Twofold Rotation Axis Research Articles

Synthesis and crystal structure of a silver(I) 6-methylmercaptopurine riboside complex.

Silver nitrate reacts with 6-methylmercaptopurine riboside (6-MMPR) in aqueous solution containing methanol and dimethyl sulfoxide at room temperature to give a colourless crystalline complex, namely, bis(6-methylmercaptopurine riboside-κN7)(nitrato-κ2O,O')silver(I) 2.32-hydrate, [Ag(NO3)(C11H14N4O4S)2]·2.32H2O. The crystal structure, determined from synchrotron diffraction data, shows a central AgI ion on a crystallographic twofold rotation axis, coordinated in an almost linear fashion by two 6-MMPR ligands via atom N7 (purine numbering), with the nitrate counter-ion loosely coordinated as a bidentate ligand, forming a discrete molecular complex as an approximate dihydrate. The complex and water molecules are connected in a three-dimensional network by hydrogen bonding.

Di-chlorido-(4,7-dimeth-oxy-1,10-phenanthroline-κ2N,N')zinc(II).

In the title complex, [ZnCl2(C14H12N2O2)], the ZnII atom is located on a twofold rotation axis and is fourfold coordinated by two chlorido ligands and a bidentate 4,7-meth-oxy-1,10-phenanthroline ligand in a distorted tetra-hedral environment. Weak π-π stacking inter-actions between adjacent 4,7-dimeth-oxy-1,10-phenanthroline rings [centroid-to-centroid distances = 3.5969 (11) and 3.7738 (11) Å] contribute to the alignment of the complexes in layers parallel to (01).

Crystal structure of a water oxidation catalyst solvate with composition (NH4)2[FeIV(L-6H)]·3CH3COOH (L = clathrochelate ligand).

The synthetic availability of mol-ecular water oxidation catalysts containing high-valent ions of 3d metals in the active site is a prerequisite to enabling photo- and electrochemical water splitting on a large scale. Herein, the synthesis and crystal structure of di-ammonium {μ-1,3,4,7,8,10,12,13,16,17,19,22-dodeca-aza-tetra-cyclo-[8.8.4.13,17.18,12]tetra-cosane-5,6,14,15,20,21-hexa-onato}ferrate(IV) acetic acid tris-olvate, (NH4)2[FeIV(C12H12N12O6)]·3CH3COOH or (NH4)2[FeIV(L-6H)]·3CH3COOH is reported. The FeIV ion is encapsulated by the macropolycyclic ligand, which can be described as a dodeca-aza-quadricyclic cage with two capping tri-aza-cyclo-hexane fragments making three five- and six six-membered alternating chelate rings with the central FeIV ion. The local coord-ination environment of FeIV is formed by six deprotonated hydrazide nitro-gen atoms, which stabilize the unusual oxidation state. The FeIV ion lies on a twofold rotation axis (multiplicity 4, Wyckoff letter e) of the space group C2/c. Its coordination geometry is inter-mediate between a trigonal prism (distortion angle φ = 0°) and an anti-prism (φ = 60°) with φ = 31.1°. The Fe-N bond lengths lie in the range 1.9376 (13)-1.9617 (13) Å, as expected for tetra-valent iron. Structure analysis revealed that three acetic acid mol-ecules additionally co-crystallize per one iron(IV) complex, and one of them is positionally disordered over four positions. In the crystal structure, the ammonium cations, complex dianions and acetic acid mol-ecules are inter-connected by an intricate system of hydrogen bonds, mainly via the oxamide oxygen atoms acting as acceptors.

Tetra-aqua-(ethane-1,2-di-amine-κ2N,N')nickel(II) naphthalene-1,5-di-sulfonate dihydrate.

The reaction of ethane-1,2-di-amine (en, C2H8N2), the sodium salt of naphthalene-1,5-di-sulfonic acid (H2NDS, C10H8O6S2), and nickel sulfate in an aqueous solution resulted in the formation of the title salt, [Ni(C2H8N2)(H2O)4](C10H6O6S2)·2H2O or [Ni(en)(H2O)4](NDS)·2H2O. In the asymmetric unit, one half of an [Ni(en)(H2O)4]2+ cation and one half of an NDS2- anion, and one water mol-ecule of crystallization are present. The Ni2+ cation in the complex is positioned on a twofold rotation axis and exhibits a slight tetra-gonal distortion of the cis-NiO4N2 octa-hedron, with an Ni-N bond length of 2.0782 (16) Å, and Ni-O bond lengths of 2.1170 (13) Å and 2.0648 (14) Å. The anion is completed by inversion symmetry. In the extended structure, the cations, anions, and non-coordinating water mol-ecules are connected by inter-molecular N-H⋯O and O-H⋯O hydrogen bonding, as well as C-H⋯π inter-actions, forming a three-dimensional network.

Accurate X-ray diffraction data required for proper evaluation of bond valence sums and global instability indexes: redetermination of the crystal structures of diamond-like Cu2CdSiS4 and Cu2HgSnS4 as a case study.

Our calculations of the global instability index (G) values for some diamond-like materials with the general formula I2-II-IV-VI4 have indicated that the structures may be unstable or incorrectly determined. To compute the G value of a given compound, the bond valence sums (BVSs) must first be calculated using a crystal structure. Two examples of compounds with high G values, based on data from the literature, are the wurtz-stannite-type dicopper cadmium silicon tetrasulfide (Cu2CdSiS4) and the stannite-type dicopper mercury tin tetrasulfide (Cu2HgSnS4), which were first reported in 1967 and 1965, respectively. In the present study, Cu2CdSiS4 and Cu2HgSnS4 were prepared by solid-state synthesis at 1000 and 900 °C, respectively. The phase purity was assessed by powder X-ray diffraction. Optical diffuse reflectance UV/Vis/NIR spectroscopy was used to estimate the optical bandgaps of 2.52 and 0.83 eV for Cu2CdSiS4 and Cu2HgSnS4, respectively. The structures were solved and refined using single-crystal X-ray diffraction data. The structure type of Cu2CdSiS4 was confirmed, where Cd2+, Si4+ and two of the three crystallographically unique S2- ions lie on a mirror plane. The structure type of Cu2HgSnS4 was also verified, where all ions lie on special positions. The S2- ion resides on a mirror plane, the Cu+ ion is situated on a fourfold rotary inversion axis and both the Hg2+ and the Sn4+ ions are located on the intersection of a fourfold rotary inversion axis, a mirror plane and a twofold rotation axis. Using the crystal structures solved and refined here, the G values were reassessed and found to be in the range that indicates reasonable strain for a stable crystal structure. This work, together with some examples gathered from the literature, shows that accurate data collected on modern instrumentation should be used to reliably calculate BVSs and G values.

Crystal structure of K6[Zn(CO3)4].

The crystal structure of K6[Zn(CO3)4], hexa-potassium tetra-carbonato-zincate(II), comprises four unique potassium cations (two located on a general position, and two on the twofold rotation axis of the space group C2/c) and a [Zn(CO3)4]6- anion. The ZnII atom of the latter is located on the twofold rotation axis and is surrounded in a slightly distorted tetra-hedral manner by two pairs of monodentately binding carbonate groups, with Zn-O distances of 1.9554 (18) and 1.9839 (18) Å. Both carbonate groups exhibit a slight deviation from planarity, with the C atom being shifted by 0.008 (2) and 0.006 (3) Å, respectively, from the plane of the three O atoms. The coordination numbers of the potassium cations range from 6 to 8, using a threshold of 3.0 Å for K-O bonding inter-actions being significant. In the crystal structure, [KOx] polyhedra and [Zn(CO3)4]6- groups share O atoms to build up the framework structure.

Metal halide coordination compounds with quinazolin-4(3H)-one.

Three coordination compounds of quinazolin-4(3H)-one (quinoz; C8H6N2O) with divalent group 12 halides are reported. In all complexes, coordination occurs via the nitro-gen atom ortho to the quinazolinone carbonyl group. In the two chain polymers with composition [MX 2(quinoz)], viz. (M = Cd, X = Br), catena-poly[[[quinazolin-4(3H)-one-κN 3]cadmium(II)]-di-μ-bromido], [CdBr2(C8H6N2O)]n (I), and M = Hg, X = Cl, catena-poly[[[quinazolin-4(3H)-one-κN 3]mercury(II)]-di-μ-chlorido], [HgCl2(C8H6N2O)]n (II), the divalent cations are five-coordinate, with four bridging halide and one terminal quinoz ligand. The CdII atom in (I) has an almost trigonal-bipyramidal coordination environment, whereas the HgII atom in (II) has a more distorted coordination environment. Likewise, the halide bridges in (II) are significantly more asymmetric than in (I). In both (I) and (II), quinoz ligands at adjacent cations along each strand are oriented in opposite directions, and the organic ligands of neighboring strands inter-digitate with resulting π-π inter-actions. In contrast to the halide-bridged chain polymers (I) and (II), the adduct of quinoz with CdI2 is the tetra-hedral complex [CdI2(quinoz)2], di-iodido-bis-[quinazolin-4(3H)-one-κN 3]cadmium(II), [CdI2(C16H12N4O2)], (III). The CdII atom in this discrete complex is located on a twofold rotation axis. Disorder in (III) is reflected in an alternative minority orientation of the mol-ecules for which the iodine sites closely match the position of the majority orientation. In view of the low site occupancy of only 0.0318 (8) Å, only the CdII position for this alternative orientation was taken into account during refinement. In all three compounds, classical N-H⋯O hydrogen bonds with donor-acceptor distances of ca 2.9 Å occur; they link the polymer chains in (I) and (II) into di-periodic networks and connect adjacent discrete complexes in (III) to mono-periodic strands.

Chiral phonons in binary compounds [formula omitted]Bi ([formula omitted] = K, Rb, Cs) with P2[formula omitted]/c structure

Binary compounds ABi (A = K, Rb, Cs) crystallize in P21/c structure containing both clockwise and anticlockwise chiral chains of Bi atoms. Electronic band structure exhibits the insulating nature of these systems, with the band gap about 0.25eV. The presented study of dynamical properties confirm a stability of the system with P21/c symmetry. The crystal structure contains the quasi-one-dimensional Bi chains, exhibiting four-fold-like rotational “local” symmetry. Nevertheless, the system formally possesses two-fold rotational symmetry. Independently of the absence of the three-fold (or higher) rotational symmetry axes for the whole crystal, the chiral modes propagate along the Bi atom chains in these systems. We discuss basic properties of these modes in monoatomic chiral chains. We show that the two-fold rotational symmetry axis affects the main properties of the chiral phonons, which are not realized at the high-symmetry points, but along some paths between them in the reciprocal space. In addition, in the doped system, the chiral phonons possess non-zero total angular momentum.

Bis[5-methyl-2,3-bis-(thio-phen-2-yl)quinoxaline-κN1](nitrato-κ2O,O')silver(I).

The crystal structure of the title silver(I) complex, [Ag(NO3)(C17H12N2S2)2], has monoclinic (C2/c) symmetry, with the silver(I) atom and the nitrate group sitting on a twofold rotation axis. The complex also exhibits a thienyl-ring flip disorder, which is common for unsubstituted thio-phene rings.

Bis[2-(thio-phen-2-yl)quinoxaline-κN4]silver(I) perchlorate.

The crystal of the title salt, [Ag(C12H8N2S)2]ClO4, has C2/c symmetry whereby the silver(I) atom sits on a twofold rotation axis, as does the perchlorate anion, which is disordered about this axis. The thienylquinoxaline ligand is nearly planar with the thienyl ring making a dihedral angle of 10.88 (8)° with respect to the quinoxaline moiety.

Syntheses, Characterization, Crystal Structures and Antimicrobial Activity of Copper(II), Nickel(II) and Zinc(II) Complexes Derived from 5-Bromo-2- ((cychlopentylimino)methyl)phenol

Four new complexes of copper(II), nickel(II) and zinc(II), [CuL2] (1), [Ni3L2(4-BrSal)2(CH3COO)2(CH3OH)2]·2CH3OH (2), [ZnBr2(HL)2] (3) and [ZnL(dca)]n (4), where L is 5-bromo-2-(cychlopentylimino)methyl)phenolate, HL is the zwitterionic form of 5-bromo-2-((cychlopentylimino)methyl)phenol, 4-BrSal is the monoanionic form of 4-bromosalicylaldehyde, dca is dicyanamide anion, were synthesized and characterized by elemental analysis, IR and UV-Vis spectroscopy. The structures of the complexes were further confirmed by single crystal X-ray structure determination. Complex 1 is a mononuclear copper(II) compound, with a crystallographic two-fold rotation axis symmetry. The Cu atom is in distorted square planar coordination. Complex 2 is a trinuclear nickel(II) compound, with an inversion center symmetry. The Ni atoms are in octahedral coordination. Complex 3 is a mononuclear zinc(II) compound, while complex 4 is a dca bridged polymeric zinc(II) compound. The Zn atoms are in tetrahedral coordination. The compounds were assayed for their antimicrobial activities.

Syntheses, Characterization, Crystal Structures and Antimicrobial Activity of Copper(II), Nickel(II) and Zinc(II) Complexes Derived from 5-Bromo-2-((cychlopentylimino)methyl)phenol.

Four new complexes of copper(II), nickel(II) and zinc(II), [CuL2] (1), [Ni3L2(4-BrSal)2(CH3COO)2(CH3OH)2]·2CH3OH (2), [ZnBr2(HL)2] (3) and [ZnL(dca)]n (4), where L is 5-bromo-2-((cychlopentylimino)methyl)phenolate, HL is the zwitterionic form of 5-bromo-2-((cychlopentylimino)methyl)phenol, 4-BrSal is the monoanionic form of 4-bromosalicylaldehyde, dca is dicyanamide anion, were synthesized and characterized by elemental analysis, IR and UV-Vis spectroscopy. The structures of the complexes were further confirmed by single crystal X-ray structure determination. Complex 1 is a mononuclear copper(II) compound, with a crystallographic two-fold rotation axis symmetry. The Cu atom is in distorted square planar coordination. Complex 2 is a trinuclear nickel(II) compound, with an inversion center symmetry. The Ni atoms are in octahedral coordination. Complex 3 is a mononuclear zinc(II) compound, while complex 4 is a dca bridged polymeric zinc(II) compound. The Zn atoms are in tetrahedral coordination. The compounds were assayed for their antimicrobial activities.

Syntheses and crystal structures of bis-(4-methyl-pyridine-κN)bis-(seleno-cyanato-κN)zinc(II) and catena-poly[[bis-(4-methyl-pyridine-κN)cadmium(II)]-di-μ-seleno-cyanato-κ2 N:Se;κ2 Se:N].

The reactions of Zn(NO3)2 .6H2O and Cd(NO3)2 .4H2O with KSeCN and 4-meth-yl-pyridine (C6H7N; 4-picoline) lead to the formation of crystals of bis-(4-methyl-pyridine-κN)bis-(seleno-cyanato-κN)zinc(II), [Cd(NCSe)2(C6H7N)2] (1), and catena-poly[[bis-(4-methyl-pyridine-κN)cadmium(II)]-di-μ-seleno-cyanato-κ2 N:Se;κ2 Se:N], [Cd(NCSe)2(C6H7N)2] n (2), suitable for single-crystal X-ray diffraction. The asymmetric unit of compound 1 consists of one Zn cation that is located on a twofold rotation axis as well as one seleno-cyanate anion and one 4-methyl-pyridine ligand in general positions. The Zn cations are tetra-hedrally coordinated by two terminal N-bonding thio-cyanate anions and two 4-methyl-pyridine ligands, forming discrete complexes. The asymmetric unit of compound 2 consists of two crystallographically independent Cd cations, of which one is located on a twofold rotation axis and the second on a center of inversion, as well as two crystallographically independent seleno-cyanate anions and two crystallographically independent 4-methyl-pyridine ligands in general positions. The Cd cations are octa-hedrally coordinated by two N- and two S-bonding seleno-cyanate anions and two 4-methyl-pyridine ligands and are linked into chains by pairs of seleno-cyanate anions. Within the chains, the Cd cations show an alternating cis-cis-trans and all-trans coordination and therefore, the chains are corrugated. PXRD investigations prove that the Zn compound was obtained as a pure phase and that the Cd compound contains a very small amount of an additional and unknown phase. In the IR spectrum of 1, the CN stretching vibration of the seleno-cyanate anion is observed at 2072 cm-1, whereas in the 2 it is shifted to 2094 cm-1, in agreement with the crystal structures.

The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids.

Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic "jelly-roll" fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.

Synthesis and structure of clozapine N-oxide hemi(hydro-chloride): an infinite hydrogen-bonded poly[n]catenane.

The structure of the title compound, 2C18H19ClN4O·HCl or (CNO)2·HCl (C36H39Cl3N8O2), at 100 K has tetra-gonal (I4/m) symmetry. The dihedral angle between the benzene rings of the fused ring system of the CNO mol-ecule is 40.08 (6)° and the equivalent angle between the seven-membered ring and its pendant N-oxide ring is 31.14 (7)°. The structure contains a very strong, symmetrical O-H⋯O hydrogen bond [O⋯O = 2.434 (2) Å] between two equivalent R 3N+-O- moieties, which share a proton lying on a crystallographic twofold rotation axis. These units then form a (CNO)4·(HCl)2 ring by way of two equivalent N-H⋯Cl hydrogen bonds (Cl- site symmetry m). These rings are catenated into infinite chains propagating along the c-axis direction by way of shape complementarity and directional C-H⋯N and C-H⋯π inter-actions.

High-pressure study of the aurophilic topological Dirac material AuI

We endeavour to explore the high-pressure study in the aurophilic AuI within the state-of-the-art of first principles. The impediment of expressing precise ground-state features of aurophilic compounds that had afflicted prior theoretical research has been resolved by incorporating van der Waals corrections (vdw). Mechanical and dynamical stability are ensured at ambient using the computed elastic constants and phonon dispersion curves. The dynamical instability is triggered by the application of pressure in AuI, as evidenced by the softening of an acoustic mode (Eu) at ∼7 GPa. Non-adherence of estimated elastic constants to the Born stability criterion at this pressure illustrates the system's mechanical instability. As previously demonstrated in experiments, the pressure-driven amorphization is rationalised by the phonon softening and elastic instability. Our calculations of the electronic band structure reveal an indirect bandgap (2.31 eV). Z2 invariants confirm that non-symmorphic AuI is a non-trivial Dirac material with the inclusion of spin-orbit coupling. Furthermore, a type-A hourglass dispersion with movable Dirac point is observed at the two-fold screw rotation axis (C2y). The pressure-dependent electronic structure reveal that the band topology is unaffected by pressure up to amorphous state. Our findings predict that this aurophilic class of material AuI possess exotic structural and electronic properties, encouraging further studies.

μ-Oxido-bis-[(5,10,15,20-tetra-phenyl-porphyrinato-κ4 N,N',N'',N''')manganese(III)].

In the crystal structure of the title oxido-bridged binuclear complex, [MnIII(TPP)]2O (TPP = tetra-phenyl-porphyrinate, C44H28N4) or [Mn2(C44H28N4)2O], the two penta-coordinate manganese(III) ions are bridged by a single oxido ligand, with an Mn-O distance of 1.7600 (3) Å and an Mn-O-Mn bridging angle of 176.1 (2)°. The bridging O2- ligand is located on a twofold rotation axis, resulting in point group 2 for the entire complex. The MnIII atom is displaced out of the 24-atom mean plane of the porphyrine entity by 0.52 Å. C-H⋯π and π-π inter-actions help to stabilize the mol-ecular packing within the crystal structure.

Crystal structure and Hirshfeld surface analysis of 2,2'-(phenyl-aza-nedi-yl)bis-(1-phenyl-ethan-1-one).

The whole mol-ecule of the title compound, C22H19NO2, is generated by twofold rotational symmetry. The N atom exhibits a trigonal-planar geometry and is located on the twofold rotation axis. In the crystal, mol-ecules are linked by C-H⋯O contacts with R 2 2(12) ring motifs, and C-H⋯π inter-actions, resulting in ribbons along the c-axis direction. van der Waals inter-actions between these ribbons consolidate the mol-ecular packing. Hirshfeld surface analysis indicates that the greatest contributions to the crystal packing are from H⋯H (45.5%), C⋯H/H⋯C (38.2%) and O⋯H/H⋯O (16.0%) inter-actions.

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.