On-Surface Molecular Recognition Driven by Chalcogen Bonding

Chalcogen bonding interactions (ChBIs) have been widely employed to create ordered noncovalent assemblies in solids and liquids. Yet, their ability to engineer molecular self-assembly on surfaces has not been demonstrated. Here, we report the first demonstration of on-surface molecular recognition solely governed by ChBIs. Scanning tunneling microscopy and ab initio calculations reveal that a pyrenyl derivative can undergo noncovalent chiral dimerization on the Au(111) surface through double Ch···N interactions involving Te- or Se-containing chalcogenazolo pyridine motifs. In contrast, reference chalcogenazole counterparts lacking the pyridyl moiety fail to form regular self-assemblies on Au, resulting in disordered assemblies.


Synthesis
The molecules studied in this work have been prepared according to a synthetic protocol previously published 1 (Scheme S1).

Surface studies
The details of the surface investigation were described in the manuscript.

Computational methodology
As for the experimental investigation on surfaces, the calculation methods were extensively described in the manuscript.

Chirality of CGP-Te dimers on Au(111)
By looking carefully at our STM images of CGP-Te dimers on Au(111) one can notice the existence of two enantiomers (Fig. S1).Statistically, after analyzing several images taken in different locations on a given sample for several samples, we found a ratio of 1.01 between the two species, as expected since they are degenerate.The image to the left was acquired in constant height mode with a CO-functionalized tip with 0.005 V, while the ones at the centre and to the right with 0.000 V. Scale bar: 1 nm.

CGP-Te dimer formation on Ag(110)
To generalize our findings, we have attempted to use chalcogen bonding interaction to form dimers on  CGP-Se molecules were sublimated in ultra-high vacuum on the Au(111) substrate held at room temperature.The coverage is close to 1 ML.The image was taken at 9.5 K with an etched W tip.

Thermal stability of CGP-Te dimers
To test the thermal stability of the CGP-Te dimers, after its deposition, we annealed a sample of CGP-Te/Au(111) to 50 °C prior to performing STM analysis.The results of the analysis are displayed in Fig. S6.No noticeable differences can be found with respect to a sample that was not annealed.

Molecular adsorption, binding and interaction energies
Adsorption, binding and interaction energies are defined in the following way.We adopt a naming convention whereby E A/B tot means the total energy of the interface formed by molecule A adsorbed on substrate B, while E C,D tot means the total energy of system C when it is in the geometry (phase) D.
The gas-phase dimer binding energy is the energy gained by forming the dimer from freestanding monomers: where the terms on the right-hand side are the DFT total energies of the isolated dimer and monomer in their fully relaxed, ground state geometry.
The gas-phase dimer interaction energy is the energy gained by forming the dimer from its constituent fragments (i.e., the monomers fixed in the geometries they take in the dimer): The difference between binding and interaction energies is the induced strain (deformation) energy.
We now introduce the corresponding expressions for the molecules adsorbed on the surface.If the molecule-substrate interaction is so weak that the substrate geometry does not change, the binding and interaction energies can be defined in a trivial way. 2 In general, however, the substrate deformation energy must be taken into account.
The surface dimer interaction energy is the energy gained by forming the dimer from its fragments: where the last term is the energy of the frozen slab (substrate) alone, when the monomer is adsorbed on top (adsorbed monomer phase).
Finally, the adsorption energy is always defined in terms of the relaxed, gas-phase monomer:

Chalcogenadiazole (diazole-Te) dimer formation on Au(111)
Chalcogen bonding between chalcogenadiazole molecules has been deeply studied in the literature [3][4][5] (e.g.Scheiner et al; Michalczyk et al; Wang et al).In Fig. S9 we demonstrate that, like for CGP-Te, chalcogen bonding in a simple chalcogenadiazole dimer (diazole-Te) persists following adsorption on Au(111).While monomer adsorption (A) occurs in the on-top (Te on Au) position with a vertical geometry, the intermolecular interaction within the dimer induces a flat geometry.In contrast to CGP-Te, lattice matching of (Te, Te) occurs with respect to the 1 st nearest neighbour Au-Au distance.
Adsorption, binding, and interaction energies are reported in Table S1.Due to the short Ch-N bonds, the interaction and binding energies are much higher than CGP-Te, although the adsorption energy is

Interaction energy analysis
The dimer interaction energy quantifies the attraction between each fragment in a dimer in gas phase (Eq.2) or when adsorbed on the surface (Eq.3).By computing ∆E dimer,peeled int , i.e. the interaction energy of the dimer in the "peeled-off" geometry (in its adsorbed geometry with the substrate removed), the change in the interaction energy due to the presence of the substrate can be analysed further.
Firstly, we define the dimer deformation energy: where ∆E dimer,surf int,CT is the energy change (penalty) in the dimer interaction energy incurred due to its electronic interaction with the surface, e.g. from charge transfer (CT), orbital mixing with Au states, etc.
Note that the surface deformation energy is excluded from the dimer interaction energy; instead, it is implicit in the dimer binding energy.
Finally, we decompose the surface dimer interaction energy into a dispersion (vdW-D3) and a nondispersion term:  The various components are reported in Table S2 for the four dimers considered in this work.A number of points can be deduced: 1) The reduction in the interaction energy upon adsorption is split equally between the deformation and electronic CT terms, which each comprise about 20% of the gas phase interaction energy.
2) For the CGP dimers, we further break down the deformation energy (1.8 kcal/mol in CGP-Te; 1.3 kcal/mol in CGP-Se).From Fig. S11 (left panel) and the computed Ch-N distances (Table S1) we estimate that the energy penalty due to lengthening the Ch-N bonds after matching to the substrate is about ~0.5 kcal/mol in both molecules.From Fig. S11 (right panel) we estimate the energy penalty associated with rotating the azole with respect to the pyrrole ring, from 25.5 in the gas phase to about ~12 when adsorbed, at about 0.2 kcal/mol (per fragment).Thus, the remaining penalty of ~0.9 kcal/mol in CGP-Te (~0.4 kcal/mol in CGP-Se) can be ascribed to the electrostatic and orbital misalignment (out-of-plane twisting) of the Te/Se and N atoms in the chalcogen bond induced by adsorption on the surface.
3) The vdW component in the interaction energy ∆E dimer,surf int,disp is fairly constant for the three dimers with Ch-N bonds.It forms a large component of the total interaction energy in the CGP-Ch dimers.It is interesting to note that despite an attractive vdW interaction present between Benzo-Te monomers, the remaining non-dispersion interaction ∆E dimer,surf int,non−disp , in the absence of chalcogen bonding, is strongly repulsive and overall destabilizes the dimer.For the smaller diazole-Te dimer, the non-dispersion contribution dominates the interaction energy.
4) Further analysis of the chalcogen bond (e.g.electrostatic, polarization, Pauli repulsion contributions) may be accessible through an energy decomposition analysis, which is however not widely available for periodic systems.

Molecular projected density of states (PDOS)
The projected density of states of the gas phase CGP-Te dimer and of one of its fragments (same geometry) is plotted in Fig. S12.A weak splitting of Te p z orbitals is observed upon dimer formation, while a much larger splitting is observed for the in-plane Te and N molecular orbitals.These calculations quantify the overlap between Te and N orbitals in forming the chalcogen bond.The HOMO remains localized on the pyrene.

Figure S1 .
Figure S1.a) 40x40 nm 2 Constant-current scanning tunnelling microscopy image collected at 11.1 K of CGP-Te deposited on Au(111).Two enantiomers can be found, as exemplified by the blow-up shown in panel b (zoom of the white square in parent: 250 pA; panel a).Tunnelling bias voltage: 0.5 V. c) Sketch of the two enantiomers.

Figure S2 .
Figure S2.Constant-current scanning tunnelling microscopy (STM) images of reference Benzo-Se molecules on Au(111) at T=9.5 K.The monomer molecules self-assemble along the herringbone reconstruction of the substrate but do not form dimers and remain well isolated.Scale bars: 20 nm (left panel) and 2 nm (right panel).Tunnelling current: 0.1 nA (left panel) and 0.08 nA (right panel); tunnelling bias: 1.000 V (left panel) and 0.100 V (right panel).

Figure S3 .
Figure S3.BRSTM images collected on the same CGP-Te dimer at T= 8.7 K.The dimer has rotated during the scan (see middle panel) due to tip-dimer interaction but remains intact after rotation, showing the stability of the dimer.The rotation angle of 60 degrees shows both the relatively strong bonding with the substrate, which forces Te atoms to be on top position with respect to the Au atoms underneath.

a
metal surface other than Au.As shown in Fig. S3, after deposition of CGP-Te molecules on a clean Ag(110) substrate held at room temperature, a number of CGP-Te dimers are observed from STM characterization.

Figure S4 .
Figure S4.Scanning tunnelling microscopy image of CGP-Te deposited on Ag(110).CGP-Te molecules were sublimated in ultra-high vacuum on the Ag(110) substrate held at room temperature.Four dimers can be spotted in this region.The image was taken at 12 K with an etched W tip. Tunnelling current: 150 pA; tunnelling bias: 1.0 V.For comparison, the inset in the top right corner shows the CGP-Te dimer on Au(111) already displayed in panel B of Figure 2 in the manuscript.

Figure S6 .
Figure S6.Constant-current STM images of a sample of CGP-Te/Au(111) that was annealed to 50 C after deposition at room temperature.Tunnelling current: 30 pA; bias voltage: 1.0 V; acquisition temperature: 10.9 K.

11.
Figure S6.(A, B) Geometry of CGP-Te monomer and dimer adsorbed on Au(111).The arrows indicate the direction of the side views.In (B), the six-fold possible orientations of the dimer are indicated.The circles indicated Te on Au matching.The CGP-Se geometry is almost identical.(C, D) Geometry of reference Benzo-Te tellurazole ("BCG-Te") molecule adsorption.

Figure S8 .
Figure S8.DFT analysis of chalcogen bonding in the CGP-Se dimer.(A, B) Gas phase and adsorption geometries (side view).The tilt angle of the azole with respect to the pyrene ring is indicated.(C, D) Electrostatic potential (in au) superimposed on a charge density ( = 0.025 au) isosurface.Atomic charges Q are reported for Se and N. Total charge transfer to the surface Q = 0.22e.(E, F) Molecular graph showing bond paths (dotted lines), bond critical points (BCP) in red, and ring critical points (in green).For clarity, critical points and bond paths between the dimer and substrate are not shown, exceptfor Se-Au and N-Au.An additional N-N bond path is found for the gas phase CGP-Se dimer that is not present in CGP-Te.(G, H) Reduced density gradient (on the 0.5 au isosurface); blue and red indicate attractive and repulsive interactions, respectively.The dashed circle highlights the attractive noncovalent interaction between Se and N, that persists in the adsorbed dimer but with a weaker intensity.

14 .Figure S10 .
Figure S9.Electronic charge density difference plots of the CGP-Te dimer, computed using (for gas phase, left)  = (dimer) -(fragment1) -(fragment2) or (for adsorbed phase, right)  = (dimer/Au) -(fragment1) -(fragment2) -(Au).Density  given in a.u.The top row shows  as a contour map on a horizontal plane containing the Te atoms; middle and bottom rows show  isosurfaces (top and side views).The dotted line indicates a weak area of electron accumulation between the Te and N atoms.Note that the intermolecular charge redistribution appears only along the Te-N axes, and persists following adsorption.Polarization is notable within the azole rings.A relatively large transfer of electrons from Te to Au is visible in the side profile, consistent with the VDD analysis reported in the main text and in Fig. 4.
much lower.Charge density difference plots (C), molecular electrostatic potential maps (D), and reduced density gradient maps (E), all indicate the presence of directional, non-covalent Te-N bonds.

Figure S11 .
Figure S11.Chalcogen bonding in a chalcogenadiazole dimer adsorbed on Au(111).(A) Adsorption geometry of the monomer and (B) dimer.(C) Electronic charge density difference plots:  = (dimer/Au) -(fragment1) -(fragment2) -(Au), as a contour map on the horizontal plane containing the Te atoms and for a single isovalue of .Density  is in a.u.(D) Molecular electrostatic potential maps (in au) superimposed on a charge density ( = 0.05 au) isosurface.(E) Reduced density gradient (on the 0.5 au isosurface); blue and red indicate attractive and repulsive interactions, respectively.

Figure S12 .
Figure S12.Left: change in dimer interaction energy with monomer separation.Energy is given with respect to that of the equilibrium geometry in the gas phase.Right: energy variation for the CGP-Te monomer with respect to the angle between planes of azole and pyrrole rings (constrained).The red dashed line is an extrapolation of the constrained lineshape to contain the freely relaxed optimized geometry and the constrained coplanar geometry at 0.

Figure S13 .
Figure S13.Projected density of states (PDOS) of CGP-Te dimer in gas phase.(A) Total PDOS of the dimer.Energy levels are indicated by vertical bars.(B) As (A), for one of the dimer fragments.(C) Molecular PDOS 6 of selected fragment states, i.e. their projection on the PDOS of the dimer.(D) PDOS for Te atom in dimer and fragment.(E) PDOS for N atom (N 1 ) involved in chalcogen bond, in dimer and fragment.Energies are shifted to align the HOMO in both systems.

Table S1 .
Binding (ΔE b ), interaction (ΔE int ), and adsorption (ΔE totis the total energy of the clean Au surface and E molecule/Au tot that of the complete interface (slab+molecule).In the limit of negligible surface strain, the adsorption and binding energies are simply related as: ads ) energies (in kcal/mol) related to dimer formation in the gas phase and adsorbed on the Au(111) surface.Ch(Te, Se)-N and Ch-Ch distances in Å.The corresponding 1 st and 2 nd nearest neighbour Au-Au distances are 2.92 Å and 5.05 Å. CGP = chalcogenazolo pyridine; Benzo = benzochalcogenazole; diazole = chalcogenadiazole.
pyridine rings) due to twisting of the azole towards the surface, the modified Te-N distance due to lattice matching, and the relative rotation of azole and pyrrole rings after adsorption.

Table S2 .
Contributions to the dimer interaction energy, in kcal/mol.See Eqs. 3, 7-10 for definitions of each quantity.