organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

(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

(Received 19 May 2010; accepted 3 June 2010; online 16 June 2010)

In the title compound, C10H19NO2, the piperidine and pyrrolidine rings of the perhydro­indolizine ring system adopt chair and envelope conformations, respectively. In the crystal structure, 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[Bermudez, J., Fake, C. S., Joiner, G. F., Joiner, K. A., Km, F. D., Miner, W. D. & Sanger, G. J. (1990). J. Med. Chem. 33, 1924-1929.]); Bonneau et al. (2003[Bonneau, R., Collado, D. & Liu, M. T. H. (2003). J. Photochem. Photobiol. A, 161, 43-50.]); Chai et al. (2003[Chai, W., Breitenbucher, J. G., Kwok, A., Li, X., Wong, V., Carruthers, N. I., Lovenberg, T. W., Mazur, C., Wilson, S. J., Axe, F. U. & Jones, T. K. (2003). Bioorg. Med. Chem. Lett. 13, 1767-1770.]); Delattre et al. (2005[Delattre, F., Woisel, P., Surpateau, G., Cazier, F. & Blach, P. (2005). Tetrahedron, 61, 3939-3945.]); Gundersen et al. (2007[Gundersen, L.-L., Charnock, C., Negussie, A. H., Rise, F. & Teklu, S. (2007). Eur. J. Pharm. Sci. 30, 26-30.]); Liu et al. (2007[Liu, Y., Hu, H.-Y., Liu, Q.-J., Hu, H.-W. & Xu, J.-H. (2007). Tetrahedron, 63, 2024-2033.]); Teklu et al. (2005[Teklu, S., Gundersen, L. L., Larsen, T., Malterud, K. E. & Rise, F. (2005). Bioorg. Med. Chem. 13, 3127-3139.]); Weide et al. (2006[Weide, T., Arve, L., Prinz, H., Waldmann, H. & Kessler, H. (2006). Bioorg. Med. Chem. Lett. 16, 59-63.]). For ring conformations, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1362.]); Nardelli (1983[Nardelli, M. (1983). Acta Cryst. C39, 1141-1142.]). For the synthesis, see: Šafař et al. (2010[Šafař, P., Žúžiová, J., Marchalín, Š., Prónayová, N., Švorc, Ľ., Vrábel, V., Comesse, S. & Daich, A. (2010). Tetrahedron Asymmetry, 21, 623-630.]).

[Scheme 1]

Experimental

Crystal data
  • C10H19NO2

  • Mr = 185.26

  • Orthorhombic, P 21 21 21

  • a = 7.20849 (17) Å

  • b = 8.83039 (19) Å

  • c = 15.6656 (4) Å

  • V = 997.18 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 298 K

  • 0.51 × 0.29 × 0.09 mm

Data collection
  • Oxford Diffraction Gemini R CCD diffractometer

  • Absorption correction: analytical (Clark & Reid, 1995[Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897.]) Tmin = 0.950, Tmax = 0.992

  • 26407 measured reflections

  • 1554 independent reflections

  • 1371 reflections with I > 2σ(I)

  • Rint = 0.023

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.099

  • S = 1.07

  • 1554 reflections

  • 124 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+2].

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]); data reduction: CrysAlis RED; 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: DIAMOND (Brandenburg, 2001[Brandenburg, K. (2001). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: enCIFer (Allen et al., 2004[Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335-338.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

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 top

The title compound (6S,7S,8R,8aS)-6-ethylperhydroindolizine-7,8-diol was prepared according literature procedures of Šafař et al. (2010).

Refinement top

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 absolute configuration 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.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Molecular structure of (I) with the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. A partial packing diagram of the molecule of (I), showing a molecular chain along the a axis. Hydrogen bonds are indicated by dashed lines. H atoms not involved in the hydrogen bonds have been omitted.
(6S,7S,8R,8aS)-6-Ethylperhydroindolizine-7,8-diol top
Crystal data top
C10H19NO2F(000) = 408
Mr = 185.26Dx = 1.234 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 17389 reflections
a = 7.20849 (17) Åθ = 3.5–29.5°
b = 8.83039 (19) ŵ = 0.09 mm1
c = 15.6656 (4) ÅT = 298 K
V = 997.18 (4) Å3Prism, white
Z = 40.51 × 0.29 × 0.09 mm
Data collection top
Oxford Diffraction Gemini R CCD
diffractometer
1554 independent reflections
Radiation source: fine-focus sealed tube1371 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
Detector resolution: 10.4340 pixels mm-1θmax = 29.5°, θmin = 3.5°
Rotation method data acquisition using ω and ϕ scansh = 99
Absorption correction: analytical
(Clark & Reid, 1995)
k = 1112
Tmin = 0.950, Tmax = 0.992l = 2120
26407 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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.099H 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 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.18 e Å3
Crystal data top
C10H19NO2V = 997.18 (4) Å3
Mr = 185.26Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.20849 (17) ŵ = 0.09 mm1
b = 8.83039 (19) ÅT = 298 K
c = 15.6656 (4) Å0.51 × 0.29 × 0.09 mm
Data collection top
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 = 0.992Rint = 0.023
26407 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.099H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.17 e Å3
1554 reflectionsΔρmin = 0.18 e Å3
124 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C20.3886 (2)0.5154 (2)0.85244 (11)0.0478 (4)
H2B0.26240.52480.87320.057*
H2A0.40430.41610.82700.057*
C30.4326 (2)0.6396 (3)0.78828 (12)0.0544 (5)
H3B0.34420.72200.79310.065*
H3A0.42840.60030.73050.065*
C40.6291 (2)0.6945 (2)0.81031 (10)0.0424 (4)
H4B0.70870.69280.76040.051*
H4A0.62660.79640.83340.051*
C50.69456 (19)0.58078 (16)0.87717 (9)0.0311 (3)
H5A0.73930.49070.84700.037*
C60.84249 (18)0.62711 (14)0.94069 (9)0.0277 (3)
H6A0.95660.65030.90930.033*
C70.8790 (2)0.49092 (15)0.99892 (9)0.0314 (3)
H7A0.92720.40980.96240.038*
C80.7028 (2)0.42864 (16)1.04186 (10)0.0346 (3)
H8A0.73530.32831.06400.042*
C90.5529 (2)0.40321 (17)0.97423 (11)0.0393 (4)
H9B0.58930.31990.93750.047*
H9A0.43760.37561.00210.047*
C100.6369 (2)0.52143 (19)1.11850 (10)0.0401 (4)
H10B0.74030.53541.15730.048*
H10A0.59870.62071.09870.048*
C110.4772 (3)0.4499 (3)1.16706 (12)0.0624 (6)
H11C0.44290.51401.21400.075*
H11B0.51470.35271.18840.075*
H11A0.37300.43771.12950.075*
N10.52295 (16)0.53891 (14)0.92216 (8)0.0319 (3)
O10.78542 (14)0.75959 (11)0.98549 (6)0.0301 (2)
H1A0.869 (3)0.7981 (19)1.0102 (12)0.036*
O121.01533 (16)0.51868 (14)1.06187 (8)0.0450 (3)
H12A1.085 (3)0.582 (2)1.0417 (14)0.054*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C20.0338 (7)0.0584 (10)0.0512 (9)0.0026 (8)0.0100 (7)0.0214 (8)
C30.0466 (9)0.0696 (12)0.0471 (9)0.0076 (9)0.0156 (8)0.0088 (9)
C40.0475 (9)0.0487 (8)0.0310 (7)0.0031 (8)0.0053 (7)0.0016 (6)
C50.0280 (6)0.0318 (6)0.0334 (6)0.0016 (6)0.0015 (5)0.0074 (5)
C60.0237 (6)0.0254 (6)0.0341 (6)0.0005 (5)0.0016 (5)0.0009 (5)
C70.0242 (6)0.0264 (6)0.0437 (8)0.0013 (5)0.0007 (5)0.0006 (5)
C80.0282 (7)0.0241 (6)0.0515 (8)0.0003 (6)0.0022 (6)0.0072 (6)
C90.0323 (7)0.0281 (7)0.0575 (9)0.0072 (6)0.0030 (7)0.0038 (6)
C100.0360 (7)0.0458 (8)0.0385 (7)0.0043 (7)0.0019 (6)0.0102 (6)
C110.0378 (8)0.0995 (16)0.0500 (9)0.0001 (10)0.0066 (8)0.0219 (11)
N10.0242 (5)0.0326 (6)0.0387 (6)0.0031 (5)0.0028 (5)0.0084 (5)
O10.0274 (5)0.0244 (4)0.0385 (5)0.0001 (4)0.0056 (4)0.0038 (4)
O120.0305 (6)0.0498 (7)0.0548 (7)0.0060 (5)0.0097 (5)0.0156 (6)
Geometric parameters (Å, º) top
C2—N11.4742 (18)C7—C81.5386 (19)
C2—C31.521 (3)C7—H7A0.9800
C2—H2B0.9700C8—C101.529 (2)
C2—H2A0.9700C8—C91.530 (2)
C3—C41.536 (2)C8—H8A0.9800
C3—H3B0.9700C9—N11.465 (2)
C3—H3A0.9700C9—H9B0.9700
C4—C51.526 (2)C9—H9A0.9700
C4—H4B0.9700C10—C111.518 (2)
C4—H4A0.9700C10—H10B0.9700
C5—N11.4710 (17)C10—H10A0.9700
C5—C61.5148 (18)C11—H11C0.9600
C5—H5A0.9800C11—H11B0.9600
C6—O11.4250 (16)C11—H11A0.9600
C6—C71.5322 (18)O1—H1A0.79 (2)
C6—H6A0.9800O12—H12A0.82 (2)
C7—O121.4137 (18)
N1—C2—C3104.54 (13)O12—C7—H7A106.7
N1—C2—H2B110.8C6—C7—H7A106.7
C3—C2—H2B110.8C8—C7—H7A106.7
N1—C2—H2A110.8C10—C8—C9113.74 (12)
C3—C2—H2A110.8C10—C8—C7114.10 (12)
H2B—C2—H2A108.9C9—C8—C7109.43 (12)
C2—C3—C4105.74 (14)C10—C8—H8A106.3
C2—C3—H3B110.6C9—C8—H8A106.3
C4—C3—H3B110.6C7—C8—H8A106.3
C2—C3—H3A110.6N1—C9—C8111.68 (11)
C4—C3—H3A110.6N1—C9—H9B109.3
H3B—C3—H3A108.7C8—C9—H9B109.3
C5—C4—C3103.41 (15)N1—C9—H9A109.3
C5—C4—H4B111.1C8—C9—H9A109.3
C3—C4—H4B111.1H9B—C9—H9A107.9
C5—C4—H4A111.1C11—C10—C8113.97 (15)
C3—C4—H4A111.1C11—C10—H10B108.8
H4B—C4—H4A109.0C8—C10—H10B108.8
N1—C5—C6110.19 (11)C11—C10—H10A108.8
N1—C5—C4103.54 (12)C8—C10—H10A108.8
C6—C5—C4119.40 (13)H10B—C10—H10A107.7
N1—C5—H5A107.7C10—C11—H11C109.5
C6—C5—H5A107.7C10—C11—H11B109.5
C4—C5—H5A107.7H11C—C11—H11B109.5
O1—C6—C5110.00 (11)C10—C11—H11A109.5
O1—C6—C7113.62 (11)H11C—C11—H11A109.5
C5—C6—C7107.46 (11)H11B—C11—H11A109.5
O1—C6—H6A108.5C9—N1—C5110.39 (11)
C5—C6—H6A108.5C9—N1—C2113.21 (12)
C7—C6—H6A108.5C5—N1—C2103.45 (11)
O12—C7—C6113.49 (11)C6—O1—H1A112.0 (13)
O12—C7—C8109.31 (11)C7—O12—H12A106.1 (15)
C6—C7—C8113.52 (12)
N1—C2—C3—C418.32 (17)O12—C7—C8—C9178.22 (11)
C2—C3—C4—C58.30 (17)C6—C7—C8—C950.40 (15)
C3—C4—C5—N132.09 (15)C10—C8—C9—N176.70 (16)
C3—C4—C5—C6154.99 (13)C7—C8—C9—N152.21 (16)
N1—C5—C6—O163.72 (14)C9—C8—C10—C1160.38 (17)
C4—C5—C6—O155.85 (16)C7—C8—C10—C11173.12 (12)
N1—C5—C6—C760.44 (14)C8—C9—N1—C560.58 (15)
C4—C5—C6—C7179.99 (12)C8—C9—N1—C2176.00 (12)
O1—C6—C7—O1258.02 (16)C6—C5—N1—C965.22 (14)
C5—C6—C7—O12179.95 (11)C4—C5—N1—C9165.98 (11)
O1—C6—C7—C867.60 (15)C6—C5—N1—C2173.37 (12)
C5—C6—C7—C854.33 (14)C4—C5—N1—C244.57 (14)
O12—C7—C8—C1049.50 (16)C3—C2—N1—C9158.49 (13)
C6—C7—C8—C1078.32 (15)C3—C2—N1—C539.00 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N1i0.79 (2)2.104 (19)2.8619 (16)160.2 (18)
O12—H12A···O1i0.82 (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 formulaC10H19NO2
Mr185.26
Crystal system, space groupOrthorhombic, P212121
Temperature (K)298
a, b, c (Å)7.20849 (17), 8.83039 (19), 15.6656 (4)
V3)997.18 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.51 × 0.29 × 0.09
Data collection
DiffractometerOxford Diffraction Gemini R CCD
diffractometer
Absorption correctionAnalytical
(Clark & Reid, 1995)
Tmin, Tmax0.950, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections
26407, 1554, 1371
Rint0.023
(sin θ/λ)max1)0.693
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.099, 1.07
No. of reflections1554
No. of parameters124
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···N1i0.79 (2)2.104 (19)2.8619 (16)160.2 (18)
O12—H12A···O1i0.82 (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.

References

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