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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2434.
Published online 2008 November 26. doi:  10.1107/S1600536808038683
PMCID: PMC2959906

3-Phenyl-2-(piperidin-1-yl)-3,5,6,8-tetra­hydro-4H-thio­pyrano[3′,4′:2,3]thieno[5,4-d]pyrimidin-4-one

Abstract

In the title compound, C20H21N3OS2, the piperidinyl ring has a distorted chair conformation. Weak inter­molecular C—H(...)O hydrogen bonds link the mol­ecules into centrosymmetric dimers. The crystal packing exhibits short inter­molecular S(...)S distances of 3.590 (2) Å.

Related literature

For properties of the compounds containing th thienopyrimidine system, see: Muller et al. (2002 [triangle]); Chambhare et al. (2003 [triangle]). For related crystal structures, see: Hu et al. (2007 [triangle]); Xie et al. (2007 [triangle]).

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Object name is e-64-o2434-scheme1.jpg

Experimental

Crystal data

  • C20H21N3OS2
  • M r = 383.52
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2434-efi1.jpg
  • a = 9.851 (2) Å
  • b = 10.755 (3) Å
  • c = 10.864 (3) Å
  • α = 117.573 (4)°
  • β = 106.099 (4)°
  • γ = 97.322 (4)°
  • V = 935.0 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.30 mm−1
  • T = 298 (2) K
  • 0.26 × 0.12 × 0.06 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.926, T max = 0.982
  • 4908 measured reflections
  • 3203 independent reflections
  • 2739 reflections with I > 2σ(I)
  • R int = 0.020

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.146
  • S = 1.08
  • 3203 reflections
  • 235 parameters
  • H-atom parameters constrained
  • Δρmax = 0.29 e Å−3
  • Δρmin = −0.35 e Å−3

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808038683/cv2480sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808038683/cv2480Isup2.hkl

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

Acknowledgments

We gratefully acknowledge financial support of this work by a key grant (No. 2008K1) from the Shanxi Datong University Foundation of Shanxi Province.

supplementary crystallographic information

Comment

The derivatives of heterocycles containing the thienopyrimidine system have proved to show significant antifungal, antibacterical, anticonvulsant and angiotensin antagonistic activities(Muller et al.,2002; Chambhare et al.2003). Recently, we have focused on the synthesis of fused heterocyclic systems containing thienopyrimidine via aza-wittig reaction at room temperature. Some X-ray crystal structures of fused pyrimidinone derivatives have been reported (Xie et al., 2007; Hu et al., 2007). The title compound (I) can be used as a new precursor for obtaining of bioactive molecules with fluorescence properties.

In (I) (Fig. 1), the piperidinyl ring has a distored chair conformation. The weak intermolecular C—H···O hydrogen bonds (Table 2) link the molecules into centrosymmetric dimers (Fig. 2). The crystal packing exhibits relatively short intermolecular S···S distances of 3.590 (2) Å (Table 1), which is shorter than the sum of the van der Waals radii of the relevent atoms.

Experimental

To a solution of iminophosphorane(2mmol) in anhyd.CH2Cl2(10ml)aromatic isocyanate(2mmol)was added under nitrogen atmosphere at room temperature.After the reaction mixture was left unstirred for 6-12h at 0-5°C,the iminophosphorane had disappeared (TLC monitored).The solvent was removed off under redunced pressure and Et2O/petroleum ether (1:2,20ml) was added to precipitate triphenylphosphine oxide. Removal of the solvent gave carbodiimides,which were used directly without further purification. To a solution of carbodiimides in CH2Cl2(10ml)dialkylamine(2mmol). After the reaction mixture was left unstirred for 4-6h. The solvent was removed and anhyd.EtOH(10ml)with several drops of EtONa in EtOH was added. The mixture was stirred for 6-12h at room temperature. The solution was condensed and residue was recrystallized from EtOH to give the expected title compound in a good yield.

Refinement

All H atoms were positioned geometrically [C-H=0.93, 0.97 Å] and allowed to ride on their parent atoms , with Uiso(H)=1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of (I) with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A portion of the crystal packing showing hydrogen bonds as dashed lines. H atoms, except for those involved in hydrogen bonds, are not included.

Crystal data

C20H21N3OS2Z = 2
Mr = 383.52F000 = 404
Triclinic, P1Dx = 1.362 Mg m3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 9.851 (2) ÅCell parameters from 2241 reflections
b = 10.755 (3) Åθ = 2.2–27.6º
c = 10.864 (3) ŵ = 0.30 mm1
α = 117.573 (4)ºT = 298 (2) K
β = 106.099 (4)ºBlock, red
γ = 97.322 (4)º0.26 × 0.12 × 0.06 mm
V = 935.0 (4) Å3

Data collection

Bruker SMART CCD area-detector diffractometer3203 independent reflections
Radiation source: fine-focus sealed tube2739 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.020
Detector resolution: 0 pixels mm-1θmax = 25.0º
T = 298(2) Kθmin = 2.2º
[var phi] and ω scansh = −11→11
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)k = −6→12
Tmin = 0.926, Tmax = 0.982l = −12→12
4908 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H-atom parameters constrained
wR(F2) = 0.146  w = 1/[σ2(Fo2) + (0.0458P)2 + 1.1731P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
3203 reflectionsΔρmax = 0.29 e Å3
235 parametersΔρmin = −0.35 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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
O10.4581 (3)0.6122 (3)0.2373 (3)0.0512 (6)
S10.01324 (10)0.73341 (11)0.03936 (9)0.0504 (3)
S20.11865 (11)0.48110 (13)−0.35508 (10)0.0600 (3)
N10.1593 (3)0.8366 (3)0.3342 (3)0.0427 (6)
N20.3694 (3)0.7625 (3)0.4072 (3)0.0365 (6)
N30.2786 (3)0.9126 (3)0.5845 (3)0.0425 (6)
C10.2676 (3)0.8387 (3)0.4386 (3)0.0376 (7)
C20.3656 (3)0.6767 (3)0.2579 (3)0.0355 (7)
C30.2474 (3)0.6762 (3)0.1466 (3)0.0365 (7)
C40.1518 (3)0.7530 (3)0.1913 (3)0.0392 (7)
C50.2090 (3)0.5983 (3)−0.0135 (3)0.0383 (7)
C60.2920 (4)0.5025 (4)−0.0928 (4)0.0468 (8)
H6A0.32310.4483−0.04490.056*
H6B0.38030.5643−0.08240.056*
C70.2004 (4)0.3946 (4)−0.2580 (4)0.0543 (9)
H7A0.12230.3216−0.26820.065*
H7B0.26290.3440−0.30530.065*
C80.0051 (4)0.5529 (4)−0.2501 (4)0.0485 (8)
H8A−0.02630.6272−0.26770.058*
H8B−0.08300.4741−0.28620.058*
C90.0850 (3)0.6190 (4)−0.0851 (3)0.0417 (7)
C100.1465 (4)0.9449 (5)0.6117 (4)0.0597 (10)
H10A0.05840.86700.53010.072*
H10B0.14041.03640.61680.072*
C110.1558 (5)0.9573 (5)0.7584 (5)0.0766 (13)
H11A0.07090.98370.77970.092*
H11B0.15190.86240.74850.092*
C120.2958 (5)1.0705 (5)0.8881 (4)0.0795 (14)
H12A0.30211.06750.97740.095*
H12B0.29311.16790.90860.095*
C130.4306 (5)1.0415 (5)0.8524 (4)0.0651 (11)
H13A0.51851.12130.93170.078*
H13B0.44200.95120.84750.078*
C140.4149 (4)1.0284 (4)0.7049 (4)0.0490 (8)
H14A0.41211.12150.71270.059*
H14B0.49981.00540.68120.059*
C150.4696 (3)0.7434 (3)0.5194 (3)0.0385 (7)
C160.4120 (4)0.6656 (4)0.5735 (4)0.0446 (8)
H16A0.31000.62870.54160.053*
C170.5068 (5)0.6429 (4)0.6754 (4)0.0562 (10)
H17A0.46840.59060.71270.067*
C180.6570 (5)0.6964 (5)0.7224 (4)0.0635 (11)
H18A0.72020.67930.79040.076*
C190.7144 (4)0.7753 (5)0.6691 (4)0.0643 (11)
H19A0.81650.81270.70210.077*
C200.6205 (4)0.7991 (4)0.5661 (4)0.0515 (9)
H20A0.65880.85190.52910.062*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0471 (14)0.0719 (16)0.0425 (13)0.0345 (13)0.0203 (11)0.0300 (12)
S10.0461 (5)0.0677 (6)0.0376 (5)0.0310 (4)0.0126 (4)0.0261 (4)
S20.0618 (6)0.0872 (8)0.0411 (5)0.0310 (5)0.0237 (4)0.0367 (5)
N10.0430 (15)0.0485 (16)0.0358 (14)0.0220 (13)0.0143 (12)0.0199 (13)
N20.0329 (13)0.0464 (15)0.0336 (13)0.0116 (12)0.0110 (11)0.0244 (12)
N30.0432 (15)0.0450 (16)0.0313 (13)0.0145 (13)0.0140 (12)0.0137 (12)
C10.0368 (16)0.0380 (17)0.0366 (16)0.0102 (14)0.0130 (13)0.0193 (14)
C20.0355 (16)0.0433 (17)0.0346 (16)0.0123 (14)0.0131 (13)0.0256 (14)
C30.0319 (16)0.0394 (17)0.0366 (16)0.0078 (13)0.0124 (13)0.0196 (14)
C40.0403 (17)0.0434 (18)0.0362 (16)0.0170 (15)0.0115 (14)0.0233 (14)
C50.0342 (16)0.0437 (18)0.0369 (16)0.0110 (14)0.0121 (13)0.0219 (14)
C60.0426 (18)0.056 (2)0.0397 (18)0.0184 (16)0.0161 (15)0.0229 (16)
C70.052 (2)0.065 (2)0.0411 (19)0.0272 (19)0.0196 (16)0.0212 (18)
C80.0454 (19)0.064 (2)0.0355 (17)0.0203 (17)0.0105 (15)0.0270 (17)
C90.0394 (17)0.0490 (19)0.0356 (17)0.0146 (15)0.0129 (14)0.0217 (15)
C100.050 (2)0.063 (2)0.049 (2)0.0232 (19)0.0186 (17)0.0146 (18)
C110.084 (3)0.083 (3)0.061 (3)0.025 (3)0.048 (2)0.026 (2)
C120.101 (4)0.087 (3)0.040 (2)0.035 (3)0.031 (2)0.021 (2)
C130.073 (3)0.064 (3)0.0358 (19)0.020 (2)0.0086 (18)0.0164 (18)
C140.052 (2)0.0406 (19)0.0397 (18)0.0122 (16)0.0104 (16)0.0147 (15)
C150.0372 (17)0.0429 (18)0.0314 (15)0.0153 (14)0.0097 (13)0.0176 (14)
C160.0477 (19)0.0467 (19)0.0401 (18)0.0159 (16)0.0159 (15)0.0234 (16)
C170.078 (3)0.064 (2)0.044 (2)0.037 (2)0.0265 (19)0.0366 (19)
C180.072 (3)0.084 (3)0.041 (2)0.047 (2)0.0161 (19)0.034 (2)
C190.038 (2)0.085 (3)0.056 (2)0.021 (2)0.0055 (17)0.033 (2)
C200.0413 (19)0.065 (2)0.048 (2)0.0136 (17)0.0137 (16)0.0320 (18)

Geometric parameters (Å, °)

O1—C21.221 (4)C10—C111.512 (6)
S1—C41.729 (3)C10—H10A0.9700
S1—C91.748 (3)C10—H10B0.9700
S2—C71.804 (4)C11—C121.508 (6)
S2—C81.806 (3)C11—H11A0.9700
N1—C11.313 (4)C11—H11B0.9700
N1—C41.361 (4)C12—C131.514 (6)
N2—C11.390 (4)C12—H12A0.9700
N2—C21.433 (4)C12—H12B0.9700
N2—C151.456 (4)C13—C141.503 (5)
N3—C11.369 (4)C13—H13A0.9700
N3—C101.462 (4)C13—H13B0.9700
N3—C141.468 (4)C14—H14A0.9700
C2—C31.426 (4)C14—H14B0.9700
C3—C41.372 (4)C15—C161.374 (5)
C3—C51.440 (4)C15—C201.379 (5)
C5—C91.360 (4)C16—C171.375 (5)
C5—C61.502 (4)C16—H16A0.9300
C6—C71.513 (5)C17—C181.369 (6)
C6—H6A0.9700C17—H17A0.9300
C6—H6B0.9700C18—C191.375 (6)
C7—H7A0.9700C18—H18A0.9300
C7—H7B0.9700C19—C201.388 (5)
C8—C91.495 (4)C19—H19A0.9300
C8—H8A0.9700C20—H20A0.9300
C8—H8B0.9700
S2···S2i3.590 (2)
C4—S1—C991.31 (15)C11—C10—H10A109.9
C7—S2—C897.82 (16)N3—C10—H10B109.9
C1—N1—C4115.4 (3)C11—C10—H10B109.9
C1—N2—C2122.6 (2)H10A—C10—H10B108.3
C1—N2—C15121.4 (2)C12—C11—C10112.3 (4)
C2—N2—C15115.1 (2)C12—C11—H11A109.1
C1—N3—C10117.7 (3)C10—C11—H11A109.1
C1—N3—C14120.9 (3)C12—C11—H11B109.1
C10—N3—C14111.8 (3)C10—C11—H11B109.1
N1—C1—N3119.5 (3)H11A—C11—H11B107.9
N1—C1—N2122.9 (3)C11—C12—C13110.6 (3)
N3—C1—N2117.5 (3)C11—C12—H12A109.5
O1—C2—C3126.9 (3)C13—C12—H12A109.5
O1—C2—N2119.6 (3)C11—C12—H12B109.5
C3—C2—N2113.5 (3)C13—C12—H12B109.5
C4—C3—C2118.4 (3)H12A—C12—H12B108.1
C4—C3—C5113.6 (3)C14—C13—C12110.4 (3)
C2—C3—C5127.9 (3)C14—C13—H13A109.6
N1—C4—C3127.1 (3)C12—C13—H13A109.6
N1—C4—S1121.6 (2)C14—C13—H13B109.6
C3—C4—S1111.2 (2)C12—C13—H13B109.6
C9—C5—C3111.4 (3)H13A—C13—H13B108.1
C9—C5—C6123.9 (3)N3—C14—C13110.4 (3)
C3—C5—C6124.7 (3)N3—C14—H14A109.6
C5—C6—C7112.8 (3)C13—C14—H14A109.6
C5—C6—H6A109.0N3—C14—H14B109.6
C7—C6—H6A109.0C13—C14—H14B109.6
C5—C6—H6B109.0H14A—C14—H14B108.1
C7—C6—H6B109.0C16—C15—C20121.0 (3)
H6A—C6—H6B107.8C16—C15—N2119.3 (3)
C6—C7—S2113.1 (3)C20—C15—N2119.7 (3)
C6—C7—H7A109.0C15—C16—C17119.3 (3)
S2—C7—H7A109.0C15—C16—H16A120.4
C6—C7—H7B109.0C17—C16—H16A120.4
S2—C7—H7B109.0C18—C17—C16120.7 (4)
H7A—C7—H7B107.8C18—C17—H17A119.6
C9—C8—S2112.4 (2)C16—C17—H17A119.6
C9—C8—H8A109.1C17—C18—C19119.9 (3)
S2—C8—H8A109.1C17—C18—H18A120.1
C9—C8—H8B109.1C19—C18—H18A120.1
S2—C8—H8B109.1C18—C19—C20120.2 (4)
H8A—C8—H8B107.9C18—C19—H19A119.9
C5—C9—C8128.4 (3)C20—C19—H19A119.9
C5—C9—S1112.4 (2)C15—C20—C19118.9 (4)
C8—C9—S1119.1 (2)C15—C20—H20A120.5
N3—C10—C11108.7 (3)C19—C20—H20A120.5
N3—C10—H10A109.9
C4—N1—C1—N3−176.1 (3)C5—C6—C7—S252.2 (4)
C4—N1—C1—N20.6 (5)C8—S2—C7—C6−61.9 (3)
C10—N3—C1—N119.5 (5)C7—S2—C8—C942.6 (3)
C14—N3—C1—N1−124.1 (3)C3—C5—C9—C8−177.1 (3)
C10—N3—C1—N2−157.4 (3)C6—C5—C9—C81.1 (6)
C14—N3—C1—N259.1 (4)C3—C5—C9—S10.3 (4)
C2—N2—C1—N10.9 (5)C6—C5—C9—S1178.6 (3)
C15—N2—C1—N1−167.9 (3)S2—C8—C9—C5−18.4 (5)
C2—N2—C1—N3177.6 (3)S2—C8—C9—S1164.27 (19)
C15—N2—C1—N38.9 (4)C4—S1—C9—C5−0.5 (3)
C1—N2—C2—O1179.9 (3)C4—S1—C9—C8177.2 (3)
C15—N2—C2—O1−10.6 (4)C1—N3—C10—C11153.3 (3)
C1—N2—C2—C3−0.7 (4)C14—N3—C10—C11−60.0 (4)
C15—N2—C2—C3168.7 (3)N3—C10—C11—C1256.0 (5)
O1—C2—C3—C4178.4 (3)C10—C11—C12—C13−53.2 (5)
N2—C2—C3—C4−0.9 (4)C11—C12—C13—C1452.7 (5)
O1—C2—C3—C51.4 (5)C1—N3—C14—C13−153.0 (3)
N2—C2—C3—C5−177.9 (3)C10—N3—C14—C1361.5 (4)
C1—N1—C4—C3−2.5 (5)C12—C13—C14—N3−56.6 (4)
C1—N1—C4—S1178.2 (2)C1—N2—C15—C1662.8 (4)
C2—C3—C4—N12.7 (5)C2—N2—C15—C16−106.7 (3)
C5—C3—C4—N1−179.9 (3)C1—N2—C15—C20−119.3 (3)
C2—C3—C4—S1−177.9 (2)C2—N2—C15—C2071.1 (4)
C5—C3—C4—S1−0.5 (4)C20—C15—C16—C17−0.2 (5)
C9—S1—C4—N1−180.0 (3)N2—C15—C16—C17177.6 (3)
C9—S1—C4—C30.6 (3)C15—C16—C17—C18−0.3 (5)
C4—C3—C5—C90.1 (4)C16—C17—C18—C190.8 (6)
C2—C3—C5—C9177.2 (3)C17—C18—C19—C20−0.9 (6)
C4—C3—C5—C6−178.2 (3)C16—C15—C20—C190.1 (5)
C2—C3—C5—C6−1.1 (5)N2—C15—C20—C19−177.7 (3)
C9—C5—C6—C7−18.4 (5)C18—C19—C20—C150.4 (6)
C3—C5—C6—C7159.7 (3)

Symmetry codes: (i) −x, −y+1, −z−1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C7—H7B···O1ii0.972.563.321 (5)136

Symmetry codes: (ii) −x+1, −y+1, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2480).

References

  • Bruker (2007). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
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