3-Nitro-N-[(pyrrolidin-1-yl)carbothioyl]benzamide

Zulkifli, N.; Yusoff, S.F.M.; Yamin, B.M.

doi:10.1107/S1600536812021319

organic compounds

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ISSN: 2056-9890

Volume 68| Part 6| June 2012| Page o1785

doi:10.1107/S1600536812021319

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3-Nitro-N-[(pyrrolidin-1-yl)carbothioyl]benzamide

Nursakinah Zulkifli,^a Siti Fairus M. Yusoff ^a and Bohari M. Yamin ^a ^*

^aSchool of Chemical Sciences and Food Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
^*Correspondence e-mail: bohari@pkrisc.cc.ukm.my

(Received 23 April 2012; accepted 10 May 2012; online 19 May 2012)

In the molecule of the title compound, C₁₂H₁₃N₃O₃S, the pyrrolidine ring adopts a half-chair conformation and the dihedral angle formed by the nitro group with the benzene ring is 15.18 (18)°. In the crystal, molecules are linked by N—H⋯S and C—H⋯O intermolecular hydrogen bonds into chains parallel to the c axis.

Related literature

For standard bond-length data, see: Allen et al. (1987 ). For related structures, see: Emen et al. (2003 ); Kayhan et al. (2003 ).

Experimental

Crystal data

C₁₂H₁₃N₃O₃S
M_r = 279.31
Monoclinic, P 2₁ /c
a = 11.331 (3) Å
b = 13.543 (3) Å
c = 8.5982 (19) Å
β = 97.168 (5)°
V = 1309.2 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.26 mm⁻¹
T = 298 K
0.28 × 0.22 × 0.09 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.932, T_max = 0.977
7272 measured reflections
2288 independent reflections
1853 reflections with I > 2σ(I)
R_int = 0.031

Refinement

R[F² > 2σ(F²)] = 0.055
wR(F²) = 0.135
S = 1.08
2288 reflections
176 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.29 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯S1ⁱ	0.86 (2)	2.55 (2)	3.406 (3)	173
C1—H1⋯O3ⁱⁱ	0.93	2.48	3.169 (3)	131
C9—H9A⋯O3ⁱⁱ	0.97	2.32	3.274 (4)	167
Symmetry codes: (i) -x, -y+1, -z; (ii) $[x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: SMART (Siemens, 1996 ); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995 ) and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812021319/rz2750sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812021319/rz2750Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812021319/rz2750Isup3.cml

checkCIF report

Comment top

The rapid increase in the number of syntheses of thiourea derivatives is driven by their applications in various fields including biology, pharmacy and materials for devices. The title compound is a thiourea derivative analogue to N'-(4-chlorobenzoyl)-N-(pyrrolidin-1-yl)thiourea (Kayhan et al., 2003) and N'-(2-chlorobenzoyl)-N-(pyrrolidin-1-yl) (Emen et al., 2003), except for the nitro substituent attached at 3-position of the benzene ring (Fig. 1). The molecule maintains a twisted conformation, but the C8-N2-C7-O3 torsion angle of 1.6 (4)° is a little larger than that found in N'-(2-chlorobenzoyl)-N-(pyrrolidin-1-yl)thiourea (0.42 (4)°). The C7-N2-C8-N3 torsion angle of 57.9 (4)° is comparable. The pyrrolidine ring adopts a half chair conformation. The bond lengths (Allen et al., 1987) and angles are in normal ranges. In the crystal structure, the molecules are linked by N2–H2···S1, C1–H1···O3 and C9–H9A···O3 intermolecular hydrogen bonds (Table 1) to form chains parallel to the c axis (Fig. 2).

Related literature top

For standard bond-length data, see: Allen et al. (1987). For related structures, see: Emen et al. (2003); Kayhan et al. (2003).

Experimental top

An ethanolic solution (10 ml) of 3-nitrobenzoyl isothiocyanate (0.416 g, 2 mmol) was added into a beaker containing pyrrolidine (0.007 g, 1 mmol) in 10 ml ethanol. The solution was refluxed for about 1 hour and left to evaporate at room temperature. Some colourless crsytals were obtained after 3 days on slow evaporation of the solvent. M. p.: 395.3-396.5 K.

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound with 50% probability displacement ellipsoids.
	Fig. 2. Packing diagram of the title compound, viewed down a axis. Dashed lines denote hydrogen bonds.

3-Nitro-N-[(pyrrolidin-1-yl)carbothioyl]benzamide top

Crystal data top

C₁₂H₁₃N₃O₃S	F(000) = 584
M_r = 279.31	D_x = 1.417 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2210 reflections
a = 11.331 (3) Å	θ = 1.8–25.0°
b = 13.543 (3) Å	µ = 0.26 mm⁻¹
c = 8.5982 (19) Å	T = 298 K
β = 97.168 (5)°	Slab, colourless
V = 1309.2 (5) Å³	0.28 × 0.22 × 0.09 mm
Z = 4

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2288 independent reflections
Radiation source: fine-focus sealed tube	1853 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.031
Detector resolution: 83.66 pixels mm^-1	θ_max = 25.0°, θ_min = 1.8°
ω scan	h = −12→13
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	k = −15→16
T_min = 0.932, T_max = 0.977	l = −10→10
7272 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.055	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.135	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ²(F_o²) + (0.063P)² + 0.5394P] where P = (F_o² + 2F_c²)/3
2288 reflections	(Δ/σ)_max = 0.001
176 parameters	Δρ_max = 0.29 e Å⁻³
1 restraint	Δρ_min = −0.18 e Å⁻³

Crystal data top

C₁₂H₁₃N₃O₃S	V = 1309.2 (5) Å³
M_r = 279.31	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 11.331 (3) Å	µ = 0.26 mm⁻¹
b = 13.543 (3) Å	T = 298 K
c = 8.5982 (19) Å	0.28 × 0.22 × 0.09 mm
β = 97.168 (5)°

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	2288 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1853 reflections with I > 2σ(I)
T_min = 0.932, T_max = 0.977	R_int = 0.031
7272 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.055	1 restraint
wR(F²) = 0.135	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	Δρ_max = 0.29 e Å⁻³
2288 reflections	Δρ_min = −0.18 e Å⁻³
176 parameters

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. 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 > 2sigma(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	−0.14867 (6)	0.55605 (5)	0.11047 (10)	0.0524 (3)
O1	0.3720 (3)	0.6242 (2)	−0.2597 (4)	0.0925 (9)
O2	0.5564 (3)	0.6408 (2)	−0.1749 (5)	0.1230 (13)
O3	0.14150 (17)	0.70007 (17)	0.3446 (2)	0.0596 (6)
N1	0.4525 (3)	0.6311 (2)	−0.1531 (5)	0.0767 (9)
N2	0.06689 (18)	0.63530 (16)	0.1098 (3)	0.0406 (5)
H2	0.081 (2)	0.5858 (13)	0.052 (2)	0.033 (7)*
N3	−0.08644 (18)	0.74365 (16)	0.1437 (3)	0.0438 (6)
C1	0.3068 (2)	0.64030 (18)	0.0326 (3)	0.0441 (6)
H1	0.2473	0.6492	−0.0509	0.053*
C2	0.4242 (3)	0.6275 (2)	0.0067 (4)	0.0548 (8)
C3	0.5143 (3)	0.6127 (2)	0.1286 (6)	0.0714 (11)
H3	0.5926	0.6047	0.1090	0.086*
C4	0.4858 (3)	0.6101 (3)	0.2790 (5)	0.0748 (11)
H4	0.5450	0.5984	0.3621	0.090*
C5	0.3705 (3)	0.6245 (2)	0.3079 (4)	0.0590 (8)
H5	0.3525	0.6242	0.4105	0.071*
C6	0.2803 (2)	0.63954 (18)	0.1845 (3)	0.0424 (6)
C7	0.1583 (2)	0.6614 (2)	0.2225 (3)	0.0425 (6)
C8	−0.0541 (2)	0.6519 (2)	0.1237 (3)	0.0395 (6)
C9	−0.0126 (3)	0.8336 (2)	0.1380 (4)	0.0558 (8)
H9A	0.0442	0.8261	0.0632	0.067*
H9B	0.0300	0.8485	0.2403	0.067*
C10	−0.1021 (3)	0.9124 (2)	0.0867 (4)	0.0656 (9)
H10A	−0.1185	0.9147	−0.0267	0.079*
H10B	−0.0738	0.9766	0.1249	0.079*
C11	−0.2110 (3)	0.8824 (2)	0.1583 (5)	0.0689 (9)
H11A	−0.2822	0.9090	0.0986	0.083*
H11B	−0.2066	0.9057	0.2656	0.083*
C12	−0.2117 (2)	0.7707 (2)	0.1528 (4)	0.0538 (8)
H12A	−0.2389	0.7434	0.2464	0.065*
H12B	−0.2629	0.7470	0.0616	0.065*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0347 (4)	0.0467 (4)	0.0771 (5)	−0.0080 (3)	0.0118 (3)	−0.0127 (4)
O1	0.106 (2)	0.100 (2)	0.0814 (19)	0.0194 (18)	0.0502 (17)	0.0123 (16)
O2	0.0760 (19)	0.122 (3)	0.189 (3)	0.0111 (17)	0.087 (2)	0.025 (2)
O3	0.0555 (13)	0.0768 (15)	0.0467 (12)	−0.0099 (10)	0.0069 (9)	−0.0160 (11)
N1	0.071 (2)	0.0548 (18)	0.114 (3)	0.0126 (15)	0.049 (2)	0.0172 (18)
N2	0.0311 (11)	0.0445 (13)	0.0471 (13)	−0.0040 (9)	0.0085 (9)	−0.0134 (10)
N3	0.0360 (12)	0.0451 (14)	0.0528 (14)	−0.0040 (9)	0.0145 (10)	−0.0083 (10)
C1	0.0323 (14)	0.0362 (15)	0.0641 (18)	−0.0005 (10)	0.0063 (12)	0.0047 (12)
C2	0.0433 (16)	0.0350 (15)	0.089 (2)	0.0002 (12)	0.0211 (16)	0.0048 (14)
C3	0.0308 (16)	0.0484 (19)	0.133 (4)	−0.0002 (13)	0.0038 (19)	−0.002 (2)
C4	0.0444 (19)	0.064 (2)	0.107 (3)	0.0044 (15)	−0.024 (2)	−0.006 (2)
C5	0.0539 (19)	0.0505 (18)	0.068 (2)	−0.0036 (14)	−0.0102 (15)	−0.0012 (15)
C6	0.0342 (14)	0.0356 (14)	0.0564 (17)	−0.0062 (10)	0.0016 (12)	−0.0010 (12)
C7	0.0398 (15)	0.0446 (15)	0.0429 (15)	−0.0078 (11)	0.0043 (12)	−0.0012 (12)
C8	0.0352 (13)	0.0474 (16)	0.0371 (13)	−0.0036 (11)	0.0091 (11)	−0.0051 (11)
C9	0.0541 (17)	0.0458 (17)	0.072 (2)	−0.0091 (14)	0.0265 (15)	−0.0099 (14)
C10	0.073 (2)	0.0493 (19)	0.077 (2)	−0.0027 (16)	0.0178 (18)	−0.0002 (16)
C11	0.065 (2)	0.056 (2)	0.089 (2)	0.0099 (16)	0.0211 (19)	−0.0054 (17)
C12	0.0409 (16)	0.0567 (19)	0.0661 (19)	0.0028 (13)	0.0155 (14)	−0.0051 (14)

Geometric parameters (Å, º) top

S1—C8	1.678 (3)	C4—C5	1.374 (5)
O1—N1	1.213 (4)	C4—H4	0.9300
O2—N1	1.222 (4)	C5—C6	1.393 (4)
O3—C7	1.209 (3)	C5—H5	0.9300
N1—C2	1.450 (5)	C6—C7	1.489 (4)
N2—C7	1.374 (3)	C9—C10	1.499 (4)
N2—C8	1.409 (3)	C9—H9A	0.9700
N2—H2	0.863 (10)	C9—H9B	0.9700
N3—C8	1.313 (3)	C10—C11	1.503 (5)
N3—C12	1.477 (3)	C10—H10A	0.9700
N3—C9	1.482 (3)	C10—H10B	0.9700
C1—C6	1.377 (4)	C11—C12	1.513 (4)
C1—C2	1.386 (4)	C11—H11A	0.9700
C1—H1	0.9300	C11—H11B	0.9700
C2—C3	1.384 (5)	C12—H12A	0.9700
C3—C4	1.372 (5)	C12—H12B	0.9700
C3—H3	0.9300

O1—N1—O2	122.7 (4)	N2—C7—C6	115.7 (2)
O1—N1—C2	118.6 (3)	N3—C8—N2	116.9 (2)
O2—N1—C2	118.7 (4)	N3—C8—S1	123.67 (19)
C7—N2—C8	123.7 (2)	N2—C8—S1	119.4 (2)
C7—N2—H2	115.4 (16)	N3—C9—C10	103.3 (2)
C8—N2—H2	115.3 (16)	N3—C9—H9A	111.1
C8—N3—C12	121.9 (2)	C10—C9—H9A	111.1
C8—N3—C9	127.3 (2)	N3—C9—H9B	111.1
C12—N3—C9	110.3 (2)	C10—C9—H9B	111.1
C6—C1—C2	118.6 (3)	H9A—C9—H9B	109.1
C6—C1—H1	120.7	C9—C10—C11	104.3 (3)
C2—C1—H1	120.7	C9—C10—H10A	110.9
C3—C2—C1	121.9 (3)	C11—C10—H10A	110.9
C3—C2—N1	119.5 (3)	C9—C10—H10B	110.9
C1—C2—N1	118.6 (3)	C11—C10—H10B	110.9
C4—C3—C2	118.7 (3)	H10A—C10—H10B	108.9
C4—C3—H3	120.7	C10—C11—C12	105.0 (2)
C2—C3—H3	120.7	C10—C11—H11A	110.8
C3—C4—C5	120.5 (3)	C12—C11—H11A	110.8
C3—C4—H4	119.8	C10—C11—H11B	110.8
C5—C4—H4	119.8	C12—C11—H11B	110.8
C4—C5—C6	120.5 (3)	H11A—C11—H11B	108.8
C4—C5—H5	119.8	N3—C12—C11	104.4 (2)
C6—C5—H5	119.8	N3—C12—H12A	110.9
C1—C6—C5	119.8 (3)	C11—C12—H12A	110.9
C1—C6—C7	121.7 (2)	N3—C12—H12B	110.9
C5—C6—C7	118.4 (3)	C11—C12—H12B	110.9
O3—C7—N2	122.5 (2)	H12A—C12—H12B	108.9
O3—C7—C6	121.8 (2)

C6—C1—C2—C3	0.9 (4)	C5—C6—C7—O3	26.7 (4)
C6—C1—C2—N1	−178.3 (2)	C1—C6—C7—N2	30.6 (4)
O1—N1—C2—C3	165.5 (3)	C5—C6—C7—N2	−153.7 (2)
O2—N1—C2—C3	−14.5 (4)	C12—N3—C8—N2	177.3 (2)
O1—N1—C2—C1	−15.3 (4)	C9—N3—C8—N2	6.5 (4)
O2—N1—C2—C1	164.7 (3)	C12—N3—C8—S1	−1.5 (4)
C1—C2—C3—C4	0.5 (5)	C9—N3—C8—S1	−172.2 (2)
N1—C2—C3—C4	179.7 (3)	C7—N2—C8—N3	58.4 (4)
C2—C3—C4—C5	−1.7 (5)	C7—N2—C8—S1	−122.9 (2)
C3—C4—C5—C6	1.6 (5)	C8—N3—C9—C10	152.1 (3)
C2—C1—C6—C5	−1.0 (4)	C12—N3—C9—C10	−19.5 (3)
C2—C1—C6—C7	174.7 (2)	N3—C9—C10—C11	33.2 (3)
C4—C5—C6—C1	−0.2 (4)	C9—C10—C11—C12	−35.2 (4)
C4—C5—C6—C7	−176.1 (3)	C8—N3—C12—C11	−174.1 (3)
C8—N2—C7—O3	0.9 (4)	C9—N3—C12—C11	−2.0 (3)
C8—N2—C7—C6	−178.8 (2)	C10—C11—C12—N3	22.8 (4)
C1—C6—C7—O3	−149.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···S1ⁱ	0.86 (2)	2.55 (2)	3.406 (3)	173
C1—H1···O3ⁱⁱ	0.93	2.48	3.169 (3)	131
C9—H9A···O3ⁱⁱ	0.97	2.32	3.274 (4)	167

Symmetry codes: (i) −x, −y+1, −z; (ii) x, −y+3/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₃N₃O₃S
M_r	279.31
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	11.331 (3), 13.543 (3), 8.5982 (19)
β (°)	97.168 (5)
V (Å³)	1309.2 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.26
Crystal size (mm)	0.28 × 0.22 × 0.09

Data collection
Diffractometer	Bruker SMART APEX CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.932, 0.977
No. of measured, independent and observed [I > 2σ(I)] reflections	7272, 2288, 1853
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.055, 0.135, 1.08
No. of reflections	2288
No. of parameters	176
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.29, −0.18

Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···S1ⁱ	0.861 (18)	2.549 (18)	3.406 (3)	173
C1—H1···O3ⁱⁱ	0.93	2.48	3.169 (3)	131
C9—H9A···O3ⁱⁱ	0.97	2.32	3.274 (4)	167

Symmetry codes: (i) −x, −y+1, −z; (ii) x, −y+3/2, z−1/2.

Acknowledgements

The authors thank the Malaysian Government and Universiti Kebangsaan Malaysia for the research grant No. UKM-GUP-NBT-68-27-110.

References

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