{[(E)-(1,3-Benzodioxol-5-yl)methyl­idene]amino}thio­urea

Mesto, E.; Okio, C.K.Y.A.; Lemus, M.A.; Schingaro, E.

doi:10.1107/S2056989024000033

research communications

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ISSN: 2056-9890

Volume 80| Part 2| February 2024| Pages 125-127

https://doi.org/10.1107/S2056989024000033

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{[(E)-(1,3-Benzodioxol-5-yl)methylidene]amino}thiourea

Ernesto Mesto,^a ^* Coco K. Y. A. Okio,^b Maria Alejandra Lemus ^b and Emanuela Schingaro ^a

^aDipartimento di Scienze della Terra e Geoambientali., Università degli Studi di Bari Aldo Moro, Via E. Orabona 4, 701125 Bari, Italy, and ^bDepartamento de Quimica, Facultad de Ciencias, Universidad Nacional de Colombia, Carerra 30 No 45-03, Bogotá, Colombia
^*Correspondence e-mail: ernesto.mesto@uniba.it

Edited by X. Hao, Institute of Chemistry, Chinese Academy of Sciences (Received 25 December 2023; accepted 2 January 2024; online 9 January 2024)

The synthesis and crystallographic analysis of the title compound, C₉H₉N₃O₂S, are reported. The compound crystallizes in the monoclinic space group P2₁/c, revealing characteristic bond lengths and angles typical of thiosemicarbazone groups. The supramolecular organization primarily arises from hydrogen bonding and π–π stacking interactions, leading to distinctive dimeric formations.

Keywords: crystal structure; thio-semicarbazone; three-dimensional network.

CCDC reference: 2190589

1. Chemical context

The group of thiosemicarbazone Schiff bases, capable of coordinating with metal centers through nitrogen and sulfur atoms, has garnered significant recent attention (Cortés et al., 2011 ; Singh et al., 2016 ) due to the exhibited biological and pharmacological properties, such as antibacterial and antiviral activities (Hu et al., 2006 ). This study focuses on describing the synthesis and the analysis of the crystal structure of the title molecule.

2. Structural commentary

The target compound (I) crystallizes in the monoclinic space group P2₁/c with one molecule in the asymmetric unit (Z = 4). A view of the molecule is shown in Fig. 1. Selected bond lengths and angles for the product are listed in Table 1. All bond lengths exhibit typical values (Dias et al., 2017 ).

Table 1
Selected geometric parameters (Å, °)

N1—C3	1.3281 (17)	N5—C6	1.2793 (17)
S2—C3	1.6899 (13)	N5—N13	1.3800 (15)
C3—N13	1.3414 (17)

S2—C3—N1	122.87 (11)	N1—C3—N13	116.82 (12)
S2—C3—N13	120.31 (10)	C6—N5—N13	117.07 (11)

Figure 1
Labelling scheme and structure of I. Displacement ellipsoids are drawn at the 50% probability level.

3. Supramolecular features

The supramolecular arrangements of I primarily result from classical and non-classical hydrogen bonds and π–π stacking interactions. These contacts were recognized by Mercury 2022 (Macrae et al., 2020 ; sum of van der Waals radii plus 0.1 Å). The hydrogen-bonding geometry is listed in Table 2, and the packing of molecules viewed down along the c axis is shown in Fig. 2. Together, the hydrogen-bonding interactions lead to the formation of a two-dimensional network parallel to (100). The molecules at (x, y, z) and (2 − x, −y, 1 − z) are components of dimers centered at (1, 0, ½), while the separation between the aryl ring centroids is 3.778 (2) Å, indicating π–π stacking interactions between the aromatic ring systems.

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H11⋯N5	0.85 (2)	2.23 (2)	2.6034 (17)	107 (1)
N1—H11⋯S2ⁱ	0.85 (2)	2.84 (2)	3.4805 (14)	134 (1)
N1—H12⋯O4ⁱⁱ	0.86 (1)	2.32 (2)	3.112 (2)	153 (2)
N13—H131⋯S2ⁱⁱⁱ	0.86 (1)	2.50 (1)	3.3550 (12)	172 (1)
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) .

Figure 2
The molecular dimers of molecule I (arbitrary view). Hydrogen bonds and π–π stacking interactions are indicated by dotted lines. [Symmetry codes: (i) 1 − x, −y, 1 − z; (ii) 2 − x, −y, 1 − z; (iii) 1 − x, $[{1\over 2}]$ + y, $[{1\over 2}]$ − z.]

4. Database Survey

Six crystal structures, authored by different researchers and featuring the [(E)-1,3-benzodioxol-5-ylmethylideneamino]thiourea fragment (piperonal, thiosemicarbazone), have been documented in the Cambridge Structural Database (CSD, WebCSD search December 2023; Groom et al., 2016 ). The crystal structure here under discussion can be considered the parent compound among those reported in the CSD. These other structures show substitutions in the imine hydrogen with methyl (de Oliveira et al., 2013 , 2015a ,b ) or nitro group (Dias et al., 2017), and in the amidic hydrogen with methyl (de Oliveira et al., 2015b), ethyl (Dias et al. 2017; de Oliveira et al., 2015a ), and phenyl (Dias et al. 2017) radicals. Some of these structures crystallize in the triclinic space group P $[\overline{1}]$ , while others in the monoclinic space group P2₁/c. Finally, Beckford et al. (2011), provide detailed information on the crystal structure of [(η⁶-p-cymene)Ru(pPhTSC)Cl]Cl, which crystallizes in the monoclinic space group P2₁/n. All of the structures reveal co-planar arrangements of the piperonal thiosemicarbazone portion along with π–π and hydrogen-bonding interactions.

5. Synthesis and crystallization

The synthesis of the Schiff base ligand (1,3-benzodioxol-5-ylformaldehyde) thiosemicarbazone was performed according to a previously published procedure (Casas et al., 2015 ). Piperonal (1.00 g, 6.66 mmol) and thiosemicarbazide (0.61 g, 6.66 mmol) were dissolved in ethanol and stirred under reflux for 2 h. Upon cooling, the solvent was removed and the remaining solid was recrystallized from ethanol/dichloromethane. Yellowish crystals suitable for X-ray diffraction were grown by slow evaporation after a couple of weeks, yield 78%; m.p. 409–411) . FT–IR (ATR, cm⁻¹): 3323 ν(N—H), 1585 ν(C=N), 1090 ν(N—N), 931 ν(C=S).

6. Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 3. The H atoms were all located in difference maps, but those attached to carbon atoms were repositioned geometrically. The H atoms were initially refined with soft restraints on the bond lengths and angles to regularize their geometry (C—H in the range 0.93–0.98 Å, N—H = 0.86 Å, O—H = 0.82 Å) and U_iso(H) (in the range 1.2–1.5 times U_eq of the parent atom), after which the positions were refined with riding constraints.

Table 3
Experimental details

Crystal data
Chemical formula	C₉H₉N₃O₂S
M_r	223.26
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	7.1189 (2), 10.9687 (2), 13.0678 (3)
β (°)	100.426 (2)
V (Å³)	1003.55 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.31
Crystal size (mm)	0.58 × 0.34 × 0.17

Data collection
Diffractometer	Bruker APEXII
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.88, 0.95
No. of measured, independent and observed [I > 2.0σ(I)] reflections	19600, 3818, 2447
R_int	0.000
(sin θ/λ)_max (Å⁻¹)	0.770

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.104, 0.95
No. of reflections	3810
No. of parameters	148
No. of restraints	10
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.32
Computer programs: APEX2 and SAINT (Bruker, 2006 ), SUPERFLIP (Palatinus & Chapuis, 2007 ), CRYSTALS (Betteridge et al., 2003 ) and Mercury (Macrae et al., 2020).

Supporting information

CCDC reference: 2190589

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989024000033/nx2003sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024000033/nx2003Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024000033/nx2003Isup3.mol

checkCIF report

Computing details top

{[(E)-(1,3-Benzodioxol-5-yl)methylidene]amino}thiourea top

Crystal data top

C₉H₉N₃O₂S	F(000) = 464
M_r = 223.26	D_x = 1.478 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3399 reflections
a = 7.1189 (2) Å	θ = 3.2–27.6°
b = 10.9687 (2) Å	µ = 0.31 mm⁻¹
c = 13.0678 (3) Å	T = 293 K
β = 100.426 (2)°	Tabular, colourless
V = 1003.55 (4) Å³	0.58 × 0.34 × 0.17 mm
Z = 4

Data collection top

Bruker APEXII diffractometer	2447 reflections with I > 2.0σ(I)
Graphite monochromator	R_int = 0.000
φ & ω scans	θ_max = 33.2°, θ_min = 3.2°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −10→10
T_min = 0.88, T_max = 0.95	k = −16→16
19600 measured reflections	l = −20→20
3818 independent reflections

Refinement top

Refinement on F²	Primary atom site location: other
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.040	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.104	Method = Modified Sheldrick w = 1/[σ²(F²) + ( 0.04P)² + 0.31P] , where P = (max(F_o²,0) + 2F_c²)/3
S = 0.95	(Δ/σ)_max = 0.001
3810 reflections	Δρ_max = 0.38 e Å⁻³
148 parameters	Δρ_min = −0.32 e Å⁻³
10 restraints

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

	x	y	z	U_iso*/U_eq
N1	0.4666 (2)	0.28730 (12)	0.27357 (10)	0.0521
S2	0.41135 (7)	0.51407 (3)	0.33300 (3)	0.0508
C3	0.4856 (2)	0.36798 (11)	0.35054 (10)	0.0378
O4	0.82417 (18)	−0.24246 (9)	0.43350 (9)	0.0596
N5	0.62732 (16)	0.20875 (9)	0.45653 (9)	0.0383
C6	0.70095 (19)	0.17336 (12)	0.54832 (10)	0.0392
O7	0.96272 (18)	−0.30444 (10)	0.59886 (10)	0.0619
C8	0.76809 (19)	0.04823 (12)	0.56576 (10)	0.0370
C9	0.75307 (19)	−0.03330 (11)	0.48105 (10)	0.0375
C10	0.8517 (2)	0.01062 (15)	0.66540 (11)	0.0497
C11	0.9050 (2)	−0.18475 (13)	0.60146 (12)	0.0451
C12	0.82203 (19)	−0.14781 (12)	0.50257 (11)	0.0389
N13	0.56921 (18)	0.32877 (10)	0.44507 (9)	0.0405
C14	0.9020 (3)	−0.34471 (13)	0.49501 (14)	0.0556
C15	0.9220 (3)	−0.10782 (16)	0.68462 (12)	0.0560
H61	0.7130	0.2267	0.6055	0.0484*
H91	0.6977	−0.0091	0.4133	0.0462*
H101	0.8592	0.0663	0.7228	0.0604*
H141	1.0143	−0.3736	0.4670	0.0677*
H142	0.8011	−0.4081	0.4918	0.0665*
H151	0.9779	−0.1327	0.7520	0.0688*
H12	0.395 (3)	0.3055 (15)	0.2155 (12)	0.0633 (19)*
H131	0.577 (2)	0.3758 (12)	0.4987 (10)	0.0488 (18)*
H11	0.498 (3)	0.2137 (13)	0.2878 (12)	0.0632 (19)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0787 (10)	0.0371 (6)	0.0379 (6)	0.0057 (6)	0.0032 (6)	−0.0042 (5)
S2	0.0777 (3)	0.03268 (16)	0.04106 (19)	0.00766 (16)	0.00842 (17)	0.00264 (13)
C3	0.0442 (7)	0.0321 (6)	0.0381 (6)	−0.0018 (5)	0.0103 (5)	−0.0016 (5)
O4	0.0838 (9)	0.0308 (5)	0.0576 (7)	0.0074 (5)	−0.0046 (6)	0.0013 (4)
N5	0.0428 (6)	0.0299 (5)	0.0426 (6)	0.0028 (4)	0.0086 (5)	−0.0001 (4)
C6	0.0410 (7)	0.0381 (6)	0.0392 (7)	0.0004 (5)	0.0090 (5)	−0.0018 (5)
O7	0.0703 (8)	0.0422 (6)	0.0685 (8)	0.0094 (5)	−0.0002 (6)	0.0207 (5)
C8	0.0353 (6)	0.0380 (6)	0.0376 (6)	−0.0017 (5)	0.0067 (5)	0.0040 (5)
C9	0.0385 (7)	0.0346 (6)	0.0374 (6)	−0.0010 (5)	0.0009 (5)	0.0055 (5)
C10	0.0577 (9)	0.0547 (8)	0.0353 (7)	0.0021 (7)	0.0048 (6)	0.0027 (6)
C11	0.0417 (7)	0.0405 (7)	0.0517 (8)	0.0005 (6)	0.0045 (6)	0.0161 (6)
C12	0.0386 (7)	0.0334 (6)	0.0430 (7)	−0.0029 (5)	0.0027 (5)	0.0046 (5)
N13	0.0534 (7)	0.0310 (5)	0.0362 (6)	0.0055 (5)	0.0060 (5)	−0.0031 (4)
C14	0.0565 (9)	0.0339 (7)	0.0760 (11)	0.0052 (6)	0.0107 (8)	0.0129 (7)
C15	0.0631 (10)	0.0617 (10)	0.0390 (7)	0.0037 (8)	−0.0016 (7)	0.0164 (7)

Geometric parameters (Å, º) top

N1—C3	1.3281 (17)	C8—C9	1.4120 (18)
N1—H12	0.858 (14)	C8—C10	1.3926 (19)
N1—H11	0.849 (14)	C9—C12	1.3592 (17)
S2—C3	1.6899 (13)	C9—H91	0.941
C3—N13	1.3414 (17)	C10—C15	1.399 (2)
O4—C12	1.3776 (17)	C10—H101	0.961
O4—C14	1.4318 (17)	C11—C12	1.3809 (19)
N5—C6	1.2793 (17)	C11—C15	1.364 (2)
N5—N13	1.3800 (15)	N13—H131	0.864 (13)
C6—C8	1.4576 (18)	C14—H141	0.990
C6—H61	0.941	C14—H142	0.995
O7—C11	1.3779 (18)	C15—H151	0.939
O7—C14	1.418 (2)

C3—N1—H12	118.5 (11)	C15—C10—H101	118.8
C3—N1—H11	118.8 (11)	O7—C11—C12	109.60 (14)
H12—N1—H11	120.3 (15)	O7—C11—C15	128.71 (13)
S2—C3—N1	122.87 (11)	C12—C11—C15	121.69 (13)
S2—C3—N13	120.31 (10)	C11—C12—O4	109.78 (12)
N1—C3—N13	116.82 (12)	C11—C12—C9	122.83 (13)
C12—O4—C14	105.76 (11)	O4—C12—C9	127.39 (12)
C6—N5—N13	117.07 (11)	N5—N13—C3	118.70 (11)
N5—C6—C8	119.96 (12)	N5—N13—H131	120.5 (9)
N5—C6—H61	121.3	C3—N13—H131	120.5 (9)
C8—C6—H61	118.7	O4—C14—O7	108.25 (12)
C11—O7—C14	106.25 (11)	O4—C14—H141	107.4
C6—C8—C9	119.84 (12)	O7—C14—H141	109.1
C6—C8—C10	119.85 (13)	O4—C14—H142	108.7
C9—C8—C10	120.28 (13)	O7—C14—H142	110.5
C8—C9—C12	116.73 (12)	H141—C14—H142	112.7
C8—C9—H91	121.3	C10—C15—C11	117.03 (13)
C12—C9—H91	122.0	C10—C15—H151	121.0
C8—C10—C15	121.44 (14)	C11—C15—H151	121.9
C8—C10—H101	119.7

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H11···N5	0.85 (2)	2.23 (2)	2.6034 (17)	107 (1)
N1—H11···S2ⁱ	0.85 (2)	2.84 (2)	3.4805 (14)	134 (1)
N1—H12···O4ⁱⁱ	0.86 (1)	2.32 (2)	3.112 (2)	153 (2)
N13—H131···S2ⁱⁱⁱ	0.86 (1)	2.50 (1)	3.3550 (12)	172 (1)

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

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