Crystal structure, Hirshfeld surface analysis and interaction energy and DFT studies of 1-methyl-3-(prop-2-yn-1-yl)-2,3-dihydro-1H-1,3-benzodiazol-2-one

The dihydrobenzimidazol-2-one moiety is essentially planar with the prop-2-yn- 1-yl substituent rotated well out of this plane. In the crystal, C—H⋯π(ring) interactions and C—H⋯O hydrogen bonds form corrugated layers parallel to (10), which are associated through additional C—H⋯O hydrogen bonds and head-to-tail, slipped, π-stacking interactions between dihydrobenzimidazol-2-one moieties


Chemical context
Benzimidazole is an aromatic heterocyclic organic compound that plays an important role in medicinal chemistry and pharmacology. The most prominent benzimidazole moiety present in nature is N-ribosyl-dimethylbenzimidazole and it serves as the axial ligand for cobalt in vitamin B12 (Walia et al., 2011). Benzimidazole derivatives possess many biological activities such as anti-microbial, anti-fungal, anti-histaminic, anti-inflammatory, anti-viral, anti-oxidant, anti-cancer and anti-ulcerative (Farukh & Mubashira, 2009;Ayhan-Kılcıgil et al., 2007;Soderlind et al., 1999;Luo et al., 2011;Navarrete-Vá zquez et al., 2011). They are considered to be an important moiety for the development of molecules of pharmaceutical interest (Mondieig et al., 2013;Lakhrissi et al., 2008). As a continuation of our research on the development of Nsubstituted benzimidazole derivatives and the evaluation of their potential pharmacological activities (Saber et al., 2018a(Saber et al., ,b, 2020Ouzidan et al., 2011), we have studied the ISSN 2056-9890 alkylation reaction of iodomethane with 1-(prop-2-ynyl)-1Hbenzoimidazol-2(3H)-one in the presence of tetra-n-butylammonium bromide as catalyst and potassium carbonate as base, to give the title compound, I in good yield. We report herein on its synthesis, the molecular and crystal structures along with the Hirshfeld surface analysis and the intermolecular interaction energies and the density functional theory (DFT) computational calculations carried out at the B3LYP/6-311 G(d,p) level for comparison with the experimentally determined molecular structure in the solid state.

Figure 3
A partial packing diagram viewed along the b-axis direction with intermolecular interactions depicted as in Fig. 2.

Figure 2
A partial packing diagram viewed along the a-axis direction with C-HÁ Á ÁO hydrogen bonds, C-HÁ Á Á(ring) and -stacking interactions shown, respectively, by black, green and orange dashed lines.

Hirshfeld surface analysis
In order to visualize the intermolecular interactions in the crystal of the title compound, a Hirshfeld surface (HS) analysis (Hirshfeld, 1977;Spackman & Jayatilaka, 2009) was carried out using Crystal Explorer 17.5 (Turner et al., 2017). In the HS plotted over d norm (Fig. 4), the white surface indicates contacts with distances equal to the sum of van der Waals radii, and the red and blue colours indicate distances shorter (in close contact) or longer (distant contact) than the van der Waals radii, respectively (Venkatesan et al., 2016). The brightred spots appearing near O1 and the hydrogen atom H11 indicate their roles as the donors and/or acceptors, respectively; they also appear as blue and red regions corresponding to positive and negative potentials on the HS mapped over electrostatic potential (Spackman et al., 2008;Jayatilaka et al., 2005) as shown in Fig View of the three-dimensional Hirshfeld surface of the title compound plotted over d norm in the range À0.3997 to 1.3219 a.u.

Figure 5
View of the three-dimensional Hirshfeld surface of the title compound plotted over electrostatic potential energy in the range À0.0500 to 0.0500 a.u. using the STO-3 G basis set at the Hartree-Fock level of theory. Hydrogen-bond donors and acceptors are shown as blue and red regions around the atoms corresponding to positive and negative potentials, respectively. Table 2 Selected interatomic distances (Å ).

Figure 6
Hirshfeld surface of the title compound plotted over shape-index.
The overall two-dimensional fingerprint plot, Fig. 7a, and those delineated into HÁ Á ÁH, HÁ Á ÁC/CÁ Á ÁH, HÁ Á ÁO/O Á Á Á H, CÁ Á ÁC, HÁ Á ÁN/NÁ Á ÁH and NÁ Á ÁC/CÁ Á ÁN contacts (McKinnon et al., 2007) are illustrated in Fig. 7b-g, respectively, together with their relative contributions to the Hirshfeld surface. The most important interaction is HÁ Á ÁH contributing 44.1% to the overall crystal packing, which is reflected in Fig. 7b as widely scattered points of high density due to the large hydrogen content of the molecule with the tip at d e = d i = 1.22 Å . The presence of C-HÁ Á Á interactions gives rise to pairs of characteristic wings in the fingerprint plot delineated into HÁ Á ÁC/CÁ Á ÁH contacts, Fig. 7c., contributing 33.5% to the HS (Table 2); these are viewed as pairs of spikes with the tips at d e + d i = 2.56 Å . The pair of wings in Fig. 7d has a symmetrical distribution of points with the edges at d e + d i = 2.09 Å arising from the HÁ Á ÁO/OÁ Á ÁH contacts (13.4% contribution). The CÁ Á ÁC contacts, Fig. 7e, have an arrow-shaped distribution of points with the tip at d e = d i = 1.75 Å . The HÁ Á ÁN/NÁ Á ÁN contacts, contributing 2.9% to the overall crystal packing, are depicted in Fig. 7f as widely scattered points. Finally, the NÁ Á ÁC/CÁ Á ÁN interactions, contributing 2.4% to the overall crystal packing, are shown in Fig. 7g as tiny characteristic wings with the tips at d e + d i = 3.45 Å .
The Hirshfeld surface analysis confirms the importance of H-atom contacts in establishing the packing. The large number of HÁ Á ÁH, HÁ Á ÁC/CÁ Á ÁH and HÁ Á Á O/OÁ Á ÁH interactions suggest that van der Waals interactions and hydrogen bonding play the major roles in the crystal packing (Hathwar et al., 2015).

DFT calculations
The optimized structure of the title compound in the gas phase was generated theoretically via density functional theory (DFT) using the standard B3LYP functional and 6-311 G(d,p) basis-set calculations (Becke, 1993)    experimental results are in good agreement ( Table 3). The highest-occupied molecular orbital (HOMO), acting as an electron donor, and the lowest-unoccupied molecular orbital (LUMO), acting as an electron acceptor, are very important parameters for quantum chemistry. When the energy gap is small, the molecule is highly polarizable and has high chemical reactivity. The DFT calculations provide some important information on the reactivity and site selectivity of the molecular framework. E HOMO and E LUMO clarify the inevitable charge-exchange collaboration inside the studied material and are given in Table 4 along with the electronegativity (), hardness (), potential (), electrophilicity (!) and softness (). The significance of and is for the evaluation of both the reactivity and stability. The electron transition from the HOMO to the LUMO energy level is shown in Fig. 9. The HOMO and LUMO are localized in the plane extending from the whole 1-methyl-3-(prop-2-yn-1-yl)-2,3-dihydro-1H-1,3benzodiazol-2-one ring. The energy band gap [ÁE = E LUMO À E HOMO ] of the molecule is about 5.4115 eV, and the frontier molecular orbital energies, E HOMO and E LUMO are À5.8885 and À0.4770 eV, respectively.

Database survey
The syntheses of several N-substituted benzimidazol-2-one analogues have been reported (Saber et al., 2018a,b;2020;Belaziz et al., 2012;Bouayad et al., 2015;Belaziz et al., 2013). In a search of the Cambridge Crystallographic Database (CSD; Version 5.40, update of September 2019; Groom et al., 2016) using benzimidazol-2-one with an exocyclic carbon atom bound to each nitrogen generated 94 hits. In these, the bicyclic ring system is either planar, has a slight twist end-to-end, or, in the cases where the exocyclic substituents form a ring, has a very shallow bowl shape. The energy band gap of the title compound. Table 3 Comparison of the selected (X-ray and DFT) geometric data (Å , ).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 5. Hydrogen atoms were located in a difference Fourier map and refined freely.

Funding information
The support of NSF-MRI grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged. TH is grateful to Hacettepe University Scientific Research Project Unit (grant No. 013 D04 602 004).  program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008). Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc * =kFc[1+0.001xFc 2 λ 3 /sin(2θ)] -1/4 Extinction coefficient: 0.0100 (12) 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. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > 2sigma(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.