Surface-assisted cyclodehydrogenation provides a synthetic ... · Surface-assisted...

SUPPLEMENTARY INFORMATIONdoi: 10.1038/nchem.891

nature chemistry | www.nature.com/naturechemistry 1

1

Supporting information for

Surface-assisted cyclodehydrogenation provides a

synthetic route towards easily processable and

chemically tailored nanographenes

Matthias Treier1#

, Carlo Antonio Pignedoli1, Teodoro Laino

2+, Ralph Rieger

3, Klaus Müllen

3, Daniele

Passerone1, Roman Fasel

1,4*

1 Empa, Swiss Federal Laboratories for Materials Science and Technology, nanotech@surfaces

laboratory, 3602 Thun and 8600 Dübendorf, Switzerland

2 Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland

3 Max-Planck Institute for Polymer Research, 55128 Mainz, Germany

4 Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland

* Corresponding author: [email protected]

# Present address: Institut de Science et d'Ingénierie Supramoléculaires, Université de Strasbourg, 67000

Strasbourg, France

+Present address: IBM Zurich Research Laboratory, 8803 Rueschlikon, Switzerland

© 2010 Macmillan Publishers Limited. All rights reserved.

2 nature chemistry | www.nature.com/naturechemistry

SUPPLEMENTARY INFORMATION doi: 10.1038/nchem.891

2

X-Ray photoelectron diffraction

The planarization of CHP upon annealing on Cu(111) has also been observed by synchrotron-based X-

ray photoelectron diffraction (XPD) [1] performed at the Swiss Light Source. Figure S1a shows the C1s-

XPD pattern of a monolayer of CHP after deposition at room temperature. The pattern only exhibits very

broad diffraction maxima and the overall anisotropy is small (~3%). Following a stepwise annealing, the

anisotropy of the pattern increases and diffraction features get sharper. After sufficiently long annealing,

when all molecules are expected to have fully reacted, the diffraction pattern (Fig. S1d) is nearly

identical to the corresponding pattern produced by the fully planar polycyclic hydrocarbon hexa-peri-

hexabenzocoronene (HBC), confirming the overall planarity of the final reaction product.

Figure S1: C1s-XPD patterns of CHP as deposited (a) and after different annealing steps (b-d).

Annealing time and temperatures are increased from b) to d). e) shows a corresponding C1s-XPD of the

fully planar polycyclic aromatic hydrocarbon HBC on Cu(111) for comparison. All patterns have been

recorded at a photon energy of 920eV.




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Extended version of Figure 4A and corresponding numerical values

Figure S2: Extended version of Figure 4A, including structural models of the transition states. The

corresponding numerical values are given in Table S1.

1 2 3 4 5 6 7

total energy (eV) 1.08 1.90 1.11 1.96 2.00 1.66 0.00

reaction barrier (eV) 1.4 1.5 1.6 0.9 0.3 1.5

Table S1: Total energies and reaction barriers computed by DFT for 1 to 7 adsorbed on Cu(111). The

total energies are relative to the fully planar TBC 7.




4

Simulated STM images

STM images of the surface-stabilized reaction intermediates and of the initial and final products have

been generated and compared to the experimental observations (see Fig. S3). The images were obtained

employing the Tersoff-Hamann approximation on a charge density constructed using all the electronic

states within the experimental bias from the Fermi level. To account for the finite size of a real tip, we

approximated the tip apex as a hemisphere of radius 6 Å, and considered that tunneling could occur

from/to the entire hemisphere. This translates into varying the height of the tip when moved along the

surface such as to keep constant the value of the charge density integrated over the hemisphere. The

reference value that we choose corresponds to an isosurface of 1*10-4 e/ Å 3 . This approach is an

improvement of the “rolling ball” approach to represent finite size effects within a Tersoff-Hamann

approach and revealed good agreement with experimental images in different cases (see e.g. [2]).

There is a good overall agreement between the most distinguishable features of each type of species

for the simulations and the experiments. As can be seen by comparing Figures S3A and S3E, both

experiment and simulation show that there are two stronger and one fainter protrusion present on the

initial CHP which has an overall triangular shape. The following surface-stable reaction intermediate 3

only has one protrusion (Fig. S3B and S3F). The next stable intermediate 6 exhibits an inwards bent side

for both simulation and experiment. The simulation also suggests that the two other sides would be

slightly bent outwards which is however not observed experimentally.

It should be noted that simulations have been performed for individual molecules while – except for

the final TBC – molecules have been observed within aggregated structures and not individually which

might slightly change the appearance of the former.




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Figure S3: Experimental and simulated STM images of the surface-stable species. (A) Initial CHP 1

(B) Intermediate 3 (C) Intermediate 6 (D) final reaction product 7. (A-D) are identical to the STM

images presented in Figure 2 of the manuscript. (E-H) Simulated STM images corresponding to the

measured configurations right above. The models overlaid on one of the simulated molecules are the

same as those used in Figure 2 of the manuscript, highlighting protrusions and the inwards-bent shape.




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Further details for the ab initio calculations

The exploration of large multidimensional free energy surfaces is a computationally extremely

expensive task, to date unaffordable if performed within a DFT framework. In order to retrieve similar

information, but without an extensive sampling of the free energy surfaces, combinations of different

computational approaches have to be employed. In this work we decided to characterize the reaction

pathway by means of NEB calculations, based on initial guesses obtained from molecular dynamics

simulations (MD) and from constrained geometry optimizations. Therefore, all intermediate states

presented in the manuscript were identified either by molecular dynamics simulations based on a

simplified scheme (see next section ‘Potential cyclodehydrogenation along a non-catalytic reaction

path’) or by a series of constrained geometry optimizations. Once a constraint is defined (e.g. the

distance between two atoms) a geometry optimization is performed forcing the constraint to preserve a

given value.

In the following we briefly describe all constraints that were used to obtain an initial guess for the

NEB calculations

For step 1-2 we constrained the distance C1-H1 to values increasing from the equilibrium distance up

to the adsorption of H1 to the surface. In this way intermediate 2, as expected, was found and a NEB

from 1 to 2 was run to find the correct transition state (TS).

For the step 2 to 3 we constrained the distance C1-C3 from the initial value of configuration 2 down to

the distance of C-C bonding. During the series of constrained optimizations H3 was spontaneously

detached, and intermediate 3 was reached. The NEB from 2 to 3 confirmed that the transition state is

characterized by partial formation of the C-C bond and partial detachment of H3.

Step 3 to 4 is analoguous to step 1-2.

For step 4-5 we constrained the distance C6-C4 to decrease up to the C-C bond distance, hydrogen H2

and H4 spontaneously lifted outwards and intermediate 5 was obtained. The NEB calculation from 4 to

5 revealed the TS described in the manuscript.




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For step 5 to 6 we removed H5 from 5 and geometry optimization resulted spontaneously in

configuration 6. We thus computed a NEB from 5 to 6 with H5 going from C5 to the surface.

Finally, for step 6-7 we obtained an initial guess for the NEB path constraining the H2-H4 distance

down to the formation of the H2 molecule. The sequence of constrained minima obtained was used as an

initial path for the NEB that revealed the TS shown in the manuscript.

We note that with respect to the lateral position of the molecule, the geometries presented in Fig. 3

and 4 of the manuscript and in Fig. S2 do not necessarily correspond to a global minimum: depending

on the location of the molecule (bridge/top/hollow position) with respect to the copper atoms, a large set

of minimum geometries is found, differing 0.1-0.2 eV one from the other (see e.g. [3]). Dynamical

simulations at the experimental temperature reveal that the molecule, if not chemically bonded to the

substrate, diffuses almost freely across the different local minima and spontaneous rotations of the

phenylene rings is also possible. Crossing of a transition state, instead, is a rare event that has to be

investigated with proper methods such as NEB. The configurations shown in Fig. 4A correspond to the

local minima closest to a transition state as prescribed by the NEB algorithm. The different local minima

at the surface for a given geometry are not distinguishable by STM.




8

Potential cyclodehydrogenation along a non-catalytic reaction path

In order to explore alternative possible dehydrogenation reaction pathways that are not catalytically

enhanced by the substrate, we performed simulations within a hybrid scheme that allows to drastically

reduce the computational effort. Within this approach the computational cost of dynamical simulations

such as metadynamics [4] become affordable. The simulation scheme can be outlined as follows: the

molecule is treated ab initio using density functional theory (DFT), the Cu substrate is mimicked via

empirical potentials (EAM) [5] and the surface/molecule interaction is modeled through a potential that

reproduces the van-der-Waals interaction in the form of C6/R6 and the core repulsion in exponential

form [6]:

VX-Cu(r)=AX*exp(-αvX*r)+BX*exp(-αcX*r)-CX-Cu/r6 where X=C,H.

This potential is added to the Hamiltonian of the system that contains two other contributions: the DFT

contribution for the isolated molecule in the given geometry and the EAM contribution of the

corresponding isolated Cu system.

The parameters for the potential were fitted to ab initio DFT simulations with inclusion of van-der-

Waals corrections [7] performed on several model geometries for CHP and TBC on Cu. The CP2K [8]

code has been used for the calculations.

The Cu substrate has been modelled with 10 Cu layers and a cell of ~40Åx40Å containing a total of

2880 Cu atoms. The molecule is treated either within empirical DFT (PM6) [9] or within standard DFT

with Goedecker pseudopotentials and BLYP [10,11] parameterization of the exchange correlation

functional.

PM6 allows to evaluate the electronic ground state of the molecule with a negligible computational cost

and an accuracy adequate to compare the energies of different geometries for the molecule. In this way it

is possible to simulate long dynamics trajectories to identify intermediate states relevant for the reaction.




9

The configurations of interest are then refined within standard DFT. The energy table reported in the

following is obtained refining PM6 results with standard DFT. Further details on the newly developed

computational methodology can be found elsewhere [12].

The complexity of the dehydrogenation process for the CHP molecule is reflected in the difficulty to

identify a unique path for the reaction; the presence of large barriers in the dehydrogenation reaction

does not allow reaching the relevant intermediate states within normal MD simulation times. We

therefore used the metadynamics method [4] that allows for an efficient sampling of the free energy

surface as a function of reaction coordinates. In brief, a potential energy surface is continuously

modified while it is being explored and dynamics simulations are being performed on it. This method

allows to both locate new equilibrium states and to evaluate free energy barriers between stable or

metastable configurations. We performed several metadynamics simulations at a temperature of 450 K

with an adequate choice of reaction coordinates [12].

The role played by van-der-Waals interactions in the dehydrogenation reaction is correctly described

within our method and, due to the empirical representation of the Cu substrate, catalytic effects

originating from the Cu electrons are neglected. As already stated in the manuscript, a similar approach

for a fully ab initio description of the substrate/molecule system is nowadays unaffordable.

The results from this alternative modelling are summarized in Figure S4A and Table S2 As shown in

Figure S4A, we identify a possible non-catalytic reaction path that contains four reaction intermediates

(II to V). Our reaction path is analogous to the one investigated by Violi [13] for the

benzo[c]phenanthrene molecule. In our case, van-der-Waals interactions and temperature effects

enhance the pathway. Compared to the reaction path that we obtained including catalytic effects, two

different reaction intermediates (II and IV) have been identified while intermediate III is the same than

3. Intermediate V is similar to the corresponding configuration (6) described in the main manuscript.

Also in this case, due to the two hydrogen atoms which are attached to sp3 bonded carbon atoms, one

side of V is bent inwards.




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The simulations show that steps a and b involve hydrogen 1-2 shifts and that H2 is released in steps b,

d and e. It should be noted that H2 readily desorbs from Cu(111) at the employed sample temperatures

(~500K), making these steps non-reversible. On the other hand, steps a and c which only involve a

rearrangement of H atoms are reversible.

As shown in table S2, the gain in adsorption energy increases (except for configurations IV and V for

which it remains approximately constant) along the reaction. This is due to an increase in efficient van-

der-Waals contact surface upon planarization of the molecule as the reaction proceeds. The total energy

gain of the reaction within this modelling approach is 1.84 eV with the final product being considerably

more stable than all the precursors. In particular, precursors I, III, and V have a lower total energy than

the intermediates II and IV. We note that the increase in adsorption energy (1 eV) accounts for more

than half of the total energy gain, which underlines the prominent role of van-der-Waals attraction in

driving this non-catalytic reaction. Computed reaction barriers are between 1.6-1.8 eV for the forward

reaction, with steps a and d having barriers of 1.7 eV and 1.6 eV, respectively, and b, c and e 1.8 eV.

Since this modelling neglected any possible catalytic role of the substrate it can be concluded that the

main driving force behind such a reaction would be the force-field acting on the molecule due to van-

der-Waals interactions with the substrate. This is also evidenced from a comparison to calculations for

the same reaction in vacuum (Fig. S4A, blue lines), where the energy gain from the initial CHP species I

to the fully planar TBC reaction product VI amounts to less than 1 eV, compared to 1.84 eV for the on-

surface reaction discussed here.

The barriers obtained within this hybrid approach are somewhat higher than those of the catalytically

promoted pathway (see Figure S2 and Table S1). This non-catalytic reaction pathway can thus be

excluded on Cu(111), but is expected to be activated on non-catalytic substrates provided that van-der-

Waals interactions are of similar strength.




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Figure S4: (A) Simulation of intramolecular aryl-aryl coupling in CHP (I) adsorbed on Cu(111) based

on the hybrid approach, i.e neglecting the catalytic activity of the substrate. The reaction proceeds via

four (meta)stable reaction intermediates (II-V). Blue lines denote relative energies for conformations

relaxed in the gas phase. All energies are relative to the final TBC (VI) reaction product. (B) Detailed

scheme of the reaction path. Structures labeled by primed numbers (I’, II’) are drawn to illustrate the

atomistic details of the corresponding reaction steps - they are neither stable intermediates nor transition

states.

I II III IV V VI

total energy (eV) 1.84 2.43 1.50 2.88 1.88 0.00

adsorption energy (eV) -2.83 -3.07 -3.51 -3.71 -3.69 -3.85

reaction barrier (eV)

(step)

1.7 a

1.8 b

1.8 c

1.6 d

1.8 e

Table S2: Energetics of the alternative, non-catalytic reaction pathway, computed by DFT for I to VI

adsorbed on Cu(111). The total energies are relative to VI.




12

References

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[8] http://cp2k.berlios.de

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