[4 + 4]-Imine Cage Compounds with Nitrogen-Rich Cavities and Tetrahedral Geometry

Key words

organic cage compounds - imines - pyrrols - dynamic covalent chemistry

Introduction

Organic cage compounds have gained a lot of interest in the past decades[1]–[5] due to emerging applications in materials science. They found their use in sensor films,[6] as coatings for quartz crystal microbalances,[7],[8] for selective ion recognition,[9] to make porous membranes,[10],[11] for selective gas sorption[12]–[15] and separation,[16]–[20] catalysis,[21] or as stationary phases for gas chromatography.[22],[23] To create cages for specific applications it is important to control parameters such as size,[24] shape,[25] geometry[3],[4] as well as number and positions of functional groups.[9],[26] Most cage compounds are synthesized by dynamic covalent chemistry (DCC).[27] Among DCC reactions, the reactions forming boronic acid esters or imines are the most common ones and for the latter a huge variety of geometries such as (truncated)[28],[29] tetrahedra,[30]–[33] trigonal prisms,[34]–[36] cubes,[16],[37],[38] rhombicuboctahedra,[39]–[41] adamantoids,[35],[42],[43] tetrapods,[44] cucurbitimines[45] or more complex structures such as catenanes[46],[47] have been realized and some of these structures have even been post-stabilized to enhance their chemical robustness.[6],[48]–[50] Cages with nitrogen-containing pyridine[9],[51] or pyrrol-units[52] showed superior behavior in, e.g., ion recognition and could act as ligands for several transition metal ions as shown for numerous metal–organic cage compounds or complexes.[53],[54] To extend the portfolio of organic cage compounds, we envisioned the synthesis of tetrahedral [4 + 4] imine cages, which are based on a trispyrrol aldehyde, a unit used by Beer and co-workers for flexible [2 + 3] cages,[55],[56] yet this time with substituted 1,3,5-trimethylamino benzenes[9],[28] to retain a higher degree of shape persistency.

Results and Discussion

The desired cage compounds were synthesized by condensation reactions of methyl-trispyrrolyl-aldehyde 1 [56] with equimolar amounts of the differently substituted triamines 2-Me, 2-Et, 2-OPr and 2-Br in chloroform at room temperature or 60 °C ([Scheme 1]). Due to their solubility in common organic solvents, cage compounds 3-Me, 3-Et and 3-OPr were successfully isolated by recycling gel permeation chromatography (rec-GPC) in THF after 6 (3-Me and 3-Et) or 15 (3-OPr) recycling cycles in yields between 10 and 18% (for chromatograms, see the Supporting Information, SI).

Scheme 1 Synthesis of the cage compounds. a) CHCl₃, TFA (3 mol-%), rt or 60 °C, 2 d.

Due to its low solubility, the purification of 3-Br by rec-GPC was not possible and attempts to remove impurities by recrystallization failed, so that minor impurities remained. The successful synthesis of the cages was verified by ¹H NMR spectroscopy by the disappearance of the signals of the aldehyde units of 1 (δ = 9.13 ppm) as well as of the amine units of 2-Me, 2-Et, 2-OPr and 2-Br (δ = 1.30 – 1.63 ppm). Instead, signals of the imine protons of cages 3-Me, 3-Et, 3-OPr and 3-Br at δ = 8.15 – 8.24 ppm were found (labeled as protons 7 in [Figure 1a – d]). Furthermore, MALDI-TOF mass spectrometry shows signals at m/z 1850.0210 (3-Me; calc: 1850.0201), m/z 2018.2058 (3-Et; calc: 2018.2079), m/z 2378.3341 (3-OPr; calc: 2378.3346) and m/z 2618.7553 (3-Br; 2618.7568) representing the corresponding [4 + 4] condensates ([Figure 1e – h]).

Figure 1 a – d) ¹H NMR spectra and of cage 3-Me (a) (600 MHz), 3-Et (b) (600 MHz), 3-OPr (c) (700 MHz) and 3-Br (d) (700 MHz) in CDCl₃. # = BHT, * = THF, $ = pentane, & = methanol. e – h) MALDI-TOF mass spectra (matrix: DCTB) of 3-Me (a), 3-Et (b), 3-OPr (c) and 3-Br (d). Simulated (top) and experimental (bottom) isotopic patterns are shown as insets.

The low isolated yields of cages 3-Me, 3-Et and 3-OPr after rec-GPC purification can be rationalized by the formation of several other species as obvious by multiple peaks in the GPC-chromatograms (see the SI). MALDI-TOF MS analyses of the isolated fractions showed the 4 + 4 condensates as main components alongside minor impurities for each fraction. Nevertheless, ¹H NMR analyses revealed more complex patterns leading to the hypothesis of isomeric cage structures. To get further insight into possible cage isomers, we conducted quantum chemical calculations at the B3LYP/6 – 31 G(d) level of theory and calculated the interconversion energy of a pro-chiral trispyrrol unit to elucidate whether these units lead to a potential mixture of diastereoisomeric cages ([Figure 2]). Even considering the highest energy barrier between intermediate II and transition state III of 23.7 kJ/mol would result in a rapid interconversion rate of 4.35·10⁸ · s⁻¹ and a half-life time of 1.59 ns, suggesting a fast interconversion in solution. This is further underlined by the comparably low relative energies of MMMM, MMMP, MMPP, MPPP and PPPP cages of 6.7 to 11.1 kJ/mol independent of the side chains (see SI), indicating again a fast interconversion excluding diastereomeric cages causing the several fractions obtained by rec-GPC. Another possibility is the formation of in–out-isomers referring to the central methyl-units of the trispyrrols. The relative energies of the possible in–out-combinations show that the all-in isomers should represent > 98.5% of the cages in a dynamic equilibrium in solution. Thus, it can be concluded that the different fractions obtained by rec-GPC contain different in–out isomers of the cages that are kinetically trapped.

Figure 2 DFT-calculated (B3LYP/6 – 31 G(d)) interconversion of P- to M-trispyrrol.

For all isolated all-in cages, suitable crystals for single-crystal X-ray diffraction (SCXRD) analyses have been obtained, unambiguously proving the molecular structures of the [4 + 4] cages ([Figure 3]). The geometrical shapes can best be described as truncated cubes with tetrahedral symmetry. In all studied cases, the central methyl group of the trispyrrols is pointing into the cage cavities resulting in distances to adjacent phenyl rings of d _Me-Ph = 1.2 – 1.3 nm and outer diameters of d = 1.5 – 1.6 nm. As previously observed, for 3-Me all ethyl substituents are conformationally stable and point outwards, whereas propoxy groups in 3-OPr point either out- or inwards.

Figure 3 Single-crystal X-ray structures of the cages 3-Me, 3-Et, 3-OPr and 3-Br as capped-stick models. The distances of a phenyl unit to the opposing internal methyl group and to the outer carbon atoms of the trispyrrol moiety are given for 3-Me exemplarily. Colors: carbon, gray; nitrogen, blue; oxygen, red; bromine, brown; hydrogen, white.

Besides the solvate 3-Et_α crystallized from dichloromethane and hexane (cubic, P _a3̄) and cage 3-OPr (orthorhombic, A_ba 2), all obtained structures crystallized in the triclinic space group P1̄. Due to steric repulsion, each trispyrrol unit adopts a chiral C ₃-symmetrical conformation (for the sake of simplicity, we name them here M or P orientation), which can interconvert quickly by rotation around the C–C single bonds to the central carbon atom. Thus, each trispyrrol unit is prochiral leading to overall five possible cage isomers due to their tetrahedral symmetry. The solid-state structures of 3-Me, 3-Et_β, 3-OPr and 3-Br adopt single enantiomeric MMMM or PPPP orientation, an effect comparable to the assembly of face-orientated polyhedra derived from prochiral building blocks as reported by Caoʼs group ([Table 1] and [Figure 5]).[57],[58] Since four out of eight “faces” of the synthesized truncated cubes possess helical chirality, the cages can be understood as semi-face-orientated polyhedra.

Table 1 Selected crystallographic data of cages 3-Me, 3-Et, 3-OPr and 3-Br.

Compound	Solvents	Crystal system	Space group	Z	Cell volume	Isomers observed	Packing
3-Me	CDCl3/MeOH	Triclinic	P1̄	2	7578.4 Å3	MMMM/PPPP	Enantiopure layers
3-Etα	CH2Cl2/C6H14	Cubic	P a3̄	8	31 222.2 Å3	MMMP/PPPM	3D-alternating
3-Etβ	CH2Cl2/MeOH	Triclinic	P1̄	2	7646.5 Å3	MMMM/PPPP	Enantiopure layers
3-Etγ	CDCl3	Triclinic	P1̄	2	8142.8 Å3	MMMP/PPPM	Enantiopure layers
3-OPr	CH2Cl2/MeOH	Orthorhombic	Aba 2̄	4	18 567.7 Å3	MMMM/PPPP	Enantiopure layers
3-Br	CH2Cl2/MeOH	Triclinic	P1̄	2	7399.5 Å3	MMMM/PPPP	Enantiopure layers

Cages 3-Me and 3-Br both pack in the triclinic space group P1̄ in an isomorphic fashion, which is obvious for example from the comparable unit cell volumes of 7578.4 ų (3-Me) and 7399.5 ų (3-Br) ([Table 1]). In both cases face-to-face π–π-stacking motifs are found on one face of each cage with distances of d _π–π = 3.43 Å (3-Br) or 3.48 Å (3-Me) ([Figure 4]). The residual faces interact, e.g., via C – H⋯π interactions in the case of 3-Me with d _{C – H⋯π} = 2.99 Å ([Figure 4c]). This interaction is mimicked in 3-Br by C–Br⋯π interactions of d _C–Br⋯π = 3.26 Å ([Figure 4f]), leading in both cases to enantiopure layers within the crystallographic ab-planes ([Figure 5f]).

Figure 4 Intermolecular interactions found in the single-crystal X-ray structures of 3-Me (a – c) and 3-Br (d – f).

Changing the solvent diffused into saturated solutions of 3-Et from methanol (leading to 3-Et_β with enantiopure cages) to hexane or if the crystals were grown by slow evaporation of a CDCl₃ solution of 3-Et, solvates 3-Et_α and 3-Et_γ are obtained showing the MMMP and PPPM isomers exclusively ([Figure 5]).

In the case of 3-OPr, packing in the orthorhombic space group A_ba 2, similar layers as in 3-Me and 3-Br are found in the crystallographic bc-plane with one-dimensional channels along the c-axis filled with methanol and water molecules (see [Table 1], [Figure 5], [Figure 6] and discussion below). For 3-Et, the homochiral solvate 3-Et_β, as well heterochiral solvate 3-Et_γ , form layered structures as well, while 3-Et_α crystallizes in the cubic space group P _a3̄ and the enantiomeric cages MMMP- 3-Et and PPPM- 3-Et can be found in an alternating order in all three dimensions ([Figure 5f]).

Figure 5 a) Schematical depiction of the P- and M-alignment of the prochiral trispyrrol units. Note: The methyl group pointing out of the paper plane here is pointing inside the cage voids, which has to be taken into account in the following figures. b) Schematic representations of the homochiral PPPP (shown in blue for 3-Me) and MMMM (shown in red for 3-Me) as well as heterochiral PPPM (shown in green for 3-Et_α ) and MMMP (shown in orange for 3-Et_α ) cages. d – h) Packing motifs of the obtained solvates with different enantiomers colored according to [Figure 3b] as capped-stick models. One cage each is shown as space-fill model in element colors.

Figure 6 Residual solvent analysis of single-crystal X-ray structures of cages 3-Me and 3-OPr. a) Cage 3-Me (shown in black as capped-stick model) with 12 molecules of methanol and one molecule of CHCl₃ (shown as space-fill models). b) Top-view and c) side-view of the hydrogen bonding pattern in detail. d) Crystal packing of cage 3-OPr (shown as capped-stick models in white with one molecule shown as space-fill model in element colors) with ten methanol molecules (shown as capped-stick model in element colors) and ten water molecules (shown as a space-fill model in red without hydrogen atoms).

The nitrogen-rich inside of the cagesʼ cavities should be a perfect environment for polar guests. Crystallizing 3-Me using CHCl₃ and methanol led to 12 enclathrate-ordered methanol molecules in defined H-bonded arrays interacting with the pyrrol-imine subunits via synergetic H-bonds of d _N–H⋯O = 2.00 Å and d _O–H⋯N = 2.11 Å ([Figure 6a – c]). This alignment generates a “shell” of methanol molecules by the interaction of the highly polar OH-groups and the inner surface of the cage leaving the methyl groups pointing to the inside of the cage creating a more nonpolar environment. Inside this nonpolar pocket, exactly one molecule of CHCl₃ can be found to be interacting via van-der-Waals interactions ([Figure 6a]).

While Russian-doll alignments with three spheres have been realized on a molecular level;[59]–[62] to the best of our knowledge, the structure discussed here is the first organic cage compound with two of these spheres being two different solvents. Furthermore, seven more methanol and one water molecule fill the inter-cage voids in the crystalline packing. For 3-Et_β , 10 methanol molecules are found in similar alignments as discussed for 3-Me ([Figure 6]), yet due to disorder the residual solvent molecules had to be SQUEEZED. Ten methanol molecules are also found in the cavity in 3-OPr ([Figure 6d]). This time the residual voids are filled with ten water molecules which align in a chain-like fashion along the crystallographic a-axis ([Figure 6d]). Due to fast exchange, the H-atoms of the water molecules were not crystallographically found and a detailed discussion of the hydrogen bonding pattern is not possible.

Conclusions

To summarize, we have constructed four cage molecules based on a trispyrroltrialdehyde. While 3-Me, 3-Et and 3-OPr have been successfully isolated and fully characterized, 3-Br was mainly investigated by SCXRD. A detailed study of six single-crystal X-ray structures in total revealed that the prochiral trispyrroltrialdehyde orient in homoenantiomeric PPPP and MMMM cages in four cases and only cage 3-Et can be found in the heteroenantiomeric MMMP and PPPM form in two solvates in the solid state. Furthermore, the nitrogen-rich interior of the cages is able to interact with polar molecules such as methanol or water and defined alignments like methanol shells or hydrogen-bonded chain-like structures were obtained. These findings can be beneficial for applications of the cages in the selective binding of polar guests or proton conductivity.[63]–[65] Furthermore, the nitrogen-rich cavity can be used as a cage ligand for transition metal ions or clusters.[66]–[69]

Funding Information

We thank the European Research Council (ERC) in the frame of the consolidator grant CaTs n DOCs (grant no. 725 765) and Deutsche Forschungsgemeinschaft (DFG) under Germanyʼs Excellence Strategy Cluster 3D Matter Made to Order (EXC-2082/1 – 390 761 711) for funding this project. The authors acknowledge support by the state of Baden-Württemberg through bwHPC and the German Research Foundation (DFG) through grant no. INST 40/575 – 1 FUGG (JUSTUS 2 cluster).

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