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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2539.
Published online 2009 September 26. doi:  10.1107/S1600536809037945
PMCID: PMC2970255

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

Abstract

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 [triangle]). For applications of pyrimidine derivatives, see: Mahboobi et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2539-scheme1.jpg

Experimental

Crystal data

  • C10H9N3S
  • M r = 203.26
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2539-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.051
  • wR(F 2) = 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

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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.

Experimental

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

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.

Figures

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.

Crystal data

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

Enraf–Nonius CAD-4 diffractometer1340 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.025
graphiteθmax = 25.3°, θmin = 1.9°
ω/2θ scansh = 0→4
Absorption correction: ψ scan (Vorob'ev et al., 2006)k = 0→16
Tmin = 0.918, Tmax = 0.971l = −21→21
2025 measured reflections3 standard reflections every 200 reflections
1758 independent reflections intensity decay: 1%

Refinement

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 = 1.02w = 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

Special details

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)

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)

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, °)

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—N1−1.7 (4)N2—C5—C6—C7−171.2 (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—S−177.23 (19)C4—C5—C6—C10−172.7 (3)
C1—S—C2—N22.4 (3)C10—C6—C7—C80.7 (4)
C1—S—C2—N1−177.8 (2)C5—C6—C7—C8179.7 (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—N30.0 (5)
C2—N2—C5—C6179.0 (2)C9—N3—C10—C60.5 (5)
C3—C4—C5—N21.7 (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, °)

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 codes: (i) x, −y+5/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: VM2004).

References

  • 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.
  • Enraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands.
  • Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
  • Mahboobi, S., Sellmer, A., Eswayah, A., Elz, S., Uecker, A. & Bohmer, F. D. (2008). Eur. J. Med. Chem.43, 1444–1453. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Vorob’ev, E. V., Kurbatov, E. S., Krasnikov, V. V., Mezheritskii, V. V. & Usova, E. V. (2006). Russ. Chem. Bull.55, 1492–1497.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography