organic compounds
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
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 is stabilized by π–π 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); 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
Crystal data
|
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell CrysAlis PRO; data reduction: CrysAlis PRO; 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, PLATON (Spek, 2009) and publCIF (Westrip, 2010).
Supporting information
10.1107/S1600536813017935/pk2490sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536813017935/pk2490Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536813017935/pk2490Isup3.cml
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.
The hydrogen atoms were placed geometrically (with C–H distances of 0.97 Å for CH2) and included in the
in a riding motion approximation with Uiso=1.2Ueq(C).Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
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).Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. Reaction scheme for the formation of the title compound. |
C12H12N2OS | F(000) = 488 |
Mr = 232.30 | Dx = 1.428 Mg m−3 |
Monoclinic, P21/c | Melting point: 475(1) K |
Hall symbol: -P 2ybc | Cu Kα radiation, λ = 1.54184 Å |
a = 10.181 (2) Å | Cell parameters from 3341 reflections |
b = 12.163 (2) Å | θ = 3.6–75.5° |
c = 8.8624 (18) Å | µ = 2.48 mm−1 |
β = 100.17 (3)° | T = 292 K |
V = 1080.2 (4) Å3 | Prismatic, light yellow |
Z = 4 | 0.20 × 0.17 × 0.15 mm |
Oxford Diffraction Xcalibur Ruby diffractometer | 2225 independent reflections |
Radiation source: Enhance (Cu) X-ray Source | 1874 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
Detector resolution: 10.2576 pixels mm-1 | θmax = 75.7°, θmin = 4.4° |
ω scans | h = −12→12 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | k = −15→14 |
Tmin = 0.639, Tmax = 0.689 | l = −9→11 |
5655 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | H-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 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C12H12N2OS | V = 1080.2 (4) Å3 |
Mr = 232.30 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 10.181 (2) Å | µ = 2.48 mm−1 |
b = 12.163 (2) Å | T = 292 K |
c = 8.8624 (18) Å | 0.20 × 0.17 × 0.15 mm |
β = 100.17 (3)° |
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 = 0.689 | Rint = 0.022 |
5655 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.124 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.25 e Å−3 |
2225 reflections | Δρmin = −0.20 e Å−3 |
145 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.30220 (5) | 0.15857 (4) | 0.11554 (6) | 0.05357 (19) | |
O1 | 0.23418 (14) | 0.55482 (10) | −0.02313 (17) | 0.0605 (4) | |
N5 | 0.08460 (14) | 0.42802 (12) | −0.13884 (16) | 0.0443 (3) | |
N9 | 0.09373 (15) | 0.23714 (13) | −0.08909 (19) | 0.0531 (4) | |
C2 | 0.41506 (17) | 0.25495 (15) | 0.2035 (2) | 0.0463 (4) | |
C3 | 0.38380 (17) | 0.35900 (14) | 0.15532 (19) | 0.0436 (4) | |
C3A | 0.26442 (16) | 0.36454 (13) | 0.04359 (18) | 0.0417 (4) | |
C4 | 0.19968 (16) | 0.45820 (14) | −0.03696 (19) | 0.0439 (4) | |
C6 | 0.0044 (2) | 0.50792 (17) | −0.2400 (2) | 0.0543 (4) | |
H6A | 0.0578 | 0.5446 | −0.3053 | 0.065* | |
H6B | −0.0338 | 0.5627 | −0.1810 | 0.065* | |
C7 | −0.1031 (3) | 0.4386 (2) | −0.3334 (3) | 0.0831 (8) | |
H7A | −0.1903 | 0.4673 | −0.3247 | 0.100* | |
H7B | −0.0942 | 0.4403 | −0.4405 | 0.100* | |
C8 | −0.0894 (2) | 0.3233 (2) | −0.2749 (3) | 0.0686 (6) | |
H8A | −0.0839 | 0.2721 | −0.3575 | 0.082* | |
H8B | −0.1647 | 0.3033 | −0.2272 | 0.082* | |
C8A | 0.03749 (18) | 0.32290 (16) | −0.1596 (2) | 0.0485 (4) | |
C9A | 0.20876 (16) | 0.26112 (14) | 0.0111 (2) | 0.0451 (4) | |
C10 | 0.5408 (2) | 0.24589 (17) | 0.3183 (2) | 0.0588 (5) | |
H10A | 0.6061 | 0.2001 | 0.2806 | 0.071* | |
H10B | 0.5240 | 0.2165 | 0.4148 | 0.071* | |
C11 | 0.5869 (2) | 0.36625 (19) | 0.3350 (3) | 0.0713 (6) | |
H11A | 0.5949 | 0.3891 | 0.4411 | 0.086* | |
H11B | 0.6737 | 0.3735 | 0.3052 | 0.086* | |
C12 | 0.4854 (2) | 0.43942 (16) | 0.2330 (2) | 0.0571 (5) | |
H12A | 0.4453 | 0.4918 | 0.2938 | 0.069* | |
H12B | 0.5268 | 0.4790 | 0.1587 | 0.069* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0499 (3) | 0.0376 (3) | 0.0673 (3) | −0.00227 (17) | −0.0058 (2) | 0.00621 (18) |
O1 | 0.0616 (8) | 0.0397 (7) | 0.0736 (9) | −0.0042 (6) | −0.0058 (7) | 0.0034 (6) |
N5 | 0.0413 (7) | 0.0445 (8) | 0.0446 (7) | 0.0029 (6) | 0.0010 (6) | 0.0028 (6) |
N9 | 0.0455 (8) | 0.0439 (8) | 0.0636 (9) | −0.0057 (6) | −0.0080 (7) | −0.0022 (7) |
C2 | 0.0415 (8) | 0.0443 (9) | 0.0501 (9) | −0.0001 (7) | −0.0002 (7) | 0.0022 (7) |
C3 | 0.0412 (8) | 0.0415 (8) | 0.0461 (8) | −0.0018 (6) | 0.0019 (7) | −0.0006 (7) |
C3A | 0.0401 (8) | 0.0387 (8) | 0.0443 (8) | −0.0013 (6) | 0.0021 (6) | −0.0012 (7) |
C4 | 0.0425 (8) | 0.0412 (8) | 0.0459 (9) | −0.0004 (6) | 0.0024 (6) | 0.0003 (7) |
C6 | 0.0516 (9) | 0.0579 (11) | 0.0499 (9) | 0.0109 (8) | −0.0002 (7) | 0.0097 (8) |
C7 | 0.0787 (16) | 0.0799 (18) | 0.0743 (15) | −0.0024 (13) | −0.0312 (12) | 0.0092 (13) |
C8 | 0.0481 (11) | 0.0695 (14) | 0.0780 (14) | −0.0021 (9) | −0.0167 (10) | −0.0014 (11) |
C8A | 0.0404 (8) | 0.0516 (10) | 0.0501 (9) | −0.0021 (7) | −0.0011 (7) | −0.0034 (7) |
C9A | 0.0420 (8) | 0.0392 (8) | 0.0517 (9) | −0.0009 (7) | 0.0013 (7) | 0.0002 (7) |
C10 | 0.0482 (10) | 0.0584 (12) | 0.0631 (11) | 0.0020 (8) | −0.0086 (8) | 0.0058 (9) |
C11 | 0.0600 (12) | 0.0613 (13) | 0.0799 (14) | −0.0044 (10) | −0.0226 (11) | 0.0019 (11) |
C12 | 0.0504 (10) | 0.0495 (10) | 0.0640 (11) | −0.0065 (8) | −0.0101 (8) | −0.0023 (8) |
S1—C2 | 1.7278 (18) | C6—H6B | 0.9700 |
S1—C9A | 1.7339 (18) | C7—C8 | 1.493 (3) |
O1—C4 | 1.226 (2) | C7—H7A | 0.9700 |
N5—C8A | 1.367 (2) | C7—H7B | 0.9700 |
N5—C4 | 1.396 (2) | C8—C8A | 1.499 (2) |
N5—C6 | 1.468 (2) | C8—H8A | 0.9700 |
N9—C8A | 1.296 (2) | C8—H8B | 0.9700 |
N9—C9A | 1.371 (2) | C10—C11 | 1.536 (3) |
C2—C3 | 1.355 (2) | C10—H10A | 0.9700 |
C2—C10 | 1.492 (2) | C10—H10B | 0.9700 |
C3—C3A | 1.427 (2) | C11—C12 | 1.532 (3) |
C3—C12 | 1.500 (2) | C11—H11A | 0.9700 |
C3A—C9A | 1.389 (2) | C11—H11B | 0.9700 |
C3A—C4 | 1.441 (2) | C12—H12A | 0.9700 |
C6—C7 | 1.508 (3) | C12—H12B | 0.9700 |
C6—H6A | 0.9700 | ||
C2—S1—C9A | 90.63 (9) | C7—C8—H8A | 110.8 |
C8A—N5—C4 | 124.57 (15) | C8A—C8—H8A | 110.8 |
C8A—N5—C6 | 113.15 (15) | C7—C8—H8B | 110.8 |
C4—N5—C6 | 122.23 (16) | C8A—C8—H8B | 110.8 |
C8A—N9—C9A | 113.28 (15) | H8A—C8—H8B | 108.9 |
C3—C2—C10 | 114.15 (16) | N9—C8A—N5 | 125.00 (16) |
C3—C2—S1 | 113.02 (13) | N9—C8A—C8 | 125.83 (17) |
C10—C2—S1 | 132.81 (14) | N5—C8A—C8 | 109.16 (16) |
C2—C3—C3A | 112.72 (15) | N9—C9A—C3A | 126.71 (15) |
C2—C3—C12 | 111.10 (15) | N9—C9A—S1 | 121.22 (13) |
C3A—C3—C12 | 136.18 (16) | C3A—C9A—S1 | 112.07 (12) |
C9A—C3A—C3 | 111.55 (14) | C2—C10—C11 | 101.88 (15) |
C9A—C3A—C4 | 118.64 (15) | C2—C10—H10A | 111.4 |
C3—C3A—C4 | 129.80 (15) | C11—C10—H10A | 111.4 |
O1—C4—N5 | 120.62 (16) | C2—C10—H10B | 111.4 |
O1—C4—C3A | 127.61 (16) | C11—C10—H10B | 111.4 |
N5—C4—C3A | 111.77 (15) | H10A—C10—H10B | 109.3 |
N5—C6—C7 | 103.66 (17) | C12—C11—C10 | 109.51 (16) |
N5—C6—H6A | 111.0 | C12—C11—H11A | 109.8 |
C7—C6—H6A | 111.0 | C10—C11—H11A | 109.8 |
N5—C6—H6B | 111.0 | C12—C11—H11B | 109.8 |
C7—C6—H6B | 111.0 | C10—C11—H11B | 109.8 |
H6A—C6—H6B | 109.0 | H11A—C11—H11B | 108.2 |
C8—C7—C6 | 108.70 (17) | C3—C12—C11 | 103.34 (16) |
C8—C7—H7A | 109.9 | C3—C12—H12A | 111.1 |
C6—C7—H7A | 109.9 | C11—C12—H12A | 111.1 |
C8—C7—H7B | 109.9 | C3—C12—H12B | 111.1 |
C6—C7—H7B | 109.9 | C11—C12—H12B | 111.1 |
H7A—C7—H7B | 108.3 | H12A—C12—H12B | 109.1 |
C7—C8—C8A | 104.84 (17) | ||
C9A—S1—C2—C3 | −0.38 (15) | C9A—N9—C8A—N5 | −0.2 (3) |
C9A—S1—C2—C10 | −178.7 (2) | C9A—N9—C8A—C8 | −179.6 (2) |
C10—C2—C3—C3A | 178.91 (16) | C4—N5—C8A—N9 | −0.8 (3) |
S1—C2—C3—C3A | 0.3 (2) | C6—N5—C8A—N9 | 176.90 (19) |
C10—C2—C3—C12 | −0.5 (2) | C4—N5—C8A—C8 | 178.62 (17) |
S1—C2—C3—C12 | −179.19 (14) | C6—N5—C8A—C8 | −3.7 (2) |
C2—C3—C3A—C9A | 0.0 (2) | C7—C8—C8A—N9 | −174.1 (2) |
C12—C3—C3A—C9A | 179.3 (2) | C7—C8—C8A—N5 | 6.5 (3) |
C2—C3—C3A—C4 | −178.74 (17) | C8A—N9—C9A—C3A | 1.6 (3) |
C12—C3—C3A—C4 | 0.5 (4) | C8A—N9—C9A—S1 | −178.89 (14) |
C8A—N5—C4—O1 | −178.76 (18) | C3—C3A—C9A—N9 | 179.23 (17) |
C6—N5—C4—O1 | 3.7 (3) | C4—C3A—C9A—N9 | −1.8 (3) |
C8A—N5—C4—C3A | 0.6 (2) | C3—C3A—C9A—S1 | −0.3 (2) |
C6—N5—C4—C3A | −176.96 (15) | C4—C3A—C9A—S1 | 178.60 (12) |
C9A—C3A—C4—O1 | 179.91 (18) | C2—S1—C9A—N9 | −179.18 (16) |
C3—C3A—C4—O1 | −1.4 (3) | C2—S1—C9A—C3A | 0.40 (14) |
C9A—C3A—C4—N5 | 0.6 (2) | C3—C2—C10—C11 | −0.4 (3) |
C3—C3A—C4—N5 | 179.35 (17) | S1—C2—C10—C11 | 177.87 (17) |
C8A—N5—C6—C7 | −0.8 (2) | C2—C10—C11—C12 | 1.2 (3) |
C4—N5—C6—C7 | 177.02 (18) | C2—C3—C12—C11 | 1.3 (2) |
N5—C6—C7—C8 | 4.9 (3) | C3A—C3—C12—C11 | −178.0 (2) |
C6—C7—C8—C8A | −6.9 (3) | C10—C11—C12—C3 | −1.5 (3) |
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 | D···A | D—H···A |
C6—H6B···Cg2i | 0.97 | 2.85 | 3.770 (2) | 159 |
C10—H10B···Cg1ii | 0.97 | 2.95 | 3.735 (2) | 139 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x, −y−1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C12H12N2OS |
Mr | 232.30 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 292 |
a, b, c (Å) | 10.181 (2), 12.163 (2), 8.8624 (18) |
β (°) | 100.17 (3) |
V (Å3) | 1080.2 (4) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 2.48 |
Crystal size (mm) | 0.20 × 0.17 × 0.15 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Ruby diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.639, 0.689 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5655, 2225, 1874 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.628 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.124, 1.06 |
No. of reflections | 2225 |
No. of parameters | 145 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
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 | D···A | D—H···A |
C6—H6B···Cg2i | 0.97 | 2.85 | 3.770 (2) | 159 |
C10—H10B···Cg1ii | 0.97 | 2.95 | 3.735 (2) | 139 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x, −y−1/2, z−1/2. |
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).
References
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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 (C4═O1).
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).