supplementary materials


Acta Cryst. (2009). E65, o2466    [ doi:10.1107/S1600536809036356 ]

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

I. Caracelli, J. Zukerman-Schpector, M. F. Z. J. Amaral, H. A. Stefani and E. R. T. Tiekink

Abstract top

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...[pi] interactions.

Comment top

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 φ2 = 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 {OC—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.

Related literature top

For background to the use of potassium organotrifluoroborate salts in organic synthesis, see: Caracelli et al. (2007); Stefani et al. (2007); Vieira et al. (2008). For a related structure, see: Vega-Teijido et al. (2007). For conformational analysis, see: Cremer & Pople (1975); Iulek & Zukerman-Schpector (1997). Cg is the centroid of the C14–C19 ring.

Experimental top

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 top

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).

Computing details top

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

Figures top
[Figure 1] 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).
[Figure 2] Fig. 2. Supramolecular chain in (I) comprising centrosymmetric dimers mediated by {OC—N—H···}2 synthons (hydrogen bonds shown as orange dashed lines) linked by C—H···π interactions (shown as purple dashed lines).
1-Benzoyl-5-phenyl-2-(propan-2-yl)-1,2,3,4-tetrahydropyrimidin-4-one top
Crystal data top
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 top
Rigaku AFC12/SATURN724
diffractometer
3094 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 = 118
Tmin = 0.811, Tmax = 1k = 69
5658 measured reflectionsl = 2627
Refinement top
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 = 1.09 w = 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
Crystal data top
C20H20N2O2V = 1672.6 (12) Å3
Mr = 320.38Z = 4
Monoclinic, P21/nMo Kα radiation
a = 9.346 (4) ŵ = 0.08 mm1
b = 8.001 (3) ÅT = 98 K
c = 22.528 (9) Å0.35 × 0.22 × 0.10 mm
β = 96.843 (9)°
Data collection top
Rigaku AFC12/SATURN724
diffractometer
2636 reflections with I > 2σ(I)
Absorption correction: multi-scan
ABSCOR (Higashi, 1995)
Rint = 0.035
Tmin = 0.811, Tmax = 1θmax = 25.5°
5658 measured reflectionsStandard reflections: 0
3094 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.049H-atom parameters constrained
wR(F2) = 0.126Δρmax = 0.22 e Å3
S = 1.09Δρmin = 0.20 e Å3
3094 reflectionsAbsolute structure: ?
213 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

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) top
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)
H150.69770.29930.10050.028*
C160.49504 (18)0.3061 (2)0.14248 (7)0.0264 (4)
H160.52010.33270.18010.032*
C170.35113 (18)0.2865 (2)0.13443 (8)0.0279 (4)
H170.27960.30000.16650.033*
C180.31473 (18)0.2469 (2)0.07842 (8)0.0285 (4)
H180.21840.23390.07290.034*
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) top
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, °) top
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—C170.1 (3)
N3—C4—C5—C69.5 (2)C15—C16—C17—C180.0 (3)
O1—C4—C5—C147.5 (2)C16—C17—C18—C190.1 (3)
N3—C4—C5—C14177.25 (14)C15—C14—C19—C180.4 (3)
C4—C5—C6—N16.5 (2)C5—C14—C19—C18179.68 (16)
C14—C5—C6—N1179.57 (15)C17—C18—C19—C140.3 (3)
O2—C7—C8—C9129.50 (19)N3—C2—C20—C22171.05 (13)
N1—C7—C8—C949.6 (2)N1—C2—C20—C2268.70 (17)
O2—C7—C8—C1345.5 (2)N3—C2—C20—C2148.23 (18)
N1—C7—C8—C13135.33 (17)N1—C2—C20—C21168.48 (13)
C13—C8—C9—C100.1 (3)O2—C7—N1—C6173.99 (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—C121.0 (3)C8—C7—N1—C2171.89 (14)
C10—C11—C12—C130.3 (3)C5—C6—N1—C7155.06 (17)
C11—C12—C13—C81.5 (3)C5—C6—N1—C223.7 (2)
C9—C8—C13—C121.4 (3)N3—C2—N1—C7132.30 (15)
C7—C8—C13—C12176.52 (15)C20—C2—N1—C7104.00 (17)
C6—C5—C14—C1938.0 (2)N3—C2—N1—C646.57 (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—C1544.3 (2)C5—C4—N3—C219.2 (2)
C19—C14—C15—C160.3 (3)N1—C2—N3—C446.0 (2)
C5—C14—C15—C16179.55 (15)C20—C2—N3—C477.04 (19)
Hydrogen-bond geometry (Å, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °)
top
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.
Acknowledgements top

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.

references
References top

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