Hydrogen atoms in direct methanol fuel cells are produced ’in situ’ by dissociation of methanol on precious metal catalysts (Pt, Pt/Ru) in an aqueous environment. The abstraction of the first hydrogen atom via C–H bond cleavage is generally considered to be the rate-limiting step of dissociative methanol adsorption on the catalyst surface. This oxidation reaction on platinum particles in a fuel cell is investigated by means of a combined approach of classical molecular dynamics (MD) simulations and ab initio calculations in order to obtain an understanding of the role of the solvent for the stabilization of intermediates and for the enhancement of proton desorption from the catalyst surface and subsequent transfer into the nearby polymer electrolyte membrane (PEM). The anodically generated protons need to migrate efficiently through the membrane to the cathode were they are consumed. At the same time water and methanol (in a direct methanol fuel cell) transport should be slow. Humidified PEMs are considered to consist of a nanometer-scale phase-separated bicontinuous network of polymer regions providing structural integrity, and of aqueous regions providing the pathways for proton conduction. MD simulations provide a powerful theoretical tool for the investigation and clarification of the relationship between molecular structure and these transport phenomena. In order to atomistically model larger fractions of a humidified PEM, a coarse-grained model of humidified polymer electrolyte membranes has been developed.