Crystal structure of the complex of trichosanthin with NADPH at 0.172 nm resolution

The orthorhombic crystal structure of the complex of trichosanthin with nicotinamide adenine dinucleotide phosphate has been determined by molecular replacement method using one of the molecules of the monoclinic crystal structure of trichosanthin at 0.27 nm resolution as the search model. The crystallographic refinement at 0.172 nm resolution led to a final R-factor of 17.4% with root-mean-square deviations of 0.0013 nm and 3.8 from the ideal bond lengths and bond angles, respectively. The quality of the structure, the polypeptide chain fold and the comparison of it with that of the monoclinic trichosanthin structure, the location of nicotinamide adenine dinucleotide phosphate, the active site structure as well as the solvent structure are described.     

High pressure synthesis and crystal structure of two forms of a new tellurium–silicon clathrate related to the classical type I

Two new clathrate-type structures have been identified in the samples obtained by high pressure–high temperature treatment of appropriate mixtures of elemental silicon and tellurium at 5 GPa and 1200 °C for 60 min reaction time. They are both related to the classical type I silicon clathrate, G₈Si₄₆ (G=guest species). The corresponding structures have been solved by X-ray single crystal diffraction analysis. They proved to correspond to a cubic and rhombohedral forms of the same compound, Te₁₆Si₃₈ (or more precisely Te₈@(Si₃₈Te₈)), in which eight extra tellurium atoms are substituted for silicon ones in the 16i crystallographic sites of the parent structure. In the cubic form, the space group is reduced from Pm-3n to P-43n, and the formation of strong bonds between the Te atoms at the centre of the tetrakaidecahedral cages and one or two silicon atoms of the surrounding cage is clearly observed, which is followed by a decrease of the coordination number of the Te atoms in substitutional position from 4 to 3. In the more distorted rhombohedral form, the 16i and 24k sites of the parent structure are both split in four sites. The formation of strong bonds involving the Te atoms at the centre of the tetrakaidecahedral cages is confirmed, but the main characteristic comes from the formation of another kind of strong bonds involving the Te atoms at the centre of the dodecahedral cages. These bonds are at the origin of the elongation of the structure along the [111] direction, which corresponds to the polar axis.     

Crystal structure and thermal decomposition mechanism of the supramolecular complex of barium chloride with inositol

The single crystal of [Ba(H2O)2(C6H12O6)2Cl2] was obtained based on the phase equilibrium results. Its structure was determined by X-ray crystallographic analysis. The crystals are monoclinic and in space group C2/c with a=1.901 7(2) nm, b = 0.682 13(8) nm, c = 0.162 60(2) nm,β=96.593(2)°and V= 2.095 3(4) nm3, Z= 4, DC=1.917 g·cm-3. In its solid state, this supramolecular complex is a three-dimensional network with double layers connected by hydrogen bondings. The molecule structure of [Ba(H2O)2(C6H12O6)2Cl2] has a central barium ion that is coordinated to two water molecules, two chlorides, and four hydroxyls from the two inosi-tols. Losing the coordinating water is controlled by random nucleation and growth mechanism (n = 2/3) and 3-dimensional diffusion mechanism (n=2).     

Electronic and geometric structure of the protonated forms of nickel β-diketonates

The effect of protonation on the electronic and spatial structure of nickel malonodialdehynate Ni(Mal)₂ and acetylacetonate Ni(Acac)₂ were studied by quantum chemical density functional theory (DFT) method. The metal ring geometry, the energies and the composition of molecular orbitals (MO), the effective charges on atoms, and the total overlap populations were determined, and the possible proton location sites were identified. The variation of the MO energy depending on the electron density distribution on the protonated and non-protonated ligands was considered. Proton addition to one of the oxygen atoms was shown to be most likely.     

Crystal structure of the clathrate compound [dibromotetra(pyridine)copper(II)]·pyridine. Characterization by EXAFS of the pyridine desorption product

Powder samples of the new compound [Cu(C₅H₅N)₄·Br₂](C₅H₅N) and of its desorption product have been studied by EXAFS. The crystal structure of [Cu(C₅H₅N)₄Br₂]·(C₅H₅N) has been determined from three-dimensional X-ray diffraction data and refined to theR value 0.038 for 379 observed reflections. (orthorhombic,Ccca,a=12.033(8),b=14.764(3),c=16.768 Å,V=1897(3) ų,Z=4). The copper atom lies on a 222 symmetry site and is hexacoordinated with four nitrogen and two bromine atoms, forming an elongated octahedron with the bromine atoms in apical positions (Cu–Br distance: 3.201(2) , Cu–N1/N2 distances: 2.02(1)/2,07(1) ). The host molecules (Cu(C₅H₅N)₄Br₂) form layers parallel to the (001) plane. Cavities in the space between these layers, bound by pyridine ligands protruding into this space, are occupied by the guest molecules (C₅H₅N). The guest desorption at room temperature is accompanied by a chemical and structural destruction of the host, leading to the known compound Cu(C₅H₅N)₂Br₂.Supplementary Data relevant to this article (lists of observed and calculated structure factors, calculated positional parameters of H atoms, root-mean-square amplitudes of thermal vibration and anisotropic thermal parameters) have been deposited with the British Library as Supplementary Publication SUP 82163 (5 pages)     

Crystal structure of Co(III) α-dimethylglyoximates with imidazole

Two new dimethylglyoximate complexes [Co(DmgH)₂(Im)Cl] (I) and (ImH)[Co(DmgH₂)₂Cl₂] (II), where DmgH^? is the dimethylglyoxime residue and Im is the imidazole molecule, are synthesized. The composition and structure of the crystals are determined from the elemental analysis, IR spectra, and single crystal X-ray diffraction. Complex I is molecular, containing the Im molecule as a coordinated ligand; complex II is of the ionic type with (ImH)⁺ involved as an outer-sphere organic cation. The mode of component packing in the crystals mainly depends on the imidazole position in the compounds.     

Crystal structure of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane solvate with ɛ-caprolactam

The crystal structure of the CL-20 solvate with ?-caprolactam in the 1:6 ratio is obtained and studied.     

Crystal structure of the polycyclic oxidation product of 1′-phthalazinylhydrazone of 2-formylpyrrole

Phthalazinylhydrazone of 2-formylpyrrole is synthesized, the values of ionization constants are determined, and quantum chemical calculation of the geometry and total energy of possible tautomers is performed. The structure of the cyclic oxidation product of hydrazone 3-(1H-pyrrolyl-2)-[1,2,4]-triazolo(3,4-a)phthalazine existing in the crystal in the form of dimers linked by two hydrogen bonds is described.     

Interpenetrating inclusion lattices: Comparison of the Β-hydroquinone and ellipsoidal clathrate structures

Crystallization of 2,7-dimethyltricyclo[43.1.1^3,8]undecane-syn-2,syn-7-diol 2 from acetonitrile or dichloro-methane yields the compounds (2)₄-(guest) in space group 14₁/acd which are further examples of the ellipsoidal clathrate structure. Both enantiomers of 2 are linked through (O-H)₄ cycles of hydrogen bonds to form a three-dimensional sublattice. Two inversion related sublattices interpenetrate thereby generating a superlattice with guest-occupied voids situated between the two individual sublattices. The two X-ray structures are compared and contrasted with that of Powell’s (hydroquinone)₃ (SO₂) clathrate compound. Translated fromZhurnal Strukturnoi Khimii, Vol. 40, No. 5, pp. 822–831, September–October, 1999.     

Crystal structure of three solvates of 1,1′-binaphthyl-2,2′-bicarboxylic acid with 2-picoline

From solutions in 2-picoline (2-methylpyridine), depending on the temperature of crystallization, the universal clathratogen — 1,1′-binaphthyl-2,2′-bicarboxylic acid (BBA) — precipitates as crystals of three types with different composition and structure. Under normal conditions (room temperature), the precipitate is crystals of BBA disolvate with 2-picoline; a temperature reduction of 20°C results in the crystallization of monosolvate dihydrate; and a temperature increase of the same level results in the precipitation of monosolvate. That is, as the temperature of crystallization rises, the number of included guest molecules gradually decreases and the space where they are located becomes more closed. In 1:1:2 BBA/2-picoline/H₂O solvate (space group P2₁/n, a = 11.991(2) Å, b = 9.317(2) Å, c = 22.283(5) Å, β = 99.77(3)○, V = 2453.3(9) ų, Z = 4), the carboxyl groups of the BBA molecule at the C21 atom are deprotonated and the released proton goes to the nitrogen atom of 2-picoline. BBA molecules interact with those of 2-picoline and water via H bonds to form infinite chains in direction [111], which, in their turn, join together into infinite two-dimensional sheets parallel to plane (?101). 2-Picoline molecules are located in the channels. In BBA/2-picoline disolvate (space group C ₂/c, a = 11.7523(11) Å, b = 13.8563(13) Å, c = 17.9615(13) Å, β = 108.044(9)○, V = 2781.1(4) ų, Z = 4), one BBA molecule and two H bond 2-picoline molecules form a 0-dimensional associate of the type G-H-G. The solvent molecules are also located in the channels. In BBA/2-picoline monosolvate (space group P2₁/c, a = 9.299(5) Å, b = 12.727(5) Å, c = 19.011(5) Å, β = 95.248(5)○, V = 2240.5(16) ų, Z = 4), each BBA molecule is H-bonded with a 2-picoline molecule to form a 0-dimensional associate of the type H-G. Guest molecules are located in closed cavities.     

The structure of the VO2F3−4 ion: Crystal structure of (NH4)3VO2F4

The VO₂F³⁻₄ ion has a cis octahedral structure, as is shown by single crystal structure analysis of the title compound. The unit cell of (NH₄)₃VO₂F₄ (space group Immm or I222, a = 912.6(2), b = 1881.8(4), c = 626.4(1) pm, Z = 6) contains two symmetrically independent anions. One is rotationally disordered. Oxo and fluoro ligands cannot be distinguished. But the second one has a distorted cis octahedral structure with the lengths 170.0(4), 186.1(4), and 202.3(4) pm for the VO, VF (axial), and VF (equatorial) bonds. Infrared and Raman spectra as well as theoretical considerations support the crystallographic results. The phase transitions at 418 and 215 K were confirmed by variable temperature X-ray powder diffraction. Above 418 K the cubic cryolite type structure is adopted with a = 902.6(2) pm. Plausible mechanisms for the phase transitions are suggested.     

Crystal structure of two new molecular adducts of uranyl nitrate with 2,2′-6,2″-terpyridine

The crystal structures of two uranyl nitrate complexes with 2,2′-6,2″-terpyridine (Trpy), [(UO (Trpy)-[(UO₂)₂(Trpy)₂(OH)₂][UO₂(NO₃)₂(OH)₂] · 2CH₃OH (I) and [(UO₂)₂(Trpy)₂(OH)₂]₂[UO₂(NO₃)₃(H₂O)](NO₃)₃ · 3H₂O (II), were studied. Compound I consists of the centrosymmetric dimeric cations [(UO₂)₂(Trpy)₂(OH)₂]²⁺, the anions [UO₂(NO₃)₂(OH)₂]^2?, and solvation methanol molecules. Complex II consists of dimeric cations [(UO₂)₂(Trpy)₂(OH)₂]²⁺, the complex anions [UO₂(NO₃)₃(H₂O)]^?, nitrate anions, and water molecules of crystallization. The uranium atom in the [UO₂(NO₃)₃(H₂O)]^? anion in II has an unusual coordination polyhedron representing a hexagonal bipyramid in which one oxygen atom in the equatorial plane is replaced by two atoms equidistant from this plane.     

Crystal structure of a trinuclear complex of zinc(II) with 2,6-Di-tert-butyl-p-quinone 1′-phthalazinylhydrazone

2,6-Di-tert-butyl-p-quinone 1′-phthalazynylhydrazone (HL) is synthesized; the total energies and geometry of the possible hydrazone tautomeric forms are calculated by quantum chemical methods. The hydrazone phthalazone tautomer is shown to be the most stable, which is well consistent with the ¹H NMR spectroscopic data for hydrazone. An X-ray crystallographic analysis is performed of the hydrazone-based Zn(II) trinuclear complex, in which zinc atoms are linked by the diazine bridge of the phthalazine cycle and two pivalate bridges. The geometric properties of the monodeprotonated hydrazone residue in the complex are similar to the calculated data for the phthalazone hydrazone tautomeric form.     

Crystal structure and electrical conductivity of the “one-dimensional solid electrolyteN,N-dimethylmorpholinium pentaiodotetraargentate

The new solid electrolyteN, N-dimethylmorpholinium pentaiodotetraargentate, [(CH₃)N(CH₂)₂-(CH₂)₂O]Ag₄I₅ (DMMAg₄I₅), has a crystal structure which allows the Ag⁺ ions to move effectively in only one dimension. The channels for this motion result from the sharing of opposite faces of icosahedra, having iodides at their centers, forming infinite chains of icosahedra along thea axis. The joining of the icosahedra forms three more face-sharing tetrahedra at each junction, or a total of 23 tetrahedra per eight Ag⁺ ions, which are distributed non-uniformly over the tetrahedral sites. The limited number of pathways for the Ag⁺ ion diffusion leads to a low average conductivity, 1 × 10⁻⁴ Ω⁻¹ cm⁻¹ and a high activation enthalpy, 0.35 eV. Crystals of DMMAg₄I₅ belong to space groupP2₁2₁2₁ (D⁴₂) witha = 13.167(4), b = 23.437(3), c = 12.758(3)A˚; the unit cell contains eight formula units. The structure of dimethylmorpholinium iodide (DMMI) confirms the chair model for the DMM⁺ ion. Crystals of DMMI belong to space groupP2₁m(C²_2h), witha = 8.861(4), b = 8.020(2), c = 6.685(2)A˚, β = 101.07(3)°; each unit cell contains two formula units.     

Molecular dynamics simulation of local motion of polystyrene chain end—comparison with the fluorescence depolarization study

Molecular dynamics (MD) simulation of the local motion of a polystyrene (PS) chain with anthryl group at the chain end surrounded by benzene molecules was performed and the results were compared with those obtained experimentally by the fluorescence depolarization method. The molecular weight dependence of the relaxation time of the probe obtained by the MD simulation was qualitatively in agreement with the results obtained by the fluorescence depolarization method. We also estimated the molecular weight dependence of the relaxation time for the end-to-end vector. Below the degree of polymerization (DP)≤3, the mean relaxation time T_m for the end-to-end vector was similar to that for the vector corresponding to the transition moment of the probe. With the increase of DP, the T_m for the probe tended to reach an asymptotic value unlike that for the end-to-end vector, which monotonically increased with DP. This indicates that the entire motion of a polymer coil contributes to the local motion to a lesser extent as the molecular weight increases. The MD simulations using artificial restraints showed that the rotational relaxation of the probe at the chain end for a dynamically stiff PS chain is realized by the cooperative rotation of the main chain bonds. The internal modes which takes place below 5 monomer units mainly led to the rotational relaxation of the probe at the PS chain end. Finally, the change of T_m with the position along the PS main chain was examined.     

Crystal structure of palladium(II) complex with 2,2′-dipyridylamine and 4-toluenesulfonyl-L-serine

The [Pd(dpa)(tsser)] complex (1) is prepared from the reaction of PdCl₂ and 2,2′-dipyridylamine (dpa) with 4-toluenesulfonyl-L-serine (tsserH₂). This complex is characterized by spectral methods (IR, UV-Vis, ¹H NMR, and luminescence), elemental analysis, thermal analysis (TG, DTA), and single crystal X-ray diffraction. X-ray structure determinations show that in this complex, Pd^II atoms are four-coordinated in a distorted square-planar configuration by two N atoms from a bidentate 2,2′-dipyridylamine ligand and one N atom and one O atom from a bidentate tsser^2– ligand.     

Crystal structure of a hydroxo-bridged dimeric uranyl complex with a 2,2′:6′,2″-terpyridine ligand

A new dimeric compound [{UO₂(μ-OH)(terpy)}₂](ClO₄)₂·0.67CH₃CN, containing an uranyl cation and a tridentate 2,2′:6′,2″-terpyridine (terpy) ligand, is synthesized from an acetonitrile solution of uranyl perchlorate and terpy. The crystal structure of the compound is determined by single crystal X-ray diffraction. The crystal structure shows the formation of symmetric and asymmetric cationic hydroxo-bridged uranyl dimers. The uranium atoms adopt a distorted pentagonal bipyramidal configuration with a UO₄N₃ coordination environment formed by two uranyl O atoms, three N atoms from the terpy ligand, and two O atoms from the hydroxide anions.     

Crystal structure and spectroscopic properties of polymeric adducts of the tetra-μ-haloaspirinate-dicopper(II)

Eight new copper(II) complexes with halo-aspirinate anions have been synthesized: [Cu₂(Fasp)₄(MeCN)₂]?·?2MeCN (1), [Cu₂(Clasp)₄(MeCN)₂]?·?2MeCN (2), [Cu₂(Brasp)₄(MeCN)₂]?·?2MeCN (3), {[Cu₂(Fasp)₄(Pyrz)]?·?2MeCN} _n (4), {[Cu₂(Clasp)₄(Pyrz)]?·?2MeCN} _n (5), [Cu₂(Brasp)₄(Pyrz)] _n (6), [Cu₂(Clasp)₄(4,4′-Bipy)] _n (7), and [Cu₂(Brasp)₄(4,4′-Bipy)] _n (8) (Fasp: fluor-aspirinate; Clasp: chloro-aspirinate; Brasp: bromo-aspirinate; MeCN: acetonitrile; Pyrz: pyrazine; 4,4′-Bipy: 4,4′-bipyridine). The crystal structure of two 2 and 4 have been determined by X-ray diffraction methods. All compounds have been studied employing elemental analysis, IR, and UV-Visible spectroscopic techniques. The results have been compared with previous data reported for complexes with similar structures.