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In most cases, if you have to calculate change in entropy and change in enthalpy separately before using the Gibbs Free Equation, entropy tends to be in J/mol whereas enthalpy tends to be in kJ/mol. When calculating each of the constituent thermodynamic values, it doesn't really matter if it's in J/mol or kJ/mol as long as it's consistent. When using the actual delta G equation, it is important, however, to either convert both to kJ/mol or J/mol before getting the final answer.
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