The dynamical behavior of the [Mo12O12S12(OH)(12){O2C-(CH2)(N)-CO2}](2-) complexes is analyzed via first-principles molecular dynamics simulations. Experimental X-ray data play the role of initial configurations for our search in the configuration space. We show that different stable and metastable conformers are possible, and these are thermally accessible at relatively low temperatures. This is the main outcome of our first-principles molecular dynamics approach in which the temperature allowing for thermal activation has been set to T = 500 K, which is consistent with the variable temperature H-1 NMR spectra of these complexes in solution taken at comparable, although moderately lower, temperature. This implies that a relatively large manifold of folding configurations is available to the encapsulated guest species. Moreover, the high flexibility of both the host cage and the inserted guests allows for the accommodation of a rather wide variety of functional groups with potential applications in several fields.