Separation of motional processes in a [2]catenane by combining synthetic, dual-frequency EPR and molecular modelling approaches

Article abstract of DOI:10.1002/mrc.1687

Continuous-wave EPR of nitroxide spin labels at conventional (9.4 GHz) and high (94.2 GHz) frequencies is applied to characterize molecular dynamics in [2]catenanes composed of macrocycles with rigid phenyleneethynylene and flexible alkyl chain building b

Full text of DOI:10.1002/mrc.1687

MAGNETIC RESONANCE IN CHEMISTRY
Magn. Reson. Chem. 2005; 43: S110–S118
Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/mrc.1687
Separation of motional processes in a [2]catenane by
combining synthetic, dual-frequency EPR and
molecular modelling approaches†
A. Godt1 and G. Jeschke2∗
1
Universita¨ t Bielefeld, Fakulta¨ t fu¨ r Chemie, Universita¨ tsstraße 25, 33615 Bielefeld, Germany
Max Planck Institute for Polymer Research, Postfach 3148, 55021 Mainz, Germany
2
Received 31 March 2005; Revised 16 June 2005; Accepted 16 June 2005
Continuous-wave EPR of nitroxide spin labels at conventional (9.4 GHz) and high (94.2 GHz) frequencies
is applied to characterize molecular dynamics in [2]catenanes composed of macrocycles with rigid
phenyleneethynylene and flexible alkyl chain building blocks. By using a set of compounds with
increasing complexity, which were all labelled at the centre of a rigid building block, it was possible to
find regimes where spectral lineshapes were dominated by local motion of the spin label or those that
contained information on tumbling of the building blocks. In chloroform, the macrocycles do not move as
rigid objects, rather the rigid building block can reorient with some ease, with respect to the rest of the
molecule. Furthermore, in that solvent the [2]catenane samples the co-conformational space on a timescale
of microseconds or shorter. In a mechanical picture, chloroform can thus be considered as an effective
lubricant that prevents the macrocycles from sticking together. Copyright  2005 John Wiley & Sons, Ltd.
KEYWORDS: EPR; nitroxide spin labels; molecular dynamics; macrocycles; catenanes; molecular devices
In a recent study, we have demonstrated by pulse
EPR measurements of distance distributions10–12 that the
two concatenated macrocycles of certain [2]catenanes can
be approximated as circular rings and that they populate
uniformly all possible co-conformations, i.e. all possible
relative orientations.13 Furthermore, we found that the
macrocycles are largely expanded in chloroform. For the
medium-sized [2]catenane 3c we find an experimental
inner diameter of 3 nm for the macrocycles, which is
much larger than the thickness of an alkyl chain or of
a phenyleneethynylene unit. This suggests that the two
macrocycles move rather unhindered, relative to each other.
However, such measurements of distance distributions have
to be performed at low temperatures in frozen solutions.
Hence, they cannot provide an estimate for the timescale of
this relative motion. We do know that the co-conformational
distribution may change during the few minutes that it takes
to dissolve and shock-freeze a sample, as we find different
distance distributions when using o-terphenyl (OTP) or
chloroform as the solvent.13 We also know that the proximity
and relative motion of the macrocycles in these [2]catenanes
do not manifest themselves in high-resolution 1H NMR
spectra14 or NOESY spectra. In the present study, we try to
obtain an estimate for the timescale of the relative motion in
liquid solution by analysing spin-label dynamics for a singly
labelled [2]catenane and line broadening due to the presence
of an additional spin label in the second macrocycle of a
[2]catenane.
INTRODUCTION
Ideas for nanostructured functional materials are often based
on analogies to macroscopic or microscopic electrical and
mechanical devices.1–5 In particular, proposed toolboxes of
molecules and supramolecular assemblies for nanomechani-
cal purposes imitate sets of simple geometrical objects, such
as rings and cylinders. To what extent such analogies extend
into nanoscopic dimensions is a matter of debate, since
interactions between molecules have different relative mag-
nitudes and a different scaling behaviour with distance than
interactions between macroscopic objects. In addition, even
shape-persistent molecules are usually much more flexible
than the units of macroscopic mechanical devices.6 To learn
about the mechanical behaviour of real molecular assem-
blies, such as [2]catenanes,7 methods are required that give
information about the geometry and the dynamics of the
molecular assemblies. As magnetic resonance techniques
such as solid-state NMR8 and spin-label EPR9 can provide
detailed information on molecular dynamics (MD) in soft
matter, they appear as good candidates for such studies.
For large, complex assemblies, labelling approaches may be
more suitable.
†Presented as part of a special issue on High-field EPR in Biology,
Chemistry and Physics.
ŁCorrespondence to: G. Jeschke, Max Planck Institute for Polymer
Research, Postfach 3148, 55021 Mainz, Germany.
E-mail: jeschke@mpip-mainz.mpg.de
Such an estimate of the timescale can only be obtained
from a rather detailed analysis of spin-label dynamics, as for
Contract/grant sponsor: Deutsche Forschungsgemeinschaft;
Contract/grant number: SPP 1051 (Hochfeld-EPR).
Copyright  2005 John Wiley & Sons, Ltd.

Separation of motional processes in a [2]catenane by EPR S111
a spin label attached to a macromolecule several motional
modes are superimposed.15,16 The present paper thus also
has a methodological aspect, namely, the separation of
contributions of local spin-label dynamics from those of
global tumbling. This problem is approached by synthesizing
a set of structurally related spin-labelled compounds that
introduce additional influences on the nitroxide spectra step
by step (Scheme 1). On the basis of this set of compounds, it
is then tested whether variations in temperature, matrix
viscosity, and microwave frequency can reliably help
discriminate between the motional modes. To differentiate
between the global motion of the [2]catenane and the relative
motion of the two macrocycles, we compare the spectra of
singly and doubly labelled [2]catenanes.
RESULTS AND DISCUSSION
Strategy for separating motional modes
Perhaps even more than high-resolution NMR spectroscopy,
EPR spectroscopy of slowly tumbling spin labels has
revealed the high complexity of macromolecular dynamics
in solution.9 Two main approaches for analysis of the
spectra were developed in recent years. The first one,
advanced mainly by the Freed group, heuristically tries
to find the minimum number of superimposed motions that
are required to fit the observed one- and two-dimensional
spectra of nitroxide spin labels.15,16 The second approach,
developed independently by Steinhoff and Hubbell17 as well
as by Levine’s group,18 uses the EPR spectra to decide
to what extent a MD simulation of the macromolecule is
in agreement with experimental observations. For the case
at hand, both approaches have drawbacks. To incorporate
relative motion of the two macrocycles of a [2]catenane into
the model of slowly relaxing local structure16 and to validate
this approach would be very tedious. MD simulations would
have to include a solvent box. Because of computation time
limitations they would not be able to extend to the timescale
on which the two macrocycles move with respect to each
other.
To reduce complexity of the problem, we try to identify
regimes in which motion can be described by simpler models.
Generally, motion of a label attached to a macromolecule can
be described as a superposition of a local tether motion,
local backbone fluctuations, and global tumbling (Fig. 1(a)).
As in our compounds, the backbone in the vicinity of the
label is rigid (Scheme 1), local backbone fluctuations are
small and therefore do not make a significant contribution
to rotational diffusion of the spin label. There should thus
be a regime at relatively low temperatures or high viscosity
of the matrix where rotational diffusion on the timescale of
the EPR experiment (tens of picoseconds to microseconds)
is dominated by tether motion. At higher temperatures
and lower viscosity, tether motion is fast on the EPR
timescale. As tether motion is restricted, it does not lead
to complete averaging of the anisotropic contributions. In
this regime, the lineshape is thus expected to be sensitive
to tumbling of the angular rigid unit (partial tumbling)
or even the whole molecule (global tumbling), Fig. 1(b–d).
To check these ideas and obtain estimates on the rate
of tumbling, we use compounds 1b, 2b, and 3b. Within
this set of compounds, local structure in the vicinity of
the spin label, and hence tether motion, are the same,
while the size of the macromolecule, and hence the rate
of tumbling, change (Fig. 1(b–d)). By comparing compound
2b to compound 1b, we can ascertain whether or not the rate
of tumbling influences the spectra and what components of
the rotational diffusion tensor are affected. By comparing
compound 3b to compound 2b, we can detect the influence
of the concatenation restraint on the motion of the labelled
macrocycle. Information on the rotational diffusion of the
spin label in compound 3b can then be used to discuss line
broadening introduced by the presence of a second spin label
in compound 3d. The type and extent of this line broadening
should, in turn, provide information on the relative motion
of the two macrocycles.
Scheme 1. Structural formulae of the investigated compounds.
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

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A. Godt and G. Jeschke
not significantly influence EPR spectra of nitroxides. Indeed,
we observe such behaviour at 330 K at both X-band (9.4 GHz)
and W-band (94.2 GHz) frequencies (Fig. 2). There are no
significant differences between the spectra of compounds
1b, 2b, and 3b except for a minor phase mismatch in the
W-band measurement of compound 2b. The small narrow
features at 337.7 mT in the X-band spectra and 3354 mT
in the W-band spectra are caused by less than 0.1% of
free spin label. Remarkably, in the X-band spectra, tether
motion is in the fast, rather than the slow, regime under
conditions where global tumbling is still insignificant. This
is manifested in the spectra in Fig. 2(a–c) by the appearance
of three relatively narrow lines that can be assigned to the
14N magnetic quantum numbers C1, 0, and ꢀ1.
As the precursor compounds are carboxylic acids, labels
can be attached via an ester13 or amide linkage. Spectra of
amide 1b and its ester analog 1c measured in OTP at 313 K at
both X- and W-band look simpler for the amide than the ester
linkage (Fig. 3). A MD simulation reveals why this is the case:
on the timescale of EPR experiments, the ester interconverts
between an E- and a Z-conformation, while the amide does
not. Surprisingly, the bimodal nature of the tether motion
for the ester linkage is more easily detected in the X-band
spectrum (arrows in Fig. 3(d)). To avoid the complication of a
bimodal tether motion, all other experiments were performed
on compounds with the amide linkage. We did not attempt
to obtain lineshape fits for the spectra shown in Fig. 3(c) and
(e), as a detailed understanding of tether motion is not the
aim of this work.
Figure 1. Motional modes expected for nitroxides (grey balls)
attached to macromolecules. (a) General case. (b) Label
attached to an angular rigid building block as in compound 1b.
(c) Label attached to a macrocycle composed of rigid and
flexible building blocks as in compound 2b. Tumbling of the
angular unit may require tumbling of the rest of the molecule.
(d) Label attached to a [2]catenane as in compound 3b.
Tumbling of the angular unit maybe further hindered by
concatenation with the second macrocycle (grey).
High viscosity – EPR spectra dominated by tether
motion
Low viscosity – extent of averaging limited by
global tumbling
In a low-viscosity solvent at high temperature global
tumbling of macromolecules with a size of a few nanometers
is expected to proceed with correlation times in the
nanosecond range or even shorter, i.e. on timescales where
Compounds 1b, c, 2b, 3b–d are well soluble in the
glass former OTP as well as in the low-viscosity solvent
chloroform. In OTP, at temperatures between the glass
transition temperature of 244 K and approximately the
melting point of 333 K, global motion is expected to have
rotational correlation times longer than 1 µs, so that it does
Figure 2. CW EPR spectra of compounds 1b, 2b, and 3b in o-terphenyl at 330 K and 9.4 GHz (a–c) and 94.2 GHz (d–f). (a,d)
Angular compound 1b. (b,e) Macrocycle 2b. (c,f) Singly labelled [2]catenane 3b.
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

Separation of motional processes in a [2]catenane by EPR S113
nitroxide lineshapes are influenced. For our compounds,
chloroform appears to be best suited, as measurements of
the distance distribution in doubly labelled [2]catenanes 3c
indicated that the macrocycles are expanded in this solvent
and adopt all possible co-conformations.13 For the diamide
3d, we found the same distance distribution as for the
diester 3c (data not shown). As Continuous-wave EPR (CW
EPR)linewidths were found to decrease significantly with
increasing temperature, we performed the measurements
at the highest possible temperature of 325 K (boiling point
of chloroform: 334 K). In this regime, we find clearly visible
differences between the spectra of angular compound 1b and
macrocycle 2b (compare Fig. 4(a) with (b) and 5(d) with (e))
and slight differences between the latter and the singly
labelled [2]catenane 3b (compare Fig. 4(b) with (c) and 5(e)
with (f)). This indicates that concatenation does not strongly
constrain motion of the macrocycle.
To quantify the differences, we fitted the spectra with
the simplest motional model that could account for the
lineshapes. We found that a model of isotropic Brownian
rotational diffusion could not reproduce the relative ampli-
tudes of the three lines for any of the compounds (data not
shown). Likewise, the rotational correlation times ꢁc0 , ꢁc00, and
ꢁc000 computed from the amplitude ratios and linewidths by
the three expressions given by Buchachenko et al.19 do not
agree, as they should for isotropic rotary diffusion. Good
fits of the X-band data (for example, Fig. 5(a, e)) are obtained
with a model of uniaxial anisotropic rotary diffusion with the
unique axis being the y-axis of the molecular frame. This axis
is perpendicular to both the N–O bond and the pꢂ orbital
lobes on the nitrogen atom. As discussed by Buchachenko
et al.,19 a reliable assignment of the unique axis may not be
possible in the regime of fast uniaxial rotary diffusion. Fur-
thermore, the spectra are rather insensitive to the principal
Figure 3. Comparison of label attachment via an amide linkage
or ester linkage through studies on compound 1b (left) and
compound 1c (right). (a,b) Tether structure and definition of
cone angle ꢀ. (c,d) CW EPR spectra in o-terphenyl at 9.4 GHz
and 313 K. (e,f) CW EPR spectra in o-terphenyl at 94.2 GHz
and 313 K. (g,h) Variation of ꢀ in a molecular dynamics
simulation in vacuum at 313 K.
value R of the rotational diffusion tensor along the unique
jj
axis. It is also clear that the actual motion is a superposi-
tion of fast partial averaging by tether motion and slower
Figure 4. CW EPR spectra of compounds 1b, 2b, and 3b in chloroform at 325 K and 9.4 GHz (a–c) and 94.2 GHz (d–f). (a,d) Angular
compound 1b. (b,e) Macrocycle 2b. (c,f) singly labelled [2]catenane 3b.
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

S114
A. Godt and G. Jeschke
Figure 5. Analysis of line broadening due to the presence of a second label in [2]catenane 3d compared to singly labelled
[2]catenane 3b (chloroform, 325 K). Solid lines are experimental spectra; dashed lines are best fits. (a) Spectrum of [2]catenane 3b at
9.4 GHz, fit with uniaxial anisotropic rotational diffusion, R D 0.5 ð 109
s
ꢀ1, R D 4 ð 1011
s
ꢀ1. (b) Spectrum of [2]catenane 3b at
?
jj
94.2 GHz, fit with uniaxial anisotropic rotational diffusion, same parameters as in (a). (c) Spectrum of [2]catenane 3d at 9.4 GHz, fit
by convolution of the spectrum in (a) with a Lorentzian. (d) High-field detail of (c). The experimental line is shifted to low-field with
respect to the simulation (arrow). (e) Spectrum of [2]catenane 3d at 9.4 GHz, fit with uniaxial anisotropic rotational diffusion,
R
D 0.4 ð 109
s
ꢀ1, R D 4 ð 1011 sꢀ1 and a Heisenberg exchange frequency of 20 MHz. (f) High-field detail of (e). The field
?
jj
positions of the experimental line and simulated lines coincide (arrow).
isotropization by global tumbling of the molecule. In this
According to this relation, which is strictly valid only for
situation, the principal value R that is perpendicular to the
rotational diffusion of a sphere, R should scale with rꢀ3
.
?
?
eff
unique axis can be considered as a rough estimate of the
timescale of global tumbling. This value is also found to
depend on temperature (data not shown). We have obtained
Hence, the effective rotational radius for the macrocycle 2b
is only by a factor of 1.08 larger than for the rigid angular
building block 1b. The concatenation constraint increases the
effective radius by another factor of 1.1. These small changes
indicate that because of the flexible alkyl chains, tumbling
of the angular building block is only weakly coupled to
tumbling of the whole molecule. In other words, neither the
macrocycle nor the [2]catenane tumble like a rigid object. The
relative motion of the building blocks is significant at 325 K
on a nanosecond timescale. The same is also true at ambient
temperature.
We can also safely conclude that the rotational correlation
time about any axis is shorter than 1 ns for all compounds.
Together with the planar extension of the rigid angular
unit (1.2 ð 2.4 nm2), this implies that the label traces a
volume of more than 5 nm3 on a nanosecond timescale.
This, in turn, means that the distance vector between the
two labels in compound 3d also rotates on this timescale.
Any residual dipole–dipole coupling between the two labels
is thus expected to be much smaller than the linewidths
of approximately 6 MHz observed at X-band for the singly
labelled [2]catenane 3b.
R
values for all compounds at 325 K in chloroform by fits
?
of X-band and W-band spectra with the Schneider/Freed
program package.15
An overview of these data is given in Table 1. Because
of slight phase errors in the experimental spectra, fits are
slightly worse at W-band frequencies (e.g., Fig. 5(b)), so that
the values obtained from those spectra are less reliable. As
the purpose of this analysis is only a timescale estimate,
we may conclude that the data at the two frequencies
agree reasonably well. As expected, R decreases with
?
increasing size of the molecule. The value for the singly
labelled [2]catenane 3b is significantly smaller than the one
for the macrocycle 2b, which implies that the concatenation
constraint influences rotational diffusion of the label. We may
roughly estimate the increase of an effective rotational radius
reff of the molecules by using the Stokes–Einstein relation.
Table 1. Perpendicular component of axial rotational diffusion
tensors obtained from fitting spectra of compounds 1b, 2b, 3b,
d in chloroform at 325 K at 9.4 GHz (R?,X) and 94.2 GHz (R
)
?,W
Line broadening in the doubly labelled
Compound
1b
2b
3b
3d
[2]catenane – relative motion of the macrocycles
The only difference between compounds 3b and 3d is
the introduction of a second spin label at a site of
the concatenated ring that is equivalent to the site of
R
R
?,X/109 sꢀ1 0.85 š 0.1 0.675 š 0.1 0.5 š 0.05 0.4 š 0.05
?,W/109 sꢀ1 0.85 š 0.2 0.55 š 0.15 0.5 š 0.05 0.5 š 0.05
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

Separation of motional processes in a [2]catenane by EPR S115
the first spin label. In the W-band spectra, where the
linewidths for compound 3b are larger than 15 MHz, this
does not cause significant changes. However, in the X-
band spectra significant additional broadening is observed
for the doubly labelled compound 3d (compare Fig. 5(c)
to (a)). As concluded in the previous section, because
of the fast motion this broadening cannot be due to
residual dipole–dipole couplings. Possible sources are a
decrease in the transverse relaxation time T2 due to dipolar
relaxation and exchange broadening. Dipolar relaxation
can be simulated by convolution of the experimental
absorption spectrum (integrated CW EPR spectrum) of
the singly labelled [2]catenane 3b with a Lorentzian line
and pseudomodulation to obtain again a first-derivative
spectrum. The width of the Lorentzian line can be treated as
a fit parameter. The best fit obtained by such a simulation
is shown in Fig. 5(c), and a detailed plot of the high-field
line in Fig. 5(d). Although the fit is not poor, one notices a
small low-field shift of the experimental high-field line with
respect to the simulated line (arrow in Fig. 5(d)). Similarly,
a slight high-field shift of the low-field line is observed. In
other words, the apparent hyperfine coupling is smaller for
compound 3d than for compound 3b. Such a reduction in
the apparent hyperfine coupling is expected for exchange
coupling as a broadening mechanism.20
and of sampling the co-conformational distribution are not
separated. We may thus conclude that the co-conformational
space is sampled on a timescale of microseconds or less.
It thus appears that in chloroform, the two macrocycles in
[2]catenanes 3 move relatively unhindered with respect to
each other; they are not sticky.
CONCLUSION
The dynamics of a [2]catenane composed of macrocycles with
both rigid and flexible building blocks could be unravelled
by analysing CW EPR lineshapes of nitroxide spin labels
attached to one or both of the angular rigid building blocks.
Tethering of the spin label via an amide linkage gave simpler
spectra than tethering via an ester linkage. A small increase
in the rotational correlation time when going from just
the angular building block to a macrocycle implies that
the macrocycles do not move as rigid objects. Rather, the
angular units can rotate considerably with respect to the rest
of the molecule. Analysis of the line broadening imposed
by attaching a second label to a [2]catenane reveals that the
two macrocycles do not stick together in chloroform, and that
they move freely with respect to each other on a microsecond
timescale. To return to a macroscopic mechanical picture,
this means that chloroform acts as an effective lubricant
for molecules composed of phenyleneethynylene and alkyl
chain building blocks.
Indeed, the best fit of the X-band spectrum of com-
pound 3d with the Schneider/Freed program15 including
Heisenberg exchange is better than with simple convolu-
tion (Fig. 5(e, f)). The improvement in relative amplitudes of
The method described here may open a way to investigate
entropy-driven nanomechanical devices on the basis of
flexible molecular subunits that have been recently suggested
by Hanke and Metzler.22
the lines is due to a slight change in R compared to that
?
in compound 3b (Table 1). However, the reduced hyper-
fine splitting is only reproduced if Heisenberg exchange is
included. The fit yields an exchange frequency of 20 MHz.
We cannot exclude that dipolar relaxation contributes to the
broadening to some extent, but we can safely conclude that
the reduction in the hyperfine splitting is not reproduced
for exchange frequencies smaller than 10 MHz. This implies
effective collisions of the two nitroxide labels on a submi-
crosecond timescale and as a result, relative motion of the
two macrocycles in the [2]catenane on that timescale.
Finally, we have to consider whether this relative
motion on the submicrosecond timescale samples the whole
space of co-conformations. From measurements of the dis-
tance distribution, we know that in chloroform solutions
of 3c13 and 3d the whole space of co-conformations is
almost uniformly populated. If the timescales of nitrox-
ide–nitroxide collisions and of sampling of the whole co-
conformational space were significantly different, we would
thus expect a distribution of exchange frequencies with fast
exchange for co-conformational subensembles with short
nitroxide–nitroxide distances and slow or no exchange for
subensembles with long nitroxide–nitroxide distances. The
occurrence of such subensembles with different exchange
frequencies leads to lineshapes with broad wings and nar-
row centres, as we have recently observed for counterions
near polyelectrolytes.21 Such lineshapes cannot be fitted by a
single exchange frequency. In the present case, the lineshapes
are well reproduced by a single exchange frequency, which
implies that the timescales of nitroxide–nitroxide collisions
EXPERIMENTAL
EPR spectroscopy
CW EPR at X-band frequencies of approximately 9.4 GHz
was performed with a Bruker Elexsys 580 spectrometer
equipped with a 4103 TM/0105 rectangular cavity and an
ER 4111 variable temperature unit. A microwave power of 2
mW and a modulation amplitude of 0.05 mT were used. The
sweep width was 20 mT for spectra measured in OTP (Fluka)
matrix and 10 mT for spectra measured in chloroform (Fluka,
stabilized with 1% ethanol) solution. In both cases, 2048
data points were acquired. CW EPR at W-band frequencies
of approximately 94.2 GHz was performed with a Bruker
Elexsys 680 spectrometer equipped with a Bruker ENDOR
resonator and an Oxford cryostat for temperature control.
Nitrogen gas was used as a heating medium. A microwave
power of 0.05 mW and a modulation amplitude of 0.1 mT
were used. The sweep width was 35 mT for spectra measured
in OTP matrix and 15 mT for spectra measured in chloroform
solution. In both cases, 1024 points were acquired.
All spectra were measured on samples with total label
concentrations below 1 mmol lꢀ1, so that an influence of
intermolecular Heisenberg exchange on lineshapes could
be excluded. All samples were kept in the corresponding
solvents and at the corresponding temperatures for a
sufficient time to equilibrate with the oxygen from air.
Control measurements of compound 1b revealed that for
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

S116
A. Godt and G. Jeschke
Pd(PPh3)2Cl2 (85 mg, 0.12 mmol) and CuI (44 mg, 0.23 mmol) were
added. Soon a precipitate formed. After 17 h at room temperature,
the reaction mixture was diluted with CH2Cl2, washed with 2 N
HCl (exothermic) and the combined aqueous phases were extracted
with CH2Cl2. The combined organic phases were dried (Na2SO4)
and concentrated in vacuo. Flash chromatography (petroleum
ether/CH2Cl2 1 : 2 v/v) gave 1d containing a trace of 1-isopropoxy-
4-iodobenzene. This material was dissolved in CH2Cl2 (15 ml), and
1d (5.6 g, 74%) was precipitated through addition to petroleum
the used protonated spin labels in chloroform at ambient
temperature, line broadening by oxygen is noticeable,
though not dominant. Such broadening is not significant
in chloroform at 325 K.
MD simulations
MD simulations were carried out with the program package
Cerius 2 (v. 3.8, Molecular Simulations, Inc.), using the CFF91
force field. The systems were first pre-equilibrated (canonical
ensemble in a Berendsen temperature bath, 20 000 steps, time
step 0.5 ð 10ꢀ15 s) and then sampled by a 1 ns run (Nose´-
Hoover thermostat, 2 ð 106 steps, time step 0.5 ð 10ꢀ15 s).
Structures were written to trajectory files in time intervals
of 1 ð 10ꢀ13 s. Time traces of the nitroxide and backbone
coordinates were extracted from the trajectory files using the
gOpenMol program and analysed by a home-written Matlab
(The MathWorks, Inc.) program.
1
°
ether (300 ml) as a colourless solid: m.p. D 167.2–169.3 C; H NMR:
υ D 7.98 (s, 2 H, H˛), 7.61 and 7.53 (AA0XX0, 4 H each, Hˇ), 7.46 (half
of AA0XX0, 4 H, Hꢃ -2,-6), 6.85 (half of AA0XX0, 4 H, Hꢃ -3,-5), 5.78 (s,
1 H, OH), 4.57 (sept, J D 6.0 Hz, 2 H, CHCH3), 4.36 (q, J D 7.1 Hz,
2 H, CO2CH2), 1.37 (t, J D 7.0 Hz, 3 H, CH2CH3),1.34 (d, J D 6.0 Hz,
6 H, CHCH3); 13C NMR: υ D 166.1 (CO2), 158.2 (Cꢃ -4), 153.2 (C˛-4),
135.9 (Cˇ-1), 133.1 (Cꢃ -2,-6), 132.0 (Cˇ-3,-5), 131.6 (C˛-2,-6), 129.3
(Cˇ-2,-6), 128.3 (C˛-3,-5), 123.7, 123.4 (C˛-1, Cˇ-4), 115.8 (Cꢃ -3,-5),
114.9 (Cꢃ -1), 90.6 (C CArꢃ ), 87.6 (C CArꢃ ), 70.0 (CHCH3), 60.9
(CO2CH2), 22.0 (CHCH3), 14.4 (CH2CH3).
Ethyl 3,5-di[4-(4-isopropoxyphenylethynyl)phenyl]-4-methoxyben-
zoate (1e)
A suspension of 1d (3.01 g, 4.74 mmol), methyl iodide (0.6 ml,
9.6 mmol) and K2CO3 (1.3 g, 9.4 mmol) in DMF (80 ml) was
EPR spectrum simulations
°
stirred for 15 h at 40 C. The reaction mixture was poured into
CW EPR spectral simulations were performed with a
program by Schneider and Freed assuming a uniaxial tensor
of rotational diffusion.15 The following magnetic parameters
water. The precipitate was isolated and washed well with water.
Drying (P4O10, vacuum) gave 1e (2.9 g, 94%) as a colourless solid.
m.p. D 179.1–179.4 C; 1H NMR: υ D 8.04 (s, 2 H, H˛-2,-6), 7.58
°
(apparent s, 8 H, Hˇ), 7.46 (half of AA0XX0, 4 H, Hꢃ -2,-6), 6.85 (half of
AA0XX0, 4 H, Hꢃ -3,-5), 4.57 (sept, J D 6.1 Hz, 2 H, CHCH3), 4.38 (q,
J D 7.1 Hz, 2 H, CO2CH2), 3.21(s, 3 H, OCH3), 1.38(t, J D 6.1 Hz, 3 H,
CH2CH3), 1.33 (d, J D 6.1 Hz, 12 H, CHCH3); 13C NMR: υ D 166.0
(CO2), 158.8 (Cꢃ -4), 158.2 (C˛-4), 137.3, 135.2 (C˛-3,-5, Cˇ-1), 133.1
(Cꢃ -2,-6), 131.7 (C˛-2,-6), 131.4 (Cˇ-3,-5), 129.2 (Cˇ-2,-6), 126.5 (C˛-1),
123.0 (Cˇ-4), 115.8 (Cꢃ -3,-5), 115.0 (Cꢃ -1), 90.3 (C CArꢃ ), 87.8 (Arˇ
were assumed: g-tensor: gxx D 2.0090, gyy D 2.0060, gzz
D
2.0024; hyperfine-tensor: Axx D 0.68 mT, Ayy D 0.62 mT,
Azz D 3.43 mT. Within the precision of our approach,
rotational correlation times do not depend on the small
variations of these parameters with solvent polarity.
C
C), 70.0 (CHCH3), 61.1 (CO2CH2), 60.7 (OCH3), 22.0 (CHCH3),
14.4 (CH2CH3); elemental analysis (%) calculated for C44H40O5
(648.799): C 81.46 H 6.21; found C 81.46, H 6.21.
Preparation of spin-labelled compounds
General
All reactions were carried out under inert atmosphere in
dried Schlenk flasks. THF was dried over sodium/benzo-
phenone and piperidine over CaH2. CH2Cl2 and DMF were
purchased in sealed bottles over molecular sieves. The
diethyl ether that was used for workup and chromatography
of the spin-labeled compounds was distilled from sodium
prior to use to remove the stabilizer. The petroleum
3,5-Di[4-(4-isopropoxyphenylethynyl)phenyl]-4-methoxybenzoic acid
(1a)
10 N NaOH (10 ml) was added to a suspension of 1e (2.98 g,
4.70 mmol) in THF (50 ml) and ethanol (30 ml). Upon heating to
°
45 C, the reaction mixture became a clear solution. After 16 h at
°
45 C, the reaction mixture was cooled with an ice bath and the
product 1a (2.80 g, 98%) was precipitated through the addition
of 2 N HCl as a colourless solid that was dried (P4O10, vacuum).
1
°
m.p. D 232.1–233.0 C; H NMR: υ D 8.12 (s, 2 H, H˛), 7.60 (apparent
s, 8 H, Hˇ), 7.47 (half of AA0XX0, 4 H, Hꢃ -2,-6), 6.86 (half of AA0XX0,
4 H, Hꢃ -3,-5), 4.57 (sept, J D 6.1 Hz, 2 H, CHCH3), 3.23 (s, 3 H,
OCH3), 1.34 (d, J D 6.1 Hz, 12 H, CHCH3); 13C NMR: υ D 171.4
(CO2), 159.7 (C˛-4), 158.1 (Cꢃ -4), 137.0, 135.4 (C˛-3,-5, Cˇ-1), 133.1
(Cꢃ -2,-6), 132.4 (C˛-2,-6), 131.4 (Cˇ-3,-5), 129.2 (Cˇ-2,-6), 125.2 (C˛-
1), 123.1 (Cˇ-4), 115.8 (Cꢃ -3,-5), 115.0 (Cꢃ -1), 90.4 (C CArꢃ ), 87.8
°
ether used had a boiling range of 30–40 C. For flash
chromatography, silica gel was used. The NMR spectra were
recorded on a 300-MHz instrument at room temperature
in CDCl3 as solvent and internal standard. The assignment
of the 13C NMR signals is in accordance with DEPT-135
measurements. The subscripts ˛, ˇ, ꢃ, and υ refer to the
aromatic rings. The hydroxybenzoate moiety is named ˛.
The benzene unit closest to the hydroxybenzoate moiety
is named ˇ, the benzene unit connected with Arˇ by only
one ethyne moiety is named ꢃ, and the residual benzene
unit is named υ. For the numbering of the positions, the
ethyl 4-hydroxybenzoate is considered as the substituted
parent compound. Melting points were determined in open
capillaries.
(Arˇ
C C), 70.0 (CHCH3), 60.7 (OCH3), 22.0 (CHCH3); elemental
analysis (%) calculated for C42H36O5 (620.745): C 81.27, H 5.85; found
C 81.25, H 5.80.
Compound 1b (compound 1 labelled with 4-amino-TEMPO)
N-Hydroxysuccinimide (20 mg, 0.17 mmol) was added to a suspen-
sion of acid 1a (99 mg, 0.16 mmol) in CH2Cl2 (3 ml). Upon addition
of N,N0-dicyclohexylcarbodiimide (36 mg, 0.17 mmol) the suspen-
sion turned into a clear solution. Shortly after the solution became
turbid, again. Then 4-amino-2,2,6,6-tetramethylpiperidinyloxy (4-
amino-TEMPO; 40 mg, 0.23 mmol) was added. After stirring the
reaction mixture at room temperature for 40 h, the precipitate was
removed by filtration and washed with CH2Cl2 until it was colour-
less. Removal of the solvent from the filtrate gave a reddish solid.
Chromatography using a chromatotron (petroleum ether/CH2Cl2
1 : 1 v/v ! petroleum ether/CH2Cl2/Et2O 15 : 15 : 1 ! 15 : 15 : 2
Synthesis of acid 1a
Ethyl 3,5-di[4-(4-isopropoxyphenylethynyl)phenyl]-4-hydroxyben-
zoate (1d)
°
To
a
carefully degassed (freeze-pump-thaw method) solution
v/v/v) gave 1b (79 mg, 64%) as a reddish solid. m.p. D 135 C sin-
of ethyl 3,5-di(4-ethynylphenyl)-4-hydroxybenzoate23 (4.32 g,
11.8 mmol) and 1-isopropoxy-4-iodobenzene (1-Isopropoxy-4-
iodobenzene was obtained from 4-iodophenol and 2-bromopropane
in analogy to the preparatꢀio2n of 1-ethoxy-4-iodobenzene (Ref. 24).
tering with discoloration; 1H NMR: all signals are broad. υ D 7.66
(apparent s with shoulder at 7.9 ppm, > 2 H, Hˇ and H˛), 7.53 (half
of AA0XX0, 4 H, Hꢃ -2,-6), 6.93 (half of AA0XX0, 4 H, Hꢃ -3,-5), 4.64 (t
in outlines, 2 H, CHCH3), 3.28 (s, 3 H, OCH3), 1.41 (d, J D 5.3 Hz,
12 H, CHCH3); elemental analysis (%) calculated for C51H53N2O5
(773.994): C 78.14, H 6.90, N 3.62; found C 78.53, H 6.86, N 3.57.
°
Distillation (77–83 C/10 torr) gave the colorless, slowly
solidifying product.) (7.42 g, 28.3 mmol) in piperidine (60 ml),
Copyright  2005 John Wiley & Sons, Ltd.
Magn. Reson. Chem. 2005; 43: S110–S118

Separation of motional processes in a [2]catenane by EPR S117
FD-MS: m/z D 759.7 (18%, [M ꢀ CH3]C), 775.5 (100%, MC), 1535
(10%, [2M ꢀ CH3]C), 1549.4 (10%, [2M]C).
mixture of CH2Cl2 and diethyl ether and this solution was washed
extensively with water. Drying (Na2SO4) and removal of solvent
gave a beige-coloured solid (94 mg) that was freeze-dried from
benzene to remove residual solvents. 1H NMR spectroscopy revealed
a mixture of diacid 3a and the corresponding monomethylester and
dimethylester at the ratio of 1 : 2 : 1. 1H-NMR: υ D 8.10 (s, 2 H, H˛
of the ring with the CO2H group of the monoester), 8.09 (s, 4 H,
H˛ of diacid 3a), 8.03 (s, 2 H of monoester and 4 H of diester, H˛
of the ring with the CO2Me group of mono ester and diester),
7.58, 7.57 (two apparent s, 16 H each, Hˇ), 7.45 (half of AA0XX0,
8 H, Hꢃ -2,-6), 7.38 and 7.29 (AA0XX0, 8 H each, Hυ), 6.85 (half of
AA0XX0, 8 H, Hꢃ -3,-5), 3.94 (t, J D 6.5 Hz, 8 H, ArOCH2), 3.91 (s,
3 H of monoester and 6 H of diester, CO2CH3), 3.183, 3.175, 3.166
(3 s, 6 H each, ArOCH3), 2.37 (t, J D 7.0 Hz, 8 H, CH2C C), 1.76 (m,
8 H, OCH2CH2), 1.56 (m, 8 H, CH2CH2C C), 1.5–1.2 (m, 152 H,
CH2); Mixture of C204H244O10 (2856.186), C205H246O10 (2870.213),
C206H248O10 (2884.240): MALDI-TOF (dithranol): m/z D 2856.5
(37%, [MH,H]C), 2871.5 (56%, [MH,Me]C), 2885.5 (12%, [MMe,Me]C),
2879.3 (41%, [MH,H C Na]C), 2893.3 (31%, [MH,Me C Na]C), 2908.4
(23%, [MMe,Me C Na]C).
Compound 1c (compound 1 labelled with 4-hydroxy-TEMPO)
The mixture of acid 1a (80 mg, 0.13 mmol), 4-hydroxy-TEMPO
(25 mg, 0.15 mmol), 4-(dimethylamino)pyridin (17 mg, 0.14 mmol)
and N-ethyl-N0-(3-dimethylaminopropyl)carbodiimide hydrochlo-
ride (37 mg, 0.19 mmol) were dissolved in CH2Cl2 (4 ml). This
°
solution was stirred at 45 C for 14 h. After cooling to room temper-
ature, diethyl ether and 2 N HCl were added. The aqueous phase
was extracted with diethyl ether. The combined organic phases
were washed with 2 N HCl and dried (MgSO4) and the solvent was
removed at reduced pressure. Flash chromatography (petroleum
ether/diethyl ether 2 : 1 v/v; the compound was applied as a solu-
tion in CH2Cl2) gave 1c (87 mg, 87%) contaminated with a small
amount of acid 1a (The sharp signal at 8.12 ppm (H˛) in the 1H NMR
spectrum and the signal at m/z D 620.7 (2%, [M(1a)]C) in the mass
spectrum proves the presence of acid 1a. Because of 1H NMR signal
overlap the amount can only be estimated to be rather small.) as
an orange-coloured solid (Based on our later results when working
with 4-hydroxy-TEMPO labelled catenanes (Ref. 13) using a gradi-
ent petroleum ether/CH2Cl2 ! petroleum ether/CH2Cl2/Et2O will
most probably give pure compound 1c.). 1H NMR: all signals are
broad. υ D 8.2 (very broad s, 2 H, H˛), 7.77 (apparent s, 8 H, Hˇ),
7.63 (half of AA0XX0, the fine structure is hardly resolved 4 H, Hꢃ -
2,-6), 7.03 (half of AA0XX0, the fine structure is hardly resolved 4 H,
Hꢃ -3,-5), 4.75 (m, 2 H, CHCH3), 3.40 (s, 3 H, OCH3), 1.52 (d, the fine
structure is hardly resolved 12 H, CHCH3); C51H52NO6 (774.978):
FD-MS: m/z D 387.5 (13%, M2C), 620.7 (2%, [M(1a)]C), 760.0 (23%,
[M ꢀ CH3]C), 774.9 (100%, MC), 1551.1 (3%, [2M]C).
Labelling of the catenane with 4-amino-TEMPO. N-Hydroxysuccinimide
(4.9 mg, 0.04 mmol) and N,N0-dicyclohexylcarbodiimide (9.0 mg,
0.04 mmol) were subsequently added to a solution of the obtained
mixture (86.8 mg, 0.03 mmol carboxyl groups) of catenane diacid and
its corresponding monomethylester and dimethylester in CH2Cl2
°
(4 ml). The reaction mixture was stirred at 45 C for 30 min. After
removal of the heating bath, 4-amino-TEMPO (12.0 mg, 0.07 mmol)
was added to the solution at room temperature. The solution turned
turbid. After stirring the suspension for 20 h at room temperature,
it was filtered, the precipitate was washed with CH2Cl2 and
the solvent of the filtrate was removed under reduced pressure.
The products were separated through chromatography using a
chromatotron. Elution with petroleum ether/CH2Cl2 1 : 1 v/v gave
catenane dimethylester (19 mg, 21% over two steps) as a colourless
solid; further elution with petroleum ether/CH2Cl2/Et2O 30 : 30 : 1
! 15 : 15 : 2 v/v/v gave mono-labelled [2]catenane 3b (32 mg, 34%
over two steps) as a beige-coloured solid and finally elution with
petroleum ether/CH2Cl2/Et2O 2 : 2 : 1 v/v/v gave doubly labelled
[2]catenane 3d (11 mg, 11% over two steps) as a slightly reddish
solid. The products were freeze dried from benzene.
Compound 2b (macrocycle labelled with 4-amino-TEMPO)
N-Hydroxysuccinimide (12 mg, 0.11 mmol) was added to a sus-
pension of macrocyclic acid 2a13 (100 mg, 0.07 mmol) in CH2Cl2
(5 ml). After addition of N,N0-dicyclohexylcarbodiimide (23 mg,
°
0.11 mmol) the thick suspension was heated to 44 C, whereupon
it became a very faintly turbid solution. After stirring the reaction
°
mixture at 44 C for 25 min the heating bath was removed and
4-amino-TEMPO (26 mg, 0.15 mmol) was added to the solution at
room temperature. The reddish brown, slightly turbid solution was
stirred at room temperature for 44 h. Because the TLC (silica gel;
petroleum ether/CH2Cl2/diethyl ether 15 : 15 : 2 v/v/v) suggested
an incomplete reaction, the reaction mixture was heated again to
Analytical data for mono-labelled [2]catenane 3b
m.p. D 110.2–111.3 C; 1H NMR: All signals are broad. υ D 8.04
°
°
45 C for 5.3 h, and afterwards kept for another 17 h at room tem-
(s, 2 H, H˛ of macrocycle with the ester group), 7.8 (very broad s,
H˛ of macrocycle with the amide group), 7.58 (apparent s, 16 H,
Hˇ), 7.46 (half of AA0XX0, 8 H, Hꢃ -2,-6), 7.39 and 7.30 (AA0XX0, 8 H
each, Hυ), 6.86 (half of AA0XX, 8 H, Hꢃ -3,-5), 3.96 (t, J D 6.4 Hz,
8 H, ArOCH2), 3.92 (s, 3 H, CO2CH3), 3.18 (s, 6 H, ArOCH3), 2.38
(t, J D 6.8 Hz, 8 H, CH2C C), 1.77 (m, 8 H, OCH2CH2), 1.58 (m,
8 H, CH2CH2C C), 1.5–1.2 (m, ca 163 H, CH2 of macrocycle and
protons of the spin label); elemental analysis (%) calculated for
C214H263N2O10 (3023.462): C 85.01, H 8.77, N 0.93; found C 84.68, H
8.66, N 0.84. MALDI-TOF (Dithranol, KO2CCF3): m/z D 3025 (8%,
MC), 3063 (16%, [M C K]C).
perature. Despite the longer reaction time, the TLC revealed no
change in the product composition. The reaction mixture was fil-
tered, the solid was washed with CH2Cl2 and the solvent was
removed from the filtrate at reduced pressure. Chromatography
using a chromatotron (the compound was applied as a solution in
CH2Cl2/CHCl3; elution with petroleum ether/CH2Cl2 1 : 1 v/v !
petroleum ether/CH2Cl2/Et2O 30 : 30 : 1 v/v/v ! 5 : 5 : 1 v/v/v)
°
revealed 2b (76 mg, 70%) to be a reddish solid. m.p. D 185 C sinter-
ing with decomposition (most probably the transition into a liquid
crystalline phase (Ref. 25); 1H NMR: all signals are broad. υ D 7.86
(very broad s, 2 H, H˛), 7.61 (apparent s, 8 H, Hˇ), 7.49 (half of
AA0XX0, 4 H, Hꢃ -2,-6), 7.41 and 7.33 (AA0XX0, 4 H each, Hυ), 6.89
(half of AA0XX, 4 H, Hꢃ -3,-5), 4.00 (t, J D 6.3 Hz, 4 H, ArOCH2),
3.21 (s, 3 H, OCH3), 2.41 (t in outlines, 4 H, CH2C C), 1.80 (m,
4 H, OCH2CH2), 1.60 (m, 4 H, CH2CH2C C), 1.6–1.2 (m, ca 82 H,
CH2 of macrocycle and protons of the spin label); elemental analysis
(%) calculated for C111H139N2O5 (1581.342): C 84.31, H 8.86, N 1.77;
found C 84.26, H 8.92, N 1.69. FD-MS: m/z D 789.6 (27%, M2C),
1564.2 (47%, [M ꢀ CH3]C), 1578.9 (100%, MC).
Analytical data for doubly labelled [2]catenane 3d
1H NMR: all signals are broad and the fine structures are hardly
resolved. υ D 7.57 (apparent s, ca 16 H, Hˇ; most probably
overlapping with signal of H˛), 7.45 (half of AA0XX0, 8 H, Hꢃ -2,-
6), 7.38 and 7.30 (AA0XX0, 8 H each, Hυ), 6.85 (half of AA0XX, 8 H,
Hꢃ -3,-5), 3.96 (t in outlines, 8 H, ArOCH2), 3.48 (s, signal of unknown
impurity), 3.16 (s, 6 H, ArOCH3), 2.38 (t in outlines, 8 H, CH2C C),
1.92 (m, signal of unknown impurity), 1.8–1.2 (m, ca 189 H, CH2 of
macrocycle and protons of the spin label); C222H278N4O10 (3162.684):
MALDI-TOF (dithranol, KO2CCF3): m/z D 3165 (4%, MC), 3202 (8%,
[M C K]C).
Compounds 3b and 3d-[2]catenane labelled once (3b) or twice (3d)
with 4-amino-TEMPO
Statistical methylation of catenane diacid 3a. A solution of methyliodide
[0.42 ml of a solution of MeI (50 µl) in dry DMF (10 ml); 0.034 mmol]
in DMF was added to a suspension of catenane diacid 3a13 (96.8 mg,
0.034 mmol) and K2CO3 (9.3 mg, 0.07 mmol) in DMF (2 ml) and
Acknowledgements
The authors thank Deutsche Forschungsgemeinschaft for financial
support within SPP 1051 (Hochfeld-EPR), Michael Mehring for
helpful discussions, Christian Bauer for technical support and Ju¨rgen
Thiel for assistance during the synthesis.
°
THF (2 ml). After stirring the reaction mixture at 44 C for 16 h,
it was cooled with an ice bath and 5 N HCl was added slowly.
The yellow precipitate dissolved upon addition of CH2Cl2. The
aqueous phase was extracted with CH2Cl2, the combined organic
phases were washed initially with 2 N HCl and finally with water
and were dried (Na2SO4). The solid obtained after removal of the
solvent under reduced pressure contained a substantial amount of
DMF. Therefore, the crude product was once again dissolved in a
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