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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2235–o2236.
Published online 2009 August 26. doi:  10.1107/S1600536809033030
PMCID: PMC2969908

N′-[(3-Methyl-2-thien­yl)carbon­yl]isonicotinohydrazide

Abstract

In the title compound, C12H11N3O2S, the pyridine ring is inclined to the thio­phene ring, forming a dihedral angle of 34.96 (7)°. The mean plane through the hydrazide unit forms dihedral angles of 21.57 (8) and 53.08 (8)°, respectively, with the pyridine and thio­phene rings. The two O atoms are twisted away from each other, as indicated by the C—N—N—C torsion angle of −81.27 (15)°. In the crystal structure, mol­ecules are linked into an extended three-dimensional network by inter­molecular N—H(...)N, N—H(...)O and C—H(...)O hydrogen bonds. The crystal structure also features a short S(...)O [3.2686 (10) Å] inter­action and a weak inter­molecular C—H(...)π inter­action.

Related literature

For general background to and application of isoniazid derivatives, see: Janin (2007 [triangle]); Maccari et al. (2005 [triangle]); Slayden et al. (2000 [triangle]). For the preparation of the title compound, see: Besra et al. (1993 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For a closely related structure, see: Naveenkumar et al. (2009 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2235-scheme1.jpg

Experimental

Crystal data

  • C12H11N3O2S
  • M r = 261.30
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2235-efi1.jpg
  • a = 8.9206 (1) Å
  • b = 10.7552 (2) Å
  • c = 12.4934 (2) Å
  • V = 1198.65 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.27 mm−1
  • T = 100 K
  • 0.58 × 0.20 × 0.15 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.861, T max = 0.961
  • 17333 measured reflections
  • 4355 independent reflections
  • 4078 reflections with I > 2σ(I)
  • R int = 0.025

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.097
  • S = 1.05
  • 4355 reflections
  • 165 parameters
  • H-atom parameters constrained
  • Δρmax = 0.79 e Å−3
  • Δρmin = −0.43 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1856 Friedel pairs
  • Flack parameter: −0.04 (6)

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809033030/is2451sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809033030/is2451Isup2.hkl

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

Acknowledgments

This research was supported by Universiti Sains Malaysia (USM) under the University Research Grant (No. 1001/PFARMASI/815005). HKF and JHG thank USM for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). HSNK and JHG thank USM for the award of a USM Fellowship.

supplementary crystallographic information

Comment

In the search of new compounds, isoniazid derivatives have been found to possess potential tuberculostatic activity (Janin, 2007; Maccari et al., 2005; Slayden et al., 2000). As a part of a current work on synthesis of such derivatives, in this paper we present the crystal structure of the title compound, (I) which was synthesized in our lab.

In (I), the pyridine ring (C1/C2/N1/C3-C5) is inclined to the thiophene ring (C8-C11/S1), forming a dihedral angle of 34.96 (7)° (Fig. 1). The mean plane through the hydrazide unit (C7/N2/N3/O2) forms dihedral angles of 21.57 (8) and 53.08 (8)°, respectively, with the pyridine and thiophene rings. The O1 and O2 atoms are twisted away from each other as indicated by torsion angle C6–N2–N3–C7 [-81.27 (15)°]. The bond lengths (Allen et al., 1987) and angles are comparable to a closely related structure (Naveenkumar et al., 2009).

In the crystal structure (Fig. 2), the molecules are linked into an extended three-dimensional network by intermolecular C4—H4A···O1, C10—H10A···O2, N2—H1N2···N1 and N3—H1N3···O2 hydrogen bonds (Table 1). The crystal structure is further stabilized by short S1···O2 interactions of 3.2686 (10) Å [symmetry code: 1/2+x, 3/2-y, -z] and by weak intermolecular C11—H11A···Cg1 interactions (Table 1; Cg1 is the centroid of the pyridine ring).

Experimental

Compound (I) was prepared following the procedure by literature (Besra et al., 1993). Dry dichloromethane (30 ml) and 4-dimethylaminopyridine (4-DMAP) (1.2 eq) was added to 3-methylthiophene-2-carbonyl chloride followed by isoniazid (1.1 eq). The reaction mixture was kept in an ice bath for 1 h and then left stirring under nitrogen atmosphere overnight at room temperature. Dichloromethane (20 ml) was added to the reaction mixture, which was then washed with water, and the organic layer dried over anhydrous sodium sulphate. The solvent was removed under reduced pressure to afford the crude product which was purified by column chromatography and recrystallized from ethanol to afford colorless single crystals.

Refinement

All the H atoms were placed in calculated positions, with N—H = 0.86 Å, Uiso(H) = 1.2 Ueq(N), C—H = 0.93 Å, Uiso(H) = 1.2 Ueq(C) for aromatic, and C—H = 0.96 Å, Uiso(H) = 1.5 Ueq(C) for methyl group. These H atoms were refined as riding on their parent atoms. A rotating group model was used for the methyl group.

Figures

Fig. 1.
The molecular structure of the (I), showing 50% probability displacement ellipsoids and the atom-numbering scheme. Hydrogen atoms are shown as spheres of arbitrary radius.
Fig. 2.
Three dimensional extended network, viewed along the b axis. Intermolecular interactions are shown as dashed lines.

Crystal data

C12H11N3O2SF(000) = 544
Mr = 261.30Dx = 1.448 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 9634 reflections
a = 8.9206 (1) Åθ = 2.5–32.7°
b = 10.7552 (2) ŵ = 0.27 mm1
c = 12.4934 (2) ÅT = 100 K
V = 1198.65 (3) Å3Block, colourless
Z = 40.58 × 0.20 × 0.15 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer4355 independent reflections
Radiation source: fine-focus sealed tube4078 reflections with I > 2σ(I)
graphiteRint = 0.025
[var phi] and ω scansθmax = 32.7°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −13→13
Tmin = 0.861, Tmax = 0.961k = −14→16
17333 measured reflectionsl = −17→18

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.097w = 1/[σ2(Fo2) + (0.0542P)2 + 0.3319P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
4355 reflectionsΔρmax = 0.79 e Å3
165 parametersΔρmin = −0.43 e Å3
0 restraintsAbsolute structure: Flack (1983), 1856 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.04 (6)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1)K.
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 > 2sigma(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
S10.26735 (4)0.98879 (3)0.04525 (3)0.01858 (8)
O10.29108 (13)0.48575 (10)0.02488 (8)0.0221 (2)
O20.01066 (11)0.69442 (9)0.07046 (8)0.01664 (19)
N10.03034 (14)0.21406 (11)−0.25010 (10)0.0159 (2)
N20.18343 (13)0.62066 (10)−0.09379 (9)0.0137 (2)
H1N20.14040.6288−0.15500.016*
N30.21647 (13)0.72506 (10)−0.03274 (9)0.01367 (19)
H1N30.29540.7684−0.04580.016*
C10.11893 (17)0.29049 (12)−0.08076 (11)0.0165 (2)
H1A0.13430.2764−0.00810.020*
C20.05396 (17)0.19936 (13)−0.14457 (11)0.0174 (2)
H2A0.02550.1248−0.11280.021*
C30.07732 (15)0.32069 (12)−0.29452 (11)0.0153 (2)
H3A0.06530.3306−0.36800.018*
C40.14288 (15)0.41719 (12)−0.23723 (11)0.0143 (2)
H4A0.17410.4894−0.27160.017*
C50.16079 (15)0.40323 (12)−0.12698 (10)0.0136 (2)
C60.21924 (14)0.50531 (11)−0.05670 (10)0.0138 (2)
C70.12212 (14)0.75769 (11)0.04814 (11)0.0125 (2)
C80.15680 (15)0.87488 (12)0.10399 (11)0.0142 (2)
C90.10620 (16)0.91137 (14)0.20356 (11)0.0177 (2)
C100.15852 (18)1.03210 (14)0.23047 (13)0.0209 (3)
H10A0.13561.07160.29470.025*
C110.24567 (18)1.08445 (13)0.15288 (12)0.0214 (3)
H11A0.28831.16310.15810.026*
C120.0117 (2)0.83596 (16)0.27738 (13)0.0259 (3)
H12A0.05300.75380.28350.039*
H12B−0.08840.83090.24960.039*
H12C0.00970.87450.34660.039*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.02092 (15)0.01399 (13)0.02083 (16)−0.00198 (11)0.00366 (12)−0.00283 (12)
O10.0302 (5)0.0186 (4)0.0176 (5)0.0033 (4)−0.0104 (4)−0.0021 (4)
O20.0134 (4)0.0166 (4)0.0200 (5)−0.0026 (3)0.0000 (3)0.0000 (4)
N10.0187 (5)0.0131 (5)0.0160 (5)−0.0004 (4)−0.0017 (4)−0.0018 (4)
N20.0177 (5)0.0113 (4)0.0120 (5)−0.0003 (4)−0.0028 (4)−0.0031 (4)
N30.0150 (5)0.0122 (4)0.0138 (5)−0.0024 (4)0.0005 (4)−0.0046 (4)
C10.0229 (6)0.0140 (6)0.0125 (5)0.0003 (5)−0.0015 (5)0.0011 (4)
C20.0226 (6)0.0123 (5)0.0173 (6)−0.0006 (5)−0.0006 (5)0.0004 (5)
C30.0182 (6)0.0163 (6)0.0114 (5)−0.0001 (4)0.0005 (4)−0.0028 (4)
C40.0172 (6)0.0127 (5)0.0131 (5)−0.0014 (4)−0.0001 (4)−0.0011 (4)
C50.0158 (5)0.0123 (5)0.0128 (5)0.0014 (4)−0.0015 (4)−0.0018 (4)
C60.0159 (5)0.0133 (5)0.0122 (5)0.0008 (4)−0.0012 (4)−0.0018 (4)
C70.0129 (5)0.0123 (5)0.0124 (5)0.0012 (4)−0.0020 (4)0.0002 (4)
C80.0139 (5)0.0128 (5)0.0160 (6)0.0008 (4)−0.0015 (4)−0.0016 (4)
C90.0180 (6)0.0188 (6)0.0165 (6)0.0005 (5)−0.0001 (5)−0.0021 (5)
C100.0230 (6)0.0194 (6)0.0205 (6)0.0026 (5)−0.0022 (5)−0.0084 (5)
C110.0246 (7)0.0152 (5)0.0245 (7)−0.0008 (5)−0.0006 (5)−0.0079 (5)
C120.0299 (8)0.0246 (7)0.0234 (7)−0.0028 (6)0.0019 (6)−0.0040 (6)

Geometric parameters (Å, °)

S1—C111.7041 (14)C3—C41.3898 (18)
S1—C81.7355 (14)C3—H3A0.9300
O1—C61.2222 (15)C4—C51.3948 (19)
O2—C71.2367 (15)C4—H4A0.9300
N1—C31.3412 (18)C5—C61.4994 (18)
N1—C21.3445 (18)C7—C81.4736 (17)
N2—C61.3623 (16)C8—C91.3803 (19)
N2—N31.3890 (14)C9—C101.420 (2)
N2—H1N20.8600C9—C121.489 (2)
N3—C71.3611 (17)C10—C111.364 (2)
N3—H1N30.8600C10—H10A0.9300
C1—C21.3899 (19)C11—H11A0.9300
C1—C51.3940 (18)C12—H12A0.9600
C1—H1A0.9300C12—H12B0.9600
C2—H2A0.9300C12—H12C0.9600
C11—S1—C891.61 (7)O1—C6—C5123.00 (12)
C3—N1—C2117.21 (12)N2—C6—C5112.71 (11)
C6—N2—N3119.98 (11)O2—C7—N3121.52 (11)
C6—N2—H1N2120.0O2—C7—C8122.19 (12)
N3—N2—H1N2120.0N3—C7—C8116.25 (11)
C7—N3—N2119.00 (11)C9—C8—C7126.96 (13)
C7—N3—H1N3120.5C9—C8—S1111.48 (10)
N2—N3—H1N3120.5C7—C8—S1121.53 (10)
C2—C1—C5119.18 (12)C8—C9—C10111.46 (13)
C2—C1—H1A120.4C8—C9—C12126.03 (14)
C5—C1—H1A120.4C10—C9—C12122.50 (13)
N1—C2—C1123.01 (13)C11—C10—C9113.35 (13)
N1—C2—H2A118.5C11—C10—H10A123.3
C1—C2—H2A118.5C9—C10—H10A123.3
N1—C3—C4123.85 (12)C10—C11—S1112.10 (11)
N1—C3—H3A118.1C10—C11—H11A124.0
C4—C3—H3A118.1S1—C11—H11A124.0
C3—C4—C5118.45 (12)C9—C12—H12A109.5
C3—C4—H4A120.8C9—C12—H12B109.5
C5—C4—H4A120.8H12A—C12—H12B109.5
C1—C5—C4118.16 (12)C9—C12—H12C109.5
C1—C5—C6119.18 (11)H12A—C12—H12C109.5
C4—C5—C6122.64 (12)H12B—C12—H12C109.5
O1—C6—N2124.29 (12)
C6—N2—N3—C7−81.27 (15)N2—N3—C7—C8−175.15 (11)
C3—N1—C2—C12.3 (2)O2—C7—C8—C921.3 (2)
C5—C1—C2—N10.6 (2)N3—C7—C8—C9−161.26 (13)
C2—N1—C3—C4−2.5 (2)O2—C7—C8—S1−156.60 (11)
N1—C3—C4—C5−0.2 (2)N3—C7—C8—S120.83 (16)
C2—C1—C5—C4−3.4 (2)C11—S1—C8—C9−0.12 (11)
C2—C1—C5—C6175.06 (12)C11—S1—C8—C7178.09 (12)
C3—C4—C5—C13.2 (2)C7—C8—C9—C10−178.07 (13)
C3—C4—C5—C6−175.20 (12)S1—C8—C9—C100.02 (15)
N3—N2—C6—O1−6.2 (2)C7—C8—C9—C123.3 (2)
N3—N2—C6—C5173.77 (11)S1—C8—C9—C12−178.58 (13)
C1—C5—C6—O132.1 (2)C8—C9—C10—C110.12 (19)
C4—C5—C6—O1−149.49 (14)C12—C9—C10—C11178.78 (14)
C1—C5—C6—N2−147.86 (13)C9—C10—C11—S1−0.21 (17)
C4—C5—C6—N230.54 (18)C8—S1—C11—C100.19 (12)
N2—N3—C7—O22.30 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1N2···N1i0.862.142.9068 (17)149
N3—H1N3···O2ii0.861.992.8034 (15)158
C4—H4A···O1iii0.932.583.2047 (17)125
C10—H10A···O2iv0.932.513.3928 (19)159
C11—H11A···Cg1v0.932.803.3760 (17)121

Symmetry codes: (i) −x, y+1/2, −z−1/2; (ii) x+1/2, −y+3/2, −z; (iii) −x+1/2, −y+1, z−1/2; (iv) −x, y+1/2, −z+1/2; (v) −x, y+3/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2451).

References

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