The detailed mechanism of thermal cis-trans inversion of protonated diazenes and azobenzenes has been investigated for the first time using ab initio Hartree-Fock (HF), density functional theory (DFT), second order Moller-Plesset (MP2), and complete active space self consistent field (CASSCF) approaches. Protonation of one of the nitrogens at the N=N bond leads to a considerable (5-20 kcal/mol) reduction of the activation barrier. The magnitude of this effect depends on the electron withdrawing nature of the substituents and the differential stabilization of the transition state by positively charged functional groups. In the case of 4-phenylazopirydine protonated at pyridine nitrogen, the barrier is dramatically reduced to just 7 kcal/mol. This result establishes the lowest (close to an experimental estimate) ab initio value for the cis-trans isomerization for a substituted azobenzene. The structures of neutral and protonated transition states are similar, and the correlation effects for molecular parameters as well as the energy are negligible for extended basis set calculations. (C) 2001 American Institute of Physics.