6-(2-Methyl­prop­yl)-4-oxo-2-sulfanyl­idene-1,2,3,4-tetra­hydro­pyrimidine-5-carbonitrile

Al-Deeb, O.A.; El-Emam, A.A.; Al-Turkistani, A.A.; Ng, S.W.; Tiekink, E.R.T.

doi:10.1107/S1600536812005119

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 68| Part 3| March 2012| Pages o676-o677

doi:10.1107/S1600536812005119

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6-(2-Methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile

Omar A. Al-Deeb,^a Ali A. El-Emam,^a ‡ Abdulghafoor A. Al-Turkistani,^a Seik Weng Ng ^b,^c and Edward R. T. Tiekink ^b ^*

^aDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia, ^bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, and ^cChemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203 Jeddah, Saudi Arabia
^*Correspondence e-mail: edward.tiekink@gmail.com

(Received 5 February 2012; accepted 6 February 2012; online 10 February 2012)

The title thiouracil derivative, C₉H₁₁N₃OS, exists in the thione form. The six atoms comprising the ring are almost coplanar [r.m.s. deviation = 0.015 Å] and the 2-methylpropyl group lies approximately perpendicular to this plane [the N—C—C—C torsion angle is 72.88 (14)°]. Linear supramolecular chains along [001] sustained by N—H⋯O and N—H⋯S hydrogen bonding feature in the crystal packing.

Related literature

For the biological activity of uracil and pyrimidine derivatives see: Ding et al. (2006 ); Hawser et al., (2006 ); Brunelle et al. (2007 ); Al-Safarjalani et al. (2005 ); Al-Omar et al. (2010 ); Al-Abdullah et al. (2011 ); Al-Turkistani et al. (2011 ). For related uracil structures, see: Tiekink (1989 ); Nasir et al. (2010 ); El-Emam et al. (2011 ).

Experimental

Crystal data

C₉H₁₁N₃OS
M_r = 209.27
Monoclinic, C 2/c
a = 25.8985 (6) Å
b = 7.0479 (2) Å
c = 11.1811 (2) Å
β = 98.527 (2)°
V = 2018.33 (8) Å³
Z = 8
Cu Kα radiation
μ = 2.62 mm⁻¹
T = 100 K
0.35 × 0.20 × 0.03 mm

Data collection

Agilent SuperNova Dual diffractometer with Atlas detector
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011 ) T_min = 0.461, T_max = 0.926
6870 measured reflections
2102 independent reflections
1989 reflections with I > 2σ(I)
R_int = 0.024

Refinement

R[F² > 2σ(F²)] = 0.030
wR(F²) = 0.086
S = 1.03
2102 reflections
135 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯S1ⁱ	0.87 (1)	2.51 (1)	3.3723 (11)	172 (2)
N2—H2N⋯O1ⁱⁱ	0.87 (1)	1.96 (1)	2.8210 (14)	168 (2)
Symmetry codes: (i) $[-x+1, y, -z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y, -z+{\script{3\over 2}}]$ .

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997 ) and DIAMOND (Brandenburg, 2006 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812005119/hg5174sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812005119/hg5174Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812005119/hg5174Isup3.cml

checkCIF report

Comment top

The chemotherapeutic efficacy of uracil derivatives is related to their ability to inhibit vital enzymes responsible for DNA biosynthesis. Thus, several uracil and pyrimidine non-nucleoside derivatives exhibited anti-cancer (Al-Safarjalani et al., 2005), anti-viral (Brunelle et al., 2007; Ding et al., 2006) and anti-bacterial activities (Hawser et al., 2006; Al-Abdullah et al., 2011). In continuation to our interest in the chemical and pharmacological properties of uracil and pyrimidine derivatives (Al-Omar et al., 2010; Al-Turkistani et al., 2011), and as part of on-going structural studies of uracil and pyrimidine derivatives (Nasir et al., 2010; El-Emam et al. 2011), we synthesized the title compound 6-(2-methylpropyl)-2-thiouracil-5-carbonitrile (I) as a precursor for potential chemotherapeutic agents.

The thiouracil derivative (I), Fig. 1, exists in the thione form with the C1═S1 bond length of 1.6693 (13) Å being shorter than the equivalent bond in the parent 2-thiouracil compound, i.e. 1.683 (3) Å (Tiekink, 1989). The six atoms comprising the ring are co-planar, having a r.m.s. deviation = 0.015 Å. The 2-methylpropyl group lies to one side of the central plane with the N1—C4—C6—C7 torsion angle being 72.88 (14)°.

The crystal packing features N—H···O and N—H···S hydrogen bonding involving both amide-H and the oxo and thione atoms, Table 1. The result of these hydrogen bonds is the formation of linear supramolecular chains along the c axis featuring alternating eight-membered {···HNCO}₂ and {···HNCS}₂ synthons, Fig. 2. The chains stack in the crystal structure with no specific intermolecular interactions between them, Fig. 3.

Related literature top

For the biological activity of uracil and pyrimidine derivatives see: Ding et al. (2006); Hawser et al., (2006); Brunelle et al. (2007); Al-Safarjalani et al. (2005); Al-Omar et al. (2010); Al-Abdullah et al. (2011); Al-Turkistani et al. (2011). For related uracil structures, see: Tiekink (1989); Nasir et al. (2010); El-Emam et al. (2011).

Experimental top

A mixture of 3-methylbutanal (8.61 g, 0.1 mol), ethyl cyanoacetate (11.31 g, 0.1 mol), thiourea (7.61 g, 0.1 mol) and potassium carbonate (13.8 g, 0.1 mol) was heated in in ethanol (300 ml) under reflux for 6 h. On cooling, the separated precipitate was filtered, washed with diethyl ether and dried. The obtained solid was added to water (200 ml) and the mixture was heated at 283–293 K until a clear solution was obtained. The solution was acidified with acetic acid and stirred for 30 min. The deposited precipitate was filtered, washed with cold water, dried and crystallized from acetic acid to yield 5.86 g (28%) of the title compound (I) as colourless crystals. m.p. 545–547. ¹H NMR (DMSO-d6): δ 1.07 (d, 6H, CH₃, J = 6.5 Hz), 2.18–2.24 (m, 1H, CH), 2.68 (d, 2H, CH₂, J = 6.5 Hz), 13.08 (br. s, 2H, NH). ¹³C NMR: δ 21.50 (CH₃), 29.40 (CH), 40.30 (CH₂), 92.30 (Uracil C-5), 114.80 (CN), 158.60 (C═O), 163.90 (Uracil C-6), 176.75 (C═S).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. The molecular structure of (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
	Fig. 2. A view of the linear supramolecular chain along [001] in (I). The N—H···O and N—H···S hydrogen bonds are shown as orange and blue dashed lines, respectively.
	Fig. 3. A view in projection down the c axis of the unit-cell contents for (I). The N—H···O and N—H···S interactions are shown as orange and blue dashed lines, respectively.

6-(2-Methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5- carbonitrile top

Crystal data top

C₉H₁₁N₃OS	F(000) = 880
M_r = 209.27	D_x = 1.377 Mg m⁻³
Monoclinic, C2/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -C 2yc	Cell parameters from 4317 reflections
a = 25.8985 (6) Å	θ = 4.0–76.1°
b = 7.0479 (2) Å	µ = 2.62 mm⁻¹
c = 11.1811 (2) Å	T = 100 K
β = 98.527 (2)°	Needle, colourless
V = 2018.33 (8) Å³	0.35 × 0.20 × 0.03 mm
Z = 8

Data collection top

Agilent SuperNova Dual diffractometer with Atlas detector	2102 independent reflections
Radiation source: SuperNova (Cu) X-ray Source	1989 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.024
Detector resolution: 10.4041 pixels mm^-1	θ_max = 76.3°, θ_min = 6.5°
ω scans	h = −31→32
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	k = −8→8
T_min = 0.461, T_max = 0.926	l = −14→10
6870 measured reflections

Refinement top

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)] = 0.030	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.0528P)² + 1.3984P] where P = (F_o² + 2F_c²)/3
2102 reflections	(Δ/σ)_max = 0.002
135 parameters	Δρ_max = 0.27 e Å⁻³
2 restraints	Δρ_min = −0.28 e Å⁻³

Crystal data top

C₉H₁₁N₃OS	V = 2018.33 (8) Å³
M_r = 209.27	Z = 8
Monoclinic, C2/c	Cu Kα radiation
a = 25.8985 (6) Å	µ = 2.62 mm⁻¹
b = 7.0479 (2) Å	T = 100 K
c = 11.1811 (2) Å	0.35 × 0.20 × 0.03 mm
β = 98.527 (2)°

Data collection top

Agilent SuperNova Dual diffractometer with Atlas detector	2102 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	1989 reflections with I > 2σ(I)
T_min = 0.461, T_max = 0.926	R_int = 0.024
6870 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.030	2 restraints
wR(F²) = 0.086	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	Δρ_max = 0.27 e Å⁻³
2102 reflections	Δρ_min = −0.28 e Å⁻³
135 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
S1	0.550100 (11)	0.21184 (4)	0.42164 (3)	0.01651 (12)
O1	0.43446 (3)	0.31829 (14)	0.72665 (8)	0.0189 (2)
N1	0.44705 (4)	0.25643 (16)	0.37760 (9)	0.0154 (2)
N2	0.48422 (4)	0.27666 (15)	0.57730 (9)	0.0143 (2)
N3	0.30186 (4)	0.37646 (18)	0.58639 (10)	0.0225 (3)
C1	0.49111 (5)	0.24972 (18)	0.46022 (11)	0.0144 (2)
C2	0.43658 (5)	0.30269 (17)	0.61833 (11)	0.0146 (3)
C3	0.39202 (5)	0.31030 (17)	0.52342 (11)	0.0150 (3)
C4	0.39788 (5)	0.28817 (16)	0.40487 (11)	0.0151 (3)
C5	0.34180 (5)	0.34614 (19)	0.55782 (10)	0.0166 (3)
C6	0.35440 (5)	0.29348 (18)	0.30154 (11)	0.0165 (3)
H6A	0.3644	0.3779	0.2381	0.020*
H6B	0.3232	0.3490	0.3297	0.020*
C7	0.33981 (5)	0.09633 (18)	0.24532 (10)	0.0160 (3)
H7	0.3698	0.0480	0.2073	0.019*
C8	0.29278 (5)	0.1211 (2)	0.14684 (12)	0.0246 (3)
H8A	0.3012	0.2133	0.0870	0.037*
H8B	0.2629	0.1670	0.1831	0.037*
H8C	0.2840	−0.0010	0.1071	0.037*
C9	0.32809 (5)	−0.0459 (2)	0.34028 (12)	0.0221 (3)
H9A	0.3589	−0.0599	0.4022	0.033*
H9B	0.3193	−0.1689	0.3017	0.033*
H9C	0.2986	−0.0004	0.3780	0.033*
H1N	0.4514 (7)	0.243 (3)	0.3021 (9)	0.026 (4)*
H2N	0.5113 (5)	0.275 (3)	0.6341 (13)	0.023 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.01253 (17)	0.02143 (19)	0.01565 (18)	0.00095 (10)	0.00231 (11)	0.00078 (10)
O1	0.0159 (4)	0.0270 (5)	0.0136 (4)	0.0004 (4)	0.0013 (3)	−0.0010 (3)
N1	0.0141 (5)	0.0193 (5)	0.0125 (5)	−0.0002 (4)	0.0014 (4)	−0.0001 (4)
N2	0.0112 (5)	0.0176 (5)	0.0134 (5)	0.0001 (4)	−0.0003 (4)	−0.0001 (4)
N3	0.0173 (5)	0.0264 (6)	0.0232 (5)	0.0018 (5)	0.0018 (4)	−0.0033 (5)
C1	0.0153 (6)	0.0121 (5)	0.0155 (6)	−0.0014 (4)	0.0009 (4)	0.0007 (4)
C2	0.0137 (6)	0.0130 (6)	0.0168 (6)	−0.0004 (4)	0.0016 (5)	0.0000 (4)
C3	0.0128 (6)	0.0149 (6)	0.0167 (6)	−0.0003 (4)	0.0006 (4)	−0.0003 (4)
C4	0.0139 (6)	0.0122 (6)	0.0186 (6)	−0.0003 (4)	0.0009 (5)	0.0006 (4)
C5	0.0165 (6)	0.0168 (6)	0.0152 (5)	0.0002 (5)	−0.0014 (4)	−0.0016 (4)
C6	0.0150 (6)	0.0183 (7)	0.0152 (6)	0.0013 (4)	−0.0012 (5)	−0.0003 (4)
C7	0.0122 (5)	0.0193 (6)	0.0162 (5)	0.0005 (4)	0.0011 (4)	−0.0028 (5)
C8	0.0230 (7)	0.0251 (7)	0.0224 (6)	0.0030 (5)	−0.0075 (5)	−0.0055 (5)
C9	0.0201 (6)	0.0233 (7)	0.0224 (6)	−0.0050 (5)	0.0014 (5)	0.0004 (5)

Geometric parameters (Å, º) top

S1—C1	1.6693 (13)	C6—C7	1.5486 (17)
O1—C2	1.2254 (15)	C6—H6A	0.9900
N1—C1	1.3583 (16)	C6—H6B	0.9900
N1—C4	1.3711 (16)	C7—C9	1.5232 (18)
N1—H1N	0.873 (9)	C7—C8	1.5261 (16)
N2—C1	1.3605 (16)	C7—H7	1.0000
N2—C2	1.3909 (16)	C8—H8A	0.9800
N2—H2N	0.874 (9)	C8—H8B	0.9800
N3—C5	1.1470 (17)	C8—H8C	0.9800
C2—C3	1.4482 (17)	C9—H9A	0.9800
C3—C4	1.3653 (18)	C9—H9B	0.9800
C3—C5	1.4323 (17)	C9—H9C	0.9800
C4—C6	1.4895 (17)

C1—N1—C4	124.66 (11)	C4—C6—H6B	108.8
C1—N1—H1N	116.1 (12)	C7—C6—H6B	108.8
C4—N1—H1N	119.2 (12)	H6A—C6—H6B	107.7
C1—N2—C2	125.81 (10)	C9—C7—C8	110.98 (10)
C1—N2—H2N	119.4 (12)	C9—C7—C6	111.67 (10)
C2—N2—H2N	114.7 (12)	C8—C7—C6	108.10 (10)
N1—C1—N2	115.64 (11)	C9—C7—H7	108.7
N1—C1—S1	122.58 (9)	C8—C7—H7	108.7
N2—C1—S1	121.77 (9)	C6—C7—H7	108.7
O1—C2—N2	120.65 (11)	C7—C8—H8A	109.5
O1—C2—C3	124.98 (11)	C7—C8—H8B	109.5
N2—C2—C3	114.37 (10)	H8A—C8—H8B	109.5
C4—C3—C5	121.13 (11)	C7—C8—H8C	109.5
C4—C3—C2	121.06 (11)	H8A—C8—H8C	109.5
C5—C3—C2	117.79 (11)	H8B—C8—H8C	109.5
N1—C4—C3	118.37 (11)	C7—C9—H9A	109.5
N1—C4—C6	116.87 (11)	C7—C9—H9B	109.5
C3—C4—C6	124.75 (12)	H9A—C9—H9B	109.5
N3—C5—C3	179.16 (14)	C7—C9—H9C	109.5
C4—C6—C7	113.78 (10)	H9A—C9—H9C	109.5
C4—C6—H6A	108.8	H9B—C9—H9C	109.5
C7—C6—H6A	108.8

C4—N1—C1—N2	0.16 (19)	C1—N1—C4—C3	−1.67 (19)
C4—N1—C1—S1	−179.61 (10)	C1—N1—C4—C6	179.07 (12)
C2—N2—C1—N1	2.54 (19)	C5—C3—C4—N1	179.23 (11)
C2—N2—C1—S1	−177.70 (9)	C2—C3—C4—N1	0.68 (18)
C1—N2—C2—O1	177.06 (12)	C5—C3—C4—C6	−1.58 (19)
C1—N2—C2—C3	−3.35 (18)	C2—C3—C4—C6	179.87 (11)
O1—C2—C3—C4	−178.83 (12)	N1—C4—C6—C7	72.88 (14)
N2—C2—C3—C4	1.60 (17)	C3—C4—C6—C7	−106.32 (14)
O1—C2—C3—C5	2.58 (19)	C4—C6—C7—C9	53.98 (14)
N2—C2—C3—C5	−176.99 (11)	C4—C6—C7—C8	176.33 (11)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···S1ⁱ	0.87 (1)	2.51 (1)	3.3723 (11)	172 (2)
N2—H2N···O1ⁱⁱ	0.87 (1)	1.96 (1)	2.8210 (14)	168 (2)

Symmetry codes: (i) −x+1, y, −z+1/2; (ii) −x+1, y, −z+3/2.

Experimental details

Crystal data
Chemical formula	C₉H₁₁N₃OS
M_r	209.27
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	25.8985 (6), 7.0479 (2), 11.1811 (2)
β (°)	98.527 (2)
V (Å³)	2018.33 (8)
Z	8
Radiation type	Cu Kα
µ (mm⁻¹)	2.62
Crystal size (mm)	0.35 × 0.20 × 0.03

Data collection
Diffractometer	Agilent SuperNova Dual diffractometer with Atlas detector
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2011)
T_min, T_max	0.461, 0.926
No. of measured, independent and observed [I > 2σ(I)] reflections	6870, 2102, 1989
R_int	0.024
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.030, 0.086, 1.03
No. of reflections	2102
No. of parameters	135
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.27, −0.28

Computer programs: CrysAlis PRO (Agilent, 2011), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···S1ⁱ	0.873 (9)	2.506 (10)	3.3723 (11)	171.8 (16)
N2—H2N···O1ⁱⁱ	0.874 (9)	1.960 (10)	2.8210 (14)	168.2 (17)

Symmetry codes: (i) −x+1, y, −z+1/2; (ii) −x+1, y, −z+3/2.

Footnotes

‡Additional correspondence author, e-mail: elemam5@hotmail.com.

Acknowledgements

The financial support of the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University, is greatly appreciated. We also thank the Ministry of Higher Education (Malaysia) for funding structural studies through the High-Impact Research Scheme (grant No. UM.C/HIR/MOHE/SC/12).

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ISSN: 2056-9890

Volume 68| Part 3| March 2012| Pages o676-o677

doi:10.1107/S1600536812005119

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

6-(2-Methyl­prop­yl)-4-oxo-2-sulfanyl­­idene-1,2,3,4-tetra­hydro­pyrimidine-5-carbo­nitrile

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Footnotes

Acknowledgements

References

organic compounds

6-(2-Methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile