2-(5-Iodo-2-oxoindolin-3-yl­idene)hydrazinecarbo­thio­amide including an unknown solvate

Conceição Duarte de Bittencourt, V.; Carratu Gervini, V.; Rosa de Menezes Vicenti, J.; Maciel Velasques, J.; Jussiane Zambiazi, P.

doi:10.1107/S1600536814010782

organic compounds

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ISSN: 2056-9890

Volume 70| Part 6| June 2014| Pages o666-o667

doi:10.1107/S1600536814010782

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2-(5-Iodo-2-oxoindolin-3-ylidene)hydrazinecarbothioamide including an unknown solvate

Viviane Conceição Duarte de Bittencourt,^a Vanessa Carratu Gervini,^a ^* Juliano Rosa de Menezes Vicenti,^a Jecika Maciel Velasques ^a and Priscilla Jussiane Zambiazi ^b

^aEscola de Química e Alimentos, Universidade Federal do Rio Grande, Av. Itália, km 08, Campus Carreiros, 96203-900, Rio Grande, RS, Brazil, and ^bDepartamento de Química, Universidade Federal de Santa Maria, Av. Roraima, Campus, 97105-900, Santa Maria, RS, Brazil
^*Correspondence e-mail: vanessa.gervini@gmail.com

Edited by R. F. Baggio, Comisión Nacional de Energía Atómica, Argentina (Received 2 May 2014; accepted 11 May 2014; online 17 May 2014)

The molecule of the title compound, C₉H₇IN₄OS, is almost planar (r.m.s. deviation = 0.0373 Å). In the molecule, N—H⋯N and N—H⋯O hydrogen bonds generate, respectively, S(5) and S(6) ring motifs. In the crystal, molecules are linked via N—H⋯O hydrogen bonds, forming chains propagating along [010]. These chains are linked via S⋯I contacts [3.4915 (16) Å], forming sheets lying parallel to (100). A region of disordered electron density, probably a disordered tetrahydrofuran solvent molecule, was treated using the SQUEEZE routine in PLATON [Spek (2009). Acta Cryst. D65, 148–155]. The formula mass and unit-cell characteristics were not taken into account during refinement.

CCDC reference: 1002200

Related literature

For the synthesis, see: Chiyanzu et al. (2003 ). For applications, see: Silva et al. (2001 ); Chiyanzu et al. (2003). For similar structures, see: de Bittencourt et al. (2014 ); Bandeira et al. (2013 ); de Oliveira et al. (2012 ). For S⋯I interactions, see: Auffinger et al. (2004 ).

Experimental

Crystal data

C₉H₇IN₄OS
M_r = 346.15
Monoclinic, C 2/c
a = 33.765 (5) Å
b = 4.4569 (5) Å
c = 19.977 (3) Å
β = 123.100 (4)°
V = 2518.4 (6) Å³
Z = 8
Mo Kα radiation
μ = 2.69 mm⁻¹
T = 100 K
1.15 × 0.10 × 0.09 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: numerical (SADABS; Bruker, 2009 ) T_min = 0.701, T_max = 0.777
18679 measured reflections
2892 independent reflections
2577 reflections with I > 2σ(I)
R_int = 0.036

Refinement

R[F² > 2σ(F²)] = 0.028
wR(F²) = 0.062
S = 1.05
2892 reflections
161 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 1.50 e Å⁻³
Δρ_min = −1.52 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H12⋯N3	0.85 (4)	2.28 (4)	2.633 (3)	105 (3)
N2—H21⋯O1	0.83 (4)	2.07 (4)	2.725 (3)	135 (3)
N4—H41⋯O1ⁱ	0.77 (3)	2.04 (4)	2.809 (3)	178 (3)
N1—H11⋯S1ⁱⁱ	0.79 (3)	2.66 (4)	3.448 (3)	170 (3)
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) -x, -y+4, -z+1.

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 ) and PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 1002200

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536814010782/bg2528sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814010782/bg2528Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814010782/bg2528Isup3.cml

checkCIF report

Comment top

Isatins and their derivatives are described as compounds with technological applications, such as organic analytical chemistry and pigments and dyes (Silva et al., 2001). Particularly, halogen substituted isatins containing thiosemicarbazone fragment demonstrated biological activity against some trypanosomes (cruzain and rhodesain) and malaria (falcipain-2) parasites (Chiyanzu et al., 2003). In this paper, we describe the crystal structure of 2-(5-Iodo-2-oxoindolin-3-ylidene)-hydrazinecarbothioamide, C₉H₇ON₄SI. There is one molecule in the asymmetric unit (Figure 1), and it is very similar to that of the Cl analogue previously published by us (de Bittencourt et al., 2014). The molecule is almost planar (Bandeira et al., 2013; de Oliveira et al., 2012), displaying a r.m.s. deviation of 0.0373 Å for all fitted non-hydrogenoid atoms (with maximum deviation of 0.1057 (12) observed for S1 atom). Although the same intramolecular S(5) and S(6) ring motifs are verified (Table 1), the crystal packing differs totally when compared with the chloro substituted analog. In the present case, co-operative dimmers are formed through N1—H11···S1ⁱ interactions displaying distances of 2.67 (4) Å. The crystal structure is expanded along the [010] crystallographic direction through N4—H41···O1ⁱⁱ interactions with distances of 2.08 (4) Å, generating a one-dimensional polymer-like motif. One of the most interesting features are the S···Iⁱⁱⁱ contacts which further connects the molecules along the [001] crystallographic direction, presenting distances of 3.4915 (16) Å (Figure 2, symmetry codes: (i) –x, 2–y, –z; (ii) 1/2–x, -1/2 + y, 1/2–z; (iii) x, –y, 1/2 + z). Such S···I short interactions are related to be present in sulfur-containing proteins like cysteine and methionine (Auffinger et al., 2004), being mentioned to play an important hole in biological systems. As a second interesting feature, it was noted disordered solvent molecules occupying accessible voids of 83 Å³, suggestive of tetrahydrofuran, which was indeed used for crystallization. Due to this, collected data was treated using the SQUEEZE routine of the PLATON software (Spek, 2009) in order to remove solvent electronic density. The new HKP file generated was then used for further refinement of the final solvent free crystal structure. For solvent-voids position assignement in the unit cell, a solvent plot calculated by PLATON is shown in Figure 3.

Related literature top

For the synthesis, see: Chiyanzu et al. (2003). For applications, see: Silva et al. (2001); Chiyanzu et al. (2003). For similar structures, see: de Bittencourt et al. (2014); Bandeira et al. (2013); de Oliveira et al. (2012). For S···I interactions, see: Auffinger et al. (2004).

Experimental top

To 20 ml of ethanol it was mixed 500 mg (1.83 mmol s) of 5-iodo-isatine with 170 mg (1.83 mmol s) of thiosemicarbazide. Then, it was added ten drops of glacial acetic acid and the system was kept under reflux for four hours. After this time, the reaction mixture was cooled and an orange precipitated was filtered off under vacuum and dried at room temperature. m.p. 249–253 °C. Yield: 98%. Crystallization: needle single crystals of the title compound suitable for X-ray diffraction were obtained by slow evaporating a solution containing 30 mg of the product dissolved in 5 ml of tetrahydrofuran.

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. Asymmetric unit of the title compound showing intramolecular hydrogen bond interactions represented with dashed lines. Ellipsoid probability: 50%.
	Fig. 2. Packing diagram of the title compound showing hydrogen bond network generated through interactions represented as dashed lines. Some hydrogen atoms were omitted for clarity. Symmetry codes: (i) –x, 2–y, –z; (ii) 1/2–x, -1/2 + y, 1/2–z; (iii) x, –y, 1/2 + z.
	Fig. 3. Plot generated by PLATON showing solvent accessible voids positions in the unit cell as dashed delimited circles.

2-(5-Iodo-2-oxoindolin-3-ylidene)hydrazinecarbothioamide top

Crystal data top

C₉H₇IN₄OS	F(000) = 1328
M_r = 346.15	D_x = 1.826 Mg m⁻³
Monoclinic, C2/c	Melting point: 522 K
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 33.765 (5) Å	Cell parameters from 9997 reflections
b = 4.4569 (5) Å	θ = 2.4–28.3°
c = 19.977 (3) Å	µ = 2.69 mm⁻¹
β = 123.100 (4)°	T = 100 K
V = 2518.4 (6) Å³	Needle, yellow
Z = 8	1.15 × 0.10 × 0.09 mm

Data collection top

Bruker APEXII CCD diffractometer	2892 independent reflections
Radiation source: fine-focus sealed tube	2577 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.036
ϕ and ω scans	θ_max = 28.3°, θ_min = 2.0°
Absorption correction: numerical (SADABS; Bruker, 2009)	h = −44→44
T_min = 0.701, T_max = 0.777	k = −3→5
18679 measured reflections	l = −26→26

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)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.062	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0208P)² + 10.8261P] where P = (F_o² + 2F_c²)/3
2892 reflections	(Δ/σ)_max = 0.001
161 parameters	Δρ_max = 1.50 e Å⁻³
0 restraints	Δρ_min = −1.52 e Å⁻³

Crystal data top

C₉H₇IN₄OS	V = 2518.4 (6) Å³
M_r = 346.15	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 33.765 (5) Å	µ = 2.69 mm⁻¹
b = 4.4569 (5) Å	T = 100 K
c = 19.977 (3) Å	1.15 × 0.10 × 0.09 mm
β = 123.100 (4)°

Data collection top

Bruker APEXII CCD diffractometer	2892 independent reflections
Absorption correction: numerical (SADABS; Bruker, 2009)	2577 reflections with I > 2σ(I)
T_min = 0.701, T_max = 0.777	R_int = 0.036
18679 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.028	0 restraints
wR(F²) = 0.062	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0208P)² + 10.8261P] where P = (F_o² + 2F_c²)/3
2892 reflections	Δρ_max = 1.50 e Å⁻³
161 parameters	Δρ_min = −1.52 e Å⁻³

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
C6	0.20209 (11)	0.5198 (5)	0.48073 (18)	0.0190 (6)
H6	0.2160	0.3772	0.4658	0.023*
C7	0.22592 (10)	0.6149 (6)	0.55978 (17)	0.0168 (5)
H7	0.2555	0.5382	0.5981	0.020*
C5	0.15782 (10)	0.6347 (6)	0.42365 (16)	0.0170 (6)
H41	0.2442 (12)	0.924 (7)	0.693 (2)	0.016 (8)*
H21	0.1270 (13)	1.502 (7)	0.631 (2)	0.023 (9)*
H11	0.0129 (12)	1.770 (7)	0.4600 (19)	0.019 (8)*
H12	0.0403 (15)	1.560 (9)	0.449 (3)	0.043 (12)*
I1	0.125098 (8)	0.47387 (4)	0.306159 (11)	0.02521 (7)
S1	0.06378 (3)	1.88628 (14)	0.62093 (4)	0.01889 (15)
O1	0.19376 (7)	1.3146 (4)	0.70372 (11)	0.0168 (4)
N4	0.22091 (9)	0.9605 (5)	0.65344 (15)	0.0145 (5)
N3	0.11031 (8)	1.3194 (4)	0.53273 (13)	0.0130 (4)
C9	0.18938 (9)	1.1590 (5)	0.64912 (16)	0.0137 (5)
C1	0.06744 (9)	1.6773 (5)	0.55453 (16)	0.0140 (5)
N1	0.03597 (10)	1.6699 (6)	0.47747 (15)	0.0209 (5)
C3	0.15944 (9)	0.9428 (5)	0.52186 (16)	0.0127 (5)
N2	0.10679 (9)	1.5041 (4)	0.58282 (15)	0.0145 (5)
C8	0.20411 (9)	0.8269 (5)	0.57920 (15)	0.0133 (5)
C2	0.14815 (9)	1.1580 (5)	0.56399 (15)	0.0127 (5)
C4	0.13579 (10)	0.8471 (5)	0.44356 (16)	0.0143 (5)
H4	0.1061	0.9222	0.4053	0.017*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C6	0.0251 (17)	0.0160 (11)	0.0226 (17)	0.0021 (10)	0.0173 (14)	0.0005 (9)
C7	0.0115 (15)	0.0176 (11)	0.0198 (15)	0.0015 (9)	0.0076 (12)	0.0034 (9)
C5	0.0212 (16)	0.0181 (11)	0.0129 (15)	−0.0041 (10)	0.0101 (13)	−0.0011 (9)
I1	0.04097 (15)	0.02153 (9)	0.01480 (12)	−0.00098 (7)	0.01630 (11)	−0.00167 (6)
S1	0.0206 (4)	0.0199 (3)	0.0160 (4)	0.0050 (2)	0.0099 (3)	0.0011 (2)
O1	0.0125 (10)	0.0216 (9)	0.0106 (10)	−0.0011 (7)	0.0026 (8)	−0.0027 (7)
N4	0.0091 (13)	0.0177 (10)	0.0095 (13)	0.0006 (8)	0.0005 (11)	0.0010 (8)
N3	0.0119 (12)	0.0143 (9)	0.0125 (12)	−0.0011 (8)	0.0065 (10)	−0.0002 (7)
C9	0.0106 (14)	0.0153 (11)	0.0124 (14)	−0.0029 (9)	0.0044 (12)	0.0013 (9)
C1	0.0101 (14)	0.0154 (11)	0.0160 (15)	−0.0001 (9)	0.0068 (12)	0.0019 (9)
N1	0.0137 (14)	0.0276 (12)	0.0147 (14)	0.0078 (10)	0.0034 (11)	−0.0008 (9)
C3	0.0110 (14)	0.0139 (10)	0.0123 (14)	−0.0017 (9)	0.0057 (12)	0.0019 (8)
N2	0.0130 (13)	0.0168 (10)	0.0091 (13)	0.0007 (8)	0.0030 (10)	−0.0001 (8)
C8	0.0117 (14)	0.0144 (10)	0.0111 (14)	−0.0011 (9)	0.0044 (11)	0.0020 (9)
C2	0.0131 (14)	0.0135 (10)	0.0090 (13)	−0.0025 (9)	0.0043 (11)	0.0008 (8)
C4	0.0119 (14)	0.0159 (11)	0.0110 (14)	−0.0025 (9)	0.0036 (11)	0.0010 (9)

Geometric parameters (Å, º) top

C6—C7	1.390 (4)	N3—C2	1.292 (3)
C6—C5	1.391 (4)	N3—N2	1.350 (3)
C6—H6	0.9300	C9—C2	1.498 (4)
C7—C8	1.378 (4)	C1—N1	1.309 (4)
C7—H7	0.9300	C1—N2	1.364 (3)
C5—C4	1.389 (4)	N1—H11	0.79 (3)
C5—I1	2.100 (3)	N1—H12	0.82 (4)
S1—C1	1.680 (3)	C3—C4	1.379 (4)
O1—C9	1.232 (3)	C3—C8	1.402 (4)
N4—C9	1.350 (3)	C3—C2	1.457 (3)
N4—C8	1.399 (3)	N2—H21	0.83 (4)
N4—H41	0.77 (3)	C4—H4	0.9300

C7—C6—C5	121.0 (2)	C1—N1—H11	118 (2)
C7—C6—H6	119.5	C1—N1—H12	119 (3)
C5—C6—H6	119.5	H11—N1—H12	122 (4)
C6—C7—C8	117.5 (3)	C4—C3—C8	120.7 (2)
C6—C7—H7	121.2	C4—C3—C2	133.3 (3)
C8—C7—H7	121.2	C8—C3—C2	105.9 (2)
C6—C5—C4	121.3 (2)	N3—N2—C1	119.9 (2)
C6—C5—I1	117.67 (19)	N3—N2—H21	121 (2)
C4—C5—I1	121.0 (2)	C1—N2—H21	119 (2)
C9—N4—C8	111.2 (2)	C7—C8—N4	128.4 (3)
C9—N4—H41	122 (2)	C7—C8—C3	121.6 (2)
C8—N4—H41	127 (2)	N4—C8—C3	110.0 (2)
C2—N3—N2	116.5 (2)	N3—C2—C3	126.1 (2)
O1—C9—N4	127.1 (3)	N3—C2—C9	127.4 (2)
O1—C9—C2	126.5 (2)	C3—C2—C9	106.5 (2)
N4—C9—C2	106.4 (2)	C3—C4—C5	117.8 (2)
N1—C1—N2	117.0 (2)	C3—C4—H4	121.1
N1—C1—S1	125.4 (2)	C5—C4—H4	121.1
N2—C1—S1	117.5 (2)

C5—C6—C7—C8	−0.1 (4)	C2—C3—C8—N4	−0.6 (3)
C7—C6—C5—C4	−0.3 (4)	N2—N3—C2—C3	179.7 (2)
C7—C6—C5—I1	−179.88 (19)	N2—N3—C2—C9	−2.1 (4)
C8—N4—C9—O1	−179.3 (2)	C4—C3—C2—N3	−1.1 (5)
C8—N4—C9—C2	−0.5 (3)	C8—C3—C2—N3	178.9 (2)
C2—N3—N2—C1	−178.7 (2)	C4—C3—C2—C9	−179.7 (3)
N1—C1—N2—N3	−4.7 (3)	C8—C3—C2—C9	0.3 (3)
S1—C1—N2—N3	176.33 (18)	O1—C9—C2—N3	0.4 (4)
C6—C7—C8—N4	−178.9 (2)	N4—C9—C2—N3	−178.4 (2)
C6—C7—C8—C3	0.3 (4)	O1—C9—C2—C3	179.0 (2)
C9—N4—C8—C7	−180.0 (2)	N4—C9—C2—C3	0.1 (3)
C9—N4—C8—C3	0.7 (3)	C8—C3—C4—C5	−0.4 (4)
C4—C3—C8—C7	0.0 (4)	C2—C3—C4—C5	179.5 (3)
C2—C3—C8—C7	−180.0 (2)	C6—C5—C4—C3	0.5 (4)
C4—C3—C8—N4	179.4 (2)	I1—C5—C4—C3	−179.85 (18)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H12···N3	0.85 (4)	2.28 (4)	2.633 (3)	105 (3)
N2—H21···O1	0.83 (4)	2.07 (4)	2.725 (3)	135 (3)
N4—H41···O1ⁱ	0.77 (3)	2.04 (4)	2.809 (3)	178 (3)
N1—H11···S1ⁱⁱ	0.79 (3)	2.66 (4)	3.448 (3)	170 (3)

Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) −x, −y+4, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H12···N3	0.85 (4)	2.28 (4)	2.633 (3)	105 (3)
N2—H21···O1	0.83 (4)	2.07 (4)	2.725 (3)	135 (3)
N4—H41···O1ⁱ	0.77 (3)	2.04 (4)	2.809 (3)	178 (3)
N1—H11···S1ⁱⁱ	0.79 (3)	2.66 (4)	3.448 (3)	170 (3)

Symmetry codes: (i) −x+1/2, y−1/2, −z+3/2; (ii) −x, −y+4, −z+1.

Acknowledgements

We gratefully acknowledge Professor Dr Manfredo Hörner (Federal University of Santa Maria, Brazil) for his help and support with the X-ray measurements. We also acknowledge financial support through the DECIT/SCTIE-MS-CNPq-FAPERGS-Pronem-# 11/2029–1 and PRONEX-CNPq-FAPERGS projects.

References

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ISSN: 2056-9890

Volume 70| Part 6| June 2014| Pages o666-o667

doi:10.1107/S1600536814010782

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

2-(5-Iodo-2-oxoindolin-3-yl­­idene)hydrazinecarbo­thio­amide including an unknown solvate

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

2-(5-Iodo-2-oxoindolin-3-ylidene)hydrazinecarbothioamide including an unknown solvate