Methyl 2-[(Z)-5-methyl-2-oxoindolin-3-yl­idene]hydrazinecarbodi­thio­ate

Abdul Manan, M.A.F.; Cordes, D.B.; McKay, A.P.

doi:10.1107/S2414314624009672

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 9| Part 10| October 2024| x240967

https://doi.org/10.1107/S2414314624009672

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Methyl 2-[(Z)-5-methyl-2-oxoindolin-3-ylidene]hydrazinecarbodithioate

Mohd Abdul Fatah Abdul Manan,^a ^* David B. Cordes ^b and Aidan P. McKay ^b

^aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia, and ^bEaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
^*Correspondence e-mail: abdfatah@uitm.edu.my

Edited by W. T. A. Harrison, University of Aberdeen, United Kingdom (Received 25 September 2024; accepted 1 October 2024; online 8 October 2024)

The title dithiocarbazate imine, C₁₁H₁₁N₃OS₂, was obtained from the condensation reaction of S-methyldithiocarbazate (SMDTC) and 5-methylisatin. It shows a Z configuration about the imine C=N bond, which is associated with an intramolecular N—H⋯O hydrogen bond that closes an S(6) ring. In the crystal, inversion dimers linked by pairwise N—H⋯O hydrogen bonds generate R²₂(8) loops. The extended structure features C—H⋯S contacts as well as reciprocal carbonyl–carbonyl (C=O⋯C=O) interactions.

Keywords: crystal structure; dithiocarbazate; 5-methylisatin; C=O⋯C=O interaction.

CCDC reference: 2388258

Structure description

In medicinal chemistry, isatin (1H-indole-2,3-dione, C₈H₅NO₂) and its derivatives represent an important class of heterocyclic compounds with potential pharmacological properties (Shu et al., 2024 ). Taking advantage of the versatile reactivity of the isatin nucleus, a huge library of isatin derivatives with various applications is now available. Most of these derivatives have been obtained by utilizing either the high reactivity of its 3-carbonyl group or the nucleophilic nature of its NH group. The NH group can undergo N-acylation, N-arylation or N-alkylation, whereas the C3 carbonyl group can be utilized in the synthesis of hydrazone or imine derivatives as well as oxindoles and spirocyclic compounds (Nath et al., 2020 ). These derivatives are reported to possess several biological activities and find applications in the field of crystal engineering, supramolecular chemistry and materials science (Mehreen et al., 2022a ; Ahmed et al., 2019 ).

Recently, chemists have recognized both one-sided and reciprocal carbonyl–carbonyl interactions as non-covalent interactions of significant interest due to their ability to influence the geometries of small molecules and affect the three dimensional structures of peptides, peptoids, proteins and polyesters (Rahim et al., 2017 ). Very recently, the use of isatin-derived compounds as potent α-glucosidase inhibitors in managing diabetes has been reported, highlighting the role of C=O⋯C=O interactions in inhibiting α-glucosidase and controlling postprandial hyperglycemia (Mehreen et al., 2022b ). As a continuation of our research interests in isatin derivatives, we now report the synthesis and crystal structure of the title compound, C₁₁H₁₁N₃OS₂.

The asymmetric unit of the title compound (Fig. 1) comprises one molecule and crystallizes in the monoclinic space group P2₁/c. The methyl hydrazinecarbodithioate chain connects to the nine-membered 5-methyisatin ring at C3 and adopts a near planar geometry (r.m.s. deviation from planarity = 0.033 Å). The essentially planar conformation of the molecule is associated with the formation of an intramolecular N4—H4⋯O2 hydrogen bond (Table 1), which closes an S(6) loop. In the solid state, the compound exists in its thione tautomeric form with the dithiocarbazate fragment adopting a Z conformation about the C=N bond with respect to the 5-methylisatin moiety, while the S-methyl group adopts a syn conformation relative to the azomethine nitrogen atom. Otherwise, the bond lengths and angles in the title compound may be regarded as normal.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4⋯O2	0.98 (2)	2.01 (6)	2.754 (6)	130 (6)
N1—H1⋯O2ⁱ	0.98 (2)	1.85 (2)	2.825 (6)	171 (7)
Symmetry code: (i) .

Figure 1
The molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level.

In the crystal, the molecules of the title compound form inversion dimers through pairwise N1—H1⋯O2 hydrogen bonds (Table 1) in the common R₂²(8) motif. There are additional weak, non-classical C7—H7⋯S11 hydrogen bonds, which link molecules into C(10) chains propagating along [010]. The combination of the chains and inversion dimers forms corrugated sheets lying in the (102) plane (Fig. 2). The aforementioned sheets stack by way of reciprocal carbonyl–carbonyl interactions [C2⋯O2 = 3.166 (6) Å, C=O⋯C = 75.1 (3)°, O=C⋯O = 104.8 (3)°] (Fig. 3). The contact observed differs from the ideal motif-II type interaction (Sahariah & Sarma, 2019 ) with O2 lying over the adjacent pyrrolone ring (Fig. 4).

Figure 2
View of the N—H⋯O and C—H⋯S hydrogen bonds generating R₂²(8) dimers (centre) and C(10) chains (left to right), which combine to form corrugated (102) sheets.

Figure 3
View showing the stacking of the corrugated sheets supported by reciprocal carbonyl–carbonyl interactions (green).

Figure 4
Offset geometry of the carbonyl–carbonyl interaction showing how O2 is positioned over the adjacent pyrrolone ring.

Synthesis and crystallization

The dithiocarbazate precursor (SMDTC) was prepared by the literature method (Das & Livingstone, 1976 ). The title compound was prepared by adding 5-methylisatin (1.61 g, 10.0 mmol, 1.0 eq) dissolved in hot ethanol (20 ml) to a solution of SMDTC (1.22 g, 10.0 mmol, 1.0 eq) in hot ethanol (35 ml). The mixture was heated (80°C) with continuous stirring for 15 min and later allowed to stand for 20 min at room temperature until a precipitate formed, which was then filtered and dried over silica gel, yielding orange needles of the title compound on recrystallization form ethanol solution (yield: 2.12 g, 80%). m.p. 236–237°C; ¹H NMR (400 MHz, d₆-DMSO) δ: (p.p.m): 2.31 (s, 3H), 2.62 (s, 3H), 6.84 (d, J = 7.96 Hz, 1H), 7.22 (d, J = 7.96 Hz, 1H), 7.36 (s, 1H), 11.27 (s, 1H), 14.00 (s, 1H); HRMS m/z (ESI⁺), found: [M+H]⁺ 266.0417, C₁₁H₁₂N₃OS₂ requires [M+H]⁺ 266.0422.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The structure was refined as a two-component twin with component 2 rotated by 2.05° around [001] (reciprocal) or [105] (direct), and a refined twin fraction of 0.128 (6).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₁N₃OS₂
M_r	265.35
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	125
a, b, c (Å)	4.9897 (4), 21.8014 (19), 11.3394 (9)
β (°)	92.995 (8)
V (Å³)	1231.83 (18)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	3.82
Crystal size (mm)	0.23 × 0.01 × 0.01

Data collection
Diffractometer	Rigaku XtaLAB P200K
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2023 )
T_min, T_max	0.631, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	23143, 2554, 1548
R_int	0.171
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.079, 0.185, 1.09
No. of reflections	2554
No. of parameters	165
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.46, −0.63
Computer programs: CrysAlis PRO (Rigaku OD, 2023), SHELXT (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ), Mercury (Macrae et al., 2020 ), OLEX2 (Dolomanov et al., 2009 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 2388258

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314624009672/hb4486sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624009672/hb4486Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314624009672/hb4486Isup3.cml

checkCIF report

Computing details top

Methyl 2-[(Z)-5-methyl-2-oxoindolin-3-ylidene]hydrazinecarbodithioate top

Crystal data top

C₁₁H₁₁N₃OS₂	F(000) = 552
M_r = 265.35	D_x = 1.431 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
a = 4.9897 (4) Å	Cell parameters from 2965 reflections
b = 21.8014 (19) Å	θ = 4.0–68.3°
c = 11.3394 (9) Å	µ = 3.82 mm⁻¹
β = 92.995 (8)°	T = 125 K
V = 1231.83 (18) Å³	Needle, orange
Z = 4	0.23 × 0.01 × 0.01 mm

Data collection top

Rigaku XtaLAB P200K diffractometer	2554 independent reflections
Radiation source: Rotating Anode, Rigaku MM-007HF	1548 reflections with I > 2σ(I)
Rigaku Osmic Confocal Optical System monochromator	R_int = 0.171
Detector resolution: 5.8140 pixels mm^-1	θ_max = 76.3°, θ_min = 4.1°
shutterless scans	h = −6→6
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2023)	k = −27→27
T_min = 0.631, T_max = 1.000	l = 0→14
23143 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.079	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.185	w = 1/[σ²(F_o²) + 4.5988P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max < 0.001
2554 reflections	Δρ_max = 0.46 e Å⁻³
165 parameters	Δρ_min = −0.63 e Å⁻³
2 restraints

Special details top

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

Refinement. Refined as a 2-component twin using an HKLF5 file generated by TWINROTMAT running in PLATON (Spek, 2009), with twin law [-1 0 0 0 -1 0 0.237 0 1]. N—H hydrogen atoms located from F_map and refined isotropically with appropriate distance restraints.

The N-bound H atoms were located in a difference map and refined isotropically with a distance restraint. The C-bound H atoms were located geometrically (phenyl C—H =0.95 Å, methyl C—H = 0.98 Å) and refined as riding atoms. The constraint U_iso(H) = 1.2U_eq(phenyl C) or 1.5U_eq(methyl C) was applied in all cases.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
S11	0.1241 (3)	0.27752 (7)	−0.01332 (14)	0.0469 (4)
S12	−0.0419 (3)	0.32382 (7)	0.22526 (13)	0.0413 (4)
O2	0.7445 (7)	0.43673 (16)	0.0099 (3)	0.0370 (9)
N1	0.8229 (9)	0.5243 (2)	0.1228 (4)	0.0368 (11)
H1	0.962 (11)	0.542 (3)	0.075 (6)	0.09 (3)*
N3	0.3151 (9)	0.4171 (2)	0.1850 (4)	0.0333 (10)
N4	0.3199 (9)	0.3741 (2)	0.0983 (4)	0.0348 (10)
H4	0.440 (12)	0.378 (3)	0.033 (5)	0.09 (3)*
C2	0.6980 (10)	0.4710 (2)	0.0933 (5)	0.0332 (12)
C3	0.4865 (10)	0.4614 (2)	0.1812 (5)	0.0325 (12)
C4	0.5034 (10)	0.5136 (2)	0.2617 (5)	0.0330 (12)
C5	0.3648 (11)	0.5306 (2)	0.3595 (5)	0.0364 (12)
H5	0.227148	0.505107	0.387426	0.044*
C6	0.4315 (12)	0.5858 (3)	0.4162 (5)	0.0410 (14)
C7	0.6350 (12)	0.6224 (3)	0.3727 (6)	0.0460 (15)
H7	0.678915	0.659976	0.411573	0.055*
C8	0.7741 (12)	0.6058 (3)	0.2752 (5)	0.0430 (14)
H8	0.909675	0.631488	0.246180	0.052*
C9	0.7089 (11)	0.5509 (2)	0.2222 (5)	0.0354 (12)
C10	0.2876 (13)	0.6062 (3)	0.5235 (5)	0.0503 (16)
H10A	0.195041	0.645094	0.506230	0.075*
H10B	0.418146	0.611821	0.590187	0.075*
H10C	0.156207	0.574984	0.543505	0.075*
C11	0.1427 (11)	0.3261 (3)	0.0983 (5)	0.0363 (12)
C12	−0.2434 (12)	0.2564 (3)	0.1973 (6)	0.0517 (16)
H12A	−0.344567	0.260750	0.121366	0.078*
H12B	−0.368701	0.251475	0.260409	0.078*
H12C	−0.126802	0.220314	0.195053	0.078*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S11	0.0550 (9)	0.0417 (8)	0.0435 (8)	0.0003 (7)	−0.0028 (7)	−0.0055 (7)
S12	0.0400 (8)	0.0386 (8)	0.0453 (8)	−0.0014 (6)	0.0031 (6)	0.0030 (7)
O2	0.035 (2)	0.038 (2)	0.037 (2)	0.0033 (17)	0.0029 (17)	0.0032 (17)
N1	0.033 (2)	0.035 (2)	0.043 (3)	0.002 (2)	0.002 (2)	0.003 (2)
N3	0.034 (2)	0.033 (2)	0.033 (2)	0.004 (2)	0.0005 (19)	0.0010 (19)
N4	0.035 (2)	0.034 (2)	0.036 (3)	0.001 (2)	0.002 (2)	0.001 (2)
C2	0.031 (3)	0.035 (3)	0.034 (3)	0.008 (2)	0.000 (2)	0.009 (2)
C3	0.031 (3)	0.031 (3)	0.035 (3)	0.005 (2)	−0.004 (2)	0.005 (2)
C4	0.030 (3)	0.031 (3)	0.037 (3)	0.001 (2)	−0.004 (2)	0.006 (2)
C5	0.039 (3)	0.038 (3)	0.033 (3)	0.003 (2)	0.004 (2)	0.006 (2)
C6	0.044 (3)	0.034 (3)	0.045 (3)	0.009 (3)	−0.004 (3)	−0.003 (3)
C7	0.044 (3)	0.039 (3)	0.055 (4)	0.008 (3)	−0.009 (3)	−0.008 (3)
C8	0.037 (3)	0.037 (3)	0.055 (4)	−0.001 (3)	0.004 (3)	−0.002 (3)
C9	0.032 (3)	0.037 (3)	0.036 (3)	0.005 (2)	−0.003 (2)	0.004 (2)
C10	0.063 (4)	0.045 (3)	0.043 (3)	0.010 (3)	0.001 (3)	−0.005 (3)
C11	0.037 (3)	0.034 (3)	0.038 (3)	0.003 (2)	0.001 (2)	0.006 (2)
C12	0.045 (4)	0.036 (3)	0.074 (5)	−0.002 (3)	−0.001 (3)	0.010 (3)

Geometric parameters (Å, º) top

S11—C11	1.649 (6)	C5—H5	0.9500
S12—C11	1.750 (6)	C5—C6	1.396 (8)
S12—C12	1.799 (6)	C6—C7	1.402 (8)
O2—C2	1.237 (6)	C6—C10	1.511 (8)
N1—H1	0.98 (2)	C7—H7	0.9500
N1—C2	1.354 (7)	C7—C8	1.384 (8)
N1—C9	1.412 (7)	C8—H8	0.9500
N3—N4	1.360 (6)	C8—C9	1.372 (8)
N3—C3	1.292 (7)	C10—H10A	0.9800
N4—H4	0.98 (2)	C10—H10B	0.9800
N4—C11	1.370 (7)	C10—H10C	0.9800
C2—C3	1.503 (7)	C12—H12A	0.9800
C3—C4	1.460 (7)	C12—H12B	0.9800
C4—C5	1.387 (7)	C12—H12C	0.9800
C4—C9	1.400 (7)

C11—S12—C12	101.1 (3)	C8—C7—C6	122.3 (6)
C2—N1—H1	122 (5)	C8—C7—H7	118.8
C2—N1—C9	110.5 (4)	C7—C8—H8	121.3
C9—N1—H1	128 (5)	C9—C8—C7	117.4 (5)
C3—N3—N4	117.0 (4)	C9—C8—H8	121.3
N3—N4—H4	121 (4)	C4—C9—N1	110.5 (5)
N3—N4—C11	119.3 (4)	C8—C9—N1	127.7 (5)
C11—N4—H4	119 (4)	C8—C9—C4	121.8 (5)
O2—C2—N1	127.3 (5)	C6—C10—H10A	109.5
O2—C2—C3	126.1 (5)	C6—C10—H10B	109.5
N1—C2—C3	106.6 (5)	C6—C10—H10C	109.5
N3—C3—C2	128.0 (5)	H10A—C10—H10B	109.5
N3—C3—C4	125.4 (5)	H10A—C10—H10C	109.5
C4—C3—C2	106.6 (4)	H10B—C10—H10C	109.5
C5—C4—C3	133.9 (5)	S11—C11—S12	127.0 (3)
C5—C4—C9	120.4 (5)	N4—C11—S11	120.0 (4)
C9—C4—C3	105.8 (5)	N4—C11—S12	112.9 (4)
C4—C5—H5	120.6	S12—C12—H12A	109.5
C4—C5—C6	118.7 (5)	S12—C12—H12B	109.5
C6—C5—H5	120.6	S12—C12—H12C	109.5
C5—C6—C7	119.3 (5)	H12A—C12—H12B	109.5
C5—C6—C10	120.8 (5)	H12A—C12—H12C	109.5
C7—C6—C10	119.9 (5)	H12B—C12—H12C	109.5
C6—C7—H7	118.8

O2—C2—C3—N3	−1.0 (8)	C3—C4—C9—N1	−0.8 (6)
O2—C2—C3—C4	−179.2 (5)	C3—C4—C9—C8	177.6 (5)
N1—C2—C3—N3	178.2 (5)	C4—C5—C6—C7	0.2 (8)
N1—C2—C3—C4	0.1 (5)	C4—C5—C6—C10	−179.7 (5)
N3—N4—C11—S11	173.7 (4)	C5—C4—C9—N1	179.3 (5)
N3—N4—C11—S12	−7.1 (6)	C5—C4—C9—C8	−2.3 (8)
N3—C3—C4—C5	2.1 (9)	C5—C6—C7—C8	−0.2 (9)
N3—C3—C4—C9	−177.7 (5)	C6—C7—C8—C9	−1.0 (9)
N4—N3—C3—C2	−1.5 (7)	C7—C8—C9—N1	−179.7 (5)
N4—N3—C3—C4	176.3 (5)	C7—C8—C9—C4	2.2 (8)
C2—N1—C9—C4	0.9 (6)	C9—N1—C2—O2	178.6 (5)
C2—N1—C9—C8	−177.3 (5)	C9—N1—C2—C3	−0.6 (5)
C2—C3—C4—C5	−179.7 (5)	C9—C4—C5—C6	1.0 (8)
C2—C3—C4—C9	0.5 (5)	C10—C6—C7—C8	179.7 (5)
C3—N3—N4—C11	179.9 (5)	C12—S12—C11—S11	0.1 (5)
C3—C4—C5—C6	−178.8 (5)	C12—S12—C11—N4	−179.0 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···O2	0.98 (2)	2.01 (6)	2.754 (6)	130 (6)
N1—H1···O2ⁱ	0.98 (2)	1.85 (2)	2.825 (6)	171 (7)

Symmetry code: (i) −x+2, −y+1, −z.

Funding information

The authors acknowledge Universiti Teknologi MARA for financial support.

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