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The title compound, C19H19N3OS, was synthesized by base catalytic reaction of ethyl 2-(phenyl­imino­methyl­eneamino)-5,6-dihydro-4H-cyclo­penta­[b]thio­phene-2-carboxyl­ate with pyrrolidine. In the mol­ecule, the fused thienopyrimidinone ring system is essentially planar, making a dihedral angle of 68.64 (9)° with the phenyl ring. The conformations of the cyclopentene and pyrrolidine rings are both distorted half-chair. The crystal packing is mainly stabilized by C—H...O and C—H...π inter­actions.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680703365X/is2190sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S160053680703365X/is2190Isup2.hkl
Contains datablock I

CCDC reference: 657747

Key indicators

  • Single-crystal X-ray study
  • T = 299 K
  • Mean [sigma](C-C) = 0.004 Å
  • R factor = 0.054
  • wR factor = 0.153
  • Data-to-parameter ratio = 15.3

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.72 Ratio PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C4 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.07
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 3 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 3 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check

Comment top

Derivatives of pyrimidinone are attracting increasing attention in the synthetic chemistry community because of the important role played by such systems in many natural products, also in antibiotics and drugs (Modica et al., 2004; Panico et al., 2001; Ding et al., 2004). Recently, we have been interested in the synthesis of new thieno[3,2-d]pyrimidone derivatives. Some related X-ray crystal structure reports for pyrimidinone derivatives have been published (Zheng et al., 2006; Xu et al., 2005). Here, the structure of the title compound, which may be used as a new precursor for obtaining bioactive molecules, is reported (Fig. 1). In the molecule, the bond lengths and angles are unexceptional. The fused ring of the thieno[3,2-d]pyrimidone system is essentially planar, making a dihedral angle of 68.64 (9)° with the pnenyl C14—C19 ring. C1—C5 and C10/C11/C12/C13/N3 rings have a total puckering amplitude of 0.118 (4) and 0.418 (3) Å, respectively (Cremer & Pople, 1975) and a distorted half-chair form [φ = 80.0 (2) and 93.2 (3)°]. The crystal packing is mainly stabilized by C—H···O and C—H···π interactions (Table 1 and Fig. 2). There are no π-π interactions.

Related literature top

Many derivatives of pyrimidinone have been prepared and their biological and pharmaceutical activities have been studied by Modica et al. (2004) and Panico et al. (2001). For related literature, see: Cremer & Pople (1975); Ding et al. (2004); Xu et al. (2005); Zheng et al. (2006).

Experimental top

To a solution of ethyl 2-(phenyliminomethyleneamino)-5,6-dihydro-4H- cyclopenta[b]thiophene-2-carboxylate (3 mmol) in anhydrous dichloromethane (15 ml) was added pyrrolidine (3 mmol). After stirring the reaction mixture for 2 h, the solvent was removed and anhydrous ethanol (10 ml) with several drops of EtONa in EtOH was added. The mixture was stirred for 4 h at room temperature. The solution was concentrated under reduced pressure and the residue was recrystallized from ethanol to give the title compound in a yield of 86%. Single crystals suitable for X-ray diffraction were obtained by recrystallization from a mixed solvent of ethanol and dichloromethane (1:1 v/v) at room temperature.

Refinement top

All H-atoms were positioned geometrically (C—H = 0.93 or 0.97 Å) and refined as riding, with Uiso(H) = 1.2Ueq(C).

Structure description top

Derivatives of pyrimidinone are attracting increasing attention in the synthetic chemistry community because of the important role played by such systems in many natural products, also in antibiotics and drugs (Modica et al., 2004; Panico et al., 2001; Ding et al., 2004). Recently, we have been interested in the synthesis of new thieno[3,2-d]pyrimidone derivatives. Some related X-ray crystal structure reports for pyrimidinone derivatives have been published (Zheng et al., 2006; Xu et al., 2005). Here, the structure of the title compound, which may be used as a new precursor for obtaining bioactive molecules, is reported (Fig. 1). In the molecule, the bond lengths and angles are unexceptional. The fused ring of the thieno[3,2-d]pyrimidone system is essentially planar, making a dihedral angle of 68.64 (9)° with the pnenyl C14—C19 ring. C1—C5 and C10/C11/C12/C13/N3 rings have a total puckering amplitude of 0.118 (4) and 0.418 (3) Å, respectively (Cremer & Pople, 1975) and a distorted half-chair form [φ = 80.0 (2) and 93.2 (3)°]. The crystal packing is mainly stabilized by C—H···O and C—H···π interactions (Table 1 and Fig. 2). There are no π-π interactions.

Many derivatives of pyrimidinone have been prepared and their biological and pharmaceutical activities have been studied by Modica et al. (2004) and Panico et al. (2001). For related literature, see: Cremer & Pople (1975); Ding et al. (2004); Xu et al. (2005); Zheng et al. (2006).

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 2001); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing the atom-labeling scheme and 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The packing diagram viewed along the b axis, showing the C—H···O hydrogen bonds as dashed lines.
3-Phenyl-2-(pyrrolidin-1-yl)-6,7-dihydro- 5H-cyclopenta[b]thieno[5,4-d]pyrimidin-4(3H)-one top
Crystal data top
C19H19N3OSF(000) = 1424
Mr = 337.43Dx = 1.315 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3147 reflections
a = 23.094 (3) Åθ = 2.4–25.8°
b = 8.5709 (10) ŵ = 0.20 mm1
c = 17.271 (2) ÅT = 299 K
β = 94.503 (2)°Plate, colourless
V = 3408.1 (7) Å30.30 × 0.20 × 0.06 mm
Z = 8
Data collection top
Bruker SMART CCD area-detector
diffractometer
2613 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.044
Graphite monochromatorθmax = 26.0°, θmin = 1.8°
φ and ω scansh = 2728
12733 measured reflectionsk = 1010
3323 independent reflectionsl = 2121
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)] = 0.054Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.153H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + 2.2147P]
where P = (Fo2 + 2Fc2)/3
3323 reflections(Δ/σ)max < 0.001
217 parametersΔρmax = 0.23 e Å3
0 restraintsΔρmin = 0.29 e Å3
Crystal data top
C19H19N3OSV = 3408.1 (7) Å3
Mr = 337.43Z = 8
Monoclinic, C2/cMo Kα radiation
a = 23.094 (3) ŵ = 0.20 mm1
b = 8.5709 (10) ÅT = 299 K
c = 17.271 (2) Å0.30 × 0.20 × 0.06 mm
β = 94.503 (2)°
Data collection top
Bruker SMART CCD area-detector
diffractometer
2613 reflections with I > 2σ(I)
12733 measured reflectionsRint = 0.044
3323 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.153H-atom parameters constrained
S = 1.05Δρmax = 0.23 e Å3
3323 reflectionsΔρmin = 0.29 e Å3
217 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'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
C10.39367 (11)0.0658 (3)0.13067 (14)0.0543 (6)
C20.41197 (13)0.2289 (4)0.15237 (19)0.0809 (9)
H2A0.38790.30510.12350.097*
H2B0.40990.24710.20750.097*
C30.47452 (15)0.2359 (5)0.1303 (2)0.1023 (12)
H3A0.47700.30260.08530.123*
H3B0.49940.27900.17290.123*
C40.49430 (14)0.0708 (5)0.1119 (2)0.1030 (13)
H4A0.52140.03060.15280.124*
H4B0.51210.06730.06290.124*
C50.43829 (11)0.0173 (3)0.10746 (16)0.0630 (7)
C60.34115 (9)0.0224 (2)0.12941 (13)0.0442 (5)
C70.34809 (9)0.1721 (3)0.10331 (13)0.0442 (5)
C80.28480 (9)0.0255 (2)0.14761 (13)0.0420 (5)
C90.25506 (9)0.2454 (2)0.11414 (12)0.0380 (5)
C100.16339 (9)0.3712 (2)0.15540 (14)0.0477 (6)
H10A0.17200.32760.20680.057*
H10B0.12910.32060.13090.057*
C110.15533 (11)0.5480 (2)0.15893 (16)0.0573 (7)
H11A0.11520.57500.16560.069*
H11B0.18010.59340.20100.069*
C120.17302 (11)0.6016 (2)0.08106 (16)0.0559 (6)
H12A0.18140.71250.08130.067*
H12B0.14310.57910.04000.067*
C130.22717 (10)0.5061 (2)0.07185 (14)0.0498 (6)
H13A0.23400.49310.01750.060*
H13B0.26100.55410.09880.060*
C140.18283 (9)0.0414 (2)0.14200 (13)0.0399 (5)
C150.16433 (11)0.0078 (3)0.21238 (15)0.0542 (6)
H150.18900.00140.25750.065*
C160.10902 (13)0.0664 (3)0.2147 (2)0.0689 (8)
H160.09620.09980.26160.083*
C170.07258 (12)0.0756 (3)0.1479 (2)0.0726 (9)
H170.03530.11590.14960.087*
C180.09132 (11)0.0254 (3)0.07868 (19)0.0634 (7)
H180.06630.02980.03380.076*
C190.14687 (10)0.0317 (2)0.07496 (15)0.0482 (6)
H190.15980.06320.02770.058*
N10.24184 (7)0.09507 (17)0.13812 (10)0.0381 (4)
N20.30734 (8)0.28498 (19)0.09507 (11)0.0443 (4)
N30.21341 (7)0.35543 (18)0.10766 (10)0.0402 (4)
O10.27071 (7)0.15575 (17)0.16791 (11)0.0606 (5)
S10.41935 (3)0.20650 (8)0.08088 (5)0.0691 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0435 (14)0.0687 (14)0.0502 (14)0.0220 (11)0.0003 (11)0.0011 (11)
C20.0651 (19)0.0815 (19)0.097 (2)0.0427 (16)0.0127 (17)0.0180 (16)
C30.071 (2)0.114 (3)0.123 (3)0.055 (2)0.015 (2)0.006 (2)
C40.055 (2)0.137 (3)0.121 (3)0.048 (2)0.027 (2)0.028 (2)
C50.0397 (14)0.0848 (18)0.0645 (17)0.0224 (13)0.0047 (12)0.0015 (13)
C60.0369 (12)0.0485 (11)0.0468 (13)0.0123 (9)0.0009 (9)0.0022 (9)
C70.0336 (11)0.0512 (11)0.0479 (13)0.0046 (9)0.0026 (9)0.0035 (10)
C80.0382 (12)0.0386 (10)0.0480 (13)0.0091 (8)0.0043 (9)0.0017 (9)
C90.0387 (12)0.0329 (9)0.0421 (12)0.0034 (8)0.0010 (9)0.0054 (8)
C100.0371 (12)0.0395 (10)0.0671 (15)0.0074 (9)0.0089 (11)0.0094 (10)
C110.0547 (15)0.0385 (11)0.0794 (18)0.0105 (10)0.0107 (13)0.0122 (11)
C120.0560 (15)0.0366 (11)0.0728 (17)0.0117 (10)0.0089 (12)0.0043 (10)
C130.0568 (15)0.0346 (10)0.0576 (15)0.0055 (9)0.0028 (11)0.0014 (9)
C140.0336 (11)0.0279 (9)0.0584 (13)0.0053 (8)0.0048 (10)0.0011 (8)
C150.0542 (15)0.0460 (12)0.0632 (16)0.0041 (10)0.0101 (12)0.0042 (11)
C160.0641 (18)0.0481 (13)0.099 (2)0.0045 (12)0.0351 (18)0.0120 (13)
C170.0427 (15)0.0408 (12)0.136 (3)0.0017 (10)0.0174 (18)0.0003 (15)
C180.0404 (14)0.0461 (12)0.101 (2)0.0009 (10)0.0098 (14)0.0076 (13)
C190.0428 (13)0.0361 (10)0.0653 (15)0.0062 (9)0.0009 (11)0.0031 (10)
N10.0322 (9)0.0332 (8)0.0486 (10)0.0055 (7)0.0018 (8)0.0009 (7)
N20.0362 (10)0.0399 (9)0.0573 (12)0.0035 (7)0.0064 (8)0.0003 (8)
N30.0376 (10)0.0333 (8)0.0498 (10)0.0060 (7)0.0038 (8)0.0018 (7)
O10.0515 (10)0.0365 (8)0.0931 (14)0.0106 (7)0.0001 (9)0.0087 (8)
S10.0379 (4)0.0785 (5)0.0927 (6)0.0067 (3)0.0174 (4)0.0095 (4)
Geometric parameters (Å, º) top
C1—C51.340 (4)C10—H10A0.9700
C1—C61.428 (3)C10—H10B0.9700
C1—C21.499 (3)C11—C121.507 (4)
C2—C31.524 (4)C11—H11A0.9700
C2—H2A0.9700C11—H11B0.9700
C2—H2B0.9700C12—C131.514 (3)
C3—C41.528 (5)C12—H12A0.9700
C3—H3A0.9700C12—H12B0.9700
C3—H3B0.9700C13—N31.477 (3)
C4—C51.495 (3)C13—H13A0.9700
C4—H4A0.9700C13—H13B0.9700
C4—H4B0.9700C14—C191.373 (3)
C5—S11.732 (3)C14—C151.385 (3)
C6—C71.373 (3)C14—N11.445 (3)
C6—C81.423 (3)C15—C161.376 (4)
C7—N21.350 (3)C15—H150.9300
C7—S11.745 (2)C16—C171.376 (4)
C8—O11.222 (3)C16—H160.9300
C8—N11.433 (2)C17—C181.372 (4)
C9—N21.321 (3)C17—H170.9300
C9—N31.345 (2)C18—C191.379 (3)
C9—N11.395 (2)C18—H180.9300
C10—N31.477 (3)C19—H190.9300
C10—C111.528 (3)
C5—C1—C6112.7 (2)C12—C11—H11A111.2
C5—C1—C2111.2 (2)C10—C11—H11A111.2
C6—C1—C2136.0 (2)C12—C11—H11B111.2
C1—C2—C3103.2 (3)C10—C11—H11B111.2
C1—C2—H2A111.1H11A—C11—H11B109.1
C3—C2—H2A111.1C11—C12—C13102.31 (18)
C1—C2—H2B111.1C11—C12—H12A111.3
C3—C2—H2B111.1C13—C12—H12A111.3
H2A—C2—H2B109.1C11—C12—H12B111.3
C2—C3—C4108.7 (2)C13—C12—H12B111.3
C2—C3—H3A110.0H12A—C12—H12B109.2
C4—C3—H3A110.0N3—C13—C12102.83 (18)
C2—C3—H3B110.0N3—C13—H13A111.2
C4—C3—H3B110.0C12—C13—H13A111.2
H3A—C3—H3B108.3N3—C13—H13B111.2
C5—C4—C3102.0 (3)C12—C13—H13B111.2
C5—C4—H4A111.4H13A—C13—H13B109.1
C3—C4—H4A111.4C19—C14—C15120.9 (2)
C5—C4—H4B111.4C19—C14—N1119.35 (19)
C3—C4—H4B111.4C15—C14—N1119.6 (2)
H4A—C4—H4B109.2C16—C15—C14119.2 (3)
C1—C5—C4113.5 (3)C16—C15—H15120.4
C1—C5—S1113.14 (18)C14—C15—H15120.4
C4—C5—S1133.3 (2)C15—C16—C17120.3 (3)
C7—C6—C8118.32 (18)C15—C16—H16119.8
C7—C6—C1112.3 (2)C17—C16—H16119.8
C8—C6—C1129.4 (2)C18—C17—C16119.9 (2)
N2—C7—C6127.3 (2)C18—C17—H17120.1
N2—C7—S1121.15 (17)C16—C17—H17120.1
C6—C7—S1111.55 (16)C17—C18—C19120.7 (3)
O1—C8—C6126.57 (19)C17—C18—H18119.7
O1—C8—N1119.61 (19)C19—C18—H18119.7
C6—C8—N1113.80 (17)C14—C19—C18119.0 (2)
N2—C9—N3117.44 (18)C14—C19—H19120.5
N2—C9—N1122.49 (17)C18—C19—H19120.5
N3—C9—N1120.04 (18)C9—N1—C8122.32 (17)
N3—C10—C11102.49 (17)C9—N1—C14122.50 (16)
N3—C10—H10A111.3C8—N1—C14114.33 (15)
C11—C10—H10A111.3C9—N2—C7115.67 (18)
N3—C10—H10B111.3C9—N3—C13118.14 (17)
C11—C10—H10B111.3C9—N3—C10127.09 (18)
H10A—C10—H10B109.2C13—N3—C10110.91 (15)
C12—C11—C10102.94 (18)C5—S1—C790.33 (11)
C5—C1—C2—C35.6 (3)N1—C14—C19—C18177.51 (18)
C6—C1—C2—C3175.2 (3)C17—C18—C19—C141.7 (3)
C1—C2—C3—C410.9 (4)N2—C9—N1—C83.2 (3)
C2—C3—C4—C511.9 (4)N3—C9—N1—C8178.62 (18)
C6—C1—C5—C4177.3 (3)N2—C9—N1—C14165.56 (19)
C2—C1—C5—C42.1 (4)N3—C9—N1—C1412.6 (3)
C6—C1—C5—S11.1 (3)O1—C8—N1—C9179.2 (2)
C2—C1—C5—S1179.5 (2)C6—C8—N1—C90.8 (3)
C3—C4—C5—C18.7 (4)O1—C8—N1—C149.5 (3)
C3—C4—C5—S1173.2 (3)C6—C8—N1—C14168.88 (18)
C5—C1—C6—C71.1 (3)C19—C14—N1—C963.7 (2)
C2—C1—C6—C7179.7 (3)C15—C14—N1—C9119.9 (2)
C5—C1—C6—C8178.0 (2)C19—C14—N1—C8106.0 (2)
C2—C1—C6—C82.8 (5)C15—C14—N1—C870.4 (2)
C8—C6—C7—N22.7 (4)N3—C9—N2—C7179.18 (19)
C1—C6—C7—N2180.0 (2)N1—C9—N2—C72.6 (3)
C8—C6—C7—S1177.87 (16)C6—C7—N2—C90.3 (3)
C1—C6—C7—S10.5 (3)S1—C7—N2—C9179.74 (15)
C7—C6—C8—O1176.4 (2)N2—C9—N3—C136.6 (3)
C1—C6—C8—O10.4 (4)N1—C9—N3—C13171.66 (18)
C7—C6—C8—N11.9 (3)N2—C9—N3—C10149.2 (2)
C1—C6—C8—N1178.7 (2)N1—C9—N3—C1032.6 (3)
N3—C10—C11—C1233.1 (2)C12—C13—N3—C9175.30 (18)
C10—C11—C12—C1343.4 (2)C12—C13—N3—C1015.8 (2)
C11—C12—C13—N336.1 (2)C11—C10—N3—C9146.5 (2)
C19—C14—C15—C160.3 (3)C11—C10—N3—C1310.7 (2)
N1—C14—C15—C16176.64 (19)C1—C5—S1—C70.7 (2)
C14—C15—C16—C170.1 (3)C4—C5—S1—C7177.4 (3)
C15—C16—C17—C180.4 (4)N2—C7—S1—C5179.4 (2)
C16—C17—C18—C191.3 (4)C6—C7—S1—C50.06 (19)
C15—C14—C19—C181.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C10—H10A···O1i0.972.453.309 (3)148
C10—H10B···Cg50.972.903.429 (2)115
C12—H12A···Cg5ii0.972.893.630 (2)134
C12—H12B···Cg1iii0.972.933.790 (3)148
C13—H13A···Cg4iii0.972.673.542 (3)150
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x, y+1, z; (iii) x+1/2, y+1/2, z.

Experimental details

Crystal data
Chemical formulaC19H19N3OS
Mr337.43
Crystal system, space groupMonoclinic, C2/c
Temperature (K)299
a, b, c (Å)23.094 (3), 8.5709 (10), 17.271 (2)
β (°) 94.503 (2)
V3)3408.1 (7)
Z8
Radiation typeMo Kα
µ (mm1)0.20
Crystal size (mm)0.30 × 0.20 × 0.06
Data collection
DiffractometerBruker SMART CCD area-detector
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
12733, 3323, 2613
Rint0.044
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.054, 0.153, 1.05
No. of reflections3323
No. of parameters217
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.23, 0.29

Computer programs: SMART (Bruker, 2001), SAINT-Plus (Bruker, 2001), SAINT-Plus, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Sheldrick, 2001), SHELXTL.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C10—H10A···O1i0.972.453.309 (3)148
C10—H10B···Cg50.972.903.429 (2)115
C12—H12A···Cg5ii0.972.893.630 (2)134
C12—H12B···Cg1iii0.972.933.790 (3)148
C13—H13A···Cg4iii0.972.673.542 (3)150
Symmetry codes: (i) x+1/2, y+1/2, z+1/2; (ii) x, y+1, z; (iii) x+1/2, y+1/2, z.
 

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