Conversion of Allylic Alcohols into Allylic Nitromethyl Compounds via a Palladium-Catalyzed Solvolysis: An Enantioselective Synthesis of an Advanced Carbocyclic Nucleoside Precursor(1)

A two-step reaction sequence to homoallylic nitro compounds from allylic alcohols is presented. Ethoxy carbonylation of the alcohols with ethyl chloroformate provides the corresponding allylic ethyl carbonates in high yields. Exposure of these substrates to catalytic palladium(0) in CH(3)NO(2) initiates a reaction sequence, ionization-decarboxylation-nitromethylation, that culminates with the formation of nitroalkenes. The regio- and stereochemical outcomes of the nitromethyl allylation reaction can be explained by the behavior of the transient pi-allylpalladium complexes. This methodology serves as a centerpiece for the synthesis of an important carbocyclic nucleoside intermediate.     

Transparent conducting oxides: texture and microstructure effects on charge carrier mobility in MOCVD-derived CdO thin films grown with a thermally stable, low-melting precursor

A series of low-melting, thermally stable cadmium metal-organic chemical vapor deposition (MOCVD) precursors have been synthesized, structurally and spectroscopically characterized, and implemented in growth of highly conductive and transparent CdO thin films. One member of the series, bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)(N,N-diethyl-N',N'-dimethyl-ethylenediamine)cadmium(II), Cd(hfa)(2)()(N,N-DE-N',N'-DMEDA), represents a particularly significant improvement over previously available Cd precursors, owing to the low melting point and robust thermal stability. High-quality CdO films were grown by MOCVD on glass and single-crystal MgO(100) between 300 and 412 degrees C. Film growth parameters and substrate surface have large effects on microstructure and electron carrier transport properties. Enhanced mobilities observed for highly biaxially textured films grown on MgO(100) vs glass are attributed, on the basis of DC charge transport and microstructure analysis, to a reduction in neutral impurity scattering and/or to a more densely packed grain microstructure. Although single-grained films grown on MgO(100) exhibit greater mobilities than analogues with discrete approximately 100 nm grains and similar texture, this effect is attributed, on the basis of charge transport and Hall effect measurements as well as optical reflectivity analysis, to differences in carrier concentration rather than to reduced grain boundary scattering. Unprecedented conductivities and mobilities as high as 11,000 S/cm and 307 cm(2)/V.s, respectively, are obtained for epitaxial single-grained films (X-ray diffraction parameters: fwhm(omega) = 0.30 degrees, fwhm(phi) = 0.27 degrees ) grown in situ on MgO(100) at a relatively low temperature (400 degrees C).     

Bistable ferroelectric liquid crystal photoswitch triggered by a dithienylethene dopant

The spontaneous polarization (PS) of a ferroelectric liquid crystal is modulated reversibly by photocyclization of the dopant 1,2-bis[5'-(4' '-heptyloxyphenyl)-2'-methylthien-3'-yl]perfluorocyclopentene. The magnitude of PS photomodulation increases with dopant concentration up to 3 mol %, and the resulting photoswitch is fatigue resistant and bistable. To the best of our knowledge, this is the first example of a bistable ferroelectric liquid crystal photoswitch to be reported in the literature.     

First and second derivative matrix elements for the stretching,bending, and torsional energy

Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.     

Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction

An ion-pair reversed-phase HPLC method was evaluated for the separation of synthetic oligonucleotides. Mass transfer in the stationary phase was found to be a major factor contributing to peak broadening on porous C18 stationary phases. A small sorbent particle size (2.5 microm), elevated temperature and a relatively slow flow-rate were utilized to enhance mass transfer. A short 50 mm column allows for an efficient separation up to 30mer oligonucleotides. The separation strategy consists of a shallow linear gradient of organic modifier, optimal initial gradient strength, and the use of an ion-pairing buffer. The triethylammonium acetate ion-pairing mobile phases have been traditionally used for oligonucleotide separations with good result. However, the oligonucleotide retention is affected by its nucleotide composition. We developed a mathematical model for the prediction of oligonucleotide retention from sequence and length. We used the model successfully to select the optimal initial gradient strength for fast HPLC purification of synthetic oligonucleotides. We also utilized ion-pairing mobile phases comprised of triethylamine (TEA) buffered by hexafluoroisopropanol (HFIP). The TEA-HFIP aqueous buffers are useful for a highly efficient and less sequence-dependent separation of heterooligonucleotides.     

Pyrimethamine analogs as strong inhibitors of double and quadruple mutants of dihydrofolate reductase in human malaria parasites

Pyrimethamine acts against malarial parasites by selectively inhibiting their dihydrofolate reductase-thymidylate synthase. Resistance to pyrimethamine in Plasmodium falciparum is due to point mutations in the DHFR domain, initially at residue 108 (S108N), with additional mutations imparting much greater resistance. Our previous work, the development of a simple rational drug design strategy to overcome such resistance, used suitable meta-substituents in the pyrimethamine framework to avoid the unfavorable steric clash with mutant side chains at position 108. Interestingly, the meta-chloro analog of pyrimethamine not only overcame the resistance due to S108N, but also that contributed by the more remote mutation, C59R. The present work improves on this by means of other meta-substituents. Against wild type DHFR, double mutant types A16V + S108T and C59R + S108T, and the highly pyrimethamine/cycloguanil-resistant quadruple-mutant form N51I + C59R + S108N + I164L, pyrimethamine itself gave Ki values of 1.5, 2.4, 72.3 and 859 nM, respectively. The meta-substituted analogs, especially the meta-bromo analog, were much more powerful inhibitors of these DHFRs, including the quadruple-mutant form (meta-bromo analog, Ki 5.1 nM). For comparison, the dihydropyrazine antifolate, WR99210, gave Ki values of 0.9, 3.2, 0.8 and 0.9 nM, respectively. Ki values were also measured against recombinant human DHFR, as were their activities against the growth of Plasmodium falciparum cultures bearing the double mutations (FCB and K1 strains) and quadruple mutation (V1/S) and the wild type (3D7). The meta-analogs were highly active against all of these, with the meta-bromo again being the strongest, having an IC50 of 37 nM against V1/S, compared to > 5000 nM for pyrimethamine itself and 1.1 nM for WR99210.     

Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry

A new algorithm is presented for performing molecular dynamics simulations of peptides with fixed geometry, with the aim of simulating conformational changes and of exploring conformational space. The principle of the method is to expand the potential energy as a Taylor's series in the coordinates around the current point, retaining the force and its first two derivatives, and obtain a series solution of the resulting differential equations using a method due to Lyapunov. By choosing the time step so that the second term in the series is small compared to the first, the true solution can in principle be approximated to any desired degree of accuracy. The algorithm has been used to solve numerically Lagrange's equations of motion for N-acetyl alanine amide and N-acetyl methionide amide, regarded as fixed at their C-termini, under the influence of the ECEPP/2 potential energy function, and time steps of 15–30 fsec have been achieved with little variation in the total energy. Possible directions for future development are discussed.     

Determination of nanomolar levels of formate in natural waters based on a luminescence enzymatic assay

A light-producing reaction utilizing three enzymes, bacterial luciferase, dehydrogenase and diaphorase, can be used to determine formic acid in natural waters at nanomolar concentrations. The method is rapid and convenient, requiring no preconcentration, desalting or derivatization procedures. Determinations can be done on small sample volumes (25 μl) at room temperature and pH 7. The precision (relative standard deviation for sea water samples containing 1.0 μM formate was 9.0% (n = 15). The reaction is specific for formate with a detection limit of 20 nM (signal-to-noise ratio = 3). Results for applications of the method to sea, estuarine and rain water are given.     

Spectrophotometric determination of copper after adsorption of its 1-phenyl-4,4,6-trimethyl(1H, 4H)-pyrimidine-2-thiol complex onto microcrystalline naphthalene

A selective Spectrophotometric method has been developed for the trace determination of copper after adsorption of its 1-phenyl-4,4,6-trimethyl(1H, 4H)-pyrimidine-2-thiol (PTPT) complex onto microcrystalline naphthalene. The complex is quantitatively adsorbed on naphthalene in the pH range 7.5–11.5, separated by filtration, dissolved in dimethylformamide (DMF) and determined spectrophotometrically at 400 nm. Beer's law is obeyed in the concentration range 2.5–37.5 g of copper in 10 ml of DMF. The molar absorptivity and Sandell's sensitivity are 1.30 × 10⁴1 · mol^–1 · cm^–1 and 0.0048g cm^–2, respectively. Ten replicate analyses of a solution containing 20.0 g of copper gave a mean absorbance of 0.410 with a relative standard deviation of 0.91 %. The interferences of various ions have been studied and the method has been validated by the determination of copper in various standard reference materials, beers, wines, human hair, goat liver and environmental samples.On leave from St. Stephen's College, Delhi 110 007, India     

Synthesis of pyranosyl amidoximes by addition of amines to pyranosyl nitrile oxides

Addition of amines to pyranosyl nitrile oxides, generated by base-induced dehydrochlorination of the corresponding hydroximoyl chloride, affords pyranosyl N-alkyl/aryl-formamide oximes (41-90%). Reaction with amino acid esters yields the corresponding amidoximes and/or 3-pyranosyl-1,2,4-oxadiazin-6-ones. The structure of N-phenyl-C-(2,3,4-tri-O-acetyl-β-D-xylopyranosyl)formamide oxime was established by X-ray crystallography.