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[20231125 Nat Com 2023_14_7741 s41467-023-43659-4.pdf](https://mdr.nims.go.jp/filesets/c0ae2e4f-138e-4c0d-b4ef-946e8bebcf81/download)

## Creator

[Shigeki Kawai](https://orcid.org/0000-0003-2128-0120), [Orlando J. Silveira](https://orcid.org/0000-0002-0403-9485), [Lauri Kurki](https://orcid.org/0000-0002-5027-7847), [Zhangyu Yuan](https://orcid.org/0000-0001-8028-2893), [Tomohiko Nishiuchi](https://orcid.org/0000-0002-2113-0731), [Takuya Kodama](https://orcid.org/0000-0001-8275-2393), [Kewei Sun](https://orcid.org/0000-0002-1835-243X), [Oscar Custance](https://orcid.org/0000-0001-7931-603X), [Jose L. Lado](https://orcid.org/0000-0002-9916-1589), [Takashi Kubo](https://orcid.org/0000-0001-6809-7396), [Adam S. Foster](https://orcid.org/0000-0001-5371-5905)

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[Local Probe-Induced Structural Isomerization in a One-Dimensional Molecular Array](https://mdr.nims.go.jp/datasets/365c6cba-5b5f-4e72-9266-43f698124811)

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Local probe-induced structural isomerization in a one-dimensional molecular arrayArticle https://doi.org/10.1038/s41467-023-43659-4Local probe-induced structural isomeriza-tion in a one-dimensional molecular arrayShigeki Kawai 1,2 , Orlando J. Silveira3, Lauri Kurki 3, Zhangyu Yuan1,2,TomohikoNishiuchi 4,5, TakuyaKodama 4,5, Kewei Sun 1,OscarCustance 1,Jose L. Lado 3, Takashi Kubo 4,5 & Adam S. Foster 3,6Synthesis of one-dimensional molecular arrays with tailored stereoisomers ischallenging yet has great potential for application in molecular opto-, elec-tronic- and magnetic-devices, where the local array structure plays a decisiverole in the functional properties. Here, we demonstrate the construction andcharacterization of dehydroazulene isomer and diradical units in three-dimensional organometallic compounds on Ag(111) with a combination of low-temperature scanning tunneling microscopy and density functional theorycalculations. Tip-induced voltage pulses firstly result in the formation of adiradical species via successive homolytic fission of two C-Br bonds in thenaphthyl groups, which are subsequently transformed into chiral dehy-droazulene moieties. The delicate balance of the reaction rates among thediradical and two stereoisomers, arising from an in-line configuration of tipand molecular unit, allows directional azulene-to-azulene and azulene-to-diradical local probe structural isomerization in a controlled manner. Fur-thermore, our theoretical calculations suggest that the diradical moiety hostsan open-shell singlet with antiferromagnetic coupling between the unpairedelectrons, which can undergo an inelastic spin transition of 91meV to theferromagnetically coupled triplet state.Atomic force microscopy and scanning tunnelling microscopy (STM),operating at low temperature under ultrahigh vacuum conditions, arepowerful tools to investigate single molecules down to the atomicscale1. The combination of bond-resolved imaging with a CO termi-nated tip2,3 and structural isomerization via homolytic fission4–9, inparticular, opened the field of local probe chemistry. In such studies,halo-substituted planar molecules are adsorbed on surfaces and sub-sequently the C-X bonds (where, X=Cl, Br, I) are cleaved by the tun-neling current flowing from the tip. However, a radical species directlyadsorbedon ametal surface is very short-lived, immediately stabilizingby connecting to surface atoms. A common method to electronicdecouple molecules from the metal substrate is by an NaCl ultrathinfilm10–12, and this also can be used to prevent the stabilization of theradical and allows for the realization of a non-short-lived product atlow temperature4–9(Fig. 1a, c). By connecting two radicals through tip-induced manipulations, dimers have been successfully synthesized13.This bond manipulation process can also be repeated for dihaloge-nated molecules, resulting in a highly unstable diradical species(Fig. 1)4,5,8,9.An alternative approach to an insulating layer on the metal, is touse three-dimensional (3D) hydrocarbons, in which a large gapbetween the outer group and the metal substrate also prevents theReceived: 15 September 2023Accepted: 15 November 2023Check for updates1Center for Basic Research on Materials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan. 2Graduate School of Pure and Applied Sciences,University of Tsukuba, Tsukuba, Japan. 3Department of Applied Physics, Aalto University, Helsinki, Finland. 4Department of Chemistry, Graduate School ofScience, Osaka University, Toyonaka, Japan. 5Innovative Catalysis Science Division (ICS), Institute for Open and Transdisciplinary Research Initiatives (OTRI),Osaka University, Suita, Osaka, Japan. 6WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma- machi, Kanazawa, Japan.e-mail: KAWAI.Shigeki@nims.go.jp; kubo@chem.sci.osaka-u.ac.jp; adam.foster@aalto.fiNature Communications |         (2023) 14:7741 11234567890():,;1234567890():,;http://orcid.org/0000-0003-2128-0120http://orcid.org/0000-0003-2128-0120http://orcid.org/0000-0003-2128-0120http://orcid.org/0000-0003-2128-0120http://orcid.org/0000-0003-2128-0120http://orcid.org/0000-0002-5027-7847http://orcid.org/0000-0002-5027-7847http://orcid.org/0000-0002-5027-7847http://orcid.org/0000-0002-5027-7847http://orcid.org/0000-0002-5027-7847http://orcid.org/0000-0002-2113-0731http://orcid.org/0000-0002-2113-0731http://orcid.org/0000-0002-2113-0731http://orcid.org/0000-0002-2113-0731http://orcid.org/0000-0002-2113-0731http://orcid.org/0000-0001-8275-2393http://orcid.org/0000-0001-8275-2393http://orcid.org/0000-0001-8275-2393http://orcid.org/0000-0001-8275-2393http://orcid.org/0000-0001-8275-2393http://orcid.org/0000-0002-1835-243Xhttp://orcid.org/0000-0002-1835-243Xhttp://orcid.org/0000-0002-1835-243Xhttp://orcid.org/0000-0002-1835-243Xhttp://orcid.org/0000-0002-1835-243Xhttp://orcid.org/0000-0001-7931-603Xhttp://orcid.org/0000-0001-7931-603Xhttp://orcid.org/0000-0001-7931-603Xhttp://orcid.org/0000-0001-7931-603Xhttp://orcid.org/0000-0001-7931-603Xhttp://orcid.org/0000-0002-9916-1589http://orcid.org/0000-0002-9916-1589http://orcid.org/0000-0002-9916-1589http://orcid.org/0000-0002-9916-1589http://orcid.org/0000-0002-9916-1589http://orcid.org/0000-0001-6809-7396http://orcid.org/0000-0001-6809-7396http://orcid.org/0000-0001-6809-7396http://orcid.org/0000-0001-6809-7396http://orcid.org/0000-0001-6809-7396http://orcid.org/0000-0001-5371-5905http://orcid.org/0000-0001-5371-5905http://orcid.org/0000-0001-5371-5905http://orcid.org/0000-0001-5371-5905http://orcid.org/0000-0001-5371-5905http://crossmark.crossref.org/dialog/?doi=10.1038/s41467-023-43659-4&domain=pdfhttp://crossmark.crossref.org/dialog/?doi=10.1038/s41467-023-43659-4&domain=pdfhttp://crossmark.crossref.org/dialog/?doi=10.1038/s41467-023-43659-4&domain=pdfhttp://crossmark.crossref.org/dialog/?doi=10.1038/s41467-023-43659-4&domain=pdfmailto:KAWAI.Shigeki@nims.go.jpmailto:kubo@chem.sci.osaka-u.ac.jpmailto:adam.foster@aalto.fistabilization of the radical by the underlying metal surface even underthe absence of a decoupling layer14. Furthermore, since this systemoffers an in-line configuration between the tip and the outer group ofthe molecule, the probe can directly sense hydrogen15,16 and halogenbonds17. When a tip terminated by either a bromine atomor a fullerenemolecule is brought into proximity to the unpaired electron speciespointing out from the surface, a molecule-by-molecule additionalreaction can also be conducted14. This 3D configuration is also bene-ficial to investigate the electronic property of the radical species andtheir isomerization.Here, we measure electronic and magnetic properties of radicalspecies in 3D organometallic compounds (OMCs). The C-Br bondpointing out from the surface is studied in detail by a combination oflow-temperature STM and density functional theory (DFT) calcula-tions. The electronic properties of radical species obtained by thesequential removal of bromine atoms using the tunneling current wereinvestigated by scanning tunneling spectroscopy (STS). Since the dir-adical species are energetically unstable under debromination condi-tions, isomerization to dehydroazulene is immediately caused. Tuningthe reaction rate by the tip-sample gap, we found that the array unitcan be switched between three configurations of the diradical and twodehydroazulenes by the local probe in a controlled manner (Fig. 1c).Results and DiscussionOn-surface synthesis of 3D-OMC and electronic propertiesWe employed 3D-OMC for local probe isomerization (Fig. 2a)14,18.Hexabromo-substituted trinaphtho[3.3.3]propellane (6Br-TNP) mole-cules were in situ deposited on clean Ag(111) surfaces under ultra-highvacuum conditions and subsequently annealed to synthesize 3D-OMC(Fig. 2b). Most of the out-of-plane C-Br bonds in the product remainedintact because no catalysis from the surface metal was induced(Fig. 2c). When the bias voltage was set higher than 2.5 V, the targetedC-Br bond was cleaved by the tunneling current. This process washighly reproducible, as a series of bromine atoms were removed oneby one in a controlled manner (Fig. 2d and Supplementary Figure 1)14;the remaining darker ovals indicate the absence of the bromine atoms.Since the naphthyl group missing two bromine atoms is fairly distantfrom the metal substrate, we assumed at first that the product shouldbe a diradical. Fromnowonwewill discuss the electronic properties ofthe naphthyl group before and after debromination and its con-sequential effects.We first measured the electronic property of the C-Br moiety inthe 3D-OMC with STS before the debromination (Fig. 2e) and foundthat highest occupied molecular orbital (HOMO) and lowest unoccu-pied molecular orbital (LUMO) levels are located at -1.7 V and 1.8V,respectively. Note that the debromination was caused by setting thebias voltage above the LUMO level (2.5 eV). This is consistent withother studies exploring the mechanism of debromination in detail12.Next, we measured the electronic property of the fully-debrominatedunit and found significant energy shifts depending on the measuredsites (Fig. 2f). The constant height dI/dVmaps taken at the LUMO andHOMO levels show distinct contrasts between the C-Br bond and itsdebrominated sites. While the measured dI/dVmap shows a textbook-like symmetric contrast on the C-Br bond site due to the π states(Fig. 2g), an asymmetric contrast appeared on the debrominated siterevealing the lower part brighter than the upper part (Fig. 2h andSupplementary Figure 2). In order to understand the observed differ-ence in contrast before and after debromination, we conducted DFTcalculations considering the ribbon structure on top of an Ag(111)surface (see Methods and Supplementary Fig. 3). The simulated den-sity of states (DOS)map of the dibrominated site is in good agreementwith the experimental data (Fig. 2i). However, the STM simulatedimages of the diradical 2 reveal two symmetrical bright spots at bothnegative and positive biases, which is inconsistent with our experi-mental findings and an indication that the diradical 2 is not the finalproduct of the debromination (Supplementary Fig. 4). To account forthis inconsistency, we considered a large variety of possible atomicstructures as alternatives to the diradical2, including the role of Br andH terminations, and isomerization. We found an excellent agreementfor the dehydroazulene structure 3 (Fig. 2j) and propose that theasymmetric structure corresponds to the dehydroazulene groupformed by the rearrangement of the naphthyl group19,20—this structureis about 0.5 eV lower in energy than 2. The analysis of the calculatedDOS (Fig. 2k, l) shows a sufficient decoupling of the imaged states fromthe Ag(111) substrate, with a clear gap and no states between theHOMO (-1.0 eV) and LUMO (0.5 eV), in agreement with the experi-mental spectra. The removal of Br results in the dominant states seenin simulated images (Fig. 2j), corresponding to the seven-memberedring (lower part) in thedehydroazulenemoietywith aweaker signatureof thefive-membered ring (upper part) seen in the image at -1.8 V (bothrings are seen for negative bias and only the seven membered forpositive bias). The calculated molecular orbitals in vacuum havesimilar features to the electron-rich part at the 1-, 8-, and 10-positionsof dehydroazulene (Fig. 1) producing a clover-like HOMO, whereas theelectron deficient part at the 8- and 9-positions produces a cotyledon-like LUMO (Fig. 2m, n). This consistency indicates a small interactionbetween the dehydroazulene group and the underlying metal sub-strate although the three-fold propellane core is strongly distorted bythe adsorption to the metal substrate15.Local probe-induced structural isomerizationWe found that applying a large bias voltage induces a reversible chiralswitch of the dehydroazulene unit. The tip was first positioned abovethe seven-membered ring (bright site, as indicated by a red cross inFig. 3a) and subsequently the bias voltage was swept to a more nega-tive value from zero. We detected abrupt changes in the tunnelingcurrent at an applied bias voltage of −2.3 V (Fig. 3b). In the transitionevent, the tunneling current first suddenly decreased towards a morenegative value and then abruptly decreased. This reduction of thetunneling current corresponds to an increase of the tunneling gap.Br BrBrBrBrBrBr Br1 233'12345678 910abcdFig. 1 | Local probe rearrangements of small aromatic compounds. a Tip-induced syntheses of single aryne4, b 3,4-benzocyclodeca-3,7,9-triene-1,5-diyne5,and c Songheimer-Wong diyne molecules8. d Tip-induced syntheses of diradical 2and dehydrozulene 3 units in one-dimensional molecular array.Article https://doi.org/10.1038/s41467-023-43659-4Nature Communications |         (2023) 14:7741 2Indeed, the initial bright spots darkened accompanied with an asym-metric contrast flip (Fig. 3c), indicating a successful chiral switch. Wefound that the switch can also be caused by applying a positive biasvoltage of 2.2 V at the dark site as indicated by a red cross (Fig. 3c, e).This chiral switch (3 () 3’) should occur through an energeticallyhigher lying diradical intermediate 2, which was the final productproposed before. To understand the manipulation mechanism, wecalculated the energy barrier of the isomerization to the dehy-droazulene unit 3 from the diradical unit 2 (Fig. 3f and SupplementaryNote 1) and found that it is about 1.1 eV. Therefore, the isomerizationshould not occur without the influence of the tip at low temperature.The barrier height is also of an order that could be generally overcomeby a combination of population of antibonding states weakening thebonds with a current heating due to inelastic electron tunneling, as wepreviously demonstrated14. This energy diagram also indicates thatwhen the second debromination is induced, the molecular unit isimmediately transformed to the dehydroazulene, as we very rarelyobserved a symmetric contrast (Supplementary Fig. 5). To prove thehigh-reproducibility of the local probe isomerization, we created anembedding of 19 texts with the standard 8-bit binary ASCII code in theselected heptamer units, similar to the previous demonstration withseveral arrays of Fe atoms by Loth et al.21. The breadboard was pre-pared by sequential cleavage of C-Br bonds by applying high-biasvoltages at chosen positions of the 3D-OMC (Supplementary Figure 6).Since the chirality of the isomers was initially random, we first reset allto be 0000 0000, namely “00” in the hexadecimal format. Then, thechirality of each unit was sequentially switched. Flipping four units, weembedded 0100 1110, which denotes “N”. By conducting 71 sub-sequent manipulations, we typed “Nanoprobe GRP. NIMS©” (Fig. 3g),demonstrating the high controllability of the chiral in the dehy-droazulene array by tip-induced isomerization (SupplementaryMovie 1).7600 �Z (pm)10 nm3D-OMCDebrominationTipab6380 �Z (pm)1 nm6220 �Z (pm)1 nmdcmax.min. dI/dV max.min. dI/dV-1.8 V 1.8 Vhigmax.min. dI/dV max.min. dI/dVmax.min. dI/dV max.min. dI/dVmax.min. dI/dV max.min. dI/dV300 pm-1.8 V 1.8 V-1.8 V 1.8 VHOMO LUMO300 pmHOMO LUMOnmHOMO LUMOHOMO LUMOfeSample bias (V) Sample bias (V)dI/dVdI/dV-2 -1 00 01 2 -2 -1 0 1 2kDOS (arb. u.)DOS (arb. u.)Energy (eV) Energy (eV)-220-2l240-2-4-1 0 1 2 -2 -1 0 1 2-1.8 V 1.3 Vj500 pm 500 pm300 pm300 pm300 pm 300 pm 300 pm300 pmFig. 2 | On-surface synthesis of 3D-OMC and electronic properties of the unitbefore and after debromination. a Schematic drawings of the three-dimensionalorganometallic compound (3D-OMC) and its diradical species. Red, blue and yellowballs in c,d correspond toBr, H, andAg atoms. Grey lines correspond to C-C bonds,respectively. b Large-scale STM image of 3D-OMCs synthesized on Ag(111). c Closeviewbefore andd after tip-induceddebromination. edI/dV curvesmeasured on thedibrominated naphthyl group 1 and f after the tip-induced debromination. The dI/dV curves were measured at the sites indicated by cross markers with the samecolors in e and f. g, h dI/dVmaps taken at LUMO and HOMO energy levels on 1 andthe debrominated unit. i, j Simulated constant height STM images at the labelledbias voltages and k, l the associated PDOS calculated fromm, n the DFT optimizedstructures on five-layer Ag(111) surfaces on the left, and calculated HOMO andLUMO in vacuum (ROB3LYP-D3/6-311 G**) at the middle and right, respectively.Purple, green, white balls correspond to Br, C, and H, respectively. Purple and lightred surfaces represent the relative signs of the orbital coefficients drawn at 0.04 ebohr−3 level. Measurement parameters: Sample bias voltage V = 500mV and tun-neling current I = 2 pA in b, V = 200mV and I = 5 pA in c, and V = 1 V and I = 10 pAin d.Article https://doi.org/10.1038/s41467-023-43659-4Nature Communications |         (2023) 14:7741 3To investigate the reaction path, the tunneling current wasrecorded as a function of time during the tip-induced isomerization(3→ 2→ 3’, Fig. 3h). As the bias voltagewas kept at −2.3 V, the tunnelingcurrent was constant until a sharp drop occurred, attributed to thepresence of the diradical species 2, which then quickly rebounds to alesser value in magnitude of the tunneling current. This drop in thetunneling current after the rebound is an indication of the chiralswitch, since the tunneling gap between the five-membered ring andthe tipwas larger than that between the seven-membered-ring and thetip. We also found transformation events back to the initial dehy-droazulene. In Fig. 3i, for example, it is shown a case where the tun-neling current rebounds 5 times to the same value of tunnelingcurrent, referring to the 2→ 3 event, until the chiral switch 2→ 3’ finallyoccurs. The probability of reverse isomerization to the initial chiralityfor the diradical was higher than that to another chirality (289 eventsfor 2→ 3 and 129 events for 2→ 3’), indicating that the reaction barrierof 2→ 3’ is higher than that of 2→ 3 under the tip. The short-rangeinteraction with the probe is most probably responsible for the pre-ferential 2→ 3 isomerization. Nevertheless, such tip effects played aminor role in the reaction because once the chiral switch occurred, theprobability to induce the reverse isomerization 3’→ 2 significantlyreduced due to the drastic drop of the tunneling current. We recordedthe tunneling current as a function of time during seven chiralityswitches at 15 different tip-sample distances and obtained meanreaction rates between dehydroazulene and diradical units at differentmean tunneling currents (Fig. 3j). Although the reaction rates scatteredI (pA)Reaction rate (s-1)bd00.510 0.5 1 1.5-0.522-TSTSTS-33fgEnergy (eV)22-TSTSTS-33Reaction coordinate (Å)Time (s) Time (s)0 5 10 0 5 10 15 20Sample bias (V)-10-2-3I (pA)-1000-200-300-400-500h ja 500 pmmax.min. dI/dVcmax.min. dI/dVemax.min. dI/dVI (pA)I (pA)Sample bias (V)Sample bias (V)1. Forward2. Backward1. Forward2. Backward0-1-20-200-400-6000 1 205010015010010010-110-110110-210-2Two-electron process4E 4D 53 A949BinaryHexadecimalASCII4E 61 62 656E 6F 6F70 72N00null na Po or eb20space“ ”47 70 4672RG P .0000000001001110011000010110111001101111011100000111001001101111011000100110010100100000010001110111001001110000001011100100111001001001010011010101001110101001i3 (dehydroazulene) 3 (dehydroazulene)3’ (dehydroazulene) 3’ (dehydroazulene)2 (diradical)2 (diradical)3   2  (1.9)2   3  (1.7)Fig. 3 | Local probe-induced structural isomerization. a, c, e STM topographiesof dehydroazulene units3on a 3D-OMC.b I-V curve taken in negative anddpositivevoltage ranges. Abrupt changes of the tunneling current indicate the tip-inducedisomerization of the dehydroazulene unit. f Calculated energy barrier for thestructural isomerization.g Systematic local probe isomerizationof dehydroazuleneunits on a 3D-OMC. “Nanoprobe GRP. NIMS©” in 8-bit binary ascii code isembedded via sequential 71 isomerization in the dehydroazulene array. The size ofthe image is 1.52 nm× 10.16 nm. h, i Tunneling current as a function of time mea-sured at different tip-sample gaps. Green, gray, and yellow areas indicate the pre-sence of initial dehydroazulene, short-lived diradical and final dehydroazuleneunits, respectively. j Reaction rates of azulene to diradical and diradical to azuleneat different tunneling currents. The values of 1.9 and 1.7 indicate the slopes of linearfitting of each data in the log-log scale. Measurement parameters: V = −1.8 V andVac = 10mV in a, c, e.Article https://doi.org/10.1038/s41467-023-43659-4Nature Communications |         (2023) 14:7741 4particularly at large-tip sample separations, we found that these iso-merization processes were based on a two-electron process via theslopes of the fitted data9, and that the reaction rate of 3→ 2 wasapproximately twelve times higher than that of 2→ 3. To try tounderstand this, we explored the charged states of themolecularunits,using a fragment of the ribbon structure calculated at the B3LYP level22to represent the fact that any charging of the molecular units will betransient and rapidly transferred to the metallic substrate. These cal-culations showed (Supplementary Figure 7) that the diradical−1 is89meV lower in energy than the dehydroazulene−1, suggesting thatelectron attachment plays a role in the observed reaction rates.Diradical array and its electronic and magnetic propertiesWe found that if the tipwas set at a tunneling current gapbelow 100pAwith a sample bias of −2.4 V above the seven-membered ring of thedehydroazulene unit, the diradical usually remained stable for severaltens of seconds. The lifetime was long enough to retract the tip andsubsequently set the bias voltage to 0V so that the diradical could beobtained as a product. By repeating this process, we obtained thediradical unit array in the 3D-OMC (Fig. 4a), which shows a symmetriccontrast of the unit, in good agreement with the simulations (Sup-plementary Figure 4). The tip-induced isomerization among the dir-adical and the twodehydroazulenes units was also highly reproducibleas we could embed “NIMS” in 6-bit ternary ascii code (0: low dehy-droazulene, 1: diradical, 2: high dehydroazulene, Fig. 4b, Supplemen-taryMovie 2). The radical was kept stablewhen the bias voltagewas setin the range of −2 V to 2 V, (Supplementary Figure 8). We also mea-sured the electronic properties of the diradical and the dehy-droazulene units near the Fermi level (Fig. 4c and SupplementaryFigure 9). Note that each curve is shifted for visibility. Although thedifferential conductance curve on the dehydroazulene unit is almostfeatureless, a distinct step-like feature is observedon thediradical unit,displaying a wide gap of 182meV; which is likely related to an inelasticspin flipping transition of the unpaired electrons. Due to electron-electron interactions, a spin-spin coupling between localized electronsin each radical part arises. The value of such Heisenberg couplingdepends on direct and superexchange contributions, leading to theappearance of a many-body excitation that can mediate electron tun-neling. DFT calculations reveal that the ground state of the diradicaldisplays spin-densities with opposite spins concentrated mostly ineach radical part, configuring an open-shell singlet with anti-ferromagnetic (anti-FM) coupling between the unpaired electrons ofthe radical parts, while the triplet state with similar spin-density andunpaired electrons ferromagnetically (FM) coupled is observed100meV above the ground state. Total energies of a fragment of theribbon structure containing the diradical part calculated at the B3LYPlevel shows that the triplet is 50meV above the open shell singlet. Theprevious findings show that the spin ground state of the molecule islikely a spin-singlet, where the exchange spin coupling accounts for theprevious energy difference. An open-shell singlet as the ground statehappens when no strong overlap is observed between the spin orbitalsand has been observed in other diradical-organic molecules such asbenzynes23, for instance, and graphene fragments24–26. The spin densityof anti-FM and FM configurations of the system plus the surface drawnat 0.001 e bohr−3 using the VESTA software27 are shown in Fig. 4d, whilemolecular orbitals and energy levels of a portion of the diradical cal-culated at the B3LYP level are shown in Supplementary Figure 10. Thestep-like conductance increase observed in Fig. 4c is associated withthe inelastic excitation between the singlet and triplet configurationsof themolecule as given by theHamiltonianH = 2JS1 : S2, with S1 and S2being the spin operators in the two dangling orbitals, withSi = ðSxi , Syi , Szi Þ. The energy scale J of such a Hamiltonian can beextracted from first principles by calculating the energy differencebetween the anti-FM ð"#Þ and FM ð""Þ configurations obtainedbyDFT.However, as the inelastic spin transition is given by the singlet-triplet1ffiffi2p ð"# � #"Þ )"" transition (the true eigenstates of the spin Hamil-tonian), the step in the conductance appears at an energy 2 J (Sup-plementary Note 2 and the Refs. 28,29). Based on this, the estimatedtheoretical conductance inelastic step would appear at 100meV,which is fairly close to the measured step 90meV in the dI/dV taken atthe diradical unit. Another small step is observed around ±150mV inthe dI/dV taken at the diradical unit, corresponding to a splitting of60meV. Since the anisotropy energy of the C atoms would be of lessthan 1meV (as reference, the anisotropy energy for Co is 3 meV30,Supplementary Figure 11), and given that the increase in conductanceis much smaller than the spin-flipping transition step, we attribute thisfeature to inelastic tunneling due to vibrational modes of themolecule31(Supplementary Notes 3 and 4). Further DFT calculationsconsidering only a portion of the molecule that stands out from theribbon show that several vibrational modes have the frequency com-patible with the measured gap, and some of these modes have con-tributions fromonly atoms closer to the radical parts, as can be seen inSupplementary Table 1 and Supplementary Figure 12.In summary, we present the synthesis of a dehydroazulene arrayin three-dimensional organometallic compounds via systematic tip-induced debromination and structural isomerization with scanningprobe microscopy at low temperature under ultra-high vacuum. Twochiral dehydroazulene and the diradical configurations can be swit-ched by applying bias voltages in a controlled manner and conse-quently 19 texts were embedded in 8-bit binary and 6-bit ternary asciicode via successful a number of tip-induced local reactions. Further-more, we found that the diradical moiety hosts an open-shell singletthat canundergo an inelastic spin transition fromantiferromagnetic toferromagnetic coupling. Expanding the previous local chemical5780 �Z (pm)1 nmaDiradicalDehydroazuleneDehydroazulene2Br Br BrDiradicalDehydro-     azulene300200-200 100-100-300 00180 meVSample bias (mV)dI/dVc dAg(111) x 1/5b4E 4D 5349TernaryHexadecimalASCII002220002212010002002201EnergyTripletSinglet+100 meVSpin-fliptransition1 nmFig. 4 | Synthesis of a diradical molecular unit array and its electronic andmagnetic properties. a STM topography taken after tip-induced dehalogenationand subsequent isomerization to the diradical units. b Systematic local probe iso-merization to embed “NIMS” in 5-bit ternary ascii code. The size of the image is1.62 nm× 7.66 nm. c dI/dV curves measured at the diradical and dehydroazuleneunits, as well as on Ag(111) for reference. d Schematic visualization of the inelasticspin flipping transition, and the DFT calculated spin densities of the open shell andtriplet states of the diradical unit.Article https://doi.org/10.1038/s41467-023-43659-4Nature Communications |         (2023) 14:7741 5reaction by which unprecedented planar molecules were synthesizedand analyzed at the single-molecule level, we are now able to controlthe structures of the units in themolecular array. In addition to the tip-induced stereo isomerization32, such systematic isomerization is ofimportance to advance nanochemistry towards fabrication of mole-cular systems molecule by molecule.MethodsExperimentalAll the experiments were conducted in a low temperature scanningtunneling microscopy (STM) system (homemade) at 4.3K under anultrahigh-vacuum environment (<1 × 10−10 mbar). The bias voltage wasapplied to the sample while the tip was electrically grounded. Au(111)and Ag(111) surfaces were cleaned through cyclic Ar+ sputtering for10min and annealing at 720K for 15min. Hexabromo-substituted tri-naphtho[3.3.3]propellane (6Br-TNP)14 was deposited from Knudsencells (KentaxGmbH). The impurity of 6Br-TNPwasbelow thedetectionlimit of 1H and 13C NMR measurements and was also confirmed byelemental analysis: Anal. Calcd for C32H12Br6: C, 43.88; H, 1.38. Found:C, 44.00 H, 1.44. The samples were annealed at 370K for 10min toform the organometallic bonded compounds. The STM tip was madefrom a chemically etched tungsten wire. Themodulation amplitude ofthe AC bias voltage was between 2 and 10 mV0-peak and the frequencywas 510Hz.Theoretical calculationsAll first-principles calculations including the surface in this workwereperformed using the periodic plane-wave basis Vienna Ab initiosimulation package (VASP) code33,34 implementing the spin-polarizedDensity Functional Theory. To accurately include van der Waalsinteractions in this system, we used the DFT-D3 method with Becke-Jonson damping35,36. Projected augmented wave potentials were usedto describe the core electrons37 with a kinetic energy cutoff of 500 eV(with PREC = accurate). Systematic k-point convergence was checkedfor all systems with sampling chosen according to the system size.This approach converged the total energy of all the systems to theorder of 1meV. The properties of the bulk and surface of Ag werecarefully checked within this methodology, and excellent agreementwas achievedwith experiments. For simplicity and easier comparisonof electronic structure between isolated molecules and on-surfacemolecular structures, the metallic adatoms binding the OMC to thesurface were neglected in simulations. Previous calculations14showed that there were minimal differences in the OMC and GNRmolecular structures far from the substrate. This can be further seenin a direct comparison between the two in Supplementary Fig. 3. Forcalculations of the ribbons on the surface, a vacuum gap of at least1.5 nm was used, and the size of the silver slab (7 × 6 unit cells) and3D-GNR length (2×1) were chosen to minimize the lattice mismatchcompared to the optimized structure of the unsupported 3D-GNR(4.6% for this combination). A 3 × 3 × 1 k-point grid was used and theupper three layers of Ag (five layers in total) and all atoms in theribbon were allowed to relax to a force of less than 0.01 eV Å−1.Atomic structure visualizations were made with the VMD package38.Simulated STM images were calculated using the CRITIC2package39,40 based on the Tersoff−Hamann approximation41. Anequivalent set of calculations for the azulene structure on the Ausurface was performed, but we observed no significant differenceswith respect to the results on Ag. Barrier calculations were per-formed initially using the standard Nudged Elastic Band (NEB)method with increasing image density42, before implementing theClimbing NEB approach43 to find the final barrier. For these calcula-tions, only the gamma point was used. Additional calculations ofmolecular orbitals and vibrational frequencies at the B3LYP level22were realized with the ORCA code44 using the def2-TZVP basisset45 or Gaussian-16 program (revision B.01)46 with the 6-311G** basisset. We also performed Climbing NEB calculations of the neutral andanionic systems by manually controlling the total charge of the sys-tem, which was either 0 or -1, and all possible spin multiplicities weretaken into consideration. In all calculations performed with ORCA,we considered only fragments of the structure that stand out fromthe ribbon, but appreciate all the local arrangements of the smallaromatic compounds that form the diradical and thedehydroazulene.Data availabilityThe data that support the findings of this study are available from thecorresponding author upon request. The simulateddata is available viaZenodo47.References1. Gross, L. et al. Atomic force microscopy for molecular structureelucidation. Angew. Chem. Int. Ed. 57, 3888–3908 (2018).2. 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Theoretical simulations for: local probe-inducedstructural isomerization in a one-dimensional molecular array.Zenodo https://doi.org/10.5281/zenodo.10077964 (2023).AcknowledgementsThis work was supported in part by the Japan Society for the Promotionof Science (JSPS) KAKENHI Grant Number JP22H00285, and the Acad-emy of Finland project 346824. Computing resources from the AaltoScience-IT project and CSC, Helsinki, are gratefully acknowledged.A.S.F. has been supported by the World Premier International ResearchCenter Initiative (WPI), MEXT, Japan. We thank Ondrej Krejčí for usefuldiscussions.Author contributionsS.K. planned and conducted experiments. S.K., Z.Y., K.S. and O.C. ana-lyzed and discussed the experimental data. T.N., T. Ko. and T. Ku.designed and synthesized the precursor molecule. O.S., L.K., J.L.L.and A.S.F. conducted theoretical calculations. S.K. and A.S.F. con-tributed to writing the manuscript. All authors commented on themanuscript.Competing interestsThe authors declare no competing interests.Additional informationSupplementary information The online version containssupplementary material available athttps://doi.org/10.1038/s41467-023-43659-4.Correspondence and requests for materials should be addressed toShigeki Kawai, Takashi Kubo or Adam S. Foster.Peer review information Nature Communications thanks the anon-ymous reviewers for their contribution to the peer review of this work. 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To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.© The Author(s) 2023Article https://doi.org/10.1038/s41467-023-43659-4Nature Communications |         (2023) 14:7741 7https://doi.org/10.5281/zenodo.10077964https://doi.org/10.1038/s41467-023-43659-4http://www.nature.com/reprintshttp://creativecommons.org/licenses/by/4.0/http://creativecommons.org/licenses/by/4.0/ Local probe-induced structural isomerization in a one-dimensional molecular�array Results and Discussion On-surface synthesis of 3D-OMC and electronic properties Local probe-induced structural isomerization Diradical array and its electronic and magnetic properties Methods Experimental Theoretical calculations Data availability References Acknowledgements Author contributions Competing interests Additional information