2-Methyl­sulfanyl-4-(3-pyrid­yl)pyrimidine

Du, R.-J.; Wang, J.-Q.; Bi, S.; Zhou, Y.-X.; Guo, C.

doi:10.1107/S1600536809037945

organic compounds

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ISSN: 2056-9890

Volume 65| Part 10| October 2009| Page o2539

doi:10.1107/S1600536809037945

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2-Methylsulfanyl-4-(3-pyridyl)pyrimidine

Ren-Jun Du,^a Jian-Qiang Wang,^a Sheng Bi,^a Yi-Xin Zhou ^a and Cheng Guo ^a ^*

^aCollege of Science, Nanjing University of Technology, Xinmofan Road No. 5 Nanjing, Nanjing 210009, People's Republic of China
^*Correspondence e-mail: guocheng@njut.edu.cn

(Received 2 September 2009; accepted 19 September 2009; online 26 September 2009)

In the title compound, C₁₀H₉N₃S, the dihedral angle between the aromatic rings is 8.09 (14)°. In the crystal, a C—H⋯N interaction links the molecules, forming chains.

Related literature

For bond-length data, see: Allen et al. (1987 ). For applications of pyrimidine derivatives, see: Mahboobi et al. (2008 ).

Experimental

Crystal data

C₁₀H₉N₃S
M_r = 203.26
Monoclinic, P 2₁ /c
a = 4.0010 (8) Å
b = 13.713 (3) Å
c = 17.877 (4) Å
β = 96.35 (3)°
V = 974.8 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.29 mm⁻¹
T = 293 K
0.30 × 0.10 × 0.10 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
Absorption correction: ψ scan (Vorob'ev et al., 2006 ) T_min = 0.918, T_max = 0.971
2025 measured reflections
1758 independent reflections
1340 reflections with I > 2σ(I)
R_int = 0.025
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.051
wR(F²) = 0.159
S = 1.02
1758 reflections
127 parameters
H-atom parameters constrained
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3A⋯N3ⁱ	0.93	2.58	3.487 (4)	164
C10—H10A⋯N2	0.93	2.44	2.798 (4)	103
Symmetry code: (i) $[x, -y+{\script{5\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 ); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXL97; software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809037945/vm2004sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809037945/vm2004Isup2.hkl

checkCIF report

Comment top

Some derivatives of pyrimidine are important chemical materials used as starting material for antineoplastic drugs (Mahboobi et al., 2008). We report here the crystal structure of the title compound, (I). The molecular structure of (I) is shown in Fig. 1, and the selected geometric parameters are given in Table 1. The bond lengths and angles (Table 1) are within normal ranges (Allen et al., 1987). A packing diagram of (I) is shown in Fig. 2.

Related literature top

For related literature, see: Allen et al. (1987); Mahboobi et al. (2008).

Experimental top

To a mixture of 2-methyl-4-(pyridin-3-yl)pyrimidine hydrosulfide (20.0 g, 0.11 mol) and sodium hydride solution (1M, 106 ml), methyl iodide (15 g) was added slowly and was stirred for 2 h at 273 K. The reaction mixture was filtered, washed with water, and dried to give (I) (19.9 g). Pure compound (I) was obstained by crystallizing from ethanol solution. Crystals of (I) suitable for X-ray diffraction were obstained by slow evaporation of an cyclohexane solution.

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXL97 (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of (I), showing the atom-numbering scheme and displacement ellipsoids at the 30% probability level.
	Fig. 2. A packing diagram of (I). Possible intermolecular hydrogen bonds are shown as dashed lines.

2-Methylsulfanyl-4-(3-pyridyl)pyrimidine top

Crystal data top

C₁₀H₉N₃S	F(000) = 424
M_r = 203.26	D_x = 1.385 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 4.0010 (8) Å	θ = 9–13°
b = 13.713 (3) Å	µ = 0.29 mm⁻¹
c = 17.877 (4) Å	T = 293 K
β = 96.35 (3)°	Block, colorless
V = 974.8 (3) Å³	0.30 × 0.10 × 0.10 mm
Z = 4

Data collection top

Enraf–Nonius CAD-4 diffractometer	1340 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.025
Graphite monochromator	θ_max = 25.3°, θ_min = 1.9°
ω/2θ scans	h = 0→4
Absorption correction: ψ scan (Vorob'ev et al., 2006)	k = 0→16
T_min = 0.918, T_max = 0.971	l = −21→21
2025 measured reflections	3 standard reflections every 200 reflections
1758 independent reflections	intensity decay: 1%

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.051	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.159	H-atom parameters constrained
S = 1.02	w = 1/[σ²(F_o²) + (0.1P)²] where P = (F_o² + 2F_c²)/3
1758 reflections	(Δ/σ)_max < 0.001
127 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₁₀H₉N₃S	V = 974.8 (3) Å³
M_r = 203.26	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 4.0010 (8) Å	µ = 0.29 mm⁻¹
b = 13.713 (3) Å	T = 293 K
c = 17.877 (4) Å	0.30 × 0.10 × 0.10 mm
β = 96.35 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	1340 reflections with I > 2σ(I)
Absorption correction: ψ scan (Vorob'ev et al., 2006)	R_int = 0.025
T_min = 0.918, T_max = 0.971	3 standard reflections every 200 reflections
2025 measured reflections	intensity decay: 1%
1758 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.051	0 restraints
wR(F²) = 0.159	H-atom parameters constrained
S = 1.02	Δρ_max = 0.26 e Å⁻³
1758 reflections	Δρ_min = −0.19 e Å⁻³
127 parameters

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

	x	y	z	U_iso*/U_eq
S	0.4309 (2)	0.94155 (5)	0.29123 (4)	0.0509 (3)
N1	0.6539 (7)	1.07222 (17)	0.20518 (13)	0.0457 (6)
C1	0.4170 (9)	0.9369 (2)	0.39062 (19)	0.0604 (9)
H1B	0.3104	0.8775	0.4036	0.091*
H1C	0.2913	0.9916	0.4060	0.091*
H1D	0.6417	0.9392	0.4157	0.091*
N2	0.7361 (5)	1.10742 (16)	0.33703 (12)	0.0360 (5)
C2	0.6299 (7)	1.05331 (19)	0.27802 (15)	0.0378 (6)
C3	0.8168 (8)	1.1546 (2)	0.19312 (16)	0.0477 (8)
H3A	0.8455	1.1712	0.1438	0.057*
N3	1.0852 (8)	1.2696 (2)	0.52338 (14)	0.0599 (8)
C4	0.9438 (7)	1.2158 (2)	0.24957 (15)	0.0405 (7)
H4A	1.0587	1.2722	0.2391	0.049*
C5	0.8963 (6)	1.19124 (18)	0.32285 (14)	0.0342 (6)
C6	1.0102 (7)	1.25258 (18)	0.38859 (15)	0.0362 (6)
C7	1.1366 (8)	1.3459 (2)	0.38145 (16)	0.0475 (7)
H7A	1.1536	1.3722	0.3341	0.057*
C8	1.2363 (8)	1.3989 (2)	0.44521 (17)	0.0533 (8)
H8A	1.3228	1.4615	0.4416	0.064*
C9	1.2066 (8)	1.3584 (2)	0.51438 (17)	0.0534 (8)
H9A	1.2750	1.3951	0.5571	0.064*
C10	0.9898 (8)	1.2193 (2)	0.46139 (15)	0.0498 (8)
H10A	0.9027	1.1572	0.4670	0.060*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S	0.0491 (5)	0.0433 (5)	0.0608 (6)	−0.0072 (3)	0.0091 (4)	−0.0078 (4)
N1	0.0512 (15)	0.0455 (14)	0.0405 (14)	0.0041 (11)	0.0055 (11)	−0.0050 (11)
C1	0.061 (2)	0.055 (2)	0.066 (2)	−0.0093 (16)	0.0120 (17)	0.0099 (16)
N2	0.0350 (12)	0.0345 (12)	0.0389 (12)	0.0026 (10)	0.0056 (9)	−0.0009 (10)
C2	0.0348 (14)	0.0369 (14)	0.0419 (15)	0.0070 (12)	0.0049 (11)	−0.0032 (12)
C3	0.0560 (19)	0.0532 (18)	0.0355 (14)	0.0091 (15)	0.0124 (13)	0.0025 (13)
N3	0.085 (2)	0.0567 (16)	0.0380 (14)	−0.0123 (15)	0.0048 (13)	−0.0044 (12)
C4	0.0448 (17)	0.0391 (15)	0.0389 (14)	0.0016 (12)	0.0097 (12)	0.0023 (12)
C5	0.0302 (13)	0.0338 (13)	0.0388 (14)	0.0062 (11)	0.0044 (11)	0.0028 (11)
C6	0.0340 (14)	0.0365 (15)	0.0379 (14)	0.0039 (11)	0.0033 (11)	0.0013 (11)
C7	0.0530 (18)	0.0460 (17)	0.0428 (16)	−0.0105 (14)	0.0024 (13)	0.0053 (13)
C8	0.059 (2)	0.0459 (17)	0.0540 (18)	−0.0161 (15)	0.0022 (15)	−0.0027 (15)
C9	0.058 (2)	0.0532 (19)	0.0476 (18)	−0.0074 (16)	0.0010 (15)	−0.0114 (14)
C10	0.071 (2)	0.0396 (15)	0.0402 (16)	−0.0079 (15)	0.0102 (14)	0.0009 (13)

Geometric parameters (Å, º) top

S—C2	1.755 (3)	N3—C9	1.328 (4)
S—C1	1.785 (3)	C4—C5	1.386 (4)
N1—C3	1.333 (4)	C4—H4A	0.9300
N1—C2	1.342 (3)	C5—C6	1.476 (4)
C1—H1B	0.9600	C6—C7	1.387 (4)
C1—H1C	0.9600	C6—C10	1.390 (4)
C1—H1D	0.9600	C7—C8	1.374 (4)
N2—C2	1.321 (3)	C7—H7A	0.9300
N2—C5	1.354 (3)	C8—C9	1.373 (4)
C3—C4	1.367 (4)	C8—H8A	0.9300
C3—H3A	0.9300	C9—H9A	0.9300
N3—C10	1.325 (4)	C10—H10A	0.9300

C2—S—C1	103.26 (14)	N2—C5—C4	120.0 (2)
C3—N1—C2	114.2 (2)	N2—C5—C6	116.5 (2)
S—C1—H1B	109.5	C4—C5—C6	123.5 (2)
S—C1—H1C	109.5	C7—C6—C10	116.7 (3)
H1B—C1—H1C	109.5	C7—C6—C5	122.4 (2)
S—C1—H1D	109.5	C10—C6—C5	120.9 (2)
H1B—C1—H1D	109.5	C8—C7—C6	119.2 (3)
H1C—C1—H1D	109.5	C8—C7—H7A	120.4
C2—N2—C5	116.4 (2)	C6—C7—H7A	120.4
N2—C2—N1	128.0 (3)	C9—C8—C7	119.2 (3)
N2—C2—S	119.6 (2)	C9—C8—H8A	120.4
N1—C2—S	112.4 (2)	C7—C8—H8A	120.4
N1—C3—C4	123.3 (3)	N3—C9—C8	123.3 (3)
N1—C3—H3A	118.3	N3—C9—H9A	118.3
C4—C3—H3A	118.3	C8—C9—H9A	118.3
C10—N3—C9	116.8 (3)	N3—C10—C6	124.8 (3)
C3—C4—C5	118.1 (3)	N3—C10—H10A	117.6
C3—C4—H4A	121.0	C6—C10—H10A	117.6
C5—C4—H4A	121.0

C5—N2—C2—N1	−1.7 (4)	N2—C5—C6—C7	−171.2 (3)
C5—N2—C2—S	178.06 (18)	C4—C5—C6—C7	8.4 (4)
C3—N1—C2—N2	2.6 (4)	N2—C5—C6—C10	7.7 (4)
C3—N1—C2—S	−177.23 (19)	C4—C5—C6—C10	−172.7 (3)
C1—S—C2—N2	2.4 (3)	C10—C6—C7—C8	0.7 (4)
C1—S—C2—N1	−177.8 (2)	C5—C6—C7—C8	179.7 (3)
C2—N1—C3—C4	−1.2 (4)	C6—C7—C8—C9	−0.3 (5)
N1—C3—C4—C5	−0.8 (4)	C10—N3—C9—C8	−0.1 (5)
C2—N2—C5—C4	−0.6 (4)	C7—C8—C9—N3	0.0 (5)
C2—N2—C5—C6	179.0 (2)	C9—N3—C10—C6	0.5 (5)
C3—C4—C5—N2	1.7 (4)	C7—C6—C10—N3	−0.8 (5)
C3—C4—C5—C6	−177.8 (2)	C5—C6—C10—N3	−179.8 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3A···N3ⁱ	0.93	2.58	3.487 (4)	164
C10—H10A···N2	0.93	2.44	2.798 (4)	103

Symmetry code: (i) x, −y+5/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₉N₃S
M_r	203.26
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	4.0010 (8), 13.713 (3), 17.877 (4)
β (°)	96.35 (3)
V (Å³)	974.8 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.29
Crystal size (mm)	0.30 × 0.10 × 0.10

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	ψ scan (Vorob'ev et al., 2006)
T_min, T_max	0.918, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections	2025, 1758, 1340
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.600

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.051, 0.159, 1.02
No. of reflections	1758
No. of parameters	127
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.19

Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3A···N3ⁱ	0.9300	2.5800	3.487 (4)	164.00
C10—H10A···N2	0.9300	2.4400	2.798 (4)	103.00

Symmetry code: (i) x, −y+5/2, z−1/2.

Acknowledgements

The authors thank the Center of Testing and Analysis, Nanjing University, for support.

References

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