This work addresses the ultrafast cis-trans photoreactions in retinal binding proteins using ab initio molecular dynamics and small protonated Schiff bases as retinal chromophore models. A new methodology to study the photochemistry of polyenic model systems was developed and compared with currently used methods. Factors that influence the photoreaction were investigated. For each model system an ensemble of starting conditions was generated to calculate excited state trajectories. The decay point was estimated with timedependent and with classical methods, results were analyzed statistically. The vacuum photoreaction of the model systems was found to be extremely fast and effective, in particular when all decay events take place at the first close approach of the two involved potential energy surfaces. The reaction is further accelerated, when the isomerising double bond and an adjacent singe bond are initially twisted as found in the x-ray structure of rhodopsin. In these cases the product distribution is also affected.