Abstract: The dimer and trimer of N-(1-naphthyl)-succinimide, NaS, molecules were constructed using a combination method of solvate building and conformational random searching performed in the Sybyl software, and the dimer thus obtained agreed well with the structure of the lowest energy provided by the docking method. Density function theory (DFT) simulation of the dimer of NaS could gain the minimum energy conformation, and the study of the molecular mechanics in high level on the trimer was carried out to obtain the stable conformation of lower energy. The difference between the dominant conformation in solution and the dimer calculated in this study, showed that the intermolecular interaction played an important role in the crystallization process in solution. The result might shed light on the intermolecular interaction of N-(1-naphthyl)-succinimide supermolecules and the mechanism research of crystallization in solution.

Key words: Intermolecular interaction, N-(1-naphthyl)-succinimide, Supermolecules system, Molecular docking