  Organic adlayers on inorganic substrates often contain adatoms, which can be
incorporated within the adsorbed molecular species, forming two-dimensional
metal-organic frameworks at the substrate surface. The interplay between native
adatoms and adsorbed molecules significantly changes various adlayer properties
such as the adsorption geometry, the bond strength between the substrate and
the adsorbed species, or the work function at the interface. Here we use
dispersion-corrected density functional theory to gain insight into the
energetics that drive the incorporation of native adatoms within molecular
adlayers based on the prototypical, experimentally well-characterized system of
F4TCNQ on Au(111). We explain the adatom-induced modifications in the
adsorption geometry and the adsorption energy based on the electronic structure
and charge transfer at the interface. With this, we provide deeper insight into
the general mechanisms causing the incorporation of adatoms within an adlayer
made of a strong acceptor molecular species.
