Twofold Axis Research Articles

Poly[bis[μ-4-(4-carboxyphenoxy)benzoato](μ-4,4′-oxydibenzoato)bis[μ-3-(pyridin-4-yl)-5-(pyridin-3-yl)-1H-1,2,4-triazole]dicadmium(II)

Three kinds of bridging ligands, 4,4′-oxydibenzoate, 4-(4-carboxyphenoxy)benzoate and 3-(pyridin-4-yl)-5-(pyridin-3-yl)-1H-1,2,4-triazole, link the CdIIcations to form the title polymeric complex, [Cd2(C14H8O5)(C14H9O5)2(C12H9N5)2]n, in which each CdIIcation is in a distorted N2O5pentagonal–bipyramidal coordination geometry. The 4,4′-oxydibenzoate dianion exhibits point group symmetry 2, with the central O atom located on a twofold rotation axis. Classical N—H...O, O—H...N hydrogen bonds and weak C—H...O hydrogen bonds link the complex molecules into a three-dimensional supramolecular architecture. A solvent-accessible void of 53 (2) Å3is observed, but no solvent molecule could reasonably located there.

Modeling Microvirus Capsid Protein Evolution Utilizing Metagenomic Sequence Data.

The Microviridae are increasingly becoming recognized as one of the most globally ubiquitous and highly diverse virus families, and as such, provide an advantageous model for studying virus evolution and adaptation. Here, we utilize microvirus sequences from diverse physiochemical environments, including novel sequences from a high-temperature acidic lake, to chart the outcome of natural selection in the main structural protein of the virus. Each icosahedral microvirus virion is composed of sixty identical capsid proteins that interact along twofold, threefold and fivefold symmetry axis interfaces to encapsidate a small, circular, single-stranded DNA genome. Viable assembly of the virus is guided by scaffolding proteins, which coordinate inter-subunit contacts between the capsid proteins. Structure-based analysis indicates that amino acid sequence conservation is predominantly localized to the twofold axis interface. While preservation of this quaternary interface appears to be essential, tertiary and secondary structural features of the capsid protein are permissive to considerable sequence variation.

Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas.

A novel mannose-specific lectin, named CGL1 (15.5 kDa), was isolated from the oyster Crassostrea gigas. Characterization of CGL1 involved isothermal titration calorimetry (ITC), glycoconjugate microarray, and frontal affinity chromatography (FAC). This analysis revealed that CGL1 has strict specificity for the mannose monomer and for high mannose-type N-glycans (HMTGs). Primary structure of CGL1 did not show any homology with known lectins but did show homology with proteins of the natterin family. Crystal structure of the CGL1 revealed a unique homodimer in which each protomer was composed of 2 domains related by a pseudo two-fold axis. Complex structures of CGL1 with mannose molecules showed that residues have 8 hydrogen bond interactions with O1, O2, O3, O4, and O5 hydroxyl groups of mannose. The complex interactions that are not observed with other mannose-binding lectins revealed the structural basis for the strict specificity for mannose. These characteristics of CGL1 may be helpful as a research tool and for clinical applications.

Crystal and molecular structure of 2,2’-(quinoxaline-2,3-diyl)dipyridinium dinitrate (H2 L)(NO3)2

The crystal structure of 2,2’-(quinoxaline-2,3-diyl)dipyridinium dinitrate (Н2L)(NO3)2 is studied by X-ray diffraction (T = 150 K, R1 = 0.0467). The H2L2+ cation is located on the twofold rotation axis and connected with two NO3− anions by strong N–H···O hydrogen bonds. Planar quinoxaline fragments of cations form stacks with the interplanar spacing of 3.308 A. The structure of the diprotonated H2L2+ cation is compared with those of the monoprotonated H2L2+ cation and neutral L molecule.

Vaterite: Interpretation in terms of OD theory and its next of kin

The polytypic structures of vaterite, CaCO3, described in recent literature, have been reinterpreted in terms of the order-disorder (OD) theory, which allows us to explain and systematize all the observed and predicted polytypes of the mineral in a unified fashion. In terms of this theory, the structure consists of OD layers that comprise a layer of calcium coordination polyhedra and the attached halves of the standing CO3 groups. The two-sided layer group of symmetry of the OD layer is c2/m, whereas the interlayer symmetry operations are three twofold rotation axes at 120° to one another, as well as a mirror plane in the common layer boundaries and partial c glide planes perpendicular to the boundary. Depending on the orientation of the active twofold rotation axis with respect to the above-defined layer mesh, performed independently in each stacking step, maximally ordered simple stacking sequences P6122, P6522, C2/c, C2/c2/m21/m, and a more complicated sequence P312 or P322, as well as several complicated or disordered sequences is obtained (before eventual relaxation to a subgroup of a particular space group). A perfect copy of the vaterite OD layer occurs in the structures of the bastnäsite-synchysite polysomatic series of fluorocarbonates. In these structures, the REE layers, configurationally analogous to the Ca-based OD layer, have layer symmetry p32 and their stacking does not lead to polytypism and OD phenomena; these are generated on the Ca-based OD layers.

Calcium complex of 2,5-dihydroxybenzoic acid (gentisic acid): synthesis, crystal structure, and spectroscopic properties

The synthesis, crystal structure, and spectral characteristics (IR, Raman, and 1H and 13C NMR) of a monomeric hexa(aqua)calcium compound, viz. [Ca(C7H5O4)2(H2O)6]·H2O (C7H5O4 = 2,5-dihydroxybenzoate), are reported. The central Ca(II) located on a twofold axis is eight coordinate in an approximate square antiprismatic environment, bonded to two monodentate 2,5-dihydroxybenzoate ligands via the carboxylate oxygen, and six waters. The adjacent monomeric units are linked with the aid of several O–H⋯O hydrogen bonds.

Poly[(2,2′-bipyridine-κ2N,N′)[μ4-2,2′-(1,3-phenylene)bis(imidazol-1-yl)-κ4N:N′:N′′:N′′′]dicopper(I)

Two CuIatoms are present in the asymmetric unit of the polymeric title complex, [Cu2(C20H12N4)(C10H8N2)]n. One of the cations is located on an inversion centre and is linearly coordinated by the N atoms of benzimidazolyl moieties of the 1,2-bis(2-benzimidazolium)benzene ligand, whereas the second cation is located on a twofold rotation axis and is tetrahedrally coordinated by two N atoms of a chelating 2,2′-bipyridine ligand and two other N atoms of the benzimidazolyl moieties. The bridging character of the 1,2-bis(2-benzimidazolyl)benzene leads to the formation of a three-dimensional framework structure.

Crystal structure of bis-(N,N,N',N'-tetra-methyl-guanidinium) tetra-chlorido-cuprate(II).

In the structure of the title salt, (C5H14N3)2[CuCl4], the Cu(II) atom in the anion lies on a twofold rotation axis. The tetra-chlorido-cuprate(II) anion adopts a flattened tetra-hedral coordination environment and inter-acts electrostatically with the tetra-methyl-guanidinium cation. The crystal packing is additionally consolidated through N-H⋯Cl and C-H⋯Cl hydrogen bonds, resulting in a three-dimensional network structure.

1,3-Bis(1-methyl-5-thioxo-1,2,4-triazolin-4-yl)urea

The title compound, C7H10N8OS2, was obtained by acylation of 4-amino-1-methyl-1,2,4-triazoline-5-thione with triphosgene. The asymmetric unit contains two half molecules. The full molecules are generated by twofold rotation axes. In the crystal, the molecules associate through bifurcated (N—H)2...O hydrogen bonds into chains extending in theb-axis direction.

4,4′-([4,4′-Bipyridine]-1,1′-diium-1,1′-diyl)dibenzoate dihydrate

We report here the synthesis of a neutral viologen derivative, C24H16N2O4·2H2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from the origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.

Crystal structure of trans-N,N'-bis-(3,5-di-tert-butyl-2-hy-droxy-phen-yl)oxamide methanol monosolvate.

The here crystallized oxamide was previously characterized as an unsolvated species [Jímenez-Pérez et al. (2000 ▸). J. Organomet. Chem. 614-615, 283-293], and is now reported with methanol as a solvent of crystallization, C30H44N2O4·CH3OH, in a different space group. The introduction of the solvent influences neither the mol-ecular symmetry of the oxamide, which remains centrosymmetric, nor the mol-ecular conformation. However, the unsolvated mol-ecule crystallized as an ordered system, while many parts of the solvated crystal are disordered. The hy-droxy group in the oxamide is disordered over two chemically equivalent positions, with occupancies 0.696 (4):0.304 (4); one tert-butyl group is disordered by rotation about the C-C bond, and was modelled with three sites for each methyl group, each one with occupancy 1/3. Finally, the methanol solvent, which lies on a twofold axis, is disordered by symmetry. The disorder affecting hy-droxy groups and the solvent of crystallization allows the formation of numerous supra-molecular motifs using four hydrogen bonds, with N-H and O-H groups as donors and the oxamide and methanol mol-ecule as acceptors.

Crystal structures of organoplatinum complexes containing alkyl-eugenoxyacetate and p-chloro-aniline.

In the title complexes, trans-di-chlorido-(4-chloro-aniline-κN){3-meth-oxy-4-meth-oxy-carbonyl-meth-oxy-1-[(2,3-η)-prop-2-en-1-yl]benzene}-platinum(II) 0.1-hydrate, [PtCl2(C6H6ClN)(C13H16O4)]·0.1H2O, (I), and trans-di-chlorido-(4-chloro-aniline-κN){4-eth-oxy-carbonyl-meth-oxy-3-meth-oxy-1-[(2,3-η)-prop-2-en-1-yl]benzene}-platinum(II), [PtCl2(C6H6ClN)(C14H18O4)], (II), the Pt(II) metal atom displays a slightly distorted square-planar coordination geometry defined by the aniline N atom, two chloride anions (trans-positioned) and one ethyl-enic double bond. The least-squares planes through the two aromatic ring systems make an angle of 47.3 (3)° for (I) and 38.6 (2)° for (II). Both structures show disorder for the PtCl2 fragment, in the case of (I) even further extended towards the CH2-CH=CH2 ligand. An intra-molecular C-H⋯Cl hydrogen bond occurs in (I). In the crystal packing of (I), which is dominated by N-H⋯O and C-H⋯Cl inter-actions, a partially occupied water mol-ecule is observed on a twofold rotation axis with a refined site occupancy of 0.10 (1). A C-H⋯π inter-action is also present. In (II), inversion dimers form chains along the b-axis direction by N-H⋯O hydrogen bonds.

Crystal structure of bis-(isonicotinamide-κN (1))bis-(thio-cyanato-κN)zinc.

The asymmetric unit of the title complex, [Zn(SCN)2(C6H6N2O)2], consists of one Zn(2+) cation located on a twofold rotation axis, as well as of one thio-cyanate anion and one neutral isonicotinamide ligand, both occupying general positions. The Zn(2+) cation is tetra-hedrally coordinated into a discrete complex by the N atoms of two symmetry-related thio-cyanate anions and by the pyridine N atoms of two isonicotinamide ligands. The complexes are linked by inter-molecular C-H⋯O and N-H⋯O, and weak inter-molecular N-H⋯S hydrogen-bonding inter-actions into a three-dimensional network.

Photonic crystal-based circulators with three and four ports for sub-terahertz region

Three- and four-port circulators based on resonators in 2D photonic crystals with square unit cell possessing a low symmetry are investigated. The three-ports are described by only one specific element named antiplane of symmetry. On the other hand, the four-port circulators formed by cascading these two three-ports can have one of the two symmetries. One of them is described by the antiplane of symmetry, and the other symmetry corresponds to a twofold rotational axis. The theoretical part of our paper concerns scattering matrix analysis of the devices with different symmetries and also the operation of the four-port circulator as a single-pole triple-throw switch. Finally, the calculated frequency responses of two circulators are presented.

Tubular Shape Fullerenes Inside Single Wall Boron Nitride Nanotubes: A Theoretical Simulation.

The orientations of fullerene molecules filled in nanotubes have important influence on the electronic properties of the formed peapods and their transformations such as polymerization under certain conditions. Here we present a investigation on the preferable orientations of tubular C70, C80 and C90 fullerenes confined inside single-walled boron nitride nanotubes (SWBNNTs) by calculating the van der Waals energy between the encapsulated molecule and the hosting nanotube. The minimum entering radius and the energetically favorable radius for encapsulating C70, C80 and C90 have been determined by the reaction energy calculation. We also show that the three studied molecules filled in SWBNNTs exhibit a transition from lying (five-fold axis) orientation to tilted orientation and then to standing orientation (two-fold axis) with increasing the tube radius. The preferable orientations of the encapsulated fullerenes are irrelevant on the tube chirality, but are dependent on the radius.

The stable orientations analysis of linearly arrayed C10H16 molecules in single-walled carbon nanotube by using the multiple-molecule model

A multiple-molecule model has firstly been constructed to study the stable orientations of encapsulated C10H16 molecules in single wall carbon nanotubes. The average molecular distance of adjacent C10H16 molecules is evaluated as 7.26Å. The orientational analysis show that tube’s confinement effect plays a leading role for the diameter distribution from 9.5Å to 11.75Å, in which C10H16s exhibit optimal three- and two-fold axis orientations with the diameter smaller and larger than 11.3Å, respectively. Then H…H repulsive interaction of adjacent C10H16 molecules plays an important role with diameter increased to 12.13Å, which induces a slant two-fold orientation.

4-Methyl-N-(4-methylpyridin-2-yl)-N-(3,4,5,6-tetrahydro-2H-pyran-4-yl)pyridin-2-amine

In the title compound, C17H21N3O, the pyridine rings make a dihedral angle of 84.44 (5)°. In the crystal, a C—H...N interaction forms a chain of molecules propagating along the twofold screw axis.

Crystal structure of hexa-kis-(di-methyl-formamide-κO)manganese(II) deca-kis-(di-methyl-formamide)-1κ(5) O,2κ(5) O-[μ-octa-deca-tungstodiphosphato(V)-κO:κO']dimanganate(II) di-methyl-formamide disolvate.

The crystal structure of the title compound, [Mn(C3H7NO)6][{Mn(C3H7NO)5}2(μ-P2W18O62)]·2C3H7NO, reveals that the Wells-Dawson-type polyanion [P2W18O62](6-), through terminal O atoms from the belts, bridges two Mn(II) octa-hedral complexes. In the complex anion [{Mn(dmf)5}2(μ-P2W18O62)](2-), located around a twofold rotation axis, the Mn(II) ions are coordinated by five O atoms from di-methyl-formamide (dmf) ligands and to a terminal O atom from the [P2W18O62](6-) polyanion. Another Mn(II) ion, located on an inversion centre, is coordinated by six O atoms from the dmf ligands and forms the [Mn(dmf)6](2+) cation. The crystal components are connected through numerous weak C-H⋯O hydrogen bonds to construct a three-dimensional network.

Crystal Structure of Human Herpesvirus 6B Tegument Protein U14.

The tegument protein U14 of human herpesvirus 6B (HHV-6B) constitutes the viral virion structure and is essential for viral growth. To define the characteristics and functions of U14, we determined the crystal structure of the N-terminal domain of HHV-6B U14 (U14-NTD) at 1.85 Å resolution. U14-NTD forms an elongated helix-rich fold with a protruding β hairpin. U14-NTD exists as a dimer exhibiting broad electrostatic interactions and a network of hydrogen bonds. This is first report of the crystal structure and dimerization of HHV-6B U14. The surface of the U14-NTD dimer reveals multiple clusters of negatively- and positively-charged residues that coincide with potential functional sites of U14. Three successive residues, L424, E425 and V426, which relate to viral growth, reside on the β hairpin close to the dimer's two-fold axis. The hydrophobic side-chains of L424 and V426 that constitute a part of a hydrophobic patch are solvent-exposed, indicating the possibility that the β hairpin region is a key functional site of HHV-6 U14. Structure-based sequence comparison suggests that U14-NTD corresponds to the core fold conserved among U14 homologs, human herpesvirus 7 U14, and human cytomegalovirus UL25 and UL35, although dimerization appears to be a specific feature of the U14 group.

Synthesis, structure and fluorescence properties of a novel 3D Sr(II) coordination polymer

Solvothermal reaction of 2,2′-bipyridine-5,5′-dicarboxylic acid (H2bpdc) and SrCl2 affords a novel coordination polymer [Sr(Hbpdc)2]n1. X-ray structure determination shows that 1 exhibits a novel three-dimensional network. The unique Sr II cation sits on a two-fold axis and coordinated by four O-atom donors from four Hbptc− ligands and four N-atom donors from two Hbptc− ligands in distorted dodecahedral geometry. In 1 each Sr II cation connects to six different Hbptc− ligands and each Hbptc− ligand bridges three different Sr II cations which results in the formation of a three-dimensional polymeric structure. Corresponding to the free ligand, the fluorescent emission of complex 1 display remarkable “Einstain” shifts, which may be attributed to the coordination interaction of Sr atoms, thus reduce the rigidity of pyridyl rings.