Assignment of NEXAFS Resonances in Alkanethiols and Their Implication on the Determination of Molecular Orientation of Aliphatic SAMs

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has become a widely used technique to analyze the molecular orientation of functional adlayers by analyzing the dichroism of NEXAFS resonances. In contrast to π-conjugated systems, which exhibit distinct π* resonances whose transition dipole moments are oriented perpendicular to the aromatic planes, the analysis of purely aliphatic systems is not as straightforward and requires a precise identification of the underlying resonances and their polarization. Here, we analyze the carbon K-edge NEXAFS signature and its dichroism of a self-assembling monolayer (SAM) formed by octadecanethiol (ODT) on gold, representing the widely studied class of alkanethiol SAMs. Employing density functional theory calculations and using the transition potential method, the polarizations of all NEXAFS resonances at excitation energies around and below the ionization threshold are precisely determined. This information is then used to simulate expected dichroism curves for various adlayer arrangements that are compared with our experimental findings for ODT SAMs on single-crystalline Au(111) and polycrystalline gold surfaces. This analysis demonstrates a novel strategy to precisely deduce the molecular orientation from the experimental NEXAFS data of aliphatic SAMs