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

An in situ electron microscope investigation of the icosahedral-to-decagonal quasicrystalline transformation in Al-20 at.% Mn

The solid-state transformation behaviour of the icosahedral phase in rapidly solidified Al-20 at.% Mn has been investigated by in situ heating experiments in the transmission electron microscope. As-rapidly-solidified Al-20 at.% Mn consists mainly of a dendritic icosahedral phase, with a small amount of interdendritic f.c.c. agr-Al. During subsequent heat treatment at temperatures below about 500°C, the dendritic icosahedral phase grows and consumes the interdendritic agr-Al. At about 500°C the decagonal phase nucleates near icosahedral dendrite and grain boundaries and then grows into the icosahedral matrix by lateral motion of ledges 10-20 nm high across facet planes normal to the twofold symmetry axes. At about 600°C the decagonal phase transforms into a crystalline phase. The present study suggests that solid-state decomposition of the icosahedral phase is the mechanism of decagonal phase formation in as-rapidly-solidified Al-Mn alloys.

The mobility of oxygen ions in CaF2

The a.c. conductivity of CaF2 samples containing a fine dispersion of CaO particles has been measured in the temperature range 630 to 1100 K. The conductivity of the dispersed solid electrolyte is two orders of magnitude higher than that for pure polycrystalline CaF2 in the middle of the temperature range. Transport measurements on pure single crystals of CaF2 and polycrystalline samples, with and without CaO dispersion, using Fe+FeO and pure Fe as electrodes, clearly indicate that fluorine ions are the only migrating ionic species with a transport number of almost unity, contrary to the suggestion of Chou and Rapp [1, 2]. The enhanced conductivity of the dispersed solid electrolyte probably arises from two effects. A small solubility of oxygen in CaF2 results in an increase in the fluorine vacancy concentration and conductivity. Adsorption of fluorine ions on the surface of the dispersed particles of CaO results in a space charge region around each particle with enhanced conductivity. Measurements on a galvanic cell incorporating CaF2 as the solid electrolyte and oxide electrodes show that the e.m.f. is a function of the activity of CaO at the electrode/electrolyte interface. The response to an oxygen potential gradient is, therefore, through an exchange reaction, which establishes an equivalent fluorine potential at the electrode/electrolyte interface.

Remarkably large captodative stabilisation in radical ions

Palladium complex-catalyzed carbonylation of arylsulfonyl chlorides in the presence of metal alkoxides M(OR)n (M=B, Al, and Ti) gives the corresponding esters along with diaryl disulfides. With metal carboxylates M(OCOR)n (M=Na, K, Ca, Mg, and Zn), the free acids are also obtained

Pressure-induced phase transitions in LiRbSO4: a Raman spectroscopic study

Room-temperature Raman spectra of LiRbSO4 were studied as a function of pressure up to 170 kbar for two different orientations of the crystal. Four pressure-induced phase transitions at about 2, 17, 32 and 57 kbar were observed. The transitions at 17 and 57 kbar have slow kinetics, taking about 4 h for their completion. These phase transitions are associated with the orientations of the SO4 ions in the unit cell.

Ion probing with Luminescent PbS Quantum dots in PVA

The PbS quantum dots synthesized in PVA are used to investigate their photoluminescence (PL) response to various ions such as Zn, Cd, Hg, Ag, Cu, Fe, Mn, Co, Cr and Ni ions. The enhancement in the photoluminescence intensity is observed with specific ions namely Zn, Cd, Hg and Ag. Among these four ions, the PL response to Hg and Ag even at sub-micro-molar concentrations is quite high, approximately an order of magnitude higher than Zn and Cd. It is interesting to observe that the change in Pb and S molar ratio has profound effect on the selectivity of these ions. The samples prepared under excess of S are quite effective compared to Pb. Indeed, the later one has hardly any effect on the photoluminescence response. These results also indicate that the sensitivity of these QDs could be fine-tuned by controlling the S concentration at the surface. Contrary to the above, Cu, Fe and Co quenches the photoluminescence. Another interesting property of PbS in PVA observed is photo-brightening mechanism due to the curing of the polymer with laser. However, the presence of excess ions at the surface changes its property to photo-darkening/brightening that depends on the direction of carrier transfer mechanism (from QDs to the surface adsorbed metal ions or vice-versa), which is an interesting feature for metal ion detectivity.

CoMn2O4 spinel from a MOF: synthesis, structure and magnetic studies

A hydrothermal reaction of Mn(OAc)(2)center dot 4H(2)O, Co(OAc)(2)center dot 4H(2)O and 1,2,4 benzenetricarboxylic acid at 220 degrees C for 24 h gives rise to a mixed metal MOF compound, CoMn2(C6H3(COO)(3))(2)], I. The structure is formed by the connectivity between octahedral CoO6 and trigonal prism MnO6 units connected through their vertices forming a Kagome layer, which are pillared by the trimellitate. Magnetic susceptibility studies on the MOF compound indicate a canted anti-ferromagnetic behavior, due to the large antisymmetric DM interaction between the M2+ ions (M = Mn, Co). Thermal decomposition studies indicate that the MOF compound forms a tetragonal mixed-metal spinel phase, CoMn2O4, with particle sizes in the nano regime at 400 degrees C. The particle size of the CoMn2O4 can be controlled by varying the decomposition temperature of the parent MOF compound. Magnetic studies of the CoMn2O4 compound suggests that the coercivity and the ferrimagnetic ordering temperatures are dependent on the particle size.

Electron paramagnetic resonance studies on Mn doped GaSb

We report on the X-band (similar to 9.43 GHz) electron paramagnetic resonance (EPR) investigations carried out on polycrystalline Ga1-xMnxSb (x=0.02). A strong EPR signal with an effective g factor (g(eff)) close to 2.00 was observed, suggesting that the ionic state of Mn which replaces Ga ion in the lattice, is Mn2+ attributable to Delta M=1 transition of the ionized Mn acceptor A(-), Mn (3d(5)). The apparent absence of EPR signal, typical for neutral Mn acceptor at g=2.7 suggests either no such centers are present or the signal broadens beyond detection limit. The temperature dependent EPR studies combined with dc magnetization data suggest the possible coexistence of antiferromagnetic and ferromagnetic phases at very low temperatures. (C) 2011 American Institute of Physics. doi:10.1063/1.3543983]

An electron diffraction study of quasicrystals in Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys

Electron diffraction studies were carried out to establish the icosahedral phase formation in rapidly quenched Ti-37 at% Mn and Ti-24 at% Mn-13 at% Fe alloys. Distortions in the diffraction spots and diffuse intensities in the diffraction patterns were investigated. The existence of a rational approximant structure and a decagonal like phase are also reported.

A study of cubic bismuth oxides of the type bi(26-X)m(X)O(40-delta) (m=ti, mn, fe, co, ni or pb) related to gamma-bi2O3

A structural investigation of cubic oxides (space group I23) of the formula Bi(26-x)M(x)O(40-delta) (M = Ti, Mn, Fe, Co, Ni and Pb) related to the Y-Bi2O3 phase has been carried out by the Rietveld profile analysis of high-resolution X-ray powder diffraction data in order to establish the cation distributions. Compositional dependence of the cation distribution has been examined in the case of Bi26-xCoxO40-delta (1 < x < 16). The study reveals that in Bi(26-X)M(X)O(40-delta) with M = Ti, Mn, Fe, Co or Pb, the M cations tend to occupy tetrahedral (2a) sites when x < 2 while the octahedral (24f) sites are shared by the excess Co or Ni cations with Bi atoms when x > 2. Also experimental magnetic moments of Mn, Co and Ni derivatives have been used to establish the valence state and distribution of these cations.

Distinct Allostery Induced in the Cyclic GMP-binding, Cyclic GMP-specific Phosphodiesterase (PDE5) by Cyclic GMP, Sildenafil, and Metal Ions

The activity of many proteins orchestrating different biological processes is regulated by allostery, where ligand binding at one site alters the function of another site. Allosteric changes can be brought about by either a change in the dynamics of a protein, or alteration in its mean structure. We have investigated the mechanisms of allostery induced by chemically distinct ligands in the cGMP-binding, cGMP-specific phosphodiesterase, PDE5. PDE5 is the target for catalytic site inhibitors, such as sildenafil, that are used for the treatment of erectile dysfunction and pulmonary hypertension. PDE5 is a multidomain protein and contains two N-terminal cGMP-specific phosphodiesterase, bacterial adenylyl cyclase, FhLA transcriptional regulator (GAF) domains, and a C-terminal catalytic domain. Cyclic GMP binding to the GAFa domain and sildenafil binding to the catalytic domain result in conformational changes, which to date have been studied either with individual domains or with purified enzyme. Employing intramolecular bioluminescence resonance energy transfer, which can monitor conformational changes both in vitro and in intact cells, we show that binding of cGMP and sildenafil to PDE5 results in distinct conformations of the protein. Metal ions bound to the catalytic site also allosterically modulated cGMP- and sildenafil-induced conformational changes. The sildenafil-induced conformational change was temperature-sensitive, whereas cGMP-induced conformational change was independent of temperature. This indicates that different allosteric ligands can regulate the conformation of a multidomain protein by distinct mechanisms. Importantly, this novel PDE5 sensor has general physiological and clinical relevance because it allows the identification of regulators that can modulate PDE5 conformation in vivo.

Influence of Bi 3+ ions in enhancing the magnitude of positive temperature coefficients of resistance in n-BaTiO3 ceramics

Bi3+ ions substituting at Ba-sites in a limited concentration range with another donor dopant occupying the Ti-sites in polycrystalline BaTiO3 enhanced the positive temperature coefficient of resistance (PTCR) by over seven orders of magnitude. These ceramics did not require normal post sinter annealing or a change to an oxygen atmosphere during annealing. These ceramics had low porosities coupled with better stabilities to large applied electric fields and chemically reducing atmospheres. Bi3+ ions limited the grain growth to less than 8 mum in size, they enhanced the concentration of acceptor-type trap centres at the grain-boundary-layer regions and maintained complete tetragonality at low grain sizes in BaTiO3 ceramics.

The secretion of gonadotrophin-releasing hormone by peri-implantation embryos of the rhesus monkey: comparison with the secretion of chorionic gonadotrophin

Chorionic gonadotrophin (CG) is the first clear embryonic signal during early pregnancy in primates. CG has close structural and functional similarities to pituitary luteinizing hormone (LH) which is regulated by gonadotrophin releasing hormone (GnRH). To study the regulatory mechanism of CG secretion in primate embryos, we examined the production and timing of secretion of GnRH in peri-implantation embryos of the rhesus monkey. In-vivo fertilized/developed morulae and early blastocysts, recovered from non-superovulated, naturally-bred rhesus monkeys by non-surgical uterine flushing, were cultured in vitro to hatched, attached and post-attached blastocyst stages using a well-established culture system. We measured GnRH and CG in media samples from cultured embryos with a sensitive radioimmunoassay and bioassay, respectively. The secretion of GnRH (pg/ml; mean +/- SEM) by embryos (n = 20) commenced from low levels (0.32 +/- 0.05) during the pre-hatching blastocyst stage to 0.70 +/- 0.08 at 6-12 days and 1.30 +/- 0.23 at greater than or equal to 13 days of hatched blastocyst attachment and proliferation of trophoblast cells. GnRH concentrations in culture media obtained from embryos (n = 5) that failed to hatch and attach were mostly undetectable (less than or equal to 0.1). Samples that did not contain detectable GnRH failed to show detectable CG. Immunocytochemical studies, using a specific monoclonal anti-GnRH antibody (HU4H) as well as polyclonal antisera (LR-1), revealed that immunopositive GnRH cells were localized in pre-hatching blastocysts (n = 4), in blastocysts (n = 2) after 5-10 days of attachment and in monolayer cultures (n = 4) of well-established embryonic trophoblast cells. GnRH positive staining was seen only in cytotrophoblasts but not in syncytiotrophoblasts. Similarly, cytotrophoblast, but not syncytiotrophoblast, cells of the rhesus placenta were immunopositive. In controls, either in the absence of antibody or in the presence of antibody pre-absorbed with GnRH, these cells failed to show stain. These observations indicate, for the first time, that an immunoreactive GnRH is produced and secreted by blastocysts during the peri-attachment period and by embryo-derived cytotrophoblast cells in the rhesus monkey.