Free-energy differences govern the equilibrium between bound and unbound states of a host and its guest molecules. The understanding of the underlying entropic and enthalpic contributions, and their complex interplay are crucial for the design of new drugs and inhibitors. In this study, molecular dynamics (MD) simulations were performed with inclusion complexes of a-cyclodextrin (aCD) and three monosubstituted benzene derivatives to investigate host -guest binding. aCD Complexes are an ideal model system, which is experimentally and computationally well-known. Thermodynamic integration (TI) simulations were carried out under various conditions for the free ligands in solution and bound to aCD. The two possible orientations of the ligand inside the cavity were investigated. Agreement with experimental data was only found for the more stable orientation, where the substituent resides inside the cavity. The better stability of this conformation results from stronger Van der Waals interactions and a favorable antiparallel host -guest dipole -dipole alignment. To estimate the entropic contributions, simulations were performed at three different temperatures (250, 300, and 350 K) and using positional restraints for the host. The system was found to be insensitive to both factors, due to the large and symmetric cavity of aCD, and the nondirectional nature of the host -guest interactions.Introduction. -a-Cyclodextrin (aCD) belongs to a family of cyclically closed oligosaccharides linked by a-bonds, where the number of glucose units ranges from six (aCD) to eight (gCD). The central cone-shaped cavity of cyclodextrins has hydrophobic character relative to bulk water, although actually semipolar [1] [2], while the rims of the cavity are hydrophilic due to the OH groups of glucose. The ability of aCD to bind small organic compounds in this cavity together with its small size renders it an ideal model for computational studies of host -guest binding [3 -5]. In addition, the system is well-studied experimentally [2] [6 -12]. Molecular dynamics (MD) simulations have reproduced the experimental relative free energies of binding [3]. These free-energy differences are a complex interplay of enthalpic and entropic contributions; however, the main driving force of complexation has not been identified yet. [16] found the electronic effects to be more important in aCD inclusion complexes, whereas Cai et al. [13] concluded that Van der Waals interactions are the most decisive ones. In addition, guest orientation in the cavity, steric effects, and the flexibility of the host may affect the equilibrium of the system. As the relative contributions of the