File Name : s1_bare au_100_.tif

Caption : (a) topography stm image (100 nm x 100 nm) of a clean au(100) single-crystal surface. (b) apparent height profile plotted along the blue straight line depicted in image (a). (c) detail topography stm image (5 nm  5 nm) showing atomic resolution of the same surface shown in image (a). (d) 2d-fft filtered image obtained from image (c). (e) height threshold filtered image applied the image (d). acquisition conditions: (a) vs = +0.10 v and it = 0.3 na; (c) vs = -0.002 v and it = 16.0 na.

File Name : s2_cys on gold surfaces.tif

Caption : topography stm images. (a) and (b) (150 nm x 150 nm); (c) and (d) (25 nm x 25 nm). (a) and (c) are of the surface of a au(100) single-crystal substrate incubated in a l-cys methanolic solution. (b) and (d) are of the surface of a au(111) single-crystal substrate incubated in a l-cys methanolic solution. acquisition conditions: (a) vs = -0.78 v and it = 6.6 na; (b) vs = -0.12 v and it = 1.3 na; (c) vs = -0.78 v and it = 6.6 na; (d) vs = -0.60 v and it = 6.7 na.

File Name : s3_fl width.tif

Caption : (a) dot matrix obtained from a topography stm image (252 pixels x 252 pixels) of the fl structures assembled on the surface of a au(100) single-crystal substrate incubated during 10 minutes in a 10 mm methanol solution of l-cys.  acquisition conditions:  vs = -0.78 v and it = 6.0 na. (b) apparent heights histogram obtained from image (a), red dot line in blue line gaussian fitting of the histogram. (c) discretized matrix obtained filtering matrix in (a) with a threshold resulting of averaging the peaking apparent heights in (b). (d) histogram of finger widths in pixels.

File Name : s4_teo.tif

Caption : systems studied. (a) l-cys parallel to the au(100) surface (system i), (b) -nh2 pointing towards the au(100) surface (system ii), (c) -cooh pointing towards the au(100) surface (system iii), (d) s atom facing the au(100) surface (system iv), before relaxation. (e), (f), (g) and (h) are systems i, ii, iii and iv after relaxation, respectively.


File Name : s5_meoh adsorption.tif

Caption : orientations of a meoh molecule on a au(100) surface before relaxation, (a) c and (b) o atoms pointing towards the au(100) surface. (c) likely adsorption sites. the au atoms of the second layer are represented in light yellow.

File Name : s6_teo.tif

Caption : optimized structure for the meoh molecule adsorbed on the au(100) surface. (a) top and (b) side views. (c) difference charge density, where the blue regions correspond to d>0, i.e. higher charge density due to adsorption, and red regions correspond to d<0, i.e. lower charge density due to adsorption. the au atoms of the second layer l2 are represented in light yellow.

File Name : s7_stm_cys_.tif

Caption : simulated stm image 2.5 nm x 2.5 nm of l-cys molecules adsorbed on a au(100) surface. the image was simulated with a vs = -0.80 v. the dashed line box corresponds to the simulated unit cell.

File Name : s8_stm_cys_au.tif

Caption : l-cys pairs of molecules adsorbed on a au(100) surface, (a) supercell (top view), (b) simulated stm image 5.0 nm  5.0 nm. the image was simulate with a vs = -0.80 v, (c) pro file of apparent heights acquired along the straight blue line depicted in image (b). (d) side view of the supercell, the average height obtained from image (b) is 0.48 nm. the dashed line boxes in (a) and (b) correspond to the simulated unit cell.