Role of edge-to-face interaction between aromatic rings in clathrate formation of 1-benzoyl-2-hydroxyindoline derivatives with benzene. X-ray crystal and PM6 analyses of the interaction

Article abstract of DOI:10.1016/j.tet.2011.07.021

(4-Nitrophenyl- and 4-chlorophenyl)(2-hydroxy-3,3-dimethylindolin-1-yl) methanone (4a,b) serve as clathrate hosts for benzene guests. X-ray crystal analyses of the inclusion compounds of 4a and 4b with benzene indicate that the 'edge-to-face interaction' plays an important role in the formation of the inclusion complexes with benzene as well as in the host-host interactions. PM6 molecular orbital calculations were found to reproduce the characteristic structural features of both intra- and intermolecular edge-to-face interactions.

Full text of DOI:10.1016/j.tet.2011.07.021

Tetrahedron 67 (2011) 7400e7405
Contents lists available at ScienceDirect
Tetrahedron
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Role of edge-to-face interaction between aromatic rings in clathrate formation of
1-benzoyl-2-hydroxyindoline derivatives with benzene. X-ray crystal and PM6
analyses of the interaction
*
Masashi Eto , Koki Yamaguchi, Itaru Shinohara, Fumikazu Ito, Yasuyuki Yoshitake, Kazunobu Harano
Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 7 June 2011
Received in revised form 6 July 2011
Accepted 9 July 2011
Available online 3 August 2011
(4-Nitrophenyl- and 4-chlorophenyl)(2-hydroxy-3,3-dimethylindolin-1-yl)methanone (4a,b) serve as
clathrate hosts for benzene guests. X-ray crystal analyses of the inclusion compounds of 4a and 4b with
benzene indicate that the ‘edge-to-face interaction’ plays an important role in the formation of the in-
clusion complexes with benzene as well as in the hostehost interactions. PM6 molecular orbital cal-
culations were found to reproduce the characteristic structural features of both intra- and intermolecular
edge-to-face interactions.
Keywords:
Edge-to-face interaction
CH/O interaction
Ó 2011 Elsevier Ltd. All rights reserved.
1-Benzoyl-2-hydroxyindoline
PM6 calculation
1. Introduction
The CH/
which occurs between a soft acid and a soft base. Nishio et al.1,2
indicated that the CH/ interaction is not only a conventional van
p interaction can be regarded as a weak hydrogen bond,
p
der Waals force but also has hydrogen-bond-like properties. High-
level ab initio molecular orbital (MO) calculations support this
concept. The enthalpy of a single-unit CH/
p interaction is small
(around 1 kcal/mol). However, CH/ interactions have been shown
p
to play significant roles in various fields of chemistry, e.g., in de-
termining the conformation of molecules, crystal packing and in
the assembly of molecular units into an organized supramolecular
structure. It has also been suggested the CH/p interaction plays an
important role in the structure of proteins and DNA.3
During the course of the studies4 of the isolable atropisomers
caused by restricted rotation around the Csp3eCsp2 bond of [2-(2-
hydroxynaphthalen-1-yl)-3,3-dimethyl-2,3-dihydroindol-1-yl](4-
nitrophenyl)methanone (5a and 6a), we recognized the formation
of a crystalline inclusion compound of 4a (Scheme 1) with benzene.
The inclusion behavior of 4 is discussed in this study along with
newly obtained X-ray diffraction data, which are used to clarify the
overall character of the hydroxylic hosts.
Scheme 1.
* Corresponding author. E-mail address: meto@ph.sojo-u.ac.jp (M. Eto).
0040-4020/$ e see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tet.2011.07.021

M. Eto et al. / Tetrahedron 67 (2011) 7400e7405
7401
2. Results
2.1. Inclusion properties
The host compounds (4aed) were synthesized by treatment of
the corresponding 2-chloro derivatives (3aed) with water.4c A va-
riety of solvents (benzene, acetone, chloroform, ethanol, and tolu-
ene) were used to explore the inclusion properties of 4aed. The
inclusion compounds were obtained by slow evaporation of a so-
lution of the host compounds in the respective guest solvents at
ambient temperature. Of several substituted benzoyl derivatives,
the 4-nitro (4a) and 4-chlorobenzoyl (4b) derivatives formed the
2:1 inclusion complexes with benzene. The host: guest stoichio-
metric ratio was confirmed by thermogravimetric (TG) analysis.
The total weight loss was observed to be 10.4% for 4a$benzene and
10.0% for 4b$benzene, in close agreement with the expected losses
of 11.1% and 11.5%, respectively, for a 2:1 host/guest ratio (see the
Supplementary data, Figs. S1 and S2).
Fig. 2. Edge-to-face interactions between the host (4a) and guest (benzene) molecules.
2.2. X-ray analysis
2.2.1. 4a$Benzene and 4b$benzene complexes. The ORTEP5 repre-
sentations of 4a$benzene and 4b$benzene are depicted in Fig. 1, in
which each complex has one-half of a benzene molecule in the
asymmetric unit, with the other half generated by a crystallo-
graphic inversion center.
Fig. 1. ORTEP drawings of 4a$benzene and 4b$benzene inclusion complexes.
In both structures, the amide carbonyl oxygen is oriented to-
ward the C7eH of the indoline moiety and the aryl ring is not co-
planar with the >NCOe plane. The interatomic distances between
ꢀ
the amide carbonyl oxygen and C7eH are 2.320 (4) A (4a) and 2.401
Fig. 3. (a)
pep Interactions between the host molecules (4a) and (b) edge-to-face
ꢀ
(3) A (4b), indicating of the presence of CH/O-type hydrogen
interactions between the host molecules (4a).
bonding.6
between the 4-nitrobenzoyl rings; this is facilitated by the hydro-
gen bond between the nitro group and the 2-hydroxy group of the
In the crystal structure of 4a$benzene, inclusion of the guest
(benzene) molecule is facilitated by edge-to-face (or T-shape) aro-
ꢀ
ꢀ
indoline moiety [O/O, 2.838 (5) A; OeH/O, 2.024 (4) A]. Edge-to-
face interactions between the host molecules were observed, in
which the distance between the ortho proton of the benzoyl group
matic CH/
suggesting the presence of potential CH/
p
interactions between the four indoline benzene rings,
interactions in which the
p
benzene rings act as both hydrogen-bond donor and acceptor
(Fig. 2 and S4). The Ha proton of the host benzene molecule is lo-
ꢀ
and the neighboring indoline ring is 2.891 A (Fig. 3b).
ꢀ
The crystal structure of the inclusion complex 4b$benzene is
depicted in Fig. 4 (see Fig. S5). The marked difference in inclusion
behavior between 4a and 4b indicates recognition of hydrogen on
the guest by the host molecules. The benzene hydrogens interact
with the oxygen atoms of the hydroxy and benzoyl groups of the
host molecules via CH/O-type hydrogen bonds.6 In contrast, the CH/
cated at a close-contact perpendicular distance of 2.796 A above the
face of the indoline ring. Additionally, the edge-to-face distance
between the C5eH of the indoline ring and the plane of the guest
ꢀ
p
-system was 3.167 A.
The host molecules are linked by
pep and edge-to-face in-
teractions, depicted in Fig. 3a and b. There are two types of
pep
p
interaction between the p plane of the benzene (guest) and the
interaction between the 4-nitrobenzoyl rings. The interaction
pep
host molecule (4b) is similar to that observed in 4a, in which the
distance between the C4eH and the plane of the guest benzene is
2.916 A. In the inclusion complex, the host molecules are firmly
stacking distance between the 4-nitrobenzoyl rings is considerably
shorter than the typical values (<3.6 A), which is the result of an
additional coulombic interaction force between the benzoyl car-
ꢀ
ꢀ
bounds together by C]O/HeO hydrogen bonds [Oe(H)/O, 2.665
(4) A, OeH/O, 2.016 (3) A].
bonyl oxygen and the nitrogen atom of the nitro group [O$$$N,
ꢀ
ꢀ
ꢀ
2.899 (5) A]. Another mode of
pep interaction stacking is found

7402
M. Eto et al. / Tetrahedron 67 (2011) 7400e7405
interactions such as the edge-to-face interaction forces between
aromatic rings. The objective was to determine whether the guest
p
benzene is hold by edge-to-face interactions during optimization,
in which a partial structure (six hosts and three guests) of the
crystal packing diagram of 4a is used, as shown in Fig. 6.
Fig. 4. Edge-to-face and CH/O interactions in clathrate of 4b$benzene.
2.2.2. Guest-free host (4c). The crystal structure of the free host 4c
is depicted in Fig. 5. The host molecules are linked by in-
termolecular hydrogen bonds between the amide carbonyl oxygen
and the 2-hydroxy group of the neighboring molecule [Oe(H)/O,
ꢀ
ꢀ
2.764 (4) A, OeH/O, 1.953 (3) A]. In contrast to the case for 4a, the
2-nitro group does not form a hydrogen bond with the 2-hydroxy
group. The benzoyl ring interacts with the adjacent indoline ben-
zene ring in an overlapping face-to-face manner, thus stabilizing
the host network. The closest interatomic distance between the
ꢀ
carbon atoms is 3.52 (1) A.
Fig. 6. PM6- and AM1-calculated partial packing structure of 4a$benzene complex
looking through the central benzene molecule.
The geometry of the complex was fully optimized by AM1,7
PM3,8 and PM69 methods without imposing any symmetrical re-
strictions. The X-ray structure and PM6-calculated interatomic
distances, intermolecular edge-to-face interaction distances and
interplane distances are summarized in Table 1.
Fig. 5. Guest-free hostehost interactions of 4c.
Table 1
3. Discussion
Comparison of the important distances between the crystal structure (4a$benzene)
and the computed structure
The hydroxylic host compound 4a enclathrated guest benzene
ꢀ
Distance (A)
molecules with
a 2:1 host/guest stoichiometric ratio. The
X-ray
PM6a
hostehost framework is assembled by tight hydrogen bonds be-
tween the 4-nitro group of the benzoyl ring and the 2-hydroxy
group of the indoline ring. In addition to this, the dimeric host
molecules are linked intermolecularly in edge-to-face and face-to-
face manner by interaction between the aryl groups (Fig. 3). The
benzene guest is located inside the space surrounded by four aryl
Host/host
N (amide)/N (amide) [cross]
N (amide)/N (amide)
Guest/guest
C/C
Host/guest
10.978 (5)
7.189 (4)
10.375
7.233
7.19 (1)
7.449
Guest-H/host indoline benzene ring
Guest plane/C6eH of host indoline ring
2.796
3.167
2.636
2.511
groups stabilized by CH/p interactions.
Semi-empirical MO calculations were performed in order to
assess the geometric features involving weak intermolecular
a
Average. For atomic coordinates see Table S7.

M. Eto et al. / Tetrahedron 67 (2011) 7400e7405
7403
The results show that the newly parameterized PM6 calculation
approximately reproduced the spatial orientation of the guest
molecule, whereas the AM1 and PM3 methods did not show sat-
isfactory results (Fig. 6).10
In the AM1-optimized geometry, there was no evidence of the
characteristic structural features of the edge-to-face interaction;
instead, weak CH/O-type interactions between the carbonyl oxygen
atom of the host and the hydrogen atom of benzene (guest) operate
inplace of edge-to-face interactions. The PM6 stabilization energy of
benzene arising from its inclusion by four edge-to-face interactions
(Fig. 2) is estimated to be 3.90 kcal/mol.11 This result seems to be
reliable because high-level ab initio MO calculations12 suggest that
the enthalpy of a single-unit CH/p interaction is around 1 kcal/mol.
As shown in Figs. 2 and 6, the edge-to-face structural features were
approximately reproduced by PM6 calculation. Inspection of the
intermolecular distances indicates that the distance between the
benzene-ring plane of the guest molecule and the hydrogen atom of
the phenyl group of the neighboring host molecule is significantly
short. This may be the result of a movement of the edge-to-face
interaction position on the guest plane from the peri position of
benzene (X-ray structure) to the central position of the guest in the
PM6-calculated geometry.
The host 4c did not enclathrate any guest molecules. This lack of
the inclusion ability toward benzene can be attributed to the
hostehost network mode. By replacing 4-nitrobenzoyl with a 2-
nitrobenzoyl group, the host becomes tightly linked by in-
termolecular hydrogen bonding between the 2-hydroxy group and
the amide carbonyl oxygen of the neighboring molecules. It is in-
teresting to note that the nitro group of 4c does not form hydrogen
bonds despite its strong hydrogen-bond acceptor ability. In addi-
tion, arylearyl interactions between the indoline rings further
stabilize the host network.
The host 4b enclathrated benzene with a 2:1 host/guest ratio.
However, the inclusion pattern of the guest is different from that of
4a. Comparison of the inclusion behavior of 4a with that of 4b
suggests that the replacement of the 4-nitro group by the chloro
group causes a change in the hostehost network, resulting in the
recognition mode toward benzene.
These findings in 4aec suggest that the hydrogen-bond network
between the host molecules plays an important role in complex
formation with guests.
Fig. 7. Crystal structure of 5d$acetone complex.
5d indicate that the amide nitrogen has a large negative charge
(ꢀ0.418) and HOMO coefficient, suggesting that the attractive
coulombic interaction and the favorable orbital interaction be-
tween the nitrogen atom and CH group can be expected (Fig. 8).
On the basis of these findings, the inclusion behavior of 5d was
reinvestigated. During a synthetic study of the atropisomers (5), it
was found that 5d (anti)4g formed a crystalline inclusion complex13
with the recrystallization solvent (acetone). A computer-generated
drawing of the crystal structure of inclusion complex 5d$acetone is
depicted in Fig. 7.
In the crystal packing, the host molecules form a dimeric unit
linked by hydrogen bonds between the amide carbonyl and the
ꢀ
naphthyl OH group [C]O/(H)eO, 2.666 (7) A; O/HeO, 1.861 (5)
ꢀ
A], resulting in a 16-membered cyclic hydrogen-bonded structure.
The edge-to-face interaction is found between the aromatic pro-
tons of the benzoyl group and the indoline moiety. The closest
ꢀ
distances between the carbon atoms are 3.87 (1) and 3.90 (1) A. In
Fig. 8. HOMO of 5d (net charges are shown in parentheses).
addition, the dimeric host molecules are considered to be in-
termolecularly linked by a CH/N interaction between the 3-methyl
group of the benzoyl ring and the amide group conjugated with the
phenyl ring of the indoline moiety.14 The methyl group is located
almost perpendicularly to the amide plane. The interatomic dis-
tance between the methyl carbon atom and the nitrogen atom is
The guest structure of the complex is disordered in the crystal.
The guest acetones are aligned almost parallel along the c-axis;
however, only an approximate structure can be obtained by the
calculation of differential Fourier synthesis. Inspection of the
packing structure suggests that the acetone molecule assumes
several possible orientations related by rotation around the car-
bonyl carbon atom. One of the possible models is shown in Fig. 7, in
which the oxygen was assigned based on the highest Fourier peak.
In this model, along the cavity created by the host dimers, the
methyl hydrogen of the guest seems to be linked with the carbonyl
oxygen of neighboring guests by weak CH/O interactions [C]
ꢀ
3.82 (1) A. In the previous paper, we reported that the presence of
the intramolecular ArOH/N interactions of 5 (anti isomer) affects
the stabilization of the rotamers based on the DFT calculations and
the equilibrium constants including the solvent and the sub-
stituents effects,4j in which the amide nitrogen atom acts as a hy-
drogen-bond acceptor.15 Inspection of the PM6 calculation data of

7404
M. Eto et al. / Tetrahedron 67 (2011) 7400e7405
ꢀ
O/(H)eC, 3.67 (2) A]. A weak CH/
p
interaction is expected between
4. Experimental section
4.1. Materials
the benzoyl ring and one of the methyl group of the acetone, inwhich
the distance between the methyl hydrogen atom and the least-
ꢀ
ꢀ
squares plane of the phenyl ring is 3.70 A [Ce(H)/plane, 3.21 A].
To assess the guest orientation, the PM6 calculation was per-
formed for the partial structures extracted from the inclusion
complex (18 hosts and six guests; Fig. 9), in which only the guest
molecules were optimized.
(4-Substitutedphenyl)(2-hydroxy-3,3-dimethylindolin-1-yl)
methanones (4aed) were prepared by the addition of substituted
benzoyl chloride to 3,3-dimethyl-3H-indole (1) followed by treat-
ment of the corresponding 2-chloro derivatives (3) with water.4b
Compound 5d (anti) was prepared according to the previously
reported method.4c
4.2. Thermal analysis
Thermal analyses of 4a, 4b, and 5d$acetone were performed on
a Shimadzu DTG-50/50H simultaneous TG/DTA instrument.
4.3. Crystal structure analysis
The single crystals for the 2:1 inclusion complexes of 4a and 4b
with benzene were prepared by slow evaporation of its benzene
solution at room temperature. All measurements were performed
on a Rigaku RAXIS RAPID imaging plate area detector with
ꢀ
graphite-monochromated Mo K
a
radiation (
l
¼0.7107 A). The data
Fig. 9. PM6-Calculated partial structure extracted from 5d$acetone complex.
were collected at a temperature of 23ꢁ1 ꢂC to a maximum 2
q value
of 55ꢂ. The structure was solved by direct method (SIR200817a), and
all hydrogen atoms were located at calculated positions. The
structure was refined by a full-matrix least-squares technique using
anisotropic thermal parameters for non-hydrogen atoms and
a riding model for hydrogen atoms. All calculations were performed
using the crystallographic software package Crystal Structure.17b,c
These X-ray crystallographic data have been deposited at the
Cambridge Crystallographic Data Centre (CCDC).
From the PM6 method, the CH/O interaction between the
methyl hydrogen and carbonyl oxygen of acetone was predicted.
The average distances between CeH/O and C(H)/O are 2.246 and
ꢀ
3.283 A, respectively. The interaction between the host and guest
molecules is considered to be mainly the result of van der Waals
forces. The calculated guest plane is somewhat rotated around the
c-axis compared to that in the crystal structure (see Figs. S6 and S8).
This suggests that the hosteguest CH/p interaction expected from
X-ray analysis is not strong enough to hold acetone in a uniform
restricted space.
4.3.1. Crystal data of 4a$benzene. C20H19N2O4, M¼351.38, triclinic,
space group P(ꢀ1) (#2), a¼8.5800 (12), b¼15.4573 (15), c¼7.1887
The phenolic OH group of the host is expected to stabilize the
hostehost network by hydrogen bonds. In the packing structure of
the 5d$acetone complex, the two host molecules form a dimeric
unit by means of intermolecular hydrogen bonding and along the
host channel, the guests (acetone) are infinitely linked to other
neighboring guests by weak CH/O interactions via the carbonyl
oxygen. The dimer was linked with the neighboring host by a weak
CH/N interaction. The fact that the guest-free crystal of 5d was
obtained from slow evaporation of protic solvent (i.e., ethanol)16
suggests that the OH/O and CH/N interaction are necessary for
the construction of the hostehost network in the formation of the
inclusion cavity.
ꢀ
(8) A,
a
¼102.557 (5)ꢂ,
b
¼97.441 (4)ꢂ,
g
¼101.661 (4)ꢂ, V¼896.2 (2)
3
3
ꢀ
A , Z¼2, Dc¼1.302 g/cm , R¼0.080, Rw¼0.170, GOF¼1.000, CCDC ref.
No. 825568; 4b$benzene C20H19ClNO2, M¼340.83, monoclinic,
space group P21/n (#14), a¼10.3816 (6), b¼12.5590 (9), c¼14.6984
3
ꢀ
3
ꢂ
ꢀ
(8) A,
b
¼108.7417 (13) , V¼1814.8 (2) A , Z¼4, Dc¼1.247 g/cm ,
R¼0.083, Rw¼0.160, GOF¼1.001, CCDC ref. No. 825569; 4c
C17H16N2O4, M¼312.32, monoclinic, space group P21/c (#14),
a¼9.6035 (12), b¼110.3597 (9), c¼15.5415 (13) A,
b
¼97.953 (4)ꢂ,
ꢀ
3
ꢀ
V¼1531.3 (3) A , Z¼4, Dc¼1.355 g/cm3, R¼0.068, Rw¼0.122,
GOF¼1.002, CCDC ref. No. 825570.
The packing structures of these complexes are shown in the
provided Supplementary data (Figs. S4eS6).
It is interesting that even if the guest is a strong hydrogen-bond
acceptor, such as acetone, the host, which contains the ArOH group,
does not form hydrogen bonds with the guest. This information
may be useful for the design of new hydroxylic clathrate hosts
containing aromatic rings. Reinvestigation of other atropisomers
(5) as new clathrate hosts is in progress.
In summary, the inclusion properties of the clathrate crystals of
4a and 4b have been investigated by means of X-ray crystallog-
raphy. Benzene is embedded in a host lattice constituted of the
intermolecular ‘edge-to-face’ interactions of the host aromatic
rings.
4.4. Molecular orbital (MO) calculations
Semi-empirical MO (PM6, PM3, AM1) calculations were run
through Winmostar18 interface using MOPAC20099 on a DELL Di-
mension9200 computer.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.tet.2011.07.021.
Inter- and intra-molecular edge-to-face attractive interactions
become important factors in stabilization of ground-state and
transition-state geometries and determination of reaction selec-
tivity. PM6 semi-empirical MO calculations seem to provide an
References and notes
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teraction are available from http://www.tim.hi-ho.ne.jp/dionisio/page/other.html.
p Interaction; Evidence Nature and
excellent clue for prediction of aromatic CH/p interaction. The
present work serves as a calculation model for understanding
molecular recognition in organic reactions.
p

M. Eto et al. / Tetrahedron 67 (2011) 7400e7405
7405
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13. The DTA (differential thermal analysis) of 5d$acetone complex showed a broad
endothermic peak corresponding to the guest losses at 89 ꢂC, followed by an
endothermic peak at 221 ꢂC caused by melting of the host. The total weight loss
was 7.7%. The value is much smaller than the expected loss of 15.2% for a 1:1
ratio. These facts indicated that the measurement sample used is the mixture of
the complex and the guest-free crystal (see Fig. S3).
14. A reviewer pointed out that the existence of the CH/N interaction between the
methyl hydrogen and NCO
p system is a questionable. Only a few examples
(NH/N type) of protonation toward amide nitrogen atom were known as ‘amide
proton sponge’. (a) Cox, C.; Wack, H.; Lectka, T. Angew. Chem., Int. Ed. 1999, 38,
798e800; (b) Cox, C.; Lectka, T. Org. Lett. 1999, 1, 749e752.
15. B3LYP/6-31G(d) estimated ground-state structures and energies of 5 (anti)
with/without intramolecular OH/N interaction are depicted as follows: the GSa
including intramolecular OH/N hydrogen bond between the OH and NCO
moiety is ca. 2.3 kcal/mol more stable than that of GSbThe details will be re-
ported in the near future.
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8. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 209e220.
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(http://OpenMOPAC.net).
10. To confirm the reliability of PM6 method, typical compounds (A,19 B,20 C21
)
containing intramolecular edge-to-face conformation were examined.
16. Recrystallization of 5d from ethanol afforded colorless prisms. The elemental
analysis indicates that the crystal did not enclathrate ethanol. Calcd for
C28H27NO2: C, 82.53: H, 6.18: N, 3.44. Found: C, 82.36, H, 6.21: N, 3.64. The X-
ray analysis also indicated the crystal is guest-free. The crystal data of guest-
free 5d are as follows: C28H25NO2, M¼407.5, triclinic, space group P(ꢀ1) (#2),
¼88.318 (5)ꢂ,
b
¼67.844 (4)ꢂ,
ꢀ
The calculations well reproduced the structural features of the crystal geometry.
For details of the PM6 investigations see the Supplementary data (Figs. S9eS11).
11. In the calculation, the central benzene molecule is freely optimized and the
coordinates of surrounding molecules are frozen. The stabilization energy due
to inclusion of benzene by four edge-to-face interactions is calculated.
a¼12.4728 (16), b¼13.676 (3), c¼14.200 (2) A,
a
3
3
ꢂ
ꢀ
g
¼84.314 (5) , V¼2232.3 (6) A , Z¼4, Dc¼1.212 g/cm , R¼0.089, Rw¼0.112,
GOF¼1.063. The maximum peaks on the final difference Fourier map corre-
3
ꢀ
sponded to 0.64 e/A .
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Crystallogr. 2007, 40, 609e613; (b) CrystalStructure 4.0: Crystal Structure
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