Twofold Axis Research Articles

Syntheses and crystal structures of 2-(p-tol-yl)-1H-perimidine hemihydrate and 1-methyl-2-(p-tol-yl)-1H-perimidine.

The title compounds, 2-(4-methylphenyl)-1H-perimidine hemihydrate (1, C18H14N2·0.5H2O) and 1-methyl-2-(4-methylphenyl)-1H-perimidine (2, C19H16N2), were prepared and characterized by 1H NMR and single-crystal X-ray diffraction. The organic mol-ecule of the hemihydrate lies on a twofold rotation axis while the water mol-ecule lies on the inter-section of three twofold rotation axes (point group symmetry 222). As a consequence, the hydrogen atoms that are part of the N-H group and the water mol-ecule as well as the CH3 group of the p-tolyl ring are disordered over two positions. In compound 1, the perimidine and the 2-aryl rings are slightly twisted while its N-methyl-ated derivative 2 has a more distorted conformation because of the steric repulsion between the N-methyl group and the 2-aryl ring. In the crystal structures, mol-ecules of perimidine 2 are held together only by C-H⋯π contacts while the parent perimidine 1 does not exhibit this type of inter-action. Its crystal packing is established by inter-molecular N-H⋯O hydrogen bonds with the solvent water mol-ecules and additionally stabilized by π-π stacking.

Synthesis, crystal structure and thermal properties of bis-(1,3-di-cyclo-hexyl-thio-urea-κS)bis(iso-thiocyanato-κN)cobalt(II).

Crystals of the title compound, [Co(NCS)2(C13H24N2S)2], were obtained by the reaction of Co(NCS)2 with 1,3-di-cyclo-hexyl-thio-urea in ethanol. Its crystal structure consists of discrete complexes that are located on twofold rotation axes, in which the CoII cations are tetra-hedrally coordinated by two terminal N-bonded thio-cyanate anions and two 1,3-di-cyclo-hexyl-thio-urea ligands. These complexes are linked via inter-molecular N-H⋯S and C-H⋯S hydrogen bonding into chains, which elongate in the b-axis direction. These chains are closely packed in a pseudo-hexa-gonal manner. The CN stretching vibration of the thio-cyanate anions located at 2038 cm-1 is in agreement with only terminal bonded anionic ligands linked to metal cations in a tetra-hedral coordination. TG-DTA measurements prove the decomposition of the compound at about 227°C. DSC measurements reveal a small endothermic signal before decomposition at about 174°C, which might correspond to melting.

Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.

The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P21212 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P21212 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus particle. RNA segments organized about the icosahedral twofold axes were present in crystals grown from ammonium sulfate and sodium chloride, as in the canonical I222 crystals (PDB entry 4oq8), but were not observed in crystals grown from sodium bromide and sodium nitrate. Bromide and nitrate ions generally replaced the RNA phosphates present in the I222 crystals, including the phosphates seen on fivefold axes, and were also found at threefold vertices in both the rhombohedral and cubic forms. An additional anion was also found on the fivefold axis 5 Å from the first anion, and slightly outside the capsid in crystals grown from sodium chloride, sodium bromide and sodium nitrate, suggesting that the path along the symmetry axis might be an ion channel. The electron densities for RNA strands at individual icosahedral dyads, as well as at the amino-terminal peptides of protein subunits, exhibited a diversity of orientations, in particular the residues at the ends.

Key carboxylate residues for iron transit through the prokaryotic ferritin SynFtn.

Ferritins are proteins forming 24meric rhombic dodecahedral cages that play a key role in iron storage and detoxification in all cell types. Their function requires the transport of Fe2+ from the exterior of the protein to buried di-iron catalytic sites, known as ferroxidase centres, where Fe2+ is oxidized to form Fe3+-oxo precursors of the ferritin mineral core. The route of iron transit through animal ferritins is well understood: the Fe2+ substrate enters the protein via channels at the threefold axes and conserved carboxylates on the inner surface of the protein cage have been shown to contribute to transient binding sites that guide Fe2+ to the ferroxidase centres. The routes of iron transit through prokaryotic ferritins are less well studied but for some, at least, there is evidence that channels at the twofold axes are the major route for Fe2+ uptake. SynFtn, isolated from the cyanobacterium Synechococcus CC9311, is an atypical prokaryotic ferritin that was recently shown to take up Fe2+ via its threefold channels. However, the transfer site carboxylate residues conserved in animal ferritins are absent, meaning that the route taken from the site of iron entry into SynFtn to the catalytic centre is yet to be defined. Here, we report the use of a combination of site-directed mutagenesis, absorbance-monitored activity assays and protein crystallography to probe the effect of substitution of two residues potentially involved in this pathway. Both Glu141 and Asp65 play a role in guiding the Fe2+ substrate to the ferroxidase centre. In the absence of Asp65, routes for Fe2+ to, and Fe3+ exit from, the ferroxidase centre are affected resulting in inefficient formation of the mineral core. These observations further define the iron transit route in what may be the first characterized example of a new class of ferritins peculiar to cyanobacteria.

Crystal structure of the potato leafroll virus coat protein and implications for viral assembly

Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.

Construction of novel hexanuclear Co(II) and dinuclear Ni(II) bis(salamo)‐type complexes

Two novel homomultinuclear complexes [Co6(L)2(μ‐OAc)4]·2CHCl3·CH3COCH3 (1) and [Ni2(L)(H2O)2(Py)2]·2CHCl3 (2) with a newly designed rigid bis(salamo)‐type tetraoxime ligand (H4L) were synthesized and characterized by elemental analyses, Fourier transform infrared (FT‐IR) spectra, UV–Vis absorption spectra, and X‐ray single‐crystal diffractions. Complex 1 is a novel triple‐decker symmetrical six‐core cluster structure with twofold axis and inversion center. The Co(II) atoms were sandwiched between the bis(salamo)‐type ligands and possess two different geometries of distorted tetragonal pyramid and octahedron, respectively. Complex 2 possesses a dinuclear structure and the Ni(II) atoms are located in the N2O2 cavities of the ligand, and axial coordination atoms come from the coordinated water and pyridine molecules. Both Ni(II) atoms adopt distorted octahedral geometries. The interactions were quantitatively determined by Hirshfeld surfaces analyses of complexes 1 and 2. The coordination ratios were determined by studying the fluorescence properties of complexes 1 and 2. The results of fluorescence titration experiment show that the metals to ligand binding ratios are 6:2 and 2:1 for complexes 1 and 2, respectively.

The structures of 1:1 and 1:2 adducts of phosphane-tricarbo-nitrile with 1,4-di-aza-bicyclo[2.2.2]octa-ne.

In the structures of 1:1 and 1:2 adducts of phosphanetricarbo-nitrile (C3N3P) with 1,4-di-aza-bicyclo-[2.2.2]octane (C6H12N2), the 1:1 adduct crystallizes in the ortho-rhom-bic space group, Pbcm, with four formula units in the unit cell (Z' = 0.5). The P(CN)3 unit lies on a crystallographic mirror plane while the C6H12N2 unit lies on a crystallographic twofold axis passing through one of the C-C bonds. The P(CN)3 moiety has close to C 3v symmetry and is stabilized by forming adducts with two symmetry-related C6H12N2 units. The phospho-rus atom is in a five-coordinate environment. As a result of the symmetry, the two trans angles are equal so τ5 = 0.00 and thus the geometrical description could be considered to be square pyramidal. However, the electronic geometry is distorted octa-hedral with the lone pair on the phospho-rous occupying the sixth position. As would be expected from VSEPR considerations, the repulsion of the lone-pair electrons with the equatorial bonding electrons means that the trans angles for the latter are considerably reduced from 180° to 162.01 (4)°, so the best description of the overall geometry for phospho-rus is distorted square pyramidal. The 1:2 adduct crystallizes in the monoclinic space group, P21/m with two formula units in the asymmetric unit (i.e. Z' = 1/2). The P(CN)3 moiety lies on a mirror plane and one of the two C6H12N2 (dabco) mol-ecules also lies on a mirror plane. The symmetry of the P(CN)3 unit is close to C 3v. There are three P⋯N inter-actions and consequently the mol-ecular geometry of the phospho-rus atom is distorted octa-hedral. This must mean that the lone pair of electrons on the phospho-rus atom is not sterically active. For the 1:1 adduct, there are weak associations between the phospho-rus atom and one of the terminal nitro-gen atoms from the C≡ N moiety, forming chains in the a-axis direction. In addition there are weak C-H⋯N inter-actions between a terminal nitro-gen atoms from the C≡N moiety and the C6H12N2 mol-ecules, which form sheets perpendicular to the a axis.

Synthesis, characterization and catalytic studies of chromium(III) porphyrin complex with axial cyanate ligands

We report the synthesis and the spectroscopic, structural and electrochemical characterization of a new chromium(III) coordination compound namely the bis(cyanato-κN)[meso-tetratolylporphyrinato]chromate(III) (cryptand-222)potassium dihydrate [K(crypt-222)][CrIII(TTP)(NCO)2]·2H2O (complex I). This compound crystallizes in the orthorhombic crystal system with the non-centrosymmetric space group C2221. The chromium and the potassium atoms are located at special positions in a two-fold axis. The crystal lattice of complex I is stabilized by O__H…O, C__H…O, C__H…N and C__H…π intermolecular contacts involving the negatively charged [CrIII(TTP)(NCO)2]− species, the [K(crypt-222)]+ counterions and the two non-coordinated water molecules. Further insights on these weak intermolecular contacts are provided by the Hirshfeld surface analysis. Molecular electrostatic potential (MEP) theoretical calculation on [K(crypt-222)][CrIII(TTP)(NCO)2]·2H2O are reported. The new Cr(III) complex was efficient as a catalyst in the decomposition of the Rhodamine B (RbH) dye by hydrogen peroxide. This coordination compound was also tested as a photocatalyst of the photodecomposition of the RbH dye by molecular oxygen.

Isostructural rubidium and caesium 4-(3,5-di-nitro-pyrazol-4-yl)-3,5-di-nitro-pyrazolates: crystal engineering with polynitro energetic species.

In the structures of the title salts, poly[[μ4-4-(3,5-di-nitro-pyrazol-4-yl)-3,5-di-nitro-pyrazol-1-ido]rubidium], [Rb(C6HN8O8)] n , (1), and its isostructural caesium analogue [Cs(C6HN8O8) n , (2), two independent cations M1 and M2 (M = Rb, Cs) are situated on a crystallographic twofold axis and on a center of inversion, respectively. Mutual inter-molecular hydrogen bonding between the conjugate 3,5-dinito-pyrazole NH-donor and 3,5-di-nitro-pyrazole N-acceptor sites of the anions [N⋯N = 2.785 (2) Å for (1) and 2.832 (3) Å for (2)] governs the self-assembly of the translation-related anions in a predictable fashion. Such one-component modular construction of the organic subtopology supports the utility of the crystal-engineering approach towards designing the structures of polynitro energetic materials. The anionic chains are further linked by multiple ion-dipole inter-actions involving the 12-coordinate cations bonded to two pyrazole N-atoms [Rb-N = 3.1285 (16), 3.2261 (16) Å; Cs-N = 3.369 (2), 3.401 (2) Å] and all of the eight nitro O-atoms [Rb-O = 2.8543 (15)-3.6985 (16) Å; Cs-O = 3.071 (2)-3.811 (2) Å]. The resulting ionic networks follow the CsCl topological archetype, with either metal or organic ions residing in an environment of eight counter-ions. Weak lone pair-π-hole inter-actions [pyrazole-N atoms to NO2 groups; N⋯N = 2.990 (3)-3.198 (3) Å] are also relevant to the packing. The Hirshfeld surfaces and percentage two-dimensional fingerprint plots for (1) and (2) are described.

Hexa-μ-acetato-chlorido-(μ-N,2-dioxodo-benzene-1-carboximidato)-μ3-oxido-tetra-iron(III)-water (1/1) and hexa-μ-acetato-(μ-N,2-dioxodo-benzene-1-carboximidato)fluorido-μ3-oxido-tri-pyridine-tetra-iron(III)-pyridine-water (1/1/0.24).

The title compounds, [Fe4(C2H3O2)6(C7H4O3)FO(C5H5N)3]·C5H5N·0.24H2O (1-F) and [Fe4(C2H3O2)6(C7H4O3)ClO(C5H5N)3]·H2O (1-Cl) were synthesized using a self-assembly reaction in methanol and pyridine with stoichiometric addition of salicyl-hydroxamic acid (H3shi), acetic acid (HOAc), and the appropriate ferric halide salt. The compounds crystallize as solvates, where 1-F has one pyridine mol-ecule that is disordered about a twofold axis and one water mol-ecule with an occupancy of 0.24 (2); and 1-Cl has one water mol-ecule that is disordered over two sites with occupancies of 0.71 (1) and 0.29 (1). The space groups for each analog differ as 1-F crystallizes in Fdd2 while 1-Cl crystallizes in P21. The difference in packing is due to changes in the inter-molecular inter-actions involving the different halides. The two mol-ecules are mostly isostructural, differing only by the torsion of the pyrine ligands and slight orientation changes in the acetate ligands. All of the iron(III) ions are in six-coordinate octa-hedral ligand field geometries but each one exhibits a unique coordination environment with various numbers of O (four to six) and N (nought to two) atom donors. Bond-valence sums confirm each iron is trivalent. The hydroximate ligand is bound to three iron(III) ions using a fused chelate motif similar to those in metallacrown compounds.

The role of conformational epitopes in the evolutionary divergence of enterovirus D68 clades: A bioinformatics-based study.

Enterovirus D68 (EV-D68), as one of the major pathogens of paediatric respiratory disease, has been widely spread in the population in recent years. As the basis of virus antigenicity, antigenic epitopes are essential to monitoring the transformation of virus antigenicity. However, there is a lack of systematic studies on the antigenic epitopes of EV-D68. In this study, a bioinformatics-based prediction algorithm for human enteroviruses was used to predict the conformational epitopes of EV-D68. The prediction results showed that the conformational epitopes of EV-D68 were clustered into three sites: site 1, site 2, and site 3. Site 1 was located in the "north rim" region of the canyon near the fivefold axis; site 2 was located in the "puff" region near the twofold axis; and site 3 consisted of two parts, one in the "knob" region on the south rim of the canyon and the other in the threefold axis region. The predicted epitopes overlapped highly with the binding regions of four reported monoclonal antibodies (mAbs), indicating that the predictions were highly reliable. Phylogenetic analysis showed that amino acid mutations in the epitopes of the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop played a crucial role in the evolutionary divergence of EV-D68 clades/subclades and epidemics. This finding indicated that the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop were the most important epitopes of EV-D68. Research on the epitopes of EV-D68 will contribute to outbreak surveillance and to the development of diagnostic reagents and recombinant vaccines.

Thermally Induced Reversible Metal-to-Metal Charge Transfer in Mixed-Valence {Fe III 4 Fe II 4 } Cubes

Thermally Induced Reversible Metal-to-Metal Charge Transfer in Mixed-Valence {Fe ^III ₄ Fe ^II ₄ } Cubes

1,1'-Methyl-enebis(4-tert-butyl-pyridinium) dichloride hemihydrate.

The structure of the title hydrated salt, C19H28N2 2+·2Cl-·0.5H2O, at 150 K has monoclinic (C2/c) symmetry. The water mol-ecule is located on a twofold rotation axis.

The order/disorder phase transition of hypophosphorous acid H3PO2

Abstract Hypophosphorous acid, H3PO2 is dimorphic with a phase transition in the 200–225 K range. The H3PO2 molecules are connected by hydrogen bonding to infinite chains extending in the [100] direction. In the high-temperature phase (P21212, Z ′ = 1 2 ${Z}^{\prime }=\frac{1}{2}$ ), the hydrogen bonds are disordered about a two-fold rotation axis. On cooling below the phase transition temperature, the hydrogen bonds become ordered, resulting in a symmetry reduction of the klassengleiche type of index 2. In the low-temperature phase (P212121, Z ′ = 1 ${Z}^{\prime }=1$ ), the c parameter is doubled with respect to the high-temperature phase. The hydrogen-bonding topology of the high- and low-temperature phases are double-infinite directed and undirected linear graphs, respectively.

Structure and Properties of Ln2MoO6 Oxymolybdates (Ln = La, Pr, Nd) Doped with Magnesium

The literature data and the results obtained by the authors on the study of the structure and properties of a series of polycrystalline and single-crystal samples of pure and Mg-doped oxymolybdates Ln2MoO6 (Ln = La, Pr, Nd) are analyzed. Presumably, the high-temperature phase I41/acd of Nd2MoO6 single crystals is retained at room temperature. The reason for the loss of the center of symmetry in the structures of La2MoO6 and Pr2MoO6 and the transition to the space group I4¯c2 is the displacement of oxygen atoms along the twofold diagonal axes. In all structures, Mg cations are localized near the positions of the Mo atoms, and the splitting of the positions of the atoms of rare-earth elements is found. Thermogravimetric studies, as well as infrared spectroscopy data for hydrated samples of Ln2MoO6 (Ln = La, Pr, Nd), pure and with an impurity of Mg, confirm their hygroscopic properties.

μ-Methyl-ene-bis-[di-bromido(diethyl ether-κO)aluminium(III)]: crystal structure and chemical exchange in solution.

In the title compound, [Al2Br4(CH2)(C4H10O)2], the mol-ecule lies on a crystallographic twofold axis passing through the bridging C atom. Each AlIII atom is four-coordinate, being bonded to two bromide ions, bridging the CH2 group as well as the oxygen atom of a diethyl ether ligand in a slightly distorted tetra-hedral arrangement with angles ranging from 101.52 (8) to 116.44 (5)°. The Al-CH2-Al angle, 118.4 (2)°, is the smallest observed for a structure where this moiety is not part of a ring. In the crystal, weak C-H⋯Br inter-actions, characterized as R 2 2(12) rings, link the mol-ecules into ribbons in the [101] direction. The title compound is monomeric and coordinatively saturated in the solid state, as each aluminum is four-coordinate, but in solution the ether mol-ecules from either or both Al atoms can dissociate, and would be expected to rapidly exchange, and this is supported by NMR data.

Aqua-(1,4,7,10-tetra-aza-cyclo-dodeca-ne)zinc(II) bis-(perchlorate).

The cationic ZnII part of aqua-(1,4,7,10-tetra-aza-cyclo-dodeca-ne)zinc(II) bis-(perchlorate), [Zn(C8H20N4)(H2O)](ClO4)2, exhibits a slightly distorted square-pyramidal coordination environment with a water mol-ecule in the apical position. In the crystal, the macrocyclic ring alternates between two conformations with equal occupancies. Two of the three perchlorate anions are situated about a twofold rotation axis, and one of them shows disorder of the O atoms with occupancies of 0.62 (7) and 0.38 (7). In the crystal, the complexes are connected by inter-molecular hydrogen bonding via the perchlorate anions.

Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase)

The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with two molecules as asymmetric unit. Both crystal forms were obtained from trace contaminants of an old commercial lipase preparation. Structures were determined and refined to 1.65Å and 1.43Å resolution respectively. The latter crystal has a non-crystallographic (NCS) twofold axis within the asymmetric unit. Glycosylation at Asn197 is evident, and in the tetragonal crystal can be seen to include three, partially disordered sugar residues following the initial N-acetyl glucosamine (NAG). Superposition of the tetragonal crystal model on the α-amylases from Bacillus subtilis (PDB:1BAG), pig pancreas (PDB:3L2L), and barley (PDB:1AMY), show a high degree of coincidence, particularly for the (β/α)8-barrel domains, and especially within the active site. Using this structural agreement between amylases, we extrapolated the binding model of a six residue, limit dextrin found in pig pancreas α-amylase to the A.oryzae enzyme model, which predicts substrate interacting amino acid residues.

Atomically Precise Insights into Metal–Metal Bonds Using Comparable Endo-Units of Sc 2 and Sc 2 C 2

The precise identification of metal–metal bonds is critical to fully understanding the nature of metal–metal bonding but remains a fundamental challenge. Herein, we show the essence of Sc–Sc bonds ...

Di-chlorido-(pyridine-κN)[2,3,5,6-tetra-kis-(pyridin-2-yl)pyrazine-κ3 N 2,N 1,N 6]nickel(II).

In the title complex, [NiCl2(C5H5N)(C24H16N6)], the NiII ion is six-coordinated in a distorted octa-hedral coordination environment defined by three N atoms of the tridentate 2,3,5,6-tetra-2-pyridyl-pyrazine ligand, one N atom of the pyridine ligand and two Cl- anions, with the latter being mutually trans. The complex is disposed about a twofold rotation axis along the a axis. The complex molecules are connected in the crystal via C-H⋯Cl, C-H⋯N and π-π [closest inter-centroid separation = 3.7446 (14) Å between pyridyl rings].