Molecular structure is often considered as emerging from the decoherence effect of the environment. Electrons are part of the environment of the nuclei in a molecule. Here, we investigate their contribution to the classical-like geometrical relationships often observed between nuclei in molecular systems. Our numerical computations of reduced density matrix (RDM) elements are made from accurate all-particle wave functions. However, we found that, as in the Born-Oppenheimer picture, the electrons play an essential rôle in localizing nuclei in specific "equilibrium" geometries. Although the electronic environment alone cannot explain molecular symmetry-broken isomers, it can contribute to their dynamical stability by significantly reducing off-diagonal RDM elements.