Derivatives of benzo[b]furan. Part I. Conformational studies of khellinone and visnaginone

Article abstract of DOI:10.1007/s11224-012-9959-4

The structural analysis of khellinone and visnaginone indicated the planarity of the benzo[b]furan ring system. The oxygen or carbon atoms of the substituents, -OH, -OCH₃, and -C(=O)CH₃, are nearly coplanar with the aromatic ring. The molecular conformation is stabilized by the intramolecular O-H..O hydrogen bond formed between the ortho-substituted hydroxyl and acetyl groups. The intermolecular contacts present in the crystal structure are the C-H..O and C-H..π interactions and the π..π stacking. The energy surface for the internal rotation about the C_sp2-O/C bonds in the khellinone and visnaginone molecules has been explored by quantum-chemical calculations. The density functional theory (DFT) methods yielded three stable conformers of khellinone and two of visnaginone obtained by a rotation of the methoxy group about the C4_sp2-OCH₃ bond. The most stable conformation in the gas phase is consistent with the stereochemistry of the molecules adopted in the solid. The secondary minima conformers have energies higher by 0.3-1.8 kcal/mol. The energy of the intramolecular O-H..O interactions, present in the molecular structure of all stable conformers, is around 18 kcal/mol at the DFT level. A complete and reliable assignment of the bands in the IR and Raman spectra of both compounds has been performed.

Full text of DOI:10.1007/s11224-012-9959-4

Struct Chem (2012) 23:1573–1584
DOI 10.1007/s11224-012-9959-4
ORIGINAL RESEARCH
Derivatives of benzo[b]furan. Part I. Conformational studies
of khellinone and visnaginone
•
Tomas Pena Ruiz Aleksandra Drzewiecka
•
•
Anna E. Koziol Manuel Fernandez Gomez
•
•
Kinga Ostrowska Marta Struga Jerzy Kossakowski
•
Received: 16 November 2011 / Accepted: 24 January 2012 / Published online: 24 February 2012
Ó The Author(s) 2012. This article is published with open access at Springerlink.com
Abstract The structural analysis of khellinone and visn-
aginone indicated the planarity of the benzo[b]furan ring
system. The oxygen or carbon atoms of the substituents,
–OH, –OCH3, and –C(=O)CH3, are nearly coplanar with
the aromatic ring. The molecular conformation is stabilized
by the intramolecular O–HÁÁÁO hydrogen bond formed
between the ortho-substituted hydroxyl and acetyl groups.
The intermolecular contacts present in the crystal structure
are the C–HÁÁÁO and C–HÁÁÁp interactions and the pÁÁÁ p
stacking. The energy surface for the internal rotation about
the Csp2–O/C bonds in the khellinone and visnaginone
molecules has been explored by quantum-chemical calcu-
lations. The density functional theory (DFT) methods
yielded three stable conformers of khellinone and two of
visnaginone obtained by a rotation of the methoxy group
about the C4sp2–OCH3 bond. The most stable conformation
in the gas phase is consistent with the stereochemistry of the
molecules adopted in the solid. The secondary minima
conformers have energies higher by 0.3–1.8 kcal/mol. The
energy of the intramolecular O–HÁÁÁO interactions, present
in the molecular structure of all stable conformers, is around
18 kcal/mol at the DFT level. A complete and reliable
assignment of the bands in the IR and Raman spectra of
both compounds has been performed.
Keywords Khellinone Á Visnaginone Á Benzo[b]furan Á
Conformational analysis Á Molecular structure Á DFT
calculation Á Crystal structure
Electronic supplementary material The online version of this
article (doi:10.1007/s11224-012-9959-4) contains supplementary
material, which is available to authorized users.
Introduction
T. Pena Ruiz Á M. Fernandez Gomez
The benzo[b]furan system, as an important pharmacophore,
is present in numerous compounds which can be isolated
from the natural sources, and is an essential fragment of
newly synthesized pharmaceuticals (e.g., amiodarone [1]
and bergapten [2]). These heterocyclic compounds show a
variety of pharmacological properties and a change of their
structure is useful in the search of new therapeutic agents
[3, 4].
Department of Physical and Analytical Chemistry,
University of Jaen, 23071 Jaen, Spain
A. Drzewiecka Á A. E. Koziol (&)
Faculty of Chemistry, Maria Curie-Sklodowska University,
23-031 Lublin, Poland
e-mail: anna.koziol@poczta.umcs.lublin.pl
A. Drzewiecka
Institute of Physics, Polish Academy of Sciences,
02-668 Warsaw, Poland
Two benzofuran derivatives, khellinone (1: 5-acetyl-4,7-
dimethoxy-6-hydroxy-benzo[b]furan) and visnaginone (2:
5-acetyl-4-methoxy-6-hydroxybenzo[b]furan) (Fig. 1), are
the product of the hydrolysis of khellin and visnagin,
respectively. Both khellin and visnagin are the chemical
constituents of Ammi visnaga Lam. (Apiaceae) fruits [5],
and their applications in pharmacology and biomedicine
have been known for long. Ammi visnaga (toothpick
K. Ostrowska
Department of Organic Chemistry, Faculty of Pharmacy,
Medical University of Warsaw, 02-097 Warsaw, Poland
K. Ostrowska Á M. Struga Á J. Kossakowski
Department of Medicinal Chemistry, Faculty of Medicine I,
Medical University of Warsaw, 02-007 Warsaw, Poland
123

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Struct Chem (2012) 23:1573–1584
Experimental
CH3
CH3
O
4
Synthesis of visnaginone and khellinone
3
O
H
5
The chemicals were purchased from Sigma-Aldrich and
used without further purification. Khellinone 1 and visn-
aginone 2 were obtained by the method of Spaeth and
Gruber [30, 31], i.e., by the ring-opening reactions of
khellin and visnagin in the alkaline solution. Single crystals
of 1 and 2 suitable for an X-ray diffraction were prepared
by a slow evaporation of the solvent from an ethanolic
solution at room temperature.
2
6
O
O
7
R
R = OCH3
R = H
khellinone
visnaginone
1
2
Fig. 1 Molecular formula of khellinone and visnaginone
ammi), possessing the Arabic name khella and the Spanish
name visnaga, has been used in the folk medicine
throughout the Mediterranean countries in treating various
ailments of the urinary (kidney stones) and respiratory tract
(asthma) [6].
Table 1 Crystal data and experimental parameters for 1 and 2
The synthetic derivatives of khellinone and visnaginone
show antibacterial and antimicrobial activities [7–13],
exhibit also antiarrhythmic, antiatherosclerotic, and/or
cardiovascular properties [14–18], insect antifeedant
activity [19], and others. Recently, it has been proved that
khellinone, visnaginone, and their derivatives are able to
block the Kv1.3 potassium channel with a different kind
and degree of selectivity [20–26]. The Kv1.3 ion channel
is involved in the pathogenesis of autoimmune diseases
such as multiple sclerosis. The structure–activity rela-
tionship (SAR) and Quantitative SAR (QSAR) studies
on the series of khellinone and visnaginone derivatives
revealed that higher hydrophobicity improves their
blocking activity.
Compounds
1
2
Molecular formula
Crystal system
Space group
C12H12O5
Triclinic
P¯ı
C11H10O4
Monoclinic
P21/n
˚
a (A)
7.322(1)
8.580(1)
9.859(1)
70.57(1)
78.94(1)
72.72(1)
554.8(1)
2
7.906(2)
7.337(1)
17.060(3)
90
˚
b (A)
˚
c (A)
a (°)
b (°)
c (°)
102.55(3)
90
3
˚
V (A )
965.9(3)
4
Z
d (g cm-3
Absorption coefficient
(mm-1
F(000)
)
1.414
1.418
Although the synthesis of khellinone 1 and visnaginone
2 is known for long, their molecular structures have not yet
been characterized. Up to date, vibrational spectroscopic
studies for khellinone and its derivatives are very scarce.
Musante et al. [27] reported the infrared spectra of visn-
aginone and its derivatives, but without any comprehensive
analysis, while Epstein et al. [28] gave a primary descrip-
tion of the infrared spectrum of khellinone in the region
1,180–1,020 cm-1. The vibrational spectra of benzofuran
itself were fully interpreted by Singh [29].
0.940
0.916
)
248
432
Crystal size (mm)
0.38 9 0.15 9 0.12 0.40 9 0.19 9 0.11
h range for data
collection (°)
Index ranges
4.78–75.06
5.31–75.13
0 B h B 9
-10 B k B 10
-12 B l B 12
2397
-9 B h B 9
0 B k B 9
-21 B l B 0
2027
Reflections collected
The main goal of this study is to explain how the
molecular conformations depend on the methoxy substit-
uents, and whether different conformers can be distin-
guished by the vibrational analysis. To compare the
molecular structure of the title compounds in the solid state
and gas phase, an X-ray crystal structure analysis and DFT/
B3LYP/B1B95 theoretical calculations were performed.
Afterwards, the IR and Raman spectra were also recorded,
and a reliable interpretation of the spectroscopic data has
been performed by a comparison with theoretical data and
scaling of the force fields.
Independent reflections 2211
1965
Number of parameters
Goodness-of-fit on F2
R1 [I [ 2r(I)]
157
139
1.043
1.046
0.0627
0.0374
wR2 [I [ 2r(I)]
Largest diff. peak and
0.1808
0.1107
0.30 and -0.27
0.22 and -0.18
-3
˚
hole (e A
CCDC Noa
a
)
849 114
849 115
Copies of the data can be obtained free of charge on application
to The Director, CCDC, 12 Union Road, Cambridge CB2 1EZ, UK
(http://www.ccdc.cam.ac.uk)
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Struct Chem (2012) 23:1573–1584
1575
1 (1a in gas phase)
2 (2a in gas phase)
Fig. 2 Molecular structure with atom-numbering scheme of khellinone (1) and visnaginone (2). View perpendicular and parallel to
benzo[b]furan system
Table 2 Selected geometric parameters of molecules 1 and 2 observed in solid state
1
2
Torsion angles (°)
C6–C5–C9–O3 (acetyl group)
-5.3(4)
-4.0(2)
C11–O5–C7–C6 (methoxy group) t1
C8–O4–C4–C3A (methoxy group) t2
Interplanar angles (°)
83.4(3)
–
-16.4(4)
-16.0(3)
Benzofuran ring/acetyl group [C5–C9(=O3)–C10]
Benzofuran ring/methoxy group (C4–O4–C8)
Benzofuran ring/methoxy group (C7–O5–C11)
6.6(1)
15.3(2)
82.0(3)
4.8(1)
15.7(2)
–
˚
d(D–H) (A)
˚
˚
Intramolecular hydrogen-bond
D–HÁÁÁA
d(HÁÁÁA) (A)
d(DÁÁÁA) (A)
\D–HÁÁÁA (°)
1
2
O2–H2ÁÁÁO3
1.02
1.07
1.46
1.48
2.463(3)
2.464(2)
165
149
X-ray crystallography
displacement parameters. All carbon-bonded H-atoms were
positioned geometrically and allowed to ride on the
attached atom. The coordinates of the hydroxyl group
H-atoms were found in the difference electron density
maps and they were riding during the refinement with the
fixed O–H distance. The isotropic displacement parameters
of the H-atoms were Uiso(H) = 1.3 Ueq(C) for the methyl
groups and Uiso(H) = 1.2 Ueq(C/O) for the rest of atoms.
The diffraction data were collected on an Oxford KM4
diffractometer with the Cu Ka radiation at room tempera-
ture. The structure was solved by direct methods using the
SHELXS-97 program and refined by the full-matrix least-
squares method on F2 using the SHELXL-97 program [32].
The non-hydrogen atoms were refined with anisotropic
123

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Struct Chem (2012) 23:1573–1584
Table 3 Geometry of intermolecular contacts in crystal of 1 and 2
˚
d(D–H) (A)
˚
˚
D–HÁÁÁA
d(HÁÁÁA) (A)
d(DÁÁÁA) (A)
\D–HÁÁÁA (°)
Symmetry code for A
1
C2–H4ÁÁÁO1
C10–H102ÁÁÁO5
C8–H83ÁÁÁO2
C3–H3ÁÁÁO2
2
0.93
0.96
0.96
0.93
2.84
2.68
2.77
2.49
3.205(3)
3.613(4)
3.378(3)
3.409(3)
105
166
122
172
-x, 1 - y, 2 - z
-x, 1 - y, 1 - z
x, 1 ? y, z
x, 1 ? y, z
C8–H8AÁÁÁO2
C3–H3ÁÁÁO2
C2–H2ÁÁÁO3
C7–H7ÁÁÁO1
C10–H10CÁÁÁCg
0.96
0.93
0.93
0.93
0.96
2.67
2.71
2.56
2.69
2.88
3.227(2)
3.640(3)
3.426(2)
3.606(2)
3.574(3)
117
175
155
171
141
-1/2 ? x, 1/2 - y, -1/2 ? z
-1/2 ? x, 1/2 - y, -1/2 ? z
1/2 ? x, 1/2 - y, -1/2 ? z
2 - x, -y, 1 - z
1 - x, 1 - y, 1 - z
Cg centre of gravity of the benzene ring
Fig. 3 Centrosymmetric tetramer and dimer of molecules present in crystal of 1. The C–HÁÁÁO interactions linking the molecules are shown by
broken lines
The crystallographic data and details of the data collection
and refinement are given in Table 1.
The gas-phase IR spectra were recorded with a gas
cell Specac 5650 (KBr windows). The solid samples
were melted and evaporated at ca 10 mmHg. The best
spectra were obtained at ca 205 and 190 °C for 1 and 2,
respectively. The liquid phase spectrum for 1 was
recorded in the CCl4 solution (Fluka 99.8%, iden.
HPLC). For this measurement a liquid cell Buck Scien-
tific (CsI windows with spacers of 0.1 and 0.2 mm) was
used. The solid phase spectra for 1 and 2 were
recorded in the KBr (Sigma-Aldrich ?99% iden. IR)
matrix.
Vibrational data
The IR and Raman spectra were recorded at the resolution
of 1 cm-1 on a Bruker FTIR Vector 22 equipped with a
DTGS detector, and a Bruker FT-Raman RFS 100/S with a
Nd:YAG laser emitting at 1,064 nm (laser power 500 mW)
and a liquid N2-cooled Ge detector. The spectra were
managed by using the OPUS 2.2 package [33, 34].
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Struct Chem (2012) 23:1573–1584
1577
Fig. 4 Layer viewed down the b-axis in crystal of 2. The C–HÁÁÁO interactions linking the molecules are shown by broken lines
Computational details
The Gaussian 03 package [35] was used for all the theo-
retical calculations. The density functional theory (DFT)
functionals B3LYP and B1B95 [36–38] as well as the
ab-initio MP2 [39] approximation were the initial selected
methods to run the simulations. The choice of those theo-
retical methods was based on the analysis of Riley et al.
[40] who evaluated an assortment of density functionals on
the calculation of bond distances, bond angles, and
hydrogen bond energies. As a result, B1B95 was placed in
the first position of the ranking (or second depending on the
basis set) and B3LYP was classified as the sixth one (or the
fifth). MP2 has been used for comparative purposes.
Further tests on the performance of these methods were
conducted to reproduce the solid-state molecular confor-
Fig. 5 Calculated energy curve of 1 for the rotation of the methoxy
group around the C7–O5 bond
mation and the vibrational spectrum. The 6-31G(d),
6-31?G(d), 6-31?G(d,p), and 6-311??G(d,p) basis sets
were implemented (Supplementary material).
The potential energy surface (PES) for the rotation of
the methoxy groups in 1 and 2 was simulated with both
DFT functionals and the MP2 approach along with the
6-31G(d) basis set [41–43].
scheme [45, 46] using natural coordinates and MOLVIB
[47, 48] code.
Finally, the intramolecular –O–HÁÁÁO hydrogen bond
was characterized by NBO methodology [49] and the
barrier to rotation of the acetyl group. The latter parameter
was estimated with both B3LYP/6-31G(d) and B3LYP/
aug-cc-pVDZ//B3LYP/6-31G(d) approximations and cor-
rected for the Basis Set Superposition Error (BSSE) [50]
with Boys and Bernardi’s counterpoise approach (Supple-
mentary material).
The Polarizable Continuum Model within the Integral
Equation Formalism Model (IEFPCM) [44] was used to
simulate the most stable minima in aqueous solution.
In order to perform an adequate vibrational analysis the
B3LYP/6-31G(d) force field was scaled according to
Pulay’s Scaled Quantum Mechanics Force Field (SQMFF)
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Struct Chem (2012) 23:1573–1584
Table 4 Torsion angles (°), t1
(C11–O5–C7–C6) and t2
(C8–O4–C4–C3A), and relative
energy (kcal/mol) for
Molecule
1
2
Conformer
1a
1b (trans)
1c (cis)
2a
2b
conformers of 1 and 2 in gas
phase calculated with different
methods
Method: B3LYP/6-31G(d)
t1
70.1
68.4
-73.1
0.34
68.1
72.4
0.42
–
–
t2
-0.9
0.0
0.0
71.0
Relative energy
0.0
1.36
Method: B1B95/6-31G(d)
t1
71.4
-0.5
0.0
70.0
-73.6
0.75
69.8
72.8
0.82
–
–
t2
0.0
0.0
71.7
Relative energy
1.78
Method: MP2/6-31G(d)
t1
70.0
-77.5
0.0
-70.2
-80.0
0.07
–
–
t2
79.0
0.0
Relative energy
Results and discussion
The structure of 1 is stabilized by the intermolecular
C–HÁÁÁO hydrogen bonds (Table 3). The C2–H4ÁÁÁO1
interactions link the molecules into the ring R22(6) and the
‘‘chelating’’ hydrogen bonds (C3–H;C8–H)ÁÁÁO2 connect
molecules to form a centrosymmetric tetramer (Fig. 3).
The main pattern in the crystal of 2 is a folded layer
(Fig. 4; Table 3) stabilized by the intermolecular C–HÁÁÁO
Molecular structure in solid
The bond lengths and angles of both molecules are within
the expected ranges and are equal within the experimental
error. The benzo[b]furan unit is almost planar; the maximal
deviations from the best-plane are observed for the C6
˚
atom [0.012(2) and 0.025(2) A for 1 and 2, respectively].
The hydroxyl group of 1 and 2 is in the ortho position to
the acetyl group (Fig. 2) and this substitution promotes
formation of the stable intramolecular O–HÁÁÁO hydrogen
bond with the S(6) motif [51, 52] (Table 2). The dihedral
angle between the plane of the acetyl group and the plane
of the benzo[b]furan atoms is 6.6(1)° and 4.8(1)° for 1 and
2, respectively.
The molecule 2 contains one methoxy group connected
with the benzo[b]furan ring system, whereas the molecule
of its derivative 1 has two –OCH3 groups in the para
position. One of these methoxy groups (at C4) is nearly
coplanar with the ring; the torsion angle C8–O4–C4–C3A
is -16.4(4)° and -16.0(3)° for 1 and 2, respectively. For
the methoxy group at C7, the torsion angle C11–O5–C7–
C6 is 83.4(3)° (Table 2). This almost perpendicular ori-
entation of the second –OCH3 substituent is in good
agreement with molecular conformation observed for
similar benzo[b]furan derivatives [21, 53].
Crystal structure
Since the hydroxyl group of both molecules forms a strong
intramolecular O–HÁÁÁO hydrogen bond, other types of
weak and less directional forces, such as C–HÁÁÁO and
C–HÁÁÁp interactions, play an important role in generating
the supramolecular architecture [54–57].
Fig. 6 Energy surface of the methoxy group rotated around the
O4–C4 bond for 1 and 2
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Struct Chem (2012) 23:1573–1584
1579
Fig. 7 Structure of the stable
conformers 1b (trans) and 1c
(cis) of molecule 1 optimized at
the B3LYP/6-31G(d) level of
theory
hydrogen bonds. These layers interact by the C10–HÁÁÁ p
contacts.
stable conformers, with the trans and the cis orientations of
the –OCH3 substituents (Table 4).
The introduction of the second methoxy group, per-
pendicular to the benzo[b]furan ring system in 1, does not
influence significantly the relative arrangement within the
pairs of parallel molecules observed around the symmetry
centers. In the crystals of 1 and 2, the CÁÁÁp distances
between the parallel molecules (with the partial overlap-
Energy surface for (C4)–OCH3 groups in 1 and 2
The PES for internal rotation about the C4–O4 bond, cal-
culated using the DFT functionals with 6-31G(d) basis set,
yields three minima for both molecules (Fig. 6). In addition
to 1a, khellinone has two new conformers with the trans
(1b) and cis (1c) orientations of the methoxy groups
(Fig. 7; Table 4). These conformers are energetically less
stable than 1a [\0.5 kcal/mol for B3LYP/6-31G(d) and
0.9 kcal/mol for B1B95/6-31G(d)].
˚
ping of the phenyl rings) are about 3.36–3.45 A.
Conformational analysis in gas phase
The benzo[b]furan ring is rigid and the intramolecular
O–HÁÁÁO hydrogen bond stabilizes the orientation of the
acetyl group; the theoretical approximations reveal a sta-
bilization energy of the intramolecular O–HÁÁÁO hydrogen
bond around 18 kcal/mol (Supplementary material
Table 1S; Fig. 1S). Thus, the search for stable conformers
of the compounds 1 and 2 was focused on the rotation of
their –OCH3 groups. The PES for the torsion angles t1
(C11–O5–C7–C6; for 1 only) and t2 (C8–O4–C4–C3A, for
both molecules) was scanned within the isolated molecule
approximation.
A similar pattern of the equivalent torsional surface is
observed for visnaginone (2) (Fig. 6). The methoxy group
of the most energetically favorable conformer 2a is
coplanar to the benzo[b]furan ring system, and this ste-
reochemistry corresponds to that observed in the crystal
(Fig. 2). The secondary minima, being the mirror images,
represent the second conformer 2b described by t2 71°
(Table 4). The energy differences between the stable con-
formers are slightly higher for 2 than for 1. The barriers
to torsion are in the range 1.0–1.5 kcal/mol for both
compounds.
Energy surface for (C7)–OCH3 group in 1
The data obtained using the MP2(full)/6-31G(d) approach
are different from those obtained with the DFT methods.
Moreover, the MP2 method does not predict a coplanarity of
the (C4)–OCH3 group with the benzo[b]furan system
(Table 4).
The rotation about the C7–O5 bond, calculated by the DFT
functionals with the 6-31G(d) basis set, for 1 gives one
stable conformer (1a). The methoxy group at C7 of 1a is
almost perpendicular to the benzo[b]furan fragment (t1
70°) and the second substituent (C4)–OCH3 is coplanar
to the aromatic ring (Fig. 5; Table 4). The calculated
geometry of the molecule in the gas phase, 1a, is in the
agreement with its structure observed in the crystal (Fig. 2;
Table 2). The barriers to torsion are in the range
2.0–2.5 kcal/mol what suggest a significant rigidity for the
position of this group.
The behavior of the (C4)–OCH3 group for 1 and 2
can be compared with the results established by Bzh-
ezovskii et al. [58] for anisol and para-methoxyanisol.
The most stable structure for the latter compounds shows
the methoxy group coplanar to the benzene ring and a
perpendicular conformation occurs as a less stable
geometry. Both 1 and 2 show a similar energetic profile
for the torsion angle t2. For the benzo[b]furan deriva-
tives the secondary minima and the barriers to rotation
are shifted to the lower values of t2, probably due to the
bulky acetyl group in the ortho position. Analogous to
The energy profile for MP2(full)/6-31G(d) yielded dif-
ferent results than DFT/6-31G(d). Both methoxy groups
are nearly perpendicular to the aromatic ring, giving two
123

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Struct Chem (2012) 23:1573–1584
Table 5 Comparison of the experimental and calculated vibrational spectra of khellinone (1) and assignments
Experimental frequencies (cm-1
)
Scaled theoretical
frequencies
Assignmentsa
IR gas IR CCl4 IR solid Raman solid 1a
1b
1c
3,160
3,140
3,161
3,140
3,180
3,159
3,039
3,028
3,170
3,144
3,044
3,033
3,031
3,028
3,015
3,170
3,144
3,043
3,033
3,031
3,028
3,015
C(furan)–H sym str.
C(furan)–H asym str.
C(CH3)–H asym str.
C(CH3)–H asym str.
O–H strS
3,014
3,016
2,975
3,028
3,015
2,993
2,992
2,980
2,949
2,922
2,913
1,627
1,618
1,590
1,552
1,475
1,475
1,465
1,460
1,451
1,440
1,434
1,426
1,422
1,415
1,373
1,359
1,347
1,291
1,287
1,280
1,212
1,199
1,180
1,157
1,153
1,152
1,152
1,083
1,064
1,049
1,036
985
C(CH3)–H asym str.
C(CH3)–H asym str.
2,989
2,962
2,933
2,991
2,963
2,933
1,626
C(CH3)–H asym str.
2,998
2,997
2,977
2,949
2,917
2,912
1,632
1,619
1,593
1,542
1,476
1,473
1,463
1,451
1,451
1,442
1,435
1,426
1,420
1,413
1,368
1,362
1,350
1,302
1,290
1,281
1,200
1,194
1,171
1,154
1,152
1,148
1,131
1,066
1,060
1,034
1,027
972
2,997
2,977
2,949
2,915
2,912
1,632
1,619
1,592
1,542
1,476
1,473
1,463
1,451
1,451
1,442
1,435
1,426
1,420
1,413
1,368
1,362
1,350
1,301
1,290
1,281
1,199
1,194
1,172
1,154
1,152
1,148
1,131
1,066
1,061
1,034
1,028
973
C(CH3)–H asym str.
O–H str.|C(CH3)–H asym str.S
C(CH3)–H sym str.
2,939 2,936
1,624 1,631
1,582
C(CH3)–H sym str.
C(CH3)–H sym str.
1,625
1,619
1,586
1,548
1,472
C=O str., rocking acetyl
Phenyl ring str., furan ring def.
Phenyl ring str.
1,587
1,549
1,474
Furan ring str., C(furan)–H rocking
CH3(methoxy) asym. def.
CH3(methoxy) asym. def.
CH3(methoxy) sym. def.
1,472 1,472
1,456
CH3(methoxy) asym. def.
CH3(methoxy) asym. def.
CH3(acetyl), asym. def.
1,442
1,444
1,424
CH3(methoxy) sym. def.
1,417 1,414
1,429
CH3(methoxy) sym. def.
C–O–H def., C–OH str.
CH3(acetyl), asym. def., C–O–H def.
CH3(acetyl), sym.
1,380
1,364
1,352
1,303
1,379
1,366
1,350
1,302
1,363 1,366
1,351 1,352
1,302
CH3(acetyl), sym.
Benzofuran ring str.
C–C(acetyl) str., rocking C(furan)–H
C–O(methoxy), phenyl ring str.
Phenyl ring str.
1,291 1,291
1,276 1,277
1,266
1,212
1,199
1,171
1,150
1,265
1,211
Furan ring def., C–O(methoxy) str.
CH3(methoxy) rocking
1,170 1,172
1,141 1,146
1,177
1,155
Furan ring str.–def.
C–O(methoxy) str., CH3(methoxy) rocking|CH3(methoxy) rockingS
C(furan)–H rocking, furan ring def.|CH3(methoxy) rockingS
CH3(methoxy) rocking|CH3(methoxy) rocking, furan ring def.S
CH3(methoxy) rocking|furan ring str., C(furan)–H rockingS
Furan ring str.|CH3(acetyl) rocking, C–O methoxy str.S
Furan ring str.–def.
1,065 1,063
1,079
1,062
1,041
1,029
987
1,078
1,040
Furan ring str.–def.
CH3(acetyl) rocking
985
974
985
975
990
980
O–C(CH3) str.
977
969
966
966
CH3(acetyl) rocking, C–C(CH3) str.
123

Struct Chem (2012) 23:1573–1584
1581
Table 5 continued
Experimental frequencies (cm-1
)
Scaled theoretical
frequencies
Assignmentsa
IR gas IR CCl4 IR solid Raman solid 1a
1b
1c
938
940
878
843
944
878
942
881
851
937
876
845
836
796
737
790
690
685
666
633
589
577
558
523
483
460
938
Furan ring str.–def.|O–C(CH3) str., furan ring str.–def.S
Furan ring def.
881
847
874
845
835
794
752
772
715
689
676
627
593
580
567
531
484
438
874
845
835
794
752
772
714
689
675
631
594
578
565
514
489
457
Furan ring str.–def.
C(furan)–H opl def.
788
777
756
701
688
791
777
754
690
C–OH rocking, C–C(acetyl) rocking
C(furan)–H opl def.
737
694
–OH torsion
C–OH opl def., phenyl ring torsion, C–OCH3 opl def.
Phenyl ring torsions
669
633
590
Phenyl ring torsions, C–C(acetyl) opl def., C–OCH3 opl def.
Acetyl group def.
631
594
638
597
589
570
538
640
600
588
571
536
496
455
Phenyl ring def.
Furan ring torsions
573
572
530
Furan ring torsions
C–OH opl def., C–O–CH3 def.
Phenyl ring def.
475
440
C–O–CH3 def., C(acetyl)–C(phenyl) rocking
419
395
376
341
324
280
418
398
370
332
316
284
277
266
242
233
222
191
162
138
104
79
416
388
364
333
309
292
272
246
227
200
173
153
138
133
100
91
417
394
350
325
311
295
267
247
230
202
173
155
138
132
100
92
C–OH rocking, C(acetyl)–C(phenyl) rocking
C(acetyl)–C(phenyl) rocking, phenyl ring def.
Phenyl ring def., C–O–CH3 def.
Phenyl ring def., C–O–CH3 def.
C(phenyl)–C(acetyl) opl def., butterfly
C–OCH3 rocking, phenyl ring def.
CH3(methoxy) rotation
385
260
Acetyl group rocking
C–OCH3 rocking
CH3(acetyl) rotation
Acetyl group rocking, C–O–CH3 def.
Phenyl ring torsions, butterfly
Phenyl ring torsions, –OH torsion
CH3(methoxy) rotation
206
175
125
105
83
–OH torsion, acetyl group torsion
CH3(methoxy) torsion, phenyl ring torsions
CH3(methoxy) torsion
64
70
69
39
62
62
Acetyl group torsion, CH3(methoxy) torsion
CH3(methoxy) rotation
30
41
41
str. stretching, def. deforming, opl out of plane deformations
a
Description of normal modes is based on the potential energy distribution matrix for the most stable conformer 1a. Description of modes for
the secondary minima, 1b and 1c, has been also included for bands interesting for the conformational analysis when a significant difference
respect to 1a is expected
The symbol ‘‘|’’ and superindex ‘‘S’’ indicate that the description corresponds to the secondary minima
Conformational analysis in liquid phase
the conformers of anisol and para-methoxyanisol [58],
the second para-methoxy group in the conformers of 1 is
responsible for the smaller torsional barrier and lower
relative energy than those observed for 2.
As 1 and 2 show their action in aqueous cellular media, the
energy surfaces were explored by changing the torsion
123

1582
Struct Chem (2012) 23:1573–1584
Fig. 8 Left column IR spectra
in the range 1,250–1,000 cm-1
for 1. Right column second
derivative. a Gas phase; b black
solid line CCl4 solution of 1, red
dashed line CCl4; c solid phase;
d black solid line conformer 1a,
red dashed dotted line
conformer 1b, blue dotted line
conformer 1c (Color figure
online)
Vibrational analysis
angles t1 and t2 in an aqueous solution; B3LYP/6-
31G(d) was the method of choice. The internal rotation
around the C7–OCH3 single bond for 1 yielded two mirror
images (analogous to those obtained for the isolated mol-
ecule) with the methoxy group at the C7 atom almost
perpendicular to the benzo[b]furan fragment (t1 is shifted
to 80°) (Fig. 5). The PES for the internal rotation about
the C4–O4 single bond yields also three minima for both
molecules (Fig. 6). However, the secondary minima for 1
and 2 almost disappear and their relative energy to the most
stable conformer increases (Fig. 6).
The discussion is focussed on the region of spectra from
1,250 to 1,000 cm-1 to support the previous conforma-
tional analysis. Since the low barriers to rotation result in
the overlapping of bands of different conformers, the sec-
ond derivative of the spectrum was used to reveal peaks
under the broad bands.
The full assignment of the vibrational spectra for 1 is
presented in Table 5, and for 2 is reported as Supplemen-
tary material (Table 2S).
123

Struct Chem (2012) 23:1573–1584
1583
On the spectrum of 1 in the region 1,250–1,000 cm-1
(Fig. 8) an evidence for the existence of several conformers
appears. Thus, two different scaled theoretical bands for
the conformers 1a and 1b/1c appear at 1,157 cm-1 (1a,
C–O stretching of the methoxy groups) and 1,131 cm-1
(1b/1c, furan ring stretching), respectively (Fig. 8d).This
couple corresponds to a broad band appearing in the gas
phase at 1,141 cm-1 and at 1,146 cm-1 in the CCl4 solu-
tion (Fig. 8a, b, respectively). Both broad bands of the IR
spectra split into two peaks in the second derivative that
match the two corresponding bands of the scaled theoret-
ical spectrum (Fig. 8d). This splitting is more visible in the
spectrum of the CCl4 solution than in the gas phase which
is consistent with the temperature of recording; the first
spectrum was recorded at room temperature and the latter
at 205 °C. In the solid phase a sharpened band is observed
at 1,150 cm-1 (Fig. 8c). The second derivative of the IR
spectrum in the solid phase, where only one conformer is
present, confirms the presence of one single band.
all three states of matter—solid, liquid, and gas phase—is
observed. The presence of this intramolecular bond in the
form of six-membered ring is energetically favorable for
the molecules, its strength is around 18 kcal/mol.
For both molecules several conformers are observed,
they differ in the orientation of methoxy groups. For the
energetically favorable forms, 1a and 2a, representative for
the solid phase, the –OCH3 substituent is coplanar to the
benzo[b]furan system. In the gas phase, this group can be
also perpendicular to the benzene ring. The introduction of
the second para-substituted methoxy group (in 1) creates a
conformer for which one –OCH3 group is perpendicular
and the second one coplanar to the benzo[b]furan moiety.
Thus, in the gas phase, apart from conformer 1a, two other
conformers were identified in which the Csp2–O-CH3
bonds are in the trans and the cis orientations (the con-
formers 1b and 1c).
The vibrational spectroscopy is a good technique to
study a conformational equilibrium. In case of khellinone
(1), the second derivative of the IR spectra (in the region
1,250–1,000 cm-1), in the gas phase and the CCl4 solution,
provide evidences of the conformational equilibrium as
compared to the solid-phase spectrum and the scaled
theoretical ones of the different conformers.
Other regions of the spectra show no significant evi-
dences to support the conformational equilibrium. The
region of the X–H stretching could be interesting because
the scaled theoretical spectra reveal a clear difference
among the O–H stretching bands of the conformers 1a and
1b/1c. In the gas phase and the CCl4 solution broad bands
are observed, and—as a consequence of this—the large
number of bands appear in the second derivative which
prevent unequivocal interpretation of results.
Supplementary material
For visnaginone (2), less visible evidences are observed
in the same region of the respective spectra, nevertheless
they are conclusive. Two IR scaled theoretical bands
appear at 1,105/1,078 cm-1 (furan ring deformations,
O–CH3 stretching) for 2a and 2b, respectively (Fig. 3S,C).
In the IR gas-phase spectrum of 2, the broad band at
1,091 cm-1 corresponds to the respective theoretical bands
(Fig. 3S,A). The second derivative of that spectrum reveals
a band and a shoulder at lower frequency that match the
scaled theoretical bands (Fig. 3S,A). The IR spectrum in
the solid phase, where only one conformer is present,
shows the sharpened band (1,107 cm-1, Fig. 3S,B) that it
is consistent with the second derivative of the IR spectrum.
However, it was impossible to record a reasonable liquid
phase IR spectra for 2 due to its low solubility in different
solvents.
Data on detailed characterization of the intramolecular
O–H...O hydrogen bond, the fullassignment of vibrational
spectra for 2, and optimized geometry of the most stable
conformersof 1 and 2 are included as electronic supplement
(14 pages).
Acknowledgments AD would like to thank Prof. Manuel
´
´
Fernandez Gomez and his research group for hospitality and financial
support during her stay in Jaen. TPR thanks Dr Francisco Partal Uren˜a
for helpful discussions. The study was performed within the Inter-
national European LLP-Erasmus program (University of Jaen,
Spain—Maria Curie-Sklodowska University, Lublin, Poland).
Open Access This article is distributed under the terms of the
Creative Commons Attribution License which permits any use, dis-
tribution, and reproduction in any medium, provided the original
author(s) and the source are credited.
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