5-Amino-1H-benzimidazole-2(3H)-thione: molecular, crystal structure and Hirshfeld surface analysis

The molecular and crystal structures of the anhydrous form of 5-amino-1H-benzimidazole-2(3H)-thione were determined. Hirshfeld surfaces and fingerprint plots were studied.


Chemical context
Benzimidazoles belong to an important class of heterocyclic compounds because of their wide spectra of biological activity. In particular, benzimidazole derivatives are known to possess antibacterial (Chkirate et al., 2020), antimicrobial (Alam et al., 2014), antitumor (Kharitonova et al., 2018;Galal et al., 2010), anti-inflammatory (Rathore et al., 2017), antioxidant (Anastassova et al., 2017), anthelmintic (Kenchappa et al., 2017), antifungal and cytotoxic (Leila et al., 2019) activity. They are also important as starting materials for terminal alkyne cyclotrimerization reactions (Xi et al., 2013) and are used as highly active catalysts for ethylene oligomerization (Haghverdi et al., 2018). The synthesis of 2-amino-1,3-benzimidazole-2-thione has been reported, prepared by first treating o-phenylenediamine CS 2 in the presence of KOH under microwave irradiation to give the intermediate 1,3benzimidazole-2-thione. Nitration of the intermediate followed by reduction of the nitro group with iron powder and concentrated hydrochloric acid gave 2-amino-1,3-benzimidazole-2-thione in a moderately good yield (Samanta et al., 2013;Ahamed et al., 2013). Taking into account the possible biological activity of the obtained compound, it is important to study its molecular and crystal structures.

Structural commentary
Two independent molecules (A and B) comprise the asymmetric unit of the title compound (Fig. 1). The molecules ISSN 2056-9890 slightly differ from each other in their degree of planarity: all non-hydrogen atoms lie in the same plane with an accuracy of 0.05 Å in molecule A and with an accuracy of 0.02 Å in molecule B. Analysis of the molecular structure revealed that the C S tautomer is found in the crystal, as confirmed by the length of the C7-S1 bond [1.687 (3) Å in molecule A and 1.684 (3) Å in molecule B], the equal lengths of the C7-N1 and C7-N2 bonds [1.345 (3) and 1.347 (3) Å in molecule A and 1.351 (3) and 1.349 (3) Å in molecule B] and the localization of hydrogen atoms at all the nitrogen atoms from the electron-density difference maps. The amino groups in both molecules are pyramidal, the sum of the bond angles centered at the nitrogen atom is 331.5 in molecule A and 340.9 in molecule B.

Hirshfeld surface analysis
One of the modern methods for analysing intermolecular interactions is Hirshfeld surface analysis (Spackman & Jaya-tilaka, 2009;Turner et al., 2017), which allows analysis of the interactions between molecules in a quantitative manner. The Hirshfeld surfaces of molecules A and B mapped over d norm proved to be very similar (Fig. 5). The red spots indicating strong interactions are found at both hydrogen atoms of the NH fragments as well as in the area of the nitrogen lone pair of the amino group. In addition, red spots are seen at the sulfur atom. Tetramer of molecules A and B formed by N2A-H2NAÁ Á ÁS1B and N2B-H2NBÁ Á ÁS1A hydrogen bonds. Table 1 Hydrogen-bond geometry (Å , ).

Figure 1
Molecular structures of molecules A and B showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
Analysis of the fingerprint plots showed the presence of strong intermolecular interactions indicated as sharp spikes (Fig. 6a, 6b). The most significant contribution to the total Hirshfeld surface is provided by HÁ Á ÁH interactions in both molecules (Fig. 6c, 6g). The contributions of SÁ Á ÁH/HÁ Á ÁS and CÁ Á ÁH/HÁ Á ÁC interactions associated with X-HÁ Á ÁS and X-HÁ Á ÁC () hydrogen bonds are similar ( Fig. 6d-i). Surprisingly, the contribution of NÁ Á ÁH/HÁ Á ÁN interactions proved to be the lowest (Fig. 6f, 6j). It may be explained by the participation of the nitrogen lone pair in hydrogen bonding as a proton acceptor.

Database survey
A search of the Cambridge Structural Database (Version 5.42, update of November 2020; Groom et al., 2016) revealed the structure of the monohydrate of the title compound (ODAXID; Hadjikakou & Light, 2016). It should be noted that the amino group was refined as planar in this structure. However, analysis of the intermolecular interactions showed that this amino group participates in a hydrogen bond with the hydrate water molecule as a proton acceptor. Such a hydrogen bonding has to result in pyramidalization of the amino group.
To check this presumption, we have optimized the ODAXID structure with a periodic boundary using the PBE functional (Adamo & Barone, 1999) within Quantum Espresso (Giannozzi et al., 2009(Giannozzi et al., , 2017. The unit-cell parameters were fixed while the molecular structures of both molecules found in the asymmetric unit were optimized. The result of this optimization shows that the amino group has to be pyramidal (Fig. 7).

Crystallization
5-Amino-1H-benzimidazole-2(3H)-thione was purchased from Sigma-Aldrich for use as a ligand in complexation with metals. The reaction of the title compound with nickel acetate in an aqueous alcoholic medium did not result in complex formation. The formed colourless needle-like crystals proved to be anhydrous form of the ligand with T melt. = 513-517 K.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. All the hydrogen atoms were located in difference-Fourier maps and refined using an isotropic approximation. Projection of a tube in the b-axis direction.

5-Amino-1H-benzimidazole-2(3H)-thione
Crystal data Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.