E.V. thanks the Brazilian agencies CAPES for funding the grant through the Capes/PrInt project (Grant number 88887.467063/2019-00). E.V. and S. A. M. thank the Brazilian agency CNPq (Grant Numbers 303884/2018-5, 423112/2018-0, and 310123/2020-8) for support. M. T. do C., J. M. T. and M. B thank the support of the FetOpen grant BoostCrop (Grant agreement 828753). M. P. and M.B. thank the funding provided by European Research Council (ERC) Advanced grant SubNano (Grant agreement 832237). Centre de Calcul Intensif d'Aix-Marseille is acknowledged for granting access to its high-performance computing resources.

The dataset includes all trajectories for the nonadiabatic (QM/MM) molecular dynamics simulations of cytosine in argon, benzene and water. Each tar.gz directory contains two directories: INPUT and RESULTS. In this latter one has the 50 trajectories for cytosine in argon and benzene and the 75 trajectories for cytosine in water. In the files named dyn.out one has the atomic coordinates, velocities and energies for each time step.