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organic compounds
Deacetylnomilin monohydrate
aGuangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People's Republic of China, and bInfinitus (China) Company Ltd, Guangzhou 510665, People's Republic of China
*Correspondence e-mail: tliyl@jnu.edu.cn
In the title compound (systematic name 1-hydroxy-1,2-dihydroobacunoic acid 3,4-lactone monohydrate), C26H32O8·H2O, the dihedral angles between the planes of the ester groups and the furan plane are 43.06 (12) and 56.06 (7)°, while that between the furan plane and the keto group is 58.50 (9)°. The A/B, B/C and C/D ring junctions are all trans-fused. Intermolecular O—H⋯O hydrogen bonds between the hydroxy and carbonyl groups and the water molecule give rise to a three-dimensional structure.
Related literature
For general background to the title compound, see: Dreyer (1965); Munehiro et al. (1989
). For the of (−)-nomilin, see: Zhang et al. (2006
). For details of ring conformations and puckering parameters, see: Cremer & Pople (1975
); Boeyens (1978
).
Experimental
Crystal data
|
|
Data collection: CrysAlis PRO (Agilent, 2011); cell 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: OLEX2 (Dolomanov et al., 2009
); software used to prepare material for publication: OLEX2.
Supporting information
https://doi.org/10.1107/S1600536811035033/zs2135sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811035033/zs2135Isup2.hkl
The title compound was isolated from the traditional Chinese medicine Pericarpium Citri Reticulatae, 500g of which was extracted with boiling water, then concentrated by rotary evaporator. The crude extract was subjected to silica gel
eluted using a methanol/chloroform gradient. Further purification of the cloroform/methanol (92/8) fraction by silica gel with EtOAc/cyclohexane (35/65) gave the title compound (4 mg). Crystals of the title compound were obtained after slow evaporation of a methanolic solution at room temperature.The C-bound H atoms were positioned geometrically and were included in the
in the riding-model approximation, with C—H = 0.93 Å (alkenyl H), 0.96 Å (CH3), 0.97 Å (CH2), 0.98 Å (CH) and O—H = 0.82 Å and with Uiso(H) = 1.2Ueq(C) (alkenyl, methylene and methine) and = 1.5Ueq[C(methyl) and O]. The determined for (-)-nomilin (Zhang et al., 2006) was invoked: the determined for the parent compound not being definitive [-0.19 (1) for 1213 Friedel pairs].The title compound C26H32O8 . H2O (Fig. 1) is the monohydrate of deacetylnomilin (systematic name: 1-hydroxy-1,2-dihydroobacunoic acid 3,4 -lactone monohydrate), which was originally isolated from the seeds of the genera Citrus and Poncirus (Dreyer, 1965; Munehiro et al., 1989). With the present compound, which was isolated from the traditional Chinese medicine Pericarpium Citri Reticulatae, the dihedral angles between the planes of the ester groups and the furan plane are 43.06 (12)° and 56.06 (7)°, while that between the furan plane and the keto group is 58.50 (9)°. The title compound is composed of five rings, one seven–membered, one five-membered and three six–membered. The seven–membered ring (A) adopts a chair conformation as does the six–membered ring (B), which has puckering parameters (Cremer & Pople, 1975; Boeyens, 1978) Q = 0.588 (2) Å, θ = 5.2 (2)°, φ = 239 (2)°. The rings C and D adopt skew–boat conformations with puckering paramaters Q = 0.775 (2) Å, θ = 98.35 (15)°, φ = 94.92 (15)° and Q = 0.512 (2) Å, θ = 110.4 (2)°, φ = 92.9 (2)°, respectively. The A/B, B/C and C/D ring junctions are all trans- fused. Intermolecular O—H···O hydrogen bonds (Table 1) involving the hydroxy and carbonyl groups and the water molecule give a three-dimensional structure (Fig. 2). The determined for the parent (-)-nomilin (Zhang et al., 2006) was invoked, giving the assignments C1(S), C5(R), C8(R), C9(R), C10(S), C12(S), C13(S), C16(R), C17(R) for the 9 chiral centres in the molecule (using the numbering scheme employed in Fig. 1).
For general background to the title compound, see: Dreyer (1965); Munehiro et al. (1989). For the
of (-)-nomilin, see: Zhang et al. (2006). For details of ring conformations and puckering parameters, see: Cremer & Pople (1975); Boeyens (1978).Data collection: CrysAlis PRO (Agilent, 2011); cell
CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009). ![]() | Fig. 1. The molecular structure of the title compound showing 50% probability displacement ellipsoids and the atom-numbering scheme. |
![]() | Fig. 2. The packing in the unit cell viewed down the a axis. |
C26H32O8·H2O | Dx = 1.381 Mg m−3 |
Mr = 490.53 | Cu Kα radiation, λ = 1.5418 Å |
Orthorhombic, P212121 | Cell parameters from 3366 reflections |
a = 10.6037 (2) Å | θ = 3.2–62.6° |
b = 13.6564 (3) Å | µ = 0.86 mm−1 |
c = 16.2893 (4) Å | T = 298 K |
V = 2358.82 (9) Å3 | Prism, colourless |
Z = 4 | 0.42 × 0.23 × 0.20 mm |
F(000) = 1048 |
Oxford Diffraction Xcalibur Sapphire3 Gemini Ultra CCD diffractometer | 3378 independent reflections |
Radiation source: Enhance Ultra (Cu) X-ray Source | 3206 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.019 |
Detector resolution: 16.0288 pixels mm-1 | θmax = 62.7°, θmin = 4.2° |
ω scans | h = −12→11 |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011) | k = −15→9 |
Tmin = 0.819, Tmax = 1.000 | l = −15→18 |
5397 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.032 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.085 | w = 1/[σ2(Fo2) + (0.0494P)2 + 0.2836P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
3378 reflections | Δρmax = 0.14 e Å−3 |
329 parameters | Δρmin = −0.17 e Å−3 |
1 restraint | Absolute structure: Flack (1983), 1213 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.19 (1) |
C26H32O8·H2O | V = 2358.82 (9) Å3 |
Mr = 490.53 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 10.6037 (2) Å | µ = 0.86 mm−1 |
b = 13.6564 (3) Å | T = 298 K |
c = 16.2893 (4) Å | 0.42 × 0.23 × 0.20 mm |
Oxford Diffraction Xcalibur Sapphire3 Gemini Ultra CCD diffractometer | 3378 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011) | 3206 reflections with I > 2σ(I) |
Tmin = 0.819, Tmax = 1.000 | Rint = 0.019 |
5397 measured reflections |
R[F2 > 2σ(F2)] = 0.032 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.085 | Δρmax = 0.14 e Å−3 |
S = 1.03 | Δρmin = −0.17 e Å−3 |
3378 reflections | Absolute structure: Flack (1983), 1213 Friedel pairs |
329 parameters | Absolute structure parameter: −0.19 (1) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.14223 (12) | 1.05987 (10) | 0.53350 (8) | 0.0411 (3) | |
O3 | 0.23637 (13) | 0.84306 (10) | 0.45658 (8) | 0.0419 (3) | |
H3 | 0.2592 | 0.8159 | 0.4142 | 0.063* | |
O5 | 0.44209 (13) | 0.58155 (10) | 0.73498 (8) | 0.0427 (3) | |
O4 | 0.13428 (16) | 0.74314 (12) | 0.75935 (11) | 0.0580 (4) | |
O2 | 0.14192 (16) | 1.07137 (13) | 0.40087 (9) | 0.0592 (4) | |
O6 | 0.21183 (16) | 0.44886 (12) | 0.84070 (10) | 0.0594 (4) | |
O7 | 0.26007 (14) | 0.42551 (10) | 0.71158 (8) | 0.0462 (4) | |
O8 | 0.2620 (3) | 0.29900 (14) | 0.45914 (12) | 0.0827 (6) | |
C3 | 0.19938 (19) | 1.04622 (14) | 0.46131 (13) | 0.0402 (5) | |
C17 | 0.34443 (17) | 0.88604 (13) | 0.58418 (11) | 0.0311 (4) | |
C10 | 0.3221 (2) | 0.57743 (16) | 0.77603 (12) | 0.0428 (5) | |
H10 | 0.3120 | 0.6192 | 0.8245 | 0.051* | |
C2 | 0.3284 (2) | 1.00257 (14) | 0.45659 (13) | 0.0414 (4) | |
H2A | 0.3861 | 1.0439 | 0.4871 | 0.050* | |
H2B | 0.3555 | 1.0028 | 0.3997 | 0.050* | |
C5 | 0.22296 (17) | 0.92924 (13) | 0.62505 (10) | 0.0319 (4) | |
H5 | 0.1527 | 0.8962 | 0.5974 | 0.038* | |
C15 | 0.43123 (19) | 0.70549 (14) | 0.55659 (12) | 0.0381 (4) | |
H15A | 0.4517 | 0.7327 | 0.5032 | 0.046* | |
H15B | 0.5087 | 0.6996 | 0.5879 | 0.046* | |
C26 | 0.14800 (18) | 0.58545 (14) | 0.60780 (13) | 0.0418 (5) | |
H26A | 0.1291 | 0.6541 | 0.6051 | 0.063* | |
H26B | 0.1028 | 0.5565 | 0.6527 | 0.063* | |
H26C | 0.1231 | 0.5545 | 0.5574 | 0.063* | |
C11 | 0.2616 (2) | 0.48032 (15) | 0.77933 (13) | 0.0451 (5) | |
C16 | 0.33892 (17) | 0.77336 (13) | 0.60152 (11) | 0.0307 (4) | |
H16 | 0.2558 | 0.7535 | 0.5812 | 0.037* | |
C8 | 0.33860 (18) | 0.74107 (13) | 0.69383 (11) | 0.0331 (4) | |
C6 | 0.2122 (2) | 0.89767 (15) | 0.71652 (12) | 0.0422 (5) | |
H6A | 0.2792 | 0.9287 | 0.7476 | 0.051* | |
H6B | 0.1324 | 0.9208 | 0.7384 | 0.051* | |
C14 | 0.3705 (2) | 0.60464 (14) | 0.54619 (12) | 0.0403 (5) | |
H14A | 0.4364 | 0.5567 | 0.5367 | 0.048* | |
H14B | 0.3170 | 0.6058 | 0.4979 | 0.048* | |
C1 | 0.33849 (18) | 0.89800 (13) | 0.48969 (11) | 0.0341 (4) | |
H1 | 0.4163 | 0.8699 | 0.4674 | 0.041* | |
C7 | 0.2202 (2) | 0.78844 (15) | 0.72810 (11) | 0.0387 (4) | |
C19 | 0.1464 (2) | 0.35218 (16) | 0.56310 (17) | 0.0573 (6) | |
H19 | 0.0785 | 0.3626 | 0.5981 | 0.069* | |
C24 | 0.47170 (17) | 0.93032 (15) | 0.61138 (13) | 0.0405 (5) | |
H24A | 0.4921 | 0.9850 | 0.5768 | 0.061* | |
H24B | 0.5366 | 0.8816 | 0.6069 | 0.061* | |
H24C | 0.4656 | 0.9519 | 0.6673 | 0.061* | |
C9 | 0.33382 (18) | 0.62767 (14) | 0.69640 (11) | 0.0344 (4) | |
C13 | 0.29043 (17) | 0.57139 (14) | 0.62084 (11) | 0.0342 (4) | |
C23 | 0.0774 (2) | 1.06898 (17) | 0.66732 (13) | 0.0497 (5) | |
H23A | 0.0486 | 1.1325 | 0.6505 | 0.075* | |
H23B | 0.0991 | 1.0705 | 0.7245 | 0.075* | |
H23C | 0.0117 | 1.0218 | 0.6585 | 0.075* | |
C4 | 0.19324 (19) | 1.04057 (14) | 0.61709 (12) | 0.0374 (4) | |
C25 | 0.4526 (2) | 0.77543 (16) | 0.74614 (14) | 0.0465 (5) | |
H25A | 0.5296 | 0.7580 | 0.7188 | 0.070* | |
H25B | 0.4497 | 0.7444 | 0.7990 | 0.070* | |
H25C | 0.4491 | 0.8452 | 0.7530 | 0.070* | |
C18 | 0.2691 (2) | 0.39381 (14) | 0.57069 (13) | 0.0434 (5) | |
C21 | 0.3345 (3) | 0.35915 (16) | 0.50605 (15) | 0.0616 (7) | |
H21 | 0.4183 | 0.3743 | 0.4949 | 0.074* | |
C22 | 0.2986 (2) | 1.11287 (15) | 0.63681 (15) | 0.0493 (5) | |
H22A | 0.3660 | 1.1049 | 0.5980 | 0.074* | |
H22B | 0.3296 | 1.1007 | 0.6912 | 0.074* | |
H22C | 0.2665 | 1.1785 | 0.6336 | 0.074* | |
C20 | 0.1471 (3) | 0.29599 (17) | 0.49702 (18) | 0.0644 (7) | |
H20 | 0.0786 | 0.2594 | 0.4788 | 0.077* | |
C12 | 0.31795 (19) | 0.46163 (14) | 0.63545 (12) | 0.0392 (4) | |
H12 | 0.4095 | 0.4529 | 0.6396 | 0.047* | |
O9 | 0.3772 (3) | 0.74718 (16) | 0.33392 (16) | 0.0972 (8) | |
H9A | 0.351 (4) | 0.6885 (14) | 0.329 (3) | 0.146* | |
H9B | 0.431 (4) | 0.752 (3) | 0.293 (3) | 0.129 (16)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0374 (7) | 0.0466 (7) | 0.0392 (7) | 0.0056 (6) | −0.0025 (6) | 0.0043 (6) |
O3 | 0.0418 (7) | 0.0472 (7) | 0.0365 (7) | −0.0089 (6) | −0.0064 (6) | −0.0033 (6) |
O5 | 0.0352 (7) | 0.0476 (8) | 0.0453 (8) | 0.0078 (6) | −0.0121 (6) | 0.0058 (6) |
O4 | 0.0504 (9) | 0.0554 (9) | 0.0682 (10) | 0.0080 (8) | 0.0211 (9) | 0.0130 (8) |
O2 | 0.0604 (10) | 0.0724 (10) | 0.0448 (8) | 0.0074 (9) | −0.0090 (8) | 0.0125 (8) |
O6 | 0.0657 (10) | 0.0636 (10) | 0.0488 (9) | 0.0012 (9) | 0.0103 (8) | 0.0182 (8) |
O7 | 0.0538 (9) | 0.0401 (7) | 0.0448 (8) | −0.0002 (7) | −0.0012 (7) | 0.0086 (6) |
O8 | 0.1235 (18) | 0.0628 (11) | 0.0619 (11) | −0.0171 (12) | 0.0025 (13) | −0.0107 (9) |
C3 | 0.0456 (11) | 0.0362 (10) | 0.0387 (10) | −0.0033 (9) | −0.0035 (10) | 0.0041 (9) |
C17 | 0.0256 (9) | 0.0340 (9) | 0.0338 (10) | −0.0016 (8) | −0.0032 (8) | −0.0022 (8) |
C10 | 0.0459 (11) | 0.0495 (11) | 0.0330 (9) | 0.0060 (10) | −0.0050 (9) | 0.0049 (9) |
C2 | 0.0401 (10) | 0.0445 (10) | 0.0395 (10) | −0.0049 (9) | 0.0026 (9) | 0.0041 (9) |
C5 | 0.0283 (8) | 0.0353 (9) | 0.0320 (9) | −0.0001 (8) | −0.0007 (8) | −0.0029 (8) |
C15 | 0.0347 (10) | 0.0404 (10) | 0.0391 (11) | 0.0046 (9) | 0.0038 (9) | −0.0005 (8) |
C26 | 0.0360 (10) | 0.0377 (10) | 0.0517 (12) | 0.0021 (9) | −0.0112 (10) | 0.0027 (9) |
C11 | 0.0423 (11) | 0.0496 (12) | 0.0433 (11) | 0.0088 (10) | −0.0030 (10) | 0.0117 (10) |
C16 | 0.0245 (8) | 0.0372 (9) | 0.0302 (9) | −0.0006 (8) | −0.0006 (8) | −0.0012 (8) |
C8 | 0.0326 (9) | 0.0368 (9) | 0.0300 (9) | 0.0011 (8) | −0.0035 (8) | 0.0002 (8) |
C6 | 0.0470 (11) | 0.0459 (11) | 0.0337 (10) | 0.0104 (10) | 0.0053 (9) | −0.0024 (9) |
C14 | 0.0487 (11) | 0.0353 (9) | 0.0369 (10) | 0.0055 (9) | 0.0032 (9) | −0.0011 (9) |
C1 | 0.0277 (9) | 0.0394 (9) | 0.0351 (10) | −0.0059 (8) | 0.0017 (8) | −0.0001 (8) |
C7 | 0.0415 (10) | 0.0451 (10) | 0.0295 (9) | 0.0036 (10) | −0.0006 (9) | 0.0033 (9) |
C19 | 0.0556 (14) | 0.0407 (11) | 0.0755 (16) | −0.0016 (11) | −0.0116 (13) | −0.0010 (12) |
C24 | 0.0288 (9) | 0.0427 (10) | 0.0501 (11) | −0.0054 (9) | −0.0061 (9) | −0.0001 (10) |
C9 | 0.0279 (9) | 0.0414 (10) | 0.0337 (10) | 0.0067 (9) | −0.0058 (8) | 0.0039 (8) |
C13 | 0.0317 (9) | 0.0358 (9) | 0.0351 (9) | 0.0034 (8) | −0.0035 (8) | 0.0017 (8) |
C23 | 0.0533 (13) | 0.0476 (11) | 0.0481 (12) | 0.0155 (11) | 0.0057 (11) | −0.0003 (10) |
C4 | 0.0370 (10) | 0.0397 (10) | 0.0356 (10) | 0.0029 (8) | −0.0044 (9) | −0.0008 (8) |
C25 | 0.0497 (12) | 0.0471 (12) | 0.0427 (11) | −0.0013 (10) | −0.0168 (10) | −0.0013 (10) |
C18 | 0.0516 (12) | 0.0306 (9) | 0.0479 (11) | 0.0008 (9) | −0.0073 (10) | 0.0048 (9) |
C21 | 0.0777 (17) | 0.0480 (12) | 0.0590 (14) | −0.0140 (13) | 0.0107 (14) | −0.0097 (12) |
C22 | 0.0537 (13) | 0.0368 (10) | 0.0574 (13) | −0.0023 (10) | −0.0100 (11) | −0.0068 (10) |
C20 | 0.0799 (19) | 0.0411 (11) | 0.0721 (17) | −0.0100 (13) | −0.0256 (16) | 0.0015 (12) |
C12 | 0.0370 (10) | 0.0391 (10) | 0.0413 (10) | 0.0040 (9) | −0.0010 (9) | 0.0065 (9) |
O9 | 0.130 (2) | 0.0746 (14) | 0.0870 (15) | −0.0275 (14) | 0.0387 (15) | −0.0335 (12) |
O1—C3 | 1.336 (2) | C8—C7 | 1.519 (3) |
O1—C4 | 1.489 (2) | C8—C9 | 1.550 (3) |
O3—H3 | 0.8200 | C8—C25 | 1.552 (3) |
O3—C1 | 1.424 (2) | C6—H6A | 0.9700 |
O5—C10 | 1.439 (3) | C6—H6B | 0.9700 |
O5—C9 | 1.452 (2) | C6—C7 | 1.506 (3) |
O4—C7 | 1.213 (3) | C14—H14A | 0.9700 |
O2—C3 | 1.208 (2) | C14—H14B | 0.9700 |
O6—C11 | 1.209 (3) | C14—C13 | 1.551 (3) |
O7—C11 | 1.333 (3) | C1—H1 | 0.9800 |
O7—C12 | 1.469 (2) | C19—H19 | 0.9300 |
O8—C21 | 1.360 (3) | C19—C18 | 1.425 (3) |
O8—C20 | 1.366 (4) | C19—C20 | 1.322 (4) |
C3—C2 | 1.495 (3) | C24—H24A | 0.9600 |
C17—C5 | 1.565 (2) | C24—H24B | 0.9600 |
C17—C16 | 1.566 (2) | C24—H24C | 0.9600 |
C17—C1 | 1.549 (3) | C9—C13 | 1.522 (3) |
C17—C24 | 1.544 (2) | C13—C12 | 1.546 (3) |
C10—H10 | 0.9800 | C23—H23A | 0.9600 |
C10—C11 | 1.474 (3) | C23—H23B | 0.9600 |
C10—C9 | 1.473 (3) | C23—H23C | 0.9600 |
C2—H2A | 0.9700 | C23—C4 | 1.526 (3) |
C2—H2B | 0.9700 | C4—C22 | 1.525 (3) |
C2—C1 | 1.530 (3) | C25—H25A | 0.9600 |
C5—H5 | 0.9800 | C25—H25B | 0.9600 |
C5—C6 | 1.555 (3) | C25—H25C | 0.9600 |
C5—C4 | 1.558 (3) | C18—C21 | 1.346 (3) |
C15—H15A | 0.9700 | C18—C12 | 1.496 (3) |
C15—H15B | 0.9700 | C21—H21 | 0.9300 |
C15—C16 | 1.534 (3) | C22—H22A | 0.9600 |
C15—C14 | 1.530 (3) | C22—H22B | 0.9600 |
C26—H26A | 0.9600 | C22—H22C | 0.9600 |
C26—H26B | 0.9600 | C20—H20 | 0.9300 |
C26—H26C | 0.9600 | C12—H12 | 0.9800 |
C26—C13 | 1.537 (3) | O9—H9A | 0.854 (10) |
C16—H16 | 0.9800 | O9—H9B | 0.87 (5) |
C16—C8 | 1.567 (2) | ||
C3—O1—C4 | 127.99 (15) | O3—C1—C17 | 110.60 (15) |
C1—O3—H3 | 109.5 | O3—C1—C2 | 107.78 (16) |
C10—O5—C9 | 61.24 (12) | O3—C1—H1 | 107.1 |
C11—O7—C12 | 120.34 (15) | C17—C1—H1 | 107.1 |
C21—O8—C20 | 105.6 (2) | C2—C1—C17 | 116.82 (16) |
O1—C3—C2 | 121.08 (18) | C2—C1—H1 | 107.1 |
O2—C3—O1 | 116.68 (18) | O4—C7—C8 | 123.90 (18) |
O2—C3—C2 | 122.2 (2) | O4—C7—C6 | 121.00 (19) |
C5—C17—C16 | 105.25 (14) | C6—C7—C8 | 115.01 (17) |
C1—C17—C5 | 110.46 (15) | C18—C19—H19 | 126.3 |
C1—C17—C16 | 106.34 (14) | C20—C19—H19 | 126.3 |
C24—C17—C5 | 116.71 (15) | C20—C19—C18 | 107.3 (3) |
C24—C17—C16 | 111.46 (15) | C17—C24—H24A | 109.5 |
C24—C17—C1 | 106.22 (15) | C17—C24—H24B | 109.5 |
O5—C10—H10 | 116.6 | C17—C24—H24C | 109.5 |
O5—C10—C11 | 115.90 (18) | H24A—C24—H24B | 109.5 |
O5—C10—C9 | 59.84 (12) | H24A—C24—H24C | 109.5 |
C11—C10—H10 | 116.6 | H24B—C24—H24C | 109.5 |
C9—C10—H10 | 116.6 | O5—C9—C10 | 58.92 (12) |
C9—C10—C11 | 119.22 (18) | O5—C9—C8 | 114.78 (16) |
C3—C2—H2A | 108.6 | O5—C9—C13 | 111.70 (15) |
C3—C2—H2B | 108.6 | C10—C9—C8 | 119.47 (17) |
C3—C2—C1 | 114.70 (17) | C10—C9—C13 | 116.83 (16) |
H2A—C2—H2B | 107.6 | C13—C9—C8 | 119.51 (15) |
C1—C2—H2A | 108.6 | C26—C13—C14 | 113.12 (16) |
C1—C2—H2B | 108.6 | C26—C13—C12 | 109.14 (16) |
C17—C5—H5 | 104.9 | C9—C13—C26 | 110.22 (16) |
C6—C5—C17 | 111.32 (15) | C9—C13—C14 | 108.71 (15) |
C6—C5—H5 | 104.9 | C9—C13—C12 | 107.95 (15) |
C6—C5—C4 | 109.59 (14) | C12—C13—C14 | 107.54 (15) |
C4—C5—C17 | 119.92 (15) | H23A—C23—H23B | 109.5 |
C4—C5—H5 | 104.9 | H23A—C23—H23C | 109.5 |
H15A—C15—H15B | 108.3 | H23B—C23—H23C | 109.5 |
C16—C15—H15A | 109.9 | C4—C23—H23A | 109.5 |
C16—C15—H15B | 109.9 | C4—C23—H23B | 109.5 |
C14—C15—H15A | 109.9 | C4—C23—H23C | 109.5 |
C14—C15—H15B | 109.9 | O1—C4—C5 | 108.81 (14) |
C14—C15—C16 | 109.15 (16) | O1—C4—C23 | 98.80 (15) |
H26A—C26—H26B | 109.5 | O1—C4—C22 | 110.13 (16) |
H26A—C26—H26C | 109.5 | C23—C4—C5 | 111.49 (17) |
H26B—C26—H26C | 109.5 | C22—C4—C5 | 117.79 (16) |
C13—C26—H26A | 109.5 | C22—C4—C23 | 108.17 (17) |
C13—C26—H26B | 109.5 | C8—C25—H25A | 109.5 |
C13—C26—H26C | 109.5 | C8—C25—H25B | 109.5 |
O6—C11—O7 | 118.7 (2) | C8—C25—H25C | 109.5 |
O6—C11—C10 | 122.6 (2) | H25A—C25—H25B | 109.5 |
O7—C11—C10 | 118.69 (18) | H25A—C25—H25C | 109.5 |
C17—C16—H16 | 104.2 | H25B—C25—H25C | 109.5 |
C17—C16—C8 | 116.73 (14) | C19—C18—C12 | 128.6 (2) |
C15—C16—C17 | 118.95 (15) | C21—C18—C19 | 105.2 (2) |
C15—C16—H16 | 104.2 | C21—C18—C12 | 126.2 (2) |
C15—C16—C8 | 106.81 (15) | O8—C21—H21 | 124.4 |
C8—C16—H16 | 104.2 | C18—C21—O8 | 111.1 (2) |
C7—C8—C16 | 103.57 (15) | C18—C21—H21 | 124.4 |
C7—C8—C9 | 112.87 (17) | C4—C22—H22A | 109.5 |
C7—C8—C25 | 108.27 (16) | C4—C22—H22B | 109.5 |
C9—C8—C16 | 107.88 (15) | C4—C22—H22C | 109.5 |
C9—C8—C25 | 108.22 (16) | H22A—C22—H22B | 109.5 |
C25—C8—C16 | 116.11 (16) | H22A—C22—H22C | 109.5 |
C5—C6—H6A | 109.0 | H22B—C22—H22C | 109.5 |
C5—C6—H6B | 109.0 | O8—C20—H20 | 124.6 |
H6A—C6—H6B | 107.8 | C19—C20—O8 | 110.8 (2) |
C7—C6—C5 | 112.98 (16) | C19—C20—H20 | 124.6 |
C7—C6—H6A | 109.0 | O7—C12—C13 | 112.14 (15) |
C7—C6—H6B | 109.0 | O7—C12—C18 | 104.05 (15) |
C15—C14—H14A | 108.7 | O7—C12—H12 | 108.4 |
C15—C14—H14B | 108.7 | C13—C12—H12 | 108.4 |
C15—C14—C13 | 114.03 (16) | C18—C12—C13 | 115.24 (16) |
H14A—C14—H14B | 107.6 | C18—C12—H12 | 108.4 |
C13—C14—H14A | 108.7 | H9A—O9—H9B | 102 (4) |
C13—C14—H14B | 108.7 | ||
O1—C3—C2—C1 | 62.1 (2) | C16—C8—C9—C10 | −175.00 (16) |
O5—C10—C11—O6 | 136.4 (2) | C16—C8—C9—C13 | −18.7 (2) |
O5—C10—C11—O7 | −44.6 (2) | C8—C9—C13—C26 | −70.9 (2) |
O5—C10—C9—C8 | −102.8 (2) | C8—C9—C13—C14 | 53.6 (2) |
O5—C10—C9—C13 | 100.31 (18) | C8—C9—C13—C12 | 169.94 (17) |
O5—C9—C13—C26 | 151.02 (16) | C6—C5—C4—O1 | −152.42 (15) |
O5—C9—C13—C14 | −84.47 (18) | C6—C5—C4—C23 | −44.5 (2) |
O5—C9—C13—C12 | 31.9 (2) | C6—C5—C4—C22 | 81.4 (2) |
O2—C3—C2—C1 | −118.3 (2) | C14—C15—C16—C17 | −150.82 (16) |
C3—O1—C4—C5 | −61.7 (2) | C14—C15—C16—C8 | 74.43 (19) |
C3—O1—C4—C23 | −178.13 (18) | C14—C13—C12—O7 | 172.34 (15) |
C3—O1—C4—C22 | 68.7 (2) | C14—C13—C12—C18 | −68.9 (2) |
C3—C2—C1—O3 | 46.6 (2) | C1—C17—C5—C6 | 167.17 (16) |
C3—C2—C1—C17 | −78.6 (2) | C1—C17—C5—C4 | −63.0 (2) |
C17—C5—C6—C7 | −53.6 (2) | C1—C17—C16—C15 | 51.7 (2) |
C17—C5—C4—O1 | 77.03 (19) | C1—C17—C16—C8 | −177.88 (15) |
C17—C5—C4—C23 | −175.05 (15) | C7—C8—C9—O5 | −128.10 (17) |
C17—C5—C4—C22 | −49.2 (2) | C7—C8—C9—C10 | −61.2 (2) |
C17—C16—C8—C7 | 60.5 (2) | C7—C8—C9—C13 | 95.1 (2) |
C17—C16—C8—C9 | −179.60 (15) | C19—C18—C21—O8 | −0.2 (3) |
C17—C16—C8—C25 | −58.0 (2) | C19—C18—C12—O7 | 38.5 (3) |
C10—O5—C9—C8 | 110.76 (19) | C19—C18—C12—C13 | −84.7 (3) |
C10—O5—C9—C13 | −109.10 (18) | C24—C17—C5—C6 | −71.4 (2) |
C10—C9—C13—C26 | 85.9 (2) | C24—C17—C5—C4 | 58.4 (2) |
C10—C9—C13—C14 | −149.55 (17) | C24—C17—C16—C15 | −63.7 (2) |
C10—C9—C13—C12 | −33.2 (2) | C24—C17—C16—C8 | 66.8 (2) |
C5—C17—C16—C15 | 168.90 (15) | C24—C17—C1—O3 | 168.87 (15) |
C5—C17—C16—C8 | −60.7 (2) | C24—C17—C1—C2 | −67.4 (2) |
C5—C17—C1—O3 | −63.67 (19) | C9—O5—C10—C11 | 110.20 (19) |
C5—C17—C1—C2 | 60.1 (2) | C9—C10—C11—O6 | −155.2 (2) |
C5—C6—C7—O4 | −120.2 (2) | C9—C10—C11—O7 | 23.8 (3) |
C5—C6—C7—C8 | 56.6 (2) | C9—C8—C7—O4 | 4.7 (3) |
C15—C16—C8—C7 | −163.55 (15) | C9—C8—C7—C6 | −171.99 (16) |
C15—C16—C8—C9 | −43.7 (2) | C9—C13—C12—O7 | 55.2 (2) |
C15—C16—C8—C25 | 77.9 (2) | C9—C13—C12—C18 | 173.99 (17) |
C15—C14—C13—C26 | 100.8 (2) | C4—O1—C3—O2 | −176.60 (18) |
C15—C14—C13—C9 | −22.0 (2) | C4—O1—C3—C2 | 3.0 (3) |
C15—C14—C13—C12 | −138.65 (16) | C4—C5—C6—C7 | 171.35 (17) |
C26—C13—C12—O7 | −64.6 (2) | C25—C8—C7—O4 | −115.1 (2) |
C26—C13—C12—C18 | 54.2 (2) | C25—C8—C7—C6 | 68.2 (2) |
C11—O7—C12—C13 | −40.8 (2) | C25—C8—C9—O5 | −8.3 (2) |
C11—O7—C12—C18 | −166.02 (17) | C25—C8—C9—C10 | 58.6 (2) |
C11—C10—C9—O5 | −104.7 (2) | C25—C8—C9—C13 | −145.11 (17) |
C11—C10—C9—C8 | 152.49 (18) | C18—C19—C20—O8 | −1.1 (3) |
C11—C10—C9—C13 | −4.4 (3) | C21—O8—C20—C19 | 1.0 (3) |
C16—C17—C5—C6 | 52.78 (18) | C21—C18—C12—O7 | −141.6 (2) |
C16—C17—C5—C4 | −177.44 (15) | C21—C18—C12—C13 | 95.2 (3) |
C16—C17—C1—O3 | 50.0 (2) | C20—O8—C21—C18 | −0.5 (3) |
C16—C17—C1—C2 | 173.79 (15) | C20—C19—C18—C21 | 0.8 (3) |
C16—C15—C14—C13 | −38.0 (2) | C20—C19—C18—C12 | −179.3 (2) |
C16—C8—C7—O4 | 121.1 (2) | C12—O7—C11—O6 | 179.16 (18) |
C16—C8—C7—C6 | −55.6 (2) | C12—O7—C11—C10 | 0.1 (3) |
C16—C8—C9—O5 | 118.09 (16) | C12—C18—C21—O8 | 179.87 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O9 | 0.82 | 2.04 | 2.817 (3) | 158 |
O9—H9A···O6i | 0.85 (1) | 2.00 (1) | 2.841 (3) | 169 (4) |
O9—H9B···O4ii | 0.87 (5) | 2.33 (5) | 3.124 (3) | 152 (4) |
Symmetry codes: (i) −x+1/2, −y+1, z−1/2; (ii) x+1/2, −y+3/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C26H32O8·H2O |
Mr | 490.53 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 298 |
a, b, c (Å) | 10.6037 (2), 13.6564 (3), 16.2893 (4) |
V (Å3) | 2358.82 (9) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 0.86 |
Crystal size (mm) | 0.42 × 0.23 × 0.20 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Sapphire3 Gemini Ultra CCD |
Absorption correction | Multi-scan (CrysAlis PRO; Agilent, 2011) |
Tmin, Tmax | 0.819, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5397, 3378, 3206 |
Rint | 0.019 |
(sin θ/λ)max (Å−1) | 0.576 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.032, 0.085, 1.03 |
No. of reflections | 3378 |
No. of parameters | 329 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.14, −0.17 |
Absolute structure | Flack (1983), 1213 Friedel pairs |
Absolute structure parameter | −0.19 (1) |
Computer programs: CrysAlis PRO (Agilent, 2011), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O9 | 0.82 | 2.04 | 2.817 (3) | 158 |
O9—H9A···O6i | 0.854 (10) | 1.998 (13) | 2.841 (3) | 169 (4) |
O9—H9B···O4ii | 0.87 (5) | 2.33 (5) | 3.124 (3) | 152 (4) |
Symmetry codes: (i) −x+1/2, −y+1, z−1/2; (ii) x+1/2, −y+3/2, −z+1. |
Acknowledgements
This work was supported financially by the National Natural Science Foundation of China (No. 81072535) and the Team Project of the Natural Science Foundation of Guangdong Province (No. 8351063201000003).
References
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The title compound C26H32O8 . H2O (Fig. 1) is the monohydrate of deacetylnomilin (systematic name: 1-hydroxy-1,2-dihydroobacunoic acid 3,4 -lactone monohydrate), which was originally isolated from the seeds of the genera Citrus and Poncirus (Dreyer, 1965; Munehiro et al., 1989). With the present compound, which was isolated from the traditional Chinese medicine Pericarpium Citri Reticulatae, the dihedral angles between the planes of the ester groups and the furan plane are 43.06 (12)° and 56.06 (7)°, while that between the furan plane and the keto group is 58.50 (9)°. The title compound is composed of five rings, one seven–membered, one five-membered and three six–membered. The seven–membered ring (A) adopts a chair conformation as does the six–membered ring (B), which has puckering parameters (Cremer & Pople, 1975; Boeyens, 1978) Q = 0.588 (2) Å, θ = 5.2 (2)°, φ = 239 (2)°. The rings C and D adopt skew–boat conformations with puckering paramaters Q = 0.775 (2) Å, θ = 98.35 (15)°, φ = 94.92 (15)° and Q = 0.512 (2) Å, θ = 110.4 (2)°, φ = 92.9 (2)°, respectively. The A/B, B/C and C/D ring junctions are all trans- fused. Intermolecular O—H···O hydrogen bonds (Table 1) involving the hydroxy and carbonyl groups and the water molecule give a three-dimensional structure (Fig. 2). The absolute configuration determined for the parent (-)-nomilin (Zhang et al., 2006) was invoked, giving the assignments C1(S), C5(R), C8(R), C9(R), C10(S), C12(S), C13(S), C16(R), C17(R) for the 9 chiral centres in the molecule (using the numbering scheme employed in Fig. 1).