Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle 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(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 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. There 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 Angstrom 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 Nai 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, O6 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.

Formation of crystalline diamond from amorphous diamond-like carbon films by pulsed laser irradiation

The formation of crystalline diamond films from amorphous diamond-like carbon films by pulsed laser irradiation with a 300 μs non-Q-switched Nd:YAG laser has been established by a combined study of transmission electron microscopy, x-ray photoelectron spectroscopy, and electrical resistivity. The films have been prepared by glow discharge decomposition of a mixture of propane, n-butane, and hydrogen in a rf plasma operating at a frequency of 13.56 MHz. Prior to laser irradiation, the films have been found to be amorphous by transmission electron microscope studies. After irradiation, the electron diffraction patterns clearly point out the formation of cubic diamond structure with a lattice spacing of 3.555 Å. However, the close similarity between diamond and graphite electron diffraction patterns could sometimes be misleading regarding the formation of a diamond structure, and hence, x-ray photoelectron spectroscopic studies have been carried out to confirm the results. A chemical shift in the C 1s core level binding energies towards higher values, viz., from 286.5 to 287.8 eV after laser irradiation, and a high electrical resistivity >1013 Ω cm are consistent with the growth of diamond structure. This novel "low-temperature, low-pressure" synthesis of diamond films offers enormous potential in terms of device compatibility with other solid-state devices.

Novel phase-transition behavior in an aqueous electrolyte solution

We have investigated the near-critical behavior of the susceptibility of a ternary liquid mixture of 3-methylpyridine. water, and sodium bromide as a function of the salt concentration. The susceptibility was determined from light-scattering measurements performed at a scattering angle of 90 degrees in the one-phase region near the locus of lower consolute points. A sharp crossover from asymptotic Ising behavior to mean-field behavior has been observed at concentrations ranging from 8 to 16.5 mass% NaBr. The range of asymptotic Ising behavior shrinks with increasing salt concentration and vanishes at a NaBr concentration of about 17 mass%. where complete mean-field-like behavior of the susceptibility is observed. A simultaneous pronounced increase in the background scattering at concentrations above 15 mass%, as well as a dip in the critical locus at 17 mass % NaBr, suggests that this phenomenon can be interpreted as mean-field tricritical behavior associated with the formation of a microheterogeneous phase due to clustering of the molecules and ions. An analogy with tri critical behavior observed in polymer solutions as well as the possibility of a charge-density-wave phase is also discussed. In addition, we, have observed a third soap-like phase an the liquid-liquid interface in several binary and ternary liquid mixtures.

Quantitative structural refinement of mn K edge XANES in LaMnO3 and CaMnO3 perovskites

The special magnetotransport properties of hole doped manganese perovskites originate from a complex interplay among structural, magnetic and electronic degree of freedom. In this picture the local atomic structure around Mn ions plays a special role and this is the reason why short range order techniques like X-ray absorption spectroscopy (XAS) have been deeply exploited for studying these compounds. The analysis of near edge region features (XANES) of XAS spectra can provide very fine details of the local structure around Mn, complementary to the EXAFS, so contributing to the full understanding of the peculiar physical properties of these materials. Nevertheless the XANES analysis is complicated by the large amount of structural and electronic details involved making difficult the quantitative interpretation.This work exploits the recently developed MXAN code to achieve a full structural refinement of the Mn K edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3, in which the Mn ions are present only in one charge state as Mn3+ and Mn4+ respectively. The good agreement between the results derived from the analysis of near edge and extended region of the XAS spectra demonstrates that a quantitative picture of the local structure call be obtained from structural refinement of Mn K edge XANES data in these crystalline compounds. The XANES analysis offers, in addition.. the possibility to directly achieve information on the topology of local atomic structure around the absorber not directly achievable from EXAFS.

Biosorption of iron(III) from aqueous solutions using the husk of Cicer arientinum

Iron is a major pollutant released as a by-product during several industrial operations especially during acid mining of metal ores. In this paper, the use of Bengal gram husk (husk of channa dal, Cicer arientinum) in the biosorption of Fe(III) from aqueous solutions is discussed. Parameters like agitation time, adsorbent dosage and pH were studied at different Fe(Ill) concentrations. The adsorption data fit well with Langmuir and Freundlich isotherm models. The adsorption capacity (q(max)) calculated from the Langmuir isotherm was 72.16 mg of Fe(III)/g of the biosorbent at an initial pH of 2.5. Desorption Studies were performed at different concentrations of hydrochloric acid showing that quantitative recovery of the metal ion is possible. The infrared spectra of the biomass before and after treatment with Fe(III), revealed that hydroxyl, carboxyl and amide bonds are involved in the uptake of Fe(III) ions.

Towards a green synthesis of LAB's: Effect of rare earth metal ions on the benzene alkylation with 1-dodecene over NaFAU-Y zeolites

Chemically modified microporous materials can be prepared as robust catalysts suitable for application in vapor phase processes such as Friedel-Crafts alkylation. In the present paper we have investigated the use of rare earth metal (Ce3+, La3+, RE3+, and Sm3+) exchanged Na-Y zeolites as catalysts for the alkylation of benzene with long chain linear 1-olefin; 1-dodecene. Thermodesorption studies of 2,6-dimethylpyridine adsorbed catalysts (in the temperature range 573 to 873 K) show that the rare earth zeolites are highly Bronsted acidic in nature. A perfect correlation between catalyst selectivity towards the desired product (2-phenyldodecane) and Bronsted acid sites amount has been observed. (c) 2006 Springer Science + Business Media, Inc.

Studies on removal of metal ions and sulphate reduction using rice husk and Desulfotomaculum nigrificans with reference to remediation of acid mine drainage

The utility of rice husk as an adsorbent for metal ions such as iron, zinc and copper from acid mine water was assessed. The adsorption isotherms exhibited Langmuirian behavior and were endothermic in nature. The free energy values for adsorption of the chosen metal ions onto rice husk were found to be highly negative attesting to favorable interaction. Over 99% Fe3+, 98% of Fe2+ and Zn2+ and 95% Cu2+ uptake was achieved from acid mine water, with a concomitant increase in the pH value by two units using rice husk. The remediation studies carried out on acid mine water and simulated acid mine water pretreated with rice husk indicated successful growth of Desulfotomaculum nigrificans (D. nigrificans). The amount of sulphate bioreduction in acid mine water at an initial pH of 5.3 was enhanced by D. nigrificans from 21% to 40% in the presence of rice husk filtrate supplemented with carbon and nitrogen. In simulated acid mine water with fortified husk filtrate, the sulphate reduction was even more extensive, with an enhancement to 73%. Concurrently, almost 90% Fe2+, 89% Zn2+ and 75% Cu2+ bioremoval was attained from simulated acid mine water. Metal adsorption by rice husk was confirmed in desorption experiments in which almost complete removal of metal ions from the rice husk was achieved after two elutions using 1 M HCl. The possible mechanisms of metal ion adsorption onto rice husk and sulphate reduction using D. nigrificans are discussed.

Heisenberg-like critical properties in ferromagnetic Nd1-xPbxMnO3 single crystals

Static magnetization for single crystals of insulating Nd0.85Pb0.15MnO3 and marginally conducting Nd0.70Pb0.30MnO3 has been studied around the ferromagnetic to paramagnetic transition temperature T-C. Results of measurements carried out in the critical range vertical bar(T - T-C)/T-C vertical bar <= 0.1 are reported. Critical exponents beta and gamma for the thermal behaviour of magnetization and susceptibility have been obtained both by modified Arrott plots and the Kouvel-Fisher method. The exponent delta independently obtained from the critical isotherm was found to satisfy the Widom scaling relation delta = gamma/beta + 1. For both compositions the values of exponents are consistent with those expected for isotropic magnets belonging to the Heisenberg universality class with short-range exchange in three dimensions. Correspondingly, the specific heat displays only a cusp-like anomaly at the critical temperature of these crystals which is consistent with an exponent alpha < 0. The results show that the ferromagnetic ordering transition in Nd1-xPbxMnO3 in the composition range 0.15 <= x <= 0.40 is continuous. This mixed-valent manganite displays the conventional properties of a Heisenberg-like ferromagnet, irrespective of the differing transport properties and in spite of low ordering temperatures T-C = 109 and 147.2 K for x = 0.15 and 0.30, respectively.

Synthesis of S-functionalized thioesters using thioaroylate ions derived from carboxylic acids and tetrathiomolybdate via acyloxyphosphonium intermediates

Thioaroylate ions generated in situ from acyloxyphosphonium salts and tetrathiomolybdate upon Michael addition or ring opening of three membered systems led to a facile synthesis of S-funcationalized thioesters. While the ring opening of aziridines gave very good yield of the products, Micheal addition and epoxide ring opening gave moderate yields.(C) 2010 Elsevier Ltd. All rights reserved.

ESR and optical studies of Mo5+ and W5+ ions in phosphomolybdate and phosphotungstate glasses

ESR and optical studies of phosphomolybdate and phosphotungstate glasses are discussed. Both the ESR and optical results indicate that molybdenum or tungsten ions are present in distorted octahedral environments in these glasses. In addition, ESR spectra of Mo5+ and W5+ ions show that the d electrons are localized on molybdenum and tungsten sites respectively. The variation of gperpendicular and gshort parallel values has been examined using appropriate structural models of these glasses.

On the admittance of lipid bilayer membranes: Part I. Membrane-permeable ions

The modular formalism of Rangarajan [J. Electroanal. Chem., 55 (1974) 297] has been applied to the admittance of lipid bilayer membranes. The method leads to equations which clearly show the interrelations between the various partial processes involved in ion transport, and which allow examination of model assumptions without the need for a complete rederivation of the membrane admittance. Explicit expressions are given for both the continuum and single jump models. The former includes the ionic displacement component, important mostly at high frequencies.

Interaction of metal ions with 6-oxopurine nucleotides. Part 1. X-Ray structures of ternary cobalt(III) complexes with inosine 5'-monophosphate or guanosine 5'-monophosphate

The crystal structures of two ternary metal nucleotide complexes of cobalt, [Co(en)2(H2O)2]-[Co(5?-IMP)2(H2O)4]Cl2·4H2O (1) and [Co(en)2(H2O)2][Co(5?-GMP)2(H2O)4]Cl2·4H2O (2), have been analysed by X-ray diffraction (en = ethylenediamine, 5?-IMP = inosine 5?-monophosphate, and 5?-GMP = guanosine 5?-monophosphate). Both complexes crystallize in the orthorhombic space group C2221 with a= 8.725(1), b= 25.891(5), c= 21.212(5)Å, Z= 4 for (1) and a= 8.733(2), b= 26.169(4), c= 21.288(4)Å, Z= 4 for (2). The structure of (1) was solved by the heavy-atom method, while that of (2) was deduced from (1). The structures were refined to R values of 0.09 and 0.10 for 1 546 and 1 572 reflections for (1) and (2) respectively. The two structures are isomorphous. A novel feature is that the chelate ligand en and the nucleotide are not co-ordinated to the same metal ion. One of the metal ions lying on the two-fold a axis is octahedrally co-ordinated by two chelating en molecules and two water oxygens, while the other on the two-fold b axis is octahedrally co-ordinated by two N(7) atoms of symmetry-related nucleotides in a cis position and four water oxygens. The conformations of the nucleotides are C(2?)-endo, anti, and gauche�gauche. In both (1) and (2) the charge-neutralising chloride ions are disordered in the vacant space between the molecules. These structures bear similarities to the mode of nucleotide co-ordination to PtII complexes of 6-oxopurine nucleotides, which are the proposed models for intrastrand cross-linking in DNA by a metal complex.

On the admittance of lipid bilayer membranes: Part I. Membrane-permeable ions

The modular formalism of Rangarajan [J. Electroanal. Chem., 55 (1974) 297] has been applied to the admittance of lipid bilayer membranes. The method leads to equations which clearly show the interrelations between the various partial processes involved in ion transport, and which allow examination of model assumptions without the need for a complete rederivation of the membrane admittance. Explicit expressions are given for both the continuum and single jump models. The former includes the ionic displacement component, important mostly at high frequencies.

Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.