Phosphonomethyl (Thio)Phosphonamidite Reagents for the Construction of Phosphonylmethyl Phosphono(Di)Thioate Mono‐ and Diesters

ABSTRACT A repertoire of phosphonomethyl (thio)phosphonamidite reagents has been developed to enable the controlled synthesis of phosphonylmethyl phosphono(di)thioate analogues of intrinsically labile pyrophosphates. Selective amidophosphonitylation of an alcohol or thiol of choice with a phosphonomethyl phosphonbisamidite allows access to four (thio)phosphonamidite reagents bearing three orthogonal protecting groups that can be chemoselectively addressed. These reagents were isolated in homogeneous form in yields up to 95% and applied in a sequence involving azole‐mediated phosphonamidite coupling with an alcohol and successive in situ sulfurization of the P III ‐P V intermediate, which affords protected phosphonylmethyl phosphono(di)thioate tetraesters. The coupling and sulfurization steps were monitored with 31 P‐NMR, revealing the nature of the key intermediates and corroborating the high efficiency of the coupling and sulfurization reactions. Immediate global deprotection or subsequent site‐selective deprotection of the terminal phosphonate followed by a phosphonodiester condensation furnishes unprecedented phosphonylmethyl phosphono(di)thioate mono‐ and nonsymmetrical diesters, respectively. Using this method, we have assembled four nucleoside diphosphate analogs as well as a set of eight stable CDP‐glycerol and CDP‐ribitol mimics, all in multimilligram amounts.