Structural characterisation of molecular conformation and the incorporation of adatoms in an on-surface Ullmann-type reaction

The on-surface synthesis of covalently bonded materials differs from solution-phase synthesis in several respects. The transition from a three-dimensional reaction volume to quasi-two-dimensional confinement, as is the case for on-surface synthesis, has the potential to facilitate alternative reaction pathways to those available in solution. Ullmann-type reactions, where the surface plays a role in the coupling of aryl-halide functionalised species, has been shown to facilitate extended one- and two-dimensional structures. Here we employ a combination of scanning tunnelling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and X-ray standing wave (XSW) analysis to perform a chemical and structural characterisation of the Ullmann-type coupling of two iodine functionalised species on a Ag(111) surface held under ultra-high vacuum (UHV) conditions. Our results allow characterisation of molecular conformations and adsorption geometries within an on-surface reaction and provide insight into the incorporation of metal adatoms within the intermediate structures of the reaction.

. Comparisons of Hard XPS measurements for 1,3,5-triphenylbenzene (TPB), left, and m-terphenyl (TP), right, before and after annealing (blue and orange curves respectively). Spectra calibrated such that peaks positions are at the same binding energy as observed in soft XP spectra. Figure S1 shows hard X-ray photoelectron spectroscopy (XPS) measurements (incident photons at 2629 eV) of the C 1s region for 1,3,5-triphenylbenzene (TPB) and m-terphenyl (TP) molecules before and after annealing (metal-organic (MO) phase and covalently coupled phase, respectively). Figure S2. Hard X-ray photoelectron spectra for the I 3d5/2 region, comparing Ag(111) samples with TPB and TP species, before (MO phase) and after annealing (covalently coupled product). Graphs averaged from 6 scans of the region. Spectra calibrated such that peaks positions are at the same binding energy as observed in soft XP spectra. Figure S2 shows hard XPS measurements (2629 eV) for TP and TPB, before and after annealing the surface (I 3d5/2 region). Each graph shows a single peak centred on 619.0 eV, indicating that the iodine moieties on the surface exist in a single chemical state. Figure S3. Examples of methods used to fit curves to pre-anneal (MO phase) C 1s data for TPBMO (left) and TPMO (right). Four peaks are used to create the shape of the curve observed in the data. The areas of the three peaks at higher binding energies (green) are summed to extract data for the main peak. The peak at lower binding energy (red) is used to gain information on the shoulder feature. The black line shows the overall fit, summed from all four peaks, to the data, shown in grey.

C 1s NIXSW Analysis
The three peaks shown in green at higher binding energies (centred on, from left to right, 285.1 eV, 284.4 eV, 283.9 eV for TPBMO and 284.8 eV, 284.3 eV, 283.8 eV for TPMO) are summed to obtain the fitting for the main peak, and are attributed to aromatic carbon atoms. Three components were necessary to reproduce the shape of the main peak, and allow the intensity of the shoulder peak due to C-Ag-C to be evaluated. We do not consider the three main peak components to be sufficiently unique or attributable to specific chemical environments within the molecule to allow them to be used for adsorption site. The single peak shown in red (centred on 283.1 for both TPBMO and TPMO) is used to extract information from the shoulder feature, attributed to the organometallic carbon species.

Model for obtaining the dihedral angle (Θ)
In order to determine the dihedral angle, Θ, for the rotated side groups in TP and TPB, a simplified model was developed based upon the NIXSW data (as employed in the 'Molecular adsorption and conformation: chemically sensitive NIXSW analysis' section of the main manuscript). The geometric model is shown in Figure S5. Within this model, the central aryl groups are flat and planar relative to the surface plane resting at a single distance d from the closest reflecting plane; this is defined as the molecular plane. The central aryl groups are connected by side aryl groups by C-C bonds that are colinear and lie within the molecular plane. The side aryl groups are twisted by an angle Θ about these bonds (orange dot in Fig S5 inset) causing two side aryl carbon atoms to be displaced upwards, and two downwards, by dtwist. Figure S5. Model for calculating twisting angle for TP and TPB using NIXSW measurements.
Average molecule height is shown as the molecular plane a distance d above the closest reflecting plane. Grey circles represent carbon atoms as part of the aryl side groups of TP/TPB, with blue highlighted atoms in line with the molecular plane and green highlighted atoms twisted by angle Θ such that they are offset from the molecular plane by distance dtwist. Green carbon atoms are a distance r from the axis of rotation (orange dot). Inset (top left) shows an example TPB unit with twisted side aryl groups as in this model.

S8
The total coherent fraction, Cf, and coherent position, Cp, for a system with n different positions, each with a coherent fraction and position (fn and pn), is defined by 1 (1) Carbon atoms within this model can be separated into two types: either remaining fixed (fixed) at the molecular plane or located above or below due to twisting (twist). The fractions, f, for each of these atoms are given by The coherent position for the fixed atoms, which due to symmetry is equal to the total coherent fraction, is given by where D is the separation of the reflecting planes [this holds for d ≤ D ]. Similarly the coherent position for the displaced carbon atoms can be written as with r being the separation between a twisted atom and the axis of rotation.
Applying the details of the twisting model shown above to equation (1), Cf and Cp values can be calculated such that Utilising the fact that the total coherent position is equivalent to the coherent position of fixed carbon atoms (equation (3)), equation 4 simplifies to = + cos ( 2 sin ) . (6) Finally, using equation 2 yields Cf was determined experimentally from NIXSW measurements and all other values are known.
Therefore     Figure S8. Comparisons of Hard XPS measurements of the C 1s region for TPB (a) and TP (b) in MO and covalent phases (blue and orange curves respectively). (c) NIXSW photoemission yields obtained using the (200) reflection for the C 1s core level, comparing TP (red) and TPB (blue) in MO and covalent phases. Each profile is normalised to 1, away from the Bragg condition, with TP results offset by 1 unit for clarity. The obtained coherent fraction (Cf ) and position (Cp) values are shown for each profile.  Figure S9. Table of  The method used for building a model of molecules is described in Figure S9. Firstly, (a) shows the simplified model of TPB molecules used. Only organometallic carbon atoms (black circles)

Fitting NIXSW Measurements of Organometallic Carbon Atoms
were considered as only these atoms contribute to the organometallic carbon features seen in XSW measurements. The distance, D, between the carbon atoms and the centre of the molecule (blue cross) can be varied by small amounts to account for stretching of the molecule and the end phenyl groups bending down towards the surface (from (111) XSW results). Next, an additional molecule is added (rotated by 180°) to create the molecular overlayer structure observed in STM images. The separation of molecule centres, s, as well as the unit cells rotation relative to the x-axis, α, can be varied ( Figure S9b) to account for different positioning of molecules on the surface. Then, the unit cell is repeated N = 6 times to create an extended structure ( Figure S9c). This accounts for the fact that the molecular adlayer has a regular S17 periodicity but is not necessarily coincident with the underlying Ag (111)  Using a similar method to that used for TPB, the lateral adsorption geometry of TP on Ag (111) was investigated by combining NIXSW and STM measurements. Room temperature STM images of TP on Ag(111), in both the metal-organic and covalently coupled phases, were obtained previously. 5 An example STM image of the metal-organic phase is shown in Figure   S10a. TPMO Figure S10b. Molecule centres are adsorbed at similar bridge sites, with molecules in adjacent chains adsorbed at a different bridge site. Ag adatoms are found to alternate between adsorbing at bridge and atop sites and only bridge sites for adjacent chains.
The adsorption model shows zigzag chains to have a period 2.60 nm, at an angle of 0° relative to the <1 ̅ 10> set of crystal directions, in agreement with STM measurements (2.63 ± 0.05 nm and -5° respectively). Additionally, the adsorption model has molecular chains separated by 1.13 nm which is in good agreement with the measured value of 1.14 ± 0.05 nm.
An argand diagram showing the resultant Cf and Cp values for this model is shown in Figure   S10c. S20 STM experiments were also performed for the covalent phase of TP (TPCC) and an example STM image of an island of molecules is shown in Figure S10d. Zigzag chains have constant apparent height along their lengths, indicating that molecules are covalently bonded. A molecular structure for the zigzag chains is overlaid. TPCC molecular chains were found to have a period of 2.24 ± 0.05 nm at an angle of 31° to the underlying surface. Chains were found to be separated by 1.19 ± 0.05 nm.
As with TPBCC, simulations using NIXSW measurements of Cf and Cp values were not used to develop adsorption models of covalent TPCC, due to the complexity of molecules and the number of possible variables within the system. Instead, adsorption models were developed based on measured dimensions and angles relative to the surface, attempting to align molecule centres to high symmetry sites. A tentative adsorption model developed using these methods is shown in Figure S10e. Chains in this model have a period of 2.25 nm, are oriented at 30° to the underlying surface and are separated by 1.15 nm.