Conformational Flexibility of Hybrid [3]- A nd [4]-Rotaxanes

Article abstract of DOI:10.1021/jacs.0c06547

The synthesis, structures, and properties of [4]- A nd [3]-rotaxane complexes are reported where [2]-rotaxanes, formed from heterometallic {Cr7Ni} rings, are bound to a fluoride-centered {CrNi2} triangle. The compounds have been characterized by single-cr

Full text of DOI:10.1021/jacs.0c06547

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Article
Conformational flexibility of hybrid [3]- and [4]-rotaxanes
Selena J. Lockyer, Selina Nawaz, Adam Brookfield, Alistair J. Fielding, Inigo J. Vitorica-Yrezabal,
Grigore A. Timco, Neil A Burton, Alice M Bowen, Richard E. P. Winpenny, and Eric J.L. McInnes
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.0c06547 • Publication Date (Web): 21 Aug 2020
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Conformational flexibility of hybrid [3]- and [4]-rotaxanes
Selena J. Lockyer,a Selina Nawaz,a Adam Brookfield,a Alistair J. Fielding,b Inigo J. Vitorica-
Yrezabal,a Grigore A. Timco,a Neil A. Burton,a Alice M. Bowen,a Richard E. P. Winpennya* and Eric J.
L. McInnesa*
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a Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL,
U.K.
b School of Pharmacy and Biomolecular sciences, Liverpool John Moores University, Liverpool L3 3AF, U.K.
ABSTRACT: The synthesis, structures and properties of [4]- and [3]-rotaxane complexes are reported where [2]rotaxanes, formed
from heterometallic {Cr7Ni} rings, are bound to a fluoride-centered {CrNi2} triangle. The compounds have been characterized by
single crystal X-ray diffraction and have the formulae [CrNi2(F)(O2CtBu)6]{(BH)[Cr7NiF8(O2CtBu)16]}3 (3) and
[CrNi2(F)(O2CtBu)6(THF)]{(BH)[Cr7NiF8(O2CtBu)16]}2 (4); where B = py-CH2CH2NHCH2C6H4SCH3. The [4]rotaxane 3 is an isos-
celes triangle of three [2]rotaxanes bound to the central triangle while the [3]rotaxane 4 contains only two [2]rotaxanes bound to the
central triangle. Studies of the behavior of 3 and 4 in solution by small angle X-ray scattering (SAXS) and atomistic molecular
dynamic simulations (AMDS) show that the structure of 3 is similar to that found in the crystal but that 4 has a different conformation
to the crystal. C.w. and pulsed EPR spectroscopy were used to study the structures present and demonstrate that in frozen solutions
(at 5 K) 4 forms more extended molecules than 3 and with a wider range of conformations.
Introduction
complexes.13, 14 Here we extend this approach, binding [2]rotax-
anes
to
a
fluoride-centred
triangle
[CrNi2(μ3-
The flexibility of supramolecular assemblies has long been of
interest. For example, the rigidity of molecular capsules has
been used to allow them to act as reactors to catalyse specific
reactions1 or to stabilise reactive species.2,3 Interlocked struc-
tures such as the various knots reported4-6 also introduce rigidity
and have been proposed as means of making less flexible poly-
mers.7 Studying rigidity is possible using NMR spectroscopy
where the species is diamagnetic; for example, the demetallated
knots made by Zhang et al show broad NMR spectra that be-
come sharper when diamagnetic Zn2+ ions are added which in-
creases the rigidity. Studying the flexibility of interlocked struc-
tures where building blocks are paramagnetic is far harder as
the NMR is paramagnetically broadened before the conforma-
tional flexibility is considered. Small angle X-ray scattering
(SAXS) has been previously used to show supramolecular as-
semblies are present in solution;8, 9 we have used SAXS sup-
ported by atomistic molecular dynamics simulations (AMDS)
to demonstrate that a [13]rotaxane maintained its structure in
solution.10 Here we use SAXS on two related rotaxanes to show
that the larger [4]rotaxane has a more similar structure between
solution and crystalline phases, while a [3]rotaxane has a much
more open structure in solution. The studies require the com-
parison of SAXS and double electron-electron resonance
(DEER) spectroscopy while remembering they operate at 300
and 5 K, respectively.
F)(O2CtBu)6(HO2CtBu)3] 1 (Figure S2) which has a labile ter-
minal ligand (HO2CtBu) at each vertex. By small changes in the
synthesis [3]- and [4]-rotaxanes can be made and which show
very different solution flexibility.
Such assemblies have been proposed as routes to implement
qubit gates. Both the {Cr7Ni} ring and the {CrNi2} triangle have
S = ½ ground states, but with very different g-values of ca. 1.8
and 2.5.15 This gives supramolecular assemblies where we can
potentially address different components by EPR spectroscopy.
This has also been investigated.
Results: Synthesis and Structural Analysis
The
F)(O2CtBu)6(HO2CtBu)3] (1; Figure S2) was prepared as re-
ported Attempts to coordinate
previously.15
parent
{CrNi2}
triangle
[CrNi2(μ3-
(AH)[Cr7NiF8(O2CtBu)16]13 to 1, were unsuccessful probably
due to the thread being too short, leading to repulsive steric in-
teractions between the components. Hence, we made py-
CH2CH2NHCH2C6H4SCH3 (B) which has a greater distance be-
tween the secondary amine site and the pyridyl head group.16 A
[2]rotaxane can then be prepared, of formula
(BH)[Cr7NiF8(O2CtBu)16] (2); the thread is protonated at the
amine site during this reaction (Figure S3).
Reaction of three equivalents of 2 with 1 in THF at 40 °C
We have previously reported hybrid [2]rotaxanes where the
ring is a [Cr7NiF8(O2CtBu)16]− unit and the thread is a secondary
ammonium with suitable sterically-demanding stoppers.11, 12 If
there is a pyridyl (py) head group on the thread, for example py-
produces
the
3:1
{Cr7Ni}:{CrNi2}
adduct
[CrNi2(F)(O2CtBu)6]{(BH)[Cr7NiF8(O2CtBu)16]}3 3 (Figure 1a)
as shown by X-ray diffraction. The structure contains three mol-
ecules of 2 each bound to a metal site of the central triangle 1
via the py head groups of the (BH)+ threads. Compound 3 is
CH2NHCH2CH2Ph
(A),
the
[2]rotaxane
(AH)[Cr7NiF8(O2CtBu)16] can be used to bind to Lewis acid
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Figure 1. The structures of 3 and 4 in the crystal, with select metric parameters indicated (black, XRD; red, AMDS). (a) 3 showing
angles between the mean planes of the {Cr7Ni} rings, and the distances between N atoms of secondary ammonium groups; (b) 4 showing
angles between the mean planes of the {Cr7Ni} rings and the distances between N atoms of secondary ammonium groups. Colors: Cr,
green; Ni, purple; O, red; F, yellow; N, blue; C, silver; S, dull yellow. H-atoms and methyl groups of pivalates excluded for clarity.
therefore a [4]rotaxane. It crystallises with a 2-fold axis of rota-
tion passing through the molecule and therefore the asymmetric
unit comprises half of the complete molecule.
all eight metal positions. Although elemental analysis gives a
slight excess of Ni with a Ni:Cr ratio of 6:22 (5:22 expected for
a 2:{CrNi2} ratio of 3:1), EPR spectroscopy unequivocally
demonstrates that there is no scrambling of the metal ions, i.e.
all the rings are {Cr7Ni} and all the triangles are {CrNi2} (see
below).
In the central {CrNi2} triangle each metal ion is in a pseudo-
octahedral geometry, with the pyridyl bound trans to the central
μ3-fluoride, which is planar (Ni-F-Cr and Ni-F-Cr angles all
around 120°). In the solid state, the pyridyl groups are almost
perpendicular to the {CrNi2} plane; angles between the py and
{CrNi2} planes vary from 75.14(1) – 80.88(1)°. Each {Cr7Ni}
ring sits about the secondary ammonium group (Nam) of (BH)+,
with hydrogen bonds to two of the bridging fluorides on the in-
terior of the ring.
If the reaction is carried out using two equivalents of 2 to 1
and in THF at 20 °C, we isolate the 2:1 {Cr7Ni}:{CrNi2} adduct
where only two sites of 1 have been substituted by 2 and the
third site is occupied by a THF molecule. The product is a [3]ro-
taxane [CrNi2(F)(O2CtBu)6(THF)]{(BH)[Cr7NiF8(O2CtBu)16]}2
(4; Figure 1b). X-ray diffraction shows that the THF substituted
metal site of the {CrNi2} triangle has a shorter M-F bond dis-
tance of 1.89(3) Å cf. 2.06(1) and 2.06(1) Å and hence the CrIII
site is localised. The μ3-F– of the triangle is again planar with
Ni-F-Cr and Ni-F-Cr angles near 120°. The planes of the py
groups are almost perpendicular to the {CrNi2} plane, with di-
hedral angles of 77.48(1) and 84.04(1)°, which are similar to
those of 3.
The CrIII site in the triangle is disordered over the three sites.
Similarly, in the {Cr7Ni} rings the NiII site is disordered over
Table 1. Metric parameters defining the shape of the [n]ro-
taxanes
3
4
X-ray
AMDS
X-ray
AMDS
To define the shape of the two supramolecules we report
some simple metric parameters (Figure 1, Table 1). Firstly, we
consider the distance from the central fluoride in each case to
the protonated secondary ammonium in each thread about
which the {Cr7Ni} rings are grown: this is the Nam…F distance
for each thread. We then consider the Nam…Nam distances; these
define the edges of the triangle of {Cr7Ni} rings in 3. The angles
between the mean planes of the {Cr7Ni} rings on each [2]rotax-
ane are given as the ring…ring angles. In each case the mean
plane of the ring is essentially perpendicular to the thread pass-
ing through it.
10.56(1) 10.31(1)
10.57(1) 10.31(1)
10.57(1) 10.31(1)
17.83(1) 21.21(1)
Nam..F
10.82(1) 10.31(1)
10.84(1) 10.31(1)
distance/ Å
Nam..Nam
18.43(1) 21.21(1) 19.07(1) 23.01(1)
18.83(1) 22.19(1)
distance/ Å
56.61(1) 62.71(1)
Ring..ring
angle/ °
56.61(1) 62.95(1) 65.83(1) 66.32(1)
66.99(1) 63.11(1)
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The X-ray diffraction results show that 3 contains an approx-
between {Cr7Ni} rings. Note that this inter-ring distribution has
greater amplitude for 3 than for 4, consistent with the 3:1 vs. 2:1
{Cr7Ni}:{CrNi2} stoichiometries. The shorter distances within
the peak centered at ca. 7 Å are due to distances within individ-
ual {Cr7Ni} rings, agreeing with the crystallographic values that
range from 3.3(1) Å (neighboring sites) to 8.7(1) Å (antipodal
sites). The combination of AMDS/SAXS confirm that 3 and 4
are distinct compounds in solution and, for example, 3 does not
exist in equilibrium with 4 and a dissociated [2]rotaxane 2.
1
2
3
4
imately isosceles triangle of {Cr7Ni} rings, with one ring…ring
angle noticeably more obtuse than the other two. The Nam…F
distances are constant. For 4 the angle between the two rings is
similar to the most obtuse angle for 3 and the Nam…Nam and
Nam…F distances are both longer than in 3.
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Atomistic Molecular Dynamic Simulations (AMDS) and
Small Angle X-ray Scattering (SAXS)
The AMDS structures calculated by molecular dynamics are
also in good agreement with the single crystal structures (see
Table 1 for selected metric parameters) but with some subtle
and intriguing variations. Compound 3 is noticeably more equi-
lateral in solution, with the ring…ring angles all very similar.
While the three angles in the crystal structure sum to close to
180°, in the AMDS structure they sum to an average of 189°
over the last 5 ns of the simulations, which corresponds to the
rings tilting away from the normal to the {CrNi2} plane in solu-
tion. The Nam…F distances are shorter but Nam…Nam distances
are 17% longer. These observations indicate that the rings are
packed together more closely than they would like in the crystal
and the structure relaxes in solution. Compound 4 has a very
similar ring…ring angle in solution and crystal structure (Table
1) but the Nam…Nam distance is 20% longer in solution than in
the crystal. This again suggests that the structure in the solution
has relaxed compared with the crystal structure.
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To study the stability and structures of 3 and 4 in solution
atomistic molecular dynamic simulations (AMDS) were per-
formed with an all-atom simulation of the two crystal structures
(in a concentrated THF solution) using GROMACS 5.1.4 mo-
lecular dynamics package.17, 18 The crystal structures of 3 and 4
were parameterised using the AMBER95 forcefield, augmented
by parameters consistent with the General Amber forcefield.19
8 nm cubic simulation boxes were set up containing a single
molecule of 3 or 4 in a solution of 2774 THF molecules and run
in an NPT ensemble for the solvent density to reach ~890 kg
m−3.
The calculated AMDS structures were then compared with
experimental solution structure information from SAXS data.
SAXS profiles calculated from the AMDS structures used Har-
tree-Fock scattering factors, with 100 nm boxes and X-ray
wavelength of 0.154209 nm. Experimental and AMDS-model
calculated SAXS intensity profiles (plotted as ln[I(q)] (a.u.),
where q (Å) is the scattering vector) are in Table S2 and Figure
S12. The corresponding pair distribution functions P(r) for 3
and 4 are in Figure 2.
Electron Paramagnetic Resonance Spectroscopy
Continuous Wave (c.w.) Q-band (ca. 34 GHz) EPR spectros-
copy measurements were performed on 3 and 4 at 5 K for pow-
der samples and for frozen 3 mM toluene solutions. The spectra
are dominated by the S = ½ ground states of the {Cr7Ni} and
{CrNi2} components, that arise from internal antiferromagnetic
coupling.
There is remarkable agreement between AMDS and SAXS
for both 3 and 4, demonstrating that both structures are stable
in THF solution (Figure 2). The very slight discrepancies be-
tween the experimental SAXS and corresponding pair distribu-
tion function is less than 1 Å, for both 3 and 4, which can be
accountable by forcefield errors. This discrepancy is also seen
in the radius of gyration (Rg) values shown in Table S2. The
radius of gyration for the simulated structures of both 3 and 4
are slightly higher indicating the calculated structures are more
extended in comparison to the experimental data.
The powder spectra for 3 and 4 (Figure S4; left and right, re-
spectively) both contain two slightly asymmetric features, cen-
tred on 995 and 1382 mT. The frozen solution spectra (Figure
3) have narrower linewidths, which for both 3 and 4 reveal ap-
proximately axial splitting of the lower field feature, while the
higher field feature remains largely unchanged. The spectra
were simulated20 using a spin-Hamiltonian incorporating only
the individual g-matrices for the S = ½ {CrNi2} and {Cr7Ni}
components and an isotropic exchange interaction:
Ĥ = μBŜCrNi2∙gCrNi2∙B + ΣμBŜCr7Ni.gCr7Ni∙B - 2JΣŜCrNi2∙ŜCr7Ni
where the summation is over three (compound 3) or two (com-
pound 4) {Cr7Ni} centres.
For the frozen solutions, the lower field feature due to
{CrNi2} can be fitted with: for 3, gx,y,z = 2.425, 2.425, 2.520; for
4, gx,y,z = 2.420, 2.425, 2.515. These agree well with the spectra
found for 1.15 The high field feature due to {Cr7Ni} can be fitted
with: 3, gx,y,z = 1.785, 1.778, 1.730 ; and 4, gx,y,z, = 1.782, 1.782,
1.740. These agree with the spectra of {Cr7Ni} rings.21 Reason-
able fits can be achieved with these g-values for J = 0.
Figure 2. Observed and calculated SAXS data for 3 and 4,
in THF solution at 20 °C. The experimental data is shown in
blue and red, respectively, for 3 and 4. The calculated traces are
shown in grey and yellow, respectively, for 3 and 4.
A slight improvement in the agreement between the simu-
lated and observed spectra is found with the inclusion of a small
exchange interaction of |J| = 0.003 cm-1. However, this only
serves to broaden the transitions. This broadening can also be
achieved by inclusion of a small (1%) g-strain for each {Cr7Ni}
component. Frozen solution spectra of 3 at lower frequencies
The P(r) distributions are dominated by a short distance (ca.
6 Å) and a longer distance at ca. 18 and 20 Å for 3 and 4, re-
spectively. The longer distance can be attributed to the distances
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(X- and S-band) fit better with the g-strain model than with the
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3
small, but unresolved J model (Figure S5). We conclude that
there are no measurable features due to exchange coupling in
the c.w. EPR spectra.
Double Electron-Electron Resonance Spectroscopy
(DEER)
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5
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7
8
9
DEER is an established method for measuring inter-spin dis-
tances in biological systems.22-24 Previously we have reported
DEER measured on supramolecular compounds containing two
{Cr7Ni} rings and demonstrated that we could measure the
weak {Cr7Ni}…{Cr7Ni} interactions.25 In those studies the two
rings were co-planar, linked along the normal to the planes of
the rings, either by forming a [3]rotaxane, or linked covalently
via a diamagnetic bridge. In 3 and 4 the planes of the rings make
angles of ~60° to one another (see Table 1), which introduces a
further structural complexity to interpreting the results.
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Four-pulse DEER experiments were performed on solutions
of 3 and 4 to probe the {Cr7Ni}…{Cr7Ni}interactions. The
pump pulse was set on the {Cr7Ni} maximum (B0 = 1373 mT)
with the observer pulse set 100 MHz higher in frequency than
the pump pulse. For both compounds, we observe oscillations
in the DEER traces (Figures 4 and 5). For 3, Fourier transfor-
mation of the background corrected data gives a frequency do-
main spectrum with peaks at ±5 MHz, with a slight shoulder at
±3 MHz, and broad wings between ±10-30 MHz. For 4, we ob-
tain similar oscillations but with weaker modulation depth, giv-
ing a frequency domain spectrum with two distinct peaks at
±2.5 and ±5 MHz. There appears to be less intensity in the
wings.
Figure 3. c.w. Q-Band EPR (ca. 34 GHz) spectra for a 3
mM solution sample in dry toluene for 3 (left) and 4 (right) at
5 K. Black: experimental, and green: simulation.
Pulsed EPR spectroscopy (Q-band, 3 K) was used to measure
the phase memory times (Tm) for 3 and 4 using standard Hahn
echo decay measurements: [π/2-τ-π-τ-echo]. Spin lattice relax-
ation (T1) measurements were carried out by inversion recovery
[π-T-π/2-τ-π-τ-echo]. We have also done comparable measure-
ments on the isolated triangle [CrNi2(F)(O2CtBu)6(py)3] 5.15
Measurements were made at magnetic fields (B0) corresponding
to resonances of the {Cr7Ni} ring and the gxy and gz features for
the {CrNi2} triangle (Table 2 and Figure S6). The phase
memory (Tm) times are similar for all components in both struc-
tures at around 700 ns, with the exception of the gz values for
the {CrNi2} fragment in 3 and 4 which is shorter (ca. 570 ns),
and shorter than in the isolated {CrNi2} triangle 5. The T1 times
vary more and the times for the isolated triangle are signifi-
cantly longer than for the {CrNi2} g-values in 3 and 4 (Table 2
and Figures S7, S9).
Two analysis methods were used to extract inter-spin dis-
tance distribution from the time traces. Firstly, a Tikhonov reg-
ularization26 using the orientation independent kernel in Deer-
Analysis,27 with a correction for the g-values corresponding to
the pump and detection frequencies, yields three main compo-
nents for 3 (Figure 4c) and gives four clear groups of distances
for 4 (Figure 5c).
Secondly, a simulation library approach was used (see SI). A
series of geometric models were developed based on the crystal
structures of 3 and 4. For each model the expected orientation
dependent DEER trace for pairwise ring-ring dipolar interac-
tions was calculated using an algorithm described elsewhere.28
The unpaired spin density in each {Cr7Ni} was equally distrib-
uted on each metal ion, reflecting the fact that the Ni position in
the ring is not localized. The calculations used the anisotropic
g-values from c.w. spectra, and the mw pulse and magnetic field
parameters used in the experimental acquisition. This library of
simulated DEER traces was fitted to the experimental data
traces using an iterative procedure over 50 iterations, similar to
that described elsewhere.29 The time and frequency domain fits
and the corresponding distance distributions, presented as both
the inter-ring M…M distances and ring centroid-to-centroid
distances, are presented in Figures 4 and 5.
Table 2. Q-band relaxation times for 3, 4 and 5 measured at
3 K in 0.2 mM solution in toluene.
Com-
pound
g-
value
Assignment
gxy {CrNi2}
gz {CrNi2}
Tm/ns
T1/ µs
3
3
2.41
2.47
713 (0.42)
562 (2.96)
172
(0.38)
108
(1.78)
4
4
2.41
2.47
gxy {CrNi2}
gz {CrNi2}
689 (2.46) 258 (3.34)
165
578 (3.61)
(1.43)
5
5
3
4
2.41
2.47
1.78
1.78
gxy {CrNi2}
gz {CrNi2}
{Cr7Ni}
863 (0.4)
848 (0.5)
713 (0.42)
826 (0.56)
840 (17)
813 (24)
62 (0.38)
Power scaling of the DEER data for 3 was used to test for the
presence of significant multi-spin effects and ghost peaks in the
extracted distance distribution.30 The contribution of the multi-
spin effects to the data set is vanishingly small (see SI): this is
because the inversion efficiency of the DEER experiment is
very low (λ = 0.0135). This validates the application of the pair-
wise analysis approaches described above for 3. The greater
modulation depth for 3 than for 4 is consistent with the presence
of three {Cr7Ni} rings in the former and two in the latter.31
108
{Cr7Ni}
(0.75)
ESEEM modulations are observed in the Hahn echo decay
measurements at B0 values corresponding to the {CrNi2} but not
for the {Cr7Ni} components. Fourier transforms of the time-do-
main data for the {CrNi2} measurements are similar for 3 and
4, with series of low-frequency (< 10 MHz) peaks (Figure S8).
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Figure 4. a) Q-Band experimental DEER trace of 3, after background subtraction, (black crosses, 0.2 mM solution in dry and de-
gassed toluene at 3 K) and fitted data; using DeerAnalysis (solid green line) and using an iterative orientation procedure (solid red
line), with vertical enlargement (insert). A four-pulse DEER sequence was used, with the ELDOR pulse at the {Cr7Ni} maximum
(B0 = 1373 mT) and observation pulse positioned at +100 MHz. Pulse lengths were 20 and 40 ns for π/2 and π, respectively, with ꢀ1
= 200 ns and ꢀ2 = 1000 ns. b) Pake pattern from Fourier transformation of dipolar evolution (solid black line); fitted data using
DeerAnalysis (solid green line) and the iterative orientation procedure (solid red line). c) Distance distribution using Tikhonov reg-
ularizations in DeerAnalysis and corrected g-values (solid green line), and from the model from the iterative orientation procedure
showing inter-ring metal-metal distances (dashed purple line) and ring centroid-centroid distances (dotted red line).
Figure 5. a) Q-Band experimental DEER trace of 4, after background subtraction, (black crosses, 0.2 mM solution in dry and de-
gassed toluene at 3 K) and fitted data; using DeerAnalysis (solid green line) and using an iterative orientation procedure (solid red
line), with vertical enlargement (insert). A four-pulse DEER sequence was used, with the ELDOR pulse at the {Cr7Ni} maximum
(B0 = 1373 mT) and observation pulse positioned at +100 MHz. Pulse lengths were 20 and 40 ns for π/2 and π, respectively, with τ1
= 200 ns and τ2 = 1000 ns. b) Pake pattern from Fourier transformation of dipolar evolution (solid black line); fitted data using
DeerAnalysis (solid green line) and the iterative orientation procedure (solid red line). c) Distance distribution using Tikhonov reg-
ularizations in DeerAnalysis and corrected g-values (solid green line), and from the model from the iterative orientation procedure
showing inter-ring metal-metal distances (dashed purple line) and ring centroid-centroid distances (dotted red line).
It is not possible to probe the {Cr7Ni}…{CrNi2} interactions
spin…spin interaction between the {Cr7Ni} and {CrNi2} com-
ponents in the c.w. EPR data, hence any interaction must be
very weak with respect to the intrinsic linewidths. The c.w. EPR
spectra of 3 and 4 are very similar in powder and frozen solu-
tion. However, given the lack of resolution of any interaction,
this does not prove that the structure is stable in solution (only
that the separate components are stable). This evidence comes
from the SAXS and AMDS data, and also from DEER meas-
urements that reveal {Cr7Ni}…{Cr7Ni} interactions.
by DEER due to the very different g-values leading to spectra
that do not overlap and the limited bandwidth of the resonator
used (ca. 200 MHz when over-coupled).
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Discussion
The c.w. EPR spectra prove unambiguously that there is no
scrambling of metal ions in either the {Cr7Ni} or {CrNi2} com-
ponents in 3 or 4. We only observe the S = ½ ground states of
either component which arises from internal antiferromagnetic
coupling. Any scrambling of the metal ions would lead to the
observation of other spin states. There is no evidence of
The weak coupling regime between {Cr7Ni} or {CrNi2} is
further proven from electron spin relaxation measurements on
the separate components.
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Electron Spin Relaxation: The T1 and Tm values for the measuring {Cr7Ni} ring…ring contacts. From the AMDS cal-
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{Cr7Ni} components of 3 and 4 (ca. 60-100 μs and 700-800 ns,
respectively, at 3 K) are in the range observed for the free ring
and in other supramolecular assemblies containing this frag-
ment (Table 2; some caution needs to be taken when comparing
data measured at Q- and X-band).14 Hence, there seems to be
relatively little variation in the {Cr7Ni} relaxation regardless of
the complexity of the supramolecular structure (we have meas-
ured similar Tm in a complex bearing twelve {Cr7Ni} rings).10
culations we also have a structure in a mobile solution at 300 K
(confirmed by the SAXS measurement, Figure 2). From single
crystal diffraction we have a structure at 200 K in a crystalline
material. It is interesting to compare these three structures of 3
and 4 (Figure 6, Table 3).
The T1 and Tm values for the {CrNi2} components of 3 and 4
are ca. 110 - 260 μs and 600 - 700 ns, respectively. Measure-
ments on the isolated {CrNi2} complex [CrNi2F(O2CtBu)6(py)3]
(5) under the same conditions give T1 ca. 800 µs, and Tm ca. 800
ns; we have chosen this complex to give a direct comparison
with the pyridyl-terminated {CrNi2} units in 3 and 4. Hence, in
contrast to {Cr7Ni}, incorporating {CrNi2} into the supramolec-
ular structures 3 and 4 results in a significant decrease in T1.
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In the free complexes, T1 for {Cr7Ni} (ca. 100 μs) is signifi-
cantly shorter than that of {CrNi2} (ca. 800 μs). Both com-
pounds are antiferromagnetically coupled CrIII…NiII clusters
that give rise to S = ½ ground states. {Cr7Ni} is a much bigger
spin system hence has a higher density of spin states, while the
exchange coupling within {CrNi2} is weaker15 leading to lower
lying excited states. It would appear that the former is the dom-
inant effect in determining the relative magnitude of T1 in these
two species. The difference between the T1 times of the two
components is much reduced in 3 and 4. The effect of a fast
relaxing spin on a slower relaxing spin depends on the relative
magnitude of the coupling and the difference in resonance fre-
quency.32 Even where the coupling is weak it can enhance the
1/T1 relaxation rate of the slow spin. This appears to be the case
in 3 and 4, where T1 of the {CrNi2} components (110-260 µs)
is still longer than that of the {Cr7Ni} rings (60-100 µs), but
reduced from the free {CrNi2}. This is also the reason for the
stability of the {Cr7Ni} T1 values across a wide range of supra-
molecular assemblies: in all these systems the rings are the fast-
est relaxing components.
The Tm values for the slower relaxing {CrNi2} components in
both 3 and 4 (600-700 ns) are similar to isolated {CrNi2} (800
ns). This implies that the 1/T1 relaxation rate of the faster relax-
ing {Cr7Ni} spin (of the order 10−1 MHz) is still slow with re-
spect to the interaction frequency.33 This is consistent with
MHz-scale coupling between the components of 3 and 4 (see
DEER section).
Note that low-frequency ESEEM effects (< 10 MHz) are ob-
served in the primary echo decay experiments of 3 and 4 when
monitoring the {CrNi2} components (20 and 40 ns π/2 and π
pulses, respectively), but not on the {Cr7Ni} components. The
fact that they are only observed on the {CrNi2} resonances im-
plies that they are due to the 14N of the {CrNi2}-bound pyridyl
groups (Larmor frequency 3.03 MHz at B0 = 983 mT).
Figure 6. The distribution of inter-{Cr7Ni} metal...metal con-
tacts by three methods, in (a) 3 and (b) 4. AMDS calculation
(brown); XRD (dark blue); metal-to-metal (purple) and cen-
troid-to-centroid (red) distances found by iterative fit of DEER
data; fit from DeerAnalysis (Tikhonov regularizations; green).
The AMDS distances were calculated using the centre of mass
of the atoms involved and calculated for every timestep over
10 ns; the average was then taken throughout the simulation to
determine the distances. The XRD distances between metal
ions for each {Cr7Ni}…{Cr7Ni} are plotted in 0.5 Å incre-
ments using a spline function. The DEER data are taken di-
rectly from the distance distributions in Figures 4 and 5.
Structures in three phases and at three temperatures
DEER spectroscopy gives us spin…spin distances at 3 K in a
dilute frozen solution. Triangular, organic three-spin systems
have been studied previously by DEER (with one arm missing
in the biradical system), and the effect of three-spin correlations
on the distance distribution data examined by comparison to
equivalent two-spin molecules, where one arm of the triangle is
missing.31, 34 In 3 and 4, we have analogues of such systems but
based on delocalised multi-centre spin systems. Here we are
We make the assumption that the electron spin on the
{Cr7Ni} rings in 3 and 4 sits on the metal sites. The DEER anal-
ysis is therefore giving us the distribution of inter-ring M…M
distances in frozen solution at 3 K. We are not seeing any
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metal…metal contacts involving the central {CrNi2} triangle M…M distribution gives peaks between 12 and 26 Å, with the
(see above). We first used DeerAnalysis software27 using
Tikhonov regularisations,26 to calculate a distance distribution
based on dipolar coupling. DeerAnalysis assumes an average
nitroxide g-value, and a correction factor is required based upon
the g-values of the experimental pump and observation pulses
(1.76 and 1.77, respectively): this results in shifts to slightly
shorter distances. The more significant difference here is that
the spin on each {Cr7Ni} ring is distributed across eight sites.35
Therefore in 3 we have contacts between three sets of eight sites
and in 4 we have contacts between two sets of eight sites. Such
effects can lead to deviations in distance distributions based on
point-dipole models and the cluster centroids, as has been
shown with biological FeS clusters.36
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4
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bulk of contacts between 18-24 Å (Figure 6a).
To compare this with the inter-ring M…M distances in 3 as
observed by single crystal X-ray diffraction we have arranged
the M…M distances from diffraction in distributions of 0.5 Å
and then broadened the distribution (dark blue line in Figure
6a). There are two maxima at 15.0 and 16.9 Å, reflecting the
rings being arranged in an isosceles triangle in the crystal. There
is then a gap in the distribution before we reach a maximum at
19.3 Å, consistent with the broad maximum in the DEER fit
M…M data and the maximum in the DeerAnalysis distribution.
There is then a small fall before a peak at 21.1 Å.
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If we then compare with the AMDS structure (brown line in
Figure 6a) we see a very similar shape to the DeerAnalysis dis-
tribution, but shifted to longer distances with two maxima at
16.0 and 20.7 Å. The simpler distribution from AMDS cf. XRD
suggests that the structure in fluid solution is relaxing to an
equilateral triangle of rings compared to the crystal structure.
The DEER fit M…M distribution is more complex, with shorter
and longer distances, reflecting the fact that a number of con-
formations are trapped on freezing the solution, and there are
also possible differences in librational effects due to the extreme
difference in temperatures of measurement (3 and 300 K). Some
of this detail is lost in the simpler DeerAnalysis treatment. How-
ever, the dominant DEER fit M…M distances around 21 Å
agree with that from AMDS.
Table 3. Maxima (Å) in distribution of intra-ring
M…M distances. (a) M…M DEER fit, (b) DeerAnalysis
3
4
AMDS 16.0 20.7
XRD
15.0 16.9 19.3 21.1
DEERa 12.1 14.5 17.9 20.9 22.9 26.0
DEERb 13.1 19.4 24.4
AMDS 18.0 22.7 26.9
XRD
12.9 15.2 18.2 20.0 21.8
DEERa 12.0 13.9 16.0 18.0 21.7 24.2 25.8
DEERb 12.7 15.0 18.1 20.7 24.7
The conclusion is that in fluid solution at room temperature 3
has a structure where the rings in the three [2]rotaxanes form an
equilateral triangle. Additional structure is seen in the XRD as
packing leads to a change in the overall structure towards an
isosceles triangle, but with similar size. While a range of con-
formations are found in the frozen solution at 3 K, the dominant
distances are similar to the fluid solution.
Hence, we also fit the DEER data with a structural model,
allowing for distribution of the spin over the eight sites of the
{Cr7Ni} rings and accounting for orientation selection due to
the g-anisotropy. In Figures 4(c) and 5(c), we compare the dis-
tance distributions extracted from the conformer library, pre-
sented both as M…M distances and as ring centroid…centroid
distances, with those obtained from model-free DeerAnalysis.
It is striking that, for both 3 and 4, the DEER fit centroid…cen-
troid distribution strongly resembles the DeerAnalysis results in
terms of the dominant distances, with the exception that the
DeerAnalysis distributions (a) are shifted to longer distances by
1-2 Å, and (b) pick up short distances (< 15 Å) that are not
found in the centroid…centroid distribution.
For compound 4 the result is very different (Figure 6b). The
XRD distance distribution has a similar longest distance at 22
Å, cf. 21 Å for 3. However, there are significantly shorter con-
tacts at 13 Å, cf. 15 Å in 3. In 4 the AMDS and XRD structures
are radically different from one another. In AMDS the shortest
contact has a maximum at 18.0 Å, with the shortest contacts
found in XRD and DEER (see below) entirely missing. The ma-
jority of M…M contacts by AMDS are around 22.7 Å, around
the longest contact from XRD and the dominant contact by
DEER fit. Finally, the AMDS has a much longer and significant
contact at above 26 Å which is absent in the XRD. Hence, the
AMDS structure is much more extended than the structure as
observed by crystallography.
The agreement, despite the neglect of DEER orientation se-
lectivity in {Cr7Ni} due to g-aniostropy,25 is because the rings
are essentially axially symmetric and we are pumping at gx,y. In
this case we will always detect the perpendicular component of
the dipolar coupling pattern, such that a single DEER measure-
ment can yield reasonable distance distributions obtained from
Tikhonov regularizations.28, 37 We have tested and validated this
assumption by simulation (see SI).
The DeerAnalysis distance distribution for 4 gives short dis-
tances at 12.7 and 15.0 Å, the majority of contacts from 17.5-
21.9 Å, and a long-distance peak at 24.7 Å. The DEER fit
M…M distribution gives peaks between shortest and longest
distances of 12 and 28 Å, with the dominant peak at around 22
Å. Comparing these to equivalent data for 3, both analyses show
that in 4 there is a broader distance distribution, extending to
longer distances, in the frozen solution. The DEER fit M…M
distribution for 4 appears to combine features of those from the
XRD and AMDS, with the short distances from the former and
the long distances from the latter. However, although the M…M
DEER fit result contains distances that extend beyond those
found in the AMDS distributions, the dominant distance is sig-
nificantly shorter.
For both 3 and 4, the DEER fit M…M distance distributions
are broader than either the centroid…centroid or DeerAnalysis
results, notably picking up the shorter distances (< 15 Å) and
extending to longer distances (> 25 Å). The closer agreement
between the DeerAnalysis and DEER fit centroid…centroid
distributions is likely a result of the fact that DeerAnalysis uses
the point dipole approach, and given that the spin is evenly dis-
tributed around the {Cr7Ni} ring (once positional disorder of the
Ni(II) ion is considered) this seems to average out to give dis-
tances similar to a spin localised at the centre of the ring.
For 3 the distance distribution from DeerAnalysis has three
maxima (Figure 6a), at 13.1 Å (towards the lower end of dis-
tances that can be measured by DEER),38, 39 a dominant peak at
19.4 Å, and a smaller peak at around 24.4 Å. The DEER fit
All these results say that the [3]-rotaxane (4) relaxes much
more in solution than the [4]-rotaxane (3). The presence of only
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Page 8 of 10
EPR Facility at Manchester (NS/A000055/1). This work was sup-
two large [2]rotaxanes attached to the central triangle in 4 leads
to steric repulsion between these groups. The result is a bigger
structure in mobile solution (also shown by the radius of gyra-
tion data, see SI) and also a broader range of conformations on
freezing the solutions as shown by DEER. Hence, the fluid and
frozen solution structures differ more significantly from each
other for 4 than for 3.
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8
ported by the EPSRC(UK) (grant number EP/L018470/1) and a
Established Career Fellowship (EP/R011079/1) to REPW, We
also thank EPSRC (UK) for funding an X-ray diffractometer
(EP/K039547/1). We also thank the European Research Council
for an Advanced Grant (ERC-2017-ADG-786734). We thank Dia-
mond Light Source for access to synchrotron X-ray facilities.
AMB thanks the Royal Society and EPSRC for a Dorothy Ho-
dgkin Fellowship (DH160004). We dedicate this paper to Profes-
sor Alan J. Welch on the occasion of his retirement.
Conclusion
9
We have prepared two large supramolecular assemblies 3 and
4, containing twenty-seven and twenty-one paramagnetic cen-
tres respectively. Single crystal diffraction studies allow us to
show these are [4]- and [3]rotaxanes with three or two {Cr7Ni}
rings attached to a central {CrNi2} triangle.
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AUTHOR INFORMATION
Corresponding Author
* Prof Eric J. L. McInnes, School of Chemistry and Photon Sci-
ence Institute, The University of Manchester. Email: eric.mcin-
nes@manchester.ac.uk
* Prof Richard E. P. Winpenny, School of Chemistry and Photon
Science Institute, The University of Manchester. Email: rich-
ard.winpenny@manchester.ac.uk
Author Contributions
The manuscript was written through contributions of all authors.
All authors have given approval to the final version of the manu-
script.
Funding Sources
This work was supported by the EPSRC through the award of a
doctoral training grant to SJL and funding of the EPSRC National
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