organic compounds
(5S,11aS)-5-Hydroperoxy-1,5,11,11a-tetrahydro[1]benzothieno[3,2-f]indolizin-3(2H)-one
aInstitute of Analytical Chemistry, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, SK-812 37 Bratislava, Slovak Republic, and bInstitute of Organic Chemistry, Catalysis and Petrochemistry, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, SK-812 37 Bratislava, Slovak Republic
*Correspondence e-mail: viktor.vrabel@stuba.sk
The 14H13NO3S, was assigned from the synthesis and confirmed by the The central six-membered ring of the indolizine moiety adopts an with the greatest deviation from the mean plane of the ring being 0.661 (2) Å for the bridgehead C atom. The benzothiene ring attached to the indolizine ring system is planar to within 0.008 (2) Å. In the crystal, molecules form chains parallel to the b axis via O—H⋯O hydrogen bonds.
of the title compound, CRelated literature
For background to indolizines and their biological activity, see: Malonne et al. (1998); Medda et al. (2003); Sonnet et al. (2000); Campagna et al. (1990); Pearson & Guo (2001). For their synthesis, see: Šafář et al. (2009a,b). For compounds with similar properties, see: Švorc et al. (2008, 2009). For IR spectroscopy on similar compounds, see: Šafář et al. (2009a). For see: Nardelli (1983).
Experimental
Crystal data
|
Data collection
Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND, (Brandenburg, 2001), PLATON (Spek, 2009) and WinGX (Farrugia, 1999); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S1600536812045394/bg2481sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812045394/bg2481Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812045394/bg2481Isup3.cml
To a solution of (11aS)-1,5,11,11a-tetrahydro[1]benzothieno[3,2-f] indolizin-3(2H)-one (0.041 mmol) in THF (2 ml) was added 3 drops of H2O2 at 0°C and the mixture was allowed to react at room temperature for 72 h. The colorless crystals were filtered off, and washing with dry n-hexane (1 ml) gave pure indolizinhydroperoxid.
All H atoms bonded to C were positioned with idealized geometry using a riding model with C–H = 0.93, 0.97 and 0.98 Å for aromatic, methylene and methine H, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C). The H3 atom on O3 was located in a difference map and finally refined isotropically with O—H distance fixed at 0.84 Å. The
has been determined. The number of Friedel pairs is 1185.Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell
CrysAlis CCD (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND, (Brandenburg, 2001), PLATON (Spek, 2009) and WinGX (Farrugia, 1999); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C14H13NO3S | F(000) = 288 |
Mr = 275.31 | Dx = 1.446 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 10799 reflections |
a = 7.8040 (5) Å | θ = 3.2–29.6° |
b = 7.9800 (4) Å | µ = 0.26 mm−1 |
c = 10.2903 (5) Å | T = 295 K |
β = 99.458 (5)° | Block, colourless |
V = 632.13 (6) Å3 | 0.25 × 0.20 × 0.15 mm |
Z = 2 |
Oxford Diffraction Xcalibur (Ruby, Gemi) diffractometer | 2555 independent reflections |
Radiation source: fine-focus sealed tube | 2162 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.028 |
Detector resolution: 10.4340 pixels mm-1 | θmax = 26.4°, θmin = 4.4° |
ω scans | h = −9→9 |
Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)] | k = −9→9 |
Tmin = 0.947, Tmax = 0.974 | l = −12→12 |
21595 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.068 | w = 1/[σ2(Fo2) + (0.0441P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.00 | (Δ/σ)max < 0.001 |
2555 reflections | Δρmax = 0.13 e Å−3 |
176 parameters | Δρmin = −0.14 e Å−3 |
2 restraints | Absolute structure: Flack (1983), 1185 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.05 (6) |
C14H13NO3S | V = 632.13 (6) Å3 |
Mr = 275.31 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 7.8040 (5) Å | µ = 0.26 mm−1 |
b = 7.9800 (4) Å | T = 295 K |
c = 10.2903 (5) Å | 0.25 × 0.20 × 0.15 mm |
β = 99.458 (5)° |
Oxford Diffraction Xcalibur (Ruby, Gemi) diffractometer | 2555 independent reflections |
Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)] | 2162 reflections with I > 2σ(I) |
Tmin = 0.947, Tmax = 0.974 | Rint = 0.028 |
21595 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.068 | Δρmax = 0.13 e Å−3 |
S = 1.00 | Δρmin = −0.14 e Å−3 |
2555 reflections | Absolute structure: Flack (1983), 1185 Friedel pairs |
176 parameters | Absolute structure parameter: −0.05 (6) |
2 restraints |
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 | ||
C2 | −0.1152 (2) | 0.0934 (2) | 0.10939 (14) | 0.0487 (4) | |
C3 | −0.2994 (2) | 0.1556 (3) | 0.07868 (18) | 0.0625 (5) | |
H3B | −0.3714 | 0.1014 | 0.1347 | 0.075* | |
H3A | −0.3483 | 0.1340 | −0.0127 | 0.075* | |
C4 | −0.2872 (2) | 0.3432 (3) | 0.1057 (2) | 0.0662 (5) | |
H4B | −0.3852 | 0.3817 | 0.1447 | 0.079* | |
H4A | −0.2838 | 0.4054 | 0.0252 | 0.079* | |
C5 | −0.1161 (2) | 0.3639 (3) | 0.20284 (16) | 0.0527 (4) | |
H5 | −0.0563 | 0.4666 | 0.1834 | 0.063* | |
C6 | −0.1345 (2) | 0.3584 (3) | 0.34751 (18) | 0.0584 (4) | |
H6B | −0.1750 | 0.4661 | 0.3741 | 0.070* | |
H6A | −0.2190 | 0.2739 | 0.3613 | 0.070* | |
C7 | 0.0371 (2) | 0.31816 (19) | 0.42819 (16) | 0.0490 (4) | |
C8 | 0.2927 (2) | 0.2798 (2) | 0.60665 (15) | 0.0497 (4) | |
C9 | 0.4223 (3) | 0.2701 (3) | 0.71705 (16) | 0.0633 (5) | |
H9 | 0.4012 | 0.3056 | 0.7990 | 0.076* | |
C10 | 0.5810 (3) | 0.2073 (3) | 0.70255 (19) | 0.0707 (6) | |
H10 | 0.6691 | 0.2028 | 0.7752 | 0.085* | |
C11 | 0.6131 (3) | 0.1499 (3) | 0.58133 (19) | 0.0634 (5) | |
H11 | 0.7218 | 0.1064 | 0.5743 | 0.076* | |
C12 | 0.4862 (2) | 0.1569 (2) | 0.47181 (16) | 0.0511 (4) | |
H12 | 0.5084 | 0.1174 | 0.3912 | 0.061* | |
C13 | 0.3233 (2) | 0.22356 (19) | 0.48218 (15) | 0.0428 (4) | |
C14 | 0.17251 (19) | 0.24634 (19) | 0.38248 (14) | 0.0412 (4) | |
C15 | 0.15873 (19) | 0.1929 (2) | 0.24080 (14) | 0.0413 (4) | |
H15 | 0.1927 | 0.0751 | 0.2363 | 0.050* | |
N1 | −0.01704 (17) | 0.21547 (16) | 0.17396 (12) | 0.0447 (3) | |
O1 | −0.06189 (17) | −0.04709 (17) | 0.08604 (12) | 0.0627 (3) | |
O2 | 0.27750 (15) | 0.29669 (15) | 0.18624 (11) | 0.0513 (3) | |
O3 | 0.28192 (17) | 0.23328 (18) | 0.05339 (11) | 0.0597 (3) | |
H3 | 0.207 (2) | 0.299 (3) | 0.013 (2) | 0.098 (9)* | |
S1 | 0.08315 (6) | 0.35880 (6) | 0.59656 (4) | 0.06228 (15) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C2 | 0.0512 (10) | 0.0610 (11) | 0.0332 (7) | −0.0060 (9) | 0.0043 (7) | 0.0038 (8) |
C3 | 0.0518 (11) | 0.0782 (14) | 0.0546 (10) | −0.0038 (10) | 0.0001 (8) | 0.0057 (9) |
C4 | 0.0501 (10) | 0.0692 (13) | 0.0765 (12) | 0.0052 (11) | 0.0018 (9) | 0.0209 (11) |
C5 | 0.0440 (9) | 0.0452 (9) | 0.0699 (10) | 0.0038 (9) | 0.0121 (8) | 0.0093 (9) |
C6 | 0.0508 (9) | 0.0560 (9) | 0.0702 (10) | 0.0095 (10) | 0.0151 (8) | −0.0066 (10) |
C7 | 0.0520 (10) | 0.0446 (10) | 0.0529 (9) | −0.0003 (8) | 0.0156 (8) | −0.0048 (7) |
C8 | 0.0679 (11) | 0.0400 (8) | 0.0435 (9) | 0.0012 (8) | 0.0161 (8) | 0.0007 (7) |
C9 | 0.0933 (15) | 0.0563 (11) | 0.0402 (9) | 0.0050 (11) | 0.0102 (9) | 0.0006 (8) |
C10 | 0.0872 (16) | 0.0703 (14) | 0.0492 (10) | 0.0112 (12) | −0.0050 (10) | 0.0097 (9) |
C11 | 0.0673 (12) | 0.0648 (12) | 0.0560 (10) | 0.0171 (10) | 0.0042 (9) | 0.0099 (9) |
C12 | 0.0589 (11) | 0.0514 (10) | 0.0439 (9) | 0.0086 (9) | 0.0111 (8) | 0.0041 (7) |
C13 | 0.0549 (9) | 0.0338 (8) | 0.0411 (7) | −0.0015 (7) | 0.0120 (7) | 0.0016 (6) |
C14 | 0.0467 (9) | 0.0354 (8) | 0.0433 (8) | −0.0009 (7) | 0.0125 (7) | −0.0009 (6) |
C15 | 0.0405 (8) | 0.0433 (9) | 0.0408 (8) | −0.0002 (7) | 0.0084 (6) | 0.0009 (6) |
N1 | 0.0429 (7) | 0.0457 (7) | 0.0458 (7) | 0.0001 (6) | 0.0082 (6) | 0.0021 (6) |
O1 | 0.0674 (9) | 0.0619 (8) | 0.0554 (7) | −0.0007 (7) | 0.0000 (6) | −0.0159 (6) |
O2 | 0.0498 (6) | 0.0609 (7) | 0.0445 (6) | −0.0061 (5) | 0.0121 (5) | 0.0000 (5) |
O3 | 0.0607 (8) | 0.0756 (9) | 0.0452 (7) | 0.0118 (7) | 0.0163 (6) | 0.0007 (6) |
S1 | 0.0745 (3) | 0.0630 (3) | 0.0537 (2) | 0.0086 (3) | 0.0234 (2) | −0.0118 (2) |
C2—O1 | 1.233 (2) | C8—C13 | 1.414 (2) |
C2—N1 | 1.345 (2) | C8—S1 | 1.7400 (19) |
C2—C3 | 1.505 (3) | C9—C10 | 1.366 (3) |
C3—C4 | 1.523 (3) | C9—H9 | 0.9300 |
C3—H3B | 0.9700 | C10—C11 | 1.390 (3) |
C3—H3A | 0.9700 | C10—H10 | 0.9300 |
C4—C5 | 1.539 (3) | C11—C12 | 1.374 (3) |
C4—H4B | 0.9700 | C11—H11 | 0.9300 |
C4—H4A | 0.9700 | C12—C13 | 1.398 (2) |
C5—N1 | 1.471 (2) | C12—H12 | 0.9300 |
C5—C6 | 1.519 (2) | C13—C14 | 1.440 (2) |
C5—H5 | 0.9800 | C14—C15 | 1.506 (2) |
C6—C7 | 1.490 (2) | C15—O2 | 1.4252 (19) |
C6—H6B | 0.9700 | C15—N1 | 1.441 (2) |
C6—H6A | 0.9700 | C15—H15 | 0.9800 |
C7—C14 | 1.353 (2) | O2—O3 | 1.4634 (16) |
C7—S1 | 1.7411 (17) | O3—H3 | 0.841 (2) |
C8—C9 | 1.393 (3) | ||
O1—C2—N1 | 124.86 (17) | C13—C8—S1 | 110.95 (13) |
O1—C2—C3 | 126.89 (16) | C10—C9—C8 | 118.72 (16) |
N1—C2—C3 | 108.17 (16) | C10—C9—H9 | 120.6 |
C2—C3—C4 | 104.88 (16) | C8—C9—H9 | 120.6 |
C2—C3—H3B | 110.8 | C9—C10—C11 | 121.29 (18) |
C4—C3—H3B | 110.8 | C9—C10—H10 | 119.4 |
C2—C3—H3A | 110.8 | C11—C10—H10 | 119.4 |
C4—C3—H3A | 110.8 | C12—C11—C10 | 120.70 (18) |
H3B—C3—H3A | 108.8 | C12—C11—H11 | 119.7 |
C3—C4—C5 | 104.22 (16) | C10—C11—H11 | 119.7 |
C3—C4—H4B | 110.9 | C11—C12—C13 | 119.67 (15) |
C5—C4—H4B | 110.9 | C11—C12—H12 | 120.2 |
C3—C4—H4A | 110.9 | C13—C12—H12 | 120.2 |
C5—C4—H4A | 110.9 | C12—C13—C8 | 118.72 (15) |
H4B—C4—H4A | 108.9 | C12—C13—C14 | 129.82 (14) |
N1—C5—C6 | 108.21 (14) | C8—C13—C14 | 111.46 (14) |
N1—C5—C4 | 102.19 (16) | C7—C14—C13 | 113.53 (14) |
C6—C5—C4 | 114.92 (14) | C7—C14—C15 | 121.41 (14) |
N1—C5—H5 | 110.4 | C13—C14—C15 | 125.04 (13) |
C6—C5—H5 | 110.4 | O2—C15—N1 | 111.66 (12) |
C4—C5—H5 | 110.4 | O2—C15—C14 | 105.62 (12) |
C7—C6—C5 | 109.33 (13) | N1—C15—C14 | 109.74 (12) |
C7—C6—H6B | 109.8 | O2—C15—H15 | 109.9 |
C5—C6—H6B | 109.8 | N1—C15—H15 | 109.9 |
C7—C6—H6A | 109.8 | C14—C15—H15 | 109.9 |
C5—C6—H6A | 109.8 | C2—N1—C15 | 124.42 (15) |
H6B—C6—H6A | 108.3 | C2—N1—C5 | 114.03 (14) |
C14—C7—C6 | 125.42 (15) | C15—N1—C5 | 119.65 (13) |
C14—C7—S1 | 112.32 (13) | C15—O2—O3 | 106.49 (11) |
C6—C7—S1 | 122.26 (12) | O2—O3—H3 | 97.2 (18) |
C9—C8—C13 | 120.88 (17) | C8—S1—C7 | 91.72 (7) |
C9—C8—S1 | 128.16 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O1i | 0.84 (1) | 1.86 (1) | 2.6962 (19) | 173 (2) |
Symmetry code: (i) −x, y+1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C14H13NO3S |
Mr | 275.31 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 295 |
a, b, c (Å) | 7.8040 (5), 7.9800 (4), 10.2903 (5) |
β (°) | 99.458 (5) |
V (Å3) | 632.13 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.25 × 0.20 × 0.15 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur (Ruby, Gemi) diffractometer |
Absorption correction | Analytical [CrysAlis RED (Oxford Diffraction, 2009), based on expressions derived by Clark & Reid (1995)] |
Tmin, Tmax | 0.947, 0.974 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 21595, 2555, 2162 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.068, 1.00 |
No. of reflections | 2555 |
No. of parameters | 176 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.13, −0.14 |
Absolute structure | Flack (1983), 1185 Friedel pairs |
Absolute structure parameter | −0.05 (6) |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND, (Brandenburg, 2001), PLATON (Spek, 2009) and WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O1i | 0.841 (2) | 1.859 (4) | 2.6962 (19) | 173 (2) |
Symmetry code: (i) −x, y+1/2, −z. |
Acknowledgements
The authors thank the Grant Agency of Slovak Republic, Grant Nos. 1/0429/11, 1/0679/11 and the Slovak Research and Development Agency under contract Nos. APVV-0797–11 and APVV-0204–10 for financial support for this research program.
References
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Heterocycles are involved in a wide range of biologically important chemical reactions in living organisms, and therefore they form one of the most important and well investigated classes of organic compounds. One group of heterocycles, indolizines, has received much scientific attention during the recent years. Indolizine derivatives have been found to possess a variety of biological activities such as antiinflammatory (Malonne et al., 1998), antiviral (Medda et al., 2003), aromatase inhibitory (Sonnet et al., 2000), analgestic (Campagna et al., 1990) and antitumor (Pearson & Guo, 2001) activities. As part of our recent efforts to synthesize novel polycyclic indolizine derivative, we report here the synthesis and molecular and crystal structure of the title compound, (I) (Fig. 1). The absolute configuration has been established without ambiguity from the anomalous dispersion of the S atom (Flack, 1983) and assigned consistent with the starting material. The expected stereochemistry of both atoms C5 and C15 was confirmed as S, see Fig. 1. The central N-heterocyclic ring is not planar and adopts a envelope conformation (Nardelli, 1983). A calculation of least-squares planes shows that this ring is puckered in such a manner that the five atoms C6, C7, C14, C15 and N1 are planar to within 0.075 (3) Å, while atom C5 is displaced from this plane with out-of-plane displacement of 0.661 (2) Å. The pyrrolidine ring is distorted towards a flat-envelope conformation, with atom C4 on the flap. Atom C4 is 0.402 (2) Å from the mean plane defined by atoms C5, N1, C2 and C3. The dihedral angle between the plane of the central N-heterocyclic ring and the plane of the pyrrolidine ring is 44.6 (1)°. Atom N1 is sp2-hybridized, as evidenced by the sum of the valence angles around it (358.1°). These data are consistent with conjugation of the lone-pair electrons on N1 with the adjacent carbonyl, similar to what is observed for amides. Intermolecular O—H···O hydrogen bonds link the molecules into infinite chains, which run parallel to the b axis (Fig. 2) and help to stabilize the crystal structure of the compound. The bond lengths of the carbonyl group C2=O1 is 1.233 (2) Å somewhat longer than typical carbonyl bonds. This may be due to the fact that atom O1 participates in intermolecular hydrogen bond.