Introduction of peripheral nitrogen atoms to cyclo-meta-phenylenes

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Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Guest Editor: Y. Yamakoshi
Beilstein J. Org. Chem. 2024, 20, 1207–1212.
Received 29 Feb 2024, Accepted 13 May 2024, Published 24 May 2024


Cyclo-meta-phenylenes doped with nitrogen atoms at the periphery were designed and synthesized. The syntheses of the macrocyclic structures were achieved with one-pot Suzuki–Miyaura coupling to arrange phenylene rings and pyridinylene rings in an alternating fashion. Analyses with UV–vis spectroscopy showed changes in the photophysical properties with nitrogen doping, and X-ray crystallographic analyses experimentally revealed the presence of biased charges on the peripheral nitrogen atoms.


Graphitic carbonaceous sheets of graphene continue to attract considerable attention, which lead us to explore structural defects such as heteroatom doping and porous defects for unique properties and functions. For instance, with nitrogen atoms as dopants [1-3], a range of applications, such as electrocatalysis [4] and gas storage [5], has been exploited. Although the locations of nitrogen, in addition to the types, including pyridinic, pyrrolic and graphitic nitrogen, play important roles in determining the properties and functions (Figure 1a), top-down, physical production does not enable control of the doped structures with atomic precision. The bottom-up chemical syntheses of molecular nanocarbons have thus become attractive for controlling the nitrogen-doped structures embedded in large, molecular π-systems [6,7]. As a versatile synthetic strategy for defective molecular nanocarbons, we recently introduced phenine design [8,9], which allowed us to introduce nitrogen dopants, as was demonstrated with nitrogen-doped phenine nanocarbons such as 1 and 2 [10,11]. The nitrogen dopants were introduced in an inward-focused manner to decorate the inner rims of [n]cyclo-meta-phenylenes ([n]CMP) (Figure 1b) and captured other entities such as protons and metal atoms at the porous defect. In this study, the nitrogen dopants were installed in an outward-radiated manner, which expands the structural diversity to exploit the chemistry at the periphery of [n]CMP (Figure 1b). Through the use of Suzuki–Miyaura coupling for macrocyclisation, pyridinyl and phenylene rings were assembled in an alternating fashion, which afforded nitrogen-doped [n]CMPs (3) containing outward-radiating nitrogen dopants. The properties and structures were investigated with UV–vis spectroscopy and X-ray crystallography, which revealed the fundamental properties of the nitrogen dopants in the macrocyclic structures.


Figure 1: Nitrogen-doped nanocarbons. (a) Schematic illustration of pyridinic nitrogen atoms installed at the interior and periphery of a graphene sheet. (b) Phenine nanocarbon molecules with nitrogen dopants.

Results and Discussion

Nitrogen-doped [n]CMPs, 3a and 3b, were synthesized via one-pot Suzuki–Miyaura coupling [12] (Scheme 1). Previously, we synthesized [n]CMPs with inward-focused nitrogen dopants by using Suzuki–Miyaura coupling with Pd(PPh3)4 as the catalyst [13] and applied this method to outward-radiated congeners in this work. However, a MALDI-TOF MS analysis of the crude mixture showed that macrocyclisation did not complete to afford a complex mixture containing noncyclic, linear oligomers (Figure S1, Supporting Information File 1). After examining the Pd-catalysts, we found that macrocyclisation with PdCl2(dppf)·CH2Cl2 worked best and afforded cyclic congeners from N3-[6]CMP to N6-[12]CMP (Figure S1, Supporting Information File 1) and isolated N3-[6]CMP (3a) and N4-[8]CMP (3b) in 7% and 3% yields, respectively [14].


Scheme 1: Syntheses of 3a and 3b.

Comparisons of the UV–vis spectra of the doped and undoped congeners revealed dopant-induced changes in the electronic properties. The UV–vis spectra of 3a and 3b were recorded in chloroform and are shown in Figure 2, with spectra of the undoped [n]CMP congeners shown as references [15]. The nitrogen-doped [n]CMPs 3a and 3b commonly showed minor yet new absorptions at approximately 280 nm, with major absorptions appearing at 250 nm (Figure 2). As shown with the reference spectra of [6]CMP and [8]CMP, the absorption at 280 nm was absent for the corresponding hydrocarbon congeners. These results showed that the nitrogen-dopants induced novel transitions for photoexcitation.


Figure 2: Photophysical properties of 3a and 3b. (a) UV–vis spectrum of 3a in CHCl3. (b) UV–vis spectrum of 3b in CHCl3. For reference, the spectra of [6]CMP and [8]CMP from the literature are also shown in gray [15].

Crystallographic analyses revealed the structural features of nitrogen-doped [n]CMPs. The crystal molecular structures of 3a and 3b are shown in Figure 3. The hexagonal macrocyclic structure of 3a showed a chair-like conformation with alternating biaryl dihedral angles showing +/– values. The octagonal structure of 3b exhibited a saddle-like conformation with an average dihedral angle of 45.0°, which was slightly larger than that of 3a (30.4°). The shapes of nitrogen-doped [n]CMPs did not deviate from those of hydrocarbon [n]CMPs, with similar average dihedral angles (32.4° for [6]CMP and 40.6° for [8]CMP) [15]. Likewise, the crystal packings of 3a and 3b resembled those of the hydrocarbon congeners, forming one-dimensional columns of stacked macrocycles (Figure 3b).


Figure 3: Crystal structures of 3a and 3b. (a) Molecular structures. Biaryl dihedral angles (ω) are shown. (b) Packing structures. Chloroform molecules in the crystal of 3b are omitted for clarity.

The electronic effects of the nitrogen dopants in 3a were examined with X-ray charge density analyses [10,16]. For the crystal structures shown in Figure 3, we used a standard method with spherical independent atom models (IAM) [17], whereas for the charge density analyses, we used the transferrable aspherical atom models (TAAM) from the Hansen and Coppens formalism [18,19]. The TAAM analysis with parameters from the University at Buffalo pseudoatom databank (UBDB) [20] was performed on XD2016 [21] to obtain an R factor of R(F) = 0.0269, which was better than that of the IAM on XD2016 with R(F) = 0.0382. As shown in Figure 4, the TAAM analysis allowed us to obtain a deformation map that located bonding and lone-pair electron densities of the nitrogen atom (Figure 4a). The analyses also allowed us to visualise experimental electrostatic potential (ESP) maps to reveal the presence of negative potentials on the nitrogen atoms (Figure 4b). For comparison, we performed TAAM analyses of hydrocarbon [6]CMP by reanalysing previous diffraction data [15] and obtained the corresponding ESP maps. A comparison of the ESP maps of 3a and hydrocarbon [6]CMP showed induction of biased densities by the nitrogen dopants. Similar biased densities were previously found to be critical in determining the packing structures of nitrogen-doped π-systems to make parallel-displaced configurations preferred over T-shaped stackings [22]. In our study, we observed that pyridine–pyridine stacks were preferred in the crystal stacking (Figure 3), which might be attributed to the biased ESPs on the macrocycles.


Figure 4: X-ray charge density analyses of 3a and [6]CMP. (a) Deformation map (FoFc) of a pyridine ring in 3a (contour interval: 0.05 e·Å−3, positive: red, negative: blue). (b) Electrostatic potential maps mapped on the 0.0067 e·Å−3 isosurface for the electron density.

Finally, we found that nitrogen locations altered chemical characteristics of nitrogen-doped CMPs. Thus, when trifluoroacetic acid (TFA) was added to a solution of 3a in chloroform, bathochromic shifts in UV spectra were observed, indicating protonation-induced changes in the electronic properties [10]. Because of the weakly acidic nature of pyridinic nitrogen atoms, an excess amount of acid was necessary for this effect to be observed with a maximum equivalent of TFA at 2 × 105, and the absorption band at the longest wavelength gradually shifted as shown in Figure 5a. When we added TFA to a solution of a reference compound 6 having inward-focused nitrogen atoms with a maximum equivalent of TFA at 2 × 105 [13], bathochromic shifts were also observed. However, unlike the case with 3a, gradual absorption shifts were not observed, and the absorption changed from 299 nm to 320 nm with an isosbestic point at 303 nm as shown in Figure 5b. This observation indicated that the protonation-induced change of UV spectra for 6 involved two equilibrating states, which most likely originated from single protonation at the centre of the CMP pore. On the other hand, the gradual absorption shifts observed with 3a might thus be ascribed to the presence of multiple protonated species involved in the equilibrium. These results show that the coordination chemistry associated with nitrogen dopants may well be controlled by the locations and directions of the nitrogen atoms.


Figure 5: Response towards acid treatment with nitrogen-doped CMPs. (a) Absorption spectra of 3a (CHCl3, 2.3 × 10−6 M) in the absence (black) and presence of trifluoroacetic acid (green: 4.3 × 10−2 M, blue: 2.1 × 10−1 M, red: 4.2 × 10−1 M). (b) Absorption spectra of 6 (CHCl3, 1.9 × 10−6 M) in the absence (black) and presence of trifluoroacetic acid (green: 4.3 × 10−2 M, blue: 2.1 × 10−1 M, red: 4.2 × 10−1 M).


Macrocycles with nitrogen atoms doped at the periphery were designed and synthesised, and their electronic properties were experimentally investigated with UV–vis and X-ray charge density analyses. The changes in the UV–vis transitions caused by nitrogen dopants may be useful for designing doped materials for optical applications, and the biased ESPs on the macrocycles should also be considered for material design. Nitrogen-induced π-stacking may also enable exploration of molecular assemblies. The experimental lone-pair electron densities were directed outward in 3a and could be used as linkers for metal atoms to assemble trigonal pyramidal macrocycles, for instance, in networks of metal organic frameworks [23,24]. Investigations of the nitrogen dopants in molecular nanocarbons should enrich the chemistry of nanocarbons.


Syntheses of N3-[6]CMP (3a) and N4-[8]CMP (3b) [14]: A mixture of 3,5-dibromopyridine (4, 7.11 g, 30.0 mmol), diborylbenzene (5, 9.90 g, 30.0 mmol), PdCl2(dppf)·CH2Cl2 (2.50 g, 3.0 mmol), and Cs2CO3 (48.9 g, 150 mmol) in 3.0 L of DMF was stirred at 110 °C for 24 h. After the addition of H2O (2.5 L) and CHCl3 (3.0 L), the precipitate was removed by filtration. The organic layer was separated, dried over Na2SO4, and concentrated in vacuo. To eliminate the soluble by-products, the crude material was first washed with CHCl3 (100 mL), and a residue comprising 3a and 3b was obtained. The residue was then suspended in CHCl3 (100 mL) and sonicated for 10 min. After separating the solid and the filtrate, each sample was purified as follows: The former was subjected to Soxhlet extraction with CHCl3 overnight to give 3a in 6% yield (272 mg, 0.592 mmol) after the extraction. The latter was purified by silica gel short path and GPC (column: YMC-GPC T30000-40 + T4000-40 + T2000-40, eluent: CHCl3, flow rate: 30 mL/min) to give 3a in 1% yield (52.8 mg, 0.115 mmol) and 3b in 3% yield (118 mg, 0.193 mmol). In total, 3a was obtained in 7% yield (325 mg, 0.707 mmol). N3-[6]CMP (3a): 1H NMR (CDCl3, 600 MHz) δ 9.05 (d, J = 2.1 Hz, 6H), 8.58 (t, J = 2.1 Hz, 3H), 8.23 (t, J = 2.1 Hz, 3H), 7.89 (dd, J = 7.6, 2.1 Hz, 6H), 7.69 (t, J = 7.6 Hz, 3H); 13C NMR (CDCl3, 150 MHz) δ 146.6 (CH), 138.3, 135.7, 133.9 (CH), 130.2 (CH), 127.5 (CH), 125.9 (CH); HRMS (APCI) (m/z): [M + H]+ calcd. for C33H22N3, 460.1808; found, 460.1808. N4-[8]CMP (3b): 1H NMR (CDCl3, 600 MHz) δ 8.81 (d, J = 1.4 Hz, 8H), 8.13 (t, J = 1.4 Hz, 4H), 7.76 (s, 4H), 7.66–7.73 (m, 12H); 13C NMR (CDCl3, 150 MHz) δ 147.9 (CH), 139.2, 137.0, 133.5 (CH), 129.9 (CH), 127.5 (CH), 127.3 (CH); HRMS (APCI) (m/z): [M + H]+ calcd. for C44H29N4, 613.2387; found, 613.2366.

Supporting Information

Supporting Information File 1: Experimental and copies of spectra.
Format: PDF Size: 1.0 MB Download
Supporting Information File 2: Crystallographic data of N3-[6]CMP (3a) analysed by SHELX (CCDC 2335441).
Format: CIF Size: 452.8 KB Download
Supporting Information File 3: Crystallographic data of N4-[8]CMP (3b) analysed by SHELX (CCDC 2335442).
Format: CIF Size: 477.1 KB Download
Supporting Information File 4: Crystallographic data of N3-[6]CMP (3a) analysed by XD2016 (CCDC 2335443).
Format: CIF Size: 197.4 KB Download
Supporting Information File 5: Crystallographic data of [6]CMP analysed by XD2016 (CCDC 2335444).
Format: CIF Size: 102.4 KB Download


This study was partly supported by KAKENHI (20H05672, 22H02059).

Data Availability Statement

All data that supports the findings of this study is available in the published article and/or the supporting information to this article. The crystallographic data were deposited in the Cambridge Crystallographic Data Centre (CCDC 2335441–2335444). The data can be obtained free of charge from the CCDC via


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