For the simulation of proton transfer, usually it needs to be done by means of the techniques such as molecular dynamics. For the compound mentioned by you, I think that it just contains ionized H (its electron transfers to the other part of the compound) rather than proton transfer. In vacuum, the mobility of this H ion in your mentioned compound may be very lower, while in the water it may be very high. So in the former case, the effect of movement of H ion on the electronic transport properties of a system consisting of your mentioned compound may be negligible. From this sense, the usual way of calculating the electron transport properties of your mentioned compound may be feasible, and you can neglect the proton transfer.
