Anchor effect on pedal motion observed in crystal phase of an azobenzene derivative

Article abstract of DOI:10.1007/s10870-011-0152-1

Some molecules having a molecular skeleton similar to that of stilbenes and azobenzenes show orientational disorder in the crystals due to pedal motion. Heretofore, the orientational disorder through pedal motion has been observed for the compounds contai

Full text of DOI:10.1007/s10870-011-0152-1

J Chem Crystallogr (2011) 41:1642–1648
DOI 10.1007/s10870-011-0152-1
ORIGINAL PAPER
Anchor Effect on Pedal Motion Observed in Crystal Phase
of an Azobenzene Derivative
•
•
Hasan Karabıyık Hande Petek
˙
Nazan Ocak Iskeleli C¸ igdem Albayrak
•
•
˘
˘
Erbil Agar
Received: 5 March 2009 / Accepted: 9 June 2011 / Published online: 7 July 2011
Ó Springer Science+Business Media, LLC 2011
Abstract Some molecules having a molecular skeleton
similar to that of stilbenes and azobenzenes show orienta-
tional disorder in the crystals due to pedal motion. Hereto-
fore, the orientational disorder through pedal motion has
been observed for the compounds containing only two aro-
matic rings in the absence of bulky substituent groups. Here
we report that the pedal motion can be detected even in the
presence of a bulky substituent group to which orientational
disorder becomes invisible as a result of anchor effect arising
from phenoxyphtalonitrile group. X-ray crystallographic
analysis of the compound, C23H18N4O, reveals the existence
of partially overlapped two pedal conformers. The com-
pound crystallizes in the monoclinic space group P21/c with
calculations at B3LYP/6-311G?(d,p) level suggest that the
stabilization of the compound decreases with increasing
deviation from the planar geometry of trans-azobenzene
fragment.
Keywords Pedal motion Á Azobenzene Á Orientational
disorder Á Conformational interconversion
Introduction
Solid-state conformational changes have received consid-
erable attention for the past three decades in order to
explain the dynamic aspects associated with certain fea-
tures of the molecules having photoreactivity and photo-
chemical properties [1–4]. In this sense, molecular motions
in crystals are of great importance in determining the
effects on their physical properties and in understanding
structure–activity relationship. It has been already well-
known that molecules having skeletons similar to those of
stilbenes and azobenzenes show orientational disorder in
the crystal phase [5–10]. The disorder observed in some
azobenzenes is dynamic, and therefore ascribed to an
interconversion between the two pedal conformers [11].
The conformational interconversion occurred in crystal
phase of such compounds is due to unusual molecular
motion referred to as the pedal motion: a pair of benzene
rings moving like the pedals of a bicycle [12]. Pedal-like
motion (or crankshaft motion) is not only peculiar to stil-
bene and azobenzene type molecules, it is also one of the
key processes in the photochromism of salicylideneanilines
[13], the photodimerization of trans-cinnamides [14, 15]
and photoisomerization of 1,4-diaryl-1,3-butadienes [16].
On the other hand, azobenzene moieties have been recently
used in preparation of molecular machines [17, 18], and
˚
˚
˚
a = 12.9429(11) A, b = 8.5075(5) A, c = 21.063(2) A
and b = 123.155(6)°. Major pedal conformer is stabilized
by weak C–HÁÁÁO type hydrogen bond and C–HÁÁÁp type
edge-to-face interactions in solid state. Quantum chemical
H. Karabıyık (&)
Department of Physics, Dokuz Eylu¨l Universitesi, Fen Faku¨ltesi,
¨ ¨
Fizik Bolumu, Tinaztepe Kampusu, 35160 Buca, Izmir, Turkey
e-mail: hasan.karabiyik@deu.edu.tr
¨
H. Petek
Department of Physics, Ondokuz Mayıs University,
55139 Samsun, Turkey
˙
N. O. Iskeleli
Department of Science Education, Ondokuz Mayıs University,
55139 Samsun, Turkey
C¸ . Albayrak
Department of Science Education, Sinop University,
57010 Sinop, Turkey
˘
E. Agar
Department of Chemistry, Ondokuz Mayıs University,
55139 Samsun, Turkey
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J Chem Crystallogr (2011) 41:1642–1648
1643
pedal motion is of great importance to put them into ver-
satile practise.
chemical calculations by means of Density Functional
Theory at B3LYP/6-311?G(d,p) level.
The absence of orientational disorder in azobenzene
compounds should be attributable to the destabilization of
the minor conformer and the non-disordered crystal struc-
tures of them do not mean that the pedal motion is inhibited.
In general, the low occupancy factor (less than 0.1) of the
minor pedal conformer makes the disorder invisible in most
crystals. Ogawa and Harada [19, 20] reported that the pedal
motion takes place even in crystal samples without disorder.
As a result of this, orientational disorder arising from
dynamical reasons and conformational interconversion
through pedal-like motion has been overlooked in most
crystal structures of such compounds [19, 20].
Experimental
Synthesis of the Compound
A mixture of 4-ethylaniline (2.5 g, 20.6 mmol), water
(50 ml) and concentrated hydrochloric acid (5 ml,
61.8 mmol) was stirred until a clear solution was obtained.
This solution was cooled to 273–278 K and a solution
sodium nitrite (1.42 g, 29.2 mmol) in water was added
dropwise while the temperature was maintained below
278 K. The resulting mixture was stirred for 30 min in an
ice bath. O-Cresol (2.23 g, 20.6 mmol) solution (pH *9)
was gradually added to a cooled solution of 4-ethyl-
benzenediazonium chloride, prepared as described above,
and the resulting mixture was stirred at 273–278 K for
60 min in ice bath. The product was recrystallized
from ethyl alcohol to obtain solid 2-Methyl-4-(4-ethyl-
phenyldiazenyl)phenol (yield 76%, m.p. 398–400 K). To a
solution of solid (1 g, 4.1 mmol) in DMF was added
potassium carbonato (1.15 g, 8.2 mmol). The mixture was
stirred for 30 min under N2. 4-nitrophtalonitrile solution in
DMF was added. The mixture was stirred for 48 h at 323 K
under N2 and poured into ice-water (150 g). The product
was filtered off and washed with water. The product was
recrystallized from ethyl alcohol to obtain solid 4-[2-
methyl-4-(4-ethylphenyldiazenyl)]phenoxyphtalonitrile.
Crystals of 4-[2-methyl-4-(4-ethylphenyldiazenyl)]pheno-
xyphtalonitrile were obtained from ethanol: CCl4 (1:2)
mixture at room temperature via slow evaporation (yield
67%, m.p. 401–403 K) (Scheme 1).
Pedal motion in azobenzene-like compounds has been
generally observed in the compounds containing two aro-
matic rings carrying small substituent groups up to the
present [19–23]. Since such compounds do not have a
bulky substituent group, it is reasonable to consider that the
detection of an unfavorable (minor) pedal conformer in
their crystal structures is become difficult by anchor effect
arising from the presence of a bulky substituent group.
Another factor affecting the population of unfavorable
minor conformer is also temperature in data collection
stage. According to the Boltzmann distribution law, the
population of an energetically unfavorable conformer in
equilibrating systems increases as the temperature is raised.
Therefore, the population of a minor conformer is detect-
able only at a high temperature [19, 20]. Under certain
circumstances, even if temperature is high enough, the
detection of unfavorable conformer is limited by the fol-
lowing reasons. The intensity of diffraction spots at high
temperature rapidly drops off at higher scattering angles
due to large thermal motion of atoms at lattice sites. In this
regard, it is reliable to measure only reflections with low
angles. Moreover, structure of the disordered conformers is
blurred by the thermal motion of the molecules in crystal
phase. Therefore, a high-quality X-ray diffraction analysis
of such crystals is needed to detect minor conformer in the
presence of bulky substituents.
X-ray Crystallography
A suitable sample of size 0.60 9 0.33 9 0.11 mm was cho-
sen for the crystallographic study and then carefully mounted
on goniometer of a STOE IPDS II diffractometer. All dif-
fraction measurements were performed at 296 K using
Possible effects of various substituent groups on pedal
motion in solid-state have not been well-recognized yet.
Recently, we have showed that small aryl substituents on
the phenyl rings accompany pedal motion synchronously
[23]. However, it is not fully understood how pedal motion
is affected by the presence of bulky substituents on the
phenyl rings. In a continuation of our interest regarding
pedal motion, here we report that the effect of a bulky
substituent group such as phenoxyphtalonitrile on pedal
motion occurred in crystal-phase and trans stereochemistry
of an azobenzene derivative, 4-[2-Methyl-4-(4-ethyl-
phenyldiazenyl)]phenoxyphtalonitrile, are investigated by
single crystal X-ray diffraction technique and quantum
˚
graphite monochromated MoKa radiation (k = 0.71073 A).
The systematic absences and intensity symmetries indicated
the monoclinic P21/c space group. A total of 19,409 reflec-
tions (3,798 unique) within the h range of [1.88° \
h \ 26.00°] for -15 B h B 15, -10 B k B 10, -25 B
l B 25 were collected in the rotation mode with Rint = 0.072.
The intensities collected were corrected for Lorentz and
polarization factors, absorption correction (l = 0.08 mm-1
by integration method via X-RED software [24] and cell
parameters were determined byusing X-AREA software [24].
Extinction correction was not applied. The structure was
)
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J Chem Crystallogr (2011) 41:1642–1648
Scheme 1 Synthesis route for
the compound
H3C
H3C
NaNO2
HCl
-
+
NH2
N
N Cl
OH
pH ~ 8-9
CH3
H3C
N
N
OH
CH3
K2CO3
DMF
NO2
CN
CN
H3C
N
CH3
O
N
NC
CN
Computational Details
solved by direct methods using SHELXS-97 [25]. The
refinement was carried out by full-matrix least-squares
method on the positional and anisotropic temperature
parameters of the non-hydrogen atoms, or equivalently cor-
responding to 347 crystallographic parameters. All H atoms
were refined using pertinent riding models, with C–H dis-
All quantum chemical calculations for the compound was
performed by utilizing DFT computation with the use of
Becke’s three-parameters hybrid exchange–correlation
functional B3LYP [26] incorporating B88 gradient-cor-
rected exchange [27] and Lee–Yang–Parr non-local cor-
relation functional [28] by means of 6-311?G(d,p) basis
set implemented in Gaussian 03W program package [29].
Geometry optimization of the compound was achieved
by the application of Berny optimization algorithm [30].
Instead of conventional SCF iterations, quadratically con-
vergent SCF [31] routine was used to guarantee to reach a
stationary point on the potential energy surface. The values
of the convergence criteria for geometry optimization
are below 4.5 9 10-4 hartree/bohr for maximum force,
˚
tances of 0.96 A for methyl groups, 0.97 A for methylene
˚
˚
groups, 0.93 A for aromatic groups. The displacement
parameters of H atoms were fixed at 1.2 Ueq of their parent
carbon atoms for aromatic groups, 1.5 Ueq of their parent
atoms for methyl and methylene groups. The structure was
refined to R1 = 0.059 for observed 2,196 reflections pre-
scribed by the condition of I [ 2r(I) and to R1 = 0.134 for all
3,798 data used in refinement process. The maximum peaks
and deepest hole observed in the final Dq map were 0.29 and
-0.30 eA-3, respectively. The scattering factors were taken
˚
3 9 10-4 hartree/bohr for RMS force, 1.8 9 10-3 A for
maximum displacement, and 1.2 9 10-3 A for RMS dis-
˚
from SHELXL-97 [25]. Other details of the data collection
conditions and parameters of refinement process are sum-
marized in Table 1.
˚
placement. To be able to compare stabilization levels of the
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J Chem Crystallogr (2011) 41:1642–1648
1645
conformers obtained from crystallographic analysis and the
computational study are listed in Table 2.
Table 1 Crystallographic data for the compound
Crystal data
Pedal motion is essentially related to the molecular
fragments around azo-bridge, and therefore conformational
interconversion through pedal motion is primarily observed
in the orientations of two aromatic rings lying at opposite
sides of azo-bridge in such compounds. It is worth noting
certain differences in relative orientations of the molecular
fragments around azo-bridge (N=N). Although the differ-
ence between the orientations of the major and minor
component in 4-ethylphenyl ring is evident, the orienta-
tions of the major and minor component of the other ring
participating to pedal motion are slightly different. While
dihedral angle between the mean planes through major and
minor component of 2-methylphenyl ring is 4.4(1)°, dihe-
dral angle between the mean planes through major and
minor component of 4-ethylphenyl ring is 20.2(6)°. The
difference between relative orientations of the major and
minor components of the substituted rings linked by azo-
bridge is due to the presence of bulky substituent group,
i.e., phenoxyphtalonitrile. It is inferred from these results
that the difference in atomic positions of the major and
minor components is reduced to being more negligible
toward bulky substituent and therefore residual peaks
corresponding to phenoxyphtalonitrile fragment of the
minor conformer can not be appeared independently. Thus,
positional separations of certain atom pairs such as C9A/B,
C10A/B, C14A/B and C15A/B on 2-methylphenoxy frag-
ment are not sufficiently distinguishable. In particular, C9A
and C9B (nearest atoms to phenoxyphtalonitrile fragment)
have almost coincident atomic positions with interatomic
Crystal size
0.60 9 0.33 9 0.11 mm
Orange, prism
C23H18N4O
Color, shape
Chemical formula
Formula weight
Crystal system
Space group
366.41
Monoclinic
P21/c
˚
a = 12.9429 (11) A
Unit cell parameters
˚
b = 8.5075 (5) A
˚
c = 21.063 (2) A
b = 123.155 (6)°
3
˚
Volume
1941.7 (3) A
Z
4
Dx (Mg m-3
F(000)
)
1.253
768
Data collection
Diffractometer/meas. meth.
Absorption correction type
STOE IPDS 2/--scan
Integration
T
min, Tmax
0.960, 0.985
No. of measured, independent and
observed reflections
19,409, 3,798, 2,196
Criterion for observed reflections
Rint
I [ 2r(I)
0.072
hmax (°)
Refinement
26.00
Refinement on
R[I [ 2r(I)], GoF(S)
Weighting scheme
F2
0.059, 0.923
w = 1/
[r2(F2o) ? (0.1223P)2]
P = (F2o ? 2 F2c)/3
˚
separation of 0.127 A. Therefore, phenoxyphtalonitrile
(D/r)max
\0.001
0.29, –0.30
fragments belonging to major and minor pedal conformers
of the compound are properly overlapped and the crystal
structure of the compound can not be completely refined as
a superposition of two pedal conformers.
-3
)
˚
Dqmax, Dqmin (eA
Pairs of formally single C–N bonds at opposite sides
around azo-bridges in both pedal conformers of the
compound are slightly different from each other due to a
possible through-resonance effect between the electron-
donating O atom and the two-electron accepting N atom in
azo-bridge as being in general agreement with those in
previously reported azobenzene compounds [33–38]. N=N
bond distances in the disordered azo-bridge are compara-
ble with those of similar compound previously reported
[33–38].
crystallographically observed pedal conformers, their total
energies were calculated at the same level of theory on the
crystallographically observed geometries with the aid of
single-point calculations.
Results and Discussion
X-ray crystallographic analysis of the compound reveals that
two pedal conformers partially overlapped coexist in the
same crystal lattice at 296 K. A thermal ellipsoid view [32]
of them is shown in Fig. 1. The compound crystallizes in the
monoclinic space group P21/c. Minor conformer (B) of the
compound having 44% site occupancy factor coexist with
stable major pedal conformer (A) 56% site occupancy factor
in crystal phase. Selected geometrical parameters for both
Solid-state conformational changes are proceeded in a
different way from those in gas-phase and coupled with
changes in supramolecular environment of the compounds.
During these changes, an intermediate crystal phase may be
regarded as either mixed crystals in which various con-
formers are held together in the same crystal lattice or pure
crystals in which only one conformer is trapped during the
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J Chem Crystallogr (2011) 41:1642–1648
Fig. 1 Orientation of thermal ellipsoid views of the major (A) and
minor (B) conformers of the title compound with the atom numbering
scheme of non-H atoms. Displacement ellipsoids are drawn at the
30% probability level. Major and minor conformers are represented
by solid and broken lines, respectively
˚
Table 2 Selected geometrical parameters (A, °) for the crystallo-
(C23A–H23BÁÁÁO1) between the major components and
C–HÁÁÁp type edge-to-face interaction involving 2-methyl-
phenyl rings of the major components. Distance of HÁÁÁCg1
[at (1 - x, 1/2 ? y, 3/2 - z)] and C–HÁÁÁp angle for the
graphically observed conformers and optimized geometry of the
compound
Bond lengths
X-ray
B3LYP/6-311?G(d, p)
˚
interaction of C10A–H10AÁÁÁp are found as 2.95 A and
O1–C9A
1.400(9)
1.40(1)
1.143(4)
1.139(4)
1.44(1)
1.43(2)
1.250(6)
1.246(8)
1.53(1)
1.54(3)
1.413
158°. Donor acceptor distance and the D–HÁÁÁA angle
O1–C9B
regarding the weak intermolecular hydrogen bonding are
˚
N1–C1
1.172
1.173
1.406
found as 3.460(9) A and 149.4° with the symmetry code
N2–C2
[1 - x, 1 - y, 1 - z]. These intermolecular interactions
serve to stabilize major components in crystal structure.
According to graph-set notation [39], C–HÁÁÁO type weak
H-bond generates R22(14) pseudo-cyclic centrosymmetric
dimers having symmetry centre at (‘, ‘, ‘) for major
components in the crystal structure as shown in Fig. 2 and
C–HÁÁÁp interactions serve to be strengthened dimeric
packing arrangement.
C16A–N4A
C16B–N4B
N3A–N4A
N3B–N4B
N3A–C12A
N3B–C12B
1.292
1.410
Bond angles
X-ray
B3LYP/6-311?G(d, p)
Conformational discrepancies between the optimized
molecule and the crystallographically observed geometries
of the compound were quantitatively analyzed by r.m.s.
overlays including H atoms as shown in Fig. 3. While the
r.m.s. fits of the atomic positions of the optimized geom-
etry (green) to their corresponding values in the major (red)
and minor (blue) conformer of the compound are obtained
N3A–N4A–C16A
N3B–N4B–C16B
N4A–N3A–C12A
N4B–N3B–C12B
115(1)
115.00
108.0(2)
103(1)
93(1)
114.47
Torsion angles
X-ray
B3LYP/6-311?G(d, p)
C17A–C16A–N4A–N3A
C21A–C16A–N4A–N3A
N4B–N3B–C12B–C11B
N4B–N3B–C12B–C13B
5.5(14)
0.43
-179.57
0.26
˚
˚
as 0.125 A and 0.139 A respectively, the r.m.s. fit of the
atomic positions in major and minor component is
-174.1(9)
171.7(4)
˚
0.104 A. These values correlate well with the stabilization
-15.4(6)
179.46
levels of the conformers. As far as the results from com-
putational study concerned that, as expected, major pedal
conformer is more stable than minor component by
13.297 kcal/mol. Total energy values of the major and
minor pedal conformers with respect to the optimized
geometry of the compound are 55.420 and 68.717 kcal/
mol, respectively.
molecular motion in solid-state. In this sense, changes in
supramolecular environment as well as the conformational
changes accompanied with intermolecular interactions are
of special importance in terms of conformational stabilities
of the conformers. Two type crystal packing interactions
associated with the major conformer of the compound
are observed in the crystal structure. Molecular packing
arrangement of both pedal conformers of the compound is
shown in Fig. 2. The crystal structure is stabilized by
C–HÁÁÁO type weak intermolecular hydrogen bonding
There are some noteworthy geometrical discrepancies
between the optimized and crystallographically observed
geometries, in particular orientations of aryl (–C2H5) and
phenoxyphtalonitrile fragment. In the optimized geome-
try, trans-azobenzene fragment is planar as expectedly
[40, 41], whereas crystallographically observed azobenzene
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J Chem Crystallogr (2011) 41:1642–1648
1647
Fig. 2 Packing of the dimers
formed by C–HÁÁÁO type weak
H-bonds and C–HÁÁÁp
interactions. Minor pedal
conformers and H atoms not
involved in the motif have been
ignored for the sake of clarity.
Symmetry operations used to
generate equivalent atomic
positions: (1) 1 - x, 1 - y,
1 - z and (2) 1 - x, 1/2 ? y,
3/2 - z
from the planar geometry of trans-azo benzene fragment has
an adverse effect on the stabilization of the compound.
Therefore, co-planarity of aromatic rings participating in
pedal motion supplies primary contribution to stabilization
of the compound. On the other hand, C23A and C23B are out
˚
˚
of plane with deviations of -0.42(2) A and -0.19(3) A from
their related ring planes. It can be inferred from these results
that the stabilities of pedal conformers are proportional to the
amount of the out-of-plane separation of ethyl group, and
their stability is increased as the amount of deviation of ethyl
group from the related ring plane increases.
Conclusion
In conclusion, X-ray crystallographic study of the com-
pound reveals that detection of pedal conformers becomes
difficult by anchor effect accompanying pedal motion from
the presence of bulky substituent group. Quantum chemical
calculations suggest a guiding rule of how far breaking the
planarity of trans-azobenzene moiety decreases the stabil-
ization level of whole molecule. Intermolecular interac-
tions and weak H-bonds supply leading contribution to the
stabilization of the major pedal conformers. More inter-
estingly, an important effect on the pedal motion in terms
of molecular motions occurred in solid state have been
firstly recognized and examined in this study. As known,
some of recent technological advances have based on the
tools to manipulate and measure the properties of single
molecules. After this study was submitted to publish, Kim
et al. [42] have reported that molecular rotors based on
Fig. 3 Superimpositions of a the major conformer (red) and the
optimized geometry (green), b the minor conformer (blue) and the
optimized geometry (green) and c the major (red) and minor
conformer (blue) (Color figure online)
fragments are not planar due to pedal motion. Dihedral angle
between the mean planes through planar azobenzene frag-
ment and phenoxyphtalonitrile fragment is 74.20° in the
optimized geometry. Dihedral angles between substituted
aromatic rings lying at opposite sides of azo-bridge are
12.6(9)° for major component and 23.3(8)° for minor com-
ponent. Considering these, it can be stated that deviation
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J Chem Crystallogr (2011) 41:1642–1648
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Acknowledgments The authors wish to acknowledge Ondokuz
Mayıs University for the use of the STOE IPDS II diffractometer
purchased under Grants F.279 and F.377.
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