atoms form rhombohedral structures (space group R3), whereas phosphates with small tetrahedrally coordinated Mg²⁺, Ni²⁺, Cu²⁺, Co²⁺, Zn ²⁺, and Mn²⁺-cations are monoclinic (space group P2₁/n). The effect of various structure-forming factors on the M_0.5Zr₂(PO₄)₃ compounds with a common structural motif but different symmetries are discussed.     

Synthesis and structure of oxovanadium(IV) complexes [VO(<Emphasis Type="Italic">Acac</Emphasis>)<Subscript>2</Subscript>] and [VO(<Emphasis Type="Italic">Sal</Emphasis>: <Emphasis Type="Italic">L</Emphasis>-alanine)(H<Subscript>2</Subscript>O)]

Bis(acetylacetonato)oxovanadium C₁₀H₁₄O₅V (I) and (S)-[2-(N-salicylidene)aminopropionate]oxovanadium monohydrate C₁₀H₉NO₅V (II) are synthesized. The crystal structures of compounds I and II are determined using single-crystal X-ray diffraction. Crystals of compound I are triclinic, a = 7.4997(19) Å, b = 8.2015(15) Å, c = 11.339(3) Å, α = 91.37(2)°, β = 110.36(2)°, γ = 113.33(2)°, Z = 2, and space group \(P\bar 1\). Crystals of compound II are monoclinic, a = 8.5106(16) Å, b = 7.373(2) Å, c = 9.1941(16) Å, β = 101.88(1)°, Z = 2, and space group P2₁. The structures of compounds I and II are solved by direct methods and refined to R₁ = 0.0382 and 0.0386, respectively. The oxovanadium complexes synthesized are investigated by vibrational spectroscopy.     

Structural Features of <Emphasis Type="Italic">Ortho</Emphasis>-hydroxy Bis-phenols and Their Comparison with <Emphasis Type="Italic">Para</Emphasis>-hydroxy Bis-phenols

Abstract The crystal structures of four bis-phenols are reported to substantiate the fact that the weak interactions play a major role in the crystal packing of bis-phenols. The reaction of 2,4-dimethylphenol with aldehydes such as 2-naphthaldehyde, terephthaldehyde in the presence of trifluoracetic acid gave 2-[bis(2-hydroxy 3,5-dimethylphenyl)methyl]naphthalene (1) and 4-[bis(2-hydroxy 3,5-dimethylphenyl) methyl]benzaldehyde (2), respectively. The 2-[bis-(2-hydroxy 3,5-dimethylphenyl)-methyl]naphthalene (1) crystallizes in orthorhombic, Pbca, a = 11.905(3) ?, b = 18.788(5) ?, c = 18.894(5) ?, 4-[bis(2-hydroxy 3,5-dimethylphenyl)methyl] benzaldehyde (2) in monoclinic, Cc, a = 8.880(3) ?, b = 16.394(7) ?, c = 13.700(5) ?, γ = 104.542(2)°. The reaction of 2-nitrobenzaldehyde with 2,4-dimethylphenol gave 2-benzo[c] isoxazo-3-yl 4,6-dimethylphenol (3) and its crystal parameters are orthorhombic, P2₁2₁2₁, a = 7.737(6) ?, b = 11.885(9) ?, c = 13.336(8) ?. The reaction of 2,6-dimethylphenol with 4-nitrobenzaldehyde and 2-chlorobenzaldehyde gave bis(4-hydroxy 3,5-dimethylphenyl)(4-nitrophenyl)methane (4) and bis(4-hydroxy 3,5-dimethylphenyl)(2-chlorophenyl)methane (5), respectively. The bis(4-hydroxy 3,5dimethylphenyl)(4-nitrophenyl)methane (4) crystallizes in monoclinic, C2/c, a = 25.921(1) ?, b = 12.202(4) ?, c = 15.6084(7) ?, β = 122.172(4)°, and bis(4-hydroxy 3,5-dimethylphenyl) (2-chlorophenyl)methane crystallizes as acetonitrile solvate (5) in triclinic, P-1, a = 12.314(3) ?, b = 14.111(3) ?, c = 15.078(5) ?, α = 98.268(2)°, β = 111.268(2)°, γ = 114.304(1)˚. The unit cell of 5 contains two pairs of crystallographically unsymmetric molecules of bis-phenols. Index abstract The crystal structures of four bis-phenols are reported to substantiate the fact that the weak interactions plays a major role in crystal packing and can induce symmetry non-equivalence among bis-phenols in unit cell of bis-phenols.      

Crystal Structure and Conformational Analysis of 4-[(<Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-Dimethylamino)Benzylidene]-2-Phenyloxazole-5-One

Abstract  

Molecular and crystal structure of 4-[(p-N,N-dimethylamino)benzylidene]-2-phenyloxazol-5-one, C₁₈H₁₆N₂O₂, have been determined by single crystal X-ray diffraction study. The title compound is monoclinic, with a = 12.1704(23) ?, b = 3.9810(5) ?, c = 30.9603(56) ?, β = 101.176(15)°, Z = 4, D _x = 1.32 g/cm³, μ(Mo Kα) = 0.087 mm⁻¹, and space group is P12₁/c1. The structure was solved by direct methods and refined to a final R = 0.047 for 3166 reflections with I > 2σ(I). The crystal structure is stabilized by C–H⋯O and C–H⋯N type intra-molecular, C–H⋯O type inter-molecular interactions. To enlighten the flexibility and the geometric isomerism (E or Z) of the title compound, the selected torsion angle is varied from −180 to 180° in every 10° separately and molecular energy profile is calculated and analyzed.     

Phase equilibria of <Emphasis Type="Italic">A</Emphasis><Superscript>3</Superscript><Emphasis Type="Italic">B</Emphasis><Superscript>5</Superscript> quinary systems with an elastically strained solid phase

The contribution of the elastic component of the excess energy of mixing is determined for A³B⁵ quinary solid solutions. A relationship is derived for the activities of the components in an elastically strained solid phase of the quinary solid solutions. The correctness of the possible assumptions used in the calculation of the activity coefficients of the solid phase of a quinary solution is analyzed. The contact supercooling in the vicinity of the binary substrate isoperiods is calculated for a number of A³B⁵ quinary systems. It is shown that the negative contact supercoolings correspond to the thermodynamic instability boundaries of the quinary solid solutions.     

Synthesis and structure of fullerene halides C<Subscript>70</Subscript><Emphasis Type="Italic">X</Emphasis><Subscript>10</Subscript> (<Emphasis Type="Italic">X</Emphasis> = Br,Cl) and C<Subscript>78</Subscript>Cl<Subscript>18</Subscript>

The crystal and molecular structures of the fullerene halides C₇₀Br₁₀ · 3C₆H₂Cl₄, C₇₀Cl_8.4Br_1.6, and C₇₈Cl₁₈ have been determined and refined using single-crystal X-ray diffraction with synchrotron radiation. In the molecular structure of C₇₀ X ₁₀ (X = Br, Cl), ten X halogen atoms are located in the equatorial region of the molecule and form one 1,2 and nine 1,4 contacts in C₆ X ₂ hexagons. The structure of the higher fullerene chloride C₇₈Cl₁₈ contains two isomers with symmetry C _2v , which results in the hexagonal symmetry of the crystal due to disordering.     

Internal deformations in substitutional quaternary solid solution <Emphasis Type="Italic">A</Emphasis><Superscript>3</Superscript><Emphasis Type="Italic">B</Emphasis><Superscript>5</Superscript>

A model that describes the bond-length distributions in quaternary A³B⁵ solid solutions and allows one to consider large clusters using a minimum of computational resources is suggested. The analytical expression for the radial-distribution function is obtained. The results of the modeling describe the known experimental data well. For a number of solid solutions, the deformation energy is evaluated in the approximation of the valent force field. It is shown that the main contribution to the energy comes from the bond-length dispersion.