Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CpG)

The crystal and molecular structure of the ammonium salt of deoxycytidylyl-(3'-5')-deoxyguanosine has been determined from 0.85 A resolution single crystal X-ray diffraction data. The crystals obtained by acetone diffusion technique at -20 degrees C, are orthorhombic, P212121, a = 12.880(2), b = 17444(2) and c = 27.642(2) A. The structure was solved by high resolution Patterson and Fourier methods and refined to R = 0.136. There are two d(CpG) molecules in the asymmetric unit forming a mini left handed Z-DNA helix. This is in contrast to the earlier reported forms of d(CpG) where the molecules form self base paired duplexes. There are two ammonium ions in the asymmetric unit. The major groove NH+4 ion interacts with N7 of guanines through water bridges besides making H-bonded interactions directly with the phosphate oxygen atoms. A second NH+4 ion is found in the minor groove interacting directly with the phosphate oxygen atoms. Symmetry related molecules pack in such a way that the cytosine base stacks on cytosine and guanine base on guanine. Our structure demonstrates that alternating d(CpG) sequences have the ability to adopt the left handed Z-DNA structure even at the dimer level i.e., in a sequence which is only two base pairs long.

Molecular structure-activity relationship study of some non-steroidal antiinflammatory agents using electrostatic potential mapping

A series of 6,11-dihydro-11-oxodibenz[b,e]oxepin-2-acetic acids (DOAA) which are known to be anti-inflammatory agents were studied. The geometries of some of the molecules obtained from X-ray crystallography were used in the calculations as such while the geometries of their derivatives were obtained by local, partial geometry optimization around the Sites of substitution employing the AMI method, keeping the remaining parts of the geometries the same as those in the parent molecules. Molecular electrostatic potential (MEP) mapping was performed for the molecules using optimized hybridization displacement charges (HDC) combined with Lowdin charges, as this charge distribution has been shown earlier to yield near ab initio quality results. A good correlation has been found between the MEP values near the oxygen atoms of the hydroxyl groups of the carboxy groups of the molecules and their anti-inflammatory activities. The result is broadly in agreement with the model proposed earlier by other authors regarding the structure-activity relationship for other similar molecules.

Synthesis, Structure, and Solid-State Transformation Studies of Phosphonoacetate Based Hybrid Compounds of Uranium and Thorium

Three new phosphonoacetate hybrid frameworks based on the actinide elements uranium and thorium have been synthesized. The compounds [C4N2H14][(UO2)(2)(O3PCH2COO)(2)]center dot H2O, I,[C4N2H14][(UO2)(2)(C2O4)(O3PCH2COOH)(2)], II, and Th(H2O)(2)(O3PCH2COO)(C2O4)(0.5). H2O, III, are built up from the connectivity between the metal polyhedra and the phosphonoacetate/oxalate units. Compound II has been prepared using a solvent-free approach, by a solid state reaction at 150 degrees C. It has been shown that II can also be prepared through a room temperature mechanochemical (grinding) route. The layer arrangement in III closely resembles to that observed in I. The compounds have been characterized by powder X-ray diffraction, IR spectroscopy, thermogravimetric analysis, and fluorescence studies.

A series of transition metal-azido extended complexes with various anionic and neutral co-ligands: synthesis, structure and their distinct magnetic behavior

The crystal structures and magnetic properties of five new transition metal-azido complexes with two anionic [pyrazine-2-carboxylate (pyzc) and p-aminobenzoate (paba)] and two neutral [pyrazine (pyz) and pyridine (py)] coligands are reported All five complexes were synthesized bysolvothermal methods The complex [Co-2(pyzc)(2)(N-3)(2)(H2O)(2)](n) (1) is 1D and exhibit canted antiferromagnetism, while the 3D complex [MnNa(pyzc)(N-3)(2)(H2O)(2)](n) (2) has a complicated structure and is weakly ferromagnetic in nature [Mn-2(paba)(2)(N-3)(2)(H2O)(2)](n) (3). is a 2D sheet and the Mn-II ions are found to be antiferromagnetically coupled The isostructural 2D complexes [Cu-3(pyz)(2)(N-3)(6)](n) (4) and [Cu-3(py)(2)(N-3)(6)](n) (5) resemble remarkably in their magnetic properties exhibiting moderately strong ferromagnetism. Density functional theory calculations (B3LYP functional) have been performed to provide a qualitative theoretical interpietation of the overall magnetic behavior shown by these complexes.

Electronic structure of high-Tc superconductors from core-level spectroscopies

Using the configuration-interaction approach, we show that various core-level spectroscopic observations on the high-Tc superconducting oxides can be consistently described in terms of mixing between d9 and d10 configurations, with a negligible amount of the d8 (Cu3+) state. From our analysis of the existing experimental data, we provide evidence of a wide and continuous valence transition in these systems as a function of temperature. The changes in the hybridization strengths deduced here are indicative of structural modifications of the square-planar CuO4 clusters with decreasing temperature.

Electronic structure of square planar CuO46− clusters

The results of spin-polarized MSXagr calculations show that the ground state of the CuO 4 6– cluster is essentially non-magnetic in spite of odd number of electrons in the system for short Cu–O distances (1.90 Å) as found in the highT c superconductors. This arises due to the fact that the unpaired electron resides in a molecular orbital with primarily oxygen 3s character. The stability of this molecular orbital is found to be sensitive to the cluster geometry and thus, increase in Cu–O distance (as well as other changes affecting oxygen-oxygen distance) tend to favour a magnetic state. From these calculations we have also estimated the Coulomb correlation strength within the Cu 3d to be about 5.3 eV.

Use of Polyazaheterocycles in the Assembly of New Cadmium Sulfate Frameworks: Synthesis, Structure, and Properties

The reaction of cadmium sulfate in the presence of polyazaheterocyclic organic molecules gave rise to a variety of new cadmium sulfate phases in water containing solvothermal reaction. The compounds have two- (I) and three-dimensionally (II-VI) extended structures. All the compounds have structures built up by the connectivity involving the cadmium octahedra and the sulfate tetrahedra in which the heterocyclic organic molecules act as the ligand. The linkages between the Cd2+ and (SO4)2- ions form one- (II), two- (I, III, and IV), and three- (V and VI) dimensionally extended cadmium sulfate phases. The connectivity between Cd2+ ion and the heterocyclic ligand also gives rise to one- and two-dimensional structures. The inter-connectivity between the two units gives rise to the observed structures. The presence of Cd-O-Cd chains and Cd-O-Cd layers in some of the structures is noteworthy. The adsorption/desorption studies suggest that the cadmium sulfate phases adsorb/desorb anionic dyes selectively in the presence of water/ethanol, respectively. The photocatalytic degradation studies on cationic dyes under UV-irradiation indicate modest activity. The cyanosilylation of imines using the present compounds as heterogeneous catalyst indicate good catalytic behavior. The various properties exhibited by the cadmium sulfate phases suggest that these compounds are versatile. All the compounds were characterized by powder X-ray diffraction, thermogravimetric analysis, infrared (IR) and UV-visible studies.

HNbWO6 and HTaWO6: Novel layered oxides related to the rutile structure. Synthesis and investigation of ion-exchange and intercalation behaviour

New protonated layered oxides, HMWO6·1.5H2O (M=Nb or Ta), have been synthesized by topotactic exchange of lithium in trirutile LiMWO6 with protons by treatment with dilute HNO3. The tetragonal cell constants are a=4.71 (2) and c=25.70 (8)Å for HNbWO6·1.5H2O and a=4.70 (2) and c=25.75 (9) Å for HTaWO6·1.5H2O. Partially hydrated compounds, HMWO6·0.5H2O and anhydrous compounds, HMWO6 retain the layered structure. The structure of these oxides consists of MWO6 sheets built up of M/W-oxygen octahedra with rutile type corner- and edge-sharing. Interlayer protons in HMWO6 are exchanged with Li+, Na+, K+ and Tl+. HMWO6 exhibit Brønsted acidity intercalating n-alkylamines and pyridine.

Conformational analysis of the right-hand twisted antiparallel β-Structure

The conformational analysis of a pair of two-linked peptide units in the anti-parallel arrangement is reported here with a view to study the effect of association of one chain with the other. The pair of two-linked peptide units were fixed in space through the hydrogen bonds between them, in accordance with certain hydrogen bond criteria. Model building was undertaken to ascertain whether the proximity of the side-chains could be used to eliminate any one of the right-hand twisted, left-hand twisted or regular β-structures. Stereochemically, it was found possible with all of them. The preference for a right-hand twisted β-structure, however, was indicated by the classical energy calculations. The relevance of the results thus obtained is discussed in the context of the preferential right-hand twist of the β-pleated sheets present in globular proteins. The agreement between the minimum energy conformations obtained for the pair of two-linked peptide units and the globular protein data is also indicated.

Some implications of an alternative structure for DNA

We have constructed a space-filling (Corey-Pauling-Koltun) model of an alternative structure for DNA. This structure is not a double helix, but consists of a pair of polynucleotide strands lying side by side and held together by Watson-Crick base pairing. Each of the two strands has alternating right- and left-handed helical segments approximately five base pairs in length. Sugar residues in alternating segments along a strand point in opposite directions. A structure slightly different from the present one proposed earlier by ourselves and another group and in which sugars in a strand all point in the same direction is ruled out. The present structure yields natural solutions to the problems of supercoiling of DNA and of strand separation during DNA replication. This model is energetically more favorable than the double helix.

Oxygen stoichiometry and structure of YBa2Cu3O7−δ and their relation to superconductivity

Thermogravimetric curves of the superconducting samples (0.0 ≤ δ left angle bracket0.5) of YBa2Cu3O7−δ are shown to be characteristically different from those of the non-superconducting samples (δreverse similar, equals0.5–1.0). The variation of Tc (from resistivity measurements) with δ confirms for a change from Image to Image Bands found in bright or dark field electron micrographs are shown to arise for different orientations of the [CuO2]∞ planes, causing oxygen enrichment in the boundaries. A new defect with missing Y-rows is found in the images of Y1−xBa2Cu3O7.

Synthesis, structure and DNA cleavage studies of coumarin analogues of tetrahydroisoquinoline and protoberberine alkaloids

Novel molecular matrices have been derived from coumarin-4-acetic acids and beta-phenylethylamines using the Bischler-Napieralski protocol which has led to the synthesis of analogues of tetrahydropapaverine in which the dimethoxybenzene moiety has been replaced by substituted coumarins. One carbon homologation has led to cyclization at the C3 position of coumarin generating the protoberberine skeleton. Structures have been confirmed by diffraction studies. The results showed that compounds 6e, 6f, 7e and 7f were found to be very effective against DNA samples of Gram positive bacterium Staphylococcus aureus and fungus Aspergillus niger. (C) 2010 Elsevier Masson SAS. All rights reserved.

Crystal structure of 8-methoxy-3-dibromoacetylcoumarin, C12H8Br2O4

C12H8BT2O4. monoclinic, P12(1)/cl (No. 14), a = 11.546(2) Angstrom, b = 6.885(4) Angstrom,= 15.949(3) Angstrom, beta = 101.75(2)degrees, V= 1241.3 Angstrom(3), Z = 4, p(m) = 2.040 g.cm(-3), R-all(F) = 0.039, wR(all)(F) = 0.043, T = 300 K.