Home Crystal structure of (R)-1-(2,3-dihydro-1H-pyrrolizin-5-yl)-2,3-dihydroxypropan-1-one, C10H13NO3
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Crystal structure of (R)-1-(2,3-dihydro-1H-pyrrolizin-5-yl)-2,3-dihydroxypropan-1-one, C10H13NO3

  • Jun-Jie Tan , Xiao-Yu Liu , Jie Zhang , Xi Chen , Yi-Ming Li EMAIL logo and Bing-Hua Jiao EMAIL logo
Published/Copyright: October 22, 2016

Abstract

C10H13NO3, monoclinic, P21 (no. 4), a = 11.8118(5) Å, b = 4.9299(2) Å, c = 14.5436(7) Å, β = 89.011(3)°, V = 945.28(7) Å3, Z = 4, Rgt(F) = 0.0302, wRref(F2) = 0.0774, T = 170 K.

CCDC no.:: 1470598

One of two crystallographically independant molecules of the title structure is shown in the figure. Tables 1 and 2 contain details of the measurement method and a list of the atoms including atomic coordinates and displacement parameters.

Table 1

Data collection and handling.

Crystal:Colourless block
Size:0.20 × 0.08 × 0.03 mm
Wavelength:Cu Kα radiation (1.54178 Å)
μ:8.4 cm−1
Diffractometer, scan mode:Bruker APEX-II, φ and ω
2θmax, completeness:130°, >99%
N(hkl)measured, N(hkl)unique, Rint:10070, 2946, 0.041
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2898
N(param)refined:216
Programs:SHELX [3], Bruker programs [4]
Table 2

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

AtomxyzUiso*/Ueq
O60.61299(10)0.9928(3)0.11529(8)0.0363(3)
H60.55361.05600.08780.055*
O50.59988(10)0.6984(3)−0.03748(7)0.0399(3)
H50.63670.8158−0.05620.060*
O40.80900(10)0.8687(3)−0.00537(7)0.0408(3)
O30.37342(9)0.1183(3)0.30346(8)0.0349(3)
H30.3995−0.02810.32190.052*
O20.47257(10)0.6339(2)0.36607(7)0.0304(3)
O10.57102(10)0.2859(2)0.47526(7)0.0292(3)
N150.98851(11)0.6759(3)0.12807(8)0.0290(3)
N40.74433(11)−0.0991(3)0.45470(8)0.0266(3)
C220.61006(14)0.7074(4)0.10931(11)0.0335(4)
H22A0.53050.64670.10090.040*
H22B0.65070.63030.16070.040*
C210.66478(13)0.6034(4)0.03881(10)0.0310(4)
H210.66390.40460.03900.037*
C200.78949(13)0.7019(4)0.04525(10)0.0293(4)
C160.87513(13)0.5894(4)0.10990(10)0.0289(4)
C141.05908(13)0.8670(4)0.09102(11)0.0350(4)
H14A1.02821.04960.08960.042*
H14B1.06470.81230.03560.042*
C131.17633(16)0.8466(6)0.15000(13)0.0505(5)
H13A1.23670.81110.11910.061*
H13B1.19371.01600.17960.061*
C191.04638(14)0.5346(4)0.19192(11)0.0348(4)
C180.97262(15)0.3489(5)0.21740(11)0.0375(4)
H180.99090.22590.26060.045*
C170.86532(14)0.3827(4)0.16557(10)0.0318(4)
H170.79880.28430.16780.038*
C121.17049(16)0.6190(6)0.20972(15)0.0563(6)
H12A1.22010.47000.20060.068*
H12B1.19330.68110.26610.068*
C110.45855(14)0.2603(4)0.27099(10)0.0314(4)
H11A0.42100.37890.22710.038*
H11B0.50500.13130.24740.038*
C100.53723(13)0.4293(3)0.33602(10)0.0261(4)
H100.59570.51660.31000.031*
C90.59878(12)0.2567(3)0.40769(9)0.0236(3)
C50.68662(12)0.0693(3)0.39377(9)0.0240(3)
C30.73494(14)−0.1636(4)0.53988(10)0.0335(4)
H3A0.6661−0.26880.54190.040*
H3B0.7347−0.00060.57270.040*
C20.84450(17)−0.3304(5)0.56835(13)0.0520(5)
H2A0.8290−0.48110.60230.062*
H2B0.9044−0.21850.60040.062*
C10.88310(14)−0.4353(4)0.49058(13)0.0413(5)
H1A0.9663−0.42680.49630.050*
H1B0.8577−0.62050.47830.050*
C80.82480(13)−0.2445(4)0.42592(11)0.0322(4)
C70.82227(14)−0.1706(4)0.34472(11)0.0365(4)
H70.8691−0.23860.31020.044*
C60.73589(13)0.0257(4)0.32457(11)0.0312(4)
H6A0.71490.11220.27390.037*
H20.474(2)0.594(6)0.4151(17)0.051(7)*

Source of material

The title compound was isolated from the fungus Eutypella sp. D-1, which was harvested from the soil of London Island of Kongsfjorden of Nylesund District (altitude of 100 m) in the Arctic [1]. The culture (150 L) was centrifuged to give the broth and mycelia. The broth was exhaustively extracted with EtOAc three times, then the EtOAc layers were combined and evaporated under reduced pressure at a temperature not exceeding 40 °C to yield a dark brown gum (200 g), which was subjected to column chromatography (CC) on silica gel and eluted with EtOH in petroleum ether (PE) (0 to 100%, stepwise) to yield 5 fractions (Fr.1 to Fr.5). Fr.4 (25 g) was applied to a MCI gel CC (MeOH/H2O, 50 to 100%) to obtain 12 fractions (Fr.4A-Fr.4L). Fr.4C (1.99 g) was subjected to a Sephadex LH-20 CC that was eluted with MeOH to obtain 8 subfractions (Fr.4C1-Fr.4C8). Fr.4C6 was further separated using the ODS-A—HG reversed-phase silica gel CC (MeOH/H2O, 20 to 30%), silica gel CC (CH2Cl2/MeOH = 50/1) and semi-preparative HPLC (CH3CN/H2O = 15/85, 4 mL/min) to give the title compound (14 mg, Rt = 18.62 min). Colorless crystals were obtained by slow evaporation at room temperature from PE and acetone in a 5:1 ratio.

Experimental details

Hydrogen atoms of O—H were found from a Fourier difference map, and refined with a fixed distance of 0.86 Å and isotropic displacement parameters of 1.5 Ueq of the parent atoms. The remaining hydrogen atoms were placed in calculated positions and refined with a riding model with isotropic displacement parameters set to 1.2 (sp2) and 1.5 (sp3) times Ueq of the parent atom. The absolute structure was confirmed by the Flack parameter x = 0.03(15).

Discussion

The title compound is a new substituted pyrrolizine alkaloid and its planar structure has been elucidated by spectroscopic methods (including NMR, MS and IR). The absolute stereochemistry of the chiral centres at C10 were determined as R by X-ray diffraction using CuKα radiation [2]. In both independent molecules there is one intramolecular hydrogen bond (cf. the figure) and there are some other intermolecular ones connecting adjacent molecules.

Acknowledgements

The project was financially supported by the National Hi-tech R&D Program of China (863 Program; 2012AA092105), Guangdong Innovative Development of Marine Economy Regional Demonstration Project (GD2012-D01-001), Eastern Scholar Tracking Program of Shanghai Municipal Education Commission (2012-90), and Shanghai E-Research Institute of Bioactive Constituent in TCM Plan.

References

1. Zhang, L. Q.; Chen, X. C.; Chen, Z. Q.; Wang, G. M.; Zhu, S. G.; Yang, Y. F.; Chen, K. X.; Liu, X. Y.; Li, Y. M.: Eutypenoids A-C: novel pimarane diterpenoids from the Arctic fungus Eutypella sp. D-1. Mar. Drugs 14 (2016) 44.10.3390/md14030044Search in Google Scholar PubMed PubMed Central

2. Flack, H. D.: On enantiomorph-polarity estimation. Acta Crystallogr. A39 (1983) 876–881.10.1107/S0108767383001762Search in Google Scholar

3. Sheldrick, G. M.: A short history of SHELX. Acta Crystallogr. A64 (2008) 112–122.10.1107/S0108767307043930Search in Google Scholar PubMed

4. Bruker. APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, WI, USA, 2009.Search in Google Scholar

Received: 2016-3-30
Accepted: 2016-9-18
Published Online: 2016-10-22
Published in Print: 2017-1-1

©2016 Jun-Jie Tan et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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