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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 3| March 2012| Pages o676-o677

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

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[Ding, Y., Girardet, J.-L., Smith, K. L., Larson, G., Prigaro, B., Wu, J. Z. & Yao, N. (2006). Bioorg. Chem. 34, 26-38.]); Hawser et al., (2006[Hawser, S., Lociuro, S. & Islam, K. (2006). Biochem. Pharmacol. 71, 941-948.]); Brunelle et al. (2007[Brunelle, M. N., Lucifora, J., Neyts, J., Villet, S., Holy, A., Trepo, C. & Zoulim, F. (2007). Antimicrob. Agents Chemother. 51, 2240-2243.]); Al-Safarjalani et al. (2005[Al-Safarjalani, O. N., Zhou, X., Rais, R. H., Shi, J., Schinazi, R. F., Naguib, F. N. M. & El Kouni, M. H. (2005). Cancer Chemother. Pharmacol. 55, 541-551.]); Al-Omar et al. (2010[Al-Omar, M. A., Al-Obaid, A. M., El-Brollosy, N. R. & El-Emam, A. A. (2010). Synth. Commun. 40, 1530-1538.]); Al-Abdullah et al. (2011[Al-Abdullah, E. S., Al-Obaid, A. M., Al-Deeb, O. A., Habib, E. E. & El-Emam, A. A. (2011). Eur. J. Med. Chem. 46, 4642-4647.]); Al-Turkistani et al. (2011[Al-Turkistani, A. A., Al-Deeb, O. A., El-Brollosy, N. R. & El-Emam, A. A. (2011). Molecules, 16, 4764-4774.]). For related uracil structures, see: Tiekink (1989[Tiekink, E. R. T. (1989). Z. Kristallogr. 187, 79-84.]); Nasir et al. (2010[Nasir, S. B., Abdullah, Z., Fairuz, Z. A., Ng, S. W. & Tiekink, E. R. T. (2010). Acta Cryst. E66, o2187.]); El-Emam et al. (2011[El-Emam, A. A., Al-Deeb, O. A., Al-Turkistani, A. A., Ng, S. W. & Tiekink, E. R. T. (2011). Acta Cryst. E67, o3126.]).

[Scheme 1]

Experimental

Crystal data
  • C9H11N3OS

  • Mr = 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[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]) Tmin = 0.461, Tmax = 0.926

  • 6870 measured reflections

  • 2102 independent reflections

  • 1989 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.28 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


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 C1S1 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 (CO), 163.90 (Uracil C-6), 176.75 (CS).

Refinement top

Carbon-bound H atoms were placed in calculated positions [C—H = 0.95 to 1.00 Å, Uiso(H) = 1.2–1.5Ueq(C)] and were included in the refinement in the riding model approximation. The amide H atoms were located in a difference Fourier map, and were refined with a distance restraint of N—H = 0.88±0.01 Å; their Uiso values were refined.

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
[Figure 1] Fig. 1. The molecular structure of (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
[Figure 2] 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.
[Figure 3] 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
C9H11N3OSF(000) = 880
Mr = 209.27Dx = 1.377 Mg m3
Monoclinic, C2/cCu Kα radiation, λ = 1.54184 Å
Hall symbol: -C 2ycCell parameters from 4317 reflections
a = 25.8985 (6) Åθ = 4.0–76.1°
b = 7.0479 (2) ŵ = 2.62 mm1
c = 11.1811 (2) ÅT = 100 K
β = 98.527 (2)°Needle, colourless
V = 2018.33 (8) Å30.35 × 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 Source1989 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.024
Detector resolution: 10.4041 pixels mm-1θmax = 76.3°, θmin = 6.5°
ω scansh = 3132
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
k = 88
Tmin = 0.461, Tmax = 0.926l = 1410
6870 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.030Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0528P)2 + 1.3984P]
where P = (Fo2 + 2Fc2)/3
2102 reflections(Δ/σ)max = 0.002
135 parametersΔρmax = 0.27 e Å3
2 restraintsΔρmin = 0.28 e Å3
Crystal data top
C9H11N3OSV = 2018.33 (8) Å3
Mr = 209.27Z = 8
Monoclinic, C2/cCu Kα radiation
a = 25.8985 (6) ŵ = 2.62 mm1
b = 7.0479 (2) ÅT = 100 K
c = 11.1811 (2) Å0.35 × 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)
Tmin = 0.461, Tmax = 0.926Rint = 0.024
6870 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0302 restraints
wR(F2) = 0.086H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.27 e Å3
2102 reflectionsΔρmin = 0.28 e Å3
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
xyzUiso*/Ueq
S10.550100 (11)0.21184 (4)0.42164 (3)0.01651 (12)
O10.43446 (3)0.31829 (14)0.72665 (8)0.0189 (2)
N10.44705 (4)0.25643 (16)0.37760 (9)0.0154 (2)
N20.48422 (4)0.27666 (15)0.57730 (9)0.0143 (2)
N30.30186 (4)0.37646 (18)0.58639 (10)0.0225 (3)
C10.49111 (5)0.24972 (18)0.46022 (11)0.0144 (2)
C20.43658 (5)0.30269 (17)0.61833 (11)0.0146 (3)
C30.39202 (5)0.31030 (17)0.52342 (11)0.0150 (3)
C40.39788 (5)0.28817 (16)0.40487 (11)0.0151 (3)
C50.34180 (5)0.34614 (19)0.55782 (10)0.0166 (3)
C60.35440 (5)0.29348 (18)0.30154 (11)0.0165 (3)
H6A0.36440.37790.23810.020*
H6B0.32320.34900.32970.020*
C70.33981 (5)0.09633 (18)0.24532 (10)0.0160 (3)
H70.36980.04800.20730.019*
C80.29278 (5)0.1211 (2)0.14684 (12)0.0246 (3)
H8A0.30120.21330.08700.037*
H8B0.26290.16700.18310.037*
H8C0.28400.00100.10710.037*
C90.32809 (5)0.0459 (2)0.34028 (12)0.0221 (3)
H9A0.35890.05990.40220.033*
H9B0.31930.16890.30170.033*
H9C0.29860.00040.37800.033*
H1N0.4514 (7)0.243 (3)0.3021 (9)0.026 (4)*
H2N0.5113 (5)0.275 (3)0.6341 (13)0.023 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.01253 (17)0.02143 (19)0.01565 (18)0.00095 (10)0.00231 (11)0.00078 (10)
O10.0159 (4)0.0270 (5)0.0136 (4)0.0004 (4)0.0013 (3)0.0010 (3)
N10.0141 (5)0.0193 (5)0.0125 (5)0.0002 (4)0.0014 (4)0.0001 (4)
N20.0112 (5)0.0176 (5)0.0134 (5)0.0001 (4)0.0003 (4)0.0001 (4)
N30.0173 (5)0.0264 (6)0.0232 (5)0.0018 (5)0.0018 (4)0.0033 (5)
C10.0153 (6)0.0121 (5)0.0155 (6)0.0014 (4)0.0009 (4)0.0007 (4)
C20.0137 (6)0.0130 (6)0.0168 (6)0.0004 (4)0.0016 (5)0.0000 (4)
C30.0128 (6)0.0149 (6)0.0167 (6)0.0003 (4)0.0006 (4)0.0003 (4)
C40.0139 (6)0.0122 (6)0.0186 (6)0.0003 (4)0.0009 (5)0.0006 (4)
C50.0165 (6)0.0168 (6)0.0152 (5)0.0002 (5)0.0014 (4)0.0016 (4)
C60.0150 (6)0.0183 (7)0.0152 (6)0.0013 (4)0.0012 (5)0.0003 (4)
C70.0122 (5)0.0193 (6)0.0162 (5)0.0005 (4)0.0011 (4)0.0028 (5)
C80.0230 (7)0.0251 (7)0.0224 (6)0.0030 (5)0.0075 (5)0.0055 (5)
C90.0201 (6)0.0233 (7)0.0224 (6)0.0050 (5)0.0014 (5)0.0004 (5)
Geometric parameters (Å, º) top
S1—C11.6693 (13)C6—C71.5486 (17)
O1—C21.2254 (15)C6—H6A0.9900
N1—C11.3583 (16)C6—H6B0.9900
N1—C41.3711 (16)C7—C91.5232 (18)
N1—H1N0.873 (9)C7—C81.5261 (16)
N2—C11.3605 (16)C7—H71.0000
N2—C21.3909 (16)C8—H8A0.9800
N2—H2N0.874 (9)C8—H8B0.9800
N3—C51.1470 (17)C8—H8C0.9800
C2—C31.4482 (17)C9—H9A0.9800
C3—C41.3653 (18)C9—H9B0.9800
C3—C51.4323 (17)C9—H9C0.9800
C4—C61.4895 (17)
C1—N1—C4124.66 (11)C4—C6—H6B108.8
C1—N1—H1N116.1 (12)C7—C6—H6B108.8
C4—N1—H1N119.2 (12)H6A—C6—H6B107.7
C1—N2—C2125.81 (10)C9—C7—C8110.98 (10)
C1—N2—H2N119.4 (12)C9—C7—C6111.67 (10)
C2—N2—H2N114.7 (12)C8—C7—C6108.10 (10)
N1—C1—N2115.64 (11)C9—C7—H7108.7
N1—C1—S1122.58 (9)C8—C7—H7108.7
N2—C1—S1121.77 (9)C6—C7—H7108.7
O1—C2—N2120.65 (11)C7—C8—H8A109.5
O1—C2—C3124.98 (11)C7—C8—H8B109.5
N2—C2—C3114.37 (10)H8A—C8—H8B109.5
C4—C3—C5121.13 (11)C7—C8—H8C109.5
C4—C3—C2121.06 (11)H8A—C8—H8C109.5
C5—C3—C2117.79 (11)H8B—C8—H8C109.5
N1—C4—C3118.37 (11)C7—C9—H9A109.5
N1—C4—C6116.87 (11)C7—C9—H9B109.5
C3—C4—C6124.75 (12)H9A—C9—H9B109.5
N3—C5—C3179.16 (14)C7—C9—H9C109.5
C4—C6—C7113.78 (10)H9A—C9—H9C109.5
C4—C6—H6A108.8H9B—C9—H9C109.5
C7—C6—H6A108.8
C4—N1—C1—N20.16 (19)C1—N1—C4—C31.67 (19)
C4—N1—C1—S1179.61 (10)C1—N1—C4—C6179.07 (12)
C2—N2—C1—N12.54 (19)C5—C3—C4—N1179.23 (11)
C2—N2—C1—S1177.70 (9)C2—C3—C4—N10.68 (18)
C1—N2—C2—O1177.06 (12)C5—C3—C4—C61.58 (19)
C1—N2—C2—C33.35 (18)C2—C3—C4—C6179.87 (11)
O1—C2—C3—C4178.83 (12)N1—C4—C6—C772.88 (14)
N2—C2—C3—C41.60 (17)C3—C4—C6—C7106.32 (14)
O1—C2—C3—C52.58 (19)C4—C6—C7—C953.98 (14)
N2—C2—C3—C5176.99 (11)C4—C6—C7—C8176.33 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···S1i0.87 (1)2.51 (1)3.3723 (11)172 (2)
N2—H2N···O1ii0.87 (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 formulaC9H11N3OS
Mr209.27
Crystal system, space groupMonoclinic, C2/c
Temperature (K)100
a, b, c (Å)25.8985 (6), 7.0479 (2), 11.1811 (2)
β (°) 98.527 (2)
V3)2018.33 (8)
Z8
Radiation typeCu Kα
µ (mm1)2.62
Crystal size (mm)0.35 × 0.20 × 0.03
Data collection
DiffractometerAgilent SuperNova Dual
diffractometer with Atlas detector
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2011)
Tmin, Tmax0.461, 0.926
No. of measured, independent and
observed [I > 2σ(I)] reflections
6870, 2102, 1989
Rint0.024
(sin θ/λ)max1)0.630
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.086, 1.03
No. of reflections2102
No. of parameters135
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N1—H1N···S1i0.873 (9)2.506 (10)3.3723 (11)171.8 (16)
N2—H2N···O1ii0.874 (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).

References

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