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

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ISSN: 2056-9890
Volume 67| Part 5| May 2011| Page o1083

3-[2-(1H-1,3-Benzo­diazol-2-yl)eth­yl]-1,3-oxazolidin-2-one

aDipartimento di Chimica Inorganica Chimica Analitica e Chimica Fisica, Universitá degli Studi di Messina, Via Salita Sperone 31, I-98166 Vill. S. Agata - Messina, Italy, and bDipartimento Farmaco-Chimico, Università di Messina, Viale Annunziata, 98168, Messina, Italy
*Correspondence e-mail: gbrancatelli@unime.it

(Received 18 February 2011; accepted 1 April 2011; online 13 April 2011)

In the title compound, C12H13N3O2, the dihedral angle between the oxazolone ring and the benzimidazole unit is 45.0 (5)°, exhibiting a staggered conformation at the Cα—Cβ bond. In the crystal, a strong N—H⋯N hydrogen bond links the mol­ecules into a C(4) chain along the c axis while a C—H⋯O hydrogen-bonding inter­action generates a C(5) chain along the a axis, i.e. perpendicular to the other chain.

Related literature

For the therapeutic activity of benzimidazole and oxazolid­in­one derivatives, see: Niño et al. 2001[Niño, V. M., Daza, C. E. & Tello, M. (2001). J. Chem. Inf. Comput. Sci. 41, 495-504.]; Siva Kumar et al. 2010[Siva Kumar, R., Kumarnallasivan, P., Vijai Anand, P. R., Pradeepchandran, R., Jayaveera, K. N. & Venkatnarayanan, R. (2010). Pharma Chem. 2, 100-108.]; Zappia et al. 2007[Zappia, G., Gacs-Baitz, E., Delle Monache, G., Misiti, D., Nevola, L. & Botta, B. (2007). Curr. Org. Synth. 4, 81-135.]. For the drug linezolid [systematic name (S)-N-({3-[3-fluoro-4-(morpholin-4-yl)phen­yl]-2-oxo-1,3-oxazolidin-5-yl}meth­yl)acetamide], see: Brickner et al. (2008[Brickner, S. J., Barbachyn, M. R., Hutchinson, D. K. & Manninen, P. R. (2008). J. Med. Chem. 51, 1981-1990.]). For asymmetry of the exocyclic angles in oxazolone rings, see: Grassi et al. (2001[Grassi, G., Bruno, G., Risitano, F., Foti, F., Caruso, F. & Nicolò, F. (2001). Eur. J. Org. Chem. pp. 4671-4678.]). For the structures of benzimidazole and oxazolidine, see: Totsatitpaisan et al. (2008[Totsatitpaisan, P., Tashiro, K. & Chirachanchai, S. (2008). J. Phys. Chem. A, 112, 10348-10358.]); Wouters et al. (1997[Wouters, J., Ooms, F. & Durant, F. (1997). Acta Cryst. C53, 895-897.]).

[Scheme 1]

Experimental

Crystal data
  • C12H13N3O2

  • Mr = 231.25

  • Monoclinic, P 21 /c

  • a = 6.0940 (2) Å

  • b = 18.1570 (6) Å

  • c = 10.0740 (3) Å

  • β = 90.696 (1)°

  • V = 1114.59 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 296 K

  • 0.51 × 0.43 × 0.21 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • 34135 measured reflections

  • 1951 independent reflections

  • 1830 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.033

  • wR(F2) = 0.089

  • S = 1.05

  • 1951 reflections

  • 155 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯N8i 0.86 2.08 2.8959 (13) 158
C11—H11A⋯O14ii 0.97 2.53 3.2876 (16) 135
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) x-1, y, z.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Heterocyclic compounds containing 5- or 6-membered rings are important for their diverse biological activities. In particular, the chemistry of oxazolidinone and benzimidazole has received considerable attention owing to their synthetic and biological importance.

Benzimidazole and oxazolidinone derivatives have been studied for the treatment of different pathologies. Their scaffold has been incorporated into a wide variety of therapeutically interesting compounds that show antibacterial, antifungal, antiviral, antineoplastics and cholinergic activity among others (Niño et al., 2001; Siva Kumar et al., 2010; Zappia et al., 2007). Furthermore, the introduction in the pharmaceutical market of Linezolid, an oxazolidin-2-one-based antibacterial drug, attracted the interest of the scientists on this scaffold (Brickner et al., 2008). On the basis of some common properties, such as antibacterial activity, of these two classes of heterocyclic compounds, in this study we synthesized the title molecule, in which the benzimidazole ring is linked to an oxazolidinone scaffold, with the aim to obtain a compound having two different moieties in the same molecular entity, and then a synergism of activity.

The one-pot synthetic route employed to obtain the title compound is depicted in Figure 1. Treatment of the commercially available 2-(2-aminoethyl)-benzimidazole dihydrochloride with dibromoethane and potassium carbonate gave the desired product. The proposed mechanism for the synthesis is shown in Figure 2. The nucleophilic attack of the 2-(2-aminoethyl)-benzimidazole primary amine function on the dibromoethane is followed by oxazolidinone ring formation. An excess of potassium carbonate is necessary both to create the basic medium for the N-alkylation and for the formation of the oxazolidinone moiety.

The molecule crystallizes in the centrosymmetric P21/c space group. The asymmetric unit contains one molecule, shown in Figure 3. The dihedral angle between the oxazolone ring and the benzimidazole unit is 45.0 (5)°, exhibiting a staggered conformation at the Cα—Cβ bond. The carbonyl fragment displays pronounced asymmetry at the exo-cyclic angles, being N12—C13—O14 and O14—C13—O15 of 128.4 (1)° and 121.9 (1)°, respectively, because of both electronic and steric factors due to the presence of different atoms bound to C13 (Grassi et al., 2001). The dimensions within the benzimidazole and the oxazolidine moieties are in excellent agreement with those found in the benzimidazole and oxazolidine crystal structures (Totsatitpaisan et al., 2008; Wouters et al., 1997).

Packing analysis of the crystal lattice indicates that the tridimensional molecular arrangement is ruled by many H-bonding interactions. A strong H-bond N1—H1···N8 gives rise to a molecular chain [C(4)] along the c axis (Figure 4). Another H-bonding interaction C11—H11···O14 generates a chain [C(5)] along the a axis, perpendicular to the previous one.

Related literature top

For the therapeutic activity of benzimidazole and oxazolidinone derivatives, see: Niño et al. 2001; Siva Kumar et al. 2010; Zappia et al. 2007. For the drug linezolid [systematic name (S)-N-({3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide], see: Brickner et al. (2008). For asymmetry of the exocyclic angles in oxazolone rings, see: Grassi et al. (2001). For the structures of benzimidazole and oxazolidine, see: Totsatitpaisan et al. (2008); Wouters et al. (1997).

Experimental top

A solution of dibromoethane (3 mmol, 0.258 ml) in ethyl acetate (2 ml) was added over 10 minutes to a stirred mixture of 2-(2-aminoethyl)-benzimidazole dihydrochloride (1 mmol, 0.234 g), potassium carbonate (10 mmol, 1.38 g), ethyl acetate (5 ml) and water (2 ml). After the reaction mixture was refluxed for 36 h, the two phases were separated and the aqueous layer was extracted with ethyl acetate (2 x 5 ml). The combined organic phases were dried over anhydrous Na2SO4, filtered and concentrated. Elution with a mixture of chloroform and methanol (99:1) gave the title molecule as colourless crystals (yield: 30%). 1H-NMR (CDCl3, 300 MHz) δ 3.30 (t, J = 6.59, 2H, CH2), 3.61 (t, J = 6.71, 2H, CH2), 3.83 (t, J = 6.59, 2H, CH2), 4.28–4.34 (t, J = 6.71, 2H, CH2), 7.22–7.25 (m, 4H, Ar), 7.56 (bs, 1H, NH).

Refinement top

H atoms were located in a difference Fourier map and placed in idealized positions using the riding-model technique, with C—H = 0.93 and 0.97Å for aromatic H and methylene H, respectively, and N—H = 0.86Å, and with Uiso(H) = 1.2Ueq(C, N).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Synthesis reaction scheme of the title compound.
[Figure 2] Fig. 2. Mechanism proposed for the synthesis of the title compound.
[Figure 3] Fig. 3. ORTEP drawing of the title molecule. Non H-atoms represented as displacement ellipsoids are plotted at the 50% probability level, while H atoms are shown as small spheres of arbitrary radius. In this view the staggered conformation around the Cα—Cβ bond is visible.
[Figure 4] Fig. 4. Arrangement of the molecules in perpendicular chains. The chain [C(5)] ruled by the C11—H11A···O14 interaction prolongs the crystal packing along the a axis; the other one [C(4)] generated by the N1—H1···N8 interaction is extended along the c axis. Dotted lines indicate H-bonding interactions.
3-[2-(1H-1,3-benzodiazol-2-yl)ethyl]-1,3-oxazolidin-2-one top
Crystal data top
C12H13N3O2F(000) = 488
Mr = 231.25Dx = 1.378 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9799 reflections
a = 6.0940 (2) Åθ = 2.3–30.0°
b = 18.1570 (6) ŵ = 0.10 mm1
c = 10.0740 (3) ÅT = 296 K
β = 90.696 (1)°Prism, colourless
V = 1114.59 (6) Å30.51 × 0.43 × 0.21 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
Rint = 0.021
Graphite monochromatorθmax = 25°, θmin = 3.0°
ϕ and ω scansh = 77
34135 measured reflectionsk = 2121
1951 independent reflectionsl = 1111
1830 reflections with I > 2σ(I)
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)] = 0.033H-atom parameters constrained
wR(F2) = 0.089 w = 1/[σ2(Fo2) + (0.0448P)2 + 0.2758P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1951 reflectionsΔρmax = 0.21 e Å3
155 parametersΔρmin = 0.22 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
0 constraintsExtinction coefficient: 0.031 (3)
Primary atom site location: structure-invariant direct methods
Crystal data top
C12H13N3O2V = 1114.59 (6) Å3
Mr = 231.25Z = 4
Monoclinic, P21/cMo Kα radiation
a = 6.0940 (2) ŵ = 0.10 mm1
b = 18.1570 (6) ÅT = 296 K
c = 10.0740 (3) Å0.51 × 0.43 × 0.21 mm
β = 90.696 (1)°
Data collection top
Bruker APEXII CCD
diffractometer
1830 reflections with I > 2σ(I)
34135 measured reflectionsRint = 0.021
1951 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0330 restraints
wR(F2) = 0.089H-atom parameters constrained
S = 1.05Δρmax = 0.21 e Å3
1951 reflectionsΔρmin = 0.22 e Å3
155 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C20.68193 (19)0.18737 (6)0.48419 (11)0.0360 (3)
C30.8441 (2)0.14478 (8)0.54393 (13)0.0495 (3)
H30.84940.13750.63530.059*
C40.9971 (2)0.11369 (8)0.46129 (15)0.0556 (4)
H41.10780.08450.49780.067*
C50.9903 (2)0.12476 (8)0.32465 (15)0.0523 (4)
H51.09710.10320.27220.063*
C60.8292 (2)0.16686 (7)0.26555 (12)0.0452 (3)
H60.8250.17390.17410.054*
C70.67213 (19)0.19869 (6)0.34697 (11)0.0350 (3)
C90.40064 (19)0.25761 (6)0.42951 (11)0.0352 (3)
C100.2094 (2)0.30701 (7)0.44963 (13)0.0439 (3)
H10A0.11520.2860.51670.053*
H10B0.12520.31040.36750.053*
C110.2802 (2)0.38413 (7)0.49276 (13)0.0439 (3)
H11A0.15170.41190.51870.053*
H11B0.37660.38020.56980.053*
C130.6099 (2)0.43147 (7)0.38402 (14)0.0457 (3)
C160.4669 (3)0.49106 (10)0.20459 (17)0.0682 (5)
H16A0.46730.46730.11840.082*
H16B0.4550.54390.19170.082*
C170.2788 (3)0.46309 (11)0.28639 (17)0.0693 (5)
H17A0.1930.50330.32210.083*
H17B0.18350.43080.2350.083*
N10.50576 (16)0.22534 (6)0.53358 (9)0.0379 (3)
H10.46890.22810.61560.045*
N80.49276 (16)0.24297 (6)0.31510 (9)0.0376 (3)
N120.39262 (16)0.42375 (6)0.38915 (11)0.0440 (3)
O140.74742 (17)0.40717 (7)0.45882 (13)0.0730 (4)
O150.66295 (17)0.47348 (6)0.27768 (11)0.0606 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C20.0400 (6)0.0367 (6)0.0314 (6)0.0057 (5)0.0019 (5)0.0004 (5)
C30.0553 (8)0.0536 (8)0.0394 (7)0.0006 (6)0.0045 (6)0.0092 (6)
C40.0496 (8)0.0541 (8)0.0630 (9)0.0100 (6)0.0035 (7)0.0054 (7)
C50.0466 (7)0.0547 (8)0.0558 (8)0.0051 (6)0.0086 (6)0.0087 (6)
C60.0471 (7)0.0533 (8)0.0352 (6)0.0018 (6)0.0067 (5)0.0050 (5)
C70.0379 (6)0.0370 (6)0.0300 (6)0.0057 (5)0.0017 (5)0.0015 (4)
C90.0360 (6)0.0383 (6)0.0315 (6)0.0071 (5)0.0025 (5)0.0013 (5)
C100.0346 (6)0.0494 (7)0.0478 (7)0.0031 (5)0.0067 (5)0.0006 (6)
C110.0395 (7)0.0483 (7)0.0440 (7)0.0040 (5)0.0050 (5)0.0045 (5)
C130.0392 (7)0.0457 (7)0.0521 (7)0.0010 (5)0.0014 (6)0.0063 (6)
C160.0762 (11)0.0666 (10)0.0618 (10)0.0016 (8)0.0012 (8)0.0156 (8)
C170.0548 (9)0.0894 (12)0.0634 (10)0.0038 (8)0.0136 (7)0.0212 (9)
N10.0433 (6)0.0459 (6)0.0246 (5)0.0031 (4)0.0056 (4)0.0011 (4)
N80.0386 (5)0.0459 (6)0.0283 (5)0.0023 (4)0.0020 (4)0.0011 (4)
N120.0341 (5)0.0451 (6)0.0527 (6)0.0013 (4)0.0023 (5)0.0048 (5)
O140.0389 (6)0.0963 (9)0.0835 (8)0.0045 (5)0.0103 (5)0.0128 (7)
O150.0534 (6)0.0681 (7)0.0605 (6)0.0114 (5)0.0104 (5)0.0016 (5)
Geometric parameters (Å, º) top
C2—N11.374 (2)C10—H10A0.97
C2—C31.387 (2)C10—H10B0.97
C2—C71.398 (2)C11—N121.447 (2)
C3—C41.378 (2)C11—H11A0.97
C3—H30.93C11—H11B0.97
C4—C51.391 (2)C13—O141.204 (2)
C4—H40.93C13—N121.333 (2)
C5—C61.374 (2)C13—O151.357 (2)
C5—H50.93C16—O151.432 (2)
C6—C71.3934 (17)C16—C171.508 (2)
C6—H60.93C16—H16A0.97
C7—N81.391 (2)C16—H16B0.97
C9—N81.315 (2)C17—N121.430 (2)
C9—N11.355 (2)C17—H17A0.97
C9—C101.487 (2)C17—H17B0.97
C10—C111.5269 (19)N1—H10.86
N1—C2—C3132.72 (11)N12—C11—H11A109.1
N1—C2—C7105.08 (10)C10—C11—H11A109.1
C3—C2—C7122.20 (12)N12—C11—H11B109.1
C4—C3—C2116.75 (12)C10—C11—H11B109.1
C4—C3—H3121.6H11A—C11—H11B107.8
C2—C3—H3121.6O14—C13—N12128.4 (1)
C3—C4—C5121.75 (13)O14—C13—O15121.9 (1)
C3—C4—H4119.1N12—C13—O15109.6 (1)
C5—C4—H4119.1O15—C16—C17106.2 (1)
C6—C5—C4121.43 (13)O15—C16—H16A110.5
C6—C5—H5119.3C17—C16—H16A110.5
C4—C5—H5119.3O15—C16—H16B110.5
C5—C6—C7117.89 (12)C17—C16—H16B110.5
C5—C6—H6121.1H16A—C16—H16B108.7
C7—C6—H6121.1N12—C17—C16101.45 (13)
N8—C7—C6130.32 (11)N12—C17—H17A111.5
N8—C7—C2109.70 (10)C16—C17—H17A111.5
C6—C7—C2119.98 (11)N12—C17—H17B111.5
N8—C9—N1112.8 (1)C16—C17—H17B111.5
N8—C9—C10125.8 (1)H17A—C17—H17B109.3
N1—C9—C10121.3 (1)C9—N1—C2107.50 (9)
C9—C10—C11111.88 (10)C9—N1—H1126.2
C9—C10—H10A109.2C2—N1—H1126.2
C11—C10—H10A109.2C9—N8—C7104.90 (10)
C9—C10—H10B109.2C13—N12—C17113.11 (12)
C11—C10—H10B109.2C13—N12—C11124.01 (11)
H10A—C10—H10B107.9C17—N12—C11122.74 (11)
N12—C11—C10112.67 (10)C13—O15—C16109.01 (11)
N1—C2—C3—C4179.30 (13)C3—C2—N1—C9179.94 (13)
C7—C2—C3—C40.01 (19)C7—C2—N1—C90.55 (12)
C2—C3—C4—C50.4 (2)N1—C9—N8—C70.69 (13)
C3—C4—C5—C60.5 (2)C10—C9—N8—C7176.10 (11)
C4—C5—C6—C70.3 (2)C6—C7—N8—C9179.88 (12)
C5—C6—C7—N8179.73 (12)C2—C7—N8—C90.32 (13)
C5—C6—C7—C20.05 (18)O14—C13—N12—C17177.42 (16)
N1—C2—C7—N80.15 (13)O15—C13—N12—C172.03 (17)
C3—C2—C7—N8179.62 (11)O14—C13—N12—C111.5 (2)
N1—C2—C7—C6179.68 (11)O15—C13—N12—C11177.92 (11)
C3—C2—C7—C60.20 (18)C16—C17—N12—C135.96 (19)
N8—C9—C10—C1197.20 (14)C16—C17—N12—C11178.09 (13)
N1—C9—C10—C1179.34 (14)C10—C11—N12—C13101.12 (15)
C9—C10—C11—N1268.0 (1)C10—C11—N12—C1783.38 (16)
O15—C16—C17—N127.44 (18)O14—C13—O15—C16177.27 (14)
N8—C9—N1—C20.81 (13)N12—C13—O15—C163.24 (16)
C10—C9—N1—C2176.15 (10)C17—C16—O15—C136.84 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N8i0.862.082.8959 (13)158
C11—H11A···O14ii0.972.533.2876 (16)135
C11—H11B···O140.972.582.9019 (16)100
C3—H3···O15i0.932.733.3820 (17)128
C5—H5···O15iii0.932.823.6229 (17)145
C6—H6···O14iv0.932.663.4008 (17)137
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x1, y, z; (iii) x+2, y1/2, z+1/2; (iv) x, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC12H13N3O2
Mr231.25
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)6.0940 (2), 18.1570 (6), 10.0740 (3)
β (°) 90.696 (1)
V3)1114.59 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.51 × 0.43 × 0.21
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
34135, 1951, 1830
Rint0.021
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.033, 0.089, 1.05
No. of reflections1951
No. of parameters155
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.21, 0.22

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N8i0.862.082.8959 (13)157.9
C11—H11A···O14ii0.972.533.2876 (16)134.9
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x1, y, z.
 

Acknowledgements

The authors thank the University of Messina and the MIUR (Ministero dell'Istruzione, dell'Universitá e della Ricerca) for financial support.

References

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Volume 67| Part 5| May 2011| Page o1083
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