Adsorption of alanine on a Ni(111) surface: A multiscale modeling oriented density functional study

A first principle density functional study of the adsorption of neutral and zwitterionic alanine on the Ni(111) surface is presented. Adsorption energies and geometries are reported for a set of possible initial orientations of both alanine forms with respect to the surface. The most energetically favorable adsorption of neutral alanine occurs via the bonding of the nitrogen to the top site. Adsorption of zwitterionic alanine is possible only via the bonding of one oxygen to the bridge site. Application of the current results to a multiscale modeling of oligopetides interacting with metal surfaces is discussed.

Figure 1

(Color online) Two adsorption geometries for the neutral alanine, with electron density difference plots. In both cases the accumulation/depletion regions are displayed in mauve(dark)∕yellow(light), respectively; the isosurface level is $\pm 0.05e∕{\mathrm{\AA }}^3$ and only the upper of four Ni layers contained in the simulation supercell is shown. Top panel: the conformation with one oxygen bonded to the surface, with $E_{\mathrm{ad}}=-0.37$. Bottom panel: the conformation with the nitrogen bonded to the surface yielding $E_{\mathrm{ad}}=-0.57\mathrm{eV}$. Not clearly visible in these perspective views is that in both cases the bonded Ni moves $0.2\mathrm{\AA }$ upwards from the average vertical position of the upper layer of the surface.

Figure 2

(Color online) Three snapshots taken along one of the proton transfer trajectories for the isolated alanine. In the left-hand configuration the proton is bonded to the charged amino group $\left(\mathrm{N}\mathrm{H}_3{}^{+}\right)$. In the center configuration the proton is approximatively at the same distance from the nitrogen and the oxygen. In the right-hand configuration the proton is bonded to one oxygen of the carboxylic group. In the transfer the energy of the system decreases by $0.7\mathrm{eV}$.

Figure 3

(Color online) Perspective view of the final configuration of the adsorbed zwitterionic alanine, with the electron density difference map. The accumulation/depletion regions are displayed in mauve(dark)∕yellow(light), respectively; the isosurface level is $\pm 0.05e∕{\mathrm{\AA }}^3$. Only the upper of four Ni layers contained in the simulation supercell is shown.

Figure 4

(Color online) Top view of the $3\times 3$ sample with three periodic images. Only the upper of four Ni layers contained in the simulation supercell is shown. The distance between images of the same atom, equal to the supercell lattice parameter, is $7.5\mathrm{\AA }$. The distance between the nonbonded oxygen and the closest hydrogen of the charged amino group, which belongs to one of the periodic images, is $3.1\mathrm{\AA }$. Similar distance relationships we found for the isolated molecule: in fact, the supercell has the same size and only small internal rearrangements of the molecule take place during the adsorption. For a reference of the distances, note that the crystal (surface) lattice parameter is $2.5\mathrm{\AA }$.

Figure 5

(Color online) Top view of the $4\times 4$ sample with three periodic images. Only the upper of four Ni layers contained in the simulation supercell is shown. The distance between images of the same atom, equal to the supercell lattice parameter, is $10.0\mathrm{\AA }$. The distance between the nonbonded oxygen and the closest hydrogen of the charged amino group, which belongs to one of the periodic images, is $5.9\mathrm{\AA }$.

Figure 6

(Color online) Snapshot of the final configuration of the system representing the solvated alanine. Only the upper of four Ni layers contained in the simulation supercell is shown. The oxygen in the bottom right water molecule is hydrogen bonded to one of the hydrogen atoms of the charged amino group.