3-Benzoyl-5-chloro­uracil

Gainsford, G.J.; Clinch, K.

doi:10.1107/S1600536809001287

organic compounds

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ISSN: 2056-9890

Volume 65| Part 2| February 2009| Page o342

doi:10.1107/S1600536809001287

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3-Benzoyl-5-chlorouracil

Graeme J. Gainsford ^a ^* and Keith Clinch ^a

^aIndustrial Research Limited, PO Box 31-310, Lower Hutt, New Zealand
^*Correspondence e-mail: g.gainsford@irl.cri.nz

(Received 4 January 2009; accepted 11 January 2009; online 17 January 2009)

The dihedral angle between the planes of two aromatic rings in the title compound [systematic name: 3-benzoyl-5-chloro-pyrimidine-2,4(1H,3H)-dione], C₁₁H₇ClN₂O₃, is 86.79 (6)°. Centrosymmetric dimers formed by N—H⋯O hydrogen bonds are linked through C—H⋯O interactions, forming a two-dimensional network parallel to (10 $[\overline{1}]$ ).

Related literature

For a related structure, see: Parvez et al. (2007 ). For graph-set notation, see: Bernstein et al. (1995 ). For the synthesis, see: Birck et al. (2009 ).

Experimental

Crystal data

C₁₁H₇ClN₂O₃
M_r = 250.64
Monoclinic, C 2/c
a = 21.9357 (9) Å
b = 5.4020 (2) Å
c = 19.9642 (9) Å
β = 113.169 (2)°
V = 2174.89 (16) Å³
Z = 8
Mo Kα radiation
μ = 0.35 mm⁻¹
T = 133 (2) K
0.34 × 0.21 × 0.03 mm

Data collection

Bruker APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Blessing, 1995 ; Bruker, 2006 ) T_min = 0.810, T_max = 0.990
24616 measured reflections
2899 independent reflections
2189 reflections with I > 2σ(I)
R_int = 0.047

Refinement

R[F² > 2σ(F²)] = 0.041
wR(F²) = 0.110
S = 1.07
2899 reflections
162 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.37 e Å⁻³
Δρ_min = −0.42 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯O14ⁱ	0.86 (3)	1.91 (3)	2.770 (2)	173 (3)
C9—H9⋯O15ⁱⁱ	0.95	2.46	3.182 (3)	133
C10—H10⋯O15ⁱⁱⁱ	0.95	2.57	3.447 (3)	153
Symmetry codes: (i) $[-x+{\script{3\over 2}}, -y+{\script{5\over 2}}, -z+1]$ ; (ii) x, y+1, z; (iii) $[-x+1, y+1, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP in WinGX (Farrugia, 1999 ) and Mercury (Bruno et al., 2002 ); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809001287/ci2757sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809001287/ci2757Isup2.hkl

checkCIF report

Comment top

The title compound, (I), was prepared for incorporation into potential thymidine phosphorylase inhibitors (Birck et al., 2009). Its molecular structure is shown in Fig.1, labelled in the same way as the closely related 5-methyl adduct, 3-benzoylthymine (II) (Parvez et al., 2007). The dihedral angle between the aromatic rings in (I) is 86.79 (10)° compared with 83.82 (6)° in (II). The N3–C7–C8–C9 torsion angle of the ring-linkage is -6.9 (2)° in (I) and -11.8 (2)° in (II). Bond distances are normal.

The crystal packing is dominated by centrosymmetric N1—H1N···O14 hydrogen bonded dimers (common graph-set R₂²(8), Bernstein et al., 1995) linked by weaker C–H···O interactions (Table 1). These two types of packing interactions are also found in (II), though not reported, as is illustrated in the comparison Fig 2. The replacement of the methyl group in (II) by chlorine in (I) has not enhanced the packing interactions: neither group/atom play a significant role.

Related literature top

For a related structure, see: Parvez et al. (2007). For graph-set notation, see: Bernstein et al. (1995). For the synthesis, see: Birck et al. (2009).

Experimental top

Synthetic details are given in Birck et al. (2009).

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP in WinGX (Farrugia, 1999) and Mercury (Bruno et al., 2002); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures top

Fig. 1. Molecular structure of the title compound. Displacement ellipsoids are shown at the 30% probability level.

Fig. 2. Comparison of similar hydrogen bond interactions (dotted lines) in (I) & (II) (MERCURY; Bruno et al., 2002). Only the hydrogen atoms involved are included. Nitrogen and Oxygen atoms are shown as balls. Colours: Nitrogen, blue (light gray); Oxygen, red (black); Carbon, (gray); Hydrogen, dark blue. Coordinates of (II) are labelled as in deposited data (SEVQUG) and additional molecules shown in purple for clarity. Symmetry Codes: (i) 3/2 - x, 5/2 - y, 1 - z (ii) x, y + 1, z (iii) 3/2 - x, 3/2 - y, 1 - z (iv) 2 - x, 1 - y, -z (v) 1/2 + x, 1/2 - y, -z (vi) 3/2 - x, 1/2 + y, z

3-Benzoyl-5-chloro-pyrimidine-2,4(1H,3H)-dione top

Crystal data top

C₁₁H₇ClN₂O₃	F(000) = 1024
M_r = 250.64	D_x = 1.531 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 6298 reflections
a = 21.9357 (9) Å	θ = 2.2–28.7°
b = 5.4020 (2) Å	µ = 0.35 mm⁻¹
c = 19.9642 (9) Å	T = 133 K
β = 113.169 (2)°	Plate, colourless
V = 2174.89 (16) Å³	0.34 × 0.21 × 0.03 mm
Z = 8

Data collection top

Bruker–Nonius APEXII CCD area-detector diffractometer	2899 independent reflections
Radiation source: fine-focus sealed tube	2189 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.047
Detector resolution: 8.333 pixels mm^-1	θ_max = 29.0°, θ_min = 3.5°
ϕ and ω scans	h = −29→29
Absorption correction: multi-scan (SADABS; Blessing, 1995; Bruker, 2006)	k = −7→7
T_min = 0.810, T_max = 0.990	l = −27→27
24616 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)] = 0.041	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.110	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0468P)² + 2.9413P] where P = (F_o² + 2F_c²)/3
2899 reflections	(Δ/σ)_max = 0.001
162 parameters	Δρ_max = 0.37 e Å⁻³
0 restraints	Δρ_min = −0.42 e Å⁻³

Crystal data top

C₁₁H₇ClN₂O₃	V = 2174.89 (16) Å³
M_r = 250.64	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 21.9357 (9) Å	µ = 0.35 mm⁻¹
b = 5.4020 (2) Å	T = 133 K
c = 19.9642 (9) Å	0.34 × 0.21 × 0.03 mm
β = 113.169 (2)°

Data collection top

Bruker–Nonius APEXII CCD area-detector diffractometer	2899 independent reflections
Absorption correction: multi-scan (SADABS; Blessing, 1995; Bruker, 2006)	2189 reflections with I > 2σ(I)
T_min = 0.810, T_max = 0.990	R_int = 0.047
24616 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.041	0 restraints
wR(F²) = 0.110	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.37 e Å⁻³
2899 reflections	Δρ_min = −0.42 e Å⁻³
162 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. An extinction parameter was refined. 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
Cl16	0.72366 (2)	0.47956 (9)	0.28923 (3)	0.03151 (14)
O14	0.68050 (6)	1.0941 (2)	0.50072 (7)	0.0230 (3)
O15	0.61273 (7)	0.4522 (3)	0.34170 (8)	0.0316 (3)
O17	0.60738 (6)	0.5865 (3)	0.49746 (7)	0.0259 (3)
N1	0.73929 (7)	1.0080 (3)	0.43155 (8)	0.0196 (3)
H1N	0.7670 (11)	1.123 (5)	0.4545 (12)	0.034 (6)*
N3	0.64590 (6)	0.7803 (3)	0.41885 (8)	0.0185 (3)
C2	0.68836 (8)	0.9710 (3)	0.45337 (9)	0.0178 (3)
C4	0.65184 (8)	0.6191 (3)	0.36658 (10)	0.0212 (4)
C5	0.70867 (8)	0.6748 (3)	0.34898 (10)	0.0206 (3)
C6	0.74965 (8)	0.8616 (3)	0.38121 (10)	0.0204 (3)
H6	0.7865 (11)	0.905 (4)	0.3704 (11)	0.025 (5)*
C7	0.59307 (8)	0.7215 (3)	0.44632 (10)	0.0189 (3)
C8	0.52873 (8)	0.8413 (3)	0.40703 (10)	0.0204 (4)
C9	0.51969 (9)	1.0174 (4)	0.35368 (11)	0.0280 (4)
H9	0.5554	1.0604	0.3403	0.034*
C10	0.45871 (10)	1.1310 (4)	0.31977 (12)	0.0367 (5)
H10	0.4524	1.2524	0.2832	0.044*
C11	0.40709 (10)	1.0666 (5)	0.33943 (13)	0.0398 (5)
H11	0.3650	1.1426	0.3156	0.048*
C12	0.41587 (10)	0.8944 (5)	0.39288 (14)	0.0458 (6)
H12	0.3800	0.8527	0.4061	0.055*
C13	0.47664 (10)	0.7816 (4)	0.42752 (13)	0.0375 (5)
H13	0.4830	0.6640	0.4651	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl16	0.0351 (3)	0.0321 (3)	0.0358 (3)	−0.0100 (2)	0.0230 (2)	−0.0132 (2)
O14	0.0189 (6)	0.0250 (6)	0.0294 (7)	−0.0055 (5)	0.0141 (5)	−0.0060 (5)
O15	0.0311 (7)	0.0315 (8)	0.0372 (8)	−0.0164 (6)	0.0186 (6)	−0.0120 (6)
O17	0.0181 (6)	0.0285 (7)	0.0323 (7)	0.0009 (5)	0.0112 (5)	0.0095 (6)
N1	0.0141 (6)	0.0217 (7)	0.0250 (8)	−0.0068 (6)	0.0098 (6)	−0.0051 (6)
N3	0.0131 (6)	0.0190 (7)	0.0249 (8)	−0.0042 (5)	0.0091 (6)	−0.0012 (6)
C2	0.0122 (7)	0.0185 (8)	0.0225 (8)	−0.0023 (6)	0.0065 (6)	0.0010 (6)
C4	0.0189 (8)	0.0226 (8)	0.0230 (9)	−0.0047 (7)	0.0091 (7)	−0.0011 (7)
C5	0.0193 (8)	0.0212 (8)	0.0239 (9)	−0.0016 (6)	0.0112 (7)	−0.0022 (7)
C6	0.0157 (7)	0.0232 (8)	0.0236 (9)	−0.0014 (7)	0.0092 (7)	−0.0001 (7)
C7	0.0138 (7)	0.0194 (8)	0.0257 (9)	−0.0047 (6)	0.0099 (7)	−0.0015 (7)
C8	0.0143 (7)	0.0212 (8)	0.0259 (9)	−0.0010 (6)	0.0079 (7)	0.0027 (7)
C9	0.0210 (8)	0.0324 (10)	0.0341 (10)	0.0011 (8)	0.0145 (8)	0.0095 (8)
C10	0.0299 (10)	0.0415 (12)	0.0403 (13)	0.0105 (9)	0.0156 (9)	0.0181 (10)
C11	0.0218 (9)	0.0514 (14)	0.0462 (13)	0.0136 (9)	0.0136 (9)	0.0153 (11)
C12	0.0188 (9)	0.0631 (16)	0.0621 (16)	0.0099 (10)	0.0229 (10)	0.0265 (13)
C13	0.0210 (9)	0.0467 (13)	0.0504 (13)	0.0052 (9)	0.0202 (9)	0.0245 (10)

Geometric parameters (Å, º) top

Cl16—C5	1.7179 (18)	C7—C8	1.468 (2)
O14—C2	1.222 (2)	C8—C9	1.383 (3)
O15—C4	1.209 (2)	C8—C13	1.394 (2)
O17—C7	1.192 (2)	C9—C10	1.382 (3)
N1—C2	1.364 (2)	C9—H9	0.95
N1—C6	1.366 (2)	C10—C11	1.381 (3)
N1—H1N	0.87 (3)	C10—H10	0.95
N3—C2	1.378 (2)	C11—C12	1.371 (3)
N3—C4	1.404 (2)	C11—H11	0.95
N3—C7	1.498 (2)	C12—C13	1.379 (3)
C4—C5	1.453 (2)	C12—H12	0.95
C5—C6	1.336 (2)	C13—H13	0.95
C6—H6	0.94 (2)

C2—N1—C6	122.97 (15)	C8—C7—N3	115.49 (14)
C2—N1—H1N	115.5 (15)	C9—C8—C13	119.96 (17)
C6—N1—H1N	121.3 (15)	C9—C8—C7	122.09 (15)
C2—N3—C4	126.39 (14)	C13—C8—C7	117.87 (16)
C2—N3—C7	116.31 (14)	C10—C9—C8	120.02 (17)
C4—N3—C7	116.87 (13)	C10—C9—H9	120.0
O14—C2—N1	123.34 (15)	C8—C9—H9	120.0
O14—C2—N3	121.36 (14)	C11—C10—C9	119.52 (19)
N1—C2—N3	115.29 (15)	C11—C10—H10	120.2
O15—C4—N3	120.65 (15)	C9—C10—H10	120.2
O15—C4—C5	126.35 (17)	C12—C11—C10	120.82 (19)
N3—C4—C5	113.00 (15)	C12—C11—H11	119.6
C6—C5—C4	121.21 (16)	C10—C11—H11	119.6
C6—C5—Cl16	121.45 (13)	C11—C12—C13	120.15 (19)
C4—C5—Cl16	117.23 (13)	C11—C12—H12	119.9
C5—C6—N1	121.09 (16)	C13—C12—H12	119.9
C5—C6—H6	123.4 (13)	C12—C13—C8	119.51 (19)
N1—C6—H6	115.4 (13)	C12—C13—H13	120.2
O17—C7—C8	126.97 (15)	C8—C13—H13	120.2
O17—C7—N3	117.53 (15)

C6—N1—C2—O14	176.60 (17)	C2—N3—C7—O17	−84.6 (2)
C6—N1—C2—N3	−2.5 (2)	C4—N3—C7—O17	88.4 (2)
C4—N3—C2—O14	−176.59 (17)	C2—N3—C7—C8	94.63 (18)
C7—N3—C2—O14	−4.3 (2)	C4—N3—C7—C8	−92.32 (19)
C4—N3—C2—N1	2.6 (2)	O17—C7—C8—C9	172.27 (19)
C7—N3—C2—N1	174.86 (14)	N3—C7—C8—C9	−6.9 (3)
C2—N3—C4—O15	177.38 (17)	O17—C7—C8—C13	−4.6 (3)
C7—N3—C4—O15	5.1 (3)	N3—C7—C8—C13	176.25 (18)
C2—N3—C4—C5	−1.5 (2)	C13—C8—C9—C10	−1.2 (3)
C7—N3—C4—C5	−173.75 (15)	C7—C8—C9—C10	−177.94 (19)
O15—C4—C5—C6	−178.47 (19)	C8—C9—C10—C11	−0.2 (4)
N3—C4—C5—C6	0.3 (3)	C9—C10—C11—C12	1.0 (4)
O15—C4—C5—Cl16	−2.2 (3)	C10—C11—C12—C13	−0.4 (4)
N3—C4—C5—Cl16	176.58 (12)	C11—C12—C13—C8	−0.9 (4)
C4—C5—C6—N1	−0.4 (3)	C9—C8—C13—C12	1.7 (4)
Cl16—C5—C6—N1	−176.52 (14)	C7—C8—C13—C12	178.6 (2)
C2—N1—C6—C5	1.6 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O14ⁱ	0.86 (3)	1.91 (3)	2.770 (2)	173 (3)
C9—H9···O15ⁱⁱ	0.95	2.46	3.182 (3)	133
C10—H10···O15ⁱⁱⁱ	0.95	2.57	3.447 (3)	153

Symmetry codes: (i) −x+3/2, −y+5/2, −z+1; (ii) x, y+1, z; (iii) −x+1, y+1, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₁H₇ClN₂O₃
M_r	250.64
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	133
a, b, c (Å)	21.9357 (9), 5.4020 (2), 19.9642 (9)
β (°)	113.169 (2)
V (Å³)	2174.89 (16)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.35
Crystal size (mm)	0.34 × 0.21 × 0.03

Data collection
Diffractometer	Bruker–Nonius APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Blessing, 1995; Bruker, 2006)
T_min, T_max	0.810, 0.990
No. of measured, independent and observed [I > 2σ(I)] reflections	24616, 2899, 2189
R_int	0.047
(sin θ/λ)_max (Å⁻¹)	0.682

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.041, 0.110, 1.07
No. of reflections	2899
No. of parameters	162
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.37, −0.42

Computer programs: APEX2 (Bruker, 2006), SAINT (Bruker, 2006), SHELXS97 (Sheldrick, 2008), ORTEP in WinGX (Farrugia, 1999) and Mercury (Bruno et al., 2002), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O14ⁱ	0.86 (3)	1.91 (3)	2.770 (2)	173 (3)
C9—H9···O15ⁱⁱ	0.95	2.46	3.182 (3)	133
C10—H10···O15ⁱⁱⁱ	0.95	2.57	3.447 (3)	153

Symmetry codes: (i) −x+3/2, −y+5/2, −z+1; (ii) x, y+1, z; (iii) −x+1, y+1, −z+1/2.

Acknowledgements

We thank Dr J. Wikaira and Dr C. Fitchett of the University of Canterbury, New Zealand, for their assistance with the data collection.

References

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