Side Reactions in the H-Phosphonate Approach to Oligonucleotide Synthesis: A Kinetic Investigation on Bisacylphosphite Formation and 5′-O-Acylation

Abstract

A kinetic study on the reactions of pivaloyl chloride with a nucleoside H-phosphonate (bisacylphosphite formation), or a protected nucleoside with a free 5′-OH (5′-O-pivaloylation) has been carried out in the presence of differently substituted pyridines. The bisacylphosphite formation is a result of acylation of the mixed carboxylic-phosphonic acid anhydride to give the corresponding bispivaloylphosphite derivative. The rate of this reaction is dependent on the concentration of pyridine derivative and pivaloyl chloride. The 5′-O-pivaloylation reaction is also dependent on the concentration of pyridine derivative and pivaloyl chloride. The rate of both reactions is dependent on the basicity of the pyridine derivative, displaying a higher rate with more basic pyridines. The dependence of log k vs. pKa of pyridine is linear but the slopes are quite different for the two reactions (0.84 for bisacylation and 0.21 for 5′-O-pivaloylation). For both reactions considerably lower rates in the presence of sterically hindered pyridines suggest the existence of nucleophilic catalysis on pivaloyl chloride in reactions with non-hindered pyridines.