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ISSN: 2414-3146

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

CROSSMARK_Color_square_no_text.svg

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 ππ stacking inter­actions.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Heterocyclic systems with benzimidazole as a significant component have been widely used in medicinal chemistry and drug development (Wang et al., 2015[Wang, M., Han, X. & Zhou, Z. (2015). Expert Opin. Ther. Pat. 25, 595-612.]). They possess anti­tumor (Soderlin et al., 1999[Soderlin, K. J., Gorodetsky, B., Singh, A. K., Bachu, N. R., Milla, G. G. & Lown, J. W. (1999). Anticancer Drug. Des. 14, 19-36.]), anti­fungal (Ke et al., 2014[Ke, Y., Zhi, X., Yu, X., Ding, G., Yang, C. & Xu, H. (2014). Combin. Chem. High Throughput Screen. 17, 89-95.]), anti­viral (Tonelli et al., 2008[Tonelli, M., Paglietti, G., Boido, V., Sparatore, F., Marongiu, E., Marongiu, E., La Colla, P. & Loddo, R. (2008). Chem. Biodivers. 5, 2386-2401.]) and anti­diabetic properties (Bansal & Silakari, 2012[Bansal, Y. & Silakari, O. (2012). Bioorg. Med. Chem. 20, 6208-6236.]). 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[link] and Table 1[link]).

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 DA 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⋯Cg3iv 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]
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 ππ 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[link]) into chains of mol­ecules stacked along the c-axis direction (Fig. 2[link]). 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[link]) 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[link]).

[Figure 2]
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 ππ 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]
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[link]. 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
Mr 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)
V3) 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[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.83, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections 4587, 2249, 1810
Rint 0.032
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.24, −0.26
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS, Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg & Putz, 2012[Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Structural data


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
C16H11N3OZ = 2
Mr = 261.28F(000) = 272
Triclinic, P1Dx = 1.412 Mg m3
a = 6.6849 (3) ÅCu Kα radiation, λ = 1.54178 Å
b = 8.9428 (5) ÅCell parameters from 3426 reflections
c = 10.7445 (5) Åθ = 5.2–72.5°
α = 103.935 (3)°µ = 0.74 mm1
β = 95.015 (4)°T = 150 K
γ = 96.860 (3)°Plate, colourless
V = 614.44 (5) Å30.21 × 0.15 × 0.02 mm
Data collection top
Bruker D8 VENTURE PHOTON 100 CMOS
diffractometer
2249 independent reflections
Radiation source: INCOATEC IµS micro-focus source1810 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.032
Detector resolution: 10.4167 pixels mm-1θmax = 72.5°, θmin = 5.2°
ω scansh = 87
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 119
Tmin = 0.83, Tmax = 0.98l = 1313
4587 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: difference Fourier map
wR(F2) = 0.136All H-atom parameters refined
S = 1.09 w = 1/[σ2(Fo2) + (0.0532P)2 + 0.4943P]
where P = (Fo2 + 2Fc2)/3
2249 reflections(Δ/σ)max = 0.001
225 parametersΔρmax = 0.24 e Å3
0 restraintsΔρmin = 0.26 e Å3
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
xyzUiso*/Ueq
O10.9044 (2)0.95697 (17)0.15628 (15)0.0297 (4)
N10.7919 (3)0.4128 (2)0.07214 (17)0.0235 (4)
N20.6348 (3)0.60823 (19)0.17826 (16)0.0205 (4)
N30.9139 (3)0.6904 (2)0.09709 (17)0.0237 (4)
H3A1.019 (4)0.680 (3)0.047 (3)0.044 (8)*
C10.6146 (3)0.3508 (2)0.11504 (19)0.0215 (4)
C20.5370 (3)0.1964 (2)0.1005 (2)0.0245 (5)
H20.609 (4)0.114 (3)0.058 (3)0.039 (7)*
C30.3508 (3)0.1635 (2)0.1428 (2)0.0262 (5)
H30.285 (4)0.056 (3)0.127 (3)0.031 (6)*
C40.2429 (3)0.2818 (3)0.1978 (2)0.0267 (5)
H40.107 (4)0.254 (3)0.222 (2)0.027 (6)*
C50.3203 (3)0.4385 (2)0.21698 (19)0.0223 (4)
H50.247 (4)0.526 (3)0.260 (3)0.029 (6)*
C60.5095 (3)0.4707 (2)0.17753 (19)0.0212 (4)
C70.6545 (3)0.7717 (2)0.21504 (19)0.0219 (4)
C80.8346 (3)0.8244 (2)0.15278 (19)0.0232 (5)
C90.7924 (3)0.5630 (2)0.11100 (19)0.0216 (4)
C100.5593 (3)0.8678 (2)0.2973 (2)0.0234 (5)
H100.599 (4)0.983 (3)0.307 (2)0.031 (6)*
C110.4150 (3)0.8193 (2)0.3810 (2)0.0232 (5)
C120.4692 (4)0.7249 (3)0.4607 (2)0.0273 (5)
H120.607 (4)0.693 (3)0.460 (3)0.041 (8)*
C130.3346 (4)0.6764 (3)0.5388 (2)0.0333 (5)
H130.375 (4)0.610 (3)0.596 (3)0.039 (7)*
C140.1420 (4)0.7199 (3)0.5370 (2)0.0373 (6)
H140.044 (5)0.685 (3)0.592 (3)0.052 (9)*
C150.0887 (4)0.8166 (3)0.4608 (3)0.0365 (6)
H150.049 (5)0.846 (4)0.462 (3)0.057 (9)*
C160.2245 (3)0.8687 (3)0.3846 (2)0.0288 (5)
H160.189 (4)0.940 (3)0.329 (3)0.039 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0337 (9)0.0220 (8)0.0333 (9)0.0005 (6)0.0081 (7)0.0075 (6)
N10.0260 (9)0.0214 (9)0.0234 (9)0.0039 (7)0.0091 (7)0.0040 (7)
N20.0202 (9)0.0188 (8)0.0215 (8)0.0019 (6)0.0053 (7)0.0029 (6)
N30.0243 (9)0.0213 (9)0.0251 (9)0.0010 (7)0.0090 (7)0.0041 (7)
C10.0234 (10)0.0218 (10)0.0190 (9)0.0034 (8)0.0058 (8)0.0035 (7)
C20.0290 (11)0.0209 (10)0.0217 (10)0.0031 (8)0.0050 (9)0.0016 (8)
C30.0325 (12)0.0208 (10)0.0232 (10)0.0019 (9)0.0064 (9)0.0033 (8)
C40.0272 (12)0.0281 (11)0.0241 (11)0.0011 (9)0.0089 (9)0.0056 (9)
C50.0212 (10)0.0266 (11)0.0170 (9)0.0026 (8)0.0011 (8)0.0022 (8)
C60.0268 (11)0.0187 (10)0.0176 (9)0.0031 (8)0.0062 (8)0.0028 (7)
C70.0244 (11)0.0204 (10)0.0207 (10)0.0022 (8)0.0045 (8)0.0046 (8)
C80.0260 (11)0.0229 (11)0.0191 (10)0.0006 (8)0.0029 (8)0.0037 (8)
C90.0216 (10)0.0224 (10)0.0198 (10)0.0017 (8)0.0064 (8)0.0028 (8)
C100.0254 (11)0.0218 (11)0.0224 (10)0.0051 (8)0.0047 (8)0.0034 (8)
C110.0263 (11)0.0204 (10)0.0202 (10)0.0033 (8)0.0051 (8)0.0008 (8)
C120.0303 (12)0.0262 (11)0.0253 (11)0.0066 (9)0.0052 (9)0.0045 (9)
C130.0447 (14)0.0325 (12)0.0239 (11)0.0055 (10)0.0095 (10)0.0073 (9)
C140.0415 (14)0.0399 (14)0.0296 (12)0.0019 (11)0.0173 (11)0.0045 (10)
C150.0282 (13)0.0410 (14)0.0388 (13)0.0076 (10)0.0115 (11)0.0037 (11)
C160.0288 (12)0.0292 (12)0.0276 (11)0.0079 (9)0.0044 (9)0.0034 (9)
Geometric parameters (Å, º) top
O1—C81.212 (3)C5—C61.388 (3)
N1—C91.306 (3)C5—H51.01 (3)
N1—C11.409 (3)C7—C101.337 (3)
N2—C91.375 (3)C7—C81.509 (3)
N2—C61.401 (3)C10—C111.472 (3)
N2—C71.406 (3)C10—H101.01 (3)
N3—C91.365 (3)C11—C121.394 (3)
N3—C81.392 (3)C11—C161.397 (3)
N3—H3A0.93 (3)C12—C131.384 (3)
C1—C21.382 (3)C12—H121.00 (3)
C1—C61.418 (3)C13—C141.388 (4)
C2—C31.386 (3)C13—H131.00 (3)
C2—H20.97 (3)C14—C151.382 (4)
C3—C41.394 (3)C14—H140.99 (3)
C3—H30.98 (3)C15—C161.386 (3)
C4—C51.394 (3)C15—H150.98 (3)
C4—H40.98 (2)C16—H161.01 (3)
C9—N1—C1103.06 (16)O1—C8—N3126.4 (2)
C9—N2—C6106.03 (16)O1—C8—C7127.33 (19)
C9—N2—C7109.67 (17)N3—C8—C7106.19 (17)
C6—N2—C7144.18 (18)N1—C9—N3134.23 (19)
C9—N3—C8109.39 (17)N1—C9—N2115.54 (18)
C9—N3—H3A121.3 (18)N3—C9—N2110.20 (17)
C8—N3—H3A128.7 (18)C7—C10—C11125.17 (19)
C2—C1—N1128.60 (19)C7—C10—H10116.6 (14)
C2—C1—C6120.20 (19)C11—C10—H10118.1 (14)
N1—C1—C6111.18 (17)C12—C11—C16118.8 (2)
C1—C2—C3118.06 (19)C12—C11—C10119.93 (19)
C1—C2—H2120.3 (16)C16—C11—C10121.3 (2)
C3—C2—H2121.6 (16)C13—C12—C11120.8 (2)
C2—C3—C4121.4 (2)C13—C12—H12120.8 (16)
C2—C3—H3120.7 (15)C11—C12—H12118.5 (16)
C4—C3—H3117.6 (15)C12—C13—C14120.0 (2)
C3—C4—C5121.7 (2)C12—C13—H13120.2 (16)
C3—C4—H4119.3 (14)C14—C13—H13119.7 (16)
C5—C4—H4119.0 (14)C15—C14—C13119.6 (2)
C6—C5—C4116.56 (19)C15—C14—H14119.8 (18)
C6—C5—H5120.6 (14)C13—C14—H14120.6 (18)
C4—C5—H5122.8 (14)C14—C15—C16120.7 (2)
C5—C6—N2133.96 (19)C14—C15—H15117.5 (19)
C5—C6—C1121.92 (18)C16—C15—H15121.8 (19)
N2—C6—C1104.03 (17)C15—C16—C11120.1 (2)
C10—C7—N2131.17 (19)C15—C16—H16121.8 (16)
C10—C7—C8124.17 (19)C11—C16—H16118.1 (16)
N2—C7—C8104.25 (16)
C9—N1—C1—C2179.9 (2)N2—C7—C8—O1178.3 (2)
C9—N1—C1—C61.4 (2)C10—C7—C8—N3167.8 (2)
N1—C1—C2—C3175.2 (2)N2—C7—C8—N35.5 (2)
C6—C1—C2—C33.1 (3)C1—N1—C9—N3176.5 (2)
C1—C2—C3—C40.5 (3)C1—N1—C9—N21.3 (2)
C2—C3—C4—C52.3 (3)C8—N3—C9—N1176.2 (2)
C3—C4—C5—C60.5 (3)C8—N3—C9—N21.6 (2)
C4—C5—C6—N2179.0 (2)C6—N2—C9—N13.5 (2)
C4—C5—C6—C13.1 (3)C7—N2—C9—N1179.52 (17)
C9—N2—C6—C5172.6 (2)C6—N2—C9—N3174.82 (17)
C7—N2—C6—C52.6 (5)C7—N2—C9—N32.2 (2)
C9—N2—C6—C13.9 (2)N2—C7—C10—C115.8 (4)
C7—N2—C6—C1179.1 (3)C8—C7—C10—C11165.6 (2)
C2—C1—C6—C55.0 (3)C7—C10—C11—C1251.9 (3)
N1—C1—C6—C5173.59 (19)C7—C10—C11—C16129.4 (2)
C2—C1—C6—N2177.99 (19)C16—C11—C12—C132.1 (3)
N1—C1—C6—N23.4 (2)C10—C11—C12—C13179.1 (2)
C9—N2—C7—C10168.0 (2)C11—C12—C13—C141.0 (3)
C6—N2—C7—C1016.9 (5)C12—C13—C14—C152.6 (4)
C9—N2—C7—C84.7 (2)C13—C14—C15—C161.0 (4)
C6—N2—C7—C8170.4 (3)C14—C15—C16—C112.2 (4)
C9—N3—C8—O1179.3 (2)C12—C11—C16—C153.7 (3)
C9—N3—C8—C74.5 (2)C10—C11—C16—C15177.6 (2)
C10—C7—C8—O18.3 (4)
Hydrogen-bond geometry (Å, º) top
Cg3 and Cg4 are the centroids of the C1–C6 and C11–C16 rings, respectively.
D—H···AD—HH···AD···AD—H···A
N3—H3A···N1i0.93 (3)1.98 (3)2.876 (2)162 (3)
C16—H16···O1ii1.01 (3)2.58 (3)3.412 (3)139 (2)
C5—H5···Cg41.01 (3)2.65 (3)3.512 (2)143 (3)
C10—H10···Cg4iii1.01 (3)2.88 (2)3.606 (2)129.0 (15)
C13—H13···Cg3iv1.00 (3)2.73 (3)3.474 (2)132 (2)
Symmetry codes: (i) x+2, y+1, z; (ii) x1, 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.

References

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