Theoretical Study of Substrate and Molecular Density Effects on Molecular Self-assembly
This work is aiming at theoretically exploring the substrate and molecular density effects on molecular self-assembly. The density functional theory (DFT) and molecular dynamics (MD) simulation were used to investigate the atomic arrangement of a sulfur-bridged annulene (ie, DPTTA) on both Au and highly oriented pyrolytic graphite (HOPG) substrates. Critical molecular density of DPTTA/Au self-assembled structure was determined to be 0.52/nm2 by the construction and simulation of different DPTTA molecular density models. By extracting and optimizing the self-assembled unit, clearly identification of self-assembled atomic structure and STM image was realized. It was found that DPTTA molecules can not form 2D self-assembled structure on HOPG substrate. The reason for different configurations of DPTTA/Au and DPTTA/HOPG systems was successfully revealed by the calculations of adsorption energy, weak interaction energy and electron density difference. This study provides a reference for the quantitative prediction of self-assembled critical molecular density and the accurate determination of self-assembled atomic structures by theoretical simulation.