Home Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3
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Halogen bonds in the crystal structure of 4,3′:5′,4″-terpyridine — 1,3-diiodotetrafluorobenzene (1/1), C21H11F4I2N3

  • Weizhou Wang ORCID logo EMAIL logo
Published/Copyright: January 14, 2022

Abstract

C21H11F4I2N3, orthorhombic, Pnma (no. 62), a = 11.0042(4) Å, b = 20.6209(5) Å, c = 9.2371(3) Å, V = 2096.05(11) Å3, Z = 4, R gt (F) = 0.0316, wR ref (F 2) = 0.0556, T = 293(2) K.

CCDC no.: 2125796

Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colorless block
Size: 0.21 × 0.20 × 0.17 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 3.05 mm−1
Diffractometer, scan mode: SuperNova, ω
θ max, completeness: 28.5°, >99%
N(hkl)measuredN(hkl)uniqueR int: 22,257, 2503, 0.037
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 1994
N(param)refined: 145
Programs: CrysAlisPRO [1], Olex2 [2], SHELX [3, 4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

Atom x y z U iso*/U eq
I1 0.78735 (2) 0.39662 (2) 0.40387 (3) 0.05317 (9)
F1 0.7038 (2) 0.2500 0.3986 (3) 0.0510 (7)
F2 1.07476 (18) 0.36309 (10) 0.4135 (2) 0.0690 (6)
F3 1.1960 (2) 0.2500 0.4129 (3) 0.0676 (8)
C9 0.8271 (4) 0.2500 0.4033 (5) 0.0419 (10)
C10 0.8855 (3) 0.30881 (15) 0.4064 (3) 0.0419 (7)
C11 1.0108 (3) 0.30739 (16) 0.4100 (3) 0.0481 (8)
C12 1.0736 (4) 0.2500 0.4106 (5) 0.0494 (12)
N1 0.6466 (3) 0.51087 (14) 0.3922 (4) 0.0630 (8)
N2 0.2858 (4) 0.7500 0.2470 (5) 0.0577 (11)
C1 0.6649 (3) 0.56103 (17) 0.4795 (4) 0.0619 (10)
H1 0.7206 0.5564 0.5545 0.074*
C2 0.6057 (3) 0.61982 (16) 0.4653 (4) 0.0533 (9)
H2 0.6222 0.6533 0.5298 0.064*
C3 0.5224 (3) 0.62892 (15) 0.3557 (4) 0.0427 (7)
C4 0.5012 (3) 0.57571 (17) 0.2666 (4) 0.0583 (9)
H4 0.4445 0.5784 0.1921 0.070*
C5 0.5646 (4) 0.51908 (18) 0.2892 (5) 0.0727 (12)
H5 0.5487 0.4843 0.2281 0.087*
C6 0.5184 (4) 0.7500 0.3608 (5) 0.0421 (11)
H6 0.5960 0.7500 0.4008 0.051*
C7 0.4610 (3) 0.69167 (15) 0.3312 (3) 0.0413 (7)
C8 0.3444 (3) 0.69504 (17) 0.2751 (4) 0.0506 (8)
H8 0.3045 0.6563 0.2557 0.061*

Source of material

The 4,3′:5′,4″-terpyridine was purchased from Jinan Heng Hua Technology Co. Ltd. (Shandong, China), and 1,3-diiodotetrafluorobenzene was purchased from J&K Scientific Ltd. (Beijing, China). Both of them were used without further purification. The halogen bond acceptor 4,3′:5′,4″-terpyridine (2.33 mg, 0.01 mmol) and the halogen bond donor 1,3-diiodotetrafluorobenzene (4.02 mg, 0.01 mmol) were dissolved in 15 mL of trichloromethane with gentle stirring at room temperature. The undissolved materials were removed by filtration. The filtrate was set aside for crystallization by slow evaporation at room temperature conditions. After about three days, colorless block crystals of title compound were obtained.

Experimental details

The structure was solved with the SHELXT [3] program using Intrinsic Phasing and refined with the SHELXL [4] refinement package. H atoms were placed in calculated positions and were included in the refinement in the riding model approximation, with U iso(H) set to 1.2U eq(C).

Comment

In recent years, the theoretical and experimental studies of the halogen bonds have attracted considerable attention [5], [6], [7], [8], [9]. The halogen bonds in the crystal structure of the cocrystal formed between 4,3′:5′,4″-terpyridine and 1,4-diiodotetrafluorobenzene have been reported in a previous study [10]. In this work, the cocrystal formed between 4,3′:5′,4″-terpyridine and 1,3-diiodotetrafluorobenzene was synthesized and the halogen bonds in its crystal structure was investigated.

All bond lengths and angles in the title crystal structure are in the normal ranges. The 4,3′:5′,4″-terpyridine molecules and 1,3-diiodotetrafluorobenzene molecules are linked by the halogen bonds with d(I1⃛N1) = 2.822 Å and <(C10–I1⃛N1) = 177.05° to form a zigzag chain. Similar to the case in the crystal structure of the cocrystal formed between 4,3′:5′,4″-terpyridine and 1,4-diiodotetrafluorobenzene [10], the electron-rich N2 atom does not form any halogen bond. In the crystal structure of the cocrystal formed between 4,3′:5′,4″-terpyridine and 1,4-diiodotetrafluorobenzene, the zigzag chains are linked mainly through the π⃛π stacking interactions to form a 3D structure [10]. In the title structure, there are no π⃛π stacking interactions found; the zigzag chains are linked together through the C8–H8⃛N1 and C6–H6⃛N2 hydrogen bonds to form the 3D structure. According to the dispersion-corrected density functional theory calculations at the PBE0-D3/def2-TZVPP level of theory [11, 12], the binding energy of one strong C6–H6⃛N2 hydrogen bond and two weak C8–H8⃛N1 hydrogen bonds formed between two 4,3′:5′,4″-terpyridine molecules is 7.77 kcal/mol, and the binding energy of one C10–I1⃛N1 halogen bond formed between 4,3′:5′,4″-terpyridine and 1,3-diiodotetrafluorobenzene is 8.00 kcal/mol. The details and reliability of the PBE0-D3/def2-TZVPP calculations for the study of the noncovalent interactions can be found elsewhere [13], [14], [15]. Evidently, the strength of one C–I⃛N halogen bond is much stronger than the strength of one C–H⃛N hydrogen bond.

In conclusion, the 4,3′:5′,4″-terpyridine molecule only forms two strong halogen bonds with two 1,3-diiodotetrafluorobenzene molecules. The third electron-rich nitrogen atom of 4,3′:5′,4″-terpyridine forms a hydrogen bond with one C–H bond of another 4,3′:5′,4″-terpyridine molecule.


Corresponding author: Weizhou Wang, College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, China, E-mail:

Award Identifier / Grant number: 21773104

Funding source: Program for Science & Technology Innovation Talents in Universities of Henan Province

Award Identifier / Grant number: 13HASTIT015

Acknowledgment

Computer time was provided by the National Supercomputing Center in Shenzhen.

  1. Author contributions: The author has accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by the National Science Foundation of China (Grant No. 21773104) and the Program for Science & Technology Innovation Talents in Universities of Henan Province (Grant No. 13HASTIT015).

  3. Conflict of interest statement: The author declares no conflicts of interest regarding this article.

References

1. Rigaku. CrysAlisPro; Rigaku Inc.: Tokyo, Japan, 2015.Search in Google Scholar

2. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K., Puschmann, H. OLEX2: a complete structure solution, refinement and analysis program. J. Appl. Crystallogr. 2009, 42, 339–341; https://doi.org/10.1107/s0021889808042726.Search in Google Scholar

3. Sheldrick, G. M. SHELXTL – integrated space-group and crystal-structure determination. Acta Crystallogr. 2015, A71, 3–8; https://doi.org/10.1107/s2053273314026370.Search in Google Scholar

4. Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Crystallogr. 2015, C71, 3–8; https://doi.org/10.1107/s2053229614024218.Search in Google Scholar

5. Gilday, L. C., Robinson, S. W., Barendt, T. A., Langton, M. J., Mullaney, B. R., Beer, P. D. Halogen bonding in supramolecular chemistry. Chem. Rev. 2015, 115, 7118–7195; https://doi.org/10.1021/cr500674c.Search in Google Scholar

6. Wang, H., Wang, W., Jin, W. J. σ-Hole bond vs π-hole bond: a comparison based on halogen bond. Chem. Rev. 2016, 116, 5072–5104; https://doi.org/10.1021/acs.chemrev.5b00527.Search in Google Scholar

7. Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G., Terraneo, G. The halogen bond. Chem. Rev. 2016, 116, 2478–2601; https://doi.org/10.1021/acs.chemrev.5b00484.Search in Google Scholar

8. Kolář, M. H., Hobza, P. Computer modeling of halogen bonds and other σ-hole interactions. Chem. Rev. 2016, 116, 5155–5187.10.1021/acs.chemrev.5b00560Search in Google Scholar PubMed

9. Wang, W., Zhang, Y., Jin, W. J. Halogen bonding in room-temperature phosphorescent materials. Coord. Chem. Rev. 2020, 404, 213107; https://doi.org/10.1016/j.ccr.2019.213107.Search in Google Scholar

10. Wang, W. Halogen bonds in the crystal structure of 4,3:5,4-terpyridine—1,4-diiodotetrafluorobenzene (1/1), C21H11F4I2N3. Z. Kristallogr. NCS 2019, 234, 935–937; https://doi.org/10.1515/ncrs-2019-0155.Search in Google Scholar

11. Adamo, C., Barone, V. Toward reliable density functional methods without adjustable parameters: the PBE0 model. J. Chem. Phys. 1999, 110, 6158–6169; https://doi.org/10.1063/1.478522.Search in Google Scholar

12. Grimme, S., Antony, J., Ehrlich, S., Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 154104; https://doi.org/10.1063/1.3382344.Search in Google Scholar

13. Wang, W., Zhang, Y., Wang, Y. B. Noncovalent π⃛π interaction between graphene and aromatic molecule: structure, energy, and nature. J. Chem. Phys. 2014, 140, 094302; https://doi.org/10.1063/1.4867071.Search in Google Scholar

14. Wang, W., Sun, T., Zhang, Y., Wang, Y. B. The benzene⃛naphthalene complex: a more challenging system than the benzene dimer for newly developed computational methods. J. Chem. Phys. 2015, 143, 114312; https://doi.org/10.1063/1.4931121.Search in Google Scholar

15. Wang, W., Zhang, Y., Wang, Y. B. Highly accurate benchmark calculations of the interaction energies in the complexes C6H6⃛C6X6 (X = F, Cl, Br, and I). Int. J. Quant. Chem. 2017, 117, e25345; https://doi.org/10.1002/qua.25345.Search in Google Scholar

Received: 2021-10-29
Accepted: 2021-12-02
Published Online: 2022-01-14
Published in Print: 2022-02-23

© 2021 Weizhou Wang, published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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