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

Zhao, Q.-H.; Li, L.-N.; Wang, K.-M.

doi:10.1107/S1600536809024891

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1793

doi:10.1107/S1600536809024891

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

Qi-Hua Zhao,^a ^* Li-Nan Li ^a and Kun-Miao Wang ^a

^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 π–π 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 ). For the synthesis 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

Crystal data

C₁₁H₁₀ClN₃S
M_r = 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 ) T_min = 0.925, T_max = 0.964
7825 measured reflections
2800 independent reflections
1841 reflections with I > 2σ(I)
R_int = 0.050

Refinement

R[F² > 2σ(F²)] = 0.049
wR(F²) = 0.096
S = 1.01
2800 reflections
145 parameters
H-atom parameters constrained
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.20 e Å⁻³
Absolute structure: Flack (1983 ), 1061 Friedel pairs
Flack parameter: 0.02 (10)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT; 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 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809024891/si2183sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809024891/si2183Isup2.hkl

checkCIF report

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 π—π 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···Cg2^iv 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.

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

	Fig. 1. The molecular structure of the title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
	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

C₁₁H₁₀ClN₃S	F(000) = 520
M_r = 251.73	D_x = 1.401 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 3984 reflections
a = 6.8148 (11) Å	θ = 2.3–28.4°
b = 10.6107 (16) Å	µ = 0.47 mm⁻¹
c = 16.509 (3) Å	T = 293 K
V = 1193.7 (3) Å³	Block, yellow
Z = 4	0.25 × 0.14 × 0.08 mm

Data collection top

Bruker APEXII 1K CCD area-detector diffractometer	2800 independent reflections
Radiation source: fine-focus sealed tube	1841 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.050
ϕ and ω scans	θ_max = 28.4°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −8→8
T_min = 0.925, T_max = 0.964	k = −13→11
7825 measured reflections	l = −21→22

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.049	H-atom parameters constrained
wR(F²) = 0.096	w = 1/[σ²(F_o²) + (0.036P)²] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
2800 reflections	Δρ_max = 0.19 e Å⁻³
145 parameters	Δρ_min = −0.20 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 1061 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.02 (10)

Crystal data top

C₁₁H₁₀ClN₃S	V = 1193.7 (3) Å³
M_r = 251.73	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.8148 (11) Å	µ = 0.47 mm⁻¹
b = 10.6107 (16) Å	T = 293 K
c = 16.509 (3) Å	0.25 × 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)
T_min = 0.925, T_max = 0.964	R_int = 0.050
7825 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	H-atom parameters constrained
wR(F²) = 0.096	Δρ_max = 0.19 e Å⁻³
S = 1.01	Δρ_min = −0.20 e Å⁻³
2800 reflections	Absolute structure: Flack (1983), 1061 Friedel pairs
145 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
Cl1	1.15208 (14)	1.01534 (10)	0.62970 (5)	0.0694 (3)
S1	−0.01688 (13)	0.85410 (8)	0.91781 (5)	0.0522 (2)
N1	0.4426 (3)	1.1541 (2)	0.89640 (13)	0.0357 (6)
N2	0.1442 (4)	1.0763 (2)	0.95722 (13)	0.0338 (6)
N3	0.2824 (4)	1.2627 (2)	0.99649 (16)	0.0423 (6)
H3A	0.3713	1.3201	0.9931	0.051*
H3B	0.1880	1.2708	1.0307	0.051*
C1	0.9466 (5)	1.0272 (3)	0.69138 (17)	0.0454 (8)
C2	0.8052 (5)	0.9354 (3)	0.68825 (18)	0.0508 (9)
H2B	0.8186	0.8682	0.6526	0.061*
C3	0.6427 (5)	0.9430 (3)	0.73817 (19)	0.0473 (8)
H3C	0.5474	0.8803	0.7359	0.057*
C4	0.6197 (4)	1.0437 (3)	0.79209 (16)	0.0359 (7)
C5	0.7638 (5)	1.1359 (3)	0.79272 (17)	0.0427 (8)
H5A	0.7502	1.2044	0.8274	0.051*
C6	0.9275 (5)	1.1292 (3)	0.74324 (18)	0.0484 (9)
H6A	1.0228	1.1919	0.7448	0.058*
C7	0.4499 (4)	1.0503 (3)	0.84876 (16)	0.0343 (7)
C8	0.3107 (5)	0.9576 (3)	0.85466 (18)	0.0438 (8)
H8A	0.3171	0.8859	0.8224	0.053*
C9	0.1589 (4)	0.9737 (3)	0.91043 (17)	0.0366 (7)
C10	0.2911 (4)	1.1611 (3)	0.94864 (16)	0.0333 (7)
C11	−0.1656 (6)	0.9020 (4)	1.0015 (2)	0.0811 (13)
H11A	−0.2674	0.8410	1.0102	0.122*
H11B	−0.2235	0.9826	0.9900	0.122*
H11C	−0.0858	0.9083	1.0493	0.122*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0647 (6)	0.0800 (7)	0.0634 (6)	0.0144 (6)	0.0276 (5)	−0.0046 (5)
S1	0.0488 (5)	0.0391 (4)	0.0686 (5)	−0.0083 (5)	0.0010 (5)	−0.0064 (5)
N1	0.0339 (13)	0.0370 (14)	0.0361 (13)	0.0013 (12)	0.0010 (10)	−0.0044 (12)
N2	0.0334 (13)	0.0344 (14)	0.0336 (13)	0.0003 (12)	−0.0039 (11)	−0.0010 (12)
N3	0.0381 (16)	0.0411 (16)	0.0476 (14)	−0.0054 (12)	0.0095 (13)	−0.0139 (13)
C1	0.048 (2)	0.053 (2)	0.0349 (16)	0.0154 (18)	0.0071 (15)	0.0003 (16)
C2	0.056 (2)	0.049 (2)	0.0468 (19)	0.0101 (18)	0.0025 (18)	−0.0163 (17)
C3	0.045 (2)	0.046 (2)	0.0516 (19)	0.0008 (17)	−0.0012 (17)	−0.0137 (17)
C4	0.0367 (18)	0.0368 (18)	0.0344 (15)	0.0061 (14)	−0.0056 (13)	−0.0035 (14)
C5	0.0501 (19)	0.0398 (19)	0.0381 (17)	0.0023 (18)	0.0065 (15)	−0.0044 (16)
C6	0.051 (2)	0.049 (2)	0.0446 (18)	−0.0049 (17)	0.0095 (16)	−0.0024 (17)
C7	0.0310 (17)	0.0373 (18)	0.0347 (15)	0.0058 (14)	−0.0033 (12)	−0.0044 (14)
C8	0.044 (2)	0.0382 (19)	0.0489 (19)	−0.0005 (16)	0.0015 (15)	−0.0105 (15)
C9	0.0346 (16)	0.0341 (17)	0.0411 (16)	0.0000 (14)	−0.0101 (15)	0.0027 (15)
C10	0.0319 (16)	0.0346 (18)	0.0334 (15)	0.0036 (14)	−0.0043 (12)	−0.0021 (14)
C11	0.077 (3)	0.065 (3)	0.101 (3)	−0.021 (2)	0.037 (3)	−0.001 (2)

Geometric parameters (Å, º) top

Cl1—C1	1.736 (3)	C3—C4	1.400 (4)
S1—C9	1.750 (3)	C3—H3C	0.9300
S1—C11	1.788 (4)	C4—C5	1.387 (4)
N1—C10	1.347 (3)	C4—C7	1.490 (4)
N1—C7	1.354 (3)	C5—C6	1.384 (4)
N2—C9	1.339 (3)	C5—H5A	0.9300
N2—C10	1.353 (4)	C6—H6A	0.9300
N3—C10	1.338 (4)	C7—C8	1.370 (4)
N3—H3A	0.8600	C8—C9	1.395 (4)
N3—H3B	0.8600	C8—H8A	0.9300
C1—C2	1.371 (5)	C11—H11A	0.9600
C1—C6	1.386 (4)	C11—H11B	0.9600
C2—C3	1.383 (4)	C11—H11C	0.9600
C2—H2B	0.9300

C9—S1—C11	103.63 (16)	C5—C6—C1	118.7 (3)
C10—N1—C7	116.4 (2)	C5—C6—H6A	120.6
C9—N2—C10	115.1 (2)	C1—C6—H6A	120.6
C10—N3—H3A	120.0	N1—C7—C8	121.1 (3)
C10—N3—H3B	120.0	N1—C7—C4	115.6 (2)
H3A—N3—H3B	120.0	C8—C7—C4	123.3 (3)
C2—C1—C6	120.8 (3)	C7—C8—C9	118.2 (3)
C2—C1—Cl1	119.6 (3)	C7—C8—H8A	120.9
C6—C1—Cl1	119.7 (3)	C9—C8—H8A	120.9
C1—C2—C3	120.0 (3)	N2—C9—C8	122.4 (3)
C1—C2—H2B	120.0	N2—C9—S1	119.9 (2)
C3—C2—H2B	120.0	C8—C9—S1	117.7 (2)
C2—C3—C4	120.8 (3)	N3—C10—N1	117.1 (3)
C2—C3—H3C	119.6	N3—C10—N2	116.2 (2)
C4—C3—H3C	119.6	N1—C10—N2	126.7 (3)
C5—C4—C3	117.7 (3)	S1—C11—H11A	109.5
C5—C4—C7	120.8 (3)	S1—C11—H11B	109.5
C3—C4—C7	121.4 (3)	H11A—C11—H11B	109.5
C6—C5—C4	122.0 (3)	S1—C11—H11C	109.5
C6—C5—H5A	119.0	H11A—C11—H11C	109.5
C4—C5—H5A	119.0	H11B—C11—H11C	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, −y+5/2, −z+2; (ii) x−1/2, −y+5/2, −z+2; (iii) x−1/2, −y+3/2, −z+2.

Experimental details

Crystal data
Chemical formula	C₁₁H₁₀ClN₃S
M_r	251.73
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	6.8148 (11), 10.6107 (16), 16.509 (3)
V (Å³)	1193.7 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.47
Crystal size (mm)	0.25 × 0.14 × 0.08

Data collection
Diffractometer	Bruker APEXII 1K CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.925, 0.964
No. of measured, independent and observed [I > 2σ(I)] reflections	7825, 2800, 1841
R_int	0.050
(sin θ/λ)_max (Å⁻¹)	0.670

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.096, 1.01
No. of reflections	2800
No. of parameters	145
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.20
Absolute structure	Flack (1983), 1061 Friedel pairs
Absolute structure parameter	0.02 (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···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2ⁱ	0.86	2.31	3.095 (3)	151.6
N3—H3B···N1ⁱⁱ	0.86	2.21	3.045 (3)	163.6
C11—H11A···S1ⁱⁱⁱ	0.96	2.93	3.859 (4)	163.1

Symmetry codes: (i) x+1/2, −y+5/2, −z+2; (ii) x−1/2, −y+5/2, −z+2; (iii) x−1/2, −y+3/2, −z+2.

Acknowledgements

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

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