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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoIUCrDATA
ISSN: 2414-3146
Volume 1| Part 12| December 2016| x161895
https://doi.org/10.1107/S2414314616018952

3-[2-(2-Amino-1H-benzo[d]imidazol-1-yl)eth­yl]-1,3-oxazolidin-2-one

CROSSMARK_Color_square_no_text.svg
Abdellatif Bouayyadi,a,b* Ahmed Moussaif,b Abdelhalim Mesfioui,a Mohammed Mzibri,b Mohamed Saadic and Lahcen El Ammaric

aLaboratory of Genetic, Endocrinology and Biotechnology–Faculty of Sciences, Ibn Tofaïl University, Kenitra, Morocco, bNational Center of Energy Sciences and Nuclear Techniques, Rabat, Morocco, and cLaboratoire de Chimie du Solide Appliquée, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, Rabat, Morocco
*Correspondence e-mail: abouayyadi@yahoo.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 25 November 2016; accepted 27 November 2016; online 2 December 2016)

In the title compound, C12H14N4O2, the benzimidazole ring is almost planar (r.m.s. deviation = 0.03 Å), with the fused ring system slightly folded at the shared atoms, with a dihedral angle of 3.4 (1)°. The oxazolidinone ring displays a twisted conformation on the –CH2–CH2– bond and its mean plane makes a dihedral angle of 57.4 (1)° with the benzimidazole ring mean plane. In the crystal, mol­ecules are linked by N—H⋯O and N—H⋯N hydrogen bonds, forming chains propagating along the a-axis direction. The chains are linked by C—H⋯O and C—H⋯N hydrogen bonds, forming a three-dimensional structure, which is reinforced by C—H⋯π inter­actions.

CCDC reference: 1519450

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

Structure description

Mol­ecules containing an heterocycle, include compounds with organic, chemical and many pharmacological inter­ests (Komeilizadeh, 2006[Komeilizadeh, H. (2006). Iranian J. Pharm. Res. 5, 229-230.]). Two-thirds of organic compounds, known in the literature, are heterocyclic (Brandi et al., 2003[Brandi, A., Cicchi, S., Cordero, F. M. & Goti, A. (2003). Chem. Rev. 103, 1213-1270.]; Ansar et al., 2009[Ansar, M., Zellou, A., Faouzi, M. E. A., Zahidi, A., Serroukh, S., Lmimouni, B. E., Cherrah, Y. & Taoufik, J. (2009). Annales Pharmaceutiques Françaises, 67, 78-83.]). Benzimid­azole and oxazoline derivatives have attracted considerable inter­est because of their important biological activities, such as anti­depressant and anxiolytic (Ahabchane et al., 1999[Ahabchane, N. H., Keita, A. & Essassi, E. M. (1999). C. R. Acad. Sci. Ser. IIc, 2, 519-523.], 2000[Ahabchane, N. H., Essassi, E. M., Lopez, L., Bellan, J. & Lamandé, L. (2000). C. R. Acad. Sci. Ser. IIc Chem. 3, 313-319.]; Alinezhad et al., 2013[Alinezhad, H., Tajbakhsh, M., Rouzi, M. & Baghery, S. (2013). World Appl. Sci. J. 22, 1711-1717.]; Ansari & Lal, 2009[Ansari, K. F. & Lal, C. (2009). Eur. J. Med. Chem. 44, 2294-2299.]). The importance of these pharmacological activities encouraged us to combine both benzimidazole and oxazoline units in one mol­ecule and to assess their toxicity (acute and chronic), and also their psychotropic activity. It involves the synthesis by the transfer phase catalysis (PTC) of a novel benzimidazole derivative from 2-amino-benzimidazole, combined with an oxazolidin-2-one unit.

The title compound, Fig. 1[link], is build up from an amino-benzimidazole ring linked to an oxazolidin-2-on through an ethylene group. The benzimidazole ring is virtually planar with the maximum deviation from the mean plane being 0.037 (2) Å for atom C7. The oxazoline ring displays a twisted conformation on the C10–C11 bond [puckering amplitude Q2 = 0.107 (3) Å, and the spherical polar angle φ2 = 50.5 (2)°]. The dihedral angle between the mean planes of the benzimidazole system and the oxazoline ring is 57.4 (1)°.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

In the crystal, mol­ecules are linked by N—H⋯O and N—H⋯N hydrogen bonds, forming chains propagating along the a-axis direction (Fig. 2[link] and Table 1[link]). The chains are linked by C—H⋯O and C—H⋯N hydrogen bonds, forming a three-dimensional structure, which is reinforced by C—H⋯π inter­actions (Fig. 2[link] and Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of C1–C6 ring.
D—H⋯A D—H H⋯A D⋯A D—H⋯A
N3—H3A⋯O2i 0.86 2.29 2.994 (2) 140
N3—H3B⋯N1ii 0.86 2.39 3.020 (2) 131
C8—H8A⋯O1iii 0.97 2.49 3.410 (3) 158
C8—H8B⋯N1ii 0.97 2.50 3.425 (2) 159
C9—H9A⋯Cg1iv 0.97 2.80 3.571 (2) 137
C11—H11B⋯Cg1v 0.97 2.80 3.730 (3) 161
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (ii) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z]; (iii) [-x+1, -y+1, z-{\script{1\over 2}}]; (iv) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z]; (v) [-x+{\script{3\over 2}}, y-{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A view along the b axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines (see Table 1[link]) and, for clarity, only the H atoms involved in hydrogen bonding have been included.

Synthesis and crystallization

Phase transfer catalysis (PTC) is a well established technique, widely used in synthetic chemistry and applied in many industrial processes. Here, we present the principle of the PTC and its benefits for the development of more eco-friendly processes. The alkyl­ation reaction, from the starting product of 2-amino-benzimidazole, was carried out under the same reaction conditions, to form an oxazolidin-2-one unit, which was alkyl­ated to the benzimidazole unit.

To the solution of 2-amino-benzimidazole (1.35 g, 9 mmol) and di­chloro­ethyl amine hydro­chloride (2.41 g, 13.5 mmol) in di­methyl­formamide (80 ml) were added potassium carbonate (4.14 g, 30 mmol) and tetra-n-butyl­ammonium bromide (0.10 g, 0.3 mmol). The resulting mixture was refluxed for 4 h, then filtered and the solvent removed. The residue was purified by column chromatography on silica gel (hexa­ne/AcOEt: 60/40) to afford the title compound (Yield 70%, m.p. 504 K). 1H NMR (dppm): 3.35: SCH2 (2H, t, J = 6.3 Hz); 3.37: NCH2 (4H, m); 4.16: OCH2 (2H, t, J = 6.6 Hz); 7.09–7.12: CH-benzenic (4H, m); 12.54: NH (1H, s).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C12H14N4O2
Mr 246.27
Crystal system, space group Orthorhombic, Pna21
Temperature (K) 296
a, b, c (Å) 9.0504 (2), 9.0612 (1), 14.3565 (2)
V (Å3) 1177.34 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.44 × 0.34 × 0.26
 
Data collection
Diffractometer Bruker X8 APEX
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.663, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 46121, 3320, 3097
Rint 0.034
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.100, 1.07
No. of reflections 3320
No. of parameters 163
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.20, −0.24
Absolute structure Flack x determined using 1380 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter −0.3 (3)
Computer programs: APEX2 and SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), ORTEPIII (Burnett & Johnson, 1996[Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII. Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.]), ORTEP-3 Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Structural data

CCDC reference: 1519450

Crystal structure: contains datablocks I, Global. DOI: https://doi.org/10.1107/S2414314616018952/su4100sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314616018952/su4100Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314616018952/su4100Isup3.cml

checkCIF report


Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 Farrugia, 2012) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015b), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

3-[2-(2-Amino-1H-benzo[d]imidazol-1-yl)ethyl]-1,3-oxazolidin-2-one top
Crystal data top
C12H14N4O2Dx = 1.389 Mg m−3
Mr = 246.27Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna21Cell parameters from 3320 reflections
a = 9.0504 (2) Åθ = 2.7–29.6°
b = 9.0612 (1) ŵ = 0.10 mm−1
c = 14.3565 (2) ÅT = 296 K
V = 1177.34 (3) Å3Block, colourless
Z = 40.44 × 0.34 × 0.26 mm
F(000) = 520
Data collection top
Bruker X8 APEX
diffractometer		3320 independent reflections
Radiation source: fine-focus sealed tube3097 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
φ and ω scansθmax = 29.6°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		h = −12→12
Tmin = 0.663, Tmax = 0.746k = −12→12
46121 measured reflectionsl = −19→19
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.035H-atom parameters constrained
wR(F2) = 0.100 w = 1/[σ2(Fo2) + (0.0582P)2 + 0.1462P]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
3320 reflectionsΔρmax = 0.20 e Å−3
163 parametersΔρmin = −0.24 e Å−3
1 restraintAbsolute structure: Flack x determined using 1380 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: −0.3 (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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.98692 (19)0.55021 (18)0.54222 (14)0.0305 (3)
C21.1216 (2)0.5197 (2)0.49961 (18)0.0408 (4)
H21.20960.55670.52370.049*
C31.1210 (3)0.4324 (2)0.42002 (19)0.0480 (5)
H31.21020.41100.39080.058*
C40.9909 (3)0.3764 (2)0.38293 (17)0.0479 (5)
H40.99470.31770.32980.057*
C50.8550 (2)0.4067 (2)0.42404 (15)0.0396 (4)
H50.76740.36980.39950.047*
C60.85612 (19)0.49410 (19)0.50313 (13)0.0292 (3)
C70.80874 (18)0.63783 (18)0.62457 (12)0.0276 (3)
C80.58530 (19)0.5271 (2)0.54381 (13)0.0318 (4)
H8A0.56350.53170.47770.038*
H8B0.53050.60550.57430.038*
C90.5335 (2)0.3792 (2)0.58184 (13)0.0346 (4)
H9A0.42740.37180.57370.042*
H9B0.57880.30090.54570.042*
C100.6839 (4)0.2609 (4)0.7117 (2)0.0633 (8)
H10A0.78060.29720.69360.076*
H10B0.67120.16120.68840.076*
C110.6626 (4)0.2679 (3)0.8156 (2)0.0661 (8)
H11A0.62340.17530.83890.079*
H11B0.75570.28790.84660.079*
C120.5022 (2)0.4301 (2)0.74885 (15)0.0357 (4)
N10.95466 (16)0.63860 (17)0.61871 (12)0.0322 (3)
N20.74285 (16)0.55200 (16)0.55759 (10)0.0285 (3)
N30.73039 (18)0.71167 (19)0.69026 (12)0.0362 (3)
H3A0.77560.76320.73170.043*
H3B0.63550.70690.69050.043*
N40.56840 (19)0.35663 (18)0.67963 (12)0.0337 (3)
O10.5596 (3)0.3860 (2)0.83151 (12)0.0560 (5)
O20.4053 (2)0.52092 (19)0.74365 (15)0.0548 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0284 (8)0.0282 (7)0.0350 (9)−0.0007 (6)0.0017 (7)0.0036 (7)
C20.0310 (8)0.0388 (9)0.0526 (12)0.0001 (7)0.0087 (9)0.0003 (9)
C30.0476 (12)0.0429 (10)0.0534 (13)0.0076 (9)0.0210 (10)0.0027 (10)
C40.0621 (14)0.0433 (10)0.0383 (11)0.0036 (10)0.0122 (10)−0.0042 (9)
C50.0464 (11)0.0388 (9)0.0335 (9)−0.0026 (8)0.0000 (8)−0.0018 (8)
C60.0301 (7)0.0289 (7)0.0286 (8)−0.0002 (6)0.0030 (7)0.0041 (6)
C70.0263 (7)0.0289 (7)0.0276 (7)−0.0008 (6)−0.0032 (6)0.0024 (6)
C80.0257 (7)0.0387 (8)0.0312 (9)−0.0022 (6)−0.0056 (7)0.0034 (7)
C90.0317 (8)0.0397 (9)0.0325 (9)−0.0070 (7)−0.0013 (7)−0.0038 (7)
C100.0683 (17)0.0687 (17)0.0529 (13)0.0356 (14)−0.0008 (13)0.0052 (12)
C110.093 (2)0.0564 (15)0.0491 (14)0.0210 (15)−0.0150 (15)0.0098 (12)
C120.0363 (9)0.0335 (8)0.0373 (9)−0.0036 (7)0.0085 (8)−0.0001 (8)
N10.0249 (6)0.0339 (7)0.0377 (8)−0.0011 (6)−0.0009 (6)−0.0027 (6)
N20.0240 (6)0.0331 (7)0.0282 (7)−0.0026 (5)−0.0008 (5)−0.0002 (5)
N30.0268 (7)0.0458 (8)0.0362 (8)0.0023 (6)−0.0011 (6)−0.0089 (7)
N40.0347 (8)0.0340 (7)0.0325 (8)0.0049 (6)0.0030 (6)0.0008 (6)
O10.0754 (12)0.0597 (10)0.0330 (7)0.0104 (9)0.0072 (8)0.0016 (7)
O20.0462 (8)0.0498 (9)0.0685 (12)0.0139 (7)0.0149 (9)−0.0051 (8)
Geometric parameters (Å, º) top
C1—N11.390 (3)C8—H8A0.9700
C1—C21.392 (3)C8—H8B0.9700
C1—C61.405 (2)C9—N41.453 (3)
C2—C31.390 (4)C9—H9A0.9700
C2—H20.9300C9—H9B0.9700
C3—C41.388 (4)C10—N41.434 (3)
C3—H30.9300C10—C111.506 (4)
C4—C51.392 (3)C10—H10A0.9700
C4—H40.9300C10—H10B0.9700
C5—C61.384 (3)C11—O11.437 (3)
C5—H50.9300C11—H11A0.9700
C6—N21.392 (2)C11—H11B0.9700
C7—N11.323 (2)C12—O21.206 (3)
C7—N31.356 (2)C12—N41.337 (3)
C7—N21.373 (2)C12—O11.356 (3)
C8—N21.457 (2)N3—H3A0.8600
C8—C91.522 (3)N3—H3B0.8600
N1—C1—C2130.21 (18)N4—C9—H9B108.8
N1—C1—C6110.30 (15)C8—C9—H9B108.8
C2—C1—C6119.38 (18)H9A—C9—H9B107.7
C3—C2—C1118.1 (2)N4—C10—C11101.5 (2)
C3—C2—H2121.0N4—C10—H10A111.5
C1—C2—H2121.0C11—C10—H10A111.5
C4—C3—C2121.8 (2)N4—C10—H10B111.5
C4—C3—H3119.1C11—C10—H10B111.5
C2—C3—H3119.1H10A—C10—H10B109.3
C3—C4—C5121.0 (2)O1—C11—C10105.8 (2)
C3—C4—H4119.5O1—C11—H11A110.6
C5—C4—H4119.5C10—C11—H11A110.6
C6—C5—C4117.0 (2)O1—C11—H11B110.6
C6—C5—H5121.5C10—C11—H11B110.6
C4—C5—H5121.5H11A—C11—H11B108.7
C5—C6—N2132.14 (17)O2—C12—N4128.3 (2)
C5—C6—C1122.73 (17)O2—C12—O1122.3 (2)
N2—C6—C1105.05 (16)N4—C12—O1109.41 (17)
N1—C7—N3124.29 (17)C7—N1—C1104.88 (15)
N1—C7—N2113.07 (16)C7—N2—C6106.68 (14)
N3—C7—N2122.63 (15)C7—N2—C8127.43 (15)
N2—C8—C9112.90 (15)C6—N2—C8125.88 (15)
N2—C8—H8A109.0C7—N3—H3A120.0
C9—C8—H8A109.0C7—N3—H3B120.0
N2—C8—H8B109.0H3A—N3—H3B120.0
C9—C8—H8B109.0C12—N4—C10112.89 (19)
H8A—C8—H8B107.8C12—N4—C9123.40 (17)
N4—C9—C8113.80 (16)C10—N4—C9123.59 (19)
N4—C9—H9A108.8C12—O1—C11109.20 (18)
C8—C9—H9A108.8
N1—C1—C2—C3−176.61 (19)N1—C7—N2—C8−179.77 (16)
C6—C1—C2—C3−0.8 (3)N3—C7—N2—C81.1 (3)
C1—C2—C3—C40.1 (3)C5—C6—N2—C7−176.61 (19)
C2—C3—C4—C50.5 (4)C1—C6—N2—C70.17 (18)
C3—C4—C5—C6−0.2 (3)C5—C6—N2—C82.3 (3)
C4—C5—C6—N2175.75 (19)C1—C6—N2—C8179.11 (16)
C4—C5—C6—C1−0.6 (3)C9—C8—N2—C7−101.4 (2)
N1—C1—C6—C5177.68 (17)C9—C8—N2—C679.8 (2)
C2—C1—C6—C51.1 (3)O2—C12—N4—C10177.6 (3)
N1—C1—C6—N20.51 (19)O1—C12—N4—C10−3.2 (3)
C2—C1—C6—N2−176.04 (17)O2—C12—N4—C91.5 (3)
N2—C8—C9—N455.4 (2)O1—C12—N4—C9−179.31 (18)
N4—C10—C11—O1−10.9 (4)C11—C10—N4—C128.9 (3)
N3—C7—N1—C1−179.78 (16)C11—C10—N4—C9−175.0 (2)
N2—C7—N1—C11.1 (2)C8—C9—N4—C1270.4 (2)
C2—C1—N1—C7175.1 (2)C8—C9—N4—C10−105.2 (3)
C6—C1—N1—C7−1.0 (2)O2—C12—O1—C11174.7 (2)
N1—C7—N2—C6−0.9 (2)N4—C12—O1—C11−4.5 (3)
N3—C7—N2—C6−179.95 (16)C10—C11—O1—C129.9 (4)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of C1–C6 ring.
D—H···AD—HH···AD···AD—H···A
N3—H3A···O2i0.862.292.994 (2)140
N3—H3B···N1ii0.862.393.020 (2)131
C8—H8A···O1iii0.972.493.410 (3)158
C8—H8B···N1ii0.972.503.425 (2)159
C9—H9A···Cg1iv0.972.803.571 (2)137
C11—H11B···Cg1v0.972.803.730 (3)161
Symmetry codes: (i) x+1/2, −y+3/2, z; (ii) x−1/2, −y+3/2, z; (iii) −x+1, −y+1, z−1/2; (iv) x−1/2, −y+1/2, z; (v) −x+3/2, y−1/2, z+1/2.
 

Acknowledgements

The authors thank the Unit of Support for Technical and Scientific Research (UATRS, CNRST) for the X-ray measurements and the Ibn Tofaïl University, Kenitra, Morocco, for financial support.

References

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ISSN: 2414-3146
Volume 1| Part 12| December 2016| x161895
https://doi.org/10.1107/S2414314616018952
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