Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229616000577/yo3016sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S2053229616000577/yo3016Isup2.hkl | |
Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229616000577/yo3016Isup3.cml |
CCDC reference: 1446723
Nobiletin, (I), is a flavonoid compound that can be found in large quantities in citrus peels. Nobiletin and its metabolites (Lai et al., 2008; Li et al., 2014) have been reported to possess a variety of interesting physiological properties, including anti-inflammatory (Lin et al., 2003), anticancer (Kunimasa et al., 2010), anti-apoptosis (Akao et al., 2008), antidementia (Nagase et al., 2005) and neuroprotective (Yasuda et al., 2014) activities. Based on its potent physiological activities, nobiletin has become an attractive candidate for use as a therapeutic agent. The physiological activities of nobiletin have been attributed to its ability to modulate cell signaling pathways, including cAMP response elements (Nagase et al., 2005) and NF-κB (Cui et al., 2010), as well as its ability to alter the expression of specific genes (Nemoto et al., 2013; Kimura et al., 2014). However, the molecular mechanisms of nobiletin are not clear because the target receptor molecules to which this compound might bind have not yet been definitively identified. Investigations to identify the receptors are currently underway.
The three-dimensional molecular structure of nobiletin had been identified as a complex structure with a porous material using the `crystalline sponge' method (Inokuma et al., 2013). However, the quality of the electron-density map for nobiletin did not appear to be satisfactory in terms of its atomic resolution, probably because of its high thermal vibrations, disorder or the low occupancy levels of the nobiletin molecules in the complex structure. We have determined a single-crystal structure of nobiletin and compared the differences in the molecular conformations of nobiletin in a variety of different crystal-packing environments.
Nobiletin was synthesized according to a previously reported procedure and crystallized from aqueous methanol to give the desired material as fine needles (Asakawa et al., 2011). Nobiletin was dissolved in ethyl acetate and the resulting solution was filtered through a 0.45 µm membrane filter. A sample of the filtered solution (500 µl) was then poured into a Petri dish with a diameter of 15 mm. The solution was allowed to evaporate slowly at 298 K over a period of 2 d to give fine white crystals with a columnar shape. The crystals were analyzed by powder X-ray diffraction (PXRD) using a Rigaku Mini Flex II X-ray diffractometer. The PXRD pattern of the crystals prepared from ethyl acetate was identical to that of the crystals prepared from an aqueous methanol solution. This result confirmed that the crystal form of nobiletin had not changed through the recrystallization process.
Crystal data, data collection and structure refinement details are summarized in Table 1. The diffraction images indicated that the crystal used for the data collection process was a twin crystal made of two separate crystals, and that the c axes of the two crystals were almost parallel. Given that the diffraction spots from each crystal were well separated in the diffraction images, it was possible to collect diffraction data from one of the crystals that diffracted more than sinθ/λ = 0.625 Å-1. During the refinement process, the H atoms were located in a difference Fourier map and were constrained as riding, with Uiso(H) = 1.2Ueq(C).
The X-ray crystal structure of nobiletin, (I), solved in the current study revealed that the asymmetric unit contained one molecule (Fig. 1). Furthermore, no voids were identified in the crystal structure that could accommodate solvent molecules, confirming that this crystal had been isolated in the unsolvated form. The planes of the chromene and benzene rings of nobiletin were almost parallel, as exemplified by the torsion angle of the covalent bond between the chromene and benzene rings (O1—C2—C11—C12) of -0.6 (5)°. The C atoms of the two methoxy groups at the 3'- and 4'-positions of the benzene ring (see Scheme) were also located in the plane of the flavone. In contrast, the C atoms of the methoxy moieties on the chromene ring were not in the same plane as the flavone. The C5 methyl group projects forwards away from the plane of the chromene ring, whilst the C6, C7 and C8 methyl groups project backwards away from the plane of the ring. The molecular structure of nobiletin in this crystal was therefore chiral because of its conformational characteristics, despite the fact that nobiletin does not contain an asymmetric C atom. However, it was not possible to determine which enantiomorph was responsible for this crystal based on the differences in the intensities of the Friedel pair reflections. This could be attributable to the scattering of the C and O atoms of the anomalous imaginary part being too small to be detected at the wavelength used for the data collection in this study [i.e. 0.7004 (1) Å]. The crystals grown from an ethyl acetate solution may therefore have been a mixture of two enantiomorphic forms, as is often the case for the crystals of organic compounds (Koizumi et al., 2008).
The plane of best fit for the flavone ring of nobiletin forms an angle of 31° with the ab plane and is stacked along the c axis (Fig. 2). The distance between the planes of the flavone rings, as represented by the distance between atom C13 and atom C15 at (x, y, z+1), is 3.497 (7) Å. Table 2 shows details of the close intermolecular contacts, which were less than the sum of the van der Waals radii, between the H atoms of the methoxy groups and the O atoms. The O2 atom of the carbonyl group, which is capable of forming a strong hydrogen bond as a hydrogen-bond acceptor, is in contact with atom H00E of the C22 methyl group. The distances between the C22—H22B···O2 and C22···O2 bonds are smaller than the average values reported for C—H···O and C···O contacts of methyl groups and carbonyl O atoms [2.761 (6) and 3.590 (7) Å, respectively; Steiner & Desiraju, 1998]. The C22—H22B···O2 angle is greater than 100°, which is the value needed for a C—H group to form a hydrogen-bonding interaction (Jensen et al., 2003). The geometrical characteristics of this structure suggest that the C22—H22B···O2 contacts could possess a weak hydrogen-bonding characteristic. All of the other close contacts between the H and O atoms of the methoxy groups have C—H···O angles greater than 100°, which implies that these contacts also possess some hydrogen-bonding characteristics (Pingali et al., 2015). However, these hydrogen bonds are weaker than that of the C22—H22B···O2 hydrogen bond because a carbonyl O atom is a better hydrogen bond acceptor than a methoxy O atom.
Fig. 3 shows the superimposition of the molecular structure of nobiletin determined in this study (denoted NOB-1) on the molecular structure determined using the `crystalline sponge' method (denoted NOB-2). The O1—C2—C15—C16 torsion angle in NOB-2 is -172 (2)°, which shows that the benzene ring of the NOB-2 structure is almost flipped compared with that of the NOB-1 structure. Unlike the NOB-1 structure, the benzene and chromene rings of the NOB-2 structure are not coplanar and are distorted by approximately 8°. The other main difference between the two structures is the conformation of the methoxy groups bound to the chromene ring. The C20 methyl group in the NOB-1 structure extends towards the same side of the chromene ring as the C18 and C19 methyl groups, whereas the C20 methyl in the NOB-2 structure extends towards the opposite side of the ring. The superimposition of the two structures also suggests that it would not be possible to pack the NOB-1 structure into the cavities of the crystalline sponge in the same way as the NOB-2 structure because of the steric hindrance between the methoxy moieties of nobiletin and the sponge. Close contacts less than van der Waals distances were found between the C20 methyl group of the superimposed NOB1 structure and a pyridine ring of the sponge, and between the C21 methyl group of the NOB1 structure and an I atom bound to a Zn atom of the sponge. In solution, nobiletin may be in equilibrium with a variety of different conformers, which could differ, at least, in the conformation of the methoxy groups bound to the chromene ring and the torsion angle around the covalent bond between the chromene and benzene rings. The NOB1 and NOB2 structures may be involved in these conformers, with the former of these two structures crystalizing as single crystals and with the latter soaking and being bound into the sponge.
As mentioned above, nobiletin has been reported to elicit a wide range of physiological responses. The key steps in these physiological responses are presumed to involve the binding of nobiletin to the target receptor molecules responsible for each physiological response. Nobiletin could bind to a wide range of receptors based on its conformational variety.
Nobiletin, (I), is a flavonoid compound that can be found in large quantities in citrus peels. Nobiletin and its metabolites (Lai et al., 2008; Li et al., 2014) have been reported to possess a variety of interesting physiological properties, including anti-inflammatory (Lin et al., 2003), anticancer (Kunimasa et al., 2010), anti-apoptosis (Akao et al., 2008), antidementia (Nagase et al., 2005) and neuroprotective (Yasuda et al., 2014) activities. Based on its potent physiological activities, nobiletin has become an attractive candidate for use as a therapeutic agent. The physiological activities of nobiletin have been attributed to its ability to modulate cell signaling pathways, including cAMP response elements (Nagase et al., 2005) and NF-κB (Cui et al., 2010), as well as its ability to alter the expression of specific genes (Nemoto et al., 2013; Kimura et al., 2014). However, the molecular mechanisms of nobiletin are not clear because the target receptor molecules to which this compound might bind have not yet been definitively identified. Investigations to identify the receptors are currently underway.
The three-dimensional molecular structure of nobiletin had been identified as a complex structure with a porous material using the `crystalline sponge' method (Inokuma et al., 2013). However, the quality of the electron-density map for nobiletin did not appear to be satisfactory in terms of its atomic resolution, probably because of its high thermal vibrations, disorder or the low occupancy levels of the nobiletin molecules in the complex structure. We have determined a single-crystal structure of nobiletin and compared the differences in the molecular conformations of nobiletin in a variety of different crystal-packing environments.
The X-ray crystal structure of nobiletin, (I), solved in the current study revealed that the asymmetric unit contained one molecule (Fig. 1). Furthermore, no voids were identified in the crystal structure that could accommodate solvent molecules, confirming that this crystal had been isolated in the unsolvated form. The planes of the chromene and benzene rings of nobiletin were almost parallel, as exemplified by the torsion angle of the covalent bond between the chromene and benzene rings (O1—C2—C11—C12) of -0.6 (5)°. The C atoms of the two methoxy groups at the 3'- and 4'-positions of the benzene ring (see Scheme) were also located in the plane of the flavone. In contrast, the C atoms of the methoxy moieties on the chromene ring were not in the same plane as the flavone. The C5 methyl group projects forwards away from the plane of the chromene ring, whilst the C6, C7 and C8 methyl groups project backwards away from the plane of the ring. The molecular structure of nobiletin in this crystal was therefore chiral because of its conformational characteristics, despite the fact that nobiletin does not contain an asymmetric C atom. However, it was not possible to determine which enantiomorph was responsible for this crystal based on the differences in the intensities of the Friedel pair reflections. This could be attributable to the scattering of the C and O atoms of the anomalous imaginary part being too small to be detected at the wavelength used for the data collection in this study [i.e. 0.7004 (1) Å]. The crystals grown from an ethyl acetate solution may therefore have been a mixture of two enantiomorphic forms, as is often the case for the crystals of organic compounds (Koizumi et al., 2008).
The plane of best fit for the flavone ring of nobiletin forms an angle of 31° with the ab plane and is stacked along the c axis (Fig. 2). The distance between the planes of the flavone rings, as represented by the distance between atom C13 and atom C15 at (x, y, z+1), is 3.497 (7) Å. Table 2 shows details of the close intermolecular contacts, which were less than the sum of the van der Waals radii, between the H atoms of the methoxy groups and the O atoms. The O2 atom of the carbonyl group, which is capable of forming a strong hydrogen bond as a hydrogen-bond acceptor, is in contact with atom H00E of the C22 methyl group. The distances between the C22—H22B···O2 and C22···O2 bonds are smaller than the average values reported for C—H···O and C···O contacts of methyl groups and carbonyl O atoms [2.761 (6) and 3.590 (7) Å, respectively; Steiner & Desiraju, 1998]. The C22—H22B···O2 angle is greater than 100°, which is the value needed for a C—H group to form a hydrogen-bonding interaction (Jensen et al., 2003). The geometrical characteristics of this structure suggest that the C22—H22B···O2 contacts could possess a weak hydrogen-bonding characteristic. All of the other close contacts between the H and O atoms of the methoxy groups have C—H···O angles greater than 100°, which implies that these contacts also possess some hydrogen-bonding characteristics (Pingali et al., 2015). However, these hydrogen bonds are weaker than that of the C22—H22B···O2 hydrogen bond because a carbonyl O atom is a better hydrogen bond acceptor than a methoxy O atom.
Fig. 3 shows the superimposition of the molecular structure of nobiletin determined in this study (denoted NOB-1) on the molecular structure determined using the `crystalline sponge' method (denoted NOB-2). The O1—C2—C15—C16 torsion angle in NOB-2 is -172 (2)°, which shows that the benzene ring of the NOB-2 structure is almost flipped compared with that of the NOB-1 structure. Unlike the NOB-1 structure, the benzene and chromene rings of the NOB-2 structure are not coplanar and are distorted by approximately 8°. The other main difference between the two structures is the conformation of the methoxy groups bound to the chromene ring. The C20 methyl group in the NOB-1 structure extends towards the same side of the chromene ring as the C18 and C19 methyl groups, whereas the C20 methyl in the NOB-2 structure extends towards the opposite side of the ring. The superimposition of the two structures also suggests that it would not be possible to pack the NOB-1 structure into the cavities of the crystalline sponge in the same way as the NOB-2 structure because of the steric hindrance between the methoxy moieties of nobiletin and the sponge. Close contacts less than van der Waals distances were found between the C20 methyl group of the superimposed NOB1 structure and a pyridine ring of the sponge, and between the C21 methyl group of the NOB1 structure and an I atom bound to a Zn atom of the sponge. In solution, nobiletin may be in equilibrium with a variety of different conformers, which could differ, at least, in the conformation of the methoxy groups bound to the chromene ring and the torsion angle around the covalent bond between the chromene and benzene rings. The NOB1 and NOB2 structures may be involved in these conformers, with the former of these two structures crystalizing as single crystals and with the latter soaking and being bound into the sponge.
As mentioned above, nobiletin has been reported to elicit a wide range of physiological responses. The key steps in these physiological responses are presumed to involve the binding of nobiletin to the target receptor molecules responsible for each physiological response. Nobiletin could bind to a wide range of receptors based on its conformational variety.
Nobiletin was synthesized according to a previously reported procedure and crystallized from aqueous methanol to give the desired material as fine needles (Asakawa et al., 2011). Nobiletin was dissolved in ethyl acetate and the resulting solution was filtered through a 0.45 µm membrane filter. A sample of the filtered solution (500 µl) was then poured into a Petri dish with a diameter of 15 mm. The solution was allowed to evaporate slowly at 298 K over a period of 2 d to give fine white crystals with a columnar shape. The crystals were analyzed by powder X-ray diffraction (PXRD) using a Rigaku Mini Flex II X-ray diffractometer. The PXRD pattern of the crystals prepared from ethyl acetate was identical to that of the crystals prepared from an aqueous methanol solution. This result confirmed that the crystal form of nobiletin had not changed through the recrystallization process.
Crystal data, data collection and structure refinement details are summarized in Table 1. The diffraction images indicated that the crystal used for the data collection process was a twin crystal made of two separate crystals, and that the c axes of the two crystals were almost parallel. Given that the diffraction spots from each crystal were well separated in the diffraction images, it was possible to collect diffraction data from one of the crystals that diffracted more than sinθ/λ = 0.625 Å-1. During the refinement process, the H atoms were located in a difference Fourier map and were constrained as riding, with Uiso(H) = 1.2Ueq(C).
Data collection: RAPID-AUTO (Rigaku, 2010); cell refinement: RAPID-AUTO (Rigaku, 2010); data reduction: RAPID-AUTO (Rigaku, 2010); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b) and shelXle (Hübschle et al., 2011); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).
C21H22O8 | Dx = 1.458 Mg m−3 |
Mr = 402.38 | Synchrotron (SPring-8 BL02B1) radiation, λ = 0.70041 Å |
Orthorhombic, P212121 | Cell parameters from 377 reflections |
a = 19.3239 (17) Å | θ = 2.8–29.5° |
b = 22.921 (2) Å | µ = 0.11 mm−1 |
c = 4.1385 (4) Å | T = 100 K |
V = 1833.0 (3) Å3 | Column, colourless |
Z = 4 | 0.5 × 0.02 × 0.01 mm |
F(000) = 848 |
Rigaku Mercury2 CCD four-circle diffractometer | Rint = 0.043 |
ω scan | θmax = 29.6°, θmin = 1.4° |
13177 measured reflections | h = −26→25 |
4894 independent reflections | k = −32→30 |
4091 reflections with I > 2σ(I) | l = −5→5 |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.065 | w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.192 | (Δ/σ)max < 0.001 |
S = 1.29 | Δρmax = 0.42 e Å−3 |
4894 reflections | Δρmin = −0.29 e Å−3 |
268 parameters | Absolute structure: An arbitrary choice of enantiomer has been made. |
0 restraints |
C21H22O8 | V = 1833.0 (3) Å3 |
Mr = 402.38 | Z = 4 |
Orthorhombic, P212121 | Synchrotron (SPring-8 BL02B1) radiation, λ = 0.70041 Å |
a = 19.3239 (17) Å | µ = 0.11 mm−1 |
b = 22.921 (2) Å | T = 100 K |
c = 4.1385 (4) Å | 0.5 × 0.02 × 0.01 mm |
Rigaku Mercury2 CCD four-circle diffractometer | 4091 reflections with I > 2σ(I) |
13177 measured reflections | Rint = 0.043 |
4894 independent reflections |
R[F2 > 2σ(F2)] = 0.065 | 0 restraints |
wR(F2) = 0.192 | H-atom parameters constrained |
S = 1.29 | Δρmax = 0.42 e Å−3 |
4894 reflections | Δρmin = −0.29 e Å−3 |
268 parameters | Absolute structure: An arbitrary choice of enantiomer has been made. |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
O2 | 0.86158 (13) | 0.29414 (11) | 0.2767 (8) | 0.0202 (6) | |
C2 | 0.70156 (19) | 0.36216 (16) | 0.4652 (10) | 0.0159 (7) | |
O1 | 0.66854 (13) | 0.32043 (11) | 0.6357 (7) | 0.0166 (6) | |
O3 | 0.85629 (13) | 0.18115 (11) | 0.5377 (7) | 0.0165 (6) | |
C3 | 0.76441 (19) | 0.35347 (16) | 0.3380 (11) | 0.0178 (8) | |
H3 | 0.7845 | 0.3837 | 0.2118 | 0.021* | |
O4 | 0.77681 (14) | 0.10365 (12) | 0.8750 (7) | 0.0196 (6) | |
C4 | 0.80334 (18) | 0.29972 (16) | 0.3846 (10) | 0.0157 (7) | |
C7 | 0.68406 (19) | 0.17222 (16) | 0.8978 (10) | 0.0160 (7) | |
O7 | 0.49217 (13) | 0.47574 (11) | 0.7082 (8) | 0.0213 (7) | |
O6 | 0.59535 (14) | 0.24399 (13) | 0.9566 (8) | 0.0218 (6) | |
C6 | 0.7513 (2) | 0.15775 (15) | 0.7931 (10) | 0.0164 (8) | |
O5 | 0.64380 (15) | 0.13367 (12) | 1.0635 (8) | 0.0247 (7) | |
C5 | 0.79098 (18) | 0.19812 (16) | 0.6319 (10) | 0.0154 (7) | |
C9 | 0.69935 (18) | 0.26729 (15) | 0.6807 (10) | 0.0147 (7) | |
O8 | 0.53896 (14) | 0.56400 (12) | 0.4006 (8) | 0.0220 (6) | |
C8 | 0.65893 (18) | 0.22752 (17) | 0.8452 (10) | 0.0161 (8) | |
C10 | 0.76586 (18) | 0.25431 (16) | 0.5686 (10) | 0.0143 (7) | |
C17 | 0.90960 (18) | 0.20222 (16) | 0.7489 (10) | 0.0172 (8) | |
H17A | 0.9536 | 0.1834 | 0.6937 | 0.021* | |
H17B | 0.8975 | 0.1930 | 0.9731 | 0.021* | |
H17C | 0.9141 | 0.2446 | 0.7240 | 0.021* | |
C11 | 0.66062 (19) | 0.41593 (16) | 0.4440 (10) | 0.0164 (7) | |
C18 | 0.7924 (2) | 0.06551 (17) | 0.6135 (12) | 0.0259 (9) | |
H18A | 0.7526 | 0.0634 | 0.4673 | 0.031* | |
H18B | 0.8027 | 0.0265 | 0.6977 | 0.031* | |
H18C | 0.8327 | 0.0804 | 0.4956 | 0.031* | |
C12 | 0.59492 (19) | 0.41848 (16) | 0.5923 (10) | 0.0169 (8) | |
H12 | 0.5775 | 0.3855 | 0.7054 | 0.020* | |
C19 | 0.6239 (2) | 0.08263 (18) | 0.8898 (14) | 0.0314 (11) | |
H19A | 0.6101 | 0.0935 | 0.6700 | 0.038* | |
H19B | 0.5849 | 0.0639 | 0.9999 | 0.038* | |
H19C | 0.6630 | 0.0555 | 0.8802 | 0.038* | |
C13 | 0.55586 (19) | 0.46892 (16) | 0.5732 (11) | 0.0176 (8) | |
C20 | 0.5402 (2) | 0.2274 (2) | 0.7441 (13) | 0.0325 (11) | |
H20A | 0.5338 | 0.1850 | 0.7530 | 0.039* | |
H20B | 0.5516 | 0.2390 | 0.5226 | 0.039* | |
H20C | 0.4973 | 0.2467 | 0.8115 | 0.039* | |
C14 | 0.58174 (19) | 0.51748 (16) | 0.4071 (11) | 0.0178 (8) | |
C15 | 0.64615 (19) | 0.51500 (16) | 0.2609 (10) | 0.0179 (8) | |
H15 | 0.6635 | 0.5480 | 0.1478 | 0.021* | |
C16 | 0.68554 (19) | 0.46417 (16) | 0.2797 (11) | 0.0183 (8) | |
H16 | 0.7297 | 0.4626 | 0.1793 | 0.022* | |
C21 | 0.4644 (2) | 0.42762 (18) | 0.8763 (12) | 0.0229 (9) | |
H21A | 0.4580 | 0.3950 | 0.7263 | 0.027* | |
H21B | 0.4197 | 0.4385 | 0.9704 | 0.027* | |
H21C | 0.4963 | 0.4160 | 1.0488 | 0.027* | |
C22 | 0.5608 (2) | 0.61381 (17) | 0.2152 (12) | 0.0234 (9) | |
H22A | 0.5690 | 0.6020 | −0.0091 | 0.028* | |
H22B | 0.6036 | 0.6296 | 0.3072 | 0.028* | |
H22C | 0.5246 | 0.6438 | 0.2213 | 0.028* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O2 | 0.0153 (12) | 0.0178 (12) | 0.0276 (16) | 0.0012 (10) | 0.0076 (12) | 0.0015 (12) |
C2 | 0.0165 (16) | 0.0169 (17) | 0.0142 (18) | −0.0031 (14) | −0.0036 (15) | −0.0003 (14) |
O1 | 0.0135 (11) | 0.0127 (12) | 0.0235 (15) | 0.0001 (9) | 0.0000 (11) | 0.0013 (11) |
O3 | 0.0160 (11) | 0.0156 (12) | 0.0181 (14) | 0.0003 (10) | −0.0015 (11) | −0.0037 (11) |
C3 | 0.0184 (17) | 0.0144 (16) | 0.020 (2) | 0.0014 (14) | 0.0019 (15) | 0.0023 (16) |
O4 | 0.0237 (13) | 0.0166 (12) | 0.0187 (15) | 0.0024 (10) | −0.0003 (12) | 0.0032 (11) |
C4 | 0.0143 (15) | 0.0151 (16) | 0.0177 (19) | −0.0015 (13) | −0.0007 (15) | −0.0028 (15) |
C7 | 0.0160 (15) | 0.0181 (17) | 0.0138 (18) | −0.0056 (13) | −0.0016 (15) | 0.0018 (15) |
O7 | 0.0149 (12) | 0.0183 (13) | 0.0306 (18) | 0.0019 (10) | 0.0031 (12) | 0.0034 (13) |
O6 | 0.0144 (12) | 0.0283 (15) | 0.0228 (16) | −0.0025 (11) | 0.0022 (12) | −0.0031 (13) |
C6 | 0.0188 (16) | 0.0134 (16) | 0.0169 (19) | 0.0009 (13) | −0.0025 (15) | −0.0030 (15) |
O5 | 0.0276 (14) | 0.0228 (14) | 0.0238 (17) | −0.0083 (12) | 0.0021 (13) | 0.0049 (13) |
C5 | 0.0149 (15) | 0.0163 (16) | 0.0150 (18) | −0.0011 (13) | −0.0029 (15) | −0.0030 (15) |
C9 | 0.0156 (16) | 0.0125 (16) | 0.0161 (18) | −0.0012 (13) | −0.0056 (14) | −0.0008 (14) |
O8 | 0.0188 (12) | 0.0181 (13) | 0.0290 (17) | 0.0040 (10) | 0.0027 (12) | 0.0030 (13) |
C8 | 0.0101 (14) | 0.0251 (19) | 0.0132 (18) | −0.0014 (13) | −0.0010 (14) | −0.0018 (15) |
C10 | 0.0138 (15) | 0.0156 (16) | 0.0136 (18) | −0.0020 (13) | −0.0012 (14) | −0.0026 (14) |
C17 | 0.0123 (15) | 0.0190 (17) | 0.020 (2) | 0.0041 (13) | −0.0013 (15) | 0.0005 (16) |
C11 | 0.0147 (15) | 0.0156 (17) | 0.0188 (19) | −0.0003 (13) | −0.0019 (15) | −0.0031 (15) |
C18 | 0.033 (2) | 0.0142 (17) | 0.030 (2) | 0.0000 (16) | 0.001 (2) | −0.0003 (17) |
C12 | 0.0165 (16) | 0.0162 (17) | 0.018 (2) | −0.0010 (13) | −0.0003 (15) | 0.0001 (16) |
C19 | 0.027 (2) | 0.0213 (19) | 0.046 (3) | −0.0099 (16) | 0.001 (2) | 0.002 (2) |
C13 | 0.0131 (15) | 0.0188 (17) | 0.021 (2) | −0.0019 (13) | −0.0032 (15) | −0.0008 (16) |
C20 | 0.0175 (19) | 0.056 (3) | 0.024 (2) | 0.0059 (19) | −0.0008 (18) | −0.002 (2) |
C14 | 0.0195 (16) | 0.0157 (17) | 0.018 (2) | −0.0006 (13) | −0.0058 (16) | 0.0002 (16) |
C15 | 0.0178 (16) | 0.0135 (16) | 0.022 (2) | −0.0006 (13) | 0.0010 (16) | 0.0003 (16) |
C16 | 0.0127 (15) | 0.0189 (18) | 0.023 (2) | −0.0013 (13) | −0.0009 (15) | 0.0001 (16) |
C21 | 0.0199 (17) | 0.025 (2) | 0.024 (2) | −0.0033 (15) | 0.0063 (17) | 0.0017 (18) |
C22 | 0.0254 (19) | 0.0159 (17) | 0.029 (2) | 0.0043 (15) | −0.0011 (18) | 0.0020 (17) |
O2—C4 | 1.217 (4) | C17—H17B | 0.9800 |
C2—C3 | 1.339 (5) | C17—H17C | 0.9800 |
C2—O1 | 1.349 (4) | C11—C16 | 1.384 (5) |
C2—C11 | 1.467 (5) | C11—C12 | 1.411 (5) |
O1—C9 | 1.368 (4) | C18—H18A | 0.9800 |
O3—C5 | 1.377 (4) | C18—H18B | 0.9800 |
O3—C17 | 1.435 (5) | C18—H18C | 0.9800 |
C3—C4 | 1.456 (5) | C12—C13 | 1.383 (5) |
C3—H3 | 0.9500 | C12—H12 | 0.9500 |
O4—C6 | 1.376 (4) | C19—H19A | 0.9800 |
O4—C18 | 1.424 (5) | C19—H19B | 0.9800 |
C4—C10 | 1.479 (5) | C19—H19C | 0.9800 |
C7—O5 | 1.362 (5) | C13—C14 | 1.401 (5) |
C7—C8 | 1.375 (5) | C20—H20A | 0.9800 |
C7—C6 | 1.410 (5) | C20—H20B | 0.9800 |
O7—C13 | 1.361 (4) | C20—H20C | 0.9800 |
O7—C21 | 1.410 (5) | C14—C15 | 1.385 (5) |
O6—C8 | 1.365 (4) | C15—C16 | 1.394 (5) |
O6—C20 | 1.434 (5) | C15—H15 | 0.9500 |
C6—C5 | 1.374 (5) | C16—H16 | 0.9500 |
O5—C19 | 1.426 (5) | C21—H21A | 0.9800 |
C5—C10 | 1.401 (5) | C21—H21B | 0.9800 |
C9—C8 | 1.380 (5) | C21—H21C | 0.9800 |
C9—C10 | 1.398 (5) | C22—H22A | 0.9800 |
O8—C14 | 1.349 (4) | C22—H22B | 0.9800 |
O8—C22 | 1.439 (5) | C22—H22C | 0.9800 |
C17—H17A | 0.9800 | ||
C3—C2—O1 | 122.0 (3) | O4—C18—H18B | 109.5 |
C3—C2—C11 | 126.2 (4) | H18A—C18—H18B | 109.5 |
O1—C2—C11 | 111.8 (3) | O4—C18—H18C | 109.5 |
C2—O1—C9 | 119.8 (3) | H18A—C18—H18C | 109.5 |
C5—O3—C17 | 113.0 (3) | H18B—C18—H18C | 109.5 |
C2—C3—C4 | 122.8 (4) | C13—C12—C11 | 120.0 (3) |
C2—C3—H3 | 118.6 | C13—C12—H12 | 120.0 |
C4—C3—H3 | 118.6 | C11—C12—H12 | 120.0 |
C6—O4—C18 | 116.2 (3) | O5—C19—H19A | 109.5 |
O2—C4—C3 | 121.2 (3) | O5—C19—H19B | 109.5 |
O2—C4—C10 | 124.6 (3) | H19A—C19—H19B | 109.5 |
C3—C4—C10 | 114.2 (3) | O5—C19—H19C | 109.5 |
O5—C7—C8 | 118.4 (3) | H19A—C19—H19C | 109.5 |
O5—C7—C6 | 121.9 (3) | H19B—C19—H19C | 109.5 |
C8—C7—C6 | 119.6 (3) | O7—C13—C12 | 124.5 (3) |
C13—O7—C21 | 117.2 (3) | O7—C13—C14 | 115.7 (3) |
C8—O6—C20 | 112.9 (3) | C12—C13—C14 | 119.8 (3) |
C5—C6—O4 | 121.8 (3) | O6—C20—H20A | 109.5 |
C5—C6—C7 | 120.3 (3) | O6—C20—H20B | 109.5 |
O4—C6—C7 | 117.8 (3) | H20A—C20—H20B | 109.5 |
C7—O5—C19 | 115.6 (3) | O6—C20—H20C | 109.5 |
C6—C5—O3 | 117.3 (3) | H20A—C20—H20C | 109.5 |
C6—C5—C10 | 121.1 (3) | H20B—C20—H20C | 109.5 |
O3—C5—C10 | 121.6 (3) | O8—C14—C15 | 125.1 (4) |
O1—C9—C8 | 114.1 (3) | O8—C14—C13 | 114.8 (3) |
O1—C9—C10 | 123.0 (3) | C15—C14—C13 | 120.2 (3) |
C8—C9—C10 | 122.9 (3) | C14—C15—C16 | 120.0 (4) |
C14—O8—C22 | 117.3 (3) | C14—C15—H15 | 120.0 |
O6—C8—C7 | 121.3 (3) | C16—C15—H15 | 120.0 |
O6—C8—C9 | 119.6 (3) | C11—C16—C15 | 120.3 (3) |
C7—C8—C9 | 119.2 (3) | C11—C16—H16 | 119.8 |
C9—C10—C5 | 116.9 (3) | C15—C16—H16 | 119.8 |
C9—C10—C4 | 118.1 (3) | O7—C21—H21A | 109.5 |
C5—C10—C4 | 125.0 (3) | O7—C21—H21B | 109.5 |
O3—C17—H17A | 109.5 | H21A—C21—H21B | 109.5 |
O3—C17—H17B | 109.5 | O7—C21—H21C | 109.5 |
H17A—C17—H17B | 109.5 | H21A—C21—H21C | 109.5 |
O3—C17—H17C | 109.5 | H21B—C21—H21C | 109.5 |
H17A—C17—H17C | 109.5 | O8—C22—H22A | 109.5 |
H17B—C17—H17C | 109.5 | O8—C22—H22B | 109.5 |
C16—C11—C12 | 119.6 (3) | H22A—C22—H22B | 109.5 |
C16—C11—C2 | 120.8 (3) | O8—C22—H22C | 109.5 |
C12—C11—C2 | 119.6 (3) | H22A—C22—H22C | 109.5 |
O4—C18—H18A | 109.5 | H22B—C22—H22C | 109.5 |
Experimental details
Crystal data | |
Chemical formula | C21H22O8 |
Mr | 402.38 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 19.3239 (17), 22.921 (2), 4.1385 (4) |
V (Å3) | 1833.0 (3) |
Z | 4 |
Radiation type | Synchrotron (SPring-8 BL02B1), λ = 0.70041 Å |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.5 × 0.02 × 0.01 |
Data collection | |
Diffractometer | Rigaku Mercury2 CCD four-circle |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13177, 4894, 4091 |
Rint | 0.043 |
(sin θ/λ)max (Å−1) | 0.705 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.065, 0.192, 1.29 |
No. of reflections | 4894 |
No. of parameters | 268 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.42, −0.29 |
Absolute structure | An arbitrary choice of enantiomer has been made. |
Computer programs: RAPID-AUTO (Rigaku, 2010), SHELXT (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b) and shelXle (Hübschle et al., 2011), Mercury (Macrae et al., 2008), publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
C22—H22B···O2i | 0.98 | 2.70 | 3.479 (5) | 136.8 |
C17—H17B···O3ii | 0.98 | 2.48 | 3.457 (5) | 172.4 |
C18—H18A···O4iii | 0.98 | 2.66 | 3.193 (6) | 114.4 |
C20—H20B···O6iii | 0.98 | 2.49 | 3.450 (6) | 165.4 |
C22—H22A···O8iii | 0.98 | 2.66 | 3.584 (6) | 157.8 |
C19—H19B···O7iv | 0.98 | 2.65 | 3.346 (5) | 127.9 |
C19—H19B···O8iv | 0.98 | 2.43 | 3.292 (5) | 146.7 |
Symmetry codes: (i) -x+3/2, -y+1, z+1/2; (ii) x, y, z+1; (iii) x, y, z-1; (iv) -x+1, y-1/2, -z+3/2. |