  We have performed a density functional theory study of the possible layered
geometries occurring after dehydrogenation of a self-assembled monolayer (SAM)
of biphenyl-thiol molecules (BPTs) adsorbed on a Au(111), as it has been
experimentally observed for low energy electron irradiated SAMs of
4'-nitro-1,1'-biphenyl-thiol adsorbed on a Au(111) surface. [Eck, W. et al.,
Advanced Materials 2000, 12, 805] Cross-link formation between the BPT
molecules has been analyzed using different models with different degrees of
complexity. We start by analyzing the bonding between biphenyl (BP) molecules
in a lineal dimer and their characteristic vibration frequencies. Next, we
consider the most stable cross-linked structures formed in an extended
free-standing monolayer of fully dehydrogenated BP molecules. Finally, we
analyze a more realistic model where the role of the Au(111) substrate and
sulphur head groups is explicitly taken into account. In this more complex
model, the dehydrogenated BPT molecules are found to interact covalently to
spontaneously form "graphene-like" nanoflakes. We propose that these
nanographenes provide plausible building-blocks for the structure of the carbon
layers formed by electron irradiation of BPT-SAMs. In particular, it is quite
tempting to visualize those structures as the result of the cross-link and
entanglement of such graphene nanoflakes.
