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Acta Crystallogr Sect E Struct Rep Online. 2008 March 1; 64(Pt 3): o617.
Published online 2008 February 22. doi:  10.1107/S1600536808004418
PMCID: PMC2960789

5-Fluoro-1-(penta­noyl)pyrimidine-2,4(1H,3H)-dione

Abstract

The penta­noyl group and the 5-fluoro­uracil moiety of the title compound, C9H11FN2O3, are essentially coplanar, with the penta­noyl carbonyl group oriented towards the ring CH group and away from the nearer ring carbonyl group. In the crystal structure, two inversion-related mol­ecules form a dimer structure, in which two N—H(...)O hydrogen bonds generate an inter­molecular R 2 2(8) ring. In addition, there are intra- and inter­molecular C—H(...)O inter­actions.

Related literature

For similar 5-fluoro­pyrimidine-2,4(1H,3H)-dione structures with N1-acyl substituents, see: Beall et al. (1997 [triangle]); Jiang et al. (1988 [triangle]); Lehmler & Parkin (2000 [triangle]). For related literature, see: Roberts & Sloan (1999 [triangle]).

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Object name is e-64-0o617-scheme1.jpg

Experimental

Crystal data

  • C9H11FN2O3
  • M r = 214.20
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o617-efi1.jpg
  • a = 5.3165 (2) Å
  • b = 9.3986 (4) Å
  • c = 10.1895 (5) Å
  • α = 96.000 (3)°
  • β = 100.957 (3)°
  • γ = 105.539 (3)°
  • V = 475.04 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 87.8 (2) K
  • 0.30 × 0.30 × 0.03 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997 [triangle]) T min = 0.963, T max = 0.996
  • 12409 measured reflections
  • 2167 independent reflections
  • 1727 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.092
  • S = 1.02
  • 2167 reflections
  • 137 parameters
  • H-atom parameters constrained
  • Δρmax = 0.23 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: COLLECT (Nonius, 1998 [triangle]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO-SMN (Otwinowski & Minor, 1997 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP in SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97 and local procedures.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808004418/at2544sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808004418/at2544Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

Despite the potential pharmaceutical application of acyl-5-fluorouracil prodrugs, the crystal structures of only three acyl derivatives have been reported (Beall et al., 1997; Jiang et al., 1988; Lehmler & Parkin, 2000). We herein describe the crystal structures of another acyl-5-fluorouracil prodrug, 5-fluoro-1-(1-oxopentyl)-2,4(1H,3H)-pyrimidinedione.

The molecular structures of the title compound and the other 1-acyl-5-fluorouracil derivatives are very similar. Specifically, the 1-acyl group and the 5-fluorouracil moiety are almost coplanar, with the C7?O7 carbonyl group oriented towards the C6—H group and away from the C2?O2 group in all four crystal structures. The C6—N1—C7—O7 dihedral angle of all 1-acyl-5-fluorouracil derivatives is comparable and ranges from 1.6 to 17.3° (Beall et al., 1997; Jiang et al., 1988; Lehmler & Parkin, 2000). In the crystal structure, two inversion-related molecules form a dimer structure, in which two N—H···O hydrogen bonds generate an intermolecular R22(8) ring. In addition, there are C—H···O type-intra and intermolecular interactions.

Experimental

5-Fluoro-1-(1-oxopentyl)-2,4(1H,3H)-pyrimidinedione was synthesized by acylation of 5-fluorouracil with pentanoyl chloride and recrystallized from diethylether at 253 K (Beall et al., 1997; Lehmler & Parkin, 2000; Roberts & Sloan, 1999).

Refinement

H atoms were found in difference Fourier maps and subsequently placed in idealized positions with constrained C—H distances of 0.98 Å (RCH3), 0.99 Å (R2CH2), 0.95 Å (CArH) and 0.88 Å (NH) with Uiso(H) values set to either 1.2Ueq or 1.5Ueq (RCH3 only) of the attached atom.

Figures

Fig. 1.
View of the title compound showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C9H11FN2O3Z = 2
Mr = 214.20F000 = 224
Triclinic, P1Dx = 1.497 Mg m3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 5.3165 (2) ÅCell parameters from 6994 reflections
b = 9.3986 (4) Åθ = 1.0–27.5º
c = 10.1895 (5) ŵ = 0.13 mm1
α = 96.000 (3)ºT = 87.8 (2) K
β = 100.957 (3)ºIrregular plate, colourless
γ = 105.539 (3)º0.30 × 0.30 × 0.03 mm
V = 475.04 (4) Å3

Data collection

Nonius KappaCCD diffractometer2167 independent reflections
Radiation source: fine-focus sealed tube1727 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.037
Detector resolution: 18 pixels mm-1θmax = 27.5º
T = 87.8(2) Kθmin = 2.1º
ω scans at fixed χ = 55°h = −6→6
Absorption correction: multi-scan(SCALEPACK; Otwinowski & Minor, 1997)k = −12→12
Tmin = 0.963, Tmax = 0.996l = −13→13
12409 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.092  w = 1/[σ2(Fo2) + (0.0269P)2 + 0.2309P] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
2167 reflectionsΔρmax = 0.23 e Å3
137 parametersΔρmin = −0.24 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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 > 2σ(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)

xyzUiso*/Ueq
N10.4196 (2)0.37039 (13)0.62262 (12)0.0131 (3)
O20.7435 (2)0.24634 (12)0.65488 (10)0.0208 (3)
C20.6455 (3)0.33911 (17)0.69638 (15)0.0146 (3)
N30.7532 (2)0.42493 (13)0.82378 (12)0.0149 (3)
H30.89130.40490.87230.018*
O40.7890 (2)0.60838 (12)0.99779 (10)0.0176 (3)
C40.6725 (3)0.53737 (16)0.88432 (15)0.0148 (3)
F50.34305 (17)0.66618 (10)0.85412 (8)0.0198 (2)
C50.4391 (3)0.56025 (16)0.80080 (15)0.0142 (3)
C60.3224 (3)0.48168 (16)0.67833 (14)0.0135 (3)
H60.16980.50130.62730.016*
O70.1183 (2)0.35259 (12)0.42664 (10)0.0189 (3)
C70.2850 (3)0.30070 (16)0.48388 (15)0.0139 (3)
C80.3615 (3)0.17280 (17)0.41877 (15)0.0162 (3)
H8A0.34940.09490.47750.019*
H8B0.55000.20880.41080.019*
C90.1823 (3)0.10375 (17)0.27854 (15)0.0170 (3)
H9A0.16440.18530.22670.020*
H9B0.27100.04180.23020.020*
C10−0.0962 (3)0.00735 (17)0.28048 (16)0.0192 (4)
H10A−0.18280.06680.33300.023*
H10B−0.0809−0.07880.32620.023*
C11−0.2706 (3)−0.0500 (2)0.13778 (17)0.0266 (4)
H11A−0.28900.03510.09290.040*
H11B−0.4482−0.11170.14270.040*
H11C−0.1868−0.11030.08600.040*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0116 (6)0.0140 (6)0.0139 (6)0.0054 (5)0.0013 (5)0.0013 (5)
O20.0197 (6)0.0233 (6)0.0206 (6)0.0133 (5)−0.0006 (5)−0.0007 (5)
C20.0119 (7)0.0156 (8)0.0167 (8)0.0044 (6)0.0029 (6)0.0047 (6)
N30.0117 (6)0.0165 (7)0.0155 (7)0.0060 (5)−0.0016 (5)0.0023 (5)
O40.0164 (6)0.0196 (6)0.0153 (6)0.0061 (5)0.0002 (4)0.0007 (5)
C40.0141 (8)0.0139 (8)0.0170 (8)0.0031 (6)0.0050 (6)0.0047 (6)
F50.0199 (5)0.0208 (5)0.0193 (5)0.0116 (4)0.0009 (4)−0.0027 (4)
C50.0142 (7)0.0139 (8)0.0170 (8)0.0069 (6)0.0049 (6)0.0033 (6)
C60.0106 (7)0.0152 (8)0.0166 (8)0.0062 (6)0.0037 (6)0.0043 (6)
O70.0197 (6)0.0210 (6)0.0163 (6)0.0108 (5)−0.0009 (5)0.0011 (5)
C70.0115 (7)0.0153 (8)0.0149 (7)0.0030 (6)0.0035 (6)0.0036 (6)
C80.0159 (8)0.0166 (8)0.0172 (8)0.0066 (6)0.0035 (6)0.0037 (6)
C90.0175 (8)0.0176 (8)0.0156 (8)0.0064 (7)0.0026 (6)−0.0006 (6)
C100.0189 (8)0.0175 (8)0.0219 (8)0.0066 (7)0.0051 (7)0.0029 (7)
C110.0242 (9)0.0236 (9)0.0270 (9)0.0045 (7)0.0013 (7)−0.0024 (7)

Geometric parameters (Å, °)

N1—C61.3999 (18)C7—C81.499 (2)
N1—C21.4093 (19)C8—C91.526 (2)
N1—C71.4526 (18)C8—H8A0.9900
O2—C21.2084 (17)C8—H8B0.9900
C2—N31.3837 (18)C9—C101.520 (2)
N3—C41.3743 (19)C9—H9A0.9900
N3—H30.8800C9—H9B0.9900
O4—C41.2291 (17)C10—C111.523 (2)
C4—C51.446 (2)C10—H10A0.9900
F5—C51.3462 (16)C10—H10B0.9900
C5—C61.325 (2)C11—H11A0.9800
C6—H60.9500C11—H11B0.9800
O7—C71.2077 (17)C11—H11C0.9800
C6—N1—C2120.42 (12)C9—C8—H8A109.1
C6—N1—C7115.53 (12)C7—C8—H8B109.1
C2—N1—C7123.89 (12)C9—C8—H8B109.1
O2—C2—N3121.00 (13)H8A—C8—H8B107.9
O2—C2—N1124.45 (13)C10—C9—C8114.16 (12)
N3—C2—N1114.55 (13)C10—C9—H9A108.7
C4—N3—C2128.41 (13)C8—C9—H9A108.7
C4—N3—H3115.8C10—C9—H9B108.7
C2—N3—H3115.8C8—C9—H9B108.7
O4—C4—N3122.41 (13)H9A—C9—H9B107.6
O4—C4—C5124.89 (14)C9—C10—C11111.57 (13)
N3—C4—C5112.70 (13)C9—C10—H10A109.3
C6—C5—F5120.95 (13)C11—C10—H10A109.3
C6—C5—C4122.57 (14)C9—C10—H10B109.3
F5—C5—C4116.48 (13)C11—C10—H10B109.3
C5—C6—N1121.32 (13)H10A—C10—H10B108.0
C5—C6—H6119.3C10—C11—H11A109.5
N1—C6—H6119.3C10—C11—H11B109.5
O7—C7—N1116.83 (13)H11A—C11—H11B109.5
O7—C7—C8123.69 (13)C10—C11—H11C109.5
N1—C7—C8119.47 (12)H11A—C11—H11C109.5
C7—C8—C9112.37 (12)H11B—C11—H11C109.5
C7—C8—H8A109.1
C6—N1—C2—O2−179.04 (14)F5—C5—C6—N1−179.41 (12)
C7—N1—C2—O2−3.7 (2)C4—C5—C6—N10.2 (2)
C6—N1—C2—N30.63 (19)C2—N1—C6—C50.1 (2)
C7—N1—C2—N3175.95 (12)C7—N1—C6—C5−175.62 (13)
O2—C2—N3—C4177.79 (14)C6—N1—C7—O75.59 (19)
N1—C2—N3—C4−1.9 (2)C2—N1—C7—O7−169.94 (13)
C2—N3—C4—O4−178.30 (14)C6—N1—C7—C8−175.64 (12)
C2—N3—C4—C52.1 (2)C2—N1—C7—C88.8 (2)
O4—C4—C5—C6179.25 (14)O7—C7—C8—C9−6.9 (2)
N3—C4—C5—C6−1.2 (2)N1—C7—C8—C9174.46 (12)
O4—C4—C5—F5−1.1 (2)C7—C8—C9—C10−74.69 (17)
N3—C4—C5—F5178.46 (12)C8—C9—C10—C11176.35 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3···O4i0.881.992.8588 (16)170
C6—H6···O70.952.282.6102 (17)100
C6—H6···O7ii0.952.343.2266 (19)154

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2544).

References

  • Beall, H. D., Prankerd, R. J. & Sloan, K. B. (1997). Drug Dev. Ind. Pharm.23, 517–525.
  • Jiang, A., Hu, S., Wang, Y. & Chen, Q. (1988). Gaodeng Xuexiao Huaxue Xuebao, 9, 307–309.
  • Lehmler, H.-J. & Parkin, S. (2000). Acta Cryst. C56, e518–e519.
  • Nonius (1998). COLLECT Nonius BV, Delft, The Netherlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
  • Roberts, W. J. & Sloan, K. B. (1999). J. Pharm. Sci.88, 515–522. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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