The effectiveness of the kinetic method for estimating the proton affinities of bases that di-coordinate the proton is evaluated using alpha,omega-diaminoalkanes as model bases. The proton affinities of these diamines have previously been examined using the equilibrium method and critically evaluated. Calculations using density functional theory at the B3LYP/6-31++G(d,p) level confirm that protonated alpha,omega-diaminoalkanes have cyclic structures with the proton covalently bound to one of the amino nitrogen atoms and hydrogen-bended to the other. Furthermore, this cyclic structure persists in the protonated heterodimer ion between an alpha,omega-diaminoalkane and ammonia (the model reference base); binding of the two bases takes place via a second hydrogen bond between the RNH3+ and ammonia. Measuring the proton affinities under several collision energies and extrapolating to zero collision energy yields proton affinities that are smaller than the reference values by -2.8 kcal/mol, on average. Application of the Fenselau correction gives proton affinities that differ from the reference values by +/-1.0 kcal/mol. These results indicate that the kinetic method is effective for estimating the proton affinities of molecules that tend to have more than one potential protonation site. Application of this method is particularly suited to biological molecules, such as peptides, where application of the equilibrium method is impossible due to low sample volatility.