The bonding of atoms to form molecules or solids changes the orbitals that electrons can occupy, and therefore also changes the energies of the electrons. Bonded atoms also can vibrate and the vibrations will have quantized energy states. Molecules in the gas phase or in solution can rotate, which just like vibrations will have definite rotational energy states.
Examples: Ground state of a diatomic moleculeFluorescence from a molecular excited stateJablonski diagram showing molecular relaxation pathways
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