Hydrogen bonds and π-π stacking interaction in 4′, 7-dimethoxylisoflavone and 4′,7-diacetyl-O-isoflavone

Article abstract of DOI:10.1007/s10870-005-5175-z

4′,7-dimethoxylisoflavone, C₁₇H₁₄O₄, (I), is linked into a supramolecular structure by a variety of weak but direction-specific intermolecular forces, the molecules are linked into chains through C-H...O hydrogen bonds, th

Full text of DOI:10.1007/s10870-005-5175-z

Journal of Chemical Crystallography, Vol. 35, No. 11, November 2005 (ꢀC 2005)
DOI: 10.1007/s10870-005-5175-z
ꢀ
Hydrogen bonds and π–π stacking interaction in 4 ,
7
ꢀ
-dimethoxylisoflavone and 4 ,7-diacetyl-O-isoflavone
(1)∗
(1)
(1)
(1)
Zun-Ting Zhang, Xiao-Bing Wang, Qiu-Ya Wang, and Li-Na Wu
Received November 24, 2004; accepted April 12, 2005
ꢁ
4
,7-dimethoxylisoflavone, C17H14O4, (I), is linked into a supramolecular structure by a
variety of weak but direction-specific intermolecular forces, the molecules are linked into
chains through C--- H· · ·O hydrogen bonds, these chains are further linked by face-to-face
(
F-tape) π–π stacking into a one-dimensional bi-chain, another type π–π stacking, edge-
to-face (T-tape), assemble the bi-chain into framework together with C--- H· · ·O hydrogen
ꢁ
bonds. 4 ,7-diacetyl-O-isoflavone, C19H15O6, (II), shows some discrepancies with I and the
molecules are assembled into framework all by C--- H· · ·O hydrogen bonds. The molecules
2
are linked into centrosymmetric dimers built from classic R (8) rings by pairs of C--- H· · ·O
2
2
2
hydrogen bonds, the dimers are linked into (011) sheets by combination of the R (8) ring
and C--- H· · ·O hydrogen bonds, another C--- H· · ·O hydrogen bond assemble the sheets into
three-dimensional network.
KEY WORDS: Daidzein; crystal structure; supramolecule; hydrogen bond; π–π stacking interaction.
Introduction
Hydrogen bonds and aromatic π–π stack-
tribute to the stability of the tertiary structure of
10
protein.
Daidzein, a natural soy isoflavone, holds
1
1
ing interactions, including two basic classes
either face-to-face (F-tape) or edge-to-face
promise in the effects of antidysrhythmic,
antioxidant
12,13
14
and getting rid of hyperkinesias.
1,2
(T-tape) orientation,
are an important re-
Studies have also found daidzein effective in
1
5,16
search area in supramolecular chemistry and
inhibiting cancer cells growth,
accelerat-
3
17
crystal engineering. They play an impor-
ing the formation of bone cells and bal-
18
ꢁ
tant role in self-assembly and recognition of
ancing women’s hormone. Compounds 4 ,
4
ꢁ
aromatic compounds as an auxiliary stabiliz-
7-dimethoxylisoflavone (I) and 4 , 7-diacetyl-O-
5–7
ing short contact. In biomacromolecular sys-
tems the base stacking interactions and hydro-
gen bonds are important for the double-helical
isoflavone (II) are the derivatives of daidzein with
potential medical applications. We report here the
crystal structures of I and II (Scheme 1).
8
DNA structure, they can direct the intercala-
9
tion of drugs into DNA and they also con-
Experimental
Synthesis of the title compound
(
1)
School of Chemistry and Materials Science, Shaanxi Normal
University, Xi’an 710062, PRC.
∗
Daidzein was purchased from the State-
owned Pharmaceutical Company of Wu-Gong.
To whom correspondence should be addressed; e-mail; zhangzt@
snnu.edu.cn.
9
23
1
074-1542/05/1100-0923/0 ꢀC 2005 Springer Science+Business Media, Inc.

9
24
Zhang, Wang, Wang, and Wu
Scheme 1.
Other chemicals were of analytical reagent grade
and were used directly without further purifica-
tion. The infrared spectra were recorded as KBr
pellets on a Nicolet 170SX FT-IR spectropho-
tometer. The H NMR Spectra were recorded on
a Bruker Am-300 spectrometer with TMS as in-
appear. The precipitate was filtered and recrystal-
lized from ethanol, the product has melting point
of 468 K. Crystals of II suitable for X-ray anal-
ysis were obtained from slow evaporation from
ethanol after two days at room temperature. IR
(KBr) υ: 1750, 1644, 1615, 1440, 1369, 1326,
1
−
1 1
ternal reference and DMSO-d as solvent. The
1184, 1129, 959, 883 cm . H NMR(DMSO-d ,
6
6
crystal structures were determined using Siemens
P4 and Bruker Smart-1000 CCD Diffractometer
instruments.
300 MHz): 8.13 (1H, S, H---C ), 7.73 (1H, d, J =
2
8.8 Hz, H---C ), 7.17 (2H, d, J = 8.4 Hz, H---C
ꢁ
,
5
2
H---C
ꢁ
), 7.13 (1H, d, J = 2.3 Hz, H---C ), 6.87
6
8
For the preparation of I, daidzein (0.2 g) was
dissolved into acetone (50 ml) and a little an-
hydrous Na CO . Dimethyl sulfate (0.5 ml) was
(1H, dd, J = 8.8 Hz, J = 2.2 Hz, H---C ), 6.74
6
(2H, d, J = 8.4 Hz, H---C
ꢁ
, H---C
ꢁ
), 2.04(6H, s,
3
5
H---CH ).
2
3
3
added dropwise to the solution with vigorous stir-
ring. The mixture was stirred for 2.5 h at room
temperature and colorless precipitation began to
appear. The precipitate was filtered and washed
with water until the pH of the filtrate was 8. After
recrystallization from ethyl acetate, the product
has melting point of 431 K. Crystals of I suitable
for X-ray analysis were obtained from slow evap-
oration from ethyl acetate after three days at room
temperature. IR (KBr) υ: 2971, 2833, 1628, 1597,
X-ray crystal structure determination
The sample of I and II selected for
investigation had dimensions of 0.58 mm ×
0.56 mm × 0.48 mm and 0.37 mm × 0.29 mm ×
0.21 mm, respectively. The data were collected
with graphite monochromated Mo Kα radiation
˚
(λ = 0.71073 A). The structures were solved
1
8
508, 1436, 1293, 1248, 1204, 1118, 1029, 878,
using direct methods with SHELXTL software
−
1
−1
20
06, 542 cm . The peaks at 1628 cm belong
package and refined by full-matrix least-squares
19
to the ---C -- -- -- O vibration of the group of I and
the disappear of the peak at about 3450 cm
techniques. The non-hydrogen atoms were as-
signed anisotropic displacement parameters in the
refinement. The hydrogen atoms were treated us-
ing a riding model. The structures were refined on
−
1
means the hydroxyl groups were substituted by
the methoxyl groups.
For the preparation of II, daidzein (0.3 g)
was dissolved into anhydrous pyridine (20 ml).
Acetic anhydride (0.3 ml) was added dropwise
to the solution. The mixture was left to sit for
2
21
F using SHELX-97. The final R values (on F)
were 0.0356 of I and 0.0476 of II.
The crystal and refinement data are listed
in Table 1. Selected bond lengths, bond angles
and torsion angles are given in Tables 2 and 3,
respectively.
4
h at room temperature then poured the mix-
ture into water and white precipitation began to

Hydrogen bonds and π–π stacking interaction
925
Table 1. Crystal Data and Structure Refinement for I and II
Crystal data Compound I Compound II
Empirical formula
C17H14O4
C19H16O6
CCDC deposit no.
Formula weight
Temperature (K)
CCDC-222301
282.28
298(2)
CCDC-254156
338.30
298(2)
˚
Wavelength (A)
0.71073
0.71073
Crystal system
Space group
Monoclinic
P 2(1)/c
Triclinic
P1
¯
Unit cell dimensions
˚
a (A)
11.116(2)
8.4625(5)
15.070(2)
90.00
109.34(2)
90.00
1343.6(3)
4
1.395
7.207(10)
7.571(10)
14.458(19)
95.244(19)
93.69(2)
97.07(2)
777.3(18)
2
˚
b (A)
˚
c (A)
◦
α ( )
◦
β ( )
◦
γ ( )
˚
3
Volume (A )
Z
Density (calculated, Mg m 3)
Absorption coefficient (mm 1)
−
−
1.445
0.109
0.100
F(000)
592
352
◦
θ range for data collection ( )
Limiting indices
1.00–27.00
0 ≤ h ≤ 14
2.725–24.691
−8 ≤ h ≤ 4
−9 ≤ k ≤ 9
−17 ≤ l ≤ 16
2741
0
≤ k ≤ 10
−
19 ≤ l ≤ 18
Reflections collected
Independent reflections
Absorption correction
Transmission factors
Data/restraints/parameters
Final R indices [I > 2σ(I)]
R indices (all data)
2932
1933
None
None
1933/0/193
R1 = 0.0356, wR2 = 0.0879
R1 = 0.0581, wR2 = 0.0935
0.185 and −0.143
1433
Empirical
0.963 and 0.977
1433/0/275
R1 = 0.0476, wR2 = 0.0935
R1 = 0.1040, wR2 = 0.1122
0.233 and −0.174
Largest diff. peak and hole (eA 3)
−
◦
Results and discussion
C17---O4---C13---C12 = 177.5 . In the crystal
structure of II, the acetyl groups at C3 and C13 are
not coplanar with their attached rings, A and B,
shown by the torsion angles C16---O3---C3---C4=
In each of I and II (Figs. 1 and 2), the
atoms of benzopyranone moiety, containing rings
A (C1---C6) and C (O1/C1/C6---C9), display an
◦
◦
65.6 and C18---O4---C13---C14 = 77.9 .
almost coplanar configuration with a mean devi-
Viewed from Fig. 3, a bi-chain viewing
downing b-axis is formed through face-to-face (F-
tape) π–π stacking and hydrogen bonds. A chain
is formed via hydrogen bond C17---H17B· · ·O3
with a distance being 2.607 A˚ and bond angle
˚
ation to their least-squares planes being 0.0265 A
˚
of I and 0.0302 A of II. To avoid steric con-
flicts, the two rigid ring systems, phenyl rings
B (C10---C15) and benzopyranone moieties are
◦
◦
◦
rotated by 24.4 of I and 44.0 of II with re-
spect to one another, respectively. In the crys-
tal structure of I, the methoxyl groups at C3
and C13 are nearly coplanar with its attached
rings, ring A and ring B, indicative of the tor-
of 142.2 . The molecules are translated into a
[1 0 1] chain via these hydrogen bonds. The chain
is assembled into a bi-chain through F-tape π–π
stacking interaction. Methoxyl oxygen atom O4,
which is nearly coplanar with ring B as indi-
cated by the mean deviation being 0.011 A˚ from
◦
sion angles C16---O3---C3---C4 = 176.3 and

9
26
Zhang, Wang, Wang, and Wu
Table 2. Selected Bond Lengths, Bond Angles,
Table 3. Selected Bond Lengths, Bond Angles
˚
◦
˚
◦
and Torsion Angles for I (A, )
and Torsion Angles for II (A, )
˚
˚
Bond lengths (A)
Bond lengths (A)
O1 ---- C9
O1 ---- C1
O2 ---- C7
O3 ---- C3
O3 ---- C16
O4 ---- C13
O4 ---- C17
C1 ---- C6
C6 ---- C7
C7 ---- C8
1.3526(16)
1.3710(15)
1.2330(15)
1.3564(16)
1.4322(16)
1.3689(16)
1.4219(18)
1.3845(18)
1.4588(18)
1.4703(18)
O1 ---- C9
O1 ---- C1
O2 ---- C7
O3 ---- C16
O3 ---- C3
O5 ---- C16
O4 ---- C18
O4 ---- C13
O6 ---- C18
C9 ---- C8
C8 ---- C7
C8 ---- C10
C7 ---- C6
C6 ---- C1
C4 ---- C3
C3 ---- C2
C16 ---- O3 ---- C3
O6 ---- C18 ---- C19
Bond angles ( )
O4 ---- C18 ---- C19
C9 ---- C8 ---- C7
C9 ---- C8 ---- C10
C7 ---- C8 ---- C10
C2 ---- C3 ---- C4
1.357(3)
1.367(3)
1.222(3)
1.358(3)
1.415(3)
1.192(3)
1.354(4)
1.409(3)
1.188(3)
1.333(4)
1.458(4)
1.482(4)
1.472(4)
1.381(4)
1.380(4)
1.357(4)
◦
Bond angles ( )
C8 ---- C9
C8 ---- C10
1.3467(18)
1.4895(19)
−4.8(2)
C16 ---- O3 ---- C3 ---- C2
C16 ---- O3 ---- C3 ---- C4
O1 ---- C1 ---- C6 ---- C5
C2 ---- C1 ---- C6 ---- C5
O1 ---- C1 ---- C6 ---- C7
C2 ---- C1 ---- C6 ---- C7
C9 ---- C8 ---- C10 ---- C15
C7 ---- C8 ---- C10 ---- C15
176.32(12)
−176.97(12)
2.10(19)
116.7(2)
125.9(3)
2.64(19)
◦
−178.29(12)
−151.59(13)
28.5(2)
111.8(3)
119.1(3)
119.7(3)
121.2(3)
122.7(3)
116.6(3)
120.7(3)
118.0(3)
122.2(3)
119.7(3)
121.5(3)
118.9(3)
119.4(3)
122.8(3)
126.5(3)
122.3(3)
110.7(3)
118.7(2)
◦
Torsion angles ( )
C9 ---- C8 ---- C10 ---- C11
C7 ---- C8 ---- C10 ---- C11
C17 ---- O4 ---- C13 ---- C14
C17 ---- O4 ---- C13 ---- C12
O3 ---- C3 ---- C2
O3 ---- C3 ---- C4
C2 ---- C3 ---- C4
O4 ---- C13 ---- C14
O4 ---- C13 ---- C12
27.21(19)
−152.68(12)
−1.9(2)
C2 ---- C3 ---- O3
C4 ---- C3 ---- O3
177.51(12)
125.30(13)
114.44(12)
120.26(13)
125.11(13)
115.75(12)
119.14(13)
C15 ---- C10 ---- C11
C15 ---- C10 ---- C8
C11 ---- C10 ---- C8
C12 ---- C13 ---- C14
C12 ---- C13 ---- O4
C14 ---- C13 ---- O4
O5 ---- C16 ---- O3
O5 ---- C16 ---- C17
O6 ---- C18 ---- O4
O3 ---- C16 ---- C17
C18 ---- O4 ---- C13
C14 ---- C13 ---- C12
the O4/C10---C15 least-squares plane, conjugated
with ring B with a lone pair to form a π system.
The systems stack with each other with the inter-
planar distance of 3.655 A and the intercentroid
◦
Torsion angles ( )
8
7
C13 ---- O4 ---- C18 ---- C19
C13 ---- O4 ---- C18 ---- O6
C16 ---- O3 ---- C3 ---- C2
C16 ---- O3 ---- C3 ---- C4
C5 ---- C6 ---- C1 ---- O1
C7 C6 C1 O1
−173.2(2)
7.6(4)
˚
−117.8(3)
65.6(3)
˚
distance of 3.904 A, the displacement of the two
−177.1(3)
3.2(4)
˚
rings is 1.371 A. The other part, including ring A,
---- ---- ----
C5
---- C6 ---- C1 ---- C2
4.1(4)
ring C, and O3 of methoxyl group at C3, forms a
1
3
C7 ---- C6 ---- C1 ---- C2
C9 ---- C8 ---- C10 ---- C15
C7 ---- C8 ---- C10 ---- C15
−175.5(3)
137.8(3)
−41.5(4)
−40.9(4)
139.8(3)
−106.9(3)
77.9(3)
π
system and the system is coplanar indicated
˚
1
1
by the mean deviation being 0.027 A from the
O3/O1/C1---C9 least-squares plane. The systems
C9
---- C8 ---- C10 ---- C11
C7 ---- C8 ---- C10 ---- C11
C18 ---- O4 ---- C13 ---- C12
---- ----
C18 O4 C13 C14
stack with each other with the interplanar dis-
˚
tance of 3.408 A and the intercentroid distance
----
----
˚
---- ----
of 3.886 A, the displacement of the two rings
C3 O3 C16 O5
--- O3 ---- C16 ---- C17
2.5(4)
−178.9(2)
C3
-
˚
is 1.867 A. A larger superimposition is favored
between the two enlarged π systems.2

Hydrogen bonds and π–π stacking interaction
927
Fig. 2. Molecular structure and atomic numbering for II.
Displacement ellipsoids are plotted at the 30% probability
level.
Fig. 1. Molecular structure and atomic numbering for I. Dis-
placement ellipsoids are plotted at the 30% probability level.
Furthermore, each ring B is almost perpen-
π–π stacking interactions.1,2 These two kinds
of aromatic T-tape π–π staking interaction are
like a thread and link the bi-chain into a three-
dimensional structure. Otherwise, two kinds of
hydrogen bonds, which form a tri-centric hydro-
gen bonding, are another kind of short contact
in forming the three-dimensional network. The
carbonyl oxygen atom O2, acts as a donor, via
H11 and H16A, to C11 and C16 from the ad-
jacent molecule, respectively. Details of the hy-
drogen bonds see Table 4. The most interesting
thing is that the F-tape and T-tape π–π stack-
ing interactions existed together in I harmony and
dicular with each benzopyranone moiety with a
◦
dihedral angle of 86.8(9) and this configuration
favor the formation of the other kind of aromatic
stacking interactions, T-tape π–π stacking, in the
cell of I(Fig. 4). The distance from H9 to CgC,
˚
the centroid of ring B, is 2.861 A and the distance
˚
from C9 to CgC is 3.492 A. Secondly, ring B inter-
acts with ring C with a distance between H14 and
˚
CgA, the centroid of ring C, being 3.117 A and
˚
distance from C14 to CgA of 3.986 A. Though
the later is somewhat weaker than the former,
they are all in the normal range of the T-tape
Fig. 3. Part of the crystal structure of I, showing the formation of the bi-chain via hydrogen
∗
bonds and the π–π stacking interactions. Atom marked with an asterisk ( ) is at the symmetry
positions (1 + x, y, 1 + z). For clarity, some H atoms are omitted.

9
28
Zhang, Wang, Wang, and Wu
Fig. 4. Part of the crystal structure of I, showing the T-tape aromatic π–π stacking inter-
∗
actions and hydrogen bonds. Atoms marked with an asterisk ( ) and ampersand (&) are at
the symmetry positions (1 − x, −0.5 + y, 1.5 − z) and (x, 1.5 − y, z − 0.5). Cgs are the
centroids of the rings B and C. For clarity, some H atoms are omitted.
they are the notable short contacts in assembling
supramolecular structure of I.
acts as hydrogen-bond acceptor, via atom H19B,
to atom C19. The dimers are linked into a (0 1 1)
sheets via C2---H2· · ·O2 hydrogen bonds. Car-
Figure 5 shows the formation of II. A classic
R (8) ring is formed via paired C19---H19B· · ·O4
2
2
bonyl oxygen atom O2 at (x, 1 + y, z) acts as
hydrogen-bond acceptor, via atom H2, to atom
C2. The sheets are linked into the framework by
C9---H9· · ·O5 hydrogen bonds. Carbonyl oxygen
hydrogen bonds at the inversion position, a cen-
trosymmetric dimer is formed by this way, of
which oxygen atom O4 at (1 − x, −2 − y, −z)
˚
◦
Table 4. Hydrogen-Bonding Geometry of I and II (A, )
D--- H
H· · ·A D· · ·A
D--- H· · ·A Symmetry code
D--- H· · ·A
I
C11--- H11· · ·O2
C16--- H16A· · ·O2
C17--- H17B· · ·O3
0.93
0.96
0.96
2.62
2.51
2.61
3.326 (6)
3.444 (2)
3.416 (2)
133.1
164.2
142.2
1 − x, y − 0.5, 1.5 − z
x, 1.5− y, z − 0.5
1 + x, y, 1 + z
II
C2--- H2· · ·O2
C9--- H9· · ·O5
C19--- H19B· · ·O4
0.96
0.99
0.96
2.24
2.58
2.59
3.175 (6)
3.432 (6)
3.399 (6)
165.8
144.0
142.2
x, 1 + y, z
1 − x, 2 − y, 1 − z
1 − x, −y, −z

Hydrogen bonds and π–π stacking interaction
929
∗
Fig. 5. Part of the crystal structure of II, showing the hydrogen bonds. Atoms marked with an asterisk ( ), hash (#), and
ampersand (&) are at the symmetry positions (x, −1 − y, z), (1 − x, −y, 1 − z) and (1 − x, −2 − y, −z), respectively.
For clarity, some H atoms are omitted.
atom O5 at (1 − x, −y, 1 − z) acted as hydrogen-
bond acceptor, via atom H9, to atom C9. Details
of the hydrogen bonds see Table 4. Combina-
tion of these hydrogen bonds generates the three-
dimensional network of II.
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