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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2437–o2438.
Published online 2010 August 28. doi:  10.1107/S1600536810034227
PMCID: PMC3007931

Absolute configuration of odorine

Abstract

The title compound, known as odorine or roxburghiline {systematic name: (S)-N-[(R)-1-cinnamoylpyrrolidin-2-yl]-2-methyl­butanamide}, C18H24N2O2, is a nitro­genous compound isolated from the leaves of Aglaia odorata. The absolute configuration was determined by refinement of the Flack parameter with data collected using Cu Kα radiation showing positions 2 and 2′ to be S and R, respectively. The pyrrolidine ring adopts an envelope conformation. In the crystal, mol­ecules are linked into chains along [010] by inter­molecular N—H(...)O hydrogen bonds.

Related literature

For ring conformations, see: Cremer & Pople (1975 [triangle]). For standard bond-length data, see: Allen et al. (1987 [triangle]). For background to the Aglaia plants and their biological activity, see: Brader et al. (1998 [triangle]); Cui et al. (1997 [triangle]); Engelmeier et al. (2000 [triangle]); Hayashi et al. (1982 [triangle]); Inada et al. (2001 [triangle]); Nugroho et al. (1999 [triangle]); Purushothaman et al. 1979 [triangle]); Saifah et al. (1993 [triangle]); Shiengthong et al. (1979 [triangle]). For related structures, see: Babidge et al. (1980 [triangle]); Dumontet et al. (1996 [triangle]); Hayashi et al. (1982 [triangle]). For the stability of the temperature controller used in the data collection, see Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2437-scheme1.jpg

Experimental

Crystal data

  • C18H24N2O2
  • M r = 300.39
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2437-efi1.jpg
  • a = 18.8909 (3) Å
  • b = 6.8398 (1) Å
  • c = 13.4174 (2) Å
  • β = 107.054 (1)°
  • V = 1657.43 (4) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 0.63 mm−1
  • T = 100 K
  • 0.57 × 0.16 × 0.13 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.718, T max = 0.924
  • 10656 measured reflections
  • 2625 independent reflections
  • 2606 reflections with I > 2σ(I)
  • R int = 0.042

Refinement

  • R[F 2 > 2σ(F 2)] = 0.033
  • wR(F 2) = 0.096
  • S = 1.16
  • 2625 reflections
  • 205 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.27 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1036 Friedel pairs
  • Flack parameter: 0.03 (18)

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810034227/lh5122sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810034227/lh5122Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

OY thanks the Office of the Higher Education Commission, Thailand, for support by grant funding under the program Strategic Scholarships for Frontier Research Network for the Joint PhD Program Thai Doctoral degree. The authors thank the Thailand Research Fund (BRG5280013) and Prince of Songkla University for financial support. The authors also thank Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

supplementary crystallographic information

Comment

Several species of the genus Aglaia of the family Meliaceae are of ethnomedicinal values and have insecticidal (Brader et al., 1998), antifungal (Engelmeier et al., 2000) and cytotoxic (Saifah et al., 1993; Cui et al., 1997) activities. These interesting activities have prompted us to screen for further bioactive compounds from Aglaia odorata. Aglaia odorata known locally in Thai as "Pra-yong" or "Hom-glai" is a small tree occurring primarily in South-East Asia. The leaves and roots of this plant have been used in local folk medicine as a heart stimulant, febrifuge and to retrieve toxin by causing vomiting. The isolated compounds from this plant also show interesting biological activities such as anticancer (Inada et al., 2001), insecticidal (Nugroho et al., 1999) and anti-leukemic (Hayashi et al., 1982) activities. In the course of our research of chemical constituents and bioactive compounds from the leaves of A. odorata which were collected from Songkhla province in the southern part of Thailand, the title aminopyrrolidine odorine (I), also known as odorine (Shiengthong et al., 1979) or roxburghiline or N-cinnamoyl-2-(2-methylbutanoylamino)pyrrolidine (Purushothaman et al., 1979) was isolated. The previous report showed that (I) possesses cancer-chemopreventive activity (Inada et al., 2001). The absolute configuration of (I) was determined by making use of the anomalous scattering of Cu KαX-radiation with the Flack parameter being refined to 0.03 (18). We report herein the crystal structure of (I).

Fig. 1 shows that the molecule of (I) possesses a 2-aminopyrrolidine ring linked by two amide functions to 2-methylbutyric acid and cinnamic acid. The pyrrolidine ring adopts an envelope conformation with the puckered C12 atom having a deviation of 0.223 (1) Å and with the puckering parameters Q = 0.3522 (15) Å and θ = 281.3 (2)° (Cremer & Pople, 1975). Atoms of the cinnamoyl (C1–C9/O1) moiety essentially lie on the same plane (r.m.s. 0.0216 (1) Å) with a max. deviation of 0.0583 (1) Å for atom O1. Atoms C13, C14, C15, N2 and O2 lie on the same plane (r.m.s. 0.0216 (1) Å). The mean plane through C13/C14/C15/N2/O2 makes the dihedral angle of 88.80 (7)° with the mean plane through the cinnamoyl moiety. The 2-methylbutanamide chain at C13 is pseudo-axial with the C14–N2–C13–C12 torsion angle = 125.55 (13)°. The orientation of the butyl group is described by the torsion angle C14–C15–C17–C18 = 68.78 (18)°. The bond distances in (I) are within normal ranges (Allen et al., 1987) and comparable with the related structures which are odorinol (Hayashi et al., 1982) and forbaglin A (Dumontet et al., 1996). The absolute configuration at atoms C15 and C13 or positions 2 and 2' of the odorine are S,R configurations which agree with the previous stereochemistry of odorine (Babidge et al., 1980).

In the crystal packing of (I) (Fig. 2), the molecules are linked into chains along [010] through N2—H1N2···O1i hydrogen bonds (Fig. 2 and Table 1).

Experimental

Ground-dried leaves of A. odorata (53.70 g) were extracted with CH2Cl2 and CH3OH (each of 2 x 2 L) for a duration of 3 days at room temperature. The solvents were evaporated under reduced pressure to afford CH2Cl2 (23.50 g) and CH3OH (5.23 g) crude extracts, respectively. The CH2Cl2 crude extract (23.50 g) was further purified by quick column chromatography (QCC) over silica gel using hexane as eluent and increasing polarity with EtOAc and CH3OH to afford 10 fractions (F1-F10). Fraction F10 (231.6 mg) was further separated by column chromatography with acetone-hexane (3:7), yielding the title compound as white solid (15.6 mg). Colorless needle-shaped single crystals of the title compound suitable for x-ray structure determination were recrystallized from CH2Cl2 by the slow evaporation of the solvent at room temperature after several days, Mp. 476-478 K.

Refinement

The amide H atom was located in a difference map and refined isotropically. The remaining H atoms were placed in calculated positions with (C—H) = 0.98 for CH, 0.97 for CH2 and 0.96 Å for CH3 atoms. The Uiso values were constrained to be 1.5Ueq of the carrier atom for methyl H atoms and 1.2Ueq for the remaining H atoms. A rotating group model was used for the methyl groups. The highest residual electron density peak is located at 0.73 Å from C6 and the deepest hole is located at 0.71 Å from C9. 1036 Friedel pairs were used to determine the absolute configuration.

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of (I) viewed approximately along the c axis, showing one dimensional chains along [0 1 0]. N—H···O hydrogen bonds are shown as dashed lines.

Crystal data

C18H24N2O2F(000) = 648
Mr = 300.39Dx = 1.204 Mg m3
Monoclinic, C2Melting point = 476–478 K
Hall symbol: C 2yCu Kα radiation, λ = 1.54178 Å
a = 18.8909 (3) ÅCell parameters from 2625 reflections
b = 6.8398 (1) Åθ = 6.8–67.4°
c = 13.4174 (2) ŵ = 0.63 mm1
β = 107.054 (1)°T = 100 K
V = 1657.43 (4) Å3Needle, colorless
Z = 40.57 × 0.16 × 0.13 mm

Data collection

Bruker APEXII DUO CCD area-detector diffractometer2625 independent reflections
Radiation source: sealed tube2606 reflections with I > 2σ(I)
graphiteRint = 0.042
[var phi] and ω scansθmax = 67.4°, θmin = 6.8°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −22→22
Tmin = 0.718, Tmax = 0.924k = −7→6
10656 measured reflectionsl = −16→16

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.096w = 1/[σ2(Fo2) + (0.0595P)2 + 0.2381P] where P = (Fo2 + 2Fc2)/3
S = 1.16(Δ/σ)max = 0.001
2625 reflectionsΔρmax = 0.21 e Å3
205 parametersΔρmin = −0.27 e Å3
1 restraintAbsolute structure: Flack (1983), 1036 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.03 (18)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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 > 2sigma(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)

xyzUiso*/Ueq
O10.68617 (5)0.99471 (16)0.55658 (7)0.0243 (2)
O20.97777 (6)0.88734 (17)0.73395 (8)0.0315 (3)
N10.79446 (6)0.99195 (19)0.51776 (8)0.0218 (2)
H1N20.8859 (10)0.691 (3)0.5433 (14)0.030 (5)*
N20.90244 (6)0.78710 (19)0.57796 (9)0.0217 (3)
C10.87323 (8)0.9894 (3)0.92951 (11)0.0299 (3)
H1A0.90381.00590.88700.036*
C20.90374 (8)0.9818 (3)1.03621 (11)0.0348 (4)
H2A0.95480.99231.06510.042*
C30.85882 (8)0.9585 (3)1.10083 (11)0.0325 (4)
H3A0.87970.95381.17280.039*
C40.78306 (9)0.9425 (3)1.05783 (11)0.0337 (4)
H4A0.75280.92731.10080.040*
C50.75221 (8)0.9490 (2)0.95025 (11)0.0285 (3)
H5A0.70120.93760.92170.034*
C60.79653 (7)0.9725 (2)0.88465 (10)0.0233 (3)
C70.76210 (7)0.9768 (2)0.77145 (10)0.0236 (3)
H7A0.71070.96790.74810.028*
C80.79691 (7)0.9920 (2)0.69898 (9)0.0219 (3)
H8A0.84831.00190.71900.026*
C90.75502 (7)0.9936 (2)0.58677 (9)0.0207 (3)
C100.75678 (7)0.9890 (2)0.40514 (9)0.0233 (3)
H10A0.73081.11090.38260.028*
H10B0.72170.88190.38710.028*
C110.81922 (8)0.9613 (2)0.35579 (10)0.0275 (3)
H11A0.80971.03480.29140.033*
H11B0.82530.82430.34140.033*
C120.88773 (8)1.0396 (2)0.43814 (11)0.0276 (3)
H12A0.93250.98080.43030.033*
H12B0.89121.18050.43290.033*
C130.87590 (7)0.9813 (2)0.54206 (10)0.0222 (3)
H13A0.89901.07810.59560.027*
C140.95055 (7)0.7544 (2)0.67329 (11)0.0237 (3)
C150.97075 (8)0.5412 (2)0.69919 (11)0.0293 (3)
H15A0.93320.45760.65270.035*
C161.04558 (10)0.5039 (3)0.67983 (16)0.0512 (5)
H16A1.04130.52720.60770.077*
H16B1.06030.37080.69710.077*
H16C1.08210.59030.72250.077*
C170.97552 (9)0.4934 (3)0.81232 (12)0.0356 (4)
H17A0.99710.36440.82900.043*
H17B1.00850.58650.85760.043*
C180.90143 (10)0.4977 (3)0.83531 (12)0.0406 (4)
H18A0.90890.47290.90810.061*
H18B0.86960.39900.79480.061*
H18C0.87900.62380.81760.061*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0229 (5)0.0260 (6)0.0230 (4)0.0040 (4)0.0051 (3)0.0031 (4)
O20.0301 (5)0.0298 (6)0.0277 (5)−0.0005 (4)−0.0025 (4)−0.0062 (5)
N10.0222 (5)0.0231 (6)0.0193 (5)0.0013 (5)0.0045 (4)0.0013 (5)
N20.0225 (5)0.0209 (7)0.0202 (6)−0.0006 (5)0.0039 (4)−0.0046 (5)
C10.0277 (7)0.0399 (9)0.0226 (6)0.0012 (7)0.0080 (5)0.0015 (7)
C20.0269 (7)0.0507 (10)0.0245 (7)0.0036 (7)0.0038 (5)−0.0006 (8)
C30.0384 (8)0.0390 (10)0.0180 (6)0.0045 (7)0.0050 (5)0.0014 (6)
C40.0379 (8)0.0409 (11)0.0253 (7)0.0019 (7)0.0137 (6)0.0029 (6)
C50.0263 (7)0.0324 (9)0.0264 (7)0.0017 (6)0.0074 (5)0.0016 (6)
C60.0268 (6)0.0209 (8)0.0217 (6)0.0049 (6)0.0063 (5)0.0022 (6)
C70.0234 (6)0.0214 (7)0.0246 (7)0.0038 (6)0.0048 (5)0.0019 (6)
C80.0228 (6)0.0194 (7)0.0215 (6)0.0031 (6)0.0032 (5)0.0014 (6)
C90.0239 (6)0.0153 (7)0.0221 (6)0.0031 (6)0.0053 (5)0.0014 (6)
C100.0275 (6)0.0218 (7)0.0187 (6)0.0032 (6)0.0037 (5)0.0011 (6)
C110.0354 (7)0.0280 (8)0.0201 (6)0.0028 (6)0.0098 (5)0.0017 (6)
C120.0304 (7)0.0277 (8)0.0276 (7)−0.0002 (6)0.0132 (5)0.0028 (6)
C130.0219 (6)0.0214 (7)0.0234 (6)−0.0015 (5)0.0070 (5)−0.0018 (6)
C140.0174 (6)0.0291 (9)0.0244 (7)0.0013 (5)0.0058 (5)−0.0013 (6)
C150.0278 (7)0.0293 (9)0.0290 (7)0.0059 (6)0.0058 (6)−0.0003 (6)
C160.0451 (9)0.0479 (13)0.0675 (12)0.0202 (9)0.0274 (9)0.0085 (10)
C170.0397 (8)0.0319 (9)0.0304 (7)0.0055 (7)0.0027 (6)0.0066 (7)
C180.0535 (9)0.0358 (10)0.0347 (8)0.0013 (8)0.0163 (7)0.0039 (8)

Geometric parameters (Å, °)

O1—C91.2437 (16)C10—C111.5243 (18)
O2—C141.2280 (19)C10—H10A0.9700
N1—C91.3480 (17)C10—H10B0.9700
N1—C101.4695 (15)C11—C121.531 (2)
N1—C131.4780 (16)C11—H11A0.9700
N2—C141.3529 (17)C11—H11B0.9700
N2—C131.451 (2)C12—C131.5284 (18)
N2—H1N20.81 (2)C12—H12A0.9700
C1—C21.3787 (19)C12—H12B0.9700
C1—C61.401 (2)C13—H13A0.9800
C1—H1A0.9300C14—C151.522 (2)
C2—C31.389 (2)C15—C171.529 (2)
C2—H2A0.9300C15—C161.532 (2)
C3—C41.382 (2)C15—H15A0.9800
C3—H3A0.9300C16—H16A0.9600
C4—C51.3898 (19)C16—H16B0.9600
C4—H4A0.9300C16—H16C0.9600
C5—C61.3907 (19)C17—C181.519 (2)
C5—H5A0.9300C17—H17A0.9700
C6—C71.4667 (17)C17—H17B0.9700
C7—C81.3282 (18)C18—H18A0.9600
C7—H7A0.9300C18—H18B0.9600
C8—C91.4813 (17)C18—H18C0.9600
C8—H8A0.9300
C9—N1—C10120.52 (10)C10—C11—H11B111.0
C9—N1—C13126.73 (10)C12—C11—H11B111.0
C10—N1—C13112.65 (10)H11A—C11—H11B109.0
C14—N2—C13122.40 (12)C13—C12—C11104.37 (11)
C14—N2—H1N2116.5 (13)C13—C12—H12A110.9
C13—N2—H1N2120.9 (13)C11—C12—H12A110.9
C2—C1—C6120.50 (13)C13—C12—H12B110.9
C2—C1—H1A119.7C11—C12—H12B110.9
C6—C1—H1A119.7H12A—C12—H12B108.9
C1—C2—C3120.45 (13)N2—C13—N1110.75 (11)
C1—C2—H2A119.8N2—C13—C12114.38 (12)
C3—C2—H2A119.8N1—C13—C12101.95 (10)
C4—C3—C2119.75 (13)N2—C13—H13A109.8
C4—C3—H3A120.1N1—C13—H13A109.8
C2—C3—H3A120.1C12—C13—H13A109.8
C3—C4—C5119.91 (14)O2—C14—N2122.61 (14)
C3—C4—H4A120.0O2—C14—C15122.00 (12)
C5—C4—H4A120.0N2—C14—C15115.36 (12)
C4—C5—C6120.94 (13)C14—C15—C17111.68 (13)
C4—C5—H5A119.5C14—C15—C16107.63 (14)
C6—C5—H5A119.5C17—C15—C16110.13 (13)
C5—C6—C1118.44 (12)C14—C15—H15A109.1
C5—C6—C7119.43 (12)C17—C15—H15A109.1
C1—C6—C7122.13 (12)C16—C15—H15A109.1
C8—C7—C6126.53 (12)C15—C16—H16A109.5
C8—C7—H7A116.7C15—C16—H16B109.5
C6—C7—H7A116.7H16A—C16—H16B109.5
C7—C8—C9120.87 (11)C15—C16—H16C109.5
C7—C8—H8A119.6H16A—C16—H16C109.5
C9—C8—H8A119.6H16B—C16—H16C109.5
O1—C9—N1120.81 (11)C18—C17—C15114.07 (12)
O1—C9—C8121.80 (11)C18—C17—H17A108.7
N1—C9—C8117.39 (11)C15—C17—H17A108.7
N1—C10—C11104.19 (10)C18—C17—H17B108.7
N1—C10—H10A110.9C15—C17—H17B108.7
C11—C10—H10A110.9H17A—C17—H17B107.6
N1—C10—H10B110.9C17—C18—H18A109.5
C11—C10—H10B110.9C17—C18—H18B109.5
H10A—C10—H10B108.9H18A—C18—H18B109.5
C10—C11—C12103.95 (11)C17—C18—H18C109.5
C10—C11—H11A111.0H18A—C18—H18C109.5
C12—C11—H11A111.0H18B—C18—H18C109.5
C6—C1—C2—C3−0.4 (3)N1—C10—C11—C12−24.24 (15)
C1—C2—C3—C40.2 (3)C10—C11—C12—C1335.81 (15)
C2—C3—C4—C50.2 (3)C14—N2—C13—N1−119.95 (13)
C3—C4—C5—C6−0.3 (3)C14—N2—C13—C12125.55 (13)
C4—C5—C6—C10.0 (2)C9—N1—C13—N272.51 (17)
C4—C5—C6—C7179.40 (15)C10—N1—C13—N2−103.96 (13)
C2—C1—C6—C50.4 (3)C9—N1—C13—C12−165.39 (14)
C2—C1—C6—C7−179.02 (17)C10—N1—C13—C1218.14 (16)
C5—C6—C7—C8−177.81 (15)C11—C12—C13—N286.96 (14)
C1—C6—C7—C81.6 (3)C11—C12—C13—N1−32.61 (14)
C6—C7—C8—C9179.71 (14)C13—N2—C14—O2−3.6 (2)
C10—N1—C9—O1−0.7 (2)C13—N2—C14—C15178.31 (11)
C13—N1—C9—O1−176.95 (14)O2—C14—C15—C1741.89 (18)
C10—N1—C9—C8178.64 (13)N2—C14—C15—C17−139.99 (13)
C13—N1—C9—C82.4 (2)O2—C14—C15—C16−79.11 (18)
C7—C8—C9—O15.1 (2)N2—C14—C15—C1699.01 (15)
C7—C8—C9—N1−174.23 (14)C14—C15—C17—C1868.78 (18)
C9—N1—C10—C11−172.93 (12)C16—C15—C17—C18−171.68 (16)
C13—N1—C10—C113.78 (17)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1N2···O1i0.81 (2)2.09 (2)2.8789 (16)163 (2)

Symmetry codes: (i) −x+3/2, y−1/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5122).

References

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