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The title compound, C9H8INO2S, was synthesized by starting from ethyl 5-amino-4-cyano-3-methyl­thio­phene-2-carboxyl­ate via Sandmeyer-type deamination, replacing the NH2 group by iodine. In the crystal structure, mol­ecules form a two-membered cyclamer held together by CN...I inter­molecular Lewis acid–base inter­actions. The N...I distance, and C—I...N and N...I—C angles are 3.142 (3) Å, 166.9 (1)° and 123.1 (1)°, respectively.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807041451/hk2315sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807041451/hk2315Isup2.hkl
Contains datablock I

CCDC reference: 660376

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](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

Comment top

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).

Related literature top

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).

Experimental top

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).

Refinement top

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.

Structure description top

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).

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Two-membered cyclamers of (I), through CN···I intermolecular interactions.
Ethyl 4-cyano-5-iodo-3-methylthiophene-2-carboxylate top
Crystal data top
C9H8INO2SZ = 2
Mr = 321.12F(000) = 308
Triclinic, P1Dx = 1.910 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71069 Å
a = 4.3132 (1) ÅCell parameters from 9412 reflections
b = 9.4355 (3) Åθ = 3.6–29.5°
c = 13.8210 (4) ŵ = 3.03 mm1
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
Data collection top
Oxford Diffraction Gemini R CCD
diffractometer
2663 independent reflections
Radiation source: fine-focus sealed tube1947 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.039
Detector resolution: 10.4340 pixels mm-1θmax = 28.0°, θmin = 3.6°
ω and φ scansh = 55
Absorption correction: analytical
(Clark & Reid, 1995)
k = 1212
Tmin = 0.383, Tmax = 0.872l = 1818
16856 measured reflections
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)] = 0.026Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.067H-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 parametersΔρmax = 0.95 e Å3
0 restraintsΔρmin = 0.47 e Å3
Crystal data top
C9H8INO2Sγ = 86.166 (2)°
Mr = 321.12V = 558.23 (3) Å3
Triclinic, P1Z = 2
a = 4.3132 (1) ÅMo Kα radiation
b = 9.4355 (3) ŵ = 3.03 mm1
c = 13.8210 (4) ÅT = 298 K
α = 87.736 (2)°0.73 × 0.10 × 0.06 mm
β = 84.396 (2)°
Data collection top
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 = 0.872Rint = 0.039
16856 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0260 restraints
wR(F2) = 0.067H-atom parameters constrained
S = 1.02Δρmax = 0.95 e Å3
2663 reflectionsΔρmin = 0.47 e Å3
129 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
I10.22760 (4)0.076548 (19)0.127435 (14)0.05116 (10)
S10.53223 (18)0.09997 (8)0.29133 (6)0.04452 (18)
N10.0199 (8)0.3059 (3)0.0005 (2)0.0684 (8)
O10.7918 (5)0.2529 (2)0.43010 (15)0.0511 (5)
O20.7225 (6)0.4763 (2)0.36908 (17)0.0631 (6)
C10.3505 (6)0.1064 (3)0.1876 (2)0.0417 (7)
C20.3038 (6)0.2436 (3)0.1528 (2)0.0407 (6)
C30.4183 (7)0.3469 (3)0.2102 (2)0.0425 (7)
C40.5503 (7)0.2834 (3)0.2882 (2)0.0400 (6)
C50.6954 (7)0.3497 (3)0.3649 (2)0.0438 (7)
C60.9331 (8)0.3055 (4)0.5121 (2)0.0561 (8)
H6A0.78020.36400.55150.067*
H6B1.10520.36290.48890.067*
C71.0460 (11)0.1831 (4)0.5701 (3)0.0777 (12)
H7A0.87130.13600.60180.117*
H7B1.16980.21470.61810.117*
H7C1.17100.11820.52830.117*
C80.1475 (8)0.2777 (3)0.0666 (2)0.0494 (8)
C90.3939 (9)0.5037 (3)0.1845 (3)0.0615 (9)
H9A0.21950.54830.22290.092*
H9B0.36450.51750.11670.092*
H9C0.58210.54520.19750.092*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.05619 (16)0.04507 (14)0.05412 (16)0.00672 (9)0.00908 (10)0.00998 (9)
S10.0518 (4)0.0387 (4)0.0444 (4)0.0020 (3)0.0121 (3)0.0014 (3)
N10.086 (2)0.0612 (18)0.0629 (19)0.0001 (16)0.0329 (17)0.0107 (15)
O10.0613 (13)0.0456 (12)0.0504 (13)0.0053 (10)0.0236 (10)0.0031 (10)
O20.0886 (17)0.0412 (12)0.0651 (15)0.0122 (11)0.0278 (12)0.0065 (11)
C10.0403 (15)0.0451 (16)0.0405 (16)0.0021 (13)0.0063 (12)0.0069 (13)
C20.0416 (15)0.0429 (16)0.0380 (16)0.0045 (13)0.0059 (12)0.0019 (13)
C30.0412 (15)0.0398 (15)0.0468 (17)0.0028 (13)0.0050 (13)0.0029 (13)
C40.0427 (16)0.0338 (14)0.0433 (16)0.0007 (12)0.0047 (13)0.0005 (12)
C50.0403 (16)0.0478 (18)0.0437 (17)0.0058 (14)0.0028 (13)0.0043 (14)
C60.068 (2)0.057 (2)0.0474 (18)0.0104 (17)0.0223 (16)0.0065 (15)
C70.109 (3)0.069 (2)0.061 (2)0.021 (2)0.031 (2)0.0047 (19)
C80.0560 (19)0.0422 (17)0.0503 (19)0.0011 (15)0.0094 (16)0.0001 (14)
C90.079 (2)0.0405 (18)0.068 (2)0.0041 (17)0.0247 (19)0.0023 (16)
Geometric parameters (Å, º) top
I1—C12.067 (3)C3—C91.507 (4)
S1—C11.697 (3)C4—C51.464 (4)
S1—C41.736 (3)C6—C71.463 (5)
N1—C81.138 (4)C6—H6A0.9700
O1—C51.333 (4)C6—H6B0.9700
O1—C61.457 (4)C7—H7A0.9600
O2—C51.212 (4)C7—H7B0.9600
C1—C21.372 (4)C7—H7C0.9600
C2—C31.424 (4)C9—H9A0.9600
C2—C81.440 (4)C9—H9B0.9600
C3—C41.367 (4)C9—H9C0.9600
C1—S1—C491.75 (14)O1—C6—H6A110.1
C5—O1—C6116.8 (2)C7—C6—H6A110.1
C2—C1—S1111.3 (2)O1—C6—H6B110.1
C2—C1—I1127.3 (2)C7—C6—H6B110.1
S1—C1—I1121.34 (16)H6A—C6—H6B108.4
C1—C2—C3114.0 (2)C6—C7—H7A109.5
C1—C2—C8122.1 (3)C6—C7—H7B109.5
C3—C2—C8123.9 (3)H7A—C7—H7B109.5
C4—C3—C2110.7 (3)C6—C7—H7C109.5
C4—C3—C9126.6 (3)H7A—C7—H7C109.5
C2—C3—C9122.7 (3)H7B—C7—H7C109.5
C3—C4—C5128.7 (3)N1—C8—C2178.8 (4)
C3—C4—S1112.2 (2)C3—C9—H9A109.5
C5—C4—S1119.1 (2)C3—C9—H9B109.5
O2—C5—O1124.4 (3)H9A—C9—H9B109.5
O2—C5—C4124.4 (3)C3—C9—H9C109.5
O1—C5—C4111.2 (2)H9A—C9—H9C109.5
O1—C6—C7108.2 (3)H9B—C9—H9C109.5
C4—S1—C1—C20.5 (2)C9—C3—C4—S1179.7 (3)
C4—S1—C1—I1179.25 (17)C1—S1—C4—C30.5 (2)
S1—C1—C2—C30.5 (3)C1—S1—C4—C5179.8 (2)
I1—C1—C2—C3179.3 (2)C6—O1—C5—O21.2 (4)
S1—C1—C2—C8178.6 (2)C6—O1—C5—C4178.3 (3)
I1—C1—C2—C81.6 (4)C3—C4—C5—O21.0 (5)
C1—C2—C3—C40.1 (4)S1—C4—C5—O2179.3 (3)
C8—C2—C3—C4179.0 (3)C3—C4—C5—O1178.5 (3)
C1—C2—C3—C9179.4 (3)S1—C4—C5—O11.1 (3)
C8—C2—C3—C91.6 (5)C5—O1—C6—C7175.3 (3)
C2—C3—C4—C5180.0 (3)C1—C2—C8—N1116 (18)
C9—C3—C4—C50.5 (5)C3—C2—C8—N163 (18)
C2—C3—C4—S10.3 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C9—H9C···O20.962.553.031 (4)111

Experimental details

Crystal data
Chemical formulaC9H8INO2S
Mr321.12
Crystal system, space groupTriclinic, 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)
V3)558.23 (3)
Z2
Radiation typeMo Kα
µ (mm1)3.03
Crystal size (mm)0.73 × 0.10 × 0.06
Data collection
DiffractometerOxford Diffraction Gemini R CCD
Absorption correctionAnalytical
(Clark & Reid, 1995)
Tmin, Tmax0.383, 0.872
No. of measured, independent and
observed [I > 2σ(I)] reflections
16856, 2663, 1947
Rint0.039
(sin θ/λ)max1)0.660
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.067, 1.02
No. of reflections2663
No. of parameters129
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C9—H9C···O20.962.553.031 (4)110.9
 

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