Single cysteine adsorption on Au(110): A first-principles study

The single-molecule adsorption of cysteine on the Au(110) surface is investigated by means of density-functional theory. The amino-gold and thiolate-gold bonds are studied separately to assess their relative contribution to the molecule-substrate bond. We analyze the bonding strength, electron redistribution, and changes in the density of states for the isolated bonds of these functional groups to the surface and for simultaneous bonding via both groups. Adsorbate-substrate geometries are obtained from total-energy minimizations. Flat adsorption configurations with S-Au at an off-bridge site and ${\text{NH}}_2\text{-Au}$ at an off-top site are found to be energetically favored.

Figure 1

(Color online) (a) Used notation for atoms of cysteine. The red enclosed area marks the side group that is replaced by $-\text{H}$ for the glycine calculations (see text). (b) Unreconstructed (110) surface unit cell. High symmetry positions are indicated as follows: top site (1), [001] bridge site (2), $\left[1\overline{1}0\right]$ bridge site (3), and $\left[1\overline{1}0\right]$ off-bridge site (4).

Figure 2

(Color online) (a) Illustration of the tilt angle $\alpha$ (in red) between the Au bridge atoms and the S-C3 bond in the thiolate bonding configuration. (b) Energy variation versus the tilt angle $\alpha$ of the thiolate bond at the $\left[1\overline{1}0\right]$ off-bridge site.

Figure 3

(Color online) Charge-density-difference plots for the thiolate bond, S at [001] bridge site. Regions of electron accumulation/depletion are marked in $\text{blue}(+)/\text{red}(-)$. Isosurface value: $\pm 0.025e{\text{Å}}^{-3}$. The surface unit cell is indicated.

Figure 4

(Color online) Total-charge difference for the thiolate bond, S at [001] bridge site: total-charge difference $\Delta Q\left(z\right)$ at given height $z$ (black) and total-charge transfer from above $z$ to below $Q\left(z\right)$ (red). The position of the Au top layer, the position of S, and $z_0$, the starting point of the integral in Eq. (4), are marked.

Figure 5

(Color online) Plane-averaged potential of adsorbate-substrate system (black) and free deprotonized cysteine radical (red). The position of the top-row Au layer and the S atom are indicated. The vacuum levels (plateaus) outside the systems are aligned.

Figure 6

(Color online) (a) Au PDOS of the adsorbate-substrate system. (b) Cysteine-radical PDOS of the adsorbate-substrate system (black) and of the free cysteine radical (red, from right to left). (c) S PDOS of the adsorbate-substrate system (black) and of the free cysteine radical (red, from right to left). The S PDOS of the adsorbate-substrate system has been magnified by a factor of 3 to allow for better visibility of the lineshape. Energy alignment was obtained using the vacuum level of the electrostatic potential. The energy zero is set to the Fermi level of the metal.

Figure 7

(Color online) (a) Charge-density difference for the amino bond, N at top site. Regions of electron accumulation/depletion are indicated in $\text{blue}(+)/\text{red}(-)$. Isosurface value: $\pm 0.025e{\text{Å}}^{-3}$. The surface unit cell is indicated. The inlet depicts the free glycine HOMO, isosurface value: $0.3e{\text{Å}}^{-3}$. (b) Isosurfaces of the spatially resolved electrostatic potential difference $\Delta V_{el}\left(\mathit{x}\right)$ (5). Isosurface values are $-1$ (blue) and $-2$ (red) eV.

Figure 8

(Color online) Total-charge difference for the amino bond, N at top site: total-charge difference $\Delta Q\left(z\right)$ at given height $z$ (black) and total charge transfer from above $z$ to below $Q\left(z\right)$ (red). The position of the Au top layer, the position of N, the starting point of the integral $z_0$ from Eq. (4) and the dividing plane $z_d$ are marked.

Figure 9

(Color online) (a) Au-projected DOS of the adsorbate-substrate system. (b) Glycine-projected DOS of the adsorbate-substrate system (black) and of the free glycine molecule (red, from right to left). (c) N-projected DOS of adsorbed (black) and gas-phase (red, from right to left) system. The Fermi level of the metal is used as energy zero.

Figure 10

(Color online) Au-projected, cysteine-projected, S-projected, and N-projected density of states of the four relaxed adsorbed cysteine configurations. The Fermi level is aligned with the origin of the energy scale. For colors, see text.

Figure 11

(Color online) Charge-density difference plots for the relaxed adsorbed cysteine configurations. Regions of electron accumulation/depletion are marked of in $\text{blue}(+)/\text{red}(-)$. Isosurface value:$\pm 0.025e{\text{Å}}^{-3}$. (a) Configuration 1, (b) configuration 2, (c) configuration 3, and (d) upright configuration. In (d) the surface unit cell is indicated.