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The way I see it is that as noted in the textbook, matter has internal energy (U) which includes the energy of an atom, its electrons, protons, neutrons, and the bonds it forms with other atoms. All of this is energy within the matter, so when it is removed, energy is subtracted
In all systems, the matter/substance involved in the system contributes to its energy. Because matter can be exchanged with the surroundings of an open system, the addition or removal of substance from the system can change its energy.
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