Conformational properties of diastereomeric 5'-O-DMT-2'deoxythymidine 3'-O-(S-methyl-methanephosphonothiolate)s and -(se-methyl-methanephosphonoselenolate)s in solution as studied by NMR methods

Synthesis and structural study of variously oxidized diastereomeric 5'-dimethoxytrityl-thymidine-3'-O-[O-(2-cyanoethyl)-N,N-diisopropyl]-phosphoramidite derivatives. Comparison of the effects of the P=O, P=S, and P=Se functions on the NMR spectral and chromatographic properties

R(P)- and S(P)-diastereomers of 5'-dimethoxytrityl-thymidine-3'-O-[O-(2-cyanoethyl)-N,N-diisopropyl]-phosphoramidite (T-CED) were separated by silica gel chromatography. Oxidation of both isomers with H(2)O(2), elemental sulfur and selenium, respectively, resulted in the corresponding oxidized analogues in nearly quantitative yields. All reactions were found to proceed with retention of P-configuration. This was confirmed by thorough NMR analysis which, in addition, aimed to study the spectral properties of the diastereomers with special respect to differences in the heteroatom effect of the O, S and Se atoms, double-bonded to the phosphorus, on the vicinal carbon-phosphorus couplings. It was found that the changes in the DeltaJ (=(3)J(P,C4') - (3)J(P,C2')) values were basically induced by the electronegativity of the heteroatoms, rather than differences in the rotational preferences about the C3'-O3' bond. The impact of the benzene solvent on the above couplings is also discussed. The effect of these heteroatoms on the chromatographic (normal and reverse phase HPLC) behavior of the compounds was also investigated and the reverse phase HPLC profiles showed an unambiguous correlation between the electronegativity of the heteroatoms and the chromatographic mobility of the analogues.

X-ray Diffraction and Solid-State NMR Studies of a Germanium Binuclear Complex

A compound formulated as (C4H12N2)[Ge2(pmida)2(OH)2] x 4 H2O (where pmida(4-) = N-(phosphonomethyl)iminodiacetate and C4H12N2(2+) = piperazinedium cation), containing the anionic [Ge2(pmida)2(OH)2]2- complex, has been synthesised by the hydrothermal approach and its structure determined by single-crystal X-ray diffraction analysis. Several high-resolution solid-state magic-angle spinning (MAS) NMR techniques, in particular two-dimensional 1H-X(13C,31P) heteronuclear correlation (HETCOR) and 1H-1H homonuclear correlation (HOMCOR) experiments incorporating a frequency-switched Lee-Goldburg (FS-LG) decoupling scheme, have been employed for the first time in such a material. Using these tools in tandem affords an excellent general approach to study the structure of other inorganic-organic hybrids. We assigned the NMR resonances with the help of C...H and P...H internuclear distances obtained through systematic statistical analyses of the crystallographic data. The compound was further characterised by powder X-ray diffraction techniques, IR and Raman spectroscopy, and by elemental and thermal analyses (thermogravimetric analysis and differential scanning calorimetry).

13C-31P couplings in the study of conformational properties of some diastereomeric nucleoside-3'-thiophosphate derivatives

Synthesis and stereochemical characterization of enantiomerically pure nucleoside-3'-phosphorothioate esters and salts are reported. Vicinal carbon phosphorus couplings reflect different predominance of the epsilon conformation in the isomeric (Rp and Sp) esters, while for the salts the epsilont conformation prevails in both stereoisomers. The influence of solvent and temperature on the conformational preferences is also described.

Solution structure of diastereomeric thymidine 3'-O(N,N-diisopropyl-O-beta-cyanoethyl-phosphoramidothioate)s by NMR spectroscopy

The conformational properties of a diastereomeric nucleoside-phosphorothioate pair is reported as reflected by different NMR parameters. Configurational assessment is based partly on the different NOE (nuclear overhauser enhancement) effects of the individual isomers and on the trends observed in other NMR parameters. Vicinal carbon-phosphorus couplings reflect the predominance of the epsilon(-) conformation for the Sp isomer and the epsilon(t) conformation for the Rp isomer. The effects of solvent and temperature on these vicinal couplings are described and the results are interpreted in terms of conformational shift towards the preferred epsilon(t) conformation.

Direct assignment of the absolute configuration of a distinct class of deoxyribonucleoside cyclic N-acylphosphoramidites at phosphorus by M-GOESY nuclear magnetic resonance spectroscopy

The determination of the absolute configuration of deoxyribonucleoside cyclic N-acylphosphoramidites at phosphorus toward the synthesis of P-stereodifined phosphorothioated oligodeoxyribonucleotides is easily accomplished with computer-assisted molecular modeling and M-GOESY NMR spectroscopy. Specifically, computer-modeling diasteromeric phosphoramidite 3 has identifed a proximal (2.55 A) through-space interaction between benzylic H-5 and sugar H-2' ', which can predictably be detected by M-GOESY NMR in SP-3 but not in RP-3 because of being too distant (5.85 A). Consistent with computer-assisted modeling predictions, M-GOESY NMR spectra of SP-3 and RP-3 revealed NOE signals generated from nuclei near the selectively excited H-2' ' that are common to both SP-3 and RP-3, namely those of H-2', H-4', H-3', and H-1'. In addition, a diagnostic NOE signal at 5.5 ppm (benzylic H-5) is, as predicted, only detected in SP-3 and thus provides an unequivocal assessment of the configuration of the diastereomer at phosphorus. M-GOESY NMR data also confirm that the condensation of deoxyribonucleoside cyclic N-acylphosphoramidites with base-activated nucleosidic or nucleotidic 5'-hydroxyls proceeds via a single nucleophilic event.

Synthesis and stereochemical characterization of diastereomeric nucleoside-phosphorothioselenoates by NMR methods

Synthesis and stereochemical characterization of enantiomerically pure nucleoside-phosphorothioselenoates are reported. The effects of solvent and temperature on the vicinal carbon-phosphorus couplings are described and the results are interpreted in terms of conformational changes influenced by stacking interactions between the bases and the phenyl rings.