Pyridinium 5-nitro­thio­phene-2-carboxyl­ate

Yang, X.-Y.; Xu, N.; Liu, S.

doi:10.1107/S1600536810016089

organic compounds

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ISSN: 2056-9890

Volume 66| Part 6| June 2010| Page o1287

https://doi.org/10.1107/S1600536810016089

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Pyridinium 5-nitrothiophene-2-carboxylate

Xiao-Yan Yang,^a Ning Xu ^a and Shan Liu ^a ^*

^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 ). For the synthesis, see: Marques et al. (2002 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₅H₆N⁺·C₅H₂NO₄S⁻
M_r = 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 ) 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[F² > 2σ(F²)] = 0.039
wR(F²) = 0.080
S = 1.00
1990 reflections
155 parameters
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: CAD-4 Software; 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.

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810016089/ci5088Isup2.hkl

checkCIF report

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.

Structure description 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).

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

	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.

Pyridinium 5-nitrothiophene-2-carboxylate top

Crystal data top

C₅H₆N⁺·C₅H₂NO₄S⁻	Z = 2
M_r = 252.24	F(000) = 260
Triclinic, P1	D_x = 1.533 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.0940 (12) Å	Cell parameters from 25 reflections
b = 7.3390 (15) Å	θ = 10–13°
c = 13.296 (3) Å	µ = 0.30 mm⁻¹
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 tube	R_int = 0.019
Graphite monochromator	θ_max = 25.3°, θ_min = 1.6°
ω/2θ scans	h = 0→7
Absorption correction: ψ scan (North et al., 1968)	k = −8→8
T_min = 0.915, T_max = 0.971	l = −15→15
2194 measured reflections	3 standard reflections every 200 reflections
1990 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.080	w = 1/[σ²(F_o²) + (0.01P)² + 0.48P] where P = (F_o² + 2F_c²)/3
S = 1.00	(Δ/σ)_max = 0.001
1990 reflections	Δρ_max = 0.25 e Å⁻³
155 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0313 (18)

Crystal data top

C₅H₆N⁺·C₅H₂NO₄S⁻	γ = 71.00 (3)°
M_r = 252.24	V = 546.6 (2) Å³
Triclinic, P1	Z = 2
a = 6.0940 (12) Å	Mo Kα radiation
b = 7.3390 (15) Å	µ = 0.30 mm⁻¹
c = 13.296 (3) Å	T = 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)	R_int = 0.019
T_min = 0.915, T_max = 0.971	3 standard reflections every 200 reflections
2194 measured reflections	intensity decay: 1%
1990 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.080	H-atom parameters constrained
S = 1.00	Δρ_max = 0.25 e Å⁻³
1990 reflections	Δρ_min = −0.22 e Å⁻³
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

	x	y	z	U_iso*/U_eq
S	0.14233 (10)	0.12191 (9)	0.65371 (4)	0.04471 (19)
O1	−0.0782 (3)	−0.1820 (3)	0.90222 (13)	0.0592 (5)
O2	0.2305 (3)	−0.0690 (3)	0.86414 (12)	0.0534 (5)
O3	−0.1575 (4)	0.3584 (3)	0.40288 (14)	0.0753 (6)
O4	0.1837 (3)	0.3262 (3)	0.44510 (14)	0.0691 (6)
N2	−0.0093 (4)	0.3011 (3)	0.46450 (15)	0.0538 (5)
C6	0.0413 (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	−0.0095	0.7374	0.053*
C9	−0.2565 (4)	0.1453 (4)	0.59945 (18)	0.0469 (6)
H9	−0.3833	0.1760	0.5608	0.056*
C10	−0.0599 (4)	0.1972 (3)	0.56517 (17)	0.0427 (5)
N1	0.3544 (3)	−0.2797 (3)	1.04230 (14)	0.0437 (5)
H6	0.3164	−0.2065	0.9836	0.052*
C1	0.4731 (4)	−0.5108 (4)	1.22741 (19)	0.0518 (6)
H1	0.5143	−0.5902	1.2908	0.062*
C2	0.2816 (4)	−0.5107 (4)	1.18469 (19)	0.0521 (6)
H2	0.1911	−0.5896	1.2189	0.063*
C3	0.2254 (4)	−0.3937 (4)	1.09159 (18)	0.0481 (6)
H3	0.0960	−0.3932	1.0620	0.058*
C4	0.5408 (4)	−0.2773 (4)	1.08249 (18)	0.0496 (6)
H4	0.6285	−0.1969	1.0470	0.060*
C5	0.6035 (4)	−0.3923 (4)	1.17561 (19)	0.0529 (6)
H5	0.7335	−0.3906	1.2038	0.063*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S	0.0397 (3)	0.0594 (4)	0.0383 (3)	−0.0262 (3)	−0.0043 (2)	0.0019 (3)
O1	0.0587 (11)	0.0758 (13)	0.0452 (10)	−0.0380 (10)	−0.0053 (8)	0.0121 (9)
O2	0.0500 (10)	0.0674 (12)	0.0460 (10)	−0.0303 (9)	−0.0133 (8)	0.0084 (8)
O3	0.0928 (15)	0.0900 (16)	0.0461 (11)	−0.0385 (12)	−0.0276 (11)	0.0126 (10)
O4	0.0766 (13)	0.0872 (15)	0.0508 (11)	−0.0496 (12)	0.0058 (10)	0.0027 (10)
N2	0.0697 (15)	0.0555 (14)	0.0393 (11)	−0.0277 (12)	−0.0060 (11)	−0.0010 (10)
C6	0.0437 (13)	0.0418 (13)	0.0382 (12)	−0.0141 (11)	−0.0038 (10)	−0.0016 (10)
C7	0.0373 (12)	0.0384 (12)	0.0370 (12)	−0.0159 (10)	0.0013 (9)	−0.0035 (9)
C8	0.0355 (12)	0.0505 (14)	0.0459 (13)	−0.0190 (11)	−0.0012 (10)	−0.0024 (11)
C9	0.0389 (13)	0.0553 (15)	0.0485 (14)	−0.0182 (11)	−0.0105 (10)	−0.0030 (11)
C10	0.0470 (13)	0.0473 (14)	0.0340 (12)	−0.0180 (11)	−0.0057 (10)	−0.0009 (10)
N1	0.0438 (11)	0.0481 (12)	0.0353 (10)	−0.0144 (9)	−0.0036 (8)	0.0016 (9)
C1	0.0519 (15)	0.0557 (16)	0.0409 (13)	−0.0138 (12)	−0.0077 (11)	0.0037 (11)
C2	0.0538 (15)	0.0504 (15)	0.0527 (15)	−0.0254 (12)	−0.0040 (12)	0.0041 (12)
C3	0.0437 (13)	0.0541 (15)	0.0491 (14)	−0.0214 (12)	−0.0086 (11)	−0.0014 (12)
C4	0.0424 (13)	0.0602 (16)	0.0479 (14)	−0.0237 (12)	0.0007 (11)	−0.0040 (12)
C5	0.0417 (14)	0.0702 (18)	0.0484 (14)	−0.0199 (13)	−0.0078 (11)	−0.0074 (13)

Geometric parameters (Å, º) top

S—C10	1.705 (2)	N1—C4	1.331 (3)
S—C7	1.717 (2)	N1—C3	1.335 (3)
O1—C6	1.233 (3)	N1—H6	0.86
O2—C6	1.275 (3)	C1—C2	1.371 (3)
O3—N2	1.218 (3)	C1—C5	1.374 (3)
O4—N2	1.230 (3)	C1—H1	0.93
N2—C10	1.432 (3)	C2—C3	1.361 (3)
C6—C7	1.492 (3)	C2—H2	0.93
C7—C8	1.364 (3)	C3—H3	0.93
C8—C9	1.400 (3)	C4—C5	1.364 (3)
C8—H8	0.93	C4—H4	0.93
C9—C10	1.360 (3)	C5—H5	0.93
C9—H9	0.93

C10—S—C7	89.85 (11)	C4—N1—C3	121.1 (2)
O3—N2—O4	123.7 (2)	C4—N1—H6	119.4
O3—N2—C10	118.7 (2)	C3—N1—H6	119.4
O4—N2—C10	117.6 (2)	C2—C1—C5	119.3 (2)
O1—C6—O2	126.8 (2)	C2—C1—H1	120.3
O1—C6—C7	118.1 (2)	C5—C1—H1	120.3
O2—C6—C7	115.03 (19)	C3—C2—C1	119.2 (2)
C8—C7—C6	129.1 (2)	C3—C2—H2	120.4
C8—C7—S	112.21 (16)	C1—C2—H2	120.4
C6—C7—S	118.70 (16)	N1—C3—C2	120.6 (2)
C7—C8—C9	113.0 (2)	N1—C3—H3	119.7
C7—C8—H8	123.5	C2—C3—H3	119.7
C9—C8—H8	123.5	N1—C4—C5	120.2 (2)
C10—C9—C8	110.8 (2)	N1—C4—H4	119.9
C10—C9—H9	124.6	C5—C4—H4	119.9
C8—C9—H9	124.6	C4—C5—C1	119.5 (2)
C9—C10—N2	126.6 (2)	C4—C5—H5	120.3
C9—C10—S	114.08 (17)	C1—C5—H5	120.3
N2—C10—S	119.34 (17)

O1—C6—C7—C8	7.6 (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—S	2.3 (3)
O2—C6—C7—S	7.3 (3)	C7—S—C10—C9	0.4 (2)
C10—S—C7—C8	−0.19 (19)	C7—S—C10—N2	−178.2 (2)
C10—S—C7—C6	179.87 (19)	C5—C1—C2—C3	0.3 (4)
C6—C7—C8—C9	179.9 (2)	C4—N1—C3—C2	0.1 (4)
S—C7—C8—C9	−0.1 (3)	C1—C2—C3—N1	−0.2 (4)
C7—C8—C9—C10	0.3 (3)	C3—N1—C4—C5	0.0 (4)
C8—C9—C10—N2	178.0 (2)	N1—C4—C5—C1	0.1 (4)
C8—C9—C10—S	−0.5 (3)	C2—C1—C5—C4	−0.2 (4)
O3—N2—C10—C9	3.4 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Experimental details

Crystal data
Chemical formula	C₅H₆N⁺·C₅H₂NO₄S⁻
M_r	252.24
Crystal system, space group	Triclinic, 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)
V (Å³)	546.6 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.30
Crystal size (mm)	0.30 × 0.20 × 0.10

Data collection
Diffractometer	Enraf–Nonius CAD-4
Absorption correction	ψ scan (North et al., 1968)
T_min, T_max	0.915, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections	2194, 1990, 1657
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.601

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.080, 1.00
No. of reflections	1990
No. of parameters	155
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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.

Acknowledgements

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

References

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