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

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ISSN: 2056-9890

Pyridinium 5-nitro­thio­phene-2-carboxyl­ate

aDepartment of Chemical Engineering, Nanjing College of Chemical Technology, Nanjing 210048, People's Republic of China
*Correspondence e-mail: dols80@163.com

(Received 28 April 2010; accepted 1 May 2010; online 8 May 2010)

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[Cao, S. L., Wan, R. & Feng, Y. P. (2003). Synth. Commun. 33, 3519-3526.]). For the synthesis, see: Marques et al. (2002[Marques, M. A., Doss, R. M., Urbach, A. R. & Dervan, P. B. (2002). Helv. Chim. Acta, 85, 4485-4517.]). For bond-length data, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C5H6N+·C5H2NO4S

  • Mr = 252.24

  • Triclinic, [P \overline 1]

  • 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[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.915, Tmax = 0.971

  • 2194 measured reflections

  • 1990 independent reflections

  • 1657 reflections with I > 2σ(I)

  • Rint = 0.019

  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H6⋯O2 0.86 1.74 2.594 (3) 176
C3—H3⋯O1 0.93 2.49 3.156 (3) 129
C1—H1⋯O3i 0.93 2.55 3.254 (3) 133
C4—H4⋯O1ii 0.93 2.44 3.210 (3) 141
Symmetry codes: (i) x+1, y-1, z+1; (ii) x+1, y, z.

Data collection: CAD-4 Software (Enraf–Nonius, 1985[Enraf-Nonius (1985). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); 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

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.

Related literature top

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

Experimental top

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 top

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).

Structure description top

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.

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

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell refinement: CAD-4 Software (Enraf–Nonius, 1985); data reduction: XCAD4 (Harms & Wocadlo, 1995); 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 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.
[Figure 2] Fig. 2. Crystal packing of the title compound. hydrogen bonds are shown as dashed lines.
Pyridinium 5-nitrothiophene-2-carboxylate top
Crystal data top
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 top
Enraf–Nonius CAD-4
diffractometer
1657 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.019
Graphite monochromatorθmax = 25.3°, θmin = 1.6°
ω/2θ scansh = 07
Absorption correction: ψ scan
(North et al., 1968)
k = 88
Tmin = 0.915, Tmax = 0.971l = 1515
2194 measured reflections3 standard reflections every 200 reflections
1990 independent reflections intensity decay: 1%
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)] = 0.039H-atom parameters constrained
wR(F2) = 0.080 w = 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)
Crystal data top
C5H6N+·C5H2NO4Sγ = 71.00 (3)°
Mr = 252.24V = 546.6 (2) Å3
Triclinic, P1Z = 2
a = 6.0940 (12) ÅMo Kα radiation
b = 7.3390 (15) ŵ = 0.30 mm1
c = 13.296 (3) ÅT = 298 K
α = 77.30 (3)°0.30 × 0.20 × 0.10 mm
β = 81.52 (3)°
Data collection top
Enraf–Nonius CAD-4
diffractometer
1657 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968)
Rint = 0.019
Tmin = 0.915, Tmax = 0.9713 standard reflections every 200 reflections
2194 measured reflections intensity decay: 1%
1990 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.080H-atom parameters constrained
S = 1.00Δρmax = 0.25 e Å3
1990 reflectionsΔρmin = 0.22 e Å3
155 parameters
Special details top

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) top
xyzUiso*/Ueq
S0.14233 (10)0.12191 (9)0.65371 (4)0.04471 (19)
O10.0782 (3)0.1820 (3)0.90222 (13)0.0592 (5)
O20.2305 (3)0.0690 (3)0.86414 (12)0.0534 (5)
O30.1575 (4)0.3584 (3)0.40288 (14)0.0753 (6)
O40.1837 (3)0.3262 (3)0.44510 (14)0.0691 (6)
N20.0093 (4)0.3011 (3)0.46450 (15)0.0538 (5)
C60.0413 (4)0.0881 (3)0.84465 (17)0.0419 (5)
C70.0384 (4)0.0149 (3)0.74043 (16)0.0375 (5)
C80.2423 (4)0.0392 (3)0.70084 (17)0.0438 (6)
H80.35980.00950.73740.053*
C90.2565 (4)0.1453 (4)0.59945 (18)0.0469 (6)
H90.38330.17600.56080.056*
C100.0599 (4)0.1972 (3)0.56517 (17)0.0427 (5)
N10.3544 (3)0.2797 (3)1.04230 (14)0.0437 (5)
H60.31640.20650.98360.052*
C10.4731 (4)0.5108 (4)1.22741 (19)0.0518 (6)
H10.51430.59021.29080.062*
C20.2816 (4)0.5107 (4)1.18469 (19)0.0521 (6)
H20.19110.58961.21890.063*
C30.2254 (4)0.3937 (4)1.09159 (18)0.0481 (6)
H30.09600.39321.06200.058*
C40.5408 (4)0.2773 (4)1.08249 (18)0.0496 (6)
H40.62850.19691.04700.060*
C50.6035 (4)0.3923 (4)1.17561 (19)0.0529 (6)
H50.73350.39061.20380.063*
Atomic displacement parameters (Å2) top
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, º) top
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—C9176.1 (2)
O2—C6—C7—C8172.7 (2)O3—N2—C10—S178.2 (2)
O1—C6—C7—S172.45 (18)O4—N2—C10—S2.3 (3)
O2—C6—C7—S7.3 (3)C7—S—C10—C90.4 (2)
C10—S—C7—C80.19 (19)C7—S—C10—N2178.2 (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—C90.1 (3)C1—C2—C3—N10.2 (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—S0.5 (3)C2—C1—C5—C40.2 (4)
O3—N2—C10—C93.4 (4)
Hydrogen-bond geometry (Å, º) top
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, y1, z+1; (ii) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC5H6N+·C5H2NO4S
Mr252.24
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)6.0940 (12), 7.3390 (15), 13.296 (3)
α, β, γ (°)77.30 (3), 81.52 (3), 71.00 (3)
V3)546.6 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.30
Crystal size (mm)0.30 × 0.20 × 0.10
Data collection
DiffractometerEnraf–Nonius CAD-4
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.915, 0.971
No. of measured, independent and
observed [I > 2σ(I)] reflections
2194, 1990, 1657
Rint0.019
(sin θ/λ)max1)0.601
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.080, 1.00
No. of reflections1990
No. of parameters155
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.25, 0.22

Computer programs: CAD-4 Software (Enraf–Nonius, 1985), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
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, y1, z+1; (ii) x+1, y, z.
 

Acknowledgements

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

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CSD CrossRef Web of Science Google Scholar
First citationCao, S. L., Wan, R. & Feng, Y. P. (2003). Synth. Commun. 33, 3519–3526.  Web of Science CrossRef CAS Google Scholar
First citationEnraf–Nonius (1985). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.  Google Scholar
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.  Google Scholar
First citationMarques, M. A., Doss, R. M., Urbach, A. R. & Dervan, P. B. (2002). Helv. Chim. Acta, 85, 4485–4517.  Web of Science CrossRef CAS Google Scholar
First citationNorth, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.  CrossRef IUCr Journals Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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ISSN: 2056-9890
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