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

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ISSN: 2056-9890

Ethyl 3-bromo-4-cyano-5-[(2-eth­­oxy-2-oxoeth­yl)sulfan­yl]thio­phene-2-carboxyl­ate

aTianjin Entry–Exit Inspection and Quarantine Bureau, Youyi road No. 33, Tianjin, People's Republic of China
*Correspondence e-mail: xpli0705@163.com

(Received 14 March 2013; accepted 18 April 2013; online 11 May 2013)

The title compound, C12H12BrNO4S2, was obtained by the Sandmeyer reaction from ethyl 3-amino-4-cyano-5-[(2-eth­oxy-2-oxoeth­yl)sulfan­yl]thio­phene-2-carboxyl­ate. The dihedral angle between the thiophene ring and linked CO2 ester group is 2.0 (5)°.

Related literature

For background literature on the use of 3-amino-4-cyano-5-eth­oxy­carbonyl­methyl­sulfanyl-thio­phene-2-carb­oxy­lic acid ethyl ester as an important inter­mediate compound for the synthesis of thieno­pyrimidine derivatives, which are thought to be potential biologically active compounds or pharmaceuticals, see: Liu et al. (2008[Liu, M. G., Hu, Y. G. & Ding, M. W. (2008). Tetrahedron, 64, 9052-9059.]). For a related compound, see: Padmavathi et al. (2011[Padmavathi, V., Reddy, G. D., Reddy, S. N. & Mahesh, K. (2011). Eur. J. Med. Chem. 46, 1367-1373.]).

[Scheme 1]

Experimental

Crystal data
  • C12H12BrNO4S2

  • Mr = 378.26

  • Monoclinic, P 21 /c

  • a = 8.5896 (17) Å

  • b = 10.837 (2) Å

  • c = 16.584 (3) Å

  • β = 99.44 (3)°

  • V = 1522.8 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 2.98 mm−1

  • T = 293 K

  • 0.20 × 0.18 × 0.12 mm

Data collection
  • Rigaku Saturn diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.587, Tmax = 0.716

  • 15211 measured reflections

  • 3596 independent reflections

  • 2224 reflections with I > 2σ(I)

  • Rint = 0.067

Refinement
  • R[F2 > 2σ(F2)] = 0.052

  • wR(F2) = 0.157

  • S = 1.00

  • 3596 reflections

  • 184 parameters

  • H-atom parameters constrained

  • Δρmax = 0.43 e Å−3

  • Δρmin = −0.71 e Å−3

Data collection: CrystalClear (Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; 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

3-Amino-4-cyano-5-ethoxycarbonylmethylsulfanyl-thiophene-2-carboxylic acid ethyl ester is an important intermediate compound for sythesis of thienothienopyrimidines derivatives, which are thought to be potential biological active compounds or pharmaceuticals (Liu, et al.,2008). We obtained the title compound by the Sandmeyer reaction from compound 3-Amino-4-cyano-5-ethoxycarbonylmethylsulfanyl-thiophene-2-carboxylic acid ethyl ester.The crystal for X-ray crystal structure analysis was obtained by recrystallizing the title compound in petroleum ether. In the crystal, the thiophene ring together with its four adjoint groups, i.e. CN, Br, S—CH2 and COO–,was located at one perfect plane, which is consistent with the crystal of 3-Amino-4-cyano-5-ethoxycarbonylmethylsulfany- thiophene-2-carboxylic acid ethyl ester reported in the literature (Padmavathi et al., 2011). The title compound cyrstal demonstrated a crystal system of monoclinic and a spce group of P2(1)/c. There existed hydrogen bond with length of 2.554 Å between one of –SCH2 H atom and the O atom of carbonyl adjoined with thiophene ring of neighbor molecule.

Related literature top

For background literature on the use of 3-amino-4-cyano-5-ethoxycarbonylmethylsulfanyl-thiophene-2-carboxylic acid ethyl ester as an important intermediate compound for the synthesis of thienothienopyrimidines derivatives, which are thought to be potential biologically active compounds or pharmaceuticals, see: Liu et al. (2008). For a related compound, see: Padmavathi et al. (2011).

Experimental top

To a solution of 3-Amino-4-cyano-5-ethoxycarbonylmethylsulfanyl -thiophene-2-carboxylic acid ethyl ester (1.57 g, 5 mmol) in 70% H2SO4 (13 mL) was added NaNO2 (0.4 g,5,7 mmol) in 5 minutes under ice water temperature. After addition, the solution was stirred for 30 min at room temperature. Then, the reaction mixture was transfered to HBr solution containing CuBr (1 g, 7 mmol). After standing overnight, water (100 mL) was added. The precipitate was collected by filtration and recrystallized from petroleum ether to afford the title compound as colourless crystals, yield 50%.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); 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. The structure of the title compound showing 30% probability ellipsoids.
[Figure 2] Fig. 2. Packing structure of the title compound.
Ethyl 3-bromo-4-cyano-5-[(2-ethoxy-2-oxoethyl)sulfanyl]thiophene-2-carboxylate top
Crystal data top
C12H12BrNO4S2F(000) = 760
Mr = 378.26Dx = 1.650 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3404 reflections
a = 8.5896 (17) Åθ = 3.1–27.9°
b = 10.837 (2) ŵ = 2.98 mm1
c = 16.584 (3) ÅT = 293 K
β = 99.44 (3)°Block, colorless
V = 1522.8 (5) Å30.20 × 0.18 × 0.12 mm
Z = 4
Data collection top
Rigaku Saturn
diffractometer
3596 independent reflections
Radiation source: rotating anode2224 reflections with I > 2σ(I)
Confocal monochromatorRint = 0.067
ω scansθmax = 27.9°, θmin = 3.1°
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
h = 1111
Tmin = 0.587, Tmax = 0.716k = 1414
15211 measured reflectionsl = 2121
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)] = 0.052H-atom parameters constrained
wR(F2) = 0.157 w = 1/[σ2(Fo2) + (0.0817P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max = 0.003
3596 reflectionsΔρmax = 0.43 e Å3
184 parametersΔρmin = 0.71 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.018 (2)
Crystal data top
C12H12BrNO4S2V = 1522.8 (5) Å3
Mr = 378.26Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.5896 (17) ŵ = 2.98 mm1
b = 10.837 (2) ÅT = 293 K
c = 16.584 (3) Å0.20 × 0.18 × 0.12 mm
β = 99.44 (3)°
Data collection top
Rigaku Saturn
diffractometer
3596 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku, 2005)
2224 reflections with I > 2σ(I)
Tmin = 0.587, Tmax = 0.716Rint = 0.067
15211 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0520 restraints
wR(F2) = 0.157H-atom parameters constrained
S = 1.00Δρmax = 0.43 e Å3
3596 reflectionsΔρmin = 0.71 e Å3
184 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
Br11.34684 (5)0.05401 (5)0.13435 (3)0.0723 (3)
S10.95059 (11)0.19092 (9)0.04312 (6)0.0421 (3)
S20.75972 (12)0.13383 (10)0.17935 (7)0.0505 (3)
O11.3519 (4)0.1042 (3)0.0246 (2)0.0703 (9)
O21.1477 (3)0.2261 (3)0.07630 (18)0.0577 (8)
O30.4240 (3)0.3685 (3)0.10494 (18)0.0559 (8)
O40.4796 (4)0.2478 (3)0.2147 (2)0.0744 (10)
N11.0569 (5)0.0869 (4)0.2904 (3)0.0784 (13)
C11.3411 (7)0.3617 (5)0.1215 (3)0.0825 (16)
H1A1.28900.42770.09800.124*
H1B1.37940.39120.16920.124*
H1C1.42820.33250.08230.124*
C21.2285 (6)0.2598 (5)0.1446 (3)0.0667 (13)
H2A1.15100.28470.19110.080*
H2B1.28450.18850.16070.080*
C31.2245 (5)0.1481 (4)0.0215 (3)0.0468 (10)
C41.1325 (4)0.1209 (3)0.0445 (2)0.0420 (9)
C51.1667 (5)0.0433 (3)0.1088 (3)0.0440 (9)
C61.0474 (4)0.0400 (3)0.1587 (2)0.0427 (9)
C70.9215 (4)0.1161 (3)0.1300 (2)0.0390 (8)
C81.0542 (5)0.0323 (4)0.2309 (3)0.0551 (11)
C90.6413 (4)0.2381 (4)0.1105 (2)0.0473 (10)
H9A0.70500.30720.09790.057*
H9B0.60030.19600.05990.057*
C100.5069 (4)0.2838 (4)0.1508 (3)0.0464 (10)
C110.2964 (6)0.4242 (5)0.1395 (3)0.0632 (13)
H11A0.33730.46300.19140.076*
H11B0.22050.36170.14880.076*
C120.2186 (6)0.5190 (5)0.0800 (4)0.0903 (18)
H12A0.29570.57820.06910.135*
H12B0.13710.56030.10290.135*
H12C0.17330.47910.02990.135*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.0499 (4)0.0728 (4)0.0911 (5)0.0186 (2)0.0023 (3)0.0000 (3)
S10.0381 (5)0.0419 (5)0.0472 (6)0.0045 (4)0.0093 (4)0.0038 (4)
S20.0452 (6)0.0526 (6)0.0570 (7)0.0040 (5)0.0186 (5)0.0114 (5)
O10.0539 (19)0.088 (2)0.075 (2)0.0161 (18)0.0267 (16)0.0067 (19)
O20.0532 (18)0.0659 (19)0.0574 (18)0.0027 (15)0.0195 (14)0.0111 (16)
O30.0464 (16)0.0658 (19)0.0585 (19)0.0130 (15)0.0177 (14)0.0037 (15)
O40.074 (2)0.088 (2)0.070 (2)0.0212 (18)0.0363 (18)0.0164 (19)
N10.073 (3)0.077 (3)0.087 (3)0.012 (2)0.020 (2)0.035 (3)
C10.100 (4)0.089 (4)0.064 (3)0.022 (3)0.030 (3)0.002 (3)
C20.076 (3)0.072 (3)0.056 (3)0.004 (3)0.022 (2)0.008 (2)
C30.040 (2)0.049 (2)0.052 (2)0.0011 (19)0.0102 (18)0.005 (2)
C40.034 (2)0.039 (2)0.054 (2)0.0016 (16)0.0101 (17)0.0058 (18)
C50.036 (2)0.041 (2)0.054 (2)0.0013 (16)0.0032 (18)0.0033 (18)
C60.041 (2)0.039 (2)0.047 (2)0.0030 (17)0.0034 (18)0.0045 (17)
C70.036 (2)0.0346 (19)0.046 (2)0.0006 (16)0.0064 (16)0.0012 (16)
C80.045 (2)0.051 (2)0.070 (3)0.006 (2)0.011 (2)0.011 (2)
C90.036 (2)0.059 (3)0.048 (2)0.0034 (19)0.0114 (18)0.003 (2)
C100.039 (2)0.053 (2)0.049 (2)0.0003 (19)0.0099 (18)0.003 (2)
C110.050 (3)0.070 (3)0.074 (3)0.018 (2)0.023 (2)0.008 (3)
C120.068 (3)0.097 (4)0.108 (5)0.036 (3)0.021 (3)0.015 (4)
Geometric parameters (Å, º) top
Br1—C51.864 (4)C2—H2A0.9700
S1—C71.707 (4)C2—H2B0.9700
S1—C41.734 (4)C3—C41.480 (6)
S2—C71.735 (4)C4—C51.352 (5)
S2—C91.798 (4)C5—C61.418 (6)
O1—C31.202 (5)C6—C71.381 (5)
O2—C31.335 (5)C6—C81.425 (6)
O2—C21.468 (5)C9—C101.509 (5)
O3—C101.323 (5)C9—H9A0.9700
O3—C111.449 (5)C9—H9B0.9700
O4—C101.188 (5)C11—C121.504 (7)
N1—C81.147 (6)C11—H11A0.9700
C1—C21.477 (7)C11—H11B0.9700
C1—H1A0.9600C12—H12A0.9600
C1—H1B0.9600C12—H12B0.9600
C1—H1C0.9600C12—H12C0.9600
C7—S1—C492.15 (19)C5—C6—C8124.7 (4)
C7—S2—C9100.55 (18)C6—C7—S1111.1 (3)
C3—O2—C2116.1 (3)C6—C7—S2123.1 (3)
C10—O3—C11115.6 (3)S1—C7—S2125.8 (2)
C2—C1—H1A109.5N1—C8—C6177.4 (5)
C2—C1—H1B109.5C10—C9—S2108.6 (3)
H1A—C1—H1B109.5C10—C9—H9A110.0
C2—C1—H1C109.5S2—C9—H9A110.0
H1A—C1—H1C109.5C10—C9—H9B110.0
H1B—C1—H1C109.5S2—C9—H9B110.0
O2—C2—C1111.0 (4)H9A—C9—H9B108.4
O2—C2—H2A109.4O4—C10—O3125.0 (4)
C1—C2—H2A109.4O4—C10—C9124.4 (4)
O2—C2—H2B109.4O3—C10—C9110.6 (4)
C1—C2—H2B109.4O3—C11—C12108.0 (4)
H2A—C2—H2B108.0O3—C11—H11A110.1
O1—C3—O2124.9 (4)C12—C11—H11A110.1
O1—C3—C4123.6 (4)O3—C11—H11B110.1
O2—C3—C4111.4 (3)C12—C11—H11B110.1
C5—C4—C3129.3 (3)H11A—C11—H11B108.4
C5—C4—S1111.1 (3)C11—C12—H12A109.5
C3—C4—S1119.5 (3)C11—C12—H12B109.5
C4—C5—C6113.1 (3)H12A—C12—H12B109.5
C4—C5—Br1126.6 (3)C11—C12—H12C109.5
C6—C5—Br1120.4 (3)H12A—C12—H12C109.5
C7—C6—C5112.6 (3)H12B—C12—H12C109.5
C7—C6—C8122.7 (4)
C3—O2—C2—C183.9 (5)C5—C6—C7—S10.2 (4)
C2—O2—C3—O10.4 (6)C8—C6—C7—S1179.4 (3)
C2—O2—C3—C4179.9 (3)C5—C6—C7—S2178.6 (3)
O1—C3—C4—C52.5 (7)C8—C6—C7—S20.9 (6)
O2—C3—C4—C5177.2 (4)C4—S1—C7—C60.1 (3)
O1—C3—C4—S1179.4 (4)C4—S1—C7—S2178.3 (3)
O2—C3—C4—S11.0 (5)C9—S2—C7—C6178.3 (3)
C7—S1—C4—C50.4 (3)C9—S2—C7—S13.5 (3)
C7—S1—C4—C3178.9 (3)C7—C6—C8—N136 (12)
C3—C4—C5—C6178.9 (4)C5—C6—C8—N1144 (11)
S1—C4—C5—C60.6 (4)C7—S2—C9—C10169.7 (3)
C3—C4—C5—Br10.6 (6)C11—O3—C10—O43.5 (6)
S1—C4—C5—Br1178.9 (2)C11—O3—C10—C9176.8 (4)
C4—C5—C6—C70.5 (5)S2—C9—C10—O45.4 (6)
Br1—C5—C6—C7179.0 (3)S2—C9—C10—O3174.9 (3)
C4—C5—C6—C8179.0 (4)C10—O3—C11—C12178.9 (4)
Br1—C5—C6—C81.5 (5)

Experimental details

Crystal data
Chemical formulaC12H12BrNO4S2
Mr378.26
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)8.5896 (17), 10.837 (2), 16.584 (3)
β (°) 99.44 (3)
V3)1522.8 (5)
Z4
Radiation typeMo Kα
µ (mm1)2.98
Crystal size (mm)0.20 × 0.18 × 0.12
Data collection
DiffractometerRigaku Saturn
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.587, 0.716
No. of measured, independent and
observed [I > 2σ(I)] reflections
15211, 3596, 2224
Rint0.067
(sin θ/λ)max1)0.658
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.052, 0.157, 1.00
No. of reflections3596
No. of parameters184
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.43, 0.71

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

Acknowledgements

The authors appreciate the help of Dr Haibin Song in Nankai University for the crystal X-ray measurement.

References

First citationLiu, M. G., Hu, Y. G. & Ding, M. W. (2008). Tetrahedron, 64, 9052–9059.  Web of Science CSD CrossRef CAS
First citationPadmavathi, V., Reddy, G. D., Reddy, S. N. & Mahesh, K. (2011). Eur. J. Med. Chem. 46, 1367–1373.  Web of Science CSD CrossRef CAS PubMed
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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ISSN: 2056-9890
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