A formate bridged Ni(II) sheet and its 3D analogue in presence of a linear organic linker: Synthesis, crystal structure and magnetic properties

Reaction of formamide with Ni(NO3)(2)center dot 6H(2)O under hydrothermal condition in a mixture of MeOH/H2O forms a two-dimensional formate bridged sheet Ni(HCOO)(2)(MeOH)(2) (1). X-ray structure analysis reveals the conversion of formamide to formate which acts as a bridging ligand in complex 1 where the axial sites of Ni(II) are occupied by methanol used as a solvent. An analogous reaction in presence of 4,4'-bipyridyl (4,4'-bipy) yielded a three-dimensional structure Ni(HCOO)(2)(4,4'-bpy) (2). DC magnetic measurements as a function of temperature and field established the presence of spontaneous magnetization with T-c (Curie temperature) = 17 and 20.8 K in 1 and 2, respectively, which can be attributed due to spin-canting. DFT calculations were performed to corroborate the magnetic results of 1 and 2. (C) 2010 Elsevier Ltd. All rights reserved.

Ruthenium-Oxygen Coordination-Driven Self-Assembly of a Ru-8(II) Incomplete Prism: Synthesis, Structure, and Shape-Selective Molecular Recognition Study

Coordination-driven self-assembly of 1,3,5-benzenetricarboxylate (tma; 1) and oxalato-bridged p-cymeneruthenium(II) building block Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (2) affords an unusual octanuclear incomplete prism Ru-8(eta(6)-p-cymene)(8)(tma)(2)(mu-eta(4)-C2O4)(2)(OMe)(4)](O3SCF3)( 2) (3), which exhibits a remarkable shape-selective binding affinity for neutral phenolic compounds via hydrogen-bonding interactions (p-cymene = p-(PrC6H4Me)-Pr-i). Such a binding was confirmed by single-crystal X-ray diffraction analysis using 1,3,5-trihydroxybenzene as an analyte.

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions

The nucleotide sequence of cosmid B1790, carrying the Rif-Str regions of the Mycobacterium leprae chromosome, has been determined. Twelve open reading frames were identified in the 36716bp sequence, representing 40% of the coding capacity. Five ribosomal proteins, two elongation factors and the β and β'subunits of RNA polymerase have been characterized and two novel genes were found. One of these encodes a member of the so-called ABC family of ATP-binding proteins while the other appears to encode an enzyme involved in repairing genomic lesions caused by free radicals. This finding may well be significant as M. leprae, an intracellular pathogen, lives within macrophages.

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.

Structure and properties of Tl0.5Pb0.5Sr2Gd2−xCexCu2O9−δ

A systematic study of the Tl0.5Pb0.5Sr2Gd2−xCexCu2O9−δ system has revealed the existence of a pure phase in the compositional. range 0.0≤x≤0.6 crystalizzing in the 1222 structure. It has an intersheet distance of approximately 6 Å, a value much higher than those found in other cuprates with double CuO2 sheets interleaved by a single fluorite layer. Superconductivity has been observed in the range 0.1≤x≤0.4 with a Tc of 45 K and a superconductive volume fraction up to 20% for the optimal composition. An interesting variation of the superconducting properties of the above system with the composition, i.e. cerium content, has also been noticed. A possible dependence of superconductivity on the coupling between CuO2 sheets in the layered cuprates has been pointed out to bring out a correlation between structure and properties.

Structure and superconducting properties of a new family of thallium cuprates, TlSr3−xLnxCu2O7

Cuprates of the formula TlSr3−xLnxCu2O7 (Ln=Pr, NdorY) derived from the hypothetical TlSr3Cu2O7 show superconductivity with Tcs up to 95 K when 0.5less, approximatex≤0.75, the x=1.0 compositions being insulators. Rietveld analysis of X-ray diffraction profiles has been carried out for two superconducting members of this family. The unit cell a-parameter, and hence the in-plane Cu-O distance, increases with increase in x. The Tc value decreases with increase in x or the in-plane Cu-O distance in all the series of cuprates. Superconductivity in the Tl1−yPbySr3−xNdxCu2O7 systems is found with the highest Tc of 95 K when y=0.2 and x=0.5. The in-plane Cu-O distances in all the cuprates studied fall in the range found in the Sr-class of cuprate superconductors.

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Synthesis, structure and electrochemical properties of complexes with a (μ-oxo)bis-(μ-carboxylato)diruthenium(III) core

Reaction of [Ru2O(O2CR)2(MeCN)4(PPh3)2](ClO4)2 (1) with 1,2-diaminoethane (em) in MeOH---H2O yielded a mixture of products, from which a purple diamagnetic and 1:2 electrolytic diruthenium(III) complex, [Ru2O(O2CR)2(en)2(PPh3)2](ClO4)2 (2), was isolated along with a trace by-product of [Ru2O(O2CR)2(en)2(PPh3)2](ClO4)(MeCONH) (3) (R = C6H4-p-X : X = H, a; OMe, b; Me, c). Complex 3b has been characterized by X-ray diffraction analysis. The structure shows the presence of a (Ru2(?-O)(?-O2CR)22+)_core, with the metal centre bonded to an unidentate PPh3 and a bidentate chelating en terminal ligand. The Ru�Ru distance and the Ru�O�Ru angle in the core are 3.255(3) Å and 119.1(4)°. The amidate anion, formed presumably by nucleophilic attack of OH? on the MeCN ligand in complex 1, remains uncoordinated to the metal. In MeCN/0.1 M [NBun4]ClO4 complex 2 exhibits a nearly reversible Ru2III,III?Ru2III,IV couple near 0.9 V and an irreversible Ru2III,III?Ru2III,II process at ?0.6 V (vs S.C.E.). The mechanistic aspects of the substitution and nucleophilic reactions in the formation of complexes 2 and 3 are discussed. References

Synthesis, structure and redox properties of (?-oxo)bis(?-carboxylato)diruthenium(III) complexes containing three different terminal ligands

Blue coloured, unstable, essentially diamagnetic and non-electrolytic diruthenium(III) complexes of the formation [Ru2O(O2CR)4(en)2(PPh3)2] were prepared by reacting [Ru2O(O2CR)4(PPh3)2] with 1,2-diaminoethane (en) in CH2Cl2 (R = C6H4-p-X; X = H, Me and OMe). The molecular structure of the complexes is proposed as [{(?1-O2CR)(?1-en)(PPH3)Ru}2(?-O)(?-O2CR)2] based on the 1H NMR spectral data. The electronic spectra of the complexes display a band near 569 nm with a shoulder at 630 nm. In CH2Cl2-0.1 M [Bun4N]ClO4, the complexes exhibit redox couples Ru2III,III/Ru2III,IV and Ru2III,IV/Ru2IV,IV near 0.1 and 1.2 V (vs SCE), respectively. The potentials are the lowest among diruthenium(III) complexes with a similar core structure.