If you have, for instance, 2 oxygen atoms and do E=mc2 to get their equivalent energy, you get about 2.38nJ. However, if you have diatomic oxygen, there's also the energy of the bond; about 0.8aJ. Nonetheless, if you measure the masses of oxygen and diatomic oxygen separately, they would weigh the same, but would have a different energy. How does this agree with Einstein's equation?
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