organic compounds
(Z)-2-(5-Fluoro-2-oxoindolin-3-ylidene)-N-methylhydrazinecarbothioamide
aDepartment of Chemistry, Faculty of Science, Sebha University, Libya, bDepartment of Chemistry, Rabigh College of Science and Arts, King Abdulaziz University, PO Box 344, Rabigh 21911, Saudi Arabia, and cSchool of Chemical Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
*Correspondence e-mail: nasertaha90@hotmail.com
In the title compound, C10H9FN4OS, which is approximately planar with a maximum deviation of 0.0881 (10) Å from the mean plane of the non-H atoms, an intramolecular N—H⋯O hydrogen bond generates an S(6) ring. In the crystal, molecules are linked via N—H⋯O hydrogen bonds, forming a helical chain along the a axis. The chains are linked by N—H⋯S, C—H⋯S and C—H⋯F hydrogen bonds and C—H⋯ π interactions into a three-dimensional network.
Keywords: crystal structure; Schiff base; isatin.
CCDC reference: 909982
Structure description
The title Schiff base was synthesized by the condensation reaction of 5-fluoroisatin with 4-methyl-3-thiosemicarbazide. In numerous cases, isatins react with nucleophiles, even in the absence of any catalyst, either at room temperature or by heating for a few hours (Singh & Desta, 2012). Thiosemicarbazones are a class of small molecules that display numerous biological activities as antivirals and as anticancer therapeutics, as well as parasiticidal action against Plasmodium falciparum and Trypanasoma cruzi which are the causative agents of malaria and Chagas's disease, respectively (Er et al., 2008). The crystal structures of (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide (Ali et al., 2012a) and bis[2-(2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamidato-κ3O,N2,S]nickel(II) dimethylformamide monosolvate (Ali et al., 2012b), closely related to the title compound, have been reported.
The title compound is approximately planar (Fig. 1); the dihedral angle between the benzene C1–C6 ring and the five-membered ring C1/C6/N1/C7/C8 is 1.24 (7)°, and the C8—N2—N3—C9, N2—N3—C9—N4 and N2—N3—C9—S1 torsion angles are 176.91 (12), 0.33 (18) and −178.81 (9)°, respectively.
In the crystal (Fig. 2), the molecules are linked through N1—H1N1⋯O1i hydrogen bonds, forming a helical chain along the a axis. The chains are linked by N4—H1N4⋯S1ii, C2—H2A⋯S1ii and C10—H10C⋯F1iii hydrogen bonds and a C4—H4A⋯Cg2iv interaction (symmetry codes as given in Table 1), forming a three-dimensional network. No significant aromatic π–π stacking interactions are observed, the shortest centroid–centroid separation being 4.715 Å.
Synthesis and crystallization
The title compound was synthesized by refluxing the reaction mixture of hot ethanolic solutions (30 ml each) of 4-methyl-3-thiosemicarbazide (0.01 mol) and 5-fluoroisatin (0.01 mol) for 2 h. The precipitates formed during reflux were filtered and washed with cold ethanol and finally stored in a vacuum desiccator over P2O5 (yield 94%, m.p. 512.4–513.8 K). Yellow crystals were grown from acetone–dimethylformamide (3:1) by slow evaporation at room temperature.
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2
|
Structural data
CCDC reference: 909982
10.1107/S2414314616006593/is4006sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2414314616006593/is4006Isup2.hkl
Supporting information file. DOI: 10.1107/S2414314616006593/is4006Isup3.cml
The title compound was synthesized by refluxing the reaction mixture of hot ethanolic solutions (30 ml each) of 4-methyl-3-thiosemicarbazide (0.01 mol) and 5-fluoroisatin (0.01 mol) for 2 h. The precipitates formed during reflux were filtered and washed with cold ethanol and finally stored in a vacuum desiccator over P2O5 (yield 94%, m.p. 512.4–513.8 K). Yellow crystals were grown from acetone–dimethylformamide (3:1) by slow evaporation at room temperature.
The title Schiff base was synthesized by the condensation reaction of 5-fluoroisatin with 4-methyl-3-thiosemicarbazide. In numerous cases, isatins react with nucleophiles, even in the absence of any catalyst, either at room temperature or by heating for a few hours (Singh & Desta, 2012). Thiosemicarbazones are a class of small molecules that display numerous biological activities as antivirals and as anticancer therapeutics, as well as parasiticidal action against Plasmodium falciparum and Trypanasoma cruzi which are the causative agents of malaria and Chagas's disease, respectively (Er et al., 2008). The crystal structures of compounds, (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide (Ali et al., 2012a) and bis[2-(2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamidato-κ3O,N2,S]nickel(II) dimethylformamide monosolvate (Ali et al., 2012b), closely related to the title compound, have been reported.
The title compound is approximately planar (Fig. 1); the dihedral angle between the benzene C1–C6 ring and the five-membered ring C1/C6/N1/C7/C8 is 1.24 (7)°, and the C8—N2—N3—C9, N2—N3—C9—N4 and N2—N3—C9—S1 torsion angles are 176.91 (12), 0.33 (18) and -178.81 (9)°, respectively.
In the crystal (Fig. 2), the molecules are linked through N1—H1N1···O1i hydrogen bonds, forming a helical chain along the a axis. The chains are linked by N4—H1N4···S1ii, C2—H2A···S1ii and C10—H10C···F1iii hydrogen bonds and a C4—H4A···Cg2iv interaction (symmetry codes as given in Table 1), forming a three-dimensional network. No significant aromatic π–π stacking interactions are observed, the shortest centroid–centroid separation being 4.715 Å.
Data collection: APEX2 (Bruker, 2005); cell
SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); 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 50% probability displacement ellipsoids and the atom-numbering scheme. | |
Fig. 2. The crystal packing of the title compound, viewed down the a axis. Hydrogen bonds are shown as dashed lines. |
C10H9FN4OS | Dx = 1.466 Mg m−3 |
Mr = 252.27 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 9924 reflections |
a = 5.7058 (1) Å | θ = 3.7–32.6° |
b = 10.6201 (2) Å | µ = 0.28 mm−1 |
c = 18.8688 (4) Å | T = 100 K |
V = 1143.38 (4) Å3 | Block, yellow |
Z = 4 | 0.53 × 0.30 × 0.17 mm |
F(000) = 520 |
Bruker APEXII CCD diffractometer | 3953 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.019 |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | θmax = 32.6°, θmin = 2.2° |
Tmin = 0.782, Tmax = 0.854 | h = −8→8 |
16340 measured reflections | k = −16→14 |
4144 independent reflections | l = −28→28 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.027 | w = 1/[σ2(Fo2) + (0.0376P)2 + 0.2071P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.069 | (Δ/σ)max < 0.001 |
S = 1.05 | Δρmax = 0.31 e Å−3 |
4144 reflections | Δρmin = −0.19 e Å−3 |
167 parameters | Absolute structure: Flack x determined using 1583 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
0 restraints | Absolute structure parameter: 0.031 (15) |
C10H9FN4OS | V = 1143.38 (4) Å3 |
Mr = 252.27 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.7058 (1) Å | µ = 0.28 mm−1 |
b = 10.6201 (2) Å | T = 100 K |
c = 18.8688 (4) Å | 0.53 × 0.30 × 0.17 mm |
Bruker APEXII CCD diffractometer | 4144 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 3953 reflections with I > 2σ(I) |
Tmin = 0.782, Tmax = 0.854 | Rint = 0.019 |
16340 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.069 | Δρmax = 0.31 e Å−3 |
S = 1.05 | Δρmin = −0.19 e Å−3 |
4144 reflections | Absolute structure: Flack x determined using 1583 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
167 parameters | Absolute structure parameter: 0.031 (15) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.74472 (6) | 0.26837 (3) | 0.22344 (2) | 0.01730 (8) | |
F1 | −0.37420 (18) | 0.87584 (8) | 0.12143 (5) | 0.0246 (2) | |
O1 | 0.13905 (19) | 0.26894 (10) | 0.06783 (5) | 0.0189 (2) | |
N1 | −0.1734 (2) | 0.39611 (11) | 0.03438 (6) | 0.0166 (2) | |
N2 | 0.2390 (2) | 0.48908 (9) | 0.16490 (5) | 0.01366 (19) | |
N3 | 0.3829 (2) | 0.39002 (10) | 0.17279 (6) | 0.0149 (2) | |
N4 | 0.6013 (2) | 0.50266 (10) | 0.25329 (6) | 0.0156 (2) | |
C1 | −0.1048 (2) | 0.57160 (12) | 0.10271 (6) | 0.0129 (2) | |
C2 | −0.1426 (2) | 0.69283 (12) | 0.12782 (7) | 0.0150 (2) | |
H2A | −0.0423 | 0.7308 | 0.1619 | 0.018* | |
C3 | −0.3354 (2) | 0.75503 (12) | 0.10026 (7) | 0.0165 (2) | |
C4 | −0.4878 (3) | 0.70357 (13) | 0.05128 (7) | 0.0176 (3) | |
H4A | −0.6193 | 0.7504 | 0.0352 | 0.021* | |
C5 | −0.4470 (2) | 0.58177 (13) | 0.02560 (7) | 0.0166 (2) | |
H5A | −0.5480 | 0.5444 | −0.0084 | 0.020* | |
C6 | −0.2538 (3) | 0.51798 (11) | 0.05173 (6) | 0.0140 (2) | |
C7 | 0.0219 (2) | 0.36665 (12) | 0.07190 (7) | 0.0150 (2) | |
C8 | 0.0724 (2) | 0.47780 (12) | 0.11870 (6) | 0.0135 (2) | |
C9 | 0.5714 (2) | 0.39599 (11) | 0.21827 (7) | 0.0135 (2) | |
C10 | 0.7908 (3) | 0.52261 (14) | 0.30366 (8) | 0.0211 (3) | |
H10A | 0.7855 | 0.6095 | 0.3211 | 0.032* | |
H10B | 0.9414 | 0.5074 | 0.2802 | 0.032* | |
H10C | 0.7730 | 0.4644 | 0.3436 | 0.032* | |
H1N3 | 0.362 (4) | 0.324 (2) | 0.1503 (10) | 0.022 (5)* | |
H1N1 | −0.234 (5) | 0.346 (2) | 0.0038 (11) | 0.035 (6)* | |
H1N4 | 0.502 (4) | 0.562 (2) | 0.2464 (12) | 0.027 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.01617 (14) | 0.01296 (12) | 0.02276 (14) | 0.00254 (12) | −0.00245 (14) | 0.00152 (10) |
F1 | 0.0294 (5) | 0.0163 (4) | 0.0280 (4) | 0.0105 (4) | −0.0010 (4) | −0.0041 (3) |
O1 | 0.0242 (5) | 0.0144 (4) | 0.0181 (4) | 0.0039 (4) | 0.0004 (4) | −0.0035 (4) |
N1 | 0.0205 (6) | 0.0137 (4) | 0.0157 (5) | −0.0002 (4) | −0.0029 (4) | −0.0032 (4) |
N2 | 0.0144 (5) | 0.0122 (4) | 0.0144 (4) | 0.0011 (4) | 0.0003 (4) | 0.0011 (3) |
N3 | 0.0164 (5) | 0.0117 (4) | 0.0167 (5) | 0.0019 (4) | −0.0028 (4) | −0.0011 (4) |
N4 | 0.0152 (5) | 0.0137 (5) | 0.0180 (5) | 0.0008 (4) | −0.0015 (4) | −0.0002 (4) |
C1 | 0.0139 (5) | 0.0125 (5) | 0.0125 (5) | 0.0002 (4) | 0.0003 (4) | 0.0001 (4) |
C2 | 0.0168 (6) | 0.0133 (5) | 0.0150 (5) | 0.0023 (4) | −0.0005 (5) | −0.0010 (4) |
C3 | 0.0178 (6) | 0.0142 (5) | 0.0175 (5) | 0.0045 (5) | 0.0023 (5) | −0.0001 (4) |
C4 | 0.0142 (6) | 0.0200 (6) | 0.0186 (5) | 0.0028 (5) | 0.0005 (5) | 0.0038 (5) |
C5 | 0.0141 (6) | 0.0193 (6) | 0.0163 (5) | −0.0013 (5) | −0.0017 (5) | 0.0018 (4) |
C6 | 0.0152 (5) | 0.0135 (4) | 0.0131 (4) | −0.0013 (5) | 0.0007 (5) | 0.0002 (4) |
C7 | 0.0195 (6) | 0.0129 (5) | 0.0125 (5) | −0.0002 (5) | 0.0003 (5) | −0.0018 (4) |
C8 | 0.0157 (6) | 0.0119 (4) | 0.0129 (5) | 0.0012 (4) | 0.0009 (4) | −0.0011 (4) |
C9 | 0.0134 (5) | 0.0130 (5) | 0.0140 (5) | 0.0001 (4) | 0.0010 (4) | 0.0021 (4) |
C10 | 0.0189 (7) | 0.0212 (6) | 0.0232 (6) | −0.0033 (5) | −0.0049 (5) | −0.0026 (5) |
S1—C9 | 1.6804 (13) | C1—C6 | 1.4043 (18) |
F1—C3 | 1.3618 (15) | C1—C8 | 1.4509 (18) |
O1—C7 | 1.2366 (16) | C2—C3 | 1.3843 (19) |
N1—C7 | 1.3567 (18) | C2—H2A | 0.9500 |
N1—C6 | 1.4116 (16) | C3—C4 | 1.3819 (19) |
N1—H1N1 | 0.86 (2) | C4—C5 | 1.4009 (19) |
N2—C8 | 1.2957 (17) | C4—H4A | 0.9500 |
N2—N3 | 1.3426 (15) | C5—C6 | 1.3847 (19) |
N3—C9 | 1.3775 (17) | C5—H5A | 0.9500 |
N3—H1N3 | 0.83 (2) | C7—C8 | 1.5020 (17) |
N4—C9 | 1.3225 (16) | C10—H10A | 0.9800 |
N4—C10 | 1.4549 (18) | C10—H10B | 0.9800 |
N4—H1N4 | 0.86 (2) | C10—H10C | 0.9800 |
C1—C2 | 1.3887 (17) | ||
C7—N1—C6 | 110.94 (11) | C6—C5—C4 | 117.45 (12) |
C7—N1—H1N1 | 122.6 (16) | C6—C5—H5A | 121.3 |
C6—N1—H1N1 | 126.5 (16) | C4—C5—H5A | 121.3 |
C8—N2—N3 | 116.80 (10) | C5—C6—C1 | 121.83 (12) |
N2—N3—C9 | 120.70 (11) | C5—C6—N1 | 128.66 (12) |
N2—N3—H1N3 | 121.2 (15) | C1—C6—N1 | 109.51 (12) |
C9—N3—H1N3 | 118.1 (14) | O1—C7—N1 | 127.23 (12) |
C9—N4—C10 | 123.16 (12) | O1—C7—C8 | 126.33 (12) |
C9—N4—H1N4 | 117.9 (15) | N1—C7—C8 | 106.43 (11) |
C10—N4—H1N4 | 118.9 (15) | N2—C8—C1 | 126.00 (11) |
C2—C1—C6 | 121.04 (12) | N2—C8—C7 | 127.51 (12) |
C2—C1—C8 | 132.37 (12) | C1—C8—C7 | 106.49 (11) |
C6—C1—C8 | 106.60 (11) | N4—C9—N3 | 116.83 (11) |
C3—C2—C1 | 115.96 (12) | N4—C9—S1 | 125.88 (10) |
C3—C2—H2A | 122.0 | N3—C9—S1 | 117.29 (9) |
C1—C2—H2A | 122.0 | N4—C10—H10A | 109.5 |
F1—C3—C4 | 117.79 (12) | N4—C10—H10B | 109.5 |
F1—C3—C2 | 117.95 (12) | H10A—C10—H10B | 109.5 |
C4—C3—C2 | 124.24 (13) | N4—C10—H10C | 109.5 |
C3—C4—C5 | 119.46 (13) | H10A—C10—H10C | 109.5 |
C3—C4—H4A | 120.3 | H10B—C10—H10C | 109.5 |
C5—C4—H4A | 120.3 | ||
C8—N2—N3—C9 | 176.91 (12) | C6—N1—C7—O1 | −177.89 (13) |
C6—C1—C2—C3 | 0.79 (19) | C6—N1—C7—C8 | 0.88 (14) |
C8—C1—C2—C3 | −179.31 (13) | N3—N2—C8—C1 | 178.69 (12) |
C1—C2—C3—F1 | −177.62 (11) | N3—N2—C8—C7 | −0.75 (19) |
C1—C2—C3—C4 | 0.7 (2) | C2—C1—C8—N2 | 2.3 (2) |
F1—C3—C4—C5 | 176.88 (12) | C6—C1—C8—N2 | −177.77 (13) |
C2—C3—C4—C5 | −1.4 (2) | C2—C1—C8—C7 | −178.15 (14) |
C3—C4—C5—C6 | 0.64 (19) | C6—C1—C8—C7 | 1.76 (13) |
C4—C5—C6—C1 | 0.80 (19) | O1—C7—C8—N2 | −3.3 (2) |
C4—C5—C6—N1 | −179.45 (13) | N1—C7—C8—N2 | 177.88 (13) |
C2—C1—C6—C5 | −1.56 (19) | O1—C7—C8—C1 | 177.15 (13) |
C8—C1—C6—C5 | 178.52 (12) | N1—C7—C8—C1 | −1.64 (14) |
C2—C1—C6—N1 | 178.64 (12) | C10—N4—C9—N3 | 179.35 (12) |
C8—C1—C6—N1 | −1.28 (14) | C10—N4—C9—S1 | −1.59 (19) |
C7—N1—C6—C5 | −179.55 (13) | N2—N3—C9—N4 | 0.33 (18) |
C7—N1—C6—C1 | 0.23 (15) | N2—N3—C9—S1 | −178.81 (9) |
Cg2 is the centroid of the C1–C6 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1N3···O1 | 0.83 (2) | 2.09 (2) | 2.7407 (15) | 135 (2) |
N1—H1N1···O1i | 0.86 (2) | 1.96 (2) | 2.8173 (15) | 178 (3) |
N4—H1N4···S1ii | 0.86 (2) | 2.67 (2) | 3.4718 (11) | 157.0 (19) |
C2—H2A···S1ii | 0.95 | 2.78 | 3.6979 (13) | 163 |
C10—H10C···F1iii | 0.98 | 2.55 | 3.1746 (19) | 122 |
C4—H4A···Cg2iv | 0.95 | 2.62 | 3.4291 (15) | 143 |
Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) −x+1, y+1/2, −z+1/2; (iii) −x, y−1/2, −z+1/2; (iv) x−1/2, −y+3/2, −z. |
Cg2 is the centroid of the C1–C6 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1N3···O1 | 0.83 (2) | 2.09 (2) | 2.7407 (15) | 135 (2) |
N1—H1N1···O1i | 0.86 (2) | 1.96 (2) | 2.8173 (15) | 178 (3) |
N4—H1N4···S1ii | 0.86 (2) | 2.67 (2) | 3.4718 (11) | 157.0 (19) |
C2—H2A···S1ii | 0.95 | 2.78 | 3.6979 (13) | 163 |
C10—H10C···F1iii | 0.98 | 2.55 | 3.1746 (19) | 122 |
C4—H4A···Cg2iv | 0.95 | 2.62 | 3.4291 (15) | 143 |
Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) −x+1, y+1/2, −z+1/2; (iii) −x, y−1/2, −z+1/2; (iv) x−1/2, −y+3/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C10H9FN4OS |
Mr | 252.27 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 5.7058 (1), 10.6201 (2), 18.8688 (4) |
V (Å3) | 1143.38 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.28 |
Crystal size (mm) | 0.53 × 0.30 × 0.17 |
Data collection | |
Diffractometer | Bruker APEXII CCD |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.782, 0.854 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16340, 4144, 3953 |
Rint | 0.019 |
(sin θ/λ)max (Å−1) | 0.758 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.069, 1.05 |
No. of reflections | 4144 |
No. of parameters | 167 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.31, −0.19 |
Absolute structure | Flack x determined using 1583 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Absolute structure parameter | 0.031 (15) |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXS2014 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia for the RU research grant (1001/PKIMIA/815067). AQA thanks the Ministry of Higher Education and the University of Sabha (Libya) for a scholarship.
References
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