The inelastic neutron scattering (INS), spectra of the isophthaloyl [2]catenane and the sebacoyl [2]catenane are measured and compared with simulated spectra obtained by molecular dynamics (MD), based on a molecular mechanics model (MM), that has been extensively used before to treat this class of molecules. Both the isolated molecule approximation (IMA), and the crystal approach, implemented through boundary conditions, are used. Good agreement with the experiments is met for the spectra of the two catenanes for the location of the most prominent bands. The crystal calculations give better intensity distributions than the IMA. Further analysis of the simulations shows that the combination of INS spectroscopy and MD is well suited to assess the strength of intramolecular and intermolecular hydrogen bonds that are the crucial interactions that govern the dynamics of these systems. (C) 2001 American Institute of Physics.