Because an empirical formula only shows the most simple ratio between elements in a compound while the molecular formula gives the actual number of each element in a certain molecule. Take the example of glucose. It has a molecular formula of [tex]C_6H_{12}O_6[/tex]. However, the smallest ratio between the atoms are 1:2:1 respectively. So the empirical formula would be [tex]CH_2O[/tex]. Clearly not representing the molecular formula.
