© 2015 American Chemical Society. Quantum mechanics/molecular mechanics (QM/MM) models are applied to investigate the adsorption and cracking of n-hexane on ZSM-5 and Faujasite zeolite structures. These simulations account for the long-range electrostatic and midrange van-der-Waals interactions in the zeolite and provide energy barriers that are close to experimental data. The active acidic site was modeled by dispersion corrected density functional theory (DFT, ω B97X-D6-311/G∗). The long-range interactions were calculated by molecular mechanics (MM). The adsorbed molecules under investigation are characterized by their thermodynamic properties (adsorption energy and enthalpy). The influence of the zeolite type on the thermodynamic properties is also pointed out. The results reveal that the kinetics of cracking is insensitive to differences in acid strengths. The thermodynamic data obtained are mainly influenced by the adsorption energy of n-hexane on ZSM-5 and/or Faujasite (Y) structures. The pore sizes of the zeolite types can lead to a stronger or weaker adsorption energy. Except for the thermodynamic property investigations in this article, the quasi-classical trajectory method (QCT) is used for investigating the pathways along metastable intermediates toward various cracking products. Not only the reaction barriers but also the reaction dynamics determine the reaction selectivity.