organic compounds
N′-(Cyclohexylcarbonyl)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, C13H17N3O2, the mean plane of the cyclohexane ring forms a dihedral angle of 33.12 (5)° with the pyridine ring. The two O atoms are twisted away from each other, as indicated by the C—N—N—C torsion angle of −74.97 (9)°. In the molecules are linked into a three-dimensional network by intermolecular N—H⋯N, N—H⋯O and C—H⋯O hydrogen bonds. The structure is also stabilized by C—H⋯π interactions.
Related literature
For bond-length data, see: Allen et al. (1987). For applications of isoniazid derivatives, see: Janin (2007); Maccari et al. (2005); Slayden & Barry (2000). For the preparation, see: Besra et al. (1993). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Refinement
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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/S1600536809027469/kj2133sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809027469/kj2133Isup2.hkl
The isoniazid (INH) derivative 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 cyclohexane carbonyl chloride followed by INH (1.1 eq). The reaction mixture was kept in an ice bath for 1 h and then left stirring under nitrogen 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 methanol to afford colorless crystals.All hydrogen atoms were located from the difference Fourier map and refined freely. As there are not enough
effects to determine the 2499 Friedel pairs were merged before final refinement.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 title compound with atom labels and 50% probability ellipsoids for non-H atoms. |
C13H17N3O2 | F(000) = 528 |
Mr = 247.30 | Dx = 1.276 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 9922 reflections |
a = 9.1184 (2) Å | θ = 2.8–35.1° |
b = 11.5989 (2) Å | µ = 0.09 mm−1 |
c = 12.1684 (2) Å | T = 100 K |
V = 1286.97 (4) Å3 | Block, colourless |
Z = 4 | 0.60 × 0.40 × 0.33 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 3210 independent reflections |
Radiation source: fine-focus sealed tube | 3124 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
ϕ and ω scans | θmax = 35.1°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −14→14 |
Tmin = 0.941, Tmax = 0.971 | k = −18→17 |
27969 measured reflections | l = −19→19 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.032 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.084 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0593P)2 + 0.0754P] where P = (Fo2 + 2Fc2)/3 |
3210 reflections | (Δ/σ)max < 0.001 |
231 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.34 e Å−3 |
C13H17N3O2 | V = 1286.97 (4) Å3 |
Mr = 247.30 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 9.1184 (2) Å | µ = 0.09 mm−1 |
b = 11.5989 (2) Å | T = 100 K |
c = 12.1684 (2) Å | 0.60 × 0.40 × 0.33 mm |
Bruker SMART APEXII CCD area-detector diffractometer | 3210 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 3124 reflections with I > 2σ(I) |
Tmin = 0.941, Tmax = 0.971 | Rint = 0.022 |
27969 measured reflections |
R[F2 > 2σ(F2)] = 0.032 | 0 restraints |
wR(F2) = 0.084 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | Δρmax = 0.25 e Å−3 |
3210 reflections | Δρmin = −0.34 e Å−3 |
231 parameters |
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 | ||
O1 | 0.75737 (8) | 1.01913 (6) | 1.03928 (5) | 0.02041 (13) | |
O2 | 0.99005 (6) | 0.79925 (5) | 1.04401 (5) | 0.01593 (11) | |
N1 | 1.02861 (8) | 1.26064 (6) | 0.76325 (6) | 0.01714 (12) | |
N2 | 0.80178 (7) | 0.89033 (6) | 0.90156 (5) | 0.01293 (11) | |
N3 | 0.76418 (7) | 0.79834 (6) | 0.96907 (5) | 0.01347 (11) | |
C1 | 0.94236 (10) | 1.18220 (7) | 0.93422 (6) | 0.01703 (14) | |
C2 | 1.01495 (11) | 1.26604 (7) | 0.87318 (7) | 0.01889 (14) | |
C3 | 0.96940 (10) | 1.16932 (7) | 0.71250 (6) | 0.01606 (13) | |
C4 | 0.89624 (9) | 1.08036 (7) | 0.76639 (6) | 0.01426 (12) | |
C5 | 0.88303 (8) | 1.08714 (6) | 0.88042 (6) | 0.01264 (12) | |
C6 | 0.80847 (8) | 0.99670 (6) | 0.94875 (6) | 0.01322 (12) | |
C7 | 0.86549 (7) | 0.75756 (6) | 1.04018 (6) | 0.01175 (11) | |
C8 | 0.81852 (8) | 0.65554 (6) | 1.10913 (6) | 0.01238 (11) | |
C9 | 0.87614 (11) | 0.54417 (7) | 1.05682 (7) | 0.02033 (15) | |
C10 | 0.83192 (15) | 0.43958 (8) | 1.12611 (10) | 0.0300 (2) | |
C11 | 0.88525 (14) | 0.45089 (10) | 1.24449 (11) | 0.0315 (2) | |
C12 | 0.82967 (13) | 0.56214 (10) | 1.29578 (7) | 0.02597 (18) | |
C13 | 0.87382 (11) | 0.66737 (8) | 1.22748 (7) | 0.02036 (15) | |
H1 | 0.936 (2) | 1.1925 (16) | 1.0135 (14) | 0.033 (4)* | |
H2 | 1.062 (2) | 1.3365 (15) | 0.9082 (14) | 0.032 (4)* | |
H3 | 0.9786 (19) | 1.1702 (14) | 0.6350 (14) | 0.027 (4)* | |
H4 | 0.8560 (17) | 1.0205 (13) | 0.7227 (12) | 0.018 (3)* | |
H8 | 0.7101 (18) | 0.6508 (14) | 1.1062 (12) | 0.021 (3)* | |
H9A | 0.837 (2) | 0.5361 (17) | 0.9849 (16) | 0.042 (5)* | |
H9B | 0.9813 (19) | 0.5498 (15) | 1.0523 (14) | 0.028 (4)* | |
H10A | 0.869 (2) | 0.3690 (19) | 1.0921 (16) | 0.046 (5)* | |
H10B | 0.722 (3) | 0.4297 (19) | 1.1277 (16) | 0.047 (5)* | |
H11A | 0.860 (2) | 0.3808 (16) | 1.2833 (14) | 0.031 (4)* | |
H11B | 0.995 (3) | 0.454 (2) | 1.249 (2) | 0.053 (6)* | |
H12A | 0.872 (2) | 0.5711 (18) | 1.3708 (15) | 0.043 (5)* | |
H12B | 0.722 (2) | 0.5602 (16) | 1.2991 (13) | 0.032 (4)* | |
H13A | 0.8388 (18) | 0.7410 (13) | 1.2598 (12) | 0.018 (3)* | |
H13B | 0.985 (2) | 0.6778 (15) | 1.2258 (14) | 0.030 (4)* | |
H1N2 | 0.862 (2) | 0.8724 (16) | 0.8443 (15) | 0.036 (5)* | |
H1N3 | 0.6729 (18) | 0.7705 (13) | 0.9596 (12) | 0.022 (3)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0286 (3) | 0.0174 (3) | 0.0152 (2) | 0.0016 (2) | 0.0095 (2) | 0.0005 (2) |
O2 | 0.0107 (2) | 0.0156 (2) | 0.0215 (2) | −0.00104 (18) | −0.00008 (19) | 0.0012 (2) |
N1 | 0.0205 (3) | 0.0136 (2) | 0.0173 (3) | −0.0004 (2) | 0.0028 (2) | 0.0031 (2) |
N2 | 0.0148 (2) | 0.0104 (2) | 0.0135 (2) | −0.00010 (19) | 0.00287 (19) | 0.00212 (19) |
N3 | 0.0116 (2) | 0.0128 (2) | 0.0159 (2) | −0.00129 (19) | −0.0005 (2) | 0.0046 (2) |
C1 | 0.0258 (3) | 0.0126 (3) | 0.0127 (3) | −0.0015 (3) | 0.0022 (2) | −0.0006 (2) |
C2 | 0.0263 (4) | 0.0129 (3) | 0.0175 (3) | −0.0031 (3) | 0.0013 (3) | 0.0000 (2) |
C3 | 0.0198 (3) | 0.0155 (3) | 0.0129 (3) | 0.0002 (3) | 0.0022 (2) | 0.0030 (2) |
C4 | 0.0179 (3) | 0.0133 (3) | 0.0115 (2) | −0.0005 (2) | 0.0009 (2) | 0.0011 (2) |
C5 | 0.0158 (3) | 0.0107 (3) | 0.0115 (2) | 0.0009 (2) | 0.0018 (2) | 0.0012 (2) |
C6 | 0.0149 (3) | 0.0116 (3) | 0.0131 (3) | 0.0016 (2) | 0.0026 (2) | 0.0014 (2) |
C7 | 0.0111 (2) | 0.0111 (2) | 0.0131 (2) | 0.0007 (2) | 0.0008 (2) | −0.0001 (2) |
C8 | 0.0125 (2) | 0.0115 (3) | 0.0131 (3) | 0.0003 (2) | 0.0005 (2) | 0.0015 (2) |
C9 | 0.0292 (4) | 0.0117 (3) | 0.0202 (3) | −0.0009 (3) | 0.0069 (3) | −0.0015 (2) |
C10 | 0.0457 (6) | 0.0107 (3) | 0.0336 (5) | −0.0014 (4) | 0.0128 (4) | 0.0013 (3) |
C11 | 0.0324 (5) | 0.0236 (4) | 0.0386 (5) | 0.0063 (4) | 0.0018 (4) | 0.0171 (4) |
C12 | 0.0337 (5) | 0.0278 (4) | 0.0164 (3) | −0.0030 (4) | −0.0022 (3) | 0.0080 (3) |
C13 | 0.0275 (4) | 0.0196 (3) | 0.0139 (3) | −0.0032 (3) | −0.0030 (3) | 0.0010 (2) |
O1—C6 | 1.2241 (9) | C7—C8 | 1.5125 (10) |
O2—C7 | 1.2353 (9) | C8—C13 | 1.5321 (11) |
N1—C3 | 1.3397 (11) | C8—C9 | 1.5329 (11) |
N1—C2 | 1.3448 (11) | C8—H8 | 0.990 (16) |
N2—C6 | 1.3622 (10) | C9—C10 | 1.5315 (13) |
N2—N3 | 1.3895 (9) | C9—H9A | 0.95 (2) |
N2—H1N2 | 0.910 (19) | C9—H9B | 0.963 (18) |
N3—C7 | 1.3513 (9) | C10—C11 | 1.5260 (19) |
N3—H1N3 | 0.900 (17) | C10—H10A | 0.98 (2) |
C1—C2 | 1.3912 (11) | C10—H10B | 1.01 (2) |
C1—C5 | 1.3917 (11) | C11—C12 | 1.5203 (18) |
C1—H1 | 0.973 (18) | C11—H11A | 0.967 (19) |
C2—H2 | 1.017 (18) | C11—H11B | 1.00 (3) |
C3—C4 | 1.3927 (11) | C12—C13 | 1.5306 (13) |
C3—H3 | 0.946 (17) | C12—H12A | 0.997 (19) |
C4—C5 | 1.3950 (10) | C12—H12B | 0.98 (2) |
C4—H4 | 0.948 (15) | C13—H13A | 0.993 (15) |
C5—C6 | 1.5014 (10) | C13—H13B | 1.02 (2) |
C3—N1—C2 | 117.26 (7) | C13—C8—H8 | 111.5 (8) |
C6—N2—N3 | 117.22 (6) | C9—C8—H8 | 106.3 (9) |
C6—N2—H1N2 | 120.2 (12) | C10—C9—C8 | 110.40 (7) |
N3—N2—H1N2 | 115.2 (11) | C10—C9—H9A | 109.4 (13) |
C7—N3—N2 | 118.60 (6) | C8—C9—H9A | 109.8 (13) |
C7—N3—H1N3 | 126.1 (10) | C10—C9—H9B | 110.4 (10) |
N2—N3—H1N3 | 115.3 (10) | C8—C9—H9B | 107.9 (11) |
C2—C1—C5 | 119.18 (7) | H9A—C9—H9B | 109.0 (17) |
C2—C1—H1 | 118.0 (11) | C11—C10—C9 | 111.57 (9) |
C5—C1—H1 | 122.8 (11) | C11—C10—H10A | 111.1 (12) |
N1—C2—C1 | 122.85 (8) | C9—C10—H10A | 109.8 (12) |
N1—C2—H2 | 114.5 (10) | C11—C10—H10B | 107.9 (11) |
C1—C2—H2 | 122.6 (10) | C9—C10—H10B | 111.2 (12) |
N1—C3—C4 | 124.18 (7) | H10A—C10—H10B | 105.1 (17) |
N1—C3—H3 | 114.5 (10) | C12—C11—C10 | 110.75 (8) |
C4—C3—H3 | 121.3 (10) | C12—C11—H11A | 115.7 (11) |
C3—C4—C5 | 117.90 (7) | C10—C11—H11A | 108.2 (11) |
C3—C4—H4 | 117.7 (9) | C12—C11—H11B | 106.4 (14) |
C5—C4—H4 | 124.4 (9) | C10—C11—H11B | 112.2 (15) |
C1—C5—C4 | 118.62 (7) | H11A—C11—H11B | 103.5 (18) |
C1—C5—C6 | 117.98 (6) | C11—C12—C13 | 111.48 (8) |
C4—C5—C6 | 123.41 (7) | C11—C12—H12A | 109.6 (12) |
O1—C6—N2 | 123.70 (7) | C13—C12—H12A | 108.2 (12) |
O1—C6—C5 | 121.48 (7) | C11—C12—H12B | 109.3 (11) |
N2—C6—C5 | 114.82 (6) | C13—C12—H12B | 107.7 (11) |
O2—C7—N3 | 121.04 (7) | H12A—C12—H12B | 110.6 (16) |
O2—C7—C8 | 123.07 (7) | C12—C13—C8 | 110.63 (7) |
N3—C7—C8 | 115.81 (6) | C12—C13—H13A | 112.7 (9) |
C7—C8—C13 | 110.98 (6) | C8—C13—H13A | 110.1 (9) |
C7—C8—C9 | 109.38 (6) | C12—C13—H13B | 111.5 (10) |
C13—C8—C9 | 110.67 (7) | C8—C13—H13B | 108.6 (9) |
C7—C8—H8 | 107.9 (9) | H13A—C13—H13B | 103.0 (14) |
C6—N2—N3—C7 | −74.97 (9) | N2—N3—C7—O2 | −1.43 (11) |
C3—N1—C2—C1 | −0.37 (13) | N2—N3—C7—C8 | −178.54 (6) |
C5—C1—C2—N1 | 1.17 (14) | O2—C7—C8—C13 | 43.39 (10) |
C2—N1—C3—C4 | −0.43 (13) | N3—C7—C8—C13 | −139.56 (7) |
N1—C3—C4—C5 | 0.40 (13) | O2—C7—C8—C9 | −79.00 (9) |
C2—C1—C5—C4 | −1.15 (12) | N3—C7—C8—C9 | 98.04 (8) |
C2—C1—C5—C6 | 178.57 (8) | C7—C8—C9—C10 | 179.16 (8) |
C3—C4—C5—C1 | 0.42 (12) | C13—C8—C9—C10 | 56.58 (10) |
C3—C4—C5—C6 | −179.29 (7) | C8—C9—C10—C11 | −56.32 (12) |
N3—N2—C6—O1 | −14.45 (11) | C9—C10—C11—C12 | 55.80 (13) |
N3—N2—C6—C5 | 166.16 (6) | C10—C11—C12—C13 | −55.73 (12) |
C1—C5—C6—O1 | 23.87 (12) | C11—C12—C13—C8 | 56.45 (11) |
C4—C5—C6—O1 | −156.42 (8) | C7—C8—C13—C12 | −178.34 (7) |
C1—C5—C6—N2 | −156.72 (7) | C9—C8—C13—C12 | −56.70 (10) |
C4—C5—C6—N2 | 22.99 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···N1i | 0.911 (18) | 2.095 (18) | 2.9456 (10) | 155.0 (16) |
N3—H1N3···O2ii | 0.900 (16) | 1.854 (16) | 2.7486 (9) | 172.4 (14) |
C2—H2···O1iii | 1.017 (18) | 2.527 (18) | 3.4971 (11) | 159.4 (14) |
C4—H4···O1iv | 0.948 (15) | 2.502 (15) | 3.3062 (10) | 142.6 (12) |
C10—H10B···Cg1v | 1.01 (2) | 2.78 (3) | 3.7299 (14) | 157.1 (16) |
C13—H13A···Cg1vi | 0.993 (15) | 2.958 (16) | 3.7039 (10) | 132.7 (12) |
Symmetry codes: (i) −x+2, y−1/2, −z+3/2; (ii) x−1/2, −y+3/2, −z+2; (iii) x+1/2, −y+5/2, −z+2; (iv) −x+3/2, −y+2, z−1/2; (v) −x−1, y+3/2, −z+5/2; (vi) −x+3/2, −y+2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C13H17N3O2 |
Mr | 247.30 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 9.1184 (2), 11.5989 (2), 12.1684 (2) |
V (Å3) | 1286.97 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.60 × 0.40 × 0.33 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.941, 0.971 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 27969, 3210, 3124 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.810 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.032, 0.084, 1.11 |
No. of reflections | 3210 |
No. of parameters | 231 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.25, −0.34 |
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 | 0.911 (18) | 2.095 (18) | 2.9456 (10) | 155.0 (16) |
N3—H1N3···O2ii | 0.900 (16) | 1.854 (16) | 2.7486 (9) | 172.4 (14) |
C2—H2···O1iii | 1.017 (18) | 2.527 (18) | 3.4971 (11) | 159.4 (14) |
C4—H4···O1iv | 0.948 (15) | 2.502 (15) | 3.3062 (10) | 142.6 (12) |
C10—H10B···Cg1v | 1.01 (2) | 2.78 (3) | 3.7299 (14) | 157.1 (16) |
C13—H13A···Cg1vi | 0.993 (15) | 2.958 (16) | 3.7039 (10) | 132.7 (12) |
Symmetry codes: (i) −x+2, y−1/2, −z+3/2; (ii) x−1/2, −y+3/2, −z+2; (iii) x+1/2, −y+5/2, −z+2; (iv) −x+3/2, −y+2, z−1/2; (v) −x−1, y+3/2, −z+5/2; (vi) −x+3/2, −y+2, z+1/2. |
Acknowledgements
This research is supported by Universiti Sains Malaysia (USM) under the University Research Grant (No. 1001/PFARMASI/815005). HKF and CSY thank USM for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CSY thanks the Malaysian Government and USM for the award of the post of Research Officer under the Science Fund Grant (No. 305/PFIZIK/613312). HSNK is grateful for a USM fellowship for financial assistance.
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 & Barry, 2000). As a part of a current work of synthesis of such derivatives, in this paper we present the crystal structure of the title compound which was synthesized in our lab.
Bond lengths and angles of the title compound (I), (Fig. 1) are within the normal range (Allen et al., 1987). The mean plane of cyclohexane ring forms dihedral angle of 33.12 (5)° with the pyridine ring. The O1 and O2 atoms are twisted away from each other as is indicated by torsion angle C6–N2–N3–C7 [-74.97 (9)°]. In the crystal structure, the molecules are linked into three-dimensional network by the intermolecular N2—H1N2···N1, N3—H1N3···O2, C2—H2···O1 and C4—H4···O1 hydrogen bonds. The structure is also stabilized by C—H···π interactions (Table 1).