organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 10 July 2009; accepted 11 July 2009; online 18 July 2009)

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[Salas, J. M., Romero, M. A. & Faure, R. (1995). Acta Cryst. C51, 2532-2534.]); Holy et al. (1974[Holy, A., Votruba, I. & Jost, K. (1974). Collect. Czech. Chem. Commun. 39, 634-646.]); Hunt et al. (1980[Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J. 187, 533-536.]); Baker & Santi, (1965[Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252-1257.]) 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 the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C7H10N2O2S

  • Mr = 186.23

  • Orthorhombic, P 21 21 21

  • 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[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.838, Tmax = 0.985

  • 4467 measured reflections

  • 1620 independent reflections

  • 1555 reflections with I > 2σ(I)

  • Rint = 0.033

Refinement
  • R[F2 > 2σ(F2)] = 0.056

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 584 Friedel pairs

  • Flack parameter: 0.2 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C7—H7A⋯N1i 0.96 2.62 3.573 (6) 171
Symmetry code: (i) x+1, y-1, z.

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2005[Bruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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).

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] 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.
4,6-Dimethoxy-2-(methylsulfanyl)pyrimidine top
Crystal data top
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 top
Bruker SMART APEXII CCD area-detector
diffractometer
1620 independent reflections
Radiation source: fine-focus sealed tube1555 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
ϕ and ω scansθmax = 26.0°, θmin = 1.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
h = 44
Tmin = 0.838, Tmax = 0.985k = 68
4467 measured reflectionsl = 3737
Refinement top
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) = 0.133 w = 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 methodsAbsolute structure parameter: 0.2 (2)
Crystal data top
C7H10N2O2SV = 868.14 (8) Å3
Mr = 186.23Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 3.9537 (2) ŵ = 0.33 mm1
b = 7.1822 (4) ÅT = 100 K
c = 30.5723 (15) Å0.55 × 0.31 × 0.05 mm
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
1620 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)
1555 reflections with I > 2σ(I)
Tmin = 0.838, Tmax = 0.985Rint = 0.033
4467 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.056H-atom parameters constrained
wR(F2) = 0.133Δρmax = 0.42 e Å3
S = 1.28Δρmin = 0.47 e Å3
1620 reflectionsAbsolute structure: Flack (1983), 584 Friedel pairs
112 parametersAbsolute structure parameter: 0.2 (2)
0 restraints
Special details top

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) top
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)
H3A0.99980.11130.20920.022*
C40.7818 (11)0.1081 (7)0.17698 (13)0.0159 (9)
C50.7262 (13)0.0160 (7)0.01606 (14)0.0206 (10)
H5A0.66510.02170.01300.031*
H5B0.60690.12790.02360.031*
H5C0.96530.03850.01730.031*
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)
H7A1.32110.53850.11150.032*
H7B1.31700.34920.08600.032*
H7C0.97970.45980.09310.032*
Atomic displacement parameters (Å2) top
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, º) top
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—C3179.4 (4)
C2—N2—C1—S1179.3 (3)N2—C2—C3—C40.3 (7)
C4—N1—C1—N21.1 (7)O2—C2—C3—C4179.6 (4)
C4—N1—C1—S1179.1 (3)C1—N1—C4—O1179.7 (4)
C5—S1—C1—N21.6 (4)C1—N1—C4—C30.4 (6)
C5—S1—C1—N1178.5 (3)C6—O1—C4—N10.9 (6)
C1—N2—C2—O2179.9 (4)C6—O1—C4—C3179.3 (4)
C1—N2—C2—C30.2 (7)C2—C3—C4—N10.1 (7)
C7—O2—C2—N20.4 (6)C2—C3—C4—O1179.7 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C7—H7A···N1i0.962.623.573 (6)171
Symmetry code: (i) x+1, y1, z.

Experimental details

Crystal data
Chemical formulaC7H10N2O2S
Mr186.23
Crystal system, space groupOrthorhombic, P212121
Temperature (K)100
a, b, c (Å)3.9537 (2), 7.1822 (4), 30.5723 (15)
V3)868.14 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.33
Crystal size (mm)0.55 × 0.31 × 0.05
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2005)
Tmin, Tmax0.838, 0.985
No. of measured, independent and
observed [I > 2σ(I)] reflections
4467, 1620, 1555
Rint0.033
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.056, 0.133, 1.28
No. of reflections1620
No. of parameters112
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.42, 0.47
Absolute structureFlack (1983), 584 Friedel pairs
Absolute structure parameter0.2 (2)

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C7—H7A···N1i0.962.623.573 (6)171
Symmetry code: (i) x+1, y1, z.
 

Footnotes

Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

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.

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 citationBaker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252–1257.  CrossRef CAS PubMed Web of Science Google Scholar
First citationBruker (2005). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationHoly, A., Votruba, I. & Jost, K. (1974). Collect. Czech. Chem. Commun. 39, 634–646.  CAS Google Scholar
First citationHunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J. 187, 533–536.  CAS PubMed Web of Science Google Scholar
First citationSalas, J. M., Romero, M. A. & Faure, R. (1995). Acta Cryst. C51, 2532–2534.  CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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