Clathrate formation of Diels-Alder adduct of phencyclone and acenaphthylene. Key role of CH/π and bidentate CH/O interactions of the phenanthrene ring in construction of host framework

Article abstract of DOI:10.1016/j.tet.2012.03.005

Two clathrate hosts (3a and 3b) were synthesized via the Diels-Alder reaction of phencyclone (1a) and tetracyclone (1b) with acenaphthylene (2), and the clathrate formation properties of these hosts towards a variety of organic guests were investigated. I

Full text of DOI:10.1016/j.tet.2012.03.005

Tetrahedron 68 (2012) 3566e3576
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Clathrate formation of DielseAlder adduct of phencyclone and acenaphthylene.
Key role of CH/p and bidentate CH/O interactions of the phenanthrene ring
in construction of host framework
,
a
a
a
Masaki Abe a, Masashi Eto a , Koki Yamaguchi , Masatoshi Yamasaki , Junichi Misaka , Yasuyuki
*
Yoshitake a, Masami Otsuka b, Kazunobu Harano a
a Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
b Faculty of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
a r t i c l e i n f o
a b s t r a c t
Article history:
Two clathrate hosts (3a and 3b) were synthesized via the DielseAlder reaction of phencyclone (1a) and
tetracyclone (1b) with acenaphthylene (2), and the clathrate formation properties of these hosts towards
a variety of organic guests were investigated. In the presence of aprotic solvents (i.e., aromatic, ketonic and
etheric solvents), host 3a formed inclusion complexes with a 2:1 stoichiometric host/guest ratio, whereas
3b primarily formed 1:1 complexes. The desolvation temperatures of the 3a$guest complexes were ex-
tremely high in comparison to the boiling points of the pure guest liquids and were also much higher than
those of the corresponding 3b$guest complexes, which contain the conformationally flexible stilbene
moiety. Structural analyses of the 3a$guest complexes (i.e., 3a$benzene, 3a$toluene, 3a$1,4-dioxane,
Received 18 January 2012
Received in revised form 29 February 2012
Accepted 2 March 2012
Available online 8 March 2012
Keywords:
CH/
p interaction
CH/O interaction
Phencyclone
3a$acetone and 3a$pentan-3-one) show that the aromatic CH/
p (edge-to-face) interactions between
phenanthrene and the acenaphthene ring as well as the interaction of the ‘bidentate’ CH/O hydrogen bond
between the phenanthrene-ring hydrogen and the bridged carbonyl oxygen play a key role in the con-
struction of the characteristic host ‘column’ structures. The guest molecule of the 3a$benzene complex is
PM6 calculation
held between the stacking columns by aromatic CH/p interactions of the acenaphthene rings of adjacent
host molecules. The stable clathrate formation of 3a is discussed based on X-ray structural analyses of six
clathrates and PM6 molecular orbital calculations for the clathration model of 3a$benzene.
Ó 2012 Elsevier Ltd. All rights reserved.
1. Introduction
structural illustration presented in Fig. 1 shows that the space
above the phenanthrene plane (region A) is occupied by aromatic
Crystalline host–guest compounds (clathrates) are an important
topic of supramolecular chemistry.1 During the last decade, exhaus-
tive studies on clathrate host molecules with typical shapes, inwhich
particular steric requirements of the host molecule and the role of
aromatic ring interactions between host and guest have been clari-
fied, have given rise to new strategies for crystalline inclusion com-
plex formation, leading to the design of new types of clathrate hosts.2
guests or the aromatic ring of adjacent host molecules.
In a previous study, we demonstrated that the [4þ2]
p cyclo-
adducts of phencyclone (1a) and N-arylmaleimides act as non-
hydroxylic clathrate hosts capable of aprotic solvent inclusion,3a,b
whereas the hydroxylic clathrate hosts derived from the cyclo-
adduct of phencyclone and acrylic acids or amides enclathrate polar
guest molecules, such as alcohols.3c
Fig. 1. Recognition sites of [4þ2]
p cycloadducts (3) of phencyclone (1a) and
In both cases, the presence of the phenanthrene-condensed
bicyclo[2.2.1]hept-2-en-7-one moiety played an important role in
the recognition of the aromatic rings of guest and hosts. The
dienophiles.
In the guest-free non-hydroxylic hosts, edge-to-face in-
teractions are operative between the phenanthrene and phenyl
* Corresponding author. E-mail address: meto@ph.sojo-u.ac.jp (M. Eto).
rings attached to the a-positions of the bridged carbonyl group. The
0040-4020/$ e see front matter Ó 2012 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tet.2012.03.005

M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
3567
Table 1
aromatic guests in the inclusion complexes of these molecules are
likewise engaged by a similar recognition mechanism involving the
phenanthrene ring.3b
The endo-oriented dienophilic residue of these adducts in-
terferes with the approach of guest molecules from region B. For
example, the N-naphthyl maleimide derivative of phencyclone
prefers to adopt a congested T-shaped conformation with an
Crystalline inclusion compounds of 3a and 3b (host/guest molar ratio and de-
sorption endotherm peak temperature)
Guest solvent (bp/ꢀC)
Host compound
3a
3b
Host/guest Desolvation Host/guest Desolvation
ratio
temp/ꢀC
ratio
temp/ꢀC
intramolecular AreH/p interaction between the phenanthrene ring
and naphthyl ring within region B.
Acetone (56)
2:1
2:1
1:1
da
2:1
(221)
(194, 224)
(121)
2:1
2:1
1:1
da
1:1
1:2
1:1
1:1
1:1
1:1
1:1
(102, 111)
(118)
(78)
Butan-2-one (80)
Pentan-3-one (101.5)
Alcohols
THF (65e67)
1,4-Dioxane (100e102) 2:1
In the host of 1a with cinnamic acid and trans-2-pentenoic acid,
the host molecules are also linked by a ‘bidentate’ CeH/O]C< type
interaction4 between the phenanthrene-ring hydrogens and the
bridged carbonyl oxygen or the carboxylic carbonyl group, which
stabilizes the host-host framework.3c
Based on these observations, we postulated that the re-
placement of the substituent (R) of the known hosts with a less
bulky and aromatic group should facilitate complex formation with
small-sized or aromatic guest molecules by allowing guest mole-
cules to approach through region B, leading to a new type of non-
hydroxylic clathrate host.
(221)
(233)
(213)
(174)
(93, 137)
(78, 140)
(131)
Benzene (80)
2:1
2:1
db
2:1
2:1
Toluene (110e111)
o-Xylene (143e145)
m-Xylene (138e139)
p-Xylene (138)
(118)
(99, 129)
(93, 118)
(105, 151)
(132)
(164)
a
Slightly soluble in alcohols (methanol, ethanol, 1-propanol, 2-propanol, 1-
butanol, 2-butanol, 2-methyl-1-propanol, 2-methyl-2-propanol).
b
Ratio dependent on recrystallization condition.
In this paper, we wish to describe the inclusion behaviour of the
phencyclone (1a) [4þ2]
p cycloadduct of acenaphthylene in com-
parisonwith those of analogous host derived from tetracyclone (1b).
(ESI-S12). The desolvation may proceed by single-step release of all
guest molecules forming the guest-free host. The difference be-
tween the onset temperature of desolvation and the boiling point of
the pure solvent may be taken as a measure of the thermal stability
of a clathrate. The differences observed herein indicate that the
guest molecules are strongly held within the host lattice (Table 2).
2. Results
2.1. Preparation of the clathrate hosts
The endo[4þ2]
p cycloadducts (3a, 3b) of phencyclone (1a) and
tetracyclone (1b) with acenaphthylene (2) were prepared accord-
Table 2
Differential thermal analysis (DTA) and thermogravimetry (TG) data for important
clathrates
ing to known methods (Fig. 2).3
Host compound (3a)
Guest solvent
Host/guest ratio
Bp (guest)/ꢀC
DTA:
Acetone Pentan-3-one Benzene 1,4-Dioxane
2:1
56
1:1
101.5
2:1
80
2:1
100e102
Desorption endotherm
onset temperature/ꢀC
TG:
221
121
213
233
Weight loss expected (%) 5.2
Weight loss observed (%) 5.1
13.9
12.2
6.8
6.8
7.6
7.5
Fig. 2. Cycloadducts (3) of cyclopentadienones with acenaphthylene (2).
In the case of 3b, the aromatic guest compounds are loosely
included as reflected by the desolvation temperatures, which are
nearly equal to or lower than the boiling points of pure guests,
except for benzene, indicating that the inclusion pattern is different
from that of 3a (Table 1). Two endothermic peaks corresponding
the guest loss were observed for the complexes of 3b with acetone,
THF, 1,4-dioxane and xylenes.
The guest selectivity of 3a was evaluated by recrystallization
from equimolar mixed solvents, the results of which are summa-
rized in Table 3.
2.2. Inclusion behaviour
The inclusion properties of host compounds 3a and 3b were
evaluated with a variety of solvents (18 solvents of four types: al-
cohols, ketones, ethers and aromatics). Recrystallization of the host
compounds from the respective guest solvents afforded the corre-
sponding inclusion complexes, the details of which are summa-
rized in Table 1.
The host/guest ratio was evaluated based on the integrated in-
tensity of methine signals of the host in the 1H NMR spectrum and
the weight-loss curve in the thermogravimetric (TG) analysis.
As shown inTable 1, 3a formed 2:1 complexes withaproticsolvents
(i.e., aromatic, ketonic and etheric solvents), whereas 3b primarily
formed 1:1 complexes with these solvents, with a few exceptions.
The typical TG and DTA (differential thermal analysis) data of
the 3a$guest complexes showed an endothermic pattern corre-
sponding to loss of guests, followed by an endothermic peak caused
by melting of the host. For example, the desolvation of 3a$acetone,
3a$1,4-dioxane and 3a$benzene, indicated by an endothermic loss
of mass corresponding to the guest removal, occurred at temper-
atures of 221, 233 and 213 ꢀC, respectively, which are extremely
high in comparison to the boiling point of the pure guest liquids
Table 3
Selective guest inclusion of 3a from a two-component solvent system
Guest solvents (I/II)
3a/I/II molar ratio
Benzene/acetone
Benzene/1,4-dioxane
Benzene/toluene
1,4-Dioxane/acetone
Benzene/methanol
1,4-Dioxane/methanol
Acetone/methanol
2.0:0.9:0.1
2.0:0.1:0.9
2.0:0.8:0.2
2.0:1.0:0.0
2.0:1.0:0.0
2.0:1.0:0.0
2.0:1.0:0.0
Overall, the enclathration of guests by 3a proceeded with some
selectivity, showing preferential enclathration with guests accord-
ing to the sequence: 1,4-dioxane>benzene>acetone. In the case of

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M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
recrystallization from the benzene/toluene mixture, benzene was
preferentially included over toluene, which is indicative of the size
and shape recognition capacity of 3a for aromatic guests. Re-
crystallization of the host 3a from solvent mixtures containing al-
cohols proceeded with the selective guest inclusion of the non-
alcoholic molecules.
Another edge-to-face (AreH/p) interaction is found between the
phenanthrene ring plane (region A) and the phenyl ring of the ad-
ꢀ
jacent host molecule [C/plane, 3.456(2) A]. Thus, host 3a is as-
sembled to give an infinite ‘column’ structure parallel to the c-axis.
Qualitative evaluation of the shapes, sizes and directions of the
cavities within the host lattice was performed by investigation of
the clipped solid-surface representation using the program Chi-
mera.6 The representation of the van der Waals surface of the
clathrate (Fig. 4a) shows that the channel is oriented along the
direction of the ‘bidentate’ CH/O interaction of the host columns (c-
axis direction). The guest benzene is well accommodated in the
narrow cavity that runs through the lattice of host molecules, and
guest benzene is held between these stacking columns of the host
2.3. X-ray crystal analysis
The structures of the inclusion compounds were determined by
single-crystal X-ray analyses of 3a$benzene (2:1), 3a$toluene (2:1),
3a$1,4-dioxane (2:1), 3a$acetone (2:1), 3a$pentan-3-one (1:1) and
3b$acetone (2:1). However, single crystals of guest-free 3a and 3b
have not yet been obtained.
molecules by aromatic CH/p (edge-to-face) interactions of the two
acenaphthene rings (Figs. 4 and 16a). The plane of benzene is ori-
ented at an angle of 67.3ꢀ relative to the acenaphthene ring and the
edge-to-face distance between the carbon atoms (3- and 4-
2.3.1. 3a$Benzene complex. The host framework of the 3a$benzene
complex is assembled by ‘bidentate’ AreH/O] band CH/
p in-
position) of the acenaphthene ring and the plane of the guest
p-
teractions. Inspection of the crystal-packing diagram shows that
the bridged carbonyl oxygen is positioned relative to the two hy-
drogen atoms (4- and 5-position) of the phenanthrene moiety to
form a ‘head-to-tail’ arrangement of the hosts along the c-axis, in
ꢀ
system are 3.718(5) and 3.793(4) A [the CeH/plane distances are
ꢀ
2.87(3) and 3.07(3) A, respectively.].
ꢀ
which the C/O distances are 3.463(3) and 3.349(3) A [the CeH/O
ꢀ
distances are 2.52(3) and 2.42(3) A, respectively.] (Fig. 3).
Fig. 3. CH/O and CH/p hostehost network of 3a$benzene complex.
The host molecules are firmly interconnected to form a dimeric
structure (demarcated by a dotted line in Fig. 3) in a typical fashion,
such that the 5,6-hydrogens of the acenaphthene ring of the host
are located on the opening of a V-shaped cavity created by the
phenanthrene and acenaphthene rings of a neighbouring host
molecule, in which the CH/
p
(edge-to-face) interactions5 are op-
erative. The closest distances between the acenaphthene carbon
atoms and the respective benzene ring of the phenanthrene moiety
ꢀ
are 3.641(3) and 3.776(3) A [the CeH/plane distances are 2.75(3)
ꢀ
and 2.85(3) A.]. The resulting host dimers are connected by the
‘bidentate’ pC]O/He hydrogen bonds as well as apparent face-to-
face manner between the neighbouring acenaphthene moieties.
CH/p interactions are operative between the methine hydrogens of
the acenaphthene moiety and the adjacent acenaphthene ring, in
which the distances between the methine carbon and the plane are
ꢀ
3.450(2) and 3.494(2) A [the CeH/plane distances are 2.61(2) and
2.68(2) A.].
Fig. 4. Crystal packing of 3a$benzene complex. (a) Clipped solid-surface representa-
tion (b) edge-to-face interactions between host and guest.
ꢀ

M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
3569
2.3.2. 3a$Toluene complex. The 3a$toluene complex exhibits
a packing arrangement that is essentially the same as that of
3a$benzene (Fig. 5). In both cases, the host framework of the
complex is built by CH/p (edge-to-face) and ‘bidentate’ AreH/O]
interactions. The guest toluene occupies the space between the
host molecules by means of aromatic CH/
acenaphthene rings.
p interactions of the two
Fig. 5. Crystal packing of 3a$toluene complex (toluene presents a disorder).
The position of the guest methyl group is disordered in the
crystal. The guest assumes two possible orientations related by
180ꢀ rotation around the centre of the benzene ring. On this basis,
3a might enclathrate p-xylene via a similar inclusion mode. The
methyl group of toluene is extruded into a void space of the channel
created by the host columns. The edge-to-face distance between
the carbon atom of the acenaphthene ring and the plane of the
ꢀ
guest
p
-system is 3.766(7) A. The interatomic distance between the
carbon atoms (3- and 4-position) of the acenaphthene ring via the
guest molecule is approximately equal to that of 3a$benzene.
2.3.3. 3a$1,4-Dioxane complex. The packingarrangements of3a$1,4-
dioxane isquite similartothatof the 3a$benzenecomplex (Fig. 6). The
host molecules are held together by CH/p (edge-to-face) interactions
to form a dimeric structure in which the 5-hydrogen atom of the
acenaphthene ring is located at the opening of a V-shaped cavity
created by the phenanthrene and acenaphthene ring, in which the
closest distance between the carbon atom of the acenaphthene ring
and the respective benzene ring of the phenanthrene plane is
Fig. 6. Crystal packing of 3a$1,4-dioxane complex (a) hostehost network (b) hoste
guest network.
ꢀ
3.763(5) A. The hosts are also arranged in a head-to-tail fashion by the
host molecules. The carbonyl oxygen atom interacts with the 3- and
‘bidentate’ CH/O-type hydrogen bonds [C/O, 3.413(5) and
3.422(4) A] between the phenanthrene ring hydrogens and bridged
4-hydrogens of the phenanthrene ring, in which the C/O distances
are 3.357(8) and 3.416(9) A (Fig. 7).
ꢀ
ꢀ
carbonyl oxygen as well as the CH/
stacked acenaphthene moieties, thus forming a ‘column’.
p
interactions between the offset-
The relative disposition of the host molecules affects the face-to-
face stacking between neighbouring acenaphthene moieties. The
distance between the methine carbon of the acenaphthene moiety
and the neighbouring acenaphthene ring of the host A molecules is
The guest dioxane is held between these stacking columns of
the host molecules. Each ether oxygen of dioxane forms a CH/O-
type hydrogen bond with the 2-hydrogen of the host phenyl
ꢀ
ꢀ
3.483(7) A [CeH/plane, 2.671(7) A], whereas the corresponding
ꢀ
ꢀ
group [C/O, 3.554(6) A]. The analysis also suggests the presence of
separations are 3.488(7) and 3.487(7) A [CeH/plane, 2.704(7) and
ꢀ
the CH/
p
interaction between the 2-methylene hydrogen of di-
2.704(7) A] with respect to host B molecules (Fig. 7b,c). Each type of
oxane and the phenanthrene ring, in which the nearest C/C dis-
tance is 3.572(7) A.
host is independently linked head-to-tail to form a ‘column’
structure via ‘bidentate’ CH/O and CH/
p interactions.
ꢀ
The phenanthrene rings of the host A are oriented in an edge-to-
face manner with respect to host B. The 2-hydrogen atom of the
phenanthrene ring is located perpendicular to the middle benzene
ring of an adjacent phenanthrene ring with a C/plane distance of
3.876(9) A (Fig. 8). In addition to the CH/O interaction between the
carbonyl oxygen and the phenyl group, this interaction may play
a leading role in the construction of the host framework.
The guest acetone is located above the phenanthrene ring (re-
gion A) of host B and is accommodated in the space surrounded by
two types of stacking host columns that are alternately arranged
(Figs. 8 and 16b). Van der Waals forces are thought to be the pri-
mary interactions connecting the host and the guest in conjunction
2.3.4. 3a$Acetone complex. The crystal structure of the 3a$acetone
complex has two independent hosts (hosts A and B) and an acetone
molecule in the asymmetric unit. The network between host A mol-
ecules includes a ‘bidentate’ AreH/O interaction that is different from
that observed in the 3a$benzene and 3a$1,4-dioxane complexes. The
bridged carbonyl oxygen forms a CH/O-type hydrogen bond with the
ꢀ
ꢀ
4-hydrogen atom of the phenanthrene ring [O/C, 3.614(10) A]. An-
other close contact is found between the carbonyl oxygen and the
ꢀ
phenyl hydrogen of the adjacent host B [O/C, 3.279(10) A].
On the other hand, the network pattern between host B mole-
cules is also unique with regard to the relative disposition of the

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M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
Fig. 9. Hostehost and guesteguest network of 3a$pentan-3-one complex.
Fig. 7. Hostehost network of 3a$acetone complex.
Fig. 10. Packing diagram of 3a$pentan-3-one complex (solid-surface representation).
Fig. 8. Packing diagram of 3a$acetone complex.
guest ketones are arranged along the host layer in such a way as to
cancel the dipoleedipole interaction of the carbonyl functions. A
pair of guest molecules forms a cyclic dimer unit by means of weak
CH/O-type hydrogen bonds between the carbonyl oxygen and the
with a weak AreH/O] interaction between the carbonyl oxygen of
acetone and the hydrogen (2-position) of the phenyl group of host
ꢀ
A [C/O, 3.410(13) A].
ꢀ
hydrogen of the methyl group [C]O/(H)eC, 3.56(3) A]. The guests
2.3.5. 3a$Pentan-3-one complex. The hostehost network of the
3a$pentan-3-one complex is stabilized by a ‘bidentate’ CH/O link-
form a layer-like structure located within the relatively large space
created by the phenanthrene ring, bridged carbonyl group, and
diphenyl group of the bicyclo[2.2.1]hept-2-en-7-one moiety,
without remarkable attractive host-guest interactions. The edge-
age and two types of CH/
between the acenaphthene hydrogen atoms and the phenanthrene
ring and CH/ interactions between the methine hydrogens of the
p interactions (i.e., AreH/p interactions
p
to-face (AreH/
plane and the phenyl ring of the adjacent host molecule found in
3a$benzene and the AreH/ interactions between the phenan-
p) interactions between the phenanthrene ring
acenaphthene ring and the neighbouring acenaphthene ring). The
distances are shown in Fig. 9.
p
The solid-surface representation of the clathrate indicates
a characteristic layer-like structure having channels within a close
distance along the crystallographic c-axis direction (Fig. 10). The
threne rings found in 3a$acetone are not observed in the
3a$pentan-3-one complex, the absence of which should prove
unfavourable for the stability of the host framework.

M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
3571
2.3.6. 3b$Acetone complex. Two independent hosts (host A and B)
are observed in the asymmetric unit of the crystal structure of the
3b$acetone complex along with an acetone molecule. The packing
diagram and notable hostehost and hosteguest interactions are
shown in Figs. 11 and 12.
Fig. 12. Crystal packing of 3b$acetone complex (stereoview).
ꢀ
3.515(7) A for host B. The dimeric structures are connected infinitely
along the a-axis by pC]O/He hydrogen bonds between the car-
bonyl oxygen and the hydrogen of the acenaphthene ring of host A.
On the other hand, the dimer unit of host B is connected to the
neighbouring unit by a CH/O-type hydrogen bond (between the
carbonyl oxygen and methine carbon of the acenaphthene moiety)
and an AreH/
teratomic and C/plane distances are 3.565(6) and 3.374(7) A, re-
spectively. Besides these interactions, the interaction between
p interaction (between the phenyl rings). The in-
ꢀ
p/p
the offset stacked acenaphthene rings of host B (plane/plane,
ꢀ
3.472 A) and edge-to-face interaction between acenaphthene rings
ꢀ
of hosts A and B [C/plane, 3.709(6) A] stabilize the host-host
network (Fig. 11c).
The guest acetone is accommodated in the space surrounded by
two types of stacking host column structures, which are alternately
arranged (Figs. 11 and 16d). The guest oxygen atom interacts with
the hydrogen at the 3-position of a phenyl ring attached to the a-
positions of the bridged carbonyl group by a pC]O/HeAr in-
teraction, and the methyl hydrogen of the guest acetone interacts
with this phenyl ring by a CH/p interaction, respectively (Fig. 11c).
2.4. Molecular modelling of 3a$guest complex
We tried to assess the geometric features involving weak in-
termolecular interactions, such as edge-to-face or CH/O interaction
forces and the energies of clathrate formation with guest molecules
by semi-empirical MO calculations on the basis of successful ap-
plication of the PM67e9 method to modelling of organic crystalline
solids.10,11
The geometries of clathration models (involving one guest and
eight hosts that interact with the guest as a minimal molecular
unit) of the 3a$benzene and 3a$1,4-dioxane complexes were opti-
mized by the PM6 method without imposing any symmetrical re-
strictions (Fig. 13).12 However, the stationary point of 3a$acetone
(eight hosts and one guest) and 3a$pentan-3-one complexes (eight
hosts and four guests) could not be found by means of similar
calculations. Based on the structural information of the clathration
models, the stabilization energy due to the formation of the
clathrate was estimated as the energy difference between
clathration model) and
Hf (3aꢁ8þguest) (Table 4).
The stabilization energy arising from intermolecular interactions
of the host molecules in dimeric structures related by AreH/ (di-
mer A), CH/
(dimer B) and ‘bidentate’ CH/O (dimer C13) in-
DHf (the
D
p
p
teractions (Fig. 14) was also calculated in a similar way. The energy
of the various dimeric structures is 4e5 kcal/mol more stable than
that of the components (Table 4). In the case of the host dimer
Fig. 11. Hostehost network of 3b$acetone.
formed by the ‘bidentate’ CH/O interaction, a CH/p interaction be-
Both of the host molecules are loosely interconnected by the
phenyl rings of the stilbene moieties to form a dimeric structure, in
which the distances between the closest carbon atom (3-position)
of a phenyl ring of the stilbene moiety and the phenyl ring plane of
tween the hydrogen of the phenanthrene ring and the phenyl ring
of the neighbouring host was suggested. The degree of stabilization
due to the purely CH/O interaction is assumed to be 2.5 kcal/mol on
the basis of a calculation involving a model structure in which the
two phenyl groups are replaced by hydrogen atoms.
ꢀ
the neighbouring host molecule is 3.610(8) A for host A and

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M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
Table 4
(a) PM6-optimized structure for the clathrate model of 3a benzene
PM6-optimized heats of formation (DHf, kcal/mol) for the clathration model and the
stabilization energies
Calculation model
D
Hf
Stabilization
energy, DDHfa
Clathration model of 3a$benzene
(eight hosts and one guest)
Clathration model of 3a$1,4-dioxane
1120.3
1007.3
52.7
55.9
(eight hosts and one guest)
Host dimer by AreH/
Host dimer by CH/ interactions [dimer B]
Host dimer by ‘bidentate’ CH/O interactions
including AreH/ interactions [dimer C]
Host (3a)
p
interactions [dimer A]
283.2
282.0
283.5
4.0
5.2
3.7
p
p
143.6
24.2
e85.6
d
d
d
Benzene
1,4-Dioxane
(b) X-Ray structure of 3a benzene complex
a
DDHf¼S
D
Hf (components)ꢂDHf (calculation model).
(a)
(b)
(c) PM6-optimized structure for the clathrate model of 3a 1,4-dioxane
(c)
(d) X-Ray structure of 3a 1,4-dioxane complex
Fig. 14. PM6-calculated partial interaction structures: (a) host dimer by AreH/
p
(edge-
to-face) interaction; (b) host dimer by CH/p interaction; (c) host dimer by ‘bidentate’
CH/O interaction.
acenaphthene and phenanthrene rings necessarily confer addi-
tional strength to the host network, leading to the formation of
stable clathrates. In fact, the desolvation temperatures of the
3a$guest complexes are markedly higher than those of the corre-
sponding 3b complexes, the latter of which contains the con-
formationally flexible stilbene moiety. The stabilization of the host
network of 3b is significantly lowered by the lack of these re-
markable attractive interactions between the aromatic rings of the
host molecule. The host molecules of 3a are also linked head-to-tail
to form a ‘column’ structure by means of ‘bidentate’ CH/O hydrogen
bonds between the phenanthrene ring hydrogens and bridged
Fig. 13. PM6-calculated structure of 3a$benzene complex and 3a$1,4-dioxane (eight
hosts and one guest) and the X-ray structures looking through the central guest
molecule.
3. Discussion
The structural feature of the hostehost network of 3a, in which
the edge-to-face (between phenanthrene and phenyl rings) and
‘bidentate’ CH/O (between phenanthrene protons and carbonyl
oxygen) interactions are operative, was consistent with those
expected on the basis of the known clathrate of the carboxylic
host.3c However, contrary to our expectations, the V-shaped cavity
(region B) created by the phenanthrene and acenaphthene rings
carbonyl oxygen as well as via CH/p interactions between the
stacked acenaphthene moieties.
The crystal structures of the 3a$guest complexes that were
evaluated in this study show that the carbonyl oxygen atom con-
tributes to the linkage of the host molecules without exception.
This ‘column’ structure of the host/host network found in the
clathrates of 3a is a common characteristic feature (Fig. 15a). The
cooperative effects of these weak intermolecular interactions
does not interact with aromatic guest molecules by aromatic CH/
or interactions, but instead, the acenaphthene ring of an ad-
jacent host molecule is included in this region (Fig. 15a). These
additional aromatic CH/ interactions between the rigidly oriented
p
p/p
p

M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
3573
which has a packing structure similar to 3a$benzene. The energy
difference for 3a$1,4-dioxane versus 3a$benzene was ca. 3 kcal/
mol, suggesting that enclathration of 3a with 1,4-dioxane is ther-
modynamically more favourable than formation of the 3a$benzene
complex.
(a)
The stabilization energy of benzene arising from its inclusion in
3a by means of double edge-to-face interactions is 4.0 kcal/mol,
which was calculated from the difference between the optimized
energy (DHf) of the clathration model and the corresponding single
point (1SCF) calculation in the absence of the guest. The value
seems to be acceptable judging from the fact that the interaction
energy of the T-shaped benzene dimer derived from CCSD(T)
(coupled cluster calculations with single and double substitutions
with non-iterative triple excitations) calculation is ꢂ2.46 kcal/mol
at the maximum.16
(b)
(c)
The clathration model includes two dimer A, four dimer B and
four dimer C units (see Fig. 14). The sum of the stabilization ener-
gies from each of these units is 43.6 kcal/mol, which accounts for
a major portion (ca. 83%) of the stabilization energy derived by
formation of the clathrate, suggesting that the weak AreH/p, CH/p
and ‘bidentate’ CH/O interactions associated with dimer formation
play a major role in the construction of the host framework.
PM6 method seems to be a useful tool for estimation of in-
teraction in organic crystalline solids that are hard to be subjected
to high-level MO calculation.
Fig. 15. Characteristic host/host network found in 3a$guest complex.
should play a leading role in the construction of the host frame-
work. The inability of 3a to enclathrate methanol (see Table 3) can
be attributed to the prevention of the formation of the head-to-tail
linkage by typical hydrogen bonding between the bridged carbonyl
of the host and methanol.
The additional CH/p interactions between the phenyl ring and
the phenanthrene ring plane of the adjacent host molecule (in-
teractions between the column structures) in the 3a$benzene
complex further strengthen the host/host network (Fig. 15b). A
similar structural feature is found in the 3a$toluene and 3a$1,4-
dioxane complexes, which exhibit high desolvation temperatures
in comparison to the boiling point of the pure guests. In the case of
the 3a$acetone complex, the host framework is constructed by CH/
O interactions between the bridged carbonyl oxygen and the phe-
For the quantitative evaluation of weak interactions, such as CH/
p, high-level quantum chemical calculations using MP2/cc-pVXZ
(X¼T or Q) or MP2/aug-cc-pVXZ (X¼D or T) level, which include
a large basis set and electron correlation correction are desirable in
general.14,15 However, the performance of such calculations for
a crystal packing model consisting of a large number of molecules is
still beyond the current computational feasibility. In order to com-
pensate the disadvantage in the process of such high-level calcula-
tions, we examined the applicability of recently developed PM6
method that is aimed at providing a reasonable balance between
speed and accuracy for investigation of molecular species of bio-
chemical interest. The clathrates of 3a seem to be a suitable model for
testing applicability of PM6 to modelling of organic crystalline solids.
The spatial orientation of the guest molecule of the crystal
nyl ring hydrogen as well as the CH/
phenanthrene rings in lieu of the CH/
p
interaction between the
interactions found in
p
3a$benzene (Fig. 15c), whereas such interactions between the hosts
are inoperative in the case of 3a$pentan-3-one.
The flexible network constructed by the weak hostehost in-
teractions is guest-inclusion dependent whereby the arrangement
of the columns is affected by the size and character of the guest
molecule; the guest molecules might act as ‘glue’ that binds the
host column structures. The inclusion pattern of 3a clarified in this
study is shown in Fig. 16aec.
structure as well as characteristic networks (AreH/
p
, CH/
p
, and
The host molecule (3a) enclathrated ketones, cyclic ethers and
aromatics. Benzene was particularly strongly incorporated within
the host lattice, and the desolvation temperatures were extremely
high relative to the boiling point of the pure guest (Table 2). The host
lattice contains channels along the crystallographic c-direction. The
aromatic guests are located in the spaces between region C of the
‘bidentate’ CH/O) between host molecules in the case of both
clathrate models (3a$benzene and 3a$1,4-dioxane) were approxi-
mately reproduced by the PM6 calculation (Fig. 13). For the clath-
ration model of 3a$benzene, the guest is held between the host
molecules by aromatic CH/p (edge-to-face) interactions of the two
acenaphthene rings, in which the edge-to-face distances between
host columns and are held by edge-to-face (CH/p) interactions be-
the carbon atoms (3- and 4-positions) of the acenaphthene ring and
tween acenaphthene ring hydrogens and the benzene ring
(Fig. 16a). The importance of the rigid acenaphthene moiety for
aromatic guest recognition is supported by the fact that the endo
ꢀ
the plane of the guest
p
-system are 3.39 and 3.42 A (the
ꢀ
CeH/plane distances are 2.61 and 2.67 A, respectively). In the
clathrate model of 3a$1,4-dioxane, CH/O interactions were found
between the ether oxygen and the hydrogen of the phenyl group of
the host. The closest distance between the carbon atom and the
[4þ2]
p cycloadduct of 1a and styrene did not show inclusion abil-
ity.3a On the other hand, the desolvation temperatures of toluene
and p-xylene enclathrated in 3a were not remarkably high in
comparisonwith the boiling point of the pure liquid, suggesting that
steric crowding within the space weakened host lattice. However,
the possibility that the packing pattern of 3a$m-xylene is different
from that of 3a$benzene cannot be denied because the desolvation
temperature is exceptionally low in the latter complexes. Judging
from the cavity of 3a$toluene, sufficient space may not be available
in the void to extrude the m-methyl group of m-xylene.
ꢀ
ꢀ
oxygen atom is 3.378 A [X-ray, 3.554(6) A]. Compared to the X-ray
analysis data, these calculated distances seem to be somewhat
underestimated. This may be due to the minimal clathration model,
in which the interactions with the external environment of the
model are oversimplified.
The stabilization energy of 3a$benzene clathration model was
estimated to be 52.7 kcal/mol, indicating that the formation of the
clathrate generates a sizable stabilization. Similar stabilization was
observed for the 3a$1,4-dioxane clathration model (55.9 kcal/mol),
Ketones tend to occupy the space within region A. In the
3a$acetone complex, the host network is strengthened by an edge-

3574
M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
Fig. 17. Composite diagram of the cavity (a) 3a$benzene (b) 3a$pentan-3-one (The
ꢀ
radius of each sphere is taken to be 1.2 A greater than the van der Waals radius of the
corresponding atom.).
Fig. 16. Schematic drawing of inclusion mode of host 3a: (a) 3a$benzene or 3a$1,4-
dioxane (2:1). (b) 3a$Acetone (2:1). (c) 3a$Pentan-3-one (1:1). (d) 3b$Acetone (2:1).
the ‘bidentate’ CH/O interaction between the phenanthrene ring
and the bridged carbonyl oxygen as well as the AreH/p interaction
to-face interaction between the phenanthrene rings of adjacent
hosts (Fig. 15c). The difference between the onset temperature for
desolvation and the boiling point of the pure solvent for 3a$pentan-
3-one is much lower than that for 3a$acetone, which may be
explained by the difference in their inclusion modes as well as the
strength of the hostehost network stated above.
between phenanthrene and the phenyl rings. As pointed out above,
the host/host network of 3b is primarily constructed by interactions
among the phenyl rings. These interactions among the conforma-
tionally flexible phenyl groups are considered to be relatively weak
as reflected in the DTA data.
On the other hand, the acenaphthene ring plays an important
Fig. 17 shows the cavities limited by a concave surface of the
sphere from the surrounding atoms, which was created by using
the program CAVITY.17 The cavity shows the area accessed by the
centres of atoms of the guest. The guest 3a$pentan-3-one is loosely
fitted in the cavity encapsulated by the host and guest molecules,
whereas 3a$benzene exhibits the typical tight fitting in which there
are several significant close contacts between the carbon atoms of
the host and guest. Only CH/O-type interactions between the guest
role in the construction of the hostehost network of 3b. CH/
p and
p/p
interactions between the acenaphthene rings are operative in
3b$acetone (Fig. 11). This shows that a suitable spatial arrangement
of the aromatic recognition motif (i.e., acenaphthene, phenan-
threne and phenyl rings) will produce similar inclusion behaviour
in various host molecules. This information should prove useful in
the design of suitable hosts for recognition of aromatic guests via
CH/p and p/p interactions.
molecules are found in 3a$pentan-3-one; CH/p-type close contacts
between the host and the guest molecules also confer a stabilizing
effect on the crystal packing. The dimeric units of 3a$pentan-3-one
also form a layer that is interdigitated with region A of the host
columns, without remarkable attractive interactions between the
dimeric units. The absence of these interactions in conjunction with
the void space might facilitate the ready collapse of the clathrate.
The inclusion behaviour exhibited by host 3b, which contains the
stilbene moiety, is different from that of host 3a in that the aromatic
guests are included in a 1:1 host/guest ratio. The desolvation
temperatures of the 3b clathrates are appreciably lower than those
observed with host 3a. The replacement of the phenanthrene
moiety of 3a with the stilbene moiety in 3b may decrease the
stability of the 3b hostehost network due to the absence of both
4. Conclusion
This study demonstrated that the clathrate hosts (3a) derived
from the [4þ2] cycloaddition of phencyclone (1a) to acenaph-
thylene (2) effectively furnishes the aromatic CH/ (edge-to-face)
interactions between the phenanthrene unit and acenaphthene
ring, leading to strong hostehost networks. These weak in-
teractions as well as ‘bidentate’ CH/O interactions between
phenanthrene-ring hydrogens and a bridged carbonyl group con-
tribute to the formation of characteristic host ‘column’ structures,
which facilitates the inclusion of various guest molecules within
the void space between the host columns.
p
p

M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
3575
5. Experimental section
5.1. General
were performed using the crystallographic software package Crystal
Structure.22b,c These X-ray crystallographic data have been deposited
at the Cambridge Crystallographic Data Centre (CCDC).
Crystal data of 3a$benzene: C41H26O$C3H3 (1/2 benzene),
Melting points were uncorrected. The IR spectra were taken
with a Hitachi 270e30 spectrophotometer. 1H NMR and 13C NMR
spectra were taken with JEOL JNM-A 500 and JNM-ECA 500
(500 MHz) spectrometers for ca. 10% solution (CDCl3) with TMS as
M¼573.71, triclinic, space group P(ꢂ1) (#2), a¼12.328(2),
ꢀ
b¼13.637(5ꢀ),
c¼9.613(2)
A,
a¼103.89(2),
b¼103.83(1),
3
g
¼95.09(2) , V¼1505.1(6) A , Z¼2, Dc¼1.266 g cmꢂ3, R¼0.069,
ꢀ
Rw¼0.081, GOF¼1.16, CCDC ref. No. 857594; 3a$acetone:
an internal standard; chemical shifts are expressed as
d
values
2C41H26O$C3H6O, M¼1127.39, triclinic, space group P(ꢂ1) (#2),
ꢀ
(ppm) and the coupling constants (J) are expressed in hertz. Mass
spectra were obtained using a JEOL JMS-DX 303 instrument. Ther-
mal analyses were performed on a Shimadzu DTG-50/50H Simul-
taneous TG/DTA instrument.
a¼10.0359(8), b¼14.863(2), c¼20.408(2) A,
a
¼88.332(3),
3
ꢀ
ꢂ3
ꢀ
b¼87.334(2),
g
¼79.546(3) , V¼2989.7(5) A , Z¼2, Dc¼1.252 g cm
,
R¼0.1271, Rw¼0.1870, GOF¼1.020, CCDC ref. No. 857595; 3a$1,4-
dioxane: C41H26O$C2H4O (1/2 1,4-dioxane), M¼578.71, triclinic,
ꢀ
space group P(ꢂ1) (#2), a¼9.679(1), b¼12.103(2), c¼13.501(2) A,
3
ꢀ
ꢀ
5.2. Materials
a¼86.521(6),
b
¼76.752(4),
g
¼76.084(5) , V¼1494.2(4) A , Z¼2,
Dc¼1.286 g cmꢂ3, R¼0.0789, Rw¼0.1224, GOF¼1.001, CCDC ref. No.
Phencyclone (1a)18 and tetracyclone (1b)19 were prepared
according to the reported methods.
857596; 3a$pentan-3-one: C41H26O$C5H10O, M¼620.79, triclinic,
ꢀ
space group P(ꢂ1) (#2), a¼9.849(3), b¼11.896(3), c¼16.596(5) A,
3
ꢀ
ꢀ
a¼70.257(8),
b¼77.572(9),
g
¼69.623(9) , V¼1705.2(8) A , Z¼2,
5.3. [4D2]
p
Cycloadducts (3) of 1 with acenaphthylene (2)
Dc¼1.209 g cmꢂ3, R¼0.1107, Rw¼0.1821, GOF¼1.001, CCDC ref. No.
(general procedure)
857597; 3a$toluene: C41H26O$C3.5H4 (1/2 toluene), M¼580.73, tri-
clinic, space group P(ꢂ1) (#2), a¼9.5582(9), b¼12.509(2),
¼103.573(4)ꢀ,
ꢀ
3
ꢀ
A solution of 1a (3.82 g, 10 mmol) and 2 (1.83 g, 12 mmol) in
toluene (20 mL) was refluxed until the dark green colour had faded
out (2 h). After cooling, the precipitated crystals were collected and
washed with cold ether and dried under vacuum. Recrystallization
from benzene gave colourless needles 3a.20
c¼13.767(2) A,
a
¼95.406(4),
b¼104.253(3),
g
V¼1530.6(3) A , Z¼2, Dc¼1.260 g cmꢂ3, R¼0.0742, Rw¼0.1067,
GOF¼1.167, CCDC ref. No. 857598; 3b$acetone: 2C41H28O$C3H6O,
M¼1131.42, triclinic, space group P(ꢂ1) (#2), a¼11.0417(6),
ꢀ
b¼12.351 (ꢀ1), c¼23.719(2) A,
a
¼103.558(3),
b
¼90.791(3),
3
Compound 3a: Yield 83%, colourless needles; mp 307e308 ꢀC. IR
g
¼90.867(4) , V¼3143.8(4) A , Z¼2, Dc¼1.195 g cmꢂ3, R¼0.1018,
ꢀ
(KBr): 1782 (bridged pC]O) cmꢂ1.1H NMR (500 MHz, CDCl3)
d: 5.38
Rw¼0.1723, GOF¼1.000, CCDC ref. No. 857599.
(s, 2H, exo-methine), 6.98e7.80 (m, 20H, aromatic H), 8.28 (d, 2H,
The checkCIF reports for 3a$benzene, 3a$toluene and
3a$pentan-3-one revealed level-A alerts relating to the bond
lengths of the guest molecule. This alert is due to a disorder of
a guest molecule and does not affect the results of the structure
determination. Inspection of the packing structure of 3b$acetone
suggests that the guest acetone assumes several possible orienta-
tions related by rotation around the carbonyl carbon atom; this has
resulted in a level-A alert in the CIF check.
J¼7.9, aromatic H), 8.31 (d, 2H, J¼7.3, aromatic H). 13C NMR
(125 MHz, CDCl3) d: 48.5 (methine), 66.2 (pCo), 120.9, 122.6, 123.2,
125.2, 125.6, 126.2, 127.1, 127.6, 128.0, 129.0, 129.1, 132.1 (aromatic
CH), 126.9, 130.4, 130.5, 134.6, 135.9, 141.8, 142.3 (aromatic pCo),
201.8 (bridged pC]O). MS (EI, m/z): 534 (Mþ), 506 (MþꢂCO). Anal.
Calcd for C41H26O: C, 92.11; H, 4.90. Found: C, 91.82; H, 5.13.
Compound 3b:21 Yield 78%, colourless prisms; mp 215e217 ꢀC.
IR (KBr): 1774 (bridged pC]O) cmꢂ1 1H NMR (500 MHz, CDCl3)
.
d
: 5.16 (s, 2H, exo-methine), 6.06 (d, 4H, J¼7.9, aromatic H),
6.61e6.64 (m, 4H, aromatic H), 6.75e6.78 (m, 2H, aromatic H),
7.14e7.65 (m, 16H, aromatic H). 13C NMR (125 MHz, CDCl3)
: 49.2
Acknowledgements
d
We thank Mr. T. Miyagoe, Ms. K. Fukumatsu and Mr. R. Mizukami
for experimental assistances.
(methine), 68.1 (pCo), 122.2, 123.9, 126.4, 126.9, 127.5, 127.7, 128.2,
129.1, 130.5 (aromatic CH), 131.7, 134.4, 134.5, 142.2, 142.7, 143.4
(aromatic pCo), 200.7 (bridged pC]O). MS (EI, m/z): 536 (Mþ),
508 (MþꢂCO). Anal. Calcd for C41H28O: C, 91.76; H, 5.26. Found:
C, 92.00; H, 5.31.
Supplementary data
Further crystal packing drawings and DTA/TG diagrams. Sup-
plementary data associated with this article can be found, in the
online version, at doi:10.1016/j.tet.2012.03.005.
5.4. Preparation of inclusion complexes
The host compound was dissolved under heating in the mini-
mum amount of a guest solvent. The solution was allowed to stand
for several days at room temperature. The crystals were collected
by suction filtration and dried.
References and notes
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The single crystalsforinclusioncomplexes were prepared byslow
evaporation of solution at room temperature. All measurements
were performed on a Rigaku RAXIS RAPID imaging plate area de-
ꢀ
tector with graphite-monochromatedMo-K
a
radiation (
l¼0.7107 A).
The data were collected at a temperature of 23ꢃ1 ꢀC to a maximum
2
q
value of 55ꢀ. The structure was solved by direct method
(SIR200822a), 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

3576
M. Abe et al. / Tetrahedron 68 (2012) 3566e3576
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