A flexible thioether-based MOF as a crystalline sponge for structural characterization of liquid organic molecules

Abstract

Herein, we present a flexible MOF (PCN-41) composed of a thioether-based linker and a stair-like {Cu₄I₄} cluster. Upon the inclusion of liquid organic molecules, PCN-41 undergoes a single crystal to single crystal transformation to allow for ordered arrangement of the guest molecules. By virtue of the low symmetry, structural flexibility, and the electron-rich cavity environment, PCN-41 exhibits crystalline sponge behavior toward a series of electron-deficient liquid molecules including DMF, MeCN, NMP, DMSO and benzaldehyde.

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Single-crystal X-ray diffraction (SCXRD) is a powerful and ubiquitous technique to definitively elucidate structures at the molecular level.¹ It has been widely used to determine static structures as well as provide direct evidence for consecutive chemical transformations.² However, this technique requires the targeted compound in a single crystalline phase, which prohibits the structural determination of liquids and amorphous solids. The preparation of crystals suitable for analysis can be a severe bottleneck for a great number of molecules that generally do not crystallize owing to their particular properties. For instance, compounds with low melting points do not maintain the single crystalline form at room temperature, which hampers the implementation of SCXRD. In macromolecular chemistry, it is observed that some guest molecules, such as solvent molecules, can be absorbed and arranged in coordination cages or MOFs.³ These molecules can sometimes be detected using single crystal X-ray crystallography. Recently, Fujita and co-workers developed this further into a new method for molecular detection and identification, the crystalline sponge method.⁴ In this method, a crystalline porous coordination polymer is chosen as a crystalline sponge.⁵ If a crystalline sponge is soaked in a solution containing a compound, the compound is absorbed into the cavities and the molecules arrange themselves in a fixed orientation. Furthermore, the structure of the targeted compound can be clearly elucidated using the X-ray crystallography method.^6–8 Using this method, not only did researchers realize the structural determination of targeted guest molecules that hardly crystallize, but they also determined the absolute configuration of natural products as well as transient species of several reactions.

To be utilized as a matrix for the crystalline sponge method, several requirements should be satisfied. Firstly, the pore size of crystalline sponges needs to be optimized.⁹ It should be large enough to accommodate guest molecules but not too large to result in a weak interaction between guest molecules and the framework. Secondly, the pore environment of the crystalline sponge should have strong affinity to guest molecules.¹⁰ Thirdly, because guest molecules are likely to be disordered in a highly symmetric structure, the crystalline sponge must possess low symmetry in order to be anisotropic. In addition, the slow diffusion of guest molecules into the solvent-filled voids of the crystalline sponge is important to render the guests thermodynamically well equilibrated at the specific molecular-recognition sites of the hosts.¹¹ Moreover, the host MOF should bear a certain extent of flexibility to change its conformation in order to accommodate different substrates.¹²

Bearing these in mind, we designed and synthesized a MOF built with a flexible tritopic ligand (Fig. 1a) and a stair-like {Cu₄I₄} cluster, namely PCN-41·2DMA. A flexible thioether-based linker (1,3,5-tris(4-pyridylsulfanylmethyl)-2,4,6-trimethylbenzene, L, Fig. S1, ESI†) was designed for the following reasons: (i) the flexible linker in combination with the stair-like {Cu₄I₄} cluster is likely to result in the formation of a MOF that crystallizes in a relatively low-symmetric space group. In fact, PCN-41·2DMA crystallizes in triclinic P1̄ which is the lowest space group reported for crystalline sponge MOFs, (ii) the flexible linker possesses variable configurations and endows the resultant framework with certain flexibility, which is critical for the incorporation of different substrates, and (iii) the thioether-based ligand provides an electron-rich pore environment, which possesses a strong affinity for electron-deficient guest molecules. Therefore, this MOF would be a good complement to the triazine-based crystalline sponge.

Fig. 1 The structure of PCN-41·2DMA: (a) the flexible thioether-based ligand L, (b) the stair-like {Cu₄I₄} cluster, (c) the 2D layer and (d) the (3,6)-connected kgd topology. Symmetry transformations used to generate equivalent atoms: #1 −x − 1, −y − 1, −z, #2 −x, −y, −z + 1, #3 x − 1, −y + 1, z − 1, #4 −x + 1, −y, −z, #5 x − 2, y − 1, z.

The reaction of CuI and L in the presence of hydroiodic acid in the DMA/H₂O system yields [Cu₂I₂L] 2DMA (PCN-41·2DMA) as yellow crystals. Single-crystal X-ray diffraction analysis reveals that PCN-41·2DMA crystallizes in the triclinic space group P1̄ (Table S1, ESI†). In the asymmetrical unit, there are two distinct copper and iodine ions, one kind of neutral L moiety, and two DMA molecules. In this compound, the connection between copper and iodine ions leads to a stair-like {Cu₄I₄} cluster (Fig. 1b). Both of the two types of Cu(I) ions in this structure are four-coordinated nodes with a tetrahedral geometry. Cu1 is coordinated with three iodine ions and one N from ligand L with distances of 2.59–2.73 Å and 2.04 Å, respectively. Cu2 is coordinated with two bridging iodide ions with a distance of 2.68 Å, as well as two N atoms from two ligand fragments with a distance of 2.05 Å, which are consistent with the distances in the literature.¹³ The distance between Cu1 and Cu2, 2.659 Å, is shorter than the sum of two copper atoms’ van der Waals radii (2.8 Å), indicating that there is some attractive interaction between these closed shell d¹⁰ metal ions. The two different types of iodide ligands exhibit doubly bridging μ₂-I (I1) and triply bridging μ₃-I (I2) modes. The stair-like {Cu₄I₄} clusters and neutral ligands can be viewed as 6- and 3-connected nodes, respectively. Therefore, topologically, the framework of this compound can be classified as a 2D (3,6)-connected kgd net with the point symbol (4³)₂(4⁶·6⁶·8³) (Fig. 1c and d).¹⁴ On the other hand, two adjacent ligand fragments were both connected with two {Cu₄I₄} clusters, and can be considered as a 4-connected node (Fig. S2, ESI†). In this sense, the {Cu₄I₄} cluster can be considered as another kind of 4-coordinated node, and the overall framework can be regarded as a (4,4)-connected sheet with square lattice sql.^14a Such connectivity results in the formation of two kinds of DMA containing cavities (11.585 × 12.441 Å and 10.899 × 12.441 Å), which are created with two moieties of L and two {Cu₄I₄} clusters. The adjacent layers were packed in an AAA sequence with an interlayer distance of 6.078 Å (Fig. S3a, ESI†).

The powder X-ray diffraction (PXRD) pattern of the as-synthesized samples matches well with the simulations (Fig. S4, ESI†), thus indicating the phase purity of PCN-41·2DMA. The framework of PCN-41·2DMA satisfied the requirements of a crystalline sponge, offering us the opportunity for crystallographic study of the uptake and specific locations of a series of chemically related simple guest molecules. As a proof of concept, five liquid samples, namely, DMF, CH₃CN, NMP, DMSO and benzaldehyde (PhCHO), were chosen as target guest molecules. We conducted solvent-soaking tests; the as-synthesized crystals of PCN-41·2DMA were immersed in these solvents at room temperature overnight. As a result, guest-exchanged samples were obtained. After the exchange process, DMA molecules were fully removed and the guest molecules were adsorbed in the flexible cavities, leading to the formation of PCN-41·DMF, PCN-41·2CH₃CN, PCN-41·2NMP, PCN-41·2DMSO and PCN-41·PhCHO. Fortunately, in the flexible crystalline 2D layers of this system, the guest inclusion can be monitored easily in a single-crystal to single-crystal (SCSC) fashion. Furthermore, their molecular structures were unambiguously determined using SCXRD and the crystallographic data are presented in Table S1 (ESI†).

X-ray diffraction analysis suggests that PCN-41·DMF, PCN-41·2CH₃CN, PCN-41·2NMP, PCN-41·2DMSO and PCN-41·PhCHO also crystallized in the P1̄ space group. Similar architectures of these products were derived from PCN-41·2DMA, in which stair-like {Cu₄I₄} clusters were connected with L fragments to form similar cavities (Fig. 2). The malleability of final networks results from the flexible ligand L, allowing the cavity sizes and angles to adjust to accommodate different guest molecules. The relevant information of cavities in these products is summarized in Table 1. Similarly, the adjacent layers were stacked in an AAA sequence (Fig. S3, ESI†). The guest molecules resided in the cavities of each layer; as a result, the interlayer distances of AAA arrays after guest-exchange were almost unchanged (Table 1).

Fig. 2 The structures of PCN-41·2DMA (a) before and after immersion in different solvents to generate PCN-41·DMF (b), PCN-41·2CH₃CN (c), PCN-41·2NMP (d), PCN-41·2DMSO (e) and PCN-41·PhCHO (f).

Table 1 Information on the two kinds of cavities and the interlayer distances

	Cavity A (a × c, Å)	α (°)	Cavity B (b × c, Å)	β (°)	D (Å)
a The interlayer distances of AAA sequences in these compounds.
PCN-41·2DMA	11.585 × 12.441	69.91	10.899 × 12.441	77.24	6.0870
PCN-41·DMF	11.539 × 12.433	72.50	10.976 × 12.433	75.20	6.0712
PCN-41·2CH3CN	11.499 × 12.205	73.41	10.935 × 12.205	75.25	5.9950
PCN-41·2NMP	11.479 × 12.432	73.09	10.946 × 12.432	73.72	6.1046
PCN-41·2DMSO	11.656 × 12.541	66.43	10.843 × 12.541	80.20	6.0708
PCN-41·PhCHO	11.626 × 12.566	66.09	10.924 × 12.566	80.95	6.1586

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Note that these liquid compounds require low temperatures to crystallize, which hampers the implementation of SCXRD. By means of synthesizing flexible crystalline networks, we transferred solution-state host–guest chemistry into the solid-state. The cavities in the electron-rich layers encapsulate the solvent guest molecules in a SCSC manner that enables a straightforward analysis of the final structure after guest inclusion using X-ray crystallography. PCN-41·2DMA as a crystal sponge provides a facile way to determine the crystal structure of liquid samples.

In conclusion, a flexible MOF, PCN-41·2DMA, was prepared, which is composed of a thioether-based linker and a stair-like {Cu₄I₄} cluster. The flexible framework and electron-rich pore environment provide the possibility to be utilized as a crystalline sponge for a series of electron-deficient guest molecules. In this work, the transfer of solution-state host–guest chemistry into the solid-state was realised through the preparation of flexible crystalline networks. This work not only offers a successful case to construct a flexible MOF for single-crystal-to-single-crystal guest inclusion studies but also enriches the crystalline sponge family. Considering its low symmetry, structural flexibility, and the electron-rich cavity environment, a variety of applications related to the crystal sponge method is envisioned for the PCN-41 system.

The Distinguished Scientist Fellowship Program (DSFP) at KSU is gratefully acknowledged for supporting this work. This work was also supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award Number DE-SC0001015, and the Hydrogen and Fuel Cell Program under Award Number DE-EE0007049. The authors also acknowledge the financial support of the U.S. Department of Energy, Office of Fossil Energy, National Energy Technology Laboratory (DE-FE0026472). S. Yuan also acknowledges the Texas A&M Energy Institute Graduate Fellowship Funded by ConocoPhillips and Dow Chemical Graduate Fellowship.

Notes and references

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Footnote

† Electronic supplementary information (ESI) available: Experimental details and crystallographic data. CCDC 1541830–1541835. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7qm00152e

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