Crystal structure of 1-(cyclo-pentyl-idene-amino)-3-(prop-2-en-1-yl)thio-urea.

In the title compound, C9H15N3S, the cyclo-pentyl ring adopts an envelope conformation with one of the methyl-ene C atoms as the flap. The thio-semicarbazide fragment is almost planar (r.m.s. deviation = 0.038 Å) and a short intra-molecular N-H⋯N contact occurs. In the crystal, mol-ecules 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 inter-action is also observed.

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 ▸).

Experimental

Crystal data

C9H15N3S

M = 197.30

Tetragonal,

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

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

Refinement

R[F 2 > 2σ(F 2)] = 0.041

wR(F 2) = 0.109

S = 1.10

1990 reflections

119 parameters

1 restraint

H-atom parameters constrained

Δρmax = 0.70 e Å−3

Δρmin = −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)

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 ▸).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015021003/hb7535sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015021003/hb7535Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989015021003/hb7535Isup3.cml

Click here for additional data file.

. DOI: 10.1107/S2056989015021003/hb7535fig1.tif

The title mol­ecule, shown with 50% probability ellipsoids.

Click here for additional data file.

b . DOI: 10.1107/S2056989015021003/hb7535fig2.tif

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.

CCDC reference: 1435175

Additional supporting information: crystallographic information; 3D view; checkCIF report

C9H15N3S	Dx = 1.259 Mg m−3
Mr = 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

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	Rint = 0.032
Detector resolution: 10.4167 pixels mm-1	θmax = 72.4°, θmin = 4.9°
ω scans	h = −10→11
Absorption correction: multi-scan (SADABS; Bruker, 2014)	k = −11→11
Tmin = 0.67, Tmax = 0.79	l = −15→15
7869 measured reflections

Refinement on F2	Hydrogen site location: mixed
Least-squares matrix: full	H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.041	w = 1/[σ2(Fo2) + (0.0616P)2 + 0.3211P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.109	(Δ/σ)max < 0.001
S = 1.10	Δρmax = 0.70 e Å−3
1990 reflections	Δρmin = −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)

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.

	x	y	z	Uiso*/Ueq
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*

	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)

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)

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

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) ; (ii) ; (iii) .