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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): o1287.
Published online 2010 May 8. doi:  10.1107/S1600536810016089
PMCID: PMC2979441

Pyridinium 5-nitro­thio­phene-2-carboxyl­ate

Abstract

The anion of the title compound, C5H6N+·C5H2NO4S, is approximately planar, with the carboxyl­ate and nitro group planes forming dihedral angles of 7.5 (3) and 3.5 (3)°, respectively, with the thio­phene ring. In the crystal structure, the cations and anions are linked into a two-dimensional network parallel to (011) by N—H(...)O and C—H(...)O hydrogen bonds.

Related literature

For the uses of 5-nitro­thio­phene-2-carboxylic acid, see: Cao et al. (2003 [triangle]). For the synthesis, see: Marques et al. (2002 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

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Object name is e-66-o1287-scheme1.jpg

Experimental

Crystal data

  • C5H6N+·C5H2NO4S
  • M r = 252.24
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1287-efi1.jpg
  • a = 6.0940 (12) Å
  • b = 7.3390 (15) Å
  • c = 13.296 (3) Å
  • α = 77.30 (3)°
  • β = 81.52 (3)°
  • γ = 71.00 (3)°
  • V = 546.6 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.30 mm−1
  • T = 298 K
  • 0.30 × 0.20 × 0.10 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: ψ scan (North et al., 1968 [triangle]) T min = 0.915, T max = 0.971
  • 2194 measured reflections
  • 1990 independent reflections
  • 1657 reflections with I > 2σ(I)
  • R int = 0.019
  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.080
  • S = 1.00
  • 1990 reflections
  • 155 parameters
  • H-atom parameters constrained
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1985 [triangle]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810016089/ci5088sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810016089/ci5088Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Center of Testing and Analysis, Nanjing University, for the data collection.

supplementary crystallographic information

Comment

5-Nitrothiophene-2-carboxylic acid is an important intermediate used to synthesize raltitrexed (trade name Tomudex), an antimetabolite drug used in cancer chemotherapy (Cao et al., 2003). We report here the crystal structure of the title compound (Fig. 1).

Bond lengths and angles in both cation and anion are within normal ranges (Allen et al., 1987). The anion is approximately planar; the C6/O1/O2 and N2/O3/O4 planes form dihedral angles of 7.5 (3)° and 3.5 (3)°, respectively, with the thiophene ring. In the crystal structure, the cations and anions are linked into a two-dimensional network (Fig. 2) by N—H···O and C—H···O hydrogen bonds.

Experimental

5-Nitrothiophene-2-carboxylic acid was prepared by the method reported in literature (Marques et al., 2002). Single crystals were obtained by dissolving 5-nitrothiophene-2-carboxylic acid (0.5 g, 2.89 mmol) in pyridine (50 ml) and evaporating the solvent slowly at room temperature for about 20 d.

Refinement

After checking their presence in the difference map, all the H atoms were positioned geometrically [N—H = 0.86 and C—H = 0.93 Å] and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,N).

Figures

Fig. 1.
The asymmetric unit of the title compound, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. Hydrogen bonds are shown as dashed lines.
Fig. 2.
Crystal packing of the title compound. hydrogen bonds are shown as dashed lines.

Crystal data

C5H6N+·C5H2NO4SZ = 2
Mr = 252.24F(000) = 260
Triclinic, P1Dx = 1.533 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.0940 (12) ÅCell parameters from 25 reflections
b = 7.3390 (15) Åθ = 10–13°
c = 13.296 (3) ŵ = 0.30 mm1
α = 77.30 (3)°T = 298 K
β = 81.52 (3)°Block, colourless
γ = 71.00 (3)°0.30 × 0.20 × 0.10 mm
V = 546.6 (2) Å3

Data collection

Enraf–Nonius CAD-4 diffractometer1657 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.019
graphiteθmax = 25.3°, θmin = 1.6°
ω/2θ scansh = 0→7
Absorption correction: ψ scan (North et al., 1968)k = −8→8
Tmin = 0.915, Tmax = 0.971l = −15→15
2194 measured reflections3 standard reflections every 200 reflections
1990 independent reflections intensity decay: 1%

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H-atom parameters constrained
wR(F2) = 0.080w = 1/[σ2(Fo2) + (0.01P)2 + 0.48P] where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max = 0.001
1990 reflectionsΔρmax = 0.25 e Å3
155 parametersΔρmin = −0.22 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: 0.0313 (18)

Special details

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

xyzUiso*/Ueq
S0.14233 (10)0.12191 (9)0.65371 (4)0.04471 (19)
O1−0.0782 (3)−0.1820 (3)0.90222 (13)0.0592 (5)
O20.2305 (3)−0.0690 (3)0.86414 (12)0.0534 (5)
O3−0.1575 (4)0.3584 (3)0.40288 (14)0.0753 (6)
O40.1837 (3)0.3262 (3)0.44510 (14)0.0691 (6)
N2−0.0093 (4)0.3011 (3)0.46450 (15)0.0538 (5)
C60.0413 (4)−0.0881 (3)0.84465 (17)0.0419 (5)
C7−0.0384 (4)0.0149 (3)0.74043 (16)0.0375 (5)
C8−0.2423 (4)0.0392 (3)0.70084 (17)0.0438 (6)
H8−0.3598−0.00950.73740.053*
C9−0.2565 (4)0.1453 (4)0.59945 (18)0.0469 (6)
H9−0.38330.17600.56080.056*
C10−0.0599 (4)0.1972 (3)0.56517 (17)0.0427 (5)
N10.3544 (3)−0.2797 (3)1.04230 (14)0.0437 (5)
H60.3164−0.20650.98360.052*
C10.4731 (4)−0.5108 (4)1.22741 (19)0.0518 (6)
H10.5143−0.59021.29080.062*
C20.2816 (4)−0.5107 (4)1.18469 (19)0.0521 (6)
H20.1911−0.58961.21890.063*
C30.2254 (4)−0.3937 (4)1.09159 (18)0.0481 (6)
H30.0960−0.39321.06200.058*
C40.5408 (4)−0.2773 (4)1.08249 (18)0.0496 (6)
H40.6285−0.19691.04700.060*
C50.6035 (4)−0.3923 (4)1.17561 (19)0.0529 (6)
H50.7335−0.39061.20380.063*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S0.0397 (3)0.0594 (4)0.0383 (3)−0.0262 (3)−0.0043 (2)0.0019 (3)
O10.0587 (11)0.0758 (13)0.0452 (10)−0.0380 (10)−0.0053 (8)0.0121 (9)
O20.0500 (10)0.0674 (12)0.0460 (10)−0.0303 (9)−0.0133 (8)0.0084 (8)
O30.0928 (15)0.0900 (16)0.0461 (11)−0.0385 (12)−0.0276 (11)0.0126 (10)
O40.0766 (13)0.0872 (15)0.0508 (11)−0.0496 (12)0.0058 (10)0.0027 (10)
N20.0697 (15)0.0555 (14)0.0393 (11)−0.0277 (12)−0.0060 (11)−0.0010 (10)
C60.0437 (13)0.0418 (13)0.0382 (12)−0.0141 (11)−0.0038 (10)−0.0016 (10)
C70.0373 (12)0.0384 (12)0.0370 (12)−0.0159 (10)0.0013 (9)−0.0035 (9)
C80.0355 (12)0.0505 (14)0.0459 (13)−0.0190 (11)−0.0012 (10)−0.0024 (11)
C90.0389 (13)0.0553 (15)0.0485 (14)−0.0182 (11)−0.0105 (10)−0.0030 (11)
C100.0470 (13)0.0473 (14)0.0340 (12)−0.0180 (11)−0.0057 (10)−0.0009 (10)
N10.0438 (11)0.0481 (12)0.0353 (10)−0.0144 (9)−0.0036 (8)0.0016 (9)
C10.0519 (15)0.0557 (16)0.0409 (13)−0.0138 (12)−0.0077 (11)0.0037 (11)
C20.0538 (15)0.0504 (15)0.0527 (15)−0.0254 (12)−0.0040 (12)0.0041 (12)
C30.0437 (13)0.0541 (15)0.0491 (14)−0.0214 (12)−0.0086 (11)−0.0014 (12)
C40.0424 (13)0.0602 (16)0.0479 (14)−0.0237 (12)0.0007 (11)−0.0040 (12)
C50.0417 (14)0.0702 (18)0.0484 (14)−0.0199 (13)−0.0078 (11)−0.0074 (13)

Geometric parameters (Å, °)

S—C101.705 (2)N1—C41.331 (3)
S—C71.717 (2)N1—C31.335 (3)
O1—C61.233 (3)N1—H60.86
O2—C61.275 (3)C1—C21.371 (3)
O3—N21.218 (3)C1—C51.374 (3)
O4—N21.230 (3)C1—H10.93
N2—C101.432 (3)C2—C31.361 (3)
C6—C71.492 (3)C2—H20.93
C7—C81.364 (3)C3—H30.93
C8—C91.400 (3)C4—C51.364 (3)
C8—H80.93C4—H40.93
C9—C101.360 (3)C5—H50.93
C9—H90.93
C10—S—C789.85 (11)C4—N1—C3121.1 (2)
O3—N2—O4123.7 (2)C4—N1—H6119.4
O3—N2—C10118.7 (2)C3—N1—H6119.4
O4—N2—C10117.6 (2)C2—C1—C5119.3 (2)
O1—C6—O2126.8 (2)C2—C1—H1120.3
O1—C6—C7118.1 (2)C5—C1—H1120.3
O2—C6—C7115.03 (19)C3—C2—C1119.2 (2)
C8—C7—C6129.1 (2)C3—C2—H2120.4
C8—C7—S112.21 (16)C1—C2—H2120.4
C6—C7—S118.70 (16)N1—C3—C2120.6 (2)
C7—C8—C9113.0 (2)N1—C3—H3119.7
C7—C8—H8123.5C2—C3—H3119.7
C9—C8—H8123.5N1—C4—C5120.2 (2)
C10—C9—C8110.8 (2)N1—C4—H4119.9
C10—C9—H9124.6C5—C4—H4119.9
C8—C9—H9124.6C4—C5—C1119.5 (2)
C9—C10—N2126.6 (2)C4—C5—H5120.3
C9—C10—S114.08 (17)C1—C5—H5120.3
N2—C10—S119.34 (17)
O1—C6—C7—C87.6 (4)O4—N2—C10—C9−176.1 (2)
O2—C6—C7—C8−172.7 (2)O3—N2—C10—S−178.2 (2)
O1—C6—C7—S−172.45 (18)O4—N2—C10—S2.3 (3)
O2—C6—C7—S7.3 (3)C7—S—C10—C90.4 (2)
C10—S—C7—C8−0.19 (19)C7—S—C10—N2−178.2 (2)
C10—S—C7—C6179.87 (19)C5—C1—C2—C30.3 (4)
C6—C7—C8—C9179.9 (2)C4—N1—C3—C20.1 (4)
S—C7—C8—C9−0.1 (3)C1—C2—C3—N1−0.2 (4)
C7—C8—C9—C100.3 (3)C3—N1—C4—C50.0 (4)
C8—C9—C10—N2178.0 (2)N1—C4—C5—C10.1 (4)
C8—C9—C10—S−0.5 (3)C2—C1—C5—C4−0.2 (4)
O3—N2—C10—C93.4 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H6···O20.861.742.594 (3)176
C3—H3···O10.932.493.156 (3)129
C1—H1···O3i0.932.553.254 (3)133
C4—H4···O1ii0.932.443.210 (3)141

Symmetry codes: (i) x+1, y−1, z+1; (ii) x+1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI5088).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Cao, S. L., Wan, R. & Feng, Y. P. (2003). Synth. Commun.33, 3519–3526.
  • Enraf–Nonius (1985). CAD-4 Software Enraf–Nonius, Delft, The Netherlands.
  • Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
  • Marques, M. A., Doss, R. M., Urbach, A. R. & Dervan, P. B. (2002). Helv. Chim. Acta, 85, 4485–4517.
  • North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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