Reductive allylation of 1H-pyridine-2-(thio)ones by means of the novel lithium allyldibutylmagnesate reagent

A new, highly efficient allylation reagent—lithium allyldibutylmagnesate (allylBu₂MgLi)—was obtained by mixing allyl-magnesium chloride (1 equiv) and n-BuLi (2 equiv). N-Lithiated and N-methyl substituted 1H-pyridine-2-thiones and -ones were successfully and regioselectively allylated by treatment with allylBu₂MgLi yielding 6-allyl-3,6-dihydro-1H-pyridine-2-(thio)ones and 4-allyl-3,4-di-hydro-1H-pyridine-2-(thio)ones. The latter were formed by a 3,3-sigmatropic Cope rearrangement of the former.     

Dipole‐bound anions supported by charge–transfer interaction: Anionic states of HnF3−nN → BH3 and H3N → BHnF3−n (n = 0, 1, 2, 3)

The possibility of electron binding to five molecules (i.e., F₃N → BH₃, H₂FN → BH₃, HF₂N → BH₃, H₃N → BH₂F, H₃N → BHF₂) was studied at the coupled cluster level of theory with single, double, and noniterative triple excitations and compared to earlier results for H₃N → BH₃ and H₃N → BF₃. All these neutral complexes involve dative bonds that are responsible for significant polarization of these species that generates large dipole moments. As a consequence, all of the neutral systems studied, except F₃N → BH₃, support electronically stable dipole‐bound anionic states whose calculated vertical electron detachment energies are 648 cm^?1 ([H₂FN → BH₃]^?), 234 cm^?1 ([HF₂N → BH₃]^?), 1207 cm^?1 ([H₃N → BH₂F]^?), and 1484 cm^?1 ([H₃N → BHF₂]^?). In addition, we present numerical results for a model designed to mimic charge–transfer (CT) and show that the electron binding energy correlates with the magnitude of the charge flow in the CT complex. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Structural factors determining DNA length limitations in conformation-sensitive mutation detection methods

Numerous mutations and polymorphisms in human genes remain to be identified using reliable methods. Of the available mutation scanning methods those dependent on structural change-induced mobility shifts are highly effective. Their efficiency is, however, DNA length-sensitive and the reasons for that are poorly understood. In this study, we explain why scanning genes for mutations is less effective in longer DNA fragments, and reveal the factors which are behind this effect. We have performed a systematic analysis of the same sequence variants of exon 11 of the BRCA1 gene in DNA fragments of three different lengths using the combined single-strand conformation polymorphism (SSCP) and heteroduplex analysis (DA) by capillary electrophoresis (CE). There are two major structural factors responsible for the reduced mutation detection rate in long amplicons. The first is increased contribution from other secondary structure modules and domains in longer fragments, which mask the structural change induced by the mutation. The second is higher frequency of single-nucleotide polymorphisms (SNPs) including common polymorphisms in longer fragments. This makes it necessary to distinguish the structural effect of the mutation from that of each polymorphic variant, which is often difficult to achieve. Taking these factors into account, an efficient scanning of genes for sequence variants by conformation-sensitive methods may be performed.     

Validated capillary electrophoretic method for the analysis of ivermectin in plasma after intragastric administration in pigs and horses

A capillary electrophoretic (CE) method has been developed for the determination of ivermectin (CAS 70288-86-7), a new generation drug with antiparasitic activity, in pig and horse plasma. The method was statistically validated for its linearity, accuracy, precision and selectivity. The linear range was from 1 to 30 ng mL(-1) with correlation coefficients greater than 0.999. The limit of detection was 0.3 ng mL(-1), while the quantitative limit was 1 ng mL(-1), using a 0.5 mL sample size. The validated procedure was used to determination of pharmacokinetic parameters of ivermectin after ingestion of 0.1 mg for pigs and 0.2 mg dose per kg body weight for horses, respectively. Studies were performed on a group of eight pigs and six horses. There were no significant differences between pigs and horses in any of the estimated pharmacokinetic parameters.     

Extension of N-confused porphyrin by an o-xylene fragment

[reaction: see text] A simple method of modification of N-confused porphyrin is provided by reactions of 5,10,15,20-tetraaryl-2-aza-21-carbaporphyrin with alpha,alpha'-dibromoxylene. The N-bromoxylene-substituted monomer formed in a first step of alkylation can be converted to the products with the extended structure on the N-confused pyrrole for which formation of organometallic silver(III) complexes has been shown.     

Theory of retention in reversed phase liquid chromatography with ternary mobile phases

The partition model of retention is developed for reversed phase liquid chromatography with multicomponent mobile phases. Simple equations for the retention and selectivity in ternary mobile phases are derived. For the systems in which the ratio of volume fractions of organic modifiers remains fixed, new linear dependences for retention factor and selectivity are proposed. These equations are successfully used to describe experimental data found in the literature. An influence of the nature of organic solvents and proportion in which they are mixed on retention and selectivity is discussed.     

Davydov splitting of Herzberg—Teller-induced vibronic transitions

Based on a simple dimer model of vibronic coupling it is demonstrated that, contrary to the conventional notion, the Davydov splitting of the fundamental vibronic transition in non-totally symmetric vibrations, induced by the Herzberg—Teller mechanism, does not need to be very small.     

Facile construction of the benzofuran and chromene ring systems via PdII-catalyzed oxidative cyclization

[reaction: see text]. We herein report the development of one-pot procedures for the conversion of allyl aryl ethers to 2-methylbenzofurans (via sequential Claisen rearrangement and oxidative cyclization) and for the conversion of aryl homoallyl ethers to chromenes (via direct oxidative cyclization). It is likely that both reactions proceed via a common Pd-catalyzed pathway involving olefin activation, nucleophilic attack, and beta-hydride elimination.     

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed.