supplementary materials


bt5233 scheme

Acta Cryst. (2010). E66, o1135-o1136    [ doi:10.1107/S1600536810013036 ]

1,3-Bis(ethoxymethyl)-1H-benzimidazole-2(3H)-thione

A. Rivera, A. Mejia-Camacho, J. Ríos-Motta, M. Dusek and K. Fejfarová

Abstract top

In the structure of the title compound, C13H18N2O2S, molecules are linked together by intermolecular C-H...S interactions into one-dimensional extended chains along the a axis. The crystal packing is further influenced by weak C-H...O interactions.

Comment top

Benzimidazole-2-thione and their derivatives exhibit potential applications in many areas such as: pharmacological (Zhang et al. 2001, 2007; Monforte et al. 2008) and industrial (Mazloum et al. 2000; Perrin & Pagetti, 1998). This compound has been synthesized by reaction of o-phenylenediamine with carbon disulfide in presence of KOH (Wang & Liu, 2007 ) or tertiary amines (Wang & Liu,1996). Further substitution of heterocyclic system could be obtained by N-alkylation with an alkylating agent. As a part of our research on the structure and properties of aminals cage, we have recently started a study on the reactivity of 6H,13H-5:12,7:14-dimethanedibenzo-[d,i][1,3,6,8]-tetraazecine (DMDBTA) (Rivera et al., 2008, Rivera & Maldonado 2006). In our recent investigation, when we carried out the reaction between DMDBTA and carbon disulfide in ethyl alcohol, the cyclic thiourea 1,3-bis(ethoxymethyl)-1,3-dihydro-2H-benzimidazole-2-thione was obtained and its crystal structure was determined.

The molecular structure of the title compound, a new benzimidazole-2-thione derivative, is shown in Fig. 1. The bond lengths and angles are within normal ranges and are comparable with the related structures (Odabaşoğlu et al., 2007). The crystal structure is further stabilized by intermolecular C—H···S interactions which link neighbouring molecules into 1-D extended chains along the a axis. The interesting feature of the crystal structure is C—H···S distance (2.88 Å), which is shorter than the sum of the Van der Waals radii of S and H by 0.12 Å. A weak intermolecular C—H···O interaction helps to establish the crystal packing which link neighbouring molecules into 1-D extended chains along the b-axis (Fig. 2). This X-ray analysis also shows that both the C8—O1 [1.406 (2) A] and C11—O2 [1.407 (2) A] bonds appear to be shorter than the normal C—O bond-length, whereas the other C—O bond lengths are more agreement with the typical 1.45 Å. This information indicates that the shortening of these bonds suggests some degrees of double bond character.

Related literature top

For related structures, see: Odabaşoğlu et al. (2007). For applications and uses of benzimidazole-2-thiones, see: Zhang et al. (2001, 2007); Monforte et al. (2008); Mazloum et al. (2000); Perrin & Pagetti (1998). For chemical background on the synthesis of the title compound, see: Wang & Liu (1996, 2007); Rivera et al. (2006, 2008).

Experimental top

A mixture of CS2 (0,95 mmol) and DMDBTA (0,95 mmol) in ethanol (30 ml) was stirred at room temperature for 72 hours. After completion of reaction as monitored by TLC the solvent was distilled off in vacuo. The crude residue was purified by column chromatography over silica gel (60-120 mesh), using benzene:ethyl acetate mixture (80:20) as eluent to give the title compound. A suitable single crystal (m.p. 377-379 K) of the product was formed by slow evaporation of an acetone solution at room temperature.

The NMR spectra were acquired at room temperature on a Bruker AMX 400 Advanced spectrometer. 1H NMR (δ, 399.9 MHz, CDCl3) δ: 1.18 (6H, t, J=6.7 Hz –CH3), 3.64 (4H, q, J= 6.7 Hz, O—CH2-CH3) 5.82 (4H, s, N—CH2—O-), 7.27 (2H, m). 13C NMR (100 MHz, CDCl3) δ: 15.0, 64.9, 74.3, 110.1, 123.7, 131.7, 171.8. MS (ESI): [M+H]+ 267.

Refinement top

All hydrogen atoms were discernible in difference Fourier maps and could be refined to reasonable geometry. According to common practice H atoms attached to C atoms were nevertheless kept in ideal positions during the refinement. The isotropic atomic displacement parameters of hydrogen atoms were evaluated as 1.2*Ueq of the parent atom.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: JANA2006 (Petříček et al., 2006); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al., 2006).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing the atom-numbering scheme, with atomic displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. Packing diagram with two different views; hydrogen bonds drawn as dashed lines.
1,3-Bis(ethoxymethyl)-1H-benzimidazole-2(3H)-thione top
Crystal data top
C13H18N2O2SF(000) = 568
Mr = 266.4Dx = 1.341 Mg m3
Monoclinic, P21/nCu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ynCell parameters from 7933 reflections
a = 4.7176 (2) Åθ = 3.7–62.4°
b = 16.0664 (6) ŵ = 2.14 mm1
c = 17.5128 (6) ÅT = 120 K
β = 96.524 (3)°Needle, colorless
V = 1318.78 (9) Å30.36 × 0.09 × 0.07 mm
Z = 4
Data collection top
Oxford diffraction Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
2096 independent reflections
Radiation source: X-ray tube1718 reflections with I > 3σ(I)
mirrorRint = 0.035
Detector resolution: 10.3784 pixels mm-1θmax = 62.3°, θmin = 3.7°
Rotation method data acquisition using ω scansh = 55
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
k = 1718
Tmin = 0.239, Tmax = 1.000l = 1919
11526 measured reflections
Refinement top
Refinement on F272 constraints
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.110Weighting scheme based on measured s.u.'s w = 1/[σ2(I) + 0.0016I2]
S = 2.09(Δ/σ)max = 0.001
2096 reflectionsΔρmax = 0.40 e Å3
163 parametersΔρmin = 0.20 e Å3
0 restraints
Crystal data top
C13H18N2O2SV = 1318.78 (9) Å3
Mr = 266.4Z = 4
Monoclinic, P21/nCu Kα radiation
a = 4.7176 (2) ŵ = 2.14 mm1
b = 16.0664 (6) ÅT = 120 K
c = 17.5128 (6) Å0.36 × 0.09 × 0.07 mm
β = 96.524 (3)°
Data collection top
Oxford diffraction Xcalibur
diffractometer with an Atlas (Gemini ultra Cu) detector
2096 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
1718 reflections with I > 3σ(I)
Tmin = 0.239, Tmax = 1.000Rint = 0.035
11526 measured reflectionsθmax = 62.3°
Refinement top
R[F2 > 2σ(F2)] = 0.038H-atom parameters constrained
wR(F2) = 0.110Δρmax = 0.40 e Å3
S = 2.09Δρmin = 0.20 e Å3
2096 reflectionsAbsolute structure: ?
163 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. CrysAlisPro, Oxford Diffraction Ltd., Version 1.171.33.51 (release 27-10-2009 CrysAlis171 .NET) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Refinement. The refinement was carried out against all reflections. The conventional R-factor is always based on F. The goodness of fit as well as the weighted R-factor are based on F and F2 for refinement carried out on F and F2, respectively. The threshold expression is used only for calculating R-factors etc. and it is not relevant to the choice of reflections for refinement.

The program used for refinement, Jana2006, uses the weighting scheme based on the experimental expectations, see _refine_ls_weighting_details, that does not force S to be one. Therefore the values of S are usually larger than the ones from the SHELX program.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S10.66272 (9)0.13029 (3)0.10850 (3)0.01931 (18)
O10.2405 (3)0.07593 (7)0.17048 (7)0.0188 (4)
O20.2199 (3)0.33197 (7)0.16433 (7)0.0195 (4)
N10.3657 (3)0.06085 (9)0.21698 (8)0.0149 (5)
N20.3556 (3)0.19758 (9)0.21569 (8)0.0145 (5)
C10.4612 (4)0.12960 (10)0.18039 (10)0.0155 (5)
C20.1990 (4)0.08518 (11)0.27371 (10)0.0146 (5)
C30.1912 (4)0.17210 (11)0.27292 (10)0.0139 (5)
C40.0581 (4)0.03918 (11)0.32458 (10)0.0177 (6)
C50.0933 (4)0.08446 (12)0.37497 (11)0.0208 (6)
C60.0995 (4)0.17090 (12)0.37354 (11)0.0206 (6)
C70.0434 (4)0.21684 (11)0.32276 (10)0.0175 (6)
C80.4585 (4)0.02431 (11)0.20549 (11)0.0176 (6)
C90.1567 (4)0.05799 (11)0.09047 (10)0.0184 (6)
C100.0375 (4)0.12746 (11)0.05950 (11)0.0226 (6)
C110.4382 (4)0.28343 (10)0.20354 (11)0.0175 (6)
C120.1586 (4)0.31173 (12)0.08429 (10)0.0202 (6)
C130.0308 (4)0.37927 (12)0.04732 (12)0.0271 (7)
H40.0639370.0205410.3252880.0212*
H50.1948310.0551950.4111910.0249*
H60.2061350.1998060.4088440.0247*
H70.0395870.2765810.3223320.021*
H8a0.6153690.0239370.1750680.0211*
H8b0.533830.0477670.2540050.0211*
H9a0.3227430.0569050.0634750.0221*
H9b0.0545160.0062290.0859290.0221*
H10a0.1136170.1149920.0075830.0271*
H10b0.0684390.1785480.0604770.0271*
H10c0.1910540.1331560.0906880.0271*
H11a0.501220.3087830.2521590.021*
H11b0.6025470.2843510.175850.021*
H12a0.0601430.2593950.0790390.0242*
H12b0.3332160.310090.0610160.0242*
H13a0.0912550.3646750.0051650.0325*
H13b0.1948050.3854610.074620.0325*
H13c0.072970.4307620.0489060.0325*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0197 (3)0.0185 (3)0.0207 (3)0.00013 (18)0.0067 (2)0.00118 (18)
O10.0274 (7)0.0112 (6)0.0176 (7)0.0036 (5)0.0012 (5)0.0003 (5)
O20.0273 (8)0.0129 (7)0.0181 (7)0.0033 (5)0.0022 (6)0.0001 (5)
N10.0165 (8)0.0109 (8)0.0174 (8)0.0002 (6)0.0020 (6)0.0006 (6)
N20.0164 (8)0.0103 (7)0.0169 (8)0.0000 (6)0.0025 (6)0.0016 (6)
C10.0147 (9)0.0146 (10)0.0164 (9)0.0007 (7)0.0020 (7)0.0016 (7)
C20.0136 (9)0.0145 (9)0.0155 (9)0.0008 (7)0.0003 (7)0.0027 (7)
C30.0128 (9)0.0140 (9)0.0141 (9)0.0018 (7)0.0013 (7)0.0009 (7)
C40.0194 (10)0.0124 (10)0.0205 (10)0.0012 (7)0.0008 (8)0.0005 (7)
C50.0210 (10)0.0232 (10)0.0179 (10)0.0055 (8)0.0015 (8)0.0052 (8)
C60.0211 (10)0.0212 (10)0.0201 (10)0.0027 (8)0.0051 (8)0.0025 (8)
C70.0191 (10)0.0124 (10)0.0205 (10)0.0017 (7)0.0003 (8)0.0009 (7)
C80.0203 (10)0.0106 (9)0.0215 (10)0.0029 (7)0.0006 (8)0.0028 (7)
C90.0219 (10)0.0148 (9)0.0185 (9)0.0028 (7)0.0029 (7)0.0016 (7)
C100.0255 (11)0.0201 (11)0.0216 (10)0.0000 (8)0.0003 (8)0.0013 (8)
C110.0220 (11)0.0115 (9)0.0186 (10)0.0033 (7)0.0007 (7)0.0005 (7)
C120.0244 (11)0.0182 (10)0.0181 (10)0.0043 (8)0.0026 (8)0.0014 (7)
C130.0275 (11)0.0282 (12)0.0246 (11)0.0005 (8)0.0011 (9)0.0036 (8)
Geometric parameters (Å, °) top
S1—C11.6618 (19)C6—H60.96
O1—C81.406 (2)C7—H70.96
O1—C91.441 (2)C8—H8a0.96
O2—C111.407 (2)C8—H8b0.96
O2—C121.436 (2)C9—C101.505 (3)
N1—C11.378 (2)C9—H9a0.96
N1—C21.392 (2)C9—H9b0.96
N1—C81.457 (2)C10—H10a0.96
N2—C11.376 (2)C10—H10b0.96
N2—C31.397 (2)C10—H10c0.96
N2—C111.456 (2)C11—H11a0.96
C2—C31.397 (2)C11—H11b0.96
C2—C41.384 (3)C12—C131.504 (3)
C3—C71.379 (3)C12—H12a0.96
C4—C51.401 (3)C12—H12b0.96
C4—H40.96C13—H13a0.96
C5—C61.389 (3)C13—H13b0.96
C5—H50.96C13—H13c0.96
C6—C71.388 (3)
C8—O1—C9114.35 (13)N1—C8—H8b109.4708
C11—O2—C12113.95 (13)H8a—C8—H8b105.1992
C1—N1—C2110.36 (14)O1—C9—C10106.89 (14)
C1—N1—C8124.70 (15)O1—C9—H9a109.4714
C2—N1—C8124.42 (15)O1—C9—H9b109.4714
C1—N2—C3110.40 (14)C10—C9—H9a109.4711
C1—N2—C11124.75 (15)C10—C9—H9b109.4713
C3—N2—C11124.23 (15)H9a—C9—H9b111.9358
S1—C1—N1127.08 (13)C9—C10—H10a109.4709
S1—C1—N2127.05 (13)C9—C10—H10b109.4709
N1—C1—N2105.86 (15)C9—C10—H10c109.4713
N1—C2—C3106.86 (15)H10a—C10—H10b109.4713
N1—C2—C4131.39 (16)H10a—C10—H10c109.4718
C3—C2—C4121.75 (16)H10b—C10—H10c109.4711
N2—C3—C2106.50 (15)O2—C11—N2113.78 (14)
N2—C3—C7131.54 (16)O2—C11—H11a109.4713
C2—C3—C7121.95 (17)O2—C11—H11b109.4723
C2—C4—C5116.41 (16)N2—C11—H11a109.4702
C2—C4—H4121.7924N2—C11—H11b109.4712
C5—C4—H4121.793H11a—C11—H11b104.7886
C4—C5—C6121.26 (18)O2—C12—C13107.50 (15)
C4—C5—H5119.3691O2—C12—H12a109.4709
C6—C5—H5119.369O2—C12—H12b109.4714
C5—C6—C7122.17 (18)C13—C12—H12a109.4711
C5—C6—H6118.9156C13—C12—H12b109.4711
C7—C6—H6118.916H12a—C12—H12b111.3742
C3—C7—C6116.46 (17)C12—C13—H13a109.4719
C3—C7—H7121.7704C12—C13—H13b109.4712
C6—C7—H7121.771C12—C13—H13c109.471
O1—C8—N1113.43 (14)H13a—C13—H13b109.471
O1—C8—H8a109.4721H13a—C13—H13c109.4706
O1—C8—H8b109.4715H13b—C13—H13c109.4717
N1—C8—H8a109.4706
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C4—H4···O2i0.952.573.489 (2)158.46
C7—H7···O1ii0.952.583.480 (2)155.41
C8—H8a···S10.952.753.2180 (19)110.16
C11—H11b···S10.952.773.2166 (19)109.21
C12—H12a···S1iii0.962.883.7915 (19)158.58
Symmetry codes: (i) −x+1/2, y−1/2, −z+1/2; (ii) −x+1/2, y+1/2, −z+1/2; (iii) x−1, y, z.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
C4—H4···O2i0.952.573.489 (2)158.46
C7—H7···O1ii0.952.583.480 (2)155.41
C12—H12a···S1iii0.962.883.7915 (19)158.58
Symmetry codes: (i) −x+1/2, y−1/2, −z+1/2; (ii) −x+1/2, y+1/2, −z+1/2; (iii) x−1, y, z.
Acknowledgements top

The authors acknowledge the Dirección de Investigaciones Sede Bogotá (DIB) of Universidad Nacional de Colombia, the institutional research plan No. AVOZ10100521 of the Institute of Physics and the project Praemium Academiae of the Academy of Sciences of the Czech Republic for financial support.

references
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