Crystal structure of (Z)-2-(5-fluoro-2-oxoindolin-3-yl­idene)hydrazinecarbo­thio­amide

Bittencourt, V.C.D.; Almeida, V.Y.G.; Back, D.F.; Gervini, V.C.; Oliveira, A.B. de

doi:10.1107/S2056989015008609

organic compounds

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Volume 71| Part 6| June 2015| Pages o383-o384

doi:10.1107/S2056989015008609

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Crystal structure of (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide

Viviane C. D. Bittencourt,^a Vitor Y. G. Almeida,^a Davi F. Back,^b Vanessa C. Gervini ^a ^* and Adriano Bof de Oliveira ^c

^aEscola de Química e Alimentos, Universidade Federal do Rio Grande, Av. Itália km 08, Campus Carreiros, 96203-900 Rio Grande-RS, Brazil, ^bDepartamento de Química, Universidade Federal de Santa Maria, Av. Roraima s/n, Campus Universitário, 97105-900 Santa Maria-RS, Brazil, and ^cDepartamento de Química, Universidade Federal de Sergipe, Av. Marechal Rondon s/n, Campus Universitário, 49100-000 São Cristóvão-SE, Brazil
^*Correspondence e-mail: vanessa.gervini@gmail.com

Edited by M. Lopez-Rodriguez, Universidad de La Laguna, Tenerife (Received 22 April 2015; accepted 3 May 2015; online 9 May 2015)

In the title compound, C₉H₇FN₄OS, the molecules are almost planar, with an r.m.s. deviation of 0.047 (3) Å from the mean plane defined by the non-H atoms and a maximum deviation of 0.123 (2) Å for the amine N atom. The torsion angle for the N—N—C—S unit is 176.57 (19)°. In the crystal, molecules are linked into inversion dimers via pairs of N—H⋯F hydrogen bonds and, additionally, through N—H⋯O and N—H⋯S hydrogen bonds, building a two-dimensional hydrogen-bond network parallel to the (103) plane. An intramolecular N—H⋯O interaction is also observed.

Keywords: crystal structure; thiosemicarbazone derivative; isatin; two-dimensional hydrogen-bonding network; natural product.

CCDC reference: 1062930

1. Related literature

For one of the first reports of the synthesis of thiosemicarbazone derivatives, see: Freund & Schander (1902 ). For the synthesis and crystal structure of a similar compound, namely (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide, see: Ali et al. (2012 ). For a review on hydrogen bonding, see: Steiner (2002 ).

2. Experimental

2.1. Crystal data

C₉H₇FN₄OS
M_r = 238.25
Monoclinic, P 2₁ /n
a = 4.7151 (1) Å
b = 15.4517 (4) Å
c = 13.9645 (4) Å
β = 93.921 (2)°
V = 1015.02 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.32 mm⁻¹
T = 293 K
0.44 × 0.16 × 0.11 mm

2.2. Data collection

Bruker X8 Kappa APEXII diffractometer
Absorption correction: numerical (SADABS; Bruker 2009 ) T_min = 0.954, T_max = 0.966
12531 measured reflections
2239 independent reflections
1390 reflections with I > 2σ(I)
R_int = 0.064

2.3. Refinement

R[F² > 2σ(F²)] = 0.049
wR(F²) = 0.140
S = 1.01
2239 reflections
145 parameters
H-atom parameters constrained
Δρ_max = 0.20 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯O1	0.86	2.12	2.781 (3)	133
N1—H1⋯S1ⁱ	0.86	2.55	3.367 (2)	158
N4—H4A⋯F1ⁱⁱ	0.86	2.24	2.956 (3)	140
N4—H4B⋯O1ⁱⁱⁱ	0.86	2.03	2.879 (3)	171
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) -x+2, -y, -z+1; (iii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1062930

Crystal structure: contains datablocks I, publication_text. DOI: 10.1107/S2056989015008609/lr2136sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015008609/lr2136Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015008609/lr2136Isup3.cml

checkCIF report

Structural commentary top

\ Concerning our interest on the study of the supramolecular chemistry of thiosemicarbazone derivatives from natural products, we report herein the crystal structure of the (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-\ hydrazinecarbothioamide, a thiosemicarbazone derivative from 5-fluorisatin (Fig. 1). The molecular structure of the title compound matches the asymmetric unit and itsn't planar. The maximum deviation from the mean plane of the non-H atoms amounts to 0.1229 (22) Å for N4 and the torsion angle for the N2–N3–C9–S1–entity amounts to 176.57 (19)°. All bond distances and angles are consistent with literature data of a similiar compound, (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-\ phenylhydrazinecarbothioamide (Ali et al., 2012). In the crystal of the title compound, the molecules are linked into dimers via pairs of N4—H4A···F1 hydrogen bonds. The dimers are linked into a two dimensional hydrogen bonded network through the N1—H1···S1, O1···H4B—N4 and S1···H1—N1 hydrogen bonds. In addition, an intramolecular N3—H3···O1 interaction is also observed and the O1 atom builds a bifurcated hydrogen bonding with the H3 and H4B atoms (Table 1, Fig. 2 and Steiner, 2002). The 2-D H-bonded polymers are stacked along the a-axis without any strong or relevant intermolecular interactions between themselves. The molecules of the title compound are also related by two fold screw axis parallel to the b-direction (Fig. 2)

Synthesis and crystallization top

Starting materials were commercially available and were used without further purification. The synthesis was adapted from a procedure reported previously (Freund & Schander, 1902). The hydrochloric acid catalyzed reaction of 5-fluorisatin (8,83 mmol) and thiosemicarbazide (8,83 mmol) in ethanol (50 ml) was refluxed for 6 h. After cooling and filtering, the title compound was obtained. Crystals suitable for X-ray diffraction of title compound were obtained in ethanol by the slow evaporation of the solvent.

Refinement top

All aromatic H atoms were positioned with idealized geometry and were refined isotropic with U_iso(H) = 1.2 U_eq(C) using a riding model with C—H = 0.93 Å. The other H atoms were located in difference map but were positioned with idealized geometry and refined isotropic with U_iso(H) = 1.2 U_eq(N) using a riding model with N—H = 0.86 Å.

Related literature top

For one of the first reports of the synthesis of thiosemicarbazone derivatives, see: Freund & Schander (1902). For the synthesis and crystal structure of a similar compound, namely (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)-N-phenylhydrazinecarbothioamide, see: Ali et al. (2012). For a review on hydrogen bonding, see: Steiner (2002).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. : The molecular structure of the title compound with labeling and displacement ellipsoids drawn at the 40% probability level. H atoms are drawn isotropically.
	Fig. 2. : A view, down the c axis, of the packing of the title compound showing the two dimensional hydrogen-bond network. Hydrogen bonds are shown as dashed lines.

(Z)-2-(5-Fluoro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide top

Crystal data top

C₉H₇FN₄OS	F(000) = 488
M_r = 238.25	D_x = 1.559 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1744 reflections
a = 4.7151 (1) Å	θ = 2.6–22.4°
b = 15.4517 (4) Å	µ = 0.32 mm⁻¹
c = 13.9645 (4) Å	T = 293 K
β = 93.921 (2)°	Block, orange
V = 1015.02 (4) Å³	0.44 × 0.16 × 0.11 mm
Z = 4

Data collection top

Bruker X8 Kappa APEXII diffractometer	2239 independent reflections
Radiation source: fine-focus sealed tube, Bruker X8 Kappa APEX II	1390 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.064
Detector resolution: 8.3333 pixels mm^-1	θ_max = 27.2°, θ_min = 2.0°
0.5 ° ω & ϕ scans	h = −3→6
Absorption correction: numerical (SADABS; Bruker 2009)	k = −19→19
T_min = 0.954, T_max = 0.966	l = −17→17
12531 measured reflections

Refinement top

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)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.140	H-atom parameters constrained
S = 1.01	w = 1/[σ²(F_o²) + (0.0642P)² + 0.1779P] where P = (F_o² + 2F_c²)/3
2239 reflections	(Δ/σ)_max < 0.001
145 parameters	Δρ_max = 0.20 e Å⁻³
0 restraints	Δρ_min = −0.29 e Å⁻³

Crystal data top

C₉H₇FN₄OS	V = 1015.02 (4) Å³
M_r = 238.25	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 4.7151 (1) Å	µ = 0.32 mm⁻¹
b = 15.4517 (4) Å	T = 293 K
c = 13.9645 (4) Å	0.44 × 0.16 × 0.11 mm
β = 93.921 (2)°

Data collection top

Bruker X8 Kappa APEXII diffractometer	2239 independent reflections
Absorption correction: numerical (SADABS; Bruker 2009)	1390 reflections with I > 2σ(I)
T_min = 0.954, T_max = 0.966	R_int = 0.064
12531 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	0 restraints
wR(F²) = 0.140	H-atom parameters constrained
S = 1.01	Δρ_max = 0.20 e Å⁻³
2239 reflections	Δρ_min = −0.29 e Å⁻³
145 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > σ(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) top

	x	y	z	U_iso*/U_eq
S1	0.02917 (16)	0.03364 (5)	0.86791 (6)	0.0558 (3)
O1	0.3669 (4)	0.28879 (12)	0.73620 (14)	0.0506 (5)
F1	1.2874 (4)	0.11434 (14)	0.40106 (15)	0.0840 (7)
N3	0.3467 (4)	0.10914 (14)	0.74614 (16)	0.0452 (6)
H3	0.2958	0.1572	0.7708	0.054*
N1	0.6921 (4)	0.32661 (14)	0.62633 (16)	0.0472 (6)
H1	0.6864	0.3820	0.6319	0.057*
N2	0.5310 (4)	0.10861 (14)	0.67623 (16)	0.0433 (5)
N4	0.3217 (5)	−0.03703 (14)	0.73181 (19)	0.0587 (7)
H4A	0.4327	−0.0322	0.6857	0.070*
H4B	0.2628	−0.0872	0.7481	0.070*
C1	0.8212 (5)	0.19327 (16)	0.57361 (19)	0.0411 (6)
C8	0.6233 (5)	0.18194 (16)	0.64722 (19)	0.0402 (6)
C7	0.5406 (5)	0.27122 (16)	0.67762 (19)	0.0413 (6)
C6	0.8603 (5)	0.28250 (17)	0.56272 (19)	0.0412 (6)
C5	1.0436 (6)	0.31552 (19)	0.4996 (2)	0.0502 (7)
H5	1.0706	0.3748	0.4936	0.060*
C3	1.1423 (6)	0.1702 (2)	0.4555 (2)	0.0549 (8)
C2	0.9634 (5)	0.13570 (19)	0.5189 (2)	0.0507 (7)
H2	0.9393	0.0762	0.5246	0.061*
C9	0.2420 (5)	0.03249 (16)	0.7774 (2)	0.0431 (6)
C4	1.1869 (6)	0.2569 (2)	0.4450 (2)	0.0553 (8)
H4	1.3129	0.2766	0.4015	0.066*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0683 (5)	0.0365 (4)	0.0666 (5)	−0.0055 (3)	0.0331 (4)	−0.0047 (3)
O1	0.0629 (11)	0.0349 (10)	0.0560 (12)	0.0082 (9)	0.0181 (10)	−0.0011 (9)
F1	0.0816 (12)	0.0853 (15)	0.0906 (15)	0.0084 (11)	0.0470 (11)	−0.0180 (12)
N3	0.0534 (12)	0.0273 (11)	0.0571 (15)	0.0001 (9)	0.0209 (11)	−0.0011 (10)
N1	0.0558 (13)	0.0259 (11)	0.0614 (15)	−0.0024 (9)	0.0153 (12)	0.0024 (10)
N2	0.0457 (11)	0.0331 (12)	0.0526 (14)	0.0004 (9)	0.0150 (10)	−0.0001 (10)
N4	0.0721 (15)	0.0292 (12)	0.0798 (18)	−0.0060 (11)	0.0412 (14)	−0.0022 (12)
C1	0.0408 (13)	0.0347 (14)	0.0484 (16)	0.0003 (11)	0.0082 (12)	−0.0001 (11)
C8	0.0407 (13)	0.0317 (14)	0.0486 (16)	0.0020 (11)	0.0064 (12)	0.0014 (11)
C7	0.0489 (14)	0.0289 (13)	0.0466 (15)	0.0025 (11)	0.0062 (12)	0.0000 (11)
C6	0.0422 (13)	0.0339 (14)	0.0478 (16)	−0.0016 (11)	0.0037 (12)	0.0036 (11)
C5	0.0495 (15)	0.0470 (17)	0.0544 (18)	−0.0081 (13)	0.0065 (13)	0.0096 (14)
C3	0.0513 (16)	0.060 (2)	0.0551 (19)	0.0032 (14)	0.0170 (14)	−0.0062 (15)
C2	0.0497 (14)	0.0437 (16)	0.0604 (19)	0.0022 (13)	0.0157 (13)	−0.0020 (14)
C9	0.0452 (14)	0.0314 (13)	0.0537 (17)	−0.0003 (11)	0.0106 (12)	0.0004 (12)
C4	0.0484 (15)	0.068 (2)	0.0514 (18)	−0.0079 (14)	0.0127 (14)	0.0075 (15)

Geometric parameters (Å, º) top

S1—C9	1.667 (3)	C1—C2	1.377 (4)
O1—C7	1.227 (3)	C1—C6	1.401 (4)
F1—C3	1.365 (3)	C1—C8	1.446 (3)
N3—N2	1.351 (3)	C8—C7	1.503 (3)
N3—C9	1.366 (3)	C7—O1	1.227 (3)
N3—H3	0.8600	C6—C5	1.374 (3)
N1—C7	1.351 (3)	C5—C4	1.388 (4)
N1—C6	1.407 (3)	C5—H5	0.9300
N1—H1	0.8600	C3—C4	1.365 (4)
N2—C8	1.289 (3)	C3—C2	1.371 (4)
N4—C9	1.316 (3)	C2—H2	0.9300
N4—H4A	0.8600	C4—H4	0.9300
N4—H4B	0.8600

N2—N3—C9	119.3 (2)	C5—C6—C1	121.9 (2)
N2—N3—H3	120.3	C5—C6—N1	129.2 (3)
C9—N3—H3	120.3	C1—C6—N1	108.9 (2)
C7—N1—C6	111.7 (2)	C6—C5—C4	117.4 (3)
C7—N1—H1	124.2	C6—C5—H5	121.3
C6—N1—H1	124.2	C4—C5—H5	121.3
C8—N2—N3	118.0 (2)	F1—C3—C4	118.3 (3)
C9—N4—H4A	120.0	F1—C3—C2	117.9 (3)
C9—N4—H4B	120.0	C4—C3—C2	123.8 (3)
H4A—N4—H4B	120.0	C3—C2—C1	116.8 (3)
C2—C1—C6	120.2 (2)	C3—C2—H2	121.6
C2—C1—C8	132.8 (2)	C1—C2—H2	121.6
C6—C1—C8	107.0 (2)	N4—C9—N3	115.6 (2)
N2—C8—C1	125.3 (2)	N4—C9—S1	125.6 (2)
N2—C8—C7	128.2 (2)	N3—C9—S1	118.83 (19)
C1—C8—C7	106.4 (2)	C3—C4—C5	119.8 (3)
O1—C7—N1	127.9 (2)	C3—C4—H4	120.1
O1—C7—C8	126.1 (2)	C5—C4—H4	120.1
N1—C7—C8	106.0 (2)

C9—N3—N2—C8	179.0 (2)	C2—C1—C6—N1	179.9 (2)
N3—N2—C8—C1	179.8 (2)	C8—C1—C6—N1	−0.5 (3)
N3—N2—C8—C7	−3.6 (4)	C7—N1—C6—C5	−179.5 (3)
C2—C1—C8—N2	−1.7 (5)	C7—N1—C6—C1	−1.0 (3)
C6—C1—C8—N2	178.8 (3)	C1—C6—C5—C4	1.1 (4)
C2—C1—C8—C7	−178.9 (3)	N1—C6—C5—C4	179.5 (3)
C6—C1—C8—C7	1.5 (3)	F1—C3—C2—C1	179.4 (3)
C6—N1—C7—O1	−177.1 (3)	C4—C3—C2—C1	0.6 (5)
C6—N1—C7—C8	1.9 (3)	C6—C1—C2—C3	0.5 (4)
N2—C8—C7—O1	−0.2 (5)	C8—C1—C2—C3	−178.9 (3)
C1—C8—C7—O1	176.9 (3)	N2—N3—C9—N4	−3.3 (4)
N2—C8—C7—N1	−179.2 (3)	N2—N3—C9—S1	176.57 (19)
C1—C8—C7—N1	−2.1 (3)	F1—C3—C4—C5	−179.8 (3)
C2—C1—C6—C5	−1.4 (4)	C2—C3—C4—C5	−0.9 (5)
C8—C1—C6—C5	178.2 (2)	C6—C5—C4—C3	0.0 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O1	0.86	2.12	2.781 (3)	133
N1—H1···S1ⁱ	0.86	2.55	3.367 (2)	158
N4—H4A···F1ⁱⁱ	0.86	2.24	2.956 (3)	140
N4—H4B···O1ⁱⁱⁱ	0.86	2.03	2.879 (3)	171

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O1	0.86	2.12	2.781 (3)	133.2
N1—H1···S1ⁱ	0.86	2.55	3.367 (2)	158.1
N4—H4A···F1ⁱⁱ	0.86	2.24	2.956 (3)	140.0
N4—H4B···O1ⁱⁱⁱ	0.86	2.03	2.879 (3)	170.5

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

Acknowledgements

We gratefully thank Professor Dr Manfredo Hörner (Federal University of Santa Maria, Brazil) for his help and support with the X-ray measurements.

References

Ali, A. Q., Eltayeb, N. E., Teoh, S. G., Salhin, A. & Fun, H.-K. (2012). Acta Cryst. E68, o285–o286. Web of Science CSD CrossRef IUCr Journals Google Scholar
Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Freund, M. & Schander, A. (1902). Chem. Ber. 35, 2602–2606. CrossRef CAS Google Scholar
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Steiner, T. (2002). Angew. Chem. Int. Ed. 41, 48–76. Web of Science CrossRef CAS Google Scholar
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Crystal structure of (Z)-2-(5-fluoro-2-oxoindolin-3-yl­­idene)hydrazinecarbo­thio­amide

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of (Z)-2-(5-fluoro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide