Crystal structure of 1-(cyclo­pentyl­idene­amino)-3-(prop-2-en-1-yl)thio­urea

Mohamed, S.K.; Mague, J.T.; Akkurt, M.; Hassan, A.A.; Abdel-Aziz, A.T.; Albayati, M.R.

doi:10.1107/S2056989015021003

organic compounds

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ISSN: 2056-9890

Volume 71| Part 12| December 2015| Pages o924-o925

https://doi.org/10.1107/S2056989015021003

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Crystal structure of 1-(cyclopentylideneamino)-3-(prop-2-en-1-yl)thiourea

Shaaban K. Mohamed,^a,^b Joel T. Mague,^c Mehmet Akkurt,^d Alaa A. Hassan,^b Ahmed T. Abdel-Aziz ^b and Mustafa R. Albayati ^e ^*

^aFaculty of Science & Engineering, School of Healthcare Science, Manchester Metropolitan University, Manchester M1 5GD, England, ^bChemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt, ^cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, ^dDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey, and ^eKirkuk University, College of Education, Department of Chemistry, Kirkuk, Iraq
^*Correspondence e-mail: shaabankamel@yahoo.com

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 3 November 2015; accepted 5 November 2015; online 11 November 2015)

In the title compound, C₉H₁₅N₃S, the cyclopentyl ring adopts an envelope conformation with one of the methylene C atoms as the flap. The thiosemicarbazide fragment is almost planar (r.m.s. deviation = 0.038 Å) and a short intramolecular N—H⋯N contact occurs. In the crystal, molecules are linked into helical (4₁ symmetry) chains propagating in [001] by N—H⋯N and N—H⋯S hydrogen bonds. A very weak C—H⋯S interaction is also observed.

Keywords: crystal structure; thiosemicarbazides; hydrogen bonding.

CCDC reference: 1435175

1. Related literature

For the biological activities of thiosemicarbazide-containing compounds, see: Hu et al. (2010 ); da Costa et al. (2015 ). For the synthesis of the title compound, see: Mague et al. (2014 ).

2. Experimental

2.1. Crystal data

C₉H₁₅N₃S
M_r = 197.30
Tetragonal, P 4₁
a = 9.0124 (2) Å
c = 12.8200 (2) Å
V = 1041.28 (5) Å³
Z = 4
Cu Kα radiation
μ = 2.42 mm⁻¹
T = 150 K
0.21 × 0.16 × 0.10 mm

2.2. Data collection

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2014 ) T_min = 0.67, T_max = 0.79
7869 measured reflections
1990 independent reflections
1901 reflections with I > 2σ(I)
R_int = 0.032

2.3. Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.109
S = 1.10
1990 reflections
119 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.70 e Å⁻³
Δρ_min = −0.18 e Å⁻³
Absolute structure: Flack x determined using 826 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter: 0.04 (3)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2C⋯N1ⁱ	0.91	2.29	3.194 (4)	177
N3—H3C⋯N1	0.91	2.25	2.642 (4)	106
N3—H3C⋯S1ⁱⁱ	0.91	2.49	3.310 (3)	151
C3—H3A⋯S1ⁱⁱⁱ	0.99	2.86	3.663 (4)	139
Symmetry codes: (i) $[-y+1, x, z+{\script{1\over 4}}]$ ; (ii) $[y, -x+1, z-{\script{1\over 4}}]$ ; (iii) $[-y, x, z+{\script{1\over 4}}]$ .

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2015a ); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b ); molecular graphics: DIAMOND (Brandenburg & Putz, 2012 ); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 ).

Supporting information

CCDC reference: 1435175

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989015021003/hb7535sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015021003/hb7535Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989015021003/hb7535Isup3.cml

checkCIF report

Comment top

The thiosemicarbazones comprise a class of molecules known for their diverse biological activities (Hu et al., 2010; Costa et al., 2015). In this context we report here the synthesis and crystal structure determination of the title compound.

In the title compound (Fig. 1), a Cremer-Pople analysis of the conformation of the 5-membered ring gave puckering parameters Q(2) = 0.380 (4) Å and φ(2) = 285.3 (6)°. The molecules pack in helical chains about the 4₁ axis assisted by an N2—H2C···N1ⁱ and an N3—H3C···S1ⁱⁱ (i: 1 - y, x, 1/4 + z; ii: y, 1 - x, -1/4 + z) hydrogen bond between each pair of adjacent molecules (Table 1 and Fig. 2).

Related literature top

For the biological activities of thiosemicarbazide-containing compounds, see: Hu et al. (2010); da Costa et al. (2015). For the synthesis of the title compound, see: Mague et al. (2014).

Experimental top

The title compound was prepared according to our recently reported method (Mague et al., 2014). Colourless blocks were grown from ethanol solution by slow evaporation. M. p. 374–375 K; 89% yield.

Structure description top

For the biological activities of thiosemicarbazide-containing compounds, see: Hu et al. (2010); da Costa et al. (2015). For the synthesis of the title compound, see: Mague et al. (2014).

Computing details top

Data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: DIAMOND (Brandenburg & Putz, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The title molecule, shown with 50% probability ellipsoids.
	Fig. 2. The packing in the title molecule, viewed down the b axis. N—H···N and N—H···S hydrogen bonds are shown, respectively, as blue and brown dotted lines.

1-(Cyclopentylideneamino)-3-(prop-2-en-1-yl)thiourea top

Crystal data top

C₉H₁₅N₃S	D_x = 1.259 Mg m⁻³
M_r = 197.30	Cu Kα radiation, λ = 1.54178 Å
Tetragonal, P4₁	Cell parameters from 7005 reflections
Hall symbol: P 4w	θ = 3.5–72.4°
a = 9.0124 (2) Å	µ = 2.42 mm⁻¹
c = 12.8200 (2) Å	T = 150 K
V = 1041.28 (5) Å³	Block, colourless
Z = 4	0.21 × 0.16 × 0.10 mm
F(000) = 424

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	1990 independent reflections
Radiation source: INCOATEC IµS micro–focus source	1901 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.032
Detector resolution: 10.4167 pixels mm^-1	θ_max = 72.4°, θ_min = 4.9°
ω scans	h = −10→11
Absorption correction: multi-scan (SADABS; Bruker, 2014)	k = −11→11
T_min = 0.67, T_max = 0.79	l = −15→15
7869 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.041	w = 1/[σ²(F_o²) + (0.0616P)² + 0.3211P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.109	(Δ/σ)_max < 0.001
S = 1.10	Δρ_max = 0.70 e Å⁻³
1990 reflections	Δρ_min = −0.18 e Å⁻³
119 parameters	Absolute structure: Flack x determined using 826 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute structure parameter: 0.04 (3)

Crystal data top

C₉H₁₅N₃S	Z = 4
M_r = 197.30	Cu Kα radiation
Tetragonal, P4₁	µ = 2.42 mm⁻¹
a = 9.0124 (2) Å	T = 150 K
c = 12.8200 (2) Å	0.21 × 0.16 × 0.10 mm
V = 1041.28 (5) Å³

Data collection top

Bruker D8 VENTURE PHOTON 100 CMOS diffractometer	1990 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2014)	1901 reflections with I > 2σ(I)
T_min = 0.67, T_max = 0.79	R_int = 0.032
7869 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	H-atom parameters constrained
wR(F²) = 0.109	Δρ_max = 0.70 e Å⁻³
S = 1.10	Δρ_min = −0.18 e Å⁻³
1990 reflections	Absolute structure: Flack x determined using 826 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
119 parameters	Absolute structure parameter: 0.04 (3)
1 restraint

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 on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs 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	0.50830 (11)	0.10489 (10)	0.51268 (7)	0.0404 (3)
N1	0.2886 (3)	0.4807 (3)	0.5217 (2)	0.0312 (8)
N2	0.3701 (3)	0.3575 (3)	0.5510 (2)	0.0325 (8)
N3	0.3362 (3)	0.2660 (3)	0.3854 (2)	0.0357 (9)
C1	0.2584 (4)	0.5764 (4)	0.5926 (3)	0.0293 (9)
C2	0.3050 (4)	0.5761 (4)	0.7060 (3)	0.0339 (10)
C3	0.2402 (4)	0.7223 (4)	0.7498 (3)	0.0362 (10)
C4	0.2242 (4)	0.8220 (4)	0.6547 (3)	0.0389 (11)
C5	0.1737 (4)	0.7160 (4)	0.5686 (3)	0.0359 (11)
C6	0.3975 (4)	0.2491 (4)	0.4790 (3)	0.0331 (10)
C7	0.3533 (5)	0.1587 (5)	0.3012 (3)	0.0430 (11)
C8	0.2503 (6)	0.0262 (6)	0.3117 (4)	0.0617 (17)
C9	0.1462 (7)	−0.0066 (7)	0.2532 (5)	0.079 (2)
H2A	0.41450	0.57460	0.71240	0.0410*
H2B	0.26350	0.48910	0.74300	0.0410*
H2C	0.41060	0.34020	0.61480	0.0390*
H3A	0.14260	0.70480	0.78310	0.0430*
H3B	0.30820	0.76700	0.80170	0.0430*
H3C	0.27400	0.34430	0.37540	0.0430*
H4A	0.32000	0.86910	0.63660	0.0470*
H4B	0.14930	0.90050	0.66700	0.0470*
H5A	0.06530	0.69880	0.57190	0.0430*
H5B	0.19970	0.75490	0.49880	0.0430*
H7A	0.45720	0.12310	0.30000	0.0520*
H7B	0.33340	0.20860	0.23380	0.0520*
H8	0.26760	−0.03810	0.36910	0.0740*
H9A	0.12420	0.05410	0.19460	0.0950*
H9B	0.08830	−0.09250	0.26690	0.0950*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0529 (6)	0.0352 (4)	0.0332 (4)	0.0076 (4)	−0.0021 (4)	−0.0046 (4)
N1	0.0366 (14)	0.0334 (13)	0.0235 (12)	−0.0002 (11)	−0.0003 (12)	0.0003 (12)
N2	0.0433 (16)	0.0325 (15)	0.0217 (12)	0.0033 (12)	−0.0040 (12)	−0.0021 (11)
N3	0.0413 (17)	0.0387 (17)	0.0272 (15)	0.0005 (12)	−0.0016 (13)	−0.0047 (12)
C1	0.0316 (16)	0.0328 (17)	0.0236 (16)	−0.0033 (13)	0.0013 (13)	0.0030 (13)
C2	0.0415 (19)	0.0357 (18)	0.0245 (17)	0.0010 (15)	−0.0038 (14)	0.0002 (13)
C3	0.0379 (18)	0.0401 (18)	0.0307 (17)	−0.0040 (14)	0.0039 (15)	−0.0051 (15)
C4	0.047 (2)	0.0338 (18)	0.036 (2)	0.0042 (15)	0.0050 (17)	−0.0026 (15)
C5	0.0389 (18)	0.0392 (19)	0.0297 (18)	0.0042 (15)	−0.0013 (14)	0.0033 (15)
C6	0.0372 (17)	0.0361 (18)	0.0260 (16)	−0.0053 (13)	0.0023 (14)	−0.0018 (13)
C7	0.044 (2)	0.055 (2)	0.0299 (17)	−0.0055 (17)	0.0020 (15)	−0.0131 (17)
C8	0.065 (3)	0.061 (3)	0.059 (3)	−0.002 (2)	0.005 (2)	−0.018 (2)
C9	0.075 (3)	0.090 (4)	0.073 (4)	−0.040 (3)	0.019 (3)	−0.028 (3)

Geometric parameters (Å, º) top

S1—C6	1.695 (4)	C8—C9	1.237 (8)
N1—N2	1.383 (4)	C2—H2A	0.9900
N1—C1	1.282 (5)	C2—H2B	0.9900
N2—C6	1.367 (5)	C3—H3A	0.9900
N3—C6	1.330 (5)	C3—H3B	0.9900
N3—C7	1.457 (5)	C4—H4A	0.9900
C1—C2	1.513 (5)	C4—H4B	0.9900
C1—C5	1.503 (5)	C5—H5A	0.9900
C2—C3	1.547 (5)	C5—H5B	0.9900
N2—H2C	0.9100	C7—H7A	0.9900
C3—C4	1.521 (5)	C7—H7B	0.9900
N3—H3C	0.9100	C8—H8	0.9500
C4—C5	1.529 (5)	C9—H9A	0.9500
C7—C8	1.519 (7)	C9—H9B	0.9500

N2—N1—C1	117.4 (3)	C2—C3—H3B	111.00
N1—N2—C6	119.1 (3)	C4—C3—H3A	111.00
C6—N3—C7	123.3 (3)	C4—C3—H3B	111.00
N1—C1—C2	128.4 (3)	H3A—C3—H3B	109.00
N1—C1—C5	121.7 (3)	C3—C4—H4A	111.00
C2—C1—C5	109.8 (3)	C3—C4—H4B	111.00
C1—C2—C3	104.0 (3)	C5—C4—H4A	111.00
N1—N2—H2C	127.00	C5—C4—H4B	111.00
C6—N2—H2C	114.00	H4A—C4—H4B	109.00
C2—C3—C4	104.4 (3)	C1—C5—H5A	111.00
C6—N3—H3C	118.00	C1—C5—H5B	111.00
C7—N3—H3C	118.00	C4—C5—H5A	111.00
C3—C4—C5	103.8 (3)	C4—C5—H5B	111.00
C1—C5—C4	102.9 (3)	H5A—C5—H5B	109.00
S1—C6—N2	118.9 (3)	N3—C7—H7A	109.00
N2—C6—N3	116.9 (3)	N3—C7—H7B	109.00
S1—C6—N3	124.2 (3)	C8—C7—H7A	109.00
N3—C7—C8	113.1 (3)	C8—C7—H7B	109.00
C7—C8—C9	126.7 (5)	H7A—C7—H7B	108.00
C1—C2—H2A	111.00	C7—C8—H8	117.00
C1—C2—H2B	111.00	C9—C8—H8	117.00
C3—C2—H2A	111.00	C8—C9—H9A	120.00
C3—C2—H2B	111.00	C8—C9—H9B	120.00
H2A—C2—H2B	109.00	H9A—C9—H9B	120.00
C2—C3—H3A	111.00

C1—N1—N2—C6	176.4 (3)	N1—C1—C2—C3	177.8 (4)
N2—N1—C1—C2	2.3 (5)	C5—C1—C2—C3	1.3 (4)
N2—N1—C1—C5	178.5 (3)	N1—C1—C5—C4	−154.9 (3)
N1—N2—C6—S1	175.4 (2)	C2—C1—C5—C4	21.9 (4)
N1—N2—C6—N3	−3.5 (5)	C1—C2—C3—C4	−24.2 (4)
C7—N3—C6—S1	2.2 (5)	C2—C3—C4—C5	38.1 (3)
C7—N3—C6—N2	−179.0 (3)	C3—C4—C5—C1	−36.6 (3)
C6—N3—C7—C8	80.2 (5)	N3—C7—C8—C9	113.4 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2C···N1ⁱ	0.91	2.29	3.194 (4)	177
N3—H3C···N1	0.91	2.25	2.642 (4)	106
N3—H3C···S1ⁱⁱ	0.91	2.49	3.310 (3)	151
C3—H3A···S1ⁱⁱⁱ	0.99	2.86	3.663 (4)	139

Symmetry codes: (i) −y+1, x, z+1/4; (ii) y, −x+1, z−1/4; (iii) −y, x, z+1/4.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2C···N1ⁱ	0.91	2.29	3.194 (4)	177
N3—H3C···N1	0.91	2.25	2.642 (4)	106
N3—H3C···S1ⁱⁱ	0.91	2.49	3.310 (3)	151
C3—H3A···S1ⁱⁱⁱ	0.99	2.86	3.663 (4)	139

Symmetry codes: (i) −y+1, x, z+1/4; (ii) y, −x+1, z−1/4; (iii) −y, x, z+1/4.

Acknowledgements

The support of NSF–MRI Grant No. 1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.

References

Brandenburg, K. & Putz, H. (2012). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2014). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Costa, P. M. da, da Costa, M. P., Carvalho, A. A., Cavalcanti, M. S., de Oliveira Cardoso, M. V., de Oliveira Filho, G. B., de Araújo Viana, D., Fechine-Jamacaru, F. V., Leite, A. C., de Moraes, M. O., Pessoa, C. & Ferreira, P. M. (2015). Chem. Biol. Interact. 239, 174–183. Web of Science PubMed Google Scholar
Hu, K., Yang, Z., Pan, S., Xu, H. & Ren, J. (2010). Eur. J. Med. Chem. 45, 3453–3458. Web of Science CrossRef CAS PubMed Google Scholar
Mague, J. T., Mohamed, S. K., Akkurt, M., Hassan, A. A. & Albayati, M. R. (2014). Acta Cryst. E70, o515. CSD CrossRef IUCr Journals Google Scholar
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar