Alejandro
Jiménez-Martín‡
abc,
Tatiana
Munteanu‡
d,
Qifan
Chen‡
be,
Simon
Pascal
df,
Aura
Tintaru
d,
Benjamin
Mallada
ab,
Pingo
Mutombo
b,
Olivier
Siri
*d,
Pavel
Jelínek
*ab and
Bruno
de la Torre
*ag
aRegional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN) Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic. E-mail: bruno.de@upol.cz
bInstitute of Physics of the Czech Academy of Sciences, Cukrovanická 10, 16200 Prague, Czech Republic. E-mail: jelinekp@fzu.cz
cFaculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 7, 11519 Prague, Czech Republic
dAix Marseille Univ., CNRS UMR 7325 Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Campus de Luminy, 13288 Marseille cedex 09, France. E-mail: olivier.siri@univ-amu.fr
eFaculty of Mathematics and Physics, Charles University, V Holešovičkách 2/747, 18000 Prague, Czech Republic
fNantes Université, CEISAM UMR 6230, CNRS, Nantes F-44000, France
gNanomaterials and Nanotechnology Research Center (CINN) CSIC-UNIOVI-PA, 33940 El Entrego, Spain
First published on 16th January 2025
On-surface synthesis under ultra-high vacuum (UHV) conditions facilitates the fabrication of unique molecular compounds, replicating established in-solution protocols. However, the intramolecular hydroamination and cyclization (IHC) of alkynes on surfaces remain unexplored due to the challenges posed by the repulsion between the nitrogen lone pair and the alkyne π-system. Here we describe the first on-surface IHC of alkyne-functionalized molecular precursors in UHV environment on the Au(111) surface. Notably, the synthesis introduces two pyrrole groups into the quinoidal-based precursor, enabling the formation of two fused pyrrolo-benzoquinonediimine compounds not achievable in solution chemistry. To analyze the resulting reaction products, we utilized scanning tunneling microscopy and non-contact atomic force microscopy with single bond resolution, comparing these products to those obtained through traditional solution methods. In parallel to the experimental results, we provide a detailed computational description of the key role of single gold adatoms during the complete on-surface reaction.
One of the most appealing features of on-surface reactions is the access to remarkably original mechanisms and products, otherwise challenging to isolate under conventional chemical practices. Classic organic reactions have been adapted to the UHV conditions and interpreted within the newly established environment and conditions. Ullmann coupling, Bergman cyclization, Glaser coupling, Scholl reaction and ring-opening polymerization are just a few to mention.1,2 Reactions based on engineering the properties of the alkyne triple bond are of particular interest because of its unique reactivity, which has enabled it to be used in various surface coupling reactions. Among these, the intriguing rearrangement of Bergman reaction19 involving the intramolecular cyclization of an alkyne-containing precursor, remains one of the most extensively studied.1,20,21 With their seminal work, de Oteyza et al. transferred the concept to metallic surfaces and have shown in a very elegant manner that the thermal activation of the ethynyl-bearing phenyl A on Ag(100) surface triggered an intramolecular Bergman cyclization, with the formation of three isomeric products6 resulting from multiple reactions (Scheme 1).
Another alkyne-based reaction transferred from solution to surface chemistry is the Glaser coupling. This is a well-known and one of the oldest protocols employed in solution synthesis to obtain homocoupled diynes under copper catalysis.19 The reaction was revitalized by the group of Ruben and Barth and by Fuchs and coworkers as a method for designing conjugated materials directly on surfaces.22,23 Bisethynylarene monomers of type B (Scheme 1) upon annealing on Au(111), Ag(111) or Cu(111) surfaces were reported to undergo oligomerization, efficiently promoting the formation of linear polymeric chains with higher selectivity on Ag(111) substrate. The well-liked metal-catalyzed Sonogashira C–C coupling was also reported on Au(110) and Au(111) surfaces,5,24,25 for instance generating diphenylacetylene as a cross-coupling product described by Lambert et al. from a reaction between phenylacetylene and iodobenzene (Scheme 1).
Despite the recent advancement in on-surface synthesis, examples of C–N bond formation through the intramolecular hydroamination/cyclization (IHC) reaction of alkynes are hitherto unknown probably because this reaction presents a considerable challenge due to the repulsion between a nitrogen lone pair and the alkyne π-system.26 In solution, this reaction is a versatile and robust strategy for crafting multifunctional N-heterocycles27,28 associated with substantial activation energy barriers that can be achieved through the use of expensive transition metal catalysts. Gold complexes, at different oxidation state, have thus emerged as highly effective catalysts for the electrophilic activation of alkynes, enabling nucleophilic additions to proceed under mild reaction conditions.29 Notably, these gold catalysts selectively activate π-bonds of alkynes, facilitating the attack of various nucleophiles. Specifically, Au(I)-catalyzed hydroamination reactions have yielded notable success in formally adding N–H reagents onto triple bonds in both intermolecular30,31 and intramolecular32 contexts. Despite these advancements in solution, examples of on-surface IHC reactions are still missed.
In this study, we provide an innovative approach for the efficient synthesis of N-heterocyclic compounds via hydroamination and subsequent cyclization on Au(111) substrate and compare with that obtained by traditional methods in solution-phase chemistry. The precursor, 2,5-diamino-1,4-benzoquinonediimines (1, 4), featuring a central quinoidal ring with two alkyne moieties and two amine functions, appears to be prime candidates for tandem hydroamination reactions of the alkynes, followed by cyclization under mild conditions (Scheme 2). On surface, the presence of single Au(0) adatoms nearby facilitates low-energy hydrogen migration from the amino group to the CC triple bond. This process evolves into fused N-heterocyclic compounds through an intramolecular cyclization reaction, leading to the high-yield production of compounds 2 and 3 (in a 4
:
1 ratio in favour of isomer 2). Leveraging scanning tunneling microscopy (STM) and advanced bond-resolved non-contact atomic force microscopy (nc-AFM),33 we effectively discerned the molecular configurations of reaction products formed on surfaces, unambiguously determining their structural changes. The reaction mechanism was further evaluated through density functional theory (DFT) calculations and quantum mechanics/molecular mechanics (QM/MM) calculations, rationalizing the occurrence of the final products. Interestingly, the same reaction was investigated in solution-phase chemistry with an Au(III) catalyst, showing the formation of the monocyclized compound 5 as model product of the unprecedented formation of pyrrolo fused benzoquinonediimine derivatives.
Subsequent elevation of the temperature of the surface to approximately 370 K initiated a pivotal transformation of the precursor, leading to the emergence of distinctly different molecular products and its subsequent self-assembly, as captured in the topographic image provided in Fig. 1c. The STM images prominently display single structures of the resulting products, which distinctly form one-dimensional chains guided by the intricate herringbone reconstruction of the surface Au(111). These molecular chains consist of two distinct molecular products, designated as type A (yield: 79%) and type B (yield: 21%) (see methods for calculation of yield in the ESI†), easily identifiable by their characteristic elongated and boomerang-like topographic shapes, respectively. Nc-AFM imaging of type A and type B products (Fig. 1d) unequivocally mirrors their chemical architectures. Each manifests a central hexagonal arrangement flanked by two pentagonal moieties in antisymmetric and symmetric configurations, respectively. The intricate intramolecular rearrangement potentially generates diverse isomeric variants for both molecular species considering the distribution of H atoms within the molecular structure.
The exact atomic structure of both products can be elucidated by combining a set of experimental and simulated nc-AFM images at different tip-sample distances. We conducted a series of nc-AFM simulations using fully optimized molecular structures obtained through total energy DFT calculations of potential isomeric variants of type A and B, considering the distribution of H atoms within the molecular structure. Fig. S1 (ESI†) presents the simulated nc-AFM images of the examined structures. Based on the agreement with experimental observations, we unambiguously identified the chemical structure of type A and type B molecules as products 2 and 3, respectively (Fig. 1d). Moreover, we should note that this configuration of type A also has the lowest total energy between all considered structures, optimizing the strength of the dispersive and electrostatic intermolecular interactions (see Fig. S1 and S2, ESI†). In addition, the high-resolution nc-AFM images enable us to identify the supramolecular arrangement of both types of chains. While the type A chain formed by molecule 2 adopted a truncated configuration, molecule 3 organizes itself in a head-to-tail arrangement, culminating in chains characterized by specific intermolecular distances measuring 7.51 (±0.05) Å and 7.39 (±0.05) Å, respectively (see Fig. S3, ESI†). An in-depth analysis of consecutive sequences of products 2 and 3 revealed the presence of hydrogen bonds between the imine and amine units of adjacent molecules similarly to reported on quinoid molecule (2,5-diamino-1,4-benzoquinonediimine) deposited on Au(111).13 The shape, whether linear or truncated, of the resulting chain was determined by the symmetric or antisymmetric configuration of the pyrrole moieties inherent in molecules 2 and 3. Remarkably, we discovered that the molecular chains can be manipulated effortlessly by inducing lateral displacements with the STM tip (Fig. S4, ESI†). This investigation serves to probe the chemical stability of the hydrogen-bonded molecular chains. It was observed that segments could be easily displaced, with the molecules moving collectively while preserving their chain configuration. We observed that the precise positioning of pyrrole units significantly influences not only the molecular arrangement but also the electronic structure of the molecules. The calculated electronic gap for free-standing 2 and 3 shows a renormalization with the HOMO shifted closer to the Fermi level by ∼1 eV, reducing the molecular gap from 3.7 eV to ∼3 eV in good agreement with our experimental observations and calculations (see Fig. S5, ESI†).
Firstly, three distinct rotamers of the precursor, namely IS1, IS2, and IS3, were initially identified, with IS2 being the most stable according to free-standing DFT calculations optimizing steric strain and electrostatic interaction between nitrogen lone pairs and hydrogen atoms (see Fig. S6, ESI†). However, the experimental situation provides a different scenario due to the presence of the gold surface. On the surface at moderated temperatures, there is an abundant amount of diffusing single gold atoms, so-called adatoms.39 These gold adatoms have a neutral charge due to the presence of a gold surface underneath. Moreover, it has been recently demonstrated that these Au(0) adatoms may steer on-surface reactions.40–42 The presence of the surface Au(0) adatoms on the Au(111) surface at RT, results in an average increase in the stability of IS4 by about 0.35 eV (see Fig. S7, ESI†). In addition, the electrostatic potential map of IS4 rotamer favours the presence of the single Au adatom nearby being electrostatically attracted by the nitrogen lone pair (Fig. S8, ESI†). Consequently, this rotamer becomes the most populated, assuming its dominant role in the reaction course.
Thus, Fig. 2a shows the initial reaction step entails the migration of a single hydrogen atom from the amine moiety to the central carbon of the terminal alkyne leading to IM1. For this specific step, the presence of the single Au(0) adatom nearby plays a key role, reducing the energy barrier of the hydrogen transfer from 2.78 eV to 1.48 eV compared to the reaction without Au adatoms (as depicted in Fig. S9, ESI†). In contrast to our findings, dehydrogenation of the terminal alkyne typically results in the manifestation of Glaser-like coupling. This phenomenon has, indeed, been documented on Au(111)22 under higher temperature conditions and on surfaces characterized by increased reactivity, such as Ag(111)23,43 and Cu(111).22
We estimated reaction rates directly from the calculated barriers using the Arrhenius equation. For a barrier of 1.5 eV at 370 K, our calculations predict a reaction time of approximately 10000 hours (not shown here) which is much longer than the experimental duration of 30 minutes. However, increasing the temperature to 400 K reduces the reaction time to around 20 minutes, aligning with experimental timescales. It is important to note that, in the experiment, the sample temperature was measured externally using a pyrometer, which introduces potential errors in the observed temperature (see methods in ESI†). These measurement uncertainties could result in a higher effective temperature than the reported 370 K, helping to reconcile the experimental timescales with our calculated barriers. Additionally, slight overestimations in the theoretical barriers, common in computational approaches, may also contribute to the apparent discrepancy.
Similarly, other competing dehydrogenation processes of the alkyne group, as well as hydrogen transfer within the alkyne group assisted by a single Au adatom, shown in Fig. S10 (ESI†), have a much larger activation barrier compared to the hydrogen transfer from the amine to central carbon atom of the alkyne segment. This modification renders the process more thermodynamically feasible at the experimentally relevant temperatures.
This primary step carries significant importance in unravelling the reaction mechanism. A detailed analysis of this reaction step reveals that the proximity of the Au adatom in IS4 weakens the triple carbon bond on alkyne, as indicated by our DFT bond-length analysis (Fig. 2b and Fig. S11, ESI†). This prompts a redistribution of molecular charge, triggering the transfer of a hydrogen atom from the NH2 to the central carbon in a sigmatropic reaction, culminating in forming a sp3 central carbon (IM1). These findings strongly indicate a deviation from the conventional nucleophilic attack of the terminal alkyne,44,45 providing an alternative mechanism on the surface. The efficacy of the metal catalysts in the hydroamination/cyclization in solution supports the involvement of a reaction pathway wherein the CC bond coordinates with the nucleophilic metal. Without this coordination, the amino group cannot effectively attack the alkyne carbon bonded to the phenyl group due to the molecular rigidity that inhibits bond bending.46 Furthermore, the two-dimensional constraint imposed by the surface impacts the behaviour of individual gold adatoms and reactants, respectively, confining their movement and consequently limiting the effective coordination compared to that in solution chemistry. This first transformation serves as a pivotal precursor for understanding the subsequent steps of the reaction. It is succeeded by a cyclization process, resulting in the formation of the primary pyrrole moiety, leading to IM2, a common intermediate state for both 2 and 3 (see Fig. S12. ESI†).
The critical step determining the formation of either product 2 or 3 from IM2 entails hydrogenation and cyclization processes of the second terminal alkyne, involving the amino group (refer to Fig. 3). At this bifurcation point, the positioning of the surrounding Au(0) adatom leads to different initial states (IS′s). Fig. S13 (ESI†) shows that IS′1, being 0.58 eV more favourable than the next one (IS′3), emerges as the leading state considered for further analysis. As shown in Fig. 3, the ground state IS′1 undergoes a sigmatropic adatom-mediated hydrogen transfer from the NH2 amino group to the central carbon alkyne (IM3), induced by the proximity of a single Au(0) adatom, similar to the formation of the first pyrrole unit. A subsequent antisymmetric cyclization reaction leads to the formation of 2 with low energy barriers reachable with the mild conditions of the experiment, as depicted in Fig. 3a. On the other hand, the formation of 3 requires a unique starting point to enable the cyclization reaction (Fig. 3b).
Its notably lower yield compared to 2 implies a less likely reaction path for 3. Hence, our focus shifts to IS′s states with elevated energy. Among IS′2, IS′3 and IS′4, the former stands out, showing lower energy barriers, consistent with the experimental conditions. Proceeding from IS′2, the reaction closely mirrors IS’1, where Au(0) adatom mediates hydrogenation of the central alkyne, leading to the IM4 state. This state marginally differs from IM3 in the Au adatom's position and relative hydrogen conformations. At the subsequent stage, newly two channels appear, describing the pyrrole construction. The straightforward cyclization process yields again 2 with an energy barrier of 1.16 eV (see Fig. S12, ESI†). However, an alternate channel emerges with a lower energy barrier (0.47 eV) involving the alkyne's rotation guided by the gold adatom, leading to IM5 and subsequent cycling toward the ortho position with a significantly lower energy barrier of 0.69 eV. Despite identifying other potential reaction pathways, this one is favored by approximately 0.24 eV (see Fig. S12, ESI†). The identified energy barrier giving rise to product 3 may provide a route for the selection of a pure (only 2) or mixed (2 and 3) sample by fine-tuning the thermal energy reservoir in the experiment.
Finally, the structure of 5 was fully established by X-ray diffraction studies that clearly confirmed the formation of a fused pyrrolo-benzoquinonediimine derivative incorporating the CC triple bond (Fig. 4b and Fig. S14, ESI†). Further examination of the bond distances of 5 does not show the expected bond equalization for an aromatic pyrrole. This observation can be explained by the fused pyrrolo-benzoquinonediimine arrangement, in which the shared carbon–carbon bond functions as a C
C double bond, preserving the conjugation (rather than delocalization) of the π system within the benzoquinonediimine unit. These characteristics account for the absence of double cyclization in molecule 5 that can be rationalized by the nature of the catalyst.
In fact, HAuCl4 is an anionic gold complex with an H+ counterion, which might participate in an acid–base reaction (protonation of an imine function in 4) to generate the stabilized cationic species 6, as depicted in Fig. 4a. This diminishes the nucleophilic character of the NH2 function, thereby decreasing reactivity. To validate this, we sought to synthesize bicycled molecule 7 from monocyclized 4 under identical conditions (same catalyst), resulting in the complete recovery of the precursor. This underscores the influence of a “parasitic” acid–base reaction in our study.
Certainly, on-surface hydroamination reactions illustrate stark differences compared to the traditional synthesis in solution-phase. Specifically, the on-surface synthesis reveals a high yield with no evident side reactions compared to the moderate yield achieved in solution. Moreover, the on-surface reaction facilitates the complete cyclization of both alkynes, forming two pyrrole moieties per molecule, and conversely in solution, only one pyrrole unit was detected per molecule.
Footnotes |
† Electronic supplementary information (ESI) available: Methods, synthesis of the materials, Fig. S1–S14, X-ray structure, NMR spectra, HRMS spectra, references. CCDC 2314122. For ESI and crystallographic data in CIF or other electronic format see DOI: https://doi.org/10.1039/d4qm00866a |
‡ These authors contributed equally to this work. |
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