Phosphoramidites as Synthons for Polynucleotide Synthesis

Abstract

Methods for the rapid synthesis of DNA and RNA are described. The procedures involve using nucleoside phosphoramidites as synthons and silica as a polymeric support. Additionally, a novel reaction involving nucleoside O-alkyl methylphosphonothioates is described.     

Rapid Conventional and Microwave-Assisted Decarboxylation of L-Histidine and Other Amino Acids via Organocatalysis with R-Carvone Under Superheated Conditions

This article reports a new methodology taking advantage of superheated chemistry via either microwave or conventional heating for the facile decarboxylation of alpha amino acids using the recoverable organocatalyst, R-carvone. The decarboxylation of amino acids is an important synthetic route to biologically active amines, and traditional methods of amino acid decarboxylation are time consuming (taking up to several days in the case of L-histidine), are narrow in scope, and make use of toxic catalysts. Decarboxylations of amino acids including L-histidine occur in just minutes while replacing toxic catalysts with green catalyst, spearmint oil. Yields are comparable to or exceed previous methods and purification of product ammonium chloride salts is aided by an isomerization reaction of residual catalyst to phenolic carvacrol. The method has been shown to be effective for the decarboxylations of a range of natural, synthetic, and protected amino acids.     

A cytotoxic dimeric furanoheliangolide from Piptocoma rufescens

A new sesquiterpene lactone, rufescenolide C (1), the first furanoheliangolide dimer, was isolated from the leaves of Piptocoma rufescens, collected in the Dominican Republic. Its structure was determined by interpretation of its spectroscopic data, with the absolute configuration being established by analysis of the CD spectrum. A plausible biogenesis of this dimer is proposed. This compound showed potent cytotoxicity with an IC₅₀ value of 150 nM, when tested against HT-29 human colon cancer cells.     

Enumeration of substitutional isomers with restrictive mutual positions of ligands: I. Overall counts

We address systematics for the enumeration of substitutional isomers when there is constrained positioning of ligands on a molecular skeleton. One constraint involves ‘restrictive ligands’ where two of the same kind are forbidden to occupy adjacent sites in a molecular skeleton. This may arise because of steric hindrance, or because of groups which in neighbor proximity react to eliminate one. For instance, no pair of –OH groups attach to the same C atom in a molecular skeleton. In another case, malonic acid residues decarboxylate leaving no more than one decarboxylation in each residue. The enumeration with such restrictive ligands may be addressed via a Polya-theoretic cycle index hybridized with the graph-theoretic independence polynomial (when there is just a single such neighbor-excluding ligand and another which is not), while more generally a hybridization with the chromatic polynomial is needed. Another substitional-isomer constraint involves bidentate ligands, with each ligand-part occupying adjacent sites, and possibly also with additional separate unidentate ligands. Here, the set of all pure & mixed such ligand placements is analytically represented by a ‘symmetry-reduced’ matching polynomial (which is a hybrid now of the matching polynomial and Polya’s cycle index). This result gives the generating function for isomer enumeration, taking into account every possible so-restricted assortment of the employed ligands. Here we make such novel hybridizations (for these and other graphtheoretic polynomials) to deal with such oft-encountered chemical problems, which nevertheless transcend typical earlier unconstrained formulizations. Further subsymmetry classification & enumerations, along with examples are considered in a further article.     

Conformational and dynamic effects of pendant-PEK chains on rigid-rod polymers by molecular dynamics simulation

Molecular dynamics simulations were performed with models of a single-component ‘hairy-rod’ molecular composite composed of flexible meta poly(aryl ether ketone) (mPEK) chains (the ‘hairs’) grafted to a poly(p-phenylene benzobisthiazole) (PBZT) rigid-rod backbone. The molecular-composite concept, conceived to circumvent solubility problems and improve compressive strength of PBZT, relies on an even distribution of rods in a coil-like matrix. Two-molecule simulations show that the pendant mPEK chains associate with the rods causing large bends in the rod backbone. Simulations of bulk systems imply that the mPEK chains greatly reduce the correlation of rod orientation without altering rod spacing. Radial distribution and orientation correlation functions as well as correlation volumes are computed.     

Simulation of Organic Liquid Product Deoxygenation through Multistage Countercurrent Absorber/Stripping Using CO2 as Solvent with Aspen-HYSYS: Process Modeling and Simulation

In this work, the deoxygenation of organic liquid products (OLP) obtained through the thermal catalytic cracking of palm oil at 450 °C, 1.0 atmosphere, with 10% (wt.) Na₂CO₃ as a catalyst, in multistage countercurrent absorber columns using supercritical carbon dioxide (SC-CO₂) as a solvent, with an Aspen-HYSYS process simulator, was systematically investigated. In a previous study, the thermodynamic data basis and EOS modeling necessary to simulate the deoxygenation of OLP was presented. This work addresses a new flowsheet, consisting of 03 absorber columns, 10 expansions valves, 10 flash drums, 08 heat exchanges, 01 pressure pump, and 02 make-ups of CO₂, aiming to improve the deacidification of OLP. The simulation was performed at 333 K, 140 bar, and (S/F) = 17; 350 K, 140 bar, and (S/F) = 38; 333 K, 140 bar, and (S/F) = 25. The simulation shows that 81.49% of OLP could be recovered and that the concentrations of hydrocarbons in the extracts of absorber-01 and absorber-02 were 96.95 and 92.78% (wt.) on a solvent-free basis, while the bottom stream of absorber-03 was enriched in oxygenated compounds with concentrations of up to 32.66% (wt.) on a solvent-free basis, showing that the organic liquid products (OLP) were deacidified and SC-CO₂ was able to deacidify the OLP and obtain fractions with lower olefin contents. The best deacidifying condition was obtained at 333 K, 140 bar, and (S/F) = 17.     

Collision cross sections for protein ions

A method for the determination of cross sections for gas-phase protein ions, based on the energy loss of ions as they pass through a collision gas, is described. A simple model relates the energy loss to the number of collisions and hence the cross section. Results from a Monte Carlo model that support the validity of this approach are described. Experimental cross sections are reported for motilin, ubiquitin, cytochrome c, myoglobm, and bovine serum albumin. Cross sections range from approximately 800 Ų for motilin to approximately 14,000 Ų for bovine serum albumin and generally increase with the number of charges on the ion. Cytochrome c ions from aqueous solution show somewhat smaller cross sections than ions formed from solutions of higher organic content, suggesting that the gas-phase ions may retain some memory of their solution conformation.