Direct observation of change in the molecular structure of benzyl (Z,Z)-muconate during photoisomerization in the solid state

Article abstract of DOI:10.1039/b714792a

For the solid-state photoisomerization of benzyl (Z,Z)-muconate to the corresponding (E,E)-muconate, the direct observation of a change in the crystal structure has revealed that the isomerization occurs by a topochemical reaction process according to a b

Full text of DOI:10.1039/b714792a

View Article Online / Journal Homepage / Table of Contents for this issue
COMMUNICATION
www.rsc.org/chemcomm | ChemComm
Direct observation of change in the molecular structure of benzyl
(Z,Z)-muconate during photoisomerization in the solid state{
Daisuke Furukawa, Seiya Kobatake and Akikazu Matsumoto*
Received (in Cambridge, UK) 2nd October 2007, Accepted 6th November 2007
First published as an Advance Article on the web 16th November 2007
DOI: 10.1039/b714792a
independently discussed volume-conserving reaction mechanisms
for the isomerization of 1,4-diphenyl-1,3-butadienes, 1,6-disubsti-
tuted hexatrienes13 and muconates in the crystalline state and the
other confined media. In the present study, we have revealed the
reaction mechanism of the solid-state photoisomerization of benzyl
(Z,Z)-muconate (1) to benzyl (E,E)-muconate (2) by the direct
observation of a change in the single crystal structure during the
photoisomerization in the solid state.
For the solid-state photoisomerization of benzyl (Z,Z)-muco-
nate to the corresponding (E,E)-muconate, the direct observa-
tion of a change in the crystal structure has revealed that the
isomerization occurs by a topochemical reaction process
according to a bicycle-pedal model and is finally accompanied
by a phase transition to a stable crystal structure.
Organic reactions performed in the solid state have many intrinsic
features and merits for synthetic and materials chemistry because
of the extremely high selectivity under crystalline-lattice control.1,2
A limited number of isomerizations of olefins between E and Z
forms in the crystalline state have been reported because of the
difficulty in the inevitable change in the size and shape of the space
occupied by the substituents of a double bond.3 The isomerization
of polyenes is an important photochemical process in biological
systems, and a bicycle-pedal model as the volume-conserving
reaction mechanism was first pointed out by Warshel in 1976.4
Later, Liu et al.5 proposed the hula-twist process to explain the
results of the picosecond time-resolved kinetics of the reaction in
the visual pigment rhodopsin. This model has been applied to not
The single crystal structures of 1 and 2, which were recrystallized
from n-hexane and ethanol, respectively, are shown in Fig. 1.{ The
crystallographic parameters are summarized in Table 1. The
monitoring of the change in the single-crystal structure of 1 was
successfully carried out during the photoisomerization using a
band path filter (UV-D36B) to irradiate light of wavelength longer
than 300 nm, corresponding to the absorption edge of 1. The
crystal structure of 1 after UV light irradiation was solved using
the structure before photoirradiation. The space group was the
same as the crystal before photoirradiation. They have crystal-
lographically imposed inversion symmetry. As shown in Table 1,
the crystal of 1 after the 27 h photoirradiation has cell volume and
density values (V 5 858.8 A , r 5 1.247 g cm23) identical to those
3
only photoisomerization in
a biosystem, but also various
˚
3
isomerization reactions in confined media such as viscous fluid,
rigid matrix, organic glass, and organic crystals, as well as the
isomerization of olefins with bulky substituents.6,7 Reactions
proceeding according to the bicycle-pedal8,9 and hula-twist
models,5–7 as well as reactions including crankshaft motion,10
require only a small change in the molecular shape, differing from
the conventional one-bond flip motion, which is usually observed
during many reactions in solution.
˚
of the crystal of 2 prepared by recrystallization (V 5 859.5 A ,
r 5 1.246 g cm23), but the packing mode of the molecules in the
crystals is different; the crystal of 1 has the space group of P21/c
while the crystal of 2 has P21. For the crystal structure after
photoirradiation, a disordered structure was observed around the
diene moiety, as shown by the ORTEP drawing in Fig. 2(b). This
disordered structure contains both 1 and 2 as the molecular
structures. Fig. 2(c) shows the separated structures. The conversion
after the photoirradiation was estimated to be 35% from the site
occupancy factor of the produced 2 in the crystal. Both the Z,Z
and E,E isomers included in the crystal after photoirradiation in
Fig. 2(c) have similar molecular shapes and planar conformations.
The direct observation of a crystal structure during the reaction
has revealed that the diene moiety changes its geometric structure
of the Z,Z isomer into the E,E isomer consistent with the bicycle-
pedal model (Scheme 1). This is evidenced by the fact that the s-cis
conformation of the reactant 1 is maintained in the product 2. The
change in the volume and shape of the reacting molecule is small as
expected for a reaction proceeding via the bicycle-pedal mechan-
ism. In fact, no large space is seen nearby to the diene moiety in the
crystals in Fig. 1(c). Bicycle-pedal motion needs a smaller space in
the solid, and a direct relationship is not observed between the
bicycle-pedal process and void space14 for the photoisomerization
of muconates.
Several years ago, we found that the isomerization of
n-butylammonium (Z,Z)-muconate produces the corresponding
E,E isomer in the crystalline state under photoirradiation.11 This
solid-state photoisomerization has some characteristics: no forma-
tion of E,Z isomer and one-way reaction from the Z,Z to E,E
form. In general, it is well-known that unsaturated compounds
such as olefins, polyenes, and azo compounds undergo reversible
one-bond photoisomerization12 to form a mixture of isomers. In
our preliminary studies, we pointed out the possibility that the
topochemical isomerization of the muconic derivatives in the solid
state follows the bicycle-pedal reaction mechanism,2 but the
molecular dynamics and mechanism of the reaction have not yet
been clarified. Recently, Saltiel et al.9 and Liu et al.6 have
Department of Applied Chemistry, Graduate School of Engineering,
Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka 558-8585,
Japan. E-mail: matsumoto@a-chem.eng.osaka-cu.ac.jp;
Fax: +81-6-6605-2981
{ Electronic supplementary information (ESI) available: Experimental
procedures, crystal structures and CIF files. See DOI: 10.1039/b714792a
The molecular conformation observed during the isomerization
of 1 to 2 was compared with the geometrical parameters
This journal is ß The Royal Society of Chemistry 2008
Chem. Commun., 2008, 55–57 | 55

View Article Online
Fig. 1 Single crystal structures of (a) 1 and (b) 2. Gray and red circles represent carbon and oxygen atoms, respectively. Hydrogen atoms are omitted for
clarity. (c) Drawing of void space (blue) in the unit cell for 1.
Table 1 Selected cell parameters for the crystals of 1 and 2
1
1 (after UV irrad.)a
2
Space group
˚
P21/c
P21/c
P21
9.167(3)
a/A
˚
10.332(4)
5.682(2)
14.791(7)
105.86(4)
835.2(6)
2
10.328(6)
5.765(4)
15.005(9)
106.00(3)
858.8(9)
2
b/A
˚
c/A
5.7038(11)
17.002(5)
104.803(4)
859.5(4)
2
b/u
Scheme 1 Solid-state photoisomerization of 1 via the bicycle-pedal
3
˚
V/A
model. The phenyl ring is omitted for clarity.
Z
r
calc/g cm23
1.282
1.247
1.246
a
determined for the 1 and 2 molecules in each crystal, as well as the
structures optimized by DFT calculation (See Table S2 in the ESI
for detailed results{). The geometrical parameters include a small
change in the molecular structure of 1 during the photoisomeriza-
tion from the structure of Fig. 2(a) to that of Fig. 2(c). The small
geometry difference between the reactant and the product
minimizes crystal lattice strain as the reaction progresses. The
topochemical isomerization of 1 is accompanied by the expansion
of the lattice lengths and the cell volume, but without changing the
space group of the crystals, as shown in Table 1. Eventually, a
structural strain is included in the molecules of 2 as the primary
photoproduct, because the produced 2 molecules exist in the
crystal lattice of the 1 molecules. Furthermore, a structural change
in the crystals of 1 was observed at a higher conversion based on a
powder X-ray diffraction analysis. The conversion of 1 to 2
achieved 97.5%, which was determined by NMR spectroscopy,
after 120 h photoirradiation. X-Ray diffraction lines after the
reaction agreed well with those for the recrystallized 2 (Fig. 3). The
molecular conformation of 2 includes an asymmetric structure
with a bent benzyl moiety, as shown in Fig. 1(b), being different
from the symmetric conformation of 1 in the crystals of 1, and also
2 in the co-crystals formed during photoirradiation. These results
indicate that a phase transition occurs at the final stage of the
isomerization process. The molecules of 2 change their conforma-
tion in the solid state using the void space around the benzyl
moiety shown in Fig. 1(c) during the phase transition. Namely, the
primary E,E isomer produced on photoirradiation has a molecular
length similar to that of the original Z,Z isomer 1 at the initial
stage of the reaction, but the cell length increased along the
After the photoirradiation of 1 for 27 h at room temperature using
an ultra-high pressure mercury lamp (500 W), a band path filter
UV-D36B and an infrared absorption filter IRA-25S. The
conversion to 2 was 35%.
Fig. 2 ORTEP drawings of (a) 1 crystals as the initial molecular
structure, (b) disordered structure after a 27 h photoirradiation, and (c) the
structure separated into 1 and 2 with a site occupancy factor of 35% for 2.
The hydrogen atoms are omitted for clarity. The thermal ellipsoids are
plotted at the 50% probability level.
56 | Chem. Commun., 2008, 55–57
This journal is ß The Royal Society of Chemistry 2008

View Article Online
P21/c to P21 during the phase transition. The void space included
in the crystals plays an important role in the phase transition
rather than in the isomerization.
This work was supported by a Grant-in-Aid for Scientific
Research on Priority Areas (Area No. 432) from the Ministry of
Education, Culture, Sports, Science and Technology (MEXT) of
Japan. We thank Prof. Norimitsu Tohnai, Osaka University, for
his kind assistance for the calculation of a void space.
Notes and references
{ CCDC 662879–662881. For crystallographic data in CIF format see
DOI: 10.1039/b714792a
1 Reviews: V. Ramamurthy and K. Venkatesan, Chem. Rev., 1987, 87,
433; K. Tanaka and F. Toda, Chem. Rev., 2000, 100, 1025;
ˇ ´
L. R. MacGillivray, G. S. Papaefstathiou, T. Friˇscic, D. B. Varshney
and T. D. Hamilton, Top. Curr. Chem., 2004, 248, 201; G. Kaupp, Top.
Curr. Chem., 2005, 254, 95; D. Braga and F. Grepioni, Chem. Commun.,
2005, 3635; J. Harada and K. Ogawa, Top. Stereochem., 2006, 25, 31;
T. A. V. Khuong, J. E. Nunez, C. E. Godinez and M. A. Garcia-
Garibay, Acc. Chem. Res., 2006, 39, 413.
2 A. Matsumoto, Top. Curr. Chem., 2005, 254, 263.
3 S. M. Alfimov and V. F. Razumov, Mol. Cryst. Liq. Cryst., 1978, 49,
95; K. Kinbara, A. Kai, Y. Maekawa, Y. Hashimoto, S. Naruse,
M. Hasegawa and K. Saigo, J. Chem. Soc., Perkin Trans. 2, 1996, 247;
G. Kaupp, Photochem. Photobiol., 2002, 76, 590; J. N. Moorthy,
P. Venkatakrishnan, G. Savitha and R. G. Weiss, Photochem. Photobiol.
Sci., 2006, 5, 903; A. Natarajan, J. T. Mague, K. Venkatesan, T. Arai
and V. Ramamurthy, J. Org. Chem., 2006, 71, 1055.
4 A. Warshel, Nature, 1976, 260, 679.
5 R. S. H. Liu and A. E. Asato, Proc. Natl. Acad. Sci. U. S. A., 1985, 82,
259; R. S. H. Liu and G. S. Hammond, Acc. Chem. Res., 2005,
38, 396.
Fig. 3 Powder X-ray diffraction profile of 1 at different conversions
during the photoisomerization at room temperature. (a) 10.6%, (b) 34.0%,
(c) 97.5%, and (d) 2 recrystallized from a solution. (e) Change in the profile
during the photoirradiation for 20 to 120 h at 10 h interval. For the
photoirradiation, an ultra-high pressure mercury lamp (500 W) and an
infrared absorption filter IRA-25S were used.
6 R. S. H. Liu, Photochem. Photobiol., 2002, 76, 580; R. S. H. Liu,
L.-Y. Yang and J. Liu, Photochem. Photobiol., 2007, 83, 2.
7 S. Schieffer, J. Pescatore, R. Ulsh and R. S. H. Liu, Chem. Commun.,
2004, 2680; L.-Y. Yang, R. S. H. Liu, K. J. Boarman, N. L. Wendt and
J. Liu, J. Am. Chem. Soc., 2005, 127, 2404; L.-Y. Yang, M. Harigai,
Y. Imamoto, M. Kataoka, T.-I. Ho, E. Andrioukhina, O. Federova,
S. Shevyakov and R. S. H. Liu, Photochem. Photobiol. Sci., 2006, 5, 874.
8 J. Saltiel, T. S. R. Krishna, A. M. Turek and R. J. Clark, Chem.
Commun., 2006, 1506.
9 J. Saltiel, T. S. R. Krishna and R. J. Clark, J. Phys. Chem. A, 2006, 110,
1694.
10 T.-A. V. Khuong, G. Zepeda, C. N. Sanrame, H. Dang,
M. D. Bartberger, K. N. Houk and M. A. Garcia-Garibay, J. Am.
Chem. Soc., 2004, 126, 14778.
directions of the b- and c-axes during the reaction, leading to an
increase in the total volume of the crystals. Drastic changes in
molecular conformation and packing structure (the slide of
molecules resulting in further increase in the c-axis length) occur
during the crystal-to-crystal transition to the stable crystal
structure of 2, accompanying a phase separation as shown in
Fig. 3(e).
11 T. Odani, A. Matsumoto, K. Sada and M. Miyata, Chem. Commun.,
2001, 2004.
12 Isomerization of 1,3-dienes in solution: J. H. Pinckard, B. Wille and
L. Zechmeister, J. Am. Chem. Soc., 1948, 70, 1938; J. Saltiel, L. Metts
and M. Wrighton, J. Am. Chem. Soc., 1970, 92, 3227; W. A. Yee,
S. J. Hug and D. S. Kliger, J. Am. Chem. Soc., 1988, 110, 2164.
13 Y. Sonoda, Y. Kawanishi, S. Tsuzuki and M. Goto, J. Org. Chem.,
2005, 70, 9755.
14 M. D. Cohen, Angew. Chem., Int. Ed. Engl., 1975, 14, 386;
A. Gavezzotti, J. Am. Chem. Soc., 1983, 105, 5220; Y. Ohashi, Acc.
Chem. Res., 1988, 21, 268.
In conclusion, an X-ray single-crystal structure analysis has
revealed that the isomerization of 1 proceeds according to a
bicycle-pedal model. The isomerization occurs via a topochemical
reaction process which does not require the significant movement
of atoms. The reaction finally causes a phase transition to crystals
of 2 with a molecular packing structure identical to that of the
recrystallized 2. At the same time, the space group changes from
This journal is ß The Royal Society of Chemistry 2008
Chem. Commun., 2008, 55–57 | 57