Effects of the atom model and the atomic charge parameters on the calculated free energy of hydration (FEH) have been studied for CH3OH, CH3NH2, CH3CN, and N(CH3)3 with the all-atom vs the united-atom model for the CH3 group. Monte Carlo simulations using the free energy perturbation method have been performed in a TIP4P water box at T = 298 and p = 1 atm. Different sets of charge parameters obtained by fits to the gas-phase and in-solution B3LYP/6-31G* molecular electrostatic potentials (ELPO) and to the in-solution B3LYP/6-311++G** ELPO have been applied. Calculations with OPLS and RESP charges have been also completed. FEH values were calculated by charge and volume annihilations and developments. Volume development has also been studied for aniline, using the all-atom approach with explicit C−H atoms. For considering the concentration effect on the calculated standard free energy in solution, the (CH3OH)2, (CH3NH2)2, and (CH3CN)2 dimers, and the (CH3NH2)9 ninemer have been studied in aqueous solution ...