AFM Imaging of Mercaptobenzoic Acid on Au(110): Sub-Molecular Contrast with Metal Tips

A self-assembled monolayer of mercaptobenzoic acid (MBA) on Au(110) is investigated with scanning tunneling and atomic force microscopy (STM, AFM) and density functional calculations. High-resolution AFM images obtained with metallic tips show clear contrasts between oxygen atoms and phenyl moieties. The contrast above the oxygen atoms is due to attractive covalent interactions which is different from previously reported high-resolution images where Pauli repulsion dominated the image contrast. We show that the bonding of MBA to the substrate occurs mainly through dispersion interactions while the thiol-Au bond contributes only a quarter of the adsorption energy. No indication of Au adatoms mediating the thiol-Au interaction was found in contrast to other thiol-bonded systems. However, MBA lifts the Au(110)-(2 × 1) reconstruction.

Combined scanning tunneling and atomic force microscopy (STM and AFM) delivers information on molecular structures and chemical interactions on the atomic scale. The method was used for sub-molecular resolution imaging of pure hydrocarbons [1][2][3][4][5][6] as well as other carbon-based molecules like fullerenes 7-10 or π-conjugated polymers. 11 In nearly all of these works, the tip of the scanning tunneling microscope was functionalized by a single CO molecule. The observed sharply localized contrasts are interpreted in terms of Pauli repulsion and the bendability of the bond between CO and the tip apex atom. 12,13 Recently, molecules comprising heteroatoms have been addressed. [14][15][16][17][18][19][20][21][22][23][24] As soon as electrostatic dipoles in the molecule or tip are present, the electrostatic force plays an important role in interpreting the images. 20,22,[24][25][26][27] Thiols are of great interest owing to their capacity to self-assemble and to create various structures thanks to their functionalizing groups. 28 The adsorption of thiols on Au(111) has been investigated over a range of coverages using a variety of methods including STM and X-ray diffraction. [29][30][31][32][33][34] There is consensus concerning the observed structural 2-dimensional phases, [35][36][37][38][39][40][41] but the discussion about involved Au adatoms at the S-Au interface is still ongoing. 42 Among the thiol-based molecules, 4-Mercaptobenzoic acid (MBA) has received particular attention because it led to the unraveling of thiol-gold structures based on an adatom model on gold nanoclusters. [43][44][45] However, no adatoms appeared to be involved in the formation MBA monolayers on Au(111). 46 The structural phases of MBA monolayers are similar as for other thiols according to X-ray photoelectron spectroscopy 47,48 and STM data. 46,49 However, a recent STM study of a MBA related molecule (4-mercaptopyridine) on Au(111) suggested an upright orientation at low coverages 50 where other thiols lie flat on the substrate. Indeed, MBA is an intriguing molecule despite its simple structure. It consists of a phenyl ring with a π-electron system that gives rise to interesting van der Waals interaction and molecular stacking in crystals. In addition, its carboxyl group leads to hydrogen-bonding while the thiol group provides covalent binding to metal atoms.
Here, we use high-resolution AFM and STM to image arrays of MBA with metallic tips.
High-resolution images are obtained at tip-sample distances where the molecules cause an increased attraction. The oxygen atoms appear as remarkably sharp features in frequencyshift AFM images. This chemical contrast provided by metallic tips is different from the results mentioned above that involved functionalized tips. Moreover, repulsive force contributions were identified as the origin of the sub-molecular resolution. We disentangle the various forces acting on MBA by means of density functional theory (DFT) calculations, which show that a covalent interaction of the metallic tip with the oxygen atoms is predominant. An electrostatic force is present but less important. Concerning the adsorption of MBA on the Au(110) surface we find that the molecules form a zigzag pattern of dimers that are due to hydrogen bonding of the carboxylic groups. Our calculations reveal that the dispersion interaction of π-electrons of the phenyl ring with the metal substrate is essential for the MBA-Au bond. The Au(110)-(2 × 1) reconstruction is lifted. The experimental data do not indicate an involvement of Au adatoms in binding the MBA molecules.
In constant-current STM images MBA molecules appear as elliptical protrusions on the Au(110) surface ( Fig. 1(a) and (h)). At coverages of ≈ 0.3 monolayers (one monolayer being defined as a coverage of one molecule per five surface gold atoms) the molecules aggregate into compact islands. Within these islands the long axes of the ellipses are aligned along the [001] direction with spacings of (7.8 ± 0.3)Å and (12.3 ± 0.3)Å. A unit cell comprising four MBA molecules is depicted by a white rectangle in Fig. 1(a). Its dimensions of (20.1 ± 0.3) × (10 ± 1)Å 2 correspond to a (5 × 4) overlayer. The distances, sizes and corrugations in our measurements indicate that MBA molecules adsorb in a nearly planar orientation on Au(110), contrary to what has been reported for other surfaces. [46][47][48][49][50] Further details of the molecular structure are resolved in constant height measurements of the tunneling current and the frequency shift. The tunneling-current map ( Fig. 1 shows an asymmetry of the molecular protrusions with maxima of the current localized close to the phenyl rings. In the frequency-shift map of Fig. 1(c), each molecule gives rise to three features. The frequency shift is negative in two well-defined spots and a more diffuse area.  The distances between the sharp depressions are y = (2.1 ± 0.2)Å and x = (2.8 ± 0.2)Å.
y matches the oxygen-oxygen distance in MBA. x is consistent with hydrogen bonding between O atoms of adjacent molecules. Therefore, these spots are suggested to stem from the oxygen atoms while the diffuse areas, corresponding to the maxima in the current, are ascribed to the phenyl rings. The oxygen-induced features in the frequency shifts appear surprisingly sharp. ∆f changes from ≈ −45 Hz to ≈ −23 Hz back to ≈ −40 Hz over a lateral distance of only 2.1Å. As discussed below, we attribute the high resolution to an attractive interaction localized to the oxygen atoms.
As the tip approaches any part of the molecule, the force becomes increasingly attractive ( Fig. 1(g)). The maximal force above the phenyl ring occurs at a slightly smaller tip-molecule distance (by ≈ 0.2Å) than above or between the oxygen atoms. Compared to forces obtained with CO tips, the present force values are roughly one order of magnitude larger. 1,27 The strong attractive forces are the origin of the sub molecular resolution as further discussed below.
The conductances show the expected exponential distance dependence at large tipmolecule distances until a change in the slope indicates the transition from the tunneling range to contact ( Fig. 1(g)). This transition occurs close to the maximal attractive force as observed for single atoms and other molecules before. 26,[51][52][53] The conductance at contact    , an adsorbed molecule with its phenyl ring parallel to the surface (horizontal), and an adsorbed molecular dimer. The considered energies are the total adsorption energy, E total , the contribution coming from the van der Waals interaction (vdW), the interaction energy between molecules due to the formation of H-bonds (O··H··O), and the contribution of the S-metal bond (S-Au).
vertical horizontal in adsorbed dimer E total -1.00 In many thiols, the S-metal bonding largely drives the adsorption of molecules on gold. 28,45,54,58 In the present case, however, this kind of bond accounts for only 25% of the molecular adsorption energy in dimers. To first approximation, MBA is adsorbed via the dispersion interaction while the S-metal bond introduces selectivity for a specific site. Indeed, the S atoms are located close to the short-bridge site of Au(110) and 1.95Å away from the surface plane. This site specificity forces a zigzag structure of the aligning rows of dimers because dimers can only form compact structures if their S atoms adsorb to adjacent Au rows, Fig. 2(a). Otherwise, the steric repulsion between hydrogen atoms of adjacent MBA molecules would be too large.
A further important contribution to the dimer stability is due to hydrogen bonding. In gas phase, the formation energy of a dimer is −0.41 eV per molecule. It reduces to −0.55 eV for the intramolecular coordinates frozen. This value is very close to the energy due to the formation of H-bonds between molecules in adsorbed dimers, see Table 1, implying that the intramolecular geometries are largely fixed by the adsorption to the substrate.
On the Au surface, the energy due to hydrogen bond formation in dimers is comparable with that of the S-metal bond. As a result of these interactions the MBA molecules are fixed on both sides. The sulfur side binds to the Au substrate while the carboxylic group causes hydrogen bonding. surface. This is consistent with the observations that fairly straight MBA dimer rows extend far into well-ordered (2 × 1) terraces and that smaller clusters of MBA grow on the next higher Au terrace (Figs. 1(h) and S1). If the mechanism were the addition of Au adatoms (so filling the existing missing-row reconstruction), the adatoms would stem from the step edges and diffuse along the [110] direction. 60,61 In this case, the diffusion and addition of adatoms would stop as soon as the first row of MBA pairs adsorbs to the step edges. Hence, a large-island (as shown in Fig. S1) would not be expected. As described by Kühnle et al., 62 the removal of a row atom becomes easier when an atom has already been extracted.
Consequently, continued growth of an existing dimer row is more likely than the creation of new rows.
Single gold adatoms have been shown to direct the interaction between some thiol-based molecules. 54,56,58 In the present case, however, we did not observe evidence of adatommediated interaction. Indeed, the frequent detection of single dimer rows (red boxes in  64 The vertical force component is where V ( r) is the electrostatic potential of the full system comprising the molecule and the surface. The force analysis shows that for d > 9Å, the van der Waals interaction dominates the force between the molecule and the model tip. In this range, the tip is largely insensitive to the molecular structure. When the tip is brought closer to the molecule, the covalent interaction first sets in over the O atoms. Our model tip reproduces the enhanced attractive signal in AFM images over the oxygen atoms shown in Fig. 1(c) since the interaction is more attractive on the oxygen atoms than in between ( Fig. 3(a)). A significant contribution to the signal over oxygen atoms comes from a mechanical deformation of the molecule, Fig. 3(b).
The relatively small interaction of the oxygen groups with the surface allows for a motion of the oxygen atoms to the tip (see also Fig. S5). At the largest attractive force (tip-surface distance of ∼ 8.4Å, red squares in Fig. 3(a)) the displacement of the oxygen atom to the tip (black squares in Fig. 3(b)) is larger than the variation of d. This leads to a marked non-linear behavior of the curves in Fig. 3(b). The oxygen distance to the tip decreases by ∼ 1Å, roughly 0.5Å more than expected from a rigid behavior following the motion of the tip. In comparison, the tip-apex atom is stiffer, moving less than 0.08Å from its equilibrium distance, and basically following the variation of d. The oxygen motion towards the tip apex takes place in a very narrow region of d ∼ 8.4 . . . 8.9Å. Experimentally, we find a smoother variation of the frequency shift between two oxygen atoms of different molecules than between oxygen atoms of the same molecule ( Fig. S4(b)). This indicates that relaxations are stronger when the tip is positioned between oxygen atoms of the same molecule. According to the calculated force curves in Fig. 3(b), ∆z = −0.8Å corresponds to a tipmolecule distance d ∼ 3.3Å. This is similar to the distance reported for atomic resolution imaging of C 60 with a CO-functionalized tip. 8 Given the absence of dipolar contributions from our model tip, we conclude that the sharp features above the oxygen atoms in the AFM images ( Fig. 1(c)) are mainly due to the covalent interaction with the tip enhanced by the motion of the carboxylic group during the approach of the tip. This is different compared to a recent work that used a CO-functionalized tip to image a molecule with carboxylic groups. 24 Sub-molecular contrast is observed on the oxygen atoms, but it is due to the repulsive electrostatic interaction between the partially negatively charged oxygen atoms of both the CO and the carboxylic group. Although we cannot rule out some contribution from electrostatic interactions between the oxygen atoms and metallic tips of more than 1 Debye of dipolar moment, see diamonds in Fig. 3(a) and Fig. S6, our calculations show that the covalent interaction is the dominating one.
As to the position above the phenyl rings, where the maximum force occurs ( Fig.1(g)), the calculations show that the electrostatic and van der Waals forces are outgrown by the covalent contribution for distances shorter than 9Å. Thus, the large contrast measured over the phenyl ring is due to the covalent interaction between the metallic tip and the π-electron system.
In conclusion, we combined STM and AFM measurements with DFT calculations aspects of the geometry and interactions of self-assembled layer of MBA on Au(110) are unraveled.
The attractive interaction between MBA molecules and the metallic tip leads to remarkably sharp features in frequency-shift AFM images above the oxygen atoms and also above the

STM and AFM measurements
Our measurements were performed in a combined STM/AFM setup in ultra-high vacuum at 5 K. Au (110)

DFT calculations
All calculations were carried out with the VASP 69 code by solving the one-electron Kohn-

Supporting Information Available
Overview STM image of a MBA island, details on the distant-dependent measurements, tip preparation, cross-sectional profiles, asymmetries and dissipation in AFM images, as well as details on the calculation of the adsorption energies, the covalent and the electrostatic forces, and the relaxed geometries of tip-molecule junctions. This material is available free of charge via the Internet at http://pubs.acs.org/.