LAUSR

Abstract Self-assembly is a bottom-up approach to prepare nanostructures with tailored properties. However, to utilize them as functional 2D layers, it is mandatory to understand their formation and its kinetics. Here, we describe the phase transformations in the full monolayer coverage of 4,4′-biphenyl-dicarboxylic acid (BDA) on the Ag(0 0 1) substrate. The phase transformations occur as a response to a thermally induced deprotonation of carboxyl groups. Contrary to the sub-monolayer coverage, the mass transport via on-surface diffusion in the full monolayer is hindered. We highlight two possible scenarios for the deprotonation of BDA in the full layer. For deprotonation of up to half of the carboxyl groups, the altered molecules can be incorporated within the existing α phase structure, forming a new binding motif. For structural changes that are required to respond to the further deprotonation, free substrate areas are necessary. The free surface is provided either by voids in the original layer or by removing excessive molecules, resulting in incomplete layers. This knowledge is essential in the fabrication of molecular layers that are part of hybrid organic–inorganic devices based on layered materials.