The electron impact (EI) mass spectrometric behaviour of 11 recently synthesized 5′-phosphordiamidates with various bases and amidate groups has been studied by low and high resolution techniques. Trimethylsilylation of these compounds yields derivatives which are sufficiently volatile for direct evaporation in the ion source. Structural relationships for the main fragment ions are given and compared with those of the previously studied analogous trimethylsilylated mononucleotides. Decomposition routes related to and specific for the primary, secondary or tertiary character of the amide functions were observed. Tertiary diamidates studied were found to be evaporable in underivatized form without significant thermal decomposition and gave very simple spectra with characteristic fragments for the base and the sugar, as well as the phosphordiamidate moieties.

The mass spectra of trimethylsilyl (TMS) derivatives of some 3′ and 5′-isomers were compared and found to be characteristically different.