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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2466.
Published online 2009 September 16. doi:  10.1107/S1600536809036356
PMCID: PMC2970446

1-Benzoyl-5-phenyl-2-(propan-2-yl)-1,2,3,4-tetra­hydro­pyrimidin-4-one

Abstract

The tetra­hydro­pyrimidinone ring in the title compound, C20H20N2O2, is in a half-boat conformation with the N—C—N C atom 0.580 (2) Å out of the plane defined by the remaining five atoms. In the crystal structure, mol­ecules are connected into centrosymmetric dimers via N—H(...)O inter­actions. The dimeric aggregates are linked into supra­molecular chains along the a axis via C—H(...)π inter­actions.

Related literature

For background to the use of potassium organotrifluoro­borate salts in organic synthesis, see: Caracelli et al. (2007 [triangle]); Stefani et al. (2007 [triangle]); Vieira et al. (2008 [triangle]). For a related structure, see: Vega-Teijido et al. (2007 [triangle]). For conformational analysis, see: Cremer & Pople (1975 [triangle]); Iulek & Zukerman-Schpector (1997 [triangle]).

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Object name is e-65-o2466-scheme1.jpg

Experimental

Crystal data

  • C20H20N2O2
  • M r = 320.38
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2466-efi1.jpg
  • a = 9.346 (4) Å
  • b = 8.001 (3) Å
  • c = 22.528 (9) Å
  • β = 96.843 (9)°
  • V = 1672.6 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 98 K
  • 0.35 × 0.22 × 0.10 mm

Data collection

  • Rigaku AFC12/SATURN724 diffractometer
  • Absorption correction: multi-scan ABSCOR (Higashi, 1995 [triangle]) T min = 0.811, T max = 1
  • 5658 measured reflections
  • 3094 independent reflections
  • 2636 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.049
  • wR(F 2) = 0.126
  • S = 1.09
  • 3094 reflections
  • 213 parameters
  • H-atom parameters constrained
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: CrystalClear (Rigaku, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 2006 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809036356/ng2639sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809036356/ng2639Isup2.hkl

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

Acknowledgments

We thank FAPESP (grant Nos. 07/59404-2 to HAS and 08/02531-5 to JZS), CNPq (grant Nos. 472237/2008-0 to IC, 300613/2007 to HAS and 307121/2006-0 to JZS) and CAPES for financial support.

supplementary crystallographic information

Comment

As part of our on-going research interest efforts exploring the chemistry of potassium organotrifluoroborate salts, including their potential use as intermediates in organic synthesis (Caracelli et al., 2007; Stefani et al., 2007; Vieira et al. 2008), we have started to use the Suzuki–Miyaura cross-coupling reaction as a new tool to synthesize β-amino acids. Herein, the crystal structure of (I) is described.

The molecular structure of (I), Fig. 1, shows the tetrahydropyrimidinone ring to adopt a half-boat conformation with the C2 atom being displaced 0.580 (2) Å out of the plane defined by the remaining five atoms. The ring-puckering parameters are q2 = 0.374 (2) Å, q3 = 0.187 (1) Å, Q = 0.418 (2) Å, and [var phi]2 = 54.0 (2)° (Cremer & Pople, 1975; Iulek & Zukerman-Schpector, 1997). The dihedral angle between the aryl rings is 55.55 (8)°. The deviation of the torsion angle C4—C5—C14—C15 from the ideal value of 60°, which would indicate bisection of the dihydripyrimidinone ring by the plane of the phenyl ring, is of 15.7°.

In the crystal packing, centrosymmetric dimers are formed being consolidated by eight-membered {O═C—N—H···}2 synthons, Table 1. The carbonyl-O2 atom is involved in an intramolecular C—H···O contact with the C—H2 atom (2.34 Å) and does not particiate in a significant intermolecular contact. The aggregates thus formed are linked into supramolecular chains, Fig. 2, aligned along the a axis via C—H···π interactions: C9—H9···Cg(C14–C19)i = 2.82 Å, C9···Cg(C14–C19)i = 3.632 (2) Å with an angle of 147° at H9; symmetry operation i: 1 - x, -y, -z.

Experimental

A 50 ml flask under N2 atmosphere was charged with potassium phenyltrifluoroborate (1.2 mmol), (S)-5-iodopyrimidinone 3 (1.0 mmol, 370 mg), Pd(OAc)2 (9 mol%, 20.02 mg), K2CO3 (2 mmol, 276 mg), and 16 ml of degassed dioxane/H2O (3/1). The reaction mixture was refluxed at 383 K and the reaction followed by TLC and GC. After completion, the reaction mixture was cooled and then extracted with ethyl acetate (3 × 50 ml). The organic layers were combined, dried (MgSO4), and the solvent removed under vacuum to give a viscous oil. The oil was purified via column chromatography using a mixture of ethyl acetate/hexane (1:1) as the eluent. Single crystals of (I) were obtained by slow evaporation from ethyl acetate.

Refinement

The H atoms were positioned with idealized geometry using a riding model with N—H = 0.93 Å and C—H = 0.93–0.98 Å, and with Uiso set to 1.2 times (1.5 for methyl) Ueq(parent atom).

Figures

Fig. 1.
The molecular structure of (I) showing atom labelling scheme and displacement ellipsoids at the 50% probability level (arbitrary spheres for the H atoms).
Fig. 2.
Supramolecular chain in (I) comprising centrosymmetric dimers mediated by {O═C—N—H···}2 synthons (hydrogen bonds shown as orange dashed lines) linked by C—H···π interactions ...

Crystal data

C20H20N2O2F(000) = 680
Mr = 320.38Dx = 1.272 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 6484 reflections
a = 9.346 (4) Åθ = 2.5–40.2°
b = 8.001 (3) ŵ = 0.08 mm1
c = 22.528 (9) ÅT = 98 K
β = 96.843 (9)°Prism, colourless
V = 1672.6 (12) Å30.35 × 0.22 × 0.10 mm
Z = 4

Data collection

Rigaku AFC12/SATURN724 diffractometer3094 independent reflections
Radiation source: fine-focus sealed tube2636 reflections with I > 2σ(I)
graphiteRint = 0.035
ω scansθmax = 25.5°, θmin = 2.5°
Absorption correction: multi-scan ABSCOR (Higashi, 1995)h = −11→8
Tmin = 0.811, Tmax = 1k = −6→9
5658 measured reflectionsl = −26→27

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)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.126H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.0541P)2 + 0.6346P] where P = (Fo2 + 2Fc2)/3
3094 reflections(Δ/σ)max < 0.001
213 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.20 e Å3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
C20.91894 (17)0.2343 (2)0.10191 (7)0.0228 (4)
H20.97910.18680.13640.027*
C40.81099 (17)0.1247 (2)0.00497 (7)0.0227 (4)
C50.68065 (16)0.2234 (2)0.01348 (7)0.0215 (4)
C60.66388 (17)0.2745 (2)0.06922 (7)0.0225 (4)
H60.57820.32640.07590.027*
C70.74672 (18)0.2425 (2)0.17669 (7)0.0250 (4)
C80.59340 (18)0.2378 (2)0.19000 (7)0.0249 (4)
C90.49283 (19)0.1281 (2)0.16115 (8)0.0289 (4)
H90.51770.06060.13040.035*
C100.3547 (2)0.1194 (3)0.17838 (8)0.0346 (4)
H100.28770.04480.15960.041*
C110.3174 (2)0.2217 (3)0.22339 (9)0.0362 (5)
H110.22480.21710.23450.043*
C120.4177 (2)0.3315 (2)0.25215 (8)0.0346 (4)
H120.39170.40050.28230.041*
C130.5563 (2)0.3389 (2)0.23625 (8)0.0296 (4)
H130.62390.41070.25620.036*
C140.56628 (17)0.2461 (2)−0.03774 (7)0.0219 (4)
C150.60156 (17)0.2860 (2)−0.09467 (7)0.0235 (4)
H150.69770.2993−0.10050.028*
C160.49504 (18)0.3061 (2)−0.14248 (7)0.0264 (4)
H160.52010.3327−0.18010.032*
C170.35113 (18)0.2865 (2)−0.13443 (8)0.0279 (4)
H170.27960.3000−0.16650.033*
C180.31473 (18)0.2469 (2)−0.07842 (8)0.0285 (4)
H180.21840.2339−0.07290.034*
C190.42147 (17)0.2262 (2)−0.03020 (7)0.0245 (4)
H190.39580.19900.00730.029*
C200.98292 (17)0.4034 (2)0.08670 (7)0.0260 (4)
H200.91350.45970.05730.031*
C211.12258 (19)0.3783 (2)0.05890 (8)0.0323 (4)
H21A1.16050.48510.04920.048*
H21B1.10350.31250.02320.048*
H21C1.19160.32150.08680.048*
C221.01001 (18)0.5154 (2)0.14175 (8)0.0318 (4)
H22A0.92390.52230.16100.048*
H22B1.03670.62520.12980.048*
H22C1.08650.46920.16910.048*
N10.77103 (14)0.25198 (17)0.11728 (6)0.0226 (3)
N30.91274 (14)0.11564 (18)0.05278 (6)0.0232 (3)
H1N30.99780.06220.04630.028*
O10.82249 (12)0.04539 (16)−0.04171 (5)0.0292 (3)
O20.84733 (13)0.23635 (17)0.21657 (5)0.0335 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C20.0202 (8)0.0296 (9)0.0179 (8)0.0028 (7)0.0000 (6)−0.0023 (7)
C40.0207 (8)0.0246 (8)0.0227 (8)−0.0016 (7)0.0022 (6)−0.0002 (7)
C50.0201 (8)0.0254 (8)0.0191 (8)−0.0008 (7)0.0022 (6)0.0008 (7)
C60.0198 (7)0.0273 (8)0.0203 (8)0.0023 (7)0.0018 (6)0.0029 (7)
C70.0308 (9)0.0247 (9)0.0192 (8)0.0059 (7)0.0015 (7)0.0028 (7)
C80.0307 (9)0.0265 (9)0.0180 (8)0.0051 (7)0.0047 (6)0.0049 (7)
C90.0337 (9)0.0316 (9)0.0220 (8)0.0023 (8)0.0061 (7)0.0021 (7)
C100.0345 (10)0.0382 (11)0.0318 (10)−0.0026 (8)0.0072 (7)0.0062 (8)
C110.0342 (10)0.0420 (11)0.0346 (10)0.0079 (9)0.0129 (8)0.0104 (9)
C120.0454 (11)0.0349 (10)0.0257 (9)0.0146 (9)0.0137 (8)0.0055 (8)
C130.0383 (10)0.0281 (9)0.0226 (8)0.0056 (8)0.0041 (7)0.0020 (7)
C140.0223 (8)0.0227 (8)0.0206 (8)0.0007 (7)0.0026 (6)−0.0009 (6)
C150.0220 (8)0.0266 (8)0.0220 (8)−0.0008 (7)0.0030 (6)−0.0003 (7)
C160.0306 (9)0.0292 (9)0.0191 (8)−0.0001 (7)0.0024 (7)0.0012 (7)
C170.0272 (8)0.0317 (9)0.0228 (8)0.0052 (8)−0.0049 (6)−0.0012 (7)
C180.0199 (8)0.0370 (10)0.0283 (9)0.0023 (7)0.0012 (7)−0.0021 (8)
C190.0232 (8)0.0311 (9)0.0194 (8)0.0012 (7)0.0037 (6)0.0007 (7)
C200.0243 (8)0.0282 (9)0.0242 (8)0.0011 (7)−0.0026 (6)−0.0001 (7)
C210.0334 (9)0.0343 (10)0.0297 (9)−0.0054 (8)0.0060 (7)−0.0005 (8)
C220.0281 (9)0.0325 (10)0.0338 (10)0.0004 (8)−0.0006 (7)−0.0090 (8)
N10.0212 (7)0.0292 (8)0.0169 (7)0.0030 (6)0.0008 (5)0.0012 (6)
N30.0196 (6)0.0270 (7)0.0223 (7)0.0034 (6)0.0003 (5)−0.0030 (6)
O10.0247 (6)0.0379 (7)0.0243 (6)0.0044 (5)0.0001 (4)−0.0091 (5)
O20.0325 (7)0.0468 (8)0.0197 (6)0.0053 (6)−0.0031 (5)0.0007 (6)

Geometric parameters (Å, °)

C2—N31.454 (2)C12—H120.9300
C2—N11.471 (2)C13—H130.9300
C2—C201.534 (2)C14—C191.393 (2)
C2—H20.9800C14—C151.399 (2)
C4—O11.244 (2)C15—C161.386 (2)
C4—N31.351 (2)C15—H150.9300
C4—C51.483 (2)C16—C171.387 (2)
C5—C61.347 (2)C16—H160.9300
C5—C141.488 (2)C17—C181.382 (3)
C6—N11.396 (2)C17—H170.9300
C6—H60.9300C18—C191.394 (2)
C7—O21.222 (2)C18—H180.9300
C7—N11.386 (2)C19—H190.9300
C7—C81.499 (2)C20—C221.526 (2)
C8—C91.389 (3)C20—C211.527 (2)
C8—C131.395 (2)C20—H200.9800
C9—C101.394 (2)C21—H21A0.9600
C9—H90.9300C21—H21B0.9600
C10—C111.380 (3)C21—H21C0.9600
C10—H100.9300C22—H22A0.9600
C11—C121.387 (3)C22—H22B0.9600
C11—H110.9300C22—H22C0.9600
C12—C131.386 (3)N3—H1N30.9300
N3—C2—N1106.75 (12)C16—C15—C14120.86 (15)
N3—C2—C20112.78 (14)C16—C15—H15119.6
N1—C2—C20111.71 (13)C14—C15—H15119.6
N3—C2—H2108.5C15—C16—C17120.20 (15)
N1—C2—H2108.5C15—C16—H16119.9
C20—C2—H2108.5C17—C16—H16119.9
O1—C4—N3121.55 (15)C18—C17—C16119.55 (15)
O1—C4—C5122.39 (14)C18—C17—H17120.2
N3—C4—C5115.88 (14)C16—C17—H17120.2
C6—C5—C4118.07 (15)C17—C18—C19120.48 (16)
C6—C5—C14122.20 (15)C17—C18—H18119.8
C4—C5—C14119.36 (14)C19—C18—H18119.8
C5—C6—N1122.08 (15)C14—C19—C18120.44 (16)
C5—C6—H6119.0C14—C19—H19119.8
N1—C6—H6119.0C18—C19—H19119.8
O2—C7—N1120.79 (16)C22—C20—C21110.07 (14)
O2—C7—C8121.49 (15)C22—C20—C2111.56 (15)
N1—C7—C8117.71 (14)C21—C20—C2110.53 (14)
C9—C8—C13120.04 (16)C22—C20—H20108.2
C9—C8—C7122.16 (15)C21—C20—H20108.2
C13—C8—C7117.61 (16)C2—C20—H20108.2
C8—C9—C10119.94 (17)C20—C21—H21A109.5
C8—C9—H9120.0C20—C21—H21B109.5
C10—C9—H9120.0H21A—C21—H21B109.5
C11—C10—C9119.90 (18)C20—C21—H21C109.5
C11—C10—H10120.0H21A—C21—H21C109.5
C9—C10—H10120.0H21B—C21—H21C109.5
C10—C11—C12120.21 (17)C20—C22—H22A109.5
C10—C11—H11119.9C20—C22—H22B109.5
C12—C11—H11119.9H22A—C22—H22B109.5
C13—C12—C11120.43 (17)C20—C22—H22C109.5
C13—C12—H12119.8H22A—C22—H22C109.5
C11—C12—H12119.8H22B—C22—H22C109.5
C12—C13—C8119.46 (18)C7—N1—C6124.81 (14)
C12—C13—H13120.3C7—N1—C2119.25 (13)
C8—C13—H13120.3C6—N1—C2115.93 (13)
C19—C14—C15118.46 (15)C4—N3—C2122.15 (14)
C19—C14—C5120.67 (15)C4—N3—H1N3115.7
C15—C14—C5120.87 (14)C2—N3—H1N3117.6
O1—C4—C5—C6165.73 (16)C14—C15—C16—C17−0.1 (3)
N3—C4—C5—C6−9.5 (2)C15—C16—C17—C180.0 (3)
O1—C4—C5—C14−7.5 (2)C16—C17—C18—C19−0.1 (3)
N3—C4—C5—C14177.25 (14)C15—C14—C19—C18−0.4 (3)
C4—C5—C6—N16.5 (2)C5—C14—C19—C18−179.68 (16)
C14—C5—C6—N1179.57 (15)C17—C18—C19—C140.3 (3)
O2—C7—C8—C9−129.50 (19)N3—C2—C20—C22−171.05 (13)
N1—C7—C8—C949.6 (2)N1—C2—C20—C2268.70 (17)
O2—C7—C8—C1345.5 (2)N3—C2—C20—C21−48.23 (18)
N1—C7—C8—C13−135.33 (17)N1—C2—C20—C21−168.48 (13)
C13—C8—C9—C100.1 (3)O2—C7—N1—C6−173.99 (16)
C7—C8—C9—C10175.01 (16)C8—C7—N1—C66.9 (2)
C8—C9—C10—C111.1 (3)O2—C7—N1—C27.3 (2)
C9—C10—C11—C12−1.0 (3)C8—C7—N1—C2−171.89 (14)
C10—C11—C12—C13−0.3 (3)C5—C6—N1—C7−155.06 (17)
C11—C12—C13—C81.5 (3)C5—C6—N1—C223.7 (2)
C9—C8—C13—C12−1.4 (3)N3—C2—N1—C7132.30 (15)
C7—C8—C13—C12−176.52 (15)C20—C2—N1—C7−104.00 (17)
C6—C5—C14—C19−38.0 (2)N3—C2—N1—C6−46.57 (18)
C4—C5—C14—C19134.97 (17)C20—C2—N1—C677.13 (17)
C6—C5—C14—C15142.74 (18)O1—C4—N3—C2165.52 (15)
C4—C5—C14—C15−44.3 (2)C5—C4—N3—C2−19.2 (2)
C19—C14—C15—C160.3 (3)N1—C2—N3—C446.0 (2)
C5—C14—C15—C16179.55 (15)C20—C2—N3—C4−77.04 (19)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H1N3···O1i0.931.902.827 (2)174
C9—H9···Cgii0.932.823.632 (2)147

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2639).

References

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  • Vega-Teijido, M., Zukerman-Schpector, J., Nunes, F. M., Gatti, P. M., Stefani, H. A. & Caracelli, I. (2007). Z. Kristallogr.222, 705–712.
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