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

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1-(2-Chloro­benzo­yl)-3-(pyrimidin-2-yl)thio­urea

aDepartment of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan, and bDepartment of Chemistry, Faculty of Engineering, Gifu University Yanagido, Gifu 501-1193, Japan
*Correspondence e-mail: mkhawarrauf@yahoo.co.uk,aminbadshah@yahoo.com

(Received 29 November 2012; accepted 7 December 2012; online 15 December 2012)

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

Related literature

For background to our work on structural and coordination chemistry of N,N′-disubstituted thio­ureas, see: Rauf et al. (2012[Rauf, M. K., Ebihara, M., Badshah, A. & Imtiaz-ud-Din, (2012). Acta Cryst. E68, o119.]). For a related structure, see: Sultana et al. (2007[Sultana, S., Khawar Rauf, M., Ebihara, M. & Badshah, A. (2007). Acta Cryst. E63, o2674.]).

[Scheme 1]

Experimental

Crystal data
  • C12H9ClN4OS

  • Mr = 292.74

  • Triclinic, [P \overline 1]

  • 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)

  • Rint = 0.032

Refinement
  • R[F2 > 2σ(F2)] = 0.034

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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) -x+1, -y+2, -z+2; (ii) x-1, y+1, z.

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2001[Molecular Structure Corporation & Rigaku (2001). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear (Molecular Structure Corporation & Rigaku, 2001[Molecular Structure Corporation & Rigaku (2001). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); data reduction: CrystalClear; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: Yadokari-XG 2009 (Kabuto et al., 2009[Kabuto, C., Akine, S., Nemoto, T. & Kwon, E. (2009). J. Cryst. Soc. Jpn, 51, 218-224.]).

Supporting information


Comment top

In continuation of our work on the structural and coordination chemistry of N,N'-disubstituted thioureas (Rauf et al., 2012) the structure of the title compound (Fig. 1) is described in this article. The bond lengths and angles in the title compound agree very well with the corresponding bond legths and angles reported in a closely related compound (Sultana et al., 2007). The molecule exists in its thione form with typical thiourea C—S and C—O bond distances, as well as shortened C—N bonds. The plane containing the S1, C2, N1 & N2 atoms is almost parallel to the pyrimidine ring, forming a dihedral angle of 9.09 (13)°. The molecules also feature intra & intermolecular N—H···N, C—H···O and C—H···S hydrogen bonds (Table 1 & Fig. 2).

Related literature top

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 top

Freshly prepared 2-chlorobenzoylisothiocyanate (1.98 g, 10 mmol) was dissolved in tetrahydrofuran (35 ml) and stirred for 40 minutes. Afterwards neat 2-aminopyrimidine (1.0 g, 10 mmol) was added and the resulting mixture was stirred for 1 h. The reaction mixture was then poured into acidified water and stirred well. The solid product was separated and washed with deionized water and purified by recrystallization from chloroform to give fine crystals of the title compound, with an overall yield of 92% (2.8 g).

Refinement top

All H atoms were positioned geometrically and refined using a riding model, with C—H = 0.95 and N—H = 0.88 Å, and Uiso(H) set at 1.2Ueq(C/N).

Computing details top

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2001); cell refinement: CrystalClear (Molecular Structure Corporation & Rigaku, 2001); data reduction: CrystalClear (Molecular Structure Corporation & Rigaku, 2001); 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. H atoms are presented as small spheres of arbitrary radius. Hydrogen bond is shown as a dashed line.
[Figure 2] Fig. 2. A view of the N—-H···N, C—H···O and C—H···S hydrogen bonds (dotted lines) in the crystal structure of the title compound.
1-(2-Chlorobenzoyl)-3-(pyrimidin-2-yl)thiourea top
Crystal data top
C12H9ClN4OSZ = 2
Mr = 292.74F(000) = 300
Triclinic, P1Dx = 1.584 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71070 Å
a = 7.167 (3) ÅCell parameters from 2102 reflections
b = 8.000 (4) Åθ = 3.0–27.5°
c = 11.252 (5) ŵ = 0.48 mm1
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
Data collection top
Rigaku/MSC Mercury CCD
diffractometer
2590 reflections with I > 2σ(I)
Radiation source: Rotating AnodeRint = 0.032
Graphite Monochromator monochromatorθmax = 27.5°, θmin = 3.0°
Detector resolution: 14.62 pixels mm-1h = 89
ω scansk = 910
4888 measured reflectionsl = 1414
2759 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.034Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.082H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0275P)2 + 0.4951P]
where P = (Fo2 + 2Fc2)/3
2759 reflections(Δ/σ)max = 0.001
172 parametersΔρmax = 0.29 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C12H9ClN4OSγ = 83.979 (15)°
Mr = 292.74V = 613.8 (5) Å3
Triclinic, P1Z = 2
a = 7.167 (3) ÅMo Kα radiation
b = 8.000 (4) ŵ = 0.48 mm1
c = 11.252 (5) ÅT = 123 K
α = 81.625 (14)°0.30 × 0.26 × 0.18 mm
β = 74.580 (12)°
Data collection top
Rigaku/MSC Mercury CCD
diffractometer
2590 reflections with I > 2σ(I)
4888 measured reflectionsRint = 0.032
2759 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0340 restraints
wR(F2) = 0.082H-atom parameters constrained
S = 1.07Δρmax = 0.29 e Å3
2759 reflectionsΔρmin = 0.34 e Å3
172 parameters
Special details top

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
xyzUiso*/Ueq
C10.5699 (2)0.40086 (19)0.77222 (14)0.0168 (3)
O10.66497 (17)0.29064 (14)0.81927 (11)0.0232 (3)
N10.54980 (19)0.57016 (16)0.79213 (12)0.0174 (3)
H10.48080.63850.74890.021*
C20.6242 (2)0.64410 (19)0.87083 (14)0.0167 (3)
S10.80674 (6)0.56064 (5)0.93013 (4)0.02194 (12)
N20.53983 (18)0.80178 (16)0.89581 (12)0.0172 (3)
H20.59870.85640.93620.021*
C30.4553 (2)0.36848 (18)0.68461 (14)0.0160 (3)
C40.5267 (2)0.25791 (19)0.59525 (15)0.0175 (3)
C50.4187 (2)0.2281 (2)0.51587 (15)0.0206 (3)
H50.47130.15490.45400.025*
C60.2331 (2)0.3058 (2)0.52718 (16)0.0225 (3)
H60.15860.28570.47300.027*
C70.1569 (2)0.4122 (2)0.61713 (16)0.0222 (3)
H70.02900.46340.62600.027*
C80.2671 (2)0.44417 (19)0.69453 (15)0.0190 (3)
H80.21410.51870.75540.023*
Cl10.75833 (5)0.15669 (5)0.57492 (4)0.02521 (12)
C90.3753 (2)0.88839 (19)0.86695 (14)0.0162 (3)
N30.2989 (2)0.83057 (17)0.78621 (13)0.0208 (3)
C100.1374 (2)0.9160 (2)0.76400 (15)0.0215 (3)
H100.07700.87660.70870.026*
C110.0568 (2)1.0582 (2)0.81851 (15)0.0191 (3)
H110.05761.11790.80280.023*
C120.1518 (2)1.10993 (19)0.89792 (15)0.0185 (3)
H120.10151.20960.93560.022*
N40.31077 (18)1.02648 (16)0.92412 (12)0.0169 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0139 (7)0.0176 (7)0.0177 (7)0.0017 (5)0.0021 (5)0.0037 (6)
O10.0235 (6)0.0197 (5)0.0287 (6)0.0079 (4)0.0125 (5)0.0064 (5)
N10.0190 (6)0.0162 (6)0.0180 (6)0.0043 (5)0.0074 (5)0.0039 (5)
C20.0149 (7)0.0182 (7)0.0160 (7)0.0011 (5)0.0025 (5)0.0029 (5)
S10.01718 (19)0.0234 (2)0.0285 (2)0.00729 (14)0.01126 (16)0.01008 (16)
N20.0159 (6)0.0175 (6)0.0198 (6)0.0030 (5)0.0070 (5)0.0060 (5)
C30.0147 (7)0.0139 (6)0.0184 (7)0.0000 (5)0.0043 (6)0.0001 (5)
C40.0136 (7)0.0165 (7)0.0210 (7)0.0011 (5)0.0028 (6)0.0009 (6)
C50.0217 (8)0.0207 (7)0.0197 (7)0.0044 (6)0.0048 (6)0.0024 (6)
C60.0210 (8)0.0240 (8)0.0248 (8)0.0064 (6)0.0112 (6)0.0029 (6)
C70.0154 (7)0.0210 (7)0.0298 (8)0.0003 (6)0.0085 (6)0.0029 (6)
C80.0156 (7)0.0166 (7)0.0235 (8)0.0009 (6)0.0041 (6)0.0010 (6)
Cl10.01698 (19)0.0298 (2)0.0311 (2)0.00670 (15)0.00699 (15)0.01528 (17)
C90.0153 (7)0.0164 (7)0.0156 (7)0.0008 (5)0.0029 (5)0.0011 (5)
N30.0226 (7)0.0209 (6)0.0213 (7)0.0062 (5)0.0107 (5)0.0063 (5)
C100.0228 (8)0.0230 (8)0.0210 (8)0.0032 (6)0.0113 (6)0.0035 (6)
C110.0160 (7)0.0197 (7)0.0202 (7)0.0033 (6)0.0053 (6)0.0001 (6)
C120.0165 (7)0.0151 (7)0.0212 (7)0.0023 (5)0.0021 (6)0.0010 (6)
N40.0155 (6)0.0157 (6)0.0189 (6)0.0005 (5)0.0036 (5)0.0026 (5)
Geometric parameters (Å, º) top
C1—O11.2051 (19)C6—C71.380 (2)
C1—N11.391 (2)C6—H60.9500
C1—C31.504 (2)C7—C81.386 (2)
N1—C21.374 (2)C7—H70.9500
N1—H10.8800C8—H80.9500
C2—N21.374 (2)C9—N31.334 (2)
C2—S11.6596 (16)C9—N41.338 (2)
N2—C91.3937 (19)N3—C101.344 (2)
N2—H20.8800C10—C111.371 (2)
C3—C41.395 (2)C10—H100.9500
C3—C81.403 (2)C11—C121.386 (2)
C4—C51.386 (2)C11—H110.9500
C4—Cl11.7420 (17)C12—N41.339 (2)
C5—C61.390 (2)C12—H120.9500
C5—H50.9500
O1—C1—N1125.24 (14)C7—C6—H6120.0
O1—C1—C3122.86 (14)C5—C6—H6120.0
N1—C1—C3111.90 (12)C6—C7—C8119.97 (15)
C2—N1—C1128.18 (13)C6—C7—H7120.0
C2—N1—H1115.9C8—C7—H7120.0
C1—N1—H1115.9C7—C8—C3121.20 (15)
N1—C2—N2114.75 (13)C7—C8—H8119.4
N1—C2—S1125.09 (12)C3—C8—H8119.4
N2—C2—S1120.12 (12)N3—C9—N4126.22 (14)
C2—N2—C9129.89 (13)N3—C9—N2118.96 (14)
C2—N2—H2115.1N4—C9—N2114.82 (13)
C9—N2—H2115.1C9—N3—C10116.63 (14)
C4—C3—C8117.63 (14)N3—C10—C11122.19 (15)
C4—C3—C1122.04 (13)N3—C10—H10118.9
C8—C3—C1120.26 (14)C11—C10—H10118.9
C5—C4—C3121.41 (14)C10—C11—C12116.25 (14)
C5—C4—Cl1117.02 (12)C10—C11—H11121.9
C3—C4—Cl1121.54 (12)C12—C11—H11121.9
C4—C5—C6119.70 (15)N4—C12—C11123.30 (14)
C4—C5—H5120.2N4—C12—H12118.3
C6—C5—H5120.2C11—C12—H12118.3
C7—C6—C5120.06 (15)C9—N4—C12115.35 (13)
O1—C1—N1—C23.0 (3)C4—C5—C6—C70.0 (2)
C3—C1—N1—C2176.24 (14)C5—C6—C7—C81.3 (2)
C1—N1—C2—N2163.48 (14)C6—C7—C8—C30.9 (2)
C1—N1—C2—S118.9 (2)C4—C3—C8—C70.9 (2)
N1—C2—N2—C99.3 (2)C1—C3—C8—C7178.10 (14)
S1—C2—N2—C9172.89 (13)C2—N2—C9—N312.7 (2)
O1—C1—C3—C439.8 (2)C2—N2—C9—N4168.18 (15)
N1—C1—C3—C4140.94 (14)N4—C9—N3—C102.7 (2)
O1—C1—C3—C8137.32 (16)N2—C9—N3—C10178.32 (14)
N1—C1—C3—C841.99 (19)C9—N3—C10—C111.7 (2)
C8—C3—C4—C52.2 (2)N3—C10—C11—C120.2 (2)
C1—C3—C4—C5179.40 (14)C10—C11—C12—N41.5 (2)
C8—C3—C4—Cl1179.94 (11)N3—C9—N4—C121.5 (2)
C1—C3—C4—Cl12.8 (2)N2—C9—N4—C12179.46 (13)
C3—C4—C5—C61.8 (2)C11—C12—N4—C90.7 (2)
Cl1—C4—C5—C6179.74 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N30.881.932.611 (2)133
N2—H2···N4i0.882.213.068 (2)166
C11—H11···O1ii0.952.283.200 (2)163
C12—H12···S1i0.952.773.568 (2)142
Symmetry codes: (i) x+1, y+2, z+2; (ii) x1, y+1, z.

Experimental details

Crystal data
Chemical formulaC12H9ClN4OS
Mr292.74
Crystal system, space groupTriclinic, P1
Temperature (K)123
a, b, c (Å)7.167 (3), 8.000 (4), 11.252 (5)
α, β, γ (°)81.625 (14), 74.580 (12), 83.979 (15)
V3)613.8 (5)
Z2
Radiation typeMo Kα
µ (mm1)0.48
Crystal size (mm)0.30 × 0.26 × 0.18
Data collection
DiffractometerRigaku/MSC Mercury CCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
4888, 2759, 2590
Rint0.032
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.034, 0.082, 1.07
No. of reflections2759
No. of parameters172
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.29, 0.34

Computer programs: CrystalClear (Molecular Structure Corporation & Rigaku, 2001), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), ORTEPII (Johnson, 1976), Yadokari-XG 2009 (Kabuto et al., 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···N30.881.932.611 (2)133
N2—H2···N4i0.882.213.068 (2)166
C11—H11···O1ii0.952.283.200 (2)163
C12—H12···S1i0.952.773.568 (2)142
Symmetry codes: (i) x+1, y+2, z+2; (ii) x1, y+1, z.
 

Acknowledgements

MKR is grateful to The Quaid-i-Azam University, Islamabad, for financial support of a postdoctoral fellowship.

References

First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals
First citationJohnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.
First citationKabuto, C., Akine, S., Nemoto, T. & Kwon, E. (2009). J. Cryst. Soc. Jpn, 51, 218–224.  CrossRef
First citationMolecular Structure Corporation & Rigaku (2001). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.
First citationRauf, M. K., Ebihara, M., Badshah, A. & Imtiaz-ud-Din, (2012). Acta Cryst. E68, o119.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSultana, S., Khawar Rauf, M., Ebihara, M. & Badshah, A. (2007). Acta Cryst. E63, o2674.  Web of Science CSD CrossRef IUCr Journals

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