Electrospray ionization is used to create what are demonstrated to be highly reactive, metastable clusters of alkylammonium cations and triphosphate dianions. Collision-induced activation of the clusters leads to either S(N)2 or E2 reactions, resulting in the formation of an alkyltriphosphate or triphosphate anion, respectively. The series of tetraalkylammonium ions from tetramethyl ammonium to tetraheptylammonium is studied. The SN2 pathway is favored over the E2 pathway. The replacement of a proton in the triphosphate dianion with a sodium cation in these clusters leads to enhanced yields of the E2 product. PM5 calculations of the reaction energetics correlate well with the observed product distributions. The doubly deprotonated DNA oligomer CCGG can also be alkylated by CID of its cluster with a tetraalkyl ammonium cation. The cluster phase reactions described in this study serve to illustrate a general scheme which we propose for the rational design of ionic clusters where reactivity is ensured by inhibiting direct dissociation. The experimental methodology implied by the cluster design criteria expands the utility of small molecular clusters for structure-reactivity studies and directed chemical synthesis.