PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 November 1; 66(Pt 11): o3013.
Published online 2010 October 31. doi:  10.1107/S1600536810041188
PMCID: PMC3009306

Yuzurimine from of Daphniphyllum macropodum Miq.

Abstract

The title compound, C27H37NO7, is a Daphniphyllum alkaloid isolated from a branch of Daphniphyllum macropodum Miq. All of the five-membered rings adopt envelope conformations while the six- and seven-membered ring adopt chair conformations. Classical inter­molecular O—H(...)O and weak C—H(...)N hydrogen bonds are present in the crystal structure.

Related literature

For the chemical structure of the title compound established from NMR and MS data, see: Li et al. (2009 [triangle]). For structures of Daphniphyllum alkaloids, see: Yamamura & Terada (1976 [triangle]); Kubota et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o3013-scheme1.jpg

Experimental

Crystal data

  • C27H37NO7
  • M r = 487.58
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3013-efi1.jpg
  • a = 9.5980 (3) Å
  • b = 9.7437 (2) Å
  • c = 26.0986 (6) Å
  • V = 2440.74 (11) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 294 K
  • 0.60 × 0.45 × 0.20 mm

Data collection

  • Oxford Xcalibur diffractometer with an Eos CCD detector
  • 8335 measured reflections
  • 2836 independent reflections
  • 2236 reflections with I > 2σ(I)
  • R int = 0.019

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.120
  • S = 1.04
  • 2836 reflections
  • 317 parameters
  • H-atom parameters constrained
  • Δρmax = 0.48 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: CrysAlis PRO CCD (Oxford Diffraction, 2009 [triangle]); cell refinement: CrysAlis PRO CCD; data reduction: CrysAlis PRO RED (Oxford Diffraction, 2009 [triangle]); 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.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810041188/xu5044sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810041188/xu5044Isup2.hkl

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

Acknowledgments

This project was supported by grants from the PhD Programs Foundation of the Ministry of Education of China (grant No. 20090181110064) and the Scientific Reseach Fund of Leshan Teachers’ College, China (grant No. Z0975). We thank Professor F.-Z. Chen of Leshan Teachers College for the isolation of the title compound.

supplementary crystallographic information

Comment

The title compound, yuzurimine, was previously isolated from Daphniphyllum macropodum Miq. (Li et al. 2009), and its structure was established from the NMR and MS data. In our recent investigation, it was isolation from the branch of Daphniphyllum macropodum Miq. collected in the Emei Mountain, Sichuan Province of China in 2008. Its crystal structure is reported here.

The molecular structure of the title compound is shown in Fig. 1. Six-membered ring A (C1/C2/C3/C4/C5/C8) adopts chair conformation; Six-membered heterocyclic ring B (C1/N1/C7/C6/C5/C8) displays the same chair conformation; seven-membered ring C (C5/C6/C12/C11/C10/C9/C8) adopts a screw-chair conformation; five-membered rings D (C8/C9/C13/C14/C15) and E (C10/C9/C15/C16/C17) adopt an envelope conformations. While the five-membered heterocyclic F (C1/N1/C19/C18/C2) displays an envelope conformation.

Experimental

The title compound was isolated from the branch of Daphniphyllum macropodum Miq. And crystals suitable for X-ray structure analysis was obtained by slow evaporation from an acetone solution at room temperature.

Refinement

H atoms were located geometrically with C—H distance of 0.93–0.98 Å, and refined using a riding model with Uiso(H) = 1.2 Ueq(C). As no significant anomalous scatterings, Friedel pairs were merged.

Figures

Fig. 1.
The molecular structure of the title compound with 30% probabiliy displacement ellipsoids for no-H atoms. H atoms have been omitted clarity. Dashed line indicates hydrogen bonding.

Crystal data

C27H37NO7F(000) = 1048
Mr = 487.58Dx = 1.327 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 4404 reflections
a = 9.5980 (3) Åθ = 3.0–27.0°
b = 9.7437 (2) ŵ = 0.10 mm1
c = 26.0986 (6) ÅT = 294 K
V = 2440.74 (11) Å3Block, colorless
Z = 40.60 × 0.45 × 0.20 mm

Data collection

Oxford Xcalibur diffractometer with an Eos CCD detector2236 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.019
graphiteθmax = 26.4°, θmin = 3.1°
ω scansh = −4→11
8335 measured reflectionsk = −12→6
2836 independent reflectionsl = −32→25

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.120H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0793P)2] where P = (Fo2 + 2Fc2)/3
2836 reflections(Δ/σ)max = 0.001
317 parametersΔρmax = 0.48 e Å3
0 restraintsΔρmin = −0.19 e Å3

Special details

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.
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)

xyzUiso*/Ueq
O10.6702 (2)0.3147 (2)0.46602 (7)0.0382 (5)
H10.73800.31700.44690.057*
O20.1503 (2)0.46110 (19)0.39329 (7)0.0362 (5)
O3−0.0227 (3)0.3209 (3)0.41677 (10)0.0737 (8)
O40.1867 (2)0.2863 (2)0.31031 (7)0.0404 (5)
O50.1503 (4)0.0913 (3)0.26965 (11)0.0921 (11)
O60.3018 (3)−0.1150 (3)0.40070 (9)0.0687 (7)
O70.4426 (3)−0.0900 (3)0.33499 (9)0.0768 (9)
N10.6017 (2)0.4877 (2)0.41036 (8)0.0332 (5)
C10.5508 (3)0.3699 (3)0.43982 (9)0.0295 (6)
C20.4577 (3)0.4292 (3)0.48146 (9)0.0342 (6)
H20.44510.36300.50940.041*
C30.3173 (3)0.4728 (3)0.45943 (10)0.0380 (7)
H3B0.25050.47790.48730.046*
H3A0.32690.56450.44530.046*
C40.2579 (3)0.3794 (3)0.41792 (9)0.0314 (6)
H40.21340.30060.43460.038*
C50.3605 (3)0.3247 (2)0.37656 (9)0.0273 (5)
C60.4181 (3)0.4432 (3)0.34171 (10)0.0327 (6)
H60.33560.49560.33130.039*
C120.4869 (3)0.3971 (3)0.29090 (9)0.0395 (7)
H12B0.42720.32830.27540.047*
H12A0.48820.47550.26800.047*
C110.6344 (3)0.3386 (4)0.29319 (10)0.0462 (8)
H11B0.66220.31290.25880.055*
H11A0.69690.41070.30450.055*
C100.6540 (3)0.2175 (3)0.32725 (10)0.0381 (7)
C170.7564 (4)0.1055 (4)0.31502 (12)0.0595 (10)
H17A0.85100.13920.31850.071*
H17B0.74330.07370.28010.071*
C160.7302 (4)−0.0094 (4)0.35225 (12)0.0604 (10)
H16A0.8171−0.04560.36550.073*
H16B0.6784−0.08320.33610.073*
C150.6441 (3)0.0580 (3)0.39524 (11)0.0411 (7)
H150.70770.07960.42350.049*
C140.5100 (3)−0.0001 (3)0.41841 (11)0.0389 (7)
H140.5328−0.06410.44610.047*
C130.4398 (3)0.1315 (3)0.44104 (9)0.0336 (6)
H13A0.47090.14650.47600.040*
H13B0.33930.12130.44120.040*
C80.4837 (3)0.2571 (2)0.40589 (9)0.0268 (6)
C90.5948 (3)0.1916 (3)0.37249 (10)0.0316 (6)
C190.6329 (4)0.5914 (3)0.45071 (11)0.0467 (8)
H19B0.60760.68240.43880.056*
H19A0.73160.59100.45860.056*
C180.5466 (3)0.5536 (3)0.49960 (11)0.0438 (7)
H180.61190.52040.52560.053*
C70.5085 (3)0.5450 (3)0.37085 (11)0.0406 (7)
H7B0.56510.59430.34620.049*
H7A0.44770.61140.38720.049*
C200.4694 (5)0.6767 (4)0.52205 (14)0.0678 (11)
H20A0.41260.64710.55020.102*
H20C0.41140.71710.49620.102*
H20B0.53570.74340.53390.102*
C210.0177 (3)0.4231 (3)0.39505 (10)0.0393 (7)
C22−0.0720 (3)0.5211 (4)0.36612 (12)0.0503 (8)
H22B−0.16800.50480.37440.076*
H22C−0.05810.50820.33000.076*
H22A−0.04760.61340.37530.076*
C230.2849 (3)0.2182 (3)0.34440 (10)0.0339 (6)
H23B0.35180.16610.32440.041*
H23A0.23540.15490.36660.041*
C240.1298 (3)0.2110 (3)0.27347 (10)0.0407 (7)
C250.0380 (4)0.2931 (4)0.24032 (11)0.0509 (8)
H25C−0.01150.23340.21740.076*
H25B0.09300.35670.22080.076*
H25A−0.02730.34270.26110.076*
C260.4157 (4)−0.0727 (3)0.37809 (12)0.0462 (8)
C270.2020 (5)−0.1746 (4)0.36432 (14)0.0790 (12)
H27B0.2100−0.27280.36480.118*
H27C0.2217−0.14130.33050.118*
H27A0.1091−0.14870.37390.118*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0288 (10)0.0501 (11)0.0357 (9)−0.0001 (11)−0.0087 (8)0.0011 (9)
O20.0214 (9)0.0407 (10)0.0465 (11)0.0010 (9)−0.0012 (8)0.0061 (9)
O30.0356 (13)0.0947 (19)0.0909 (18)−0.0145 (15)−0.0098 (13)0.0483 (17)
O40.0387 (11)0.0407 (10)0.0417 (10)0.0026 (11)−0.0183 (9)−0.0028 (9)
O50.124 (3)0.0572 (15)0.0951 (19)0.020 (2)−0.068 (2)−0.0273 (15)
O60.0680 (17)0.0769 (17)0.0612 (13)−0.0202 (16)0.0013 (13)−0.0102 (13)
O70.087 (2)0.097 (2)0.0469 (13)−0.0159 (19)0.0028 (14)−0.0190 (14)
N10.0290 (12)0.0368 (12)0.0337 (11)−0.0056 (11)−0.0028 (10)−0.0008 (10)
C10.0264 (14)0.0326 (13)0.0295 (12)−0.0026 (12)−0.0045 (10)0.0003 (11)
C20.0357 (15)0.0407 (15)0.0263 (12)−0.0004 (15)−0.0025 (11)−0.0016 (11)
C30.0315 (14)0.0489 (16)0.0337 (13)0.0044 (14)0.0017 (12)−0.0054 (13)
C40.0242 (13)0.0365 (14)0.0334 (13)−0.0002 (12)0.0003 (11)0.0068 (12)
C50.0250 (13)0.0295 (12)0.0273 (11)−0.0013 (12)−0.0020 (10)0.0023 (11)
C60.0270 (14)0.0394 (14)0.0318 (13)0.0008 (14)−0.0029 (11)0.0093 (12)
C120.0400 (16)0.0497 (16)0.0288 (13)−0.0013 (16)−0.0002 (12)0.0097 (13)
C110.0383 (17)0.067 (2)0.0333 (14)0.0026 (18)0.0104 (13)0.0074 (14)
C100.0314 (15)0.0524 (16)0.0305 (12)0.0035 (16)0.0028 (12)−0.0027 (13)
C170.054 (2)0.078 (2)0.0459 (16)0.025 (2)0.0068 (16)−0.0050 (17)
C160.057 (2)0.064 (2)0.0599 (19)0.024 (2)0.0079 (18)−0.0019 (18)
C150.0401 (17)0.0439 (15)0.0392 (14)0.0125 (16)−0.0056 (13)0.0039 (13)
C140.0404 (17)0.0360 (14)0.0404 (15)0.0080 (15)−0.0078 (13)0.0043 (13)
C130.0374 (16)0.0346 (13)0.0287 (12)−0.0016 (13)−0.0036 (11)0.0043 (12)
C80.0260 (13)0.0311 (12)0.0235 (12)−0.0009 (12)−0.0037 (10)0.0013 (10)
C90.0275 (13)0.0361 (13)0.0313 (13)0.0042 (13)−0.0051 (11)−0.0010 (12)
C190.0461 (19)0.0435 (15)0.0506 (16)−0.0104 (16)−0.0060 (15)−0.0084 (14)
C180.0455 (18)0.0479 (17)0.0381 (14)−0.0005 (16)−0.0063 (14)−0.0115 (14)
C70.0438 (17)0.0350 (14)0.0429 (15)−0.0026 (15)−0.0021 (14)0.0063 (13)
C200.072 (3)0.062 (2)0.069 (2)−0.002 (2)0.001 (2)−0.0308 (19)
C210.0271 (15)0.0557 (17)0.0352 (14)−0.0062 (15)0.0004 (12)0.0056 (14)
C220.0322 (16)0.066 (2)0.0526 (18)0.0039 (17)−0.0034 (14)0.0042 (17)
C230.0349 (15)0.0344 (13)0.0326 (12)0.0024 (14)−0.0091 (12)0.0024 (12)
C240.0372 (16)0.0472 (16)0.0377 (14)−0.0017 (16)−0.0084 (13)−0.0042 (14)
C250.052 (2)0.0589 (18)0.0421 (16)−0.0022 (19)−0.0180 (15)0.0047 (15)
C260.060 (2)0.0328 (14)0.0455 (18)0.0046 (16)0.0151 (16)0.0020 (14)
C270.073 (3)0.075 (3)0.089 (3)−0.017 (2)−0.021 (2)−0.022 (2)

Geometric parameters (Å, °)

O1—C11.439 (3)C17—H17A0.9700
O1—H10.8200C17—H17B0.9700
O2—C211.327 (4)C16—C151.540 (4)
O2—C41.454 (3)C16—H16A0.9700
O3—C211.209 (4)C16—H16B0.9700
O4—C241.327 (3)C15—C91.508 (4)
O4—C231.456 (3)C15—C141.531 (5)
O5—C241.187 (4)C15—H150.9800
O6—C261.309 (4)C14—C261.558 (5)
O6—C271.468 (4)C14—C131.564 (4)
O7—C261.166 (4)C14—H140.9800
N1—C11.465 (4)C13—C81.586 (4)
N1—C71.475 (4)C13—H13A0.9700
N1—C191.490 (4)C13—H13B0.9700
C1—C21.521 (4)C8—C91.518 (4)
C1—C81.552 (4)C19—C181.565 (4)
C2—C31.526 (4)C19—H19B0.9700
C2—C181.556 (4)C19—H19A0.9700
C2—H20.9800C18—C201.527 (4)
C3—C41.526 (4)C18—H180.9800
C3—H3B0.9700C7—H7B0.9700
C3—H3A0.9700C7—H7A0.9700
C4—C51.555 (4)C20—H20A0.9600
C4—H40.9800C20—H20C0.9600
C5—C231.520 (4)C20—H20B0.9600
C5—C81.555 (3)C21—C221.491 (4)
C5—C61.570 (3)C22—H22B0.9600
C6—C71.522 (4)C22—H22C0.9600
C6—C121.548 (4)C22—H22A0.9600
C6—H60.9800C23—H23B0.9700
C12—C111.528 (4)C23—H23A0.9700
C12—H12B0.9700C24—C251.471 (4)
C12—H12A0.9700C25—H25C0.9600
C11—C101.489 (4)C25—H25B0.9600
C11—H11B0.9700C25—H25A0.9600
C11—H11A0.9700C27—H27B0.9600
C10—C91.335 (4)C27—H27C0.9600
C10—C171.502 (4)C27—H27A0.9600
C17—C161.504 (5)
C1—O1—H1109.5C15—C14—C13102.0 (2)
C21—O2—C4120.9 (2)C26—C14—C13112.1 (2)
C24—O4—C23117.2 (2)C15—C14—H14109.8
C26—O6—C27112.2 (3)C26—C14—H14109.8
C1—N1—C7117.4 (2)C13—C14—H14109.8
C1—N1—C19103.1 (2)C14—C13—C8107.5 (2)
C7—N1—C19111.0 (2)C14—C13—H13A110.2
O1—C1—N1106.1 (2)C8—C13—H13A110.2
O1—C1—C2105.67 (19)C14—C13—H13B110.2
N1—C1—C2105.9 (2)C8—C13—H13B110.2
O1—C1—C8109.7 (2)H13A—C13—H13B108.5
N1—C1—C8113.19 (19)C9—C8—C1109.5 (2)
C2—C1—C8115.6 (2)C9—C8—C5115.43 (18)
C1—C2—C3110.8 (2)C1—C8—C5107.3 (2)
C1—C2—C18101.0 (2)C9—C8—C13101.2 (2)
C3—C2—C18112.4 (2)C1—C8—C13109.08 (18)
C1—C2—H2110.7C5—C8—C13114.2 (2)
C3—C2—H2110.7C10—C9—C15112.2 (3)
C18—C2—H2110.7C10—C9—C8136.7 (3)
C4—C3—C2115.5 (2)C15—C9—C8111.0 (2)
C4—C3—H3B108.4N1—C19—C18108.1 (2)
C2—C3—H3B108.4N1—C19—H19B110.1
C4—C3—H3A108.4C18—C19—H19B110.1
C2—C3—H3A108.4N1—C19—H19A110.1
H3B—C3—H3A107.5C18—C19—H19A110.1
O2—C4—C3104.6 (2)H19B—C19—H19A108.4
O2—C4—C5109.29 (19)C20—C18—C2117.6 (3)
C3—C4—C5117.4 (2)C20—C18—C19112.6 (3)
O2—C4—H4108.4C2—C18—C19103.0 (2)
C3—C4—H4108.4C20—C18—H18107.7
C5—C4—H4108.4C2—C18—H18107.7
C23—C5—C8110.21 (19)C19—C18—H18107.7
C23—C5—C4108.4 (2)N1—C7—C6116.7 (2)
C8—C5—C4106.53 (18)N1—C7—H7B108.1
C23—C5—C6110.51 (19)C6—C7—H7B108.1
C8—C5—C6109.2 (2)N1—C7—H7A108.1
C4—C5—C6111.9 (2)C6—C7—H7A108.1
C7—C6—C12112.0 (2)H7B—C7—H7A107.3
C7—C6—C5113.0 (2)C18—C20—H20A109.5
C12—C6—C5115.7 (2)C18—C20—H20C109.5
C7—C6—H6105.0H20A—C20—H20C109.5
C12—C6—H6105.0C18—C20—H20B109.5
C5—C6—H6105.0H20A—C20—H20B109.5
C11—C12—C6118.0 (2)H20C—C20—H20B109.5
C11—C12—H12B107.8O3—C21—O2123.6 (3)
C6—C12—H12B107.8O3—C21—C22125.4 (3)
C11—C12—H12A107.8O2—C21—C22110.9 (3)
C6—C12—H12A107.8C21—C22—H22B109.5
H12B—C12—H12A107.1C21—C22—H22C109.5
C10—C11—C12115.8 (2)H22B—C22—H22C109.5
C10—C11—H11B108.3C21—C22—H22A109.5
C12—C11—H11B108.3H22B—C22—H22A109.5
C10—C11—H11A108.3H22C—C22—H22A109.5
C12—C11—H11A108.3O4—C23—C5109.6 (2)
H11B—C11—H11A107.4O4—C23—H23B109.8
C9—C10—C11128.6 (3)C5—C23—H23B109.8
C9—C10—C17109.2 (3)O4—C23—H23A109.8
C11—C10—C17122.1 (3)C5—C23—H23A109.8
C10—C17—C16107.1 (3)H23B—C23—H23A108.2
C10—C17—H17A110.3O5—C24—O4122.4 (3)
C16—C17—H17A110.3O5—C24—C25125.8 (3)
C10—C17—H17B110.3O4—C24—C25111.8 (3)
C16—C17—H17B110.3C24—C25—H25C109.5
H17A—C17—H17B108.5C24—C25—H25B109.5
C17—C16—C15104.1 (3)H25C—C25—H25B109.5
C17—C16—H16A110.9C24—C25—H25A109.5
C15—C16—H16A110.9H25C—C25—H25A109.5
C17—C16—H16B110.9H25B—C25—H25A109.5
C15—C16—H16B110.9O7—C26—O6125.0 (4)
H16A—C16—H16B109.0O7—C26—C14126.0 (3)
C9—C15—C14102.1 (2)O6—C26—C14108.9 (2)
C9—C15—C16104.5 (2)O6—C27—H27B109.5
C14—C15—C16125.6 (3)O6—C27—H27C109.5
C9—C15—H15107.8H27B—C27—H27C109.5
C14—C15—H15107.8O6—C27—H27A109.5
C16—C15—H15107.8H27B—C27—H27A109.5
C15—C14—C26112.9 (2)H27C—C27—H27A109.5

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1···O3i0.822.433.216 (3)161
C22—H22B···N1ii0.962.413.354 (4)169

Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU5044).

References

  • Kubota, T., Matsuno, Y., Morita, H., Shinzato, T., Sekiguchi, M. & Kobayashi, J. (2006). Tetrahedron, 62, 4743–4746.
  • Li, Z.-Y., Gu, Y.-C., Irwin, D., Sheridan, J., Clough, J., Chen, P., Peng, S.-Y., Yang, Y.-M. & Guo, Y.-W. (2009). Chem. Biodivers.6, 1744–1750. [PubMed]
  • Oxford Diffraction (2009). CrysAlis PRO CCD and CrysAlis PRO RED Oxford Diffraction Ltd, Yarnton, England.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Yamamura, S. & Terada, Y. (1976). Chem. Lett.5, 1381–1385.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography