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An empirical formula is a chemical formula that shows the simplest ratio of elements in a compound, without indicating the actual number of atoms. On the other hand, a molecular formula is a chemical formula that displays the actual number of atoms of each element in a compound.

Two compounds can have the same empirical formula if they have the same ratio of elements but different molecular formulas if they contain different numbers of atoms of each element. For example, hydrogen peroxide (H2O2) and water (H2O) have different molecular formulas but share the same empirical formula (HO).

The molecular structure of a compound plays a significant role in determining its properties such as boiling point, melting point, viscosity, and volatility. Factors that influence these properties include strength of intermolecular forces (e.g. hydrogen bonding, dipole-dipole, and London dispersion forces), molecular size, and shape. As a result, two compounds with the same empirical formula but different molecular structures can have distinct properties.

One example of two substances with the same empirical formula but different properties is ethene (C2H4) and benzene (C6H6). Both compounds have the empirical formula CH2, but ethene is a gas at room temperature, while benzene is a liquid. The different properties are due to the varying molecular structures and intermolecular forces – ethene has a simple linear structure with weak London dispersion forces, whereas benzene has a cyclic structure and exhibits stronger pi-pi stacking interactions resulting in its liquid state. In conclusion, two substances with the same empirical formula can have markedly different properties due to differences in their molecular formulas and structures, which influence the strength of intermolecular forces and other factors that dictate their properties.