Controlled magnetic bistability of a helical non-Kekulé hydrocarbon on a Au(111) surface

Domain: physics
Published: 2026-01-09
Editorial outcome: major_revision

Abstract
Recent advances in the synthesis of graphene fragments that possess unpaired π-electrons and display high-spin ground states have unlocked possibilities to explore exotic physical phenomena related to magnetism. The high degree of spin-delocalisation makes these non-metal-based systems ideal building blocks for the construction of chains and lattices with strongly correlated magnetic ground states, which is the main requisite for measurement-based quantum computation. In this work, we demonstrate the magnetic bistability of a diradical nanographene that allows direct spin manipulation at the single-molecule level. To this end, we make use of solution-phase synthesis and tip-induced activation on a metallic surface to construct a helical non-Kekulé hydrocarbon spin switch, with a reversible transformation between a magnetic ground state and a non-magnetic one via intramolecular bond formation/breaking. The switching process is monitored by scanning tunnelling spectroscopy measurements, illustrating that this, and related systems, hold potential as spin-switch units for direct manipulation of magnetism and quantum information in entangled spin systems.

Introduction
Magnetic ground states in molecular graphene fragments, referred to as nanographenes, emerge from specific conjugation topologies1,2, which give rise to an entire family of structures termed non-Kekulé3,4, with unique electronic and magnetic properties compared to traditional Kekulé structures. The direct correlation between structure and ground-state spin enables precise control over π-electron magnetism through molecular design5,6. The emergence of π-magnetism has been reported to arise from sublattice imbalance7,8, topological frustrations9 and the interplay between hybridisation energy and Coulomb repulsion10. In contrast to systems with mostly localised unpaired electrons, such as in metal complexes11, the unpaired electrons in non-Kekulé nanographenes are highly delocalised12 within the molecular unit. This feature makes this class of carbon-based compounds ideal building blocks to construct covalently linked oligomeric arrays with strongly correlated magnetic ground states13 useful for quantum computation14. The prototypical class of such systems are triangular polybenzenoid hydrocarbons15, exemplified by the first two homologues, phenalenyl 2T16 and triangulene 3T17, as shown in Fig. 1a. These nanographene π-radicals adhere to Hund’s rule and possess ground states of the highest possible spin multiplicity (S = 1/2 and 1 for 2T and 3T, respectively), as predicted by Ovchinnikov18 and Lieb1. Despite their high reactivity19,20, several triangular nanographenes have been successfully synthesised and characterised: five pristine homologues, recently achieved7,8,21–23 by means of on-surface synthesis and tip-induced atomic manipulation, and kinetically stabilised derivatives of the first two homologues, accomplished24–26 via solution-phase synthesis. Both approaches provided direct evidence for the magnetic ground state of the first two species, 2T and 3T.

Using on-surface scanning probe techniques such as non-contact atomic force microscopy (nc-AFM), and scanning tunnelling microscopy (STM) and spectroscopy (STS), 2T and 3T were studied as building blocks or subunits of more complex structures, including dimers10,27, chains13,28, sheets9,29, and macrocycles30,31. These systems—so far limited exclusively to planar structures—enabled the realisation of non-trivial magnetic ground states32 as well as observation of spin excitations and edge fractionalisation13. To allow controlled manipulation of quantum information, it is essential to devise a structural unit that displays directed magnetic bistability33; that is, its spin can be changed on demand. Recently, a non-directed switching between π-diradical open-shell and closed-shell states in indeno[1,2-a]fluorene molecules on an insulating surface was reported34; however, it was not possible to control the formation of one or the other species, when changing the adsorption site on NaCl.

Under this scenario, a suitable molecular platform to realise such a function was lately discovered, namely, cethrene35 (Fig. 1b, top), which belongs to a class of polybenzenoid helical hydrocarbons formally built from two 2T units (white) fused to an aromatic unit (grey). Their most characteristic feature is the alteration of the electronic structure between quinoidal Kekulé and diradical non-Kekulé forms, with each additional benzenoid ring expanding the helical backbone36. The first homologue in this series, Kekulé [7]cethrene, possesses a singlet ground state (S = 0) and a low-energy triplet excited state whose thermal population is dictated by the magnitude of the energy gap between the two spin states37. Using a dimethyl derivative of this homologue, [7]cethrene-Me2, it has been demonstrated38 that reversible ring closure of the cethrene scaffold can be promoted by light or heat in solution (Fig. 1b, top). Although this switch did not produce a magnetic response, as the triplet state of [7]cethrene-Me2 is thermally inaccessible at room temperature, an analogous magnetic photoswitch operating at cryogenic temperatures was later reported39 by Dumele and coworkers, validating the concept (Fig. 1b, bottom).

Here, we present the second homologue in the cethrene series, a helical non-Kekulé diradical with a triplet ground state—[8]cethrene (Fig. 1c). Using a STM tip-induced bond formation/breakage, this molecular system can be switched controllably and reversibly between two distinct structures: an open-shell form (1) with ferromagnetically coupled spins (S = 1) and a closed-shell form (2), therefore behaving as a spin switch, as we experimentally demonstrate by means of low-temperature STM and STS.

On metal surfaces, the magnetic ground state of open-shell species typically manifests as zero- or low-bias features in the STS spectra40 that can be assigned to the total spin of the system according to the observed line shape. The appearance/disappearance of such spectral features (e.g., zero-bias Kondo resonance41) can thus be attributed to a switching behaviour between magnetic/non-magnetic states. Up until now, the on–off switching of the Kondo resonance has been achieved by covalent bonding to the surface42 or to a hydrogen atom43, intra-44 and intermolecular45 conformational changes, geometrical distortion46, magnetic field47, electron-injection-induced coordination48, and variation of a tip–sample distance49. In addition, a molecular switch based on Bergman cyclisation of a diyne system on NaCl/Cu(111) was described, although the on–off switching was tracked via the observation of structural changes, and no low-bias spectroscopy was reported50. In our system, the appearance/disappearance of an under-screened Kondo resonance relies on a controlled chemical transformation that alters the chemical bonding within the molecular skeleton, making [8]cethrene a prototypic single-molecule system in which fully directed and reversible switching of the magnetic ground state is achieved via an intramolecular reaction. The switching process can be observed by monitoring such an under-screened Kondo resonance, attributed to ferromagnetic correlations (triplet ground state, S = 1), that is either on or off depending on the form that the switch adopts upon the application of bias voltage or specific scanning parameter conditions with the STM tip: open = Kondo on, closed = Kondo off. Because of its spin-delocalised open-shell electronic structure, [8]cethrene is suited for implementation into nanographene-based spin chains and lattices as a spin-switch unit for controlling magnetism and quantum information.

Results
The target [8]cethrene was prepared by combining51 the solution-phase synthesis (Fig. 2a) with a tip-induced activation on a metal surface (Fig. 2b). The key intermediate in our synthetic strategy was the dihydro-precursor of [8]cethrene (2H-1) comprising two phenalene units fused to a naphthalene unit, synthesised starting from dialdehyde352. In the first step, the Wittig reaction of 3 and 4 was performed to quantitatively afford intermediate 5 equipped with side chains required for the closure of the last two rings of the skeleton. Photocyclodehydrogenation of 5 was employed to construct the [6]helicene backbone, affording intermediate 6 in 56% yield. Subsequently, hydrolysis, acyl chloride formation, and Friedel–Crafts acylation provided diketo compound 7 in 66% yield over the three steps. Finally, 7 was subjected to reduction and dehydration to afford dihydro-precursor 2H-1 in 32% yield, which was used for on-surface deposition. All intermediates and the target compound were characterised by nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HRMS); the structures of 7 and 2H-1 are additionally supported by single-crystal X-ray diffraction analysis (XRD; see Supplementary Information), both revealing the fully assembled helical skeleton composed of eight six-membered rings.

To probe whether [8]cethrene can be generated in solution, 2H-1 was oxidised with p-chloranil in toluene under oxygen-free conditions, leading to the formation of a precipitate within 30 minutes. On exposure of this suspension to air, diketo compound 8 was isolated, the structure of which was confirmed by NMR spectroscopy and XRD analysis (see Supplementary Information). These observations suggest that oxidation of 2H-1 generates reactive mono- and/or diradical species, which form under the reaction conditions insoluble σ-oligomers. Upon exposure to air, these oligomers may transform into 8 either directly or via dissociation into monomeric mono- and/or diradical species. However, because the formation of free [8]cethrene in solution could not be directly confirmed and the involvement of monoradical intermediates cannot be excluded, its solution-phase generation remains inconclusive.

To investigate the electronic properties and switching behaviour of [8]cethrene, the dihydro-precursor 2H-1 was deposited onto a clean Au(111) surface at room temperature under ultra-high vacuum (UHV) conditions. At low molecular coverage, after cooling the sample down to 4.7 K, the molecules are found as isolated species, preferably adsorbed at the elbow site of the 22×√3 (“herringbone”) surface reconstruction. While still offering interesting details to unravel the general picture9, molecular adsorption on such under-coordinated sites53–56 may affect the electronic properties of the species under investigation. Therefore, lateral manipulation of the molecules away from these reactive sites was routinely performed with the STM tip to reduce the interaction with the substrate and access the intrinsic electronic properties of the studied species (Supplementary Fig. 18).

An overview of the observed structures on the Au(111) surface upon deposition of 2H-1 and after applying different bias voltages from the STM tip is shown in Fig. 2b. It should be noted that the observed transformations were not always occurring in a stepwise manner according to the sequences shown in the chemical sketch of Fig. 2b, but an event promoted by applying voltage could entail more than one reaction step, as shown by the corresponding arrows (e.g., direct transformation of 2H-1 to 1). The DFT-computed STM images of all the structures adsorbed on the Au(111) surface offered excellent agreement with the experimental images, thus confirming our assignment of the different species (Fig. 2c, experimental and theoretical STM images).

The pristine precursor 2H-1 displays a characteristic trapezoidal shape with a bright lobe non-symmetrically displaced with respect to the molecular centre, representing the upper end of the helical moiety that is more distant from the surface plane (Fig. 2c). Annealing of the as-prepared sample until complete molecular desorption did not induce any intramolecular chemical transformations. Thus, a voltage pulse (see Methods) from the STM tip was applied to induce dehydrogenation57 of 2H-1 in an attempt to achieve the target [8]cethrene. Initially, monoradical species H-1 and H-1’ were obtained, with one hydrogen atom being removed in each case from the lower or upper half of the molecule, respectively. Experimentally, such events result in the appearance of characteristic lobes at one of the two ends of the molecule (white arrows in the STM images of H-1 and H-1’ in Fig. 2c). Further hydrogen atom removal from H-1 and H-1’ was achieved by applying a stronger voltage pulse to afford species 1, which could also be accessed directly from the precursor 2H-1. The STM image of 1 features two pairs of lobes, one at the lower and one at the upper end of the molecule, indicating the formation of the target diradical [8]cethrene (1). In some cases, when attempting the dehydrogenation of specie H-1 to 1, a skeletal rearrangement accompanied by the loss of five hydrogen atoms was observed, affording planar specie 10. The planarity of the molecule facilitated us to confirm its chemical structure by nc-AFM measurements using a CO-functionalized tip, which was not possible for all previous, highly non-planar species. The resulting constant-height frequency-shift image of 10 features two five- and one seven- in addition to six-membered rings.

To obtain information about the electronic nature of 1, we performed low-bias dI/dV spectroscopy (Fig. 3). We observed two types of spectroscopic features, one for molecules located on the elbows of the Au(111) herringbone reconstruction (Fig. 3a, d, g) and another one for molecules located in other areas of the Au(111) surface (Fig. 3b, e, h). When 1 is located on the elbow, we observe a spectroscopic feature centred at the Fermi level, which we attribute to an narrow Kondo resonance (FWHM ∼3 meV), consistent with an unpaired electron spin (S = ½) interacting with the electron bath of Au(111) (Fig. 3g). This finding suggests that 1 might be pinned to the elbow site of the herringbone ridge, possibly binding to an under-coordinated gold atom9,53–56, which could lead to a reduction in the number of unpaired electrons from two to one (see Fig. 3a for the corresponding chemical sketch).

The spectrum on 1 located in other areas (out of elbow) of the Au(111) reconstruction reveals a subtle but noticeable difference with respect to 1 pinned to the elbow (Fig. 3h). Herein, a Kondo feature is also observed. However, this feature is now accompanied by two small and symmetric shoulders around the Fermi energy (Fig. 3h). These shoulders can be attributed to spin-flip features suggesting very low ferromagnetic correlations (triplet ground state, S = 1) with an exchange coupling energy of J_eff ∼ 8 meV. The emergence of magnetism in 1 is qualitatively reproduced by gas-phase calculations via mean-field Hubbard (MFH, Supplementary Fig. 24) and DFT, with a triplet ground state preferred over a singlet antiferromagnetic one by a few meV (7 meV by MFH and 20 meV by DFT). Therefore, this underscreened S = 1 Kondo effect implies that, when 1 is away from the elbow site, it is no longer pinned to the gold surface with one unpaired electron being “quenched”, and the two unpaired electrons in 1 interact ferromagnetically with one another. Interestingly, the detection of such spin-flip features in molecules with a triplet ground state and small exchange coupling energies explored on metal surfaces by STS measurements is often challenging. Rather small magnetic fields58 or fittings using the Frota function21,59 have already been reported to confirm their magnetic nature. However, in the present case, and other reported ones displaying relatively large exchange coupling energies60, the spin-flip features can be directly detected by STS. Finally, to discard any mechanical manipulation or influence of the spin state caused by the STM tip while scanning over the molecule, we have acquired dI/dV spectra measured at different tip heights. Retracting or approaching the tip ±200 pm with respect to the starting position did not give rise to any noticeable modification of the dI/dV spectra (Supplementary Fig. 19), while approaching closer than 200 pm leads to the lateral displacement/desorption of 1.

Next, we addressed the challenge of reversible intramolecular transformation with the aim of switching the magnetic character of 1 off and then turning it on again. To our delight, the switching was achieved by applying a voltage of 3.2 V to 1 or by scanning over the molecule with very low bias voltages (V_b = 5 to −200 mV, I_t = 20 to 100 pA). These specific experimental conditions promoted the transformation of 1 into 2 (Fig. 4). During this intramolecular process, a new C–C bond is formed, which alters the electronic configuration of the molecule and renders it formally a closed-shell structure (Fig. 3c, f, i). Indeed, low-bias dI/dV spectroscopy of 2 did not reveal any features that could be ascribed to the presence of unpaired electrons (Fig. 3i). Notably, this process was found to be reversible, and species 2 could be transformed back into species 1 by scanning over the molecule with a large bias (V_b = −1.5 V, I_t = 20 pA). The energy barrier to convert 1 into 2 (the latter being more stable by 0.08 eV) is 0.29 eV, while that of the reverse transformation is 0.37 eV, as computed by climbing image nudged elastic band (CI-NEB) calculations61. The switching from species 1 to 2 and vice versa was experimentally tested 40 times (20 times transforming 1 into 2 and 20 times transforming 2 into 1). The switching was successfully achieved in all cases when induced during the scan, with a 100% yield. When applying a higher voltage instead, the result of the transformation was sometimes different; namely, a hydrogen atom was removed from 2, yielding species 9, a monoradical with one hydrogen atom protruding out of the molecule (Fig. 2b). Note that scanning over 1 or 2 using intermediate voltage parameters (from 0.1 V to 1.4 V and from –0.2 V to –1.4 V, with I = 20 pA) does not give rise to any molecular transformation. An illustrative sequence of the reversible switching process of [8]cethrene, including the employed scanning parameters, is shown in Fig. 4 (complete series of seven transformations is shown in Supplementary Fig. 20).

We also notice that the molecule under investigation often moved during the transformation from 1 to 2 (i.e., it slightly changed its adsorption location on the Au(111) surface, see Supplementary Fig. 21) in both cases of “voltage pulses” and the “scanning method”. In contrast, the molecule preserved its adsorption location during the transformation of 2 into 1. Finally, in one case, we observed the transformation from 1 to 2 during the lateral manipulation of specie 1 (while dragging the molecule out of an elbow site). All these observations suggest the following scenario for the reversible switching between 1 and 2: In both cases of “voltage pulse” or “scanning method”, molecule 1 receives a mechanical excitation that makes it relax into specie 2, which is slightly more stable than 1 (by 0.08 eV; as computed by DFT for the two species adsorbed on Au(111)). On the other hand, specie 2 can be converted back into 1 while scanning at bias voltages close to the energy of its frontier orbitals (i.e., –1.5 V, as shown in Supplementary Fig. 22), suggesting a mechanism based on hole-injection into the HOMO.

We have demonstrated the directed magnetic bistability in a non-Kekulé nanographene diradical, where reversible switching of the ground-state spin—from triplet (S = 1) to singlet (S = 0)—is enabled through intramolecular ring-closing reaction promoted by tip-induced voltage pulses at the helical [8]cethrene molecule. This hydrocarbon spin switch was achieved by combining a solution-phase synthesis employed to construct the dihydro-precursor with a stepwise tip-induced activation on a metallic surface to yield mono- and diradical species in two consecutive dehydrogenation steps. The low-bias dI/dV spectra of the open diradical form of the switch located outside the Au(111) elbow sites show a Kondo feature that is accompanied by a spin-flip signature attributed to an under-screened spin triplet, in agreement with theoretical calculations. Upon applying a bias voltage pulse of 3.2 V or specific scanning conditions, the open-shell form undergoes an intramolecular transformation to the closed-shell form, during which a new bond and a new ring are formed. The low-bias dI/dV spectra of the closed-shell form do not display any features that would indicate the presence of unpaired electrons, which is in accord with the closed-shell electronic structure of this species. This switching process was found to be fully reversible. In light of the recent developments enabling bottom-up construction of nanographene-based multispin arrays, this work puts forward a tool for direct manipulation of spin and thereby brings prospects for applications in the areas of carbon magnetism and quantum information processing.

Methods
Solution-phase synthesis
Synthetic protocols and characterisation data for all compounds are compiled in the Supplementary Information.

X-ray crystallography
Single crystals for all three compounds were obtained from the corresponding CD2Cl2 solutions by slow evaporation of the solvent in an NMR tube under a stream of nitrogen. Single-crystal X-ray diffraction data were collected at 160(1) K on a Rigaku OD SuperNova/Atlas area-detector diffractometer using a single-wavelength X-ray source (Cu Kα radiation: λ = 1.54184 Å62) or an Oxford Instruments Cryojet XL cooler. The selected suitable single crystal was mounted using polybutene oil on a flexible loop fixed on a goniometer head and immediately transferred to the diffractometer. Pre-experiment, data collection, data reduction and analytical absorption correction63 were performed with the programme suite CrysAlisPro64. Using Olex265, the structure was solved with the SHELXT66 small-molecule structure-solution programme and refined with the SHELXL2018/3 programme package62 by full-matrix least-squares minimisation on F2. PLATON67 was used to check the result of the X-ray analysis. For more details about the data collection and refinement parameters, see the CIF files. Crystal parameters are available in the Supplementary Information.

On-surface experiments
Synthesis and measurements were performed under UHV conditions in two independent custom-designed ultra-high vacuum systems (base pressure below 2×10−10 mbar) hosting commercial low-temperature microscopes with STM/AFM capabilities from Scienta Omicron. Au(111) substrates (MaTeck GmbH) were cleaned by repeated cycles of Ar+ sputtering (1 keV) and annealing (470 °C). The precursor molecules were thermally evaporated onto the clean Au(111) surface from quartz crucibles heated at 165 °C, which resulted in a deposition rate of ~0.5 Å·min–1. STM images were acquired at 4.7 K in constant-current mode using an etched tungsten tip. Bias voltages are given with respect to the sample. nc-AFM measurements were performed at 4.7 K with a tungsten tip placed on a qPlus tuning fork sensor68. The tip was functionalized with a single CO molecule at the tip apex picked up from the previously CO-dosed surface69. The sensor was driven at its resonance frequency (24800 Hz) with a constant amplitude of 70 pm. The frequency shift from resonance of the tuning fork was recorded in constant-height mode using Omicron Matrix electronics and HF2Li PLL by Zurich Instruments. The Δz is positive (negative) when the tip-surface distance is increased (decreased) with respect to the STM set point at which the feedback loop is opened.

In our work, we have used two types of external stimuli to achieve the molecular transformations: (i) “voltage pulses” (i.e., bias ramping with the tip at a constant height, far from the molecule, as described below) and (ii) “scanning method”, i.e., specific scanning conditions during constant-current STM image acquisition. While voltage pulses have been successfully used for all molecular transformations depicted in Fig. 2, they could not induce the transformation of 2 into 1 (i.e., the reversible switching described in our manuscript). In this case, the only successful strategy found by us was the “scanning method” (–1.5 V/20 pA). Regarding the voltage applications reported in Fig. 2, they are not standard pulses applied within a short time frame, but performed by placing the tip on top of the molecule and ramping up the bias voltage until an event occurs. This method guarantees more controlled and reproducible modifications and assessing of voltage thresholds. Standard procedure is as follows: (i) stop the tip on top of the molecule – in the centre, as the electric field will interest the entire molecule – with scanning parameters V_b = 0.1 V, I_t = 10 pA; (ii) open the feedback loop; (iii) increase Δz of +0.5 nm (tip moves away from the molecule) such that the tunnelling current is almost zero; (iv) slowly ramp up the bias voltage while monitoring the current-vs-time signal: a sudden jump indicates an event, which typically occurs within a few seconds after reaching of the required voltage; (v) ramp down the bias to V_b = 0.1 V, I_t = 10 pA; (vi) close the feedback-loop; (vii) restart the scan.

The dI/dV measurements were obtained with a lock-in amplifier operating at a frequency of 800 Hz. Modulation voltages for each measurement are reported as root-mean-squared amplitude (V_rms). Tunnelling bias voltages are given with respect to the sample.

Theory
All DFT calculations were performed using the AiiDA lab platform70 and AiiDA workflows71 based on the CP2K code72. The surface–adsorbate systems were modelled in the repeated slab scheme. The simulation cell consisted of four atomic layers of gold along the [111] direction. A layer of hydrogen atoms was used to passivate one side of the slab to suppress the Au(111) surface state. A vacuum of 40 Å was included in the simulation cell to decouple the system from its periodic replicas in the direction perpendicular to the surface. The electronic states were expanded using a TZV2P Gaussian basis set73 for carbon and hydrogen species and a DZVP basis set for gold species. A cutoff of 600 Ry was used for the plane-wave basis set. Norm-conserving Goedecker–Teter–Hutter pseudo-potentials74 were used to represent the frozen core electrons of the atoms. We used the Perdew–Burke–Ernzerhof parameterisation for the generalised gradient approximation of the exchange-correlation functional75. To account for van der Waals interactions, we used the D3 scheme proposed by Grimme76. The gold surface was modelled using a super-cell, with a size of 41.3 × 40.8 Å2 (896 gold atoms corresponding to 224 surface unit cells). The Au(111) slab was planar, and the herringbone reconstruction associated with this surface was not considered, as it would greatly expand the supercell and not substantially change the chemical activity of the surface77. 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. STM images were simulated within the Tersoff–Hamann approximation78 based on the Kohn–Sham orbitals of the slab/adsorbate systems. The orbitals were extrapolated to the vacuum region in order to correct the wrong decay of the charge density due to the localised basis set. To compute the triplet/singlet energy difference in the gas phase, we used the geometry of the adsorbed molecule and unrestricted Kohn–Sham DFT, starting from a ferromagnetic (antiferromagnetic) guess and imposing a multiplicity of 3 (1). From the same geometries, we built a tight-binding model considering one orbital and one electron per carbon atom. Given the non-planarity of the molecules considered, we computed the hoppings t_ij between carbon sites i and j using a Slater–Koster formalism for the angular dependence, and assuming an exponential decay with the distance (see ref. 79 for details and parameters). In the mean-field Hubbard routine, we considered an on-site Hubbard repulsion of U = 3 eV, and a tolerance of 10–6 for the convergence of the spin-resolved densities in the self-consistent loops.

Data availability
All data associated with this study are available in the published Article and its Supplementary Information. The raw NMR and IR data generated in this study have been deposited in the public repository Zenodo under the accession link https://zenodo.org/record/8253265 (https://doi.org/10.5281/zenodo.8253265). The X-ray crystallographic coordinates for structures reported in this study have been deposited at the Cambridge Crystallographic Data Centre (CCDC), under deposition numbers 2289143 (7), 2289144 (2H-1) and 2446997 (8). These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif. The on-surface data (experimental and computational, including Cartesian coordinates) generated in this study have been deposited in the Materials Cloud repository under the accession link https://doi.org/10.24435/materialscloud:ae-s0. All data are available from the corresponding authors upon request.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "This work used solution-phase synthesis to synthesize the key precursor 2H-1, and then obtained a helical two-radical molecule-[8]cethrene with a ferromagnetically coupled ground state by tip-induced dehydrogenation on the Au(111) surface. By detecting zero-bias or low-bias characteristics in STS spectra, specifically, Kondo effect and spin-flip feature, the authors demonstrated that reversible magnetic ground state switching can be achieved by tip-induced intramolecular transformation on [8]cethrene. The manuscript is well-written and the target helical molecule-[8]cethrene is novel. However, the understanding of the mechanism of tip manipulation deserves further exploration. More experimental data and mechanistic discussion should be supplied before it can be published in Nature Communication.\n1. The experimental conditions for realizing the conversion from 1 to 2 are confusing. For voltage ramping, the bias threshold is 3.2 V, and molecule 1 also can be activated with very low bias voltages (V = -5 mV). Why is the bias difference between the two ways is so great? Generally, the bias voltages of electronic excitation are high, because the holes/electrons are injected into the molecular orbital. But the vibration excitation mechanism is often accompanied by a lower bias threshold (for example, the energy of C–H vibrational modes is about ~400 meV). Additionally, can the conversion from 2 to 1 be achieved by biasing ramping?\n2. The mechanism of the tip manipulation is not clear. Referring to the reported studies, detailed statistical data of reversible experiments and manipulation mechanism should be provided. Specifically, Is tip-induced manipulation due to the electronic excitation, vibrational excitation or electric field? Is the process one electron process or a multiple-electron process? What about switching yields?\n3. What are the energy barriers for bond formation/breakage between molecules 1 and 2? Whether they are related to the bias thresholds for tip manipulation?\n4. Is it possible to obtain STS spectra with wide ranges of molecules 1 and 2 and dI/dV maps of corresponding peak positions, and explain them through DFT calculations?\n5. Although the authors write in the Method section that the tip is placed at the center of the molecule during the tip manipulation, no indication is marked in Figure 4. The site of manipulation on molecules 1 and 2 should be clearly indicated. In addition, have the authors attempted manipulation at different positions of the molecule 1 and 2 and does their voltage thresholds change? Regardless of whether it changes or not, manipulation experiments on different positions would benefit the understanding of the manipulation mechanism.\n6. In Page 8, line 194, the authors mentioned that the exchange coupling energy of molecule 1 was calculated using DFT in gas phase. However, the detailed description of the calculation is not found in the Method section and Supporting Information.\nAdditionally, some minor issues should be noticed:\n1. Page 6, line 137. The subgraphs in Figure 2 were not labeled with a, b, c….\n2. Page 8, line 176. The values of scale bars should be provided, although they are same.", "reviewer_2": "In this manuscript, the authors report the new non-Kekulé hydrocarbon [8]cethrene and its on surface synthesis. The hydrogenated precursor is prepared in solution, deposited on an Au(111) surface and dehydrogenated applying a voltage. The subsequent chemical reaction sequence is studied in detail using scanning tunnelling microscopy (STM) and further supported by theoretical computations. The dehydrogenated target diradical 1 can be reversibly converted to a closed form non-radical molecule 2 by applying different scanning voltages. Further dehydrogenations from 2 were also observed and thoroughly characterized.\nOverall, the manuscript is at a high level of scientific presentation. For an expert reader, it is well-written and clearly understandable. The characterization of all compounds synthesized in solution is conclusive and partially unambiguous structural proof is provided by single-crystal X-ray diffraction. The on-surface characterization is conclusive but could perhaps extended using more specialized techniques to express the magnetic key features of the molecule, such as EPR-sensitive STM (Physical Review Research 2, 013032 (2020)). However, this could be done in a follow-up study and is not required to publish the current manuscript.\nIn summary, I highly recommend publication after minor revisions of some points as listed below. Congratulations to the authors on this fantastic piece. This study closes the gap of on-surface spin state switching with all-organic molecules (see my comments below).\n1: It remains open whether the authors have attempted the full solution-phase synthesis of the targeted structures 1 or 2 (or 8), starting from 2H-1 or 7? What experiments were conducted (conditions, outcome, observations), and did any of the attempts lead to similar side products, such as compound 9?\n2: The citation of references 39 (and 40) is misleading when describing the [7]cethrene-Me2 case. It should be clarified that these references refer not to dimethyl[7]cethrene but to a different spin-state switch. The difference in structure and properties should also be shown in Figure 1 to give context of the current design. I admit this is the previous work of this reviewer and typically I refrain from suggesting references to my own work during the peer review process. However, it might be the most relevant context to this study.\n3: Previous work on spin state switching on an Ag-surface based on an organic ligand system on a metal-porphyrin was reported. The switching trigger was the injection of an electron. The paper should be cited: Nature Nanotechnology 2020, 15, 18–21. Their read-out was also based on the Kondo resonance.\n4: The solvent system to obtain single-crystal of 2H-1 is inconsistent. In figure 2 (top right); CH2Cl2 and in X-ray crystallography methods CD2Cl2.\n5: I highly suggest specifying the title and mentioning the “on surface” study in the title. The field of surface science is clearly distinguished and many phenomena that can be observed on surface are practically impossible to achieve in bulk solution. The current study is one such example and it should be reflected in the title, maybe as “On-surface controlled magnetic bistability of a helical non-Kekulé hydrocarbon” or “Controlled magnetic bistability of a helical non-Kekulé hydrocarbon on Au(111) surface”.", "reviewer_3": "The authors report the synthesis of an interesting molecule revealing a bistability as a diradical and as a closed-shell structure. The molecules are characterized on a Au(111) surface under vacuum by STM, whose spectroscopic variant allows probing magnetic fingerprints of the molecules. The switching is triggered by the STM current, allowing for an in-situ characterization of the reversible switching process. The results are very interesting and the data convincing. I thus consider the manuscript appropriate for publication, provided the authors address the following issues:\n- Although the Introduction and Conclusion sections are labelled, there is no label for Results, which is very confusing in the first reading, knowing this is not a letter.\n- As the authors describe in the main text, there have been many reports on the on and off switching of Kondo resonances by various means. In this respect, to really warrant sufficient novelty to this work, they should show that the switching is really controllable and at least provide a better characterization of it (e.g. switching traces or average life time as a function of bias, switching probability as a function of bias and/or current…). Right now it is extremely vaguely described, providing three “switching conditions” (3.2 V pulse, U=-5mV/I=20pA scan and U=-1.5V/I=20pA scan) that are neither compared nor quantitatively analyzed by any means.\n- The assignment of 1 at the herringbone elbows to S=1/2 is not fully convincing. The tails around the Kondo resonance actually cause an impression as if they could be made up by the same lateral side-peaks/excitations as out-of-elbow, only a little bit broader or worse resolved. The authors should discuss this option."}, "author_response": "Response to Reviewer's Comments\nReviewer 1\n1. The experimental conditions for realizing the conversion from 1 to 2 are confusing. For voltage\nramping, the bias threshold is 3.2 V, and molecule 1 also can be activated with very low bias\nvoltages (V = -5 mV). Why is the bias difference between the two ways is so great? Generally, the\nbias voltages of electronic excitation are high, because the holes/electrons are injected into the\nmolecular orbital. But the vibration excitation mechanism is often accompanied by a lower bias\nthreshold (for example, the energy of C–H vibrational modes is about ~400 meV).\nWe appreciate the reviewer’s comment. We understand that the conditions required for the\nconversion from 1 to 2 and vice versa may need further clarification. First, we would like to stress\nthat our main purpose was to find conditions to achieve a reversible and controllable switching\nbetween the two species, while a detailed mechanistic insight into the processes driving the\nconversion is out of the scope of the present study. In our work, we have used two types of external\nstimuli to achieve the molecular transformations: (i) “voltage pulses” (i.e., bias ramping with the\ntip at constant heigh, far from the molecule, as described in the methods) and (ii) “scanning\nmethod”, i.e., specific scanning conditions during constant current STM image acquisition. While\nvoltage pulses have been successfully used for all molecular transformation depicted in Figure 2,\nthey could not induce the transformation of 2 into 1 (i.e., the reversible switching described in our\nmanuscript). In this case, the only successful strategy found by us was the “scanning method”\n(–1.5 V / 20 pA). After discovering this pathway, we also applied the “scanning method” to attempt\nthe transformation from 1 to 2 and found that indeed the expected product was achieved when\nscanning in the range +5… –200 mV / 20…100 pA (updated in the new Figure 2 in our revised\nmanuscript).\nWe also notice that the molecule under investigation moved during the transformation from 1 to 2\n(i.e., it slightly changed its adsorption location on the Au(111) surface) in both cases of “voltage\npulses” and the “scanning method”. In contrast, the molecule preserved its adsorption location\nduring the transformation of 2 into 1. Finally, in one case, we observed the transformation from 1\nto 2 during the lateral manipulation of specie 1 (while dragging the molecule out of an elbow site).\nAll these observations suggest the following scenario for the reversible switching between 1 and 2:\nIn both cases of “voltage pulse” or “scanning method”, molecule 1 receives a mechanical excitation\nthat makes it relax into the slightly more stable (by 0.08 eV) specie 2 (see the energy landscape in\nour reply to point 3 and Figure R1 below). On the other hand, specie 2 can be converted back into\n1 while scanning at bias voltages close to the energy of its frontier orbitals (i.e. –1.5 V, as shown in\nour reply to point 4 and Figure R2 below), suggesting a mechanism based on hole-injection into the\nHOMO.\nAdditionally, can the conversion from 2 to 1 be achieved by biasing ramping?\nNo, when ramping the bias on molecule 2, we have only observed the transformation of 2 into 8, as\nindicated in Figure 2 of our manuscript.\n1/9\nAction: We have included a Figure in the SI (Supplementary Fig. 21) showing the displacement of\nmolecules 1 and their subsequent transformation to 2 while scanned at certain parameters.\nAdditionally, we have improved the description of external stimuli application to achieve the\ndesired molecular transformations (both in the Methods and in the main text) and included a\ndiscussion of the possible mechanisms driving the switching behavior, as follows:\n• In the Methods: “[…]The Δz is positive (negative) when the tip-surface distance is increased\n(decreased) with respect to the STM set point at which the feedback loop is opened. In our work,\nwe have used two types of external stimuli to achieve the molecular transformations: (i) “voltage\npulses” (i.e., bias ramping with the tip at a constant height, far from the molecule, as described\nbelow) and (ii) “scanning method”, i.e., specific scanning conditions during constant current STM\nimage acquisition. While voltage pulses have been successfully used for all molecular\ntransformation depicted in Figure 2, they could not induce the transformation of 2 into 1 (i.e., the\nreversible switching described in our manuscript). In this case, the only successful strategy found\nby us was the “scanning method” (–1.5 V / 20 pA). Regarding the voltage applications reported in\nFigure 2, they are not standard pulses[…]”\n• In the main text: “[…]An illustrative sequence of the reversible switching process of [8]cethrene\nincluding the employed scanning parameters is shown in Fig. 4 (complete series of seven\ntransformations is shown in Supplementary Fig. 20). We also notice that the molecule under\ninvestigation often moved during the transformation from 1 to 2 (i.e., it slightly changed its\nadsorption location on the Au(111) surface, see Supplementary Fig. 21) in both cases of “voltage\npulses” and the “scanning method”. In contrast, the molecule preserved its adsorption location\nduring the transformation of 2 into 1. Finally, in one case, we observed the transformation from 1\nto 2 during the lateral manipulation of specie 1 (while dragging the molecule out of an elbow site).\nAll these observations suggest the following scenario for the reversible switching between 1 and 2:\nIn both cases of “voltage pulse” or “scanning method”, molecule 1 receives a mechanical excitation\nthat makes it relax into specie 2, which is slightly more stable than 1 (by 0.08 eV; as computed by\nDFT for the two species adsorbed on Au(111)). On the other hand, specie 2 can be converted back\ninto 1 while scanning at bias voltages close to the energy of its frontier orbitals (i.e., –1.5 V, as\nshown in Supplementary Fig. 22), suggesting a mechanism based on hole-injection into the HOMO.”\n2. The mechanism of the tip manipulation is not clear. Referring to the reported studies, detailed\nstatistical data of reversible experiments and manipulation mechanism should be provided.\nSpecifically, Is tip-induced manipulation due to the electronic excitation, vibrational excitation or\nelectric field? Is the process one electron process or a multiple-electron process? What about\nswitching yields?\nWe are grateful to the reviewer for this comment. Our reply to point 1 offers clarifications regarding\nthe switching mechanisms occurring during tip manipulation. When using the methods and\nconditions described in our manuscript, the switching yields between 1 and 2 are found to be 100%.\n2/9\nAction: We have included new description and discussions, as per our reply to point 1, and added\nthe switching yield value, as follows: “[…]The switching was successfully achieved in all cases\nwhen induced during the scan, with a 100% yield. When applying a higher voltage instead[…]”\n3. What are the energy barriers for bond formation/breakage between molecules 1 and 2? Whether\nthey are related to the bias thresholds for tip manipulation?\nThe energy barrier for bond formation/breakage was found to be 0.29/0.37 eV, respectively. The\ndiagram showing the energy landscape is reported below for completeness. The energy values were\nobtained by performing a climbing image nudged elastic band (CI-NEB) calculations [Ref. 60].\nThe activation barriers for the two processes are similar and could not directly justify the difference\nobserved in the scanning parameters used for the switching from 1 to 2 and vice versa. Instead, we\nprovide a different argument in our reply to point 1.\nFigure R1. Energy landscape for the bond formation/breakage leading to the transformation of 1 to\n2 and vice versa, computed by CI-NEB calculations.\nAction: We have included these values in the text:\n“Notably, this process was found to be reversible, and species 2 could be transformed back into\nspecies 1 by scanning over the molecule with a large bias (V = −1.5 V, I = 20 pA). The energy barrier\nb t\nto convert 1 into 2 (the latter being more stable by 0.08 eV) is 0.29 eV, while that of the reverse\ntransformation is 0.37 eV, as computed by climbing image nudged elastic band (CI-NEB)\ncalculations60. The switching from…”\n4. Is it possible to obtain STS spectra with wide ranges of molecules 1 and 2 and dI/dV maps of\ncorresponding peak positions, and explain them through DFT calculations?\nWe thank the reviewer for this valuable comment. We have acquired STS spectra for both\nmolecules obtaining the dI/dV maps of corresponding frontier orbitals for 1. Due to the three-\ndimensional geometry of the molecule, it was difficult to achieve clear DOS distributions to be\nassociated to specific molecular orbitals. Moreover, the acquisition of the dI/dV maps for 2 at the\ncorresponding peak positions led to the transformation of the molecule. Therefore, we decided to\nonly include the STS point spectra in the SI file.\nAction: STS point spectra showing the energy position of the frontier orbitals (Figure R2) have now\nbeen added to the SI file.\n3/9\nFigure R2. Long-range scanning tunneling spectroscopy of species 1 and 2. a) Differential\nconductance spectra on selected positions of 1; the positions at which the spectra on the\nmolecule were acquired is highlighted in the inset STM topography image with filled blue and\ngreen circles. Open feedback parameters: V = 2.3 V, I = 100 pA, V = 20 mV. b) Differential conductance spectra\nb t rms\non selected positions of 2. The purple and red circles highlight the positions at where the spectra\nwere acquired, showing features assigned to the HOMO and LUMO frontier orbitals. Open feedback\nparameters: (positive region) V = -1.0 V, I = 100 pA, V = 20 mV; (negative region) V = 1.0 V, I =100\nb t rms b t\npA, V = 20 mV. The orange circles in the inset images of (a and b) correspond to the reference\nrms\ndI/dV spectra acquired on Au(111).\n5. Although the authors write in the Method section that the tip is placed at the center of the\nmolecule during the tip manipulation, no indication is marked in Figure 4. The site of manipulation\non molecules 1 and 2 should be clearly indicated. In addition, have the authors attempted\nmanipulation at different positions of the molecule 1 and 2 and does their voltage thresholds\nchange? Regardless of whether it changes or not, manipulation experiments on different positions\nwould benefit the understanding of the manipulation mechanism.\nWe thank the reviewer for their useful comment which has helped us to improve the manuscript.\nThe switching between 1 and 2 described in Figure 4 has been realized by acquiring STM images\nwith specific scanning parameters (see i) and ii) in its figure caption). Therefore, following such\nprotocol the tip is not located at a precise position of the molecule. We apologize if the description\nin the Methods was not clear enough and we have now modified the corresponding text accordingly,\nalso in reply to previous points, highlighting the difference between the “voltage pulses” and\n“scanning method”.\nDuring “voltage pulses” (i.e., bias ramping with the tip at constant heigh, far from the molecule, as\ndescribed in the revised version of the Methods) the tip was located at the “brighter” positions of\nmolecules 1 and 2 (observed in the STM images), which, according with DFT calculations\ncorrespond to the segments of the molecules that are adsorbed further away from the surface.\nThese locations provide, in our opinion, a more accessible point for achieving the transformation,\nwhile we have not systematically varied the manipulation site across the molecular structure.\n4/9\nHowever, we have acquired repeated STM images varying the bias voltage (from 0.1 V to 1.4 V and\nfrom –0.2 V to –1.4V, with I = 20 pA) without observing the switching between 1 and 2, suggesting\nthat there is no voltage threshold change within the applied parameters.\nAction: We have added a clarification sentence in the figure caption, the Method section and the\ntext related to the scanning parameters used in the transformation between 1 and 2.\n• Figure caption of Figure 2: “Middle: Chemical sketch of the structures observed on the Au(111)\nsurface upon deposition of 2H-1 and applying voltage from the STM tip (see Method section for\nexperimental details and voltage application procedure). Arrows indicate the direction of the\nobserved transformations and the numbers bellow arrows specify the voltage between the tip and\nthe sample at which the transformation was observed (ranges arise from multiple experiments).”\n• Methods section: “Regarding the voltage applications reported in Figure 2, they are not standard\npulses applied within a short time frame, but performed by placing the tip on top the molecule and\nramping up the bias voltage until an event occurs.”\n• Main text: “[…]protruding out of the molecule (Fig. 2 middle). Note that scanning over 1 or 2 using\nintermediate voltage parameters (from 0.1 V to 1.4 V and from –0.2 V to –1.4 V, with I = 20 pA) does\nnot give rise to any molecular transformation. An illustrative sequence of the reversible switching\nprocess[…]”\n6. In Page 8, line 194, the authors mentioned that the exchange coupling energy of molecule 1 was\ncalculated using DFT in gas phase. However, the detailed description of the calculation is not found\nin the Method section and Supporting Information.\nWe are thankful to the reviewer for pointing out this missing information.\nAction: We have added the missing information to the Methods section as follows:\n“[…]The orbitals were extrapolated to the vacuum region in order to correct the wrong decay of the\ncharge density due to the localized basis set. To compute the triplet/singlet energy difference in the\ngas phase, we used the geometry of the adsorbed molecule and unrestricted Kohn–Sham DFT,\nstarting from a ferromagnetic (antiferromagnetic) guess and imposing a multiplicity of 3 (1). From\nthe same geometries, we built a tight-binding model considering[…]”.\nAdditionally, some minor issues should be noticed:\n1. Page 6, line 137. The subgraphs in Figure 2 were not labeled with a, b, c….\nWe thank the Reviewer for noticing this inconsistency.\nAction: We now refer to the respective parts of Fig. 2 as top, middle, and bottom in accordance\nwith the Fig. 2 caption.\n2. Page 8, line 176. The values of scale bars should be provided, although they are same.\nIn Figure 3, the image sizes change slightly.\nAction: Hence, we left the scale bars at each STM image and added the value on top of the first one,\nto be consistent with the layout of Figure 4.\n5/9\nReviewer 2\n1. It remains open whether the authors have attempted the full solution-phase synthesis of the\ntargeted structures 1 or 2 (or 8), starting from 2H-1 or 7? What experiments were conducted\n(conditions, outcome, observations), and did any of the attempts lead to similar side products, such\nas compound 9?\nWe thank the Reviewer for raising this point. We had not included the solution-phase results in the\noriginal manuscript, as the primary focus was on surface chemistry. However, we agree that these\nfindings provide valuable supporting information and may be of interest to solution chemists. We\nhave now incorporated a description of these results into the main text and added the\ncorresponding characterization data for compound 8 (NMR, HRMS, XRD) to the Supplementary\nInformation. Please note that due to these additions, the numbering of compounds has been\nupdated: compounds 8 and 9 are now referred to as 9 and 10, respectively.\nAction: We have added the following paragraph in the main text:\n“[...]both revealing the fully assembled helical skeleton composed of eight six-membered rings.\nTo probe whether [8]cethrene can be generated in solution, 2H-1 was oxidised with p-chloranil in\ntoluene under oxygen-free conditions, leading to the formation of a precipitate within 30 minutes.\nOn exposure of this suspension to air, diketo compound 8 was isolated, the structure of which was\nconfirmed by NMR spectroscopy and XRD analysis (see Supplementary Information). These\nobservations suggest that oxidation of 2H-1 generates reactive mono- and/or diradical species,\nwhich form under the reaction conditions insoluble σ-oligomers. Upon exposure to air, these\noligomers may transform into 8 either directly or via dissociation into monomeric mono- and/or\ndiradical species. However, because the formation of free [8]cethrene in solution could not be\ndirectly confirmed and the involvement of monoradical intermediates cannot be excluded, its\nsolution-phase generation remains inconclusive.\nTo investigate the electronic properties and switching behaviour of [8]cethrene, the dihydro-\nprecursor 2H-1 was deposited[...]”\n2: The citation of references 39 (and 40) is misleading when describing the [7]cethrene-Me2 case.\nIt should be clarified that these references refer not to dimethyl[7]cethrene but to a different spin-\nstate switch. The difference in structure and properties should also be shown in Figure 1 to give\ncontext of the current design. I admit this is the previous work of this reviewer and typically I\nrefrain from suggesting references to my own work during the peer review process. However, it\nmight be the most relevant context to this study.\nWe agree with the Reviewer that this aspect was not sufficiently clear and that featuring this switch\nin Figure 1 is important, as it represents the most relevant example of a solution-phase magnetic\nswitch. We thank the Reviewer for raising this important point.\nAction: We modified the main text (as well as Fig. 1) accordingly:\n6/9\n“[...]can be promoted by light or heat in solution (Fig. 1, middle). Although this switch did not\nproduce a magnetic response, as the triplet state of [7]cethrene-Me is thermally inaccessible at\n2\nroom temperature, an analogous magnetic photoswitch operating at cryogenic temperatures was\nlater reported39 by Dumele and coworkers, validating the concept (Fig. 1, middle).\nHere, we present the second homolog in the cethrene series[...]”\n3: Previous work on spin state switching on an Ag-surface based on an organic ligand system on a\nmetal-porphyrin was reported. The switching trigger was the injection of an electron. The paper\nshould be cited: Nature Nanotechnology 2020, 15, 18–21. Their read-out was also based on the\nKondo resonance.\nWe appreciate the Reviewer’s careful reading and for noting the absence of this important\nreference.\nAction: We have mentioned this example and included the corresponding reference:\n“Up until now, the on–off switching of the Kondo resonance has been achieved by covalent bonding\nto the surface42 or to a hydrogen atom43, intra-44 and intermolecular45 conformational changes,\ngeometrical distortion46, magnetic field47, electron-injection-induced coordination48 and variation\nof a tip–sample distance49”\n4: The solvent system to obtain single-crystal of 2H-1 is inconsistent. In figure 2 (top right); CH2Cl2\nand in X-ray crystallography methods CD2Cl2.\nWe thank the Reviewer for spotting this mistake. The correct solvent is CD₂Cl₂. However, since the\nXRD structure in Fig. 2 has been replaced with that of compound 8, the product obtained after\nexposing 2H-1 to oxidant and then air, this correction is no longer necessary.\n5: I highly suggest specifying the title and mentioning the “on surface” study in the title. The field of\nsurface science is clearly distinguished and many phenomena that can be observed on surface are\npractically impossible to achieve in bulk solution. The current study is one such example and it\nshould be reflected in the title, maybe as “On-surface controlled magnetic bistability of a helical\nnon-Kekulé hydrocarbon” or “Controlled magnetic bistability of a helical non-Kekulé hydrocarbon\non Au(111) surface”.\nWe thank the Reviewer for this suggestion, with which we fully agree. We adopted the second\nproposed option.\nAction: The title was modified to “Controlled magnetic bistability of a helical non-Kekulé\nhydrocarbon on a Au(111) surface”.\nReviewer 3\n1. Although the Introduction and Conclusion sections are labelled, there is no label for Results,\nwhich is very confusing in the first reading, knowing this is not a letter.\nWe thank the Reviewer for bringing this to our attention.\n7/9\nAction: The label \"Results and discussion\" was added in the main text.\n2. As the authors describe in the main text, there have been many reports on the on and off\nswitching of Kondo resonances by various means. In this respect, to really warrant sufficient\nnovelty to this work, they should show that the switching is really controllable and at least provide\na better characterization of it (e.g. switching traces or average life time as a function of bias,\nswitching probability as a function of bias and/or current...). Right now it is extremely vaguely\ndescribed, providing three \"switching conditions\" (3.2 V pulse, U=-5mV/I=20pA scan and U=-\n1.5V/I=20pA scan) that are neither compared nor quantitatively analyzed by any means.\nWe appreciate the reviewer’s insightful comment. Previously reported studies on on/off Kondo\nresonances induced by lateral manipulation (Mishra, S., et al., Nat. Nanotechnol. 15, 81 (2020)) or\ntip-controlled dehydrogenation (Zhao, C., et al., Phys. Rev. Lett. 132, 046201 (2024)) describe\nirreversible processes, where a specific nanographene reaches a final magnetic ground state. The\nkey novelty of our work lies in achieving a reversible spin switch, where the system can be\ntoggled between two magnetic states in a controlled and repeatable manner via external\nstimuli. This switching is highly reproducible, as highlighted in the manuscript:\n“The switching from species 1 to 2 and vice versa was experimentally tested 40 times (20 times\ntransforming 1 into 2 and 20 times transforming 2 into 1). The switching was successfully achieved\nin all cases when induced during the scan.”\nRegarding the characterization of switching conditions, we have conducted additional experiments\nto deepen our understanding of the phenomenon. The corresponding modifications in the main text\nand supporting information have been addressed in our response to Reviewer 1 (questions 1 and\n5).\n3. The assignment of 1 at the herringbone elbows to S=1/2 is not fully convincing. The tails around\nthe Kondo resonance actually cause an impression as if they could be made up by the same lateral\nside-peaks/excitations as out-of-elbow, only a little bit broader or worse resolved. The authors\nshould discuss this option.\nWe appreciate the Reviewer’s observation. The interpretation of S = 1/2 state at the herringbone\nelbows for 1 is based on both the experimentally obtained Kondo resonances and reinforced by\nseveral previous works of magnetic nanographenes pinned by gold at the reactive elbow sites.\nThough the three spectra shown in Figure 3 were acquired with identical open-feedback\nparameters (see Figure caption), we acknowledge that the spectral tails of the Kondo resonance\ncould, at first glance, resemble the lateral side-peaks observed for species 1 in out-of-elbow\nlocations. Therefore, we have performed more spectroscopic measurements of different species 1\nlocated on the elbows observing always the same symmetric profile, consistent with a single\nscreening channel for an S = 1/2 system (Figure R3).\n8/9\nFigure R3. Electronic characterization of species 1 on the elbow. For four different species 1 no\nlateral side-peaks/excitations can be discerned. Open-feedback parameters for the dI/dV spectra:\na) V = 50 mV, I = 0.35 nA; root mean squared modulation voltage V = 0.8 mV. b) V = -1 V,\nb t rms b\nI = 0.1 nA; root mean squared modulation voltage V = 10 mV. c,d) V = 50 mV, I = 0.5 nA; root\nt rms b t\nmean squared modulation voltage V = 0.8 mV. (a, b and c) were acquired with a CO-\nrms\nfunctionalized tip while (c) was acquired with a metal tip.\nAction: We have included more references to literature where a magnetic nanographene is pinned\nto the gold substrate at an elbow site as well as softened our statement regarding the assignment\nof 1 at the herringbone elbows and now the text reads as follows:\n“When 1 is located on the elbow, we observe a spectroscopic feature centered at the Fermi level,\nwhich we attribute to a narrow Kondo resonance (FWHM ∼3 meV), consistent with an unpaired\nelectron spin (S = ½) interacting with the electron bath of Au(111) (Fig. 3g). This finding suggests\nthat 1 might be pinned to the elbow site of the herringbone ridge, possibly binding to an under-\ncoordinated gold atom9,52,53,54,55, which could lead to a reduction in the number of unpaired\nelectrons from two to one (see Fig. 3a for the corresponding chemical sketch).”\n9/9"}, {"round": 2, "reviewer_comments": {"reviewer_1": "The long-range STS of species 1 and 2 were provided in the revised SI. The results reveal a significant difference in term of HOMO-LUMO energy gap and their energy level. For instance, the HOMO position shifts nearly 1 eV lower from specie 1 to specie 2. How does this experimental finding compare with the theoretical results?", "reviewer_2": "The authors present a fully revised version of their manuscript. All my comments have been addressed perfectly. I want to congratulate the authors on these results. Great job.\nI recommend publication without further changes.", "reviewer_3": "The authors have satisfactorily answered my comments and I find the article now acceptable for publication."}, "author_response": "Response to Reviewer's Comments\nReviewer 1\nRemarks to the Author:\nThe long-range STS of species 1 and 2 were provided in the revised SI. The results reveal a\nsignificant difference in term of HOMO-LUMO energy gap and their energy level. For instance,\nthe HOMO position shifts nearly 1 eV lower from specie 1 to specie 2. How does this\nexperimental finding compare with the theoretical results?\nFigure S1. Long-range scanning tunneling spectroscopy of species 1 and 2. a) Differential\nconductance spectra on selected positions of 1; the positions at which the spectra on the\nmolecule were acquired is highlighted in the inset STM topography image with filled blue and\ngreen circles. Open feedback parameters: V = 2.3 V, I = 100 pA, V = 20 mV. b) Differential\nb t rms\nconductance spectra on selected positions of 2. The purple and red circles highlight the\npositions at where the spectra were acquired, showing features assigned to the HOMO and\nLUMO frontier orbitals. Open feedback parameters: (positive region) V = –1.0 V, I = 100 pA,\nV = 20 mV; (negative region) V = 1.0 V, I =100 pA, V = 20 mV. The orange circles in the\nrms b t rms\ninset images of (a and b) correspond to the reference dI/dV spectra acquired on Au(111).\n1/4\nReply:\nWe thank the reviewer for pointing out the ambiguity in the labeling of Figure S22. The\nsignificant difference in the observed energy gaps arises from their fundamentally different\nphysical origins. For species 2, the gap corresponds to the conventional HOMO–LUMO gap in\nclosed-shell molecules, determined by the hybridization of the two zero modes (see Figure\nR1b). In contrast, species 1 is an open-shell system with two ferromagnetically coupled spins\nin two singly occupied molecular orbitals (SOMOs). In this case, the gap is not governed by\nhybridization but instead by the Coulomb gap, which must be overcome to add an additional\nelectron to a SOMO (see Figure R1a). Theoretical results confirm that the Coulomb gap is\nsmaller than the HOMO–LUMO gap. In the experiments, we have attempted measuring LDOS\nmaps at relevant bias values, but the bulky and 3D structure of the molecules prevented a\nclear distinction of the specific orbitals in play. However, according to the new theoretical\ninsights, we can assign the states observed in the experimental long-range STS spectra. For\nspecies 1, the peak observed at about –0.5 V (previously assigned to HOMO) is now identified\nas SOMO. The SUMO is not visible, as sometimes experienced in similar systems (K. Biswas,\net al. Nanomaterials 2022, 12, 224; S. Mishra, et al. Nat. Chem. 2021, 13, 581–586; A. Sanchez-\nGrande, et al. Angew. Chem. Int. Ed. 2020, 59, 17594-17599). The state observed at +2.1 V\n(previously assigned to LUMO) is assigned to the LUMO+1. For species 2, we confirm the\ncorrect assignment of HOMO and LUMO for the states at –1.3 V and +1.4 V, respectively.\nFigure R1: Energy levels of molecule 1 (a) and molecule 2 (b), obtained for the ground state\nsolution of the corresponding MFH models (see Methods for details). Solid black line denotes\nthe Fermi level.\n2/4\nAction taken:\nWe have revised the labeling of the ion resonances in Figure S22a to \"SOMO\" and \"LUMO+1\".\nMoreover, we have included the new theoretical results in the same figure, for a\ncomprehensive description of the observed spectral features. Finally, the corresponding\ndescription of the long-range STS spectra has been revised as follows:\nFigure S22. Long-range scanning tunneling spectroscopy of species 1 and 2. a. Differential\nconductance spectra on selected positions of 1; the positions at which the spectra on the\nmolecule were acquired is highlighted in the inset STM topography image with filled blue and\ngreen circles. Open feedback parameters: V = 2.3 V, I = 100 pA, V = 20 mV. b. Differential\nb t rms\nconductance spectra on selected positions of 2. The purple and red circles highlight the\npositions at where the spectra were acquired. Open feedback parameters: (positive region)\nV = –1.0 V, I = 100 pA, V = 20 mV; (negative region) V = 1.0 V, I =100 pA, V = 20 mV. The\nb t rms b t rms\norange circles in the inset images of a and b correspond to the reference dI/dV spectra\nacquired on Au(111). c,d. Energy levels of molecule 1 (c) and molecule 2 (d), obtained for the\nground state solution of the corresponding MFH models (see Methods for details). Solid black\nline denotes the Fermi level.\n3/4\nFor species 2, the gap corresponds to the conventional energy difference between the highest\noccupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO)\n(HOMO–LUMO gap) in closed-shell molecules, determined by the hybridization of the two zero\nmodes (see panel d). In contrast, species 1 is an open-shell system with two ferromagnetically\ncoupled spins in two singly occupied molecular orbitals (SOMOs). In this case, the gap is not\ngoverned by hybridization but instead by the Coulomb gap, which must be overcome to add\nan additional electron to a SOMO (see panel c). The experimental scanning tunneling\nspectroscopy (STS) results detect the HOMO and LUMO states for species 2 at –1.3 V and +1.4\nV, respectively. In the case of molecule 1, instead, we revealed the SOMO at –0.5 V and the\nLUMO+1 at +2.1 V, while the SUMO was not experimentally detected. Both the experimental\nand theoretical results confirm that the Coulomb gap is smaller than the HOMO–LUMO gap.\n4/4"}, {"round": 3, "reviewer_comments": {"reviewer_1": "The revision is recommended for publishing"}, "author_response": ""}]

Decision letter