Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

The effect of Cu substitution on the A1g mode of La0.7Sr0.3MnO3 manganites

We report on the first Raman data of Cu substituted La_1−ySr_yMn_1−xCu_xO₃ (0≤x≤0.10 and 0.17≤y≤0.3, accordingly in order to have the same Mn⁴⁺/[Mn⁴⁺+Mn³⁺] ratio), collected in the frequency range 100-900 cm⁻¹ and at room temperature, with parallel (e_i∥e_s) and crossed (e_i⊥e_s) polarizations of the incident (e_i) and scattered (e_s) light. Spectra were fitted with a Drude-Lorentz model, and peaks at 190-220 and 430 cm⁻¹, together with two broad structures centered at near 500 and 670 cm⁻¹, have been found. We also have observed that the A_1g mode is substantially shifted with increasing Cu substitution. The A_1g phonon shift is a linear function of the tolerance factor t and the rhombohedral angle α_r, thus following the structural changes of the MnO₆ octahedra in the system.     

Synthesis and characterization of novel perfluorinated polyimides with 3D‐controlled structures for photonic applications

We have designed and synthesized novel perfluorinated polyimides with 3D controlled structure. At first, we successfully developed the new synthetic routes to diamines with pendant bulky perfluorinated aromatic units in a multi‐step synthetic procedure. Novel perfluorinated polyimides were prepared in a two‐step reaction in N‐methyl‐2‐pyrrolidinone (NMP) solution: The first step was for the synthesis of polyamic acids (PAAs) and the second reaction was for the imidization of PAA. The polymer yield was over 89% and the inherent viscosity of PAAs was in the range of 0.24–0.36 dL/g. The thin films were prepared by spin‐coating the PAA solution in NMP onto various substrates such as a Si wafer or a KBr pellet, dried at 80 °C and further cured at 230 °C. The resultant polyimides are thermally stable over 400 °C. The refractive index and birefringence of the resultant polyimides are 1.5858–1.6452 and 0.01–0.005, respectively. The refractive index of polyimide decreases with increasing the fluorine content. The copolymerization and the ether linkages into the backbone reduce the birefringence of polyimides. Surprisingly, the pendant ether linkage is not a crucial factor in reducing the polyimide birefringence. Their birefringence is comparatively very low, compared with that of previous polyimides. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1326–1342, 2006     

Influence of the reaction temperature and ph on the coordination modes of the 1,4-benzenedicarboxylate (BDC) ligand: a case study of the Ni(II)(BDC)/2,2'-bipyridine system

Three new Ni(BDC)/2,2'-bipy compounds, Ni2(BDC)(HBDC)2(2,2'-bipy)2 (2), Ni3(BDC)3(2,2'-bipy)2 (3), and Ni(BDC)(2,2-bipy)2.2H2O (5), in addition to the previously reported Ni(BDC)(2,2'-bipy).0.75H2BDC (1) and Ni(BDC)(2,2'-bipy)(H2O) (4) [BDC = 1,4-benzenedicarboxylate; 2,2'-bipy = 2,2'-bipyridine], have been synthesized by hydrothermal reactions. A systematic investigation of the effect of the reaction temperature and pH resulted in a series of compounds with different compositions and dimensionality. The diverse product slate illustrates the marked sensitivity of the structural chemistry of polycarboxylate aromatic ligands to synthesis conditions. Compound 1, which has a channel structure containing guest H2BDC molecules, is formed at the lowest pH. The guest H2BDC molecules are connected by hydrogen bonds and form extended chains. At a slightly higher pH, a dimeric molecular compound 2 is formed with a lower number of protonated carboxylate groups per nickel atom and per BDC ligand. Reactions at higher temperature and the same pH lead to the transformation of 1 and 2 into the two-dimensional, layered trinuclear compound 3. As the pH is increased, a one-dimensional polymer 4 is formed with a water molecule coordinated to Ni2+. Bis-monodentate and bischelating BDC ligands alternate along the chain to give a crankshaft rather than a regular zigzag arrangement. A further increase of the pH leads to the one-dimensional chain compound 5, which has two chelating 2,2'-bipy ligands. Crystal data: 2, triclinic, space group P, a = 7.4896(9) angstroms, b = 9.912(1) angstroms, c = 13.508(2) angstroms, alpha = 86.390(2) degrees , beta = 75.825(2) degrees, gamma = 79.612(2) degrees, Z = 2; 3, orthorhombic, space group Pbca, a = 9.626(2) angstroms, b = 17.980(3) angstroms, c = 25.131(5) angstroms, Z = 4; 5, orthorhombic, space group Pbcn, a = 14.266(2) angstroms, b = 10.692(2) angstroms, c = 17.171(2) angstroms, Z = 8.     

Method for measuring the electron distribution function in the low temperature plasma with a high time resolution

A hybrid method for measuring the electron distribution function in the low temperature plasma is described. The time resolution of the measurement is of the order of several sec.     

Synthesis and Structures of Titanosiloxane Cage Compounds

Reaction of (triphenylmethyl)silanetriol (1) with cyclopentadienyltitanium trichloride (CpTiCl₃) in the presence of triethylamine as a HCl scavenger gave both compounds of a partial open-cage type {[Ph₃CSiO(OH)]₃(Ph₃CSiO_3/2)(CpTiO_3/2)₄} (2) and cube type (Ph₃CSiO_3/2CpTiO_3/2)₄ (3). The 1:1 reaction of 1 and CpTiCl₃ in toluene solvent at reflux temperature for 3 d afforded compounds 2 (22%) and 3 (36%). When 1 is reacted with a 1.5 fold excess of CpTiCl₃ under the same conditions, compound 3 was obtained in high yield (81%) along with 2 in trace quantities. Compounds 2 and 3 were fully characterized by the analyses of ¹H, ¹³C, ²⁹Si NMR, IR, and FAB MS data. The solid-state structure of 3 was determined by a single crystal X-ray diffraction study. Compound 3 had shown to have catalytic activity for the oxidation of alkenes such as 1-octene, cyclooctene, and norbornene with t-butyl hydrogen peroxide. The effect of solvent was observed in this epoxidation reaction. The order of reactivity were decreased as follows: CHCl₃ > hexane THF.     

Selective Recognition of Calcium Ion through Liquid Membrane

The mole transport rate of alkaline earth metal ions through a bulk liquid membrane and a supported liquid membrane using a series of proton diionizable acyclic polyethers was measured. Among alkaline earth metal ions, the calcium ion was observed to be selectively transported in both single and competitive transport experiments. Potentiometric titration and solution calorimetric titration also gave calcium selectivity over other alkaline earth metal ions. Acyclic polyether bearing a diethylene glycol unit andn-tetradecyl lipophilic chain at the α position of carboxylic acid affords the best selectivity for the calcium ion in bulk and supported liquid membranes.     

Ruthenium-catalyzed reductive cyclization of nitroarenes with trialkylamines leading to quinolines

Nitroarenes react with trialkylamines in the presence of a catalytic amount of a ruthenium catalyst together with tin(II) chloride dihydrate at 180 °C in an aqueous medium (toluene–H₂O) to afford the corresponding quinolines in moderate to good yields. The catalytic pathway seems to be proceeded via a sequence involving initial reduction of nitroarenes to anilines, alkyl group transfer from alkylamines to anilines to form an imine, dimerization of imine, and heterocyclization.