(3Z)-3-Benzyl­idene-1H-benzimidazo[1,2-a]imidazol-2(3H)-one

Rida, M.; El Bakri, Y.; Essassi, E.M.; Mague, J.T.

doi:10.1107/S2414314616019088

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 1| Part 12| December 2016| x161908

https://doi.org/10.1107/S2414314616019088

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(3Z)-3-Benzylidene-1H-benzimidazo[1,2-a]imidazol-2(3H)-one

Mohammed Rida,^a ^* Youness El Bakri,^a El Mokhtar Essassi ^a and Joel T. Mague ^b

^aLaboratoire de Chimie Organique Hétérocyclique, URAC 21, Pôle de Compétence, Pharmacochimie, Av Ibn Battouta, BP 1014, Faculté des Sciences, Mohammed V University, Rabat, Morocco, and ^bDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA
^*Correspondence e-mail: rida.m.b@hotmail.com

Edited by J. Simpson, University of Otago, New Zealand (Received 23 November 2016; accepted 30 November 2016; online 9 December 2016)

In the title compound, C₁₆H₁₁N₃O, the molecular conformation is partially determined by an intramolecular C—H⋯π(ring) interaction. In the crystal, pairwise N—H⋯N hydrogen bonds form dimers, which associate into stacks through a combination of C—H⋯O, C—H⋯π(ring) and offset π–π stacking interactions.

Keywords: crystal structure; hydrogen bonds; π–π stacking.

CCDC reference: 1519973

Structure description

Heterocyclic systems with benzimidazole as a significant component have been widely used in medicinal chemistry and drug development (Wang et al., 2015 ). They possess antitumor (Soderlin et al., 1999 ), antifungal (Ke et al., 2014 ), antiviral (Tonelli et al., 2008 ) and antidiabetic properties (Bansal & Silakari, 2012 ). The title compound was obtained by the action of 2-aminobenzimidazole on ethyl glycidate in hot n-butanol.

In the title molecule, the tricyclic core is approximately planar with an r.m.s. deviation of 0.062 Å for the 12 non-H atoms making up the ring system. The dihedral angle between the C1–C6 and the central five-membered ring is 4.21 (1)°, while that between the central and outer five-membered rings is 4.1 (1)°. The pendant phenyl group makes a dihedral angle of 52.61 (6)° with the N2/C9/N3/C8/C7 ring, and its orientation appears to be determined in part by an intramolecular C5—H5⋯Cg4 contact (Fig. 1 and Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

Cg3 and Cg4 are the centroids of the C1–C6 and C11–C16 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N1ⁱ	0.93 (3)	1.98 (3)	2.876 (2)	162 (3)
C16—H16⋯O1ⁱⁱ	1.01 (3)	2.58 (3)	3.412 (3)	139 (2)
C5—H5⋯Cg4	1.01 (3)	2.65 (3)	3.512 (2)	143 (3)
C10—H10⋯Cg4ⁱⁱⁱ	1.01 (3)	2.88 (2)	3.606 (2)	129.0 (15)
C13—H13⋯Cg3^iv	1.00 (3)	2.73 (3)	3.474 (2)	132 (2)
Symmetry codes: (i) -x+2, -y+1, -z; (ii) x-1, y, z; (iii) -x+1, -y+2, -z+1; (iv) -x+1, -y+1, -z+1.

Figure 1
The title molecule with the atom-labeling scheme and 50% probability ellipsoids. The intramolecular C—H⋯π(ring) interaction is shown by a dotted line.

In the crystal, significant π–π stacking interactions [Cg1⋯Cg1ⁱⁱ = 3.5537 (12) Å and Cg2⋯Cg3ⁱⁱ = 3.4421 (12) Å; symmetry code: −x + 1, −y + 1, −z] link adjacent molecules into inversion dimers in a head-to-tail fashion. These dimers are further linked by C—H⋯π(ring) contacts (Table 1) into chains of molecules stacked along the c-axis direction (Fig. 2). Adjacent chains are connected by C10—H10⋯Cg4 contacts, forming sheets of molecules in the bc plane. Pairs of N3—H3A⋯N1 hydrogen bonds (Table 1) form inversion dimers with R₂²(8) rings and, together with C16—H16⋯O1 hydrogen bonds, stack the molecules along the a-axis direction (Fig. 3).

Figure 2
Details of the hydrogen bonding [N—H⋯N hydrogen bonds are represented by blue dashed lines and C—H⋯π(ring) interactions are represented by purple dashed lines] and π–π stacking interactions (orange dashed lines). Cg1–Cg4 are the centroids of the N1/C1/C6/N2/C9, N2/C9/N3/C8/C7, C1–C6 and C11–C16 rings, respectively. [Symmetry codes: (i) 1 − x, 1 − y, 1 − z; (ii) 1 − x, 1 − y, −z; (iii) x, −1 + y, z; (iv) −1 + x, y, 1 + z.]

Figure 3
Packing viewed along the a axis, with C—H⋯O and some of the C—H⋯π(ring) interactions shown, respectively, as black and orange dashed lines.

Synthesis and crystallization

A mixture of 2-aminobenzimidazole (0.03 mol) and ethyl glycidate (0.03 mol) was refluxed in 80 ml of n-butanol for 48 h. The resulting solution was concentrated under reduced pressure and the crude solid obtained was chromatographed on a silica gel column with a mixture of ethyl acetate/ethanol (80/20) as eluent. The 3-benzylidene-1H-benzimidazo[1,2-a]imidazol-2(3H)-one obtained was recrystallized from ethanol solution to afford the title compound as colorless crystals.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. Three reflections (5 $[\overline{1}]$ 4, 5 $[\overline{2}]$ 8 and 5 $[\overline{2}]$ 7) were omitted from the final refinement since they fell very close to the edge of a frame and were therefore felt to be poorly recorded.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₆H₁₁N₃O
M_r	261.28
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	150
a, b, c (Å)	6.6849 (3), 8.9428 (5), 10.7445 (5)
α, β, γ (°)	103.935 (3), 95.015 (4), 96.860 (3)
V (Å³)	614.44 (5)
Z	2
Radiation type	Cu Kα
μ (mm⁻¹)	0.74
Crystal size (mm)	0.21 × 0.15 × 0.02

Data collection
Diffractometer	Bruker D8 VENTURE PHOTON 100 CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2016 )
T_min, T_max	0.83, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections	4587, 2249, 1810
R_int	0.032
(sin θ/λ)_max (Å⁻¹)	0.618

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.136, 1.09
No. of reflections	2249
No. of parameters	225
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.24, −0.26
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), DIAMOND (Brandenburg & Putz, 2012 ) and SHELXTL (Sheldrick, 2008 ).

Structural data

CCDC reference: 1519973

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314616019088/sj4073sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616019088/sj4073Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019088/sj4073Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314616019088/sj4073Isup4.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

(3Z)-3-Benzylidene-1H-benzimidazo[1,2-a]imidazol-2(3H)-one top

Crystal data top

C₁₆H₁₁N₃O	Z = 2
M_r = 261.28	F(000) = 272
Triclinic, P1	D_x = 1.412 Mg m⁻³
a = 6.6849 (3) Å	Cu Kα radiation, λ = 1.54178 Å
b = 8.9428 (5) Å	Cell parameters from 3426 reflections
c = 10.7445 (5) Å	θ = 5.2–72.5°
α = 103.935 (3)°	µ = 0.74 mm⁻¹
β = 95.015 (4)°	T = 150 K
γ = 96.860 (3)°	Plate, colourless
V = 614.44 (5) Å³	0.21 × 0.15 × 0.02 mm

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	2249 independent reflections
Radiation source: INCOATEC IµS micro-focus source	1810 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.032
Detector resolution: 10.4167 pixels mm^-1	θ_max = 72.5°, θ_min = 5.2°
ω scans	h = −8→7
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = −11→9
T_min = 0.83, T_max = 0.98	l = −13→13
4587 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.047	Hydrogen site location: difference Fourier map
wR(F²) = 0.136	All H-atom parameters refined
S = 1.09	w = 1/[σ²(F_o²) + (0.0532P)² + 0.4943P] where P = (F_o² + 2F_c²)/3
2249 reflections	(Δ/σ)_max = 0.001
225 parameters	Δρ_max = 0.24 e Å⁻³
0 restraints	Δρ_min = −0.26 e Å⁻³

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.9044 (2)	0.95697 (17)	0.15628 (15)	0.0297 (4)
N1	0.7919 (3)	0.4128 (2)	0.07214 (17)	0.0235 (4)
N2	0.6348 (3)	0.60823 (19)	0.17826 (16)	0.0205 (4)
N3	0.9139 (3)	0.6904 (2)	0.09709 (17)	0.0237 (4)
H3A	1.019 (4)	0.680 (3)	0.047 (3)	0.044 (8)*
C1	0.6146 (3)	0.3508 (2)	0.11504 (19)	0.0215 (4)
C2	0.5370 (3)	0.1964 (2)	0.1005 (2)	0.0245 (5)
H2	0.609 (4)	0.114 (3)	0.058 (3)	0.039 (7)*
C3	0.3508 (3)	0.1635 (2)	0.1428 (2)	0.0262 (5)
H3	0.285 (4)	0.056 (3)	0.127 (3)	0.031 (6)*
C4	0.2429 (3)	0.2818 (3)	0.1978 (2)	0.0267 (5)
H4	0.107 (4)	0.254 (3)	0.222 (2)	0.027 (6)*
C5	0.3203 (3)	0.4385 (2)	0.21698 (19)	0.0223 (4)
H5	0.247 (4)	0.526 (3)	0.260 (3)	0.029 (6)*
C6	0.5095 (3)	0.4707 (2)	0.17753 (19)	0.0212 (4)
C7	0.6545 (3)	0.7717 (2)	0.21504 (19)	0.0219 (4)
C8	0.8346 (3)	0.8244 (2)	0.15278 (19)	0.0232 (5)
C9	0.7924 (3)	0.5630 (2)	0.11100 (19)	0.0216 (4)
C10	0.5593 (3)	0.8678 (2)	0.2973 (2)	0.0234 (5)
H10	0.599 (4)	0.983 (3)	0.307 (2)	0.031 (6)*
C11	0.4150 (3)	0.8193 (2)	0.3810 (2)	0.0232 (5)
C12	0.4692 (4)	0.7249 (3)	0.4607 (2)	0.0273 (5)
H12	0.607 (4)	0.693 (3)	0.460 (3)	0.041 (8)*
C13	0.3346 (4)	0.6764 (3)	0.5388 (2)	0.0333 (5)
H13	0.375 (4)	0.610 (3)	0.596 (3)	0.039 (7)*
C14	0.1420 (4)	0.7199 (3)	0.5370 (2)	0.0373 (6)
H14	0.044 (5)	0.685 (3)	0.592 (3)	0.052 (9)*
C15	0.0887 (4)	0.8166 (3)	0.4608 (3)	0.0365 (6)
H15	−0.049 (5)	0.846 (4)	0.462 (3)	0.057 (9)*
C16	0.2245 (3)	0.8687 (3)	0.3846 (2)	0.0288 (5)
H16	0.189 (4)	0.940 (3)	0.329 (3)	0.039 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0337 (9)	0.0220 (8)	0.0333 (9)	−0.0005 (6)	0.0081 (7)	0.0075 (6)
N1	0.0260 (9)	0.0214 (9)	0.0234 (9)	0.0039 (7)	0.0091 (7)	0.0040 (7)
N2	0.0202 (9)	0.0188 (8)	0.0215 (8)	0.0019 (6)	0.0053 (7)	0.0029 (6)
N3	0.0243 (9)	0.0213 (9)	0.0251 (9)	0.0010 (7)	0.0090 (7)	0.0041 (7)
C1	0.0234 (10)	0.0218 (10)	0.0190 (9)	0.0034 (8)	0.0058 (8)	0.0035 (7)
C2	0.0290 (11)	0.0209 (10)	0.0217 (10)	0.0031 (8)	0.0050 (9)	0.0016 (8)
C3	0.0325 (12)	0.0208 (10)	0.0232 (10)	−0.0019 (9)	0.0064 (9)	0.0033 (8)
C4	0.0272 (12)	0.0281 (11)	0.0241 (11)	−0.0011 (9)	0.0089 (9)	0.0056 (9)
C5	0.0212 (10)	0.0266 (11)	0.0170 (9)	0.0026 (8)	0.0011 (8)	0.0022 (8)
C6	0.0268 (11)	0.0187 (10)	0.0176 (9)	0.0031 (8)	0.0062 (8)	0.0028 (7)
C7	0.0244 (11)	0.0204 (10)	0.0207 (10)	0.0022 (8)	0.0045 (8)	0.0046 (8)
C8	0.0260 (11)	0.0229 (11)	0.0191 (10)	0.0006 (8)	0.0029 (8)	0.0037 (8)
C9	0.0216 (10)	0.0224 (10)	0.0198 (10)	0.0017 (8)	0.0064 (8)	0.0028 (8)
C10	0.0254 (11)	0.0218 (11)	0.0224 (10)	0.0051 (8)	0.0047 (8)	0.0034 (8)
C11	0.0263 (11)	0.0204 (10)	0.0202 (10)	0.0033 (8)	0.0051 (8)	−0.0008 (8)
C12	0.0303 (12)	0.0262 (11)	0.0253 (11)	0.0066 (9)	0.0052 (9)	0.0045 (9)
C13	0.0447 (14)	0.0325 (12)	0.0239 (11)	0.0055 (10)	0.0095 (10)	0.0073 (9)
C14	0.0415 (14)	0.0399 (14)	0.0296 (12)	0.0019 (11)	0.0173 (11)	0.0045 (10)
C15	0.0282 (13)	0.0410 (14)	0.0388 (13)	0.0076 (10)	0.0115 (11)	0.0037 (11)
C16	0.0288 (12)	0.0292 (12)	0.0276 (11)	0.0079 (9)	0.0044 (9)	0.0034 (9)

Geometric parameters (Å, º) top

O1—C8	1.212 (3)	C5—C6	1.388 (3)
N1—C9	1.306 (3)	C5—H5	1.01 (3)
N1—C1	1.409 (3)	C7—C10	1.337 (3)
N2—C9	1.375 (3)	C7—C8	1.509 (3)
N2—C6	1.401 (3)	C10—C11	1.472 (3)
N2—C7	1.406 (3)	C10—H10	1.01 (3)
N3—C9	1.365 (3)	C11—C12	1.394 (3)
N3—C8	1.392 (3)	C11—C16	1.397 (3)
N3—H3A	0.93 (3)	C12—C13	1.384 (3)
C1—C2	1.382 (3)	C12—H12	1.00 (3)
C1—C6	1.418 (3)	C13—C14	1.388 (4)
C2—C3	1.386 (3)	C13—H13	1.00 (3)
C2—H2	0.97 (3)	C14—C15	1.382 (4)
C3—C4	1.394 (3)	C14—H14	0.99 (3)
C3—H3	0.98 (3)	C15—C16	1.386 (3)
C4—C5	1.394 (3)	C15—H15	0.98 (3)
C4—H4	0.98 (2)	C16—H16	1.01 (3)

C9—N1—C1	103.06 (16)	O1—C8—N3	126.4 (2)
C9—N2—C6	106.03 (16)	O1—C8—C7	127.33 (19)
C9—N2—C7	109.67 (17)	N3—C8—C7	106.19 (17)
C6—N2—C7	144.18 (18)	N1—C9—N3	134.23 (19)
C9—N3—C8	109.39 (17)	N1—C9—N2	115.54 (18)
C9—N3—H3A	121.3 (18)	N3—C9—N2	110.20 (17)
C8—N3—H3A	128.7 (18)	C7—C10—C11	125.17 (19)
C2—C1—N1	128.60 (19)	C7—C10—H10	116.6 (14)
C2—C1—C6	120.20 (19)	C11—C10—H10	118.1 (14)
N1—C1—C6	111.18 (17)	C12—C11—C16	118.8 (2)
C1—C2—C3	118.06 (19)	C12—C11—C10	119.93 (19)
C1—C2—H2	120.3 (16)	C16—C11—C10	121.3 (2)
C3—C2—H2	121.6 (16)	C13—C12—C11	120.8 (2)
C2—C3—C4	121.4 (2)	C13—C12—H12	120.8 (16)
C2—C3—H3	120.7 (15)	C11—C12—H12	118.5 (16)
C4—C3—H3	117.6 (15)	C12—C13—C14	120.0 (2)
C3—C4—C5	121.7 (2)	C12—C13—H13	120.2 (16)
C3—C4—H4	119.3 (14)	C14—C13—H13	119.7 (16)
C5—C4—H4	119.0 (14)	C15—C14—C13	119.6 (2)
C6—C5—C4	116.56 (19)	C15—C14—H14	119.8 (18)
C6—C5—H5	120.6 (14)	C13—C14—H14	120.6 (18)
C4—C5—H5	122.8 (14)	C14—C15—C16	120.7 (2)
C5—C6—N2	133.96 (19)	C14—C15—H15	117.5 (19)
C5—C6—C1	121.92 (18)	C16—C15—H15	121.8 (19)
N2—C6—C1	104.03 (17)	C15—C16—C11	120.1 (2)
C10—C7—N2	131.17 (19)	C15—C16—H16	121.8 (16)
C10—C7—C8	124.17 (19)	C11—C16—H16	118.1 (16)
N2—C7—C8	104.25 (16)

C9—N1—C1—C2	179.9 (2)	N2—C7—C8—O1	178.3 (2)
C9—N1—C1—C6	1.4 (2)	C10—C7—C8—N3	167.8 (2)
N1—C1—C2—C3	−175.2 (2)	N2—C7—C8—N3	−5.5 (2)
C6—C1—C2—C3	3.1 (3)	C1—N1—C9—N3	−176.5 (2)
C1—C2—C3—C4	0.5 (3)	C1—N1—C9—N2	1.3 (2)
C2—C3—C4—C5	−2.3 (3)	C8—N3—C9—N1	176.2 (2)
C3—C4—C5—C6	0.5 (3)	C8—N3—C9—N2	−1.6 (2)
C4—C5—C6—N2	179.0 (2)	C6—N2—C9—N1	−3.5 (2)
C4—C5—C6—C1	3.1 (3)	C7—N2—C9—N1	179.52 (17)
C9—N2—C6—C5	−172.6 (2)	C6—N2—C9—N3	174.82 (17)
C7—N2—C6—C5	2.6 (5)	C7—N2—C9—N3	−2.2 (2)
C9—N2—C6—C1	3.9 (2)	N2—C7—C10—C11	5.8 (4)
C7—N2—C6—C1	179.1 (3)	C8—C7—C10—C11	−165.6 (2)
C2—C1—C6—C5	−5.0 (3)	C7—C10—C11—C12	51.9 (3)
N1—C1—C6—C5	173.59 (19)	C7—C10—C11—C16	−129.4 (2)
C2—C1—C6—N2	177.99 (19)	C16—C11—C12—C13	2.1 (3)
N1—C1—C6—N2	−3.4 (2)	C10—C11—C12—C13	−179.1 (2)
C9—N2—C7—C10	−168.0 (2)	C11—C12—C13—C14	1.0 (3)
C6—N2—C7—C10	16.9 (5)	C12—C13—C14—C15	−2.6 (4)
C9—N2—C7—C8	4.7 (2)	C13—C14—C15—C16	1.0 (4)
C6—N2—C7—C8	−170.4 (3)	C14—C15—C16—C11	2.2 (4)
C9—N3—C8—O1	−179.3 (2)	C12—C11—C16—C15	−3.7 (3)
C9—N3—C8—C7	4.5 (2)	C10—C11—C16—C15	177.6 (2)
C10—C7—C8—O1	−8.3 (4)

Hydrogen-bond geometry (Å, º) top

Cg3 and Cg4 are the centroids of the C1–C6 and C11–C16 rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N1ⁱ	0.93 (3)	1.98 (3)	2.876 (2)	162 (3)
C16—H16···O1ⁱⁱ	1.01 (3)	2.58 (3)	3.412 (3)	139 (2)
C5—H5···Cg4	1.01 (3)	2.65 (3)	3.512 (2)	143 (3)
C10—H10···Cg4ⁱⁱⁱ	1.01 (3)	2.88 (2)	3.606 (2)	129.0 (15)
C13—H13···Cg3^iv	1.00 (3)	2.73 (3)	3.474 (2)	132 (2)

Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) −x+1, −y+2, −z+1; (iv) −x+1, −y+1, −z+1.

Acknowledgements

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.

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