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Acta Crystallogr Sect E Struct Rep Online. 2009 May 1; 65(Pt 5): o959.
Published online 2009 April 2. doi:  10.1107/S1600536809011520
PMCID: PMC2977659

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

Abstract

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 Csp 2—S bond is significantly shorter than that of the Csp 3—S bond. The crystal structure is stabilized by inter­molecular N—H(...)O, C—H(...)O and C—H(...)N hydrogen bonding, and C—H(...)π inter­actions.

Related literature

For bond-length data, see: Gao et al. (2007 [triangle]). For heteroatom-rich compounds as effective precursors for active mol­ecules, see: Huynh et al. (2005 [triangle]); Ye et al. (2006 [triangle]).

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Object name is e-65-0o959-scheme1.jpg

Experimental

Crystal data

  • C14H14ClN3OS
  • M r = 307.79
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o959-efi1.jpg
  • a = 26.494 (5) Å
  • b = 4.6736 (9) Å
  • c = 11.931 (2) Å
  • V = 1477.3 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.40 mm−1
  • T = 113 K
  • 0.30 × 0.26 × 0.20 mm

Data collection

  • Rigaku Saturn diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.890, T max = 0.925
  • 8870 measured reflections
  • 2573 independent reflections
  • 2445 reflections with I > 2σ(I)
  • R int = 0.031

Refinement

  • R[F 2 > 2σ(F 2)] = 0.024
  • wR(F 2) = 0.061
  • S = 1.07
  • 2573 reflections
  • 187 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.20 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1199 Freidel pairs
  • Flack parameter: 0.00 (5)

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 1999 [triangle]); cell refinement: CrystalClear ; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809011520/at2755sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809011520/at2755Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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).

Experimental

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

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).

Figures

Fig. 1.
View of the molecule of (I) showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 35% probability level.

Crystal data

C14H14ClN3OSF(000) = 640
Mr = 307.79Dx = 1.384 Mg m3
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 mm1
c = 11.931 (2) ÅT = 113 K
V = 1477.3 (5) Å3Prism, colourless
Z = 40.30 × 0.26 × 0.20 mm

Data collection

Rigaku Saturn diffractometer2573 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

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) = 0.061w = 1/[σ2(Fo2) + (0.0391P)2] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max = 0.001
2573 reflectionsΔρmax = 0.17 e Å3
187 parametersΔρmin = −0.20 e Å3
2 restraintsAbsolute structure: Flack (1983), 1199 Freidel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.00 (5)

Special details

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)

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)

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, °)

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, °)

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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2755).

References

  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Gao, Y., Liang, D., Gao, L.-X., Fang, G.-J. & Wang, W. (2007). Acta Cryst. E63, o4854.
  • Huynh, M. H. V., Hiskey, M. A. & Archuleta, J. G. (2005). Angew Chem. Int. Ed.44, 737–739. [PubMed]
  • Molecular Structure Corporation & Rigaku (1999). CrystalClear MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Ye, C. F., Gao, H. X. & Boatz, J. A. (2006). Angew. Chem. Int. Ed.45, 7262–7265. [PubMed]

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