Acidity constants of lumiflavin from first principles molecular dynamics simulations.

We have computed the free energy profiles of the deprotonation reactions of lumiflavin in the semiquinone and fully reduced oxidation states using constrained DFT-based molecular dynamics simulations. In the semiquinone state, the N5 nitrogen atom and the N1 nitrogen atom can become protonated. We find, in agreement with experiment, that the N5 site is the predominant proton acceptor in the semiquinone state, although the computed pKa value is somewhat smaller than the experimental number. The computed pKa for the N1 protonation in the fully reduced state is in good agreement with the experimental number. We employ two different, commonly used, reaction coordinates based on the distances between the proton and the donor and acceptor atoms. Further improvement of the accuracy of this type of pKa calculations may require development of more advanced reaction coordinates that go beyond the description of only the first proton transfer step from a donor atom to a first solvation shell water molecule.