organic compounds
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
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). For a related structure, see: Sultana et al. (2007).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2001); cell 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).
Supporting information
https://doi.org/10.1107/S1600536812050118/pv2612sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812050118/pv2612Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536812050118/pv2612Isup3.cml
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).
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).
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).
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).
Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 2001); cell
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).C12H9ClN4OS | Z = 2 |
Mr = 292.74 | F(000) = 300 |
Triclinic, P1 | Dx = 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 | Rint = 0.032 |
Graphite Monochromator monochromator | θmax = 27.5°, θmin = 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(Fo2) + (0.0275P)2 + 0.4951P] where P = (Fo2 + 2Fc2)/3 |
2759 reflections | (Δ/σ)max = 0.001 |
172 parameters | Δρmax = 0.29 e Å−3 |
0 restraints | Δρmin = −0.34 e Å−3 |
C12H9ClN4OS | γ = 83.979 (15)° |
Mr = 292.74 | V = 613.8 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.167 (3) Å | Mo Kα radiation |
b = 8.000 (4) Å | µ = 0.48 mm−1 |
c = 11.252 (5) Å | T = 123 K |
α = 81.625 (14)° | 0.30 × 0.26 × 0.18 mm |
β = 74.580 (12)° |
Rigaku/MSC Mercury CCD diffractometer | 2590 reflections with I > 2σ(I) |
4888 measured reflections | Rint = 0.032 |
2759 independent reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.082 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.29 e Å−3 |
2759 reflections | Δρmin = −0.34 e Å−3 |
172 parameters |
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 | Uiso*/Ueq | ||
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 |
Symmetry codes: (i) −x+1, −y+2, −z+2; (ii) x−1, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C12H9ClN4OS |
Mr | 292.74 |
Crystal system, space group | Triclinic, 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) |
V (Å3) | 613.8 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.48 |
Crystal size (mm) | 0.30 × 0.26 × 0.18 |
Data collection | |
Diffractometer | Rigaku/MSC Mercury CCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4888, 2759, 2590 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.082, 1.07 |
No. of reflections | 2759 |
No. of parameters | 172 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
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) −x+1, −y+2, −z+2; (ii) x−1, y+1, z. |
Acknowledgements
MKR is grateful to The Quaid-i-Azam University, Islamabad, for financial support of a postdoctoral fellowship.
References
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. Web of Science CrossRef CAS IUCr Journals Google Scholar
Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Google Scholar
Kabuto, C., Akine, S., Nemoto, T. & Kwon, E. (2009). J. Cryst. Soc. Jpn, 51, 218–224. CrossRef Google Scholar
Molecular Structure Corporation & Rigaku (2001). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan. Google Scholar
Rauf, M. K., Ebihara, M., Badshah, A. & Imtiaz-ud-Din, (2012). Acta Cryst. E68, o119. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sultana, S., Khawar Rauf, M., Ebihara, M. & Badshah, A. (2007). Acta Cryst. E63, o2674. Web of Science CSD CrossRef IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).