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

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ISSN: 2056-9890

(2Z)-N-(2-Chloro­benz­yl)-2-(2-oxo-2,3-di­hydro-1H-indol-3-yl­­idene)hydrazinecarbo­thio­amide

aDepartment of Chemistry, Bahauddin Zakariya University, Multan 60800, Pakistan, bDepartment of Chemistry, Forman Christian College, Lahore 54600, Pakistan, and cUniversity of Sargodha, Department of Physics, Sargodha, Pakistan
*Correspondence e-mail: dmntahir_uos@yahoo.com

(Received 31 July 2012; accepted 8 August 2012; online 23 August 2012)

In the title compound, C16H13ClN4OS, the isatin ring system is oriented at dihedral angles of 10.60 (7) and 72.60 (3)° with respect to the thio­semicarbazide and 2-chloro­benzyl groups, respectively. The near planarity of the isatin and thio­semicarbazide groups [r.m.s. deviations of 0.0420 and 0.0163 Å, respectively] is reinforced by intra­molecular N—H⋯O and N—H⋯N hydrogen bonds, which generate S(6) and S(5) rings, respectively. In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds generate R22(8) loops. Aromatic ππ stacking inter­actions between the centroids of heterocyclic five-membered and benzene rings [distance = 3.6866 (11) Å] are also observed.

Related literature

For biochemical background to isatins, see: Pervez et al. (2012[Pervez, H., Ramzan, M., Yaqub, M., Nasim, F. H. & Khan, K. M. (2012). Med. Chem. 8, 505-514.]). For a related structure, see: Ramzan et al. (2010[Ramzan, M., Pervez, H., Tahir, M. N., Yaqub, M. & Iqbal, M. S. (2010). Acta Cryst. E66, o2447.]). For graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C16H13ClN4OS

  • Mr = 344.81

  • Monoclinic, P 21 /c

  • a = 13.7017 (10) Å

  • b = 14.1585 (10) Å

  • c = 8.2698 (5) Å

  • β = 93.151 (3)°

  • V = 1601.88 (19) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.38 mm−1

  • T = 296 K

  • 0.32 × 0.23 × 0.20 mm

Data collection
  • Bruker Kappa APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2005[Bruker (2005). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.888, Tmax = 0.929

  • 14957 measured reflections

  • 3935 independent reflections

  • 2541 reflections with I > 2σ(I)

  • Rint = 0.033

Refinement
  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.105

  • S = 1.02

  • 3935 reflections

  • 208 parameters

  • H-atom parameters constrained

  • Δρmax = 0.21 e Å−3

  • Δρmin = −0.29 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3A⋯O1 0.86 2.05 2.7416 (19) 137
N4—H4A⋯N2 0.86 2.28 2.663 (2) 107
N1—H1⋯O1i 0.86 2.09 2.903 (2) 157
Symmetry code: (i) -x, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and PLATON.

Supporting information


Comment top

As a part of our ongoing work on the synthesis of isatin-thiosemicarbazones having certain pharmaceutical applications (Pervez et al., 2012), we report herein the synthesis and crystal structure of the title compound (Fig. 1). The crystal structure of 1-(2-oxoindolin-3-ylidene)-4-[2-(trifluoromethoxy)phenyl]thiosemicarbazide (Ramzan et al. 2010) has been published which is related to the title compound.

In the title compound, the group A (C1—C8/N1/O1) of isatin moiety, group B (N2/N3/C9/S1/N4) of thiosemicarbazide and group C (C10—C16/CL1) of 2-chlorobenzyl are planar with r.m.s. deviations of 0.0230 Å, 0.0420 Å and 0.0163 Å, respectively. The dihedral angle between A/B, A/C and B/C are 10.60 (7)°, 72.60 (3)° and 72.89 (3)°, respectively. In the title compound, S(5) and S(6) ring motifs (Bernstein et al., 1995) are formed due to intramolecular H-bondings of N—H···N and N—H···O types, respectively (Table 1, Fig. 1). The molecules are stabilized in the form of dimers due to H-bonding of N—H···O type (Table 1, Fig. 2) with R22(8) ring motif. There exists ππ interaction between Cg1···Cg2i [i = x, 1/2 - y, -1/2 + z] at a distance of 3.6866 (11) Å, where Cg1 and Cg2 are the centroids of heterocyclic five membered ring (C1/C6/N1/C7/C8) and the benzene ring (C1—C6), respectively. Similarly, ππ interaction exists between Cg2···Cg1ii [ii = x, 1/2 - y, 1/2 + z] at a distance of 3.6866 (11) Å.

Related literature top

For biochemical background to isatins, see: Pervez et al. (2012). For a related structure, see: Ramzan et al. (2010). For graph-set notation, see: Bernstein et al. (1995).

Experimental top

To a hot solution of isatin (0.74 g, 5 mmol) in 50% aqueous ethanol (15 ml) was added 4-(2-chlorobenzyl)thiosemicarbazide (1.08 g, 5 mmol) dissolved in ethanol (10 ml) under stirring. The reaction mixture was then refluxed for 2 h. The orange crystalline solid formed during heating was collected by suction filtration. Thorough washing with hot aqueous ethanol afforded the title compound in pure form (1.55 g, 90%), m.p. 525 K. The orange prisms of title compound were grown from chloroform solution by slow evaporation of the solvent.

Refinement top

The H-atoms were positioned geometrically at C—H = 0.93 Å and N—H = 0.86 Å, respectively and included in the refinement as riding with U iso(H) = xUeq(C, N), where x = 1.2 for all H-atoms.

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: ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Figures top
Fig. 1. View of the title compound with displacement ellipsoids drawn at the 50% probability level. The dotted lines represent the intramolecular hydrogen bonds.

Fig. 2. The partial packing diagram, which shows that molecules form dimers with R22(8) ring motifs.
(2Z)-N-(2-Chlorobenzyl)-2-(2-oxo-2,3-dihydro-1H-indol- 3-ylidene)hydrazinecarbothioamide top
Crystal data top
C16H13ClN4OSF(000) = 712
Mr = 344.81Dx = 1.430 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2075 reflections
a = 13.7017 (10) Åθ = 1.5–28.4°
b = 14.1585 (10) ŵ = 0.38 mm1
c = 8.2698 (5) ÅT = 296 K
β = 93.151 (3)°Prism, orange
V = 1601.88 (19) Å30.32 × 0.23 × 0.20 mm
Z = 4
Data collection top
Bruker Kappa APEXII CCD
diffractometer
3935 independent reflections
Radiation source: fine-focus sealed tube2541 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
Detector resolution: 7.50 pixels mm-1θmax = 28.4°, θmin = 1.5°
ω scansh = 1818
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
k = 1318
Tmin = 0.888, Tmax = 0.929l = 811
14957 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)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105H-atom parameters constrained
S = 1.02 w = 1/[σ2(Fo2) + (0.0415P)2 + 0.3273P]
where P = (Fo2 + 2Fc2)/3
3935 reflections(Δ/σ)max < 0.001
208 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = 0.29 e Å3
Crystal data top
C16H13ClN4OSV = 1601.88 (19) Å3
Mr = 344.81Z = 4
Monoclinic, P21/cMo Kα radiation
a = 13.7017 (10) ŵ = 0.38 mm1
b = 14.1585 (10) ÅT = 296 K
c = 8.2698 (5) Å0.32 × 0.23 × 0.20 mm
β = 93.151 (3)°
Data collection top
Bruker Kappa APEXII CCD
diffractometer
3935 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
2541 reflections with I > 2σ(I)
Tmin = 0.888, Tmax = 0.929Rint = 0.033
14957 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.105H-atom parameters constrained
S = 1.02Δρmax = 0.21 e Å3
3935 reflectionsΔρmin = 0.29 e Å3
208 parameters
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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
Cl10.34601 (5)0.04349 (4)0.12764 (8)0.0798 (3)
S10.30114 (4)0.37338 (4)0.01319 (6)0.0502 (2)
O10.07991 (10)0.44729 (9)0.35390 (16)0.0505 (5)
N10.05032 (11)0.37716 (11)0.47406 (17)0.0434 (5)
N20.11200 (10)0.24682 (10)0.24169 (15)0.0336 (4)
N30.17023 (10)0.31195 (10)0.17804 (16)0.0363 (5)
N40.26056 (11)0.19523 (11)0.06682 (17)0.0402 (5)
C10.02814 (12)0.22197 (12)0.40963 (19)0.0352 (5)
C20.04817 (15)0.12656 (14)0.4110 (2)0.0488 (7)
C30.12841 (17)0.09610 (16)0.4929 (3)0.0615 (8)
C40.18653 (16)0.16013 (18)0.5692 (3)0.0628 (8)
C50.16717 (15)0.25630 (16)0.5693 (2)0.0517 (7)
C60.08666 (13)0.28509 (13)0.48984 (19)0.0382 (6)
C70.02986 (13)0.37795 (13)0.3854 (2)0.0380 (6)
C80.04609 (12)0.27811 (12)0.33533 (18)0.0329 (5)
C90.24367 (12)0.28702 (12)0.07912 (19)0.0351 (5)
C100.34135 (14)0.15508 (15)0.0198 (2)0.0469 (7)
C110.42635 (14)0.12971 (14)0.0949 (2)0.0424 (6)
C120.43573 (15)0.04174 (14)0.1681 (2)0.0493 (7)
C130.51332 (19)0.01890 (19)0.2740 (3)0.0655 (9)
C140.5822 (2)0.0854 (2)0.3117 (3)0.0775 (10)
C150.57512 (18)0.1745 (2)0.2452 (3)0.0716 (10)
C160.49822 (16)0.19569 (16)0.1363 (3)0.0563 (8)
H10.075660.426580.515320.0520*
H20.009150.083790.358730.0585*
H30.143090.032030.496240.0737*
H3A0.161370.370630.199670.0436*
H40.240220.138100.622020.0754*
H4A0.221820.156930.112370.0482*
H50.206610.299160.620510.0620*
H10A0.362480.200520.098430.0563*
H10B0.318820.099010.078020.0563*
H130.518410.041210.319030.0786*
H140.634700.070690.383220.0930*
H150.621880.220040.273390.0861*
H160.494550.255490.089830.0676*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0945 (5)0.0626 (4)0.0842 (4)0.0105 (3)0.0230 (4)0.0024 (3)
S10.0545 (3)0.0484 (3)0.0491 (3)0.0073 (3)0.0144 (2)0.0011 (2)
O10.0604 (9)0.0332 (7)0.0602 (8)0.0045 (7)0.0230 (7)0.0027 (6)
N10.0451 (10)0.0386 (9)0.0477 (9)0.0048 (7)0.0148 (7)0.0051 (7)
N20.0338 (8)0.0342 (8)0.0326 (7)0.0000 (7)0.0002 (6)0.0001 (6)
N30.0378 (9)0.0321 (8)0.0396 (8)0.0006 (7)0.0073 (7)0.0032 (6)
N40.0364 (9)0.0423 (9)0.0424 (8)0.0042 (7)0.0080 (7)0.0018 (7)
C10.0363 (10)0.0384 (10)0.0304 (8)0.0040 (8)0.0014 (7)0.0002 (7)
C20.0574 (13)0.0422 (11)0.0466 (11)0.0061 (10)0.0023 (9)0.0018 (9)
C30.0712 (16)0.0534 (13)0.0598 (13)0.0266 (12)0.0038 (12)0.0019 (11)
C40.0571 (14)0.0799 (17)0.0526 (12)0.0262 (13)0.0135 (11)0.0042 (12)
C50.0434 (12)0.0663 (14)0.0460 (11)0.0069 (11)0.0091 (9)0.0059 (10)
C60.0381 (11)0.0440 (10)0.0323 (9)0.0036 (9)0.0007 (8)0.0011 (8)
C70.0415 (11)0.0363 (10)0.0366 (9)0.0018 (9)0.0057 (8)0.0005 (7)
C80.0350 (10)0.0340 (9)0.0295 (8)0.0011 (8)0.0010 (7)0.0008 (7)
C90.0343 (10)0.0420 (10)0.0287 (8)0.0015 (8)0.0015 (7)0.0040 (7)
C100.0504 (12)0.0531 (12)0.0376 (10)0.0165 (10)0.0065 (9)0.0019 (9)
C110.0421 (12)0.0499 (11)0.0364 (9)0.0132 (10)0.0121 (8)0.0004 (8)
C120.0519 (13)0.0535 (12)0.0439 (11)0.0106 (10)0.0159 (10)0.0010 (9)
C130.0745 (17)0.0705 (16)0.0519 (13)0.0304 (15)0.0065 (12)0.0110 (11)
C140.0614 (17)0.103 (2)0.0668 (16)0.0278 (17)0.0094 (13)0.0021 (15)
C150.0481 (14)0.090 (2)0.0766 (16)0.0000 (14)0.0015 (12)0.0178 (15)
C160.0509 (14)0.0575 (14)0.0615 (13)0.0094 (12)0.0111 (11)0.0021 (10)
Geometric parameters (Å, º) top
Cl1—C121.742 (2)C5—C61.376 (3)
S1—C91.6625 (18)C7—C81.493 (2)
O1—C71.234 (2)C10—C111.505 (3)
N1—C61.404 (2)C11—C161.387 (3)
N1—C71.354 (2)C11—C121.388 (3)
N2—N31.345 (2)C12—C131.378 (3)
N2—C81.299 (2)C13—C141.357 (4)
N3—C91.377 (2)C14—C151.378 (4)
N4—C91.325 (2)C15—C161.381 (3)
N4—C101.466 (2)C2—H20.9300
N1—H10.8600C3—H30.9300
N3—H3A0.8600C4—H40.9300
N4—H4A0.8600C5—H50.9300
C1—C81.453 (2)C10—H10A0.9700
C1—C21.379 (3)C10—H10B0.9700
C1—C61.393 (2)C13—H130.9300
C2—C31.391 (3)C14—H140.9300
C3—C41.382 (3)C15—H150.9300
C4—C51.387 (3)C16—H160.9300
C6—N1—C7111.13 (15)C10—C11—C16120.63 (18)
N3—N2—C8116.49 (14)C10—C11—C12122.63 (18)
N2—N3—C9121.67 (14)C11—C12—C13122.5 (2)
C9—N4—C10123.90 (15)Cl1—C12—C11119.38 (15)
C7—N1—H1124.00Cl1—C12—C13118.11 (17)
C6—N1—H1124.00C12—C13—C14119.1 (2)
C9—N3—H3A119.00C13—C14—C15120.7 (2)
N2—N3—H3A119.00C14—C15—C16119.6 (2)
C9—N4—H4A118.00C11—C16—C15121.4 (2)
C10—N4—H4A118.00C1—C2—H2121.00
C2—C1—C6120.31 (16)C3—C2—H2121.00
C2—C1—C8133.12 (16)C2—C3—H3120.00
C6—C1—C8106.56 (15)C4—C3—H3120.00
C1—C2—C3118.08 (18)C3—C4—H4119.00
C2—C3—C4120.6 (2)C5—C4—H4119.00
C3—C4—C5122.0 (2)C4—C5—H5122.00
C4—C5—C6116.66 (19)C6—C5—H5122.00
N1—C6—C1109.58 (15)N4—C10—H10A109.00
N1—C6—C5128.09 (17)N4—C10—H10B109.00
C1—C6—C5122.33 (18)C11—C10—H10A109.00
O1—C7—N1126.73 (17)C11—C10—H10B109.00
O1—C7—C8127.01 (16)H10A—C10—H10B108.00
N1—C7—C8106.26 (15)C12—C13—H13120.00
N2—C8—C7127.38 (15)C14—C13—H13120.00
N2—C8—C1126.22 (16)C13—C14—H14120.00
C1—C8—C7106.39 (14)C15—C14—H14120.00
S1—C9—N3117.66 (13)C14—C15—H15120.00
S1—C9—N4126.66 (13)C16—C15—H15120.00
N3—C9—N4115.68 (15)C11—C16—H16119.00
N4—C10—C11111.33 (14)C15—C16—H16119.00
C12—C11—C16116.71 (18)
C7—N1—C6—C10.42 (19)C1—C2—C3—C40.6 (3)
C7—N1—C6—C5179.26 (17)C2—C3—C4—C50.8 (4)
C6—N1—C7—O1177.87 (17)C3—C4—C5—C60.2 (3)
C6—N1—C7—C81.46 (18)C4—C5—C6—N1178.93 (18)
C8—N2—N3—C9178.97 (14)C4—C5—C6—C11.4 (3)
N3—N2—C8—C1176.21 (14)O1—C7—C8—N24.5 (3)
N3—N2—C8—C72.4 (2)O1—C7—C8—C1176.61 (17)
N2—N3—C9—S1171.76 (11)N1—C7—C8—N2176.14 (16)
N2—N3—C9—N47.8 (2)N1—C7—C8—C12.73 (18)
C10—N4—C9—S16.5 (2)N4—C10—C11—C1289.5 (2)
C10—N4—C9—N3174.00 (14)N4—C10—C11—C1688.4 (2)
C9—N4—C10—C1198.6 (2)C10—C11—C12—Cl10.3 (2)
C6—C1—C2—C30.6 (3)C10—C11—C12—C13179.54 (19)
C8—C1—C2—C3178.34 (19)C16—C11—C12—Cl1177.75 (15)
C2—C1—C6—N1178.63 (15)C16—C11—C12—C131.5 (3)
C2—C1—C6—C51.7 (3)C10—C11—C16—C15178.0 (2)
C8—C1—C6—N12.16 (18)C12—C11—C16—C150.1 (3)
C8—C1—C6—C5177.54 (16)Cl1—C12—C13—C14177.65 (19)
C2—C1—C8—N23.1 (3)C11—C12—C13—C141.7 (3)
C2—C1—C8—C7177.98 (18)C12—C13—C14—C150.1 (4)
C6—C1—C8—N2175.93 (15)C13—C14—C15—C161.4 (4)
C6—C1—C8—C72.96 (17)C14—C15—C16—C111.5 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O10.862.052.7416 (19)137
N4—H4A···N20.862.282.663 (2)107
N1—H1···O1i0.862.092.903 (2)157
Symmetry code: (i) x, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC16H13ClN4OS
Mr344.81
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)13.7017 (10), 14.1585 (10), 8.2698 (5)
β (°) 93.151 (3)
V3)1601.88 (19)
Z4
Radiation typeMo Kα
µ (mm1)0.38
Crystal size (mm)0.32 × 0.23 × 0.20
Data collection
DiffractometerBruker Kappa APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.888, 0.929
No. of measured, independent and
observed [I > 2σ(I)] reflections
14957, 3935, 2541
Rint0.033
(sin θ/λ)max1)0.670
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.105, 1.02
No. of reflections3935
No. of parameters208
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.21, 0.29

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and PLATON (Spek, 2009), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···O10.862.052.7416 (19)137
N4—H4A···N20.862.282.663 (2)107
N1—H1···O1i0.862.092.903 (2)157
Symmetry code: (i) x, y+1, z+1.
 

Acknowledgements

HP, MSI and NK thank the Higher Education Commission (HEC), Pakistan, for financial assistance under the National Research Program for Universities (project No. 20–873/R&D/07/452).

References

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