Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807041451/hk2315sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807041451/hk2315Isup2.hkl |
CCDC reference: 660376
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.004 Å
- R factor = 0.026
- wR factor = 0.067
- Data-to-parameter ratio = 20.6
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT431_ALERT_2_B Short Inter HL..A Contact I1 .. N1 .. 3.14 Ang.
Alert level C PLAT063_ALERT_3_C Crystal Probably too Large for Beam Size ....... 0.73 mm PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density .... 2.02 PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 200 Deg. PLAT371_ALERT_2_C Long C(sp2)-C(sp1) Bond C2 - C8 ... 1.44 Ang. PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 24 C1 -C2 -C8 -N1 116.00 18.00 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_C Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 25 C3 -C2 -C8 -N1 -63.00 18.00 1.555 1.555 1.555 1.555
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 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
For related literature, see: Apinitis et al. (1984); Bailey et al. (2000); Bond et al. (2001); Britton (2001, 2004); Britton & Gleason (2002); Desiraju & Harlow (1989); Metrangolo et al. (2004); Nyburg & Faerman (1985); Ojala et al. (1999).
For the preparation of the title compound, (I), etyl 5-amino-4-cyano-3-methylthiophene-2-carboxylate (12.0 mmol, 2.5 g) was added to a solution of p-toluenesulphonic acid (36.0 mmol, 6.4 g) in acetonitrile (50 ml). The resulting solution was cooled to 283–288 K and added to a solution of NaNO2 (1.6 g, 24 mmol) and KI (5.2 g, 30 mmol) in water (10 ml), gradually. The reaction mixture was stirred for 10 min, then allowed to come 293 K and stirred for 3 h. Then, H2O (50 ml), NaHCO3 (1 M, until pH = 9–10) and Na2S2O3 (2 M, 6 ml) were added to the reaction mixture. The precipitated iodine was filtered and purified by flash flow column chromatography (i-hexane/ethylacetate, 5:1) (yield: 2.7 g, 73%, m.p. 395–398 K).
H atoms were positioned geometrically, with C—H = 0.97 and 0.96 Å for methylene and methyl H, and constrained to ride on their parent atoms, with Uiso(H) = xUeq(C), where x = 1.2 for methylene H, and x = 1.5 for methyl H atoms.
The family of well defined oligothiophene derivatives is important for polymer research, electronic semiconducting materials, non-linear optical materials and highly ordered molecular assemblies. Thiophene based oligomers are among the most investigated systems for technological applications, due to their chemical stability and wide spread possibility of functionalization. Moreover, they are relative to some other conjugated systems and represent structures with high labeled molecular architecture. Etyl 5-iodo-4-cyano-3-methylthiophene-2-carboxylate represents an important building block in desing of oligothiophene structure, in terms of its well defined molecular structure. We report herein the crystal structure of the title compound, (I).
In the molecule of the title compound, (I), (Fig. 1), the bond lengths are in accordance with those observed in ethyl 5-amino-4-cyano-3-methylthiophene-2-carboxylate (refcode: DACLIC; Apinitis et al., 1984). A weak intramolecular C—H···O hydrogen bond (Table 1) is also comparable with the corresponding one in DACLIC.
A cyclamer is formed by the association of two monomers through weak intermolecular CN···I Lewis acid-base interactions (Fig. 2). The CN···I distances are in accordance with the expected values from non-spherical radii of Nyburg & Faerman (1985). The angles at the N atoms are closer to trigonal, but the angles at the I atoms are approximately linear. In (I), the N···I distance, C—I···N and N···I—C angles are 3.142 (3) Å, 166.9 (1)° and 123.1 (1)°, respectively. The significant CN···I interactions (in the range of 2.9–3.3 Å) are well known in more organic molecules containing iodo and cyano groups (Bond et al., 2001; Britton, 2001, 2004; Desiraju & Harlow, 1989; Ojala et al., 1999), and as well as in organic co-crystals, organic cyano- and iodo-compounds (Bailey et al., 2000; Britton & Gleason, 2002; Metrangolo et al., 2004).
For related literature, see: Apinitis et al. (1984); Bailey et al. (2000); Bond et al. (2001); Britton (2001, 2004); Britton & Gleason (2002); Desiraju & Harlow (1989); Metrangolo et al. (2004); Nyburg & Faerman (1985); Ojala et al. (1999).
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: enCIFer (Allen et al., 2004).
C9H8INO2S | Z = 2 |
Mr = 321.12 | F(000) = 308 |
Triclinic, P1 | Dx = 1.910 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71069 Å |
a = 4.3132 (1) Å | Cell parameters from 9412 reflections |
b = 9.4355 (3) Å | θ = 3.6–29.5° |
c = 13.8210 (4) Å | µ = 3.03 mm−1 |
α = 87.736 (2)° | T = 298 K |
β = 84.396 (2)° | Needle, colourless |
γ = 86.166 (2)° | 0.73 × 0.10 × 0.06 mm |
V = 558.23 (3) Å3 |
Oxford Diffraction Gemini R CCD diffractometer | 2663 independent reflections |
Radiation source: fine-focus sealed tube | 1947 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
Detector resolution: 10.4340 pixels mm-1 | θmax = 28.0°, θmin = 3.6° |
ω and φ scans | h = −5→5 |
Absorption correction: analytical (Clark & Reid, 1995) | k = −12→12 |
Tmin = 0.383, Tmax = 0.872 | l = −18→18 |
16856 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.026 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.067 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0398P)2] where P = (Fo2 + 2Fc2)/3 |
2663 reflections | (Δ/σ)max < 0.001 |
129 parameters | Δρmax = 0.95 e Å−3 |
0 restraints | Δρmin = −0.47 e Å−3 |
C9H8INO2S | γ = 86.166 (2)° |
Mr = 321.12 | V = 558.23 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.3132 (1) Å | Mo Kα radiation |
b = 9.4355 (3) Å | µ = 3.03 mm−1 |
c = 13.8210 (4) Å | T = 298 K |
α = 87.736 (2)° | 0.73 × 0.10 × 0.06 mm |
β = 84.396 (2)° |
Oxford Diffraction Gemini R CCD diffractometer | 2663 independent reflections |
Absorption correction: analytical (Clark & Reid, 1995) | 1947 reflections with I > 2σ(I) |
Tmin = 0.383, Tmax = 0.872 | Rint = 0.039 |
16856 measured reflections |
R[F2 > 2σ(F2)] = 0.026 | 0 restraints |
wR(F2) = 0.067 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.95 e Å−3 |
2663 reflections | Δρmin = −0.47 e Å−3 |
129 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
I1 | 0.22760 (4) | −0.076548 (19) | 0.127435 (14) | 0.05116 (10) | |
S1 | 0.53223 (18) | 0.09997 (8) | 0.29133 (6) | 0.04452 (18) | |
N1 | 0.0199 (8) | 0.3059 (3) | −0.0005 (2) | 0.0684 (8) | |
O1 | 0.7918 (5) | 0.2529 (2) | 0.43010 (15) | 0.0511 (5) | |
O2 | 0.7225 (6) | 0.4763 (2) | 0.36908 (17) | 0.0631 (6) | |
C1 | 0.3505 (6) | 0.1064 (3) | 0.1876 (2) | 0.0417 (7) | |
C2 | 0.3038 (6) | 0.2436 (3) | 0.1528 (2) | 0.0407 (6) | |
C3 | 0.4183 (7) | 0.3469 (3) | 0.2102 (2) | 0.0425 (7) | |
C4 | 0.5503 (7) | 0.2834 (3) | 0.2882 (2) | 0.0400 (6) | |
C5 | 0.6954 (7) | 0.3497 (3) | 0.3649 (2) | 0.0438 (7) | |
C6 | 0.9331 (8) | 0.3055 (4) | 0.5121 (2) | 0.0561 (8) | |
H6A | 0.7802 | 0.3640 | 0.5515 | 0.067* | |
H6B | 1.1052 | 0.3629 | 0.4889 | 0.067* | |
C7 | 1.0460 (11) | 0.1831 (4) | 0.5701 (3) | 0.0777 (12) | |
H7A | 0.8713 | 0.1360 | 0.6018 | 0.117* | |
H7B | 1.1698 | 0.2147 | 0.6181 | 0.117* | |
H7C | 1.1710 | 0.1182 | 0.5283 | 0.117* | |
C8 | 0.1475 (8) | 0.2777 (3) | 0.0666 (2) | 0.0494 (8) | |
C9 | 0.3939 (9) | 0.5037 (3) | 0.1845 (3) | 0.0615 (9) | |
H9A | 0.2195 | 0.5483 | 0.2229 | 0.092* | |
H9B | 0.3645 | 0.5175 | 0.1167 | 0.092* | |
H9C | 0.5821 | 0.5452 | 0.1975 | 0.092* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.05619 (16) | 0.04507 (14) | 0.05412 (16) | −0.00672 (9) | −0.00908 (10) | −0.00998 (9) |
S1 | 0.0518 (4) | 0.0387 (4) | 0.0444 (4) | −0.0020 (3) | −0.0121 (3) | −0.0014 (3) |
N1 | 0.086 (2) | 0.0612 (18) | 0.0629 (19) | 0.0001 (16) | −0.0329 (17) | −0.0107 (15) |
O1 | 0.0613 (13) | 0.0456 (12) | 0.0504 (13) | −0.0053 (10) | −0.0236 (10) | −0.0031 (10) |
O2 | 0.0886 (17) | 0.0412 (12) | 0.0651 (15) | −0.0122 (11) | −0.0278 (12) | −0.0065 (11) |
C1 | 0.0403 (15) | 0.0451 (16) | 0.0405 (16) | −0.0021 (13) | −0.0063 (12) | −0.0069 (13) |
C2 | 0.0416 (15) | 0.0429 (16) | 0.0380 (16) | −0.0045 (13) | −0.0059 (12) | 0.0019 (13) |
C3 | 0.0412 (15) | 0.0398 (15) | 0.0468 (17) | −0.0028 (13) | −0.0050 (13) | −0.0029 (13) |
C4 | 0.0427 (16) | 0.0338 (14) | 0.0433 (16) | −0.0007 (12) | −0.0047 (13) | −0.0005 (12) |
C5 | 0.0403 (16) | 0.0478 (18) | 0.0437 (17) | −0.0058 (14) | −0.0028 (13) | −0.0043 (14) |
C6 | 0.068 (2) | 0.057 (2) | 0.0474 (18) | −0.0104 (17) | −0.0223 (16) | −0.0065 (15) |
C7 | 0.109 (3) | 0.069 (2) | 0.061 (2) | −0.021 (2) | −0.031 (2) | 0.0047 (19) |
C8 | 0.0560 (19) | 0.0422 (17) | 0.0503 (19) | −0.0011 (15) | −0.0094 (16) | 0.0001 (14) |
C9 | 0.079 (2) | 0.0405 (18) | 0.068 (2) | −0.0041 (17) | −0.0247 (19) | 0.0023 (16) |
I1—C1 | 2.067 (3) | C3—C9 | 1.507 (4) |
S1—C1 | 1.697 (3) | C4—C5 | 1.464 (4) |
S1—C4 | 1.736 (3) | C6—C7 | 1.463 (5) |
N1—C8 | 1.138 (4) | C6—H6A | 0.9700 |
O1—C5 | 1.333 (4) | C6—H6B | 0.9700 |
O1—C6 | 1.457 (4) | C7—H7A | 0.9600 |
O2—C5 | 1.212 (4) | C7—H7B | 0.9600 |
C1—C2 | 1.372 (4) | C7—H7C | 0.9600 |
C2—C3 | 1.424 (4) | C9—H9A | 0.9600 |
C2—C8 | 1.440 (4) | C9—H9B | 0.9600 |
C3—C4 | 1.367 (4) | C9—H9C | 0.9600 |
C1—S1—C4 | 91.75 (14) | O1—C6—H6A | 110.1 |
C5—O1—C6 | 116.8 (2) | C7—C6—H6A | 110.1 |
C2—C1—S1 | 111.3 (2) | O1—C6—H6B | 110.1 |
C2—C1—I1 | 127.3 (2) | C7—C6—H6B | 110.1 |
S1—C1—I1 | 121.34 (16) | H6A—C6—H6B | 108.4 |
C1—C2—C3 | 114.0 (2) | C6—C7—H7A | 109.5 |
C1—C2—C8 | 122.1 (3) | C6—C7—H7B | 109.5 |
C3—C2—C8 | 123.9 (3) | H7A—C7—H7B | 109.5 |
C4—C3—C2 | 110.7 (3) | C6—C7—H7C | 109.5 |
C4—C3—C9 | 126.6 (3) | H7A—C7—H7C | 109.5 |
C2—C3—C9 | 122.7 (3) | H7B—C7—H7C | 109.5 |
C3—C4—C5 | 128.7 (3) | N1—C8—C2 | 178.8 (4) |
C3—C4—S1 | 112.2 (2) | C3—C9—H9A | 109.5 |
C5—C4—S1 | 119.1 (2) | C3—C9—H9B | 109.5 |
O2—C5—O1 | 124.4 (3) | H9A—C9—H9B | 109.5 |
O2—C5—C4 | 124.4 (3) | C3—C9—H9C | 109.5 |
O1—C5—C4 | 111.2 (2) | H9A—C9—H9C | 109.5 |
O1—C6—C7 | 108.2 (3) | H9B—C9—H9C | 109.5 |
C4—S1—C1—C2 | −0.5 (2) | C9—C3—C4—S1 | −179.7 (3) |
C4—S1—C1—I1 | 179.25 (17) | C1—S1—C4—C3 | 0.5 (2) |
S1—C1—C2—C3 | 0.5 (3) | C1—S1—C4—C5 | −179.8 (2) |
I1—C1—C2—C3 | −179.3 (2) | C6—O1—C5—O2 | 1.2 (4) |
S1—C1—C2—C8 | −178.6 (2) | C6—O1—C5—C4 | −178.3 (3) |
I1—C1—C2—C8 | 1.6 (4) | C3—C4—C5—O2 | −1.0 (5) |
C1—C2—C3—C4 | −0.1 (4) | S1—C4—C5—O2 | 179.3 (3) |
C8—C2—C3—C4 | 179.0 (3) | C3—C4—C5—O1 | 178.5 (3) |
C1—C2—C3—C9 | 179.4 (3) | S1—C4—C5—O1 | −1.1 (3) |
C8—C2—C3—C9 | −1.6 (5) | C5—O1—C6—C7 | −175.3 (3) |
C2—C3—C4—C5 | 180.0 (3) | C1—C2—C8—N1 | 116 (18) |
C9—C3—C4—C5 | 0.5 (5) | C3—C2—C8—N1 | −63 (18) |
C2—C3—C4—S1 | −0.3 (3) |
Experimental details
Crystal data | |
Chemical formula | C9H8INO2S |
Mr | 321.12 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 298 |
a, b, c (Å) | 4.3132 (1), 9.4355 (3), 13.8210 (4) |
α, β, γ (°) | 87.736 (2), 84.396 (2), 86.166 (2) |
V (Å3) | 558.23 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 3.03 |
Crystal size (mm) | 0.73 × 0.10 × 0.06 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini R CCD |
Absorption correction | Analytical (Clark & Reid, 1995) |
Tmin, Tmax | 0.383, 0.872 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16856, 2663, 1947 |
Rint | 0.039 |
(sin θ/λ)max (Å−1) | 0.660 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.026, 0.067, 1.02 |
No. of reflections | 2663 |
No. of parameters | 129 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.95, −0.47 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), enCIFer (Allen et al., 2004).
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The family of well defined oligothiophene derivatives is important for polymer research, electronic semiconducting materials, non-linear optical materials and highly ordered molecular assemblies. Thiophene based oligomers are among the most investigated systems for technological applications, due to their chemical stability and wide spread possibility of functionalization. Moreover, they are relative to some other conjugated systems and represent structures with high labeled molecular architecture. Etyl 5-iodo-4-cyano-3-methylthiophene-2-carboxylate represents an important building block in desing of oligothiophene structure, in terms of its well defined molecular structure. We report herein the crystal structure of the title compound, (I).
In the molecule of the title compound, (I), (Fig. 1), the bond lengths are in accordance with those observed in ethyl 5-amino-4-cyano-3-methylthiophene-2-carboxylate (refcode: DACLIC; Apinitis et al., 1984). A weak intramolecular C—H···O hydrogen bond (Table 1) is also comparable with the corresponding one in DACLIC.
A cyclamer is formed by the association of two monomers through weak intermolecular CN···I Lewis acid-base interactions (Fig. 2). The CN···I distances are in accordance with the expected values from non-spherical radii of Nyburg & Faerman (1985). The angles at the N atoms are closer to trigonal, but the angles at the I atoms are approximately linear. In (I), the N···I distance, C—I···N and N···I—C angles are 3.142 (3) Å, 166.9 (1)° and 123.1 (1)°, respectively. The significant CN···I interactions (in the range of 2.9–3.3 Å) are well known in more organic molecules containing iodo and cyano groups (Bond et al., 2001; Britton, 2001, 2004; Desiraju & Harlow, 1989; Ojala et al., 1999), and as well as in organic co-crystals, organic cyano- and iodo-compounds (Bailey et al., 2000; Britton & Gleason, 2002; Metrangolo et al., 2004).