On-surface synthesis of tailored organic platforms for single metal atoms

Domain: physics
Published: 2025-12-03
Editorial outcome: accept

Abstract
Recent advances in nanomaterials have pushed the boundaries of nanoscale fabrication to the limit of single atoms, particularly in heterogeneous catalysis. Single atom catalysts, comprising minute amounts of transition metals dispersed on inert substrates, have emerged as prominent materials in this domain. However, overcoming the tendency of these single atoms to cluster beyond cryogenic temperatures and precisely arranging them on surfaces with desired local environments pose significant challenges. Employing organic templates for orchestrating and modulating the activity of single atoms holds promise. Here, we introduce an on-surface synthesis of a single atom platform wherein atoms are firmly anchored to specific coordination sites distributed along carbon-based polymers. These platforms exhibit atomic-level structural precision and stability, even at elevated temperatures, offering arrays of undercoordinated metal centers as model active sites for single-atom catalysis. We theoretically reveal the pronounced ability of these architectures to coordinate several gas molecules and experimentally visualize their interaction with CO and CO2. Fine-tuning the structure and properties of the coordination sites offers unparalleled flexibility in tailoring functionalities, thus opening avenues for previously untapped potential in catalytic applications.

Introduction
Catalysts play a critical role in modern society: from pharmaceuticals to metallurgy, improving the catalysts involved has led to better products that are more sustainably manufactured. Many catalysts are transition or rare earth metals1, and one way to improve their efficiency, while simultaneously making them more sustainable, is to use their smallest functional units, leading to single-atom catalysts (SACs)2,3. This maximizes the utilization of the function-bearing entities, yielding an improved atom economy4,5. In SACs, the atoms are dispersed on and are supported by surfaces of host materials (Fig. 1a), typically ceramics such as zeolites6, oxides7, 2D materials such as graphene8–10, other metals such as copper11–13, as well as metal-organic frameworks14–16. The isolated single atoms (SAs) exhibit properties distinct from conventional metal clusters and nanoparticles, and closely resemble the reactive centers in solution or gas phase17. As heterogeneous catalysis reaches this atomic frontier, the exact chemical environment of the single atoms defines their catalytic properties18–20. This leads to several challenges3: attaining a high density of individual atoms without the formation of metal clusters, ensuring that the majority of these atoms are in a desirable chemical state on the surface, and developing adaptable platforms compatible with various metals.

Consequently, achieving a high-density uniformly dispersed arrangement of single atoms, each with an atomically precise local environment, remains a longstanding objective. This goal also parallels the function of biological enzymes, where individual metal atoms are precisely coordinated within a protein structure, enabling a broad spectrum of catalytic actions21,22.

Here, we introduce a surface-supported one-dimensional organic polymer with terpyridine (tpy) functional motifs23 as side groups. These motifs can be chelated, post-synthesis, with a variety of metal atoms, making these polymers versatile atomically precise single-atom platforms (SAPs) (Fig. 1b). The atomic precision is achieved by triggering selective surface-catalyzed reactions of molecular precursors on single crystal Au(111) surfaces, a process often called on-surface synthesis (OSS)24. These organic polymers have several structural advantages due to the achieved structural precision, for instance, by having all the metal atoms in the same chemical environment, the elucidation of the structure-property relationship is simplified25. Compared to coordination polymers26,27 and surface-confined metal-organic networks28–32, which are also atomically precise and chemically active towards specific reactions, these polymers have metal coordination independent from polymerization. Not only does this enable the post-synthesis metal chelation, but it allows for asymmetrically coordinated metal atoms, which can be critical in improving the catalytic efficiency21,33–35. In addition, the N3 open-site coordination achieved using the terpyridine motif also provides ample steric access to the coordinated atom. Lastly, although future catalysts for actual applications may rely on nanoparticle-based materials, having the SAPs on a clean, crystalline and atomically flat substrate such as Au(111) facilitates their fundamental characterization using powerful tools of surface science36, particularly bond resolved scanning probe imaging that allows the direct visualization of active sites and bonding motifs.

We demonstrate the on-surface synthesis of an atomically precise SAP using a 4’-{4-(2,7-dibromoanthracen-9-yl)phenyl}−2,2’:6’,2”-terpyridine (DBAP-tpy) precursor (Fig. 1c) that undergoes dehalogenative aryl-aryl coupling on an Au(111) surface in ultrahigh vacuum (UHV) conditions. Post-synthesis, these polymers are coordinated with cobalt atoms. The resulting material is characterized by scanning tunneling microscopy (STM, example large-scale image in Fig. 1d) and non-contact atomic force microscopy (nc-AFM) with functionalized tips, complemented with density functional theory (DFT) simulations (performed with AiiDAlab based applications)37. DFT calculations reveal that several gas molecules can be coordinated to these active sites and provide a rationalization of such behavior via in-depth analysis of the molecular orbital energetics and spatial localization. This theoretical investigation is complemented by the experimental visualization of CO and CO2 binding configurations (Fig. 1e), providing fundamental insights into the potential of this material for single-atom reactivity studies.

Results
The atomically precise SAP was synthesized through a three-step process. First, the DBAP-tpy precursor molecules were deposited on a clean Au(111) surface held at 200 °C under UHV conditions. This temperature promotes the debrominative homo-coupling yielding 1D polymers (Fig. 1c)38. High-resolution imaging of one of these polymer chains reveals a polyanthracene backbone with phenylene-terpyridine side moieties (Fig. 2a, b), as expected. Due to the precursor design and surface confinement, the steric hindrance operated by the tpy groups guarantees high selectivity in the covalent coupling, and only linear chains are formed39,40. While the tpy units appear as a Y-shaped feature in STM, nc-AFM with a CO-functionalized tip reveals their intramolecular structure as consisting of three planar rings. The central pyridine ring is slightly pulled up by the neighboring phenylene, which is rotated compared to the surface plane due to the hydrogen repulsion with the adjacent anthracene. Such rotation induces a periodic height modulation in the polyanthracene backbone, as highlighted in Fig. 2b. The nc-AFM image of a tpy unit (Fig. 2c) matches perfectly with the simulated one (Fig. 2d) obtained from the DFT-optimized geometry of the structure in Fig. 2e, indicating that the peripheral nitrogen atoms are pointing towards the polymer backbone. We also notice that the tpy units are slightly tilted toward the polymer long axis, probably due to the effect of the rotated phenylene rings and to a better match with the underlying surface lattice achieved in this configuration.

A sample with medium/high polymer coverage features chemisorbed bromine atoms that coexist with the polymer chains and stabilize them in islands (Supplementary Fig. 1a). If cobalt atoms are deposited on the surface at this stage, a cobalt-bromine complex is formed at the terpyridine (tpy-Co-Br, Supplementary Figs. 1b and 2).

To achieve the targeted active sites featuring only cobalt as the coordinated atom, the second step of the platform preparation consists in the removal of bromine atoms. If this is attempted by annealing the surface at higher temperatures, some intramolecular transformations occur in the polymer before complete bromine desorption. Hence, we used an alternative, well-established procedure, which exploits atomic hydrogen41. This treatment (see Methods for the experimental details) successfully removes all bromine atoms from the surface and leaves the polymer chains (nearly) unaltered (Supplementary Figs. 1c and 3).

The third procedural step involves the controlled dosing of cobalt atoms, executed with the sample held at 150 °C to enhance surface diffusion and prevent cobalt clustering into islands. We meticulously calibrated the cobalt surface coverage to achieve a precise 1:1 ratio between tpy and Co. Subsequently, the sample underwent annealing at 200 °C to enhance order and cleanliness post the aforementioned steps. Upon this procedure, we found no indications of Co incorporation into the Au surface. As a result, the Y-shaped features observed by STM appear now less dark and less sharp in their center (Fig. 2f) as compared to the pristine polymers (Fig. 2a). nc-AFM reveals that the tpy moieties are no longer planar, as their constituent rings appear tilted down at the center of the unit (Fig. 2f, h). This is consistent with the presence of a cobalt atom coordinated to the tpy and closer in height to the surface plane, as evidenced by the good match with the simulated nc-AFM image (Fig. 2i) of a tpy-Co unit (Fig. 2j) and in agreement with a previous study using iron-coordinated tpy on a silver surface42. The distal pyridine rings are now pointing toward the complex center to maximize metal-ligand interaction. The tilt of the tpy-Co units towards the polymer long axis is still present. DFT-optimized geometries indicate that cobalt atoms occupy either hollow or bridge sites on the Au(111) surface, with local lifting of nearby gold atoms from the first atomic layer.

We affirm the successful on-surface synthesis of the targeted SAP, with cobalt loading that amounts to 10.9 wt%, or 1.7 at%. Samples with medium molecular coverage facilitated the growth of the SAP with quasi-evenly spaced chains adsorbed predominantly on the fcc regions of the Au(111) 22×√3 (herringbone) reconstruction (Supplementary Fig. 1d). In such samples, the average density of active sites (tpy-Co) is approximately 0.15 per nm2, corresponding to one every 6.6 nm2. The DFT-calculated binding energy of cobalt atoms within the tpy pockets is 3.8 eV. Given that the sample underwent a temperature of 200 °C during preparation, this substantial binding energy anticipates the high stability of the active sites.

The well-defined structures obtained through our synthetic protocol feature cobalt atoms coordinated in an open N3 environment. We computed the binding energies of several gas molecules (CO2, CO, O2, and H2) at these active sites, as well as at a reference Co-porphyrin complex, with all geometries optimized on a Au(111) surface via DFT. This analysis shows that – with the exception of CO2, which interacts only weakly with both types of active sites – the tpy-Co centers exhibit stronger binding to the investigated gases than the Co-porphyrin (Fig. 3a). The enhanced binding strength at the tpy-Co sites can be advantageous for catalyzing reactions requiring selective stabilization of intermediates, such as CO in the CO2 conversion to methanol and methane or to C2 products with two or more carbon atoms. To elucidate the origin of this increased reactivity, we analyzed the gas-phase molecular orbitals of the two model systems (Fig. 3b–g). These calculations reveal that the open coordination environment in the tpy-Co complex aligns the Co d-orbitals closely with the frontier molecular orbitals. Projected density of states (PDOS) analysis indicates that the frontier states are more localized on the cobalt center in the tpy-Co than in the Co-porphyrin. Deconvolution of the PDOS show that the energy position of the 3d orbitals of cobalt are significantly different in the two cases, with the dxy, dyz, dxz orbitals of the tpy-Co being closer to the frontier molecular orbitals than in the Co-porphyrin case (Supplementary Fig. 4). Moreover, in gas phase the two systems differ by their spin multiplicity (quartet for the tpy-Co and doublet for the Co-porphyrin) and by their formal charge state, with the tpy-Co deviating from the formal 2+ charge of the cobalt in Co-porphyrin (see the natural bond analysis in Supplementary Table 1). Thus, the combination of an open metal site and cobalt-centered frontier orbitals (some of which with Rydberg-like shape, like the HOMO–1 in Fig. 3d) emerges as a crucial electronic design, enhancing the potential for catalysis by facilitating bond activation and electron transfer processes. We emphasize that the electronic properties of these molecular systems may change upon adsorption onto the Au(111) surface. To provide a flavor of these modifications, we performed DFT single-point calculation of a tpy-Co in presence of a gold cluster, which revealed a distortion and symmetry breaking of the molecular orbitals (Supplementary Fig. 5). This broken symmetry is expected to promote more efficient electron transfer and stronger interactions with reactants, ultimately offering a spatial orbital distribution that is highly favorable for catalytic activity43.

Cobalt, a pivotal metal in industrial processes and catalysis, plays a crucial role in diverse reactions, such as Fischer-Tropsch synthesis44, oxidation of methane45, steam reforming of ethanol46 and methane47, and is prohibitively expensive. The innovative SAP presented here comprises a minimal amount of this valuable material – yet our protocol is also applicable to other precious metals – and presents an ideal opportunity to explore the performance of low cobalt doses under gas exposure. Based on the theoretical results described above, we focus on CO and CO2 as model systems, also considering their central role in the mentioned industrial processes and CO2 reduction.

We exposed the SAP to CO at a partial pressure of 3×10−8 mbar for 90 s, with the Au(111) sample maintained at 9.0 K. This low dose typically results in a very low surface density of physisorbed CO molecules, used to functionalize the STM tip for improved imaging. The resulting STM image (Fig. 4a) reveals variations in tpy-Co sites, some appearing empty, while others exhibit dim or bright dots. Concurrent nc-AFM imaging clarifies these features (Fig. 4b). Empty units correspond to the tpy-Co sites described above. Dim dots in STM align with bright circular protrusions in nc-AFM (yellow arrows in Fig. 4b), resembling CO molecules physisorbed on the Au(111) surface and trapped between the polymer chains (white arrows in Fig. 4b). Hence, these units feature CO molecules standing perpendicular to the surface and stabilized by the cobalt atom without direct bonding (tpy-Co···CO in Fig. 1e). Less than 1% of units (statistics over more than 200 units) exhibit a bright center in STM (green circle in Fig. 4a). The corresponding nc-AFM image displays two faint features extending from the tpy (green circle in Fig. 4b), representing a CO molecule nearly parallel to the surface and covalently bound to the cobalt atom, i.e., tpy-Co-CO (Figs. 1e and 4c). The simulated nc-AFM image of a DFT-optimized tpy-Co-CO unit (Fig. 4f) perfectly aligns with the experimental image (Fig. 4d), confirming our assignment and consistent with a similar study on isolated molecules containing tpy-Fe moieties on Ag(111)48. We observed no appreciable structural changes with respect to the molecular adsorption site on the Au(111) surface.

Elevating the CO dose (5×10⁻⁸ mbar for 15 min) followed by a wobble stick annealing (WA, see Methods) for 15 min results in a sample, where 89% of the active sites (statistics over more than 800 units) exhibit bound CO molecules, specifically in the form of tpy-Co-CO (Fig. 4g and Supplementary Fig. 1e). First, the distinctive appearance of tpy-Co-CO sites in STM imaging demonstrates the potential for detecting CO at low temperatures, obviating the need for nc-AFM imaging. Then, it is noteworthy that the CO binds to the active sites via a post-adsorption diffusion mechanism. In fact, the tpy-Co-CO sites were only 1% before this treatment – with most CO adsorbed on the bare Au(111) or adjacent to the polymer chains – highlighting the key advantage of the tpy-based sites with open structure in contrast to closed pores or macrocycles. Complete CO desorption from the Au(111) surface and the tpy-Co sites is achieved after annealing the sample to room temperature, preserving the SAP for cyclic reuse without harm.

When exposing the SAP to CO2 (5×10‒8 mbar for 15 min) with the sample held at 30 K, the resulting surface exhibited chains with different occupation of the tpy-Co sites. Most of them show large, round features (Fig. 5a), which appear as elongated, rod-like objects in nc-AFM (Fig. 5b, c). Those next to the tpy-Co are slightly nonplanar. The simulated nc-AFM image of a DFT-optimized tpy-Co···CO2 unit (Fig. 5e, f) shows an excellent match with the experimental images. The rod-like feature of the CO2 is fully reproduced, including its nonplanar appearance due to a weak interaction with the Co. The calculated distance between cobalt and the nearest oxygen is 2.81 Å. This value, significantly larger than the distance between cobalt and carbon in the case of tpy-Co-CO units (1.74 Å), suggests that the CO2 is not bound to the cobalt, but weakly stabilized next to it (tpy-Co···CO2, see Fig. 1e and Supplementary Fig. 9). DFT-optimized geometries of this structure with varying Co-CO2 distances (Supplementary Fig. 9) offer further insights into the possible binding of CO2 to Co, which, despite being accompanied by a significant change in morphology, does not produce a significant energy gain – in agreement with our theoretical results (Fig. 3a). The coexistence of “empty” tpy-Co sites with those decorated with CO and CO2 (Fig. 5d), offers a direct comparison of the possible functionalization motifs and highlights the strength of our characterization down to the atomic level. Remarkably, we have further investigated the sample after stepwise annealing and observed the diminishing of tpy-Co···CO2 sites in favor of new species (Supplementary Fig. 10) whose morphology (studied via STM and nc-AFM) is compatible with either tpy-Co-CO (discussed previously) or tpy-Co-CO2 (Supplementary Fig. 9a, b). A definitive determination of the fate of CO2 upon annealing would require dedicated investigations using complementary spectroscopic techniques – such as x-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD) – which are beyond the scope of the present study. Nevertheless, we provide direct visualization of key molecular species and their interactions with the active sites described herein, establishing a robust platform for future studies on single-atom reactivity.

In conclusion, we have developed a strategy for the synthesis of model SAPs based on organic polymers functionalized with terpyridine side groups that can be selectively chelated post-synthesis, achieving all-equivalent and regularly spaced active sites. These structures differ from isolated molecular systems on surfaces that present a broad distribution of site occupancy and poor spacing control. The resulting asymmetric N3 coordination environment around the metal centers yields open-site structures that are highly promising for studies of single-atom reactivity. Using high-resolution scanning probe microscopy with functionalized tips, we achieved atomic-level characterization of these unique active sites. Furthermore, we computed the binding energies of several gases (CO, O2, H2, and CO2) at the tpy-Co centers and compared them to those at a metalloporphyrin reference. Our results demonstrate that the tpy-Co sites exhibit significantly stronger binding to CO, O2, and H2 – a combination of properties that is advantageous for catalytic reactions such as CO2 conversion to methanol, methane and C2+ products via Fischer-Tropsch processes. The enhanced reactivity of the tpy-Co active sites is attributed to their distinct electronic structure, characterized by frontier molecular orbitals that are more localized on the metal center than in traditional systems like porphyrins. This localization facilitates bond activation and electron transfer processes. In addition, we directly visualized the binding configurations of CO and CO2 molecules at the active sites through scanning probe microscopy, providing experimental confirmation of their adsorption behavior. Our work establishes a new route for the synthesis of single-atom platforms with an atomically defined environment that serves as a reference for understanding single-site reactivity and enables the isolation of specific chemical effects – complementary to more complex or industrially relevant systems. Given that the synthesis is based on well-established on-surface chemistry protocols, it can be readily extended to different molecular precursors, allowing systematic tuning of the structural and electronic properties of the resulting material24,49–51. In the future, we envisage that such atomically engineered platforms could be rationally designed to selectively catalyze targeted reactions, approaching the efficiency and specificity typically associated with biological enzymes.

Methods
General methods for precursor synthesis
All reactions working with air- or moisture-sensitive compounds were carried out under an argon atmosphere using standard Schlenk line techniques. All starting materials, reagents, and solvents were purchased from commercial sources and used as received unless otherwise noted. Anhydrous dimethylformamide (DMF), tetrahydrofuran (THF), and dichloromethane (CH2Cl2) were purified by a solvent purification system (GlassContour) prior to use. Thin-layer chromatography (TLC) was done on silica gel coated aluminum sheets with F254 indicator, and column chromatography separation was performed with silica gel (particle size 0.063–0.200 mm). Nuclear Magnetic Resonance (NMR) spectra were recorded in CDCl3 using Bruker Avance Neo 400 and 500 MHz NMR spectrometers. Chemical shifts (δ) were expressed in ppm relative to the residual of solvents (CDCl3, 1H: 7.26 ppm, 13C: 76.00 ppm). Coupling constants (J) were recorded in Hertz. Abbreviations: s = singlet, d = doublet, t = triplet, m = multiplet. High-resolution mass spectra (HRMS) were recorded on a Bruker ultrafleXtreme spectrometer by matrix-assisted laser desorption/ionization (MALDI) with tetracyanoquinodimethane (TCNQ) as the matrix, or on a Thermo Scientific LTQ-Orbitrap Mass Spectrometer by electrospray ionization (ESI).

On-surface experiments
The on-surface synthesis experiments were performed under ultrahigh vacuum (UHV) conditions with base pressure below 2×10‒10 mbar. Au(111) substrates (MaTeck GmbH) were cleaned by repeated cycles of Ar+ sputtering (1 keV) and annealing (460 °C). The precursor molecules were thermally evaporated onto the clean Au(111) surface held at 200 °C from quartz crucible heated at 170 °C (deposition rate of ~0.5 Å·min−1). Atomic hydrogen was dosed onto the surface held at 150 °C by using a gas cracker (Mantis) operated at 70 W with a partial pressure of 2×10‒7 mbar of molecular hydrogen (Messer, purity 5.0) for 15 min. Cobalt atoms were sublimated onto the surface held at 150 °C from a rod (Alfa Aesar, purity 4.5) heated in a home-built e-beam metal evaporator, and the surface coverage was controlled using the STM and nc-AFM images as feedback. After cobalt deposition, the sample was annealed to 200 °C for 20 min. CO, CO2, and Ar gases (Linde, purity 4.7, Pangas, purity 4.5, and Messer, purity 5.0, respectively) were dosed onto the cold sample in the STM stage with a partial pressure of 5×10‒8 mbar for 15 min. The sample temperature reached 9.5 K during the exposure with the shields of the STM cryostat kept open. In some cases, we performed an unusual annealing of the sample to prevent potential contamination from the STM stage that might occur in the case of standard resistive heating. Such wobble stick annealing (WA) consisted in extracting the cold sample from the STM stage with the (room temperature) pincer tool that is usually operated for transfers (namely, the wobble stick), and holding the sample on this pincer for a specific time. Afterwards, the sample is reinserted into the cold STM stage and cooled down to 4.7 K. While not allowing any temperature readout, this method guarantees the cleanest annealing conditions.

STM and nc-AFM imaging
STM images were acquired with a low-temperature STM/nc-AFM (Scienta Omicron) operated at 4.7 K in constant-current mode using an etched tungsten tip. The scanning parameters are indicated in the captions, with bias voltages referred to the sample. nc-AFM measurements were performed at 4.7 K with a tungsten tip placed on a qPlus force sensor52. The tip was functionalized with a single CO molecule at the tip apex picked up from the previously CO-dosed surface53. The sensor was driven at its resonance frequency (27405 Hz) with a constant amplitude of 70 pm. The frequency shift from the resonance of the tuning fork was recorded in constant-height mode using Omicron Matrix electronics and HF2Li PLL by Zurich Instruments. The Δz reported in the captions is positive (negative) when the tip-surface distance is increased (decreased) with respect to the STM setpoint at which the feedback loop is open (It = 100 pA, Vb = ‒5 mV, with the tip located on an empty area of the Au(111) surface).

Computational details
On surface. All calculations were performed with AiiDAlab37 apps based on the DFT code CP2K54. The surface/adsorbate system was modeled within the repeated slab scheme, with a simulation cell containing up to 1500 atoms, of which 4 atomic layers of Au along the [111] direction and a layer of hydrogen atoms to passivate one side of the slab in order to suppress one of the two Au(111) surface states. 40 Å of vacuum was included in the simulation cell to decouple the system from its periodic replicas in the direction perpendicular to the surface. The size of the cell was 38.3×51.1 Å2 corresponding to 260 Au(111) surface unit cells. The electronic states were expanded with a TZV2P Gaussian basis set55 for C and H species and a DZVP basis set for Au and Co species. A cutoff of 600 Ry was used for the plane wave basis set. Norm-conserving Goedecker-Teter-Hutter pseudopotentials56 were used to represent the frozen core electrons of the atoms. We used the PBE parameterization for the generalized gradient approximation of the exchange correlation functional57. To account for van der Waals interactions, we used the D3 scheme proposed by Grimme58. To obtain the equilibrium geometries, we kept the atomic positions of the bottom two layers of the slab fixed to the ideal bulk positions, and all other atoms were relaxed until forces were lower than 0.005 eV/Å. The Probe Particle model59 was used to simulate nc-AFM images. The binding energy of gas molecules to the active sites described in Fig. 3a have been computed by comparing the DFT-optimized geometries of the molecular systems with the gas molecule either bound (or in proximity) to the active sites to the case where the gas molecules were adsorbed on the Au(111) surface, far from the active sites – multiple geometries have been tested and the most stable ones were used for the comparison.

Gas phase. The molecular orbitals and PDOS reported in Fig. 3b–g have been computed using geometries optimized in Gaussian 1660 with the PBE061 exchange-correlation functional. The def2-TZVP basis set62 was used for all elements. The tpy-Co (Co-porphyrin) system displayed a quartet (doublet) spin state as the lowest energy configuration in the gas phase.

From the optimized structure of tpy-Co on an Au(111) surface discussed in the main text, a representative model containing an Au cluster and the tpy-Co molecule was defined (see its geometry in Supplementary Fig. 5a, b). In this case, pseudopotentials were employed for the Au atoms. A visualization of the resulting frontier molecular orbitals is reported in Supplementary Fig. 5c. The spin configuration of the system tpy-Co + Au cluster was evaluated for two multiplicities of Co (M = 2 and 4), with the doublet spin state identified as the lowest energy configuration (Supplementary Table 2). Geometry optimization calculations were performed on the tpy-Co molecule in the gas phase, excluding the Au cluster, using both spin multiplicities as well (Supplementary Table 3 and Supplementary Figs. 6 and 7). In addition, molecular orbitals of Co-porphyrin were computed for comparison with those of the tpy-Co complex at the gas-phase (Supplementary Fig. 8).

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The manuscript describes a method to synthesize metal-organic structures featuring cobalt atoms in asymmetric threefold-coordinated sites. These metal-organic structures were synthesized on Au(111), characterized by scanning probe microscopy (STM and ncAFM) and subsequently exposed to CO and CO2 in ultrahigh vacuum conditions at cryogenic temperatures. The individual adsorbate molecules were imaged by STM and ncAFM, and their appearance was compared to simulated ncAFM images based on DFT-optimized models.\n\nA crucial aspect of the work is the claim that the reactivity of the asymmetric cobalt sites studied in this work is very distinct from cobalt sites in other metal-organic structures. This is illustrated by DFT computations indicating that the binding strengths of adsorbed molecules (CO, CO2, O2, H2) is much higher than in a chosen reference system (Co-porphyrin).\n\nUnfortunately, this point is currently not supported by the presented experimental data, as the experiments do not provide any information about binding strengths of the imaged adsorbate molecules, nor do they provide any comparison to reference systems (such as the Co-porphyrin, which was chosen as a reference in the DFT computations).\n\nIn the cover letter (responding to a previous review of the manuscript), the authors state that traditional spectroscopic methods used in model catalysis research cannot be applied for this system due to the inherently low surface coverage of the Co sites. This limits the potential impact of the work, but the authors argue that this limitation can be outweighed by the atomic-scale definition of their system, allowing direct comparison to DFT models that can lead to fundamental insights inaccessible by ensemble-averaging methods. Such argumentation is fair, but the manuscript currently does not present the promised fundamental insights.\n\nTo provide such insights (that I would deem necessary for publication in Nature Communications), the following steps can be suggested:\n\n1. Calibrate the temperature of the very vaguely defined “wobble-stick annealing” and estimate the temperature at which the adsorbed molecules desorb from the cobalt sites. This way, it will be possible to provide experimental values that can be compared to the DFT results presented in Figure 3a.\n\n2. Provide some experimental reference of an alternative Co-site (ideally the Co-porphyrin that was analyzed by DFT in Fig. 3a), to provide experimental evidence that the binding strengths of adsorbed molecules are indeed dramatically different from the asymmetric cobalt sites.\n\n3. Analyze the DFT data: why are the binding strengths so dramatically different between the Co-tpy and Co-porphyrin sites? Do the variations in binding strengths correlate to any electronic parameters of the Co-sites? (formal charge state, spin multiplicity, d-band position, hybridization of specific d-orbitals…?)\n\n4. It is not clear why the authors chose to plot the PDOS and energy diagrams of a coordinatively saturated bis(tpy)-Co system in Figure 3e-g. The reactivity of bis(tpy)-Co was not addressed at all, thus I don’t see the point of analyzing its PDOS and relating it to reactivity. Moreover, the bis(tpy)-Co system does not seem to be a suitable reference, as it can be expected that its reactivity will be significantly reduced by steric hinderance (which may outweigh any differences stemming from the distinct electronic structure). Without any doubt, the electronic structure Co-porphyrin should be analyzed instead, and it should be clearly explained what parameters are responsible for the differences in reactivity.\n\nTo conclude, I see this manuscript as a nice surface science work. I recognize the potential of this (or similar) system to potentially serve as a suitable model for elucidating the fundamentals of “single-atom” site reactivity. Nevertheless, for publication in Nature Communications I would expect to see some of fundamental understanding that this system can bring – not only promises that it may be done in the future.\n\nWithout such deeper insights I can only recommend publication in a more specialized journal.", "reviewer_2": "This work presents an original on-surface polymerization reaction of a terpyridine based ligand which is then used to coordinate cobalt atoms (tpy-Co). The Co-terpyridine polymer system is subsequently utilized to actuate a ligation between the Co centers and C=O molecules (tpy-Co-C=O). This chemistry is studied at a single molecule level employing UHV-STM and nc-AFM. The reactivity of the on surface tpy-Co system and to a reference, Co-porphyrin molecule, toward C=O are explored using theory. The results of this study are highly relevant to the current interest in developing single-atom catalysts.\n\nOverall, I found this work quite interesting and have the following questions and comments:\n\nIt is not clear to me what exactly is calculated and depicted in Figure 3. Are these slab calculations, periodic boundary calculations, or gas phase calculations? If the former, why bother with gas phase calculations? If the later, why not use the slab or PBC calculations which will more accurately represent the energies? It is well known that the substrate can have a dramatic effect on the axial binding by Cobalt II porphyrins.\n\nTerpyridine is a labile molecule in solution or gas phase and the external N's can either be pointed to form a pocket as shown, or oriented in the opposite direction. What is causing them to all adopt the pocket configuration?\n\nThe chemistry reported here is essentially the same (Co replacing Fe) as in a previous communication (Nat. Comm. 2022, 13, 7407); reference 48 in the manuscript, mentioned in one sentence on page 6. The authors should discuss their results in the context of that work."}, "author_response": "Point-by-point response\nReviewer 1\n3. Analyze the DFT data: why are the binding strengths so dramatically different between the Co-tpy and\nCo-porphyrin sites? Do the variations in binding strengths correlate to any electronic parameters of the\nCo-sites? (formal charge state, spin multiplicity, d-band position, hybridization of specific d-orbitals…?)\nOur reply: We are grateful to the reviewer for this comment, which gives us the opportunity to further\nelucidate the origin of the higher reactivity of our tpy-Co compared to traditional system with known\nelectronic configurations, such as a Co-porphyrin. We have performed additional calculations to display\nthe electronic properties of the Co-porphyrin, including a new PDOS graph and energy diagram of the\nmolecular orbitals (new Fig. 3e-g in the main text). The PDOS comparison confirms that the frontier states\nare more localized on the cobalt center in the tpy-Co than in the Co-porphyrin. Deconvolution of the PDOS\nreveals that the energy positions of the cobalt 3d orbitals differ significantly between the two systems. In\nthe tpy-Co complex, the d , d , and d orbitals lie closer to the frontier molecular orbitals compared to the\nxy yz xz\nCo-porphyrin case (new Supplementary Fig. 4). In the Co-porphyrin, the frontier orbitals correspond to the\nwell-known π molecular orbitals, where the two HOMOs are nearly degenerate (a and a under D\n1u 2u 4h\nsymmetry) and the two LUMOs are exactly degenerate (e under D ). Moreover, the two systems differ by\ng 4h\ntheir spin multiplicity (quartet for the tpy-Co and doublet for the Co-porphyrin in gas phase). Natural Bond\nOrbital (NBO) analysis comparing the natural electron configuration of the Co atom in both systems shows\na similar overall configuration with a slight deviation of the tpy-Co from the known Co(II) complex with a\nformal charge of +2 and one unpaired electron of the Co-porphyrin. In particular, the comparison reveals\nthat the Co atom in tpy-Co exhibits a higher d-orbital occupation (new Supplementary Table 1). These\ndifferences arise from the distinct coordination environment of tpy-Co, which is less coordinated and more\nopen than that of Co-porphyrin, ultimately leading to increased chemical reactivity.\n\nNew Supplementary Fig. 4 | PDOS of Co 3d orbitals. a. PDOS of the 3d orbitals of cobalt in the tpy-Co\ncompound. b. PDOS of the 3d orbitals of cobalt in the Co-porphyrin. The graphs elucidate the origin of the\nspectral features reported in Fig. 3c,f in the main text. Positive (negative) values in the y-axis correspond to\nthe spin-up (spin-down) channel. Highest occupied molecular orbital (HOMO) levels are indicated by the\ngrey dashed lines.\nBond Orbital (NBO) Analysis of the Co atom in tpy-Co and Co-porphyrin.\nNatural electron tpy-Co Co-porphyrin\nconfiguration\nCo atom\nAlpha [core]4s(0.19)3d(4.84)4p(0.18) [core]4s(0.14)3d(4.30)4p(0.20)\nBeta [core]4s(0.07)3d(3.03)4p(0.08) [core]4s(0.10)3d(3.29)4p(0.19)\nTotal [core]4s(0.26)3d(7.86)4p(0.26)4d(0.01) [core]4s(0.25)3d(7.59)4p(0.38)4d(0.01)\nThe results are presented as the effective valence electron configuration, also referred to as the Natural\nElectron Configuration. The analysis is provided separately for the α and β spin densities, as well as for the\noverall total. The reported values show a higher d orbital occupancy for the tpy-Co.\nAction: We have performed new gas-phase calculations for a Co-porphyrin system and included the results\nin Fig. 3e-g. Moreover, we have added to the SI the deconvolution of the PDOS into the d orbitals of cobalt\nfor the two complexes (new Supplementary Fig. 4) and the NBO analysis for the description of the formal\ncharge state (new Supplementary Table 1). Finally, we have carefully described the differences in the\nelectronic properties of the tpy-Co and Co-porphyrin in light of the new computational results, offering a\nrationalization of the increased chemical reactivity of the newly developed active sites.\n4. It is not clear why the authors chose to plot the PDOS and energy diagrams of a coordinatively\nsaturated bis(tpy)-Co system in Figure 3e-g. The reactivity of bis(tpy)-Co was not addressed at all, thus I\ndon’t see the point of analyzing its PDOS and relating it to reactivity. Moreover, the bis(tpy)-Co system\ndoes not seem to be a suitable reference, as it can be expected that its reactivity will be significantly\nreduced by steric hinderance (which may outweigh any differences stemming from the distinct electronic\nstructure). Without any doubt, the electronic structure Co-porphyrin should be analyzed instead, and it\nshould be clearly explained what parameters are responsible for the differences in reactivity.\nOur reply: We understand the reviewer’s concern about our choice to display and discuss the electronic\nproperties of a bis(tpy)-Co. With this choice, we wanted to highlight the difference between our tpy-Co\nsystem and a coordinatively saturated one. However, in line with the reviewer’s request, we have now\ncomputed the electronic properties of a Co-porphyrin and discussed them in comparison to the tpy-Co. A\ndetailed description is reported in our answer to the previous point.\nAction: The theoretical results in Fig. 3e-g have been replaced with those of a Co-porphyrin. Moreover, we\nhave discussed the differences in the electronic properties of this system in comparison to the tpy-Co and\nadded in the SI a new figure (new Supplementary Fig. 4, showing a deconvolution of the PDOS into the d\norbitals of cobalt) and a new table (new Supplementary Table 1, with the NBO analysis).\n“On-Surface Synthesis of Tailored Organic Platforms for Single Metal Atoms”\nPoint-by-point response\nReviewer 2\nThis work presents an original on-surface polymerization reaction of a terpyridine based ligand which is then used\nto coordinate cobalt atoms (tpy-Co). The Co-terpyridine polymer system is subsequently utilized to actuate a ligation\nbetween the Co centers and C=O molecules (tpy-Co-C=O). This chemistry is studied at a single molecule level\nemploying UHV-STM and nc-AFM. The reactivity of the on surface tpy-Co system and to a reference, Co-porphyrin\nmolecule, toward C=O are explored using theory. The results of this study are highly relevant to the current interest\nin developing single-atom catalysts.\nOur reply: We appreciate the reviewer’s positive evaluation of our work and address their comments below.\nOverall, I found this work quite interesting and have the following questions and comments:\nIt is not clear to me what exactly is calculated and depicted in Figure 3. Are these slab calculations, periodic\nboundary calculations, or gas phase calculations? If the former, why bother with gas phase calculations? If the\nlater, why not use the slab or PBC calculations which will more accurately represent the energies? It is well known\nthat the substrate can have a dramatic effect on the axial binding by Cobalt II porphyrins.\nOur reply: We thank the reviewer for the opportunity to clarify the calculations presented in Fig. 3. The geometries\nshown in Fig. 3a correspond to DFT-optimized structures of the molecular units adsorbed on Au(111), obtained\nusing periodic boundary conditions. In contrast, Figs. 3b-g illustrate the electronic properties of two compounds\nwhose structures (indicated in Fig. 3b and Fig. 3e) were optimized via gas-phase DFT calculations. Gas-phase\noptimization was chosen to enable the use of more accurate functionals, which would be computationally prohibitive\nfor the full molecule-substrate system. Although substrate effects are neglected under these conditions, this approach\nallowed us to identify distinct differences in the electronic properties of the two systems and to gain deeper insight\ninto the higher reactivity of the tpy-Co structure relative to the reference Co-porphyrin complex.\nAction: In the caption of Figure 3, we clarified that the calculations in panel a are “optimized structures on A(111)\nobtained by DFT with periodic boundary conditions”.\nTerpyridine is a labile molecule in solution or gas phase and the external N's can either be pointed to form a pocket\nas shown, or oriented in the opposite direction. What is causing them to all adopt the pocket configuration?\nOur reply: The reviewer is correct that the distal pyridine rings can rotate, causing the external nitrogen atoms to\npoint either inward (toward the ligand center) or outward (toward the polyanthracene backbone). The rotation of\nsimilar rings in surface-adsorbed nanostructures has been previously investigated by us and was found to occur with\nonly a modest energy input (J. Am. Chem. Soc. 2018, 140, 10, 3532–3536). Consistent with this, our nc-AFM\nmeasurements of the “empty” tpy ligands (Fig. 2a,c) closely match the expected appearance of structures with\noutward-oriented distal pyridine rings (Fig. 2d,e). In certain cases – such as after prolonged annealing, as in our\n1\nhydrogen exposure experiments – we observed a different contrast in the tpy structures, in agreement with the\nsimulated nc-AFM image of the tpy ligand with inward-oriented distal pyridine rings (Supplementary Fig. 3). Upon\ncobalt coordination, the distal pyridine rings adopt the inward orientation, reflecting stabilization of the complex\nwhen all three rings participate in metal-ligand coordination (Nat. Commun. 2022, 13, 7407).\nAction: In the main text of our revised manuscript, we clarified that after coordination of cobalt atoms “the distal\npyridine rings are pointing towards the complex center to maximize metal-ligand interaction”.\nThe chemistry reported here is essentially the same (Co replacing Fe) as in a previous communication (Nat. Comm.\n2022, 13, 7407); reference 48 in the manuscript, mentioned in one sentence on page 6. The authors should discuss\ntheir results in the context of that work.\nOur reply: We thank the reviewer for their comment, which gives us the opportunity to clarify the context and\nnovelty of our work. The central innovation of our study lies in the design and on-surface synthesis of a single-atom\nplatform in which undercoordinated, open active sites are interconnected through a covalently bonded carbon-based\nnanostructure. This concept is fundamentally different from the cited work (Nat. Commun. 2022, 13, 7407), even\nthough the chemical nature of the active sites is comparable (tpy-Co on Au(111) vs. tpy-Fe on Ag(111)). Our goal\nwas not only to visualize active sites and their local environment upon gas adsorption, but to achieve such insights\nwithin an extended, well-defined platform that could serve as a prototype for studying and tuning single-atom\nreactivity. In this regard, we developed a nanomaterial featuring regularly spaced and chemically equivalent active\nsites – distinct from isolated molecules that exhibit a broad distribution of site functionalization and occupancy.\nFurthermore, the gases used to probe the platform’s response were CO and CO in our study, whereas CO and C H\n2 2 4\nwere employed in the cited work. Finally, by comparing the electronic properties of our system with reference metal-\nporphyrins, we provided a deeper understanding of the asymmetric coordination environment and its associated\nhigher reactivity. In summary, although the active site chemistries share similarities, the two studies differ in their\nobjectives, material design, and characterization strategies. Together, they address complementary aspects of the\ndynamic field of single-site molecular catalysts at the interface between homogeneous and heterogeneous catalysis.\nAction: We have highlighted the context of our study in the final part of our revised manuscript, adding that we\nachieved “all-equivalent and regularly spaced active sites” and that “these structures differ from isolated molecular\nsystems on surfaces that present a broad distribution of site occupancy and poor spacing control”.\n2"}]

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