Crystal structure of (E)-2-[(2S,5R)-2-isopropyl-5-methyl­cyclo­hexyl­idene]hydrazine-1-carbo­thio­amide

Oliveira, A.B. de; Beck, J.; Daniels, J.; Farias, R.L. de; Godoy Netto, A.V. de

doi:10.1107/S1600536814015980

organic compounds

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ISSN: 2056-9890

Volume 70| Part 9| September 2014| Pages o903-o904

doi:10.1107/S1600536814015980

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Crystal structure of (E)-2-[(2S,5R)-2-isopropyl-5-methylcyclohexylidene]hydrazine-1-carbothioamide

Adriano Bof de Oliveira,^a ^* Johannes Beck,^b Jörg Daniels,^b Renan Lira de Farias ^a and Adelino Vieira de Godoy Netto ^c

^aDepartamento de Química, Universidade Federal de Sergipe, Av. Marechal Rondon s/n, Campus, 49100-000 São Cristóvão-SE, Brazil, ^bInstitut für Anorganische Chemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany, and ^cInstituto de Química, Universidade Estadual Paulista, Rua Francisco Degni s/n, 14801-970 Araraquara-SP, Brazil
^*Correspondence e-mail: adriano@daad-alumni.de

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 7 July 2014; accepted 8 July 2014; online 1 August 2014)

The title compound, C₁₁H₂₁N₃S, consists of a menthone moiety attached to an extended thiosemicarbazone group with the N—N—C—N torsion angle being 11.92 (16)°. The cyclohexane ring has a chair conformation and the conformation about the C=N bond is E. In the crystal, molecules are linked via pairs of N—H⋯S hydrogen bonds, forming chains along the a axis. The absolute structure could be assigned with reference to the starting material, i.e. enantiopure (−)-menthone [Flack parameter = 0.05 (5)].

Keywords: thiocarbazone; hydrogen-bonding polymer; crystal structure.

CCDC reference: 1012829

1. Related literature

For one of the first reports of the synthesis of thiosemicarbazone derivatives, see: Freund & Schander (1902 ). For a report of the anti-HIV activity of thiosemicarbazone derivatives of menthone, see: Mishra et al. (2012 ).

2. Experimental

2.1. Crystal data

C₁₁H₂₁N₃S
M_r = 227.37
Orthorhombic, P 2₁ 2₁ 2₁
a = 8.2139 (1) Å
b = 11.6117 (2) Å
c = 13.8820 (2) Å
V = 1324.03 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.22 mm⁻¹
T = 123 K
0.54 × 0.10 × 0.06 mm

2.2. Data collection

Nonius KappaCCD diffractometer
Absorption correction: analytical (Alcock, 1970 ) T_min = 0.890, T_max = 0.988
22998 measured reflections
3033 independent reflections
2848 reflections with I > 2σ(I)
R_int = 0.046

2.3. Refinement

R[F² > 2σ(F²)] = 0.025
wR(F²) = 0.060
S = 1.05
3033 reflections
220 parameters
All H-atom parameters refined
Δρ_max = 0.15 e Å⁻³
Δρ_min = −0.19 e Å⁻³
Absolute structure: Flack (1983 )
Absolute structure parameter: 0.05 (5)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—HN2⋯S1ⁱ	0.858 (17)	2.525 (18)	3.3551 (11)	163.1 (15)
N3—HN3A⋯S1ⁱⁱ	0.794 (19)	2.52 (2)	3.3104 (12)	173.0 (17)
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y-{\script{1\over 2}}, -z+1]$ ; (ii) $[x-{\script{1\over 2}}, -y-{\script{1\over 2}}, -z+1]$ .

Data collection: COLLECT (Nonius, 1998 ); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ); data reduction: DENZO (Otwinowski & Minor, 1997) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1012829

Crystal structure: contains datablocks I, publication_text. DOI: 10.1107/S1600536814015980/su2751sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814015980/su2751Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814015980/su2751Isup3.cml

checkCIF report

Structural commentary top

Several thiosemicarbazone derivatives have a wide range of pharmacological properties. For example, some thiosemicarbazone derivatives of the peppermint essential oil show anti-HIV activity (Mishra et al., 2012). As part of our studies on synthesis and structural chemistry of thiosemicarbazone derivatives of natural products, we report herein the crystal structure of (-)-3-menthone thiosemicarbazone.

In the molecular structure of the title compound, Fig, 1, the thiosemicarbazone unit is not completely planar, but shows a torsion angle N1–N2–C11–N3 of 11.92 (16)°. The cyclohexane ring of the menthone unit is in the chair conformation. The molecule, shows also a trans conformation about the N1—N2 bond.

For the synthesis, enantiopure (-)-menthone was used. No change in chirality occurred in the course of the reaction with thiosemicarbazide and the obtained product emerged as chiral crystals in the non-centrosymmetric space group P2₁2₁2₁.

In the crystal, molecules are connected by a pair of N—H···S hydrogen bonds, with bridging sulfur atoms, into a one-dimensional chain along the a-axis (Fig. 2 and Table 1).

Synthesis and crystallization top

The synthesis of the title compound was adapted from a previously reported procedure (Freund & Schander, 1902). In a hydrochloric acid catalyzed reaction, a mixture of (-)-menthone (10 mmol) and thiosemicarbazide (10 mmol) in ethanol (80 ml) was refluxed for 5 h. After cooling and filtering, the title compound was obtained. Colourless needles were obtained by slow evaporation of a solution in the solvent DMSO.

Refinement top

All the H atoms were located in a difference Fourier map and freely refined. The assignment of the correct absolute configuration was assured by the Flack parameter of 0.05 (5).

Related literature top

For one of the first reports of the synthesis of thiosemicarbazone derivatives, see: Freund & Schander (1902). For a report of the anti-HIV activity of thiosemicarbazone derivatives of menthone, see: Mishra et al. (2012).

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: 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: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. The molecular structure of the title molecule, with atom labelling. Displacement ellipsoids are drawn at the 40% probability level.
	Fig. 2. A partial view along the c-axis of the crystal structure of the title compound, showing the hydrogen bonded chains (hydrogen bonds are shown as dashed lines; see Table 1 for details).

(E)-2-[(2S,5R)-2-Isopropyl-5-methylcyclohexylidene]hydrazine-1-carbothioamide top

Crystal data top

C₁₁H₂₁N₃S	F(000) = 496
M_r = 227.37	D_x = 1.141 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 37558 reflections
a = 8.2139 (1) Å	θ = 2.9–27.5°
b = 11.6117 (2) Å	µ = 0.22 mm⁻¹
c = 13.8820 (2) Å	T = 123 K
V = 1324.03 (3) Å³	Needle, colourless
Z = 4	0.54 × 0.10 × 0.06 mm

Data collection top

Nonius KappaCCD diffractometer	3033 independent reflections
Radiation source: fine-focus sealed tube, Nonius KappaCCD	2848 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
Detector resolution: 9 pixels mm^-1	θ_max = 27.5°, θ_min = 2.9°
CCD rotation images, thick slices scans	h = −10→10
Absorption correction: analytical (Alcock, 1970)	k = −15→15
T_min = 0.890, T_max = 0.988	l = −17→18
22998 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.025	All H-atom parameters refined
wR(F²) = 0.060	w = 1/[σ²(F_o²) + (0.0305P)² + 0.1951P] where P = (F_o² + 2F_c²)/3
S = 1.05	(Δ/σ)_max = 0.001
3033 reflections	Δρ_max = 0.15 e Å⁻³
220 parameters	Δρ_min = −0.19 e Å⁻³
0 restraints	Absolute structure: Flack (1983), ???? Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.05 (5)

Crystal data top

C₁₁H₂₁N₃S	V = 1324.03 (3) Å³
M_r = 227.37	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 8.2139 (1) Å	µ = 0.22 mm⁻¹
b = 11.6117 (2) Å	T = 123 K
c = 13.8820 (2) Å	0.54 × 0.10 × 0.06 mm

Data collection top

Nonius KappaCCD diffractometer	3033 independent reflections
Absorption correction: analytical (Alcock, 1970)	2848 reflections with I > 2σ(I)
T_min = 0.890, T_max = 0.988	R_int = 0.046
22998 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.025	All H-atom parameters refined
wR(F²) = 0.060	Δρ_max = 0.15 e Å⁻³
S = 1.05	Δρ_min = −0.19 e Å⁻³
3033 reflections	Absolute structure: Flack (1983), ???? Friedel pairs
220 parameters	Absolute structure parameter: 0.05 (5)
0 restraints

Special details top

Experimental. Alcock, N. W., 1970

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

	x	y	z	U_iso*/U_eq
S1	−0.08952 (3)	−0.30315 (2)	0.48771 (2)	0.02034 (8)
N1	0.04374 (12)	0.00856 (9)	0.41416 (7)	0.0177 (2)
N2	0.04891 (13)	−0.11130 (9)	0.42555 (8)	0.0186 (2)
N3	−0.22424 (13)	−0.09979 (10)	0.45259 (9)	0.0231 (2)
C1	0.16488 (14)	0.05821 (10)	0.37313 (8)	0.0168 (2)
C2	0.16273 (15)	0.18913 (11)	0.36955 (8)	0.0192 (2)
C3	0.20800 (17)	0.23095 (11)	0.26796 (10)	0.0238 (3)
C4	0.36682 (16)	0.17718 (11)	0.23241 (11)	0.0263 (3)
C5	0.35351 (16)	0.04665 (11)	0.22932 (9)	0.0217 (3)
C6	0.31196 (15)	−0.00025 (11)	0.32996 (9)	0.0193 (2)
C7	0.00597 (17)	0.24498 (11)	0.40902 (10)	0.0244 (3)
C8	−0.14038 (18)	0.23265 (14)	0.34230 (13)	0.0337 (3)
C9	0.0343 (3)	0.37222 (13)	0.43286 (15)	0.0406 (4)
C10	0.50872 (19)	−0.00988 (14)	0.19164 (12)	0.0320 (3)
C11	−0.09004 (15)	−0.16286 (9)	0.45455 (8)	0.0166 (2)
HN2	0.139 (2)	−0.1453 (14)	0.4388 (12)	0.030 (4)*
HN3A	−0.308 (2)	−0.1263 (15)	0.4708 (13)	0.038 (5)*
HN3B	−0.214 (2)	−0.0304 (16)	0.4401 (12)	0.032 (4)*
H2	0.2510 (19)	0.2111 (14)	0.4104 (11)	0.025 (4)*
H3A	0.1221 (19)	0.2081 (13)	0.2244 (11)	0.026 (4)*
H3B	0.2167 (19)	0.3172 (14)	0.2688 (11)	0.026 (4)*
H4A	0.395 (2)	0.2061 (14)	0.1673 (12)	0.038 (4)*
H4B	0.4556 (19)	0.1942 (14)	0.2754 (11)	0.027 (4)*
H5	0.2651 (19)	0.0275 (13)	0.1881 (11)	0.022 (4)*
H6A	0.2988 (18)	−0.0818 (14)	0.3277 (11)	0.024 (4)*
H6B	0.4050 (19)	0.0163 (12)	0.3714 (10)	0.021 (3)*
H7	−0.0193 (19)	0.2058 (13)	0.4704 (11)	0.032 (4)*
H8A	−0.124 (2)	0.2778 (16)	0.2830 (13)	0.046 (5)*
H8B	−0.237 (2)	0.2586 (16)	0.3744 (12)	0.040 (5)*
H8C	−0.160 (2)	0.1543 (16)	0.3249 (12)	0.033 (4)*
H9A	−0.058 (2)	0.4100 (15)	0.4585 (12)	0.037 (5)*
H9B	0.123 (3)	0.3810 (18)	0.4819 (17)	0.067 (6)*
H9C	0.063 (2)	0.4138 (15)	0.3757 (14)	0.045 (5)*
H10A	0.606 (2)	0.0073 (14)	0.2334 (12)	0.039 (4)*
H10B	0.494 (2)	−0.0917 (18)	0.1884 (13)	0.041 (5)*
H10C	0.533 (2)	0.0126 (17)	0.1271 (15)	0.053 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01461 (12)	0.01597 (13)	0.03044 (16)	−0.00151 (11)	−0.00087 (12)	0.00710 (12)
N1	0.0187 (5)	0.0138 (5)	0.0206 (5)	−0.0008 (4)	−0.0011 (4)	0.0037 (4)
N2	0.0155 (5)	0.0140 (5)	0.0264 (6)	−0.0001 (4)	0.0001 (4)	0.0059 (4)
N3	0.0150 (5)	0.0163 (5)	0.0380 (7)	−0.0007 (4)	0.0031 (5)	0.0053 (5)
C1	0.0183 (5)	0.0171 (6)	0.0151 (5)	−0.0002 (5)	−0.0028 (5)	0.0026 (4)
C2	0.0201 (5)	0.0157 (5)	0.0217 (6)	−0.0026 (5)	−0.0036 (5)	0.0016 (5)
C3	0.0251 (6)	0.0191 (6)	0.0272 (6)	0.0005 (5)	0.0023 (6)	0.0079 (5)
C4	0.0263 (7)	0.0213 (7)	0.0314 (7)	−0.0008 (5)	0.0073 (6)	0.0095 (5)
C5	0.0219 (6)	0.0219 (6)	0.0213 (6)	−0.0003 (5)	0.0018 (5)	0.0048 (5)
C6	0.0183 (5)	0.0174 (6)	0.0223 (6)	−0.0014 (5)	0.0000 (5)	0.0053 (5)
C7	0.0301 (7)	0.0171 (6)	0.0259 (7)	0.0015 (5)	0.0053 (6)	0.0013 (5)
C8	0.0249 (7)	0.0326 (8)	0.0435 (9)	0.0071 (6)	0.0017 (6)	0.0066 (7)
C9	0.0557 (11)	0.0205 (7)	0.0455 (10)	0.0015 (7)	0.0114 (8)	−0.0055 (7)
C10	0.0324 (7)	0.0295 (8)	0.0342 (8)	0.0045 (6)	0.0108 (7)	0.0073 (6)
C11	0.0159 (5)	0.0174 (5)	0.0165 (5)	−0.0012 (5)	−0.0010 (5)	0.0007 (4)

Geometric parameters (Å, º) top

S1—C11	1.6928 (11)	C4—H4B	0.963 (16)
N1—C1	1.2833 (15)	C5—C10	1.5264 (19)
N1—N2	1.4015 (14)	C5—C6	1.5377 (17)
N2—C11	1.3502 (15)	C5—H5	0.951 (15)
N2—HN2	0.858 (17)	C6—H6A	0.954 (16)
N3—C11	1.3237 (16)	C6—H6B	0.976 (15)
N3—HN3A	0.794 (19)	C7—C8	1.524 (2)
N3—HN3B	0.829 (18)	C7—C9	1.5318 (19)
C1—C6	1.5098 (17)	C7—H7	0.988 (16)
C1—C2	1.5211 (16)	C8—H8A	0.984 (19)
C2—C3	1.5372 (17)	C8—H8B	0.961 (19)
C2—C7	1.5423 (18)	C8—H8C	0.955 (18)
C2—H2	0.955 (15)	C9—H9A	0.947 (18)
C3—C4	1.5282 (18)	C9—H9B	1.00 (2)
C3—H3A	0.966 (16)	C9—H9C	0.96 (2)
C3—H3B	1.004 (16)	C10—H10A	1.008 (19)
C4—C5	1.5202 (17)	C10—H10B	0.96 (2)
C4—H4A	0.991 (16)	C10—H10C	0.95 (2)

C1—N1—N2	118.21 (10)	C1—C6—C5	112.27 (10)
C11—N2—N1	116.64 (10)	C1—C6—H6A	111.6 (9)
C11—N2—HN2	117.4 (11)	C5—C6—H6A	110.3 (9)
N1—N2—HN2	120.5 (11)	C1—C6—H6B	107.7 (8)
C11—N3—HN3A	120.0 (13)	C5—C6—H6B	107.0 (8)
C11—N3—HN3B	117.0 (12)	H6A—C6—H6B	107.6 (12)
HN3A—N3—HN3B	122.3 (17)	C8—C7—C9	109.98 (13)
N1—C1—C6	126.49 (10)	C8—C7—C2	113.76 (11)
N1—C1—C2	117.03 (11)	C9—C7—C2	110.83 (12)
C6—C1—C2	116.47 (10)	C8—C7—H7	108.4 (9)
C1—C2—C3	110.06 (10)	C9—C7—H7	106.8 (9)
C1—C2—C7	114.73 (10)	C2—C7—H7	106.7 (9)
C3—C2—C7	113.27 (10)	C7—C8—H8A	110.6 (11)
C1—C2—H2	103.8 (10)	C7—C8—H8B	110.0 (10)
C3—C2—H2	106.1 (9)	H8A—C8—H8B	109.4 (16)
C7—C2—H2	108.1 (9)	C7—C8—H8C	112.0 (10)
C4—C3—C2	111.94 (11)	H8A—C8—H8C	108.5 (15)
C4—C3—H3A	108.0 (9)	H8B—C8—H8C	106.2 (15)
C2—C3—H3A	108.1 (9)	C7—C9—H9A	113.9 (10)
C4—C3—H3B	110.5 (9)	C7—C9—H9B	110.8 (12)
C2—C3—H3B	108.8 (9)	H9A—C9—H9B	106.3 (15)
H3A—C3—H3B	109.4 (12)	C7—C9—H9C	110.1 (10)
C5—C4—C3	110.80 (10)	H9A—C9—H9C	106.0 (15)
C5—C4—H4A	109.2 (9)	H9B—C9—H9C	109.5 (16)
C3—C4—H4A	110.8 (10)	C5—C10—H10A	112.4 (10)
C5—C4—H4B	106.1 (10)	C5—C10—H10B	109.9 (11)
C3—C4—H4B	111.2 (9)	H10A—C10—H10B	108.7 (15)
H4A—C4—H4B	108.6 (13)	C5—C10—H10C	112.4 (12)
C4—C5—C10	112.23 (11)	H10A—C10—H10C	108.5 (15)
C4—C5—C6	110.09 (10)	H10B—C10—H10C	104.6 (16)
C10—C5—C6	110.15 (11)	N3—C11—N2	116.90 (10)
C4—C5—H5	107.7 (9)	N3—C11—S1	122.69 (9)
C10—C5—H5	109.3 (9)	N2—C11—S1	120.37 (9)
C6—C5—H5	107.2 (9)

C1—N1—N2—C11	−169.70 (11)	C3—C4—C5—C6	−58.39 (15)
N2—N1—C1—C6	3.59 (18)	N1—C1—C6—C5	133.17 (12)
N2—N1—C1—C2	−174.83 (9)	C2—C1—C6—C5	−48.41 (14)
N1—C1—C2—C3	−133.96 (11)	C4—C5—C6—C1	52.25 (14)
C6—C1—C2—C3	47.46 (14)	C10—C5—C6—C1	176.53 (11)
N1—C1—C2—C7	−4.82 (15)	C1—C2—C7—C8	−73.69 (14)
C6—C1—C2—C7	176.60 (11)	C3—C2—C7—C8	53.83 (15)
C1—C2—C3—C4	−52.04 (14)	C1—C2—C7—C9	161.77 (12)
C7—C2—C3—C4	178.03 (11)	C3—C2—C7—C9	−70.71 (15)
C2—C3—C4—C5	59.56 (15)	N1—N2—C11—N3	11.92 (16)
C3—C4—C5—C10	178.54 (12)	N1—N2—C11—S1	−170.14 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—HN2···S1ⁱ	0.858 (17)	2.525 (18)	3.3551 (11)	163.1 (15)
N3—HN3A···S1ⁱⁱ	0.794 (19)	2.52 (2)	3.3104 (12)	173.0 (17)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—HN2···S1ⁱ	0.858 (17)	2.525 (18)	3.3551 (11)	163.1 (15)
N3—HN3A···S1ⁱⁱ	0.794 (19)	2.52 (2)	3.3104 (12)	173.0 (17)

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

Acknowledgements

We gratefully acknowledge financial support by FAPITEC/SE/FUNTEC/CNPq through the PPP Program 04/2011.

References

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Volume 70| Part 9| September 2014| Pages o903-o904

doi:10.1107/S1600536814015980

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

Crystal structure of (E)-2-[(2S,5R)-2-iso­propyl-5-methyl­cyclo­hexyl­­idene]hydrazine-1-carbo­thio­amide

1. Related literature

2. Experimental

2.1. Crystal data

2.2. Data collection

2.3. Refinement

Supporting information

Acknowledgements

References

organic compounds

Crystal structure of (E)-2-[(2S,5R)-2-isopropyl-5-methylcyclohexylidene]hydrazine-1-carbothioamide