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
Keywords: crystal structure, benzimidazol-2-one, hydrogen bond, C—H⋯π(ring) interaction, π-stacking, Hirshfeld surface
Abstract
In the title molecule, C11H10N2O, 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—HMthy⋯π(ring) interactions and C—HProp⋯ODhyr (Mthy = methyl, Prop = prop-2-yn-1-yl and Dhyr = dihydro) hydrogen bonds form corrugated layers parallel to (10
), which are associated through additional C—HBnz⋯ODhyr (Bnz = benzene) hydrogen bonds and head-to-tail, slipped, π-stacking [centroid-to-centroid distance = 3.7712 (7) Å] interactions between dihydrobenzimidazol-2-one moieties. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (44.1%), H⋯C/C⋯H (33.5%) and O⋯H/H⋯O (13.4%) interactions. Hydrogen-bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry calculations indicate that in the crystal, C—H⋯O hydrogen-bond energies are 46.8 and 32.5 (for C—HProp⋯ODhyr) and 20.2 (for C—HBnz⋯ODhyr) kJ mol−1. Density functional theory (DFT) optimized structures at the B3LYP/6–311 G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.
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-Vázquez 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 N-substituted benzimidazole derivatives and the evaluation of their potential pharmacological activities (Saber et al., 2018a
▸,b
▸, 2020 ▸; Ouzidan et al., 2011 ▸), we have studied the alkylation reaction of iodomethane with 1-(prop-2-ynyl)-1H-benzoimidazol-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.
Structural commentary
In the title compound, the dihydrobenzimidazol-2-one moiety is planar to within 0.0160 (8) Å (r.m.s. deviation = 0.0082) with atom C7 deviating the most from the mean plane and a prop-2-yn-1-yl substituent rotated well out of this plane as shown by the C1—N2—C9—C10 torsion angle of 62.16 (13)° (Fig. 1 ▸).
Figure 1.
The molecular structure of the title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
Supramolecular features
In the crystal, inversion dimers are formed by pairs of C—HMthy⋯Cg1i interactions [Mthy = methyl; symmetry code: (i) − x, 1 − y, 1 − z; Cg1 is the centroid of the benzene (A; C1–C6), ring]; which are connected along the b-axis direction by C—HBnz⋯ODhyr hydrogen bonds (Bnz = benzene and Dhyr = dihydro) and along the a-axis direction at ca 90° to this and parallel to (10
) by inversion-related C—HProp⋯ODhyr hydrogen bonds (Table 1 ▸). The resulting corrugated layers are parallel to (10
) and are connected in pairs by slipped, head-to-tail π-stacking interactions between the dihydrobenzimidazol-2-one moieties, [Cg2⋯Cg1ii = 3.7712 (7) Å, dihedral angle = 0.96 (6)°; symmetry code: (ii) 1 – x, 1 – y, 1 – z; Cg1 and Cg2 are the centroids of rings A and B (N1/N2/C1/C6/C7) and C—HProp⋯ODhyr (Prop = prop-2-yn-1-yl) hydrogen bonds (Table 1 ▸, Figs. 2 ▸ and 3 ▸).
Table 1. Hydrogen-bond geometry (Å, °).
Cg1 is the centroid of the C1–C6 benzene ring.
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| C3—H3⋯O1ix | 1.005 (15) | 2.566 (15) | 3.4885 (15) | 152.6 (11) |
| C8—H8C⋯Cg1v | 1.004 (16) | 2.626 (15) | 3.5413 (13) | 151.1 (12) |
| C9—H9B⋯O1vi | 0.978 (15) | 2.347 (15) | 3.3198 (14) | 172.9 (12) |
| C11—H11⋯O1vii | 1.010 (15) | 2.181 (15) | 3.1569 (15) | 162.1 (12) |
Symmetry codes: (v)
; (vi)
; (vii)
; (ix)
.
Figure 2.
A partial packing diagram viewed along the a-axis direction with C—H⋯O hydrogen bonds, C—H⋯π(ring) and π-stacking interactions shown, respectively, by black, green and orange dashed lines.
Figure 3.
A partial packing diagram viewed along the b-axis direction with intermolecular interactions depicted as in Fig. 2 ▸.
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 bright-red 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. 5 ▸. The blue regions indicate positive electrostatic potential (hydrogen-bond donors), while the red regions indicate negative electrostatic potential (hydrogen-bond acceptors). The shape-index of the HS is a tool to visualize π–π stacking by the presence of adjacent red and blue triangles; if there are no adjacent red and/or blue triangles, then there are no π–π interactions. Fig. 6 ▸ clearly suggests that there are π– π interactions in (I).
Figure 4.
View of the three-dimensional Hirshfeld surface of the title compound plotted over d norm in the range −0.3997 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 −0.0500 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.
Figure 6.
Hirshfeld surface of the title compound plotted over shape-index.
The overall two-dimensional fingerprint plot, Fig. 7 ▸ a, and those delineated into H⋯H, H⋯C/C⋯H, H⋯O/O ⋯ H, C⋯C, H⋯N/N⋯H and N⋯C/C⋯N contacts (McKinnon et al., 2007 ▸) are illustrated in Fig. 7 ▸ b–g, respectively, together with their relative contributions to the Hirshfeld surface. The most important interaction is H⋯H contributing 44.1% to the overall crystal packing, which is reflected in Fig. 7 ▸ b 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—H⋯π interactions gives rise to pairs of characteristic wings in the fingerprint plot delineated into H⋯C/C⋯H contacts, Fig. 7 ▸ c., 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. 7 ▸ d has a symmetrical distribution of points with the edges at d e + d i = 2.09 Å arising from the H⋯O/O⋯H contacts (13.4% contribution). The C⋯C contacts, Fig. 7 ▸ e, have an arrow-shaped distribution of points with the tip at d e = d i = 1.75 Å. The H⋯N/N⋯N contacts, contributing 2.9% to the overall crystal packing, are depicted in Fig. 7 ▸ f as widely scattered points. Finally, the N⋯C/C⋯N interactions, contributing 2.4% to the overall crystal packing, are shown in Fig. 7 ▸ g as tiny characteristic wings with the tips at d e + d i = 3.45 Å.
Figure 7.
The full two-dimensional fingerprint plots for the title compound, showing (a) all interactions, and delineated into (b) H⋯H, (c) H⋯C/C⋯H, (d) H⋯O/O⋯H, (e) C⋯C, (f) H⋯N/N⋯H and (g) N⋯C/C⋯N interactions. The d i and d e values are the closest internal and external distances (in Å) from given points on the Hirshfeld surface contacts.
Table 2. Selected interatomic distances (Å).
| O1⋯H9A | 2.491 (14) | C11⋯O1vii | 3.1569 (15) |
| O1⋯H3i | 2.566 (15) | C2⋯H8A iv | 2.82 (2) |
| O1⋯H8B | 2.516 (19) | C3⋯H8C v | 2.859 (15) |
| O1⋯H9B ii | 2.346 (14) | C3⋯H8A iv | 2.92 (2) |
| O1⋯H11iii | 2.181 (15) | C4⋯H8C v | 2.810 (15) |
| C2⋯C10 | 3.3889 (16) | C5⋯H8C v | 2.935 (15) |
| C3⋯C8iv | 3.5335 (17) | C8⋯H5 | 2.983 (14) |
| C4⋯C8v | 3.4947 (17) | C9⋯H2 | 2.975 (14) |
| C4⋯C7iv | 3.5437 (16) | C10⋯H4viii | 2.976 (15) |
| C5⋯C8v | 3.5884 (17) | C11⋯H5iv | 2.865 (15) |
| C6⋯C6iv | 3.5349 (14) | C11⋯H4viii | 2.705 (15) |
| C9⋯O1vi | 3.3198 (14) |
Symmetry codes: (i)
; (ii)
; (iii)
; (iv)
; (v)
; (vi)
; (vii)
; (viii)
.
The Hirshfeld surface representations with the function d norm plotted onto the surface are shown for the H⋯H, H⋯C/C⋯H and H⋯O/O⋯H interactions in Fig. 8 ▸ a–c, respectively.
Figure 8.
The Hirshfeld surface representations with the function d norm plotted onto the surface for (a) H⋯H, (b) H⋯C/C⋯H and (c) H⋯O/O⋯H interactions.
The Hirshfeld surface analysis confirms the importance of H-atom contacts in establishing the packing. The large number of H⋯H, H⋯C/C⋯H and H⋯ O/O⋯H interactions suggest that van der Waals interactions and hydrogen bonding play the major roles in the crystal packing (Hathwar et al., 2015 ▸).
Interaction energy calculations
The intermolecular interaction energies were calculated using the CE–B3LYP/6–31G(d,p) energy model available in CrystalExplorer17.5 (Turner et al., 2017 ▸), where a cluster of molecules is generated by applying crystallographic symmetry operations with respect to a selected central molecule within the default radius of 3.8 Å (Turner et al., 2014 ▸). The total intermolecular energy (E tot) is the sum of electrostatic (E ele), polarization (E pol), dispersion (E dis) and exchange-repulsion (E rep) energies (Turner et al., 2015 ▸) with scale factors of 1.057, 0.740, 0.871 and 0.618, respectively (Mackenzie et al., 2017 ▸). Hydrogen-bonding interaction energies (in kJ mol−1) were calculated to be −17.4 (E ele), −3.5 (E pol), −62.6 (E dis), 46.5 (E rep) and −46.8 (E tot) for C11—H11⋯O1, −12.4 (E ele), −1.9 (E pol), −41.6 (E dis), 29.6 (E rep) and −32.5 (E tot) for C9—H9B⋯O1 and −13.7 (E ele), −3.7 (E pol), −15.5 (E dis), 17.0 (E rep) and −20.2 (E tot) for C3—H3⋯O1.
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 ▸) as implemented in GAUSSIAN 09 (Frisch et al., 2009 ▸). The theoretical and 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 (χ), hardness (η), potential (μ), electrophilicity (ω) and softness (σ). The significance of η and σ 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-1,3-benzodiazol-2-one ring. The energy band gap [ΔE = E LUMO − E HOMO] of the molecule is about 5.4115 eV, and the frontier molecular orbital energies, E HOMO and E LUMO are −5.8885 and −0.4770 eV, respectively.
Table 3. Comparison of the selected (X-ray and DFT) geometric data (Å, °).
| Bonds/angles | X-ray | B3LYP/6–311 G(d,p) |
|---|---|---|
| O1—C7 | 1.2281 (13) | 1.24660 |
| N1—C7 | 1.3735 (14) | 1.39764 |
| N1—C6 | 1.3874 (15) | 1.40100 |
| N1—C8 | 1.4526 (14) | 1.45375 |
| N2—C7 | 1.3807 (14) | 1.40268 |
| N2—C1 | 1.3910 (13) | 1.40222 |
| N2—C9 | 1.4545 (14) | 1.46036 |
| C7—N1—C6 | 110.19 (9) | 110.10303 |
| C7—N1—C8 | 124.14 (10) | 122.94288 |
| C6—N1—C8 | 125.66 (10) | 126.95366 |
| C7—N2—C1 | 110.16 (9) | 110.18664 |
| C7—N2—C9 | 123.55 (9) | 122.02491 |
| C1—N2—C9 | 126.00 (9) | 126.78733 |
| C2—C1—N2 | 131.64 (10) | 132.00719 |
Table 4. Calculated energies for the title compound.
| Molecular Energy (a.u.) (eV) | |
|---|---|
| Total Energy TE (eV) | −16594.1662 |
| E HOMO (eV) | −5.8885 |
| E LUMO (eV) | −0.4770 |
| Energy gap, ΔE (eV) | 5.4115 |
| Dipole moment, μ (Debye) | 2.8313 |
| Ionization potential, I (eV) | 5.8885 |
| Electron affinity, A | 2.6040 |
| Electro negativity, χ | 0.31828 |
| Hardness, η | 2.7058 |
| Electrophilicity index, ω | 1.8719 |
| Softness, σ | 0.3696 |
| Fraction of electron transferred, ΔN | 0.7054 |
Figure 9.
The energy band gap of the title compound.
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 closest examples to the title compound, I, are II (HISFUN; Saber et al., 2018b ▸), III (URAQAG; Ouzidan et al., 2011a ▸) and IV (AGAXOX; Kandri Rodi et al., 2013 ▸). In the title compound, the C—N bonds to the exocyclic groups are 1.4526 (14) and 1.4545 (19) Å while in II–IV the corresponding distances range from 1.445 (3) to 1.4632 (11) Å, and so are quite comparable. The exocyclic groups in I are in an anti-arrangement with the prop-2-yn-1-yl group rotated by 62.16 (13)° out of the plane of the bicyclic moiety (as measured by the C1—N2—C9—C10 torsion angle). In the other three, these substituents are also anti and in II the corresponding torsion angle is 73.46 (18)° while in III they are 82.58 (15) and 74.31 (14)°. In IV the torsion angles are 106.0 (3) and 113.4 (3)° indicating a rotation in the opposite direction from the first three.
Synthesis and crystallization
To a mixture of 1-(prop-2-ynyl)-1H-benzimidazol-2(3H)-one (3.61 mmol), iodomethane (6.73 mmol) and potassium carbonate (6.24 mmol) in DMF (15 ml) was added a catalytic amount of tetra-n-butylammonium bromide (0.37 mmol). The mixture was stirred for 24 h. The solid material was removed by filtration and the solvent evaporated under vacuum. The solid product was purified by recrystallization from ethanol to afford colorless crystals (yield: in 82%).
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.
Table 5. Experimental details.
| Crystal data | |
| Chemical formula | C11H10N2O |
| M r | 186.21 |
| Crystal system, space group | Monoclinic, P21/n |
| Temperature (K) | 150 |
| a, b, c (Å) | 7.1507 (3), 8.8177 (4), 15.4602 (7) |
| β (°) | 97.914 (2) |
| V (Å3) | 965.52 (7) |
| Z | 4 |
| Radiation type | Cu Kα |
| μ (mm−1) | 0.68 |
| Crystal size (mm) | 0.32 × 0.31 × 0.12 |
| Data collection | |
| Diffractometer | Bruker D8 VENTURE PHOTON 100 CMOS |
| Absorption correction | Multi-scan (SADABS; Krause et al., 2015 ▸) |
| T min, T max | 0.83, 0.92 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 6896, 1812, 1679 |
| R int | 0.030 |
| (sin θ/λ)max (Å−1) | 0.610 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.033, 0.086, 1.06 |
| No. of reflections | 1812 |
| No. of parameters | 168 |
| H-atom treatment | All H-atom parameters refined |
| Δρmax, Δρmin (e Å−3) | 0.18, −0.19 |
Supplementary Material
Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989019015779/lh5936sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989019015779/lh5936Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989019015779/lh5936Isup3.cdx
Supporting information file. DOI: 10.1107/S2056989019015779/lh5936Isup4.cml
CCDC reference: 1967468
Additional supporting information: crystallographic information; 3D view; checkCIF report
supplementary crystallographic information
Crystal data
| C11H10N2O | F(000) = 392 |
| Mr = 186.21 | Dx = 1.281 Mg m−3 |
| Monoclinic, P21/n | Cu Kα radiation, λ = 1.54178 Å |
| a = 7.1507 (3) Å | Cell parameters from 5848 reflections |
| b = 8.8177 (4) Å | θ = 5.8–70.1° |
| c = 15.4602 (7) Å | µ = 0.68 mm−1 |
| β = 97.914 (2)° | T = 150 K |
| V = 965.52 (7) Å3 | Plate, colourless |
| Z = 4 | 0.32 × 0.31 × 0.12 mm |
Data collection
| Bruker D8 VENTURE PHOTON 100 CMOS diffractometer | 1812 independent reflections |
| Radiation source: INCOATEC IµS micro-focus source | 1679 reflections with I > 2σ(I) |
| Mirror monochromator | Rint = 0.030 |
| Detector resolution: 10.4167 pixels mm-1 | θmax = 70.1°, θmin = 5.8° |
| ω scans | h = −8→8 |
| Absorption correction: multi-scan (SADABS; Krause et al., 2015) | k = −10→9 |
| Tmin = 0.83, Tmax = 0.92 | l = −18→18 |
| 6896 measured reflections |
Refinement
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.033 | All H-atom parameters refined |
| wR(F2) = 0.086 | w = 1/[σ2(Fo2) + (0.0402P)2 + 0.2239P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.06 | (Δ/σ)max < 0.001 |
| 1812 reflections | Δρmax = 0.18 e Å−3 |
| 168 parameters | Δρmin = −0.19 e Å−3 |
| 0 restraints | Extinction correction: SHELXL2018 (Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| Primary atom site location: dual | 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 F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > 2sigma(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| O1 | 0.31019 (11) | 0.82725 (9) | 0.64517 (6) | 0.0345 (2) | |
| N1 | 0.24854 (12) | 0.64929 (11) | 0.53316 (6) | 0.0280 (2) | |
| N2 | 0.36075 (12) | 0.56773 (10) | 0.66470 (6) | 0.0250 (2) | |
| C1 | 0.33940 (14) | 0.44082 (11) | 0.61080 (7) | 0.0235 (2) | |
| C2 | 0.37638 (15) | 0.28918 (12) | 0.62754 (8) | 0.0289 (3) | |
| H2 | 0.426 (2) | 0.2543 (16) | 0.6872 (10) | 0.039 (4)* | |
| C3 | 0.34025 (16) | 0.18941 (14) | 0.55731 (8) | 0.0353 (3) | |
| H3 | 0.364 (2) | 0.0783 (17) | 0.5684 (10) | 0.043 (4)* | |
| C4 | 0.27117 (17) | 0.24106 (15) | 0.47421 (8) | 0.0378 (3) | |
| H4 | 0.246 (2) | 0.1678 (17) | 0.4255 (10) | 0.046 (4)* | |
| C5 | 0.23359 (16) | 0.39392 (15) | 0.45751 (7) | 0.0339 (3) | |
| H5 | 0.190 (2) | 0.4305 (16) | 0.3992 (10) | 0.042 (4)* | |
| C6 | 0.26803 (14) | 0.49324 (12) | 0.52720 (7) | 0.0255 (3) | |
| C7 | 0.30715 (14) | 0.69684 (12) | 0.61712 (7) | 0.0260 (2) | |
| C8 | 0.17860 (17) | 0.75002 (16) | 0.46162 (8) | 0.0381 (3) | |
| H8A | 0.255 (3) | 0.747 (2) | 0.4146 (13) | 0.076 (6)* | |
| H8B | 0.176 (3) | 0.854 (2) | 0.4867 (13) | 0.072 (5)* | |
| H8C | 0.044 (2) | 0.7264 (17) | 0.4370 (10) | 0.047 (4)* | |
| C9 | 0.44506 (16) | 0.56993 (13) | 0.75585 (7) | 0.0283 (3) | |
| H9A | 0.4344 (19) | 0.6753 (16) | 0.7764 (9) | 0.033 (3)* | |
| H9B | 0.376 (2) | 0.5012 (16) | 0.7898 (9) | 0.038 (3)* | |
| C10 | 0.64427 (15) | 0.52362 (12) | 0.76752 (7) | 0.0281 (3) | |
| C11 | 0.80385 (17) | 0.48197 (14) | 0.77883 (8) | 0.0342 (3) | |
| H11 | 0.938 (2) | 0.4443 (17) | 0.7926 (10) | 0.050 (4)* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O1 | 0.0298 (4) | 0.0254 (4) | 0.0471 (5) | 0.0006 (3) | 0.0015 (3) | −0.0012 (3) |
| N1 | 0.0239 (4) | 0.0309 (5) | 0.0277 (5) | −0.0020 (3) | −0.0012 (4) | 0.0074 (4) |
| N2 | 0.0254 (5) | 0.0249 (5) | 0.0236 (4) | 0.0005 (3) | −0.0007 (3) | −0.0007 (3) |
| C1 | 0.0196 (5) | 0.0264 (5) | 0.0244 (5) | −0.0023 (4) | 0.0028 (4) | −0.0014 (4) |
| C2 | 0.0249 (5) | 0.0281 (6) | 0.0337 (6) | −0.0008 (4) | 0.0041 (4) | 0.0011 (4) |
| C3 | 0.0298 (6) | 0.0300 (6) | 0.0469 (7) | −0.0021 (4) | 0.0088 (5) | −0.0072 (5) |
| C4 | 0.0339 (6) | 0.0427 (7) | 0.0384 (6) | −0.0083 (5) | 0.0107 (5) | −0.0158 (5) |
| C5 | 0.0286 (6) | 0.0486 (7) | 0.0248 (6) | −0.0089 (5) | 0.0048 (4) | −0.0032 (5) |
| C6 | 0.0207 (5) | 0.0307 (6) | 0.0254 (5) | −0.0046 (4) | 0.0037 (4) | 0.0014 (4) |
| C7 | 0.0189 (5) | 0.0261 (5) | 0.0328 (6) | −0.0007 (4) | 0.0025 (4) | 0.0025 (4) |
| C8 | 0.0294 (6) | 0.0450 (7) | 0.0380 (7) | −0.0013 (5) | −0.0019 (5) | 0.0189 (6) |
| C9 | 0.0296 (6) | 0.0332 (6) | 0.0218 (5) | 0.0004 (4) | 0.0019 (4) | −0.0014 (4) |
| C10 | 0.0333 (6) | 0.0293 (5) | 0.0206 (5) | −0.0018 (4) | −0.0004 (4) | 0.0014 (4) |
| C11 | 0.0330 (6) | 0.0381 (6) | 0.0298 (6) | 0.0022 (5) | −0.0016 (4) | 0.0030 (5) |
Geometric parameters (Å, º)
| O1—C7 | 1.2281 (13) | C4—C5 | 1.3915 (19) |
| N1—C7 | 1.3735 (14) | C4—H4 | 0.989 (16) |
| N1—C6 | 1.3874 (15) | C5—C6 | 1.3839 (16) |
| N1—C8 | 1.4526 (14) | C5—H5 | 0.967 (15) |
| N2—C7 | 1.3807 (14) | C8—H8A | 0.97 (2) |
| N2—C1 | 1.3910 (13) | C8—H8B | 0.99 (2) |
| N2—C9 | 1.4545 (14) | C8—H8C | 1.004 (16) |
| C1—C2 | 1.3805 (15) | C9—C10 | 1.4689 (16) |
| C1—C6 | 1.4011 (14) | C9—H9A | 0.988 (14) |
| C2—C3 | 1.3937 (17) | C9—H9B | 0.978 (15) |
| C2—H2 | 0.991 (15) | C10—C11 | 1.1885 (17) |
| C3—C4 | 1.3883 (19) | C11—H11 | 1.009 (16) |
| C3—H3 | 1.005 (15) | ||
| O1···H9A | 2.491 (14) | C11···O1vii | 3.1569 (15) |
| O1···H3i | 2.566 (15) | C2···H8Aiv | 2.82 (2) |
| O1···H8B | 2.516 (19) | C3···H8Cv | 2.859 (15) |
| O1···H9Bii | 2.346 (14) | C3···H8Aiv | 2.92 (2) |
| O1···H11iii | 2.181 (15) | C4···H8Cv | 2.810 (15) |
| C2···C10 | 3.3889 (16) | C5···H8Cv | 2.935 (15) |
| C3···C8iv | 3.5335 (17) | C8···H5 | 2.983 (14) |
| C4···C8v | 3.4947 (17) | C9···H2 | 2.975 (14) |
| C4···C7iv | 3.5437 (16) | C10···H4viii | 2.976 (15) |
| C5···C8v | 3.5884 (17) | C11···H5iv | 2.865 (15) |
| C6···C6iv | 3.5349 (14) | C11···H4viii | 2.705 (15) |
| C9···O1vi | 3.3198 (14) | ||
| C7—N1—C6 | 110.19 (9) | C5—C6—N1 | 132.12 (10) |
| C7—N1—C8 | 124.14 (10) | C5—C6—C1 | 120.83 (11) |
| C6—N1—C8 | 125.66 (10) | N1—C6—C1 | 107.04 (9) |
| C7—N2—C1 | 110.16 (9) | O1—C7—N1 | 127.43 (10) |
| C7—N2—C9 | 123.55 (9) | O1—C7—N2 | 126.43 (10) |
| C1—N2—C9 | 126.00 (9) | N1—C7—N2 | 106.14 (9) |
| C2—C1—N2 | 131.64 (10) | N1—C8—H8A | 112.7 (12) |
| C2—C1—C6 | 121.90 (10) | N1—C8—H8B | 106.7 (11) |
| N2—C1—C6 | 106.45 (9) | H8A—C8—H8B | 111.1 (16) |
| C1—C2—C3 | 117.07 (11) | N1—C8—H8C | 111.9 (9) |
| C1—C2—H2 | 120.7 (8) | H8A—C8—H8C | 108.5 (15) |
| C3—C2—H2 | 122.3 (8) | H8B—C8—H8C | 105.7 (13) |
| C4—C3—C2 | 121.20 (11) | N2—C9—C10 | 112.38 (9) |
| C4—C3—H3 | 120.5 (9) | N2—C9—H9A | 106.5 (8) |
| C2—C3—H3 | 118.3 (9) | C10—C9—H9A | 109.8 (8) |
| C3—C4—C5 | 121.63 (11) | N2—C9—H9B | 109.9 (8) |
| C3—C4—H4 | 119.6 (9) | C10—C9—H9B | 108.2 (8) |
| C5—C4—H4 | 118.8 (9) | H9A—C9—H9B | 110.1 (11) |
| C6—C5—C4 | 117.35 (11) | C11—C10—C9 | 177.63 (12) |
| C6—C5—H5 | 120.9 (8) | C10—C11—H11 | 176.1 (9) |
| C4—C5—H5 | 121.7 (8) | ||
| C7—N2—C1—C2 | 178.91 (11) | C2—C1—C6—C5 | −0.69 (15) |
| C9—N2—C1—C2 | 4.89 (17) | N2—C1—C6—C5 | 178.96 (9) |
| C7—N2—C1—C6 | −0.69 (11) | C2—C1—C6—N1 | −179.67 (9) |
| C9—N2—C1—C6 | −174.72 (9) | N2—C1—C6—N1 | −0.02 (11) |
| N2—C1—C2—C3 | −179.33 (10) | C6—N1—C7—O1 | 179.51 (10) |
| C6—C1—C2—C3 | 0.23 (15) | C8—N1—C7—O1 | 0.13 (17) |
| C1—C2—C3—C4 | 0.37 (16) | C6—N1—C7—N2 | −1.13 (11) |
| C2—C3—C4—C5 | −0.54 (18) | C8—N1—C7—N2 | 179.49 (9) |
| C3—C4—C5—C6 | 0.08 (17) | C1—N2—C7—O1 | −179.51 (10) |
| C4—C5—C6—N1 | 179.20 (11) | C9—N2—C7—O1 | −5.31 (16) |
| C4—C5—C6—C1 | 0.52 (15) | C1—N2—C7—N1 | 1.12 (11) |
| C7—N1—C6—C5 | −178.10 (11) | C9—N2—C7—N1 | 175.32 (9) |
| C8—N1—C6—C5 | 1.27 (18) | C7—N2—C9—C10 | −111.11 (11) |
| C7—N1—C6—C1 | 0.72 (11) | C1—N2—C9—C10 | 62.16 (13) |
| C8—N1—C6—C1 | −179.91 (9) |
Symmetry codes: (i) x, y+1, z; (ii) −x+1/2, y+1/2, −z+3/2; (iii) −x+3/2, y+1/2, −z+3/2; (iv) −x+1, −y+1, −z+1; (v) −x, −y+1, −z+1; (vi) −x+1/2, y−1/2, −z+3/2; (vii) −x+3/2, y−1/2, −z+3/2; (viii) x+1/2, −y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º)
Cg1 is the centroid of the C1–C6 benzene ring.
| D—H···A | D—H | H···A | D···A | D—H···A |
| C3—H3···O1ix | 1.005 (15) | 2.566 (15) | 3.4885 (15) | 152.6 (11) |
| C8—H8C···Cg1v | 1.004 (16) | 2.626 (15) | 3.5413 (13) | 151.1 (12) |
| C9—H9B···O1vi | 0.978 (15) | 2.347 (15) | 3.3198 (14) | 172.9 (12) |
| C11—H11···O1vii | 1.010 (15) | 2.181 (15) | 3.1569 (15) | 162.1 (12) |
Symmetry codes: (v) −x, −y+1, −z+1; (vi) −x+1/2, y−1/2, −z+3/2; (vii) −x+3/2, y−1/2, −z+3/2; (ix) x, y−1, z.
Funding Statement
This work was funded by National Science Foundation grant 1228232. Tulane University grant . Hacettepe Üniversitesi grant 013 D04 602 004 to T. Hökelek.
References
- Ayhan-Kılcıgil, G., Kus, G., Özdamar, E. D., Can-Eke, B. & Iscan, M. (2007). Arch. Pharm. Chem. Life Sci. 340, 607–611. [DOI] [PubMed]
- Becke, A. D. (1993). J. Chem. Phys. 98, 5648–5652.
- Belaziz, D., Kandri Rodi, Y., Essassi, E. M. & El Ammari, L. (2012). Acta Cryst. E68, o1276. [DOI] [PMC free article] [PubMed]
- Belaziz, D., Kandri Rodi, Y., Ouazzani Chahdi, F., Essassi, E. M., Saadi, M. & El Ammari, L. (2013). Acta Cryst. E69, o122. [DOI] [PMC free article] [PubMed]
- Bouayad, K., Kandri Rodi, Y., Ouzidan, Y., Essassi, E. M., Saadi, M. & El Ammari, L. (2015). Acta Cryst. E71, o735–o736. [DOI] [PMC free article] [PubMed]
- Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.
- Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.
- Farukh, A. & Mubashira, A. (2009). Eur. J. Med. Chem. 44, 834–844.
- Frisch, M. J., et al. (2009). GAUSSIAN09. Gaussian Inc., Wallingford, CT, US
- Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]
- Hathwar, V. R., Sist, M., Jørgensen, M. R. V., Mamakhel, A. H., Wang, X., Hoffmann, C. M., Sugimoto, K., Overgaard, J. & Iversen, B. B. (2015). IUCrJ, 2, 563–574. [DOI] [PMC free article] [PubMed]
- Hirshfeld, H. L. (1977). Theor. Chim. Acta, 44, 129–138.
- Jayatilaka, D., Grimwood, D. J., Lee, A., Lemay, A., Russel, A. J., Taylor, C., Wolff, S. K., Cassam-Chenai, P. & Whitton, A. (2005). TONTO – A System for Computational Chemistry. Available at: http://hirshfeldsurface.net/
- Kandri Rodi, Y., Misbahi, K., El-Ghayoury, A., Zorina, L., Essassi, E. M. & El Ammari, L. (2013). Acta Cryst. E69, o1159. [DOI] [PMC free article] [PubMed]
- Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10. [DOI] [PMC free article] [PubMed]
- Lakhrissi, B., Benksim, A., Massoui, M., Essassi, E. M., Lequart, V., Joly, N., Beaupère, D., Wadouachi, A. & Martin, P. (2008). Carbohydr. Res. 343, 421–433. [DOI] [PubMed]
- Luo, Y., Yao, J. P., Yang, L., Feng, C. L., Tang, W., Wang, G. F., Zuo, J. P. & Lu, W. (2011). Arch. Pharm. Pharm. Med. Chem. 344, 78–83. [DOI] [PubMed]
- Mackenzie, C. F., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). IUCrJ, 4, 575–587. [DOI] [PMC free article] [PubMed]
- McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814–3816. [DOI] [PubMed]
- Mondieig, D., Lakhrissi, L., El Assyry, A., Lakhrissi, B., Negrier, P., Essassi, E. M., Massoui, M., Michel Leger, J. & Benali, B. (2013). J. Mar. Chim. Heterocycl. 12, 51–61.
- Navarrete-Vázquez, G., Cedillo, R., Hernández-Campos, A., Yépez, L., Hernández-Luis, F., Valdez, J., Morales, R., Cortés, R., Hernández, M. & Castillo, R. (2011). Bioorg. Med. Chem. 11, 187–190. [DOI] [PubMed]
- Ouzidan, Y., Kandri Rodi, Y., Fronczek, F. R., Venkatraman, R., El Ammari, L. & Essassi, E. M. (2011). Acta Cryst. E67, o362–o363. [DOI] [PMC free article] [PubMed]
- Ouzidan, Y., Kandri Rodi, Y., Jasinski, J. P., Butcher, R. J., Golen, J. A. & El Ammari, L. (2011a). Acta Cryst. E67, o1091. [DOI] [PMC free article] [PubMed]
- Saber, A., Sebbar, N. K., Hökelek, T., El hafi, M., Mague, J. T. & Essassi, E. M. (2018b). Acta Cryst. E74, 1842–1846. [DOI] [PMC free article] [PubMed]
- Saber, A., Sebbar, N. K., Hökelek, T., Hni, B., Mague, J. T. & Essassi, E. M. (2018a). Acta Cryst. E74, 1746–1750. [DOI] [PMC free article] [PubMed]
- Saber, A., Sebbar, N. K., Sert, Y., Alzaqri, N., Hökelek, T., El Ghayati, L., Talbaoui, A., Mague, J. T., Filali Baba, Y., Urrutigoîty, M. & Essassi, E. M. (2020). J. Mol. Struct. 1200, 127174.
- Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
- Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.
- Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.
- Soderlind, K. J., Gorodetsky, B., Singh, A. K., Bachur, N., Miller, G. G. & Lown, J. W. (1999). Anticancer Drug. Des. 14, 19–36. [PubMed]
- Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19–32.
- Spackman, M. A., McKinnon, J. J. & Jayatilaka, D. (2008). CrystEngComm, 10, 377–388.
- Turner, M. J., Grabowsky, S., Jayatilaka, D. & Spackman, M. A. (2014). J. Phys. Chem. Lett. 5, 4249–4255. [DOI] [PubMed]
- Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. The University of Western Australia.
- Turner, M. J., Thomas, S. P., Shi, M. W., Jayatilaka, D. & Spackman, M. A. (2015). Chem. Commun. 51, 3735–3738. [DOI] [PubMed]
- Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H. & Sundius, T. (2016). Spectrochim. Acta Part A, 153, 625–636. [DOI] [PubMed]
- Walia, R., Hedaitullah, M., Naaz, S. F., Iqbal, K. & Lamba, H. S. (2011). Int. J. Res. Pharm. Chem. 1, 565–574.
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989019015779/lh5936sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989019015779/lh5936Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989019015779/lh5936Isup3.cdx
Supporting information file. DOI: 10.1107/S2056989019015779/lh5936Isup4.cml
CCDC reference: 1967468
Additional supporting information: crystallographic information; 3D view; checkCIF report









