A comprehensive evaluation of the kinetic method applied in the determination of the proton affinity of the nucleic acid molecules.

The determination of proton affinity (PA) of 2'-deoxyadenosine (dA) is used as a case study for the evaluation of possible drawbacks in the determination of the PA of the nucleic acid molecules by the kinetic method. The observed Delta PA among the different values obtain for dA by applying this procedure in its different extensions was 0.64 Kcal/mol, which is within the uncertainties of any theoretical or experimental approach. It was demonstrated that nucleosides can be generally used as reference compounds to measure the PA of an unknown nucleoside. The evaluation of Delta Delta S value for two competing reaction channels taken by proton-bound heterodimers formed by two nucleosides provides clear information on the reference base which has to be discarded from the set of reference compounds used for the estimation of an unknown PA. The PA of dA obtained with the most elaborated kinetic method (237.00 +/- 0.07 kcal/mol) is consistent with the value of 237.0 kcal/mol obtained by a simple treatment of the relative intensities of the product ions generated by two couples of the proton bound dimers formed by the nucleoside and two reference amines. The kinetic method can be, therefore, confidently used to assess the proton affinity of the multifunctional molecules such as nucleosides and nucleobases.