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ISSN: 2056-9890

2,3-Tri­methyl­ene-7,8-di­hydro­pyrrolo­[1,2-a]thieno[2,3-d]pyrimidin-4(6H)-one

aS. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 77, Tashkent 100170, Uzbekistan, and bXinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, People's Republic of China
*Correspondence e-mail: khurshed-m@mail.ru

(Received 17 June 2013; accepted 28 June 2013; online 10 July 2013)

The title mol­ecule, C12H12N2OS, is planar, with an r.m.s. deviation of 0.04 Å. In the crystal, the N atom adjacent to the carbonyl group is sp2-hybridized. The crystal structure is stabilized by ππ stacking inter­actions observed between thio­phene and pyrimidinone rings of c-glide-related mol­ecules [centroid–centroid distance = 3.9554 (13) Å] and by C—H⋯π inter­actions, forming an infinite chain along the c-axis direction.

Related literature

For background information on related compounds, see: Ibrahim et al. (1996[Ibrahim, Y. A., Elwahy, A. H. M. & Kadry, A. M. (1996). Adv. Heterocycl. Chem. 65, 235-281.]); Litvinov (2004[Litvinov, V. P. (2004). Russ. Chem. Bull. 3, 487-516.]). For the synthesis of the title compound, see: Csukonyi et al. (1986[Csukonyi, K., Lázár, J., Bernáth, G., Hermecz, I. & Mészáros, Z. (1986). Monatsh. Chem. 117, 1295-1303.]); Elmuradov et al. (2011[Elmuradov, B. Zh., Bozorov, Kh. A. & Shakhidoyatov, Kh. M. (2011). Chem. Heterocycl. Compd, 46, 1393-1399.]). For its physiological activity, see: Lilienkampf et al. (2007[Lilienkampf, A., Heikkinen, S., Mutikainen, I. & Wähäla, K. (2007). Synthesis, pp. 2699-2705.]); Moore et al. (2006[Moore, S., Jaeschke, H., Kleinau, G., Neuman, S., Costanzi, S., Jiang, J. K., Childress, J., Raaka, B. M., Colson, A., Paschke, R., Krause, G., Thomas, C. J. & Gershengorn, M. C. (2006). J. Med. Chem. 49, 3888-3896.]). For 1H NMR and IR spectroscopy of the title compound, see: Bozorov et al. (2013[Bozorov, Kh. A., Mamadalieva, N. Z., Elmuradov, B. Zh., Triggiani, D., Egamberdieva, D., Tiezzi, A., Aisa, H. A. & Shakhidoyatov, Kh. M. (2013). J. Chem. article ID 976715, http://dx.doi.org/10.1155/2013/976715 .]). For the related structures of the thieno[2,3-d] pyrimidin-4-one derivatives, see; Lilienkampf et al. (2007[Lilienkampf, A., Heikkinen, S., Mutikainen, I. & Wähäla, K. (2007). Synthesis, pp. 2699-2705.]).

[Scheme 1]

Experimental

Crystal data
  • C12H12N2OS

  • Mr = 232.30

  • Monoclinic, P 21 /c

  • a = 10.181 (2) Å

  • b = 12.163 (2) Å

  • c = 8.8624 (18) Å

  • β = 100.17 (3)°

  • V = 1080.2 (4) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 2.48 mm−1

  • T = 292 K

  • 0.20 × 0.17 × 0.15 mm

Data collection
  • Oxford Diffraction Xcalibur Ruby diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.639, Tmax = 0.689

  • 5655 measured reflections

  • 2225 independent reflections

  • 1874 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.124

  • S = 1.06

  • 2225 reflections

  • 145 parameters

  • H-atom parameters constrained

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the S1/C2/C3/C3A/C9A (thio­phene) and C3A/C4/N5/C8A/N9/C9A rings

D—H⋯A D—H H⋯A DA D—H⋯A
C6—H6BCg2i 0.97 2.85 3.770 (2) 159
C10—H10BCg1ii 0.97 2.95 3.735 (2) 139
Symmetry codes: (i) -x, -y+1, -z; (ii) [x, -y-{\script{1\over 2}}, z-{\script{1\over 2}}].

Data collection: CrysAlis PRO (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: XP in SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL, PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

Thieno[2,3-d]pyrimidin-4-ones (Litvinov, 2004; Ibrahim, et al., 1996) are a large group of heterocyclic compounds. These compounds and their derivatives possess different pharmacological activities (Lilienkampf, et al., 2007; Moore, et al., 2006).

Interaction of ethyl 2-amino-4,5-trimethylene-thiophene-3-carboxylate with γ-butyrolactam in presence of phosphorus oxycloride leads to the formation of a new potentially active tetracyclic thieno[2,3-d] pyrimidin-4-one. Synthesis of the title compound was carried out at 368-371 K with reagents in the ratio ester:lactam:POCl3 of 1:1.5:3.6. The structure of the synthesized compound has been investigated by XRD analysis.

The molecular structure of the title compound is shown in Fig. 2. As shown in the picture, the molecule of the title compound is planar with r.m.s. deviation of 0.04 Å (non-hydrogen atoms). The sum of bond angles of atom N5 (close to 360°) and bond lengths indicate sp2 hybridization of the nitrogen atom. This indicates that the lone electron pair of N5 atom participates in a conjugation with π-electrons of carbonyl group (C4O1).

The crystal structure is stabilized by π-π interactions between neighboring molecules Cg1···Cg2 [Cg1 and Cg2 are centroids of the S1/C2/C3/C3A/C9A (thiophene) and C3A/C4/N5/C8A/N9/C9A rings]. With the distance Cg1···Cg2i of 3.9554 (13) Å [symmetry code: (i) x, 1/2 - y, 1/2 + z] (Spek, 2009). In addition, intermolecular C6–H···Cg2 and C10–H···Cg1 interactions are present (Table 1).

Related literature top

For background information on related compounds, see: Ibrahim et al. (1996); Litvinov (2004). For the synthesis of the title compound, see: Csukonyi et al. (1986); Elmuradov et al. (2011). For its physiological activity, see: Lilienkampf et al. (2007); Moore et al. (2006). For 1H NMR and IR spectroscopy of the title compound, see: Bozorov et al. (2013). For the related structures of the thieno[2,3-d] pyrimidin-4-one derivatives, see; Lilienkampf et al. (2007).

Experimental top

The title compound was synthesized on the basis of a well-known method (Elmuradov, et al., 2011) (Fig. 2). Light yellow crystals suitable for X-ray analysis (in the form of prisms with size 0.20x0.17x0.15 mm) were obtained from DMSO solvent at room temperature, m.p. 475-476 K.

Refinement top

The hydrogen atoms were placed geometrically (with C–H distances of 0.97 Å for CH2) and included in the refinement in a riding motion approximation with Uiso=1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Reaction scheme for the formation of the title compound.
15-Thia-2,7-diazatetracyclo[7.6.0.03,7.010,14]pentadeca-1(9),2,10 (14)-trien-8-one top
Crystal data top
C12H12N2OSF(000) = 488
Mr = 232.30Dx = 1.428 Mg m3
Monoclinic, P21/cMelting point: 475(1) K
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.54184 Å
a = 10.181 (2) ÅCell parameters from 3341 reflections
b = 12.163 (2) Åθ = 3.6–75.5°
c = 8.8624 (18) ŵ = 2.48 mm1
β = 100.17 (3)°T = 292 K
V = 1080.2 (4) Å3Prismatic, light yellow
Z = 40.20 × 0.17 × 0.15 mm
Data collection top
Oxford Diffraction Xcalibur Ruby
diffractometer
2225 independent reflections
Radiation source: Enhance (Cu) X-ray Source1874 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
Detector resolution: 10.2576 pixels mm-1θmax = 75.7°, θmin = 4.4°
ω scansh = 1212
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
k = 1514
Tmin = 0.639, Tmax = 0.689l = 911
5655 measured reflections
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0783P)2 + 0.1555P]
where P = (Fo2 + 2Fc2)/3
2225 reflections(Δ/σ)max < 0.001
145 parametersΔρmax = 0.25 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C12H12N2OSV = 1080.2 (4) Å3
Mr = 232.30Z = 4
Monoclinic, P21/cCu Kα radiation
a = 10.181 (2) ŵ = 2.48 mm1
b = 12.163 (2) ÅT = 292 K
c = 8.8624 (18) Å0.20 × 0.17 × 0.15 mm
β = 100.17 (3)°
Data collection top
Oxford Diffraction Xcalibur Ruby
diffractometer
2225 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
1874 reflections with I > 2σ(I)
Tmin = 0.639, Tmax = 0.689Rint = 0.022
5655 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.124H-atom parameters constrained
S = 1.06Δρmax = 0.25 e Å3
2225 reflectionsΔρmin = 0.20 e Å3
145 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
S10.30220 (5)0.15857 (4)0.11554 (6)0.05357 (19)
O10.23418 (14)0.55482 (10)0.02313 (17)0.0605 (4)
N50.08460 (14)0.42802 (12)0.13884 (16)0.0443 (3)
N90.09373 (15)0.23714 (13)0.08909 (19)0.0531 (4)
C20.41506 (17)0.25495 (15)0.2035 (2)0.0463 (4)
C30.38380 (17)0.35900 (14)0.15532 (19)0.0436 (4)
C3A0.26442 (16)0.36454 (13)0.04359 (18)0.0417 (4)
C40.19968 (16)0.45820 (14)0.03696 (19)0.0439 (4)
C60.0044 (2)0.50792 (17)0.2400 (2)0.0543 (4)
H6A0.05780.54460.30530.065*
H6B0.03380.56270.18100.065*
C70.1031 (3)0.4386 (2)0.3334 (3)0.0831 (8)
H7A0.19030.46730.32470.100*
H7B0.09420.44030.44050.100*
C80.0894 (2)0.3233 (2)0.2749 (3)0.0686 (6)
H8A0.08390.27210.35750.082*
H8B0.16470.30330.22720.082*
C8A0.03749 (18)0.32290 (16)0.1596 (2)0.0485 (4)
C9A0.20876 (16)0.26112 (14)0.0111 (2)0.0451 (4)
C100.5408 (2)0.24589 (17)0.3183 (2)0.0588 (5)
H10A0.60610.20010.28060.071*
H10B0.52400.21650.41480.071*
C110.5869 (2)0.36625 (19)0.3350 (3)0.0713 (6)
H11A0.59490.38910.44110.086*
H11B0.67370.37350.30520.086*
C120.4854 (2)0.43942 (16)0.2330 (2)0.0571 (5)
H12A0.44530.49180.29380.069*
H12B0.52680.47900.15870.069*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0499 (3)0.0376 (3)0.0673 (3)0.00227 (17)0.0058 (2)0.00621 (18)
O10.0616 (8)0.0397 (7)0.0736 (9)0.0042 (6)0.0058 (7)0.0034 (6)
N50.0413 (7)0.0445 (8)0.0446 (7)0.0029 (6)0.0010 (6)0.0028 (6)
N90.0455 (8)0.0439 (8)0.0636 (9)0.0057 (6)0.0080 (7)0.0022 (7)
C20.0415 (8)0.0443 (9)0.0501 (9)0.0001 (7)0.0002 (7)0.0022 (7)
C30.0412 (8)0.0415 (8)0.0461 (8)0.0018 (6)0.0019 (7)0.0006 (7)
C3A0.0401 (8)0.0387 (8)0.0443 (8)0.0013 (6)0.0021 (6)0.0012 (7)
C40.0425 (8)0.0412 (8)0.0459 (9)0.0004 (6)0.0024 (6)0.0003 (7)
C60.0516 (9)0.0579 (11)0.0499 (9)0.0109 (8)0.0002 (7)0.0097 (8)
C70.0787 (16)0.0799 (18)0.0743 (15)0.0024 (13)0.0312 (12)0.0092 (13)
C80.0481 (11)0.0695 (14)0.0780 (14)0.0021 (9)0.0167 (10)0.0014 (11)
C8A0.0404 (8)0.0516 (10)0.0501 (9)0.0021 (7)0.0011 (7)0.0034 (7)
C9A0.0420 (8)0.0392 (8)0.0517 (9)0.0009 (7)0.0013 (7)0.0002 (7)
C100.0482 (10)0.0584 (12)0.0631 (11)0.0020 (8)0.0086 (8)0.0058 (9)
C110.0600 (12)0.0613 (13)0.0799 (14)0.0044 (10)0.0226 (11)0.0019 (11)
C120.0504 (10)0.0495 (10)0.0640 (11)0.0065 (8)0.0101 (8)0.0023 (8)
Geometric parameters (Å, º) top
S1—C21.7278 (18)C6—H6B0.9700
S1—C9A1.7339 (18)C7—C81.493 (3)
O1—C41.226 (2)C7—H7A0.9700
N5—C8A1.367 (2)C7—H7B0.9700
N5—C41.396 (2)C8—C8A1.499 (2)
N5—C61.468 (2)C8—H8A0.9700
N9—C8A1.296 (2)C8—H8B0.9700
N9—C9A1.371 (2)C10—C111.536 (3)
C2—C31.355 (2)C10—H10A0.9700
C2—C101.492 (2)C10—H10B0.9700
C3—C3A1.427 (2)C11—C121.532 (3)
C3—C121.500 (2)C11—H11A0.9700
C3A—C9A1.389 (2)C11—H11B0.9700
C3A—C41.441 (2)C12—H12A0.9700
C6—C71.508 (3)C12—H12B0.9700
C6—H6A0.9700
C2—S1—C9A90.63 (9)C7—C8—H8A110.8
C8A—N5—C4124.57 (15)C8A—C8—H8A110.8
C8A—N5—C6113.15 (15)C7—C8—H8B110.8
C4—N5—C6122.23 (16)C8A—C8—H8B110.8
C8A—N9—C9A113.28 (15)H8A—C8—H8B108.9
C3—C2—C10114.15 (16)N9—C8A—N5125.00 (16)
C3—C2—S1113.02 (13)N9—C8A—C8125.83 (17)
C10—C2—S1132.81 (14)N5—C8A—C8109.16 (16)
C2—C3—C3A112.72 (15)N9—C9A—C3A126.71 (15)
C2—C3—C12111.10 (15)N9—C9A—S1121.22 (13)
C3A—C3—C12136.18 (16)C3A—C9A—S1112.07 (12)
C9A—C3A—C3111.55 (14)C2—C10—C11101.88 (15)
C9A—C3A—C4118.64 (15)C2—C10—H10A111.4
C3—C3A—C4129.80 (15)C11—C10—H10A111.4
O1—C4—N5120.62 (16)C2—C10—H10B111.4
O1—C4—C3A127.61 (16)C11—C10—H10B111.4
N5—C4—C3A111.77 (15)H10A—C10—H10B109.3
N5—C6—C7103.66 (17)C12—C11—C10109.51 (16)
N5—C6—H6A111.0C12—C11—H11A109.8
C7—C6—H6A111.0C10—C11—H11A109.8
N5—C6—H6B111.0C12—C11—H11B109.8
C7—C6—H6B111.0C10—C11—H11B109.8
H6A—C6—H6B109.0H11A—C11—H11B108.2
C8—C7—C6108.70 (17)C3—C12—C11103.34 (16)
C8—C7—H7A109.9C3—C12—H12A111.1
C6—C7—H7A109.9C11—C12—H12A111.1
C8—C7—H7B109.9C3—C12—H12B111.1
C6—C7—H7B109.9C11—C12—H12B111.1
H7A—C7—H7B108.3H12A—C12—H12B109.1
C7—C8—C8A104.84 (17)
C9A—S1—C2—C30.38 (15)C9A—N9—C8A—N50.2 (3)
C9A—S1—C2—C10178.7 (2)C9A—N9—C8A—C8179.6 (2)
C10—C2—C3—C3A178.91 (16)C4—N5—C8A—N90.8 (3)
S1—C2—C3—C3A0.3 (2)C6—N5—C8A—N9176.90 (19)
C10—C2—C3—C120.5 (2)C4—N5—C8A—C8178.62 (17)
S1—C2—C3—C12179.19 (14)C6—N5—C8A—C83.7 (2)
C2—C3—C3A—C9A0.0 (2)C7—C8—C8A—N9174.1 (2)
C12—C3—C3A—C9A179.3 (2)C7—C8—C8A—N56.5 (3)
C2—C3—C3A—C4178.74 (17)C8A—N9—C9A—C3A1.6 (3)
C12—C3—C3A—C40.5 (4)C8A—N9—C9A—S1178.89 (14)
C8A—N5—C4—O1178.76 (18)C3—C3A—C9A—N9179.23 (17)
C6—N5—C4—O13.7 (3)C4—C3A—C9A—N91.8 (3)
C8A—N5—C4—C3A0.6 (2)C3—C3A—C9A—S10.3 (2)
C6—N5—C4—C3A176.96 (15)C4—C3A—C9A—S1178.60 (12)
C9A—C3A—C4—O1179.91 (18)C2—S1—C9A—N9179.18 (16)
C3—C3A—C4—O11.4 (3)C2—S1—C9A—C3A0.40 (14)
C9A—C3A—C4—N50.6 (2)C3—C2—C10—C110.4 (3)
C3—C3A—C4—N5179.35 (17)S1—C2—C10—C11177.87 (17)
C8A—N5—C6—C70.8 (2)C2—C10—C11—C121.2 (3)
C4—N5—C6—C7177.02 (18)C2—C3—C12—C111.3 (2)
N5—C6—C7—C84.9 (3)C3A—C3—C12—C11178.0 (2)
C6—C7—C8—C8A6.9 (3)C10—C11—C12—C31.5 (3)
Hydrogen-bond geometry (Å, º) top
Cg1 and Cg2 are the centroids of the S1/C2/C3/C3A/C9A (thiophene) and C3A/C4/N5/C8A/N9/C9A rings
D—H···AD—HH···AD···AD—H···A
C6—H6B···Cg2i0.972.853.770 (2)159
C10—H10B···Cg1ii0.972.953.735 (2)139
Symmetry codes: (i) x, y+1, z; (ii) x, y1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC12H12N2OS
Mr232.30
Crystal system, space groupMonoclinic, P21/c
Temperature (K)292
a, b, c (Å)10.181 (2), 12.163 (2), 8.8624 (18)
β (°) 100.17 (3)
V3)1080.2 (4)
Z4
Radiation typeCu Kα
µ (mm1)2.48
Crystal size (mm)0.20 × 0.17 × 0.15
Data collection
DiffractometerOxford Diffraction Xcalibur Ruby
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
Tmin, Tmax0.639, 0.689
No. of measured, independent and
observed [I > 2σ(I)] reflections
5655, 2225, 1874
Rint0.022
(sin θ/λ)max1)0.628
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.124, 1.06
No. of reflections2225
No. of parameters145
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.25, 0.20

Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
Cg1 and Cg2 are the centroids of the S1/C2/C3/C3A/C9A (thiophene) and C3A/C4/N5/C8A/N9/C9A rings
D—H···AD—HH···AD···AD—H···A
C6—H6B···Cg2i0.972.853.770 (2)159
C10—H10B···Cg1ii0.972.953.735 (2)139
Symmetry codes: (i) x, y+1, z; (ii) x, y1/2, z1/2.
 

Acknowledgements

We thank the Academy of Sciences of the Republic of Uzbekistan for supporting this study (grants FA-F7-T185 and FA-F7-T207), and the project supported by the Funds for Inter­national Cooperation and Exchange of the National Natural Science Foundation of China (grant No. 31110103908).

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