This work presents the determination of both reference chemical potential and temperature-dependent enthalpy changes of gas hydrates using molecular dynamics simulations. We introduced a method incorporating molecular dynamic (MD) simulations to the Lee-Holder distortion model for calculating the reference properties of single component structure II gas hydrates. The guest molecules affect the interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed the simulation to validate the experimental data determining the reference chemical potential as well as the thermal expansivity of unit cell structure for structure II type gas hydrates. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. As an attempt to apply MD simulation to calculate the reference state of gas hydrate, we demonstrate lattice distortion of structure I and II gas hydrates. The reference chemical potential was generally found to increase with the size of the guest molecule. The temperature effect on the unit cell size, which will be used to calculate the enthalpy change of gas hydrate due to temperature, has been observed.