![e logo](https://journals.iucr.org/logos/jicons/e_36x36.png)
![...](/logos/entities/ctdot_rmgif.gif)
![...](/logos/entities/ctdot_rmgif.gif)
![...](/logos/entities/ctdot_rmgif.gif)
Supporting information
![]() | Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680705194X/fb2063sup1.cif |
![]() | Structure factor file (CIF format) https://doi.org/10.1107/S160053680705194X/fb2063Isup2.hkl |
CCDC reference: 667463
Key indicators
- Single-crystal X-ray study
- T = 294 K
- Mean
(C-C) = 0.002 Å
- R factor = 0.038
- wR factor = 0.105
- Data-to-parameter ratio = 21.5
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.98
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related literature see: Dubey et al., 1985; Garuti et al., 2000. For refinement weighting scheme, see: Prince (1982); Watkin (1994).
2 ml of triethylamine (19.98 mmol) and 3-chloropropan-1-ol (1.7 ml, 19.98 mmol) was added to 2-mercatobenzimidazole (1 g, 6.66 mmol) in dry ethanol (20 ml). The mixture was refluxed for 24 h. The solvent was evaporated in vacuum. The residue was purified by column chromatography on a silica gel (Elution: ethyl acetate/dichloromethane (1:9, v/v)) and the title compound was yielded as a yellow powder (1.12 g, 81%) with a melting point 395 K. The compound was dissolved in ethanol and pentane and after 72 h prismatic crystals were obtained. 1H NMR(DMSO, 300 MHz) δ (p.p.m.):1.832–1.919 (m, 2H, CH2S), 3.321–3.429 (m, 2H, CH2), 3.526 (m, 2H, CH2O), 4.774 (s, 1H, OH), 7.078–7.440 (m, 4H, C6H4), 12.556 (s, 1H, NH). 13C NMR (DMSO, 300 MHz) δ (p.p.m.):28.18 (CH2S), 32.62 (CH2), 59.09 (CH2O), 110.60, 116.85, 121.38, 135.44, 143.42 (C4, C5, C6, C7, C8, C9), 150.50 (C═N).
All the H atoms were discernable in a difference Fourier map. The C—H distances were contrained to 0.95 and 0.98 Å for aryl and methylene H atoms, respectively, while Uiso(H) = 1.2Ueq(C). The positional parameters as well as the Uiso of the H atoms H9 and H14, i.e. the H atoms involved in the N—H···O and O—H···N hydrogen bonds, respectively, were refined freely.
Benzimidazole derivatives are important pharmaceutical intermediates. They are used in the design of antihelmintic (Dubey et al., 1985) and antiviral pharmaceutics (Garuti et al., 2000). Therefore we have decided to study this class of compounds. The title compound has been synthesized and its structure has been determined in order to study influence of new substituents on the biological activity of the new benzimidazole derivative.
In the title molecule the benzimidazole unit C1/N2/C3/C4/C5/C6/C7/C8/N9 is essentially planar, with a mean deviation of 0.0087 Å. The structure packing exhibits intra and intermolecular hydrogen bonds - see also Tab. 1 and Fig. 2.
For related literature see: Dubey et al., 1985; Garuti et al., 2000. For refinement weighting scheme, see: Prince (1982); Watkin (1994).
Data collection: COLLECT (Nonius, 1997); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).
C10H12N2OS | F(000) = 440 |
Mr = 208.28 | Dx = 1.351 Mg m−3 |
Monoclinic, P21/c | Melting point: 395 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 7.1472 (3) Å | Cell parameters from 14014 reflections |
b = 11.5574 (6) Å | θ = 2–30° |
c = 12.5284 (6) Å | µ = 0.28 mm−1 |
β = 98.343 (4)° | T = 294 K |
V = 1023.93 (8) Å3 | Prism, yellow |
Z = 4 | 0.40 × 0.35 × 0.25 mm |
Nonius KappaCCD diffractometer | 2469 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.028 |
Graphite monochromator | θmax = 30.0°, θmin = 2.4° |
φ scans | h = −10→10 |
14014 measured reflections | k = −16→16 |
2905 independent reflections | l = −17→17 |
Refinement on F2 | 40 constraints |
Least-squares matrix: full | Primary atom site location: structure-invariant direct methods |
R[F2 > 2σ(F2)] = 0.039 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.105 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.96 | Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982)
[weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)]
where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)2]2 Ai are: 401. 643. 404. 180. 52.0 |
2897 reflections | (Δ/σ)max = 0.001 |
135 parameters | Δρmax = 0.24 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C10H12N2OS | V = 1023.93 (8) Å3 |
Mr = 208.28 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.1472 (3) Å | µ = 0.28 mm−1 |
b = 11.5574 (6) Å | T = 294 K |
c = 12.5284 (6) Å | 0.40 × 0.35 × 0.25 mm |
β = 98.343 (4)° |
Nonius KappaCCD diffractometer | 2469 reflections with I > 2σ(I) |
14014 measured reflections | Rint = 0.028 |
2905 independent reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.105 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.96 | Δρmax = 0.24 e Å−3 |
2897 reflections | Δρmin = −0.29 e Å−3 |
135 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.20606 (16) | 0.48268 (12) | 0.70598 (10) | 0.0398 | |
N2 | 0.33956 (14) | 0.46390 (10) | 0.64550 (9) | 0.0405 | |
C3 | 0.25166 (16) | 0.39740 (11) | 0.55977 (10) | 0.0367 | |
C4 | 0.32332 (19) | 0.35508 (12) | 0.46994 (11) | 0.0437 | |
C5 | 0.2028 (2) | 0.29163 (13) | 0.39578 (11) | 0.0500 | |
C6 | 0.0160 (2) | 0.27040 (13) | 0.41022 (12) | 0.0524 | |
C7 | −0.05715 (19) | 0.31195 (12) | 0.49875 (12) | 0.0490 | |
C8 | 0.06357 (16) | 0.37607 (11) | 0.57329 (10) | 0.0382 | |
N9 | 0.03898 (15) | 0.43166 (10) | 0.66774 (9) | 0.0419 | |
S10 | 0.22683 (5) | 0.56461 (4) | 0.82388 (3) | 0.0543 | |
C11 | 0.4478 (2) | 0.64012 (12) | 0.81673 (12) | 0.0497 | |
C12 | 0.6209 (2) | 0.58824 (14) | 0.88430 (12) | 0.0519 | |
C13 | 0.6655 (2) | 0.46502 (14) | 0.85854 (12) | 0.0506 | |
O14 | 0.70311 (14) | 0.44920 (10) | 0.75131 (9) | 0.0511 | |
H9 | −0.063 (3) | 0.4384 (16) | 0.6965 (16) | 0.061 (5)* | |
H14 | 0.602 (3) | 0.4573 (17) | 0.7080 (18) | 0.067 (6)* | |
H7 | −0.1845 | 0.2974 | 0.5083 | 0.0582* | |
H6 | −0.0628 | 0.2262 | 0.3578 | 0.0621* | |
H5 | 0.2482 | 0.2619 | 0.3337 | 0.0604* | |
H4 | 0.4506 | 0.3693 | 0.4600 | 0.0533* | |
H111 | 0.4340 | 0.7200 | 0.8407 | 0.0592* | |
H112 | 0.4698 | 0.6400 | 0.7413 | 0.0592* | |
H121 | 0.6009 | 0.5917 | 0.9600 | 0.0613* | |
H122 | 0.7308 | 0.6355 | 0.8743 | 0.0613* | |
H131 | 0.7770 | 0.4400 | 0.9081 | 0.0607* | |
H132 | 0.5569 | 0.4168 | 0.8691 | 0.0607* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0318 (5) | 0.0495 (7) | 0.0390 (6) | 0.0036 (5) | 0.0086 (4) | 0.0026 (5) |
N2 | 0.0303 (4) | 0.0541 (6) | 0.0381 (5) | −0.0015 (4) | 0.0078 (4) | −0.0024 (4) |
C3 | 0.0320 (5) | 0.0405 (6) | 0.0378 (5) | 0.0001 (4) | 0.0061 (4) | 0.0041 (4) |
C4 | 0.0423 (6) | 0.0493 (7) | 0.0414 (6) | 0.0001 (5) | 0.0117 (5) | 0.0020 (5) |
C5 | 0.0627 (8) | 0.0481 (7) | 0.0401 (6) | −0.0025 (6) | 0.0098 (6) | −0.0008 (5) |
C6 | 0.0601 (8) | 0.0460 (7) | 0.0487 (7) | −0.0118 (6) | −0.0004 (6) | 0.0013 (6) |
C7 | 0.0394 (6) | 0.0490 (7) | 0.0569 (8) | −0.0090 (5) | 0.0018 (5) | 0.0076 (6) |
C8 | 0.0331 (5) | 0.0405 (6) | 0.0413 (6) | 0.0001 (4) | 0.0068 (4) | 0.0072 (5) |
N9 | 0.0292 (5) | 0.0530 (6) | 0.0452 (6) | 0.0016 (4) | 0.0114 (4) | 0.0040 (5) |
S10 | 0.0455 (2) | 0.0749 (3) | 0.04444 (19) | 0.00492 (16) | 0.01321 (14) | −0.01196 (16) |
C11 | 0.0562 (8) | 0.0419 (6) | 0.0508 (7) | 0.0025 (6) | 0.0069 (6) | −0.0057 (5) |
C12 | 0.0499 (7) | 0.0588 (8) | 0.0460 (7) | −0.0021 (6) | 0.0037 (6) | −0.0097 (6) |
C13 | 0.0486 (7) | 0.0607 (8) | 0.0433 (7) | 0.0115 (6) | 0.0093 (5) | 0.0015 (6) |
O14 | 0.0320 (4) | 0.0762 (7) | 0.0464 (5) | 0.0055 (4) | 0.0097 (4) | −0.0085 (5) |
C1—N2 | 1.3197 (15) | C8—N9 | 1.3800 (17) |
C1—N9 | 1.3554 (16) | N9—H9 | 0.86 (2) |
C1—S10 | 1.7427 (14) | S10—C11 | 1.8182 (16) |
N2—C3 | 1.3939 (16) | C11—C12 | 1.517 (2) |
C3—C4 | 1.3912 (17) | C11—H111 | 0.980 |
C3—C8 | 1.4009 (16) | C11—H112 | 0.980 |
C4—C5 | 1.382 (2) | C12—C13 | 1.505 (2) |
C4—H4 | 0.950 | C12—H121 | 0.980 |
C5—C6 | 1.395 (2) | C12—H122 | 0.980 |
C5—H5 | 0.950 | C13—O14 | 1.4195 (17) |
C6—C7 | 1.379 (2) | C13—H131 | 0.980 |
C6—H6 | 0.950 | C13—H132 | 0.980 |
C7—C8 | 1.3899 (19) | O14—H14 | 0.84 (2) |
C7—H7 | 0.950 | ||
N2—C1—N9 | 113.50 (12) | C8—N9—H9 | 128.4 (13) |
N2—C1—S10 | 126.61 (10) | C1—N9—H9 | 124.6 (13) |
N9—C1—S10 | 119.89 (9) | C1—S10—C11 | 100.77 (6) |
C1—N2—C3 | 104.51 (10) | S10—C11—C12 | 115.24 (11) |
N2—C3—C4 | 129.75 (11) | S10—C11—H111 | 108.1 |
N2—C3—C8 | 109.70 (11) | C12—C11—H111 | 108.2 |
C4—C3—C8 | 120.55 (12) | S10—C11—H112 | 108.0 |
C3—C4—C5 | 117.63 (12) | C12—C11—H112 | 107.8 |
C3—C4—H4 | 121.2 | H111—C11—H112 | 109.5 |
C5—C4—H4 | 121.2 | C11—C12—C13 | 115.82 (12) |
C4—C5—C6 | 121.39 (13) | C11—C12—H121 | 107.6 |
C4—C5—H5 | 119.3 | C13—C12—H121 | 108.1 |
C6—C5—H5 | 119.3 | C11—C12—H122 | 108.2 |
C5—C6—C7 | 121.64 (13) | C13—C12—H122 | 107.5 |
C5—C6—H6 | 119.2 | H121—C12—H122 | 109.5 |
C7—C6—H6 | 119.2 | C12—C13—O14 | 113.58 (13) |
C6—C7—C8 | 117.08 (12) | C12—C13—H131 | 108.8 |
C6—C7—H7 | 121.5 | O14—C13—H131 | 108.3 |
C8—C7—H7 | 121.5 | C12—C13—H132 | 108.2 |
C3—C8—C7 | 121.71 (12) | O14—C13—H132 | 108.5 |
C3—C8—N9 | 105.40 (11) | H131—C13—H132 | 109.5 |
C7—C8—N9 | 132.88 (12) | C13—O14—H14 | 109.5 (14) |
C8—N9—C1 | 106.88 (10) |
D—H···A | D—H | H···A | D···A | D—H···A |
O14—H14···N2 | 0.84 (2) | 1.93 (2) | 2.746 (2) | 163 (2) |
N9—H9···O14i | 0.86 (2) | 1.90 (2) | 2.762 (2) | 176 (2) |
C11—H112···N2 | 0.98 | 2.47 | 2.978 (2) | 112 |
Symmetry code: (i) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C10H12N2OS |
Mr | 208.28 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 294 |
a, b, c (Å) | 7.1472 (3), 11.5574 (6), 12.5284 (6) |
β (°) | 98.343 (4) |
V (Å3) | 1023.93 (8) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.40 × 0.35 × 0.25 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14014, 2905, 2469 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.105, 0.96 |
No. of reflections | 2897 |
No. of parameters | 135 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.24, −0.29 |
Computer programs: COLLECT (Nonius, 1997), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
O14—H14···N2 | 0.84 (2) | 1.93 (2) | 2.746 (2) | 163 (2) |
N9—H9···O14i | 0.86 (2) | 1.90 (2) | 2.762 (2) | 176 (2) |
C11—H112···N2 | 0.98 | 2.47 | 2.978 (2) | 112 |
Symmetry code: (i) x−1, y, z. |
![](https://journals.iucr.org/logos/arrows/smarrr.png)
Subscribe to Acta Crystallographica Section E: Crystallographic Communications
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- If you have already subscribed, you may need to register
Benzimidazole derivatives are important pharmaceutical intermediates. They are used in the design of antihelmintic (Dubey et al., 1985) and antiviral pharmaceutics (Garuti et al., 2000). Therefore we have decided to study this class of compounds. The title compound has been synthesized and its structure has been determined in order to study influence of new substituents on the biological activity of the new benzimidazole derivative.
In the title molecule the benzimidazole unit C1/N2/C3/C4/C5/C6/C7/C8/N9 is essentially planar, with a mean deviation of 0.0087 Å. The structure packing exhibits intra and intermolecular hydrogen bonds - see also Tab. 1 and Fig. 2.