Umbrella Sampling Molecular Dynamics has been used to determine transition energies for different guest molecules through hydroquinoneβ-clathrate nanochannels, as well as their temperature trend. This clathrate has been shown to successfully enclathrate different types of small gases with remarkable selectivity, and thus it has been proposed as a potential gas separation and storage medium. Most of these potential guest gases can be successfully modeled as single Lennard–Jones spheres. Then, to obtain a general view of diffusion probabilities for different potential guest molecules, a comparative study for different virtual guest molecules described by different Lennard–Jones parameters has been performed. A regular temperature trend has been obtained for the transition energies for the molecular model characteristic parameter range explored. Finally, to locate the transition energy values of real gases within the space of phases explored, calculations have been repeated for molecular models of different noble gases and H2. The correlation results presented allow a wide interpolation ability for determining the transition energies of potential guest molecules stored or diffusing through the nanochannels of the studied clathrate structure.