  In this study we investigated by means of density functional theory
calculations the adsorption geometry and bonding mechanism of a single thymine
(C$_5$H$_6$N$_2$O$_2$) molecule on Cu(110) surface. In the most stable
energetic configuration, the molecular plane is oriented perpendicular to
substrate along the $[1\bar{1}0]$ direction. For this adsorption geometry, the
thymine molecule interacts with the surface via a deprotonated nitrogen atom
and two oxygen ones such that the bonding mechanism involves a strong
hybridization between the highest occupied molecular orbitals (HOMOs) and the
d-states of the substrate. In the case of a parallel adsorption geometry, the
long-range van der Waals interactions play an important role on both the
molecule-surface geometry and adsorption energy. Their specific role was
analyzed by means of a semi-empirical and the seamless methods. In particular,
for a planar configuration, the inclusion of the dispersion effects
dramatically changes the character of the adsorption process from physisorption
to chemisorption. Finally, we predict the real-space topography of the
molecule-surface interface by simulating scanning tunneling microscopy (STM)
images. From these simulations we anticipate that only certain adsorption
geometries can be imaged in STM experiments.
