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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o959
doi:10.1107/S1600536809011520

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

Qiang Li,a Wei Wang,a* Hui Wang,b Yan Gaoa and Hong Qiua

aSchool of Chemical Engineering, University of Science and Technology, Liaoning Anshan 114051, People's Republic of China, and bHermann Gmeiner Vocational Technical College, Qiqihar University, Heilongjiang, Qiqihar 161006, People's Republic of China
*Correspondence e-mail: zhao_submit@yahoo.com.cn

(Received 26 March 2009; accepted 28 March 2009; online 2 April 2009)

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⋯π inter­actions.

Related literature

For bond-length data, see: Gao et al. (2007[Gao, Y., Liang, D., Gao, L.-X., Fang, G.-J. & Wang, W. (2007). Acta Cryst. E63, o4854.]). For heteroatom-rich compounds as effective precursors for active mol­ecules, see: Huynh et al. (2005[Huynh, M. H. V., Hiskey, M. A. & Archuleta, J. G. (2005). Angew Chem. Int. Ed. 44, 737-739.]); Ye et al. (2006[Ye, C. F., Gao, H. X. & Boatz, J. A. (2006). Angew. Chem. Int. Ed. 45, 7262-7265.]).

[Scheme 1]

Experimental

Crystal data

  • C14H14ClN3OS

  • Mr = 307.79

  • Orthorhombic, P c a 21

  • 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[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.890, Tmax = 0.925

  • 8870 measured reflections

  • 2573 independent reflections

  • 2445 reflections with I > 2σ(I)

  • Rint = 0.031
Refinement

  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1199 Freidel pairs

  • Flack parameter: 0.00 (5)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1⋯O1i 0.873 (11) 2.054 (12) 2.8414 (18) 149.6 (18)
C2—H2⋯O1ii 0.93 2.46 3.213 (2) 138
C8—H8A⋯Cg1i 0.97 2.92 3.832 (2) 157
C13—H13B⋯Cg1iii 0.96 2.99 3.592 (2) 122
Symmetry codes: (i) x, y+1, z; (ii) [-x+1, -y+2, z+{\script{1\over 2}}]; (iii) x, y-1, z. Cg1 is the centroid of the N2/N3/C9–C12 ring.

Data collection: CrystalClear (Molecular Structure Corporation & Rigaku, 1999[Molecular Structure Corporation & Rigaku (1999). CrystalClear. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear ; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information

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

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

checkCIF report


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)
Confocal monochromatorRint = 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 methodsAbsolute structure 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		2573 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		2445 reflections with I > 2σ(I)
Tmin = 0.890, Tmax = 0.925Rint = 0.031
8870 measured 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 parametersAbsolute structure 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, º) 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, º) 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.

Experimental details

Crystal data
Chemical formulaC14H14ClN3OS
Mr307.79
Crystal system, space groupOrthorhombic, Pca21
Temperature (K)113
a, b, c (Å)26.494 (5), 4.6736 (9), 11.931 (2)
V (Å3)1477.3 (5)
Z4
Radiation typeMo Kα
µ (mm−1)0.40
Crystal size (mm)0.30 × 0.26 × 0.20
Data collection
DiffractometerRigaku Saturn
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.890, 0.925
No. of measured, independent and
observed [I > 2σ(I)] reflections		8870, 2573, 2445
Rint0.031
(sin θ/λ)max (Å−1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.061, 1.07
No. of reflections2573
No. of parameters187
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.17, −0.20
Absolute structureFlack (1983), 1199 Freidel pairs
Absolute structure parameter0.00 (5)

Computer programs: CrystalClear (Molecular Structure Corporation & Rigaku, 1999), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.873 (11)2.054 (12)2.8414 (18)149.6 (18)
C2—H2···O1ii0.93002.46003.213 (2)138.00
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

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

References

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ISSN: 2056-9890
Volume 65| Part 5| May 2009| Page o959
doi:10.1107/S1600536809011520
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