In this work the growth process of a self-assembled monolayer (SAM) was studied in detail by complementary microscopic and spectroscopic methods. Vapour deposited 4’-nitro-1,1’-biphenyl-4-thiol (NBPT) SAMs on Au(111) were investigated by scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) showing a complex polymorphic phase behaviour, which strongly correlates with the density of the NBPT molecules on the surface monitored by X-ray photoelectron spectroscopy (XPS) prior STM scanning in situ. In addition the molecular orientation was measured as a function of the NBPT surface coverage by near-edge X-ray absorption fine structure spectroscopy (NEXAFS) in situ as well. In combination the experimental results provide a good insight into the formation process of a SAM from the very beginning, where the NBPT molecules adsorb selectively outside the bridging regions of the herringbone reconstructed gold surface in a down tilted orientation, the formation of molecular patches and the lifting of the herringbone reconstruction, the genesis of a closed molecular layer in a upward orientation, till the very end, where the intermolecular interactions of the NBPT molecules lead to a reorganization of the Au(111) substrate visible as surface islands of gold step edge height.

The influence of two different SAM preparation methods, namely the immersion into a solvent in the chemistry laboratory and the chemical vapour deposition under ultra-high vacuum conditions, was investigated by STM for the high coverage regime of NBPT-SAMs, leading to the result that the observed surface morphologies are predominantly independent of the preparation process, except of the formation of high coverage striped phases, which was only observed for solvent immersed samples.

Altogether the results show that the conventional picture of the morphology of a SAM-surface-interface, which is laterally dominated by the surface geometry and its binding sites, must be reviewed for monolayers in the medium to high coverage regime. It also becomes clear that the observable surface height differences cannot be addressed completely to changes in the tilt angles of the molecular backbones. Instead of that it is rather likely that gold adatoms and reorganization processes in the substrate structure are dominantly responsible for the visible surface corrugations. This also reviews the perception of surface phenomena like gold islands on SAM surfaces as defect structures arisen during the SAM formation. This work points out that such effects are driven by the interplay of molecule-molecule and molecule-substrate interactions in the end of the assembly process minimizing the overall energy of the SAM-substrate complex.