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Investigations of nanodimers with different ring faces in contact by molecular dynamics

Jie Cheng, Jingchuan Zhu

Four nanodimers of cyclo-[(1R, 3S)-ã-Acc-D-Phe]3 in contactwith different ring faces as their termini in solvent CHCl3 with 300, 150 and 49 molecules are modeled to investigate the two faces of cyclic peptide ring through 8 ns molecular dynamics (MD) based on Dreiding force field. The radius of monomer rings, terminal and internal sizes of dimer tubes and distances between two neighboring ring faces are analyzed. Simulation results show that the spacing in á-á dimers (dimer-II and -IV) is larger than that in ã-ã dimers (dimer-I and -III), and for dimer-IV, the timeCHCl3 needs to enter into its cavity is the shortest, which indicates that the channel with ã-NCH3 termini (dimer-IV) is a good candidate carrier to absorpt CHCl3.