Halogen Bonding in a Crystalline Sponge - ACS Publications

Feb 18, 2019 - Cooperation Base of Pesticide and Green Synthesis, College of Chemistry, Central China Normal University, Luoyu Road 152,. Wuhan 430079...
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Halogen Bonding in a Crystalline Sponge Liangqian Yuan, Siyu Li, and Fangfang Pan* Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, College of Chemistry, Central China Normal University, Luoyu Road 152, Wuhan 430079, People’s Republic of China

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between iodoperfluorocarbons and NO3− anions or H2O molecules.26 In general, CSs with intrinsic cavities and an ability to capture guest molecules also have potential in the study of intermolecular interactions between guests, for example, XB between small halogen-bond donors and acceptors. During this course, the host−guest contacts may have a crucial influence on the bonding between guests, particularly when the host− guest binding is stronger than the guest−guest binding. Consequently, it is necessary to investigate the potential binding ability of the CS to guests of different features at the same time. However, this field is still blank. In this contribution, we made use of the most topical crystal sponge CS-1, formed by ZnI2 and a trigonal organic linker, 2,4,6tris(4-pyridyl)-1,3,5-triazine (TPT), as the host container, and two molecules of different types as guests. One guest contains electron-deficient moieties with potential as halogen-bond donors including 1,4-diiodotetrafluorobenzene (DITFB) and 1,4-diiodobenzene (DIB), and the other has electron-rich groups involving 4-(methylsulfonyl)toluene (MST) and 1,4dioxane (DOX). The guests were found to be simultaneously absorbed and sorted by the host framework via its two different cavities (Figures 1 and S1).

ABSTRACT: Host−guest interactions are the key to the supramolecular chemistry and the further application of the receptors to study the structural details of the small guest molecules. Crystalline sponges as a kind of supramolecular receptor need to be investigated in terms of the binding ability with the guests. We found in this work that one guest with σ-hole donors and another with electron-donating species were separately entrapped in two distinct channels of the host framework via the crystalline sponge method. Halogen bonding and weak hydrogen bonding were detected between the host and the two guests, respectively. The ability of the crystalline sponge to absorb and sort guests of different types was unambiguously confirmed by X-ray crystallography.

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he crystalline sponge method (CSM), since being developed in 2013 by Fujita et al., has received growing attention.1 It has been found to be extremely useful in structure determination for liquid and other noncrystallizing compounds,1−4 absolute configuration confirmation,5−8 and inspection of the intermediate state for organic reactions.9−12 The basis of the CSM is attributed to the guest absorption ability of the crystalline sponge (CS).13 Because of their relatively large pore size, most of the previously reported CS structures contained more than one type of guest in its cavity, including the target molecules and solvent.14−16 Halogen bonding (XB) was extensively studied in past decades particularly in theory and in the solid phase because of its ubiquity in biosystems, utilization in crystal engineering, and potential applications in medical chemistry and materials science.17−21 Although the definition of a halogen bond was finally given in 2013 by IUCr,22 a number of basic issues of XB are still unclear.23 For example, the structures of small XB pairs in solution are not able to be directly measured because of the paucity of current tools. Encapsulation in host−guest systems resembles the situation in liquids in terms of intermolecular contacts and packing issues.24 In this sense, X-ray crystallography could provide a way to study the XB assembly via host− guest techniques. In 2012, the Nau group encapsulated the molecular dibromine and diiodine in the cavity of cucurbit[6]uril.25 In the case of dibromine, the inclusion guest Br2 formed XB with the water molecules, while for diiodine, XB was found between the ureido carbonyl group of the host and the inclusion guest I2. In 2015, Fujita et al. reported that the confined space in a metal−organic cage could enhance XB © XXXX American Chemical Society

Figure 1. Schematic diagram of the synthesis of the CS and the entrapment of two different guests.

The ZnI2−TPT framework is the most studied CS so far,27−29 although great efforts have been made to explore new CSs. There were four different patterns of the framework reported in total. The CS-1 used here was a doubly interpenetrated structure crystallizing in the monoclinic space group C2/c. It was synthesized with an optimized method by Clardy et al.30 That is, in a test tube, a methanol solution of 3 Received: February 18, 2019

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DOI: 10.1021/acs.inorgchem.9b00482 Inorg. Chem. XXXX, XXX, XXX−XXX

Communication

Inorganic Chemistry equiv of ZnI2 was carefully layered on top of the CHCl3 solution containing 2 equiv of TPT. The test tube was sealed and left undisturbed at ambient conditions for 3 days. The crystals obtained with this method were square plates. Immersing the sponge crystals in a solution containing the corresponding guests for another 2−3 days gave rise to target crystals, as first confirmed by IR (Figures S2−S5). In the case of DITFB&MST@CS-1, the new signals at 1464 and 943 cm−1 proved the existence of DITFB and the vibration at 1147 cm−1 indicated the successful entrapment of MST. Analogously, the frequency of 1254, 1117, and 993 cm−1 clearly manifested the absorption of DOX and DIB, respectively. Thermogravimetric analysis (TGA) was also used to identify the absorption results (Figure S6 and Table S1). The weight loss from 37% at ca. 150 °C to 51% at 335 °C in DIB&DOX@CS-1 corresponds to the release of two guests, respectively. In DITFB&MTS@CS-1, the first weight loss of 21% at 166 °C is attributed to the leaving of the chloroform. The next weight loss of 25% at 320 °C indicates the simultaneous removal of DITFB and MTS. In both cases, the CS-1 collapses at around 450 °C. Finally, we examined the two structures by single-crystal Xray crystallography. After absorption of the guests, all of the crystals remained as the space group C2/c, with unit cells very similar to those of the CS (Table S2). This indicated that the replacement of the absorbed guests did not significantly affect the interpenetrated network. In detail, in the case of DITFB&MST@CS-1, the unit cell is slightly increased, while the relatively small guests DIB and DOX slightly decrease the unit cell. Crystal structure analysis revealed that interlocking of the 3D networks partitioned the channel into two parts, shown in Figures 1 and S1 as H1 and H2, respectively. They differ in shape and size. In particular, the relative positions of iodide are different for the two pores. This provides the two pores with different binding-ability electron-deficient molecules, such as molecules with σ holes. XB between metal halides and other halogen-containing compounds has been systematically studied by Brammer et al.31 Through coordination with the metal ion, the halides show strong nucleophilic sites, which were potentially able to donate electrons to halogen bond donors. Recently, Gee et al. evaluated the dynamic absorption of I2 in CS-1.32 With a different I2 amount, I−···I2···I− and I3− species were found, where the guest I2 interacted with the framework via I···I halogen bonds. It is interesting to find that only channel H1 attracts the halogen bond donors DITFB and DIB, and the channel H2 prefers the other guests MST and DOX. In DITFB&MST@ CS-1 (Figures 2 and S8), DITFB was located around the 2-fold axis, resulting in a disordered distribution over two sites. DITFB interacted with the iodides from the CS via XB at both ends, with RXB values of 0.92 and 0.97, respectively [RXB = dD···A/(rvdW(D) + rvdW(A))]. Although the halogen bonds were not strong, they showed good linearity with C−I···I angles of 157.67 and 171.25°, respectively. Note that there was a second disordered DITFB with around 0.25 occupancy parallel to the halogen bond. A weak contact between the DITFB I and triazine N atoms assisted by two pyridyl CH groups was detected. This might be the stabilizing force for the second DITFB molecule in the cavity. In H2, only a MST molecule was found. The closest contact between MST and CS was the −CH3 groups and the iodide. The C···I distance of 3.839 Å implies no real attraction between the host and guest. Nevertheless, a lone pair···π interaction between the MST O

Figure 2. Left: Structure of DITFB&MST@CS-1, with the guests in CPK mode and the host in capped sticks. Right: XB (blue broken lines) between DITFB and the ZnI2−TPT framework (top) and interactions among DITFB and MST (bottom), with hydrogen bonds in red and π···π interactions in green.

atom and DITFB molecule was detected. The distance between the O atom and the centroid of DITFB was 3.034 Å, falling in the range of the lone pair···π force.33 The attractive nature of this force was accounted for by the electron-rich site of the O atom and the electron-deficient area of the DITFB center because of the strong electron-withdrawing effect of F. In addition, the MST molecule was dimerized via two CH···O weak hydrogen bonds. In this way, all of the guests in the channel were reasonably stabilized. The absorption experiment was conducted in a solution of chloroform, and some CHCl3 residuals remained in the cavities of the CS-1. They were disorderedly distributed in both H1 and H2. In DIB&DOX@ CS-1 (Figure 3), two disordered DIB species with occupancies

Figure 3. Left: Structure of DIB&DOX@CS-1, with the guests in CPK mode and the host in capped sticks. Right: XB (blue broken lines) between DIB and the ZnI2−TPT framework (top), as well as the lone pair···π (green broken lines) and CH···O (red broken lines) between DOX and the framework (bottom).

of around 0.5 and 0.15, respectively, were assigned from the difference Fourier map. For the main part, similar XB interactions (RXB = 0.91 and 0.96, respectively) accounted for binding of the CS-1 toward DIB. Interestingly, the two DIB species also only appeared in the channel H1 (Figures 3 and S9). In H2, three sites were assigned with DOX molecules. Two were disordered with an occupancy of around 0.5. For one of the half-occupancy DOX, a crystallographic glide plane went through and additionally halved the molecule. Weak CH···O (dC···O = 3.167 Å) and O···π (dO···C = 3.153 Å) interactions were observed between the host and guest. The symmetry-related DOX locates in the middle of the other two DOX molecules and interacts with them via CH···O contacts. B

DOI: 10.1021/acs.inorgchem.9b00482 Inorg. Chem. XXXX, XXX, XXX−XXX

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In addition, we also investigated the adsorption experiment of the CS-1 with the guest combination of iodobenzene and MST, as well as pentafluoroiodobenzene and MST. Unfortunately, we were not able to locate the positions of the guests in the cavity, although the IR and TGA indicated both guests entrapped in the host. This is probably because of the weak binding between the host and guests, which resulted in severe disorder of the guests. A CSD search found in total 196 hits containing the ZnI2− TPT motif.27 Among them, 116 have similar interpenetrated networks (CS-1) crystallizing in either a monoclinic or triclinic crystal system with a space group of C2/c, C2, Cc, P21/c, P21, or P1̅, depending on the guests. CH···π or π···π interactions were the main host−guest interactions as reported. Utilizing the Zn−I2 moieties to entrap organic guests of XB donors in this study was the first attempt. For another CS formed by the same reactants via a high-temperature reaction, the Zn−I2 moieties were involved in the binding of reactive P4 and S3 via I···P or I···S contacts.34,35 We also noticed that, from tribromomethane or chloroform, noninterpenetrated threedimensional structures of ZnI2−TPT formed. Careful analysis of the structures indicated XB between the iodide in the framework and the halogen atoms in the bromoform or chloroform.28,29 Although XB interactions were not specifically mentioned in the original publications, they may play a crucial role in such framework formations. In conclusion, the ZnI2−TPT network, in particular the doubly interpenetrated pattern as CS, was demonstrated to have the ability to entrap two distinct types of guests. The ZnI2 moieties prefer donating electrons to guests with σ holes, forming halogen bonds, while the TPT sites tend to provide an electron-deficient surface via CH groups for the guests with electron-rich groups. Interpenetration of the ZnI2−TPT networks results in two slightly different channels in terms of I···I separation; thus, halogen-bonded donors with certain lengths would be absorbed into the suitable one, with the other guest in the second. In addition, weak interactions also take place between the guests because the two channels are interconnected. Although XB happens between the host and guest instead of the two guests as desired, the idea that making use of the channel of the CS as the space to investigate the intermolecular interactions between the small molecules would extend the application of the CSM. The corresponding studies are still underway.

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Communication

AUTHOR INFORMATION

Corresponding Author

*E-mail: ff[email protected] (F.P.). ORCID

Fangfang Pan: 0000-0002-3091-6795 Author Contributions

The manuscript was written by F.P. and all authors contributed to the final version of the manuscript. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We are grateful for financial support through the National Natural Science Foundation of China (Grant 21602071 to F.P.), the Fundamental Research Funds for the Central Universities (Grant CCNU17QN006 to F.P.), and the Central China Normal University, China.

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The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.inorgchem.9b00482. Full treatment procedures and refinement details, IR spectroscopy, TGA, crystallographic analyses, packing views, ORTEP plots, and UV−vis results (PDF) Accession Codes

CCDC 1895266−1895267 and 1915405−1915406 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/ data_request/cif, or by emailing [email protected]. uk, or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033. C

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DOI: 10.1021/acs.inorgchem.9b00482 Inorg. Chem. XXXX, XXX, XXX−XXX