Literature DB >> 23476466

1-(2-Chloro-benzo-yl)-3-(pyrimidin-2-yl)thio-urea.

M Khawar Rauf¹, Samad Yaseen, Masahiro Ebihara, Amin Badshah.

Abstract

In the title compound, C12H9ClN4OS, the carbonyl group is at a cis position with respect to the thio-urea unit. The dihedral angle between the phenyl and pyrimidine ring is 16.49 (6)°. An intra-molecular N-H⋯N hydrogen bond stabilizes the mol-ec-ular conformation. In the crystal, N-H⋯N, C-H⋯O and C-H⋯S hydrogen bonds generate chains along the bc axis.

Entities: Chemical Disease Species

Year: 2012 PMID： 23476466 PMCID： PMC3588338 DOI： 10.1107/S1600536812050118

Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN： 1600-5368

Related literature

For background to our work on structural and coordination chemistry of N,N′-disubstituted thioureas, see: Rauf et al. (2012 ▶). For a related structure, see: Sultana et al. (2007 ▶).

Experimental

Crystal data

C12H9ClN4OS M = 292.74 Triclinic, a = 7.167 (3) Å b = 8.000 (4) Å c = 11.252 (5) Å α = 81.625 (14)° β = 74.580 (12)° γ = 83.979 (15)° V = 613.8 (5) Å3 Z = 2 Mo Kα radiation μ = 0.48 mm−1 T = 123 K 0.30 × 0.26 × 0.18 mm

Data collection

Rigaku/MSC Mercury CCD diffractometer 4888 measured reflections 2759 independent reflections 2590 reflections with I > 2σ(I) R int = 0.032

Refinement

R[F 2 > 2σ(F 2)] = 0.034 wR(F 2) = 0.082 S = 1.07 2759 reflections 172 parameters H-atom parameters constrained Δρmax = 0.29 e Å−3 Δρmin = −0.34 e Å−3 Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2001 ▶); cell refinement: CrystalClear (Molecular Structure Corporation & Rigaku, 2001 ▶); data reduction: CrystalClear; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEPII (Johnson, 1976 ▶); software used to prepare material for publication: Yadokari-XG 2009 (Kabuto et al., 2009 ▶). Click here for additional data file. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812050118/pv2612sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812050118/pv2612Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S1600536812050118/pv2612Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C₁₂H₉ClN₄OS	Z = 2
M_r = 292.74	F(000) = 300
Triclinic, P1	D_x = 1.584 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71070 Å
a = 7.167 (3) Å	Cell parameters from 2102 reflections
b = 8.000 (4) Å	θ = 3.0–27.5°
c = 11.252 (5) Å	µ = 0.48 mm⁻¹
α = 81.625 (14)°	T = 123 K
β = 74.580 (12)°	Block, yellow
γ = 83.979 (15)°	0.30 × 0.26 × 0.18 mm
V = 613.8 (5) Å³

Rigaku/MSC Mercury CCD diffractometer	2590 reflections with I > 2σ(I)
Radiation source: Rotating Anode	R_int = 0.032
Graphite Monochromator monochromator	θ_max = 27.5°, θ_min = 3.0°
Detector resolution: 14.62 pixels mm^-1	h = −8→9
ω scans	k = −9→10
4888 measured reflections	l = −14→14
2759 independent reflections

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)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.082	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0275P)² + 0.4951P] where P = (F_o² + 2F_c²)/3
2759 reflections	(Δ/σ)_max = 0.001
172 parameters	Δρ_max = 0.29 e Å⁻³
0 restraints	Δρ_min = −0.34 e Å⁻³

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.

	x	y	z	U_iso*/U_eq
C1	0.5699 (2)	0.40086 (19)	0.77222 (14)	0.0168 (3)
O1	0.66497 (17)	0.29064 (14)	0.81927 (11)	0.0232 (3)
N1	0.54980 (19)	0.57016 (16)	0.79213 (12)	0.0174 (3)
H1	0.4808	0.6385	0.7489	0.021*
C2	0.6242 (2)	0.64410 (19)	0.87083 (14)	0.0167 (3)
S1	0.80674 (6)	0.56064 (5)	0.93013 (4)	0.02194 (12)
N2	0.53983 (18)	0.80178 (16)	0.89581 (12)	0.0172 (3)
H2	0.5987	0.8564	0.9362	0.021*
C3	0.4553 (2)	0.36848 (18)	0.68461 (14)	0.0160 (3)
C4	0.5267 (2)	0.25791 (19)	0.59525 (15)	0.0175 (3)
C5	0.4187 (2)	0.2281 (2)	0.51587 (15)	0.0206 (3)
H5	0.4713	0.1549	0.4540	0.025*
C6	0.2331 (2)	0.3058 (2)	0.52718 (16)	0.0225 (3)
H6	0.1586	0.2857	0.4730	0.027*
C7	0.1569 (2)	0.4122 (2)	0.61713 (16)	0.0222 (3)
H7	0.0290	0.4634	0.6260	0.027*
C8	0.2671 (2)	0.44417 (19)	0.69453 (15)	0.0190 (3)
H8	0.2141	0.5187	0.7554	0.023*
Cl1	0.75833 (5)	0.15669 (5)	0.57492 (4)	0.02521 (12)
C9	0.3753 (2)	0.88839 (19)	0.86695 (14)	0.0162 (3)
N3	0.2989 (2)	0.83057 (17)	0.78621 (13)	0.0208 (3)
C10	0.1374 (2)	0.9160 (2)	0.76400 (15)	0.0215 (3)
H10	0.0770	0.8766	0.7087	0.026*
C11	0.0568 (2)	1.0582 (2)	0.81851 (15)	0.0191 (3)
H11	−0.0576	1.1179	0.8028	0.023*
C12	0.1518 (2)	1.10993 (19)	0.89792 (15)	0.0185 (3)
H12	0.1015	1.2096	0.9356	0.022*
N4	0.31077 (18)	1.02648 (16)	0.92412 (12)	0.0169 (3)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0139 (7)	0.0176 (7)	0.0177 (7)	0.0017 (5)	−0.0021 (5)	−0.0037 (6)
O1	0.0235 (6)	0.0197 (5)	0.0287 (6)	0.0079 (4)	−0.0125 (5)	−0.0064 (5)
N1	0.0190 (6)	0.0162 (6)	0.0180 (6)	0.0043 (5)	−0.0074 (5)	−0.0039 (5)
C2	0.0149 (7)	0.0182 (7)	0.0160 (7)	0.0011 (5)	−0.0025 (5)	−0.0029 (5)
S1	0.01718 (19)	0.0234 (2)	0.0285 (2)	0.00729 (14)	−0.01126 (16)	−0.01008 (16)
N2	0.0159 (6)	0.0175 (6)	0.0198 (6)	0.0030 (5)	−0.0070 (5)	−0.0060 (5)
C3	0.0147 (7)	0.0139 (6)	0.0184 (7)	0.0000 (5)	−0.0043 (6)	0.0001 (5)
C4	0.0136 (7)	0.0165 (7)	0.0210 (7)	−0.0011 (5)	−0.0028 (6)	−0.0009 (6)
C5	0.0217 (8)	0.0207 (7)	0.0197 (7)	−0.0044 (6)	−0.0048 (6)	−0.0024 (6)
C6	0.0210 (8)	0.0240 (8)	0.0248 (8)	−0.0064 (6)	−0.0112 (6)	0.0029 (6)
C7	0.0154 (7)	0.0210 (7)	0.0298 (8)	−0.0003 (6)	−0.0085 (6)	0.0029 (6)
C8	0.0156 (7)	0.0166 (7)	0.0235 (8)	0.0009 (6)	−0.0041 (6)	−0.0010 (6)
Cl1	0.01698 (19)	0.0298 (2)	0.0311 (2)	0.00670 (15)	−0.00699 (15)	−0.01528 (17)
C9	0.0153 (7)	0.0164 (7)	0.0156 (7)	0.0008 (5)	−0.0029 (5)	−0.0011 (5)
N3	0.0226 (7)	0.0209 (6)	0.0213 (7)	0.0062 (5)	−0.0107 (5)	−0.0063 (5)
C10	0.0228 (8)	0.0230 (8)	0.0210 (8)	0.0032 (6)	−0.0113 (6)	−0.0035 (6)
C11	0.0160 (7)	0.0197 (7)	0.0202 (7)	0.0033 (6)	−0.0053 (6)	0.0001 (6)
C12	0.0165 (7)	0.0151 (7)	0.0212 (7)	0.0023 (5)	−0.0021 (6)	−0.0010 (6)
N4	0.0155 (6)	0.0157 (6)	0.0189 (6)	0.0005 (5)	−0.0036 (5)	−0.0026 (5)

C1—O1	1.2051 (19)	C6—C7	1.380 (2)
C1—N1	1.391 (2)	C6—H6	0.9500
C1—C3	1.504 (2)	C7—C8	1.386 (2)
N1—C2	1.374 (2)	C7—H7	0.9500
N1—H1	0.8800	C8—H8	0.9500
C2—N2	1.374 (2)	C9—N3	1.334 (2)
C2—S1	1.6596 (16)	C9—N4	1.338 (2)
N2—C9	1.3937 (19)	N3—C10	1.344 (2)
N2—H2	0.8800	C10—C11	1.371 (2)
C3—C4	1.395 (2)	C10—H10	0.9500
C3—C8	1.403 (2)	C11—C12	1.386 (2)
C4—C5	1.386 (2)	C11—H11	0.9500
C4—Cl1	1.7420 (17)	C12—N4	1.339 (2)
C5—C6	1.390 (2)	C12—H12	0.9500
C5—H5	0.9500

O1—C1—N1	125.24 (14)	C7—C6—H6	120.0
O1—C1—C3	122.86 (14)	C5—C6—H6	120.0
N1—C1—C3	111.90 (12)	C6—C7—C8	119.97 (15)
C2—N1—C1	128.18 (13)	C6—C7—H7	120.0
C2—N1—H1	115.9	C8—C7—H7	120.0
C1—N1—H1	115.9	C7—C8—C3	121.20 (15)
N1—C2—N2	114.75 (13)	C7—C8—H8	119.4
N1—C2—S1	125.09 (12)	C3—C8—H8	119.4
N2—C2—S1	120.12 (12)	N3—C9—N4	126.22 (14)
C2—N2—C9	129.89 (13)	N3—C9—N2	118.96 (14)
C2—N2—H2	115.1	N4—C9—N2	114.82 (13)
C9—N2—H2	115.1	C9—N3—C10	116.63 (14)
C4—C3—C8	117.63 (14)	N3—C10—C11	122.19 (15)
C4—C3—C1	122.04 (13)	N3—C10—H10	118.9
C8—C3—C1	120.26 (14)	C11—C10—H10	118.9
C5—C4—C3	121.41 (14)	C10—C11—C12	116.25 (14)
C5—C4—Cl1	117.02 (12)	C10—C11—H11	121.9
C3—C4—Cl1	121.54 (12)	C12—C11—H11	121.9
C4—C5—C6	119.70 (15)	N4—C12—C11	123.30 (14)
C4—C5—H5	120.2	N4—C12—H12	118.3
C6—C5—H5	120.2	C11—C12—H12	118.3
C7—C6—C5	120.06 (15)	C9—N4—C12	115.35 (13)

O1—C1—N1—C2	−3.0 (3)	C4—C5—C6—C7	0.0 (2)
C3—C1—N1—C2	176.24 (14)	C5—C6—C7—C8	1.3 (2)
C1—N1—C2—N2	−163.48 (14)	C6—C7—C8—C3	−0.9 (2)
C1—N1—C2—S1	18.9 (2)	C4—C3—C8—C7	−0.9 (2)
N1—C2—N2—C9	9.3 (2)	C1—C3—C8—C7	−178.10 (14)
S1—C2—N2—C9	−172.89 (13)	C2—N2—C9—N3	−12.7 (2)
O1—C1—C3—C4	−39.8 (2)	C2—N2—C9—N4	168.18 (15)
N1—C1—C3—C4	140.94 (14)	N4—C9—N3—C10	−2.7 (2)
O1—C1—C3—C8	137.32 (16)	N2—C9—N3—C10	178.32 (14)
N1—C1—C3—C8	−41.99 (19)	C9—N3—C10—C11	1.7 (2)
C8—C3—C4—C5	2.2 (2)	N3—C10—C11—C12	0.2 (2)
C1—C3—C4—C5	179.40 (14)	C10—C11—C12—N4	−1.5 (2)
C8—C3—C4—Cl1	−179.94 (11)	N3—C9—N4—C12	1.5 (2)
C1—C3—C4—Cl1	−2.8 (2)	N2—C9—N4—C12	−179.46 (13)
C3—C4—C5—C6	−1.8 (2)	C11—C12—N4—C9	0.7 (2)
Cl1—C4—C5—C6	−179.74 (12)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3	0.88	1.93	2.611 (2)	133
N2—H2···N4ⁱ	0.88	2.21	3.068 (2)	166
C11—H11···O1ⁱⁱ	0.95	2.28	3.200 (2)	163
C12—H12···S1ⁱ	0.95	2.77	3.568 (2)	142

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N3	0.88	1.93	2.611 (2)	133
N2—H2⋯N4ⁱ	0.88	2.21	3.068 (2)	166
C11—H11⋯O1ⁱⁱ	0.95	2.28	3.200 (2)	163
C12—H12⋯S1ⁱ	0.95	2.77	3.568 (2)	142

Symmetry codes: (i) ; (ii) .

2 in total

1. A short history of SHELX.

Authors: George M Sheldrick
Journal: Acta Crystallogr A Date: 2007-12-21 Impact factor: 2.290

2. 1-Benzoyl-3-(2,4,5-trichloro-phen-yl)thio-urea.

Authors: M Khawar Rauf; Masahiro Ebihara; Amin Badshah
Journal: Acta Crystallogr Sect E Struct Rep Online Date: 2011-12-14

2 in total