organic compounds
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
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
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Refinement
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Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell 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
10.1107/S1600536809037945/vm2004sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809037945/vm2004Isup2.hkl
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.
All H atoms bonded to the C atoms were placed geometrically at the distances of 0.93–0.97 Å, and included in the
in riding motion approximation with Uiso(H) = 1.2 or 1.5Ueq of the carrier atom.Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell
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).C10H9N3S | F(000) = 424 |
Mr = 203.26 | Dx = 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 |
Enraf–Nonius CAD-4 diffractometer | 1340 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.025 |
Graphite monochromator | θmax = 25.3°, θmin = 1.9° |
ω/2θ scans | h = 0→4 |
Absorption correction: ψ scan (Vorob'ev et al., 2006) | k = 0→16 |
Tmin = 0.918, Tmax = 0.971 | l = −21→21 |
2025 measured reflections | 3 standard reflections every 200 reflections |
1758 independent reflections | intensity decay: 1% |
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(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
1758 reflections | (Δ/σ)max < 0.001 |
127 parameters | Δρmax = 0.26 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
C10H9N3S | V = 974.8 (3) Å3 |
Mr = 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)° |
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 = 0.971 | 3 standard reflections every 200 reflections |
2025 measured reflections | intensity decay: 1% |
1758 independent reflections |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.159 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.26 e Å−3 |
1758 reflections | Δρmin = −0.19 e Å−3 |
127 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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) |
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 |
Mr | 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) |
Tmin, Tmax | 0.918, 0.971 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2025, 1758, 1340 |
Rint | 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 |
Δρmax, Δρmin (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).
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
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. CrossRef Web of Science Google Scholar
Enraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany. Google Scholar
Mahboobi, 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
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Vorob'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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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.