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

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

doi:10.1107/S2414314624007879

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 9| Part 8| August 2024| x240787

https://doi.org/10.1107/S2414314624007879

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Methyl 2-[(Z)-5-bromo-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 5 August 2024; accepted 9 August 2024; online 16 August 2024)

The title compound, C₁₀H₈BrN₃OS₂, a brominated dithiocarbazate imine derivative, was obtained from the condensation reaction of S-methyldithiocarbazate (SMDTC) and 5-bromoisatin. The essentially planar molecule exhibits a Z configuration, with the dithiocarbazate and 5-bromoisatin fragments located on the same sides of the C=N azomethine bond, which allows for the formation of an intramolecular N—H⋯O_b (b = bromoisatin) hydrogen bond generating an S(6) ring motif. In the crystal, adjacent molecules are linked by pairs of N—H⋯O hydrogen bonds, forming dimers characterized by an R²₂(8) loop motif. In the extended structure, molecules are linked into a three-dimensional network by C—H⋯S and C—H⋯Br hydrogen bonds, C—Br⋯S halogen bonds and aromatic π–π stacking.

Keywords: crystal structure; dithiocarbazate; 5-bromoisatin; Z configuration; hydrogen bonding; halogen bond.

CCDC reference: 2376721

Structure description

Isatin-derived dithiocarbazate imines have been reported to exhibit a broad spectrum of physiological properties (Yekke-ghasemi et al., 2020 ; Ramilo-Gomes et al., 2021 ). In particular, the S-methyl-substituted derivatives have received considerable attention in the field of organic transformations for the preparation of carbothiohydrazones, carbothiohydrazides and various aza-heterocyclic compounds such as pyrazoles, 1,2,4-triazoles and 1,3,4-thiadiazoles (Lin et al., 2013 ; Moustafa et al., 2021 ; Bekircan et al., 2022 ; Malakar et al., 2023 , Geoghegan et al., 2024 ). Recent study has revealed that the imine obtained from the condensation reaction of isatin and S-methyldithiocarbazate can be directly transformed into the spiro-fused 1,3,4-thiadiazole compound in a straightforward synthetic protocol (Moustafa et al., 2021). This approach opens a new avenue in accessing isatin-based spirocycle molecules. We are concerned with developing new dithiocarbazate imines containing isatin derivatives and continue research work to explore their potential applications (Abdul Manan et al., 2024 ). Therefore, as part of our ongoing research and structural studies on such molecules, we now report the synthesis and crystal structure of the title compound.

The asymmetric unit of the title compound, C₁₀H₈BrN₃OS₂ contains one molecule and crystallizes in the P2₁/n monoclinic space group with the S-methyl and thione groups being syn (Fig. 1). The non-hydrogen atoms in the molecule are close to planar, indicating electron delocalization within the molecule: the dihedral angle between the dithiocarbazate group and the 5-bromoisatin ring is 7.9 (3)°. The imine exists in its thione tautomeric form with the dithiocarbazate unit adopting a Z conformation about the C=N bond [C4—C3=N3—N4 = 177.9 (9)°] with respect to the 5-bromoisatin moiety, while the S10 thioketo sulfur atom is positioned anti to the N3 azomethine nitrogen atom [N3—N4—C10—S10 = 173.8 (7)°]. The presence of an N—H⋯O_b (b = bromoisatin) intramolecular hydrogen helps to consolidate the planar conformatic of the title molecule (Table 1). Otherwise, the bond lengths and angles are comparable to those reported for methyl 2-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)hydrazinecarbodithioate (Abdul Manan et al., 2011 ), methyl 2-(1-methyl-2-oxo-1,2-dihydro-3H-indol-3-ylidene)hydrazinecarbodithioate (Abdul Manan et al., 2012 ) and methyl (Z)-2-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)hydrazine-1-carbodithioate (Li et al., 2018 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4⋯O2	0.98 (2)	2.04 (8)	2.715 (11)	124 (7)
N1—H1⋯O2ⁱ	0.97 (2)	1.86 (4)	2.801 (11)	163 (10)
C5—H5⋯Br5ⁱⁱ	0.95	3.00	3.941 (10)	172
C7—H7⋯S10ⁱⁱⁱ	0.95	2.83	3.775 (10)	171
Symmetry codes: (i) ; (ii) ; (iii) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

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

In the crystal of the title compound, molecules are linked into dimers through pairwise N1—H1⋯O2 hydrogen bonds in a common R₂²(8) motif (Fig. 2). These dimers further pack into chains propagating along [2 $[\overline{1}]$ 0] through a combination of weak C5—H5⋯Br5 hydrogen bonds and Br5⋯S11 [Br⋯S = 3.521 (3) Å, C—S⋯Br = 135.1 (3)°, C—Br⋯S = 155.2 (3)°] halogen bonds, forming a extended R₂¹(9) R₂²(8) R₂¹(9) motif. These chains are connected into the third dimension by further weak C7—H7⋯S10 hydrogen bonds (Table 1, Fig. 3). These hydrogen bonded arrays have parallel molecules separated such that an equivalent interpenetrating molecular framework exists, interacting with the other via aromatic π–π stacking [N1/C2–C4/C9, centroid⋯centroid separation = 3.307 (9) Å].

Figure 2
View of the dimers formed by N—H⋯O hydrogen-bonding giving R₂²(8) motifs.

Figure 3
View showing both the weak hydrogen bonds and halogen bonds connecting the hydrogen-bonded dimers in three-dimensions.

Synthesis and crystallization

The dithiocarbazate precursor, SMDTC was prepared by the literature method (Das & Livingstone, 1976 ). The title compound was prepared by adding 5-bromoisatin (2.26 g, 10.0 mmol, 1.0 eq) dissolved in hot ethanol (20 ml) to a solution of the precursor, 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 about 20 min at room temperature until a precipitate was formed, which was then filtered and dried over silica gel, yielding orange crystals on recrystallization from ethanol solution (yield: 2.74 g, 83%). m.p. 259–260°C; ¹H NMR (400 MHz, d₆-DMSO) δ: (p.p.m.): 2.63 (s, 3H), 6.92 (d, J = 8.28 Hz, 1H), 7.59 (dd, J = 8.32, 2.0 Hz, 1H), 7.63 (d, J = 1.92 Hz, 1H), 11.48 (s, 1H), 13.90 (s, 1H); HRMS m/z (ESI⁺), found: [M + H]⁺ 329.9335, C₁₀H₈N₃OS₂⁷⁹Br requires [M + H]⁺ 329.9370.

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 −176.99° around [0.92 0.02 − 0.38] (reciprocal) or [1.00 0.02 0.00] (direct), and a refined twin fraction of 0.056 (3).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₀H₈BrN₃OS₂
M_r	330.22
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	125
a, b, c (Å)	6.6331 (3), 7.5726 (3), 24.6985 (10)
β (°)	97.141 (4)
V (Å³)	1230.98 (9)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	7.63
Crystal size (mm)	0.11 × 0.01 × 0.01 × 0.40 (radius)

Data collection
Diffractometer	Rigaku XtaLAB P200K
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2023 $[Rigaku OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.025, 0.114
No. of measured, independent and observed [I > 2σ(I)] reflections	11989, 2513, 1869
R_int	0.1931
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.093, 0.293, 1.14
No. of reflections	2513
No. of parameters	164
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)	1.37, −1.06
Computer programs: CrysAlis PRO (Rigaku OD, 2023 $[Rigaku OD (2023). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), 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: 2376721

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314624007879/hb4481sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624007879/hb4481Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314624007879/hb4481Isup3.cml

checkCIF report

Computing details top

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

Crystal data top

C₁₀H₈BrN₃OS₂	F(000) = 656
M_r = 330.22	D_x = 1.782 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.54184 Å
a = 6.6331 (3) Å	Cell parameters from 3279 reflections
b = 7.5726 (3) Å	θ = 3.6–75.3°
c = 24.6985 (10) Å	µ = 7.63 mm⁻¹
β = 97.141 (4)°	T = 125 K
V = 1230.98 (9) Å³	Needle, orange
Z = 4	0.11 × 0.01 × 0.01 × 0.40 (radius) mm

Data collection top

Rigaku XtaLAB P200K diffractometer	2513 independent reflections
Radiation source: Rotating Anode, Rigaku MM-007HF	1869 reflections with I > 2σ(I)
Rigaku Osmic Confocal Optical System monochromator	R_int = 0.193
Detector resolution: 5.8140 pixels mm^-1	θ_max = 76.3°, θ_min = 6.1°
shutterless scans	h = −7→7
Absorption correction: multi-scan (CrysAlisPr; Rigaku OD, 2023)	k = −9→9
T_min = 0.025, T_max = 0.114	l = −5→30
11959 measured reflections

Refinement top

Refinement on F²	Primary atom site location: dual
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.093	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.293	w = 1/[σ²(F_o²) + (0.145P)² + 4.1265P] where P = (F_o² + 2F_c²)/3
S = 1.14	(Δ/σ)_max < 0.001
2513 reflections	Δρ_max = 1.37 e Å⁻³
164 parameters	Δρ_min = −1.06 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 with HKLF5 generated by TWINROTMAT running in PLATON. NH hydrogen atoms were identifed from F_map and refined with N-H restrained to 0.98 Å.

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

	x	y	z	U_iso*/U_eq
Br5	−0.00632 (16)	0.49654 (14)	0.40002 (4)	0.0565 (4)
S11	0.3366 (4)	0.2379 (4)	0.68815 (10)	0.0606 (7)
S10	0.7209 (4)	0.0479 (4)	0.73636 (10)	0.0602 (7)
O2	0.9075 (10)	0.0482 (9)	0.5665 (3)	0.0519 (15)
N1	0.7784 (13)	0.1254 (11)	0.4779 (3)	0.0497 (17)
N4	0.6432 (12)	0.1539 (11)	0.6357 (3)	0.0500 (17)
N3	0.5194 (11)	0.2188 (10)	0.5925 (3)	0.0471 (17)
C2	0.7769 (15)	0.1156 (13)	0.5335 (4)	0.051 (2)
C6	0.2344 (13)	0.3758 (12)	0.4224 (4)	0.048 (2)
C9	0.5992 (16)	0.2052 (13)	0.4534 (4)	0.052 (2)
C4	0.4781 (16)	0.2581 (12)	0.4928 (4)	0.050 (2)
C5	0.2935 (15)	0.3440 (12)	0.4784 (4)	0.0483 (19)
H5	0.210762	0.379717	0.505144	0.058*
C10	0.5760 (17)	0.1466 (13)	0.6859 (4)	0.054 (2)
C7	0.3544 (14)	0.3217 (13)	0.3840 (4)	0.051 (2)
H7	0.309938	0.343966	0.346543	0.061*
C11	0.3089 (19)	0.2206 (17)	0.7602 (5)	0.065 (3)
H11A	0.175584	0.266410	0.766485	0.098*
H11B	0.415852	0.289473	0.781506	0.098*
H11C	0.320165	0.096497	0.771421	0.098*
C8	0.5376 (16)	0.2359 (13)	0.3979 (4)	0.053 (2)
H8	0.618622	0.199134	0.370855	0.064*
C3	0.5842 (16)	0.2045 (13)	0.5453 (4)	0.052 (2)
H4	0.753 (10)	0.069 (10)	0.633 (4)	0.04 (2)*
H1	0.881 (13)	0.046 (12)	0.467 (4)	0.05 (3)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br5	0.0560 (7)	0.0579 (7)	0.0547 (7)	0.0055 (4)	0.0036 (5)	0.0015 (4)
S11	0.0661 (15)	0.0663 (15)	0.0499 (13)	0.0133 (12)	0.0089 (11)	0.0043 (11)
S10	0.0692 (16)	0.0626 (15)	0.0472 (13)	0.0112 (12)	0.0007 (11)	0.0017 (11)
O2	0.049 (4)	0.055 (4)	0.051 (3)	0.004 (3)	0.002 (3)	−0.001 (3)
N1	0.060 (5)	0.048 (4)	0.043 (4)	0.000 (3)	0.012 (3)	−0.001 (3)
N4	0.052 (4)	0.047 (4)	0.050 (4)	0.007 (3)	0.004 (3)	0.002 (3)
N3	0.049 (4)	0.042 (4)	0.050 (4)	0.002 (3)	0.002 (3)	0.000 (3)
C2	0.058 (5)	0.047 (5)	0.047 (5)	−0.009 (4)	0.008 (4)	−0.006 (4)
C6	0.034 (4)	0.046 (4)	0.061 (5)	0.000 (3)	−0.008 (4)	0.001 (4)
C9	0.060 (6)	0.043 (5)	0.056 (5)	−0.005 (4)	0.013 (4)	−0.001 (4)
C4	0.067 (6)	0.038 (4)	0.043 (4)	−0.003 (4)	0.002 (4)	−0.003 (3)
C5	0.058 (5)	0.042 (4)	0.044 (5)	−0.007 (4)	0.002 (4)	−0.002 (3)
C10	0.074 (6)	0.043 (5)	0.046 (5)	0.004 (4)	0.007 (4)	−0.002 (4)
C7	0.052 (5)	0.055 (5)	0.046 (5)	−0.002 (4)	0.009 (4)	0.006 (4)
C11	0.070 (7)	0.070 (7)	0.058 (6)	0.009 (5)	0.019 (5)	−0.004 (5)
C8	0.060 (6)	0.052 (5)	0.049 (5)	−0.011 (4)	0.013 (4)	0.000 (4)
C3	0.059 (5)	0.046 (5)	0.052 (5)	−0.001 (4)	0.012 (4)	−0.004 (4)

Geometric parameters (Å, º) top

Br5—C6	1.863 (8)	C6—C5	1.410 (13)
S11—C10	1.739 (11)	C6—C7	1.375 (14)
S11—C11	1.816 (11)	C9—C4	1.395 (14)
S10—C10	1.654 (10)	C9—C8	1.399 (14)
O2—C2	1.224 (12)	C4—C5	1.394 (14)
N1—C2	1.378 (12)	C4—C3	1.455 (13)
N1—C9	1.402 (13)	C5—H5	0.9500
N1—H1	0.97 (2)	C7—H7	0.9500
N4—N3	1.355 (11)	C7—C8	1.383 (15)
N4—C10	1.371 (13)	C11—H11A	0.9800
N4—H4	0.98 (2)	C11—H11B	0.9800
N3—C3	1.294 (12)	C11—H11C	0.9800
C2—C3	1.505 (14)	C8—H8	0.9500

C10—S11—C11	101.9 (5)	C4—C5—C6	117.3 (9)
C2—N1—C9	110.1 (8)	C4—C5—H5	121.3
C2—N1—H1	110 (7)	S10—C10—S11	127.1 (6)
C9—N1—H1	137 (7)	N4—C10—S11	114.4 (7)
N3—N4—C10	119.6 (8)	N4—C10—S10	118.4 (8)
N3—N4—H4	124 (5)	C6—C7—H7	118.9
C10—N4—H4	111 (5)	C6—C7—C8	122.3 (9)
C3—N3—N4	116.2 (8)	C8—C7—H7	118.9
O2—C2—N1	126.5 (9)	S11—C11—H11A	109.5
O2—C2—C3	127.3 (9)	S11—C11—H11B	109.5
N1—C2—C3	106.3 (8)	S11—C11—H11C	109.5
C5—C6—Br5	119.9 (7)	H11A—C11—H11B	109.5
C7—C6—Br5	119.3 (7)	H11A—C11—H11C	109.5
C7—C6—C5	120.8 (8)	H11B—C11—H11C	109.5
C4—C9—N1	110.7 (9)	C9—C8—H8	121.2
C4—C9—C8	120.8 (10)	C7—C8—C9	117.5 (9)
C8—C9—N1	128.5 (9)	C7—C8—H8	121.2
C9—C4—C3	106.6 (9)	N3—C3—C2	126.6 (9)
C5—C4—C9	121.3 (9)	N3—C3—C4	126.9 (9)
C5—C4—C3	132.1 (9)	C4—C3—C2	106.3 (8)
C6—C5—H5	121.3

Br5—C6—C5—C4	−178.0 (7)	C9—N1—C2—O2	177.5 (9)
Br5—C6—C7—C8	178.1 (8)	C9—N1—C2—C3	−2.8 (10)
O2—C2—C3—N3	−3.0 (17)	C9—C4—C5—C6	−0.2 (14)
O2—C2—C3—C4	−178.5 (9)	C9—C4—C3—N3	−175.6 (10)
N1—C2—C3—N3	177.3 (9)	C9—C4—C3—C2	−0.2 (10)
N1—C2—C3—C4	1.8 (10)	C4—C9—C8—C7	0.6 (14)
N1—C9—C4—C5	178.7 (8)	C5—C6—C7—C8	−0.6 (15)
N1—C9—C4—C3	−1.6 (11)	C5—C4—C3—N3	4.0 (17)
N1—C9—C8—C7	−178.4 (9)	C5—C4—C3—C2	179.5 (10)
N4—N3—C3—C2	3.3 (14)	C10—N4—N3—C3	−172.9 (9)
N4—N3—C3—C4	177.9 (9)	C7—C6—C5—C4	0.7 (13)
N3—N4—C10—S11	−3.9 (12)	C11—S11—C10—S10	6.9 (9)
N3—N4—C10—S10	173.8 (7)	C11—S11—C10—N4	−175.7 (8)
C2—N1—C9—C4	2.9 (11)	C8—C9—C4—C5	−0.5 (14)
C2—N1—C9—C8	−178.0 (10)	C8—C9—C4—C3	179.2 (9)
C6—C7—C8—C9	−0.1 (15)	C3—C4—C5—C6	−179.8 (10)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···O2	0.98 (2)	2.04 (8)	2.715 (11)	124 (7)
N1—H1···O2ⁱ	0.97 (2)	1.86 (4)	2.801 (11)	163 (10)
C5—H5···Br5ⁱⁱ	0.95	3.00	3.941 (10)	172
C7—H7···S10ⁱⁱⁱ	0.95	2.83	3.775 (10)	171

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

Acknowledgements

The authors acknowledge Universiti Teknologi MARA for financial support.

References

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