The Correlation between Location Confidence and Alkanethiol Chain Tilt Direction in Alkanethiol Self-Assembled Monolayers (SAMs)*

Accurate measurements of structures at the nanoscale are of fundamental importance for nanofabrication. Using alkanethiol self-assembled monolayers (SAMs) as a model system, we demonstrate a way to measure the alkanethiol chain tilt direction from constant-current scanning tunneling microscope (STM) images. These measurements are made with a real-space image post-processing technique that compensates for image distortion using a physical model. Using this measurement, we are also able to establish the chain tilt direction without guest molecules, by using the position uncertainty of molecules about their expected lattice site position. In particular, we will show the direction of maximum position uncertainty is anticorrelated with the alkanethiol chain tilt direction. This anticorrelation is consistent across different STM tips and alkanethiol chain lengths.