Date of Award

Spring 2016

Project Type


Program or Major


Degree Name

Master of Science

First Advisor

Karsten Pohl

Second Advisor

Glen P. Miller

Third Advisor

David Mattingly


With increasing potential to serve as a basis for constructing organic photovoltaic de- vices, 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) pro- viding a limited view of assembled layer structural characteristics, molecular dynamics sim- ulations must be employed to obtain a more detailed depiction of how the structures form. With atom-scale spatial resolution and femtosecond timescale resolution, molecular simula- tion 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 con- ducted with easy manipulation of initial conditions. In this study, several arrangements of xvthe 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.