A theoretical examination of the acid-catalyzed and noncatalyzed ring-opening reaction of an oxirane by nucleophilic addition of acetate. Implications to epoxide hydrolases

Ab initio and density functional calculations have been performed to gain a better understanding of the epoxide ring-opening reaction catalyzed by epoxide hydrolase. The S(N)2 reaction of acetate with 1S,2S-trans-2-methylstyrene oxide to provide the corresponding diol acetate ester was studied with and without general-acid catalysis. MP2 and DFT (B3LYP) calculations predict, for the noncatalyzed reaction, a central barrier of approximately 20-21 kcal/mol separating the reactants from products depending on which carbon center in the epoxide is undergoing attack. From these gas-phase reactions the immediate alkoxide products are not energetically far below their associated transition states such that the reaction is predicted to be endothermic. Inclusion of aqueous solvation effects via a polarizable continuum model predicts the activation barrier to increase by almost 10 kcal/mol due to the solvation of the acetate ion nucleophile. The activation barrier for the epoxide ring-opening reaction is reduced to approximately 10 kcal/mol when phenol, as the general-acid catalyst, is included in the gas-phase calculations. This is due to the immediate product being the neutral ester rather than the corresponding alkoxide. The transition state in the general-acid-catalyzed reaction is earlier than that for the noncatalyzed reaction and the reaction is highly exothermic. Molecular mechanics calculations of 1S,2S-trans-2-methylstyrene oxide in the active site of murine epoxide hydrolase show two possible binding conformations. Both conformers have the epoxide oxygen forming hydrogen bonds with the acidic hydrogens of the catalytic tyrosines (Tyr381 and Tyr465). These two conformations likely lead to different products since the nucleophile (Asp333-CO(2)(-)) is positioned to react with either carbon center in the epoxide.     

MoSe2 and WSe2 nanotubes and related structures

MoSe2 and WSe2 nanotubes are obtained by the reduction of the corresponding triselenides in hydrogen or by the decomposition of the ammonium selenometallates in a hydrogen atmosphere.     

In vitro high throughput screening of compounds for favorable metabolic properties in drug discovery

Drug metabolism can have profound effects on the pharmacological and toxicological profile of therapeutic agents. In the pharmaceutical industry, many in vitro techniques are in place or under development to screen and optimize compounds for favorable metabolic properties in the drug discovery phase. These in vitro technologies are meant to address important issues such as: (1) is the compound a potent inhibitor of drug metabolising enzymes (DMEs)? (2) does the compound induce the expression of DMEs? (3) how labile is the compound to metabolic degradation? (4) which specific enzyme(s) is responsible for the compound's biotransformation? and (5) to which metabolites is the compound metabolized? Answers to these questions provide a basis for judging whether a compound is likely to have acceptable pharmacokinetic properties in vivo. To address these issues on the increasing number of compounds inundating the drug discovery programs, high throughput assays are essential. A combination of biochemical advances in the understanding of the function and regulation of DMEs (in particular, cytochromes P450, CYPs) and automated analytical technologies are revolutionizing drug metabolism research. Automated LC-MS based metabolic stability, fluorescence, radiometric and LC-MS based CYP inhibition assays are now in routine use. Automatible models for studying CYP induction based on enzyme activity, quantitative RT-PCR and reporter gene systems are being developed. We will review the utility and limitations of these HTS approaches and highlight on-going developments and emerging technologies to answer metabolism questions at the different stages of the drug discovery process.     

Analysis of steroids in environmental water samples using solid-phase extraction and ion-trap gas chromatography-mass spectrometry and gas chromatography-tandem mass spectrometry

This paper describes an improved method for the extraction and determination of three steroids, oestrone, 17beta-oestradiol, and the synthetic contraceptive steroid 17alpha-ethinyloestradiol in aqueous matrices. Samples of wastewater and environmental water were spiked with internal standards, comprising isotopically labelled analogues of the steroids to be determined. The samples were extracted using solid-phase extraction disks and the extracts were then derivatized to form tert.-butyldimethylsilyl derivatives. The derivatised steroids were determined in the final extracts by GC-MS or GC-MS-MS allowing an operational detection limit for each steroid in effluent samples of 1 ng l(-1).     

Replacement of the phosphorodiester linkages of RNA with guanidinium linkages: the solid-phase synthesis of ribonucleic guanidine

[reaction: see text] Replacement of the negatively charged phosphodiester linkages of RNA with positively charged guanidinium linkages provides the polycationic ribonucleic guanidine (RNG). RNG is anticipated to bind strongly to target DNA/RNA through the specific interactions of nucleobases and the attractive electrostatic interactions of backbones. Preparation of building blocks and the solid-phase synthesis of RNG are reported. Both trimeric and pentameric uridyl RNG have been synthesized.     

Density functional calculation of the electronegativity and other related properties of atoms and ions of the principal groups of the periodic table

The relation between the electronegativityχ of an atom or an ion (χ=??E(Z,N)/?N) and its finite difference (Mulliken like) counterpart has been studied for the elements of the groups IA to VIIA of the Periodic Table, using an approximate Density Functional Theory. Only the valence electrons are taken into account and the effect of the ionic core is simulated by a simple empty core pseudopotential. The first derivative ?χ/6N of the electronegativity has also been computed. The interest inχ and?χ/?N is illustrated by a simple model for the transfer of electronic charge in a molecule. Molecular electronegativities are then computed.     

Palladium-catalyzed C-O bond formation: direct synthesis of phenols and aryl/alkyl ethers from activated aryl halides

A simple and efficient palladium-catalyzed carbon-oxygen bond formation is reported. The palladium-tri-tert-butylphosphine complex was found to be effective in converting haloarenes to corresponding substituted phenols. This methodology offers a direct transformation of aryl halides to phenols, as well as the straightforward application to generate a wide variety of diaryl or alkyl/aryl ethers.     

Thermal and autoxidation reactions of poly-3-methylenecyclobutene and poly-1-methyl-3-methylenecyclobutene

The thermal ring-opening reactions, autoxidation and hydrogenation of polymethy-lenecyclobutene (PMCB) and poly-1-methyl-3-methylenecyclobutene (PMMCB), were investigated. Both polymers were prepared by cationic polymerization and consisted almost entirely of 1,5-repeating units containing cyclobutene rings in the polymer backbone. Both polymers showed well behaved exothermic processes at elevated temperatures which apparently resulted in crosslinking. These processes were investigated by differential scanning calorimetry and interpreted to involve thermal ring-opening reactions. Autoxidation occurred very rapidly in PMCB but much more slowly in PMMCB as predicted by Bolland's rules. Attempts to hydrogenate the cyclobutene rings in both polymers resulted in the occurrence of hydrogenolysis in PMCB and little or no reaction with PMMCB for a Pd-catalyzed reaction and partial hydrogenation of the latter for a diimide reaction.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.     

Transferable atom equivalent multicentered multipole expansion method

The transferability of atomic and functional group properties is an implicit concept in chemistry. The work presented here describes the use of Transferable Atom Equivalents (TAE) to represent molecular electrostatic potential fields through the use of integrated atomic multipole moments that are associated with each TAE atom type used in the reconstruction. TAE molecular surface distributions of electrostatic potentials are compared with analytical ab initio and empirical (Gasteiger) partial charge reference models for several conformations of test peptides. Surface electrostatic potential distributions computed using TAE multipole representations were found to converge at the octopole level, with incremental improvement observed when hexadecapoles were included. Molecular electrostatic potential fields that were produced using the TAE method were observed to be responsive to conformational changes and to compare well with ab initio reference distributions. Generation of TAE atom types and their associated multipoles does not involve fitting to sample electrostatic potential fields, but rather utilizes integrated AIM atomic electron density distributions within representative chemical environments. The RECON program was used for TAE reconstruction. RECON is capable of processing 5,000 drug-sized molecules or 25 proteins per minute per 1.7 GHz P4 Linux processor.