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Acta Cryst. (2009). E65, o959    [ doi:10.1107/S1600536809011520 ]

N-(2-Chlorophenyl)-2-(4,6-dimethylpyrimidin-2-ylsulfanyl)acetamide

Q. Li, W. Wang, H. Wang, Y. Gao and H. Qiu

Abstract top

In the title compound, C14H14ClN3OS, the 4,6-dimethylpyrimidine ring and the chlorobenzene ring subtend a dihedral angle of 80.0 (2)°. The length of the Csp2-S bond is significantly shorter than that of the Csp3-S bond. The crystal structure is stabilized by intermolecular N-H...O, C-H...O and C-H...N hydrogen bonding, and C-H...[pi] interactions.

Comment top

The heteroatom-rich compounds have been intensively studied due to their applications including effective precursors for active molecule (Ye et al., 2006; Huynh et al., 2005). Now, we have synthesized the title compound, (I), from 4,6-dimethylpyrimidin-2-thiol with 2-chlorophenyl carbamic chloride. Here we report the crystal structure determination of the title compound.

The molecular structure of (I) and the atom-numbering scheme are shown in Fig. 1. The molecule contains a benzene ring and a pyrimidine ring. The dihedral angle between the benzene ring and benzo[d]thiazole ring is 80.0 (2)°, which indicate the two rings are close to be perpendicular. Cl atom attached to the benzene ring is coplanar to the benzene ring with an r.m.s deviation of 0.0130 (3) Å. The deviations with the pyrimidine ring plane of C13 and C14 atoms are 0.0544 (3) and 0.0005 (3) Å, respectively. The C6—N1—C7—C8 torsion angle of 177.61 (15)° indicates that the acylamide group are nearly coplanar with the benzene ring plane. As a result of π-π conjugation, the Csp2—S bond [S1—C9 = 1.7646 (17) Å] is significantly shorter than the Csp3—S bond [S1—C8 = 1.7947 (17) Å]. These values compare with the values of 1.772 (3) and 1.801 (2) Å reported in the literature (Gao et al., 2007).

The crystal structure is stabilized by inter molecular C—H···O and C—H···N hydrogen bonding, and C—H···π interactions (Table 1).

Related literature top

For bond-length data, see: Gao et al. (2007). For heteroatom-rich compounds as effective precursors for active molecules, see: Huynh et al. (2005); Ye et al. (2006). Cg1 is the centroid of the N2/N3/C9–C12 ring.

Experimental top

The title compound was synthesized by the reaction of from the 4,6-dimethylpyrimidin-2-thiol with 2-chlorophenyl carbamic chloride in the refluxing ethanol. Crystals of (I) suitable for single-crystal X-ray analysis were grown by slow evaporation of a solution in chloroform/acetone.

Refinement top

The H atoms attached to N atom was located in a different density map and the atomic coordinates allowed to refine freely. Other H atoms were positioned geometrically and refined as riding (C—H = 0.93–0.97 Å) and allowed to ride on their parent atoms, with Uiso(H) =1.2Ueq(parent) or 1.5Ueq(parent).

Computing details top

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 1999); cell refinement: CrystalClear (Molecular Structure Corporation & Rigaku, 1999); data reduction: CrystalClear (Molecular Structure Corporation & Rigaku, 1999); 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).

Figures top
[Figure 1] Fig. 1. View of the molecule of (I) showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 35% probability level.
N-(2-Chlorophenyl)-2-(4,6-dimethylpyrimidin-2-ylsulfanyl)acetamide top
Crystal data top
C14H14ClN3OSF(000) = 640
Mr = 307.79Dx = 1.384 Mg m−3
Orthorhombic, Pca21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2acCell parameters from 4682 reflections
a = 26.494 (5) Åθ = 1.5–27.9°
b = 4.6736 (9) ŵ = 0.40 mm−1
c = 11.931 (2) ÅT = 113 K
V = 1477.3 (5) Å3Prism, colourless
Z = 40.30 × 0.26 × 0.20 mm
Data collection top
Rigaku Saturn
diffractometer		2573 independent reflections
Radiation source: rotating anode2445 reflections with I > 2σ(I)
confocalRint = 0.031
ω scansθmax = 25.0°, θmin = 1.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −23→31
Tmin = 0.890, Tmax = 0.925k = −5→5
8870 measured reflectionsl = −14→14
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.024H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.061 w = 1/[σ2(Fo2) + (0.0391P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
2573 reflectionsΔρmax = 0.17 e Å−3
187 parametersΔρmin = −0.20 e Å−3
2 restraintsAbsolute structure: Flack (1983), 1199 Freidel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.00 (5)
Crystal data top
C14H14ClN3OSV = 1477.3 (5) Å3
Mr = 307.79Z = 4
Orthorhombic, Pca21Mo Kα radiation
a = 26.494 (5) ŵ = 0.40 mm−1
b = 4.6736 (9) ÅT = 113 K
c = 11.931 (2) Å0.30 × 0.26 × 0.20 mm
Data collection top
Rigaku Saturn
diffractometer		2445 reflections with I > 2σ(I)
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		Rint = 0.031
Tmin = 0.890, Tmax = 0.925θmax = 25.0°
8870 measured reflectionsStandard reflections: 0
2573 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.024H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.061Δρmax = 0.17 e Å−3
S = 1.07Δρmin = −0.20 e Å−3
2573 reflectionsAbsolute structure: Flack (1983), 1199 Freidel pairs
187 parametersFlack parameter: 0.00 (5)
2 restraints
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
S10.689926 (15)1.07672 (8)0.28992 (4)0.02168 (11)
Cl10.53054 (2)1.55461 (10)0.63460 (4)0.03848 (14)
O10.58637 (4)0.8871 (2)0.35668 (11)0.0216 (3)
N10.55577 (5)1.3204 (3)0.40980 (12)0.0193 (3)
N20.67886 (5)1.0007 (3)0.51049 (13)0.0216 (3)
N30.74415 (5)0.7412 (3)0.41469 (12)0.0198 (3)
C10.49282 (7)1.3208 (4)0.55761 (16)0.0250 (4)
C20.44695 (7)1.2326 (4)0.60204 (17)0.0353 (5)
H20.43611.30250.67100.042*
C30.41781 (7)1.0427 (5)0.5439 (2)0.0403 (6)
H30.38730.98160.57400.048*
C40.43334 (7)0.9406 (4)0.44072 (19)0.0350 (5)
H40.41340.81060.40170.042*
C50.47894 (6)1.0334 (4)0.39558 (18)0.0254 (4)
H50.48910.96740.32560.031*
C60.50924 (6)1.2233 (3)0.45406 (14)0.0204 (4)
C70.59151 (6)1.1465 (3)0.36648 (14)0.0171 (3)
C80.63851 (6)1.3054 (4)0.32946 (15)0.0233 (4)
H8A0.64951.42870.39010.028*
H8B0.63001.42670.26630.028*
C90.70557 (6)0.9262 (3)0.42103 (14)0.0179 (3)
C100.75680 (6)0.6156 (3)0.51203 (15)0.0201 (4)
C110.73123 (6)0.6745 (4)0.61057 (15)0.0238 (4)
H110.74000.58410.67720.029*
C120.69218 (6)0.8721 (4)0.60723 (16)0.0231 (4)
C130.80089 (7)0.4138 (4)0.50769 (18)0.0280 (4)
H13A0.80460.34120.43290.042*
H13B0.79520.25760.55840.042*
H13C0.83110.51350.52910.042*
C140.66199 (8)0.9520 (5)0.70853 (18)0.0363 (5)
H14A0.66041.15670.71460.054*
H14B0.67780.87450.77430.054*
H14C0.62850.87620.70160.054*
H10.5635 (7)1.500 (2)0.4204 (17)0.027 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.02112 (19)0.0217 (2)0.0222 (2)0.00522 (16)0.00482 (17)0.0057 (2)
Cl10.0551 (3)0.0323 (3)0.0280 (3)0.0023 (2)0.0035 (2)−0.0090 (2)
O10.0241 (6)0.0138 (6)0.0270 (7)0.0011 (5)0.0005 (5)−0.0002 (5)
N10.0224 (7)0.0105 (7)0.0249 (8)−0.0024 (5)0.0059 (6)−0.0004 (6)
N20.0201 (7)0.0226 (7)0.0221 (8)−0.0003 (6)0.0016 (6)−0.0034 (7)
N30.0188 (7)0.0180 (7)0.0224 (8)−0.0013 (5)0.0005 (6)0.0008 (6)
C10.0303 (9)0.0197 (9)0.0251 (9)0.0060 (7)0.0049 (7)0.0054 (8)
C20.0357 (11)0.0317 (10)0.0386 (12)0.0123 (8)0.0153 (9)0.0113 (9)
C30.0226 (9)0.0422 (13)0.0560 (15)0.0027 (9)0.0127 (9)0.0221 (11)
C40.0235 (10)0.0342 (11)0.0474 (14)−0.0054 (8)−0.0060 (9)0.0125 (10)
C50.0239 (9)0.0234 (9)0.0290 (10)0.0000 (7)−0.0017 (8)0.0070 (8)
C60.0206 (9)0.0163 (9)0.0243 (9)0.0042 (6)0.0028 (7)0.0052 (7)
C70.0207 (8)0.0157 (8)0.0150 (8)0.0016 (6)−0.0026 (6)0.0016 (7)
C80.0232 (8)0.0168 (8)0.0299 (10)0.0042 (7)0.0048 (7)0.0043 (7)
C90.0179 (8)0.0157 (8)0.0203 (9)−0.0031 (6)0.0001 (7)−0.0007 (7)
C100.0203 (9)0.0171 (8)0.0230 (10)−0.0046 (6)−0.0050 (7)0.0011 (7)
C110.0256 (9)0.0255 (9)0.0203 (10)−0.0056 (7)−0.0047 (7)0.0038 (8)
C120.0219 (9)0.0282 (9)0.0192 (10)−0.0072 (7)0.0004 (6)−0.0042 (8)
C130.0269 (9)0.0276 (10)0.0294 (11)0.0031 (7)−0.0037 (8)0.0038 (8)
C140.0322 (11)0.0547 (13)0.0220 (11)0.0013 (9)0.0024 (8)−0.0055 (9)
Geometric parameters (Å, °) top
S1—C91.7646 (17)C4—H40.9300
S1—C81.7947 (17)C5—C61.385 (3)
Cl1—C11.742 (2)C5—H50.9300
O1—C71.2252 (19)C7—C81.516 (2)
N1—C71.351 (2)C8—H8A0.9700
N1—C61.416 (2)C8—H8B0.9700
N1—H10.874 (9)C10—C111.385 (3)
N2—C91.327 (2)C10—C131.502 (3)
N2—C121.348 (2)C11—C121.387 (2)
N3—C91.341 (2)C11—H110.9300
N3—C101.344 (2)C12—C141.497 (3)
C1—C61.387 (2)C13—H13A0.9600
C1—C21.388 (3)C13—H13B0.9600
C2—C31.365 (3)C13—H13C0.9600
C2—H20.9300C14—H14A0.9600
C3—C41.383 (3)C14—H14B0.9600
C3—H30.9300C14—H14C0.9600
C4—C51.392 (3)
C9—S1—C8100.53 (8)S1—C8—H8A108.7
C7—N1—C6124.06 (14)C7—C8—H8B108.7
C7—N1—H1117.9 (13)S1—C8—H8B108.7
C6—N1—H1117.4 (13)H8A—C8—H8B107.6
C9—N2—C12115.58 (14)N2—C9—N3128.40 (15)
C9—N3—C10115.01 (14)N2—C9—S1118.89 (12)
C6—C1—C2121.14 (18)N3—C9—S1112.71 (12)
C6—C1—Cl1119.72 (14)N3—C10—C11121.67 (15)
C2—C1—Cl1119.13 (16)N3—C10—C13116.00 (15)
C3—C2—C1119.6 (2)C11—C10—C13122.32 (16)
C3—C2—H2120.2C10—C11—C12118.23 (16)
C1—C2—H2120.2C10—C11—H11120.9
C2—C3—C4120.55 (19)C12—C11—H11120.9
C2—C3—H3119.7N2—C12—C11121.10 (16)
C4—C3—H3119.7N2—C12—C14116.10 (16)
C3—C4—C5119.7 (2)C11—C12—C14122.79 (17)
C3—C4—H4120.2C10—C13—H13A109.5
C5—C4—H4120.2C10—C13—H13B109.5
C6—C5—C4120.50 (19)H13A—C13—H13B109.5
C6—C5—H5119.8C10—C13—H13C109.5
C4—C5—H5119.8H13A—C13—H13C109.5
C5—C6—C1118.53 (16)H13B—C13—H13C109.5
C5—C6—N1121.47 (16)C12—C14—H14A109.5
C1—C6—N1120.00 (16)C12—C14—H14B109.5
O1—C7—N1123.63 (14)H14A—C14—H14B109.5
O1—C7—C8123.26 (14)C12—C14—H14C109.5
N1—C7—C8113.10 (14)H14A—C14—H14C109.5
C7—C8—S1114.09 (12)H14B—C14—H14C109.5
C7—C8—H8A108.7
C6—C1—C2—C31.2 (3)N1—C7—C8—S1171.73 (12)
Cl1—C1—C2—C3−178.03 (15)C9—S1—C8—C7−68.05 (14)
C1—C2—C3—C4−0.8 (3)C12—N2—C9—N3−0.4 (3)
C2—C3—C4—C5−0.3 (3)C12—N2—C9—S1178.49 (12)
C3—C4—C5—C61.1 (3)C10—N3—C9—N20.4 (2)
C4—C5—C6—C1−0.7 (3)C10—N3—C9—S1−178.57 (11)
C4—C5—C6—N1179.97 (16)C8—S1—C9—N20.91 (15)
C2—C1—C6—C5−0.4 (3)C8—S1—C9—N3179.98 (11)
Cl1—C1—C6—C5178.80 (13)C9—N3—C10—C110.4 (2)
C2—C1—C6—N1178.91 (16)C9—N3—C10—C13−178.32 (14)
Cl1—C1—C6—N1−1.9 (2)N3—C10—C11—C12−1.0 (2)
C7—N1—C6—C5−48.9 (2)C13—C10—C11—C12177.59 (16)
C7—N1—C6—C1131.82 (18)C9—N2—C12—C11−0.3 (2)
C6—N1—C7—O13.2 (3)C9—N2—C12—C14−179.39 (16)
C6—N1—C7—C8−177.61 (15)C10—C11—C12—N21.0 (2)
O1—C7—C8—S1−9.1 (2)C10—C11—C12—C14179.99 (17)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.87 (1)2.05 (1)2.8414 (18)150 (2)
C2—H2···O1ii0.932.463.213 (2)138
C8—H8A···Cg1i0.972.923.832 (2)157
C13—H13B···Cg1iii0.962.993.592 (2)122
Symmetry codes: (i) x, y+1, z; (ii) −x+1, −y+2, z+1/2; (iii) x, y−1, z.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.87 (1)2.05 (1)2.8414 (18)150 (2)
C2—H2···O1ii0.932.463.213 (2)138
C8—H8A···Cg1i0.972.923.832 (2)157
C13—H13B···Cg1iii0.962.993.592 (2)122
Symmetry codes: (i) x, y+1, z; (ii) −x+1, −y+2, z+1/2; (iii) x, y−1, z.
Acknowledgements top

This project was supported by the Foundation of Liaoning Province (20071103) and the Key Laboratory Project (2008S127).

references
References top

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Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany

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