Nucleophilicities and Lewis basicities of imidazoles, benzimidazoles, and benzotriazoles.

The kinetics of the reactions of some imidazoles, benzimidazoles and benzotriazoles with benzhydrylium ions (diarylcarbenium ions) have been studied photometrically in DMSO, acetonitrile, and aqueous solution at 20 degrees C. The resulting second-order rate constants have been used to determine the nucleophile-specific parameters N and s of these azoles according to the linear-free-energy relationship log k (20 degrees C) = s(N + E). With N = 11.

Nucleophilicities of amino acids and peptides.

The kinetics of the reactions of amino acids with stabilized diarylcarbenium ions (Ar(2)CH(+)) have been studied photometrically in aqueous solution at variable pH. In the range of 10.5 < pH < 12, the amino acids react much faster than the competing nucleophiles hydroxide and water.

Nucleophilicities of primary and secondary amines in water.

The kinetics of the reactions of 26 primary and secondary amines with benzhydrylium ions in water were investigated photometrically. Because the parallel reactions of the benzhydrylium ions with hydroxide and water are much slower, the second-order rate constants for the reactions of amines with benzhydrylium ions could be determined reliably. Reactivities of anilines were also studied in acetonitrile solution.

Nucleophilicities and carbon basicities of pyridines.

Rate and equilibrium constants for the reactions of pyridines with donor-substituted benzhydrylium ions have been determined spectrophotometrically. The correlation equation log k(20 degrees C)=s(N+E), in which s and N are nucleophile-specific parameters and E is an electrophile-specific parameter, has been used to determine the nucleophilicity parameters of various pyridines in CH(2)Cl(2) and aqueous solution and to compare them with N of other nucleophiles. It is found that the nucleophilic organocatalyst 4-(dimethylamino)pyridine (DMAP) and tertiary phosphanes have comparable nucleophilicities and carbon basicities despite widely differing Brønsted basicities.

Stabilizing or destabilizing oligodeoxynucleotide duplexes containing single 2'-deoxyuridine residues with 5-alkynyl substituents.

The 5-position of pyrimidines in DNA duplexes offers a site for introducing alkynyl substituents that protrude into the major groove and thus do not sterically interfere with helix formation. Substituents introduced at the 5-position of the deoxyuridine residue of dU:dA base pairs may stabilize duplexes and reinforce helices weakened by a low G/C content, which would otherwise lead to false negative results in DNA chip experiments. Here we report on a method for preparing oligonucleotides with a 5-alkynyl substituent at a 2'-deoxyuridine residue by on-support Sonogashira coupling involving the fully assembled oligonucleotide.