organic compounds
(6S,7S,8R,8aS)-6-Ethylperhydroindolizine-7,8-diol
aInstitute of Analytical Chemistry, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, SK-812 37 Bratislava, Slovak Republic 81237, bInstitute of Organic Chemistry, Catalysis and Petrochemistry, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, SK-812 37 Bratislava, Slovak Republic 81237, and cInstitute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak Technical University, Radlinského 9, Bratislava, Slovak Republic 81237
*Correspondence e-mail: viktor.vrabel@stuba.sk
In the title compound, C10H19NO2, the piperidine and pyrrolidine rings of the perhydroindolizine ring system adopt chair and envelope conformations, respectively. In the intermolecular O—H⋯N and O—H⋯O hydrogen bonds link the molecules into a chain running along the a axis.
Related literature
For indolizine derivatives, see: Bermudez et al. (1990); Bonneau et al. (2003); Chai et al. (2003); Delattre et al. (2005); Gundersen et al. (2007); Liu et al. (2007); Teklu et al. (2005); Weide et al. (2006). For ring conformations, see: Cremer & Pople (1975); Nardelli (1983). For the synthesis, see: Šafař et al. (2010).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: enCIFer (Allen et al., 2004) and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536810021240/is2552sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810021240/is2552Isup2.hkl
The title compound (6S,7S,8R,8aS)-6-ethylperhydroindolizine-7,8-diol was prepared according literature procedures of Šafař et al. (2010).
Hydroxyl H atoms were located in a difference Fourier map and their positions were refined freely, with Uiso(H) = 1.2Ueq(O). Other H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C—H distances in the range 0.93–0.98 Å, and with Uiso(H) = 1.2Ueq(C). The
could not be reliably determined for this compound using Mo radiation, and has been assigned according to the synthesis. 1061 total Friedel pairs have been merged.Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell
CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: enCIFer (Allen et al., 2004) and PLATON (Spek, 2009).C10H19NO2 | F(000) = 408 |
Mr = 185.26 | Dx = 1.234 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 17389 reflections |
a = 7.20849 (17) Å | θ = 3.5–29.5° |
b = 8.83039 (19) Å | µ = 0.09 mm−1 |
c = 15.6656 (4) Å | T = 298 K |
V = 997.18 (4) Å3 | Prism, white |
Z = 4 | 0.51 × 0.29 × 0.09 mm |
Oxford Diffraction Gemini R CCD diffractometer | 1554 independent reflections |
Radiation source: fine-focus sealed tube | 1371 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
Detector resolution: 10.4340 pixels mm-1 | θmax = 29.5°, θmin = 3.5° |
Rotation method data acquisition using ω and ϕ scans | h = −9→9 |
Absorption correction: analytical (Clark & Reid, 1995) | k = −11→12 |
Tmin = 0.950, Tmax = 0.992 | l = −21→20 |
26407 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)] = 0.035 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.099 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0669P)2 + 0.0442P] where P = (Fo2 + 2Fc2)/3 |
1554 reflections | (Δ/σ)max < 0.001 |
124 parameters | Δρmax = 0.17 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C10H19NO2 | V = 997.18 (4) Å3 |
Mr = 185.26 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 7.20849 (17) Å | µ = 0.09 mm−1 |
b = 8.83039 (19) Å | T = 298 K |
c = 15.6656 (4) Å | 0.51 × 0.29 × 0.09 mm |
Oxford Diffraction Gemini R CCD diffractometer | 1554 independent reflections |
Absorption correction: analytical (Clark & Reid, 1995) | 1371 reflections with I > 2σ(I) |
Tmin = 0.950, Tmax = 0.992 | Rint = 0.023 |
26407 measured reflections |
R[F2 > 2σ(F2)] = 0.035 | 0 restraints |
wR(F2) = 0.099 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.17 e Å−3 |
1554 reflections | Δρmin = −0.18 e Å−3 |
124 parameters |
Experimental. (face-indexed; Oxford Diffraction, 2006) |
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 > 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 | 0.3886 (2) | 0.5154 (2) | 0.85244 (11) | 0.0478 (4) | |
H2B | 0.2624 | 0.5248 | 0.8732 | 0.057* | |
H2A | 0.4043 | 0.4161 | 0.8270 | 0.057* | |
C3 | 0.4326 (2) | 0.6396 (3) | 0.78828 (12) | 0.0544 (5) | |
H3B | 0.3442 | 0.7220 | 0.7931 | 0.065* | |
H3A | 0.4284 | 0.6003 | 0.7305 | 0.065* | |
C4 | 0.6291 (2) | 0.6945 (2) | 0.81031 (10) | 0.0424 (4) | |
H4B | 0.7087 | 0.6928 | 0.7604 | 0.051* | |
H4A | 0.6266 | 0.7964 | 0.8334 | 0.051* | |
C5 | 0.69456 (19) | 0.58078 (16) | 0.87717 (9) | 0.0311 (3) | |
H5A | 0.7393 | 0.4907 | 0.8470 | 0.037* | |
C6 | 0.84249 (18) | 0.62711 (14) | 0.94069 (9) | 0.0277 (3) | |
H6A | 0.9566 | 0.6503 | 0.9093 | 0.033* | |
C7 | 0.8790 (2) | 0.49092 (15) | 0.99892 (9) | 0.0314 (3) | |
H7A | 0.9272 | 0.4098 | 0.9624 | 0.038* | |
C8 | 0.7028 (2) | 0.42864 (16) | 1.04186 (10) | 0.0346 (3) | |
H8A | 0.7353 | 0.3283 | 1.0640 | 0.042* | |
C9 | 0.5529 (2) | 0.40321 (17) | 0.97423 (11) | 0.0393 (4) | |
H9B | 0.5893 | 0.3199 | 0.9375 | 0.047* | |
H9A | 0.4376 | 0.3756 | 1.0021 | 0.047* | |
C10 | 0.6369 (2) | 0.52143 (19) | 1.11850 (10) | 0.0401 (4) | |
H10B | 0.7403 | 0.5354 | 1.1573 | 0.048* | |
H10A | 0.5987 | 0.6207 | 1.0987 | 0.048* | |
C11 | 0.4772 (3) | 0.4499 (3) | 1.16706 (12) | 0.0624 (6) | |
H11C | 0.4429 | 0.5140 | 1.2140 | 0.075* | |
H11B | 0.5147 | 0.3527 | 1.1884 | 0.075* | |
H11A | 0.3730 | 0.4377 | 1.1295 | 0.075* | |
N1 | 0.52295 (16) | 0.53891 (14) | 0.92216 (8) | 0.0319 (3) | |
O1 | 0.78542 (14) | 0.75959 (11) | 0.98549 (6) | 0.0301 (2) | |
H1A | 0.869 (3) | 0.7981 (19) | 1.0102 (12) | 0.036* | |
O12 | 1.01533 (16) | 0.51868 (14) | 1.06187 (8) | 0.0450 (3) | |
H12A | 1.085 (3) | 0.582 (2) | 1.0417 (14) | 0.054* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C2 | 0.0338 (7) | 0.0584 (10) | 0.0512 (9) | −0.0026 (8) | −0.0100 (7) | −0.0214 (8) |
C3 | 0.0466 (9) | 0.0696 (12) | 0.0471 (9) | 0.0076 (9) | −0.0156 (8) | −0.0088 (9) |
C4 | 0.0475 (9) | 0.0487 (8) | 0.0310 (7) | 0.0031 (8) | −0.0053 (7) | −0.0016 (6) |
C5 | 0.0280 (6) | 0.0318 (6) | 0.0334 (6) | 0.0016 (6) | 0.0015 (5) | −0.0074 (5) |
C6 | 0.0237 (6) | 0.0254 (6) | 0.0341 (6) | −0.0005 (5) | 0.0016 (5) | −0.0009 (5) |
C7 | 0.0242 (6) | 0.0264 (6) | 0.0437 (8) | 0.0013 (5) | 0.0007 (5) | 0.0006 (5) |
C8 | 0.0282 (7) | 0.0241 (6) | 0.0515 (8) | 0.0003 (6) | 0.0022 (6) | 0.0072 (6) |
C9 | 0.0323 (7) | 0.0281 (7) | 0.0575 (9) | −0.0072 (6) | 0.0030 (7) | −0.0038 (6) |
C10 | 0.0360 (7) | 0.0458 (8) | 0.0385 (7) | 0.0043 (7) | 0.0019 (6) | 0.0102 (6) |
C11 | 0.0378 (8) | 0.0995 (16) | 0.0500 (9) | 0.0001 (10) | 0.0066 (8) | 0.0219 (11) |
N1 | 0.0242 (5) | 0.0326 (6) | 0.0387 (6) | −0.0031 (5) | −0.0028 (5) | −0.0084 (5) |
O1 | 0.0274 (5) | 0.0244 (4) | 0.0385 (5) | −0.0001 (4) | −0.0056 (4) | −0.0038 (4) |
O12 | 0.0305 (6) | 0.0498 (7) | 0.0548 (7) | −0.0060 (5) | −0.0097 (5) | 0.0156 (6) |
C2—N1 | 1.4742 (18) | C7—C8 | 1.5386 (19) |
C2—C3 | 1.521 (3) | C7—H7A | 0.9800 |
C2—H2B | 0.9700 | C8—C10 | 1.529 (2) |
C2—H2A | 0.9700 | C8—C9 | 1.530 (2) |
C3—C4 | 1.536 (2) | C8—H8A | 0.9800 |
C3—H3B | 0.9700 | C9—N1 | 1.465 (2) |
C3—H3A | 0.9700 | C9—H9B | 0.9700 |
C4—C5 | 1.526 (2) | C9—H9A | 0.9700 |
C4—H4B | 0.9700 | C10—C11 | 1.518 (2) |
C4—H4A | 0.9700 | C10—H10B | 0.9700 |
C5—N1 | 1.4710 (17) | C10—H10A | 0.9700 |
C5—C6 | 1.5148 (18) | C11—H11C | 0.9600 |
C5—H5A | 0.9800 | C11—H11B | 0.9600 |
C6—O1 | 1.4250 (16) | C11—H11A | 0.9600 |
C6—C7 | 1.5322 (18) | O1—H1A | 0.79 (2) |
C6—H6A | 0.9800 | O12—H12A | 0.82 (2) |
C7—O12 | 1.4137 (18) | ||
N1—C2—C3 | 104.54 (13) | O12—C7—H7A | 106.7 |
N1—C2—H2B | 110.8 | C6—C7—H7A | 106.7 |
C3—C2—H2B | 110.8 | C8—C7—H7A | 106.7 |
N1—C2—H2A | 110.8 | C10—C8—C9 | 113.74 (12) |
C3—C2—H2A | 110.8 | C10—C8—C7 | 114.10 (12) |
H2B—C2—H2A | 108.9 | C9—C8—C7 | 109.43 (12) |
C2—C3—C4 | 105.74 (14) | C10—C8—H8A | 106.3 |
C2—C3—H3B | 110.6 | C9—C8—H8A | 106.3 |
C4—C3—H3B | 110.6 | C7—C8—H8A | 106.3 |
C2—C3—H3A | 110.6 | N1—C9—C8 | 111.68 (11) |
C4—C3—H3A | 110.6 | N1—C9—H9B | 109.3 |
H3B—C3—H3A | 108.7 | C8—C9—H9B | 109.3 |
C5—C4—C3 | 103.41 (15) | N1—C9—H9A | 109.3 |
C5—C4—H4B | 111.1 | C8—C9—H9A | 109.3 |
C3—C4—H4B | 111.1 | H9B—C9—H9A | 107.9 |
C5—C4—H4A | 111.1 | C11—C10—C8 | 113.97 (15) |
C3—C4—H4A | 111.1 | C11—C10—H10B | 108.8 |
H4B—C4—H4A | 109.0 | C8—C10—H10B | 108.8 |
N1—C5—C6 | 110.19 (11) | C11—C10—H10A | 108.8 |
N1—C5—C4 | 103.54 (12) | C8—C10—H10A | 108.8 |
C6—C5—C4 | 119.40 (13) | H10B—C10—H10A | 107.7 |
N1—C5—H5A | 107.7 | C10—C11—H11C | 109.5 |
C6—C5—H5A | 107.7 | C10—C11—H11B | 109.5 |
C4—C5—H5A | 107.7 | H11C—C11—H11B | 109.5 |
O1—C6—C5 | 110.00 (11) | C10—C11—H11A | 109.5 |
O1—C6—C7 | 113.62 (11) | H11C—C11—H11A | 109.5 |
C5—C6—C7 | 107.46 (11) | H11B—C11—H11A | 109.5 |
O1—C6—H6A | 108.5 | C9—N1—C5 | 110.39 (11) |
C5—C6—H6A | 108.5 | C9—N1—C2 | 113.21 (12) |
C7—C6—H6A | 108.5 | C5—N1—C2 | 103.45 (11) |
O12—C7—C6 | 113.49 (11) | C6—O1—H1A | 112.0 (13) |
O12—C7—C8 | 109.31 (11) | C7—O12—H12A | 106.1 (15) |
C6—C7—C8 | 113.52 (12) | ||
N1—C2—C3—C4 | 18.32 (17) | O12—C7—C8—C9 | 178.22 (11) |
C2—C3—C4—C5 | 8.30 (17) | C6—C7—C8—C9 | 50.40 (15) |
C3—C4—C5—N1 | −32.09 (15) | C10—C8—C9—N1 | 76.70 (16) |
C3—C4—C5—C6 | −154.99 (13) | C7—C8—C9—N1 | −52.21 (16) |
N1—C5—C6—O1 | −63.72 (14) | C9—C8—C10—C11 | 60.38 (17) |
C4—C5—C6—O1 | 55.85 (16) | C7—C8—C10—C11 | −173.12 (12) |
N1—C5—C6—C7 | 60.44 (14) | C8—C9—N1—C5 | 60.58 (15) |
C4—C5—C6—C7 | −179.99 (12) | C8—C9—N1—C2 | 176.00 (12) |
O1—C6—C7—O12 | −58.02 (16) | C6—C5—N1—C9 | −65.22 (14) |
C5—C6—C7—O12 | −179.95 (11) | C4—C5—N1—C9 | 165.98 (11) |
O1—C6—C7—C8 | 67.60 (15) | C6—C5—N1—C2 | 173.37 (12) |
C5—C6—C7—C8 | −54.33 (14) | C4—C5—N1—C2 | 44.57 (14) |
O12—C7—C8—C10 | 49.50 (16) | C3—C2—N1—C9 | −158.49 (13) |
C6—C7—C8—C10 | −78.32 (15) | C3—C2—N1—C5 | −39.00 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···N1i | 0.79 (2) | 2.104 (19) | 2.8619 (16) | 160.2 (18) |
O12—H12A···O1i | 0.82 (2) | 2.05 (2) | 2.8591 (15) | 169 (2) |
Symmetry code: (i) x+1/2, −y+3/2, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C10H19NO2 |
Mr | 185.26 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 298 |
a, b, c (Å) | 7.20849 (17), 8.83039 (19), 15.6656 (4) |
V (Å3) | 997.18 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.51 × 0.29 × 0.09 |
Data collection | |
Diffractometer | Oxford Diffraction Gemini R CCD diffractometer |
Absorption correction | Analytical (Clark & Reid, 1995) |
Tmin, Tmax | 0.950, 0.992 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 26407, 1554, 1371 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.693 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.099, 1.07 |
No. of reflections | 1554 |
No. of parameters | 124 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.17, −0.18 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2001), enCIFer (Allen et al., 2004) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···N1i | 0.79 (2) | 2.104 (19) | 2.8619 (16) | 160.2 (18) |
O12—H12A···O1i | 0.82 (2) | 2.05 (2) | 2.8591 (15) | 169 (2) |
Symmetry code: (i) x+1/2, −y+3/2, −z+2. |
Acknowledgements
The authors thank the Grant Agency of the Slovak Republic (grant Nos. 1/0161/08 and 1/0817/08) and the Structural Funds, Interreg IIIA, for financial support to purchase the diffractometer, and the Development Agency under contract No. APVV-0210–07.
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Bridgehead nitrogen heterocycles are important natural products. Among them, indolizines have received much attention in recent years due to their intriguing molecular structures featured with a 10 p-delocalized electrons. They have been extensively examined because of its wide range of potent applications such as biological activities (Bonneau et al., 2003) and a fluorescent probe (Delattre et al., 2005). These molecules have found various pharmaceutical applications as anti-tuberculosis agents (Gundersen et al., 2007), histamine H3 receptor antagonists (Chai et al., 2003), 5-HT3 receptor antagonists (Bermudez et al., 1990), associated with many infectious diseases (Weide et al., 2006) and as 15-lipoxygenase inhibitors (Teklu et al., 2005). Indolizines demonstrate also antifungal, antimycobacterial, antiherpes and antineociceptive properties (Liu et al., 2007). Thus, there is a growing interest in the synthesis and study of crystal and molecular structures of indolizine derivatives.
Based on these facts and in continuation of our interest in developing simple and efficient route for the synthesis of novel monohydroxylated indolizine derivatives, we report here the synthesis, molecular and crystal structure of the title compound, (I). The absolute configuration was established by synthesis and is depicted in the scheme and figure. The expected stereochemistry of atoms C5, C6, C7 and C8 was confirmed as S, R, S and S, respectively (Fig. 1). The central six-membered ring is not planar and adopts a chair conformation (Cremer & Pople, 1975). A calculation of least-squares planes shows that this ring is puckered in such a manner that the four atoms C6, C7, C9 and N1 are coplanar to within 0.019 (2) Å, while atoms C5 and C8 are displaced from this plane on opposite sides, with out-of-plane displacements of -0.720 (2) and 0.636 (1) Å, respectively. In the molecule, the pyrrolidine ring N1/C2–C5 exhibits an envelope conformation with envelope on atom N1 (Nardelli, 1983). The displacement of atom N1 from the mean plane of the remaining four atoms is 0.625 (2) Å. The N1—C2, N1—C5 and N1—C9 bonds are approximately equivalent. Atom N1 is sp3-hybridized, as evidenced by the sum of the valence angles around it [327.05 (2)°]. Intermolecular O—H···N and O—H···O hydrogen bonds link the neighbouring molecules of (I) into extended chains, which run parallel to the a axis (Fig. 2) and help to stabilize the crystal structure of the compound. Atom N1 (O1) participates as acceptor and atom O1 (O12) as donator in these intermolecular hydrogen bonds.