3-Benzoyl-5-chloro­uracil

Abstract

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).

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,

• a = 21.9357 (9) Å

• b = 5.4020 (2) Å

• c = 19.9642 (9) Å

• β = 113.169 (2)°

• V = 2174.89 (16) ų

• 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[F ² > 2σ(F ²)] = 0.041

• wR(F ²) = 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

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 ▶).

Supplementary Material

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

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) ; (ii) ; (iii) .

supplementary crystallographic information

Comment

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.

Experimental

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

Refinement

Atoms H1N and H6 were located in a difference map and refined freely. All other H atoms were restrained using riding models (C-H = 0.95 Å), with U_iso values constrained to 1.2 times that of the U_eq of their parent atom.

Figures

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

Crystal data

C11H7ClN2O3	F(000) = 1024
Mr = 250.64	Dx = 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

Bruker–Nonius APEXII CCD area-detector diffractometer	2899 independent reflections
Radiation source: fine-focus sealed tube	2189 reflections with I > 2σ(I)
graphite	Rint = 0.047
Detector resolution: 8.333 pixels mm-1	θmax = 29.0°, θmin = 3.5°
φ and ω scans	h = −29→29
Absorption correction: multi-scan (SADABS; Blessing, 1995; Bruker, 2006)	k = −7→7
Tmin = 0.810, Tmax = 0.990	l = −27→27
24616 measured reflections

Refinement

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(Fo2) + (0.0468P)2 + 2.9413P] where P = (Fo2 + 2Fc2)/3
2899 reflections	(Δ/σ)max = 0.001
162 parameters	Δρmax = 0.37 e Å−3
0 restraints	Δρmin = −0.42 e Å−3

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. 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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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.