Role of the van der Waals interactions on the bonding mechanism of pyridine on Cu(110) and Ag(110) surface: First-principles study

We performed density-functional calculations aimed to investigate the adsorption mechanism of a single pyridine $\left({\text{C}}_5{\text{H}}_5\text{N}\right)$ molecule on Cu(110) and Ag(110) surfaces. Our ab initio simulations show that, in the ground state, the pyridine molecule adsorbs with its molecular plane perpendicular to these substrates and is oriented along the [001] direction. In this case, the bonding mechanism involves a $\sigma$ bond through the lone-pair electrons of the nitrogen atom. When the heterocyclic ring is parallel to the surface, the bonding takes place via $\pi$-like molecular orbitals. However, depending on the position of the N atom on the surface, the planar adsorption configuration can relax to a perpendicular geometry. The role of the long-range van der Waals interactions on the adsorption geometries and energies was analyzed in the framework of the semiempirical method proposed by Grimme [J. Comput. Chem. 27, 1787 (2006)]. We demonstrate that these dispersion effects are very important for geometry and electronic structure of flat adsorption configurations.

Figure 1

(Color online) Contour plots of several molecular orbitals of the pyridine molecule in the gas phase. The HOMO and $\text{HOMO}-3$ are $\sigma$-type molecular orbitals being combinations of $s$, $p_x$, and $p_y$ atomic type orbitals. The $\text{HOMO}-2\left({\pi }_2\right)$, $\text{HOMO}-1\left({\pi }_1\right)$, LUMO $\left({\pi }_1\ast \right)$, and $\text{LUMO}+1\left({\pi }_2\ast \right)$ are $\pi$-type molecular orbitals having a node in the plane of the molecule, because they originate from a $p_z$ atomic type orbital. Note that $p_x$ and $p_y$ atomic orbitals are in the molecular plane while the $p_z$ is oriented perpendicular to it [see also text and Fig. 5a].

Figure 2

(Color online) Upper panel: The ground-state adsorption geometry ([001] adsorption configuration) of the pyridine molecule on the Cu(Ag)(110) surface. Lower panel: In the case of copper surface the most stable local minimum for the perpendicular adsorption geometry ($\left[1\overline{1}0\right]$ adsorption configuration) is separated by an energy barrier of $\approx 0.55\text{eV}$ from the ground-state [001] geometry (see also Fig. 3).

Figure 3

(Color online) Potential energy barriers obtained by rotating the pyridine on Cu(Ag)(110) surface from [001] to $\left[1\overline{1}0\right]$ adsorption configuration. At each rotation step the pyridine-substrate geometries were relaxed in a direction perpendicular to the surface. Characteristic of the Ag(110) surface is a smooth energetic transition when rotating the molecular ring from the [001] to $\left[1\overline{1}0\right]$ direction (continuous line and open circles). On the contrary, for the Cu(110) surface the $\left[1\overline{1}0\right]$ adsorption configuration is a local minimum separated by an energy barrier of $\approx 0.55\text{eV}$ from the ground-state [001] geometry (dotted line and open squares).

Figure 4

(Color online) Several flat adsorption configurations of the pyridine molecule on Cu(110) and Ag(110) surfaces. The (a), (b), and (c) starting configurations with the N atom of the molecule close to a copper atom of a $\left[1\overline{1}0\right]$ row relax to a local minimum geometry such that the pyridine is perpendicular to the metal surface as shown in (d). In the (e), (f), and (g) starting geometries the relaxed pyridine molecule remains flat on the surface. In this case the most stable local minimum corresponds to configuration (g) where the N atom is above two adjacent [001] rows.

Figure 5

(Color online) Local density of states (LDOS) calculated for the (a) gas phase, (b) perpendicular ([001] adsorption configuration; see Fig. 2), and (c) flat [see Fig. 4g] geometries of the pyridine molecule absorbed on Cu(110) and Ag(110) surfaces. The thick red (thick black) line corresponds to the $\pi$-type electrons and the thick orange (thick gray) one corresponds to the $\sigma$-type electrons. For the flat adsorption geometry, the $d$ bands of Cu underneath the C2 atom (C2 atom is equivalent to C4 atom) [see also Table and Fig. 4g] are drawn with thin black lines while the $d$ bands of the surface metal atom underneath the N atom are plotted with thin green (thin gray) lines. For (b) and (c) graphs, the upper and lower panels correspond to the Cu(110) and Ag(110) surfaces, respectively.

Figure 6

(Color online) In a very simplified chemical model, the N-metal interaction for the perpendicular adsorption takes place via two types of bonds: $\sigma$ and $\pi$. (a) Top view of the $d_{y^2}$, $d_{yz}$, and $d_{yx}$ orbitals located at the metal atom, binding the N atom of the ${\text{C}}_5{\text{H}}_5\text{N}$ molecule. (b) The $\sigma$-type bond is formed along the $y$ direction by a bonding overlap between $d_{y^2}$ orbital of the metal and ${\sigma }_1$ orbital of the pyridine. (c) The $\pi$-type bond is formed along the [001] $\left(\left[1\overline{1}0\right]\right)$ direction between $d_{yz}$ $\left(d_{yx}\right)$ orbital of the metal with the ${\pi }_2$ orbital of the pyridine molecule.

Figure 7

(Color online) Schematic view of the hybridization of pyridine molecular orbitals with Cu(110) and Ag(110) $d$ bands. (a) In the case of the perpendicular adsorption geometry, the pyridine molecule binds to surface mainly via the ${\sigma }_1$ molecular orbital. For the Cu(110) surface this orbital is drastically shifted to lower energies, well below the ${\pi }_1$ and ${\pi }_2$ orbitals, while for the Ag(110) surface the ${\sigma }_1$ orbital gives rise to a peak with small weight above the ${\pi }_1$ and ${\pi }_2$ orbitals and a broad $\sigma$-type bond having also a small intensity [see also Fig. 5b]. (b) In the flat adsorption geometry the strong hybridization of the ${\pi }_1$ and ${\pi }_2$ molecular orbitals with the metal $d$ bands leads to the formation of broad bonding ${\pi }_{2,1}$ and antibonding ${\pi }_{1,2}^{\ast }$ bands with mixed $\pi$ and metallic character. However, the shift toward lower energies of the occupied ${\pi }_{2,1}$ band is larger for the copper than for the silver surface. This effect is due to a much stronger hybridization of the $\pi$ molecular orbitals with the $d$ bands of the metal surface in the former case [see also Fig. 5c].