Molecular dynamics (MD) simulations of methylene chloride (CH2Cl2) with two different potentials are used to calculate the intermolecular static structure factor inter(q) for a series of isotopic substituted mixtures CX 2Cl2. The intermolecular structure factors are compared with corresponding experimental data obtained from neutron diffraction. We discuss the validity of the rigid molecule approximation in the MD simulation and show that the quantitative comparison of the static structure factors of molecular liquids obtained from neutron diffraction experiments and MD simulation must be considered with some care for molecules containing hydrogen atoms with low effective masses.