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

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ISSN: 2056-9890

5-[1-(1,3-Di­methyl-2,4,6-trioxohexa­hydropyrimidin-5-yl)-2-oxoprop­yl]-1,3-di­methyl­pyrimidine-2,4,6(1H,3H,5H)-trione

aDepartment of Chemistry, The University of Jordan, Amman 11942, Jordan, and bInstitut für Anorganische Chemie der Universität Tübingen, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
*Correspondence e-mail: k.sweidan@ju.edu.jo

(Received 30 April 2013; accepted 21 July 2013; online 27 July 2013)

The title compound, C15H18N4O7, is a product of the substitution reaction of 5,5-di­bromo-1,3-di­methyl­barbituric acid with sodium sulfide in aqueous acetone. In the crystal, mol­ecules display neither inter­molecular nor intra­molecular hydrogen bonding and the two barbiturate rings adopt the keto form.

Related literature

For general applications of barbituric acid, see: Negwer (2001[Negwer, M. (2001). Organic-Chemical Drugs and their Synonyms, 7th rev. and Engl. ed., Vol. 4, pp. 2873-2957, Berlin: Akademie.]); Bojarski et al. (1985[Bojarski, J. T., Mokrocz, J. L., Barton, H. J. & Paluchowska, M. H. (1985). Adv. Heterocycl. Chem. 38, 229-297.]); Sans & Chosaz (1988[Sans, S. R. G. & Chosaz, M. G. (1988). Pharmazie, 43, 827-829.]). For the structures of related compounds, see: Sweidan et al. (2009[Sweidan, K., Abu-Salem, Q., Al-Sheikh, A. & Abu-Sheikha, G. (2009). Lett. Org. Chem. 6, 669-672.]); Ahadi et al. (2012[Ahadi, S., Abaszadeh, M., Khavasi, H. R. & Bazgir, A. (2012). Tetrahedron, 68, 2906-2916.]). For the synthesis of the starting material, see: Sweidan et al. (2010[Sweidan, K., Abu-Salem, Q., Al-Sheikh, A. & Abu-Sheikha, G. (2010). J. Struct. Chem. 51, 793-797.]).

[Scheme 1]

Experimental

Crystal data
  • C15H18N4O7

  • Mr = 366.33

  • Orthorhombic, P 21 21 21

  • a = 9.253 (2) Å

  • b = 13.179 (3) Å

  • c = 13.360 (3) Å

  • V = 1629.2 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 213 K

  • 0.50 × 0.35 × 0.25 mm

Data collection
  • Enraf–Nonius CAD-4 diffractometer

  • 1911 measured reflections

  • 1911 independent reflections

  • 1265 reflections with I > 2σ(I)

  • 3 standard reflections every 200 reflections intensity decay: 1.0%

Refinement
  • R[F2 > 2σ(F2)] = 0.043

  • wR(F2) = 0.099

  • S = 1.07

  • 1911 reflections

  • 240 parameters

  • H-atom parameters constrained

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.17 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1998[Enraf-Nonius (1998). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: SET4 and CEKDIM in CAD-4 Software; data reduction: HELENA/PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

Many 1,3-dimethylbarbituric acid derivatives play important roles in the areas of pharmaceutical and medicinal chemistry (Bojarski et al., 1985; Sans & Chosaz, 1988). In the target molecule, two moieties of the 1,3-dimethylbarbiturate anion were attached to the same carbon of the acetone molecule and hydrogen sulfide and sodium bromide were produced during the course of the reaction. It is clear that each barbiturate ring adopts a keto form rather than the enol form as indicated by the bond angles C1-C2-C3 (116.1 (3)°), C3-C2-C13 (109.1 (2)°) and C1-C2-C13 (115.5 (2)°) for one barbiturate ring and C7-C8-C13 (112.6 (3)°), C9-C8-C13 (114.4 (3)°) and C7-C8-C9 (116.31 (3)°) for the second one. In addition, the bond lengths C12-C13 (153.7 (4) pm) and C13-C8 (154.3 (4) pm) lie within the normal range for a carbon-carbon (sp3-sp3) single bond length. Due to the steric bulk of the barbiturate rings, the bond angle C2-C13-C8 (116.2 (2)°) is noticeably larger than C2-C13-C14 (110.4 (3)°) or C8-C13-C14 (113.0 (3)°).

Related literature top

For general applications of barbituric acid, see: Negwer (2001); Bojarski et al. (1985); Sans & Chosaz (1988). For the structures of related compounds, see: Sweidan et al. (2009); Ahadi et al. (2012). For the synthesis of the starting material, see: Sweidan et al. (2010).

Experimental top

The title compound, C15H18N4O7, was prepared by addition of a solution of 5,5-dibromo-1,3-dimethylbarbituric acid (Sweidan et al., 2010), (0.74g, 2.4 mmol) in 10 mL of acetone to a solution of sodium sulfide (0.19g, 2.4 mmol) in 15 mL of water at room temperature. After the reaction mixture was stirred overnight, the precipitate was filtered off and dried in vacuo. The yield after recrystallisation from dichloromethane/diethyl ether was 0.24g (22%) as colorless crystals.

Refinement top

Hydrogen atoms were included in the refinement at calculated positions C—H = 0.95–1.00 Å and with Uiso(H) = 1.2Ueq(aromatic C) or 1.5Ueq(aliphatic C), using a riding-model approximation.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1998); cell refinement: SET4 and CEKDIM in CAD-4 Software (Enraf–Nonius, 1998); data reduction: HELENA/PLATON (Spek, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecule showing the atom numbering scheme with 20% probability displacement ellipsoids for non-H atoms.
5-[1-(1,3-Dimethyl-2,4,6-trioxohexahydropyrimidin-5-yl)-2-oxopropyl]-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione top
Crystal data top
C15H18N4O7F(000) = 768
Mr = 366.33Dx = 1.494 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 25 reflections
a = 9.253 (2) Åθ = 6.8–15.5°
b = 13.179 (3) ŵ = 0.12 mm1
c = 13.360 (3) ÅT = 213 K
V = 1629.2 (6) Å3Cube, colourless
Z = 40.50 × 0.35 × 0.25 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.000
Radiation source: fine-focus sealed tubeθmax = 26.4°, θmin = 3.1°
Graphite monochromatorh = 011
ω scansk = 016
1911 measured reflectionsl = 016
1911 independent reflections3 standard reflections every 200 reflections
1265 reflections with I > 2σ(I) intensity decay: 1.0%
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)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.099H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0391P)2 + 0.2519P]
where P = (Fo2 + 2Fc2)/3
1911 reflections(Δ/σ)max < 0.001
240 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C15H18N4O7V = 1629.2 (6) Å3
Mr = 366.33Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 9.253 (2) ŵ = 0.12 mm1
b = 13.179 (3) ÅT = 213 K
c = 13.360 (3) Å0.50 × 0.35 × 0.25 mm
Data collection top
Enraf–Nonius CAD-4
diffractometer
Rint = 0.000
1911 measured reflections3 standard reflections every 200 reflections
1911 independent reflections intensity decay: 1.0%
1265 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.099H-atom parameters constrained
S = 1.07Δρmax = 0.17 e Å3
1911 reflectionsΔρmin = 0.17 e Å3
240 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
N10.1811 (3)0.5023 (2)0.09198 (18)0.0356 (6)
N20.2638 (3)0.38060 (19)0.02592 (18)0.0375 (7)
N30.6557 (3)0.6949 (2)0.23141 (19)0.0404 (7)
N40.5211 (3)0.82117 (18)0.1472 (2)0.0397 (7)
O10.3230 (3)0.62919 (18)0.14586 (18)0.0551 (7)
O20.0383 (3)0.37348 (19)0.0384 (2)0.0646 (8)
O30.4834 (3)0.39452 (18)0.09365 (19)0.0559 (7)
O40.7066 (3)0.54505 (17)0.15638 (17)0.0462 (6)
O50.5992 (3)0.84280 (18)0.30569 (17)0.0576 (7)
O60.4264 (3)0.79063 (16)0.00524 (17)0.0488 (6)
O70.3341 (3)0.60948 (19)0.12316 (17)0.0517 (7)
C10.3085 (4)0.5526 (2)0.0950 (2)0.0374 (8)
C20.4327 (3)0.5085 (2)0.0391 (2)0.0347 (8)
H20.49390.47630.09090.042*
C30.3974 (4)0.4251 (2)0.0330 (2)0.0388 (8)
C40.1547 (4)0.4153 (2)0.0347 (2)0.0382 (8)
C50.0635 (4)0.5370 (3)0.1582 (2)0.0512 (10)
H5A0.09400.53120.22750.077*
H5B0.02160.49540.14740.077*
H5C0.04080.60730.14340.077*
C60.2332 (4)0.2914 (3)0.0893 (3)0.0557 (10)
H6A0.14660.25780.06540.084*
H6B0.31410.24470.08610.084*
H6C0.21890.31310.15790.084*
C70.6562 (3)0.6294 (3)0.1511 (2)0.0375 (8)
C80.5953 (3)0.6702 (2)0.0545 (2)0.0335 (7)
H80.68150.69380.01730.040*
C90.5027 (4)0.7636 (2)0.0630 (2)0.0365 (8)
C100.5932 (4)0.7903 (3)0.2325 (3)0.0429 (9)
C110.7255 (4)0.6633 (3)0.3251 (2)0.0573 (11)
H11A0.76990.59730.31590.086*
H11B0.65370.65930.37780.086*
H11C0.79890.71240.34340.086*
C120.4578 (4)0.9231 (2)0.1506 (3)0.0570 (11)
H12A0.41530.93900.08620.085*
H12B0.53270.97220.16600.085*
H12C0.38380.92550.20190.085*
C130.5319 (3)0.5860 (2)0.0127 (2)0.0359 (8)
H130.61620.54640.03640.043*
C140.4602 (4)0.6271 (2)0.1071 (2)0.0410 (8)
C150.5562 (4)0.6769 (3)0.1827 (2)0.0547 (10)
H15A0.60980.62540.21890.082*
H15B0.62320.72190.14880.082*
H15C0.49780.71570.22920.082*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0331 (18)0.0352 (16)0.0383 (16)0.0004 (16)0.0103 (15)0.0043 (15)
N20.0343 (19)0.0382 (18)0.0393 (17)0.0073 (16)0.0013 (15)0.0007 (15)
N30.038 (2)0.0413 (18)0.0420 (16)0.0019 (17)0.0140 (17)0.0002 (16)
N40.039 (2)0.0324 (15)0.0457 (18)0.0022 (16)0.0040 (17)0.0023 (15)
O10.0511 (19)0.0493 (18)0.0644 (17)0.0075 (17)0.0168 (17)0.0184 (16)
O20.0419 (19)0.0602 (19)0.090 (2)0.0187 (17)0.0097 (17)0.0099 (17)
O30.0493 (19)0.0521 (16)0.0664 (18)0.0012 (17)0.0193 (17)0.0176 (16)
O40.0379 (17)0.0378 (16)0.0616 (17)0.0044 (15)0.0089 (15)0.0006 (14)
O50.070 (2)0.0578 (17)0.0451 (15)0.0006 (18)0.0025 (17)0.0202 (14)
O60.0498 (17)0.0501 (15)0.0450 (14)0.0078 (15)0.0096 (16)0.0026 (14)
O70.0423 (19)0.0594 (19)0.0515 (17)0.0092 (17)0.0123 (15)0.0064 (15)
C10.038 (2)0.035 (2)0.038 (2)0.005 (2)0.0047 (19)0.0021 (19)
C20.026 (2)0.0382 (19)0.0401 (19)0.0016 (18)0.0017 (18)0.0050 (17)
C30.038 (2)0.037 (2)0.038 (2)0.000 (2)0.002 (2)0.0021 (18)
C40.033 (2)0.038 (2)0.044 (2)0.004 (2)0.0014 (19)0.0091 (19)
C50.043 (3)0.054 (2)0.056 (2)0.005 (2)0.021 (2)0.012 (2)
C60.054 (3)0.049 (2)0.061 (3)0.009 (3)0.001 (3)0.009 (2)
C70.024 (2)0.038 (2)0.050 (2)0.0038 (19)0.0010 (19)0.002 (2)
C80.025 (2)0.0350 (19)0.0419 (19)0.0014 (18)0.0005 (19)0.0004 (16)
C90.029 (2)0.039 (2)0.040 (2)0.0013 (19)0.0042 (19)0.0038 (18)
C100.037 (2)0.042 (2)0.049 (2)0.006 (2)0.003 (2)0.002 (2)
C110.060 (3)0.059 (3)0.054 (3)0.002 (3)0.028 (2)0.002 (2)
C120.064 (3)0.037 (2)0.070 (3)0.011 (2)0.003 (3)0.005 (2)
C130.029 (2)0.0339 (17)0.044 (2)0.0009 (18)0.0045 (19)0.0019 (17)
C140.046 (3)0.039 (2)0.036 (2)0.006 (2)0.000 (2)0.0030 (17)
C150.064 (3)0.054 (2)0.045 (2)0.016 (3)0.004 (2)0.001 (2)
Geometric parameters (Å, º) top
N1—C11.354 (4)C5—H5A0.9700
N1—C41.400 (4)C5—H5B0.9700
N1—C51.475 (4)C5—H5C0.9700
N2—C31.371 (4)C6—H6A0.9700
N2—C41.373 (4)C6—H6B0.9700
N2—C61.476 (4)C6—H6C0.9700
N3—C71.377 (4)C7—C81.507 (4)
N3—C101.384 (4)C8—C91.504 (4)
N3—C111.469 (4)C8—C131.543 (4)
N4—C91.368 (4)C8—H80.9900
N4—C101.381 (4)C11—H11A0.9700
N4—C121.466 (4)C11—H11B0.9700
O1—C11.224 (4)C11—H11C0.9700
O2—C41.211 (4)C12—H12A0.9700
O3—C31.206 (4)C12—H12B0.9700
O4—C71.208 (4)C12—H12C0.9700
O5—C101.199 (4)C13—C141.525 (4)
O6—C91.207 (4)C13—H130.9900
O7—C141.209 (4)C14—C151.496 (5)
C1—C21.489 (4)C15—H15A0.9700
C2—C31.498 (4)C15—H15B0.9700
C2—C131.537 (4)C15—H15C0.9700
C2—H20.9900
C1—N1—C4124.7 (3)N3—C7—C8116.2 (3)
C1—N1—C5118.2 (3)C9—C8—C7116.1 (3)
C4—N1—C5117.0 (3)C9—C8—C13114.6 (3)
C3—N2—C4124.1 (3)C7—C8—C13112.6 (3)
C3—N2—C6118.3 (3)C9—C8—H8103.9
C4—N2—C6117.6 (3)C7—C8—H8103.9
C7—N3—C10125.4 (3)C13—C8—H8103.9
C7—N3—C11119.0 (3)O6—C9—N4122.1 (3)
C10—N3—C11115.7 (3)O6—C9—C8121.2 (3)
C9—N4—C10125.1 (3)N4—C9—C8116.4 (3)
C9—N4—C12118.9 (3)O5—C10—N4121.7 (3)
C10—N4—C12115.9 (3)O5—C10—N3120.8 (3)
O1—C1—N1121.1 (3)N4—C10—N3117.5 (3)
O1—C1—C2121.0 (3)N3—C11—H11A109.5
N1—C1—C2117.8 (3)N3—C11—H11B109.5
C1—C2—C3116.1 (3)H11A—C11—H11B109.5
C1—C2—C13115.3 (2)N3—C11—H11C109.5
C3—C2—C13109.1 (2)H11A—C11—H11C109.5
C1—C2—H2105.0H11B—C11—H11C109.5
C3—C2—H2105.0N4—C12—H12A109.5
C13—C2—H2105.0N4—C12—H12B109.5
O3—C3—N2119.9 (3)H12A—C12—H12B109.5
O3—C3—C2122.2 (3)N4—C12—H12C109.5
N2—C3—C2117.8 (3)H12A—C12—H12C109.5
O2—C4—N2121.8 (3)H12B—C12—H12C109.5
O2—C4—N1120.4 (3)C14—C13—C2110.4 (3)
N2—C4—N1117.9 (3)C14—C13—C8113.0 (3)
N1—C5—H5A109.5C2—C13—C8116.2 (2)
N1—C5—H5B109.5C14—C13—H13105.4
H5A—C5—H5B109.5C2—C13—H13105.4
N1—C5—H5C109.5C8—C13—H13105.4
H5A—C5—H5C109.5O7—C14—C15122.5 (3)
H5B—C5—H5C109.5O7—C14—C13119.9 (3)
N2—C6—H6A109.5C15—C14—C13117.1 (3)
N2—C6—H6B109.5C14—C15—H15A109.5
H6A—C6—H6B109.5C14—C15—H15B109.5
N2—C6—H6C109.5H15A—C15—H15B109.5
H6A—C6—H6C109.5C14—C15—H15C109.5
H6B—C6—H6C109.5H15A—C15—H15C109.5
O4—C7—N3122.2 (3)H15B—C15—H15C109.5
O4—C7—C8121.5 (3)
C4—N1—C1—O1178.9 (3)O4—C7—C8—C1330.0 (4)
C5—N1—C1—O15.1 (5)N3—C7—C8—C13152.3 (3)
C4—N1—C1—C24.5 (4)C10—N4—C9—O6172.4 (3)
C5—N1—C1—C2171.5 (3)C12—N4—C9—O66.2 (5)
O1—C1—C2—C3170.6 (3)C10—N4—C9—C814.2 (5)
N1—C1—C2—C312.8 (4)C12—N4—C9—C8167.2 (3)
O1—C1—C2—C1341.1 (4)C7—C8—C9—O6165.3 (3)
N1—C1—C2—C13142.3 (3)C13—C8—C9—O631.3 (4)
C4—N2—C3—O3174.4 (3)C7—C8—C9—N421.3 (4)
C6—N2—C3—O33.9 (4)C13—C8—C9—N4155.2 (3)
C4—N2—C3—C28.0 (4)C9—N4—C10—O5176.3 (3)
C6—N2—C3—C2173.7 (3)C12—N4—C10—O52.3 (5)
C1—C2—C3—O3168.0 (3)C9—N4—C10—N32.2 (5)
C13—C2—C3—O335.6 (4)C12—N4—C10—N3179.2 (3)
C1—C2—C3—N214.5 (4)C7—N3—C10—O5179.2 (3)
C13—C2—C3—N2146.9 (3)C11—N3—C10—O51.1 (5)
C3—N2—C4—O2179.9 (3)C7—N3—C10—N42.3 (5)
C6—N2—C4—O21.6 (5)C11—N3—C10—N4177.3 (3)
C3—N2—C4—N10.8 (4)C1—C2—C13—C1475.7 (3)
C6—N2—C4—N1177.5 (3)C3—C2—C13—C1457.1 (3)
C1—N1—C4—O2178.2 (3)C1—C2—C13—C854.7 (4)
C5—N1—C4—O22.2 (4)C3—C2—C13—C8172.4 (3)
C1—N1—C4—N22.8 (4)C9—C8—C13—C1440.2 (4)
C5—N1—C4—N2178.7 (3)C7—C8—C13—C14175.8 (3)
C10—N3—C7—O4176.3 (3)C9—C8—C13—C289.0 (3)
C11—N3—C7—O43.3 (5)C7—C8—C13—C246.6 (4)
C10—N3—C7—C85.9 (4)C2—C13—C14—O711.0 (4)
C11—N3—C7—C8174.4 (3)C8—C13—C14—O7121.2 (3)
O4—C7—C8—C9164.9 (3)C2—C13—C14—C15161.4 (3)
N3—C7—C8—C917.4 (4)C8—C13—C14—C1566.5 (4)

Experimental details

Crystal data
Chemical formulaC15H18N4O7
Mr366.33
Crystal system, space groupOrthorhombic, P212121
Temperature (K)213
a, b, c (Å)9.253 (2), 13.179 (3), 13.360 (3)
V3)1629.2 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.50 × 0.35 × 0.25
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
1911, 1911, 1265
Rint0.000
(sin θ/λ)max1)0.625
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.099, 1.07
No. of reflections1911
No. of parameters240
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.17, 0.17

Computer programs: , SET4 and CEKDIM in CAD-4 Software (Enraf–Nonius, 1998), HELENA/PLATON (Spek, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

Acknowledgements

KS gratefully acknowledges financial support from the Deanship of Scientific Research at the University of Jordan.

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