Crystal structure of obscurine: a natural product isolated from the stem bark of B. obscura

Bruno N Lenta; Rodolphe J Chouna; Beate Neumann; Hans-Georg Stammler; Norbert Sewald

doi:10.1107/S2056989015010567

. 2015 Jun 10;71(Pt 7):o457–o458. doi: 10.1107/S2056989015010567

Crystal structure of obscurine: a natural product isolated from the stem bark of B. obscura

Bruno N Lenta ^a,^*, Rodolphe J Chouna ^b, Beate Neumann ^c, Hans-Georg Stammler ^c, Norbert Sewald ^c

PMCID: PMC4518939 PMID: 26279906

Abstract

The title compound, C₂₄H₃₁NO₃ {systematic name: (E)-3-[(1R*,2S*,4aS*,8aR*)-2-(benzo[d][1,3]dioxol-5-yl)-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-N-isobutylacrylamide}, is a natural product isolated from the stem bark of B. obscura. It is composed of an octahydronaphthalene ring system substituted with an essentially planar benzodioxole ring system [r.m.s. deviation = 0.012 Å] and an extended isobutylacrylamide group. In the crystal, molecules are linked by N—H⋯O hydrogen bonds, forming chains propagating along [100]. The chains are linked by pairs of C—H⋯O hydrogen bonds, involving inversion-related benzodioxole ring systems, forming ribbons lying parallel to (010). There are also C—H⋯π interactions present within the ribbons.

Keywords: crystal structure, obscurine, octahydronaphthalene, benzodioxole, isobutylacrylamide, N—H⋯O hydrogen bonds

Related literature

For background to the Beilschmiedia genus, medicinal plants used in Cameroon, see: Chouna et al. (2009 ▸, 2010 ▸, 2011 ▸); Lenta et al. (2009 ▸, 2011 ▸). For related structures, see: Balawsnt et al. (1975 ▸). graphic file with name e-71-0o457-scheme1.jpg

Experimental

Crystal data

C₂₄H₃₁NO₃
M _r = 381.50
Triclinic,
a = 5.14153 (16) Å
b = 9.7449 (3) Å
c = 20.4639 (5) Å
α = 98.839 (2)°
β = 90.946 (2)°
γ = 100.237 (3)°
V = 996.00 (5) Å³
Z = 2
Cu Kα radiation
μ = 0.66 mm⁻¹
T = 100 K
0.36 × 0.03 × 0.02 mm

Data collection

Agilent SuperNova, Dual, Cu at zero, Atlas diffractometer
Absorption correction: gaussian (CrysAlis PRO; Agilent, 2013 ▸) T _min = 0.798, T _max = 1.000
13324 measured reflections
3892 independent reflections
3425 reflections with I > 2σ(I)
R _int = 0.027

Refinement

R[F ² > 2σ(F ²)] = 0.035
wR(F ²) = 0.091
S = 1.04
3892 reflections
377 parameters
All H-atom parameters refined
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2013 ▸); cell refinement: 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: Mercury (Macrae et al., 2008 ▸); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009 ▸) and PLATON (Spek, 2009 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989015010567/su5126sup1.cif

e-71-0o457-sup1.cif^{(459.3KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010567/su5126Isup2.hkl

e-71-0o457-Isup2.hkl^{(213.5KB, hkl)}

Click here for additional data file.^{(2.1MB, tif)}

. DOI: 10.1107/S2056989015010567/su5126fig1.tif

A view of the molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 50% probabilityl evel.

Click here for additional data file.^{(1.7MB, tif)}

b . DOI: 10.1107/S2056989015010567/su5126fig2.tif

A view along the b axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1 for details).

CCDC reference: 1404418

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

Cg2 is the centroid of the benzene ring C2C7.

DHA	DH	HA	D A	DHA
N1H1O3ⁱ	0.896(16)	2.105(16)	2.8938(13)	146.3(13)
C7H7O1ⁱⁱ	0.984(16)	2.503(16)	3.4264(15)	156.3(12)
C1H1B Cg2ⁱ	0.978(16)	2.595(15)	3.4578(12)	147.4(11)

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

BNL thanks the Alexander von Humboldt Foundation for providing a fellowship to study at Bielefeld University.

supplementary crystallographic information

S1. Chemical context

Plants of the Beilschmiedia genus have been the subject of research interest (Lenta et al., 2009, 2011; Chouna et al. 2011). Our interests involve the isolation of active constituents from the stem bark and leaves of B. obscura, a medicinal plant used in Cameroon. Herein, we report on the crystal structure of the title compound, a natural product isolated from the stem bark of B. obscura.

S2. Isolation and crystallization

The air-dried stem bark of B. obscura (400 g) was macerated with methanol at room temperature for 72 h. The methanol extract was concentrated under reduced pressure to give a residue of 16 g, which was selectively extracted with CH₂Cl₂ at room temperature to afford 4 g of the CH₂Cl₂ soluble residue. This extract was subjected to column chromatography (CC) over silica gel (0.023-0.20 mesh, Merck) and eluted with a gradient system of n-hexane/ CH₂Cl₂ and ( CH₂Cl₂/MeOH,) to afford obscurine (4.2 mg), the solid obtained was grounded and then recrystallised from a mixture of petroleum ether/dichlorometahne (1:1), yielding colourless needle-like crystals.

S3. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All of the H atoms were all located in difference Fourier maps and freely refined.