In this work we present an experimental and theoretical study of the proton transfer from the pyridinium-d(5) cation to pyridine. FT-ICR measurements yield, at 331 K, an equilibrium constant K = 0.809 (Delta(r)G(m)degrees = 0.58 kJ mol(-1)) for the process, favoring the pyridine form. The structural and bonding changes on protonation of pyridine are analyzed by applying the atoms in molecules theory. As a consequence of electronic density redistribution, we found that on protonation the CN and the CC bonds placed farther from the nitrogen weaken. In addition, the CH and the CC bonds closer to the nitrogen increase their strength. Thermostatistical computation of the equilibrium constant from data obtained at the B3LYP/cc-pVTZ level, within the harmonic approximation, predicts a value of 0.827 (Delta(r)G(m)degrees value of 0.52 kJ mol(-1)), in good agreement with the 0.809 +/- 0.027 experimental result for a 99.9% confidence level. A simple statistical mechanical model intended to apply under conditions close to the present ones is developed. The model allows for a fine-tuning of the thermodynamic state functions for the equilibrium. This model shows that rather than by translational and rotational variations, the reaction is driven by the changes in zero point energies and in the density of vibrational states. In addition, theoretical analysis of the enthalpic and entropic contributions shows that the Delta(r)G(m)degrees value is determined by the enthalpic part. It is also predicted that the A(r)G(m)degrees value decreases with temperature. We found that this effect is due to a higher density of vibrational states in the pyridine-d(5) form. A new model is developed to correct the vibrational partition function for anharmonicity. This model shows that correction for anharmonicity in the low-frequency modes reduces significantly the difference between calculated and experimental K values.