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I believe empirical formula does not directly refer to the mass percent composition of a molecule because mass percent composition is based on the mass of each type of atom over the total mass(and different atoms have different masses) while the empirical formula is more about the relative ratio of each atom presented.
the empirical formula simplifies the ratio of the atoms in a formula, the molecular formula shows the actual number. as a result, the empirical formula of multiple molecules could be the same while the molecular formulas cannot
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