SUEMENTARY INRMATIN - Nature Research · .10/.2506 SUEMENTARY INRMATIN 2 Table of Contents 1....

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SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2506

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Imaging Single-Molecule Reaction Intermediates Stabilized by Surface Dissipation and Entropy

Authors: Alexander Riss1,2,‡,*, Alejandro Pérez Paz3,‡, Sebastian Wickenburg1,4,‡, Hsin-Zon Tsai1, Dimas G. de

Oteyza5,6, Aaron J. Bradley1, Miguel M. Ugeda1,7,8, Patrick Gorman9, Han Sae Jung1,9, Michael F.

Crommie1,4,10,*, Angel Rubio3,11.12,*, and Felix R. Fischer4,9,10,*

Affiliations: 1Department of Physics, University of California, Berkeley, CA 94720, USA, 2Institute of Applied

Physics, Vienna University of Technology, 1040 Wien, Austria, 3Nano-Bio Spectroscopy Group and ETSF,

Universidad del País Vasco, CFM CSIC-UPV/EHU-MPC & DIPC, 20018 San Sebastián, Spain, 4Materials

Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 5Donostia

International Physics Center, E-20018 San Sebastián, Spain and Ikerbasque, Basque Foundation for Science,

48011 Bilbao, Spain, 6Centro de Física de Materiales CSIC/UPV-EHU-Materials Physics Center, Paseo Manuel

de Lardizabal 5, 20018 San Sebastián, Spain, 7CIC nanoGUNE, 20018 Donostia-San Sebastian, Spain,

8Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain, 9Department of Chemistry, University of

California, Berkeley, CA 94720, USA, 10Kavli Energy NanoSciences Institute at the University of California

Berkeley and the Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 11Max Planck Institute

for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany and 12Center

for Free-electron Laser Science (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany.

‡ These authors contributed equally to this work.

© 2016 Macmillan Publishers Limited. All rights reserved.



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Table of Contents 1. Assignment of chemical structures to the nc-AFM images 3

2. Calculated reaction pathway from 1 to 4c 4

3. Dissipation of energy from molecular dynamics simulations 7

4. Calculated timescales of reaction steps and energy dissipation for the transformation from 2b to 3a 8

5. Supplementary Movie 9

6. Computational methods and details 9

7. Accuracy of DFTB calculations 13

8. Three-dimensional renderings 14

9. Kinetic simulations 14

10. Large-scale experimental nc-AFM image of the surface after annealing 17

11. Statistical analysis of the reaction progress 18

References 20




3

1. Assignment of chemical structures to the nc-AFM images

Figure 1| Experimental nc-AFM images (blue color) compared to the relaxed molecular geometries and

simulated nc-AFM images (grayscale) for transient intermediates along the reaction pathway from 1 to

4c. For each structure along the reaction pathway the relaxed molecular geometries were calculated by




4

DFTB. The AFM images were simulated using a mechanical model introduced by Hapala et al.,1 which

accounts for the probe relaxation (we used CO-functionalized AFM tips for the measurements). Based on

the resemblance of the experimental and simulated AFM images, we assigned the structures 1, 2b, 3c, and

4c to the nc-AFM measurements (note the obvious differences in symmetries of the linker-parts of the

structures). Most simulated images were evaluated at the same tip-sample height, except for the image of

2a (0.03 nm higher), and 3b and 3c (0.01 nm lower) due to their different adsorption configurations.

2. Calculated reaction pathway from 1 to 4c

DFTB calculations predict that both 1-cis and 1-trans monomers are nearly isoenergetic on the Ag

(100) surface. In gas phase, however, ab initio computations at the B3LYP/311G** level predict that the

trans isomer is 2.86 kcal/mol more stable than the cis conformer. The average monomer adsorption height

above the Ag(100) surface ranges from 2.6 Å on the frozen slab to 3.0 Å on the free Ag surface, according

to DFTB calculations. The terminal acetylenic carbons are typically anchored at the bridge position on the

underlying Ag surface and adopt a configuration resembling a sp2 hybridization with the terminal hydrogen

atom pointing upwards.

The activation barrier associated with the intermolecular C–C coupling of uncyclized cis-1 with

trans-1 monomers is 1.38 eV on a frozen slab. The resulting dimer 2a has biradical character and features a

central butadienyl linker with two hydrogen atoms pointing upwards and two carbon atoms anchored to

the surface. This geometry is very similar to the one reported by Björk et al.2 Similar alkyne coupling

reactions have been reported for ethynyl functionalized precursors. For instance, branched chains (from

the partial dehydrogenated products) as well as linear polymers were reported for diethynyl-substituted

systems on Au(111) and Ag(111).3 Our dimerization barrier is 1.38 eV, whereas a value of 1.4 eV was

calculated at the DFT level for the 1,3,5-triethynylbenzene (TEB) dimerization on Ag (111)4 and also a

barrier of 0.90 eV was reported for the same process with ethynylbenzene.2 The latter study showed that

the role of the surface for the TEB coupling is to provide anchoring points to the reactants (i.e. restricting

their mobility but with little molecule-surface charge transfer) but also to greatly stabilize the resulting cis




5

intermediate (resembling our 2a) where C–Ag bonds are clearly formed. In line with those results, we also

found the terminal acetylenic carbons to work as anchoring points of our precursors 1 to the Ag surface.

Previous studies2,3,5 state that the most likely reaction pathway is first the direct covalent linking of the

alkynes along similar schemes to those proposed here, followed by a dehydrogenation. For our more

complex precursors, we claim the dehydrogenation step to be substituted by intramolecular H-migrations

that allow the saturation of the radicals generated at several of the isomerization steps. Based on our

statistical analysis, we can exclude hydrogen loss (or competing side reactions that involve hydrogen

stemming from the residual gas): the number of intermediates and products within the reaction pathway

remains constant, which provides strong experimental evidence that no significant number of molecules

undergo such side reactions. Furthermore, our measurements do not show any evidence for the formation

of organometallic compounds as seen in a recent study.6 However, as we have analyzed the majority of the

formed intermediates and products, we can exclude that such mechanisms play an important role in our

system.

A formal [1,3] H-shift in the central linker leads to the eneyne intermediate 2b. On the Ag(100)

surface, however, 2a and 2b are nearly isoenergetic due to the stabilization of radicals in 2a by the

substrate. The terminal enediyne in 2b undergoes a thermally induced C1-C6 cyclization (with a barrier of

0.86 eV on a frozen slab) to form a 1,4-benzyne intermediate, which spontaneously (barrierless) undergoes

C1-C5 cyclization with the internal alkyne to form the a benzo[a]fluorene core. A series of hydrogen shifts

from the central linker to the benzo[a]fluorene leads via 3b to the eneyne 3c. A second thermally induced

C1-C6 cyclization of the enediyne in 3c (with a barrier of 0.63 eV) is followed by a C1-C5 cyclization with the

internal alkyne (with a barrier of 0.25 eV) to form the benzo[b]fluorene core in 4a. A series of H-shifts with

barriers of ~ 2 eV leads to the species 4b. All these hydrogen transfers feature a large activation barrier of

about 2.0 eV, which is in agreement with our previous work7 and gas-phase ab initio calculations.8,9 Finally,

the formation of a buta-1,2,3-triene linker (with a barrier of 0.8 eV) leads to the cumulene product 4c. The

accuracy of the calculations of the critical barrier heights (for the species 2b and 3c) was further improved

by structural relaxations of the adsorbates and the upper two Ag layers, as well as by zero-point energy




6

(ZPE) corrections leading to a slight decrease of the barriers to 0.69 eV (before: 0.86 eV) for 2b and 0.52 eV

(before: 0.63 eV) for 3c, respectively.

The classical barrier for hydrogen transfers can be reduced by nuclear quantum effects via

tunneling and zero point energy effects.10 Inclusion of such effects would, however, not affect the

conclusions of our study: The reaction kinetics are governed by the first barrier and the reaction barriers

for the transformation of 2b and 3c, changes in the barrier heights of other intermediates (which undergo

hydrogen transfer reactions) will have no relevant effect.




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3. Dissipation of energy from molecular dynamics simulations

Figure 2| Dissipation of the kinetic energy calculated by DFTB molecular dynamics simulations. The

images show the kinetic energy (averaged over 1 ps) of each atom of the transient intermediates 2a (first

panel), as well as for the products of the C1-C6 and C1-C5 cyclization, and hydrogen migration steps. Relative

atom sizes have been adjusted for clarity. (Selective dissipation calculations were omitted for 4b since its

extremely small reaction barrier implies that dissipation will not significantly affect the reaction kinetics for

this step).




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4. Calculated timescales of reaction steps and energy dissipation for

the transformation from 2b to 3a

Figure 3| Calculated time evolution of the kinetic energy (KE) of molecule and substrate for the reaction

step from 2b to 3a. The graph depicts a C1-C6 cyclization at t = 0 fs and a C1-C5 cyclization at t ≈ 920 fs

(vertical dotted lines). Results were obtained from a DFTB molecular dynamics simulation at constant

energy over a slab of 4 Ag layers. The instantaneous kinetic energy of the first three upper Ag layers is

shown, with "1st" denoting the layer closest to the adsorbate (the bottom 4th layer was fixed and is not

shown). As required, the total energy (TE; red trace) of the system stays constant. The lower graph shows

the time evolution of relevant C–C bond distances for the newly formed bonds during the C1-C6 cyclization




9

and the C1-C5 cyclization steps. The average bond lengths in the time interval 1100 fs ≤ t ≤ 2000 fs are 1.425

Å and 1.47 Å for the six- and five-membered ring, respectively.

5. Supplementary Movie

The corresponding animated simulation showing the time evolution of the calculated kinetic

energy for the transformation from 2b to 3a can be downloaded from the publisher's website. Each frame

in the movie shows the averaged atomic kinetic energy over 5 fs of the DFTB simulation.

6. Computational methods and details

We model the reaction energetics on the Ag(100) surface by a periodically-repeated 7x7x3 slab

fixed at the coordinates derived from the experimental lattice constant of Ag (4.0862 Å). The surface

normal was along the Z axis. In our previous work, we found that 3 Ag layers were sufficient to converge

energy differences.7 The 7x7x3 slab provides at least 5 Å of lateral separation between the molecule and its

nearest repeated images. The system was then placed in a cubic box of volume 23.1153 Å3 which was made

periodic in all spatial directions. With this cell there is 20 Å of vacuum between the molecular system and

the bottom of the nearest periodic slab image.

We performed Γ point calculations using the density functional based tight binding (DFTB) method

as implemented in the DFTB+ code.11 We used the Slater-Koster DFTB parameters for Ag, C, and H elements

from refs. 12–15 We set the charge self-consistent (SCC) tolerance to 10-9 electrons. We relaxed all molecular

structures until a maximum ionic force below 10-3 eV/Å was achieved. Constrained optimizations were

performed through an interface to DFTB+ implemented in the ASE code.16 We validated selected DFTB

geometries by comparing to those obtained from purely density functional theory (DFT) calculations. For

the latter, we used the real-space projector augmented wavefunction (PAW) method as implemented in

the GPAW code.17 Specifically, we optimized some of our previously-relaxed DFTB geometries until a

maximum force below 0.025 eV/Å was attained. To this end, we employed the local density approximation




10

(LDA) to the exchange-correlation functional level and a grid spacing of 0.2 Å. The rest of parameters were

the same as in our previous work.7 The root-mean-square-deviation (RSMD) between DFT and DFTB

geometries for several relevant steps were less than or equal to 0.12 Å. This result gave us confidence in

the quality of the DFTB results and allows us substantial computational savings. In particular, the use of the

DFTB method affords nearly two orders of magnitude in computational resources savings when compared

to our LDA calculations. Finally, we remark that our DFTB and LDA calculations are missing van der Waals

(vdW) interactions, which may affect energies and the molecule-substrate distance (our average separation

ranges from 2.6 to 3.0 Å for a frozen and free Ag slab, respectively).4,18 However, we expect our conclusions

to be robust with respect to the addition of vdW interactions because these interactions are of minor

importance for radical species that strongly interact with the surface.Also, we found similar reaction

intermediates for the initial dimerization step as a recent full vdW DFT calculation.2

To locate transition states and estimate activation energy barriers, we fixed the distance between

relevant atoms in steps of ~ 0.1 Å while relaxing the other degrees of freedom of the molecule (the Ag slab

was frozen) until a maximum in energy was obtained during the mapping of the energy profile. As the exact

structure and reaction coordinate of the transition state will directly affect the reaction barriers,19,20 we

further refined the transition state geometry and energy profiles by performing nudge-elastic band

calculations in selected cases. We found that the barriers calculated by this method deviate by up to 0.06

eV from the corresponding barriers found by the stepwise procedure.21

To investigate the role of heat dissipation from the transforming intermediates to the Ag surface,

we performed constant-energy (micro-canonical or NVE) molecular dynamics (MD) simulations using the

DFTB method. Initially both the molecule and the upper two Ag layers of the 7x7x3 slab were relaxed (in

contrast to energetics calculations where the whole Ag slab was frozen). The bottom Ag layer was always

frozen in all calculations. A bond constraint was used to keep the initial geometry slightly beyond its

transition state and prevent a chemical reaction during the structural relaxations. Initial ionic velocities

were set to zero so that the initial temperature was also 0 K. This particular choice of ionic velocities, albeit

somewhat artificial, facilitates the subsequent analysis of the MD trajectories because any local heating in




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the system will be solely due to the energy transfer from the reaction location and not to the random

fluctuations of the atomic velocities that follow a Maxwell-Boltzmann distribution. The MD time step was

0.2 fs and the SCC tolerance was 10-5 electrons. The non-equilibrium MD simulations were initiated by

releasing the bond constraint at time zero and we then followed the reaction as it proceeded downhill. We

monitored how atomic kinetic energy (heat) was produced locally (“hot spots”) at the reaction location and

then redistributed throughout the system. Structures and kinetic energies were averaged over 1 ps of MD

simulation once initial energy transients disappeared and the system had reached an energetic plateau. We

checked for finite-size effects by running few MD trajectories on a larger 11x11x3 and 7x7x4 surfaces to

confirm our findings on the (smaller) 7x7x3 slab. We remark that our MD simulations provide a lower

bound for the heat dissipation because we used three approximations: First, in all of our MD calculations,

we set the initial temperature to 0 K to facilitate the analysis of the heat flow in our system. Actual

experiments are conducted at finite temperatures where more phonons are excited and therefore more

efficient heat dissipation results. Second, acoustic phonons are one of the main vehicles for heat

dissipation in a solid. From the computational viewpoint, including such bulk behavior in ordinary MD

simulations is difficult because it would require very large system sizes. Thus, in our calculations there are

many phononic channels suppressed or missing that would lead to an even greater dissipation. In our case,

heat is artificially stored in the two upper Ag layers and in the molecule due to the finite-size limitations,

rather than being continuously drained from the reaction location.22 Third, we chose the initial

configurations close to the transition state along the downhill part of the potential energy surface to

facilitate the chemical reaction during the MD runs.

For the vibrational entropy and zero-point energy (ZPE) calculations, we first optimized the

geometries for each species by relaxing both the adsorbate and the upper two Ag layers (the third (bottom)

Ag layer is always frozen). We then performed a partial normal mode calculation where we only considered

the vibrations of the adsorbate and the upper Ag layer (N = 120 atoms and a total of 3*N = 360 modes).

This entails a calculation and subsequent diagonalization of a 360x360 Hessian matrix (we ignored the

contribution from the bottom two Ag layers) for each species. We observed that the ZPE increases slightly




12

as the reaction proceeds and new bonds are being formed (ZPE4c - ZPE1 ~ 0.57 eV). The ZPE arises mostly

from the higher vibrational modes of the adsorbate (~ 11.5 eV), while the surface contributes little with a

nearly constant factor of ~ 0.77 eV. The vibrational entropies are fairly constant (of the order of 0.042

eV/K) throughout the reaction, except for a small decrease at the transition states, which is consistent with

a more ordered configuration.

For the translational and rotational entropy calculations, we assume that at low coverages the

“mobile" non-radical species (1, 2b, 3c, 4c) are able to freely rotate about the normal axis to the surface

and translate on the surface.23–25 The rotational entropy for a perfect 1D rotor is Srot = kB [��+�� Qrot], where

Qrot = �� )�� is the 1D rotational partition function, T = 573.15 K, h is Planck's constant, I ~

2 x 10-43 kg m2 is the moment of inertia of the adsorbate around the rotation axis z (normal to the surface),

and σ = 1 is the rotational symmetry number. The translational entropy for a perfect 2D gas is Strans =

�� ,where A is the surface area available for the adsorbate and m is its mass,

respectively. This effective area is unknown and was approximated by A ~ � �� , where a is the adsorbate

area and ϴ ~ 0.2 is the total surface coverage of all species as estimated from the scanning probe

measurements. The “mobile" intermediates (2b, 3c, 4c), i.e. the species without carbon radicals, have an

average value of Srot ~ 0.635 meV/K and Strans ~ 1.26 meV/K. We note that vibrations contribute less to the

activation entropies than roto-translations. We must emphasize, however, that these entropy estimates

are upper bounds because surface intermediates are neither completely mobile nor rotate completely

freely as their movement is partially hindered on the surface.




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7. Accuracy of DFTB calculations

To explore the energy landscape of the reaction in Fig. 2 we relied on DFTB calculations, because a

full DFT treatment of this complex reaction pathway is computationally too expensive. We carefully

checked the accuracy of the DFTB calculations for the key steps that mainly govern the reaction kinetics

(transformation steps of 1 to 2a, 2b to 3a, and 3c to 4a)). We performed various tests to validate the results

presented here by comparing selected geometries, barriers, and reaction energies with full-fledged DFT

calculations. To this end, we used the ab initio code GPAW with LDA and PBE exchange-correlation DFT

functionals. We found minor deviations in geometries (root-mean-square deviation of less than 0.12 Å) and

differences of 0.2 to 0.3 eV in activation barriers (see Table 1). We note that the DFTB results are closer to

the LDA results than to PBE results. The difference between DFTB and LDA is comparable to the difference

between LDA and PBE.

values in eV DFTB LDA PBE

ΔE‡ (1 → 2a) 1.379 1.095 1.078

ΔE (1 → 2a) 1.767 1.93 2.035

ΔE‡ (2b → 3a) 0.859 0.881 1.033

ΔE (2b → 3a) 2.692 2.722 2.225

ΔE‡ (3c → 4a) 0.631 0.815 0.962

ΔE (3c → 4a) 3.914 3.715 3.041

Table 1| DFTB/LDA/PBE calculated activation energies (ΔE‡) and reaction energies (ΔE) for the key steps

of the reaction. Calculations were performed using DFTB relaxed geometries (structural relaxation at the

LDA level only marginally affects the values). All values are in eV and do not include ZPE.

We note that the used DFTB Slater-Koster parameters for the organic molecules were extensively

validated by Marcus Elstner and coworkers14,15 and are of B3LYP/6-31G* quality.26 For a benchmark of

36 reaction energies, they found a mean absolute deviation from experiment of 0.54 eV for DFTB,

compared to 0.48 eV for the DFT (local spin density).14 Note the small difference of 0.06 eV between DFT

and DFTB. For a set of 63 organic molecules, the DFTB geometries have an accuracy of 0.014 Å in bond




14

lengths and of about 2 degrees in bond angles with respect to experiment. Vibrational frequencies show

mean errors of 5-7%. The agreement with experiment and GGA calculations is particularly good for the C-C

stretching in aromatic molecules [Table IV of ref. 15]. Recent studies reported an activation barrier of 1.4 eV

for a similar terminal alkyne coupling (1,3,5-triethynylbenzene on Ag(111)) using DFT calculations.27 This

value is in good agreement with our results (ΔH‡ (1 → 2a) = 1.379 eV).

In summary, for the present work, DFTB provides a good compromise between accuracy and

computational effort. Such methodology is recommended for dealing with extremely complicated surface

reactions as ours, where exploring the full reaction pathway via DFT methods is prohibitively expensive.

The outputs of this comparative study can be downloaded from the Novel Materials Discovery

(NoMaD) repository at: http://nomad-repository.eu

8. Three-dimensional renderings

Interactive three-dimensional representations of the relaxed molecular geometries (Fig. 1), the

kinetic energy dissipation calculations (Fig. 2), as well as time evolution of the calculated kinetic energy for

the transformation from 2b to 3a (Fig. 3 and the corresponding movie) can be found online at:

http://alexriss.github.io/intermediates-viewer/

9. Kinetic simulations

The simulations were performed by numerically solving the following system of sequentially-

coupled rate equations:




15

�[�]�� = ��[�]�

�[��]�� = ��[�]� � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��] � ��[��]

�[��]�� = ��[��]

where [�] denotes the concentration of species x (x = 1, 2a, ..., 4c) and �� is the reaction rate constant

associated with the transformation of x. Based on our experimental data, side reactions can be excluded.

Reactions in the reverse direction are neglected (inclusion does not significantly change the results). The

reaction rate constants were determined by the Eyring equation28 � = ��

��‡��

��‡��, where � is the chemical

reaction rate constant, �� is the Boltzmann constant, ℎ is Planck's constant, � is the absolute temperature, ��‡

is the activation entropy and ��‡ is the activation enthalpy for the respective reaction step as estimated from

DFTB calculations. Selective dissipation was modeled by introducing an effective absolute temperature ��

that replaces � in the Eyring equation, with �� = �� . Here �� is the substrate temperature

before the respective reaction step. �� corresponds to the effective temperature of the molecule after it has

gained part of the chemical energy released after the respective reaction step. The increase of the molecular

temperature can be calculated via �� = �� ⁄ , where�� is the increase in

molecular internal energy after the chemical reaction step has occurred and dissipative energy transfer to the

surface has been taken into account, and �� is the molecular heat capacity. The molecular heat

capacities are determined by the vibrational heat capacities, which were calculated based on the quantum

harmonic approximation: �� = �� ∑ � ��)

��

� with �� = ��

��, where � is the

number of atoms of the molecule, and �� are the frequencies of the molecular vibrational modes (obtained

from ab initio calculations). For the relevant temperature range we obtain values of �� for

300 K and �� for 600 K (these values show little variation for different molecular species




16

along the reaction pathway). To solve the rate equations, we use an average temperature-independent value

of �� . To account for entropic effects, we calculated the activation entropies of the species

2b and 3c (��‡ � �� ‡ � ��). 2b and 3c are the only intermediates that undergo a

transformation from non-radical into radical species and thus exhibit large negative values for the activation

entropies (see main text). The activation entropies for all other species were set to 0. A linear temperature

ramp with a slope of 5 K/min was used.

Inclusion of both effects, selective dissipation and entropy, are necessary to explain the experimental

observations. Neglecting entropy (Fig. 3c) or selective dissipation (Fig. 4) in the simulations results in

qualitatively different predicted behavior.

Figure 4| Calculated temperature-dependent relative concentrations of reactant, intermediates and product

determiend by solving kinetic rate equations for the reaction pathway from 1 to 4c. Relative concentrations

of reactant, intermediates, and product when taking into account entropy but neglecting selective dissipation.

Lastly, we want to point out approximations within this approach:

- We do not explicitly account for possible further decrease of the molecular energy through additional

dissipation, such as electronic mechanisms (e.g., plasmon excitations and creation of electron-hole pairs), and




17

dissipation on longer timescales. However, we expect that electronic mechanisms will not significantly change

the selectivity of the surface dissipation since states that mediate electronic dissipation (surface states,

plasmons, electron-hole transitions) have a long-range nature and thus should not be so sensitive to specific

molecular configurations.

- The reaction kinetics will also be affected by contributions from the activation entropy for the initial

dimerization of 1 (we neglect the activation entropy of this step). These contributions, however, are not

expected to significantly affect the stabilization of the intermediates.

10. Large-scale experimental nc-AFM image of the surface after annealing




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Figure 5| nc-AFM image of the Ag(100) surface after two annealing steps. It shows the presence of

monomers, dimers and oligomers at various stages of cyclization (a maximum temperature of 460 K was

reached).

11. Statistical analysis of the reaction progress

Figure 6| Statistical analysis of the relative abundance of monomeric and dimeric species on the surface after

each annealing step. a, nc-AFM image shows 1 deposited on the Ag(100) surface. b, After annealing, uncyclized

dimers (such as b3 and b4), half-cyclized dimers (i.e. dimers consisting of one cyclized and one uncyclized

monomer such as b5 and b6), cyclized dimers (i.e. both monomer parts are cyclized such as b7 and b8) are

observed. c, shows the relative count of the precursors and the dimer species with each subsequent annealing

step from T = 290 K to T = 490 K. The relative counts are plotted in terms of the number of monomer units, i.e.




19

the dimer counts were multiplied by a factor of 2. The number of precursor molecules 1 (uncyclized monomers,

orange trace) gradually decreases as they transform into other species. After the last annealing step, all the

precursor molecules (uncyclized monomers) have reacted and cyclized dimers (black trace) constitute the main

product of the reaction. The graph also reveals a transient increase in the number of uncyclized dimers, as well

as half-cyclized dimers. This indicates that the uncyclized monomers first form uncyclized dimers, then half-

cyclized dimers, which eventually transform into cyclized dimers. The data for this plot was obtained by

statistical analysis of 1058 molecules.

The dimers b3 to b8 in Fig. 6 are not part of the reaction pathway presented in the main text. Various

other uncyclized, half-cyclized and cyclized dimers can be found on the surface. Such species are formed by

different coupling of monomer units and thus represent intermediates and products of competitive reaction

pathways.




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