Reactions of NH+4 in water solutions with self-assembled monolayer (SAM) surfaces result in the deposition of ammonia in the monolayers. Similarities between this and the soft landing of ions seen in low energy gas phase ion—surface collisions suggest that monolayers can be used as matrices to preserve species. Ammonia can be incorporated only into thicker SAMs such as those made from octadecanethiol. Reactions with larger ions do not lead to trapping. Trapped ammonia desorbs during prolonged exposure of the SAMs to vacuum. © 1999 Taylor & Francis Group, LLC.