Home Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se
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Chalcogen bonds in the crystal structure of 4,7-dibromo-2,1,3-benzoselenadiazole, C6H2Br2N2Se

  • Weizhou Wang ORCID logo EMAIL logo
Published/Copyright: December 14, 2021

Abstract

C6H2Br2N2Se, monoclinic, P21/c (no. 14), a = 7.7277(4) Å, b = 19.6360(6) Å, c = 10.8656(5) Å, β = 102.124(4)°, V = 1611.98(12) Å3, Z = 4, R gt (F) = 0.0482, wR ref (F2) = 0.1175, T = 290 K.

CCDC no.: 2125766

The asymmetric unit of the title crystal structure is shown in the Figure 1. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Figure 1: 
Molecular structure of the title compound with displacement ellipsoids draw at the 50% probability level.
Figure 1:

Molecular structure of the title compound with displacement ellipsoids draw at the 50% probability level.

Table 1:

Data collection and handling.

Crystal: Brown block
Size: 0.32 × 0.28 × 0.17 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 14.5 mm−1
Diffractometer, scan mode: SuperNova, ω
θmax, completeness: 28.5°, >99%
N(hkl)measured, N(hkl)unique, Rint: 18,469, 3636, 0.075
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2375
N(param)refined: 199
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 Uiso*/Ueq
Br1 0.51340 (11) 0.82695 (4) 0.67016 (8) 0.0569 (2)
Br2 0.56356 (10) 0.50297 (4) 0.82913 (7) 0.0510 (2)
Se1 0.25275 (9) 0.61923 (3) 0.44783 (6) 0.0386 (2)
N1 0.3403 (7) 0.6984 (3) 0.5138 (5) 0.0380 (13)
N2 0.3542 (6) 0.5706 (3) 0.5841 (5) 0.0330 (12)
C1 0.4348 (8) 0.6850 (3) 0.6276 (6) 0.0301 (14)
C2 0.5266 (8) 0.7341 (3) 0.7143 (6) 0.0377 (16)
C3 0.6242 (8) 0.7143 (3) 0.8267 (6) 0.0418 (17)
H3 0.6848 0.7469 0.8815 0.050*
C4 0.6360 (9) 0.6440 (4) 0.8628 (6) 0.0437 (17)
H4 0.7041 0.6315 0.9406 0.052*
C5 0.5482 (8) 0.5952 (3) 0.7843 (6) 0.0338 (15)
C6 0.4431 (8) 0.6140 (3) 0.6654 (5) 0.0299 (14)
Br3 −0.01261 (10) 0.22100 (4) 0.31893 (8) 0.0592 (3)
Br4 −0.06430 (10) 0.54466 (4) 0.15761 (7) 0.0482 (2)
Se2 0.25383 (8) 0.42750 (4) 0.53765 (6) 0.0379 (2)
N3 0.1699 (7) 0.3480 (3) 0.4694 (5) 0.0367 (13)
N4 0.1468 (6) 0.4774 (2) 0.4045 (5) 0.0340 (12)
C7 0.0702 (8) 0.3615 (3) 0.3575 (6) 0.0306 (14)
C8 −0.0253 (8) 0.3134 (3) 0.2715 (6) 0.0399 (16)
C9 −0.1235 (9) 0.3331 (3) 0.1608 (6) 0.0410 (17)
H9 −0.1855 0.3008 0.1063 0.049*
C10 −0.1345 (8) 0.4035 (3) 0.1250 (6) 0.0377 (16)
H10 −0.2027 0.4159 0.0471 0.045*
C11 −0.0476 (8) 0.4523 (3) 0.2019 (6) 0.0322 (14)
C12 0.0582 (7) 0.4333 (3) 0.3212 (5) 0.0269 (13)

Source of material

The 4,7-dibromo-2,1,3-benzoselenadiazole was purchased from Alfa Chemical Co. Ltd. (Zhengzhou, China) and used without further purification. The 4,7-dibromo-2,1,3-benzoselenadiazole (3.41 mg, 0.01 mmol) was dissolved in approximately 10 mL of methanol with gentle stirring at room temperature. Then, the solution was set aside for crystallization by slow evaporation of the solvent at room temperature conditions. After about two days, brown block crystals of title compound suitable for single-crystal X-ray diffraction 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 Uiso(H) set to 1.2Ueq(C).

Comment

The term chalcogen bond was coined in 2009 [5]. Ten years later, the International Union of Pure and Applied Chemistry (IUPAC) issued a formal definition of the chalcogen bond [6]. In the crystals involving 2,1,3-benzoselenadiazole or its derivatives, the four-membered [Se–N]2 cyclic double chalcogen bonds were always formed [7]. Besides the cyclic double chalcogen bonds, the other types of chalcogen bonds can also be formed between the 2,1,3-benzoselenadiazole or its derivatives and their coformers [8]. In this work, we studied the non-covalent interactions in the crystal of 4,7-dibromo-2,1,3-benzoselenadiazole. The focus of attention is: what kind of chalcogen bond can be formed in the title crystal.

All bond lengths and angles in the title crystal structure are in the normal ranges. The 4,7-dibromo-2,1,3-benzoselenadiazole molecules form 2D corrugated sheets which further self-assemble into a 3D layered structure. There are five types of non-covalent interactions in the crystal structure: the four-membered [Se–N]2 cyclic double chalcogen bonds, N–Se⃛Br chalcogen bonds, C–H⃛N hydrogen bonds, ππ stacking interactions and σ-hole(Br)⃛σ-hole(Br) stacking interactions [9, 10]; among them, the four-membered [Se–N]2 cyclic double chalcogen bonds and ππ stacking interactions are much stronger. According to the dispersion-corrected density functional theory calculations at the PBE0-D3/def2-TZVPP level of theory [11, 12], the binding energy of the four-membered [Se–N]2 cyclic double chalcogen bonds between two 4,7-dibromo-2,1,3-benzoselenadiazole molecules is 10.27 kcal/mol, and the binding energy of the ππ stacking interactions between two 4,7-dibromo-2,1,3-benzoselenadiazole molecules is 8.55 kcal/mol. The details and reliability of the PBE0-D3/def2-TZVPP calculations for the study of the non-covalent interactions can be found elsewhere [13], [14], [15]. Evidently, the larger binding energy of the four-membered [Se–N]2 cyclic double chalcogen bonds between two 4,7-dibromo-2,1,3-benzoselenadiazole molecules explains why the four-membered [Se–N]2 cyclic double chalcogen bonds were always found in the crystals involving 2,1,3-benzoselenadiazole or its derivatives.

In conclusion, there are two types of chalcogen bonds in the crystal of 4,7-dibromo-2,1,3-benzoselenadiazole. One type is of the much stronger four-membered [Se–N]2 cyclic double chalcogen bonds, and the other is of the much weaker N–Se⃛Br chalcogen bonds.


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.

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Received: 2021-10-29
Accepted: 2021-12-02
Published Online: 2021-12-14
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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