The origin of NTE in DUT-60, MOF-399 and NU-110 was investigated by calculation of phonon modes. We identified a number of low-energy phonon modes that contribute to the NTE observed in these systems. In DUT-60 these are observed to correspond to transverse "trampoline"-like vibrations of the ligands within the lattice. Subsequently, we considered temperature-induced structure changes intrinsic to the large molecular subunits, which construct the studied MOFs, and found that they alone produce considerable NTE.