Crystal structure of 5-chloro-1,3-bis­[2-(2-oxo-1,3-oxazolidin-3-yl)eth­yl]-1H-benz­imidazol-2(3H)-one

Kaoutar Bouayad; Youssef Kandri Rodi; Youness Ouzidan; El Mokhtar Essassi; Mohamed Saadi; Lahcen El Ammari

doi:10.1107/S2056989015016102

. 2015 Sep 12;71(Pt 10):o735–o736. doi: 10.1107/S2056989015016102

Crystal structure of 5-chloro-1,3-bis[2-(2-oxo-1,3-oxazolidin-3-yl)ethyl]-1H-benzimidazol-2(3H)-one

Kaoutar Bouayad ^a,^*, Youssef Kandri Rodi ^b, Youness Ouzidan ^b, El Mokhtar Essassi ^c, Mohamed Saadi ^d, Lahcen El Ammari ^d

PMCID: PMC4647354 PMID: 26594449

Abstract

In the title compound, C₁₇H₁₉ClN₄O₅, the benzimidazole fused-ring system is essentially planar, the maximum deviation from the mean plane being 0.06 (1) Å. Both oxazolidine rings are nearly planar, the maximum deviations from the mean planes are 0.071 (13) and 0.070 (10) Å. The dihedral angle between the mean planes of the oxazolidine rings is 69.9 (7)°. The benzimidazole mean plane makes the dihedral angles of 43.9 (6) and 45.6 (6)° with the two oxazolidine rings. In the crystal, the molecules are linked together by weak C—H⋯O hydrogen bonds building zigzag tapes running along the c axis. The Cl atom is split over two positions with an occupancy ratio of 0.567 (7):0.433 (7). This means that the reaction yields two isomers, A and B; the A component has the Cl-atom substituent in the 5-position of the benzimidazolone ring and the B component has the Cl atom in the 6-position. The two isomers form the disordered co-crystal, with a nearly half Cl atom in each of them, as indicated by the occupancy ratio. The crystal structure was refined as an inversion twin.

Keywords: crystal structure, benzimidazol-2-one derivative, hydrogen bonding

Related literature

For biological properties of benzimidazol-2-one derivatives, see: Gribkoff et al. (1994 ▸); Olesen et al. (1994 ▸); Soderlind et al. (1999 ▸). For antibacterial activity oxazolidin-2-ones, see: Diekema & Jones (2000 ▸); Mukhtar & Wright (2005 ▸). For asymmetric reactions of oxazolidin-2-ones, see: Evans et al. (1993 ▸); Matsunaga et al. (2005 ▸). For oxazolidin-2-one derivatives, see: Ouzidan et al. (2011 ▸); Dardouri et al. (2011 ▸).

Experimental

Crystal data

C₁₇H₁₉ClN₄O₅
M _r = 394.81
Orthorhombic,
a = 14.053 (8) Å
b = 13.438 (6) Å
c = 9.733 (4) Å
V = 1838.1 (15) Å³
Z = 4
Mo Kα radiation
μ = 0.25 mm⁻¹
T = 296 K
0.35 × 0.31 × 0.26 mm

Data collection

Bruker X8 APEX diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▸) T _min = 0.504, T _max = 0.748
9588 measured reflections
3701 independent reflections
1697 reflections with I > 2σ(I)
R _int = 0.052

Refinement

R[F ² > 2σ(F ²)] = 0.057
wR(F ²) = 0.150
S = 1.01
3701 reflections
255 parameters
4 restraints
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.16 e Å⁻³
Absolute structure: Refined as an inversion twin
Absolute structure parameter: 0.5 (5)

Data collection: APEX2 (Bruker, 2009 ▸); cell refinement: SAINT-Plus (Bruker, 2009 ▸); data reduction: SAINT-Plus ; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015 ▸); molecular graphics: ORTEP-3 (Burnett & Johnson, 1996 ▸) and ORTEP-3 for Windows (Farrugia, 2012 ▸); software used to prepare material for publication: PLATON (Spek, 2009 ▸) and publCIF (Westrip, 2010 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989015016102/xu5863sup1.cif

e-71-0o735-sup1.cif^{(459.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015016102/xu5863Isup2.hkl

e-71-0o735-Isup2.hkl^{(295.3KB, hkl)}

Click here for additional data file.^{(7.3KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015016102/xu5863Isup3.cml

Click here for additional data file.^{(1.3MB, tif)}

. DOI: 10.1107/S2056989015016102/xu5863fig1.tif

Molecular plot the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are represented as small circles.

Click here for additional data file.^{(1.5MB, tif)}

c . DOI: 10.1107/S2056989015016102/xu5863fig2.tif

Intermolecular interactions in the title compound building a zigzag tape along c axis. Hydrogen bonds are shown as dashed lines.

CCDC reference: 1421051

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C4H4AO2ⁱ	0.97	2.42	3.247(13)	143
C14H14AO4ⁱⁱ	0.97	2.48	3.315(13)	144

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Symmetry codes: (i) Inline graphic ; (ii) .

supplementary crystallographic information

S1. Comment

Benzimidazol-2-one derivatives are useful heterocyclic building blocks and are prominent structural elements of compounds demonstrating a wide variety of pharmacological and biochemical properties(Gribkoff et al., 1994; Olesen et al., 1994; Soderlind et al., 1999).

Also, oxazolidin-2-ones are a very important class of heterocyclic compounds and their derivatives have attracted attention in various areas of drug development for antibacterial activity (Diekema & Jones, 2000; Mukhtar & Wright, 2005). Some oxazolidin-2-ones have been used as chiral auxiliaries in a wide range of asymmetric reactions (Evans et al., 1993; Matsunaga et al., 2005). In a previous study, we reacted 1H-benzo[d]imidazol-2(3H)-one with bis(2-chloroethyl)amine hydrochloride in the presence of a catalytic quantity of tetra-n-butylammonium bromide to form 1,3-bis(2-(2-oxooxazolidin-3-yl)ethyl)-1H-benzo[d]imidazol-2(3H)-one (Ouzidan et al., 2011). The study is extended to the synthesis of the 5-chloro analog to furnish the title compound (Scheme 1).

The molecule of title compound is build up from a fused five- and six-membered rings linked through ethyl groups, on opposite side, to two 2-oxo-oxazolidin- 3-yl rings as shown in Fig. 1. The chlorine in 5-chloro-benzo[d]imidazol-2(3H) -one is splited in two positions with an occupancy ratio of Cl1B = 0.567 (7) and Cl1A = 0.433 (7). As a matter of fact, we have two isomers that form a disordered co-crystal, like in the 5-Chloro-1-[(E)-3-(dimethylamino)acryloyl]- 3-methyl-1H-benzimidazol-2(3H)-one-6-chloro-1-[(E)-3-(dimethylamino)acryloyl]- 3-methyl-1H-benzimidazol-2(3H)-one(4/1) (Dardouri et al., 2011), but with a nearly half chlorine atom in each of them as shown in the occupancy ratio of Cl1A and Cl1B. The fused rings system (N2N3C6 – C12) is essentially planar with the largest deviation from the mean plane being 0.06 (1) Å at C8 atom. The benzimidazole plane makes dihedral angles of 43.9 (6)° and 45.6 (6)° with the two 2-oxo-oxazolidin-3-yl rings, (O1N1C1-C3) and (O5N4C15-C17), respectively. The dihedral angle between the two 2-oxo-oxazolidin-3-yl rings is of 69.9 (7)°. In the crystal, the molecules are linked together by C4–H4A···O2 and C14–H14A···O4 hydrogen bonds in the way to build a zigzag tape along c axis as shown in Fig. 2 and Table 2.

S2. Experimental

To 5-chloro-1H-benzo[d]imidazol-2(3H)-one (0,2 g, 1.18 mmol), potassium carbonate (0.65 g, 4.74 mmol), and tetra-n-butylammonium bromide (0.05 g, 0,1 mmol) in DMF (15 ml) was added bis(2-chloroethyl)amine hydrochloride (0.52 g, 3 mmol). The mixture was heated for 48 h. After the completion of the reaction (as monitored by TLC), the inorganic material salt was filtered and the solvent was removed under reduced pressure. The residue was purified by column chromatography on silica gel by using (ethanol/ethylacetate: 1/4) as eluent to furnish colourless crystals.