First-principles and semi-empirical van der Waals study of thymine on   Cu(110) surface
  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. 
V. Caciuc, N. Atodiresei, P. Lazic, Y. Morikawa, S. Blugel