Literature DB >> 26279906

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

Bruno N Lenta1, Rodolphe J Chouna2, Beate Neumann3, Hans-Georg Stammler3, Norbert Sewald3.   

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-octa-hydro-naphthalen-1-yl]-N-iso-butyl-acryl-amide}, is a natural product isolated from the stem bark of B. obscura. It is composed of an octa-hydro-naphthalene ring system substituted with an essentially planar benzodioxole ring system [r.m.s. deviation = 0.012 Å] and an extended iso-butyl-acryl-amide group. In the crystal, mol-ecules 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 inter-actions present within the ribbons.

Entities:  

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

Year:  2015        PMID: 26279906      PMCID: PMC4518939          DOI: 10.1107/S2056989015010567

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


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 ▸).

Experimental

Crystal data

C24H31NO3 M = 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 Δρmax = 0.24 e Å−3 Δρmin = −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 ▸). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S2056989015010567/su5126sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010567/su5126Isup2.hkl Click here for additional data file. . 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. 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
C24H31NO3Z = 2
Mr = 381.50F(000) = 412
Triclinic, P1Dx = 1.272 Mg m3
a = 5.14153 (16) ÅCu Kα radiation, λ = 1.5418 Å
b = 9.7449 (3) ÅCell parameters from 7209 reflections
c = 20.4639 (5) Åθ = 4.7–76.2°
α = 98.839 (2)°µ = 0.66 mm1
β = 90.946 (2)°T = 100 K
γ = 100.237 (3)°Needle, clear colourless
V = 996.00 (5) Å30.36 × 0.03 × 0.02 mm
Agilent SuperNova, Dual, Cu at zero, Atlas diffractometer3892 independent reflections
Radiation source: SuperNova (Cu) X-ray Source3425 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.027
Detector resolution: 5.3114 pixels mm-1θmax = 72.1°, θmin = 4.4°
ω scansh = −6→5
Absorption correction: gaussian (CrysAlis PRO; Agilent, 2013)k = −11→12
Tmin = 0.798, Tmax = 1.000l = −24→24
13324 measured reflections
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035All H-atom parameters refined
wR(F2) = 0.091w = 1/[σ2(Fo2) + (0.0424P)2 + 0.3477P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.001
3892 reflectionsΔρmax = 0.24 e Å3
377 parametersΔρmin = −0.22 e Å3
0 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.
xyzUiso*/Ueq
O30.99052 (16)0.81354 (9)0.86676 (4)0.01947 (19)
O10.32116 (17)0.81350 (9)0.50886 (4)0.0198 (2)
O20.26950 (17)0.59230 (9)0.54145 (4)0.0211 (2)
N10.5440 (2)0.79089 (11)0.87047 (5)0.0177 (2)
C70.7117 (2)0.92262 (12)0.58231 (6)0.0155 (2)
C60.8900 (2)0.89637 (12)0.62993 (6)0.0149 (2)
C140.9558 (2)1.40385 (13)0.81143 (6)0.0189 (3)
C180.9906 (2)1.00932 (12)0.77808 (6)0.0161 (2)
C190.7706 (2)0.94294 (12)0.80006 (6)0.0172 (2)
C40.6528 (2)0.65272 (13)0.62212 (6)0.0183 (2)
C161.2263 (2)1.23586 (12)0.74705 (6)0.0152 (2)
C171.0186 (2)1.10091 (12)0.72506 (6)0.0147 (2)
C20.5136 (2)0.81316 (12)0.55642 (6)0.0154 (2)
C220.4536 (2)0.77083 (13)0.98764 (6)0.0195 (3)
C81.1097 (2)1.01511 (12)0.66128 (6)0.0150 (2)
C30.4823 (2)0.68151 (12)0.57583 (6)0.0162 (2)
C50.8593 (2)0.76299 (12)0.64871 (6)0.0174 (2)
C200.7803 (2)0.84434 (12)0.84886 (6)0.0161 (2)
C210.5080 (2)0.69546 (13)0.91942 (6)0.0182 (3)
C121.0346 (2)1.41782 (12)0.69190 (6)0.0174 (2)
C131.0029 (3)1.50233 (13)0.75965 (6)0.0192 (3)
C91.2170 (2)1.11024 (13)0.61238 (6)0.0163 (2)
C111.2589 (2)1.33271 (12)0.69369 (6)0.0153 (2)
C101.2835 (2)1.24957 (13)0.62661 (6)0.0166 (2)
C230.3498 (3)0.66495 (16)1.03273 (7)0.0293 (3)
C151.1801 (2)1.32087 (13)0.81431 (6)0.0178 (2)
C10.1586 (2)0.67567 (13)0.49990 (6)0.0186 (3)
C240.6991 (3)0.87158 (15)1.01892 (7)0.0260 (3)
H161.402 (3)1.2038 (15)0.7515 (7)0.016 (3)*
H111.426 (3)1.4037 (15)0.7059 (7)0.015 (3)*
H170.844 (3)1.1256 (15)0.7138 (7)0.015 (3)*
H21A0.670 (3)0.6545 (15)0.9203 (7)0.019 (4)*
H15A1.345 (3)1.3876 (15)0.8301 (7)0.017 (3)*
H40.633 (3)0.5592 (17)0.6353 (8)0.026 (4)*
H91.238 (3)1.0624 (15)0.5679 (7)0.018 (3)*
H50.986 (3)0.7444 (16)0.6806 (8)0.023 (4)*
H12A0.862 (3)1.3498 (16)0.6770 (7)0.019 (4)*
H181.159 (3)0.9934 (15)0.7974 (7)0.020 (4)*
H70.730 (3)1.0156 (17)0.5680 (7)0.022 (4)*
H13A1.169 (3)1.5731 (16)0.7739 (8)0.023 (4)*
H14A0.942 (3)1.4596 (16)0.8555 (8)0.023 (4)*
H21B0.354 (3)0.6183 (16)0.9026 (7)0.022 (4)*
H10.399 (3)0.8194 (16)0.8567 (7)0.022 (4)*
H1A0.160 (3)0.6301 (16)0.4528 (8)0.023 (4)*
H81.260 (3)0.9720 (15)0.6758 (7)0.019 (4)*
H12B1.068 (3)1.4823 (16)0.6573 (8)0.021 (4)*
H14B0.780 (3)1.3357 (16)0.7997 (8)0.023 (4)*
H1B−0.020 (3)0.6828 (15)0.5137 (7)0.021 (4)*
H220.313 (3)0.8255 (15)0.9805 (7)0.018 (3)*
H101.350 (3)1.3042 (16)0.5915 (8)0.023 (4)*
H15B1.146 (3)1.2548 (17)0.8489 (8)0.025 (4)*
H13B0.851 (3)1.5540 (17)0.7578 (8)0.026 (4)*
H24A0.841 (3)0.8171 (19)1.0287 (9)0.036 (5)*
H24B0.660 (3)0.9237 (19)1.0614 (9)0.037 (5)*
H23A0.483 (4)0.609 (2)1.0412 (9)0.041 (5)*
H190.599 (3)0.9535 (17)0.7834 (8)0.029 (4)*
H24C0.775 (3)0.9404 (19)0.9890 (9)0.036 (5)*
H23B0.304 (4)0.717 (2)1.0772 (10)0.043 (5)*
H23C0.187 (4)0.601 (2)1.0128 (9)0.043 (5)*
U11U22U33U12U13U23
O30.0158 (4)0.0234 (4)0.0221 (4)0.0068 (3)0.0012 (3)0.0090 (3)
O10.0191 (4)0.0170 (4)0.0230 (4)0.0005 (3)−0.0059 (3)0.0060 (3)
O20.0198 (4)0.0153 (4)0.0277 (5)−0.0001 (3)−0.0058 (4)0.0058 (3)
N10.0154 (5)0.0214 (5)0.0187 (5)0.0052 (4)0.0010 (4)0.0087 (4)
C70.0162 (6)0.0148 (5)0.0173 (6)0.0050 (4)0.0025 (4)0.0048 (4)
C60.0153 (5)0.0152 (5)0.0152 (5)0.0049 (4)0.0034 (4)0.0031 (4)
C140.0176 (6)0.0216 (6)0.0169 (6)0.0042 (5)0.0017 (5)0.0007 (5)
C180.0175 (6)0.0160 (5)0.0157 (6)0.0054 (4)−0.0008 (4)0.0029 (4)
C190.0161 (6)0.0199 (6)0.0176 (6)0.0060 (5)0.0000 (4)0.0059 (4)
C40.0207 (6)0.0143 (6)0.0218 (6)0.0047 (5)0.0027 (5)0.0069 (4)
C160.0134 (5)0.0160 (5)0.0171 (6)0.0040 (4)−0.0006 (4)0.0038 (4)
C170.0134 (5)0.0166 (6)0.0154 (6)0.0048 (4)−0.0001 (4)0.0041 (4)
C20.0153 (5)0.0175 (6)0.0150 (5)0.0059 (4)0.0018 (4)0.0043 (4)
C220.0195 (6)0.0213 (6)0.0200 (6)0.0066 (5)0.0031 (5)0.0070 (5)
C80.0138 (5)0.0154 (5)0.0170 (6)0.0049 (4)0.0006 (4)0.0038 (4)
C30.0147 (5)0.0146 (5)0.0188 (6)0.0020 (4)0.0022 (4)0.0019 (4)
C50.0187 (6)0.0172 (6)0.0185 (6)0.0067 (5)0.0006 (5)0.0056 (4)
C200.0175 (6)0.0158 (5)0.0156 (6)0.0043 (4)0.0004 (4)0.0027 (4)
C210.0194 (6)0.0169 (6)0.0193 (6)0.0027 (5)0.0008 (5)0.0068 (4)
C120.0185 (6)0.0172 (6)0.0181 (6)0.0060 (5)−0.0004 (5)0.0045 (4)
C130.0198 (6)0.0172 (6)0.0218 (6)0.0070 (5)0.0003 (5)0.0022 (5)
C90.0141 (6)0.0189 (6)0.0164 (6)0.0039 (4)0.0017 (4)0.0032 (4)
C110.0135 (5)0.0154 (5)0.0171 (6)0.0025 (4)0.0006 (4)0.0033 (4)
C100.0145 (6)0.0187 (6)0.0176 (6)0.0031 (4)0.0021 (4)0.0061 (4)
C230.0335 (8)0.0297 (7)0.0245 (7)−0.0006 (6)0.0050 (6)0.0109 (6)
C150.0181 (6)0.0186 (6)0.0164 (6)0.0026 (5)−0.0014 (5)0.0026 (4)
C10.0181 (6)0.0167 (6)0.0203 (6)0.0012 (5)−0.0015 (5)0.0037 (4)
C240.0296 (7)0.0235 (7)0.0233 (7)0.0028 (6)−0.0010 (6)0.0018 (5)
O3—C201.2363 (15)C2—C31.3838 (16)
O1—C21.3772 (14)C22—C211.5289 (17)
O1—C11.4341 (15)C22—C231.5213 (18)
O2—C31.3772 (14)C22—C241.5189 (18)
O2—C11.4386 (15)C22—H220.991 (15)
N1—C201.3443 (16)C8—C91.5120 (16)
N1—C211.4606 (15)C8—H81.006 (15)
N1—H10.894 (16)C5—H50.973 (16)
C7—C61.4093 (16)C21—H21A0.987 (16)
C7—C21.3705 (17)C21—H21B1.004 (16)
C7—H70.984 (16)C12—C131.5269 (16)
C6—C81.5199 (16)C12—C111.5384 (16)
C6—C51.3945 (16)C12—H12A1.020 (15)
C14—C131.5300 (17)C12—H12B1.014 (16)
C14—C151.5270 (17)C13—H13A1.007 (16)
C14—H14A0.988 (16)C13—H13B1.003 (17)
C14—H14B1.021 (16)C9—C101.3250 (17)
C18—C191.3216 (18)C9—H90.973 (15)
C18—C171.5007 (16)C11—C101.5024 (16)
C18—H180.994 (15)C11—H111.006 (15)
C19—C201.4944 (16)C10—H100.988 (16)
C19—H190.970 (17)C23—H23A0.98 (2)
C4—C31.3732 (17)C23—H23B1.025 (19)
C4—C51.4050 (17)C23—H23C0.99 (2)
C4—H40.978 (16)C15—H15A0.990 (15)
C16—C171.5411 (16)C15—H15B1.025 (16)
C16—C111.5421 (16)C1—H1A0.997 (16)
C16—C151.5385 (16)C1—H1B0.978 (16)
C16—H161.016 (15)C24—H24A1.010 (18)
C17—C81.5640 (16)C24—H24B0.980 (18)
C17—H171.002 (14)C24—H24C1.010 (19)
C2—O1—C1106.11 (9)C4—C5—H5118.5 (9)
C3—O2—C1105.76 (9)O3—C20—N1123.23 (11)
C20—N1—C21124.03 (10)O3—C20—C19121.94 (11)
C20—N1—H1119.1 (10)N1—C20—C19114.83 (10)
C21—N1—H1116.7 (10)N1—C21—C22112.10 (10)
C6—C7—H7121.2 (9)N1—C21—H21A106.5 (9)
C2—C7—C6117.32 (11)N1—C21—H21B106.8 (9)
C2—C7—H7121.5 (9)C22—C21—H21A112.0 (9)
C7—C6—C8119.41 (10)C22—C21—H21B110.2 (9)
C5—C6—C7119.69 (11)H21A—C21—H21B109.0 (12)
C5—C6—C8120.89 (10)C13—C12—C11111.67 (10)
C13—C14—H14A109.7 (9)C13—C12—H12A109.2 (8)
C13—C14—H14B108.9 (9)C13—C12—H12B110.8 (9)
C15—C14—C13111.11 (10)C11—C12—H12A108.9 (8)
C15—C14—H14A109.2 (9)C11—C12—H12B110.0 (9)
C15—C14—H14B109.8 (9)H12A—C12—H12B106.0 (12)
H14A—C14—H14B108.0 (12)C14—C13—H13A107.7 (9)
C19—C18—C17128.07 (11)C14—C13—H13B109.8 (9)
C19—C18—H18116.3 (9)C12—C13—C14110.15 (10)
C17—C18—H18115.5 (9)C12—C13—H13A110.0 (9)
C18—C19—C20120.79 (11)C12—C13—H13B110.4 (9)
C18—C19—H19120.9 (10)H13A—C13—H13B108.8 (12)
C20—C19—H19118.3 (10)C8—C9—H9115.5 (9)
C3—C4—C5116.89 (11)C10—C9—C8124.58 (11)
C3—C4—H4121.4 (9)C10—C9—H9119.9 (9)
C5—C4—H4121.7 (9)C16—C11—H11107.0 (8)
C17—C16—C11111.83 (9)C12—C11—C16112.87 (10)
C17—C16—H16106.3 (8)C12—C11—H11106.4 (8)
C11—C16—H16106.0 (8)C10—C11—C16110.93 (9)
C15—C16—C17114.84 (10)C10—C11—C12110.45 (10)
C15—C16—C11110.08 (9)C10—C11—H11109.0 (8)
C15—C16—H16107.2 (8)C9—C10—C11123.82 (11)
C18—C17—C16110.54 (9)C9—C10—H10119.5 (9)
C18—C17—C8108.26 (9)C11—C10—H10116.7 (9)
C18—C17—H17110.5 (8)C22—C23—H23A110.8 (11)
C16—C17—C8109.30 (9)C22—C23—H23B110.0 (11)
C16—C17—H17110.5 (8)C22—C23—H23C110.8 (11)
C8—C17—H17107.6 (8)H23A—C23—H23B108.3 (15)
O1—C2—C3109.80 (10)H23A—C23—H23C109.1 (16)
C7—C2—O1127.48 (10)H23B—C23—H23C107.8 (15)
C7—C2—C3122.71 (11)C14—C15—C16113.29 (10)
C21—C22—H22106.4 (8)C14—C15—H15A108.9 (8)
C23—C22—C21110.96 (11)C14—C15—H15B110.5 (9)
C23—C22—H22108.2 (9)C16—C15—H15A108.7 (8)
C24—C22—C21111.12 (11)C16—C15—H15B109.8 (9)
C24—C22—C23110.86 (11)H15A—C15—H15B105.3 (12)
C24—C22—H22109.2 (9)O1—C1—O2108.07 (9)
C6—C8—C17111.47 (9)O1—C1—H1A109.5 (9)
C6—C8—H8108.3 (8)O1—C1—H1B109.9 (9)
C17—C8—H8106.4 (8)O2—C1—H1A108.7 (9)
C9—C8—C6111.81 (9)O2—C1—H1B108.4 (9)
C9—C8—C17111.61 (9)H1A—C1—H1B112.2 (12)
C9—C8—H8107.0 (9)C22—C24—H24A110.3 (10)
O2—C3—C2110.17 (10)C22—C24—H24B110.8 (11)
C4—C3—O2128.50 (11)C22—C24—H24C112.1 (10)
C4—C3—C2121.32 (11)H24A—C24—H24B106.4 (14)
C6—C5—C4122.06 (11)H24A—C24—H24C107.5 (14)
C6—C5—H5119.5 (9)H24B—C24—H24C109.5 (14)
O1—C2—C3—O20.14 (14)C3—O2—C1—O12.82 (12)
O1—C2—C3—C4178.82 (11)C3—C4—C5—C60.73 (18)
C7—C6—C8—C1789.64 (12)C5—C6—C8—C17−88.97 (13)
C7—C6—C8—C9−36.07 (14)C5—C6—C8—C9145.33 (11)
C7—C6—C5—C4−0.73 (18)C5—C4—C3—O2178.46 (11)
C7—C2—C3—O2−179.54 (11)C5—C4—C3—C20.05 (18)
C7—C2—C3—C4−0.87 (19)C20—N1—C21—C22103.43 (13)
C6—C7—C2—O1−178.77 (11)C21—N1—C20—O32.70 (18)
C6—C7—C2—C30.86 (17)C21—N1—C20—C19−178.39 (10)
C6—C8—C9—C10140.17 (12)C12—C11—C10—C9−109.46 (13)
C18—C19—C20—O3−5.24 (18)C13—C14—C15—C16−55.96 (13)
C18—C19—C20—N1175.83 (11)C13—C12—C11—C1654.57 (13)
C18—C17—C8—C670.41 (12)C13—C12—C11—C10179.40 (10)
C18—C17—C8—C9−163.77 (10)C11—C16—C17—C18−179.76 (9)
C19—C18—C17—C16135.66 (13)C11—C16—C17—C861.18 (12)
C19—C18—C17—C8−104.64 (14)C11—C16—C15—C1452.15 (13)
C16—C17—C8—C6−169.12 (9)C11—C12—C13—C14−56.40 (13)
C16—C17—C8—C9−43.30 (12)C23—C22—C21—N1165.79 (11)
C16—C11—C10—C916.46 (16)C15—C14—C13—C1256.89 (13)
C17—C18—C19—C20173.97 (11)C15—C16—C17—C18−53.39 (13)
C17—C16—C11—C1277.81 (12)C15—C16—C17—C8−172.45 (9)
C17—C16—C11—C10−46.76 (13)C15—C16—C11—C12−51.11 (13)
C17—C16—C15—C14−75.12 (13)C15—C16—C11—C10−175.68 (10)
C17—C8—C9—C1014.53 (16)C1—O1—C2—C7−178.70 (12)
C2—O1—C1—O2−2.74 (12)C1—O1—C2—C31.63 (13)
C2—C7—C6—C8−178.69 (10)C1—O2—C3—C4179.60 (12)
C2—C7—C6—C5−0.07 (17)C1—O2—C3—C2−1.84 (13)
C8—C6—C5—C4177.87 (11)C24—C22—C21—N1−70.39 (13)
C8—C9—C10—C11−0.56 (19)
D—H···AD—HH···AD···AD—H···A
N1—H1···O3i0.896 (16)2.105 (16)2.8938 (13)146.3 (13)
C7—H7···O1ii0.984 (16)2.503 (16)3.4264 (15)156.3 (12)
C1—H1B···Cg2i0.978 (16)2.595 (15)3.4578 (12)147.4 (11)
Table 1

Hydrogen-bond geometry (, )

Cg2 is the centroid of the benzene ring C2C7.

DHA DHHA 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)

Symmetry codes: (i) ; (ii) .

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