2-[(2-Meth­oxy­eth­yl)sulfan­yl]-4-(2-methyl­prop­yl)-6-oxo-1,6-dihydro­pyrimidine-5-carbonitrile

El-Emam, A.A.; Demirtaş, G.; Dege, N.; Al-Deeb, O.A.; El-Brollosy, N.R.

doi:10.1107/S1600536812013372

organic compounds

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ISSN: 2056-9890

Volume 68| Part 5| May 2012| Page o1379

doi:10.1107/S1600536812013372

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2-[(2-Methoxyethyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile

Ali A. El-Emam,^a Güneş Demirtaş,^b Necmi Dege,^b ^* Omar A. Al-Deeb ^a and Nasser R. El-Brollosy ^a

^aDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451 Riyadh, Saudi Arabia, and ^bOndokuz Mayıs University, Arts and Sciences Faculty, Department of Physics, 55139 Samsun, Turkey
^*Correspondence e-mail: necmid@omu.edu.tr

(Received 21 March 2012; accepted 27 March 2012; online 13 April 2012)

In the title compound, C₁₂H₁₇N₃O₂S, the 4-methyl-2-methylsulfanyl-6-oxo-1,6-dihydropyrimidine-5-carbonitrile part of the molecule is almost planar (r.m.s deviation = 0.062 Å). In the crystal, molecules form centrosymmetric dimers via pairs of N—H⋯O hydrogen bonds.

Related literature

For related pyrimidine structures, see: Yan et al. (2011 ); El-Brollosy et al. (2011 ); Nasir et al. (2010 ); Tiekink (1989 ); Al-Deeb et al. (2012 ); Durkaya et al. (2011 ).

Experimental

Crystal data

C₁₂H₁₇N₃O₂S
M_r = 267.35
Triclinic, $[P \overline 1]$
a = 5.0379 (5) Å
b = 10.5453 (10) Å
c = 13.3936 (13) Å
α = 85.274 (8)°
β = 82.170 (8)°
γ = 83.034 (8)°
V = 698.14 (12) Å³
Z = 2
Mo Kα radiation
μ = 0.23 mm⁻¹
T = 296 K
0.68 × 0.47 × 0.15 mm

Data collection

Stoe IPDS 2 diffractometer
Absorption correction: integration (X-RED32; Stoe & Cie, 2002 ) T_min = 0.859, T_max = 0.966
6663 measured reflections
2725 independent reflections
2090 reflections with I > 2σ(I)
R_int = 0.062

Refinement

R[F² > 2σ(F²)] = 0.044
wR(F²) = 0.126
S = 1.02
2725 reflections
164 parameters
H-atom parameters constrained
Δρ_max = 0.28 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.86	1.89	2.747 (2)	175
Symmetry code: (i) -x+2, -y+1, -z.

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: WinGX (Farrugia, 1997 ) and SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999 ) and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812013372/bt5854sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812013372/bt5854Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812013372/bt5854Isup3.cml

checkCIF report

Comment top

In continuation to our work on the chemical and pharmacological properties of pyrimidine derivatives, we synthesized the title compound as a potential chemotherapeutic agent. The 4-methyl-2-(methylthio)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile part of the molecule is almost planar. Some pyrimidine structures have been described in the literature (Yan et al., 2011; El-Brollosy et al., 2011; Nasir et al., 2010; Tiekink 1989; Al-Deeb et al., 2012; Durkaya et al., 2011) and the bond distances of our crystal structure is comparable with these structures.

In the crystal, the molecules form centrosymmetric dimers via intermolecular N—H···O hydrogen bonds.

Related literature top

For related pyrimidine structures, see: Yan et al. (2011); El-Brollosy et al. (2011); Nasir et al. (2010); Tiekink (1989); Al-Deeb et al. (2012); Durkaya et al. (2011).

Experimental top

To a solution of 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile (2.09 g, 0.01 mol) in DMF (10 ml), 1-bromo-2-methoxyethane (1.4 g, 0.01 mol) and anhydrous potassium carbonate (1.38 g, 0.01 mol) were added and the mixture was stirred at room temperature for 12 h. Water (15 ml) was then added and the mixture was stirred for further 30 min. The separated solid was filtered, washed with cold water, dried and crystallized from water to yield 1.15 g (43%) of the title compound (C₁₂H₁₇N₃O₂S) as colorless crystals. M.P.: 113–115 ^oC. Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution of the title compound in EtOH at room temperature. ¹H NMR (DMSO-d₆, 500.13 MHz): δ 0.93 (d, 6H, CH₃, J = 7.0 Hz), 2.12–2.15 (m, 1H, CH), 2.53 (d, 2H, CH₂CH, J = 7.0 Hz), 3.27 (s, 3H, CH₃O), 3.53 (t, 2H, CH₂S, J = 6.5 Hz), 3.56 (t, 2H, OCH₂CH₂, J = 6.5 Hz), 13.55 (s, 1H, NH). ¹³C NMR (DMSO-d₆, 125.76 MHz): δ 22.55 (CH₃), 27.94 (CH), 30.19 (CH₂S), 45.30 (CH₂CH), 58.36 (CH₃O), 70.25 (OCH₂), 95.97 (C-5), 115.55 (CN), 162.05 (C-6), 166.19 (C=O), 174.50 (C-2).

Computing details top

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA (Stoe & Cie, 2002); data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: WinGX (Farrugia, 1997) and SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Figures top

Fig. 1. The asymmetric unit of the title compound, showing the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

2-[(2-Methoxyethyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine- 5-carbonitrile top

Crystal data top

C₁₂H₁₇N₃O₂S	Z = 2
M_r = 267.35	F(000) = 284
Triclinic, P1	D_x = 1.272 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.0379 (5) Å	Cell parameters from 9417 reflections
b = 10.5453 (10) Å	θ = 3.1–27.9°
c = 13.3936 (13) Å	µ = 0.23 mm⁻¹
α = 85.274 (8)°	T = 296 K
β = 82.170 (8)°	Prism, colorless
γ = 83.034 (8)°	0.68 × 0.47 × 0.15 mm
V = 698.14 (12) Å³

Data collection top

Stoe IPDS 2 diffractometer	2725 independent reflections
Radiation source: fine-focus sealed tube	2090 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.062
rotation method scans	θ_max = 26.0°, θ_min = 3.1°
Absorption correction: integration (X-RED32; Stoe & Cie, 2002)	h = −6→6
T_min = 0.859, T_max = 0.966	k = −12→12
6663 measured reflections	l = −16→16

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)] = 0.044	H-atom parameters constrained
wR(F²) = 0.126	w = 1/[σ²(F_o²) + (0.0743P)²] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max < 0.001
2725 reflections	Δρ_max = 0.28 e Å⁻³
164 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.059 (9)

Crystal data top

C₁₂H₁₇N₃O₂S	γ = 83.034 (8)°
M_r = 267.35	V = 698.14 (12) Å³
Triclinic, P1	Z = 2
a = 5.0379 (5) Å	Mo Kα radiation
b = 10.5453 (10) Å	µ = 0.23 mm⁻¹
c = 13.3936 (13) Å	T = 296 K
α = 85.274 (8)°	0.68 × 0.47 × 0.15 mm
β = 82.170 (8)°

Data collection top

Stoe IPDS 2 diffractometer	2725 independent reflections
Absorption correction: integration (X-RED32; Stoe & Cie, 2002)	2090 reflections with I > 2σ(I)
T_min = 0.859, T_max = 0.966	R_int = 0.062
6663 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.044	0 restraints
wR(F²) = 0.126	H-atom parameters constrained
S = 1.02	Δρ_max = 0.28 e Å⁻³
2725 reflections	Δρ_min = −0.22 e Å⁻³
164 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
C1	0.6121 (4)	0.32542 (17)	0.13412 (14)	0.0433 (4)
C2	0.9074 (4)	0.48214 (16)	0.15109 (15)	0.0450 (4)
C3	0.8266 (4)	0.46228 (16)	0.25758 (15)	0.0442 (4)
C4	0.6474 (4)	0.37554 (16)	0.29360 (14)	0.0437 (4)
C5	0.9463 (4)	0.53342 (18)	0.32209 (16)	0.0520 (5)
C6	0.5689 (4)	0.34539 (18)	0.40400 (14)	0.0495 (5)
H6A	0.3788	0.3735	0.4212	0.059*
H6B	0.6694	0.3929	0.4421	0.059*
C7	0.6216 (4)	0.20252 (19)	0.43492 (15)	0.0479 (4)
H7	0.5092	0.1569	0.3991	0.057*
C8	0.5377 (5)	0.1782 (2)	0.54676 (17)	0.0632 (6)
H8A	0.3491	0.2060	0.5625	0.076*
H8B	0.6398	0.2249	0.5837	0.076*
H8C	0.5710	0.0883	0.5652	0.076*
C9	0.9103 (5)	0.1502 (3)	0.4063 (2)	0.0851 (9)
H9A	1.0253	0.1946	0.4393	0.102*
H9B	0.9561	0.1620	0.3344	0.102*
H9C	0.9339	0.0606	0.4267	0.102*
C10	0.3129 (4)	0.1261 (2)	0.12329 (17)	0.0566 (5)
H10A	0.1835	0.1737	0.1707	0.068*
H10B	0.2118	0.0853	0.0808	0.068*
C11	0.4729 (5)	0.0231 (2)	0.18197 (18)	0.0646 (6)
H11A	0.5673	0.0621	0.2278	0.078*
H11B	0.3517	−0.0319	0.2218	0.078*
C12	0.7991 (8)	−0.1519 (3)	0.1697 (3)	0.1020 (10)
H12A	0.6742	−0.2072	0.2050	0.122*
H12B	0.8951	−0.1190	0.2173	0.122*
H12C	0.9246	−0.1993	0.1222	0.122*
N1	0.7874 (3)	0.40967 (14)	0.09326 (12)	0.0468 (4)
H1	0.8246	0.4179	0.0286	0.056*
N2	0.5378 (3)	0.30759 (14)	0.23047 (12)	0.0452 (4)
N3	1.0420 (5)	0.5910 (2)	0.37314 (18)	0.0761 (6)
O1	1.0717 (3)	0.55469 (13)	0.11167 (11)	0.0575 (4)
O2	0.6562 (4)	−0.04885 (17)	0.11760 (15)	0.0855 (6)
S1	0.50676 (11)	0.23771 (5)	0.04486 (4)	0.0547 (2)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0492 (9)	0.0408 (9)	0.0385 (10)	−0.0040 (7)	−0.0042 (8)	0.0019 (7)
C2	0.0564 (10)	0.0373 (9)	0.0396 (10)	−0.0048 (7)	−0.0018 (8)	0.0007 (7)
C3	0.0553 (10)	0.0365 (9)	0.0393 (10)	−0.0011 (7)	−0.0048 (8)	−0.0003 (7)
C4	0.0518 (10)	0.0375 (8)	0.0388 (10)	0.0004 (7)	−0.0015 (8)	−0.0005 (7)
C5	0.0637 (12)	0.0444 (10)	0.0473 (11)	−0.0056 (8)	−0.0067 (9)	−0.0014 (9)
C6	0.0616 (11)	0.0483 (10)	0.0365 (10)	−0.0073 (8)	0.0017 (8)	−0.0027 (8)
C7	0.0479 (10)	0.0544 (10)	0.0402 (10)	−0.0077 (8)	−0.0033 (8)	0.0033 (8)
C8	0.0734 (14)	0.0715 (14)	0.0423 (12)	−0.0143 (11)	0.0004 (10)	0.0074 (10)
C9	0.0608 (14)	0.103 (2)	0.0744 (18)	0.0151 (13)	0.0095 (12)	0.0300 (16)
C10	0.0606 (12)	0.0580 (12)	0.0512 (12)	−0.0167 (9)	0.0002 (9)	−0.0007 (9)
C11	0.0896 (16)	0.0523 (11)	0.0507 (13)	−0.0130 (11)	−0.0013 (11)	−0.0013 (10)
C12	0.127 (3)	0.0788 (18)	0.096 (3)	0.0192 (17)	−0.029 (2)	−0.0031 (17)
N1	0.0598 (9)	0.0449 (8)	0.0347 (8)	−0.0099 (7)	−0.0015 (7)	0.0027 (6)
N2	0.0537 (8)	0.0448 (8)	0.0357 (8)	−0.0073 (6)	−0.0008 (7)	0.0007 (6)
N3	0.0948 (15)	0.0671 (12)	0.0729 (15)	−0.0169 (11)	−0.0209 (12)	−0.0147 (11)
O1	0.0751 (9)	0.0526 (8)	0.0456 (8)	−0.0238 (7)	0.0009 (7)	0.0019 (6)
O2	0.1202 (15)	0.0712 (11)	0.0588 (11)	0.0131 (10)	−0.0080 (10)	−0.0074 (9)
S1	0.0701 (4)	0.0594 (3)	0.0368 (3)	−0.0201 (2)	−0.0053 (2)	−0.0007 (2)

Geometric parameters (Å, º) top

C1—N2	1.299 (2)	C8—H8B	0.9600
C1—N1	1.359 (2)	C8—H8C	0.9600
C1—S1	1.744 (2)	C9—H9A	0.9600
C2—O1	1.232 (2)	C9—H9B	0.9600
C2—N1	1.374 (2)	C9—H9C	0.9600
C2—C3	1.434 (3)	C10—C11	1.505 (3)
C3—C4	1.376 (3)	C10—S1	1.800 (2)
C3—C5	1.425 (3)	C10—H10A	0.9700
C4—N2	1.363 (2)	C10—H10B	0.9700
C4—C6	1.496 (3)	C11—O2	1.376 (3)
C5—N3	1.139 (3)	C11—H11A	0.9700
C6—C7	1.530 (3)	C11—H11B	0.9700
C6—H6A	0.9700	C12—O2	1.417 (3)
C6—H6B	0.9700	C12—H12A	0.9600
C7—C9	1.502 (3)	C12—H12B	0.9600
C7—C8	1.510 (3)	C12—H12C	0.9600
C7—H7	0.9800	N1—H1	0.8600
C8—H8A	0.9600

N2—C1—N1	123.67 (18)	C7—C9—H9A	109.5
N2—C1—S1	122.84 (14)	C7—C9—H9B	109.5
N1—C1—S1	113.43 (14)	H9A—C9—H9B	109.5
O1—C2—N1	120.88 (18)	C7—C9—H9C	109.5
O1—C2—C3	125.26 (18)	H9A—C9—H9C	109.5
N1—C2—C3	113.85 (16)	H9B—C9—H9C	109.5
C4—C3—C5	122.88 (18)	C11—C10—S1	115.59 (16)
C4—C3—C2	120.35 (18)	C11—C10—H10A	108.4
C5—C3—C2	116.75 (17)	S1—C10—H10A	108.4
N2—C4—C3	121.83 (17)	C11—C10—H10B	108.4
N2—C4—C6	115.56 (15)	S1—C10—H10B	108.4
C3—C4—C6	122.56 (18)	H10A—C10—H10B	107.4
N3—C5—C3	179.5 (2)	O2—C11—C10	110.6 (2)
C4—C6—C7	112.75 (16)	O2—C11—H11A	109.5
C4—C6—H6A	109.0	C10—C11—H11A	109.5
C7—C6—H6A	109.0	O2—C11—H11B	109.5
C4—C6—H6B	109.0	C10—C11—H11B	109.5
C7—C6—H6B	109.0	H11A—C11—H11B	108.1
H6A—C6—H6B	107.8	O2—C12—H12A	109.5
C9—C7—C8	110.84 (19)	O2—C12—H12B	109.5
C9—C7—C6	112.29 (18)	H12A—C12—H12B	109.5
C8—C7—C6	110.23 (18)	O2—C12—H12C	109.5
C9—C7—H7	107.8	H12A—C12—H12C	109.5
C8—C7—H7	107.8	H12B—C12—H12C	109.5
C6—C7—H7	107.8	C1—N1—C2	122.62 (16)
C7—C8—H8A	109.5	C1—N1—H1	118.7
C7—C8—H8B	109.5	C2—N1—H1	118.7
H8A—C8—H8B	109.5	C1—N2—C4	117.66 (16)
C7—C8—H8C	109.5	C11—O2—C12	112.2 (2)
H8A—C8—H8C	109.5	C1—S1—C10	102.06 (10)
H8B—C8—H8C	109.5

O1—C2—C3—C4	−177.90 (18)	N2—C1—N1—C2	1.5 (3)
N1—C2—C3—C4	0.9 (3)	S1—C1—N1—C2	−175.81 (14)
O1—C2—C3—C5	0.4 (3)	O1—C2—N1—C1	177.75 (17)
N1—C2—C3—C5	179.25 (15)	C3—C2—N1—C1	−1.1 (3)
C5—C3—C4—N2	−179.28 (17)	N1—C1—N2—C4	−1.5 (3)
C2—C3—C4—N2	−1.1 (3)	S1—C1—N2—C4	175.58 (13)
C5—C3—C4—C6	−1.9 (3)	C3—C4—N2—C1	1.3 (3)
C2—C3—C4—C6	176.28 (17)	C6—C4—N2—C1	−176.22 (16)
N2—C4—C6—C7	53.7 (2)	C10—C11—O2—C12	−176.3 (2)
C3—C4—C6—C7	−123.80 (19)	N2—C1—S1—C10	−3.49 (19)
C4—C6—C7—C9	56.1 (3)	N1—C1—S1—C10	173.88 (14)
C4—C6—C7—C8	−179.82 (18)	C11—C10—S1—C1	−70.78 (19)
S1—C10—C11—O2	−59.3 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.86	1.89	2.747 (2)	175

Symmetry code: (i) −x+2, −y+1, −z.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₇N₃O₂S
M_r	267.35
Crystal system, space group	Triclinic, P1
Temperature (K)	296
a, b, c (Å)	5.0379 (5), 10.5453 (10), 13.3936 (13)
α, β, γ (°)	85.274 (8), 82.170 (8), 83.034 (8)
V (Å³)	698.14 (12)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.23
Crystal size (mm)	0.68 × 0.47 × 0.15

Data collection
Diffractometer	Stoe IPDS 2 diffractometer
Absorption correction	Integration (X-RED32; Stoe & Cie, 2002)
T_min, T_max	0.859, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections	6663, 2725, 2090
R_int	0.062
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.044, 0.126, 1.02
No. of reflections	2725
No. of parameters	164
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.22

Computer programs: X-AREA (Stoe & Cie, 2002), X-RED32 (Stoe & Cie, 2002), WinGX (Farrugia, 1997) and SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.86	1.89	2.747 (2)	175.1

Symmetry code: (i) −x+2, −y+1, −z.

Acknowledgements

The authors thank Professor Orhan Büyükgüngör for his help with the data collection and acknowledge the Ondokuz Mayıs University Research Fund for financial support. The financial support of the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University is greatly appreciated.

References

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Volume 68| Part 5| May 2012| Page o1379

doi:10.1107/S1600536812013372

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

2-[(2-Meth­­oxy­eth­yl)sulfan­yl]-4-(2-methyl­prop­yl)-6-oxo-1,6-di­hydro­pyrimidine-5-carbo­nitrile

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

2-[(2-Methoxyethyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile