The question of molecular motion in response to "heat" is answered by statistical mechanics. If you have a single molecule at a temperature T, all that means is that the probability of any state of the molecule with energy E is as likely as $e^{-E\over T}$.
For the nucleus to move, it must change it's energy state by a discrete amount, and the gap between the lowest energy state and any of the excited states is thousands of eV's. In temperature units, this is millions of degrees. So the nucleus will have negligible probability to get excited at normal temperatures.
The electrons are excited in the energy range of .1-1eV, which is about 300-30000 degrees. So again, you won't get significant electronic excitations.
The rotational or bending energies of the molecule can start to get excited at relatively small temperatures, if the molecule is large, so easy to bend and rotate slowly. But the significant thing is center of mass motion. The energy levels of moving around depend on the size of the box, and if the box is arbitrarily big, these levels have energies that are arbitrarily small. So the molecule will, at low temperatures, start to move around first, before it rotates or deforms, or does anything electronic or nuclear.
The notion of a thermal ensemble for a single molecule is well defined statistically, so long as you ask about average properties over many trials, rather than single trials.