Unexpected molecular flip in solid-state photodimerization

Article abstract of DOI:10.1021/cg3016707

Three cocrystals of the light-stable compound 1,1,6,6-tetraphenyl-2,4- hexadiyne-1,6-diol (I) with light-sensitive molecules 1,2-dimethyl-2(1H)- pyridinone (a), 6-methyl-2(1H)-pyridinone (b) and 2-methyl-2(1H)-pyridinone (c) were exposed to UV light. It w

Full text of DOI:10.1021/cg3016707

Article
pubs.acs.org/crystal
Unexpected Molecular Flip in Solid-State Photodimerization
Thekku Veedu Sreevidya,†,§ Deng-Ke Cao,†,‡ Tali Lavy,† Mark Botoshansky,† and Menahem Kaftory*,†
†Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
S
* Supporting Information
ABSTRACT: Three cocrystals of the light-stable compound
1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol (I) with light-sensitive
molecules 1,2-dimethyl-2(1H)-pyridinone (a), 6-methyl-2(1H)-
pyridinone (b) and 2-methyl-2(1H)-pyridinone (c) were exposed
to UV light. It was found that the molecules undergo molecular flip
perpendicular to the molecular plane (rotation of ∼180°). In the
first two cocrystals, the light-sensitive molecules are disordered,
which means that the space provided for them is larger than needed
for ordered molecules. Therefore, rotation can take place.
Moreover, in I-b, the flip is temperature dependent and takes
place without exposure to UV light. Crystal structures at four different temperatures enable one to estimate the activation energy
of the flip to be 9.72 kJ/mol. The kinetics of the reaction of I-c was studied at room temperature and revealed a sigmoidal
behavior with Avrami exponent of n = 0.95(6) that could be explained by the JMAK model for crystal growth. It means that the
nucleation rate is constant over time and that the reaction is homogeneous with equal probability to occur in any region of the
sample. This could be explained by the fact that the voids where the reaction and the flip take place are isolated from each other.
Scheme 1
1. INTRODUCTION
There is a major advantage of studying solid-state photo-
chemical reactions of systems where the transformation from
the reactant to the product takes place homogenously, from
single-crystal to single-crystal. In all other cases where structural
information is lost, partially or completely, one has to speculate
on the events during the reaction, and one can miss some of
them. We have recently come across three examples in which
the structural behavior of the reactant molecules could not be
envisaged. We succeeded to observe the unexpected events
only due to the fact that the transformation from reactants to
products took place in a single-crystal to single-crystal mode. It
was recently demonstrated that in cocrystals composed of light-
stable host molecules and light-sensitive guest molecules, the
photochemical reaction may proceed to completion with the
preservation of the single-crystal integrity.1−9 Such systems
enable kinetic investigation of compounds that do not undergo
photochemical reactions in the solid state in their neat phase.10
It also enables the study of the effects of the environment on
the reaction product.1,11
In this Article, we would like to describe molecular flip
(rotation by 180°) while a [4 + 4] photodimerization takes
place in a system composed of light-stable host (I) and light-
sensitive guest molecules a, b, and c (Scheme 1). The flip was
observed to take place as a result of heat or of illumination by
UV light. Each example will be described separately, and
because the crystal structure of I-b, I-c was described in detail
in previous publication,4 we will mention the structures briefly.
The crystal structure of I-a is new; therefore, we describe it in
more detail.
2. EXPERIMENTAL SECTION
Preparation of the Materials. Commercially available reagents
were purchased from Aldrich and used without further purification.
1,2-Dimethyl-2(1H)-pyridinone (a). The mixture of 2-methyl-2-
pyridinone (9.16 mmol, 1.0 g), potassium carbonate (35 mmol, 4.82
g), methyl iodide (35 mmol, 2.2 mL), and acetone (100 mL) was
refluxed for 4 h in oil bath (80 °C). After being cooled, potassium
carbonate was removed. The filtrate was evaporated, and the resulting
residue was mixed with 12 mL of water, and then extracted with
Received: November 14, 2012
Revised: December 27, 2012
Published: January 7, 2013
© 2013 American Chemical Society
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chloroform (45 mL × 3). The chloroform solutions were dried with
MgSO4. After removal of chloroform, the resulting residue was
distilled (92 °C, 0.5 mbar) and was crystallized from dry ether.12
6-Methyl-2(1H)-pyridinone (b) and 2-methyl-2(1H)-pyridinone
(c) are commercially available.
1,1,6,6-Tetraphenyl-2,4-hexadiyne-1,6-diol (I). Cu(OAc)2 (5
mmol, 0.9 g) was dissolved in 60 mL of methanol−pyridine (1:1),
and then the solution of 1,1-diphenylpropyn-1-ol (purchased from
Sigma-Aldrich) (10 mmol, 2.08 g) in 60 mL of methanol−pyridine
(purchased from Sigma-Aldrich) (1:1) was added dropwise with
stirring in an oil bath (63 °C). After the mixture was stirred for 10 h, it
was cooled to room temperature. The solvent was evaporated, and the
resulting residue was mixed with 100 mL of ether−CS2 (v/v 4/1) and
250 mL of 2 M HCl. The organic phase of the mixture was separated,
and the aqueous phase was further extracted with 2 × 100 mL of
ether−CS2 (v/v 4/1). Finally, the combined organic phase was washed
with 3 × 100 mL of 2 M HCl, 3 × 100 mL of water, and 3 × 100 mL
of NaCl solution, and dried with MgSO4. After removal of solvent, the
pale yellow residue was refluxed in hexane (40 mL) to yield powder.
After recrystallization in CH2Cl2−hexane, the colorless needle-like
crystals were collected with 89% yield.13
Figure 1. The disordered light-sensitive molecule in I-a.
in Figure 2. There are three possible interactions that may lead
to photodimers: molecules A−A, B−B, and A−B. The last (A−
Cocrystals I-a, I-b, and I-c. 1:2 equivalent proportion of the
components was dissolved in a mixture of ethyl acetate and methanol.
The solution was stirred at room temperature for 1 h. The solution
was evaporated in air for a few days until colorless crystals appeared.
Irradiation Setup. The irradiation system consisted of an Osram Xe
short arc lamp (150 W), in the irradiation of I-b, and with a LED
source (UV-LED) in the range 350−390 nm with the maximum of
365 nm for the irradiation of I-a and I-c. Each single crystal was
attached with grease to a thin piece of glass and mounted at a distance
of about 2 cm in front of the focused beam on a device that revolved at
1 rpm. After each stage, diffraction intensity data were collected.
Conversion percentage was determined by the occupancy factors
obtained from the crystal structure refinement.
Figure 2. Relative geometry of light-sensitive molecules in I-a. A···A
(left), B···B (middle), and A···B (right). Carbon atoms of molecule A
are in yellow, and those of molecule B are in green.
Crystal Structure Determination and Refinement. Intensity
data have been collected on a KapaCCD Nonius diffractometer or on a
Bruker APEX2 Duo diffractometer (Mo Kα, λ = 0.71073 Å). The
following software has been used for crystal structure solution and
refinement: data collection, COLLECT;14 cell refinement and data
reduction, DENZO-SMN.15 The program used to solve and refine the
crystal structures was SHELXS-97.16 The program used for molecular
graphics was MERCURY.17
Before and after irradiation to full conversion, all non-hydrogen
atoms were refined anisotropically. The positions of the hydrogen
atoms were located in difference Fourier maps and refined by riding on
their parent atoms. At intermediate stages of irradiation, the
refinement of the crystal structure that includes the unreacted
monomers of the light-sensitive molecule and the partially produced
dimer was carried out in a procedure similar to that used above;
however, the occupancy factor of the atoms of the unreacted molecules
and the product molecules was refined. At lower and higher
conversion, the atoms of the minor species were refined isotropically;
at conversion closer to 50%, both unreacted molecules and the
product molecules were refined anisotropically.
B) is unlikely to be present at the same void due to the less
favorable interactions. The distance between the potentially
reactive atoms C17A and C20A with their counterparts related
by inversion center, C20Ai and C17Ai, is 3.652(3)Å (see Figure
2) shorter than the upper limit of 4.2 Å, set by Schmidt.18 The
equivalent distances between atoms C17B and C20B with their
counterparts, C20Bi and C17Bi, are longer than this limit
(4.640 Å), and therefore photodimer is not expected. The same
is true for the mutual relation between the two molecules A and
B, where one of the distances is much too long (5.191 Å) and
the overlap between the reactive p-orbitals is very poor.
Moreover, dimerization of A−B would lead to a head-to-head
dimer in which the N−CH3 groups will overlap, which is less
probable to occur.
As expected, the photoreaction goes to completion, leading
to dimers of A−A in a single-crystal to single-crystal mode of
reaction.
Three stages of the reaction are shown in Figure 3, before
illumination (left), at ca. 50% conversion (middle), and after
full conversion (right). There is no trace of molecules B (in
green) at the intermediate stages. This implies that molecule B
undergoes reorientation to adopt the structure and the
geometric relation of molecule A.
Because the two molecules, A and B, are related by pseudo 2-
fold axis running in the plane of the pyridine ring, molecule B
has to flip (rotation by 180°) to have the same relative
geometry of molecule A. During the flip and the photo-
dimerization, hydrogen bonds between the light-stable and the
light-sensitive molecules were broken and reformed after the
dimer was produced. Further information and results will be
given in the discussion.
3. RESULTS
3.1. 1,1,6,6-Tetraphenyl-2,4-hexadiyne-1,6-diol:2(1,6-
dimethyl-2(1H)-pyridone) (I-a). The molecular compound
crystallizes in the monoclinic system P21/c space group. The
structure may be generally described as made up of 1,6-
dimethyl-2(1H)-pyridone (a) molecules forming dimers
through hydrogen bonds. They are also hydrogen bonded to
the host molecule 1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol.
The light-sensitive (a) molecule is disordered in equal
proportion as seen in Figure 1.
Those molecules are related by inversion center to other
disordered molecules. The geometric relation between each
pair of potentially reacting molecules to form dimers is shown
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that during the flip and the photodimerization, hydrogen bonds
between the light-stable and the light-sensitive molecules, as
well as between two neighbor light-sensitive molecules, were
broken and reformed after the dimer was produced.
Further information and results will be given below in the
discussion.
3.3. 1,1,6,6-Tetraphenyl-2,4-hexadiyne-1,6-diol:2(2-
(1H)-pyridone) (I-c). The structure of I-c was published
elsewhere,4 and the flip of the light-sensitive molecules was
mentioned. Therefore, we mention it here briefly for
comparison with the previous two examples. The light-sensitive
molecules (c) are not disordered, and they are related to each
other by inversion centers. The distance between the
potentially reactive atoms, C17 and C20, with their counterpart
related by inversion center C20i and C17i, is 3.835 Å. A priori,
there is no reason for the light-sensitive molecules to flip,
because the mutual geometry between pair of molecules is
within any geometric limits set for photodimerization. Never-
theless, the dimers obtained show clearly that the molecules
have flipped. Figure 6 shows a comparison of the structure of
Figure 3. Structure of the light-sensitive molecules in I-a at three
stages: left, before irradiation; middle, after ca. 50% conversion; and
right, at full conversion. Carbon atoms of unreacted molecule A are in
yellow, and those of unreacted molecule B are in green.
3.2. 1,1,6,6-Tetraphenyl-2,4-hexadiyne-1,6-diol:2(2-
methyl-2(1H)-pyridone) (I-b). The crystal structure of I-b
was published elsewhere,4 and the molecular flip was briefly
mentioned. We have repeated the experiments mentioned in
the previous work and will elaborate in the discussion. The
guest molecule (b) is disordered with the two molecules (A and
B in Figure 4) related by a pseudo 2-fold axis running in the
Figure 6. Structure of the light-sensitive molecules in I-b at two stages:
left, before irradiation; right, after ca. 60% conversion. Carbon atoms
of unreacted molecule A are in yellow, and those of unreacted
molecule B are in green.
Figure 4. The disordered light-sensitive molecule in I-b.
plane of the pyridine ring, slightly different from that in I-a.
The relative occupation of the two molecules A/B is 86/14,
respectively. The distances between the potentially reactive
atoms C17 and C20 to their counterpart, C20i, C17i, related by
inversion centers are 4.612, 3.908 Å for molecules A···A and
B···B, respectively, 3.904, and 4.137 Å (Figure 5). The
arguments mentioned for the possible photodimers discussed
for I-a are valid also here. Indeed, at full conversion B−B is the
only dimer that is formed.
This is surprising, because molecules B are only 14% from
the total light-sensitive molecules in the crystal; nevertheless,
they photodimerize while the majority of the molecules (86%)
have to flip (rotation be 180°) to enable the photoreaction to
proceed to completion. It should be added, but not discussed,
the light-sensitive molecules before irradiation (left) and when
the conversion to dimers reached ca. 60% conversion (right). It
is clearly seen that the remaining unreacted monomers and the
dimer have a different orientation than before irradiation. This
observation can be explained by flipping of the light-sensitive
molecules. It should be added, but not discussed, that during
the flip and the photodimerization, hydrogen bonds between
the light-stable and the light-sensitive molecules, as well as
between two neighbor light-sensitive molecules, were broken
and reformed after the dimer was produced.
The open questions are when, why, and how do the
molecules flip.
4. DISCUSSION
In our previous publication11 describing the crystal structure of
I-b, we have suggested that the flip (or rotation) of the guest
molecules belonging to the major population (86%) may be a
result of the irradiation or of the heat evolved during
irradiation. Two experiments were carried out to distinguish
between the two hypotheses: first, heating the crystal without
irradiation, and, second, cooling the crystal during irradiation.
The temperature dependency of the two different populations
of the guest molecules was estimated from the refined
occupancy factors of the disordered guest molecules obtained
during the crystal structure refinement process. The initial ratio
between the guest populations at room temperature was 86/14
Figure 5. Relative geometry of light-sensitive molecules in I-b. A···A
(left), B···B (middle), and A···B (right). Carbon atoms of molecule A
are in yellow, and those of molecule B are in green.
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(major/minor). It was changed to 67/33 at 393 K and reverted
to its original ratio upon cooling to room temperature. No
change was observed when the crystal was cooled to 100 K.
Irradiation while cooling the crystal to 220 K for 20 h produced
full conversion to the same photodimerization product as that
when the photodimerization was carried out at room
temperature. These results suggest that light-induced heating
is not the sole cause of molecular rotation (flip). It is likely that
photodimerization of molecules of the minor population shifts
the equilibrium, causing molecules of the major population to
flip to adopt the orientation of molecules of the minor
population and thus re-establish the equilibrium, and the
photodimerization proceeds until completion. We have carried
out an additional experiment where the structure of the same
crystal was determined at four different temperatures, and the
results are shown in Figure 7. It was once again shown that the
flip takes place also as a result of heat.
orientation of molecules A. Thus, the photodimerization can
proceed to completion.
In crystals of I-c, there is no disorder, and the relative
geometry between light-sensitive molecules related by inversion
center (C17−C20i distance of 3.835 Å) enables photo-
dimerization. The photodimerization proceeds with minor
changes of the unit cell dimensions; however, at certain stages
of the reaction (estimated to be ∼50% conversion), both the
remaining monomers and the formed dimers flip (see Figure
6). We have no explanation for this phenomenon.
Rotation of planar molecule such as pyridone in the plane
does not need too much free space. However, rotation of such a
molecule by ∼180° perpendicular to the plane (flip) requires
much space. Moreover, the molecules are arranged in pairs so
that the interplanar distance is of the order of 3.5 Å, shorter
than the length of the molecule. The rotation of the molecules
B in I-a, and molecules A in I-b, is about an axis passing the
inversion centers and running parallel to the direction
N1A···N1B (in I-a) and parallel to C20A···C20B (in I-b).
The rotation should be concerted; the two monomers should
rotate simultaneously, and this is also true for I-c.
The voids where the reactions take place were drawn using
the software program Mercury (Cambridge Crystallographic
Data Centre),17 which find any empty spaces (voids) that are
big enough to hold spherical “probe”. The radius of the probe is
1.2 Å, and the grid spacing is 0.7 Å. The voids were calculated
using contact surface using the structure of the host light-stable
molecules and omitting the guest light-sensitive molecules. The
voids created by the host molecules and the flipping molecules
are shown in Figures 8−10 for I-a, I-b, and I-c, respectively.
The voids having a shape of slightly distorted sphere are
separated from each other, and each accommodate a pair of
monomers. The existing disorder in I-a and I-b suggests that
there is additional space in the voids to accommodate more
than that required by a single pair of molecules. The additional
length available for the rotation is 1.5 and 1.4 Å in I-a and I-b,
respectively (estimated from the distances N1A···N1B and
C20A···C20B) along the rotation axis.
The fact that there is one pair of molecules in isolated
cavities in each of the compounds I-a and I-b as well as the fact
that the dimerization proceeds to completion suggest that there
are no cavities that include the pair A···B. The possibility that
such a pair exists in a cavity is ruled out because it means that
one of the molecules (A or B) would have to flip to undergo
photodimerization. However, there is no space in the cavity for
such a rotation. These results point out that the disorder in the
Figure 7. Equilibrium constants versus 1/T plot for I-b. The
equilibrium constant at each temperature was set to the ratio between
the disordered molecules obtained by their refined occupancy factors.
The estimated activation energy of the flip is 9.72 kJ/mol.
The dependence of the equilibrium between the two
orientations of the light-sensitive molecules is demonstrated
and justified by the effect seen in the photodimerization
process, as described above.
The ratio between the disordered molecules in I-a remains
constant at the range of temperatures 213−393 K. Never-
theless, the same arguments discussed for I-b hold also in this
example. As soon as dimers are being formed from molecules A,
the equilibrium is shifted and molecules B flip to adopt the
Figure 8. The reaction cavity in the crystal structure of I-a.
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Figure 11. Plot of the fraction of the light-sensitive molecule of I-c as a
function of the irradiation time at room temperature. The data points
■
( ) are the refined occupancy factors, and the line is a fit using the
equation and the parameter shown. The time scale is based simply on
fluence of the Xe light and is not an absolute property of the sample.
Figure 9. The reaction cavity in the crystal structure of I-b.
exposure time, k is the constant of the growth rate, and n is the
Avrami exponent that shows the dimension of the growth.
When n = 2, 3, or 4, the dimensionality of the growth is 1, 2,
and 3, respectively. When n = 1, it means that the nucleation
rate is constant over time and that the reaction is homogeneous
with equal probability to occur in any region of the sample. In a
plot of ln[ln(1 − y)−1] versus ln[time], called an “Avrami plot”,
the parameters of the reaction can be easily extracted.22,23
A
straight line with slope n is obtained. Figure 12 shows the
Figure 10. The reaction cavity in the crystal structure of I-c.
crystal is due to existence of cavities having either pairs of
molecules of type A···A or B···B. The rotation takes place,
therefore, only in the cavities having the longer distances
between the reactive atoms of the two molecules related by
inversion center (C17 and C20) in a simultaneous fashion.
To understand the mechanism of the reaction and growth of
the product, a single crystal of I-c was illuminated and checked
periodically for its structure and the progress of the conversion.
Figure 11 shows the fraction of the photodimer produced
(expressed in term of conversion) by the irradiation of a single
crystal of I-c with 355 nm UV-LED. The time scale in Figure 11
is based simply on fluency of the light and is not an absolute
property of the sample. The fraction of the dimer was extracted
from a least-squares refinement of the crystal structure (the
occupancy factor). During the refinement procedure, the sum
of the occupancy factor of atoms of the monomer and the
occupancy factor of the atoms of the dimer was kept to 1.0. The
occupancy factor was free to refine until the residual electron
density, and the R value was minimal. The sigmoidal line shape
of JMAK19−22 was used in the description of the [2 + 2]
photodimerization of α-cinnamic acid.23,24 The fit of the data
points was done using the equation:19−22
Figure 12. Avrami plot of ln[ln(1 − y)−1] versus ln(time), where y is
the fraction of the conversion. The slop is the Avrami exponent.
Avrami plot for the experimental data. The linearity of the plot
indicates that this is a JMAK kinetic process. The slope of
0.95(3) is identical to that obtained above. Bertmer et al. have
used the Avrami model to fit the sigmoidal curve observed in
the kinetic study of the [2 + 2] photodimerization of α-trans-
cinnamic acid.23 The Avrami exponent was found to be
1.66(10); Benedict and Coppens24 have found 1.43(8) for the
same reaction using a two-photon absorption experiment.
Avrami exponents of 1.6(1) and 1.5(1) were found for the [4 +
4] photodimerization of 1,4-dimethyl-2-pyridone in its
cocrystal with 1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol at 230
and 280 K, respectively.10 It was found that different
substituents at the aromatic ring of the cinnamic acid influence
the reaction mechanism. For example, it was found25 that the
Avrami exponent is 0.98(11) for the kinetics curve of o-
methoxy cinnamic acid, and it was 2.22(11) for the kinetic
curve of o-ethoxy cinnamic acid.
conversion = 1 − exp(−ktn)
where conversion = 1 − occupancy factor.
This equation was used as a model for the kinetics of phase
transition involving nucleation and growth mechanism.22 In the
equation, “conversion” is the fraction of the dimer, t is the
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The first is indicative of a heterogeneous one-dimensional
linear growth, and the second is indicative of heterogeneous
two-dimensional growth, with a decreasing nucleation rate over
time. The chemical system in the present work consists of light-
sensitive guest molecules that are almost isolated within cavities
formed by light-stable host molecules; therefore, we expected
different behavior. We have found that n = 0.95(6), indicating
that the growth mechanism is similar to the kinetics of o-
methoxy cinnamic acid.25 A very different Avrami exponent of
0.55(8) was recently reported for the [4 + 4] photo-
dimerization of 9-anthracene-carboxylic acid.26 An Avrami
exponent of 0.55 would lead to a negative dimensionality,
which might suggest an auto inhibition step in the reaction. It is
important to note that in this particular case the two monomers
are related by crystallographic translation leading to head-to-
head orientation (β-type packing); therefore, the carboxylic
acid groups have to adjust their conformations to enable
dimerization with minimal interference between them. This
might lead to additional disorder in the crystal, as suggested by
the authors.
ACKNOWLEDGMENTS
This work was supported by the Israel Science Foundation, no.
499/08.
■
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5. CONCLUSION
It was shown that in illumination by UV light of three examples
of molecular compounds composed of light-stable host and
light-sensitive guest molecules, [4 + 4] photodimerization takes
place. In these examples, the dimerization takes place with
molecular flip. The photochemical reaction as well as the
molecular flip could be followed due to the fact that the whole
process proceeds in a single-crystal to single-crystal type
transformation. The driving force for the molecular flip is well
understood in the two compounds where the light-sensitive
molecules are disordered (I-a and I-b). It seems that the driving
force for the molecular flip in I-c is free-energy minimization if
the space provided for the flip is available.
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ASSOCIATED CONTENT
* Supporting Information
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S
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X-ray crystallographic information files (CIF) for compounds I-
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material is available free of charge via the Internet at http://
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AUTHOR INFORMATION
Corresponding Author
*E-mail: kaftory@tx.technion.ac.il.
■
Present Addresses
‡State Key Laboratory of Coordination Chemistry, Coordina-
tion Chemistry Institute, Nanjing University, Nanjing 210093,
People’s Republic of China.
§Structural Dynamics of (Bio)Chemical Systems, Max-Planck-
Institute for Biophysical Chemistry, Am Fassberg 11, 37077
Gottingen, Germany.
̈
Notes
The authors declare no competing financial interest.
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