organic compounds
(E)-N′-(2,4,5-Trifluorobenzylidene)isonicotinohydrazide monohydrate
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 Schiff base molecule of the title compound, C13H8F3N3O·H2O, the benzene ring and the pyridine ring are nearly coplanar, making a dihedral angle of 6.64 (7)°. The molecule exists in an E configuration with respect to the C=N double bond. In the molecules are linked via the water molecules into two-dimensional planes parallel to the ab plane through intermolecular N—H⋯O, O—H⋯O O—H⋯N and C—H⋯O hydrogen bonds.
Related literature
For applications of isoniazid (isonicotinylhydrazine) derivatives, see: Janin (2007); Maccari et al. (2005); Slayden & Barry (2000); Kahwa et al. (1986). For the preparation of the title compound, see: Lourenco et al. (2008). For related structures, see: Naveenkumar et al. (2009, 2010); Shi (2005).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); 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/S1600536810004514/sj2725sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810004514/sj2725Isup2.hkl
The isoniazid derivative was prepared following a procedure reported by Lourenco et al., (2008). 2,4,5-triflurobenzaldehyde (1.0 eq) was added to isoniazid (1.0 eq) in ethanol/water. After stirring for 1-3 h at room temperature, the resulting mixture was concentrated under reduced pressure. The residue was purified by washing with cold ethanol and diethyl ether to give the pure derivative. Colourless single crystals suitable for X-ray analysis were obtained by re-crystallization from methanol.
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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 (I) with atom labels and 50% probability ellipsoids for non-H atoms. | |
Fig. 2. The crystal packing of (I), viewed down the a axis, showing the molecules are linked into 2-dimensional planes parallel to the ab plane. Intermolecular hydrogen bonds are shown as dashed lines. |
C13H8F3N3O·H2O | Z = 2 |
Mr = 297.24 | F(000) = 304 |
Triclinic, P1 | Dx = 1.517 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.9241 (1) Å | Cell parameters from 6031 reflections |
b = 6.3915 (1) Å | θ = 2.9–30.8° |
c = 21.3387 (2) Å | µ = 0.13 mm−1 |
α = 88.616 (1)° | T = 296 K |
β = 86.556 (1)° | Plate, colourless |
γ = 76.056 (1)° | 0.32 × 0.32 × 0.13 mm |
V = 650.58 (2) Å3 |
Bruker SMART APEXII CCD area-detector diffractometer | 4024 independent reflections |
Radiation source: fine-focus sealed tube | 2730 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
ϕ and ω scans | θmax = 30.8°, θmin = 2.9° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −6→7 |
Tmin = 0.958, Tmax = 0.984 | k = −9→9 |
14710 measured reflections | l = −30→29 |
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)] = 0.046 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.146 | All H-atom parameters refined |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0764P)2 + 0.0515P] where P = (Fo2 + 2Fc2)/3 |
4024 reflections | (Δ/σ)max < 0.001 |
230 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
C13H8F3N3O·H2O | γ = 76.056 (1)° |
Mr = 297.24 | V = 650.58 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 4.9241 (1) Å | Mo Kα radiation |
b = 6.3915 (1) Å | µ = 0.13 mm−1 |
c = 21.3387 (2) Å | T = 296 K |
α = 88.616 (1)° | 0.32 × 0.32 × 0.13 mm |
β = 86.556 (1)° |
Bruker SMART APEXII CCD area-detector diffractometer | 4024 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2730 reflections with I > 2σ(I) |
Tmin = 0.958, Tmax = 0.984 | Rint = 0.022 |
14710 measured reflections |
R[F2 > 2σ(F2)] = 0.046 | 0 restraints |
wR(F2) = 0.146 | All H-atom parameters refined |
S = 1.05 | Δρmax = 0.27 e Å−3 |
4024 reflections | Δρmin = −0.22 e Å−3 |
230 parameters |
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 | ||
F1 | 1.20930 (18) | 0.63383 (14) | 0.34682 (4) | 0.0667 (3) | |
F2 | 1.2581 (2) | 1.19398 (18) | 0.48033 (4) | 0.0824 (3) | |
F3 | 0.8111 (2) | 1.44958 (15) | 0.42966 (5) | 0.0834 (3) | |
O1 | 0.1646 (2) | 1.24750 (13) | 0.19113 (5) | 0.0552 (3) | |
N1 | 0.5532 (2) | 1.00798 (15) | 0.25981 (4) | 0.0386 (2) | |
N2 | 0.4249 (2) | 0.91747 (15) | 0.21550 (4) | 0.0377 (2) | |
N3 | −0.1882 (3) | 0.7926 (2) | 0.04246 (6) | 0.0592 (3) | |
C1 | 1.1071 (3) | 0.8366 (2) | 0.36730 (6) | 0.0431 (3) | |
C2 | 1.2389 (3) | 0.9080 (3) | 0.41488 (6) | 0.0532 (3) | |
C3 | 1.1375 (3) | 1.1151 (3) | 0.43436 (6) | 0.0533 (3) | |
C4 | 0.9082 (3) | 1.2479 (2) | 0.40781 (6) | 0.0520 (3) | |
C5 | 0.7792 (3) | 1.1753 (2) | 0.36057 (6) | 0.0465 (3) | |
C6 | 0.8779 (2) | 0.96531 (19) | 0.33900 (5) | 0.0381 (3) | |
C7 | 0.7429 (2) | 0.87952 (19) | 0.28944 (5) | 0.0391 (3) | |
C8 | 0.2279 (2) | 1.05161 (17) | 0.18276 (5) | 0.0381 (3) | |
C9 | 0.0888 (2) | 0.95209 (18) | 0.13457 (5) | 0.0381 (3) | |
C10 | −0.1271 (3) | 1.0858 (2) | 0.10359 (6) | 0.0469 (3) | |
C11 | −0.2587 (3) | 0.9994 (3) | 0.05883 (6) | 0.0549 (3) | |
C12 | 0.0208 (4) | 0.6670 (3) | 0.07203 (7) | 0.0645 (4) | |
C13 | 0.1642 (3) | 0.7368 (2) | 0.11825 (7) | 0.0555 (4) | |
O1W | 0.6042 (3) | 0.46898 (15) | 0.22162 (5) | 0.0567 (3) | |
H2A | 1.388 (4) | 0.807 (3) | 0.4315 (9) | 0.079 (5)* | |
H5A | 0.619 (4) | 1.275 (3) | 0.3436 (8) | 0.069 (5)* | |
H7A | 0.798 (3) | 0.727 (2) | 0.2805 (7) | 0.054 (4)* | |
H10A | −0.178 (3) | 1.237 (3) | 0.1110 (7) | 0.061 (4)* | |
H11A | −0.398 (4) | 1.092 (3) | 0.0388 (8) | 0.069 (5)* | |
H12A | 0.087 (4) | 0.519 (3) | 0.0585 (9) | 0.084 (6)* | |
H13A | 0.316 (4) | 0.636 (3) | 0.1371 (8) | 0.073 (5)* | |
H1N2 | 0.479 (3) | 0.776 (3) | 0.2116 (8) | 0.067 (5)* | |
H1W1 | 0.759 (4) | 0.402 (3) | 0.2127 (8) | 0.071 (6)* | |
H2W1 | 0.499 (4) | 0.384 (4) | 0.2232 (10) | 0.099 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0610 (5) | 0.0571 (5) | 0.0724 (6) | 0.0110 (4) | −0.0253 (4) | −0.0153 (4) |
F2 | 0.0779 (6) | 0.1120 (8) | 0.0649 (6) | −0.0278 (6) | −0.0330 (5) | −0.0306 (5) |
F3 | 0.0999 (8) | 0.0612 (5) | 0.0897 (7) | −0.0114 (5) | −0.0295 (6) | −0.0347 (5) |
O1 | 0.0565 (6) | 0.0337 (4) | 0.0772 (6) | −0.0068 (4) | −0.0346 (5) | −0.0034 (4) |
N1 | 0.0405 (5) | 0.0378 (5) | 0.0402 (5) | −0.0114 (4) | −0.0145 (4) | −0.0050 (4) |
N2 | 0.0408 (5) | 0.0331 (5) | 0.0412 (5) | −0.0087 (4) | −0.0177 (4) | −0.0039 (4) |
N3 | 0.0653 (8) | 0.0712 (8) | 0.0501 (6) | −0.0285 (6) | −0.0241 (5) | −0.0041 (6) |
C1 | 0.0381 (6) | 0.0491 (7) | 0.0410 (6) | −0.0062 (5) | −0.0103 (5) | −0.0040 (5) |
C2 | 0.0407 (7) | 0.0730 (9) | 0.0446 (7) | −0.0073 (6) | −0.0172 (5) | −0.0031 (6) |
C3 | 0.0490 (7) | 0.0758 (9) | 0.0409 (6) | −0.0220 (7) | −0.0140 (5) | −0.0131 (6) |
C4 | 0.0593 (8) | 0.0503 (7) | 0.0499 (7) | −0.0161 (6) | −0.0125 (6) | −0.0129 (5) |
C5 | 0.0492 (7) | 0.0431 (6) | 0.0480 (7) | −0.0086 (5) | −0.0183 (5) | −0.0049 (5) |
C6 | 0.0377 (6) | 0.0422 (6) | 0.0367 (5) | −0.0119 (4) | −0.0110 (4) | −0.0020 (4) |
C7 | 0.0411 (6) | 0.0361 (5) | 0.0415 (6) | −0.0091 (4) | −0.0139 (5) | −0.0039 (4) |
C8 | 0.0372 (6) | 0.0355 (5) | 0.0442 (6) | −0.0107 (4) | −0.0138 (5) | −0.0013 (4) |
C9 | 0.0378 (6) | 0.0433 (6) | 0.0375 (6) | −0.0153 (5) | −0.0126 (4) | −0.0005 (4) |
C10 | 0.0449 (7) | 0.0509 (7) | 0.0451 (7) | −0.0084 (5) | −0.0161 (5) | −0.0017 (5) |
C11 | 0.0484 (7) | 0.0724 (9) | 0.0459 (7) | −0.0138 (7) | −0.0216 (6) | 0.0011 (6) |
C12 | 0.0858 (11) | 0.0528 (8) | 0.0630 (9) | −0.0250 (8) | −0.0335 (8) | −0.0060 (7) |
C13 | 0.0671 (9) | 0.0427 (7) | 0.0603 (8) | −0.0132 (6) | −0.0322 (7) | −0.0036 (6) |
O1W | 0.0608 (7) | 0.0322 (4) | 0.0771 (7) | −0.0067 (4) | −0.0194 (5) | −0.0063 (4) |
F1—C1 | 1.3454 (15) | C5—C6 | 1.3922 (17) |
F2—C3 | 1.3445 (13) | C5—H5A | 0.969 (18) |
F3—C4 | 1.3463 (16) | C6—C7 | 1.4660 (14) |
O1—C8 | 1.2299 (13) | C7—H7A | 0.965 (15) |
N1—C7 | 1.2737 (15) | C8—C9 | 1.5025 (14) |
N1—N2 | 1.3791 (11) | C9—C13 | 1.3835 (17) |
N2—C8 | 1.3477 (14) | C9—C10 | 1.3843 (17) |
N2—H1N2 | 0.881 (18) | C10—C11 | 1.3821 (17) |
N3—C12 | 1.326 (2) | C10—H10A | 0.953 (16) |
N3—C11 | 1.3324 (19) | C11—H11A | 0.911 (19) |
C1—C2 | 1.3800 (17) | C12—C13 | 1.3882 (17) |
C1—C6 | 1.3877 (16) | C12—H12A | 0.966 (19) |
C2—C3 | 1.363 (2) | C13—H13A | 0.963 (18) |
C2—H2A | 0.93 (2) | O1W—H1W1 | 0.79 (2) |
C3—C4 | 1.381 (2) | O1W—H2W1 | 0.83 (2) |
C4—C5 | 1.3699 (16) | ||
C7—N1—N2 | 116.55 (9) | N1—C7—C6 | 118.93 (10) |
C8—N2—N1 | 117.36 (9) | N1—C7—H7A | 121.8 (9) |
C8—N2—H1N2 | 126.2 (11) | C6—C7—H7A | 119.2 (9) |
N1—N2—H1N2 | 116.5 (11) | O1—C8—N2 | 122.04 (9) |
C12—N3—C11 | 116.24 (11) | O1—C8—C9 | 120.84 (10) |
F1—C1—C2 | 118.25 (11) | N2—C8—C9 | 117.12 (9) |
F1—C1—C6 | 118.70 (10) | C13—C9—C10 | 117.67 (10) |
C2—C1—C6 | 123.04 (12) | C13—C9—C8 | 124.60 (10) |
C3—C2—C1 | 117.80 (12) | C10—C9—C8 | 117.72 (10) |
C3—C2—H2A | 126.1 (11) | C11—C10—C9 | 119.15 (12) |
C1—C2—H2A | 116.1 (11) | C11—C10—H10A | 119.8 (9) |
F2—C3—C2 | 120.48 (12) | C9—C10—H10A | 121.0 (9) |
F2—C3—C4 | 118.53 (13) | N3—C11—C10 | 123.93 (13) |
C2—C3—C4 | 120.99 (11) | N3—C11—H11A | 119.1 (11) |
F3—C4—C5 | 120.41 (12) | C10—C11—H11A | 116.9 (11) |
F3—C4—C3 | 118.89 (11) | N3—C12—C13 | 124.42 (14) |
C5—C4—C3 | 120.70 (12) | N3—C12—H12A | 117.9 (11) |
C4—C5—C6 | 120.06 (12) | C13—C12—H12A | 117.5 (11) |
C4—C5—H5A | 117.3 (10) | C9—C13—C12 | 118.58 (13) |
C6—C5—H5A | 122.7 (10) | C9—C13—H13A | 121.8 (10) |
C1—C6—C5 | 117.41 (10) | C12—C13—H13A | 119.6 (10) |
C1—C6—C7 | 120.67 (11) | H1W1—O1W—H2W1 | 108.0 (19) |
C5—C6—C7 | 121.89 (10) | ||
C7—N1—N2—C8 | −178.64 (11) | N2—N1—C7—C6 | −177.37 (10) |
F1—C1—C2—C3 | 178.60 (12) | C1—C6—C7—N1 | −172.44 (12) |
C6—C1—C2—C3 | −0.2 (2) | C5—C6—C7—N1 | 9.12 (19) |
C1—C2—C3—F2 | −179.70 (12) | N1—N2—C8—O1 | 0.66 (18) |
C1—C2—C3—C4 | 0.8 (2) | N1—N2—C8—C9 | −179.99 (9) |
F2—C3—C4—F3 | −1.2 (2) | O1—C8—C9—C13 | 174.03 (13) |
C2—C3—C4—F3 | 178.33 (14) | N2—C8—C9—C13 | −5.32 (19) |
F2—C3—C4—C5 | 179.61 (13) | O1—C8—C9—C10 | −4.90 (18) |
C2—C3—C4—C5 | −0.8 (2) | N2—C8—C9—C10 | 175.74 (11) |
F3—C4—C5—C6 | −178.86 (13) | C13—C9—C10—C11 | 0.8 (2) |
C3—C4—C5—C6 | 0.3 (2) | C8—C9—C10—C11 | 179.78 (12) |
F1—C1—C6—C5 | −179.11 (12) | C12—N3—C11—C10 | 0.3 (2) |
C2—C1—C6—C5 | −0.3 (2) | C9—C10—C11—N3 | −1.0 (2) |
F1—C1—C6—C7 | 2.38 (18) | C11—N3—C12—C13 | 0.7 (3) |
C2—C1—C6—C7 | −178.84 (12) | C10—C9—C13—C12 | 0.1 (2) |
C4—C5—C6—C1 | 0.3 (2) | C8—C9—C13—C12 | −178.85 (13) |
C4—C5—C6—C7 | 178.75 (12) | N3—C12—C13—C9 | −0.9 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···O1W | 0.883 (19) | 1.921 (19) | 2.7910 (13) | 168.1 (16) |
O1W—H1W1···O1i | 0.79 (2) | 2.03 (2) | 2.8263 (17) | 176.3 (18) |
O1W—H2W1···O1ii | 0.84 (2) | 2.19 (2) | 2.9670 (17) | 155 (2) |
O1W—H2W1···N1ii | 0.84 (2) | 2.47 (2) | 3.1024 (14) | 133.7 (19) |
C7—H7A···O1W | 0.967 (13) | 2.492 (14) | 3.2576 (16) | 135.9 (12) |
C13—H13A···O1W | 0.963 (19) | 2.427 (18) | 3.3308 (19) | 156.2 (14) |
Symmetry codes: (i) x+1, y−1, z; (ii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C13H8F3N3O·H2O |
Mr | 297.24 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 296 |
a, b, c (Å) | 4.9241 (1), 6.3915 (1), 21.3387 (2) |
α, β, γ (°) | 88.616 (1), 86.556 (1), 76.056 (1) |
V (Å3) | 650.58 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.32 × 0.32 × 0.13 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.958, 0.984 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 14710, 4024, 2730 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.721 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.046, 0.146, 1.05 |
No. of reflections | 4024 |
No. of parameters | 230 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.27, −0.22 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1N2···O1W | 0.883 (19) | 1.921 (19) | 2.7910 (13) | 168.1 (16) |
O1W—H1W1···O1i | 0.79 (2) | 2.03 (2) | 2.8263 (17) | 176.3 (18) |
O1W—H2W1···O1ii | 0.84 (2) | 2.19 (2) | 2.9670 (17) | 155 (2) |
O1W—H2W1···N1ii | 0.84 (2) | 2.47 (2) | 3.1024 (14) | 133.7 (19) |
C7—H7A···O1W | 0.967 (13) | 2.492 (14) | 3.2576 (16) | 135.9 (12) |
C13—H13A···O1W | 0.963 (19) | 2.427 (18) | 3.3308 (19) | 156.2 (14) |
Symmetry codes: (i) x+1, y−1, z; (ii) x, y−1, z. |
Acknowledgements
This research was supported by Universiti Sains Malaysia (USM) under the University Research Grant (1001/PFARMASI/815005). HSNK and CSY each thank USM for the award of a USM Fellowship. HKF and CSY thank USM for the Research University Golden Goose Grant (1001/PFIZIK/811012).
References
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In the search for new biologically active compounds, isoniazid (isonicotinylhydrazine) derivatives have been found to possess potential tuberculostatic activity (Janin, 2007; Maccari et al., 2005; Slayden & Barry, 2000). As part of our current work on the synthesis of (E)-N'-substituted isonicotinohydrazide derivatives, in this paper we present the crystal structure of the title compound, (I).
The asymmetric unit consists of one Schiff base molecule and one water molecule (Fig. 1). The geometric parameters are comparable to those related structures (Naveenkumar et al., 2009, 2010; Shi, 2005). The molecule is nearly coplanar with a dihedral angle between the benzene ring and the pyridine ring of 6.64 (7)°. The molecule exists in an E configuration with respect to the C7=N1 double bond. In the crystal structure, the water molecules link the molecules into two-dimensional planes parallel to the ab plane through intermolecular N–H···O, O–H···O O–H···N and C–H···O hydrogen bonds (Fig. 2, Table 1).