Intensities of circular dichroism and absorption bands and the states of <Emphasis Type="Italic">d</Emphasis> ions in absorbing media: II. Tetrahedrally coordinated positions of <Emphasis Type="Italic">d</Emphasis> ions

The factors affecting the band intensity in the circular dichroism (CD) and absorption spectra of tetrahedrally coordinated d ions in an absorbing medium (symmetry selection rules, structural position, and bond covalence) are analyzed. It is shown by the examples of the Cr⁴⁺ ion in Ca₃Ga₂Ge₄O₁₄ crystal and the Fe²⁺ and Fe³⁺ ions in SiO₄ crystal that the symmetry forbiddenness of the transitions from orbitally degenerate states and the covalence of the d-ion-ligand bond lead to changes in the intensity of the corresponding CD bands in a wide range, beginning from zero. It is shown by the example of Ca₃Ga₂Ge₄O₁₄, LiAlGeO₄, LiGaGeO₄, and LiGaSiO₄ crystals activated with Cr⁴⁺ ions that the preferred ion localization position corresponds to a higher effective symmetry.     

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).     

Nanoclusters based on pentagondodecahedra with shells in the form of <Emphasis Type="Italic">D</Emphasis>32, <Emphasis Type="Italic">D</Emphasis>42, and <Emphasis Type="Italic">D</Emphasis>50 deltahedra in crystal structures of intermetallic compounds

The TOPOS software package has been used to form a database of intermetallic compounds containing pentagondodecahedral d clusters (528 crystal structures of intermetallic compounds, 111 topological types, and 47 space symmetry groups). On the whole, 606 atomic d configurations have been selected which are described by 14 point symmetry groups. Examples of nanoclusters are presented which are precursors of the crystal structures of intermetallic compounds with the outer shell in the form of deltahedra D, which are formed above dodecahedra. These nanoclusters are identified in the automatic mode of structural data processing: D32 (K₈In₆Ge₄₀, Cs₃₀Na₃Sn₁₆₂), D ₄₂ (Ru₃Be₁₇, Y₃Cd₁₈, Ca₃(Cd₁₇Al)), and D ₅₀ (Yb₃Zn₁₈, Ce₃(Au₁₄Sn₃), Pr₃Cd₁₈, Eu₄Cd₂₅), where 32, 42, and 50 are the numbers of atoms in the shell. Similar deltahedra were found previously in icosahedral nanoclusters (precursors of intermetallic compounds). Structures with the dodecahedral nanocluster precursors containing D42 and D50 deltahedra are approximants of MCd_5.7 (M = Yb or Ca) quasicrystals and belong to the family of MCd₆ (M = Ce, Pr, Nd, Sm, Eu, Gd, Dy, Yb, Y, or Ca).     

Electron diffraction study of 1<Emphasis Type="Italic">M</Emphasis> illites with interstratified <Emphasis Type="Italic">trans</Emphasis>- and <Emphasis Type="Italic">cis</Emphasis>-vacant 2 : 1 layers

Illites from the volcanogenic Zn-Au-Ag sulfide deposit Galkinskoe (Northern Urals) have been investigated using oblique-texture electron diffraction patterns in combination with the simulation of diffraction effects. Along with single-phase tv/cv1M illites, the structures of which are formed by statistically interstratified dioctahedral 2: 1 layers with vacant trans- or cis-octahedra, illites in the form of a mixture of two interstratified tv/cv1M phases, with the dominance of tv- or cv layers, are identified. It is shown that in the latter case the diffraction pattern can also be interpreted within the single-phase tv/cv model, provided that the tv- and cv layers are distributed with some tendency to segregate. The structural features indicating the preference of the two-phase model are analyzed.     

Crystal and Molecular Structures of Di-1-Adamantylthiophosphinic Chloride, <Emphasis Type="Italic">P</Emphasis>,<Emphasis Type="Italic">P</Emphasis>-Diphenyl-<Emphasis Type="Italic">N</Emphasis>-Benzyl Phosphinothioic- and Selenoic- Amides

Abstract  Synthesis and X-ray structural determination of three phosphorus compounds are reported. (3b) is monoclinic P2(1)/c with a = 11.852(1), b = 12.825(1), c = 12.445(1) ?, β = 103.693(1)o; (4a) and (4b) are monoclinic P2(1)/n with a = 12.1422(16), b = 9.0860(12), c = 14.845(2) ?, β = 96.498(3)o for (4a), and a = 12.2714(16), b = 9.2812(12), c = 14.800(2) ?, β = 97.176(2)o for (4b). They all exhibit distorted tetrahedral geometry about the P atom. Ph₂P(X)NHC₇H₇ (X=S (4a) and X=Se (4b)) show typical P–S and P–Se double bond distances and P–N single bonds, while P–S bond in 1-Ad₂P(S)Cl (3b) is comparable to P–S single bonded probably due to the largeness of 1-adamantyl groups. Graphical Abstract  Synthesis and X-ray structural determination of 1-Ad₂P(S)Cl (3b), Ph₂P(S)NHC₇H₇ (4a) and Ph₂P(Se)NHC₇H₇ (4b) are reported.      

Synthesis and structural studies of <Emphasis Type="Italic">tris</Emphasis>-2-chlorobenzylamine and <Emphasis Type="Italic">tris</Emphasis>-2-bromobenzylamine

The tris-2-chloro and 2-bromotribenzylamines are prepared from aqueous ammonia and 2-chlorobenzyl chloride and 2-bromobenzyl bromide, respectively, in ethanol. Recrystallization yielded colorless cubes of each product. The crystal structures are each solved in space group P , and are isostructural. The tris-2-chloro compound, 1, has a = 7.4226(5) Å, b = 9.0825(7) Å, c = 14.529(1) Å, = 78.279(1), = 82.389(1), = 84.661(1), and V = 948.41(12) ų with Z = 2, and d_calc = 1.368 Mg/m³. The tris-2-bromo analog, 2, has a = 7.6569(11) Å, b = 9.0922(13) Å, c = 14.614(2) Å, = 79.286(2), = 81.777(2), = 85.401(2), and V = 987.9(2) ų with Z = 2, and d_calc = 1.762 Mg/m³. Lithium–halogen exchange experiments conducted in tetrahydrofuran at –78C using n-butyl lithium revealed that no exchange occurred for the tris-2-chloro compound, but did occur for the tris-2-bromo analog to yield tribenzylamine upon quench and work-up.     

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)°.     

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.      

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)°.     

Synthesis of <Emphasis Type="Italic">E</Emphasis> Isomer and Crystal Structures of <Emphasis Type="Italic">E</Emphasis> and <Emphasis Type="Italic">Z</Emphasis> Isomers of 3-(2,5-Dimethoxyphenyl)-2-(4-methoxyphenyl)acrylonitrile

Abstract Details of the synthesis of the E isomer of 3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylonitrile, and the X-ray crystal structures of both the E and Z isomers of this compound are presented. The E isomer crystallizes in the P2₁/c space group with cell parameters, a = 8.5659(17) ?, b = 16.399(3) ?, c = 11.224(2) ?, α = 90°, β = 95.27(3)°, γ = 90°and Z = 4. The Z isomer crystallizes in the Pca2₁ space group with cell parameters, a = 4.1223(8) ?, b = 19.113(4) ?, c = 19.453(4) ?, α = 90°, β = 90°, γ = 90° and Z = 4. Index Abstract Synthesis of E isomer and X-ray crystal structure determination of both E and Z isomers of 3-(2,5-dimethoxyphenyl)-2-(4-methoxyphenyl)acrylonitrile are presented.      

Synthesis and Crystal Structure of Bis(<Emphasis Type="Italic">N</Emphasis>-alkyl-<Emphasis Type="Italic">N</Emphasis>-phenyl dithiocarbamato)mercury(II)

Abstract  

The mixed ligand dithiocarbamate complex was synthesized by the reaction between the ammonium salt of the dithiocarbamate ligands with mercury salt. There are two mercury complexes in the asymmetric unit with a compositional disorder between an ethyl group and a methyl group. A distorted tetrahedral geometry is found for each mercury atom defined by four sulphur atoms derived from two asymmetrically chelating dithiocarbamate ligands. IR spectra show thioureide υ(C–N) bands at 1491 cm⁻¹ which is higher than observed in the simple complexes of the same ligands. The effect of alkyl substituents were observed in the magnetic unequivalence of the thioureide and phenyl units in the NMR spectroscopy. The molecules are related to each other by virtue of the compositional disorder which exists at three positions in the alkyl group across the unit. The compound crystallizes in the triclinic space group P-1 with a = 10.4764(10) ?, b = 11.0433(10) ?, c = 18.5566(17) ?, α = 97.8980(10)^°, β = 95.3340(10)^°, γ = 110.3010(10)^°, and Z = 2.     

Structure of cellulose <Emphasis Type="Italic">Acetobacter xylinum</Emphasis>

The data are presented on optimization of cellulose synthesis by Acetobacter xylinum (strain VKM V-880) and the structural characteristics of A. xylinum cellulose gel film synthesized during static cultivation. The structural changes caused by the removal of water from gel films are established and the structural organization of macromolecular chains in cellulose A. xylinum is studied.     

Synthesis and crystal structure of the [WOCl<Subscript>3</Subscript>{<Emphasis Type="Italic">Ph</Emphasis>NHC(O)CHC(O-)<Emphasis Type="Italic">Me</Emphasis>}] complex

The [WOCl₃{PhNHC(O)CHC(O⁻)Me}] complex has been synthesized, and its crystal structure has been determined. The coordination polyhedron of the tungsten atom is a distorted octahedron with a meridional arrangement of three chlorine atoms. Two oxygen atoms of the acetoacetanilide bidentate chelating ligand occupy trans positions to the O(3) oxo atom and the Cl(3) atom. The crystal structures and the IR spectra of the WOCl₃{PhNHC(O)CHC(O^t-)Me} and [MoO₂Cl₂{(o-MePh)NHC(O)CH₂C(O)Me}] complexes are compared.     

2<Emphasis Type="Italic">D</Emphasis> quasi-periodic Rauzy tiling as a section of 3<Emphasis Type="Italic">D</Emphasis> periodic tiling

A method for constructing a 2D quasi-periodic Rauzy tiling Til as a section of some 3D periodic tiling Til ^3D is considered. The translation lattice of the tiling Til ^3D and its connectivity graph are constructed using the discrete modeling of packings. The calculation of the layer-by-layer growth polyhedron for the tiling Til ^3D made it possible to estimate from upper the shape of a growth polygon for the tiling Til. As a result, the growth shape in six out of eight growth sectors has been rigorously proven. A set of quasi-periodic tilings (locally indistinguishable from the Rauzy tiling Til), including seven centrosymmetric tilings, has been obtained.     

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.     

Comparative analysis of spatial organization of laccases from <Emphasis Type="Italic">Cerrena maxima</Emphasis> and <Emphasis Type="Italic">Coriolus zonatus</Emphasis>

Laccase (oxygen oxidoreductase, EC 1.10.3.2) belongs to the multicopper oxidase family. The main function of this enzyme is to perform electron transfer from the oxidized substrate through the mononuclear copper-containing site T1 to the oxygen molecule bound to the site T3 in the trinuclear T2/T3 cluster. The structures of two new fungal laccases from C. maxima and C. zonatus were solved on the basis of synchrotron X-ray diffraction data. Both laccases show high structural homology with laccases from other sources. The role of the carbohydrate component of laccases in structure stabilization and formation of ordered protein crystals was demonstrated. In the structures of C. maxima and C. zonatus laccases, two water channels of functional importance were found and characterized. The structural results reported in the present study characterize one of the functional states of the enzyme fixed in the crystal structure.     

Synthesis,Characterization and Antibacterial Activity of <Emphasis Type="Italic">N</Emphasis>-(<Emphasis Type="Italic">N</Emphasis>-Acetic Acid-yl-Phthalimide-5-yl) Maleamic Acid Dihydrate

Abstract  

The compound N-(N-acetic acid-yl-phthalimide-5-yl) maleamic acid (C₁₄H₁₀N₂O₇, M _r  = 318) was synthesized and its structure was characterized by elemental analysis, ¹H NMR and IR spectra. The single crystal of the title compound (C₁₄H₁₄N₂O₉, M _r  = 354.27) was cultured and its structure was determined by single crystal X-ray diffraction. The crystal belongs to monoclinic system, space group P21/c with a = 14.3859(19), b = 12.5835(18), c = 8.6934(15) ?, β = 102.824(2)°, V = 1534.5(4) ?³, Z = 4, D _c  = 1.534 g cm⁻³, μ(Mo Kα) = 0.131 mm⁻¹, F(000) = 736. The final refinement gave R = 0.0652, wR(F ²) = 0.1239 for 2,703 observed reflections with I > 2σ(I). X-ray diffraction analysis reveals that the asymmetric unit of the title compound contains one N-(N-acetic acid-yl-phthalimide-5-yl) maleamic acid molecule and two water molecules. One of the two water molecules is disordered. The phthalimide group is essentially planar. The crystal structure of the title compound is stabilized by N–H…O and O–H…O hydrogen bonds interactions. The compound N-(N-acetic acid-yl-phthalimide-5-yl) maleamic acid possesses moderate antibacterial activity.     

A new polymorph of tri(<Emphasis Type="Italic">p</Emphasis>-tolyl)boroxine

A new orthorhombic polymorph of tri(p-tolyl)boroxine (Pmn2₁) with relatively short intermolecular B–O distances of 3.321 Å was crystallized from CDCl₃ at ambient temperature. The crystal structure of the orthorhombic polymorph of tri(p-tolyl)boroxine shows the shortest intermolecular B–O contact yet found in boroxines. The cell dimensions of the orthorhombic polymorph of tri(p-tolyl)boroxine are a = 21.888(4) Å, b = 9.304(2) Å, and c = 4.7804(10) Å. The structural features of the orthorhombic polymorph of tri(p-tolyl)boroxine are quite different from a previously reported monoclinic (Beckett et al., J. Organomet. Chem. 1997, 535, 33–41) but similar to that of tri(p-bromophenyl)boroxine (Avent et al., Coll. Czech. Chem. Commun. 2002, 67, 1051–1060). Obviously, electronic effects of substituents on the boron centers influence the structural features of substituted boroxines less than discussed in earlier reports (Boese et al., Angew. Chem. 1987, 99, 239–241).     

Structure and features of the surface morphology of <Emphasis Type="Italic">A</Emphasis><Superscript>4</Superscript><Emphasis Type="Italic">B</Emphasis><Superscript>6</Superscript> chalcogenide epitaxial films

The structure and features of the surface morphology of Pb_{1 − x} Mn _x Se (x = 0.03) epitaxial films grown on freshly cleaved BaF₂(111) faces and PbSe_{1 − x} S _x (100) (x = 0.12) single-crystal wafers were investigated by molecular beam condensation and the hot-wall method. It is shown that the epitaxial films, in accordance with the data in the literature for other chalcogenides, grow in the (111) and (100) planes, repeating the substrate orientation. Black aggregates are observed on the film surface of the films grown. The results obtained are compared with the data in the literature and generalized for other chalcogenides: A ⁴ B ⁶:Pb (S, Se, Te); Pb_{1 − x} Sn _x (S, Se, Te); and Pb_{1 − x} Mn (Se, Te). It is established that the formation of black aggregates, which are second-phase inclusions on the surface of epitaxial films obtained by vacuum thermal deposition, is characteristic of narrow-gap A ⁴ B ⁶ chalcogenides.     

Relationship between the lengths of covalent and intermolecular bonds in <Emphasis Type="Italic">X</Emphasis>-H...<Emphasis Type="Italic">Y</Emphasis> bridges

The formula exp(−ln2((r ^XH − r ₀ ^XH)/(r _sym ^XH − r ₀ ^XH))^5/3) + exp(−ln2((r ^YH − r ₀ ^YH)/(r _sym ^YH − r ₀ ^YH))^5/3) = 1 is proposed, which relates the lengths of both covalent and hydrogen bonds in homo- and heterobridges. This formula is justified by the experimental data from the CSD bank, which was obtained by neutron diffraction for 108 O-H...N hydrogen bridges with bond angles exceeding 170°.