organic compounds
N′-[(3-Methyl-2-thienyl)carbonyl]isonicotinohydrazide
aSchool of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
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 molecules are linked into an extended three-dimensional network by intermolecular N—H⋯N, N—H⋯O and C—H⋯O hydrogen bonds. The 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); Maccari et al. (2005); Slayden et al. (2000). For the preparation of the title compound, see: Besra et al. (1993). For bond-length data, see: Allen et al. (1987). For a closely related structure, see: Naveenkumar et al. (2009). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Data collection: APEX2 (Bruker, 2005); cell SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536809033030/is2451sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809033030/is2451Isup2.hkl
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
and recrystallized from ethanol to afford colorless single crystals.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.
Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).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. |
C12H11N3O2S | F(000) = 544 |
Mr = 261.30 | Dx = 1.448 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 9634 reflections |
a = 8.9206 (1) Å | θ = 2.5–32.7° |
b = 10.7552 (2) Å | µ = 0.27 mm−1 |
c = 12.4934 (2) Å | T = 100 K |
V = 1198.65 (3) Å3 | Block, colourless |
Z = 4 | 0.58 × 0.20 × 0.15 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 4355 independent reflections |
Radiation source: fine-focus sealed tube | 4078 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.025 |
ϕ and ω scans | θmax = 32.7°, θmin = 2.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −13→13 |
Tmin = 0.861, Tmax = 0.961 | k = −14→16 |
17333 measured reflections | l = −17→18 |
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)] = 0.036 | H-atom parameters constrained |
wR(F2) = 0.097 | w = 1/[σ2(Fo2) + (0.0542P)2 + 0.3319P] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max < 0.001 |
4355 reflections | Δρmax = 0.79 e Å−3 |
165 parameters | Δρmin = −0.43 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 1856 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.04 (6) |
C12H11N3O2S | V = 1198.65 (3) Å3 |
Mr = 261.30 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.9206 (1) Å | µ = 0.27 mm−1 |
b = 10.7552 (2) Å | T = 100 K |
c = 12.4934 (2) Å | 0.58 × 0.20 × 0.15 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 4355 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 4078 reflections with I > 2σ(I) |
Tmin = 0.861, Tmax = 0.961 | Rint = 0.025 |
17333 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | H-atom parameters constrained |
wR(F2) = 0.097 | Δρmax = 0.79 e Å−3 |
S = 1.05 | Δρmin = −0.43 e Å−3 |
4355 reflections | Absolute structure: Flack (1983), 1856 Friedel pairs |
165 parameters | Absolute structure parameter: −0.04 (6) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.26735 (4) | 0.98879 (3) | 0.04525 (3) | 0.01858 (8) | |
O1 | 0.29108 (13) | 0.48575 (10) | 0.02488 (8) | 0.0221 (2) | |
O2 | 0.01066 (11) | 0.69442 (9) | 0.07046 (8) | 0.01664 (19) | |
N1 | 0.03034 (14) | 0.21406 (11) | −0.25010 (10) | 0.0159 (2) | |
N2 | 0.18343 (13) | 0.62066 (10) | −0.09379 (9) | 0.0137 (2) | |
H1N2 | 0.1404 | 0.6288 | −0.1550 | 0.016* | |
N3 | 0.21647 (13) | 0.72506 (10) | −0.03274 (9) | 0.01367 (19) | |
H1N3 | 0.2954 | 0.7684 | −0.0458 | 0.016* | |
C1 | 0.11893 (17) | 0.29049 (12) | −0.08076 (11) | 0.0165 (2) | |
H1A | 0.1343 | 0.2764 | −0.0081 | 0.020* | |
C2 | 0.05396 (17) | 0.19936 (13) | −0.14457 (11) | 0.0174 (2) | |
H2A | 0.0255 | 0.1248 | −0.1128 | 0.021* | |
C3 | 0.07732 (15) | 0.32069 (12) | −0.29452 (11) | 0.0153 (2) | |
H3A | 0.0653 | 0.3306 | −0.3680 | 0.018* | |
C4 | 0.14288 (15) | 0.41719 (12) | −0.23723 (11) | 0.0143 (2) | |
H4A | 0.1741 | 0.4894 | −0.2716 | 0.017* | |
C5 | 0.16079 (15) | 0.40323 (12) | −0.12698 (10) | 0.0136 (2) | |
C6 | 0.21924 (14) | 0.50531 (11) | −0.05670 (10) | 0.0138 (2) | |
C7 | 0.12212 (14) | 0.75769 (11) | 0.04814 (11) | 0.0125 (2) | |
C8 | 0.15680 (15) | 0.87488 (12) | 0.10399 (11) | 0.0142 (2) | |
C9 | 0.10620 (16) | 0.91137 (14) | 0.20356 (11) | 0.0177 (2) | |
C10 | 0.15852 (18) | 1.03210 (14) | 0.23047 (13) | 0.0209 (3) | |
H10A | 0.1356 | 1.0716 | 0.2947 | 0.025* | |
C11 | 0.24567 (18) | 1.08445 (13) | 0.15288 (12) | 0.0214 (3) | |
H11A | 0.2883 | 1.1631 | 0.1581 | 0.026* | |
C12 | 0.0117 (2) | 0.83596 (16) | 0.27738 (13) | 0.0259 (3) | |
H12A | 0.0530 | 0.7538 | 0.2835 | 0.039* | |
H12B | −0.0884 | 0.8309 | 0.2496 | 0.039* | |
H12C | 0.0097 | 0.8745 | 0.3466 | 0.039* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.02092 (15) | 0.01399 (13) | 0.02083 (16) | −0.00198 (11) | 0.00366 (12) | −0.00283 (12) |
O1 | 0.0302 (5) | 0.0186 (4) | 0.0176 (5) | 0.0033 (4) | −0.0104 (4) | −0.0021 (4) |
O2 | 0.0134 (4) | 0.0166 (4) | 0.0200 (5) | −0.0026 (3) | 0.0000 (3) | 0.0000 (4) |
N1 | 0.0187 (5) | 0.0131 (5) | 0.0160 (5) | −0.0004 (4) | −0.0017 (4) | −0.0018 (4) |
N2 | 0.0177 (5) | 0.0113 (4) | 0.0120 (5) | −0.0003 (4) | −0.0028 (4) | −0.0031 (4) |
N3 | 0.0150 (5) | 0.0122 (4) | 0.0138 (5) | −0.0024 (4) | 0.0005 (4) | −0.0046 (4) |
C1 | 0.0229 (6) | 0.0140 (6) | 0.0125 (5) | 0.0003 (5) | −0.0015 (5) | 0.0011 (4) |
C2 | 0.0226 (6) | 0.0123 (5) | 0.0173 (6) | −0.0006 (5) | −0.0006 (5) | 0.0004 (5) |
C3 | 0.0182 (6) | 0.0163 (6) | 0.0114 (5) | −0.0001 (4) | 0.0005 (4) | −0.0028 (4) |
C4 | 0.0172 (6) | 0.0127 (5) | 0.0131 (5) | −0.0014 (4) | −0.0001 (4) | −0.0011 (4) |
C5 | 0.0158 (5) | 0.0123 (5) | 0.0128 (5) | 0.0014 (4) | −0.0015 (4) | −0.0018 (4) |
C6 | 0.0159 (5) | 0.0133 (5) | 0.0122 (5) | 0.0008 (4) | −0.0012 (4) | −0.0018 (4) |
C7 | 0.0129 (5) | 0.0123 (5) | 0.0124 (5) | 0.0012 (4) | −0.0020 (4) | 0.0002 (4) |
C8 | 0.0139 (5) | 0.0128 (5) | 0.0160 (6) | 0.0008 (4) | −0.0015 (4) | −0.0016 (4) |
C9 | 0.0180 (6) | 0.0188 (6) | 0.0165 (6) | 0.0005 (5) | −0.0001 (5) | −0.0021 (5) |
C10 | 0.0230 (6) | 0.0194 (6) | 0.0205 (6) | 0.0026 (5) | −0.0022 (5) | −0.0084 (5) |
C11 | 0.0246 (7) | 0.0152 (5) | 0.0245 (7) | −0.0008 (5) | −0.0006 (5) | −0.0079 (5) |
C12 | 0.0299 (8) | 0.0246 (7) | 0.0234 (7) | −0.0028 (6) | 0.0019 (6) | −0.0040 (6) |
S1—C11 | 1.7041 (14) | C3—C4 | 1.3898 (18) |
S1—C8 | 1.7355 (14) | C3—H3A | 0.9300 |
O1—C6 | 1.2222 (15) | C4—C5 | 1.3948 (19) |
O2—C7 | 1.2367 (15) | C4—H4A | 0.9300 |
N1—C3 | 1.3412 (18) | C5—C6 | 1.4994 (18) |
N1—C2 | 1.3445 (18) | C7—C8 | 1.4736 (17) |
N2—C6 | 1.3623 (16) | C8—C9 | 1.3803 (19) |
N2—N3 | 1.3890 (14) | C9—C10 | 1.420 (2) |
N2—H1N2 | 0.8600 | C9—C12 | 1.489 (2) |
N3—C7 | 1.3611 (17) | C10—C11 | 1.364 (2) |
N3—H1N3 | 0.8600 | C10—H10A | 0.9300 |
C1—C2 | 1.3899 (19) | C11—H11A | 0.9300 |
C1—C5 | 1.3940 (18) | C12—H12A | 0.9600 |
C1—H1A | 0.9300 | C12—H12B | 0.9600 |
C2—H2A | 0.9300 | C12—H12C | 0.9600 |
C11—S1—C8 | 91.61 (7) | O1—C6—C5 | 123.00 (12) |
C3—N1—C2 | 117.21 (12) | N2—C6—C5 | 112.71 (11) |
C6—N2—N3 | 119.98 (11) | O2—C7—N3 | 121.52 (11) |
C6—N2—H1N2 | 120.0 | O2—C7—C8 | 122.19 (12) |
N3—N2—H1N2 | 120.0 | N3—C7—C8 | 116.25 (11) |
C7—N3—N2 | 119.00 (11) | C9—C8—C7 | 126.96 (13) |
C7—N3—H1N3 | 120.5 | C9—C8—S1 | 111.48 (10) |
N2—N3—H1N3 | 120.5 | C7—C8—S1 | 121.53 (10) |
C2—C1—C5 | 119.18 (12) | C8—C9—C10 | 111.46 (13) |
C2—C1—H1A | 120.4 | C8—C9—C12 | 126.03 (14) |
C5—C1—H1A | 120.4 | C10—C9—C12 | 122.50 (13) |
N1—C2—C1 | 123.01 (13) | C11—C10—C9 | 113.35 (13) |
N1—C2—H2A | 118.5 | C11—C10—H10A | 123.3 |
C1—C2—H2A | 118.5 | C9—C10—H10A | 123.3 |
N1—C3—C4 | 123.85 (12) | C10—C11—S1 | 112.10 (11) |
N1—C3—H3A | 118.1 | C10—C11—H11A | 124.0 |
C4—C3—H3A | 118.1 | S1—C11—H11A | 124.0 |
C3—C4—C5 | 118.45 (12) | C9—C12—H12A | 109.5 |
C3—C4—H4A | 120.8 | C9—C12—H12B | 109.5 |
C5—C4—H4A | 120.8 | H12A—C12—H12B | 109.5 |
C1—C5—C4 | 118.16 (12) | C9—C12—H12C | 109.5 |
C1—C5—C6 | 119.18 (11) | H12A—C12—H12C | 109.5 |
C4—C5—C6 | 122.64 (12) | H12B—C12—H12C | 109.5 |
O1—C6—N2 | 124.29 (12) | ||
C6—N2—N3—C7 | −81.27 (15) | N2—N3—C7—C8 | −175.15 (11) |
C3—N1—C2—C1 | 2.3 (2) | O2—C7—C8—C9 | 21.3 (2) |
C5—C1—C2—N1 | 0.6 (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—S1 | 20.83 (16) |
C2—C1—C5—C4 | −3.4 (2) | C11—S1—C8—C9 | −0.12 (11) |
C2—C1—C5—C6 | 175.06 (12) | C11—S1—C8—C7 | 178.09 (12) |
C3—C4—C5—C1 | 3.2 (2) | C7—C8—C9—C10 | −178.07 (13) |
C3—C4—C5—C6 | −175.20 (12) | S1—C8—C9—C10 | 0.02 (15) |
N3—N2—C6—O1 | −6.2 (2) | C7—C8—C9—C12 | 3.3 (2) |
N3—N2—C6—C5 | 173.77 (11) | S1—C8—C9—C12 | −178.58 (13) |
C1—C5—C6—O1 | 32.1 (2) | C8—C9—C10—C11 | 0.12 (19) |
C4—C5—C6—O1 | −149.49 (14) | C12—C9—C10—C11 | 178.78 (14) |
C1—C5—C6—N2 | −147.86 (13) | C9—C10—C11—S1 | −0.21 (17) |
C4—C5—C6—N2 | 30.54 (18) | C8—S1—C11—C10 | 0.19 (12) |
N2—N3—C7—O2 | 2.30 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···N1i | 0.86 | 2.14 | 2.9068 (17) | 149 |
N3—H1N3···O2ii | 0.86 | 1.99 | 2.8034 (15) | 158 |
C4—H4A···O1iii | 0.93 | 2.58 | 3.2047 (17) | 125 |
C10—H10A···O2iv | 0.93 | 2.51 | 3.3928 (19) | 159 |
C11—H11A···Cg1v | 0.93 | 2.80 | 3.3760 (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. |
Experimental details
Crystal data | |
Chemical formula | C12H11N3O2S |
Mr | 261.30 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 8.9206 (1), 10.7552 (2), 12.4934 (2) |
V (Å3) | 1198.65 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.27 |
Crystal size (mm) | 0.58 × 0.20 × 0.15 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.861, 0.961 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 17333, 4355, 4078 |
Rint | 0.025 |
(sin θ/λ)max (Å−1) | 0.760 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.097, 1.05 |
No. of reflections | 4355 |
No. of parameters | 165 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.79, −0.43 |
Absolute structure | Flack (1983), 1856 Friedel pairs |
Absolute structure parameter | −0.04 (6) |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···N1i | 0.86 | 2.14 | 2.9068 (17) | 149 |
N3—H1N3···O2ii | 0.86 | 1.99 | 2.8034 (15) | 158 |
C4—H4A···O1iii | 0.93 | 2.58 | 3.2047 (17) | 125 |
C10—H10A···O2iv | 0.93 | 2.51 | 3.3928 (19) | 159 |
C11—H11A···Cg1v | 0.93 | 2.80 | 3.3760 (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. |
Acknowledgements
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.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).