We report on the interaction between ZnS quantum dots and several surface ligands by means of pure Quantum Mechanical (QM) and hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) methods. To shed light on the nature of the interaction, we focus our discussion on the structural and energetic aspects. The Zn6S6 cluster has been chosen to model the quantum dot core, while trimethylamine (NMe3), trimethylphosphine (PMe3), trymethylphosphine oxide (OPMe3), methanol (MeOH), methanethiol (MeSH), and methaneselenol (MeSeH) have been employed to model the passivating ligands. Our results concerning the interaction between the cluster and one ligand of each type reveal that NMe3, PMe3, and OPMe3 show a significantly greater affinity to Zn6S6 than MeOH, MeSH, and MeSeH. We noticed that the softer the heteroatom of the ligand bonded to the cluster, the greater the interaction energy. A comparative study of different amines shows that the interaction is strengthened with the number and the length of the alkyl substituents in the ligand. We demonstrated that the interaction is mainly electrostatic, even if an important polarization of the charge density is observed. Fully passivated complexes have also been investigated, and our calculations point out that the bond is weaker than in the complexes with a single bonded ligand, suggesting that the repulsive interactions between the ligands and the diminished charge acceptor capacity of the cluster come into play.