Abstract The alkenyldiarylmethanes are a class of non‐nucleoside reverse transcriptase inhibitors that are currently being developed as potential antivirals for the treatment of HIV infection and AIDS. As part of our continuing investigations on the alkenyldiarylmethanes, a series of thioester analogues were prepared in an effort to improve upon the metabolic stability of the parent lead compound. Hydrolysis of the thioester moieties was consistently observed during ion trap electrospray ionization (ESI) mass spectrometry to the extent that the parent molecular ion was weak in intensity or simply could not be detected. The same hydrolysis observations were also made when the analogues were analyzed by ion trap electron impact (EI) ionization, indicating the hydrolysis event was the result of the ion trap and not ionization technique. Ion‐trap‐mediated hydrolysis has been observed previously in prior alkenyldiarylmethane studies and prevented characterization of certain intermediates; thus, we wished to investigate whether modifying instrument parameters and protocols affected the instrument‐mediated hydrolysis event. Unfortunately, varying the maximum injection time and the number of microscans performed, independent of each other, had little effect on the intensities of the parent ions [MH + ] or the hydrolysis products]MH + HSCH 3 ]. Copyright © 2008 John Wiley & Sons, Ltd.