Twofold Axis Research Articles

Three phenanthroline-metal complexes with topologically similar but geometrically different conformations.

The structures of three related complexes of general formula M(pds)(nab)2 [pds is the peroxodi-sulfate anion and nab is an nitro-gen-containing aromatic base], viz. bis(2,9-dimethyl-1,10-phenanthroline-κ2N,N')(peroxodi-sulfato-κ2O,O')cadmium, [Cd(S2O8)(C14H12N2)2], (V), bis-(3,4,7,8-tetra-methy-1,10-phenanthroline-κ2N,N')(peroxodi-sulfato-κ2O,O')zinc, [Zn(S2O8)(C16H16N2)2], (VI), and bis-(3,4,7,8-tetra-methy-1,10-phenanthroline-κ2N,N')(peroxodi-sulfato-κ2O,O')cadmium, [Cd(S2O8)(C16H16N2)2], (VII), present the same topological coordination, with three chelating ligands in an MN4O2 polyhedron. The main difference resides in the fact that the first two complexes are bis-ected by a crystallographic twofold axis, thus providing a symmetrical environment to the cation, while in the third one this symmetry is disrupted into a clearly unsymmetrical disposition, probably by way of an unusually strong intra-molecular C-H⋯O hydrogen bond. The situation is compared with similar inter-actions in the literature. The structure of (V) is based on a redetermination in the correct space group C2/c of the structure originally described in the Cc space group [Harvey et al. (2001). Aust. J. Chem.54, 307-311; Marsh (2004 ▸). Acta Cryst. B60, 252-253].

2,4-Dimethylpyrido[1,2-a]pyrimidin-5-ium perchlorate

In the title molecular salt, C10H11N2 +·ClO4 −, the pyrido[1,2-a]pyrimidin-5-ium cation is planar, with an r.m.s. deviation of 0.027 Å for all 12 non-H atoms. The perchlorate anions are distributed over two twofold rotation axes; for one, three of the O atoms are disordered over two sites (occupancies of 1/2). In the crystal, the cations are linked via C—H...N hydrogen bonds, forming chains propagating along [001]. The chains are linked by a C—H...O hydrogen bond involving the non-disordered perchlorate anion, forming double layers parallel to the bc plane. These layers are linked by a number of weak C—H...O hydrogen bonds involving the disordered perchlorate anion, forming a three-dimensional framework.

Ammonium hydrogen bis[4-(2-phenyl-2H-tetrazol-5-yl)benzoate

The title salt, NH4 +·H+·2C14H9N4O2 −, is composed of an ammonium cation with a strong intermolecular negatively charge-assisted hydrogen-bonded acid/conjugate base-pair monoanion. The carboxylic acid H atom is located on an inversion center, while the N atom of the ammonium cation is located on a twofold rotation axis. In the crystal, the N—H bonds of each ammonium cation act as donors with carboxylate O-atom acceptors to form chains along the a-axis direction. The chains are linked by offset π–π interactions [intercentroid distances = 3.588 (2) and 3.686 (2) Å], forming layers parallel to the ab plane.

Chloridobis[2-(pyridin-2-yl-κN)benzo[b][1,5]naphthyridine-κN 1]copper(II) perchlorate acetonitrile disolvate

The copper(II) ion in the title complex, [CuCl(C17H11N3)2]ClO4·2CH3CN, is coordinated by four N atoms from two pbn ligands and one Cl− ion in a distorted trigonal–bipyramidal geometry (τ = 0.84). The asymmetric unit comprises half of the cationic complex molecule, and complete molecules are generated by twofold rotation symmetry with the corresponding axis running through the Cu atom and the coordinating Cl atom. The perchlorate anion is also located on a twofold rotation axis (passing through the Cl atom). In the crystal, there are π–π stacking interactions between the benzonaphthyridine rings of the pbn ligand of neighbouring cations.

Crystal structure and Hirshfeld surface analysis of 1-carb-oxy-2-(3,4-di-hydroxy-phen-yl)ethan-1-aminium bromide 2-ammonio-3-(3,4-di-hydroxy-phen-yl)propano-ate.

In the title mol-ecular salt, C9H12NO4+·Br-·C9H11NO4, one of the dopa mol-ecules is in the cationic form in which the α-amino group is protonated and the α-carb-oxy-lic acid group is uncharged, while the second dopa mol-ecule is in the zwitterion form. The Br- anion occupies a special position and is located on a twofold rotation axis. The two dopa mol-ecules are inter-connected by short O-H⋯O hydrogen bonds. In the crystal, the various units are linked by O-H⋯O, N-H⋯Br and N-H⋯O hydrogen bonds, forming a three-dimensional framework. The title compound was refined as an inversion twin with an absolute structure parameter of 0.023 (8).

Syntheses, structure and properties of Alkaline-earth metal salts of 4-Nitrophenylacetic acid

The synthesis, crystal structure, spectral characteristics and thermal properties of alkaline-earth metal salts of 4-nitrophenylacetic acid (4-npaH) namely, [Mg(H2O)6](4-npa)2⋅4H 2O (4-npa = 4-nitrophenyl-acetate) (1), [Ca(H 2O) 2(4-npa) 2] (2) and [Sr(H 2O) 3(4-npa) 2] ⋅4.5H 2O(3) are reported. In 1, the 4-npa ion functions as a charge balancing counter anion for the octahedral [Mg(H 2O) 6] 2+ unit with the Mg(II) ion situated on a centre of inversion. The two unique lattice water molecules link the [Mg(H 2O) 6] 2+ cations and 4-npa anions with the aid of O-H ⋯O interactions. Compounds 2 and 3 are one-dimensional (1-D) coordination polymers containing an eight coordinated Ca(II) situated in a general position and a nine coordinated Sr(II) located on a twofold axis. The μ 2-bridging tridentate binding modes of the crystallographically independent 4-npa ligands in 2 and the unique 4-npa ligand in 3 link the bivalent metal ions into an infinite chain with alternating Ca ⋯Ca separations of 3.989 and 4.009 Å, respectively, and a single Sr ⋯Sr separation of 4.194 Å in the 1-D chain. Synthesis, structure and properties of [Mg(H2O)6](4-npa)2·4H2O (4-npa =4-nitrophenylacetate) (1), [Ca(4-npa)2(H2O)2] (2), and [Sr(4-npa)2(H2O)3]·4.5H2O (3) are reported.

Crystal structure of an HgII coordination polymer with an unsymmetrical dipyridyl ligand: catena-poly[[[di-chlorido-mercury(II)]-μ-N-(pyridin-4-ylmeth-yl)pyridin-3-amine-κ2N:N'] chloro-form hemisolvate

The asymmetric unit of the title compound, {[HgLCl2]·0.5CHCl3} n (L = N-(pyridin-4-ylmeth-yl)pyridin-3-amine, C11H11N3), contains one HgII ion, one bridging L ligand, two chloride ligands and a chloro-form solvent mol-ecule with half-occupancy that is disordered about a crystallographic twofold rotation axis. Each HgII ion is coordinated by two pyridine N atoms from two symmetry-related L ligands and two chloride anions in a highly distorted tetra-hedral geometry with bond angles falling in the range 99.05 (17)-142.96 (7)°. Each L ligand bridges two HgII ions, forming polymeric zigzag chains propagating in [010]. In the crystal, the chains are linked by inter-molecular N/C-H⋯Cl hydrogen bonds together with weak C-H⋯π inter-actions, resulting in the formation of a three-dimensional supra-molecular network, which is further stabilized by C-Cl⋯π inter-actions between the solvent chloro-form mol-ecules and the pyridine rings of L [chloride-to-centroid distances = 3.442 (11) and 3.626 (13) Å]. In addition, weak Cl⋯Cl contacts [3.320 (5) Å] between the chloro-form solvent mol-ecules and the coordinating chloride anions are also observed.

Acetic anhydride at 100 K: the first crystal structure determination.

Acetic anhydride (ethanoic anhydride), (CH3CO)2O, is a widely used acetylation reagent in organic synthesis. The crystal and molecular structure, as determined by single-crystal X-ray analysis at 100 K, is reported for the first time. A crystal of the title compound (m.p. 200 K) suitable for X-ray diffraction was grown from the melt at low temperature. The title compound crystallizes in the orthorhombic space group Pbcn, with Z = 4. In the crystal, the molecule adopts an exact C2-symmetric conformation about a crystallographic twofold axis. The molecules are densely packed. Two of the methyl H atoms form short intermolecular contacts to a neighbouring carbonyl O atom, which can be viewed as weak hydrogen bonds.

Asymmetric cryo-EM structure of the canonical Allolevivirus Qβ reveals a single maturation protein and the genomic ssRNA in situ

Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qβ, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qβ with and without symmetry applied. The icosahedral structure, at 3.7-Å resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-Å resolution, reveals A2 and the gRNA. A2 contains a bundle of α-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.

The hydrogen-bonded complex bis(tert-butylammonium) 2,6-dichlorophenolate 2,4-dichlorophenol–2,4-dichlorophenolate tetrahydrofuran disolvate containing a chiralR53(10) hydrogen-bonded ring as a supramolecular synthon

A fixed hydrogen-bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen-bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen-bonding motif R53(10) was observed previously in a cocrystal of 2,4,6-trichlorophenol, 2,4-dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C4H12N+·C6H3Cl2O-·(C6H3Cl2O-·C6H4Cl2O)·2C4H8O, five components, namely two tert-butylammonium cations, one 2,4-dichlorophenol molecule, one 2,4-dichlorophenolate anion and one 2,6-dichlorophenolate anion, are bound by N-H...O and O-H...O hydrogen bonds to form a hydrogen-bonded ring, with the graph-set motif R53(10), which is further associated with two pendant tetrahydrofuran molecules by N-H...O hydrogen bonds. The hydrogen-bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6-dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4-dichlorophenol, dicyclohexylamine and 2,4,6-trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen-bonded rings, along and across the c axis, and successive pairs of rings are associated with each other through C-H...π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.

Application of electron backscatter diffraction (EBSD) to quasicrystal-containing microstructures in the Mg-Cd-Yb system

We develop a new analysis system for identifying orientation of an icosahedral quasicrystal (iQc) in a SEM installed with an electron backscatter diffraction (EBSD) instrument. The system is successfully applied to determine the orientation of any given iQc grain by reading and assigning the Kikuchi bands obtained with the EBSD. This enables us to analyze relative orientations of iQc and αMg grains in a eutectic structure obtained through a unidirectional solidification process for the Mg-Cd-Yb system. According to EBSD analysis, growth direction of the eutectic structure is shown to be clearly parallel to a two-fold axis of the iQc and {10-10} of αMg, and a unique orientation relationship in iQc and αMg grains is verified in all iQc-αMg coexisting regions. The similarity between primary inter-planar spacings of the iQc and αMg phases is a key factor for stabilizing the interface of two phases and favoring the formation of eutectic structure. This stabilization mechanism is supported by a simple argument on the energetics of a quasiperiodic/periodic lattice interface.

1,1′-Biphenyl-2,2′,5,5′-tetracarboxylic acid

In the title compound, C16H10O8or H4bptc, the dihedral angle between the planes of the phenyl rings is 51.90 (4)°. The asymmetric unit contains one half-molecule; complete molecules are generated by a twofold rotation axis. In the crystal, O—H...O and C—H...O hydrogen-bonding generate a two-dimensional supramolecular network. In addition, weak π–π interactions are also observed.

Crystal structure of aqua-tris-(isonicotinamide-κN)bis-(thio-cyanato-κN)cobalt(II) 2.5-hydrate.

The asymmetric unit of the title compound, [Co(NCS)2(C6H6N2O)3(H2O)]·2.5H2O, comprises one CoII cation, three isonicotinamide ligands, two thio-cyanate anions, one aqua ligand and two water solvent mol-ecules in general positions, as well as one water solvent mol-ecule that is located on a twofold rotation axis. The CoII cations are octa-hedrally coordinated by two terminally N-bonded thio-cyanate anions, one water mol-ecule and three isonicotinamide ligands, each coordinating via the pyridine N atom. The discrete complexes are linked by inter-molecular O-H⋯O, N-H⋯O and N-H⋯S hydrogen bonding into a three-dimensional network that contains cavities in which the solvent water mol-ecules are located. The latter are linked by further O-H⋯O hydrogen bonds to the network. There are additional short contacts present in the crystal, indicative of weak C-H⋯S, C-H⋯O and C-H⋯N inter-actions.

Crystal structure of [tris-(4,4'-bi-pyridine)]-diium bis-(1,1,3,3-tetra-cyano-2-eth-oxy-propenide) trihydrate.

The title hydrated salt, C30H26N62+·2C9H5N4O-·3H2O, was obtained as an unexpected product from the hydro-thermal reaction between potassium 1,1,3,3-tetra-cyano-2-eth-oxy-propenide, 4,4'-bi-pyridine and iron(II) sulfate hepta-hydrate. The cation lies across a twofold rotation axis in the space group I2/a with the other components all in general positions. In the cation, the H atom linking the pyridine units is disordered over two adjacent sites having occupancies of 0.66 (4) and 0.36 (4), i.e. as N-H⋯N and N⋯H-N. The water mol-ecules of crystallization are each disordered over two sets of atomic sites, having occupancies of 0.522 (6) and 0.478 (6) for one, and 0.34 (3) and 0.16 (3) for the other, and it was not possible to reliably locate the H atoms associated with these partial-occupancy sites. In the crystal, four independent C-H⋯N hydrogen bonds link the ionic components into a three-dimensional network.

Crystal structure of hexa-aqua-nickel(II) bis-{5-bromo-7-[(2-hy-droxy-eth-yl)amino]-1-methyl-6-oxido-quinolin-1-ium-3-sulfonate} monohydrate.

The asymmetric unit of the title compound, [Ni(H2O)6](C12H12BrN2O5S)2·H2O, contains a half hexa-aqua-nickel(II) complex cation with the NiII ion lying on an inversion center, one 5-bromo-7-[(2-hy-droxy-eth-yl)amino]-1-methyl-6-oxido-quinolin-1-ium-3-sulfonate (QAO) anion and a half lattice water mol-ecule on a twofold rotation axis. In the crystal, QAO anions are stacked in a column along the c axis by π-π stacking inter-actions [centroid-centroid distances 3.5922 (10)-3.7223 (11) Å]. The columns are inter-linked by hexa-aqua-nickel(II) cations through O-H⋯O and N-H⋯O hydrogen bonds.

Synthesis, characterization, and crystal structure of cobalt(II) and zinc(II) complexes with a bulky Schiff base derived from rimantadine

Two novel complexes, C38H48CoN2O2 (I) and C38H48N2O2Zn (II), were prepared through an analogous procedure with a corresponding metal chloride and a bulky Schiff base ligand (HL) which derived from rimantadine and salicylaldehyde in appropriate solvents, respectively. They were structurally characterized by the means of IR, UV-Vis, elemental analysis, molar conductance, PXRD and single-crystal X-ray diffraction (CIF files nos. 946735 (I), 893304 (II)). Single-crystal X-ray diffraction analysis reveals that I belongs to the triclinic system, \(P\overline 1 \) space group; each asymmetric unit consists of one cobalt(II) complex and one lattice ethanol molecule. In each complex molecule, cobalt(II) atom is four-coordinated via two oxygen atoms and two nitrogen atoms from the deprotonated Schiff base ligands, forming an approximate planar geometry. The crystal structure also involves strong O–H···O intermolecular hydrogen bonds between the solvent alcoholic and phenol O atoms of complex molecule. Complex II belongs to the monoclinic system, Cc space group. Each asymmetric unit consists of one zinc(II) ion and two deprotonated ligands. Zinc(II) atom lies on a twofold rotation axis and is four-coordinated via two nitrogen atoms and two oxygen atoms from the Schiff base ligands, forming a distorted tetrahedral geometry.

Isotypic one-dimensional coordination polymers: catena-poly[[di-chlorido-cadmium]-μ-5,6-bis-(pyridin-2-yl)pyrazine-2,3-di-carboxyl-ato-κ(2) N (5):N (6)] and catena-poly[[di-chlorido-mercury(II)]-μ-5,6-bis-(pyridin-2-yl)pyrazine-2,3-di-carboxyl-ato-κ(2) N (5):N (6)

The isotypic title one-dimensional coordination polymers, [CdCl2(C18H14N4O4)] n , (I), and [HgCl2(C18H14N4O4)] n , (II), are, respectively, the cadmium(II) and mercury(II) complexes of the dimethyl ester of 5,6-bis-(pyridin-2-yl)pyrazine-2,3-di-carb-oxy-lic acid. In both compounds, the metal ions are located on a twofold rotation axis and a second such axis bis-ects the Car-Car bonds of the pyrazine ring. The metal ions are bridged by binding to the N atoms of the two pyridine rings and have an MN2Cl2 bisphenoidal coordination geometry. The metal-Npyrazine distances are much longer than the metal-Npyridine distances; the difference is 0.389 (2) Å for the Cd-N bonds but only 0.286 (5) Å for the Hg-N bond lengths. In the crystals of both compounds, the polymer chains are linked via pairs of C-H⋯Cl hydrogen bonds, forming corrugated slabs parallel to the ac plane.

1-(4-Fluorophenyl)-4,4,6-trimethyl-3,4-dihydropyrimidine-2(1H)-thione

In the title molecule, C13H15FN2S, the dihydropyrimidine ring is in a flattened boat conformation with deviations of 0.135 (2) and 0.371 (2) Å for the fluorophenyl-substituted N atom and the dimethyl-substituted C atom, respectively, from the four other essentially co-planar atoms. In the crystal, pairs of molecules related by twofold rotation axes are linked by N—H...S hydrogen bonds, forming dimers.

Crystal structure of ammonium/potassium trans-bis-(N-methyl-iminodi-acetato-κ(3) O,N,O')chromate(III) from synchrotron data.

The structure of the title compound, [(NH4)0.8K0.2][Cr(C5H7NO4)2] (C5H7NO4 is methyl-iminodi-acetate; mida), has been determined from synchrotron data. The Cr(III) atom is located on a centre of symmetry and is coordinated by two N atoms and four O atoms of two facially arranged tridentate mida ligands, displaying a slightly distorted octa-hedral coordination environment. The Cr-N and mean Cr-O bond lengths are 2.0792 (14) and 1.958 (14) Å, respectively. The cation site is located on a twofold rotation axis and shows occupational disorder, being occupied by ammonium and potassium cations in a 0.8:0.2 ratio. In the crystal, inter-molecular hydrogen bonds involving the N-H groups of the ammonium cation as donor and the two non-coordinating O atoms of the carboxyl-ate group as acceptor groups consolidate the three-dimensional packing.

Distinct coordination geometries in bis-[N,N-bis-(2-meth-oxy-eth-yl)di-thio-carbamato-κ(2) S,S']di-phenyltin(IV) and bis-[N-(2-meth-oxy-eth-yl)-N-methyl-dithio-carbamato-κ(2) S,S']di-phenyl-tin(IV): crystal structures and Hirshfeld surface analysis.

The crystal and mol-ecular structures of two di-phenyl-tin bis-(di-thio-carbamate)s, [Sn(C6H5)2(C5H10NOS2)2], (I), and [Sn(C6H5)2(C7H14NO2S2)2], (II), are described. In (I), in which the metal atom lies on a twofold rotation axis, the di-thio-carbamate ligand coordinates with approximately equal Sn-S bond lengths and the ipso-C atoms of the Sn-bound phenyl groups occupy cis-positions in the resulting octa-hedral C2S4 donor set. A quite distinct coordination geometry is noted in (II), arising as a result of quite disparate Sn-S bond lengths. Here, the four S-donors define a trapezoidal plane with the ipso-C atoms lying over the weaker of the Sn-S bonds so that the C2S4 donor set defines a skewed trapezoidal bipyramid. The packing of (I) features supra-molecular layers in the ab plane sustained by methyl-ene-C-H⋯π(Sn-ar-yl) inter-actions; these stack along the c-axis direction with no specific inter-actions between them. In (II), supra-molecular chains along the b-axis direction are formed by methyl-ene-C-O(ether) inter-actions; these pack with no directional inter-actions between them. A Hirshfeld surface analysis was conducted on both (I) and (II) and revealed the dominance of H⋯H inter-actions contributing to the respective surfaces, i.e. >60% in each case, and other features consistent with the description of the mol-ecular packing above.