1 Molecules are collections of atoms stuck to each other; an example is O2 = oxygen gas, with two oxygen atoms making one oxygen molecule. than they were prior to your rubbing. That's what heat really is: the shaking of atoms and molecules, rapid in speed, but microscopic. Heat is more than just a sensation we experience; it is a direct reflection of the unseen world of molecules in constant motion. It accounts for translational, vibrational, and rotational motion. Since it involves the random movement of molecules, thermal. Heat is another name for thermal energy, the energy contained in the vibrations of atoms and molecules. A thermodynamic system does not contain heat.