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

Balasubramani, K.; Fun, H.-K.

doi:10.1107/S1600536809027263

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1895

doi:10.1107/S1600536809027263

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

Kasthuri Balasubramani ^a and Hoong-Kun Fun ^a ^*‡

^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 ); 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

Crystal data

C₇H₁₀N₂O₂S
M_r = 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 ) 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[F² > 2σ(F²)] = 0.056
wR(F²) = 0.133
S = 1.28
1620 reflections
112 parameters
H-atom parameters constrained
Δρ_max = 0.42 e Å⁻³
Δρ_min = −0.47 e Å⁻³
Absolute structure: Flack (1983 ), 584 Friedel pairs
Flack parameter: 0.2 (2)

Table 1
Hydrogen-bond geometry (Å, °)

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

Supporting information

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

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

checkCIF report

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.

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

	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.

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

Crystal data top

C₇H₁₀N₂O₂S	F(000) = 392
M_r = 186.23	D_x = 1.425 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 3133 reflections
a = 3.9537 (2) Å	θ = 2.7–30.7°
b = 7.1822 (4) Å	µ = 0.33 mm⁻¹
c = 30.5723 (15) Å	T = 100 K
V = 868.14 (8) Å³	Plate, yellow
Z = 4	0.55 × 0.31 × 0.05 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	1620 independent reflections
Radiation source: fine-focus sealed tube	1555 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.033
ϕ and ω scans	θ_max = 26.0°, θ_min = 1.3°
Absorption correction: multi-scan (SADABS; Bruker, 2005)	h = −4→4
T_min = 0.838, T_max = 0.985	k = −6→8
4467 measured reflections	l = −37→37

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.056	H-atom parameters constrained
wR(F²) = 0.133	w = 1/[σ²(F_o²) + 2.7239P] where P = (F_o² + 2F_c²)/3
S = 1.28	(Δ/σ)_max = 0.001
1620 reflections	Δρ_max = 0.42 e Å⁻³
112 parameters	Δρ_min = −0.47 e Å⁻³
0 restraints	Absolute structure: Flack (1983), 584 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.2 (2)

Crystal data top

C₇H₁₀N₂O₂S	V = 868.14 (8) Å³
M_r = 186.23	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 3.9537 (2) Å	µ = 0.33 mm⁻¹
b = 7.1822 (4) Å	T = 100 K
c = 30.5723 (15) Å	0.55 × 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)
T_min = 0.838, T_max = 0.985	R_int = 0.033
4467 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.056	H-atom parameters constrained
wR(F²) = 0.133	Δρ_max = 0.42 e Å⁻³
S = 1.28	Δρ_min = −0.47 e Å⁻³
1620 reflections	Absolute structure: Flack (1983), 584 Friedel pairs
112 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
S1	0.6163 (3)	0.16537 (16)	0.05410 (4)	0.0194 (3)
O1	0.7269 (9)	0.2088 (4)	0.21365 (10)	0.0207 (8)
O2	1.1384 (9)	−0.3287 (4)	0.14636 (9)	0.0200 (7)
N1	0.6864 (9)	0.1795 (5)	0.13848 (11)	0.0140 (8)
N2	0.8979 (11)	−0.0980 (5)	0.10377 (11)	0.0177 (8)
C1	0.7499 (12)	0.0691 (6)	0.10392 (14)	0.0163 (9)
C2	0.9874 (12)	−0.1607 (7)	0.14346 (14)	0.0190 (10)
C3	0.9362 (12)	−0.0645 (6)	0.18210 (14)	0.0184 (10)
H3A	0.9998	−0.1113	0.2092	0.022*
C4	0.7818 (11)	0.1081 (7)	0.17698 (13)	0.0159 (9)
C5	0.7262 (13)	−0.0160 (7)	0.01606 (14)	0.0206 (10)
H5A	0.6651	0.0217	−0.0130	0.031*
H5B	0.6069	−0.1279	0.0236	0.031*
H5C	0.9653	−0.0385	0.0173	0.031*
C6	0.5624 (13)	0.3873 (6)	0.20817 (14)	0.0200 (10)
H6A	0.5276	0.4436	0.2363	0.030*
H6B	0.3481	0.3699	0.1940	0.030*
H6C	0.7023	0.4670	0.1906	0.030*
C7	1.1937 (13)	−0.4273 (7)	0.10586 (14)	0.0210 (11)
H7A	1.3211	−0.5385	0.1115	0.032*
H7B	1.3170	−0.3492	0.0860	0.032*
H7C	0.9797	−0.4598	0.0931	0.032*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0226 (6)	0.0161 (5)	0.0194 (5)	0.0009 (6)	−0.0013 (5)	0.0026 (5)
O1	0.0265 (19)	0.0147 (16)	0.0207 (15)	0.0071 (14)	0.0014 (14)	−0.0017 (12)
O2	0.0249 (17)	0.0127 (14)	0.0225 (14)	0.0059 (18)	0.0005 (14)	0.0001 (13)
N1	0.0059 (18)	0.0141 (17)	0.0221 (17)	−0.0036 (16)	0.0012 (13)	0.0001 (15)
N2	0.019 (2)	0.0143 (17)	0.0200 (17)	0.0012 (19)	−0.0030 (17)	0.0004 (14)
C1	0.019 (2)	0.012 (2)	0.019 (2)	−0.006 (2)	−0.0011 (19)	0.0031 (16)
C2	0.018 (2)	0.016 (2)	0.023 (2)	0.000 (2)	0.0023 (17)	0.005 (2)
C3	0.020 (3)	0.016 (2)	0.019 (2)	0.001 (2)	0.0027 (19)	0.0040 (18)
C4	0.010 (2)	0.019 (2)	0.018 (2)	−0.0014 (19)	0.0056 (17)	0.0014 (17)
C5	0.017 (3)	0.024 (2)	0.021 (2)	0.001 (2)	−0.0007 (19)	0.0000 (19)
C6	0.022 (3)	0.012 (2)	0.026 (2)	0.010 (2)	0.003 (2)	−0.0018 (18)
C7	0.021 (3)	0.017 (2)	0.026 (2)	0.007 (2)	−0.0007 (19)	−0.0013 (18)

Geometric parameters (Å, º) top

S1—C1	1.754 (4)	C3—C4	1.390 (7)
S1—C5	1.799 (5)	C3—H3A	0.93
O1—C4	1.352 (5)	C5—H5A	0.96
O1—C6	1.448 (5)	C5—H5B	0.96
O2—C2	1.349 (6)	C5—H5C	0.96
O2—C7	1.443 (5)	C6—H6A	0.96
N1—C4	1.338 (5)	C6—H6B	0.96
N1—C1	1.345 (6)	C6—H6C	0.96
N2—C1	1.335 (6)	C7—H7A	0.96
N2—C2	1.342 (6)	C7—H7B	0.96
C2—C3	1.384 (6)	C7—H7C	0.96

C1—S1—C5	101.7 (2)	S1—C5—H5B	109.5
C4—O1—C6	116.8 (3)	H5A—C5—H5B	109.5
C2—O2—C7	116.7 (3)	S1—C5—H5C	109.5
C4—N1—C1	114.4 (4)	H5A—C5—H5C	109.5
C1—N2—C2	114.5 (4)	H5B—C5—H5C	109.5
N2—C1—N1	127.9 (4)	O1—C6—H6A	109.5
N2—C1—S1	118.9 (3)	O1—C6—H6B	109.5
N1—C1—S1	113.2 (3)	H6A—C6—H6B	109.5
N2—C2—O2	118.4 (4)	O1—C6—H6C	109.5
N2—C2—C3	124.5 (4)	H6A—C6—H6C	109.5
O2—C2—C3	117.1 (4)	H6B—C6—H6C	109.5
C2—C3—C4	114.4 (4)	O2—C7—H7A	109.5
C2—C3—H3A	122.8	O2—C7—H7B	109.5
C4—C3—H3A	122.8	H7A—C7—H7B	109.5
N1—C4—O1	118.6 (4)	O2—C7—H7C	109.5
N1—C4—C3	124.4 (4)	H7A—C7—H7C	109.5
O1—C4—C3	117.0 (4)	H7B—C7—H7C	109.5
S1—C5—H5A	109.5

C2—N2—C1—N1	0.9 (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—C4	179.6 (4)
C4—N1—C1—S1	179.1 (3)	C1—N1—C4—O1	−179.7 (4)
C5—S1—C1—N2	1.6 (4)	C1—N1—C4—C3	0.4 (6)
C5—S1—C1—N1	−178.5 (3)	C6—O1—C4—N1	0.9 (6)
C1—N2—C2—O2	179.9 (4)	C6—O1—C4—C3	−179.3 (4)
C1—N2—C2—C3	−0.2 (7)	C2—C3—C4—N1	0.1 (7)
C7—O2—C2—N2	0.4 (6)	C2—C3—C4—O1	−179.7 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7A···N1ⁱ	0.96	2.62	3.573 (6)	171

Symmetry code: (i) x+1, y−1, z.

Experimental details

Crystal data
Chemical formula	C₇H₁₀N₂O₂S
M_r	186.23
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	100
a, b, c (Å)	3.9537 (2), 7.1822 (4), 30.5723 (15)
V (Å³)	868.14 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.33
Crystal size (mm)	0.55 × 0.31 × 0.05

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2005)
T_min, T_max	0.838, 0.985
No. of measured, independent and observed [I > 2σ(I)] reflections	4467, 1620, 1555
R_int	0.033
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.056, 0.133, 1.28
No. of reflections	1620
No. of parameters	112
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.42, −0.47
Absolute structure	Flack (1983), 584 Friedel pairs
Absolute structure parameter	0.2 (2)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7A···N1ⁱ	0.96	2.62	3.573 (6)	171

Symmetry code: (i) x+1, y−1, 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

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