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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1404–o1405.
Published online 2009 May 29. doi:  10.1107/S1600536809019035
PMCID: PMC2969686

Ethyl 4-[3,5-bis­(trifluoro­meth­yl)phen­yl]-6-methyl-2-oxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate

Abstract

In the title compound, C16H14F6N2O3, the dihydro­pyrimid­in­one ring adopts an envelope conformation. In the crystal, mol­ecules are linked by N—H(...)O and C—H(...)O hydrogen bonds into a ribbon-like structure along the b axis. In the ribbon, a pair of bifurcated acceptor N—H(...)O and C—H(...)O bonds generate an R 2 1(6) ring motif. Adjacent ribbons are linked via C—H(...)F hydrogen bonds.

Related literature

For general background and the pharmaceutical applications of pyrimidinones, see: Kalluraya & Rai (2003 [triangle]); Atwal (1990 [triangle]); Steele et al. (1998 [triangle]); Manjula et al. (2004 [triangle]); Matsuda & Hirao (1965 [triangle]). For a related structure, see: Fun et al. (2009 [triangle]). For ring conformations, see: Cremer & Pople (1975 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1404-scheme1.jpg

Experimental

Crystal data

  • C16H14F6N2O3
  • M r = 396.29
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1404-efi1.jpg
  • a = 12.6876 (2) Å
  • b = 7.3073 (1) Å
  • c = 19.9547 (3) Å
  • β = 114.443 (1)°
  • V = 1684.23 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.15 mm−1
  • T = 110 K
  • 0.45 × 0.25 × 0.22 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.908, T max = 0.967
  • 22326 measured reflections
  • 7151 independent reflections
  • 5660 reflections with I > 2σ(I)
  • R int = 0.025

Refinement

  • R[F 2 > 2σ(F 2)] = 0.046
  • wR(F 2) = 0.134
  • S = 1.04
  • 7151 reflections
  • 254 parameters
  • 36 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.49 e Å−3
  • Δρmin = −0.45 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809019035/ci2801sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809019035/ci2801Isup2.hkl

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

Acknowledgments

HKF and CKQ thank Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (No. 1001/PFIZIK/811012). CKQ also thanks USM for a Research Fellowship.

supplementary crystallographic information

Comment

3,4-Dihydropyrimidinones are compounds that have been drawn wide-spread attention due to their pharmaceutical applications. A variety of dihydropyrimidinone derivatives have been screened for antihypertension (Atwal, 1990) and antibacterial (Matsuda & Hirao, 1965) activities. Michael addition followed by aldol condensation known as the Robinson's annulation is synthetically a very useful reaction for the construction of six-membered cyclic compounds (Kalluraya & Rai, 2003). The common synthetic routes to these compounds generally involve multi-step transformations that are essentially based on the Biginelli condensation methodology (Steele et al., 1998). These pyrimidinones are also associated with activities like calcium channel blocking (Manjula et al., 2004). We report here the crystal structure of the title compound which was synthesized by means of Robinson's annulation employing microwave technique.

The bond lengths (Allen et al., 1987) and angles in the molecule (Fig. 1) are within normal ranges, and are comparable to those observed in a closely related structure (Fun et al., 2009). The dihydropyrimidinone ring adopts an envelope conformation with atom C7 as the flap. The puckering parameters (Cremer & Pople, 1975) are Q = 0.288 (1) Å; Θ = 72.0 (2)° and [var phi] = 52.3 (2)°. The dihedral angle formed by benzene ring (C1—C6) and the N1/C8/N2/C9-/C10 plane is 89.33 (3)°.

In the solid state, the molecules are linked into a ribbon-like structure (Fig. 2) along the [010] by N–H···O and C–H···O hydrogen bonds (Table 1). In the ribbon, C14–H14B···O3 and N2–H1N2···O3 interactions form a pair of bifurcated acceptor bonds, generating an R21(6) ring motif (Bernstein et al., 1995). The adjacent ribbons are linked via C—H···F hydrogen bonds (Fig. 3).

Experimental

A mixture of 3,5-bis(trifluoromethyl)benzaldehyde (0.01 mol), ethyl acetoacetate (0.015 mol), thiourea (0.01 mol) and conc. H2SO4 (2 drops) in absolute alcohol (10 ml) taken in a beaker (100 ml) was zapped inside a MW oven for a duration of 3 minutes (at 160 Watt i.e, 25% MW power). The reaction mixture was then allowed to stand at room temperature and the product formed was filtered, washed with ethanol followed by water and dried. Further purification was done by recrystallization from ethanol. Single crystals suitable for X-ray analysis were obtained by slow evaporation of an ethanol solution.

Refinement

Atoms H1N1 and H1N2 were located in a difference Fourier map and refined freely. The remaining H atoms were positioned geometrically and refined using a riding model, with C-H = 0.95–1.00 Å and Uiso(H) = 1.2 or 1.5Ueq(C). A rotating-group model was applied for the methyl groups. Some of the F atoms show elongated ellipsoids indicating disorder. Attempts to refine a disorder model resulted in large s.u's on occupancy factors and almost the same positional parameters for corresponding F atoms in the major and minor disorder components. Hence the original model was used with the Uij parameters of all F atoms restrained to an approximate isotropic behaviour.

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of the title compound, viewed along the [101]. Intermolecular interactions are shown as dashed lines.
Fig. 3.
The crystal packing viewed along the b axis. Intermolecular interactions are shown as dashed lines.

Crystal data

C16H14F6N2O3F(000) = 808
Mr = 396.29Dx = 1.563 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 9602 reflections
a = 12.6876 (2) Åθ = 3.2–35.0°
b = 7.3073 (1) ŵ = 0.15 mm1
c = 19.9547 (3) ÅT = 110 K
β = 114.443 (1)°Block, colourless
V = 1684.23 (5) Å30.45 × 0.25 × 0.22 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer7151 independent reflections
Radiation source: fine-focus sealed tube5660 reflections with I > 2σ(I)
graphiteRint = 0.025
[var phi] and ω scansθmax = 35.0°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −20→20
Tmin = 0.908, Tmax = 0.967k = −11→11
22326 measured reflectionsl = −32→32

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0681P)2 + 0.4398P] where P = (Fo2 + 2Fc2)/3
7151 reflections(Δ/σ)max = 0.001
254 parametersΔρmax = 0.49 e Å3
36 restraintsΔρmin = −0.45 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 110.0 (1) K.
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)

xyzUiso*/Ueq
F11.02153 (7)1.04916 (15)0.79988 (6)0.0546 (3)
F21.12550 (8)0.80663 (18)0.82674 (7)0.0625 (3)
F31.08940 (8)0.94509 (16)0.90918 (5)0.0510 (3)
F40.96398 (11)0.31292 (16)0.94197 (6)0.0734 (4)
F50.78290 (13)0.33990 (15)0.91770 (7)0.0721 (4)
F60.83618 (9)0.18885 (11)0.84630 (5)0.0416 (2)
O10.54733 (7)1.21425 (11)0.72029 (5)0.02532 (16)
O20.65993 (7)0.70237 (10)0.50892 (4)0.02120 (15)
O30.63160 (7)0.49775 (10)0.58404 (4)0.01973 (14)
N10.56554 (7)0.90955 (12)0.70349 (5)0.01736 (15)
H1N10.5326 (13)0.881 (2)0.7321 (8)0.024 (4)*
N20.62532 (7)1.12340 (12)0.64147 (5)0.01722 (15)
H1N20.6307 (13)1.238 (2)0.6327 (8)0.025 (4)*
C10.83363 (8)0.82264 (14)0.76186 (5)0.01796 (16)
H10.82810.93010.73380.022*
C20.93726 (9)0.77888 (16)0.82033 (5)0.02191 (19)
C30.94750 (10)0.62163 (17)0.86221 (6)0.0247 (2)
H31.01850.59270.90240.030*
C40.85233 (10)0.50878 (15)0.84400 (5)0.02311 (19)
C50.74728 (9)0.55033 (14)0.78490 (5)0.01934 (17)
H50.68290.47040.77270.023*
C60.73721 (8)0.70860 (13)0.74415 (5)0.01511 (15)
C70.62140 (7)0.75947 (13)0.68172 (5)0.01453 (15)
H70.56950.65010.67050.017*
C80.57787 (8)1.08737 (14)0.69151 (5)0.01731 (16)
C90.64143 (7)0.99139 (13)0.59672 (5)0.01476 (15)
C100.63470 (7)0.81180 (12)0.61226 (5)0.01376 (14)
C110.64206 (7)0.65599 (13)0.56809 (5)0.01450 (15)
C120.66444 (9)0.55645 (15)0.46087 (5)0.02057 (18)
H12A0.58600.50720.43170.025*
H12B0.71460.45560.49000.025*
C130.71342 (13)0.64003 (19)0.41112 (7)0.0337 (3)
H13A0.71190.54960.37450.051*
H13B0.79350.67850.44040.051*
H13C0.66690.74660.38610.051*
C140.66536 (10)1.06995 (14)0.53478 (5)0.02129 (18)
H14A0.73851.02050.53690.032*
H14B0.67091.20350.53940.032*
H14C0.60231.03710.48760.032*
C150.85946 (13)0.33881 (18)0.88774 (7)0.0338 (3)
C161.04253 (10)0.8954 (2)0.83865 (7)0.0314 (2)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.0302 (4)0.0609 (6)0.0583 (6)−0.0195 (4)0.0037 (4)0.0275 (5)
F20.0249 (4)0.0770 (8)0.0886 (8)−0.0072 (4)0.0266 (5)−0.0217 (7)
F30.0464 (5)0.0600 (7)0.0342 (4)−0.0237 (5)0.0044 (4)−0.0086 (4)
F40.0821 (8)0.0439 (6)0.0514 (6)−0.0039 (5)−0.0152 (5)0.0284 (5)
F50.1372 (11)0.0420 (6)0.0831 (8)0.0306 (6)0.0916 (9)0.0335 (6)
F60.0642 (6)0.0183 (4)0.0462 (5)0.0014 (4)0.0267 (4)0.0044 (3)
O10.0308 (4)0.0193 (4)0.0354 (4)0.0011 (3)0.0233 (3)−0.0065 (3)
O20.0373 (4)0.0144 (3)0.0191 (3)−0.0018 (3)0.0188 (3)−0.0016 (3)
O30.0293 (3)0.0120 (3)0.0219 (3)−0.0003 (3)0.0147 (3)0.0004 (2)
N10.0207 (3)0.0156 (4)0.0226 (3)−0.0005 (3)0.0157 (3)−0.0004 (3)
N20.0235 (4)0.0112 (3)0.0226 (3)−0.0007 (3)0.0151 (3)−0.0012 (3)
C10.0194 (4)0.0180 (4)0.0178 (3)−0.0003 (3)0.0091 (3)0.0019 (3)
C20.0198 (4)0.0257 (5)0.0193 (4)0.0002 (4)0.0072 (3)0.0008 (4)
C30.0265 (5)0.0266 (5)0.0185 (4)0.0059 (4)0.0069 (3)0.0033 (4)
C40.0358 (5)0.0166 (4)0.0181 (4)0.0036 (4)0.0123 (4)0.0029 (3)
C50.0284 (4)0.0149 (4)0.0176 (4)−0.0010 (3)0.0123 (3)0.0005 (3)
C60.0203 (4)0.0134 (4)0.0146 (3)0.0000 (3)0.0103 (3)0.0000 (3)
C70.0178 (3)0.0128 (4)0.0164 (3)−0.0020 (3)0.0104 (3)−0.0009 (3)
C80.0175 (4)0.0165 (4)0.0218 (4)−0.0004 (3)0.0120 (3)−0.0025 (3)
C90.0175 (3)0.0126 (4)0.0161 (3)−0.0003 (3)0.0088 (3)−0.0001 (3)
C100.0174 (3)0.0120 (4)0.0143 (3)−0.0008 (3)0.0090 (3)0.0000 (3)
C110.0167 (3)0.0138 (4)0.0143 (3)−0.0002 (3)0.0077 (3)0.0001 (3)
C120.0268 (4)0.0195 (4)0.0191 (4)−0.0007 (4)0.0131 (3)−0.0049 (3)
C130.0535 (7)0.0306 (6)0.0308 (5)0.0104 (5)0.0313 (5)0.0070 (5)
C140.0348 (5)0.0140 (4)0.0210 (4)−0.0005 (4)0.0175 (4)0.0021 (3)
C150.0523 (7)0.0227 (6)0.0262 (5)0.0061 (5)0.0159 (5)0.0083 (4)
C160.0201 (4)0.0404 (7)0.0290 (5)−0.0035 (4)0.0054 (4)0.0029 (5)

Geometric parameters (Å, °)

F1—C161.3271 (17)C3—C41.3809 (17)
F2—C161.3388 (16)C3—H30.95
F3—C161.3317 (15)C4—C51.3994 (15)
F4—C151.3334 (17)C4—C151.4991 (16)
F5—C151.3348 (17)C5—C61.3890 (13)
F6—C151.3302 (16)C5—H50.95
O1—C81.2344 (11)C6—C71.5278 (13)
O2—C111.3350 (10)C7—C101.5129 (11)
O2—C121.4508 (12)C7—H71.00
O3—C111.2210 (12)C9—C101.3593 (13)
N1—C81.3420 (13)C9—C141.5034 (12)
N1—C71.4659 (12)C10—C111.4663 (12)
N1—H1N10.860 (15)C12—C131.5017 (15)
N2—C91.3859 (12)C12—H12A0.99
N2—C81.3879 (11)C12—H12B0.99
N2—H1N20.866 (17)C13—H13A0.98
C1—C21.3867 (14)C13—H13B0.98
C1—C61.3993 (13)C13—H13C0.98
C1—H10.95C14—H14A0.98
C2—C31.3949 (16)C14—H14B0.98
C2—C161.4961 (16)C14—H14C0.98
C11—O2—C12117.75 (8)C9—C10—C11125.94 (8)
C8—N1—C7124.42 (7)C9—C10—C7119.63 (8)
C8—N1—H1N1118.3 (11)C11—C10—C7114.42 (8)
C7—N1—H1N1116.5 (11)O3—C11—O2123.19 (8)
C9—N2—C8123.71 (8)O3—C11—C10122.54 (8)
C9—N2—H1N2120.0 (10)O2—C11—C10114.26 (8)
C8—N2—H1N2115.0 (10)O2—C12—C13106.15 (9)
C2—C1—C6120.04 (9)O2—C12—H12A110.5
C2—C1—H1120.0C13—C12—H12A110.5
C6—C1—H1120.0O2—C12—H12B110.5
C1—C2—C3120.99 (10)C13—C12—H12B110.5
C1—C2—C16120.94 (10)H12A—C12—H12B108.7
C3—C2—C16118.04 (10)C12—C13—H13A109.5
C4—C3—C2118.67 (9)C12—C13—H13B109.5
C4—C3—H3120.7H13A—C13—H13B109.5
C2—C3—H3120.7C12—C13—H13C109.5
C3—C4—C5121.09 (10)H13A—C13—H13C109.5
C3—C4—C15120.40 (10)H13B—C13—H13C109.5
C5—C4—C15118.51 (11)C9—C14—H14A109.5
C6—C5—C4119.92 (9)C9—C14—H14B109.5
C6—C5—H5120.0H14A—C14—H14B109.5
C4—C5—H5120.0C9—C14—H14C109.5
C5—C6—C1119.28 (9)H14A—C14—H14C109.5
C5—C6—C7120.29 (8)H14B—C14—H14C109.5
C1—C6—C7120.42 (8)F6—C15—F4106.15 (12)
N1—C7—C10109.47 (7)F6—C15—F5105.53 (12)
N1—C7—C6111.10 (7)F4—C15—F5107.51 (12)
C10—C7—C6111.98 (7)F6—C15—C4112.10 (10)
N1—C7—H7108.0F4—C15—C4112.97 (12)
C10—C7—H7108.0F5—C15—C4112.09 (11)
C6—C7—H7108.0F1—C16—F3106.23 (12)
O1—C8—N1124.21 (8)F1—C16—F2106.83 (12)
O1—C8—N2120.35 (9)F3—C16—F2106.23 (11)
N1—C8—N2115.41 (8)F1—C16—C2113.32 (10)
C10—C9—N2119.02 (8)F3—C16—C2112.12 (10)
C10—C9—C14127.54 (8)F2—C16—C2111.64 (12)
N2—C9—C14113.44 (8)
C6—C1—C2—C30.11 (15)N2—C9—C10—C7−5.85 (13)
C6—C1—C2—C16177.92 (10)C14—C9—C10—C7173.99 (9)
C1—C2—C3—C40.49 (16)N1—C7—C10—C926.13 (11)
C16—C2—C3—C4−177.37 (10)C6—C7—C10—C9−97.55 (10)
C2—C3—C4—C5−0.12 (15)N1—C7—C10—C11−155.34 (7)
C2—C3—C4—C15−179.77 (10)C6—C7—C10—C1180.98 (10)
C3—C4—C5—C6−0.86 (15)C12—O2—C11—O31.37 (14)
C15—C4—C5—C6178.79 (9)C12—O2—C11—C10−177.99 (8)
C4—C5—C6—C11.46 (13)C9—C10—C11—O3−177.59 (9)
C4—C5—C6—C7−177.28 (8)C7—C10—C11—O34.00 (13)
C2—C1—C6—C5−1.09 (14)C9—C10—C11—O21.78 (13)
C2—C1—C6—C7177.64 (8)C7—C10—C11—O2−176.63 (8)
C8—N1—C7—C10−31.69 (12)C11—O2—C12—C13−166.51 (9)
C8—N1—C7—C692.51 (11)C3—C4—C15—F6−120.88 (13)
C5—C6—C7—N1104.84 (9)C5—C4—C15—F659.46 (15)
C1—C6—C7—N1−73.88 (10)C3—C4—C15—F4−1.01 (17)
C5—C6—C7—C10−132.40 (9)C5—C4—C15—F4179.34 (11)
C1—C6—C7—C1048.88 (11)C3—C4—C15—F5120.64 (14)
C7—N1—C8—O1−167.27 (9)C5—C4—C15—F5−59.01 (15)
C7—N1—C8—N214.68 (14)C1—C2—C16—F17.46 (17)
C9—N2—C8—O1−167.38 (9)C3—C2—C16—F1−174.67 (11)
C9—N2—C8—N110.76 (14)C1—C2—C16—F3127.71 (12)
C8—N2—C9—C10−14.76 (14)C3—C2—C16—F3−54.42 (16)
C8—N2—C9—C14165.38 (9)C1—C2—C16—F2−113.22 (13)
N2—C9—C10—C11175.81 (8)C3—C2—C16—F264.65 (14)
C14—C9—C10—C11−4.35 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O1i0.86 (2)2.05 (2)2.8641 (13)157 (1)
N2—H1N2···O3ii0.86 (2)2.13 (2)2.9796 (12)166 (1)
C5—H5···O1iii0.952.463.3797 (14)162
C14—H14B···O3ii0.982.463.3571 (13)153
C12—H12B···F3iv0.992.473.2308 (15)133

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2801).

References

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