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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1895.
Published online 2009 July 18. doi:  10.1107/S1600536809027263
PMCID: PMC2977336

4,6-Dimeth­oxy-2-(methyl­sulfan­yl)pyrimidine

Abstract

The title compound, C7H10N2O2S, is essentially planar [maximum deviation 0.018 (4) Å]. In the crystal, mol­ecules are linked into chains by C—H(...)N hydrogen bonds and the chains are arranged in layers parallel to the ab plane.

Related literature

For general background to substituted pyrimidines, see: Salas et al. (1995 [triangle]); Holy et al. (1974 [triangle]); Hunt et al. (1980 [triangle]); Baker & Santi, (1965 [triangle]) For bond-length data, see: Allen et al. (1987 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

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Object name is e-65-o1895-scheme1.jpg

Experimental

Crystal data

  • C7H10N2O2S
  • M r = 186.23
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1895-efi1.jpg
  • a = 3.9537 (2) Å
  • b = 7.1822 (4) Å
  • c = 30.5723 (15) Å
  • V = 868.14 (8) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.33 mm−1
  • T = 100 K
  • 0.55 × 0.31 × 0.05 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.838, T max = 0.985
  • 4467 measured reflections
  • 1620 independent reflections
  • 1555 reflections with I > 2σ(I)
  • R int = 0.033

Refinement

  • R[F 2 > 2σ(F 2)] = 0.056
  • wR(F 2) = 0.133
  • S = 1.28
  • 1620 reflections
  • 112 parameters
  • H-atom parameters constrained
  • Δρmax = 0.42 e Å−3
  • Δρmin = −0.47 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 584 Friedel pairs
  • Flack parameter: 0.2 (2)

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809027263/ci2850sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809027263/ci2850Isup2.hkl

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

Acknowledgments

KBS and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. KBS thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

supplementary crystallographic information

Comment

Purine and pyrimidine derivatives are the constituents of nucleic acids and play important roles in many biological systems (Salas et al., 1995). 2-Thiopyrimidine shows a strong bacteriostatic activity in vitro on E. coli (Holy et al., 1974). Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al., 1980; Baker & Santi, 1965). The crystal structure of the title compound is presented here.

The molecule (Fig.1) is essentially planar, with atom N1 deviating a maximum of 0.018 (4) Å. The bond lengths (Allen et al., 1987) and angles are normal.

The molecules are linked into chains by C—H···N hydrogen bonds (Table 1). The chains are arranged in layers parallel to the ab plane (Fig.2).

Experimental

Hot methanol solution (20 ml) of 4,6-dimethoxy-2-methylthiopyrimidine (46 mg, Aldrich) was warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of the title compound appeared from the mother liquor after a few days.

Refinement

H atoms were positioned geometrically [C–H = 0.93–0.96 Å] and refined using a riding model with Uiso(H) = 1.2Ueq(C) and 1.5Ueq(methyl C). A rotating–group model was used for the methyl groups.

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of the title compound, viewed along the c axis. H atoms not involved in hydrogen bonding (dashed line) have been omitted for clarity.

Crystal data

C7H10N2O2SF(000) = 392
Mr = 186.23Dx = 1.425 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3133 reflections
a = 3.9537 (2) Åθ = 2.7–30.7°
b = 7.1822 (4) ŵ = 0.33 mm1
c = 30.5723 (15) ÅT = 100 K
V = 868.14 (8) Å3Plate, yellow
Z = 40.55 × 0.31 × 0.05 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer1620 independent reflections
Radiation source: fine-focus sealed tube1555 reflections with I > 2σ(I)
graphiteRint = 0.033
[var phi] and ω scansθmax = 26.0°, θmin = 1.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −4→4
Tmin = 0.838, Tmax = 0.985k = −6→8
4467 measured reflectionsl = −37→37

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.056H-atom parameters constrained
wR(F2) = 0.133w = 1/[σ2(Fo2) + 2.7239P] where P = (Fo2 + 2Fc2)/3
S = 1.28(Δ/σ)max = 0.001
1620 reflectionsΔρmax = 0.42 e Å3
112 parametersΔρmin = −0.47 e Å3
0 restraintsAbsolute structure: Flack (1983), 584 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.2 (2)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
S10.6163 (3)0.16537 (16)0.05410 (4)0.0194 (3)
O10.7269 (9)0.2088 (4)0.21365 (10)0.0207 (8)
O21.1384 (9)−0.3287 (4)0.14636 (9)0.0200 (7)
N10.6864 (9)0.1795 (5)0.13848 (11)0.0140 (8)
N20.8979 (11)−0.0980 (5)0.10377 (11)0.0177 (8)
C10.7499 (12)0.0691 (6)0.10392 (14)0.0163 (9)
C20.9874 (12)−0.1607 (7)0.14346 (14)0.0190 (10)
C30.9362 (12)−0.0645 (6)0.18210 (14)0.0184 (10)
H3A0.9998−0.11130.20920.022*
C40.7818 (11)0.1081 (7)0.17698 (13)0.0159 (9)
C50.7262 (13)−0.0160 (7)0.01606 (14)0.0206 (10)
H5A0.66510.0217−0.01300.031*
H5B0.6069−0.12790.02360.031*
H5C0.9653−0.03850.01730.031*
C60.5624 (13)0.3873 (6)0.20817 (14)0.0200 (10)
H6A0.52760.44360.23630.030*
H6B0.34810.36990.19400.030*
H6C0.70230.46700.19060.030*
C71.1937 (13)−0.4273 (7)0.10586 (14)0.0210 (11)
H7A1.3211−0.53850.11150.032*
H7B1.3170−0.34920.08600.032*
H7C0.9797−0.45980.09310.032*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0226 (6)0.0161 (5)0.0194 (5)0.0009 (6)−0.0013 (5)0.0026 (5)
O10.0265 (19)0.0147 (16)0.0207 (15)0.0071 (14)0.0014 (14)−0.0017 (12)
O20.0249 (17)0.0127 (14)0.0225 (14)0.0059 (18)0.0005 (14)0.0001 (13)
N10.0059 (18)0.0141 (17)0.0221 (17)−0.0036 (16)0.0012 (13)0.0001 (15)
N20.019 (2)0.0143 (17)0.0200 (17)0.0012 (19)−0.0030 (17)0.0004 (14)
C10.019 (2)0.012 (2)0.019 (2)−0.006 (2)−0.0011 (19)0.0031 (16)
C20.018 (2)0.016 (2)0.023 (2)0.000 (2)0.0023 (17)0.005 (2)
C30.020 (3)0.016 (2)0.019 (2)0.001 (2)0.0027 (19)0.0040 (18)
C40.010 (2)0.019 (2)0.018 (2)−0.0014 (19)0.0056 (17)0.0014 (17)
C50.017 (3)0.024 (2)0.021 (2)0.001 (2)−0.0007 (19)0.0000 (19)
C60.022 (3)0.012 (2)0.026 (2)0.010 (2)0.003 (2)−0.0018 (18)
C70.021 (3)0.017 (2)0.026 (2)0.007 (2)−0.0007 (19)−0.0013 (18)

Geometric parameters (Å, °)

S1—C11.754 (4)C3—C41.390 (7)
S1—C51.799 (5)C3—H3A0.93
O1—C41.352 (5)C5—H5A0.96
O1—C61.448 (5)C5—H5B0.96
O2—C21.349 (6)C5—H5C0.96
O2—C71.443 (5)C6—H6A0.96
N1—C41.338 (5)C6—H6B0.96
N1—C11.345 (6)C6—H6C0.96
N2—C11.335 (6)C7—H7A0.96
N2—C21.342 (6)C7—H7B0.96
C2—C31.384 (6)C7—H7C0.96
C1—S1—C5101.7 (2)S1—C5—H5B109.5
C4—O1—C6116.8 (3)H5A—C5—H5B109.5
C2—O2—C7116.7 (3)S1—C5—H5C109.5
C4—N1—C1114.4 (4)H5A—C5—H5C109.5
C1—N2—C2114.5 (4)H5B—C5—H5C109.5
N2—C1—N1127.9 (4)O1—C6—H6A109.5
N2—C1—S1118.9 (3)O1—C6—H6B109.5
N1—C1—S1113.2 (3)H6A—C6—H6B109.5
N2—C2—O2118.4 (4)O1—C6—H6C109.5
N2—C2—C3124.5 (4)H6A—C6—H6C109.5
O2—C2—C3117.1 (4)H6B—C6—H6C109.5
C2—C3—C4114.4 (4)O2—C7—H7A109.5
C2—C3—H3A122.8O2—C7—H7B109.5
C4—C3—H3A122.8H7A—C7—H7B109.5
N1—C4—O1118.6 (4)O2—C7—H7C109.5
N1—C4—C3124.4 (4)H7A—C7—H7C109.5
O1—C4—C3117.0 (4)H7B—C7—H7C109.5
S1—C5—H5A109.5
C2—N2—C1—N10.9 (7)C7—O2—C2—C3−179.4 (4)
C2—N2—C1—S1−179.3 (3)N2—C2—C3—C4−0.3 (7)
C4—N1—C1—N2−1.1 (7)O2—C2—C3—C4179.6 (4)
C4—N1—C1—S1179.1 (3)C1—N1—C4—O1−179.7 (4)
C5—S1—C1—N21.6 (4)C1—N1—C4—C30.4 (6)
C5—S1—C1—N1−178.5 (3)C6—O1—C4—N10.9 (6)
C1—N2—C2—O2179.9 (4)C6—O1—C4—C3−179.3 (4)
C1—N2—C2—C3−0.2 (7)C2—C3—C4—N10.1 (7)
C7—O2—C2—N20.4 (6)C2—C3—C4—O1−179.7 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C7—H7A···N1i0.962.623.573 (6)171

Symmetry codes: (i) x+1, y−1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2850).

References

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  • Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci.54, 1252–1257. [PubMed]
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
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  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Holy, A., Votruba, I. & Jost, K. (1974). Collect. Czech. Chem. Commun.39, 634–646.
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