The unique crystal structure of hexaboride materials make them very attractive for applications related to gas storage including hydrogen and other light gases. The lattice is simple cubic with boron octahedra at each corner of the cube bonded at the apexes. The octahedra consist of the boron atoms, with four adjacent neighbors in every octahedron for every boron atom, and one on the main axes of the cube. The metal atom is located in the middle of the unit cell and can donate electrons to the structure, imparting a metallic character to hexaborides with metal ions of +3 charge, and semiconductor character to hexaborides with metal ions of +2 charge. In this presentation, we discuss the current state of the art on the fundamental modeling of these systems and present preliminary results on mass transfer of simple gases through this type of structures assuming that the metal atoms are not present. We use molecular dynamics (MD) with representative potentials to describe the interactions and diffusion of gases in the hexaboride cages. Although it might not be realistic experimentally to empty all the cages of the metal ions, molecular dynamics calculations under this scenario provides significant insight on the type of gases that could be stable in these cages and how the hexaboride structure affect their mobility and stability in the system. We also describe how the effect of external fields such as electric, pressure gradients, and heat flow affect the relative positions of the atoms in the structures and their mass transport behavior. The diffusion process is characterized using mean square displacement of atoms and the Einstein relation to evaluate diffusion coefficients. Fundamental understanding of these materials at the atomic level is crucial for the development of commercial applications of these and similar types of materials.