Microscopic dynamics of a base protonation

The protonation of the base peroxynitrite in aqueous solution is investigated by way of the Car-Parrinello molecular dynamics technique. It is found that the protonation proceeds through an increase in the vibration amplitude of the hydrogen bond between the base and the hydronium ion. When the amplitude gets sufficiently large a proton may oscillate a few times between the base and the hydronium ion before it remains as part of peroxynitrous acid. The start of the protonation requires a certain orientation of the hydrogen bond. The estimated protonation time agrees well with the one obtained from femtosecond UV experiments.