Where will the heat come from in an entirely empty space? Radiation?
When energy is added to an atom. electrons may be excited to higher energy levels, or lead to ionization of the atom. Then, when the energy is removed, electrons drop again to lower energy levels, and emit radiation (photons), with a frequence corresponding to the difference of energy levels, and according to allowed transitions. This leads to a discrete spectrum for emitted radiation.
Vibrate is a classical expression I would not use in this case.
Anyway, you can get the idea from elementary quantum ideas, there are many books about this. The key formula is E=h nu (interprate well)
Heat usually means infrared radiation, which may not be enough to excite the atom. It generally would a molecule.