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ISSN: 2056-9890

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

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[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For applications of pyrimidine derivatives, see: Mahboobi et al. (2008[Mahboobi, S., Sellmer, A., Eswayah, A., Elz, S., Uecker, A. & Bohmer, F. D. (2008). Eur. J. Med. Chem. 43, 1444-1453.]).

[Scheme 1]

Experimental

Crystal data
  • C10H9N3S

  • Mr = 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[Vorob'ev, E. V., Kurbatov, E. S., Krasnikov, V. V., Mezheritskii, V. V. & Usova, E. V. (2006). Russ. Chem. Bull. 55, 1492-1497.]) Tmin = 0.918, Tmax = 0.971

  • 2025 measured reflections

  • 1758 independent reflections

  • 1340 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.26 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Enraf-Nonius (1994). CAD-4 EXPRESS. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); 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: SHELXL97; software used to prepare material for publication: SHELXL97.

Supporting information


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.

Refinement top

All H atoms bonded to the C atoms were placed geometrically at the distances of 0.93–0.97 Å, and included in the refinement in riding motion approximation with Uiso(H) = 1.2 or 1.5Ueq of the carrier atom.

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
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-numbering scheme and displacement ellipsoids at the 30% probability level.
[Figure 2] 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
C10H9N3SF(000) = 424
Mr = 203.26Dx = 1.385 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 4.0010 (8) Åθ = 9–13°
b = 13.713 (3) ŵ = 0.29 mm1
c = 17.877 (4) ÅT = 293 K
β = 96.35 (3)°Block, colorless
V = 974.8 (3) Å30.30 × 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 tubeRint = 0.025
Graphite monochromatorθmax = 25.3°, θmin = 1.9°
ω/2θ scansh = 04
Absorption correction: ψ scan
(Vorob'ev et al., 2006)
k = 016
Tmin = 0.918, Tmax = 0.971l = 2121
2025 measured reflections3 standard reflections every 200 reflections
1758 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.159H-atom parameters constrained
S = 1.02 w = 1/[σ2(Fo2) + (0.1P)2]
where P = (Fo2 + 2Fc2)/3
1758 reflections(Δ/σ)max < 0.001
127 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = 0.19 e Å3
Crystal data top
C10H9N3SV = 974.8 (3) Å3
Mr = 203.26Z = 4
Monoclinic, P21/cMo Kα radiation
a = 4.0010 (8) ŵ = 0.29 mm1
b = 13.713 (3) ÅT = 293 K
c = 17.877 (4) Å0.30 × 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)
Rint = 0.025
Tmin = 0.918, Tmax = 0.9713 standard reflections every 200 reflections
2025 measured reflections intensity decay: 1%
1758 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.159H-atom parameters constrained
S = 1.02Δρmax = 0.26 e Å3
1758 reflectionsΔρmin = 0.19 e Å3
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
xyzUiso*/Ueq
S0.4309 (2)0.94155 (5)0.29123 (4)0.0509 (3)
N10.6539 (7)1.07222 (17)0.20518 (13)0.0457 (6)
C10.4170 (9)0.9369 (2)0.39062 (19)0.0604 (9)
H1B0.31040.87750.40360.091*
H1C0.29130.99160.40600.091*
H1D0.64170.93920.41570.091*
N20.7361 (5)1.10742 (16)0.33703 (12)0.0360 (5)
C20.6299 (7)1.05331 (19)0.27802 (15)0.0378 (6)
C30.8168 (8)1.1546 (2)0.19312 (16)0.0477 (8)
H3A0.84551.17120.14380.057*
N31.0852 (8)1.2696 (2)0.52338 (14)0.0599 (8)
C40.9438 (7)1.2158 (2)0.24957 (15)0.0405 (7)
H4A1.05871.27220.23910.049*
C50.8963 (6)1.19124 (18)0.32285 (14)0.0342 (6)
C61.0102 (7)1.25258 (18)0.38859 (15)0.0362 (6)
C71.1366 (8)1.3459 (2)0.38145 (16)0.0475 (7)
H7A1.15361.37220.33410.057*
C81.2363 (8)1.3989 (2)0.44521 (17)0.0533 (8)
H8A1.32281.46150.44160.064*
C91.2066 (8)1.3584 (2)0.51438 (17)0.0534 (8)
H9A1.27501.39510.55710.064*
C100.9898 (8)1.2193 (2)0.46139 (15)0.0498 (8)
H10A0.90271.15720.46700.060*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S0.0491 (5)0.0433 (5)0.0608 (6)0.0072 (3)0.0091 (4)0.0078 (4)
N10.0512 (15)0.0455 (14)0.0405 (14)0.0041 (11)0.0055 (11)0.0050 (11)
C10.061 (2)0.055 (2)0.066 (2)0.0093 (16)0.0120 (17)0.0099 (16)
N20.0350 (12)0.0345 (12)0.0389 (12)0.0026 (10)0.0056 (9)0.0009 (10)
C20.0348 (14)0.0369 (14)0.0419 (15)0.0070 (12)0.0049 (11)0.0032 (12)
C30.0560 (19)0.0532 (18)0.0355 (14)0.0091 (15)0.0124 (13)0.0025 (13)
N30.085 (2)0.0567 (16)0.0380 (14)0.0123 (15)0.0048 (13)0.0044 (12)
C40.0448 (17)0.0391 (15)0.0389 (14)0.0016 (12)0.0097 (12)0.0023 (12)
C50.0302 (13)0.0338 (13)0.0388 (14)0.0062 (11)0.0044 (11)0.0028 (11)
C60.0340 (14)0.0365 (15)0.0379 (14)0.0039 (11)0.0033 (11)0.0013 (11)
C70.0530 (18)0.0460 (17)0.0428 (16)0.0105 (14)0.0024 (13)0.0053 (13)
C80.059 (2)0.0459 (17)0.0540 (18)0.0161 (15)0.0022 (15)0.0027 (15)
C90.058 (2)0.0532 (19)0.0476 (18)0.0074 (16)0.0010 (15)0.0114 (14)
C100.071 (2)0.0396 (15)0.0402 (16)0.0079 (15)0.0102 (14)0.0009 (13)
Geometric parameters (Å, º) top
S—C21.755 (3)N3—C91.328 (4)
S—C11.785 (3)C4—C51.386 (4)
N1—C31.333 (4)C4—H4A0.9300
N1—C21.342 (3)C5—C61.476 (4)
C1—H1B0.9600C6—C71.387 (4)
C1—H1C0.9600C6—C101.390 (4)
C1—H1D0.9600C7—C81.374 (4)
N2—C21.321 (3)C7—H7A0.9300
N2—C51.354 (3)C8—C91.373 (4)
C3—C41.367 (4)C8—H8A0.9300
C3—H3A0.9300C9—H9A0.9300
N3—C101.325 (4)C10—H10A0.9300
C2—S—C1103.26 (14)N2—C5—C4120.0 (2)
C3—N1—C2114.2 (2)N2—C5—C6116.5 (2)
S—C1—H1B109.5C4—C5—C6123.5 (2)
S—C1—H1C109.5C7—C6—C10116.7 (3)
H1B—C1—H1C109.5C7—C6—C5122.4 (2)
S—C1—H1D109.5C10—C6—C5120.9 (2)
H1B—C1—H1D109.5C8—C7—C6119.2 (3)
H1C—C1—H1D109.5C8—C7—H7A120.4
C2—N2—C5116.4 (2)C6—C7—H7A120.4
N2—C2—N1128.0 (3)C9—C8—C7119.2 (3)
N2—C2—S119.6 (2)C9—C8—H8A120.4
N1—C2—S112.4 (2)C7—C8—H8A120.4
N1—C3—C4123.3 (3)N3—C9—C8123.3 (3)
N1—C3—H3A118.3N3—C9—H9A118.3
C4—C3—H3A118.3C8—C9—H9A118.3
C10—N3—C9116.8 (3)N3—C10—C6124.8 (3)
C3—C4—C5118.1 (3)N3—C10—H10A117.6
C3—C4—H4A121.0C6—C10—H10A117.6
C5—C4—H4A121.0
C5—N2—C2—N11.7 (4)N2—C5—C6—C7171.2 (3)
C5—N2—C2—S178.06 (18)C4—C5—C6—C78.4 (4)
C3—N1—C2—N22.6 (4)N2—C5—C6—C107.7 (4)
C3—N1—C2—S177.23 (19)C4—C5—C6—C10172.7 (3)
C1—S—C2—N22.4 (3)C10—C6—C7—C80.7 (4)
C1—S—C2—N1177.8 (2)C5—C6—C7—C8179.7 (3)
C2—N1—C3—C41.2 (4)C6—C7—C8—C90.3 (5)
N1—C3—C4—C50.8 (4)C10—N3—C9—C80.1 (5)
C2—N2—C5—C40.6 (4)C7—C8—C9—N30.0 (5)
C2—N2—C5—C6179.0 (2)C9—N3—C10—C60.5 (5)
C3—C4—C5—N21.7 (4)C7—C6—C10—N30.8 (5)
C3—C4—C5—C6177.8 (2)C5—C6—C10—N3179.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3A···N3i0.932.583.487 (4)164
C10—H10A···N20.932.442.798 (4)103
Symmetry code: (i) x, y+5/2, z1/2.

Experimental details

Crystal data
Chemical formulaC10H9N3S
Mr203.26
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)4.0010 (8), 13.713 (3), 17.877 (4)
β (°) 96.35 (3)
V3)974.8 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.29
Crystal size (mm)0.30 × 0.10 × 0.10
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correctionψ scan
(Vorob'ev et al., 2006)
Tmin, Tmax0.918, 0.971
No. of measured, independent and
observed [I > 2σ(I)] reflections
2025, 1758, 1340
Rint0.025
(sin θ/λ)max1)0.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.159, 1.02
No. of reflections1758
No. of parameters127
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
C3—H3A···N3i0.93002.58003.487 (4)164.00
C10—H10A···N20.93002.44002.798 (4)103.00
Symmetry code: (i) x, y+5/2, z1/2.
 

Acknowledgements

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

References

First citationAllen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.  CrossRef Web of Science Google Scholar
First citationEnraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands.  Google Scholar
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.  Google Scholar
First citationMahboobi, S., Sellmer, A., Eswayah, A., Elz, S., Uecker, A. & Bohmer, F. D. (2008). Eur. J. Med. Chem. 43, 1444–1453.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationVorob'ev, E. V., Kurbatov, E. S., Krasnikov, V. V., Mezheritskii, V. V. & Usova, E. V. (2006). Russ. Chem. Bull. 55, 1492–1497.  CAS Google Scholar

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