The emergence of carrier-free nanodrugs as a promising drug delivery system is a significant development in the field of pharmaceutical research. The research on molecules that can form carrier-free nanodrugs can facilitate the expansion of their applications. The capacity of molecules to self-assemble with other molecules is the foundation upon which their formation of carrier-free nanodrugs is based. In this paper, we present a computational method for evaluating the assembly ability of molecules in aqueous environments. The method begins with screening the optimal conformation of a single molecule in water, then simulates the assembly behavior of two molecules in water, and finally calculates the optimal conformation of dimer in water. In comparison to the original computational method, this method describes the effect of water on molecular assembly behavior with the greatest possible realism by utilizing high-precision water environments in each step. The accuracy of the method has been validated by classical experiments, while its rationality has been demonstrated by electronic structure calculations of single molecules and assemblies. Furthermore, we employ the method to investigate the assembly capabilities of 54 molecules in the presence of berberine. The results demonstrate that anthraquinone and flavonoid molecules readily form robustly bound assemblies with berberine. This method offers a relatively efficient approach to compositional screening of carrier-free nanodrugs, thereby contributing to the advancement of the field.
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