Generating Antiaromaticity: Thermally-selective Skeletal Rearrangements at Interfaces

doi:10.21203/rs.3.rs-2371634/v1

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Generating Antiaromaticity: Thermally-selective Skeletal Rearrangements at Interfaces

https://doi.org/10.21203/rs.3.rs-2371634/v1

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published 11 Sep, 2023

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Antiaromatic polycyclic conjugated hydrocarbons (PCHs) are attractive research targets in modern organic chemistry in view of their interesting structural, electronic and magnetic properties. Unlike aromatic compounds, the synthesis of antiaromatic PHs is challenging as a result of their high reactivity and lack of stability, stemming from the small energy gap between their highest occupied and lowest unoccupied molecular orbitals. In this work, we describe a strategy toward the introduction of antiaromatic units in PHs viathermally selective intra- and intermolecular ring-rearrangement reactions of dibromomethylene-functionalized molecular precursors upon sublimation on a hot Au(111) metal surface, not available in solution chemistry. The synthetic value of these reactions is proven by 1) the integration of pentalene segments into acene-based precursors which undergo intramolecular ring-rearrangement; 2) the formation of π-conjugated ladder polymers, linked through cyclobutadiene connections, prior to ring-rearrangement and [2+2] cycloaddition reactions of indenofluorene-based precursors. The elucidation of the reaction products of the title reactions are investigated by scanning tunneling and non-contact atomic force microscopy investigations, and the mechanistic insights are unveiled by state-of-the-art computational studies.

Physical sciences/Chemistry/Surface chemistry/Scanning probe microscopy

Physical sciences/Chemistry/Organic chemistry/Structure elucidation

The concept of antiaromaticity was first introduced by Breslow in 1967 with the aim of explaining the usual instability of molecules with [4n] π-electrons in polycyclic conjugated systems^1,2. In contrast to aromatic molecules³, polycyclic conjugated hydrocarbons (PCHs) that follow the Hückel´s rule⁴, antiaromatic PCHs present π-electron energies higher than that of their open-chain counterparts, turning them kinetically unstable and highly reactive⁵. In addition to the number of conjugated π-electrons within PCHs, the nature of their fragmental structures or subunits should also be considered for their aromatic (or antiaromatic) properties. Nowadays, antiaromatic and aromatic PCHs containing 4n π-subunits are attracting great interest as advanced materials for organic electronics and spintronics, due to a prevalent contribution of the antiaromatic segments to the overall topological, electronic and chemical properties of the PCHs⁶. In view of their high-lying highest occupied molecular orbital (HOMO) and low-lying lowest unoccupied molecular orbital (LUMO), such PCHs are considered as appealing research targets for small-molecule semiconductors^7,8, n-type materials^9,10 and organic secondary batteries¹¹. For instance, structural modifications in linear acenes such as heteroatom replacement or the incorporation of non-benzenoid rings have recently gained increased attention as an alternative to acenes, which are susceptible to oxidation and dimerization under ambient conditions, reducing their aromaticity to achieve high charge mobilities^12–14. Therefore, the development of stable compounds containing antiaromatic subunits is of utmost demand for further device application.

Modern methods in conventional organic chemistry have recently allowed the synthesis of several polycyclic antiaromatic systems, often requiring the attachment of bulky aryl substituents onto the most reactive sites of the molecule to attain a reasonable kinetic stability. During the last decade, on-surface synthesis has appeared as a profitable alternative to traditional organic chemistry, where the study of well-defined PCHs is reachable thanks to advanced scanning probe techniques, providing key mechanistic information on the reaction pathway^15,16. The two-dimensional (2D) confinement of organic precursors together with the catalytic role of the underlying metal surface are primarily key factors of desirable or unexpected intramolecular reactions and intermolecular carbon-carbon (C–C) couplings, contributing to the expansion of the chemical toolbox of organic materials. Furthermore, additional controllable factors like precursor design, activation method, growth parameters, environmental conditions or substrate nature and symmetry, among others, should also be considered and properly tuned to steer the formation of the reaction products. As a result, a large number of chemical reactions have been successfully achieved on surfaces through non-conventional reaction mechanisms in the last years. For instance, members of the long-pursued acene^17–23, periacene^24–27, indenofluorene^28,29 or triangulene³⁰ families, as well as one-dimensional (1D) polymers that present expected³¹ or unforeseen^32,33 C–C couplings have been recently achieved.

An innovative strategy toward the integration of antiaromatic units in PCHs is related to ring rearrangement reactions. In this respect, thermal rearrangements, in which an atom, ion or chemical unit of a molecule is rearranged to obtain a structural isomer of the original molecule under a thermal stimulus, represents an excellent alternative to induce the formation of novel antiaromatic PCHs and conjugated polymers not accessible otherwise. Only recently, a few strain-induced rearrangement reactions of precursors that are composed of rigid and strained three dimensional (3D) structures have shown skeletal rearrangements in their backbone after planarization on metal surfaces^34–37. In this respect, the selectivity of on-surface chemical reaction pathways is a promising approach to increase synthetic versatility, though remains largely underexplored³⁸. Interestingly, thermal selectivity was confirmed in the case of competing intra- and intermolecular C–C couplings^39,40. Although during the last years the on-surface synthesis of several antiaromatic PCHs^28,41 and polymers^42–48 has been reported, the systematic and well-defined introduction of antiaromatic segments into such carbon-based nanomaterials through skeletal ring rearrangements, however, has been rarely achieved, and disruptive chemical strategies are necessary.

Herein, we introduce new routes toward the generation of antiaromatic segments into members of the acene and indenofluorene families through thermal rearrangement reactions on a metal surface. On one hand, intramolecular skeletal rearrangements induced the formation of diaceno[a,e]pentalenes after deposition of dibromomethylene-functionalized p-quinoid-based precursors on a hot Au(111) surface. In contrast, an analogous strategy on indenofluorene-based precursors, endowed with the same functional groups attached to the apical carbon of the five-membered rings, leads to the formation of π-conjugated ladder polymers of dibenz[a,h]anthracene units linked by cyclobutadiene segments (Scheme 1). Scanning tunneling microscopy (STM) and non-contact atomic force microscopy (nc-AFM) clearly unveil the chemical structure of the thermally activated intra- and intermolecular reactions. In addition, the experimental results are complemented by density functional theory (DFT) calculations, altogether providing a rationalization of the unique mechanisms driving reaction pathways.

Intramolecular thermal rearrangement reactions of dibromomethylene-functionalized p-quinoid-based acene precursors

The reaction illustrated in Scheme 1a provides a new strategy toward the transformation of pro-aromatic p-quinoid systems into pentalene antiaromatic systems. To explore this unique on-surface reaction, 9,10-bis(dibromomethylene)-9,10-dihydroanthracene precursor (1) was synthesized in solution. As recently shown by us for 1 and other dibromomethylene-functionalized precursors, the formation of ethynylene- or cumulene-bridged π-conjugated 1D polymers under ultrahigh vacuum (UHV) conditions on an Au(111) surface was demonstrated^49–55 by depositing a submonolayer coverage of the selected precursor on a surface held at room temperature, followed by an annealing process. In fact, upon thermal annealing of 1 (150 to 250 ºC), the molecular species dehalogenate and diffuse as surface-stabilized carbenes until they homocouple yielding an ethynylene-bridged anthracene polymer, where the aromatization of the quinoid precursors is ostensible⁴⁹. However, a completely new scenario emerges when 1 is sublimed onto an already hot gold surface kept at 165 ºC. Instead of the previously found 1D molecular wires observed in STM images, individual asymmetric “cross-like” structures (2a) appear, surrounded by circular structures assigned to bromine (Br) atoms, which were dissociated from the precursor and chemisorbed on the surface (Fig. 1a). Interestingly, high-resolution STM and nc-AFM images acquired with a carbon monoxide (CO)-functionalized tip allow to resolve their chemical structure⁵⁶ (Fig. 1b,c). In particular, constant-height frequency-shift images clearly show modifications in the molecular backbone, where a central pentalene moiety is flanked by two fused planar features assigned to two benzene rings, i.e. forming a dibenzo[a,e]pentalene molecule. Furthermore, 2a presents bright lobes (Fig. 1b) or elongated straight lines (Fig. 1c) of an increased frequency shift, depending on the height of the recorded nc-AFM images, arising from the apexes of the five-membered rings that compose the pentalene subunit. This is attributed to the presence of Br atoms, still bonded to the molecular backbone, through a gold adatom, as elucidated below. The experimental features of such individual molecules are well reproduced by the DFT-optimized geometry (Fig. 1d) and the corresponding nc-AFM simulations⁵⁷ (Fig. 1e,f) on the Au(111) surface. Furthermore, analogous results are obtained for the sublimation of a fluorine-functionalized anthracene precursor on a hot Au(111) surface, i.e. 9,10-bis(dibromomethylene)-2,3,6,7-tetrafluoro-9,10-dihydroanthracene (see Fig. S1), demonstrating the versatility of the presented reaction toward modifications in the functionalization of the molecular backbone. The robustness of this individual asymmetric “cross-like” structures is confirmed by performing lateral manipulation experiments, which reveal that fluorinated Br − Au − dibenzo[a,e]pentalene molecules can be displaced and rotated along the gold surface (see Fig. S2).

Similar outcome is obtained upon the sublimation of a 9,10-bis (dibromomethylene)-9,10-dihydropentacene precursor (3) onto the gold surface kept at 200 ºC, resulting in the formation of Br − Au − dinaphtho[a,e]pentalene molecules (4a) (Fig. 2a-c).

Importantly, it is noticeable that an increase of the initial surface temperature induces a larger conversion of the precursors into diaceno[a,e]pentalenes, observing total conversion for surface temperatures of 200 ºC for 1 and 240 ºC for 3 (see graph in Fig. 2d). Thus, the thermal stimuli that the molecular precursors suffer upon absorption on the surface is crucial to drive the subsequent reaction pathways, switching from covalent polymerization (annealing from room temperature) to intramolecular ring rearrangement reactions (adsorption on a hot substrate).

In addition to the observed dominant 2a and 4a species, different reaction products can be observed after sublimation of both precursors at such temperatures. Notably, STM images reveal the appearance of new species, termed 4b, visualized as chains connected through rounded protrusions (Fig. 2e). They are assigned to dinaphtho[a,e]pentalene organometallic complexes with an observed intermolecular spacing of 2.2 ± 0.3 Å, which suggest a C − Au bond length of 2.1 ± 0.6 Å (see the Laplace filtered nc-AFM image in Fig. 2f), in agreement with previously reported works^17,58,59. Comparable results are obtained for dibenzo[a,e]pentalene organometallic complexes (2b) (see Fig. S3). Moreover, a small amount of individual dinaphtho[a,e]pentalene (4c) species could also be observed, i.e. without the Au-Br peripheral connections, being passivated by hydrogen residual gas present in the vacuum chamber, altogether giving a hint of the full reactivity scheme of the diaceno[a,e]pentalene molecules on surfaces.

Next, in order to extend the number of antiaromatic subunits that can be integrated within a certain molecular backbone, we have sublimed a molecular precursor endowed with four dibromomethylene functional groups, namely 5,7,12,14-tetrakis(dibromomethylene)-5,7,12,14-tetrahydropentacene (5) on a gold surface kept at 200 ºC.

In analogy to the previous experiments involving precursor 1 and 3, after annealing a submonolayer coverage of precursor 5 from room temperature to 220 ºC⁵², the intramolecular ring-rearrangement that gives rise to the integration of pentalene subunits was activated (see STM images in Fig. 3a,b). Therefore, the formation of diindeno[2,1-a:2',1'-g]-s-indacene (6a) was confirmed as expected, coexisting with diindeno[2,1-a:2',1'-g]-s-indacene organometallic complexes (6b) (see Fig. 3c). Again, the four elongated straight lines are attributed to four Br atoms linked to the molecular backbone through gold adatoms. It should be noted that the length of the complexes can vary ranging from two to five diindeno[2,1-a:2',1'-g]-s-indacene units under the mentioned reaction conditions, whereby 80% of the complexes present one or two molecular units (statistics out of ∼300 molecules, Figure S4).

Reaction mechanism investigated by QM/MM calculations

To get further insights into the reaction mechanism that originates the generation of pentalene subunits in the molecular backbone of the 9,10-bis(dibromomethylene)-9,10-dihydroanthracene precursor, we carried out DFT and quantum mechanics/molecular mechanics (QM/MM) simulations.

In a first step, a plausible scenario is the one where a gold adatom breaks one of the C-Br bonds of the precursor 1 and swaps positions with the Br atom forming a linear C-Au-Br complex, see Fig. S5. According to our QM/MM simulations, this process has relatively not only a low activation energy ∼10 kcal/mol, but the product is also thermodynamically more stable. Next, molecular dynamics (MD) DFT simulations reveal that the debromination of the adjacent Br atom is thermodynamically spontaneous on the gold substrate, as shown in Fig. S6. This indicates that the Br atom not attached to a gold adatom can dissociate, thus yielding an intermediate structure containing a linear C-Au-Br complex, denoted as IS in Fig. 4a.

Figure 4 shows a subsequent reaction course leading to the formation of the pentalene unit obtained from the free energy QM/MM simulations at 227 ºC. The reaction mechanism consists of several steps including two intermediate states (denoted as IM1 and IM2 in Fig. 4a). Herein, a carbon atom, bonded to the gold atom, incorporates into the central benzene ring, forming the intermediate structure IM1. This process has an activation energy 39.6 kcal/mol and the free energy of the intermediate IM1 is similar to the initial state, which makes this reaction step thermodynamically feasible. In the next step, the identical reaction mechanism takes place on the other side of the molecule forming the intermediate state IM2, see Fig. 4a. In this case the activation energy is even lower and the intermediate state IM2 is much more stable than IM1 (see Fig. S7). Notably, our QM/MM steered MD simulations show that these two reaction steps (globally, the transformation from IS to IM2 shown on Fig. 4a) occur indeed in a stepwise fashion rather than simultaneously (see video attached in the Supporting information). It is also worth mentioning the important role of the gold substrate in the reaction course. The presence of the gold substrate affects the relative stability of IM2 and the final state. Namely, without the gold substrate, the interaction of an Au atom in the C-Au-Br bonding complex would be much stronger and it would stabilize the organometallic complex, see Fig. S8. Thus, the reaction would not be thermodynamically feasible. This hints at the importance of the adatom-substrate interaction in the reaction process.

Once the intermediate IM2 is established, the final product with the pentalene unit can be formed with a very small activation barrier of 15.5 kcal/mol. Theoretically, also a final product with a four- and a six-membered ring could be alternatively formed, as shown in Fig. S9. However, according to our QM/MM free energy calculations, this product is much less stable.

Polymerization of dibromomethylene-functionalized indenofluorene-based precursors through intra- and intermolecular thermal rearrangement and [2 + 2] cycloaddition reactions

In order to extend the general application of the above-mentioned strategy into not only intramolecular ring rearrangements, but also in the formation of π-conjugated polymers, we have performed experiments under comparable conditions using a dibromomethylene-functionalized indenofluorene precursor (7 in Scheme 1b). STM images show that after sublimation of 7 on an Au(111) surface kept at 300 ºC, the spontaneous formation of 1D chains, coexisting with some concomitant fused segments is achieved (Fig. 5a). A closer look to these chains allows the clear identification of their chemical structure. The obtained high-resolution STM images (Fig. 5b) together with the Laplace filtered constant-height frequency-shift image (Fig. 5c), using a CO-functionalized tip, reveal that the formed π-conjugated ladder polymer (8a) is constituted of planar dibenz[a,h]anthracene units connected through tetragons, attributed to cyclobutadiene moieties (see chemical sketch in Fig. 5c). This experimental finding is in contrast to the pentalene-linked indeno[1,2-b]fluorene polymers achieved by RT deposition of 7 and subsequent annealing to 350 ºC on the same surface (see Fig. S10)⁵³. This type of connections is highly selective, being present in 85% of the analyzed segments (statistics out of 83 linkages).

Considering the huge computational cost that such a long series of reaction steps would require, we consider only a model case consisting of a single fluorene unit endowed with a dibromomethylene functional group, see Fig. S11. Such a simplified model can capture the main ingredients of the reaction mechanism. We assume that the first reaction step is similar to the previous case shown in Fig. 4, consisting of a partial debromination of the dibromo-methylene moiety and the formation of the linear C-Au-Br group via interaction with an Au adatom. The resulting intermediate, shown in upper left panel of Fig. S11, can be thermally activated to undergo an on-surface Fritsch-Buttenberg-Wiechell (FBW) rearrangement⁶⁰ leading to the formation of a benzyne moiety³⁸. According to our QM/MM calculations the activation barrier is ∼15 kcal/mol and the final product is thermodynamically more stable. Note, that the highly reactive intermediate is partially passivated by the presence of the Au-Br group. We assume that this complex readily reacts with each other by a [2 + 2] cycloaddition reaction to provide the observed 8a polymers (see the proposed chemical reaction pathway in Fig. 5e). In addition, a residual amount (~ 15%) of dibenz[a,h]anthracene units linked by fused five membered rings (8b) are observed (see Fig. S12). The formation mechanism of these species is tentatively rationalized as a competing side-reaction of the [2 + 2] cycloaddition (see Fig. S13), where the rearrangement of one hydrogen atom may generate a biradical species able to form a five-membered ring with a neighboring benzyne moiety.

STM and nc-AFM experiments

Experiments were performed in two independent custom-designed ultra-high vacuum systems (base pressure below 5 x 10^− 10 mbar) hosting commercial low-temperature microscopes with STM/AFM capabilities from Scienta Omicron and Createc GmbH. The Au(111) substrate (MaTeck GmbH) was cleaned by repeated cycles of Ar⁺ ion sputtering (E = 1 keV) and subsequent annealing to 740 K for 10 minutes. All STM images shown were taken in constant current mode, unless otherwise noted, with electrochemically etched tungsten and Pt/Ir tips, at a sample temperature of 4.3 K (Omicron) and 4.2 K in a custom designed LT-STM/nc-AFM system (Createc GmbH), respectively. Scanning parameters are specified in each figure caption. Molecular precursor 1, 3, 5 and 7 were thermally sublimed onto the clean Au(111) surface kept at 300 > T > 130°C temperature with a typical deposition rate of 0.5 Å/min (sublimation temperatures of 100, 160, 230 and 195°C, respectively). The surface temperature was measured by a thermocouple contact on the sample plate. Non-contact AFM measurements were performed with a tungsten or a Pt/Ir tip attached to a Qplus tuning fork sensor.⁶¹ The tip was a posteriori functionalized by a controlled adsorption of a single CO molecule at the tip apex from a previously CO-dosed surface.⁶² The functionalized tip enables the imaging of the intramolecular structure of organic molecules.⁵⁶ The sensors were driven at their resonance frequency (26/30 kHz) with a constant amplitude of ~ 60/50 pm in both the Scienta Omicron and Createc GmbH instruments. The frequency shift from resonance of the sensor (with the attached CO-functionalized tip) was recorded in a constant-height mode (Omicron Matrix electronics and MFLi PLL by Zurich Instruments for Omicron; Nanonis SPM controller with Nanonis OC4 forCreatec GmbH). The STM and nc-AFM images were analyzed using WSxM.⁶³

Computational details

We have used the Fireball/AMBER software to simulate the QM/MM Molecular Dynamics of the chemical reactions. To define the forces of the classical part (which consist in the most part of the metal surface) we employ the interface force-field and the dynamics is controlled by the AMBER code^64,65. The quantum region is treated at the BLYP-DFT level with the Fireball software⁶⁶, a local-orbital DFT code which employs an optimized basis set of pseudo-atomic orbitals. The interface between Fireball and AMBER was implemented and described in⁶⁷.

We have employed a combination of Umbrella Sampling Simulations (US)⁶⁸ and Steered Molecular Dynamics (SMD)⁶⁹ to unveil the features of the reaction mechanism and calculate the free energy profiles of the reactions.

Before the US or SMD, we have performed a QM/MM geometry optimization followed by a thermalization from 300K to 500 K in order to stabilize the system. We use the Langevin thermostat as implemented in AMBER⁷⁰ to simulate the canonical ensemble. We use the Alan Grossfield´s implementation⁷¹ for the Weighted Histogram Analysis Method (WHAM)⁷² to calculate Free Energy profiles associated to each reaction from the US. See the paragraph on the reaction mechanism of the previous section for more information about the reaction coordinates on each case. On each of these cases, an initial SMD is employed to drag the corresponding reaction coordinate and generate structures which can be used as seeds for each US window. To construct the free energy profile, we made 121 umbrella sampling windows from − 1.20 Å to 1.20 Å for the ΔD₁ (d₁-d₂) combined reaction coordinate from the Initial State (IS) to the Intermediate State 1 (IM1) and 141 windows from − 1.20 Å to 1.50 Å for the ΔD₂ (d₃-d₄) combined reaction coordinate from the IM1 to the Intermediate State 2 (IM2), while for the reaction pathway from IM2 to the Final State (FS), the free energy is reconstructed by 81 umbrella sampling windows from 3.00 Å to 1.40 Å using a single reaction coordinate D₃ = d₅. Each US window is a QM/MM Molecular Dynamics of 10000 steps at 500K with a time step of 0.5 fs.

Advancements in the field of on-surface synthesis demand new synthetic concepts and routes able to stimulate further research efforts and design innovative nanomaterials. Novel pathways toward the integration of antiaromatic subunits into PCH complexes, including polymers, is of special relevance since it can provide a wide variety of unprecedented extended π-systems with potential applications in organic materials/electronics. Here we report the synthesis of PCHs and π-conjugated ladder polymers on a metal surface integrating, in a controllable fashion, [4n] π-electrons segments in the polycyclic conjugated backbone. Combining high-resolution STM with nc-AFM for structural identification, with DFT and QM/MM based calculations for obtaining the reaction barriers has allowed for a complete elucidation of the reaction mechanisms. Sublimation of dibromomethylene-functionalized molecular precursors onto the hot Au(111) surface induces a spontaneous skeletal ring-rearrangement reaction. On the one hand, dibromomethylenes attached to six-membered rings of different precursors (1 and 3) lead to the formation of pentalene-based PCHs, i.e. diaceno[a,e]pentalenes (2a,c and 4a,c) and their organometallic derivatives (2b and 4b). Furthermore, the number of pentalene subunits introduced into a PCHs can be increased by an ingenious modification of the precursors (5), producing diindeno[2,1-a:2',1'-g]-s-indacene PCHs (6a). On the other hand, for dibromomethylenes attached to five-membered rings (7) sublimed onto a hot gold surface, π-conjugated ladder polymers linked through cyclobutadiene bridges are formed upon ring-rearrangement of the fulvene carbene segments to give a benzyne that, thereafter, undergoes [2 + 2] cycloaddition reaction with a neighboring benzyne moiety (8a). Thus, the synthetic strategies presented in this work provide the basis of the syntheses of π-systems introducing antiaromatic subunits, which can serve as a good platform to design novel spintronics and optoelectronics devices. Furthermore, our work anticipates further research efforts to elucidate the influence of thermal stimuli in the reaction pathways of on-surface synthesis.

Acknowledgements

This project has received funding from Comunidad de Madrid [projects QUIMTRONIC-CM (Y2018/NMT-4783), MAD2D, and NanoMagCost (P2018/NMT-4321)], ERC Consolidator Grant (ELECNANO, 766555), and Ministerio de Ciencia, Innovacion y Universidades (projects SpOrQuMat (PGC2018-098613-B-C21), CTQ2017-83531-R, PID2019-108532GB-I00, and CTQ2016-81911-REDT). IMDEA Nanociencia is appreciative of support from the “Severo Ochoa” Programme for Centers of Excellence in R&D (MINECO, grants SEV-2016-0686 and CEX2020-001039-S). We appreciate funding from the Praemium Academie of the Academy of Science of the Czech Republic and the CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110). A.S-G thanks the funding from the “Ministerio de Universidades” for the “Plan de Recuperación, Transformación y Resiliencia” under the Margarita Salas grant agreement CA1/RSUE/2021-00369. P.J. thanks the support of the GACR 20-13692X. J.I.U. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No [886314]. We acknowledge Dr. Borja Cirera for fruitful discussions.

Data and Code Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. The Fireball software package is available at: https://github.com/fireball-QMD and PP-SPM software package can be downloaded at: https://github.com/Probe-Particle/ppafm#probe-particle-model.

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Generating Antiaromaticity: Thermally-selective Skeletal Rearrangements at Interfaces

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Generating Antiaromaticity: Thermally-selective Skeletal Rearrangements at Interfaces

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