On-surface synthesis platform for highly branched oligomers based on sequential C—C coupling and C—H activation of carbenes

Domain: neuroscience
Published: 2026-01-30
Editorial outcome: minor_revision

Abstract
On-surface synthesis is an emerging field for fabricating low-dimensional nanostructures. While carbenes are versatile reactive intermediates in solution-phase organic synthesis, they have rarely been explored in on-surface synthesis. Here, we demonstrate the versatility of carbenes in synthesizing highly branched zero-dimensional oligomers with distinct structures on a metal surface by combining bond-resolved scanning tunneling microscopy imaging, manipulation, X-ray photoelectron spectroscopy, surface infrared spectroscopy, and ab initio theoretical modeling. We synthesize highly symmetric branched oligomers through the C−C coupling of two carbene molecules to form a core of oligomers, followed by C−H activation of the core with up to four additional carbene molecules to create branches. Branched oligomers of lower symmetry are formed through cyclodehydrogenation of the highly symmetric oligomers. Our on-surface synthetic strategy based on C−H activation of carbene building blocks provides a platform for the design and synthesis of highly branched zero-dimensional oligomers with distinct structures.

Introduction
On-surface synthesis offers opportunities to fabricate low-dimensional carbon-based nanostructures through various chemical reactions, such as Ullmann coupling1, Glaser coupling2,3, and dehydrogenative coupling4–7. In recent years, many intriguing nanostructures have been synthesized and characterized on surfaces, ranging from zero-dimensional (0D) fullerenes8 and cyclocarbons9 over one-dimensional (1D) polymers5,10 and graphene nanoribbons11 to two-dimensional(2D)networks12. However, the synthesis of nanostructures gets more challenging with increasing complexity. While generating highly reactive intermediates is essential for the synthesis, controlling these intermediates is necessary to avoid undesired side products and reduced selectivity13,14. Developing strategies for a precise and efficient coupling of reactive intermediates is of vital importance for the synthesis of sophisticated low-dimensional nanostructures.

Carbenes are archetypal reactive intermediates of key importance in organic syntheses, undergoing reactions such as dimerization, cyclopropanation, addition to C–C bonds, and insertion into C–H bonds15–17. The high reactivity of arylcarbenes (such as diphenylcarbene or fluorenylidene) results from their highly asymmetric electron distribution at the carbene center, resembling a 1,1-zwitterionic structure18. Despite their versatility in solution chemistry, the use of carbenes in on-surface synthesis has been limited to simple C–C couplings, forming either dimers19,20 or one-dimensional polymers21–23. Carbene insertion into C–H bonds, a promising strategy for C–H functionalization24, has not yet been integrated into on-surface synthesis protocols.

In this work, we demonstrate the feasibility of carbene-based C–H insertion on a silver surface. Arylcarbenes dimerize via C–C bond formation, and they insert into the C–H bonds of such dimers. Following a controlled reaction sequence of the two reaction steps, highly branched 0D oligomers composed of six carbene units are synthesized (Fig. 1). We characterize the reaction intermediates and the final products of carbenes in detail by bond-resolved scanning tunneling microscopy (STM) imaging and manipulation, X-ray photoelectron spectroscopy (XPS), surface infrared (IR) spectroscopy, and density functional theory (DFT) calculations. Our study expands the on-surface synthesis toolbox, paving the way to synthesize highly branched 0D oligomers with distinct structures using carbenes as building blocks.

Results
On-surface synthesis of carbene 1a
We use 1,8-diaza-9-diazofluorene 1a as a precursor for the synthesis of 1,8-diazafluorenylidene 2a on an Ag(111) surface. The surface is beneficial because Ag-catalyzed carbene reactions are useful for various synthetic transformations in organic chemistry, yet they are less explored compared to reactions catalyzed by gold25. Studying carbene reactions on well-defined single-crystal silver surfaces provides mechanistic insight into silver-catalyzed carbene reactions in solution. Moreover, Ag surfaces are more promising because of the weaker binding of carbenes to Ag(111) than to Au(111) surfaces26. It results from a stronger back-donation from the carbene to the gold surface than to silver at comparable donation from the metal to the carbene26.

Upon deposition at 50 K, precursor 1a self-assembles into ribbon patterns (Fig. 2a). Attractive interactions between nitrogen atoms and vicinal hydrogen atoms from a neighboring molecule promote the ribbon assembly via hydrogen bonds (Supplementary Fig. 1). According to DFT calculations and supported by IR spectroscopy (Supplementary Fig. 2), 1a is adsorbed with its π-system parallel to the surface (Fig. 2f, bottom). The adsorption geometry is similar to the related 9-diazofluorene 1b, where the two nitrogen atoms at positions N1 and N8 are replaced by CH groups (Fig. 1). Analysis of the N 1s peak in XPS spectra confirm the non-dissociative adsorption of 1a at 87 K (Supplementary Fig. 3).

9-Diazofluorene 1b has been dissociated on the same surface into fluorenylidene 2b and an N2 molecule by inelastic electron tunneling (IET) manipulation at an electron energy of 1.5 eV27. Here, IET manipulations of individual molecules 1a within the ribbon lead to bright protrusions at a low manipulation voltage of 1.0 V (Fig. 2b–d). These protrusions cannot be converted back to 1a. More molecules within an extended region around the point of electron injection react to product molecules at a higher manipulation voltage of up to 2.0 V (Supplementary Fig. 4). Based on the IET-induced dissociation of 9-diazofluorene 1b into fluorenylidene 2b27, the product molecules are assigned to carbenes 2a. The apparent height of 2a is 70% larger than 1a at a bias voltage of 50 mV (Fig. 2e). Such a height increase cannot be explained by the charge transfer from the surface, since carbene 2b, with a similar charge transfer to 2a (0.5 e vs. 0.6 e), is imaged even less high than its precursor 1b27. It suggests that the product molecules are adsorbed in another geometry than precursor 1a.

DFT calculations support the identification of the bright protrusions as perpendicularly-adsorbed carbene 2a. The calculations reveal an adsorption of carbene 2a via the reactive carbene center with the π-system of the molecule tilted with respect to Ag(111). The angle of 68° between the molecular plane of carbene 2a and the surface plane contrasts the close-to-parallel geometry of precursor 1a (Fig. 2f). The highest part of carbene 2a above the surface plane is, at h = 574 pm, around 80% higher than that of precursor 1a at h = 311 pm (Fig. 2f). This change is nicely reflected in the STM images, despite the fact that apparent heights in STM are influenced by both the geometrical heights of adsorbates and their local density of states28. The tilted geometry of 2a is further corroborated by IR spectroscopy based on the surface selection rule29 (Supplementary Fig. 2).

The carbene center of 2a is situated at a bridge site of Ag(111). Its calculated binding energy of 5.12 eV is significantly higher than the 2.95 eV of carbene 2b on the same surface27. The difference between the carbenes 2a and 2b is that the backbone of 2a comprises two nitrogen atoms next to the carbene center (Fig. 1). The enhanced binding energy of carbene 2a results from the additional interaction of the lone pairs of the two nitrogen atoms with Ag atoms. The two atoms are at a distance of approximately 3a along an Ag<112> direction, with a the lattice constant of the Ag(111) surface (Fig. 2f, right). An alternative geometry with a planar carbene 2 bonded to an Ag adatom (adsorbed atom) is not possible because there are no adatoms released from the step edges on Ag(111) at the maximum temperature of 52 K during irradiation30. For the discussion of alternative adsorption geometries, see Supplementary Note 2.

It is noteworthy that carbenes 2a and 2b differ fundamentally from the widely studied N-heterocyclic carbenes (NHCs)31. As σ donors, NHCs bind strongly to metal surfaces, leading to self-assembled monolayers with adatom extraction32–34. In contrast, carbenes 2a and 2b interact with the metal surface both as σ donors and π acceptors with a net electron transfer from the metal to the molecules (0.6 e for 2a and 0.5 e for 2b). For an in-depth discussion, see Supplementary Note 4.

Dimerization of carbene 1a
Having produced carbenes 2a locally on the surface by IET manipulation, we perform photolysis of 1a to carbene 2a on the entire Ag(111) surface. Irradiation at 365 nm for 3 h converts all the precursor molecules of 1a to 2a, the same species as obtained by IET manipulation (Fig. 3a, b; for details, see Supplementary Fig. 4). We confirm the dissociation of 1a by XPS. After irradiation, the N 1s peaks associated with diazo groups disappear, indicating the desorption of the N2 byproduct (Supplementary Fig. 3). Thus, the use of diazo compounds as precursors provides a residue-free on-surface synthesis route. It is complementary to the widely used Ullmann coupling, which produces halogen byproducts that chemisorb on the surface, hinder the diffusion of reaction intermediates35,36, and promote alternative reaction pathways37.

Carbene 2a aggregates into larger islands during subsequent annealing at temperatures up to 240 K (Supplementary Fig. 5). Other structures form upon annealing at even higher temperatures. Annealing at 292 K leads to chains oriented along the Ag<110> directions. The chains consist of alternating regularly spaced bright ellipsoidal protrusions and dimer-like species. The latter contain two pairs of three protrusions (Fig. 3d, e and Supplementary Fig. 6). Based on their apparent heights, we assign the ellipsoidal bright protrusions to unreacted carbene molecules 2a (Supplementary Fig. 7). Annealing at a higher temperature of 375 K converts the unreacted carbenes 2a to six-protrusion species. It increases the abundance of the six-protrusion species from 57.2% to 80.2% (Fig. 3h). In addition, a butterfly-shaped species is synthesized at the higher annealing temperature (Fig. 3g).

The geometry of the six-protrusion species is better visible in one of the rare isolated species on the surface (Fig. 3e). Two rows of bright protrusions are distinguished, each displaying three protrusions, with the middle ones elongated. As the six-protrusion species maintains its integrity during lateral manipulation, its internal bonding is stronger than that of the individual constituents to the surface (Supplementary Fig. 6). We propose that this species is an organometallic intermediate 3a (Fig. 1), comprising two carbene molecules linked by three Ag adatoms. In an optimized structure, the two diaza-fluorenyl groups adsorb at slightly different angles to the surface plane (Fig. 3j). The different angles in the calculated geometry are reflected in different shapes of the two halves of the isolated organometallic intermediate 3a in the STM images. The three protrusions on the right side are more elongated than those on the left side (Fig. 3e, i). The shape of the organometallic intermediate 3a depends on its neighbors. It suggests a geometric flexibility induced by non-directed intermolecular interactions (for details, see Supplementary Notes 7 and 8). Organometallic complexes are typical reaction intermediates in on-surface syntheses14,38,39.

At a higher annealing temperature of 375 K, some of these intermediates react to a butterfly-shaped species. We assign this species to the metal-free dimer 4a (cf., Fig. 1). This assignment is confirmed by direct deposition of the dimer 4a on the Ag(111) surface (see Supplementary Note 9 for its synthesis in wet chemistry). It reveals that the wet-chemistry and on-surface synthesized dimer 4a are identical. On the surface, the dimer 4a is formed from the organometallic intermediate 3a by C–C coupling under the release of the Ag adatoms (Fig. 1). The formation of organometallic intermediates 3a and dimers 4a is supported by a splitting of the N 1s peak in the XPS spectrum (Supplementary Fig. 3c).

C–H activation by carbene 1a
The organometallic intermediate 3a exhibits a high thermal stability even at 375 K, preventing its complete conversion to the dimer 4a. It enables a carbene reaction beyond C–C coupling at higher temperatures. Thus, annealing at 600 K converts the dimers 3a and 4a into a series of oligomers (Fig. 4a, b(i)–g(i)). Bond-resolved STM images recorded with a functionalized tip40 confirm these oligomers as substituted dimers 5a to 10a (Fig. 4b(ii)–g(ii), b(iii)–g(iii)). Up to four diaza-fluorenyl groups are attached to a dimer 4a core (Fig. 4b(iv)–(iv)). The covalent bonds between the dimer 4a core and the diaza-fluorenyl branches are further supported by the structural integrity of these oligomers during lateral manipulations across the surface. It is noteworthy that the C–H activation exhibit high selectivity, attaching exclusively at the C3(3’)/C6(6’) positions of the dimer 4a core (Fig. 1).

Such a site-specific C–H activation is attributed to the steric hindrance between the diaza-fluorenyl branch and the core of dimer 4a. This steric hindrance only exists under the two-dimensional confinement on the surface41–43. It facilitates the synthesis of the 0D oligomers composed of one core and four branches. As carbene 2a is largely absent on the surface after annealing at 375 K (Figs. 3h), 2a must be generated by cleavage of the organometallic intermediate 3a at 600 K. Carbene 2a formed at such a high temperature readily reacts with dimer 4a on the surface to form the substituted dimers.

The functionalization of C–H bonds by carbene insertion is a widely used strategy in solution24. It proceeds through a concerted process of C–C bond formation and hydrogen atom migration, thereby generating sp3 carbon atoms44. In on-surface synthesis of polycyclic aromatic hydrocarbons at elevated temperatures, both dehydrogenation to sp2 carbon atoms45–47 and preservation of sp2 carbon atoms48–50 have been reported. To explore whether the sp3 carbon atoms persist in substituted dimers 5a to 10a, we perform IET manipulations and confirm the result by dI/dV spectra and maps (Supplementary Fig. 11). Substituted dimers 5a to 10a contain non-dehydrogenated sp3 carbon atoms according to these experiments.

Intramolecular cyclodehydrogenation
The branched 0D tetrasubstituted dimer 10a, formed through C–H activation induced by carbenes, is highly symmetric and exhibits two mirror planes (Fig. 1). To tune the symmetry of such branched structures, we employ intramolecular cyclodehydrogenation, a reaction widely used in on-surface graphene nanoribbon synthesis11. However, the pyridine subunits of tetrasubstituted dimer 10a prevent the two diaza-fluorenyl units in the core from further reaction (Fig. 1). In contrast, such a cyclodehydrogenation reaction is feasible for the tetrasubstituted dimer 10b. It produces a fused tetrasubstituted dimer 11 with only one mirror plane (Fig. 1).

We synthesize tetrasubstituted dimer 10b using carbene 2b as a building block. Following the same procedure used to form carbene 2a, we photolyze precursor 1b using 365 nm irradiation to form carbene 2b on the Ag(111) surface (Supplementary Fig. 12). The formed carbene 2b consists of an ellipsoidal protrusion next to a depression. The depression is related to a reduced density of states because the carbene draws electron density from the metal27.

Upon annealing at 240 K, carbenes 2b form organometallic intermediates 3b (Supplementary Fig. 13). It contrasts carbene 2a, which remains stable at 240 K (Supplementary Fig. 5), and requires annealing at 292 K to form organometallic intermediates 3a (Supplementary Fig. 6). The bright protrusion in the dimer indicates an Ag adatom connecting two carbenes 2b (Supplementary Fig. 12). While many molecules of the organometallic intermediates 3b persist upon annealing at 375 K, some oligomers form. These oligomers consist of bifluorenylidene (dimer 4b) cores and fluorenyl branches. It indicates C–C coupling and C–H activation of carbene 2b at 375 K (Supplementary Fig. 13). Annealing at 500 K converts all organometallic intermediates 3b to oligomers that agglomerate to larger structures (Supplementary Fig. 14). Lateral manipulation to separate these agglomerates identifies substituted dimers of core structures with one to four branches (Fig. 5a–e). It is similar to the substituted dimers formed via C–C coupling and C–H activation of carbene 2a (Fig. 4b–g). The core structures exhibit two brighter and two less bright protrusions at opposite corners of a tetragon. It is consistent with a twisted geometry of dimer 4b (Supplementary Fig. 14). Both carbenes follow similar C−C coupling and C–H activation reactions on Ag(111) to form highly symmetric oligomers. However, the reactions proceed at different reaction temperatures because of their distinct surface interactions.

The core structures of the two tetrasubstituted dimers 10a and 10b differ (Fig. 1). The dimer 4a core of 10a has nitrogen atoms at positions N1(8)/N1’(8’). In contrast, the dimer 4b core of 10b has carbon atoms at positions C1(8)/C1’(8’). The twisted structure of the dimer 4b core facilitates its cyclodehydrogenation at 600 K (Fig. 5f). Upon cyclodehydrogenation on either side, the core structure is planar. It prohibits further cyclodehydrogenation on the opposite side. Cyclization at both sides would lead to a non-planar bowl-shaped structure, which is not observed upon annealing at 600 K (for details, see Supplementary Note 14).

Cyclodehydrogenation of asymmetric substituted dimers, such as the monosubstituted dimer 5b (Fig. 5a), yields two types of fused monosubstituted dimers 12 and 13 (Fig. 5g, h). In contrast, molecules with central inversion symmetry yield only one type of fused tetrasubstituted dimer 11 (Fig. 5i). Tetrasubstituted dimers 10b and fused tetrasubstituted dimer 11 have distinct structures: 10b has two mirror planes, while 11 has only one (blues lines in Fig. 1). We generate nine types of fused substituted dimers in two symmetries through cyclodehydrogenation of substituted dimers synthesized from carbenes 2b (Fig. 5a–e and Supplementary Fig. 15). These dimers either have or lack a mirror plane. Bond-resolved STM images confirm the successful cyclodehydrogenation (Fig. 5g–I and Supplementary Fig. 15). Our results demonstrate that intramolecular cyclodehydrogenation is a feasible approach for tuning the structures of highly branched oligomers on surfaces.

In summary, we have established an on-surface synthesis strategy based on carbenes as building blocks. Highly branched oligomers are synthesized through sequential C–C coupling and C–H activation of the carbenes. The C–C coupling generates dimer cores, which subsequently participate in cross coupling with additional carbenes via C–H activation. The created oligomers contain one to four branches. The success of the synthetic strategy is illustrated using two structurally similar carbenes, one heterocyclic with two pyridine moieties and the other based on a hydrocarbon skeleton. Both carbenes follow the same controlled reaction pathway upon annealing, despite their significantly different surface binding energies (5.12 eV vs. 2.95 eV). An essential ingredient of our strategy is the formation of thermally highly stable organometallic intermediates. Their formation prevents the complete conversion of the two carbenes to C–C coupled dimers. It enables the subsequent C–H activation at elevated temperatures to form symmetrically branched oligomers. Intramolecular cyclodehydrogenation is only feasible for hydrocarbon-based oligomers, leading to less symmetric oligomers.

Our proof-of-principle study establishes a platform for synthesizing structurally distinct branched oligomers on surfaces. The potential applications of this platform are promising. First, using diazo compounds as precursors of reactive carbenes offers a residue-free on-surface synthesis route that complements the widely used Ullmann coupling on surfaces, thus broadening the toolbox of on-surface synthesis. Second, this approach can be expanded to synthesize various N-doped 0D oligomers by replacing C2, C4, C5, or C7 atoms in carbene 2b with N atoms. Moreover, the oligomer size can be tuned by tailoring the dimensions of the carbenes. Finally, this approach could be extended to synthesize low-dimensional nanostructures on nonmetallic surfaces. The photo-induced carbene formation does not necessarily require the catalytic effects of a metal surface. The subsequent carbene coupling could be initiated by co-adsorption of single Ag atoms. The platform thus paves the way to synthesize functional materials with applications in nanoelectronics.

Methods
Experimental details
The experiments were performed in three UHV systems with similar facilities for sample preparation and molecule deposition. The first system is equipped with a low-temperature STM (Unisoku, base pressure of 1.0×10−10 mbar), the second with an X-ray photoelectron spectrometer (Specs, base pressure of 4.0×10−10 mbar), and the third with a vacuum Fourier transform infrared spectroscopy (FTIR) spectrometer (Bruker, VERTEX 80V) coupled to an IR chamber (PREVAC, base pressure of 7.0×10−10 mbar).

Sample preparation
The Ag(111) surfaces were cleaned by repeated cycles of 10 min ion sputtering and 10 min annealing at 900 K. In the STM system, the surface was sputtered with 1.0 keV Ne+ at 3×10−5 mbar, yielding an ion current of 1 μA. In the XPS system, the surface was sputtered with 1.3 keV Ar+ at 3×10−6 mbar, yielding an ion current of 12 μA. In the IR system, the surface was sputtered with 1.0 keV Ar+ at 1×10−5 mbar, yielding an ion current of 20 μA.

Molecule deposition
The depositions of precursor 1 and dimer 4a were performed in molecule deposition chambers separated from the main chambers of the set-up by gate valves. For the synthesis of 1 and 4a, see Supplementary Note 15. For the deposition of precursor 1, freshly prepared 1 was transferred in an argon atmosphere into a UHV-cleaned quartz tube sealed by an angle valve, called molecule deposition unit. After loading the molecules, the molecule deposition unit was attached to a molecule deposition chamber, a chamber separated from the preparation chamber of the set-up by a gate valve. The quartz tube was immersed in a cooling bath with an ethanol/LN2 mixture, kept always below 253 K, except during deposition, to avoid thermal dissociation of the precursor. 1 was purified by freeze-pump-thaw cycles; the purity of its vapor was checked by a mass spectrometer. For the deposition of 1a, the bare Ag(111) surface was placed on a LN2- or LHe-cooled manipulator in the preparation chamber of the STM system. Molecules were dosed through the gate-through valve from the molecule deposition chamber. Thereby, the real pressure at the surface is orders of magnitude lower than the pressure measured in the molecule deposition chamber.

For the STM system, 1a was deposited on Ag(111) at 50 K for 133 s and 313 s at a pressure of 2.4×10−7 mbar in the molecule deposition chamber prior to opening the gate-through valve. 1b was deposited on Ag(111) at 85 K for 163 s at a pressure of 2.1×10−7 mbar in the molecule deposition chamber prior to opening the gate-through valve. Dimer 4a was deposited from an organic molecular beam evaporator (OME from MBE Komponenten). The molecule was sublimed at 478 K and deposited on Ag(111) at 140 K for 600 s. After deposition, the samples were transferred to the STM head. The sample temperature increased to 70 K during the transfer.

For the XPS system, 1a was deposited on Ag(111) at 87 K for 180 s at a pressure of 2.0×10−6 mbar in the molecule deposition chamber prior to opening the gate-through valve. For the IR system, 1a was deposited on Ag(111) at 105 K for 300 s at a pressure of 5.0×10−7 mbar in the molecule deposition chamber prior to opening the gate-through valve.

The adsorption temperatures differ slightly due to the different cooling efficiency of the LN2-cooled manipulators. They are well below the thermal dissociation temperature of 1a and 1b.

For the STM and XPS system, the photolysis of precursors 1a and 1b was induced by a mercury lamp (100 W, Müller GmbH Elektronik-Optik) with a 365 nm bandpass filter (Edmund Optics GmbH) similar to earlier experiments51. In the STM system, the Ag(111) surface was in the STM head during irradiation. The sample temperature increased to 52 K during the 3 h irradiation of precursor 1a, and was below 60 K during stepwise irradiation of precursor 1b with a total time of 23.2 h. In the XPS system, the sample temperature remained constant at 87 K during irradiation. An irradiation time of one hour corresponds to a photon dose of 2.2 × 1016 photons/mm2 for the STM system and 1.0 × 1017 photons/mm2 for the XPS system. In the IR system, the photolysis of precursor 1a was induced with a 365 nm LED light (30 W, Windfire). An irradiation time of one hour corresponds to a photon dose of 4.7 × 1017 photons/mm2. The sample temperature remained constant at 105 K during irradiation.

STM measurements
STM images were recorded with a Pt/Ir tip at 5 K. The bias voltage was applied to the sample. Constant-height STM images were acquired using a functionalized tip with the feedback loop closed at a set point on the Ag(111) surface. For direct inelastic electron tunneling (IET) manipulation28, the tip was positioned above a chosen part of the molecule, and the feedback loop was switched off. A voltage was ramped from 0.01 V to 1.0 V, 2.0 V, or 2.5 V, while recording the current-voltage (I–V) trace. A steplike change in the tunneling current indicated a successful manipulation. Indirect IET was performed by injecting electrons into the sample at 2 V and 110 pA for 10 s52. For lateral manipulation, the STM tip was positioned above a chosen part of the molecule and approached by reducing the tunneling resistance from a typical value of 10 GΩ to 250 kΩ. At this resistance, the tip-molecule interaction is strong enough for manipulation. The STM tip was then moved across the surface along a predefined path in constant-current mode. At its final position, the tip was withdrawn to the imaging distance at the original resistance. The manipulation success was verified in a subsequent STM image.

The dI/dV spectra were recorded in lock-in technique by adding a 20 mV modulation at 413.3 Hz to the bias voltage. The dI/dV maps were recorded at the chosen voltages by recording the lock-in signal at each pixel with the feedback loop on.

The STM topographic images were processed using WSxM53. For the Laplace filtering, each STM image pixel is recalculated by multiplying it with the following matrix:

M = 
0 1 2 2 1 0
1 2 4 4 2 1
2 4 -4 -12 -4 4 2
2 4 -4 -12 -4 4 2
1 2 4 4 2 1
0 1 2 2 1 0 (1)

XPS measurements
XPS was performed using a Mg Kα X-ray source with a power of 300 W. The photoelectrons were collected at an angle normal to the surface by a hemispherical analyzer (PHOIBOS 100 from Specs) equipped with a multi-channel tron detector. The binding energy was calibrated at the Ag 3d5/2 peak centered at 368.3 eV. The spectra were analyzed using the commercial software CasaXPS54.

The molecule peaks in the N 1s spectra were processed before peak fitting. First, a linear background and the satellite peak of the pristine Ag(111) surface was subtracted, with weights based on the corresponding Ag 3d5/2 peaks. Second, the peaks were normalized to the intensity of their corresponding C 1s peaks. Finally, the peaks were fitted with asymmetric Gaussian/Lorentzian product function.

IRRAS measurements
The IRRAS measurements were performed in reflection absorption mode at a fixed incidence angle of 80° with a resolution of 4 cm−1. The optic bench was evacuated to eliminate absorption from gas-phase species (e.g., H2O and CO2) in the optical path. The infrared reflection absorption spectra were obtained by subtracting a background spectrum recorded before molecule exposure. Each IR spectrum represents an average of 1024 scans.

Computational details
The calculations were performed with the Quantum-ESPRESSO package55. The metal surface was simulated with a silver slab comprising four layers of Ag(111) using (6×5) atoms in each layer. For the calculations of species 1a and 2a, the bottom two layers were kept fixed at the value of the experimental lattice constant. The rest of the structure was optimized. For species 3a, the surface atoms (6 × 6 atoms per layer) were kept fixed at the value of the experimental lattice constant. The organic fragments and the three Ag adatoms were allowed to move during the optimization. The atomic simulation environment (ASE)56 was used to construct the slabs. The PBEsol functional was used for all calculations, employing D3 dispersion corrections to consider the van der Waals interactions57,58. Pseudopotentials with a wave function cut-off of 50 Ry and a charge density cut-off of 600 Ry were used. The Brillouin zone was sampled using the gamma point only algorithm, as implemented in Quantum-ESPRESSO. The adsorption distances were calculated as the distance between the adsorbed atoms and the plane formed by the first layer of the surface atoms.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "This manuscript is a continuation of the group's previous work on carbenes on metal surfaces. Here, the authors studied the\nreactions of carbene molecules on Ag(111) where 0D oligomers were formed by sequential C-C coupling and C-H\nactivation, through inelastic electron tunneling (IET) operation, photolysis and thermal control. They also modeled the\nadsorption configuration using density-functional theory (DFT) calculations. Overall, although this work may expand the\nscope of carbene chemistry on surfaces, both the significance and data quality do not meet the requirement of Nat.\nCommun.. In particular, the resolution of BR-STM is not high enough so that the assignment of each structure is not valid.\nApart from high-resolution BR-STM and qPlus nc-AFM, spectroscopic techniques like XPS, NEXAFS, IR, or\nRaman should be performed to elucidate the evolution of reaction intermediates. In addition, the English gramma should be improved.\nTherefore, I recommend the resubmission of the manuscript in Nat. Commun. or to a more specialized journal (e. g. ACS\nNano, Chemical Science) after addressing all the major points above and also scientific issues as listed below.\nMajor issues :\nA five membered ring in a branch of the products (dimers 10, 11) contains a sp3 carbon atom, as shown in Fig. 1 and\nfollowing associated figures. How can the authors exclude that a H atom is removed during annealing? The BR-STM\nimages rather suggest a planarized adsorption configuration of these products on Ag(111), which implies the sp3 carbon\natoms transformed into sp2 carbon atoms (a dehydrogenation occurred). This is very common in on-surface chemistry, in\nparticular in the formation of magnetic carbon-based structures (e.g. J. Am. Chem. Soc. 2025, 147, 23, 19530–19538;\nAngew. Chem. Int. Ed. 2023, 62, e202307884; ACS Nano 2023, 17, 20, 20237–20245).\nOnce the dehydrogenation reaction occurs, the molecules will probably become open-shell, although the magnetism might\nnot be detected because of the charge transfer from low-work-function Ag substrate to the molecules. However, STS\nanalysis and dI/dV maps of molecular orbitals will offer a guidance, which is thereof suggested to be done.\nMinor issues :\n1) The structure in Fig. 4g(i) is not clearly indicated in Fig. 4a. The authors should highlight this species in Fig. 4a. Similarly,\nin Fig. S4, the correspondence between Fig. S4a and Fig. S4f is not clear. It would be advisable to label the relevant\nstructure in Fig. S4a.\n2) It was mentioned that the constant height STM image is processed with a Laplace filter. However, this images are\nsignificantly distorted as shown in Figs. 4b(ii)-g(ii) and Figs. 5g(ii)-i(ii). I suggest that the authors provide the original images\nin the Supplementary Information.\n3) It seems that some N-N bonds are also formed according to BR-STM images in Fig. 5.\n4) In Fig. 5, the authors describe the dehydrogenation of the tetrasubstituted dimer 10b to form the fused tetrasubstituted\ndimer 11. Theoretically, it is possible to remove four hydrogen atoms within the molecule (rather than just two) to achieve\ncyclization. The authors should add some discussion to justify this. Did the authors anneal the sample to a higher\ntemperature?\n5) While the authors discuss the correlation between reaction temperature and product distribution, I recommend that they\nalso consider the reaction energy barriers and transition states using DFT to rationalize the reaction pathways.\n6) English gramma. JUST FOR EXAMPLE.\n“Developing strategies for precisely and efficiently coupling reactive intermediates is crucial for synthesizing sophisticated\nlow-dimensional nanostructures”\n“It is important to note the fundamental differences between carbenes 2 and the N- heterocyclic carbenes (NHCs) which are\nmore frequently on surfaces, which are of key importance to understand the surface reactivity of 2.”", "reviewer_2": "The manuscript entitled: “On-surface synthesis platform for highly branched oligomers based on sequential C–C coupling\nand C–H activation of carbenes” is a thorough study that employs two strategies for the formation of carbenes.\nThe work presents outstanding data, and the overall presentation is clear. The figures are also clear and self-explanatory. It\nis a very good work for the area of on-surface synthesis.\nHowever, I have some queries about it:\n1. Carbene 2a is formed either by light (Fig. 3) or tip electrons (Fig. 2). The authors claim that the same structure is formed\nbased on a height comparison. However, I have several concerns regarding this claim:\nWhen electrons are involved, the structural model shown in Fig. 2e seems to be quite accurate, as the transformation\nappears to be local and occurs in the middle of an island. However, when photons are used, the entire island appears to\nshow an increase in height. There are several issues I observe:\n1.1. Looking closely at the STM images, after light irradiation, it appears that “2a” is flat rather than nearly vertical. The most\nlikely scenario is that “2a” reacts with an adatom to form a planar structure, similar to the model proposed for “3a.” Have the\nauthors considered a simpler model for the case of light? How does it compare in terms of DFT energy?\n1.2. It is intriguing that Figs. 1e and S2c and f show a height increase of exactly 62 pm in all cases. While this value may\nhave an error, the authors should present a height histogram across different images and structures to convince the reader\nthat the increase is indeed the same (within the error bar) in all cases.\n1.3. Have the authors considered the possibility that the height increase could be due to electron transfer rather than a\nstructural change?\n1.4. The N2 groups are quite “fragile,” and I wonder whether the mechanism of removal after light-irradiation is correct, or if\nthe increase in temperature caused by 3 hours of irradiation is what actually leads to the removal of these groups. Have the\nauthors attempted thermal removal?\n1.5. It is unfortunate that the authors did not follow the reaction using XAS or XPS (at synchrotron), as this could have\nconfirmed some of the proposed mechanisms.\n2. The main drawback of the proposed mechanism is the lack of selectivity (see the dispersion of products in Fig. 4a). This is\na known issue, particularly in C–H dehydrogenation reactions. Can the carbene-based oligomer formation be directed and\ninduced in a more selective manner, perhaps through a more directional Ullmann coupling? This could improve the\nselectivity.\n3. Similarly to query 1.2, have the authors considered the possibility that in structure “3a,” the final product might involve a\nsurface metal atom rather than an adatom? DFT calculations could be helpful in addressing this.\n4. Why did the authors choose Ag? What about Au? It is likely that gold would result in more diffusion, less interaction, and a\nhigher number of adatoms, potentially leading to more complex structures. A brief discussion of how the choice of surface\naffects the results would be valuable.\n5.- Making carbenes into oligomers is important, but doing so on a metal surface reduces the applicability of those\noligomers. The article might be much more sound if the authors managed to perform the reaction on an insulating surface.\nThis could work for “2a,” but not for the C–H dehydrogenation, as C–H cleavage typically requires a catalyst. However, the\nauthors could evaporate \"adatoms\" to create a single-atom catalyst. This is just a speculative idea. Of course, this is not\nbeing requested for the manuscript publication.", "reviewer_3": "This is an elegant study on C-C coupling in carbene molecules, in the context of \"on surface synthesis\". Efforts in using\nsurfaces to obtain planar conjugated structures started less than three decades ago and are becoming increasingly popular.\nThis particular investigation focuses on obtaining highly branched oligomers.\nThe concept and results are original and the study was conducted methodically and rigorously.\nTypically the use of adjectives such as \"novel\" are discouraged, for fairly obvious reasons (novel platform... if this were not\nnovel, we shouldn't even be discussing it).\nMy main concerns are:\n- the references. At this point, forty references for this kind of study is a bare minimum.\n- the conclusions are too dry. I encourage the authors to describe a broader outlook, in the form of perspectives for future\nwork."}, "author_response": "Response letter to reviewers for manuscript NCOMMS-25-37132-T\nComments are in black, replies in blue, and amendments to the manuscript in red.\nReviewer #1\nThis manuscript is a continuation of the group's previous work on carbenes on metal surfaces.\nHere, the authors studied the reactions of carbene molecules on Ag(111) where 0D oligomers\nwere formed by sequential C-C coupling and C-H activation, through inelastic electron\ntunneling (IET) operation, photolysis and thermal control. They also modeled the adsorption\nconfiguration using density-functional theory (DFT) calculations. Overall, although this work\nmay expand the scope of carbene chemistry on surfaces, both the significance and data\nquality do not meet the requirement of Nat. Commun.. In particular, the resolution of BR-STM\nis not high enough so that the assignment of each structure is not valid. Apart from high-\nresolution BR-STM and qPlus nc-AFM, spectroscopic techniques like XPS, NEXAFS, IR, or\nRaman should be performed to elucidate the evolution of reaction intermediates. In addition,\nthe English gramma should be improved. Therefore, I recommend the resubmission of the\nmanuscript in Nat. Commun. or to a more specialized journal (e. g. ACS Nano, Chemical\nScience) after addressing all the major points above and also scientific issues as listed below.\nReply: We thank the reviewer for the helpful comments and suggestions on improving our\nmanuscript. As recommended, we have performed XPS and IR measurements to identify\nreaction intermediates chemically (see Figs. R1 and R2 and corresponding discussions). We\nhave also performed IET manipulations to confirm the assignment of the C–H activation\nproducts (see Fig. R3 and corresponding discussion). Moreover, we have improved the\nresolution of the BR-STM images (revised Figs. 4 and 5).\nIndeed, few previous studies have investigated the adsorption of carbenes on surfaces, but\nmostly those of non-reactive N-heterocyclic carbenes. However, the reactivity of reactive\ncarbenes to polycyclic aromatic hydrocarbons, particularly by C–H activation, has not yet been\nexplored. In this work, we demonstrate for the first time carbene-mediated C–H activation on\nsurfaces, which expands the toolbox for on-surface synthesis for the fabrication of\nsophisticated, low-dimensional nanostructures, such as highly branched oligomers. We have\nemphasized these results in the revised Abstract and the Introduction. We hope that the\nadditional data and clarifications provided below address the reviewer’s concerns.\n1\n XP spectra\nFig. R1. XP spectra on Ag(111). (a,b) XP spectra of the N 1s and C 1s regions on a Ag(111) surface\n(i), after adsorption of 1a at 87 K (ii), after irradiation at 365 nm for 2 h (iii), and after annealing at 400 K\n(iv) and 600 K (v). The black curve in (a) corresponds to a fit of the satellite peak of the Ag(111) surface\non a linear background (dashed line). (c) Background-subtracted N 1s spectra from (a) after subtracting\nthe Ag(111) background (curve i in (a)), normalized to the areas of the related C 1s spectra in (b). (d)\nStructural formulas of the reaction products with N atoms marked in the colors of the fits in (c).\nXPS measurements of the N 1s and C 1s regions are performed for the chemical identification\nof the species on the Ag(111) surface (Fig. R1a,b). A full quantitative analysis is challenging\ndue to the influence of a satellite peak of the pristine Ag(111) surface in the N 1s region (curve\ni in Fig. R1a) and the coexistence of multiple products with various geometries at elevated\ntemperatures and the partial desorption. Therefore, we only discuss the trends in the proposed\nreaction mechanism. To analyze the changes in the N 1s spectra, the surface-related satellite\npeak is subtracted, and the resulting spectra are normalized to the corresponding C 1s peak\nareas (Fig. R1c).\n(curve ii in Fig. R1c), corresponding to the three types of N atoms in 1a (Fig. R1d). The area\nratio suggests that the peak of higher intensity (light purple) corresponds to pyridinic N atoms\nwithin the molecular backbone (Supplementary Ref. 3). The peaks at 403.3 eV (olive) and\n401.3 eV (cyan) are assigned to the N atom binding to the C atom in 1a and the terminal N\natom, respectively, based on the N 1s spectrum of 1b on the Ag(111) surface (Ref. 20 of the\nrevised manuscript). Curve ii thus confirms that 1a adsorbs non-dissociatively at 87 K.\nUpon irradiation at 365 nm, the 403.3 eV (olive) and 401.3 eV (cyan) peaks disappear,\nconfirming that the diazo group is removed from 1a (curve iii in Fig. R1c). The byproduct,\nmolecular N , desorbs at 87 K (Supplementary Ref. 5). The dissociation of 1a is corroborated\n2\nby a shift of the C 1s peak from 285.3 eV to 284.9 eV (curves ii to iii in Fig. R1b). A similar red\nshift was observed for the dissociation of precursor 1b to carbene 2b (Ref. 20), suggesting\nthe formation of carbene 2a. It is accompanied by a shift of the pyridinic N peak from 399.2 eV\nto 399.1 eV. The broadening of the pyridinic N peak after irradiation reflects the disordered\narrangement of 2a (Supplementary Fig. 4).\nThe pyridinic N peak splits upon annealing at 400 K (curve iv in Fig. R1c). According to STM\nresults, 3a and 4a are formed at this temperature (Fig. 3f). The N atoms in 3a and 4a are in\ndifferent environments. While 3a contains all N atoms in similar chemical environments, the N\natoms of the twisted geometry of 4a are in two chemical environments, one closer to the\nsurface and the other farther away. Accordingly, the N 1s spectrum is fitted by three peaks:\n399.2 eV (orange) for 3a, and 401.2 eV (blue) and 398.1 eV (green) for 4a.\nAnnealing at 600 K converts 3a and 4a into a series of oligomers with a 4a dimer core and\ndiaza-fluorenyl branches (Fig. 4a). Consistently, the two N 1s peaks of 4a are not altered,\nwhile the 399.2 eV peak of 3a (orange) evolves into a 399.1 eV peak (dark yellow) assigned\nto the N atoms in the diaza-fluorenyl branches (curve v in Fig. R1c).\nThe C 1s peak shifts slightly to lower binding energy (Fig. R1b), from 284.9 eV (curve iii) to\n284.7 eV (curve v), consistent with the formation of C=C and C–C bonds in the branched\noligomers.\nTherefore, the XPS results support the reactions deduced in real space. The XP spectra and\ntheir interpretation are added to the Supplementary Information (Supplementary Fig. 3) and\nreferred to in the main text.\n3\n IR spectra\nFig. R2. IR spectra on Ag(111). (a) IR spectra after adsorption of 1a at 105 K (i), after irradiation at\n365 nm for 5 min (ii), 10 min (iii), 20 min (iv), 30 min (v), and 40 min (vi), and after annealing at 400 K\n(vii) and 600 K (viii). (b) Scheme of the IR surface selection rule on metal surfaces. (c) Relative\nintensities of the peaks (A/A ) marked in (b) vs. irradiation time (t). A and A represent the peak areas\ntot tot\nat time t and at 40 min, respectively.\nBesides XPS measurements, we use IR spectroscopy to determine the geometries of the\nspecies on the Ag(111) surface. The IR spectrum of precursor 1a has only a very weak peak\nat 2084 cm-1 (curve i in Fig. R2a), which is assigned to the asymmetric C=N=N stretching\nmode. It is slightly red-shifted from its value in argon matrices at 2096 cm-1 (Supplementary\nRef. 1). The low IR intensity for 1a on the Ag(111) surface is explained by the IR surface\nselection rule (Ref. 29). On metal surfaces, a vibrational mode is IR active only if there exists\na non-vanishing projection of the dynamic dipole moment along the surface normal (Fig. R2b).\nThus, the IR spectrum supports the nearly parallel geometry of 1a on the surface, as predicted\nby DFT calculations (Fig. 2f).\nAfter irradiation, the formation of carbene 2a leads to several intense IR peaks (curves ii to vi\nin Fig. R2a). The peaks at 1611 cm-1 and 1171 cm-1 are close to the frequencies of the C–C–\nC bending and asymmetric stretching modes of 2a in argon matrices, while the peaks at\n1369 cm-1, 1320 cm-1, and 1295 cm-1 fall within the ranges of the C–C stretching, C–N\nstretching, and C–H rocking modes. The dominant peak at 1369 cm-1 saturates in intensity\nafter 40 min irradiation, indicating complete conversion of precursors 1a to carbenes 2a (Fig.\nR2c). Notably, the 1369 cm-1 peak of carbene 2a is approximately 26 times more intense than\nthe 2084 cm-1 peak of precursor 1a. Such a substantial increase in intensity suggests a large\nout-of-plane dipole moment component, which suggests an adsorption geometry of 2a with a\nlarge tilt angle. It is consistent with the nearly perpendicular geometry predicted by DFT\ncalculations and the increased apparent height of 2a relative to 1a in STM experiments.\nof organometallic dimer 3a, reflecting a change in bonding environments. After annealing at\noligomers 5a to 10a are oriented nearly parallel to the surface, according to the IR surface\nselection rule.\nThe IR data clearly demonstrate the geometry change from 1a to 2a, as well as the\nsubsequent evolution of 2a upon annealing. We have included this discussion in the main text\nand added Fig. R2 in the Supplementary Information as Supplementary Fig. 2.\nMajor issues:\nA five membered ring in a branch of the products (dimers 10, 11) contains a sp3 carbon atom,\nas shown in Fig. 1 and following associated figures. How can the authors exclude that a H\natom is removed during annealing? The BR-STM images rather suggest a planarized\nadsorption configuration of these products on Ag(111), which implies the sp3 carbon atoms\ntransformed into sp2 carbon atoms (a dehydrogenation occurred). This is very common in on-\nsurface chemistry, in particular in the formation of magnetic carbon-based structures (e.g. J.\nAm. Chem. Soc. 2025, 147, 23, 19530–19538; Angew. Chem. Int. Ed. 2023, 62, e202307884;\nACS Nano 2023, 17, 20, 20237–20245).\nOnce the dehydrogenation reaction occurs, the molecules will probably become open-shell,\nalthough the magnetism might not be detected because of the charge transfer from low-work-\nfunction Ag substrate to the molecules. However, STS analysis and dI/dV maps of molecular\norbitals will offer a guidance, which is thereof suggested to be done.\nFig. R3. IET-induced dehydrogenation of sp3 carbon atoms. (a) Scheme of IET manipulations for\n5a and 10a. (b-e) STM images of substituted dimers 5a (b,c) and 10a (d,e) before and after I-V\nmanipulation up to 2.5 V at the white crosses. (f-i) STM images in (b-e) are displayed with another color\nscale to enhance the contrast. Scanning parameters: V = 5 mV, I = 20 pA. (j) dI/dV spectra recorded\nb t\nat the crosses in (e) in corresponding colors. (k, l) dI/dV maps recorded at 1.02 V (k) and 2.03 V (l) with\na tunneling current of 100 pA, a modulation voltage of 20 mV, and a modulation frequency of 413.3 Hz.\nAll images use the same length scale marked in panel (b).\nWe agree that dehydrogenation of sp3 carbon atoms is possible at elevated temperatures, as\nmentioned by the reviewer (Refs. 45-47). However, the persistence of sp3 carbon atoms at\nsimilar temperatures has also been reported in other adsorbed systems (Refs. 48-50).\nA generation of sp3 carbon atoms in our system is consistent with the carbene C–H insertion\nreaction in solution, which introduces sp3 carbon atoms through a concerted process of C–C\nbond formation and hydrogen atom migration (Ref. 44). To confirm whether or not the sp3\n6\ncarbon atoms persist, we performed IET manipulations at the carbon of interest and monitored\nthe induced changes using STM/STS and dI/dV mapping (Fig. R3). We expected that a\nhydrogen can be removed from an sp3 carbon site in the range of 2 eV to 3 eV (Refs. 45, 50).\nA similar manipulation at a dehydrogenated sp2 site should not alter the molecule\n(Supplementary Ref. 17).\nFor substituted dimers 5a and 10a, the manipulations clearly alter the molecules (Figs. R3b-\nf). The adjacent depressions in the subsequent STM images after manipulation (Figs. R3g, i)\nindicate a charge transfer from the molecule to the surface (Ref. 28), consistent with the\nconversion from an sp3 to an sp2 carbon atom. For 5a, one corner of the dimer becomes\nbrighter, most likely due to a tilting of the pyridine ring (gray arrows in Fig. R3a and Fig. 3c). It\ncan be caused by a reduced molecule–surface distance at the newly formed sp2 carbon site.\nFor 10a, a similar topographic change is quenched by a diaza-fluorenyl group at the same\nposition. Therefore, we performed dI/dV spectroscopy and dI/dV mapping to monitor the\nelectronic states of 10a after manipulation. The spectra show two unoccupied molecular states\nat 1.02 V and 2.03 V at the dimer and the manipulated part of the molecule, respectively\n(Fig. R3j). The dI/dV map at 1.02 V is dominated by a symmetric protrusion at the core of the\nmolecule (Fig. R3k). In contrast, in the dI/dV map at 2.03 V the C2 symmetry is broken and\nthe local density of states at the manipulation site is reduced (red arrow in Fig. R3l). The\nneighboring branch is brighter (gray arrow in Fig. R3l), likely due to a geometry change. No\nKondo resonance is observed in the dI/dV spectra, which is consistent with the quenched\nmagnetism caused by the charge transfer, as suggested by the reviewer.\nIn summary, the site-specific manipulation, the characteristic manipulation voltages (< 3 V),\nand the correlated topographic and electronic changes support the presence of sp3 carbon\natoms in the substituted dimers. We have incorporated this discussion into the revised\nmanuscript (page 11) and included Fig. R3 as Supplementary Fig. 11.\nMinor issues:\n1) The structure in Fig. 4g(i) is not clearly indicated in Fig. 4a. The authors should highlight\nthis species in Fig. 4a. Similarly, in Fig. S4, the correspondence between Fig. S4a and Fig.\nS4f is not clear. It would be advisable to label the relevant structure in Fig. S4a.\nReply: We are sorry for the misleading wording. There is no correspondence between Fig.\n4g(i) and Fig. 4a, or between Supplementary Fig. 6a (former Fig. S4a) and Supplementary\nFig. 6f (former Fig. S4f), as the small-scale images are from other overview images. We have\nrevised the figure captions to clarify this point.\n2) It was mentioned that the constant height STM image is processed with a Laplace filter.\nHowever, this images are significantly distorted as shown in Figs. 4b(ii)-g(ii) and Figs. 5g(ii)-\ni(ii). I suggest that the authors provide the original images in the Supplementary Information.\nFig. R4. Bond-resolved STM images of substituted dimers 5a to 10a. Top row: original constant-\nheight STM images recorded with a functionalized tip; bottom row: corresponding images processed\nwith a Laplace filter. The images are rotated or mirrored to align the central dimer 4a. Scanning\nparameters: feedback closed with a setpoint of V = 5 mV and I = 20 pA.\nb t\nWe thank the reviewer for the suggestion. The original constant-height STM images\ncorresponding to Figs. 4b(ii)-g(ii) have been added as Supplementary Fig. 10 (Fig. R4), and\nthose corresponding to Figs. 5g(ii)-i(ii) are now included in Supplementary Fig. 15.\n3) It seems that some N–N bonds are also formed according to BR-STM images in Fig. 5.\nReply:\nFig. R5. AFM imaging and simulations of a tetramer of bis(para-pyridyl)acetylene molecules. Imaging\nwith a CO tip leads to a line between the nitrogen atoms, which could be an image artifact falsely\ninterpreted as a bond (red arrow in (e), adapted from Supplementary Ref. 13).\nIn Fig. 5, only C–C bonds are formed. The reviewer may be referring to the lines (black arrows)\nin Fig. 4. These lines are well-known imaging artifacts in high-resolution AFM/STM images,\narising from bending of the probe molecule on the tip between two closely-spaced atoms in\nadjacent molecules (Supplementary Refs. 12,13). Such artifacts appear between adjacent\n8\natoms that do not bond (e.g., red arrow in Fig. R5e). We have marked these artifacts in Fig. 4\nand clarified that they are not real bonds in the figure caption (page 10).\n4) In Fig. 5, the authors describe the dehydrogenation of the tetrasubstituted dimer 10b to\nform the fused tetrasubstituted dimer 11. Theoretically, it is possible to remove four hydrogen\natoms within the molecule (rather than just two) to achieve cyclization. The authors should\nadd some discussion to justify this. Did the authors anneal the sample to a higher temperature?\nReply:\nFig. R6. Intramolecular and intermolecular dehydrogenation. (a) Ball-and-stick model of C\n60\nfullerene, with five- and six-membered rings numbered in the yellow region. (b) Large-scale STM image\nafter annealing carbenes 2a on Ag(111) at 700 K. (c) Zoomed-in image of the square in (b). Scanning\nparameters: (b) V = 50 mV, I = 10 pA, (c) V = 10 mV, I = 1 nA.\nb t b t\nCyclization of 10b by removing four hydrogen atoms would lead to a non-planar bowl-shaped\nstructure, similar to a fragment of a C molecule (yellow region in Fig. R6a). Such a structure\n60\nis energetically less favorable compared to the planar molecules (Supplementary Ref. 19). At\nthe annealing temperature of 600 K, we did not observe the formation of non-planar molecules\nindicative of the removal of four hydrogen atoms. We did not explore higher temperatures\nbecause annealing 10a at higher temperatures leads to disordered polymeric structures (Fig.\nR6b,c). We have added the discussion in the revised manuscript (page 14) and the\nSupplementary Information.\n5) While the authors discuss the correlation between reaction temperature and product\ndistribution, I recommend that they also consider the reaction energy barriers and transition\nstates using DFT to rationalize the reaction pathways.\nReply: We appreciate the reviewer’s suggestion. However, it will not be possible to explore all\nsteps of the reaction fully without an automated quantum chemistry workflow, as is already\nnecessary for much smaller systems (e.g., J. Phys. Chem. C 2025, 129, 3469). Though it is\nnowadays very popular to add some reaction energy scheme, it is unlikely that these present\nthe lowest energy pathways, as frequencies stated in the studies (ACS Catal. 2024, 14, 14206;\nJ. Phys. Chem. C 2009, 113, 710). Thus, it is not so obvious what scientific insight they provide.\nmeasurements performed for this reply and presented above to be much more valuable.\n6) English gramma. JUST FOR EXAMPLE.\n“Developing strategies for precisely and efficiently coupling reactive intermediates is crucial\nfor synthesizing sophisticated low-dimensional nanostructures”\n“It is important to note the fundamental differences between carbenes 2 and the N-\nheterocyclic carbenes (NHCs) which are more frequently on surfaces, which are of key\nimportance to understand the surface reactivity of 2.”\nReply: We apologize for the grammatical issues. We have made a thorough proofreading of\nthe manuscript and the Supplementary Information, and additionally checked the text with the\nprogram Grammarly. All corrections are highlighted in yellow.\nWith the additional XPS and IR measurements, IET manipulation, and the above clarifications,\nwe hope that we have removed the reviewer’s concerns fully.\nThe manuscript entitled: “On-surface synthesis platform for highly branched oligomers based\non sequential C–C coupling and C–H activation of carbenes” is a thorough study that employs\ntwo strategies for the formation of carbenes.\nThe work presents outstanding data, and the overall presentation is clear. The figures are also\nclear and self-explanatory. It is a very good work for the area of on-surface synthesis.\nReply: We thank the reviewer for naming our study “outstanding” and as “a very good work\nfor the area of on-surface synthesis”. The points raised by the reviewer are carefully addressed\nas detailed below.\nHowever, I have some queries about it:\n1. Carbene 2a is formed either by light (Fig. 3) or tip electrons (Fig. 2). The authors claim that\nthe same structure is formed based on a height comparison. However, I have several concerns\nregarding this claim:\nWhen electrons are involved, the structural model shown in Fig. 2e seems to be quite accurate,\nas the transformation appears to be local and occurs in the middle of an island. However,\nwhen photons are used, the entire island appears to show an increase in height.\nReply:\nFig. R7. Incomplete conversion of precursors 1a to carbenes\n2a. (a) STM images after irradiation of precursors 1a on Ag(111)\nat 365 nm for 2 h. (b) Apparent height profile along the line in (a).\nScanning parameters: V = 50 mV, I = 10 pA.\nb t\nIn the original manuscript, we presented only the complete\nphoto-induced conversion of precursors 1a to carbenes 2a.\nWe have now added data for an intermediate step with\nincomplete conversion (Fig. R7a). The height profile clearly\nreveals that 2a has a larger apparent height than 1a in the\nsame STM image (Fig. R7b).\nThere are several issues I observe:\n1.1. Looking closely at the STM images, after light irradiation, it appears that “2a” is flat rather\nthan nearly vertical. The most likely scenario is that “2a” reacts with an adatom to form a planar\nstructure, similar to the model proposed for “3a”. Have the authors considered a simpler model\nfor the case of light? How does it compare in terms of DFT energy?\nFig. R8. IR spectra of 1a and 2a on Ag(111). (a) Scheme of the IR surface selection rule on metal\nsurfaces. (b) IR spectra after adsorption of 1a on the Ag(111) surface at 105 K (i), and after irradiation\nat 365 nm for 5 min (ii), 10 min (iii), 20 min (iv), 30 min (v), and 40 min (vi). (c) Relative intensities of\nthe peaks (A/A ) marked in (b) vs. irradiation time (t). A and A represent the peak areas at time t and\ntot tot\nat 40 min, respectively.\nWe thank the reviewer for the careful analysis of the STM images and the suggestion of an\nalternative planar geometry of carbene 2a. We rule out this possibility based on the IR\nmeasurements. According to the IR surface selection rule on metal surfaces (Ref. 29 of the\nrevised manuscript), a vibrational mode is IR active only if the dynamic dipole moment has a\nnon-zero projection along the surface normal (Fig. R8a). Consequently, precursor 1a that\nadsorbs nearly parallel to the surface (Fig. 2f), shows a very weak IR peak at 2084 cm-1 (curve\ni in Fig. R8b). It contrasts a strong asymmetric C=N=N stretching peak at 2096 cm-1 of 1a in\nargon matrices (Supplementary Ref. 1). Upon irradiation, the formation of carbene 2a leads\nto several intense IR peaks (curves ii to vi in Fig. R8b). The dominant peak at 1369 cm-1\nsaturates in intensity after 40 min irradiation, indicating complete conversion of precursors 1a\nto carbenes 2a (Fig. R8c). Notably, the 1369 cm-1 peak of carbene 2a is approximately 26\ntimes more intense than the 2084 cm-1 peak of precursor 1a. Such a substantial increase in\nintensity suggests a large out-of-plane dipole moment component, which can only be\nexplained by a large tilt angle of 2a relative to the surface.\nMoreover, height profiles show the same apparent height increase of ~70% towards precursor\n1a for both photo-induced and IET-induced carbenes 2a (Supplementary Fig. 4). A height pixel\n12\nhistogram corroborates the similarity between the two experimental results (see below). Such\na substantial height increase is not consistent with a planar adsorption geometry, in particular\nin view of the reactive carbon atom being drawn closer to the surface (Ref. 27).\nIn addition, during light irradiation, the maximum surface temperature remains below 52 K (5 K\nfor IET manipulation). At these temperatures, no adatoms are released from the step edges\non the Ag(111) surface (Ref. 30). Therefore, the model “2a” with an adatom is ruled out.\nWe have clarified this point in the revised manuscript and included the IR data in the\nSupplementary Information.\n1.2. It is intriguing that Figs. 1e and S2c and f show a height increase of exactly 62 pm in all\ncases. While this value may have an error, the authors should present a height histogram\nacross different images and structures to convince the reader that the increase is indeed the\nsame (within the error bar) in all cases.\nReply:\nFig. R9. IET-induced vs. photolytic dissociation of precursor 1a to carbene 2a. (a, b) STM images\nbefore (a) and after (b) indirect IET manipulation at the white cross. Manipulation parameters: V = 2.0 V,\nb\nI = 105 pA, and t = 10 s. White circles mark the primary region of the dissociation events to guide the\nt\neye. (c, d) STM images after irradiation of 1a at 365 nm for 2 h (c) and 3 h (d). Scanning parameters:\nV = 50 mV, and (a,b) I = 5 pA, (d,e) 10 pA. (e, f) Apparent height profiles along the lines in (a) to (d).\nb t\n(g) Pixel histograms of apparent heights normalized to the total number of pixels (N ) with Gaussian\ntot\nfits. The fitted peak positions are h = (68 ± 1) pm, h = (144 ± 1) pm, and h = (147 ± 1) pm. The surface\n1 2 3\nbaselines are set to 0 pm.\nWe thank the reviewer for bringing this point to our attention. The pixel histograms of apparent\nheights for precursor 1a (gray), IET-induced carbene 2a (red), and photo-induced carbene 2a\n(cyan) each are based on statistics from approximately 1000 molecules (Fig. R9a). The peak-\n13\nto-peak height difference from 1a to IET-induced 2a is (62  7) pm, and to photo-induced 2a\nit is (68  9) pm. The two mean values are identical within the error bar. Moreover, height\nprofiles across some molecules show height increases of (76  1) pm for IET-induced 2a and\n(79  1) pm for photo-induced 2a (Fig. R9b), also identical within the error range.\nIt should be noted that pixel histograms and height profiles measure apparent heights\ndifferently. Histograms capture the most frequently occurring apparent heights in the STM\nimage, while height profiles measure the maximum apparent heights along the lines. Thus,\nthe absolute apparent height values are bigger when determined from height profiles than\nfrom pixel histograms, and the relative height values are smaller. Nonetheless, both analyses\nconfirm that the IET-induced and photo-induced 2a have the same apparent height and are\nsignificantly higher than that of 1a. We have added the error analysis in the Supplementary\nInformation and incorporated Fig. R9 as Supplementary Fig. 4.\n1.3. Have the authors considered the possibility that the height increase could be due to\nelectron transfer rather than a structural change?\nReply: We agree with the reviewer that charge transfer influences apparent heights. In our\ncase, 2b has a similar charge transfer to 2a (0.5 e vs. 0.6 e), but it is imaged at an even lower\napparent height than its precursor 1b (Supplementary Fig. 12). Therefore, charge transfer\ncannot explain the substantial height increase for 2a compared to 1a. We have clarified this\npoint in the revised manuscript (page 5).\n1.4. The N groups are quite “fragile,” and I wonder whether the mechanism of removal after\n2\nlight-irradiation is correct, or if the increase in temperature caused by 3 hours of irradiation is\nwhat actually leads to the removal of these groups. Have the authors attempted thermal\nremoval?\nReply:\nFig. R10. N 1s XP spectrum of 1a on Ag(111) with fits. The N atoms in the structural formula are\nhighlighted in the colors of the fits. The pristine Ag(111) satellite peak is subtracted for clarity.\nand 1b (below 60 K) are lower than their respective deposition temperatures (1a at 70 K and\n1b at 85 K).\nXPS confirms that the molecule remains intact upon adsorption (Fig. R10). Deposition of 1a\nat 87 K yields three well-separated peaks with an area ratio of approx.1:1:2, corresponding to\nthe three types of N atoms in 1a (Fig. R10). The area ratio suggests that the peak of higher\nintensity (light purple) corresponds to pyridinic N atoms within the molecular backbone\n(Supplementary Ref. 3). Based on the N 1s spectrum of 1b on Ag(111) (Ref. 20), the peaks at\n403.3 eV (olive) and 401.3 eV (cyan) are assigned to the N atom binding to the C atom in 1a\nand the terminal N atom, respectively. These results confirm that 1a adsorbs non-\ndissociatively at 87 K, well above the maximum temperature of 52 K during irradiation. Thus,\nthe temperature increase during irradiation is not sufficient to remove the diazo groups. We\nhave added this discussion to the revised manuscript and incorporated Fig. R10 to\nSupplementary Fig. 3.\n15\n1.5. It is unfortunate that the authors did not follow the reaction using XAS or XPS (at\nsynchrotron), as this could have confirmed some of the proposed mechanisms.\nReply:\nFig. R11. XP spectra on Ag(111). (a,b) XP spectra of the N 1s and C 1s regions on a Ag(111) surface\n(i), after adsorption of 1a at 87 K (ii), after irradiation at 365 nm for 2 h (iii), and after annealing at 400 K\n(iv) and 600 K (v). The black curve in (a) corresponds to a fit of the satellite peak of the Ag(111) surface\non a linear background (dashed line). (c) Background-subtracted N 1s spectra from (a) after subtracting\nthe Ag(111) background (curve i in (a)), normalized to the areas of the related C 1s spectra in (b). (d)\nStructural formulas of the reaction products with N atoms marked in the colors of the fits in (c).\nWe have performed XPS measurements to support the STM observations (Fig. R11). To\nanalyze the changes in the N 1s spectra, the surface-related satellite peak is subtracted, and\nthe resulting spectra are normalized to the corresponding C 1s peak areas (Fig. R11c).\nAs pointed out in the reply to the previous question, the three well-separated peaks for 1a\nconfirm non-dissociative adsorption at 87 K (Fig. R11c,d). Upon irradiation at 365 nm, the\n403.3 eV (olive) and 401.3 eV (cyan) peaks disappear, confirming that the diazo group is\nremoved from 1a (curve iii in Fig. R11c). The byproduct, molecular N , desorbs at 87 K\n2\n16\n(Supplementary Ref. 5). The dissociation of 1a is corroborated by a shift of the C 1s peak from\n285.3 eV to 284.9 eV (curves ii to iii in Fig. R11b). A similar red shift was observed for the\ndissociation of precursor 1b to carbene 2b (Ref. 20), suggesting the formation of carbene 2a.\nIt is accompanied by a shift of the pyridinic N peak from 399.2 eV to 399.1 eV. The broadening\nof the pyridinic N peak after irradiation reflects the disordered arrangement of 2a\n(Supplementary Fig. 4).\nThe pyridinic N peak splits upon annealing at 400 K (curve iv in Fig. R11c). According to STM\nresults, 3a and 4a are formed at this temperature (Fig. 3f). The N atoms in 3a and 4a are in\ndifferent environments. While 3a contains all N atoms in similar chemical environments, N\natoms of the twisted geometry of 4a are in two chemical environments, one closer to the\nsurface and the other farther away. Accordingly, the N 1s spectrum is fitted by three peaks:\n399.2 eV (orange) for 3a, and 401.2 eV (blue) and 398.1 eV (green) for 4a.\nAnnealing at 600 K converts 3a and 4a into a series of oligomers with a 4a dimer core and\ndiaza-fluorenyl branches (Fig. 4a). Consistently, the two N 1s peaks of 4a are not altered,\nwhile the 399.2 eV peak of 3a (orange) evolves into a 399.1 eV peak (dark yellow) assigned\nto the N atoms in the diaza-fluorenyl branches (curve v in Fig. R11c).\nThe C 1s peak shifts slightly to lower binding energy (Fig. R11b), from 284.9 eV (curve iii) to\n284.7 eV (curve v), consistent with the formation of C=C and C–C bonds in the branched\noligomers.\nTherefore, the XPS results support the reaction deduced in real space. The XP spectra and\ntheir interpretation are added to the Supplementary Information (Supplementary Fig. 3) and\nreferred to in the main text.\n2. The main drawback of the proposed mechanism is the lack of selectivity (see the dispersion\nof products in Fig. 4a). This is a known issue, particularly in C–H dehydrogenation reactions.\nCan the carbene-based oligomer formation be directed and induced in a more selective\nmanner, perhaps through a more directional Ullmann coupling? This could improve the\nselectivity.\nReply: We thank the reviewer for the suggestion. While Ullmann coupling is indeed a powerful\napproach in on-surface synthesis, its drawback is the generation of halogen byproducts, which\nchemisorb on the surface, hinder the diffusion of reaction intermediates (Refs. 35, 36) and\npromote alternative reaction pathways (Ref. 37). In contrast, our carbene-based strategy is\nresidue-free, as the N byproduct desorbs at 87 K (Fig. R11c). It hence provides a\n2\ncomplementary route to construct low-dimensional nanostructures on surfaces. We anticipate\nthat the selectivity can be improved through rational precursor design and careful selection of\nthe surface. A comparison between our approach and Ullmann coupling has been included in\nthe revised manuscript (pages 7,8).\n17\n3. Similarly to query 1.2, have the authors considered the possibility that in structure “3a,” the\nfinal product might involve a surface metal atom rather than an adatom? DFT calculations\ncould be helpful in addressing this.\nReply: We thank the reviewer for suggesting this structure. Following the suggestion, we have\noptimized two carbenes 2a sharing one surface atom. However, this results in two individual\ncarbenes 2a adsorbed perpendicularly to the surface at neighboring surface sites. Such a\nstructure would be imaged as two bright protrusions, similar to carbenes 2a before annealing\n(Fig. 3b). It cannot explain the dimer-like 3a, which is imaged as two pairs of three protrusions\n(Fig. 3d,e).\n4. Why did the authors choose Ag? What about Au? It is likely that gold would result in more\ndiffusion, less interaction, and a higher number of adatoms, potentially leading to more\ncomplex structures. A brief discussion of how the choice of surface affects the results would\nbe valuable.\nReply:\nFig. R12. Adsorption of carbenes on coinage metal surfaces. Calculated adsorption energies and\ncarbon-metal bond lengths for small carbenes on Cu(111), Ag(111), and Au(111) surfaces (adapted from\nRef. 26).\nWe choose silver because silver-catalyzed carbene reactions are useful for various synthetic\ntransformations, yet they are less explored compared to reactions catalyzed by gold (Ref. 25).\nStudying carbene reactions on well-defined single-crystal silver surfaces provides mechanistic\ninsight into silver-catalyzed carbene reactions in solution. Moreover, recent DFT calculations\nfor smaller carbenes reveal that carbenes interact more strongly with gold than with silver (Fig.\nR12). It is because the back-donation from the carbene to gold is stronger than that to silver\nat a similar donation from the metal to the carbene. Therefore, gold may not facilitate more\ndiffusion even at a high number of adatoms to form more complex structures. We have\nincluded a discussion of the choice of the surface in the revised manuscript (page 4).\n18\n5. Making carbenes into oligomers is important, but doing so on a metal surface reduces the\napplicability of those oligomers. The article might be much more sound if the authors managed\nto perform the reaction on an insulating surface. This could work for “2a,” but not for the C–H\ndehydrogenation, as C–H cleavage typically requires a catalyst. However, the authors could\nevaporate \"adatoms\" to create a single-atom catalyst. This is just a speculative idea. Of course,\nthis is not being requested for the manuscript publication.\nReply: We appreciate this suggestion. Carbene-based reactions on insulating surfaces have\npotential applications in nanoelectronics. As the reviewer notes, the main challenge of\nsynthesis on insulating surfaces is the lack of catalytic activity. The photo-induced carbene\nformation does not necessarily require the catalytic effects of a metal surface. The subsequent\nC–H activation could, in principle, be catalyzed by foreign metal adatoms. In the present work,\nwe focus on demonstrating the feasibility of carbene-mediated C–H activation on metal\nsurfaces. Applying this concept to insulating surfaces is undoubtedly of interest for future\nstudies. We have included an outlook in the revised manuscript discussing the potential\napplications of carbene reactions on insulating surfaces.\nThis is an elegant study on C-C coupling in carbene molecules, in the context of \"on surface\nsynthesis\". Efforts in using surfaces to obtain planar conjugated structures started less than\nthree decades ago and are becoming increasingly popular. This particular investigation\nfocuses on obtaining highly branched oligomers.\nThe concept and results are original and the study was conducted methodically and rigorously.\nTypically the use of adjectives such as \"novel\" are discouraged, for fairly obvious reasons\n(novel platform... if this were not novel, we shouldn't even be discussing it).\nReply: We thank the reviewer for the very positive evaluation of our work. We agree that\nadjectives such as “novel” should be avoided, and we have removed them throughout the\nrevised manuscript.\nMy main concerns are:\n- the references. At this point, forty references for this kind of study is a bare minimum.\nReply: In the revised manuscript, we have increased the number of references to fifty-eight.\n- the conclusions are too dry. I encourage the authors to describe a broader outlook, in the\nform of perspectives for future work.\nReply: We thank the reviewer for the suggestion. We have extended the conclusion to include\na broader outlook: “Our proof-of-principle study establishes a platform for synthesizing\nstructurally distinct branched oligomers on surfaces. The potential applications of this platform\nare promising. First, using diazo compounds as precursors of reactive carbenes offers a\nresidue-free on-surface synthesis route that complements the widely used Ullmann coupling\non surfaces, thus broadening the toolbox of on-surface synthesis. Second, this approach can\nbe expanded to synthesize various N-doped 0D oligomers by replacing C2, C4, C5, or C7\natoms in carbene 2b with N atoms. Moreover, the oligomer size can be tuned by tailoring the\ndimensions of the carbenes. Finally, this approach could be extended to synthesize low-\ndimensional nanostructures on nonmetallic surfaces. The photo-induced carbene formation\ndoes not necessarily require the catalytic effects of a metal surface. The subsequent carbene\ncoupling could be initiated by co-adsorption of single Ag atoms. The platform thus paves the\nway to synthesize functional materials with applications in nanoelectronics.”\n20"}, {"round": 2, "reviewer_comments": {"reviewer_1": "All my previous concerns are satisfactorily addressed after the major revisions. I therefore recommend its publication in Nat. Commun.", "reviewer_2": "The authors have responded to all my queries, and those of the other reviewers in a satisfactory manner, adding some new information to the manuscript. They have performed IR, and XPS experiments to confirm their models. The manuscript can be accepted for publication. no other comments."}, "author_response": ""}]

Decision letter