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ISSN: 2056-9890

4-(4-Chloro­phen­yl)-6-(methyl­sulfan­yl)pyrimidin-2-amine

aSchool of Chemical Science and Technology, Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education, Yunnan University, Kunming 650091, People's Republic of China
*Correspondence e-mail: qhzhao@ynu.edu.cn

(Received 10 June 2009; accepted 28 June 2009; online 8 July 2009)

In the title compound, C11H10ClN3S, the dihedral angle between the benzene and pyrimidine rings is 3.99 (4)°. In the crystal, inter­molecular N—H⋯N hydrogen bonds link the mol­ecules into ribbons of R22(8) rings parallel to [100]. Weak C—H⋯S contacts connect adjacent ribbons into a two-dimensional undulating layer-like structure extending parallel to (110). The benzene and pyrimidine rings of adjacent mol­ecules have the offset face-to-face ππ stacking inter­actions in a zigzag fashion along the c axis, with perpendicular ring distances of 3.463 and 3.639 Å, and a dihedral angle between the planes of 3.99 (2)°. The distance between the ring centroids is 4.420 (2) Å.

Related literature

For the synthesis of pyrimidine-5-carbaldehydes from α-formyl­aroylketene dithio­acetals, see: Mathews & Asokan (2007[Mathews, A. & Asokan, C. V. (2007). Tetrahedron, 63, 7845-7849.]). For the synthesis of a 6-aryl amino­pyrimidine compound, see: Lin et al. (2008[Lin, J., Liu, Y.-J., Yan, S.-J., Niu, Y.-F., Zheng, H. & Huang, R. (2008). CN Patent No. 101302203A.]). For the application of organic compounds as ligands, see: Li et al. (2007[Li, S.-L., Liu, J. & Ma, J.-F. (2007). Acta Cryst. E63, o4509.]). For the importance amino­pyrimidine compounds in the synthesis of complexes, see: Cui & Lan (2007[Cui, R.-H. & Lan, Y.-Q. (2007). Acta Cryst. E63, o4515.]). For a review of inter­molecular C—H⋯S contacts, see: Taylor & Kennard (1982[Taylor, R. & Kennard, O. (1982). J. Am. Chem. Soc. 104, 5063-5070.]). For graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C11H10ClN3S

  • Mr = 251.73

  • Orthorhombic, P 21 21 21

  • a = 6.8148 (11) Å

  • b = 10.6107 (16) Å

  • c = 16.509 (3) Å

  • V = 1193.7 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.47 mm−1

  • T = 293 K

  • 0.25 × 0.14 × 0.08 mm

Data collection
  • Bruker APEXII 1K CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.925, Tmax = 0.964

  • 7825 measured reflections

  • 2800 independent reflections

  • 1841 reflections with I > 2σ(I)

  • Rint = 0.050

Refinement
  • R[F2 > 2σ(F2)] = 0.049

  • wR(F2) = 0.096

  • S = 1.01

  • 2800 reflections

  • 145 parameters

  • H-atom parameters constrained

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.20 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 1061 Friedel pairs

  • Flack parameter: 0.02 (10)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3A⋯N2i 0.86 2.31 3.095 (3) 152
N3—H3B⋯N1ii 0.86 2.21 3.045 (3) 164
C11—H11A⋯S1iii 0.96 2.93 3.859 (4) 163
Symmetry codes: (i) [x+{\script{1\over 2}}, -y+{\script{5\over 2}}, -z+2]; (ii) [x-{\script{1\over 2}}, -y+{\script{5\over 2}}, -z+2]; (iii) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2].

Data collection: APEX2 (Bruker, 2004[Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2004[Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

In recent years, aminopyrimidine compounds have shown predominant bioactivity and played an important role in the drug synthesis (Mathews & Asokan, 2007). Meanwhile, these organic compounds can be used as new organic N-donor ligands, which can construct a wide range of coordination polymers with novel architectures and special properties. The selection and synthesis of proper ligands are the most important tasks (Li et al., 2007; Cui & Lan, 2007). Herein, the crystal structure of the title compound is reported. Its synthetic method followed the procedure given by Lin et al., (2008).

In the title compound (Fig. 1), all atoms are almost in the same plane and the largest distortion from the mean plane being 0.3127Å for C11, atoms S1 and Cl1 being 0.1338 (6) and 0.1251 (5) Å out-of-plane. The two aromatic rings of the molecule make a dihedral angle of 3.99 (4)°.

In the crystal structure, there are two kinds of hydrogen bonds. One group is N3—H3A···N2, N3—H3B···N1, and the other is C11—H11A···S1 (Fig. 2 and Table 1). The strong intermolecular N—H···N hydrogen bonds link the molecules into ribbons of R22(8) rings (Bernstein et al. 1995) parallel to [1 0 0]. The weak intermolecular C—H···S contacts connect the adjacent ribbons into a two-dimensional waved layer-like structure extending parallel to (1 1 0). Similar geometric parameters (H···S = 2.916 Å, angle C—H···S = 164<%) were discussed for a possible intermolecular C—H···S contact by Taylor & Kennard (1982). The phenyl and pyrimidine rings of adjacent molecules exhibit ππ stacking interactions in a zig-zag fashion along the c axis with perpendicular ring distances of 3.463 Å and 3.639 Å, and the dihedral angle α being 3.99°. The distance between the ring centroids Cg1···Cg2iv amounts to 4.420 (2) Å. Cg1 and Cg2 represent the centroids of the pyrimidine and phenyl rings. The symmetry code: (iv = -1 + x, y, z). The intermolecular forces construct a three-dimensional supramolecular architecture in the crystal.

Related literature top

For the synthesis of pyrimidine-5-carbaldehydes from α-formylaroylketene dithioacetals, see: Mathews & Asokan (2007). For the synthetic method of a 6-aryl aminopyrimidine compound, see: Lin et al. (2008). For the application of organic compounds as ligands, see: Li et al. (2007). For the importance aminopyrimidine compounds in the synthesis of complexes, see: Cui & Lan (2007). For a review of intermolecular C—H···S contacts, see: Taylor & Kennard (1982). For graph-set notation, see: Bernstein et al. (1995).

Experimental top

All chemicals used were commercially available. We first got the title compound using the reported method (Lin et al., 2008). After that 1 mmol (0.025 g) 4-(4-Chlorophenyl)-6-(methylthio)pyrimidin-2-amine was dissolved in a mixture of 15 ml methyl cyanide and 5 ml water. Then the solution was stirred for 40 min at room temperature. The solvent was removed gradually for a few weeks and faint yellow crystals for X-ray data collection were obtained by the slow evaporation method.

Refinement top

H atoms bonded to C and N atoms were calculated geometrically and allowed to ride on the C and N atoms with distance restraints of C—H = 0.93 Å and N—H = 0.86 Å, with Uiso(H) = 1.2Ueq(C, N).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); 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) and PLATON (Spek, 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 30% probability level.
[Figure 2] Fig. 2. The crystal packing diagram of the title compound, showing hydrogen bonds along the ab plane.
4-(4-Chlorophenyl)-6-(methylsulfanyl)pyrimidin-2-amine top
Crystal data top
C11H10ClN3SF(000) = 520
Mr = 251.73Dx = 1.401 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3984 reflections
a = 6.8148 (11) Åθ = 2.3–28.4°
b = 10.6107 (16) ŵ = 0.47 mm1
c = 16.509 (3) ÅT = 293 K
V = 1193.7 (3) Å3Block, yellow
Z = 40.25 × 0.14 × 0.08 mm
Data collection top
Bruker APEXII 1K CCD area-detector
diffractometer
2800 independent reflections
Radiation source: fine-focus sealed tube1841 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.050
ϕ and ω scansθmax = 28.4°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 88
Tmin = 0.925, Tmax = 0.964k = 1311
7825 measured reflectionsl = 2122
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)] = 0.049H-atom parameters constrained
wR(F2) = 0.096 w = 1/[σ2(Fo2) + (0.036P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
2800 reflectionsΔρmax = 0.19 e Å3
145 parametersΔρmin = 0.20 e Å3
0 restraintsAbsolute structure: Flack (1983), 1061 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (10)
Crystal data top
C11H10ClN3SV = 1193.7 (3) Å3
Mr = 251.73Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 6.8148 (11) ŵ = 0.47 mm1
b = 10.6107 (16) ÅT = 293 K
c = 16.509 (3) Å0.25 × 0.14 × 0.08 mm
Data collection top
Bruker APEXII 1K CCD area-detector
diffractometer
2800 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1841 reflections with I > 2σ(I)
Tmin = 0.925, Tmax = 0.964Rint = 0.050
7825 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.049H-atom parameters constrained
wR(F2) = 0.096Δρmax = 0.19 e Å3
S = 1.01Δρmin = 0.20 e Å3
2800 reflectionsAbsolute structure: Flack (1983), 1061 Friedel pairs
145 parametersAbsolute structure parameter: 0.02 (10)
0 restraints
Special details top

Experimental. 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.

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 F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > σ(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ 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
Cl11.15208 (14)1.01534 (10)0.62970 (5)0.0694 (3)
S10.01688 (13)0.85410 (8)0.91781 (5)0.0522 (2)
N10.4426 (3)1.1541 (2)0.89640 (13)0.0357 (6)
N20.1442 (4)1.0763 (2)0.95722 (13)0.0338 (6)
N30.2824 (4)1.2627 (2)0.99649 (16)0.0423 (6)
H3A0.37131.32010.99310.051*
H3B0.18801.27081.03070.051*
C10.9466 (5)1.0272 (3)0.69138 (17)0.0454 (8)
C20.8052 (5)0.9354 (3)0.68825 (18)0.0508 (9)
H2B0.81860.86820.65260.061*
C30.6427 (5)0.9430 (3)0.73817 (19)0.0473 (8)
H3C0.54740.88030.73590.057*
C40.6197 (4)1.0437 (3)0.79209 (16)0.0359 (7)
C50.7638 (5)1.1359 (3)0.79272 (17)0.0427 (8)
H5A0.75021.20440.82740.051*
C60.9275 (5)1.1292 (3)0.74324 (18)0.0484 (9)
H6A1.02281.19190.74480.058*
C70.4499 (4)1.0503 (3)0.84876 (16)0.0343 (7)
C80.3107 (5)0.9576 (3)0.85466 (18)0.0438 (8)
H8A0.31710.88590.82240.053*
C90.1589 (4)0.9737 (3)0.91043 (17)0.0366 (7)
C100.2911 (4)1.1611 (3)0.94864 (16)0.0333 (7)
C110.1656 (6)0.9020 (4)1.0015 (2)0.0811 (13)
H11A0.26740.84101.01020.122*
H11B0.22350.98260.99000.122*
H11C0.08580.90831.04930.122*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0647 (6)0.0800 (7)0.0634 (6)0.0144 (6)0.0276 (5)0.0046 (5)
S10.0488 (5)0.0391 (4)0.0686 (5)0.0083 (5)0.0010 (5)0.0064 (5)
N10.0339 (13)0.0370 (14)0.0361 (13)0.0013 (12)0.0010 (10)0.0044 (12)
N20.0334 (13)0.0344 (14)0.0336 (13)0.0003 (12)0.0039 (11)0.0010 (12)
N30.0381 (16)0.0411 (16)0.0476 (14)0.0054 (12)0.0095 (13)0.0139 (13)
C10.048 (2)0.053 (2)0.0349 (16)0.0154 (18)0.0071 (15)0.0003 (16)
C20.056 (2)0.049 (2)0.0468 (19)0.0101 (18)0.0025 (18)0.0163 (17)
C30.045 (2)0.046 (2)0.0516 (19)0.0008 (17)0.0012 (17)0.0137 (17)
C40.0367 (18)0.0368 (18)0.0344 (15)0.0061 (14)0.0056 (13)0.0035 (14)
C50.0501 (19)0.0398 (19)0.0381 (17)0.0023 (18)0.0065 (15)0.0044 (16)
C60.051 (2)0.049 (2)0.0446 (18)0.0049 (17)0.0095 (16)0.0024 (17)
C70.0310 (17)0.0373 (18)0.0347 (15)0.0058 (14)0.0033 (12)0.0044 (14)
C80.044 (2)0.0382 (19)0.0489 (19)0.0005 (16)0.0015 (15)0.0105 (15)
C90.0346 (16)0.0341 (17)0.0411 (16)0.0000 (14)0.0101 (15)0.0027 (15)
C100.0319 (16)0.0346 (18)0.0334 (15)0.0036 (14)0.0043 (12)0.0021 (14)
C110.077 (3)0.065 (3)0.101 (3)0.021 (2)0.037 (3)0.001 (2)
Geometric parameters (Å, º) top
Cl1—C11.736 (3)C3—C41.400 (4)
S1—C91.750 (3)C3—H3C0.9300
S1—C111.788 (4)C4—C51.387 (4)
N1—C101.347 (3)C4—C71.490 (4)
N1—C71.354 (3)C5—C61.384 (4)
N2—C91.339 (3)C5—H5A0.9300
N2—C101.353 (4)C6—H6A0.9300
N3—C101.338 (4)C7—C81.370 (4)
N3—H3A0.8600C8—C91.395 (4)
N3—H3B0.8600C8—H8A0.9300
C1—C21.371 (5)C11—H11A0.9600
C1—C61.386 (4)C11—H11B0.9600
C2—C31.383 (4)C11—H11C0.9600
C2—H2B0.9300
C9—S1—C11103.63 (16)C5—C6—C1118.7 (3)
C10—N1—C7116.4 (2)C5—C6—H6A120.6
C9—N2—C10115.1 (2)C1—C6—H6A120.6
C10—N3—H3A120.0N1—C7—C8121.1 (3)
C10—N3—H3B120.0N1—C7—C4115.6 (2)
H3A—N3—H3B120.0C8—C7—C4123.3 (3)
C2—C1—C6120.8 (3)C7—C8—C9118.2 (3)
C2—C1—Cl1119.6 (3)C7—C8—H8A120.9
C6—C1—Cl1119.7 (3)C9—C8—H8A120.9
C1—C2—C3120.0 (3)N2—C9—C8122.4 (3)
C1—C2—H2B120.0N2—C9—S1119.9 (2)
C3—C2—H2B120.0C8—C9—S1117.7 (2)
C2—C3—C4120.8 (3)N3—C10—N1117.1 (3)
C2—C3—H3C119.6N3—C10—N2116.2 (2)
C4—C3—H3C119.6N1—C10—N2126.7 (3)
C5—C4—C3117.7 (3)S1—C11—H11A109.5
C5—C4—C7120.8 (3)S1—C11—H11B109.5
C3—C4—C7121.4 (3)H11A—C11—H11B109.5
C6—C5—C4122.0 (3)S1—C11—H11C109.5
C6—C5—H5A119.0H11A—C11—H11C109.5
C4—C5—H5A119.0H11B—C11—H11C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N2i0.862.313.095 (3)152
N3—H3B···N1ii0.862.213.045 (3)164
C11—H11A···S1iii0.962.933.859 (4)163
Symmetry codes: (i) x+1/2, y+5/2, z+2; (ii) x1/2, y+5/2, z+2; (iii) x1/2, y+3/2, z+2.

Experimental details

Crystal data
Chemical formulaC11H10ClN3S
Mr251.73
Crystal system, space groupOrthorhombic, P212121
Temperature (K)293
a, b, c (Å)6.8148 (11), 10.6107 (16), 16.509 (3)
V3)1193.7 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.47
Crystal size (mm)0.25 × 0.14 × 0.08
Data collection
DiffractometerBruker APEXII 1K CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.925, 0.964
No. of measured, independent and
observed [I > 2σ(I)] reflections
7825, 2800, 1841
Rint0.050
(sin θ/λ)max1)0.670
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.049, 0.096, 1.01
No. of reflections2800
No. of parameters145
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.19, 0.20
Absolute structureFlack (1983), 1061 Friedel pairs
Absolute structure parameter0.02 (10)

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N2i0.862.313.095 (3)151.6
N3—H3B···N1ii0.862.213.045 (3)163.6
C11—H11A···S1iii0.962.933.859 (4)163.1
Symmetry codes: (i) x+1/2, y+5/2, z+2; (ii) x1/2, y+5/2, z+2; (iii) x1/2, y+3/2, z+2.
 

Acknowledgements

We acknowledge the National Natural Science Foundation of China for financial support.

References

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First citationLin, J., Liu, Y.-J., Yan, S.-J., Niu, Y.-F., Zheng, H. & Huang, R. (2008). CN Patent No. 101302203A.  Google Scholar
First citationMathews, A. & Asokan, C. V. (2007). Tetrahedron, 63, 7845-7849.  Web of Science CrossRef CAS Google Scholar
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First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationTaylor, R. & Kennard, O. (1982). J. Am. Chem. Soc. 104, 5063–5070.  CrossRef CAS Web of Science Google Scholar

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