Plumeridoid C from the Amazonian traditional medicinal plant Himatanthus sucuuba

Waltenberger, B.; Rollinger, J.M.; Griesser, U.J.; Stuppner, H.; Gelbrich, T.

doi:10.1107/S0108270111035761

organic compounds

STRUCTURAL
CHEMISTRY

ISSN: 2053-2296

Volume 67| Part 10| October 2011| Pages o409-o412

doi:10.1107/S0108270111035761

Plumeridoid C from the Amazonian traditional medicinal plant Himatanthus sucuuba

Birgit Waltenberger,^a Judith M. Rollinger,^a Ulrich J. Griesser,^a Hermann Stuppner ^a and Thomas Gelbrich ^a ^*

^aInstitute of Pharmacy, University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
^*Correspondence e-mail: thomas.gelbrich@uibk.ac.at

(Received 11 August 2011; accepted 2 September 2011; online 29 September 2011)

The stereochemistry of the iridoid plumeridoid C, C₁₅H₁₈O₇, was established by X-ray single-crystal structure analysis, giving (2′R,3R,4R,4aS,7aR)-methyl 3-hydroxy-4′-[(S)-1-hydroxyethyl]-5′-oxo-3,4,4a,7a-tetrahydro-1H,5′H-spiro[cyclopenta[c]pyran-7,2′-furan]-4-carboxylate. The absolute structure of the title compound was determined on the basis of the Flack x parameter and Bayesian statistics on Bijvoet differences. The hydrogen-bond donor and acceptor functions of the two hydroxy groups are employed in the formation of O—H⋯O-bonded helical chains.

Comment

As part of our search for bioactive natural products, we have investigated chemical compounds contained in the bark material of the Amazonian tree Himatanthus sucuuba (spruce) Woodson (Apocynaceae). In folk medicine, the bark and latex of this plant species are used for the treatment of tumours and inflammatory diseases. Pharmacological studies have shown that extracts and constituents of Himatanthus sucuuba possess therapeutic potential (Amaral et al., 2007 ).

Eleven compounds, denoted (I) to (XI) (see Supplementary materials ), were isolated and purified from the bark material (1.9 kg) of Himatanthus sucuuba using extraction, liquid–liquid partition, various chromatographic techniques and crystallization from solvents. The isolated compounds were identified as the iridoids plumeridoid C [(I), 60 mg] (Kuigoua et al., 2010 ), plumericin [(II), 90 mg] (Elsässer et al., 2005 ), plumieridin [(III), 8 mg] (Yamauchi et al., 1981 ) and allamandicin [(IV), 7 mg] (Abe et al., 1984 ), the flavonoids biochanin A [(V), 8 mg] (Jha et al., 1980 ; Talukdar et al., 2000 ), dihydrobiochanin A [(VI), 9 mg] (Osawa et al., 1992 ), dalbergioidin [(VII), 0.3 mg] (Osawa et al., 1992), naringenin [(VIII), 9 mg] (Hou et al., 2001 ), ferreirin [(IX), 2 mg] (Osawa et al., 1992) and dihydrocajanin [(X), 8 mg] (Osawa et al., 1992), and the lignan pinoresinol [(XI), 9 mg] (Xie et al., 2003 ) by means of mass spectrometry, one- and two-dimensional NMR experiments, optical rotation and comparison with data from the literature. Except for (II) and (XI), the isolation of these compounds from Himatanthus sucuuba is reported here for the first time.

A recent paper by Kuigoua et al. (2010) contains the first report of the existence of the iridoid plumeridoid C, (I). In order to complete the full characterization of (I) and to elucidate its absolute configuration, its crystal structure has been determined.

The asymmetric unit of (I) consists of one formula unit (Fig. 1). As the compound consists only of O, C and H atoms, Cu Kα radiation was used to enable the determination of the absolute configuration, and 1210 Friedel pairs were measured. This yielded a refined Flack (1983 ) x parameter and standard uncertainty (s.u.) of −0.01 (13). We note that the obtained s.u. value is slightly above the suggested upper confidence limit of 0.10 for the determination of the absolute structure of an enantiopure compound (Flack & Bernardinelli, 2000 ). However, additional confirmation was obtained from the examination of Bayesian statistics on 1210 Bijvoet pairs (Hooft et al., 2008 ) carried out using the program PLATON (Spek, 2009 ). The calculated Hooft y parameter was 0.07 (6) with G = 0.9 (1). The calculated probability values P3(true), P3(twin) and P3(wrong) were 1.000, 0.000 and 0.000, respectively. This confirmed the absolute configuration of the six stereocentres as 3R, 4R, 5S, 8R, 9R and 13S (see Scheme). Moreover, these results are consistent with the relative configuration of (I) that was proposed by Kuigoua et al. (2010) on the basis of NMR data.

Inspection of a plot of the Bijvoet pairs δ(F_o²) against δ(F_c²) generated with PLATON (Spek, 2009) does not reveal a clear trend. All quadrants of the plot are populated by a significant number of points. This contrasts with the observation that all of the numerical indicators (x, y, P2, P3) give a very clear indication of the absolute structure and are consistent between themselves. We note that the error bars on the plot indicate that many of the Bijvoet differences are small compared with experimental error. However, even with this limitation, the data give clear indications in terms of the numerical parameters that have been developed to distinguish absolute structures.

The cyclopentene ring of (I) displays a C9 envelope conformation, with atom C9 displaced by 0.420 (2) Å from the plane defined by atoms C5/C6/C7/C8. As indicated by its Cremer–Pople ring-puckering parameters [Q = 0.544 (2) Å, θ = 163.4 (2)° and φ = 139.7 (6)°; Cremer & Pople, 1975 ], the geometry of the tetrahydropyran ring (O3/C1/C9/C5/C4/C3) is best described as a slightly distorted chair. The mean plane of the furan ring and the plane defined by atoms C7/C8/C9 form an angle of 88.11 (8)°. The mean plane of the –CC(=O)OC fragment C4/C15/O1/O2/C16 is almost perpendicular to the plane defined by atoms C3/C4/C5, with which it forms an angle of 81.27 (10)°.

The molecule of (I) contains two OH groups, O6 in the hydroxyethyl fragment and the O7 group on the tetrahydropyran ring. The hydrogen-bond donor and acceptor functions of both are utilized to give a one-dimensional helical chain that propagates along [010] (Table 1 and Fig. 2). This hydrogen-bonded chain consists of two strands of O6—H6O⋯O7(x, y + 1, z)-bonded molecules, neighbouring molecules of which are related to one another by translational symmetry. The two strands of a chain are related by a 2₁ screw axis and linked to one another via O7—H7O⋯O6(−x + 2, y − $[{1\over 2}]$ , −z + 1) interactions. Hence, every molecule of (I) is O—H⋯O-bonded to four neighbouring molecules. Using the graph-set notation proposed by Etter et al. (1990 ) and Bernstein et al. (1995 ), the hydrogen-bonded molecules of (I) are linked together via fused R₃³(15) rings. The crystal packing of these O—H⋯O-bonded chains generates two notable short inter-chain contacts, viz. C1—H1B⋯O5(−x + 2, y − $[{1\over 2}]$ , −z) and C5—H5⋯O4(−x + 1, y − $[{1\over 2}]$ , −z), with H⋯O distances of 2.37 and 2.47 Å, respectively (Table 1). The first interchain contact is observed between the CH₂ group of the tetrahydropyran ring and the carbonyl group on the furan ring of a neighbouring molecule, while the second contact involves the chiral centre C5 of the fused cyclopentene and tetrahydropyran rings of one molecule and the furan O atom of another.

We have found that, in methanol solution, diastereomerization of (I) occurs at position 3, yielding the epiplumeridoid C [(Ia); Kuigoua et al., 2010]. This phenomenon was studied in a time-dependent ¹H NMR experiment. Compound (I) (1 mg) was dissolved in CD₃OD and isochronous ¹H NMR measurements of the (I):(Ia) ratio were started instantaneously. This experiment confirmed the diastereomerization at position 3, giving a chemical equilibrium of 1:1.05 between (I) and (Ia) [(I): 3R, 4R, 5S, 8R, 9R, 13S; (Ia): 3S, 4R, 5S, 8R, 9R, 13S] after approximately two days (Fig. 3). These results suggest that crystallization from a methanol solution yields compound (I) exclusively, even though diastereomerization takes place in a methanol solution so that the epimers (I) and (Ia) are both present. Moreover, NMR experiments have shown that both (I) and (Ia) are also contained in a deuterated pyridine solution.

Figure 1
The molecular structure of (I)

, with displacement ellipsoids drawn at the 50% probability level.

Figure 2
A single O—H⋯O-bonded helical chain in the crystal structure of (I)

, viewed along [100]. The two strands of the chain are denoted S and S′, with the hydrogen bonds α = O6—H6O⋯O7(x, y + 1, z) and β = O7—H7O⋯O6(−x + 2, y − $[{1\over 2}]$ , −z + 1).

Figure 3
Time-dependent ratio of diastereomers (I)

and (Ia)

in a CD₃OD solution, analysed by ¹H NMR. Compound (I)

was dissolved in CD₃OD at zero time.

Experimental

The general experimental conditions used for the isolation and identification of compounds (I) to (XI), including the detailed isolation protocols and chemical structures, the characteristic UV–Vis and FT–IR data for (I) and the NMR spectroscopic data for (I) and (Ia), are available in the Supplementary materials .

¹H NMR experiments for the evaluation of the diastereomerization were carried out on a Bruker TXI600 at 298 K in CD₃OD (referenced to the residual nondeuterated solvent signals). The $[[\alpha ]^{20}_D]$ values for (I) and for the 1:1.05 mixture of (I) and (Ia) were determined as +70.5 and +82.0, respectively (c = 0.97, methanol).

Simultaneous melting and decomposition of (I) were observed above 454 K. The colourless prisms of (I) used for this study were obtained by crystallization from a saturated methanol solution. The unit-cell parameters of six different crystals were determined and found to be consistent with (I). There was no indication of the presence of crystals of (Ia) in the investigated batch.

Crystal data

C₁₅H₁₈O₇
M_r = 310.29
Monoclinic, P 2₁
a = 9.6736 (2) Å
b = 7.6203 (1) Å
c = 10.6303 (2) Å
β = 107.142 (2)°
V = 748.81 (2) Å³
Z = 2
Cu Kα radiation
μ = 0.93 mm⁻¹
T = 173 K
0.20 × 0.20 × 0.15 mm

Data collection

Oxford Xcalibur Ruby Gemini Ultra diffractometer
Absorption correction: multi-scan [CrysAlis PRO (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Versions 1.171. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); multi-scan absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm] T_min = 0.766, T_max = 1.000
7011 measured reflections
2651 independent reflections
2615 reflections with I > 2σ(I)
R_int = 0.029

Refinement

R[F² > 2σ(F²)] = 0.029
wR(F²) = 0.081
S = 1.09
2651 reflections
225 parameters
3 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.19 e Å⁻³
Absolute structure: Flack (1983), with 1210 Friedel pairs
Flack parameter: −0.01 (13)

Table 1
Geometry of hydrogen bonds and other contacts (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O6—H6O⋯O7ⁱ	0.83 (2)	1.99 (2)	2.8153 (15)	174 (2)
O7—H7O⋯O6ⁱⁱ	0.80 (2)	1.92 (2)	2.7218 (15)	176 (2)
C1—H1B⋯O5ⁱⁱⁱ	0.99	2.37	3.2969 (18)	156
C5—H5⋯O4^iv	1.00	2.47	3.3243 (16)	143
Symmetry codes: (i) x, y+1, z; (ii) $[-x+2, y-{\script{1\over 2}}, -z+1]$ ; (iii) $[-x+2, y-{\script{1\over 2}}, -z]$ ; (iv) $[-x+1, y-{\script{1\over 2}}, -z]$ .

All H atoms were identified in a difference map. Methyl H atoms were idealized and included as rigid groups that were allowed to rotate but not tip (C—H = 0.98 Å). H atoms bonded to tertiary (C—H = 1.00 Å), secondary (C—H = 0.99 Å) and aromatic C atoms (C—H = 0.95 Å) were positioned geometrically. H atoms attached to O atoms were refined with restrained distances [O—H = 0.82 (2) Å]. The U_iso parameters of all H atoms were refined freely.

The absolute configuration of this structure was confirmed by the Flack (1983) parameter and Bayesian statistics on 1210 Bijvoet pairs (Hooft et al., 2008). The Flack parameter is −0.01 (13) for the reported structure and 0.99 (13) for the inverted structure. Friedif, R_A and R_D values (Flack & Shmueli, 2007 ; Flack et al., 2011 ) were calculated using PLATON (Spek, 2009). Friedif reflects the ability to determine the absolute structure, and Friedif_stat = 36 has a low value as only C, H and O atoms are present, while Friedif_obs is 1286. The R_A and R_D values are 0.050 and 0.989, respectively, for the reported structure, and 0.050 and 1.022, respectively, for the inverted structure.

Data collection: CrysAlis CCD (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Versions 1.171. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); cell refinement: CrysAlis RED (Oxford Diffraction, 2003 $[Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED. Versions 1.171. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S0108270111035761/fa3259sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S0108270111035761/fa3259Isup2.hkl

Supporting information file. DOI: 10.1107/S0108270111035761/fa3259sup3.pdf

Comment top

As part of our search for bioactive natural products, we have investigated chemical compounds contained in the bark material of the Amazonian tree Himatanthus sucuuba (Spruce) Woodson (Apocynaceae). In folk medicine, the bark and latex of this plant species are used for the treatment of tumours and inflammatory diseases. Pharmacological studies have shown that extracts and constituents of Himatanthus sucuuba possess therapeutic potential (Amaral et al., 2007).

Eleven compounds, denoted (I) to (XI) (see Supplementary materials), were isolated and purified from the bark material (1.9 kg) of Himatanthus sucuuba using extraction, liquid–liquid partition, various chromatographic techniques and crystallization from solvents. The isolated compounds were identified as the iridoids plumeridoid C [(I), 60 mg] (Kuigoua et al., 2010), plumericin [(II), 90 mg] (Elsässer et al., 2005), plumieridin [(III), 8 mg] (Yamauchi et al., 1981) and allamandicin [(IV), 7 mg] (Abe et al., 1984), the flavonoids biochanin A [(V), 8 mg] (Jha et al., 1980; Talukdar et al., 2000), dihydrobiochanin A [(VI), 9 mg] (Osawa et al., 1992), dalbergioidin [(VII), 0.3 mg) (Osawa et al., 1992), naringenin [(VIII), 9 mg] (Hou et al., 2001), ferreirin [(IX), 2 mg] (Osawa et al., 1992) and dihydrocajanin [(X), 8 mg] (Osawa et al., 1992), and the lignan pinoresinol [(XI), 9 mg] (Xie et al., 2003) by means of mass spectrometry, one-dimensional and two-dimensional NMR experiments, optical rotation and comparison with data from the literature. Except for (II) and (XI), the isolation of these compounds from Himatanthus sucuuba is reported here for the first time.

A recent paper by Kuigoua et al. (2010) contains the first report about the existence of the iridoid plumeridoid C, (I). The asymmetric unit of (I) consists of one formula unit (Fig. 1). As the compound consists only of oxygen, carbon and hydrogen atoms, Cu Kα radiation was used to enable the determination of the absolute configuration, and Friedel pairs were measured. This yielded a refined Flack (1983) x parameter and standard uncertainty (s.u.) of -0.01 (13) [number of Friedel pairs?]. We note that the obtained s.u. value is slightly above the suggested upper confidence limit of 0.10 for the determination of the absolute structure of an enantiopure compound (Flack & Bernardinelli, 2000). However, additional confirmation was obtained from the examination of Bayesian statistics on 1210 Bijvoet pairs (Hooft et al., 2008) carried out with the program PLATON (Spek, 2009). The calculated Hooft y parameter was 0.07 (6) with G = 0.9 (1). The calculated probability values P3(true), P3(twin) and P3(wrong) were 1.000, 0.000 and 0.000, respectively. This confirmed the absolute configuration of the six stereocentres as 3R, 4R, 5S, 8R, 9R, 13S (see scheme). Moreover, these results are consistent with the relative configuration of (I) that was proposed by Kuigoua et al. (2010) on the basis of NMR data.

The inspection of a plot of the Bijvoet pairs δ(F_o²) against δ(F_c²) generated with PLATON (Spek, 2009) does not reveal a clear trend. All quadrants of the plot are populated by a significant number of points. This contrasts with the observation that all of the numerical indicators (x, y, P2, P3) give a very clear indication of the absolute structure and are consistent among themselves. We note that the error bars on the plot indicate that many of the Bijvoet differences are small in comparison with experimental error. However, even with this property, the data give clear indications in terms of the numerical parameters that have been developed to distinguish absolute structures.

The cyclopentene ring of (I) displays a C9 envelope conformation with atom C9 displaced by -0.420 (2) Å from the plane defined by the atoms C5/C6/C7/C8. As indicated by its Cremer–Pople ring puckering parameters [Q = 0.544 (2) Å, Θ = 163.4 (2)°, Φ = 139.7 (6)°] (Cremer & Pople, 1975), the geometry of the tetrahydropyran ring O3/C1/C9/C5/C4/C3 is best described as a slightly distorted chair. The mean plane of the furan ring and the plane defined by C7/C8/C9 form an angle of 88.11 (8)°. The mean plane of the –CC(═O)OC fragment C4/C15/O1/O2/C16/ is almost perpendicular to the plane defined by the atoms C3/C4/C5, with which it forms an angle of 81.27 (10)°.

The molecule of (I) contains two OH groups, O6 in the hydroxyethyl fragment and the O7 group on the tetrahydropyran ring. The hydrogen-bond donor and acceptor functions of both are utilized to give a one-dimensional helical chain that propagates along [010] (Table 1, Fig. 2). This hydrogen-bonded chain consists of two strands of O6—H6O···O7(x, y + 1, z)-bonded molecules in which neighbouring molecules are related to one another by translational symmetry. The two strands of a chain are related by a 2₁ screw axis and linked to one another via O7—H7O···O6(-x + 2, y - 1/2, -z + 1) interactions. Hence, every molecule of (I) is O—H···O-bonded to four neighbouring molecules. Using the graph-set notation proposed by Etter et al. (1990) and Bernstein et al. (1995), the hydrogen-bonded molecules of (I) are linked together via fused R³₃(15) rings. The crystal packing of these O—H···O-bonded chains generates two notable short inter-chain contacts C1—H1B···O5(-x + 2, y - 1/2, -z) and C5—H5···O4(-x + 1, y - 1/2, -z) with H···O distances of 2.37 and 2.47 Å, respectively (Table 1). The first inter-chain contact is observed between the CH₂ group of the tetrahydropyran ring and the carbonyl group on the furan ring in a neighbouring molecule, while the second contact involves the chiral centre C5 of the fused cyclopentene and tetrahydropyran rings of one molecule and the furan oxygen atom of another.

We have found that in methanol solution diastereomerization of (I) occurs at position 3, yielding the epiplumeridoid C [(Ia), Kuigoua et al., 2010]. This phenomenon was studied in a time-dependent ¹H-NMR experiment. 1 mg of (I) was dissolved in CD₃OD and isochronous ¹H-NMR measurements of the (I):(Ia) ratio were started instantaneously. This experiment confirmed the diastereomerization at position 3, giving a chemical equilibrium of 1:1.05 between (I) and (Ia) [(I), 3R, 4R, 5S, 8R, 9R, 13S: (Ia), 3S, 4R, 5S, 8R, 9R, 13S] after approximately 2 d (Fig. 3). These results suggest that crystallization from a methanol solution yields compound (I) exclusively. By contrast, in a methanol solution diastereomerization takes place so that the epimers (I) and (Ia) are present. Moreover, NMR experiments have shown that both (I) and (Ia) are also contained in a deuterated pyridine solution.

Related literature top

For related literature, see: Abe et al. (1984); Amaral et al. (2007); Bernstein et al. (1995); Cremer & Pople (1975); Elsässer et al. (2005); Etter et al. (1990); Flack (1983); Flack & Bernardinelli (2000); Flack & Shmueli (2007); Flack et al. (2011); Hooft et al. (2008); Hou et al. (2001); Jha et al. (1980); Kuigoua et al. (2010); Osawa et al. (1992); Spek (2009); Talukdar et al. (2000); Xie et al. (2003); Yamauchi et al. (1981).

Experimental top

The general experimental conditions used for the isolation and identification of compounds (I) to (XI), including the detailed isolation protocols and chemical structures, characteristic UV/Vis and FT–IR data of (I) and the NMR spectral data of (I) and (Ia) are available in the Supplementary materials.

¹H-NMR experiments for the evaluation of the diastereomerization were carried out on a Bruker TXI600 at 298 K in CD₃OD (referenced to the residual non-deuterated solvent signals). The [α]²⁰ _D values for (I) and the 1:1.05 mixture of (I):(Ia) were determined as +70.5 and +82.0, respectively (c = 0.97, methanol).

Simultaneous melting and decomposition of (I) were observed above 454 K. The colourless prisms of (I) used for this study were obtained by crystallization from a saturated methanol solution. Unit-cell parameters of six different crystals were determined and found to be consistent with (I). There was no indication of the presence of crystals of (Ia) in the investigated batch.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2003); cell refinement: CrysAlis RED (Oxford Diffraction, 2003); data reduction: CrysAlis RED (Oxford Diffraction, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. The molecular structure of (I). Displacement ellipsoids are drawn at the 50% probability level, with hydrogen atoms shown as spheres of arbitrary size.
	Fig. 2. A single O—H···O-bonded helical chain in the crystal structure of (I), viewed along [100]. The two strands of the chain are denoted S and S' with the hydrogen bonds α: O6—H6O···O7(x, y + 1, z) and β: O7—H7O···O6 (-x + 2, y - 1/2, -z + 1).
	Fig. 3. Time-dependent ratio of the diastereomers (I) and (Ia) in a CD₃OD solution, analysed by ¹H-NMR. (I) was dissolved in CD₃OD at 0 time.

(2'R,3R,4R,4aS,7aR)-methyl 3-hydroxy-4'-[(S)-1-hydroxyethyl]-5'-oxo- 3,4,4a,7a-tetrahydro-1H,5'H-spiro[cyclopenta[c]pyran-7,2'-furan]-4-carboxylate top

Crystal data top

C₁₅H₁₈O₇	F(000) = 328
M_r = 310.29	D_x = 1.376 Mg m⁻³
Monoclinic, P2₁	Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2yb	Cell parameters from 6253 reflections
a = 9.6736 (2) Å	θ = 4.4–66.8°
b = 7.6203 (1) Å	µ = 0.93 mm⁻¹
c = 10.6303 (2) Å	T = 173 K
β = 107.142 (2)°	Prism, colourless
V = 748.81 (2) Å³	0.20 × 0.20 × 0.15 mm
Z = 2

Data collection top

Xcalibur, Ruby, Gemini ultra diffractometer	2651 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source	2615 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.029
Detector resolution: 10.3575 pixels mm^-1	θ_max = 67.0°, θ_min = 4.4°
ω scans	h = −11→11
Absorption correction: multi-scan CrysAlis PRO (Oxford Diffraction, 2003). Multi-scan absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.	k = −9→9
T_min = 0.766, T_max = 1.000	l = −12→12
7011 measured reflections

Refinement top

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)] = 0.029	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.081	w = 1/[σ²(F_o²) + (0.0592P)² + 0.029P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max < 0.001
2651 reflections	Δρ_max = 0.16 e Å⁻³
225 parameters	Δρ_min = −0.19 e Å⁻³
3 restraints	Absolute structure: Flack (1983), no. of Friedel pairs?
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.01 (13)

Crystal data top

C₁₅H₁₈O₇	V = 748.81 (2) Å³
M_r = 310.29	Z = 2
Monoclinic, P2₁	Cu Kα radiation
a = 9.6736 (2) Å	µ = 0.93 mm⁻¹
b = 7.6203 (1) Å	T = 173 K
c = 10.6303 (2) Å	0.20 × 0.20 × 0.15 mm
β = 107.142 (2)°

Data collection top

Xcalibur, Ruby, Gemini ultra diffractometer	2651 independent reflections
Absorption correction: multi-scan CrysAlis PRO (Oxford Diffraction, 2003). Multi-scan absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.	2615 reflections with I > 2σ(I)
T_min = 0.766, T_max = 1.000	R_int = 0.029
7011 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.029	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.081	Δρ_max = 0.16 e Å⁻³
S = 1.09	Δρ_min = −0.19 e Å⁻³
2651 reflections	Absolute structure: Flack (1983), no. of Friedel pairs?
225 parameters	Absolute structure parameter: −0.01 (13)
3 restraints

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.49325 (13)	0.09240 (16)	0.30372 (13)	0.0415 (3)
O2	0.48078 (12)	0.33663 (15)	0.41722 (11)	0.0346 (3)
O3	0.88284 (11)	0.31098 (14)	0.26013 (10)	0.0284 (2)
O4	0.73833 (11)	0.77164 (14)	0.02471 (9)	0.0264 (2)
O5	0.89875 (12)	0.96432 (15)	−0.00926 (10)	0.0314 (3)
O6	1.08252 (11)	0.93156 (14)	0.41722 (10)	0.0277 (2)
O7	0.84709 (12)	0.14430 (15)	0.42459 (10)	0.0298 (2)
C1	0.83056 (16)	0.3625 (2)	0.12495 (14)	0.0292 (3)
H1A	0.8075	0.2562	0.0692	0.032 (5)*
H1B	0.9077	0.4274	0.1008	0.034 (5)*
C3	0.77849 (15)	0.2127 (2)	0.29999 (14)	0.0248 (3)
H3	0.7422	0.1144	0.2366	0.031 (5)*
C4	0.65246 (14)	0.33404 (18)	0.30066 (13)	0.0228 (3)
H4	0.6896	0.4323	0.3639	0.024 (4)*
C5	0.58245 (14)	0.41150 (19)	0.16100 (13)	0.0246 (3)
H5	0.5168	0.3237	0.1029	0.030 (4)*
C6	0.50130 (15)	0.5778 (2)	0.17024 (14)	0.0281 (3)
H6	0.4079	0.5801	0.1824	0.040 (5)*
C7	0.57548 (15)	0.7199 (2)	0.15946 (13)	0.0270 (3)
H7	0.5437	0.8366	0.1659	0.033 (5)*
C8	0.71756 (14)	0.67248 (18)	0.13552 (12)	0.0227 (3)
C9	0.69699 (15)	0.47702 (19)	0.09750 (13)	0.0246 (3)
H9	0.6504	0.4734	0.0001	0.038 (5)*
C10	0.84851 (14)	0.72160 (19)	0.24684 (12)	0.0233 (3)
H10	0.8689	0.6787	0.3343	0.033 (5)*
C11	0.93165 (15)	0.83309 (18)	0.20614 (13)	0.0238 (3)
C12	0.86197 (14)	0.8673 (2)	0.06440 (13)	0.0244 (3)
C13	1.07174 (15)	0.9185 (2)	0.28008 (13)	0.0266 (3)
H13	1.0758	1.0388	0.2439	0.034 (5)*
C14	1.20012 (16)	0.8124 (2)	0.26770 (16)	0.0362 (4)
H14A	1.2901	0.8731	0.3139	0.048 (5)*
H14B	1.1941	0.7997	0.1745	0.046 (5)*
H14C	1.1990	0.6961	0.3067	0.057 (7)*
C15	0.53605 (16)	0.2369 (2)	0.34078 (14)	0.0271 (3)
C16	0.3586 (2)	0.2645 (3)	0.4523 (2)	0.0487 (5)
H16A	0.2769	0.2496	0.3726	0.054 (6)*
H16B	0.3310	0.3447	0.5129	0.089 (9)*
H16C	0.3852	0.1504	0.4951	0.063 (7)*
H6O	1.0132 (19)	0.990 (3)	0.4248 (19)	0.035 (5)*
H7O	0.872 (2)	0.227 (3)	0.473 (2)	0.048 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0454 (7)	0.0275 (6)	0.0593 (8)	−0.0103 (5)	0.0273 (6)	−0.0074 (5)
O2	0.0364 (6)	0.0332 (6)	0.0418 (6)	−0.0070 (5)	0.0235 (5)	−0.0054 (5)
O3	0.0223 (5)	0.0314 (5)	0.0327 (5)	0.0028 (4)	0.0100 (4)	0.0019 (4)
O4	0.0240 (5)	0.0314 (5)	0.0216 (5)	−0.0015 (4)	0.0033 (4)	0.0041 (4)
O5	0.0323 (5)	0.0336 (6)	0.0310 (5)	0.0014 (4)	0.0135 (4)	0.0076 (4)
O6	0.0233 (5)	0.0302 (5)	0.0266 (5)	0.0028 (4)	0.0027 (4)	−0.0028 (4)
O7	0.0316 (5)	0.0278 (5)	0.0285 (5)	0.0061 (4)	0.0064 (4)	0.0016 (5)
C1	0.0338 (8)	0.0277 (7)	0.0300 (7)	0.0028 (6)	0.0155 (6)	−0.0014 (6)
C3	0.0248 (7)	0.0236 (7)	0.0265 (6)	0.0022 (5)	0.0084 (5)	−0.0017 (6)
C4	0.0225 (7)	0.0205 (7)	0.0256 (6)	−0.0010 (5)	0.0074 (5)	−0.0023 (5)
C5	0.0201 (6)	0.0274 (7)	0.0240 (6)	−0.0034 (5)	0.0030 (5)	−0.0026 (5)
C6	0.0197 (6)	0.0344 (8)	0.0289 (7)	0.0034 (6)	0.0049 (5)	0.0045 (6)
C7	0.0231 (7)	0.0294 (8)	0.0268 (6)	0.0069 (6)	0.0049 (5)	0.0049 (6)
C8	0.0218 (6)	0.0248 (7)	0.0205 (6)	0.0012 (5)	0.0046 (5)	0.0024 (5)
C9	0.0241 (7)	0.0283 (7)	0.0206 (6)	−0.0023 (6)	0.0054 (5)	−0.0024 (5)
C10	0.0225 (7)	0.0242 (7)	0.0216 (6)	0.0013 (6)	0.0043 (5)	0.0006 (5)
C11	0.0229 (6)	0.0231 (7)	0.0248 (6)	0.0031 (5)	0.0063 (5)	0.0003 (5)
C12	0.0214 (6)	0.0260 (7)	0.0263 (7)	0.0041 (5)	0.0079 (5)	0.0004 (6)
C13	0.0242 (7)	0.0276 (7)	0.0264 (6)	−0.0029 (5)	0.0047 (5)	0.0004 (6)
C14	0.0235 (7)	0.0474 (10)	0.0381 (8)	−0.0014 (7)	0.0095 (6)	−0.0058 (7)
C15	0.0278 (7)	0.0252 (8)	0.0288 (7)	0.0004 (6)	0.0091 (6)	0.0020 (6)
C16	0.0481 (10)	0.0469 (10)	0.0662 (12)	−0.0114 (8)	0.0402 (9)	−0.0063 (9)

Geometric parameters (Å, º) top

O1—C15	1.201 (2)	C5—C9	1.5406 (19)
O2—C15	1.3340 (18)	C5—H5	1.0000
O2—C16	1.4483 (19)	C6—C7	1.323 (2)
O3—C3	1.4181 (17)	C6—H6	0.9500
O3—C1	1.4305 (17)	C7—C8	1.5134 (19)
O4—C12	1.3573 (18)	C7—H7	0.9500
O4—C8	1.4623 (16)	C8—C10	1.5039 (18)
O5—C12	1.2046 (18)	C8—C9	1.541 (2)
O6—C13	1.4341 (17)	C9—H9	1.0000
O6—H6O	0.830 (16)	C10—C11	1.327 (2)
O7—C3	1.3959 (18)	C10—H10	0.9500
O7—H7O	0.802 (17)	C11—C12	1.4811 (19)
C1—C9	1.515 (2)	C11—C13	1.4998 (19)
C1—H1A	0.9900	C13—C14	1.519 (2)
C1—H1B	0.9900	C13—H13	1.0000
C3—C4	1.5316 (18)	C14—H14A	0.9800
C3—H3	1.0000	C14—H14B	0.9800
C4—C15	1.5102 (19)	C14—H14C	0.9800
C4—C5	1.5551 (19)	C16—H16A	0.9800
C4—H4	1.0000	C16—H16B	0.9800
C5—C6	1.509 (2)	C16—H16C	0.9800

C15—O2—C16	116.40 (13)	C10—C8—C9	117.44 (11)
C3—O3—C1	111.90 (11)	C7—C8—C9	102.79 (12)
C12—O4—C8	110.16 (10)	C1—C9—C5	114.31 (11)
C13—O6—H6O	108.5 (14)	C1—C9—C8	118.00 (12)
C3—O7—H7O	106.3 (17)	C5—C9—C8	104.62 (11)
O3—C1—C9	112.37 (11)	C1—C9—H9	106.4
O3—C1—H1A	109.1	C5—C9—H9	106.4
C9—C1—H1A	109.1	C8—C9—H9	106.4
O3—C1—H1B	109.1	C11—C10—C8	110.71 (12)
C9—C1—H1B	109.1	C11—C10—H10	124.6
H1A—C1—H1B	107.9	C8—C10—H10	124.6
O7—C3—O3	107.43 (11)	C10—C11—C12	107.85 (12)
O7—C3—C4	112.18 (11)	C10—C11—C13	130.36 (12)
O3—C3—C4	108.69 (11)	C12—C11—C13	121.79 (12)
O7—C3—H3	109.5	O5—C12—O4	121.98 (12)
O3—C3—H3	109.5	O5—C12—C11	129.51 (13)
C4—C3—H3	109.5	O4—C12—C11	108.48 (12)
C15—C4—C3	111.49 (11)	O6—C13—C11	110.28 (11)
C15—C4—C5	107.73 (11)	O6—C13—C14	107.98 (12)
C3—C4—C5	110.36 (11)	C11—C13—C14	111.06 (12)
C15—C4—H4	109.1	O6—C13—H13	109.2
C3—C4—H4	109.1	C11—C13—H13	109.2
C5—C4—H4	109.1	C14—C13—H13	109.2
C6—C5—C9	102.21 (11)	C13—C14—H14A	109.5
C6—C5—C4	110.18 (11)	C13—C14—H14B	109.5
C9—C5—C4	111.98 (11)	H14A—C14—H14B	109.5
C6—C5—H5	110.7	C13—C14—H14C	109.5
C9—C5—H5	110.7	H14A—C14—H14C	109.5
C4—C5—H5	110.7	H14B—C14—H14C	109.5
C7—C6—C5	112.08 (12)	O1—C15—O2	124.09 (14)
C7—C6—H6	124.0	O1—C15—C4	124.76 (13)
C5—C6—H6	124.0	O2—C15—C4	111.04 (12)
C6—C7—C8	111.22 (13)	O2—C16—H16A	109.5
C6—C7—H7	124.4	O2—C16—H16B	109.5
C8—C7—H7	124.4	H16A—C16—H16B	109.5
O4—C8—C10	102.79 (11)	O2—C16—H16C	109.5
O4—C8—C7	111.06 (11)	H16A—C16—H16C	109.5
C10—C8—C7	113.85 (11)	H16B—C16—H16C	109.5
O4—C8—C9	109.02 (11)

C4—C5—C9—C8	−92.28 (13)	C10—C11—C13—C14	93.58 (18)
C1—C9—C5—C6	156.18 (11)	C10—C11—C13—O6	−26.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O6—H6O···O7ⁱ	0.83 (2)	1.99 (2)	2.8153 (15)	174 (2)
O7—H7O···O6ⁱⁱ	0.80 (2)	1.92 (2)	2.7218 (15)	176 (2)
C1—H1B···O5ⁱⁱⁱ	0.99	2.37	3.2969 (18)	156
C5—H5···O4^iv	1.00	2.47	3.3243 (16)	143

Symmetry codes: (i) x, y+1, z; (ii) −x+2, y−1/2, −z+1; (iii) −x+2, y−1/2, −z; (iv) −x+1, y−1/2, −z.

Experimental details

Crystal data
Chemical formula	C₁₅H₁₈O₇
M_r	310.29
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	173
a, b, c (Å)	9.6736 (2), 7.6203 (1), 10.6303 (2)
β (°)	107.142 (2)
V (Å³)	748.81 (2)
Z	2
Radiation type	Cu Kα
µ (mm⁻¹)	0.93
Crystal size (mm)	0.20 × 0.20 × 0.15

Data collection
Diffractometer	Xcalibur, Ruby, Gemini ultra diffractometer
Absorption correction	Multi-scan CrysAlis PRO (Oxford Diffraction, 2003). Multi-scan absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.
T_min, T_max	0.766, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7011, 2651, 2615
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.597

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.081, 1.09
No. of reflections	2651
No. of parameters	225
No. of restraints	3
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.19
Absolute structure	Flack (1983), no. of Friedel pairs?
Absolute structure parameter	−0.01 (13)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2003), CrysAlis RED (Oxford Diffraction, 2003), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O6—H6O···O7ⁱ	0.830 (16)	1.989 (16)	2.8153 (15)	174 (2)
O7—H7O···O6ⁱⁱ	0.802 (17)	1.921 (17)	2.7218 (15)	176 (2)
C1—H1B···O5ⁱⁱⁱ	0.99	2.37	3.2969 (18)	156.1
C5—H5···O4^iv	1.00	2.47	3.3243 (16)	142.7

Symmetry codes: (i) x, y+1, z; (ii) −x+2, y−1/2, −z+1; (iii) −x+2, y−1/2, −z; (iv) −x+1, y−1/2, −z.

Acknowledgements

This work was supported by the National Research Network project `Drugs from Nature Targeting Inflammation' (subproject No. S10703) granted by the Austrian Science Fund (FWF). The authors thank Peter Schneider and Professor Ernst P. Ellmerer for the NMR measurements, and Professor Volker Kahlenberg for access to the X-ray facilities used for this study.

References

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ISSN: 2053-2296

Volume 67| Part 10| October 2011| Pages o409-o412

doi:10.1107/S0108270111035761

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Plumeridoid C from the Amazonian traditional medicinal plant Himatanthus sucuuba

Comment

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds