Molecular dynamics simulations of a pentacene derivative on gold surfaces in the quantum mechanical and classical mechanics frameworks

With increasing potential to serve as a basis for constructing organic photovoltaic devices, the directed self-assembly of small organic molecules on metal substrates provides an interesting new method of bottom-up device building. By utilizing the qualities inherent in the substrate and molecules, one can manipulate surface topology to create functional layers of molecules in a desired configuration. However, tailoring these organic layers in a useful way requires detailed analysis of the substructure characteristics.;With top-down visualization approaches like Scanning Tunneling Microscopy (STM) providing a limited view of assembled layer structural characteristics, molecular dynamics simulations must be employed to obtain a more detailed depiction of how the structures form. With atom-scale spatial resolution and femtosecond timescale resolution, molecular simulation provides a means to study surface diffusion and self-assembly with a clear view of the molecular trajectories and atomic movements, and several virtual experiments can be conducted with easy manipulation of initial conditions. In this study, several arrangements of the pentacene derivative 5 6,7-trithiapentacene-13-one (TTPO) were studied on flat Au(111) surfaces and Au(788) steps. The results obtained agree with those previously obtained in STM experiments for TTPO on these surfaces. Also, details of the the diffusive properties of TTPO on gold were were obtained from analysing the trajectories at varied temperatures. Finally, different arrangements of surface defects gave insight into TTPO's interaction with substrate vacancies. The study bridges theoretical simulation with past experiment and provides insights into phenomena previously unstudied for this molecule-substrate complex.