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 $[1bar{1}0]$ 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.

Chemical versus van der Waals Interaction: The Role of the Heteroatom

We performed first-principles calculations aimed to investigate the role of an heteroatom like N in the chemical and the long-range van der Waals (vdW) interactions for a flat adsorption of several pi-conjugated molecules on the Cu(110) surface. Our study reveals that the alignment of the molecular orbitals at adsorbate-substrate interface depends on the number of heteroatoms. As a direct consequence, the molecule-surface vdW interactions involve not only pi-like orbitals which are perpendicular to the molecular plane but also sigma-like orbitals delocalized in the molecular plane.

Role of tip size, orientation, and structural relaxations in first-principles studies of magnetic exchange force microscopy and spin-polarized scanning tunneling microscopy

Using first-principles calculations based on density functional theory (DFT), we investigate the exchange interaction between a magnetic tip and a magnetic sample which is detected in magnetic exchange force microscopy (MExFM) and also occurs in spin-polarized scanning tunneling microscopy (SP-STM) experiments. As a model tip-sample system, we choose Fe tips and one monolayer Fe on W(001) which exhibits a checkerboard antiferromagnetic structure and has been previously studied with both SP-STM and MExFM. We calculate the exchange forces and energies as a function of tip-sample distance using different tip models ranging from single Fe atoms to Fe pyramids consisting of up to 14 atoms. We find that modelling the tip by a single Fe atom leads to qualitatively different tip-sample interactions than using clusters consisting of several atoms. Increasing the cluster size changes the calculated forces quantitatively enhancing the detectable exchange forces. Rotating the tip with respect to the surface unit cell has only a small influence on the tip-sample forces. Interestingly, the exchange forces on the tip atoms in the nearest and next-nearest layers from the apex atom are non-negligible and can be opposite to that on the apex atom for a small tip. In addition, the apex atom interacts not only with the surface atoms underneath but also with nearest-neighbors in the surface. We find that structural relaxations of tip and sample due to their interaction depend sensitively on the magnetic alignment of the two systems. As a result the onset of significant exchange forces is shifted towards larger tip-sample separations which facilitates their measurement in MExFM. At small tip-sample separations, structural relaxations of tip apex and surface atoms can either enhance or reduce the magnetic contrast measured in SP-STM