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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2280.
Published online 2010 August 11. doi:  10.1107/S1600536810031296
PMCID: PMC3007977

1-(6-Methyl-4-phenyl-2-sulfanyl­idene-1,2,3,4-tetrahydro­pyrimidin-5-yl)ethanone

Abstract

In the title compound, C13H14N2OS, the heterocyclic ring adopts a flattened boat conformation with the plane through the four coplanar atoms making a dihedral angle of 86.90 (13)° with the phenyl ring, which adopts an axial orientation. The thionyl, acetyl and methyl groups all have equatorial orientations. Inter­molecular N—H(...)O, N—H(...)S and C—H(...)O hydrogen bonds are found in the crystal structure.

Related literature

For chemical and biological applications of dihydro­pyrimidinone derivatives, see: Chitra et al. (2010 [triangle]). For their applications and for related structures, see: Anuradha et al. (2008 [triangle], 2009a [triangle],b [triangle],c [triangle]).

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Object name is e-66-o2280-scheme1.jpg

Experimental

Crystal data

  • C13H14N2OS
  • M r = 246.33
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2280-efi1.jpg
  • a = 7.8849 (10) Å
  • b = 7.2054 (5) Å
  • c = 21.555 (3) Å
  • β = 94.401 (12)°
  • V = 1221.0 (2) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 2.23 mm−1
  • T = 295 K
  • 0.44 × 0.31 × 0.16 mm

Data collection

  • Oxford Diffraction Xcalibur Ruby Gemini diffractometer
  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010 [triangle]) T min = 0.307, T max = 1.000
  • 4776 measured reflections
  • 2531 independent reflections
  • 2226 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.081
  • wR(F 2) = 0.236
  • S = 1.22
  • 2531 reflections
  • 164 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.62 e Å−3
  • Δρmin = −0.30 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2010 [triangle]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2002 (Burla et al., 2003 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810031296/hg2697sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810031296/hg2697Isup2.hkl

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

Acknowledgments

RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.

supplementary crystallographic information

Comment

Dihydropyrimidinone derivatives exhibit a wide range of biological effects such as antibacterial and antifungal activities (Chitra et al., 2010). The crystal structures of four very closely related compounds have recently been reported [Anuradha et al., (2008, 2009a,b,c)]. This study of the title compound, was undertaken to compare the biological activity and structure of dihydropyrimidin-2(1H)-thione and its corresponding 2(1H)-one (Anuradha et al., 2008).

In the title molecule, C13H14N2OS, Fig.1., the heterocyclic ring adopts a flattened boat conformation with the plane through the four coplanar atoms (C2,N3,C5,C6) making a dihedral angle of 86.90 (13)° with the phenyl ring, which adopts an axial orientation. The thionyl, acetyl and methyl groups all have equatorial orientations. Intermolecular N1—H1···O15, N3—H3···S2 and C61—H61B···O15 hydrogen bonds are found in the crystal structure (Fig. 2, Table 1).

Experimental

A solution of acetylacetone (1.0012 g, 0.01 mol), benzaldehyde (1.06 g, 0.01 mol) and thiourea (1.149 g, 0.015 mol) was heated under reflux in the presence of calcium fluoride (0.0780 g, 0.001 mol) for 2 h (monitored by TLC). After completion of the reaction, the reaction mixture was cooled to room temperature and poured into crushed ice. The crude product containing also the catalyst was collected on a Buchner funnel by filtration. The mixture of the product and the catalyst was digested in methanol (40 ml). The undissolved catalyst was removed by filtration. The crude product was obtained by evaporation of methanol and further purified by recrystallization from hot ethanol to afford the pure title compound. Yield 96% (2.8 g).

Refinement

The two N-bound H atoms were located in a difference Fourier map and refined freely; N1—H1 = 0.80 (6)Å and N3—H3 = 0.88 (4) Å. The remaining H atoms were positioned geometrically and allowed to ride on their parent atoms, with Csp2—H = 0.93, C(methyl)—H = 0.96, and C(methine)—H = 0.98 Å; Uiso(H) = kUeq(C), where k = 1.5 for methyl and 1.2 for all other H atoms.

Figures

Fig. 1.
The molecular structure of the title compound, showing the atom-numbering scheme and displacement ellipsoids drawn at the 30% probability level. H atoms are shown as small spheres of arbitrary radius.
Fig. 2.
The packing of the title compound, viewed down the a axis. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted.

Crystal data

C13H14N2OSF(000) = 520
Mr = 246.33Dx = 1.340 Mg m3
Monoclinic, P21/cMelting point: 523.5 K
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.54184 Å
a = 7.8849 (10) ÅCell parameters from 3041 reflections
b = 7.2054 (5) Åθ = 5.6–77.1°
c = 21.555 (3) ŵ = 2.23 mm1
β = 94.401 (12)°T = 295 K
V = 1221.0 (2) Å3Prism, colourless
Z = 40.44 × 0.31 × 0.16 mm

Data collection

Oxford Diffraction Xcalibur Ruby Gemini diffractometer2531 independent reflections
Radiation source: Enhance (Cu) X-ray Source2226 reflections with I > 2σ(I)
graphiteRint = 0.029
Detector resolution: 10.5081 pixels mm-1θmax = 77.3°, θmin = 5.6°
ω scansh = −9→9
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2010)k = −5→9
Tmin = 0.307, Tmax = 1.000l = −24→27
4776 measured reflections

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)] = 0.081Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.236H atoms treated by a mixture of independent and constrained refinement
S = 1.22w = 1/[σ2(Fo2) + (0.0912P)2 + 1.9142P] where P = (Fo2 + 2Fc2)/3
2531 reflections(Δ/σ)max = 0.001
164 parametersΔρmax = 0.62 e Å3
0 restraintsΔρmin = −0.30 e Å3

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
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 > 2σ(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
S20.49206 (14)−0.24803 (15)0.06167 (5)0.0540 (4)
O150.7124 (6)0.5124 (5)0.21330 (16)0.0771 (13)
N10.6473 (5)−0.1160 (5)0.16583 (16)0.0512 (11)
N30.5890 (4)0.0977 (5)0.08897 (16)0.0456 (10)
C20.5819 (5)−0.0771 (5)0.10664 (18)0.0444 (11)
C40.6849 (5)0.2449 (5)0.12284 (18)0.0441 (11)
C50.7078 (5)0.1972 (5)0.19220 (17)0.0432 (11)
C60.6954 (5)0.0179 (6)0.21040 (18)0.0461 (11)
C150.7438 (6)0.3575 (6)0.23320 (19)0.0516 (14)
C160.8242 (9)0.3391 (8)0.2982 (2)0.080 (2)
C410.8574 (5)0.2795 (5)0.09762 (17)0.0444 (11)
C420.9599 (6)0.1317 (7)0.0816 (2)0.0585 (16)
C431.1194 (6)0.1664 (8)0.0619 (2)0.0673 (17)
C441.1803 (6)0.3452 (9)0.0582 (2)0.0661 (16)
C451.0782 (6)0.4909 (8)0.0726 (2)0.0617 (16)
C460.9178 (6)0.4592 (7)0.0921 (2)0.0548 (12)
C610.7244 (7)−0.0627 (6)0.27457 (19)0.0603 (14)
H10.642 (7)−0.225 (8)0.173 (2)0.061 (15)*
H30.565 (5)0.118 (6)0.049 (2)0.047 (11)*
H40.618610.359720.118250.0528*
H16A0.864870.458180.312790.1193*
H16B0.917780.253750.298550.1193*
H16C0.741610.293670.324960.1193*
H420.920860.010380.084270.0701*
H431.186820.067590.050950.0807*
H441.289230.366770.046070.0796*
H451.117270.612010.069130.0739*
H460.849850.559150.101640.0657*
H61A0.84360−0.059330.287480.0904*
H61B0.68524−0.188900.274220.0904*
H61C0.662780.008530.303030.0904*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S20.0612 (7)0.0456 (6)0.0530 (6)−0.0106 (5)−0.0089 (4)−0.0029 (4)
O150.128 (3)0.0362 (17)0.065 (2)0.0011 (19)−0.007 (2)−0.0031 (14)
N10.070 (2)0.0316 (17)0.0496 (18)−0.0030 (16)−0.0112 (15)0.0024 (14)
N30.0482 (17)0.0417 (18)0.0448 (17)−0.0042 (14)−0.0101 (13)0.0047 (14)
C20.0420 (18)0.041 (2)0.049 (2)−0.0012 (15)−0.0037 (15)−0.0004 (16)
C40.049 (2)0.0365 (19)0.0455 (19)−0.0013 (15)−0.0050 (15)0.0027 (15)
C50.0472 (19)0.0370 (19)0.0447 (19)0.0005 (15)−0.0002 (15)0.0012 (15)
C60.053 (2)0.041 (2)0.0433 (19)−0.0006 (17)−0.0027 (15)0.0009 (16)
C150.069 (3)0.036 (2)0.050 (2)−0.0061 (18)0.0050 (18)−0.0008 (16)
C160.123 (5)0.055 (3)0.058 (3)−0.021 (3)−0.015 (3)−0.006 (2)
C410.0477 (19)0.045 (2)0.0390 (17)0.0012 (16)−0.0063 (14)0.0027 (15)
C420.062 (3)0.050 (2)0.063 (3)0.004 (2)0.001 (2)0.005 (2)
C430.055 (3)0.075 (3)0.072 (3)0.013 (2)0.005 (2)−0.001 (3)
C440.048 (2)0.093 (4)0.057 (2)−0.008 (2)0.0027 (19)0.005 (3)
C450.061 (3)0.068 (3)0.055 (2)−0.014 (2)−0.002 (2)0.003 (2)
C460.060 (2)0.052 (2)0.052 (2)−0.006 (2)0.0009 (18)0.0023 (18)
C610.087 (3)0.044 (2)0.048 (2)−0.005 (2)−0.007 (2)0.0057 (18)

Geometric parameters (Å, °)

S2—C21.689 (4)C42—C431.381 (7)
O15—C151.214 (6)C43—C441.379 (8)
N1—C21.368 (5)C44—C451.373 (8)
N1—C61.394 (5)C45—C461.382 (7)
N3—C21.318 (5)C4—H40.9800
N3—C41.465 (5)C16—H16A0.9600
N1—H10.80 (6)C16—H16B0.9600
N3—H30.88 (4)C16—H16C0.9600
C4—C411.524 (6)C42—H420.9300
C4—C51.531 (5)C43—H430.9300
C5—C61.356 (6)C44—H440.9300
C5—C151.469 (6)C45—H450.9300
C6—C611.501 (6)C46—H460.9300
C15—C161.499 (6)C61—H61A0.9600
C41—C461.388 (6)C61—H61B0.9600
C41—C421.396 (6)C61—H61C0.9600
S2···N3i3.436 (4)C16···H61C2.7100
S2···H45ii3.1400C16···H61A2.8900
S2···H16Ciii3.1900C42···H16Aix2.8600
S2···H3i2.57 (4)C43···H16Aix3.0800
S2···H44iv3.1200C45···H61Aviii3.0500
O15···N1v2.898 (5)C46···H61Aviii3.0900
O15···C413.283 (5)C61···H16B2.7700
O15···C463.201 (6)C61···H16C2.7900
O15···C61v3.333 (6)H1···O15vi2.14 (6)
O15···H1v2.14 (6)H1···H61B2.2000
O15···H42.3900H3···S2i2.57 (4)
O15···H462.7400H4···O152.3900
O15···H61Bv2.5400H4···H462.3700
N1···O15vi2.898 (5)H16A···C42viii2.8600
N3···S2i3.436 (4)H16A···C43viii3.0800
N3···H422.7000H16B···C63.0100
C2···C423.418 (6)H16B···C612.7700
C15···C463.509 (6)H16B···H61A2.3400
C16···C613.033 (7)H16C···C612.7900
C41···O153.283 (5)H16C···H61C2.1900
C42···C23.418 (6)H16C···S2x3.1900
C44···C46vii3.563 (6)H42···N32.7000
C44···C45vii3.552 (7)H42···C22.8200
C45···C46vii3.571 (6)H44···S2iv3.1200
C45···C61viii3.555 (6)H45···S2xi3.1400
C45···C44vii3.552 (7)H46···O152.7400
C45···C45vii3.277 (6)H46···H42.3700
C46···C153.509 (6)H61A···C162.8900
C46···O153.201 (6)H61A···H16B2.3400
C46···C45vii3.571 (6)H61A···C45ix3.0500
C46···C44vii3.563 (6)H61A···C46ix3.0900
C61···C45ix3.555 (6)H61B···O15vi2.5400
C61···C163.033 (7)H61B···H12.2000
C61···O15vi3.333 (6)H61C···C153.0200
C2···H422.8200H61C···C162.7100
C6···H16B3.0100H61C···H16C2.1900
C15···H61C3.0200
C2—N1—C6124.4 (3)C44—C45—C46120.6 (5)
C2—N3—C4125.4 (3)C41—C46—C45120.6 (5)
C2—N1—H1111 (3)N3—C4—H4108.00
C6—N1—H1124 (3)C5—C4—H4108.00
C2—N3—H3116 (3)C41—C4—H4108.00
C4—N3—H3116 (3)C15—C16—H16A109.00
S2—C2—N1119.8 (3)C15—C16—H16B109.00
S2—C2—N3123.8 (3)C15—C16—H16C110.00
N1—C2—N3116.4 (3)H16A—C16—H16B109.00
N3—C4—C5110.0 (3)H16A—C16—H16C109.00
C5—C4—C41110.1 (3)H16B—C16—H16C109.00
N3—C4—C41112.4 (3)C41—C42—H42120.00
C4—C5—C6119.4 (3)C43—C42—H42120.00
C4—C5—C15114.5 (3)C42—C43—H43119.00
C6—C5—C15126.2 (4)C44—C43—H43119.00
C5—C6—C61128.7 (4)C43—C44—H44120.00
N1—C6—C5118.8 (4)C45—C44—H44120.00
N1—C6—C61112.4 (4)C44—C45—H45120.00
O15—C15—C16118.1 (4)C46—C45—H45120.00
C5—C15—C16122.8 (4)C41—C46—H46120.00
O15—C15—C5119.0 (4)C45—C46—H46120.00
C4—C41—C42120.9 (3)C6—C61—H61A110.00
C4—C41—C46120.3 (3)C6—C61—H61B109.00
C42—C41—C46118.8 (4)C6—C61—H61C109.00
C41—C42—C43119.7 (5)H61A—C61—H61B109.00
C42—C43—C44121.1 (5)H61A—C61—H61C109.00
C43—C44—C45119.2 (5)H61B—C61—H61C109.00
C6—N1—C2—S2−167.7 (3)C4—C5—C6—N1−5.6 (6)
C6—N1—C2—N310.2 (6)C4—C5—C6—C61175.5 (4)
C2—N1—C6—C5−12.3 (6)C15—C5—C6—N1175.0 (4)
C2—N1—C6—C61166.8 (4)C15—C5—C6—C61−3.9 (7)
C4—N3—C2—S2−171.4 (3)C4—C5—C15—O1517.8 (6)
C4—N3—C2—N110.9 (6)C4—C5—C15—C16−159.8 (5)
C2—N3—C4—C5−25.7 (5)C6—C5—C15—O15−162.8 (5)
C2—N3—C4—C4197.4 (4)C6—C5—C15—C1619.6 (7)
N3—C4—C5—C622.0 (5)C4—C41—C42—C43−176.7 (4)
N3—C4—C5—C15−158.6 (3)C46—C41—C42—C431.3 (6)
C41—C4—C5—C6−102.5 (4)C4—C41—C46—C45176.3 (4)
C41—C4—C5—C1577.0 (4)C42—C41—C46—C45−1.6 (6)
N3—C4—C41—C42−42.5 (5)C41—C42—C43—C440.5 (7)
N3—C4—C41—C46139.6 (4)C42—C43—C44—C45−2.0 (7)
C5—C4—C41—C4280.5 (4)C43—C44—C45—C461.6 (7)
C5—C4—C41—C46−97.4 (4)C44—C45—C46—C410.2 (7)

Symmetry codes: (i) −x+1, −y, −z; (ii) x−1, y−1, z; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+2, −y, −z; (v) x, y+1, z; (vi) x, y−1, z; (vii) −x+2, −y+1, −z; (viii) −x+2, y+1/2, −z+1/2; (ix) −x+2, y−1/2, −z+1/2; (x) −x+1, y+1/2, −z+1/2; (xi) x+1, y+1, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O15vi0.80 (6)2.14 (6)2.898 (5)158 (5)
N3—H3···S2i0.88 (4)2.57 (4)3.436 (4)168 (4)
C61—H61B···O15vi0.962.543.333 (6)140

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2697).

References

  • Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2008). Acta Cryst. E64, o2474–o2475. [PMC free article] [PubMed]
  • Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009a). Acta Cryst. E65, o564–o565. [PMC free article] [PubMed]
  • Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009b). Acta Cryst. E65, o3036. [PMC free article] [PubMed]
  • Anuradha, N., Thiruvalluvar, A., Pandiarajan, K., Chitra, S. & Butcher, R. J. (2009c). Acta Cryst. E65, o3068. [PMC free article] [PubMed]
  • Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst.36, 1103.
  • Chitra, S., Devanathan, D. & Pandiarajan, K. (2010). Eur. J. Med. Chem.45, 367–371. [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Oxford Diffraction (2010). CrysAlis PRO Oxford Diffraction Ltd, Yarnton, England.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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