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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 11| November 2011| Page o2858
doi:10.1107/S1600536811040293

1-(5-Nitro-2-oxoindolin-3-yl­­idene)thio­semicarbazide

Katlen C. T. Bandeira,a Leandro Bresolin,a* Johannes Beck,b Jörg Danielsb and Adriano Bof de Oliveirac

aEscola de Química e Alimentos, Universidade Federal do Rio Grande, Av. Itália km 08, Campus Carreiros, 96201-900 Rio Grande, RS, Brazil, bInstitut für Anorganische Chemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany, and cDepartamento de Química, Universidade Federal de Sergipe, Av. Marechal Rondon s/n, Campus, 49100-000 São Cristóvão, SE, Brazil
*Correspondence e-mail: adriano@daad-alumni.de

(Received 10 August 2011; accepted 29 September 2011; online 5 October 2011)

In the title molecule, C9H7N5O3S, there is an intramolecular N—H⋯O. The molecule is essentially planar, with the maximum deviation from the mean plane of the 18 non-H atoms being 0.135 (2) Å for the amine N atom. In the crystal, the molecules are connected via intermolecular N—H⋯O and N—H⋯S hydrogen bonds, forming two-dimensional networks lying parallel to (10[\overline4]). They are separated by an interplanar distance of 3.3214 (9) Å, leading to π–π interactions which stabilize the crystal structure.

Related literature

For the pharmacological properties of isatine-thio­semi­carb­azone derivatives, including the title compound, against cruzain, falcipain-2 and rhodesain, see: Chiyanzu et al. (2003[Chiyanzu, I., Hansell, E., Gut, J., Rosenthal, P. J., McKerrow, J. H. & Chibale, K. (2003). Bioorg. Med. Chem. Lett. 13, 3527-3530.]). For the synthesis of 5-nitro­isatine-3-thio­semi­carbazone, see: Campaigne & Archer (1952[Campaigne, E. & Archer, W. L. (1952). J. Am. Chem. Soc. 74, 5801.]). For an example of a similar structure, 5-bromo­isatin-thio­semicarbazone, see: Pederzolli et al. (2011[Pederzolli, F. R. S., Bresolin, L., Carratu, V. S., Locatelli, A. & Oliveira, A. B. de (2011). Acta Cryst. E67, o1804.]).

[Scheme 1]

Experimental

Crystal data

  • C9H7N5O3S

  • Mr = 265.26

  • Monoclinic, P 21 /c

  • a = 5.2112 (2) Å

  • b = 15.5354 (5) Å

  • c = 13.8711 (5) Å

  • β = 105.855 (2)°

  • V = 1080.25 (7) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.31 mm−1

  • T = 293 K

  • 0.08 × 0.07 × 0.03 mm
Data collection

  • Nonius KappaCCD diffractometer

  • Absorption correction: analytical (Alcock, 1970[Alcock, N. W. (1970). Crystallographic Computing, edited by F. R. Ahmed, S. R. Hall & C. P. Huber, p. 271. Copenhagen: Munksgaard.]) Tmin = 0.966, Tmax = 0.983

  • 15688 measured reflections

  • 2469 independent reflections

  • 1646 reflections with I > 2σ(I)

  • Rint = 0.055
Refinement

  • R[F2 > 2σ(F2)] = 0.041

  • wR(F2) = 0.108

  • S = 1.02

  • 2469 reflections

  • 191 parameters

  • All H-atom parameters refined

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.27 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N4—H5⋯O1 0.93 (2) 2.08 (2) 2.791 (2) 132.6 (19)
N5—H6⋯O1i 0.83 (2) 2.13 (3) 2.957 (2) 173 (2)
N5—H7⋯O2ii 0.90 (3) 2.36 (3) 3.215 (3) 160 (2)
N1—H4⋯Siii 0.88 (3) 2.45 (3) 3.3123 (18) 170 (2)
Symmetry codes: (i) [-x-1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) -x+1, -y, -z+1; (iii) [-x-1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: COLLECT (Nonius, 1998[Nonius (1998). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811040293/vm2117sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811040293/vm2117Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811040293/vm2117Isup3.cml

checkCIF report


Comment top

Thiosemicarbazone derivatives have a wide range of biological properties. For example, isatin-based synthetic thiosemicarbazones show pharmacological activity against cruzain, falcipain-2 and rhodesain (Chiyanzu et al., 2003). As part of our study of thiosemicarbazone derivatives, we report herein the crystal structure of 5-nitroisatin-3-thiosemicarbazone. In the title compound (Fig. 1), the 5-nitroisain-3-thiosemicarbazone unit is planar and the maximal deviation from the least squares plane through all 18 non-hydrogen atoms is observed for N5 (0.135 (2) Å). The best plane through the thiosemicarbazide group (maximal deviation of 0.029 (2) Å for N4) makes an angle of 5.91 (8)° with the best plane through the isatine group (maximal deviation of 0.008 (2) Å for atoms C2, C4, C7). The nitro group is coplanar with the isatine ring (O2—N2—C5—C6 -0.7°). The bond angles suggest sp2 hybridization for the C and N atoms and explain the planarity of the title compound. The crystal packing is stabilized by intermolecular N—H···O and N—H···S (Table 1; N5-H6···O1i, N5-H7···O2ii, N1-H4···Siii) and intramolecular N—H···O1 bonds (Table 1; N4-H5···O1), building a two-dimensional H-bonded network (Fig. 2). The crystal packing is also stabilised by aromatic π–π-interactions between the isatine-thiosemicarbazone derivative molecules. The idealized plane through all 18 non-hydrogen atoms of adjacent molecules have an interplanar distance of 3.3214 (9) Å and are parallel. Symmetry codes: (i) -x-1, y-1/2, -z+1/2; (ii) -x+1, -y, -z+1; (iii) -x-1, y+1/2, -z+1/2.

Related literature top

For the pharmacological properties of isatine-thiosemicarbazone derivatives, including the title compound, against cruzain, falcipain-2 and rhodesain, see: Chiyanzu et al. (2003). For the synthesis of 5-nitroisatine-3-thiosemicarbazone, see: Campaigne & Archer (1952). For an example of a similar structure, 5-bromoisatin-thiosemicarbazone, see: Pederzolli et al. (2011).

Experimental top

Starting materials were commercially available and were used without further purification. The synthesis was adapted from a procedure reported previously (Campaigne & Archer, 1952). The hydrochloric acid catalyzed reaction of 5-nitroisatin (5,2 mmol) and thiosemicarbazide (5,2 mmol) in ethanol (60 ml) was refluxed for 6 h. After cooling and filtering, crystals suitable for X-ray diffraction were obtained.

Refinement top

All hydrogen atoms were localized in a difference density Fourier map. Their positions and isotropic displacement parameters were refined.

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. : The molecular structure of the title compound with labeling and displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. : Crystal structure of the title compound viewed in the direction of the crystallographic c-axis. Hydrogen bonding is indicated as dashed lines. The graphical representation is simplified for clarity.
1-(5-Nitro-2-oxoindolin-3-ylidene)thiosemicarbazide top
Crystal data top
C9H7N5O3SF(000) = 544
Mr = 265.26Dx = 1.631 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 26694 reflections
a = 5.2112 (2) Åθ = 2.9–27.5°
b = 15.5354 (5) ŵ = 0.31 mm−1
c = 13.8711 (5) ÅT = 293 K
β = 105.855 (2)°Prism, colourless
V = 1080.25 (7) Å30.08 × 0.07 × 0.03 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer		2469 independent reflections
Radiation source: fine-focus sealed tube1646 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.055
Detector resolution: 9 pixels mm-1θmax = 27.5°, θmin = 3.0°
CCD rotation images, thick slices scansh = −6→6
Absorption correction: analytical
(Alcock, 1970)		k = −19→20
Tmin = 0.966, Tmax = 0.983l = −18→17
15688 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: difference Fourier map
wR(F2) = 0.108All H-atom parameters refined
S = 1.02 w = 1/[σ2(Fo2) + (0.0502P)2 + 0.2777P]
where P = (Fo2 + 2Fc2)/3
2469 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.18 e Å−3
0 restraintsΔρmin = −0.27 e Å−3
Crystal data top
C9H7N5O3SV = 1080.25 (7) Å3
Mr = 265.26Z = 4
Monoclinic, P21/cMo Kα radiation
a = 5.2112 (2) ŵ = 0.31 mm−1
b = 15.5354 (5) ÅT = 293 K
c = 13.8711 (5) Å0.08 × 0.07 × 0.03 mm
β = 105.855 (2)°
Data collection top
Nonius KappaCCD
diffractometer		2469 independent reflections
Absorption correction: analytical
(Alcock, 1970)		1646 reflections with I > 2σ(I)
Tmin = 0.966, Tmax = 0.983Rint = 0.055
15688 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.108All H-atom parameters refined
S = 1.02Δρmax = 0.18 e Å−3
2469 reflectionsΔρmin = −0.27 e Å−3
191 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
xyzUiso*/Ueq
S−0.82185 (11)0.04442 (3)0.13953 (5)0.0550 (2)
O1−0.3758 (3)0.30256 (9)0.25265 (11)0.0497 (4)
O20.8282 (4)0.06044 (11)0.57143 (16)0.0833 (6)
O31.0641 (3)0.17173 (11)0.62922 (13)0.0689 (5)
N10.0324 (3)0.34347 (11)0.35807 (13)0.0456 (4)
H4−0.001 (5)0.3986 (19)0.3598 (18)0.068 (8)*
N20.8602 (4)0.13826 (13)0.57750 (14)0.0534 (5)
N3−0.1521 (3)0.12472 (10)0.31461 (13)0.0416 (4)
N4−0.3969 (3)0.12302 (10)0.24907 (13)0.0438 (4)
H5−0.481 (5)0.1742 (16)0.2237 (17)0.059 (7)*
N5−0.3935 (4)−0.02231 (12)0.26970 (16)0.0564 (5)
H6−0.469 (5)−0.0697 (16)0.2592 (18)0.059 (7)*
H7−0.234 (6)−0.0184 (18)0.315 (2)0.072 (8)*
C10.2206 (4)0.21247 (12)0.40888 (14)0.0382 (4)
C20.2575 (4)0.30160 (12)0.41775 (15)0.0407 (5)
C30.4895 (4)0.33798 (14)0.47706 (16)0.0473 (5)
H10.519 (5)0.3964 (16)0.4829 (16)0.055 (6)*
C40.6870 (4)0.28252 (14)0.52923 (16)0.0470 (5)
H20.847 (5)0.3009 (15)0.5747 (17)0.058 (6)*
C50.6461 (4)0.19440 (13)0.52072 (15)0.0423 (5)
C60.4156 (4)0.15681 (13)0.46118 (16)0.0430 (5)
H30.394 (4)0.0988 (15)0.4573 (16)0.050 (6)*
C7−0.0416 (4)0.19895 (12)0.33974 (14)0.0398 (5)
C8−0.1545 (4)0.28607 (12)0.30925 (15)0.0416 (5)
C9−0.5237 (4)0.04538 (12)0.22445 (15)0.0420 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S0.0442 (3)0.0362 (3)0.0713 (4)−0.0030 (2)−0.0065 (3)0.0049 (2)
O10.0429 (8)0.0369 (7)0.0590 (9)0.0058 (6)−0.0035 (7)−0.0004 (6)
O20.0670 (12)0.0471 (10)0.1111 (15)0.0072 (8)−0.0173 (10)0.0094 (10)
O30.0427 (9)0.0704 (11)0.0784 (12)−0.0001 (8)−0.0093 (8)0.0074 (9)
N10.0454 (10)0.0282 (8)0.0561 (11)0.0011 (7)0.0019 (8)−0.0007 (7)
N20.0430 (10)0.0537 (12)0.0571 (11)0.0054 (8)0.0030 (9)0.0054 (9)
N30.0381 (9)0.0343 (8)0.0480 (9)−0.0002 (7)0.0045 (7)−0.0019 (7)
N40.0398 (9)0.0309 (8)0.0532 (10)0.0015 (7)0.0002 (8)−0.0010 (7)
N50.0464 (11)0.0318 (9)0.0769 (14)−0.0018 (8)−0.0072 (10)0.0044 (9)
C10.0392 (10)0.0314 (9)0.0416 (10)−0.0009 (8)0.0070 (8)−0.0015 (8)
C20.0405 (11)0.0342 (10)0.0451 (11)0.0008 (8)0.0080 (9)−0.0011 (8)
C30.0484 (12)0.0355 (11)0.0541 (13)−0.0056 (9)0.0076 (10)−0.0060 (9)
C40.0415 (11)0.0466 (12)0.0483 (12)−0.0038 (9)0.0047 (10)−0.0050 (9)
C50.0378 (10)0.0432 (11)0.0427 (11)0.0043 (8)0.0055 (9)0.0028 (8)
C60.0420 (11)0.0354 (10)0.0485 (12)0.0011 (8)0.0073 (9)−0.0002 (9)
C70.0412 (11)0.0304 (9)0.0446 (11)0.0024 (8)0.0063 (9)−0.0011 (8)
C80.0406 (11)0.0344 (10)0.0463 (11)0.0014 (8)0.0058 (9)−0.0013 (8)
C90.0404 (10)0.0317 (9)0.0506 (12)0.0006 (8)0.0069 (9)−0.0014 (8)
Geometric parameters (Å, º) top
S—C91.674 (2)N5—H60.83 (2)
O1—C81.231 (2)N5—H70.90 (3)
O2—N21.220 (2)C1—C61.380 (3)
O3—N21.224 (2)C1—C21.399 (3)
N1—C81.357 (3)C1—C71.454 (3)
N1—C21.398 (2)C2—C31.384 (3)
N1—H40.88 (3)C3—C41.385 (3)
N2—C51.464 (3)C3—H10.92 (2)
N3—C71.294 (2)C4—C51.386 (3)
N3—N41.350 (2)C4—H20.94 (2)
N4—C91.373 (2)C5—C61.387 (3)
N4—H50.93 (2)C6—H30.91 (2)
N5—C91.314 (3)C7—C81.490 (3)
C8—N1—C2111.20 (17)C2—C3—H1123.6 (15)
C8—N1—H4122.3 (17)C4—C3—H1118.9 (15)
C2—N1—H4125.5 (17)C3—C4—C5119.68 (19)
O2—N2—O3122.80 (18)C3—C4—H2123.9 (14)
O2—N2—C5118.90 (18)C5—C4—H2116.3 (14)
O3—N2—C5118.30 (19)C4—C5—C6123.69 (19)
C7—N3—N4117.92 (16)C4—C5—N2117.76 (18)
N3—N4—C9119.14 (16)C6—C5—N2118.55 (18)
N3—N4—H5119.9 (15)C1—C6—C5116.30 (19)
C9—N4—H5120.9 (15)C1—C6—H3122.0 (14)
C9—N5—H6117.8 (17)C5—C6—H3121.7 (14)
C9—N5—H7122.6 (18)N3—C7—C1125.12 (17)
H6—N5—H7119 (2)N3—C7—C8128.38 (17)
C6—C1—C2120.68 (17)C1—C7—C8106.45 (15)
C6—C1—C7132.90 (17)O1—C8—N1126.92 (18)
C2—C1—C7106.43 (16)O1—C8—C7126.75 (17)
C3—C2—N1128.15 (18)N1—C8—C7106.32 (16)
C3—C2—C1122.23 (18)N5—C9—N4115.68 (18)
N1—C2—C1109.61 (16)N5—C9—S126.01 (16)
C2—C3—C4117.42 (19)N4—C9—S118.29 (14)
C7—N3—N4—C9−177.19 (19)C7—C1—C6—C5179.5 (2)
C8—N1—C2—C3179.0 (2)C4—C5—C6—C1−0.2 (3)
C8—N1—C2—C1−0.1 (2)N2—C5—C6—C1−179.71 (19)
C6—C1—C2—C31.1 (3)N4—N3—C7—C1−179.81 (19)
C7—C1—C2—C3−178.98 (19)N4—N3—C7—C83.1 (3)
C6—C1—C2—N1−179.75 (19)C6—C1—C7—N32.1 (4)
C7—C1—C2—N10.1 (2)C2—C1—C7—N3−177.7 (2)
N1—C2—C3—C4−179.6 (2)C6—C1—C7—C8179.7 (2)
C1—C2—C3—C4−0.7 (3)C2—C1—C7—C8−0.1 (2)
C2—C3—C4—C5−0.2 (3)C2—N1—C8—O1178.6 (2)
C3—C4—C5—C60.6 (3)C2—N1—C8—C70.0 (2)
C3—C4—C5—N2−179.8 (2)N3—C7—C8—O1−1.1 (4)
O2—N2—C5—C4179.7 (2)C1—C7—C8—O1−178.6 (2)
O3—N2—C5—C4−0.2 (3)N3—C7—C8—N1177.6 (2)
O2—N2—C5—C6−0.7 (3)C1—C7—C8—N10.1 (2)
O3—N2—C5—C6179.4 (2)N3—N4—C9—N51.3 (3)
C2—C1—C6—C5−0.7 (3)N3—N4—C9—S−177.56 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H5···O10.93 (2)2.08 (2)2.791 (2)132.6 (19)
N5—H6···O1i0.83 (2)2.13 (3)2.957 (2)173 (2)
N5—H7···O2ii0.90 (3)2.36 (3)3.215 (3)160 (2)
N1—H4···Siii0.88 (3)2.45 (3)3.3123 (18)170 (2)
Symmetry codes: (i) −x−1, y−1/2, −z+1/2; (ii) −x+1, −y, −z+1; (iii) −x−1, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formulaC9H7N5O3S
Mr265.26
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)5.2112 (2), 15.5354 (5), 13.8711 (5)
β (°) 105.855 (2)
V (Å3)1080.25 (7)
Z4
Radiation typeMo Kα
µ (mm−1)0.31
Crystal size (mm)0.08 × 0.07 × 0.03
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionAnalytical
(Alcock, 1970)
Tmin, Tmax0.966, 0.983
No. of measured, independent and
observed [I > 2σ(I)] reflections		15688, 2469, 1646
Rint0.055
(sin θ/λ)max (Å−1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.108, 1.02
No. of reflections2469
No. of parameters191
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å−3)0.18, −0.27

Computer programs: COLLECT (Nonius, 1998), DENZO and SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H5···O10.93 (2)2.08 (2)2.791 (2)132.6 (19)
N5—H6···O1i0.83 (2)2.13 (3)2.957 (2)173 (2)
N5—H7···O2ii0.90 (3)2.36 (3)3.215 (3)160 (2)
N1—H4···Siii0.88 (3)2.45 (3)3.3123 (18)170 (2)
Symmetry codes: (i) −x−1, y−1/2, −z+1/2; (ii) −x+1, −y, −z+1; (iii) −x−1, y+1/2, −z+1/2.
 

Acknowledgements

We gratefully acknowledge financial support by the CNPq/FAPERGS.

References

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ISSN: 2056-9890
Volume 67| Part 11| November 2011| Page o2858
doi:10.1107/S1600536811040293
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