The molecular pathways of the catalytic reactions within the direct methanol fuel cell are studied. A realistic model of the electrocatalytic system, in which both the solution phase and an applied potential are included, is used to aid in the design of effective materials for methanol oxidation and oxygen reduction. Polyoxometalates, or heteropolyacids (HPA), are active in reactions requiring a strong acid catalyst, such as the skeletal isomerization of hydrocarbons and the alkylation of isobutane with butenes, and are a potential replacement for the corrosive, toxic liquid acids currently used. Density functional theory (DFT) is used to study the energetics of proposed deactivation mechanisms. Reaction energies and activation barriers are determined by DFT and further used to establish reaction rates and equilibrium constants to clarify whether a proposed mechanism may explain the deactivation process. Emphasis is placed on understanding how including water in the reaction environment may slow or prevent deactivation. This research also seeks to further understanding of acid-catalysis mechanisms over HPA by providing insight into the requirements of an effective solid-acid catalyst for the alkylation of isobutane with n-butene. This is an abstract of a paper presented at the AIChE Annual Meeting and Fall Showcase (Cincinnati, OH 10/30/2005-11/4/2005).