2-(5-Chloro-2-oxoindolin-3-yl­­idene)hydrazinecarbo­thio­amide

The title mol­ecule, C₉H₇ClN₄OS, is almost planar, with an r.m.s. deviation of 0.034 (2) Å for the mean plane through all the non-H atoms. Intra­molecular N—H⋯O and N—H⋯N hydrogen bonds form S(6) and S(5) ring motifs, respectively. In the crystal, mol­ecules are assembled into inversion dimers through pairs of co-operative N—H⋯Cl inter­actions. These dimers are connected along the b axis by N—H⋯O and N—H⋯S hydrogen bonds, generating layers parallel to (103). The layers are further connected along the a axis into a three-dimensional network, through weak π–π stacking inter­actions [centroid–centroid distance = 3.849 (2) Å].

Related literature

For the synthesis of the title compound, see: Qasem Ali et al. (2011). For similar hydrazinecarbo­thio­amide crystal structures, see: Bandeira et al. (2013); Ali et al. (2012); de Oliveira et al. (2012). For the biological activity of isatin and derivatives, see: Cerchiaro & Ferreira (2006).

Experimental

Crystal data

• C₉H₇ClN₄OS

• M_r = 254.70

• Monoclinic, P 2₁ /n

• a = 5.260 (5) Å

• b = 15.396 (10) Å

• c = 13.215 (9) Å

• β = 96.53 (2)°

• V = 1063.4 (14) ų

• Z = 4

• Mo Kα radiation

• μ = 0.54 mm⁻¹

• T = 173 K

• 1.27 × 0.38 × 0.35 mm

Data collection

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009) T_min = 0.639, T_max = 0.746

• 6939 measured reflections

• 2540 independent reflections

• 2374 reflections with I > 2σ(I)

• R_int = 0.014

Refinement

• R[F² > 2σ(F²)] = 0.029

• wR(F²) = 0.084

• S = 0.81

• 2540 reflections

• 161 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.52 e Å⁻³

• Δρ_min = −0.30 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H21⋯O1	0.865 (18)	2.127 (18)	2.783 (2)	132.2 (15)
N4—H41⋯S1^i	0.90 (2)	2.47 (2)	3.354 (2)	169.5 (19)
N1—H11⋯O1^ii	0.88 (2)	1.98 (2)	2.848 (2)	169 (2)
N1—H12⋯N3	0.88 (3)	2.15 (3)	2.594 (2)	110 (2)
N1—H12⋯Cl1^iii	0.88 (3)	2.62 (3)	3.342 (2)	139 (2)
Symmetry codes: (i) ; (ii) ; (iii) -x+2, -y+1, -z.

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

S1. Experimental

S1.1. Synthesis and crystallization

Experimental procedures for synthesis were based on Qasem Ali et al. (2011). Thio­semicarbazide (0.25 g, 2.7 mmol) was mixed to 20 ml of an ethano­lic solution containing 5-chloro­isatin (0.50 g, 2.7 mmol), followed by addition of ten drops of glacial acetic acid. This mixture was maintained under reflux for 4 h, being a yellow precipitated obtained. The product was filtered off under vacuum, yielding 0.38 g (76.2%). Yellow single crystals suitable for X-ray diffraction measurements were grown in ethanol/aceto­nitrile (1:1), adding five drops of pyridine and slow evaporating at room temperature.

S1.2. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. H-atoms attached to aromatic C atoms were positioned with idealized geometry and were refined isotropic with U_eq(H) set to 1.2 times of the U_eq(C) using a riding model with C–H = 0.95 Å. H-atoms attached to N atoms were located in difference Fourier maps. Their coordinates and isotropic displacement parameters were refined.

S2. Results and discussion

Isatin and its derivatives are known for demonstrate biological effects, such as bactericide and fungicide activities (Cerchiaro & Ferreira, 2006). This class of compounds has been characterized through X-ray crystallography: (Ali et al., 2012; de Oliveira et al., 2012; Bandeira et al., 2013). As part of our research, in this paper we describe the synthesis (Qasem Ali et al., 2011) and present the crystal structure determination of 1-(5-Chloro-2-oxoindolin-3-yl­idene)hydrazinecarbo­thio­amide.

The molecular structure of the title compound, C₉H₇ClN₄OS, shows an E conformation about the N2–N3 bond, matching its asymmetric unit (Fig. 1). The molecule is almost planar (Bandeira et al., 2013), with a r.m.s. deviation of 0.034 Å and maximum deviation from the mean plane through non-H atoms observed for the N1 atom (0.0920 (12) Å). Individually, the mean planes defined through non-H atoms of the thio­semicarbazone fragment (S1/C1/N1–N3) and the chloro substituted aromatic ring (C3–C8/Cl1) reveals a dihedral angle of 4.75 (8)°, with maximum deviations of 0.0058 (11) Å and 0.0043 (11) Å, respectively (de Oliveira et al., 2012).

Intra-molecular N1–H12···N3 (2.15 (3) Å) and N2–H21···O1 (2.127 (18) Å) hydrogen bonds are observed, forming S(5) and S(6) ring motifs, respectively. Dimeric species are formed through inter­molecular N3–H12···Cl1ⁱ hydrogen bonds with a distance of 2.62 (3) Å (symmetry code: (i) –x + 2, –y + 1, –z) and molecular units being related by crystallographic centers of symmetry. Shorter inter­molecular hydrogen bonding with distances of 2.47 (2) Å (N4–H41···S1ⁱⁱ) and 1.98 (2) Å (N1–H11···O1ⁱⁱⁱ) occur in a R₄⁴(8) ring fashion, connecting molecules into a bi-dimensional net parallel to the [103] plane (Fig. 2, symmetry codes: (ii) –x + 1/2, y + 1/2, –z + 1/2; (iii) –x + 1/2, y - 1/2, –z + 1/2). Additional weak π–π stacking inter­actions are verified between adjacent bi-dimensional layers along the a axis, with C2^iv···C5^v and C9^iv···C7^v distances of 3.3209 (26) Å and 3.3973 (28) Å, respectively (Fig. 3, symmetry codes: (iv) x + 1/2, –y + 3/2, z + 1/2; (v) x – 1/2, –y + 3/2, z + 1/2). All these bonding features are similar to that described by Bandeira et al. (2013), despite of the different crystal symmetry verified previously.

Related literature

For the synthesis of the title compound, see: Qasem Ali et al. (2011). For similar hydrazinecarbothioamide crystal structures, see: Bandeira et al. (2013); Ali et al. (2012); de Oliveira et al. (2012). For the biological activity of isatin and derivatives, see: Cerchiaro & Ferreira (2006).

Structure description

Isatin and its derivatives are known for demonstrate biological effects, such as bactericide and fungicide activities (Cerchiaro & Ferreira, 2006). This class of compounds has been characterized through X-ray crystallography: (Ali et al., 2012; de Oliveira et al., 2012; Bandeira et al., 2013). As part of our research, in this paper we describe the synthesis (Qasem Ali et al., 2011) and present the crystal structure determination of 1-(5-Chloro-2-oxoindolin-3-yl­idene)hydrazinecarbo­thio­amide.

The molecular structure of the title compound, C₉H₇ClN₄OS, shows an E conformation about the N2–N3 bond, matching its asymmetric unit (Fig. 1). The molecule is almost planar (Bandeira et al., 2013), with a r.m.s. deviation of 0.034 Å and maximum deviation from the mean plane through non-H atoms observed for the N1 atom (0.0920 (12) Å). Individually, the mean planes defined through non-H atoms of the thio­semicarbazone fragment (S1/C1/N1–N3) and the chloro substituted aromatic ring (C3–C8/Cl1) reveals a dihedral angle of 4.75 (8)°, with maximum deviations of 0.0058 (11) Å and 0.0043 (11) Å, respectively (de Oliveira et al., 2012).

Intra-molecular N1–H12···N3 (2.15 (3) Å) and N2–H21···O1 (2.127 (18) Å) hydrogen bonds are observed, forming S(5) and S(6) ring motifs, respectively. Dimeric species are formed through inter­molecular N3–H12···Cl1ⁱ hydrogen bonds with a distance of 2.62 (3) Å (symmetry code: (i) –x + 2, –y + 1, –z) and molecular units being related by crystallographic centers of symmetry. Shorter inter­molecular hydrogen bonding with distances of 2.47 (2) Å (N4–H41···S1ⁱⁱ) and 1.98 (2) Å (N1–H11···O1ⁱⁱⁱ) occur in a R₄⁴(8) ring fashion, connecting molecules into a bi-dimensional net parallel to the [103] plane (Fig. 2, symmetry codes: (ii) –x + 1/2, y + 1/2, –z + 1/2; (iii) –x + 1/2, y - 1/2, –z + 1/2). Additional weak π–π stacking inter­actions are verified between adjacent bi-dimensional layers along the a axis, with C2^iv···C5^v and C9^iv···C7^v distances of 3.3209 (26) Å and 3.3973 (28) Å, respectively (Fig. 3, symmetry codes: (iv) x + 1/2, –y + 3/2, z + 1/2; (v) x – 1/2, –y + 3/2, z + 1/2). All these bonding features are similar to that described by Bandeira et al. (2013), despite of the different crystal symmetry verified previously.

For the synthesis of the title compound, see: Qasem Ali et al. (2011). For similar hydrazinecarbothioamide crystal structures, see: Bandeira et al. (2013); Ali et al. (2012); de Oliveira et al. (2012). For the biological activity of isatin and derivatives, see: Cerchiaro & Ferreira (2006).

Synthesis and crystallization

Experimental procedures for synthesis were based on Qasem Ali et al. (2011). Thio­semicarbazide (0.25 g, 2.7 mmol) was mixed to 20 ml of an ethano­lic solution containing 5-chloro­isatin (0.50 g, 2.7 mmol), followed by addition of ten drops of glacial acetic acid. This mixture was maintained under reflux for 4 h, being a yellow precipitated obtained. The product was filtered off under vacuum, yielding 0.38 g (76.2%). Yellow single crystals suitable for X-ray diffraction measurements were grown in ethanol/aceto­nitrile (1:1), adding five drops of pyridine and slow evaporating at room temperature.

Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 1. H-atoms attached to aromatic C atoms were positioned with idealized geometry and were refined isotropic with U_eq(H) set to 1.2 times of the U_eq(C) using a riding model with C–H = 0.95 Å. H-atoms attached to N atoms were located in difference Fourier maps. Their coordinates and isotropic displacement parameters were refined.

Computing details

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

	Fig. 1. Molecular projection showing the asymmetric unit. Intramolecular hydrogen bonds are represented with dashed lines. Ellipsoid probability: 50%.
	Fig. 2. Bi-dimensional network formed through intermolecular hydrogen bonds, represented with dashed lines. Aromatic hydrogen atoms were omitted for clarity. Symmetry codes: (i) –x + 2, –y + 1, –z; (ii) –x + 1/2, y + 1/2, –z + 1/2; (iii) –x + 1/2, y - 1/2, –z + 1/2.
	Fig. 3. Packing of bidimensional layers through π–π stacking interactions. Aromatic hydrogen atoms were omitted for clarity. Symmetry codes: (iv) x + 1/2, –y + 3/2, z + 1/2; (v) x – 1/2, –y + 3/2, z + 1/2.

2-(5-Chloro-2-oxoindolin-3-ylidene)hydrazinecarbothioamide

Crystal data

C9H7ClN4OS	Z = 4
Mr = 254.70	F(000) = 520
Monoclinic, P21/n	Dx = 1.591 Mg m^−3
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 5.260 (5) Å	θ = 2.0–28.3°
b = 15.396 (10) Å	µ = 0.54 mm^−1
c = 13.215 (9) Å	T = 173 K
β = 96.53 (2)°	Block, yellow
V = 1063.4 (14) Å^3	1.27 × 0.38 × 0.35 mm

Data collection

Bruker APEXII CCD diffractometer	2540 independent reflections
Radiation source: fine-focus sealed tube	2374 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.014
φ and ω scans	θmax = 28.3°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −6→7
Tmin = 0.639, Tmax = 0.746	k = −20→18
6939 measured reflections	l = −17→17

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.029	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.084	H atoms treated by a mixture of independent and constrained refinement
S = 0.81	w = 1/[σ^2(Fo^2) + (0.0594P)^2 + 1.1793P] where P = (Fo^2 + 2Fc^2)/3
2540 reflections	(Δ/σ)max = 0.001
161 parameters	Δρmax = 0.52 e Å^−3
0 restraints	Δρmin = −0.30 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	1.30216 (7)	0.60089 (2)	−0.07671 (3)	0.02850 (11)
S1	0.02044 (6)	0.54702 (2)	0.36977 (3)	0.01934 (10)
O1	0.35742 (18)	0.80256 (6)	0.24115 (7)	0.0187 (2)
N1	0.3377 (3)	0.47463 (8)	0.24996 (11)	0.0285 (3)
N2	0.3459 (2)	0.62260 (7)	0.25988 (8)	0.0162 (2)
N3	0.5262 (2)	0.62044 (7)	0.19443 (8)	0.0159 (2)
N4	0.6662 (2)	0.83859 (7)	0.13477 (8)	0.0166 (2)
C1	0.2444 (2)	0.54529 (8)	0.28857 (10)	0.0163 (2)
C2	0.6101 (2)	0.69327 (8)	0.16351 (9)	0.0148 (2)
C3	0.8029 (2)	0.70274 (8)	0.09346 (9)	0.0152 (2)
C4	0.9460 (2)	0.64250 (8)	0.04630 (10)	0.0173 (2)
H4	0.9271	0.5819	0.0565	0.021*
C5	1.1187 (2)	0.67488 (9)	−0.01663 (10)	0.0189 (3)
C6	1.1518 (2)	0.76349 (9)	−0.03214 (10)	0.0192 (3)
H6	1.2728	0.7829	−0.0753	0.023*
C8	0.8326 (2)	0.79228 (8)	0.07785 (9)	0.0152 (2)
C9	0.5256 (2)	0.78350 (8)	0.18693 (10)	0.0156 (2)
C7	1.0070 (3)	0.82389 (9)	0.01575 (10)	0.0180 (3)
H7	1.0274	0.8845	0.0061	0.022*
H21	0.291 (3)	0.6714 (12)	0.2814 (13)	0.017 (4)*
H41	0.637 (4)	0.8958 (15)	0.1304 (16)	0.035 (5)*
H11	0.276 (4)	0.4232 (15)	0.2616 (16)	0.033 (5)*
H12	0.459 (5)	0.4835 (18)	0.210 (2)	0.054 (7)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.02824 (19)	0.0271 (2)	0.0332 (2)	0.00156 (13)	0.01668 (14)	−0.00782 (13)
S1	0.02276 (18)	0.01321 (17)	0.02450 (18)	−0.00194 (11)	0.01337 (13)	−0.00236 (11)
O1	0.0228 (5)	0.0133 (4)	0.0215 (5)	0.0022 (3)	0.0088 (4)	0.0002 (3)
N1	0.0363 (7)	0.0112 (5)	0.0437 (8)	−0.0024 (5)	0.0288 (6)	−0.0028 (5)
N2	0.0209 (5)	0.0099 (5)	0.0195 (5)	0.0005 (4)	0.0093 (4)	0.0002 (4)
N3	0.0180 (5)	0.0136 (5)	0.0171 (5)	0.0003 (4)	0.0067 (4)	0.0007 (4)
N4	0.0199 (5)	0.0094 (5)	0.0216 (5)	0.0005 (4)	0.0066 (4)	0.0016 (4)
C1	0.0183 (6)	0.0117 (6)	0.0196 (6)	−0.0004 (4)	0.0051 (5)	0.0006 (4)
C2	0.0169 (5)	0.0117 (5)	0.0163 (5)	0.0010 (4)	0.0040 (4)	0.0002 (4)
C3	0.0168 (5)	0.0127 (6)	0.0165 (5)	−0.0006 (4)	0.0044 (4)	0.0016 (4)
C4	0.0191 (6)	0.0132 (6)	0.0202 (6)	0.0003 (4)	0.0050 (5)	−0.0010 (4)
C5	0.0184 (6)	0.0194 (6)	0.0198 (6)	0.0011 (5)	0.0061 (5)	−0.0014 (5)
C6	0.0179 (6)	0.0216 (7)	0.0191 (6)	−0.0028 (5)	0.0059 (5)	0.0018 (5)
C8	0.0164 (6)	0.0132 (6)	0.0162 (6)	0.0006 (4)	0.0024 (4)	0.0007 (4)
C9	0.0190 (6)	0.0111 (5)	0.0170 (6)	0.0004 (4)	0.0035 (4)	0.0008 (4)
C7	0.0199 (6)	0.0157 (6)	0.0187 (6)	−0.0014 (5)	0.0037 (5)	0.0036 (4)

Geometric parameters (Å, º)

Cl1—C5	1.7417 (16)	N4—H41	0.90 (2)
S1—C1	1.6816 (17)	C2—C3	1.4561 (19)
O1—C9	1.2354 (18)	C2—C9	1.5015 (19)
N1—C1	1.3196 (18)	C3—C4	1.3863 (18)
N1—H11	0.88 (2)	C3—C8	1.4052 (19)
N1—H12	0.88 (3)	C4—C5	1.3919 (19)
N2—N3	1.3548 (17)	C4—H4	0.9500
N2—C1	1.3753 (17)	C5—C6	1.393 (2)
N2—H21	0.865 (18)	C6—C7	1.398 (2)
N3—C2	1.2886 (18)	C6—H6	0.9500
N4—C9	1.3629 (17)	C8—C7	1.3869 (19)
N4—C8	1.4108 (17)	C7—H7	0.9500
C1—N1—H11	121.0 (14)	C3—C4—C5	116.98 (13)
C1—N1—H12	115.4 (18)	C3—C4—H4	121.5
H11—N1—H12	124 (2)	C5—C4—H4	121.5
N3—N2—C1	118.47 (11)	C4—C5—C6	122.65 (12)
N3—N2—H21	121.0 (12)	C4—C5—Cl1	118.11 (11)
C1—N2—H21	120.5 (12)	C6—C5—Cl1	119.23 (11)
C2—N3—N2	118.11 (11)	C5—C6—C7	120.06 (12)
C9—N4—C8	111.12 (11)	C5—C6—H6	120.0
C9—N4—H41	123.0 (14)	C7—C6—H6	120.0
C8—N4—H41	125.2 (14)	C7—C8—C3	121.54 (12)
N1—C1—N2	115.72 (13)	C7—C8—N4	129.09 (12)
N1—C1—S1	125.31 (10)	C3—C8—N4	109.36 (11)
N2—C1—S1	118.97 (10)	O1—C9—N4	127.66 (12)
N3—C2—C3	125.26 (11)	O1—C9—C2	126.00 (11)
N3—C2—C9	128.28 (12)	N4—C9—C2	106.33 (11)
C3—C2—C9	106.41 (10)	C8—C7—C6	117.75 (13)
C4—C3—C8	121.02 (12)	C8—C7—H7	121.1
C4—C3—C2	132.21 (12)	C6—C7—H7	121.1
C8—C3—C2	106.77 (11)
C1—N2—N3—C2	176.25 (12)	C4—C3—C8—C7	−0.62 (19)
N3—N2—C1—N1	1.08 (19)	C2—C3—C8—C7	178.86 (11)
N3—N2—C1—S1	180.00 (9)	C4—C3—C8—N4	−179.71 (11)
N2—N3—C2—C3	−179.99 (11)	C2—C3—C8—N4	−0.23 (14)
N2—N3—C2—C9	−3.0 (2)	C9—N4—C8—C7	−179.50 (12)
N3—C2—C3—C4	−2.3 (2)	C9—N4—C8—C3	−0.49 (15)
C9—C2—C3—C4	−179.81 (13)	C8—N4—C9—O1	−177.55 (12)
N3—C2—C3—C8	178.32 (12)	C8—N4—C9—C2	0.97 (14)
C9—C2—C3—C8	0.79 (14)	N3—C2—C9—O1	0.0 (2)
C8—C3—C4—C5	−0.01 (19)	C3—C2—C9—O1	177.47 (12)
C2—C3—C4—C5	−179.33 (13)	N3—C2—C9—N4	−178.51 (13)
C3—C4—C5—C6	0.6 (2)	C3—C2—C9—N4	−1.08 (13)
C3—C4—C5—Cl1	179.81 (9)	C3—C8—C7—C6	0.66 (19)
C4—C5—C6—C7	−0.5 (2)	N4—C8—C7—C6	179.56 (12)
Cl1—C5—C6—C7	−179.75 (10)	C5—C6—C7—C8	−0.11 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H21···O1	0.865 (18)	2.127 (18)	2.783 (2)	132.2 (15)
N4—H41···S1^i	0.90 (2)	2.47 (2)	3.354 (2)	169.5 (19)
N1—H11···O1^ii	0.88 (2)	1.98 (2)	2.848 (2)	169 (2)
N1—H12···N3	0.88 (3)	2.15 (3)	2.594 (2)	110 (2)
N1—H12···Cl1^iii	0.88 (3)	2.62 (3)	3.342 (2)	139 (2)

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