Home Physical Sciences The crystal structure of 2,2′-((pyridine-2,6-diylbis(methylene))bis(sulfanediyl))-bis(4,5-dihydro-1H-imidazol-3-ium) bromide, C13H19Br2N5S2
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The crystal structure of 2,2′-((pyridine-2,6-diylbis(methylene))bis(sulfanediyl))-bis(4,5-dihydro-1H-imidazol-3-ium) bromide, C13H19Br2N5S2

  • Václav Eigner ORCID logo EMAIL logo
Published/Copyright: September 7, 2022

Abstract

C13H19Br2N5S2, triclinic, P 1 (no. 2), a = 5.22590(10) Å, b = 9.9960(2) Å, c = 17.0076(3) Å, α = 102.1340(15)°, β = 92.9160(16)°, γ = 90.7550(13)°, V = 867.21(3) Å3, Z = 2, R gt (F) = 0.0205, wR ref (F 2) = 0.0737, T = 95 K.

CCDC no.: 2203672

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: Colourless prism
Size: 0.18 × 0.09 × 0.06 mm
Wavelength: CuKα radiation (1.54184 Å)
μ: 8.21 mm−1
Diffractometer, scan mode: SuperNova, ω
θ max, completeness: 73.1°, 98%
N(hkl)measuredN(hkl)uniqueR int: 12478, 3406, 0.014
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 3311
N(param)refined: 211
Programs: Rigaku [1], SUPERFLIP [2], JANA2006 [3], DIAMOND [4]
Table 2:

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

Atom x y z U iso*/U eq
Br1 0.33529 (4) 0.197076 (17) 0.099027 (10) 0.01685 (8)
Br2 1.01959 (4) 0.752068 (18) 0.492617 (11) 0.02181 (8)
S1 0.90807 (9) 0.55250 (4) 0.27126 (3) 0.01738 (13)
S2 0.91766 (9) 1.04456 (4) 0.23432 (3) 0.01912 (14)
N1 0.8634 (3) 0.71863 (14) 0.13947 (8) 0.0151 (4)
N2 0.6551 (3) 0.49229 (17) 0.39024 (9) 0.0234 (5)
N3 0.5189 (3) 0.36822 (16) 0.27336 (9) 0.0207 (5)
N4 0.6719 (3) 1.01812 (16) 0.36423 (10) 0.0230 (5)
N5 0.5492 (3) 0.86270 (15) 0.25689 (9) 0.0180 (4)
C1 0.9717 (3) 0.59553 (18) 0.12508 (10) 0.0152 (5)
C2 1.1844 (3) 0.56739 (18) 0.07925 (10) 0.0171 (5)
C3 1.2867 (4) 0.6717 (2) 0.04629 (11) 0.0176 (5)
C4 1.1777 (3) 0.79928 (18) 0.06116 (10) 0.0172 (5)
C5 0.9668 (3) 0.81921 (17) 0.10898 (10) 0.0151 (5)
C6 0.8508 (4) 0.48814 (18) 0.16298 (11) 0.0167 (5)
C7 0.6812 (4) 0.46424 (18) 0.31198 (11) 0.0162 (5)
C8 0.4400 (4) 0.41195 (18) 0.41111 (11) 0.0192 (5)
C9 0.3627 (4) 0.31634 (18) 0.33008 (11) 0.0193 (5)
C10 0.8420 (4) 0.95619 (17) 0.13000 (11) 0.0179 (5)
C11 0.7021 (3) 0.96934 (17) 0.28728 (11) 0.0173 (5)
C12 0.4821 (4) 0.9352 (2) 0.39584 (11) 0.0226 (6)
C13 0.4012 (4) 0.82400 (19) 0.32121 (11) 0.0196 (5)
H1n2 0.739 (4) 0.5587 (17) 0.4217 (12) 0.0281*
H1n3 0.513 (5) 0.329 (2) 0.2232 (4) 0.0249*
H1n4 0.762 (4) 1.0831 (18) 0.3947 (12) 0.0276*
H1n5 0.592 (5) 0.8053 (18) 0.2147 (8) 0.0216*
H1c2 1.259173 0.478622 0.070474 0.0206*
H1c3 1.431914 0.65493 0.013508 0.0212*
H1c4 1.245518 0.87232 0.039086 0.0206*
H1c6 0.936575 0.403167 0.147039 0.0201*
H2c6 0.669659 0.482152 0.149679 0.0201*
H1c8 0.301445 0.471526 0.427901 0.023*
H2c8 0.500871 0.358687 0.44876 0.023*
H1c9 0.410827 0.224606 0.331804 0.0232*
H2c9 0.184579 0.327135 0.316695 0.0232*
H1c10 0.659567 0.944034 0.120857 0.0215*
H2c10 0.895096 1.012692 0.094313 0.0215*
H1c12 0.3374 0.9901 0.412734 0.0271*
H2c12 0.564654 0.89361 0.436051 0.0271*
H1c13 0.454976 0.736424 0.329701 0.0235*
H2c13 0.221232 0.830057 0.30845 0.0235*

Source of material

The suspension of imidazoline-2-thione (0.435 g, 4.26 mmol) in acetonitrile (10 ml) was added to the solution of 2,6-bis(bromomethyl)pyridine (0.565 g, 2.13 mmol) in acetonitrile (10 ml). The reaction mixture was stirred for 8 h at room temperature. The resulting precipitate was filtered off, washed with acetonitrile (5 ml) and allowed to dry on air, resulting in yield of 0.915 g (91.5%). The single crystals for measurement were prepared by slow evaporation of acetonitrile solution of title compound (1 mg in 20 ml).

Experimental details

H atoms bonded at C were placed in calculated positions. H bonded to N were refined with restrained bond lengths (N—H = 0.86 Å). U iso(H) = 1.2U eq(C,N).

Comment

The title compound is a N,N′-substituted isothiouronium salt. The isothiouronium salts can act as GABAA agonists [5] and recently their antitumor activities have been described [6].

The asymmetric unit of the title compound crystal structure consists of one 2,2′-((pyridine-2,6-diylbis(methylene))bis(sulfanediyl))bis(4,5-dihydro-1H-imidazol-3-ium) dication and two bromide anions, balancing the charges, see the figure. Both substituted isothiouronium groups are located on the same side of pyridine core. Viewing along the C6—S1 bond shows that the C1 and C7 atoms are close to the anti-periplanar conformation with the torsion angle C1—C6—S1—C7 at 159.90(13)°, while along the C10—S2 bond the conformation appears to be close to gauche with the C5—C10—S2—C11 torsion angle at −81.84(14)°. In both isothiouronium groups they are almost parallel with mean planes through the thiourea atoms forming an angle of 8.30(9)°. There is a significant difference between the C(Ar)—C(me)—S angles in both groups, with C1—C6—S1 angle at 104.58(11)°, while C5—C10—S2 angle is observed at 112.64(13)°. We attribute this difference to the hydrogen bonding and steric demands of the overall structure.

There are four strong hydrogen bonds in the structure with each isothiouronium nitrogen forming one hydrogen bond. The N2, N3, and N4 atoms form intermolecular N—H⋅⋅⋅Br bonds, while N5 forms an intramolecular N—H⋅⋅⋅N bond with the pyridine nitrogen, causing the observed gauche conformation. The N—H⋅⋅⋅Br bonds involving Br2 connect two cations and two bromide anions into an R4 2(28) ring. Two N3—H1n3⋅⋅⋅Br1 bonds connect two Br1 anions to the ring, forming a neutral supramolecular block. The blocks are connected by numerous weak C—H⋅⋅⋅Br hydrogen bonds as well as C—H⋅⋅⋅S hydrogen bonds.


Corresponding author: Václav Eigner, Institute of Physics AS CR, v.v.i. Na Slovance 2, 182 21 Prague 8, Czech Republic, E-mail:

Funding source: Grant Agency of the Czech Republic 10.13039/501100001824

Award Identifier / Grant number: 20-14770Y

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This research was supported by the project 20–14770Y of the Grant Agency of the Czech Republic.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Rigaku OD. CrysAlisPRO; Rigaku Oxford Diffraction Ltd: Yarnton, Oxfordshire, England, 2020.Search in Google Scholar

2. Palatinus, L., Chapuis, G. SUPERFLIP – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. J. Appl. Crystallogr. 2007, 40, 786–790; https://doi.org/10.1107/s0021889807029238.Search in Google Scholar

3. Petricek, V., Dusek, M., Palatinus, L. Crystallographic computing system JANA2006: general features. Z. Kristallogr. Cryst. Mater. 2014, 229, 345–352.10.1515/zkri-2014-1737Search in Google Scholar

4. Brandenburg, K. DIAMOND; Crystal Impact GbR: Bonn, Germany, 1999.Search in Google Scholar

5. Allan, R. D., Dickenson, H. W., Johnston, G. A. R., Kazlauskas, R., Newett, K. N. Structural analogues of ZAPA as GABAA agonists. Neurochem. Int. 1997, 30, 583–591; https://doi.org/10.1016/s0197-0186(96)00094-0.Search in Google Scholar PubMed

6. Ferreira, M., Assuncao, L. S., Silva, A. H., Filippin-Monteiro, F. B., Creczynski-Pasa, T. B., Sa, M. M. Allylic isothiouronium salts: the discovery of a novel class of thiourea analogues with antitumor activity. Eur. J. Med. Chem. 2017, 129, 151–158; https://doi.org/10.1016/j.ejmech.2017.02.013.Search in Google Scholar PubMed

Received: 2021-10-14
Accepted: 2021-11-05
Published Online: 2022-09-07
Published in Print: 2022-12-16

© 2022 the author(s), published by De Gruyter, Berlin/Boston

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

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