Coordinate Square Research Articles

Syntheses and Characterization of Some Tetradentate Schiff‐Base Complexes and Their Heteroleptic Analogues

VO(IV), Ni(II) and Cu(II) complexes of the asymmetric Schiff base [(HOC6H3(OCH3)C(C6H5):N(CH2CH2)N:C(CH3)CH:C(C6H5)OH)], and their heteroleptic analogues with triphenyl phosphine and 2,2’‐bipyridine have been synthesized and characterized by elemental analyses, conductance, magnetic, infrared and electronic spectral measurements. The ligand is tetradentate coordinating via the imine N and enolic O atoms. The Ni(II) and Cu(II) complexes adopt a four coordinate square planar geometry, the VO(IV) complex is five coordinate square‐pyramidal and the heteroleptic complexes are 6‐coordinate, octahedral. The assignment of geometry is collaborated by magnetic moments and electronic spectra measurements. The compounds are non‐electrolyte in nitromethane and are magnetically dilute.

Trivalent metal ion directed synthesis and characterization of macrocyclic complexes

A novel series of complexes of the type [M(TML)X]X2, where TML is a tetradentate macrocyclic ligand, M = Cr(III), Mn(III) or Fe(III), X = Cl-, CH3COO- or ? NO3, were synthesized by template condensation of dibenzoyl and thiocarbohydrazide in the presence of trivalent metal salts in a methanolic medium. The complexes were characterized with the help of elemental analyses, conductance measurements, molecular weight determination, magnetic measurements, electronic, NMR, infrared and far infrared spectral studies. The electronic spectra together with the magnetic moments suggest five coordinate square pyramidal geometry for these complexes. The molar conductance indicates them to be 1:2 electrolytes.

Synthesis and biological evaluation of copper (II) complexes of sterically hindered o-aminophenol derivatives as antimicrobial agents

Cu(II) complexes with 4,6-di( tert-butyl)-2-aminophenol ( I) and 2-anilino-4,6-di( tert-butyl)phenol ( II) have been synthesized and characterized by means of elemental analysis, TG/DTA, FT-IR, UV–vis, ESR, and conductance measurements. The compounds I and II can coordinate in their singly deprotonated forms and behave as bidentate O,N-coordinated ligands; their CuL 2 complexes are characterized by CuN 2O 2 coordination modes and square planar geometry. In vitro antimicrobial screening against Gram-positive and Gram-negative bacteria, yeasts, and moulds indicated that the compound I and its Cu(II) complex were more active than Questiomycin B, the compound II, and its Cu(II) complex.

Spectroscopic characterization and EPR spectral studies on transition metal complexes with a novel tetradentate, 12-membered macrocyclic ligand

Complexes of Cr(III), Mn(II), Co(II), Ni(II) and Cu(II) containing a tetradentate macrocyclic N-donor ligand have been prepared via template reaction of 2,3-pentanedione, ethylene-di-ammine and transition metal ions. The complexes have been characterized on the basis of the elemental analysis, molar conductance, magnetic moment susceptibility, IR, electronic and EPR spectral studies. The complexes are of high spin type and possess four coordinate tetrahedral five coordinate square pyramidal and six coordinated octahedral/tetragonal geometry.

Manganese Stereochemistry in the Structures of Oxygen-Containing Compounds

The Voronoi-Dirichlet polyhedra (VDP) and the method of intersecting spheres were used to carry out crystal chemical analysis of coordination of 1304 sorts of Mn atoms in the structure of 859 oxygen-containing compounds. The manganese atoms whose oxidation number varies from 2 to 7 were found to bind 4 to 8 oxygen atoms giving rise to the MnO n coordination tetrahedra (n = 4), square pyramids (n = 5), octahedra or trigonal prisms (n = 6), pentagonal bipyramids or one-cap trigonal prisms (n = 7), trigonal dodecahedra, cubes, square antiprisms, or hexagonal bipyramids (n = 8). The effect of the valence state and the coordination number of manganese atoms on the parameters of their VDP was studied. The existence of a general linear correlation between the solid angles of the VDP faces corresponding to Mn-O bonds and the corresponding interatomic distances, which vary over a broad range (1.55–3.12 A), was established. The VDP characteristics can be used to determine the valence state of Mn atoms in the crystal structures and in the crystal chemical analysis of manganites with giant magnetoresistance.

Bis(μ-phenyl 2-pyridyl ketoneN4,N4-butane-1,4-diylthiosemicarbazonato)bis[chlorocopper(II)

The title compound, [Cu2(C17H17N4S)2Cl2], exhibits a dimeric structure related by a centre of symmetry. The monomers are linked to each other by the longest Cu-S apical distance observed to date among Cu(II) square-pyramidal complexes of N4-substituted thiosemicarbazones. Each Cu(II) atom deviates from the coordination square plane, which contains the pyridyl and imine N atoms, the thiolate S atom and the Cl- anion, towards the S atom of the adjacent monomer. The dimers pack in a zigzag manner through the crystal.

Copper(II) complexes with twelve to fourteen membered ring macrocyclic ligands

Copper(II) complexes of general composition Cu(L)X 2 [where L = 3,9-diethyl-2,10-dimethyl-1,4,8,11-tetraazacyclotetradeca1,3,8,10-tetraene (DSLB); 2,9-diethyl-2,10-dimethyl-1,4,7,10-tetraaza-5,6:11,12-dibenzotricyclo[2,4,4]dodeca-1,3,7,9-tetraene (DSLC); 3,8-diethyl-2,6,9,11-tetramethyl-1,4,7,10-tetraazacyclododeca-1,3,7,9-tetraene (DSLD); X = Cl-, NO - 3 , ½SO 2 - 4 ] have been synthesized. The complexes have been characterized on the basis of elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, electronic and EPR spectral studies. The complexes were found to stabilize tetragonal geometry except Cu(L)SO 4 which is of a five coordinate square pyramidal geometry.

Supramolecular structures of oxovanadium(IV) polymeric complexes containing quinoline azodyes

A novel series of oxovanadium(IV) monomeric and polymeric complexes with 5-(4′ derivatives phenylazo)-8-hydroxy-7-quinolinecarboxaldehyde (HLn) has been synthesized and characterized. The composition, structural, chemical and electronic properties were investigated by elemental analysis followed by 1H-NMR to determine the effect of substituents on the intramolecular hydrogen bond. The electronic properties and model of bonding of ligands as well as complexes were investigated by UV-Vis and IR spectroscopy. Comparison with reference data along with electronic and IR spectroscopies allow identification of the molecular structures for the polymeric complexes, where a six coordinate square planar with an oxygen atom in the apical position was proposed. Data from the above combined techniques reveal the formation of two isomeric forms. The polymeric structure results from intermolecular V=O…V=O interactions, whereas the ligands act as a monobasic bidentate chelating agent coordinating through CO and OH groups by replacing a proton from the latter group.

The MPSim‐Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals

To help improve the accuracy of protein-ligand docking as a useful tool for drug discovery, we developed MPSim-Dock, which ensures a comprehensive sampling of diverse families of ligand conformations in the binding region followed by an enrichment of the good energy scoring families so that the energy scores of the sampled conformations can be reliably used to select the best conformation of the ligand. This combines elements of DOCK4.0 with molecular dynamics (MD) methods available in the software, MPSim. We test here the efficacy of MPSim-Dock to predict the 64 protein-ligand combinations formed by starting with eight trypsin cocrystals, and crossdocking the other seven ligands to each protein conformation. We consider this as a model for how well the method would work for one given target protein structure. Using as a criterion that the structures within 2 kcal/mol of the top scoring include a conformation within a coordinate root mean square (CRMS) of 1 A of the crystal structure, we find that 100% of the 64 cases are predicted correctly. This indicates that MPSim-Dock can be used reliably to identify strongly binding ligands, making it useful for virtual ligand screening.

Ambivalent intercalators for DNA: L-shaped platinum(II) complexes.

Novel platinum(II) square planar coordination complexes, in which two heteroaromatic ligands are held by the metal in an unusual L-shaped geometry orthogonal to each other, have been synthesized, and their interaction with DNA was investigated with absorption and linear dichroism spectroscopy. As a rule, the ligand that is coplanar with the coordination square of Pt is found to be oriented perpendicular relative to the DNA helix axis when bound, suggestive of its intercalation between the base pairs of DNA. However, when this coplanar ligand is replaced by two pyridines, the opposite ligand, orthogonal to the coordination square, is instead preferentially intercalated. This behavior shows that these new complexes do indeed show some properties of true ambintercalators, i.e., compounds that can bind by intercalation of either of two distinct aromatic moieties.

Parametric representation of the elastic wave in anisotropic media

Shortly after his appointment to the first geophysical professorship (1895 at the Jagiellonian University of Cracow), Rudzki had published two papers in which he made a strong case for anisotropy of crustal rocks [Beitr. Geophys. 2 (1898); Bull. Acad. Sci. Crac. (1899)]. He had solved the Christoffel equation for transversely isotropic media in terms of what we today would call the “slowness surface”. Rudzki regarded this as the representation of the wave surface in line coordinates. The conversion to point coordinates lead to an equation of 12th degree. Rudzki had determined a few points, but this was not sufficient to obtain an impression of the wavefront. Costanzi [Boll. Soc. Sismol. Ital. 7 (1901)] had suggested to simplify the coordinate conversion by expressing the solution of the Christoffel equation in a parameter form. The first part of the current paper describes the implementation of this idea. For the first time, the cusps in the wave surface became visible. The results of this first part have been discussed and expanded by Helbig [Beitr. Geophys. 67 (1958) 177; Bull. Seismol. Soc. Am. 56 (1966) 527; Helbig, K., 1994. Foundations of Anisotropy for Exploration Geophysics. Pergamon] and Khatkevich [Isv. Akad. Nauk. SSSR, Ser. Geofiz. 9 (1964) 788]. In a second part, Rudzki applied the ideas to orthorhombic media. The process is straightforward: the elements of the characteristic determinant are of order 2 in the three line coordinates (the three slowness components), with squares of coordinates in the diagonal elements and products of two coordinates in the off-diagonal elements. The elements are easily manipulated so that they are expressed in terms of squares only. Next, the determinant is expanded in terms of rows. This leads to three (equivalent) expressions. The vanishing of any of the three expressions means that the characteristic determinant vanishes, i.e., it corresponds to a solution of the Christoffel equation. Each of the equations can be used to determine one of the sheets of the line coordinates of the wave surface (point coordinates of the slowness surface). To this end, it is expressed in terms of two parameters, which have been chosen strictly for mathematical convenience. After conversion of the line coordinates to point coordinates (formation of the envelopes), one obtains a parameter expression for the wave surface. Until today, the second part of the Rudzki's paper has not been closely studied. However, a blind test of the equations showed that they indeed describe the wave surface of orthorhombic media. The final sections discuss a few interesting aspects, among them the stability conditions for orthorhombic media and the condition under which a transversely isotropic medium transmits pure P- and S-waves.

Characterization of Ni–Pd alloy as anode for methanol oxidative fuel cell

Electrochemical deposition of Ni–Pd alloy films of various compositions from bath solution containing ethylenediamine (EDA) was carried out to use as anode material for methanol oxidative fuel cell in H 2SO 4 medium. Electronic absorption spectrum of bath solution containing Ni 2+, Pd 2+ ions and EDA indicated the formation of a four coordinate square planar metal–ligand complex of both the metal ions. X-ray diffraction (XRD) patterns of the deposited alloy films show an increase in Pd–Ni alloy lattice parameter with increase in Pd content, and indicate the substitution of Pd in the lattice. A nano/ultrafine kind of crystal growth was observed in the alloy film deposited at low current density (2.5 mA cm −2). X-ray photoelectron spectroscopic (XPS) studies on the successively sputtered films showed the presence of Ni and Pd in pure metallic states and the surface concentration ratio of Ni to Pd is less than bulk indicating the segregation of Pd on the surface. Electro-catalytic oxidation of methanol in H 2SO 4 medium is found to be promoted on Ni–Pd electrodeposits. The anodic peak current characteristics to oxidation reaction on Ni–Pd was found typically high when compared to pure nickel and the relative increase in surface area by alloying the Ni by Pd was found to be as much as 300 times.

Palladium (II) compounds with diaminocarboxylic acids: Crystal structures of [Pd(H2 Cdta)] · H2O, [Pd(H3 Edtp)Cl] · 2H2O, and (H6 Edtp)[PdCl4] · 4H2O

The crystal structures of three Pd(II) compounds with diamine tetracarboxylates in different protonation states are determined, namely, [Pd(H2 Cdta)] · H2O (I), [Pd(H3 EdtpCl] · 2H2O (II), and (H6 Edtp)[PdCl4] · 4H2O (III) (R 1 = 0.0230, 0.0313, and 0.0277 for 3040, 3377, and 3809 reflections with I > 2σ(I) for I–III, respectively). Crystals I and II are built of neutral complexes [Pd(H2 Cdta)] and [Pd(H3 Edtp)Cl], respectively, and crystallization water molecules. Crystal III consists of [PdCl4]2− anionic complexes, H6 Edtp 2+ cations, and water molecules. In I, one of the protonated acetate groups of the H2 Cdta 2− ligand forms a very weak additional Pd-O bond [2.968(2) A] over the 2N + 2O coordination square. In II and III, the protonated propionate groups of the H3 Edtp − ligand and the H6 Edtp 2+ cation are not involved in Pd coordination and the coordination squares consist of the 2N + O + Cl and 4Cl atoms, respectively.

Supramolecular assembly at interfaces: formation of an extended two-dimensional coordinate covalent square grid network at the air-water interface.

Reaction of a Langmuir monolayer of an amphiphilic pentacyanoferrate(3+) complex with Ni(2+) ions from the subphase results in the formation of a two-dimensional iron-nickel cyanide-bridged network at the air-water interface. The network can be transferred to various supports to form monolayer or multilayer lamellar films by the Langmuir-Blodgett (LB) technique. The same network does not form from homogeneous reaction conditions. Therefore, the results demonstrate the potential utility of an interface as a structure director in the assembly of low dimensional coordinate covalent network solids. Characterization of the LB film extended networks by X-ray photoelectron spectroscopy (XPS), FT-IR spectroscopy, SQUID magnetometry, X-ray absorption fine structure (XAFS), and grazing incidence synchrotron X-ray diffraction (GIXD) revealed a face-centered square grid structure with an average domain size of 3600 A(2). Magnetic measurements indicated that the network undergoes a transition to a ferromagnetic state below a T(c) of 8 K.

Structural isomerism among octanuclear oxomolybdenum(V) coordination compounds with pyridines. Two isomers of [Mo 8O 16(OCH 3) 8(RPy) 4

The condensation of dinuclear {Mo 2O 4} 2+ leads, under conditions of the solvothermal synthesis, to two distinct architectures: (i) the cluster species of [Mo 8O 16(OCH 3) 8Py 4]·2CH 3OH (Py=pyridine, C 5H 5N) ( 1·2CH 3OH) whose four building blocks, {Mo 2O 4} 2+ units, are linked through doubly or triply bridging oxo and methoxo groups into a compact array; and (ii) [Mo 8O 16(OCH 3) 8(4-MePy) 4] (4-MePy=4-methylpyridine, C 6H 7N) ( 2) which displays an open, bent cyclic structure made of four building blocks linked to each other by pairs of methoxo bridges. The MoMo distances within dinuclear units, 2.5638(12) and 2.6012(13) Å in 1, and 2.5661(3) Å in 2, are characteristic for single metal–metal bonds. All metal atoms of 1 are in a distorted octahedral coordination; each octahedron shares several edges (two, three or four) with its neighbors. Compound 2 displays two types of coordination polyhedra, square pyramids and octahedra (four of each) that are connected through common edges. Each polyhedron shares two edges with the adjacent polyhedra.

Synthesis, spectral and cytotoxicity studies of palladium(II) and platinum(II) amino acid Schiff base complexes

Novel PdII and PtII complexes of substituted o-hydroxyacetophenone-glycine have been synthesized, and characterized by conductivity measurements, i.r., electronic and 1H-n.m.r. spectra. The spectral data indicate that the ligands are monobasic bidentate, coordinating through imino nitrogen and the carboxylate group. A four coordinate square planar configuration has been proposed for all the complexes. The ligands, as well as their PdII and PtII complexes, exhibit potent cytotoxic activity against Ehrlich ascites tumour cells in vitro, but appear to be more active in vivo.

Metal Complexes with Cis alpha Topology from Stereoselective Quadridentate Ligands with Amine, Pyridine, and Quinoline Donor Groups.

Though the principles governing quadridentate topology and metal stereochemistry have been known for some time, the cis alpha topology has been little exploited in designing catalysts for asymmetric reactions. Investigation of the inorganic chemistry of labile metal cis alpha complexes was undertaken as a prelude to exploring their potential to serve as catalysts for a variety of different reactions. The synthesis of a series of first row transition metal complexes of quadridentate ligands with ethylenediamine (en) and S-propylenediamine (S-pn) backbones that have been alkylated at nitrogen with either pyridine (py) or quinoline (qn) donor groups as well as with noncoordinating benzyl (Bn) or pentafluorobenzyl (F(5)Bn) groups was undertaken. The steric and electronic properties vary throughout the ligand series, en(Bn)py, 1, en(F(5)Bn)py, 2, S-pn(F(5)Bn)py, 3, and S-pn(F(5)Bn)qn, 4. These ligands were reacted with MCl(n)() salts (n = 2, M = Mn, Fe, Co, Ni, Cu, Zn; n = 3, M = Fe) to generate, in most cases, octahedral complexes with the targeted cis alpha topology. UV/vis, NMR, IR, cyclic voltammetry (CV), and conductivity analysis are described for the metal compounds. X-ray structural analysis of [Cu{en(F(5)Bn)py}Cl]Cl reveals a five coordinate square pyramidal geometry. Single or major diastereomers were obtained for all diamagnetic Zn(II) complexes as well as for Co(III) analogues that were prepared by oxidation of Co(II) species using Br(2) as the oxidant. Electronic differences among ligands are reflected in the oxidation potentials of the respective metal complexes as determined by CV, with fluorinated systems showing greater resistance to oxidation, as expected.

Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model

A new, efficient method for the assembly of protein tertiary structure from known, loosely encoded secondary structure restraints and sparse information about exact side chain contacts is proposed and evaluated. The method is based on a new, very simple method for the reduced modeling of protein structure and dynamics, where the protein is described as a lattice chain connecting side chain centers of mass rather than Calphas. The model has implicit built-in multibody correlations that simulate short- and long-range packing preferences, hydrogen bonding cooperativity and a mean force potential describing hydrophobic interactions. Due to the simplicity of the protein representation and definition of the model force field, the Monte Carlo algorithm is at least an order of magnitude faster than previously published Monte Carlo algorithms for structure assembly. In contrast to existing algorithms, the new method requires a smaller number of tertiary restraints for successful fold assembly; on average, one for every seven residues as compared to one for every four residues. For example, for smaller proteins such as the B domain of protein G, the resulting structures have a coordinate root mean square deviation (cRMSD), which is about 3 A from the experimental structure; for myoglobin, structures whose backbone cRMSD is 4.3 A are produced, and for a 247-residue TIM barrel, the cRMSD of the resulting folds is about 6 A. As would be expected, increasing the number of tertiary restraints improves the accuracy of the assembled structures. The reliability and robustness of the new method should enable its routine application in model building protocols based on various (very sparse) experimentally derived structural restraints.

2,3-Bis(salicylideneamino-O,N)pyridinato]nickel(II)

The coordination around the Ni atom in the title compound, {2,2′-[2,3-pyridindiylbis(iminomethyl)]diphenolato}nickel(II), [Ni(C19H13N3O2)], is slightly distorted from square planar. Within the coordination square the bond angles are in the range 83.8 (1)–94.8 (2)°. The Ni—N and Ni—O distances are equal within experimental error with average values of 1.854 (2) and 1.835 (2) Å, respectively. Comparisons of bond lengths in free and Ni-coordinated ligands indicate shortening of the C—O bonds due to the packing effect. On complex formation, the whole molecule assumes a more planar form, which brings the Ni atoms from neighbouring molecules as close as 3.1908 (10) Å to each other.

(2,2'-Bipyridyl-N,N')dibromopalladium(II)

The title complex, [PdBr2(C10H8N2)], has square-planar geometry for Pd with Pd—N 2.047 (5) and Pd—Br 2.4102 (9) Å. The mean planes of the coordinated pyridine groups form a dihedral angle of 1.7 (3)° with the coordination square plane; the parallel complexes stack with inter­planar spacing of 3.41 (1) Å and a Pd⋯Pd separation of 5.246 (1) Å to form a chain structure as reported for isomorphous PtI2(bipy) (where bipy = C10H8N2). The structure differs from those found for related chain structures in the `red' form of PtCl2(bipy) and in PdCl2(bipy) which is isomorphous with the `yellow' form of PtCl2(bipy).