Advances in theoretical and computational chemistry are making it practical to consider fully first principles (de novo) predictions of such important complex systems as fuel cells, but the most important applications require strategies for linking the time scales from electrons to macroscale. We will illustrate the approaches we have been using with recent results on simulations of fuel cell systems. Here we will consider •QM studies of the reaction mechanisms on the anode and cathode, •Effects of catalyst alloying on the rates •ReaxFF reactive force fields that reproduce the mechanism from QM •The nanoscale structure of PEM membranes such as Nafion •MD simulations combining reactions at the catalysts with migrations of protons through the PEM. •Using these results we will suggest some new designs for the membrane and for the catalyst and for Reversible high capacity H2 storage for transportation fuel cells.