Reactions of Per-O-Acetylglucosyl Isothiocyanate with Enamines. A Route for the Synthesis of Pyrimidine Nucleosides

Abstract

The reaction of 2,3,4,6-tetra-O-acetyl-β-D-glucopyranosyl isothiocyanate with enamines in basic medium to form the glucosylthioamides 9-16, the glucosylthiourea 17, and the nucleoside analogue 18 is reported. The N-halogenophenyl-(1-3, 5-7) and the N-(3,4-dimethoxybenzyl)-(4,8) enaminoesters or enaminones were prepared as precursors for 9-18. The treatment of several of the prepared glucosylthioamides with thiophosgene yields dithioxopyrimidine nucleosides (19-22) with the sugar ring on position 3 of the heterocycle. Glucosylamides are isolated as byproducts. The enamino moieties of the prepared glucosylthioamides and glycosylamides have the EEE configuration and the thioamide or amide bond the Z, anti geometry.     

Bimolecular photoinduced electron transfer in imidazolium-based room-temperature ionic liquids is not faster than in conventional solvents

The fluorescence quenching of 3-cyanoperylene upon electron transfer from N,N-dimethylaniline in three room-temperature ionic liquids (RTILs) and in binary solvent mixtures of identical viscosity has been investigated using steady-state and time-resolved fluorescence spectroscopy. This study was stimulated by previous reports of bimolecular electron transfer reactions faster by one or several orders of magnitude in RTILs than in conventional polar solvents. These conclusions were usually based on a comparison with data obtained in low-viscous organic solvents and extrapolated to higher viscosities and not by performing experiments at similar viscosities as those of the RTILs, which we show to be essential. Our results reveal that (i) the diffusive motion of solutes in both types of solvents is comparable, (ii) the intrinsic electron transfer step is controlled by the solvent dynamics in both cases, being slower in the RTILs than in the conventional organic solvent of similar viscosity, and (iii) the previously reported reaction rates much larger than the diffusion limit at low quencher concentration in RTILs originate from a neglect of the static and transient stages of the quenching, which are dominant in solvents as viscous as RTILs.     

Spurious observation of the Marcus inverted region in bimolecular photoinduced electron transfer

The effect of viscosity on the bimolecular electron transfer quenching of a series of coumarins by N,N-dimethylaniline was investigated using steady-state and time-resolved fluorescence spectroscopy. The data reveal that the static and transient stages of the quenching become dominant as viscosity increases. When extracting the quenching rate constants using a simple Stern-Volmer analysis, a decrease of the rate constant with increasing driving force is observed above ~2 cP. However, this apparent Marcus inverted region, already reported several times with the same system in micelles and room temperature ionic liquids, totally vanishes when analyzing the data with a model accounting for the static and transient stages of the quenching. It appears that the apparent Marcus inverted region arises from the neglect of these quenching regimes together with the use of fluorophores with different excited-state lifetimes.     

Rigid-CLL: avoiding constant-distance computations in cell linked-lists algorithms

Many of the existing molecular simulation tools require the efficient identification of the set of nonbonded interacting atoms. This is necessary, for instance, to compute the energy values or the steric contacts between atoms. Cell linked-lists can be used to determine the pairs of atoms closer than a given cutoff distance in asymptotically optimal time. Despite this long-term optimality, many spurious distances are anyway computed with this method. Therefore, several improvements have been proposed, most of them aiming to refine the volume of influence for each atom. Here, we suggest a different improvement strategy based on avoiding to fill cells with those atoms that are always at a constant distance of a given atom. This technique is particularly effective when large groups of the particles in the simulation behave as rigid bodies as it is the case in simplified models considering only few of the degrees of freedom of the molecule. In these cases, the proposed technique can reduce the number of distance computations by more than one order of magnitude, as compared with the standard cell linked-list technique. The benefits of this technique are obtained without incurring in additional computation costs, because it carries out the same operations as the standard cell linked-list algorithm, although in a different order. Since the focus of the technique is the order of the operations, it might be combined with existing improvements based on bounding the volume of influence for each atom.     

Plasma fingerprinting with GC-MS in acute coronary syndrome

New biomarkers of cardiovascular disease are needed to augment the information obtained from traditional indicators and to illuminate disease mechanisms. One of the approaches used in metabolomics/metabonomics for that purpose is metabolic fingerprinting aiming to profile large numbers of chemically diverse metabolites in an essentially nonselective way. In this study, gas chromatography-mass spectrometry was employed to evaluate the major metabolic changes in low molecular weight plasma metabolites of patients with acute coronary syndrome (n = 9) and with stable atherosclerosis (n = 10) vs healthy subjects without significant differences in age and sex (n = 10). Reproducible differences between cases and controls were obtained with pattern recognition techniques, and metabolites accounting for higher weight in the classification have been identified through their mass spectra. On this basis, it seems inherently plausible that even a simple metabolite profile might be able to offer improved clinical diagnosis and prognosis, but in addition, specific markers are being identified.     

Synthesis of amine-functionalized heparin oligosaccharides for the investigation of carbohydrate-protein interactions in microtiter plates

The synthesis of well-defined oligosaccharides is crucial for the establishment of structure-activity relationships for specific sequences of heparin, contributing to the understanding of the biological role of this polysaccharide. It is highly convenient that the synthetic oligosaccharides contain an orthogonal functional group that allows selective conjugation of the probes and expands their use as chemical tools in glycobiology. We present here the synthesis of a series of amine-functionalized heparin oligosaccharides using an n+2 modular approach. The conditions of the glycosylation reactions were carefully optimized to produce efficiently the desired synthetic intermediates with an N-benzyloxycarbonyl-protected aminoethyl spacer at the reducing end. The use of microwave heating greatly facilitates O- and N-sulfation steps, avoiding experimental problems associated with these reactions. The synthesized oligosaccharides were immobilized in 384-well microtiter plates and successfully probed with a heparin-binding protein, the basic fibroblast growth factor FGF-2. The use of hexadecyltrimethylammonium bromide minimized the amount of sugar required for attachment to the solid support. Using this approach we quantified heparin-protein interactions, and surface dissociation constants for the synthetic heparin derivatives were determined.     

Ultrafast solvation dynamics of coumarin 153 in imidazolium-based ionic liquids

The dynamic Stokes shift of coumarin 153 has been measured in two room-temperature ionic liquids, 1-(3-cyanopropyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and 1-propyl-3-methylimidazolium tetrafluoroborate, using the fluorescence up-conversion technique with a 230 fs instrumental response function. A component of about 10-15% of the total solvation shift is found to take place on an ultrafast time scale < 10 ps. The amplitude of this component is substantially less than assumed previously by other authors. The origin of the difference in findings could be partly due to chromophore-internal conformational changes on the ultrafast time scale, superimposed to solvation-relaxation, or due to conformational changes of the chromophore ground state in polar and apolar environments. First three-pulse photon-echo peak-shift experiments on indocyanine green in room-temperature ionic liquids and in ethanol indicate a difference in the inertial component of the early solvent relaxation of <100 fs.