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

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].

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.036
• wR factor = 0.098
• Data-to-parameter ratio = 17.4

checkCIF/PLATON results

No syntax errors found



Alert level C
SHFSU01_ALERT_2_C  Test not performed. _refine_ls_shift/su_max and
            _refine_ls_shift/esd_max not present.
            Absolute value of the parameter shift to su ratio given   0.001
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          4
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600         88

Alert level G
PLAT128_ALERT_4_G Alternate Setting of Space-group P21/c   .......      P21/n

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 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
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check


checkCIF publication errors

Alert level A
PUBL024_ALERT_1_A The number of authors is greater than 5.
              Please specify the role of each of the co-authors
              for your paper.

Author Response:

 Fen Wang  synthesized the title compound;

 Sacha Ninkovic suggested to synthesize and to study
 the title compound;

 Michael Collins was instrumental in
 providing the starting material and suggested improvements of
 reaction conditions;

 Curtis Moore performed structure solution and refinement;

 Arnold Rheingold ran the X-ray diffraction experiment;

 Alex Yanovsky wrote most of the text parts of the CIF
 file and prepared CIF file for publication.



   1 ALERT level A = Data missing that is essential or data in wrong format
   0 ALERT level G = General alerts. Data that may be required is missing

---

S1. Comment

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

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

S2. Experimental

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

S3. Refinement

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 U_iso(H) were set to 1.2U_eq of the carrying atom. The highest residual peak of 1.41 e/ų is located at 0.91 Å from the Br1 atom.

Computing details

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

	Fig. 1. Molecular structure of (I), showing 50% probability displacement ellipsoids. H atoms are drawn as circles with arbitrary small radius.
	Fig. 2. Packing diagram of (I) viewed approximately down the a axis.

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

Crystal data

C5H3BrN2S	F(000) = 392
Mr = 203.06	Dx = 2.153 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 4198 reflections
a = 3.8917 (11) Å	θ = 2.4–27.4°
b = 17.118 (5) Å	µ = 6.79 mm^−1
c = 9.405 (3) Å	T = 100 K
β = 91.359 (3)°	Needle, light brown
V = 626.4 (3) Å^3	0.32 × 0.18 × 0.09 mm
Z = 4

Data collection

Bruker APEX CCD diffractometer	1441 independent reflections
Radiation source: fine-focus sealed tube	1270 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.043
φ and ω scans	θmax = 28.2°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −5→5
Tmin = 0.220, Tmax = 0.580	k = −22→21
9691 measured reflections	l = −11→12

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.098	H-atom parameters constrained
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0585P)^2 + 0.9841P] where P = (Fo^2 + 2Fc^2)/3
1441 reflections	(Δ/σ)max < 0.001
83 parameters	Δρmax = 1.41 e Å^−3
0 restraints	Δρmin = −0.81 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Br1	0.78267 (9)	0.43247 (2)	0.25169 (4)	0.01969 (18)
S1	0.4398 (2)	0.58614 (6)	0.13967 (10)	0.0204 (3)
N1	0.4603 (8)	0.71893 (18)	0.4614 (3)	0.0186 (7)
H1N	0.5141	0.7276	0.5515	0.022*
N2	0.2480 (8)	0.7397 (2)	0.2389 (3)	0.0212 (7)
C1	0.6366 (9)	0.5359 (2)	0.2806 (4)	0.0178 (7)
C2	0.6719 (9)	0.5760 (2)	0.4074 (4)	0.0159 (7)
H2	0.7747	0.5568	0.4932	0.019*
C3	0.5239 (9)	0.6521 (2)	0.3853 (4)	0.0169 (7)
C4	0.3908 (9)	0.6662 (2)	0.2503 (4)	0.0168 (7)
C5	0.2976 (10)	0.7690 (2)	0.3697 (4)	0.0206 (8)
H5	0.2262	0.8200	0.3960	0.025*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Br1	0.0235 (2)	0.0164 (3)	0.0190 (3)	0.00184 (12)	−0.00180 (14)	−0.00335 (13)
S1	0.0251 (5)	0.0207 (5)	0.0153 (5)	0.0007 (3)	−0.0021 (4)	−0.0008 (4)
N1	0.0240 (16)	0.0179 (16)	0.0140 (16)	−0.0007 (12)	−0.0001 (12)	−0.0003 (13)
N2	0.0225 (16)	0.0183 (18)	0.0227 (18)	−0.0007 (11)	−0.0005 (13)	0.0031 (13)
C1	0.0189 (17)	0.0149 (18)	0.0196 (19)	−0.0004 (13)	0.0011 (13)	−0.0008 (15)
C2	0.0201 (17)	0.0141 (17)	0.0137 (18)	−0.0012 (13)	0.0033 (13)	0.0018 (13)
C3	0.0195 (17)	0.0171 (18)	0.0140 (18)	−0.0024 (13)	−0.0009 (13)	0.0002 (14)
C4	0.0204 (17)	0.0140 (17)	0.0161 (19)	−0.0002 (14)	−0.0006 (13)	0.0018 (14)
C5	0.0258 (19)	0.0154 (18)	0.021 (2)	0.0007 (14)	0.0012 (15)	0.0020 (15)

Geometric parameters (Å, º)

Br1—C1	1.882 (4)	N2—C4	1.378 (5)
S1—C4	1.734 (4)	C1—C2	1.379 (5)
S1—C1	1.742 (4)	C2—C3	1.438 (5)
N1—C5	1.362 (5)	C2—H2	0.9500
N1—C3	1.375 (5)	C3—C4	1.381 (5)
N1—H1N	0.8800	C5—H5	0.9500
N2—C5	1.338 (5)
C4—S1—C1	89.20 (18)	C3—C2—H2	126.4
C5—N1—C3	106.3 (3)	N1—C3—C4	105.3 (3)
C5—N1—H1N	126.8	N1—C3—C2	139.1 (3)
C3—N1—H1N	126.8	C4—C3—C2	115.6 (3)
C5—N2—C4	102.8 (3)	N2—C4—C3	111.9 (3)
C2—C1—S1	116.5 (3)	N2—C4—S1	136.4 (3)
C2—C1—Br1	124.6 (3)	C3—C4—S1	111.6 (3)
S1—C1—Br1	118.9 (2)	N2—C5—N1	113.6 (3)
C1—C2—C3	107.1 (3)	N2—C5—H5	123.2
C1—C2—H2	126.4	N1—C5—H5	123.2

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···N2^i	0.88	2.04	2.903 (4)	165

Symmetry code: (i) x+1/2, −y+3/2, z+1/2.