Swertisin dihydrate

Article abstract of DOI:10.1107/S0108270104028355

The molecular structure of the 6-C-glucopyranosyl-7-O-methylapigenin dihydrate is discussed. The basal plane of the pyranosyl ring of the glucose moiety is found to be perpendicular to the benzopyran ring system. It is observed that the flavone skeletons are stacked along the a axis, forming layers parallel to (001). The glucose groups and water molecules of crystallization are connected via O-H···O hydrogen bonds.

Full text of DOI:10.1107/S0108270104028355

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
between insects (Harborne & Williams, 2000). Swertisin (7-O-
methylisovitexin) is a C-glucosyl¯avone isolated from the
whole herb of Swertia japonica (Komatsu & Tomimori, 1966;
Komatsu et al., 1967) and from the seeds of Ziziphus jujuba
Mill var. spinosa (Cheng et al., 2000), Piper elongatum
(Masuoka et al., 2003) and other plants. This compound has
also been obtained by acid hydrolysis of ¯avocommelin, which
was isolated from the blue petals of Commelina communis
(Takeda et al., 1966).
ISSN 0108-2701
Swertisin dihydrate
Shigeru Ohba,a* Kumi Yoshidab and Tadao Kondoc
aDepartment of Chemistry, Keio University, Hiyoshi 4-1-1, Kohoku-ku, Yokohama
223-8521, Japan, bGraduate School of Information Science, Nagoya University,
Chikusa, Nagoya 464-8601, Japan, and cGraduate School of Bioagricultural
Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
Correspondence e-mail: ohba@flet.keio.ac.jp
Received 29 September 2004
Accepted 4 November 2004
Online 30 November 2004
In the supramolecular metal complex pigment (comme-
linin) of the blue ¯owers of C. communis (Kondo et al., 1992),
six molecules of anthocyanin (malonylawobanin) and six
molecules of ¯avone (¯avocommelin) form a ¯attened sphe-
rical cluster with two metal atoms and chiral ꢀ±ꢀ stacking
interactions inside the cluster. Chiral self-association of
¯avocommelin in aqueous solution was also deduced on the
basis of CD (circular dichroism; Goto et al., 1990). In these
chiral molecular stacking phenomena, the conformation of the
glucosyl moieties and intermolecular hydrogen bonding
involving the sugar groups must play very important roles
(Kondo et al., 2001). The octaacetate derivative of ¯avo-
commelin does not show any ꢀ±ꢀ stacking in the crystal
(Ohsawa et al., 1994), possibly as a result of there being no
intermolecular hydrogen bonding. The crystal structures of
¯avone glycosides may give some features of the self-asso-
ciation. However, X-ray structural analyses of ¯avone glyco-
sides are very rare (Jin, Yamagata & Tomita, 1990; Jin, Fujii &
Tomita, 1990; Hirakura et al., 1997). We report here the crystal
structure of the title compound, (I).
The title compound, 6-C-glucopyranosyl-7-O-methylapigenin
dihydrate, C22H22O10Á2H2O, is a natural C-glucosyl¯avone.
The ¯avone skeleton is almost planar, the dihedral angle
between the pyran moiety and the 4-hydroxyphenyl ring being
9.8 (3)ꢀ. The basal plane of the pyranosyl ring of the glucose
moiety is almost perpendicular to the benzopyran ring system.
The ¯avone skeletons are stacked along the a axis, forming
layers parallel to (001). Between these hydrophobic layers, the
glucose groups and water molecules of crystallization are
connected via OÐHÁ Á ÁO hydrogen bonds, forming hydro-
philic layers.
Comment
Flavonoid compounds make up a large group of secondary
plant metabolites. Some of them exist as glycosides and show
various biological functions, such as co-pigment effects on
¯ower pigmentation, screening effects from solar UV radia-
tion, signaling between micro-organisms and chemo-attraction
Figure 1
The molecular structure of (I), showing displacement ellipsoids at the 50% probability level. H atoms bonded to atoms O8, O11 and O12 show positional
disorder, and atoms H8B, H11C and H12B have been omitted for clarity.
Acta Cryst. (2004). C60, o893±o896
DOI: 10.1107/S0108270104028355
# 2004 International Union of Crystallography o893

organic compounds
The molecular structure of (I) is shown in Fig. 1. The basal
plane of the hexopyranosyl glucose ring (de®ned by atoms O6,
C33, C31 and C30) is almost perpendicular to the plane of
benzene ring A (atoms C13±C18), the dihedral angle being
87.3 (3)ꢀ. Cheng et al. (2000) reported the existence of rota-
mers of (I) on the basis of the temperature dependence of 1H
and 13C NMR spectra in DMSO-d6 solution, and described the
contribution of the methyl group (atom C28) to the rotational
energy barrier around the C-glucopyranosyl bond (C14ÐC29
bond) on the basis of conformational analysis. The nearly
perpendicular arrangement of the basal plane of the glucose
moiety and ring A may be the result of non-bonded inter-
atomic repulsions around the C-glucopyranosyl bond.
ring B from the plane of pyran ring C. Similar bending has
been observed in ¯avocommelin octaacetate and other ¯avone
crystals (Ohsawa et al., 1994). The dihedral angles between the
planes of rings A and C, and between the planes of rings B and
C are 3.0 (2) and 9.8 (3)ꢀ, respectively.
The roughly planar 4-hydroxyphenylbenzopyranone skele-
tons are stacked along the a axis, forming hydrophobic layers
(Fig. 2). Fig. 3 shows the ꢀ±ꢀ stacking in detail by illustrating
the neighboring ꢀ systems below and above the molecule at (x,
y, z), where 0 < x < 14. There are two ꢀ systems above (related
by the 21 screw axis parallel to b) and one ꢀ system below the
¯avone plane (related by the twofold axis parallel to b). The
shortest intermolecular distances between the ¯avone skele-
vii
Ê
Phenyl ring B (atoms C22±C27) is slightly rotated out of the
plane of the pyran ring (ring C; atoms O3/C17±C21), the O3Ð
C21ÐC22ÐC23 torsion angle being 8.3 (9)ꢀ (Table 1). In
addition, there is a slight bending of ring B with respect to ring
tons are 3.263 (9) (for O2Á Á ÁC21 ) and 3.399 (10) A for
(C19Á Á ÁC20ix) [symmetry codes: (vii)
x, y, 1 z].
x, y 12, 1 z; (ix)
1
2
The glucose groups and water molecules of crystallization
are connected via OÐHÁ Á ÁO hydrogen bonds (Table 2),
forming hydrophilic layers parallel to (001) (Fig. 2). There is
positional disorder of the H atoms in a hydroxy group (O8)
and the water molecules (O11 and O12), resulting in two
possible hydrogen-bond linkages. In Fig. 4, one of two possible
linkages is shown, i.e. O8iiiÐH8AiiiÁ Á ÁO11ÐH11BÁ Á ÁO12Ð
H12CÁ Á ÁO12ivÐH12Biv (for symmetry codes, see Table 2).
The other possible linkage is H8BiiiÐO8iiiÁ Á ÁH11CÐ
O11Á Á ÁH12BÐO12Á Á ÁH12CivÐO12iv.
Ê
C, as measured by the 0.24 (1) A shift of the center of phenyl
In the supramolecular blue pigment, commelinin (Kondo et
al., 1992), the C-glucosyl moiety of ¯avocommelin is a rotamer
of (I), suggesting the ¯exibility of the relative orientation of
the glucose moiety. In commelinin, two molecules of ¯avo-
commelin are stacked anticlockwise, the torsion angle
between the C O bond axes of the ¯avone moieties being ca
100ꢀ. The C O bond direction is roughly the direction of
electric transition moment of the main absorption band of the
¯avone compound, and the chiral arrangement of the exciton
coupling will cause the CD activity (Nakanishi & Berova,
1994). On the other hand, in (I), the C O bond axes are
approximately parallel to one other. This con®guration may be
the result of the two-dimensional arrangement of the ¯avone
Figure 2
The crystal structure of (I), projected along the b axis. Thin lines indicate
hydrogen bonds. H atoms bonded to C atoms and atoms H8B, H11C and
H12B have been omitted for clarity.
Figure 3
1
4
The ꢀ±ꢀ stacking between the ¯avone moiety at (x, y, z) (0 < x < ;
Figure 4
hatched) and those of the neighboring molecules above (14 < x < 21 ) and
The hydrogen-bond network of glucose groups and water molecules. The
¯avone moieties, some atoms bonded to the sugar rings and some of the
disordered H atoms have been omitted for clarity. [Symmetry codes: (iii)
x, y, z; (iv) 1 x, y, z.]
1
4
below ( < x < 0). The substituents, such as glucose groups, have been
omitted for clarity. Rings, A, B and C are labeled. [Symmetry codes: (vii)
1
2
1
2
x, y 12, 1 z; (viii)
x, y + 12, 1 z; (ix) x, y, 1 z.]
ꢁ
o894 Ohba, Yoshida and Kondo
C22H22O10Á2H2O
Acta Cryst. (2004). C60, o893±o896

organic compounds
Table 2
Hydrogen-bonding geometry (A, ).
skeletons in (I), which is supported by a two-dimensional
hydrogen-bonding network of the sugar groups and water
molecules.
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
O1ÐH1Á Á ÁO2
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.82
1.81
2.07
2.10
2.00
1.96
1.91
2.32
2.37
2.03
2.10
1.98
1.98
2.16
2.542 (6)
2.886 (9)
2.907 (9)
2.728 (7)
2.771 (7)
2.732 (8)
2.945 (6)
3.023 (8)
2.751 (7)
2.728 (7)
2.787 (7)
2.751 (7)
2.837 (10)
148
175
170
148
173
179
133
137
146
133
168
156
140
O5ÐH5Á Á ÁO10i
Experimental
O7ÐH7Á Á ÁO5ii
O8ÐH8AÁ Á ÁO11iii
O9ÐH9Á Á ÁO8iii
Compound (I) was obtained by acid hydrolysis of the O-gluco-
pyranosyloxy group bonded to ring B of ¯avocommelin isolated from
C. communis. To ¯avocommelin (500 mg) was added 10% HCl±
methanol (500 ml) and the mixture was warmed at 333 K for 12 h.
The reaction mixture was concentrated in vacuo and the resulting
syrup was recrystallized from an aqueous methanol solution [yield of
(I): 140 mg, 38%]. The powder of (I) (280 mg) was dissolved in an
aqueous methanol solution (500 ml) at room temperature and left to
stand for slow evaporation of the solvent for ®ve months. At the
bottom of the beaker, spherical micelle-like particles were obtained
on a curved thin ®lm of (I). Inside the spherical particles were found
very thin plate-like crystals of (I) with well developed (001) faces.
O10ÐH10Á Á ÁO12iv
O11ÐH11AÁ Á ÁO4v
O11ÐH11AÁ Á ÁO6v
O11ÐH11BÁ Á ÁO12
O11ÐH11CÁ Á ÁO8iii
O12ÐH12AÁ Á ÁO9vi
O12ÐH12BÁ Á ÁO11
O12ÐH12CÁ Á ÁO12iv
1
2
Symmetry codes: (i)
x; y; z; (v) 12 x; y
x; 12 ‡ y; 1 z; (ii)
x; y 1; 1 z; (iii)
x; y; z; (iv)
1
2
1
2
1
;
z; (vi)
x; 12 ‡ y; z.
H atoms bonded to C atoms were positioned geometrically, with
Ê
CÐH distances of 0.96 (methyl group) and 0.95 A (other H atoms),
and ®xed with Uiso(H) values of 1.2Ueq(C) [Ueq(C) for the methyl
group]. The positions of these H atoms were recalculated after each
set of re®nement cycles, except for the last. About half of the H atoms
bonded to O atoms were located from difference syntheses, and
positional disorder of the water H atoms was observed, suggesting
two possible hydrogen-bond patterns, viz. O11ÐH11BÁ Á ÁO12 and
O11Á Á ÁH12BÐO12. The positions of the remaining hydroxy and
water H atoms were calculated by assuming an intermolecular
Crystal data
3
C22H22O10Á2H2O
Dx = 1.507 Mg m
Mo Kꢂ radiation
Cell parameters from 25
re¯ections
Mr = 482.44
Monoclinic, C2
Ê
a = 12.950 (3) A
ꢃ = 10.0±13.5ꢀ
ꢄ = 0.12 mm
T = 296 K
Ê
b = 8.036 (3) A
1
Ê
c = 20.436 (6) A
ꢁ = 90.14 (2)ꢀ
3
Ê
V = 2126.7 (11) A
Z = 4
Plate, pale yellow
0.40 Â 0.20 Â 0.03 mm
Ê
hydrogen-bond network, with OÐH distances of 0.82 A. The site-
Data collection
occupancy factors of atoms H8A, H8B, H11B, H11C, H12B and
H12C are 50% each. Atom H11C was introduced at one of two
possible positions, assuming sp3 hybridization of atom O11, on the
basis of the positions of atoms H11A and H11B; the other position
Rigaku AFC-7R diffractometer
! scans
Rint = 0.014
ꢃmax = 25.0ꢀ
Absorption correction: by integra-
tion (ABSCOR; Higashi, 1999)
Tmin = 0.980, Tmax = 0.997
2235 measured re¯ections
2017 independent re¯ections
1063 re¯ections with I > 2ꢅ(I)
h = 6 ! 15
k = 0 ! 9
1
Ê
was rejected because of a short contact (1.86 A) to atom H34A(2 x,
l = 24 ! 24
1
2
y
, z). In order to account for the disorder of the hydrogen bond,
3 standard re¯ections
every 150 re¯ections
intensity decay: 0.7%
O8ÐH8AÁ Á ÁO11iii [symmetry code: (iii)
x, y,
z] and
O8Á Á ÁH11CiiiÐO11Ciii, two geometrically possible positions were
calculated, assuming sp3 hybridization of atom O8, on the basis of the
positions of atoms C31 and H8A. The position close to atom H9iii was
rejected; the other position, which was assigned to atom H8B, has no
HÁ Á ÁH short contact, although there is no hydrogen-bond acceptor.
Atoms H1, H5, H7 and H9 were re®ned as riding on their parent O
atoms, with Uiso(H) values of Ueq(O). The positions of atoms H10,
H11A and H12A were re®ned for several cycles and then ®xed to
maintain a reasonable hydrogen-bonding geometry. Restraints were
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.045
wR(F2) = 0.135
S = 1.01
2017 re¯ections
w = 1/[ꢅ2(F2o) + (0.0633P)2
+ 0.191P]
where P = (F2o + 2Fc2)/3
(Á/ꢅ)max = 0.007
3
Ê
Áꢆmax = 0.21 e A
3
Ê
0.29 e A
330 parameters
H-atom parameters constrained
Áꢆmin
=
Ê
applied for the C31Á Á ÁH8A/H8B (1.88 A), H11AÁ Á ÁH11B/H11C
Ê
Ê
(1.31 A) and H12AÁ Á ÁH12B/H12C (1.31 A) distances. Friedel pairs
were merged before the ®nal re®nement, since anomalous scattering
effects were negligible. The absolute structure was assigned on the
basis of the absolute con®guration of d-(+)-glucose.
Table 1
Selected geometric parameters (A, ).
ꢀ
Ê
O1ÐC13
O2ÐC19
O3ÐC17
O3ÐC21
O4ÐC15
O5ÐC25
C13ÐC14
C13ÐC18
1.345 (11)
1.249 (11)
1.372 (8)
1.375 (9)
1.349 (8)
1.381 (9)
1.394 (9)
1.413 (9)
C14ÐC15
C14ÐC29
C15ÐC16
C16ÐC17
C17ÐC18
C18ÐC19
C19ÐC20
C20ÐC21
1.404 (11)
1.518 (9)
1.385 (9)
1.383 (10)
1.377 (12)
1.456 (10)
1.426 (10)
1.337 (13)
Data collection: WinAFC Diffractometer Control Software
(Rigaku, 1999); cell re®nement: WinAFC Diffractometer Control
Software; data reduction: TEXSAN (Molecular Structure Corpora-
tion, 2001); program(s) used to solve structure: SIR92 (Altomare et
al., 1994); program(s) used to re®ne structure: SHELXL97 (Shel-
drick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software
used to prepare material for publication: TEXSAN.
C13ÐC14ÐC29
C15ÐC14ÐC29
118.0 (7)
124.0 (6)
O4ÐC15ÐC14
O4ÐC15ÐC16
114.4 (6)
123.3 (7)
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SX1162). Services for accessing these data are
described at the back of the journal.
O3ÐC21ÐC22ÐC23
O6ÐC29ÐC14ÐC15
8.3 (9)
58.1 (8)
C15ÐC14ÐC29ÐC30
C16ÐC15ÐO4ÐC28
64.5 (9)
0.4 (9)
ꢁ
Acta Cryst. (2004). C60, o893±o896
Ohba, Yoshida and Kondo C22H22O10Á2H2O o895

organic compounds
Komatsu, M., Tomimori, T. & Ito, M. (1967). Chem. Pharm. Bull. 15, 263±269.
Kondo, T., Oyama, K. & Yoshida, K. (2001). Angew. Chem. Int. Ed. 40, 894±
897.
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o896 Ohba, Yoshida and Kondo
C22H22O10Á2H2O
Acta Cryst. (2004). C60, o893±o896