Hot electron (HE) photocatalysis is one of the most intriguing fields of nanoscience, with a clear potential for technological impact. Despite much effort, the mechanisms of HE photocatalysis are not fully understood. Here we investigate a mechanism based on transient electron spillover on a molecule and subsequent energy release into vibrational modes. We use state-of-the-art real-time Time Dependent Density Functional Theory (rt-TDDFT), simulating the dynamics of a HE moving within linear chains of Ag or Au atoms, on which CO, N2, or H2O are adsorbed. We estimate the energy a HE can release into adsorbate vibrational modes and show that certain modes are selectively activated. The energy transfer strongly depends on the adsorbate, the metal, and the HE energy. Considering a cumulative effect from multiple HEs, we estimate this mechanism can transfer tenths of an eV to molecular vibrations and could play an important role in HE photocatalysis.