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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 8| August 2010| Page o2021
https://doi.org/10.1107/S1600536810027224

5-Bromo-1H-thieno[2,3-d]imidazole

Fen Wang,a Sacha Ninkovic,a Michael Collins,a Curtis Moore,b Arnold L. Rheingoldb and Alex Yanovskya*

aPfizer Global Research and Development, La Jolla Labs, 10770 Science Center Drive, San Diego, CA 92121, USA, and bDepartment of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
*Correspondence e-mail: alex.yanovsky@pfizer.com

(Received 7 July 2010; accepted 8 July 2010; online 14 July 2010)

The crystal structure of the title compound, C5H3BrN2S, shows that bromination of 1H-thieno[2,3-d]imidazole with N-bromo­succinimide in acetonitrile occurs at position 5 of the bicyclic system. The mol­ecule is almost planar, with a mean deviation of 0.015 Å from the least-squares plane through all the non-H atoms. In the crystal, N—H⋯N hydrogen bonds link the mol­ecules into infinite C(4) chains running along [101].

Related literature

For a related structure involving the thieno[2,3-d]imidazole fragment, see: Busetti et al. (1989[Busetti, V., Guerrera, F., Siracusa, M. A., Ajo, D. & De Zuane, F. (1989). Z. Kristallogr. 187, 187-191.]).

[Scheme 1]

Experimental

Crystal data

  • C5H3BrN2S

  • Mr = 203.06

  • Monoclinic, P 21 /n

  • a = 3.8917 (11) Å

  • b = 17.118 (5) Å

  • c = 9.405 (3) Å

  • β = 91.359 (3)°

  • V = 626.4 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 6.79 mm−1

  • T = 100 K

  • 0.32 × 0.18 × 0.09 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.220, Tmax = 0.580

  • 9691 measured reflections

  • 1441 independent reflections

  • 1270 reflections with I > 2σ(I)

  • Rint = 0.043
Refinement

  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.098

  • S = 1.08

  • 1441 reflections

  • 83 parameters

  • H-atom parameters constrained

  • Δρmax = 1.41 e Å−3

  • Δρmin = −0.81 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1N⋯N2i 0.88 2.04 2.903 (4) 165
Symmetry code: (i) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}].

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

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810027224/hb5547sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810027224/hb5547Isup2.hkl

checkCIF report


Comment top

Bromination of 1H-thieno[2,3-d]imidazole by bromosuccinimide in acetonitrile may occur either at position 2,5 or 6. The present X-ray study showed that substitution occurs in fact at position 5; the molecular structure of the title compound, representing the major product of bromination is shown in Fig. 1.

The molecule of the title compound is planar; maximum deviation of the Br1 atom from the mean plane of all non-H atoms of the molecule is equal to 0.029 (3) Å. To the best of our knowledge, this is the first structural study of thieno[2,3-d]imidazole derivative with the isolated bicyclic system. In the only closely related molecule, studied by the single-crystal X-ray diffraction earlier (Busetti et al., 1989), the thieno[2,3-d]imidazole system is fused with the benzene ring, thus forming a tricyclic molecule. The geometry of the thienoimidazole fragment of the tricyclic molecule is very similar to that of the title compound.

There is one symmetry independent intermolecular H-bond in the structure (Table 1), which is responsible for the formation of infinite chains of molecules running along the [101] direction of the crystal (Fig. 2).

Related literature top

For a related structure involving the thieno[2,3-d]imidazole fragment, see: Busetti et al. (1989).

Experimental top

To a solution of 1H-thieno[2,3-d]imidazole (16 mg, 0.13 mmol) in 0.75 ml of acetonitrile at 0°C was added dropwise N-bromosuccinimide (21 mg, 0.12 mmol) in 0.25 ml of acetonitrile. The reaction mixture was stirred at 0°C for 0.5 hr. The reaction mixture was diluted with 10 ml of 1 N NaOH, and the aqueous layer was extracted with EtOAc (3 × 15 ml). The organic layers were combined, dried over Na2SO4, filtered and concentrated. The product was purified by flash chromatography (silica gel, 0–70% EtOAc/heptane) to give 22 mg (81%) 5-bromo-1H-thieno[2,3-d]imidazole as an off white solid.

Light brown needles of (I) were grown by slow evaporation of a 20/20/60 methanol/dichloromethane/toluene solution

Refinement top

All H atoms were placed in geometrically calculated positions (N—H 0.88 Å, C—H 0.95 Å) and included in the refinement in the riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom. The highest residual peak of 1.41 e/Å3 is located at 0.91 Å from the Br1 atom.

Structure description top

Bromination of 1H-thieno[2,3-d]imidazole by bromosuccinimide in acetonitrile may occur either at position 2,5 or 6. The present X-ray study showed that substitution occurs in fact at position 5; the molecular structure of the title compound, representing the major product of bromination is shown in Fig. 1.

The molecule of the title compound is planar; maximum deviation of the Br1 atom from the mean plane of all non-H atoms of the molecule is equal to 0.029 (3) Å. To the best of our knowledge, this is the first structural study of thieno[2,3-d]imidazole derivative with the isolated bicyclic system. In the only closely related molecule, studied by the single-crystal X-ray diffraction earlier (Busetti et al., 1989), the thieno[2,3-d]imidazole system is fused with the benzene ring, thus forming a tricyclic molecule. The geometry of the thienoimidazole fragment of the tricyclic molecule is very similar to that of the title compound.

There is one symmetry independent intermolecular H-bond in the structure (Table 1), which is responsible for the formation of infinite chains of molecules running along the [101] direction of the crystal (Fig. 2).

For a related structure involving the thieno[2,3-d]imidazole fragment, see: Busetti et al. (1989).

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. Molecular structure of (I), showing 50% probability displacement ellipsoids. H atoms are drawn as circles with arbitrary small radius.
[Figure 2] Fig. 2. Packing diagram of (I) viewed approximately down the a axis.
5-Bromo-1H-thieno[2,3-d]imidazole top
Crystal data top
C5H3BrN2SF(000) = 392
Mr = 203.06Dx = 2.153 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 4198 reflections
a = 3.8917 (11) Åθ = 2.4–27.4°
b = 17.118 (5) ŵ = 6.79 mm−1
c = 9.405 (3) ÅT = 100 K
β = 91.359 (3)°Needle, light brown
V = 626.4 (3) Å30.32 × 0.18 × 0.09 mm
Z = 4
Data collection top
Bruker APEX CCD
diffractometer		1441 independent reflections
Radiation source: fine-focus sealed tube1270 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.043
φ and ω scansθmax = 28.2°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −5→5
Tmin = 0.220, Tmax = 0.580k = −22→21
9691 measured reflectionsl = −11→12
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H-atom parameters constrained
S = 1.08 w = 1/[σ2(Fo2) + (0.0585P)2 + 0.9841P]
where P = (Fo2 + 2Fc2)/3
1441 reflections(Δ/σ)max < 0.001
83 parametersΔρmax = 1.41 e Å−3
0 restraintsΔρmin = −0.81 e Å−3
Crystal data top
C5H3BrN2SV = 626.4 (3) Å3
Mr = 203.06Z = 4
Monoclinic, P21/nMo Kα radiation
a = 3.8917 (11) ŵ = 6.79 mm−1
b = 17.118 (5) ÅT = 100 K
c = 9.405 (3) Å0.32 × 0.18 × 0.09 mm
β = 91.359 (3)°
Data collection top
Bruker APEX CCD
diffractometer		1441 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		1270 reflections with I > 2σ(I)
Tmin = 0.220, Tmax = 0.580Rint = 0.043
9691 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.098H-atom parameters constrained
S = 1.08Δρmax = 1.41 e Å−3
1441 reflectionsΔρmin = −0.81 e Å−3
83 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Br10.78267 (9)0.43247 (2)0.25169 (4)0.01969 (18)
S10.4398 (2)0.58614 (6)0.13967 (10)0.0204 (3)
N10.4603 (8)0.71893 (18)0.4614 (3)0.0186 (7)
H1N0.51410.72760.55150.022*
N20.2480 (8)0.7397 (2)0.2389 (3)0.0212 (7)
C10.6366 (9)0.5359 (2)0.2806 (4)0.0178 (7)
C20.6719 (9)0.5760 (2)0.4074 (4)0.0159 (7)
H20.77470.55680.49320.019*
C30.5239 (9)0.6521 (2)0.3853 (4)0.0169 (7)
C40.3908 (9)0.6662 (2)0.2503 (4)0.0168 (7)
C50.2976 (10)0.7690 (2)0.3697 (4)0.0206 (8)
H50.22620.82000.39600.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0235 (2)0.0164 (3)0.0190 (3)0.00184 (12)−0.00180 (14)−0.00335 (13)
S10.0251 (5)0.0207 (5)0.0153 (5)0.0007 (3)−0.0021 (4)−0.0008 (4)
N10.0240 (16)0.0179 (16)0.0140 (16)−0.0007 (12)−0.0001 (12)−0.0003 (13)
N20.0225 (16)0.0183 (18)0.0227 (18)−0.0007 (11)−0.0005 (13)0.0031 (13)
C10.0189 (17)0.0149 (18)0.0196 (19)−0.0004 (13)0.0011 (13)−0.0008 (15)
C20.0201 (17)0.0141 (17)0.0137 (18)−0.0012 (13)0.0033 (13)0.0018 (13)
C30.0195 (17)0.0171 (18)0.0140 (18)−0.0024 (13)−0.0009 (13)0.0002 (14)
C40.0204 (17)0.0140 (17)0.0161 (19)−0.0002 (14)−0.0006 (13)0.0018 (14)
C50.0258 (19)0.0154 (18)0.021 (2)0.0007 (14)0.0012 (15)0.0020 (15)
Geometric parameters (Å, º) top
Br1—C11.882 (4)N2—C41.378 (5)
S1—C41.734 (4)C1—C21.379 (5)
S1—C11.742 (4)C2—C31.438 (5)
N1—C51.362 (5)C2—H20.9500
N1—C31.375 (5)C3—C41.381 (5)
N1—H1N0.8800C5—H50.9500
N2—C51.338 (5)
C4—S1—C189.20 (18)C3—C2—H2126.4
C5—N1—C3106.3 (3)N1—C3—C4105.3 (3)
C5—N1—H1N126.8N1—C3—C2139.1 (3)
C3—N1—H1N126.8C4—C3—C2115.6 (3)
C5—N2—C4102.8 (3)N2—C4—C3111.9 (3)
C2—C1—S1116.5 (3)N2—C4—S1136.4 (3)
C2—C1—Br1124.6 (3)C3—C4—S1111.6 (3)
S1—C1—Br1118.9 (2)N2—C5—N1113.6 (3)
C1—C2—C3107.1 (3)N2—C5—H5123.2
C1—C2—H2126.4N1—C5—H5123.2
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···N2i0.882.042.903 (4)165
Symmetry code: (i) x+1/2, −y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H3BrN2S
Mr203.06
Crystal system, space groupMonoclinic, P21/n
Temperature (K)100
a, b, c (Å)3.8917 (11), 17.118 (5), 9.405 (3)
β (°) 91.359 (3)
V (Å3)626.4 (3)
Z4
Radiation typeMo Kα
µ (mm−1)6.79
Crystal size (mm)0.32 × 0.18 × 0.09
Data collection
DiffractometerBruker APEX CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.220, 0.580
No. of measured, independent and
observed [I > 2σ(I)] reflections		9691, 1441, 1270
Rint0.043
(sin θ/λ)max (Å−1)0.665
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.098, 1.08
No. of reflections1441
No. of parameters83
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)1.41, −0.81

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—H1N···N2i0.882.042.903 (4)165
Symmetry code: (i) x+1/2, −y+3/2, z+1/2.
 

References

First citationBruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBusetti, V., Guerrera, F., Siracusa, M. A., Ajo, D. & De Zuane, F. (1989). Z. Kristallogr. 187, 187–191.  CrossRef CAS Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 8| August 2010| Page o2021
https://doi.org/10.1107/S1600536810027224
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