organic compounds
H,3H)-dione
of 6-chloro-5-isopropylpyrimidine-2,4(1aDepartment of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia, bKing Abdullah Institute for Nanotechnology (KAIN), King Saud University, Riyadh 11451, Saudi Arabia, and cX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hfun.c@ksu.edu.sa
In the molecule of the title compound, C7H9ClN2O2, the conformation is determined by intramolecular C—H⋯O and C—H⋯Cl hydrogen bonds, which generate S(6) and S(5) ring motifs. The isopropyl group is almost perpendicular to the pyrimidine ring with torsion angles of −70.8 (3) and 56.0 (3)°. In the crystal, two inversion-related molecules are linked via a pair of N—H⋯O hydrogen bonds into R22(8) dimers; these dimers are connected into chains extending along the bc plane via an additional N—H⋯O hydrogen bond and weaker C—H⋯O hydrogen bonds. The is further stabilized by a weak π–π interaction [3.6465 (10) Å] between adjacent pyrimidine-dione rings arranged in a head-to-tail fashion, producing a three-dimensional network.
Keywords: crystal structure; pyrimidine-2,4-dione; hydrogen bonds; π–π interaction.
CCDC reference: 1026350
1. Related literature
For the biological activity of pyrimidine-2,4(1H,3H)-diones, see: Miyasaka et al. (1989); Tanaka et al. (1995); Hopkins et al. (1996); El-Brollosy et al. (2009); Klein et al. (2001); Nencka et al. (2006); El-Emam et al. (2004). For the use of 5-alkyl-6-chloropyrimidine-2,4(1H,3H)-diones in synthesis, see: El-Emam et al. (2004). For related pyrimidine-2,4-dione structures, see: El-Brollosy et al. (2011); Al-Omary et al. (2014); Haress et al. (2014). For the synthesis of the title compound, see: Al-Turkistani et al. (2011); Koroniak et al. (1993). For hydrogen-bond motifs, see: Bernstein et al. (1995).
2. Experimental
2.1. Crystal data
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2.3. Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; 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 and PLATON (Spek, 2009).
Supporting information
CCDC reference: 1026350
10.1107/S1600536814021382/sj5429sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814021382/sj5429Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814021382/sj5429Isup3.cml
5-Isopropylbarbituric acid (8.51 g, 0.05 mol) was added portionwise with stirring to a mixture of phosphorus oxychloride (19.2 ml) and N,N-dimethyl aniline (10.3 ml) over a period of 10 minutes. The mixture was then heated under reflux for one hour. On cooling, the mixture was poured onto crushed ice (200 g m), stirred for 30 minutes and extracted with diethyl ether (400 ml). The ethereal extract was dried over anhydrous sodium sulfate and evaporated under vacuum at room temperature to yield the intermediate 5-isopropyl-2,4,6-trichloropyrimidine as a white waxy solid. 10% Sodium hydroxide (20 ml) was then added to the intermediate and the mixture was heated under reflux for 30 minutes. On cooling, the mixture was acidified with hydrochloric acid to pH 1–2 and the separated precipitate was filtered, washed with cold water and crystallized from ethanol to yield 6.98 g (74%) of the title compound (C7H9ClN2O2) as colourless crystals. M.P.: 257–259 °C.
1H NMR (DMSO-d6, 500.13 MHz): δ 1.14 (d, 6H, CH3, J = 7.2 Hz), 2.51–2.63 (m, 1H, CH), 11.22 (s, 1H, NH), 11.79 (s, 1H, NH). 13C NMR (DMSO-d6, 125.76 MHz): δ 20.02 (CH3), 26.52 (CH), 113.95 (C–5), 140.95 (C-6), 149.75 (C=O), 162.75 (C=O).
The nitrogen-bound H-atoms were located in a difference Fourier map and were refined freely [N–H 0.83 (2) and 0.84 (3) Å]. Other H atoms were positioned geometrically (C=H 0.95–0.96 Å) and refined using a riding model with Uiso(H) = 1.2 Ueq(C) or 1.5 Ueq(C) for methyl H atoms. A rotating group model was used for the methyl groups.
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 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) and PLATON (Spek, 2009).Fig. 1. The molecular structure of the title compound with atom labels and 30% probability displacement ellipsoids. Fig. 2. Crystal packing of the title compound, showing the hydrogen bonding interactions as dashed lines. H-atoms not involved in the hydrogen bonding are omited for clarity. |
C7H9ClN2O2 | F(000) = 392 |
Mr = 188.61 | Dx = 1.448 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54178 Å |
Hall symbol: -P 2ybc | Cell parameters from 3341 reflections |
a = 11.2244 (4) Å | θ = 3.9–69.4° |
b = 6.8288 (3) Å | µ = 3.62 mm−1 |
c = 11.6641 (5) Å | T = 296 K |
β = 104.577 (2)° | Block, colourless |
V = 865.26 (6) Å3 | 0.45 × 0.28 × 0.26 mm |
Z = 4 |
Bruker APEXII CCD diffractometer | 1553 independent reflections |
Radiation source: fine-focus sealed tube | 1444 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.027 |
ϕ and ω scans | θmax = 69.7°, θmin = 4.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −12→13 |
Tmin = 0.292, Tmax = 0.458 | k = −8→7 |
5647 measured reflections | l = −13→10 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.040 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.114 | w = 1/[σ2(Fo2) + (0.0664P)2 + 0.3263P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
1553 reflections | Δρmax = 0.27 e Å−3 |
122 parameters | Δρmin = −0.32 e Å−3 |
0 restraints | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0181 (15) |
C7H9ClN2O2 | V = 865.26 (6) Å3 |
Mr = 188.61 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 11.2244 (4) Å | µ = 3.62 mm−1 |
b = 6.8288 (3) Å | T = 296 K |
c = 11.6641 (5) Å | 0.45 × 0.28 × 0.26 mm |
β = 104.577 (2)° |
Bruker APEXII CCD diffractometer | 1553 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 1444 reflections with I > 2σ(I) |
Tmin = 0.292, Tmax = 0.458 | Rint = 0.027 |
5647 measured reflections |
R[F2 > 2σ(F2)] = 0.040 | 0 restraints |
wR(F2) = 0.114 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.27 e Å−3 |
1553 reflections | Δρmin = −0.32 e Å−3 |
122 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.20279 (5) | 0.71985 (9) | 0.34179 (6) | 0.0644 (3) | |
O1 | 0.55744 (12) | 0.3674 (2) | 0.28760 (12) | 0.0465 (4) | |
O2 | 0.35879 (13) | 0.0719 (2) | 0.53323 (13) | 0.0522 (4) | |
N1 | 0.39383 (14) | 0.5227 (2) | 0.32786 (14) | 0.0386 (4) | |
N2 | 0.45727 (14) | 0.2261 (2) | 0.41291 (14) | 0.0394 (4) | |
C1 | 0.29636 (16) | 0.5181 (3) | 0.37878 (16) | 0.0371 (4) | |
C2 | 0.47498 (15) | 0.3710 (3) | 0.33892 (15) | 0.0354 (4) | |
C3 | 0.36295 (16) | 0.2134 (3) | 0.46972 (15) | 0.0371 (4) | |
C4 | 0.27390 (15) | 0.3729 (3) | 0.44806 (15) | 0.0368 (4) | |
C5 | 0.16037 (17) | 0.3635 (3) | 0.49593 (17) | 0.0437 (5) | |
C6 | 0.1871 (2) | 0.3338 (5) | 0.6280 (2) | 0.0697 (7) | |
H6A | 0.2438 | 0.4322 | 0.6675 | 0.105* | |
H6B | 0.2226 | 0.2065 | 0.6480 | 0.105* | |
H6C | 0.1119 | 0.3437 | 0.6527 | 0.105* | |
C7 | 0.0719 (2) | 0.2127 (5) | 0.4302 (3) | 0.0815 (9) | |
H7A | 0.0568 | 0.2355 | 0.3465 | 0.122* | |
H7B | −0.0041 | 0.2217 | 0.4533 | 0.122* | |
H7C | 0.1065 | 0.0845 | 0.4486 | 0.122* | |
H1N1 | 0.403 (2) | 0.617 (4) | 0.2856 (19) | 0.043 (6)* | |
H1N2 | 0.506 (2) | 0.132 (4) | 0.422 (2) | 0.059 (7)* | |
H5 | 0.125 (2) | 0.489 (4) | 0.481 (2) | 0.058 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0662 (4) | 0.0486 (4) | 0.0892 (5) | 0.0249 (2) | 0.0395 (3) | 0.0243 (3) |
O1 | 0.0481 (7) | 0.0421 (8) | 0.0587 (9) | 0.0001 (6) | 0.0307 (6) | −0.0012 (6) |
O2 | 0.0522 (8) | 0.0506 (9) | 0.0614 (9) | 0.0157 (6) | 0.0286 (6) | 0.0227 (7) |
N1 | 0.0458 (8) | 0.0321 (8) | 0.0424 (9) | 0.0018 (6) | 0.0197 (7) | 0.0042 (6) |
N2 | 0.0394 (8) | 0.0381 (8) | 0.0451 (9) | 0.0095 (7) | 0.0187 (7) | 0.0061 (6) |
C1 | 0.0392 (9) | 0.0358 (9) | 0.0379 (10) | 0.0053 (7) | 0.0124 (7) | −0.0011 (7) |
C2 | 0.0373 (8) | 0.0343 (9) | 0.0365 (9) | −0.0012 (7) | 0.0129 (7) | −0.0044 (7) |
C3 | 0.0376 (9) | 0.0394 (10) | 0.0361 (10) | 0.0033 (7) | 0.0125 (7) | 0.0025 (7) |
C4 | 0.0380 (9) | 0.0393 (10) | 0.0346 (9) | 0.0044 (7) | 0.0120 (7) | 0.0005 (7) |
C5 | 0.0420 (9) | 0.0460 (11) | 0.0485 (11) | 0.0095 (8) | 0.0215 (8) | 0.0060 (8) |
C6 | 0.0585 (13) | 0.108 (2) | 0.0512 (14) | 0.0016 (14) | 0.0296 (11) | −0.0019 (13) |
C7 | 0.0472 (13) | 0.120 (3) | 0.0849 (19) | −0.0208 (14) | 0.0314 (13) | −0.0335 (17) |
Cl1—C1 | 1.7200 (18) | C4—C5 | 1.516 (2) |
O1—C2 | 1.222 (2) | C5—C7 | 1.500 (3) |
O2—C3 | 1.226 (2) | C5—C6 | 1.507 (3) |
N1—C2 | 1.364 (2) | C5—H5 | 0.95 (3) |
N1—C1 | 1.370 (2) | C6—H6A | 0.9600 |
N1—H1N1 | 0.83 (2) | C6—H6B | 0.9600 |
N2—C2 | 1.360 (2) | C6—H6C | 0.9600 |
N2—C3 | 1.386 (2) | C7—H7A | 0.9600 |
N2—H1N2 | 0.84 (3) | C7—H7B | 0.9600 |
C1—C4 | 1.342 (3) | C7—H7C | 0.9600 |
C3—C4 | 1.457 (2) | ||
C2—N1—C1 | 121.92 (16) | C7—C5—C6 | 111.5 (2) |
C2—N1—H1N1 | 117.6 (15) | C7—C5—C4 | 110.49 (17) |
C1—N1—H1N1 | 120.4 (15) | C6—C5—C4 | 114.38 (17) |
C2—N2—C3 | 126.87 (16) | C7—C5—H5 | 109.6 (16) |
C2—N2—H1N2 | 116.1 (17) | C6—C5—H5 | 106.3 (15) |
C3—N2—H1N2 | 116.9 (17) | C4—C5—H5 | 104.3 (15) |
C4—C1—N1 | 124.69 (16) | C5—C6—H6A | 109.5 |
C4—C1—Cl1 | 123.17 (14) | C5—C6—H6B | 109.5 |
N1—C1—Cl1 | 112.13 (13) | H6A—C6—H6B | 109.5 |
O1—C2—N2 | 123.07 (17) | C5—C6—H6C | 109.5 |
O1—C2—N1 | 122.60 (17) | H6A—C6—H6C | 109.5 |
N2—C2—N1 | 114.32 (15) | H6B—C6—H6C | 109.5 |
O2—C3—N2 | 119.22 (16) | C5—C7—H7A | 109.5 |
O2—C3—C4 | 124.43 (16) | C5—C7—H7B | 109.5 |
N2—C3—C4 | 116.35 (16) | H7A—C7—H7B | 109.5 |
C1—C4—C3 | 115.60 (16) | C5—C7—H7C | 109.5 |
C1—C4—C5 | 123.76 (16) | H7A—C7—H7C | 109.5 |
C3—C4—C5 | 120.54 (16) | H7B—C7—H7C | 109.5 |
C2—N1—C1—C4 | 3.4 (3) | N1—C1—C4—C5 | −175.22 (17) |
C2—N1—C1—Cl1 | −175.53 (14) | Cl1—C1—C4—C5 | 3.6 (3) |
C3—N2—C2—O1 | −176.48 (18) | O2—C3—C4—C1 | 177.94 (19) |
C3—N2—C2—N1 | 4.4 (3) | N2—C3—C4—C1 | −2.5 (2) |
C1—N1—C2—O1 | 175.02 (17) | O2—C3—C4—C5 | −5.7 (3) |
C1—N1—C2—N2 | −5.8 (2) | N2—C3—C4—C5 | 173.89 (16) |
C2—N2—C3—O2 | 179.34 (18) | C1—C4—C5—C7 | 105.3 (2) |
C2—N2—C3—C4 | −0.3 (3) | C3—C4—C5—C7 | −70.8 (3) |
N1—C1—C4—C3 | 1.0 (3) | C1—C4—C5—C6 | −128.0 (2) |
Cl1—C1—C4—C3 | 179.85 (13) | C3—C4—C5—C6 | 56.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1i | 0.83 (3) | 2.01 (3) | 2.833 (2) | 169 (2) |
N2—H1N2···O2ii | 0.83 (3) | 2.03 (3) | 2.854 (2) | 171 (2) |
C5—H5···Cl1 | 0.94 (3) | 2.57 (2) | 3.132 (2) | 118.7 (17) |
C6—H6A···O1iii | 0.96 | 2.56 | 3.455 (3) | 156 |
C6—H6B···O2 | 0.96 | 2.45 | 3.034 (3) | 119 |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+1, −y, −z+1; (iii) −x+1, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1i | 0.83 (3) | 2.01 (3) | 2.833 (2) | 169 (2) |
N2—H1N2···O2ii | 0.83 (3) | 2.03 (3) | 2.854 (2) | 171 (2) |
C5—H5···Cl1 | 0.94 (3) | 2.57 (2) | 3.132 (2) | 118.7 (17) |
C6—H6A···O1iii | 0.9600 | 2.5600 | 3.455 (3) | 156.00 |
C6—H6B···O2 | 0.9600 | 2.4500 | 3.034 (3) | 119.00 |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+1, −y, −z+1; (iii) −x+1, −y+1, −z+1. |
Acknowledgements
The financial support of the Deanship of Scientific Research and the Research Center for Female Scientific and Medical Colleges, King Saud University, is greatly appreciated. CSCK thanks Universiti Sains Malaysia (USM) for a postdoctoral research fellowship.
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Pyrimidine-2,4-diones and their related derivatives have long been known for their diverse chemotherapeutic activities including antiviral activity against HIV (Miyasaka et al., 1989; Tanaka et al., 1995; Hopkins et al., 1996; El-Emam et al., 2004). In addition, potent anticancer activity was observed for several pyrimidine-2,4-diones (Klein et al., 2001; Nencka et al., 2006). In a continuation of our interest in the chemical and pharmacological properties of pyrimidine and uracil derivatives (Al-Omary et al., 2014; Haress et al., 2014, El-Brollosy et al., 2009), we have synthesized the title compound (I) as a precursor to the synthesis of a potential chemotherapeutic agent (Al-Turkistani et al., 2011).
In the title compound (Fig. 1), the molecular conformation is stabilized by intramolecular C6–H6B···O2 and C5–H5···Cl1 hydrogen bonds incorporating S(6) and S(5) ring motifs respectively (Bernstein et al., 1995). The isopropyl group is almost perpendicular to the N1/N2/C1–C4 ring with the C3–C4–C5–C7 and C3–C4–C5–C6 torsion angles of -70.8 (3)° and 56.0 (3)° respectively. In the crystal structure, two adjacent molecules are linked via a pair of N2–H1N2···O2 intermolecular hydrogen bonds forming inversion related R22(8) dimers (Fig. 2).; these dimers are connected into chains via N1–H1N1···O1 and weak C6–H6A···O1 hydrogen bonds extending along the bc plane. The crystal structure is further stabilized by a weak π···π interaction [3.6465 (10) Å] producing a three-dimensional network.