Formation of highly ordered self assembled monolayers of alkanethiol molecules on thermally annealed gold films.

We controlled the ordering between alkanethiol molecules in self-assembled monolayers (SAMs) formed on a Au surface by modifying surface topography of Au films. The ordering between molecules was evaluated using Fourier Transform infrared (FTIR) spectroscopy. A thermal annealing in hydrogen environment removed the nm-scale protrusions from the surface of as deposited Au film resulting in an increase in grain size and a decrease in roughness. This process allowed the alignment of Au atoms in the (111) direction. Together with the aligned Au surface, Au nanoparticles were also prepared as a rough surface with tiny grain size of $\sim $ 10 nm. The symmetric and asymmetric CH$_{2}$ vibrations in the FTIR spectra showed a larger blueshift from the SAMs on an flatter Au surface. Binding specificity of molecules was examined by Secondary Ion Mass Spectroscopy (SIMS) using a Au pattern formed on a SiO$_{2}$/Si wafer. The molecular signal matched with the Au pattern and the ratio of the signals on Au to SiO$_{2}$ was larger than 1000, indicating that the level of non-specific binding was negligible. This method of improving and controlling the ordering between molecules in the SAMs can be applied to sub $\mu $m patterns on a SiO$_{2}$/Si wafer.