Among the many different types of molecules that form clathrate hydrates, H-2 is unique as it can easily diffuse into and out of clathrate cages, a process that involves the physical-chemical interactions between guest (H-2) and host (water) molecules, and is unlike any other molecular system. The dynamic and nano-scale process of H-2 diffusion into binary structure II hydrates, where the large cages are occupied by larger molecules, was studied using molecular dynamics simulation. As the H-2 molecules diffused from one cage to another, two types of diffusion processes were observed: (i) when moving between a pair of large cages, the H-2 molecules pass through the central part of the hexagonal rings; (ii) however, when the H-2 molecules move from a large cage to a small one, it requires one of the pentagonal rings to partially break, as this allows the H-2 molecule to pass through the widened space. While the diffusion of H-2 molecules between large cages was found to occur more frequently, the presence of SF6 molecules in the large cages was found to inhibit diffusion. Therefore, in order to attain higher H-2 storage capacities in binary hydrates, it is suggested that there is an optimal number of large cages that should be occupied by SF6 molecules.