An allosterically regulated molecular shuttle

Article abstract of DOI:10.1002/anie.200502624

(Figure Presented) When push comes to shove: A switchable [2]rotaxane has been developed in which the binding of a metal ion (e.g. Cd²⁺, see scheme) to a bis(picolyl)amine fragment that acts as one of the stoppers induces a shift of the macrocyclic component along the thread from one binding site (green) to another weaker binding site (orange).

Full text of DOI:10.1002/anie.200502624

Angewandte
Chemie
Rotaxanes
DOI: 10.1002/anie.200502624
An Allosterically Regulated Molecular Shuttle**
Dana S. Marlin, Diego Gonzµlez Cabrera,
David A. Leigh,* and Alexandra M. Z. Slawin
One of Natureꢀs most effective ways of influencing function
from afar is through allosteric control.[1] This occurs—most
typically in proteins—when activity at a substrate-binding site
is modulated by the complexation of an effector molecule or
[*] Dr. D. S. Marlin, D. Gonzµlez Cabrera, Prof. D. A. Leigh
School ofChemistry
University ofEdinburgh
The King’s Buildings
West Mains Road
Edinburgh EH9 3JJ (UK)
Fax: (+44)131-667-9085
E-mail: David.Leigh@ed.ac.uk
Prof. A. M. Z. Slawin
School ofChemistry
University ofSt. Andrews
Purdie Building
St. Andrews
Fife KY16 9ST (UK)
[**] This work was supported by the European Union Future and
Emerging Technology Program Hy3M and the EPSRC. D.S.M. is a
Marie Curie Fellow; D.A.L. is an EPSRC Senior Research Fellow and
holds a Royal Society–Wolfson Research Merit Award.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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Communications
ion at a second site. The binding sites are frequently several
nanometers apart, and communication between them is
achieved through a variety of mechanisms, the details of
which are not well understood but often involve multiple
substrate-binding sites and cooperative complexation events
that are accompanied by large amplitude movements of
polypeptide chains and other molecular subunits.[2] However,
to achieve any kind of distant control in response to binding in
synthetic systems is far from trivial. Most of the artificial
allosteric receptors developed to date feature one or more
substrate-interaction sites directly conformationally coupled
to an effector-binding site.[3] Herein, we report on a mechan-
ically linked substrate/host ensemble (a [2]rotaxane), which
contains two spatially and chemically distinct “substrate”
hydrogen-bonding sites, only one of which is influenced by the
coordination of a metal ion (the “effector”) to an adjacent
tridentate ligand fragment. The result is a stimuli-responsive
molecular shuttle[4] that undergoes a large amplitude internal
motion (change in the position and binding strength of the
macrocycle), allosterically regulated through a small, but
highly significant, conformational change brought about by
complexation of a transition metal at the effector site.
The molecular shuttle allosteric control mechanism has its
origins in anomalous behavior observed for some simple
hydrogen-bonded rotaxanes that bear metal-chelating stop-
Scheme 1. Rotaxanes 1–4 and their attempted complexation reactions
with one (a,c) or two (b,d) equivalents ofCuCl 2 in DMF at room
temperature. Complexes 1CuCl2 and 2(CuCl2)2 are formed in near-
quantitative yield and were purified by recrystallization from CH3CN/
DMF;[8] 3CuCl2 and 4(CuCl2)2 could not be detected even upon heating
at 808C for 12 h.[7] The free threads of 1–4 each react readily with
CuCl2 in DMF at room temperature to form coordination complexes
that are analogous to 1CuCl2 and 2(CuCl2)2.
pers containing
a
bis(2-picolyl)amine (BPA)[5] moiety
(Scheme 1). Rotaxanes 1 and 2, in which the BPA unit is
connected to the hydrogen-bonding groups of the thread by
an ethylene spacer, react readily with various transition-metal
salts including CuCl2, which yields complexes 1CuCl2 and
2(CuCl2)2, respectively (Scheme 1a and b). The X-ray crystal
structures of 1CuCl2 and 2(CuCl2)2 (Figure 1a and b) show
the typical four intercomponent hydrogen bonds between the
benzylamide groups of the macrocycle and the amide groups
of the thread,[6] together with the predicted coordination of
the BPA ligands to each metal ion in a tridentate fashion.
However, to our surprise, rotaxanes 3 and 4, in which the
ethylene spacer is absent and the BPAunit is attached directly
to the hydrogen-bonding station of the thread, were found not
to react[7] with CuCl2 or similar transition-metal salts even
under forcing conditions (Scheme 1c and d). This behavior is
in marked contrast to that of their parent threads, which react
like rotaxanes 1 and 2 to give the expected coordination
complexes, indicating that the reduced electron density on the
nitrogen atom caused by the adjacent carbonyl group is not
the reason for the lack of reaction of 3 and 4.[5]
The X-ray crystal structures of 3 and 4 (Figure 1c–f)
reveal the reason for their lack of reactivity. Although the
macrocycles in 3 and 4 form hydrogen bonds to the thread
through the four intercomponent hydrogen bonds (shown in
the stick representation, Figure 1c and d) analogous to
rotaxanes 1 and 2, the pyridine arms of the BPA groups are
forced close-to-parallel with the isophthalamide groups of the
macrocycle (concomitantly forming favorable p–p-stacking
interactions) to accommodate the ring on the hydrogen-
bonding site. To chelate to a metal ion by using all three
nitrogen atoms of the BPA group, the pyridine arms must
twist orthogonally, causing them to enter space that is already
occupied by the benzylamide macrocycle. However, the
macrocycle physically has nowhere else to move to in either
3 or 4 (see the space-filling representations, Figure 1e and f)
and so the conformational change required for the BPA group
to chelate to a transition metal cannot take place in these
short congested rotaxane structures.
The prospect of a situation where, despite binding at
different sites, metal- and macrocycle-binding modes compete
for the same 3D space led us to consider whether transloca-
tion of the macrocycle to a second hydrogen-bonding site on a
thread could be induced by a metal-binding interaction. As a
model we designed rotaxane 5 (Scheme 2), which contains
three carbonyl hydrogen-bond acceptors on the thread in
what can be viewed as an elongated hydrogen-bonding station
1
(for clarity in interpreting the H NMR spectra (Figure 2),
one half of this unit is colored in green and the other in
orange). With this extended station the macrocycle in 5 has
space to occupy (and hydrogen-bonding partners) when a
metal binds to, and rearranges the conformation of, the BPA-
containing stopper. The solid-state structure of 5 (Scheme 2b)
reveals that the macrocycle is bound to the central carbonyl
group (O41) of the thread through hydrogen bonds between
the carboxamide hydrogen donors (N20H and N29H) and the
amide carbonyl group adjacent to the diphenylacetyl stopper
(O44). However, the carbonyl group (O38) adjacent to the
BPA station is also in the plane of the other two carbonyl
groups (O41 and O44) on the thread, and in solution one
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Scheme 2. Synthesis of[2]rotaxane 5 with an extended hydrogen-
bonding site and its subsequent complexation to generate 5MX2
(MX2 =CuCl2 or Cd(NO3)2): a) the solution positional equilibrium of
the macrocycle in 5 (atom-lettering scheme corresponds to 1H NMR
assignments in Figure 2). The complexes 5MX2 were prepared by
addition ofa solution ofthe appropriate metal salt in acetonitrile to a
solution of 5 in acetonitrile at room temperature and purified by
crystallization. b,c) X-ray crystal structures[8] of 5 and 5CuCl2, respec-
tively. C (thread) yellow, C (macrocycle) turquoise, O red, N dark blue,
Cu gray, Cl green, H white; all hydrogen atoms except for the amide
protons have been omitted for clarity. Selected bond lengths [Š]: 5:
N20H–O41 2.026, N29H–O41 2.192, N11H–O44 1.888; 5CuCl2: N37–
Cu1 2.432, N60–Cu1 1.976, N67–Cu1 1.987, Cl1–Cu1 2.256, Cl2–Cu1
2.227, N2H–O41 2.190, N11H–O41 2.153, N29H–O44 1.885. The red
circles highlight the enforced change in conformation of the BPA
ligand and adjacent peptide unit upon coordination to a metal ion.
Figure 1. X-ray crystal structures[8] ofa) 1CuCl2, b) 2(CuCl2)2, c) 3, and
d) 4 in stick representation, and e) 3 and f) 4 in space-filling van der
Waals radius form. C (thread) yellow, C (macrocycle) turquoise, O red,
N dark blue, Cu gray, Cl green, H white. In the stick representations, all
hydrogen atoms except for the amide and olefin protons have been
omitted for clarity. Selected bond lengths [Š]: 1CuCl2: N12–Cu2 2.075,
N42–Cu2 1.987, N112–Cu2 1.987, Cl3–Cu2 2.235, Cl4–Cu2 2.563,
N264H–O222 2.236, N354H–O222 2.353, N174H–O192 2.260, N84H–
O192 2.290; 2(CuCl2)2: N11–Cu1 2.076, N41–Cu1 2.001, N111–Cu1
2.027, Cu1–Cl1 2.497, Cu1–Cl1 2.232, N172H–O191 2.140, N82H–
O191 2.260; 3: N20H–O42 2.239, N29H–O42 2.136, N2H–O45 2.687,
N11H–O45 1.957; 4: N172H–O161 1.985, N82H–O161 2.212.
would expect an equilibrium to exist between the hydrogen
bonding of N11H and O44 and a similar interaction between
O38 and N2H (Scheme 2a). Indeed, the 1H NMR spectrum of
rotaxane 5 in CD3CN (Figure 2b) reveals that this is the case,
with the chemical shifts of both internal methylene groups Hf
and Hh (green and orange, respectively) shifted upfield
(DdHf = 0.7 ppm; DdHh = 1.0 ppm) relative to those of the
free thread (Figure 2a), as a result of shielding from the
macrocycle.
Addition of CuCl2 to 5 results in formation of complex
5CuCl2, the X-ray crystal structure of which is shown in
Scheme 2c. The most striking characteristics of this solid-state
structure are the chelation of all three BPA nitrogen atoms
(including the carboxamide nitrogen, N71) to the CuII ion,
together with the out-of-plane tilting of carbonyl oxygen O38
relative to the plane in which the other two carbonyl oxygen
atoms (O41 and O43) of the thread lie. As cadmium is a
diamagnetic metal with similar binding properties to CuII,
treatment of 5 with Cd(NO3)2 allowed us to study the solution
behavior of metal chelation to 5 using 1H NMR spectroscopy
(compare Figure 2c with Figure 2b and d). As expected, the
binding of a metal ion to the BPA stopper alters the
equilibrium of hydrogen bonding between the three carbonyl
hydrogen-bond acceptors in 5, causing a shift of the signal for
Hh (orange) further upfield and a slight downfield shift of the
resonance for Hf (green) in 5Cd(NO3)2 relative to those in the
1
free rotaxane. Comparison of the H NMR spectra of 5Cd-
(NO3)2 with the Cd(NO3)2–thread complexrevealed a similar
trend, that is, a large upfield shift of the signal for Hh and a
much smaller shift for that of Hf. The changes indicate that the
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Scheme 3. An allosterically regulated molecular shuttle. Rotaxane 6
consists of a BPA metal-chelating site (the “effector” binding site), two
hydrogen-bonding stations of different intrinsic affinities (substrate-
binding sites), and a benzylamide macrocycle substrate. Metal com-
plexation of 6 occurs quantitatively at room temperature with Cd-
(NO3)2 in CD3CN. The reverse transformation is accomplished by
treatment with excess NaCN (5 equiv).
Figure 2. Partial 1H NMR spectra (400 MHz, CD3CN, 298 K) ofa) the
thread ofrotaxane 5, b) 5, c) 5Cd(NO3)2, and d) the complex ofthe
thread ofrotaxane 5 with Cd(NO3)2. Resonances are colored and
labeled as shown in Scheme 2.
macrocycle no longer shuttles back and forth along the thread
in 5Cd(NO3)2 but is restricted mainly to a position over the Hh
methylene group between carbonyl oxygen atoms O41 and
O43.
Encouraged by the results from this model system we
prepared a two-station [2]rotaxane, 6, with hydrogen-bonding
sites of substantially differing affinities[9] for the macrocycle
separated by a C12 alkyl chain. The station of known[9] higher
binding affinity (succinamide, shown in green) is directly
attached to the metal-binding BPA unit, while the station of
inherent lower affinity[9] (succinic amide ester, shown in
orange) is attached to a nonchelating diphenylacetyl stopper
(Scheme 3). In 6, the macrocycle occupies the position over
the green station more than 95% of the time at 273 K in
CD3CN, as revealed by the large (Dd = 1.5 ppm) upfield shift
of the signals for protons Hf and Hg (compare Figure 3b and
a). In comparison, the signals for protons Hn and Ho (orange
station) appear at similar chemical shifts in rotaxane 6
(Figure 3a) and the parent thread (Figure 3a).
The addition of one equivalent of Cd(NO3)2 to 6 in
CD3CN results in a dramatic change in the 1H NMR spectrum
(Figure 3c). The major differences in the spectra of 6 and
6Cd(NO3)2 are the large (Dd = 1.1 ppm) downfield shift of the
signals for protons Hf and Hg (green station) and the upfield
shift (Dd = 0.7 ppm) of the peaks for Hn and Ho (orange
station) in the metal-coordinated rotaxane. In addition,
protons Hl, Hp, and Hq at the periphery of the orange station
are also shielded by the macrocycle (Dd ꢀ 0.3 ppm). Collec-
tively these data indicate that the macrocycle has moved from
residing predominantly over the green station to being
positioned mainly over the orange station. The difference in
the chemical shifts of 6Cd(NO3)2 relative to those of the
parent thread bound to Cd(NO3)2 (Figure 3d) confirms the
change in position of the macrocycle. The coordination
Figure 3. Partial 1H NMR spectra (400 MHz, CD3CN, 273 K) ofa) the
parent thread of 6, b) 6, c) 6Cd(NO3)2, and d) the complex ofthe
parent thread of 6 with Cd(NO3)2. Resonances are colored and labeled
as shown in Scheme 3. Peaks shown in light gray arise from residual
non-deuterated solvent and water.
reaction, and change in position of the macrocycle, is reversed
by treatment with NaCN (Scheme 3).
The stimuli-induced shuttling between 6 and 6Cd(NO3)2
(Scheme 3) corresponds to a negative heterotropic allosteric
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Angewandte
Chemie
binding event[10]—inhibition of hydrogen bonding of the
macrocycle at the succinamide unit through the conforma-
tional change induced by metal chelation at the BPA site—
that leads to translocation of the macrocycle to the inherently
weaker hydrogen-bonding succinic amide ester site, which lies
1.5 nm away. Similarly large movements in rotaxanes have
been used to bring about changes in conductivity,[4d,11] circular
dichroism,[12] fluorescence,[13] porosity,[14] and surface
energy,[15] and to carry out mechanical work,[15,16] largely as
a result of chemical (redox, acid-base, and photochemical)
reactions on the covalent structure of the rotaxane. An
allosteric shuttling mechanism offers the possibility of using
metal-binding events as the energy source or operating
stimulus for functional synthetic molecular machines.
Inorg. Chem. 2005, 44, 4796 – 4805; f) D. S. Marlin, D. Gonzµlez
Cabrera, D. A. Leigh, A. M. Z. Slawin, Angew. Chem. 2006, 118,
83 – 89; Angew. Chem. Int. Ed. 2006, 45, 77 – 83.
[6] F. G. Gatti, D. A. Leigh, S. A. Nepogodiev, A. M. Z. Slawin, S. J.
Teat, J. K. Y. Wong, J. Am. Chem. Soc. 2001, 123, 5983 – 5989.
[7] There was no indication of reaction by color change, mass
spectrometry, or thin-layer chromatography.
[8] Crystals of 1CuCl2 and 2(CuCl2)2 of suitable quality for X-ray
diffraction studies were obtained by carefully layering a solution
of the appropriate complexin N,N-dimethylformamide (DMF)
with CH3CN (approximately 1:10 v/v). Single crystals of 3, 4, 5,
and 5CuCl2 were grown from slow evaporation of saturated
solutions in CH3CN, CHCl3, CH2Cl2, and CH2Cl2/DMF (5:1 v/v),
respectively. Data for 1CuCl2, 2(CuCl2)2, 3, 4, and 5CuCl2 were
collected on a Bruker SMART CCD diffractometer, whereas
data for 5 were collected on a Rigaku Saturn (MM007 high flux
RA/MoKa radiation, confocal optic). Data were collected at
150 K for 1CuCl2, 2(CuCl2)2, and and 4, at 125 K for 3 and
5CuCl2, and at 93 K for 5. All data collections employed narrow
frames (0.3–1.08) to obtain at least a full hemisphere of data.
Intensities were corrected for Lorentz polarization and absorp-
tion effects (multiple equivalent reflections). Structures were
solved by direct methods, non-hydrogen atoms were refined
anisotropically with CH protons being refined in riding geo-
metries (SHELXTL) against F2. In most cases, amide protons
were refined isotropically subject to a distant constraint. Data
for 1CuCl2·3.75DMF: C73.75H83.75N12.25O9.25Cl2Cu, Mr = 1424.22,
crystal size 2.07 ” 0.37 ” 0.35 mm3, monoclinic, P21/c, a =
Received: July 26, 2005
Revised: October 1, 2005
Published online: January 30, 2006
Keywords: allosterism · hydrogen bonds · molecular devices ·
.
rotaxanes · transition metals
[1] For recent reviews on allostery in biological systems, see: a) J.-P.
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15.5009(8), b = 43.623(2), c = 23.9057(11) Š, Z = 8, 1calcd
=
1.231 MgmÀ3 m = 0.415 mmÀ1
;
,
92715 reflections collected,
27020 unique (Rint = 0.0521) giving R = 0.0702 for 18444
[2] a) A. Mattevi, M. Rizzi, M. Bolognesi, Curr. Opin. Struct. Biol.
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observed data [Fo > 4s(Fo)], S = 0.994 for 1481 parameters;
À3
residual electron density extremes were 0.549 and À0.566 eŠ
.
Data for 2(CuCl2)2: C70H78Cl4Cu2N14O8, Mr = 1512.34, crystal
size 0.19 ” 0.18 ” 0.08 mm3, monoclinic, P21/c, a = 12.7343(5),
b = 19.0061(8), c = 15.7470(7) Š, Z = 2, 1calcd = 1.438 MgmÀ3
;
m = 0.828 mmÀ1
, 20841 reflections collected, 7515 unique
(Rint = 0.0450) giving R = 0.0791 for 5367 observed data [Fo >
4s(Fo)], S = 1.112 for 444 parameters; residual electron density
extremes were 0.663 and À0.851 eŠÀ3. Data for 3: C62H56N8O6,
Mr = 1009.15, crystal size 0.21 ” 0.1 ” 0.1 mm3, monoclinic, C2/c,
a = 31.107(10), b = 18.677(6), c = 21.001(7) Š, Z = 8, 1calcd
=
1.318 MgmÀ3 m = 0.086 mmÀ1
;
,
31645 reflections collected,
9198 unique (Rint = 0.5301) giving R = 0.1611 for 2791 observed
data [Fo > 4s(Fo)], S = 0.994 for 707 parameters; residual
electron density extremes were 0.383 and À0.380 eŠÀ3. Data
[4] a) Molecular Catenanes, Rotaxanes, and Knots:
A Journey
Through the World of Molecular Topology (Eds.: J.-P. Sauvage,
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for 4·(CHCl3)3: C64H58Cl12N10O6, Mr = 1488.66, crystal size 0.59 ”
3
¯
0.46 ” 0.41 mm , triclinic, P1, a = 11.8069(7), b = 12.2006(7) Š,
Z = 4, 1calcd = 1.485 MgmÀ3; m = 0.559 mmÀ1, 16004 reflections
collected, 7684 unique (Rint = 0.04) giving R = 0.0526 for 6362
observed data [Fo > 4s(Fo)], S = 0.9917 for 415 parameters;
À3
residual electron density extremes were 0.44 and À0.36 eŠ
.
Data for 5: C62H59N9O8, Mr = 1058.18, crystal size 0.1 ” 0.03 ”
0.03 mm3, triclinic, P1, a = 10.9491(5), b = 14.8382(2), c =
¯
18.5719(8) Š, Z = 2, 1calcd = 1.311 MgmÀ3
;
m = 0.716 mmÀ1
,
32650 reflections collected, 7414 unique (Rint = 0.0782) giving
R = 0.0806 for 5270 observed data [Fo > 4s(Fo)], S = 1.051 for
[5] For examples of CuII and CdII bound to BPA tertiary amide
ligands, including several with a central carboxamide nitrogen
and discussions of the thermodynamics and kinetics of these
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746 parameters; residual electron density extremes were 0.288
À3
and
C
À0.313 eŠ
.
Data
for
5CuCl2·3DMF·2H2O:
68.75H75.75Cl2CuN11.25O10.75, Mr = 1366.1, crystal size 0.16 ” 0.1 ”
0.1 mm3, monoclinic, P2(1)/n, a = 25.279(6), b = 10.970(3), c =
25.649(6) Š, Z = 4, 1calcd = 1.288 MgmÀ3; m = 0.451 mmÀ1, 44451
reflections collected, 12876 unique (Rint = 0.4536) giving R =
0.1614 for 4795 observed data [Fo > 4s(Fo)], S = 1.038 for 856
parameters; residual electron density extremes were 1.180 and
À0.718 eŠÀ3. The protons on solvate molecules were not allowed
for in the refinement. CCDC 281563–281568 (1CuCl2, 2(CuCl2)2,
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3, 4, 5, and 5CuCl2, respectively) contain the supplementary
crystallographic data for this paper. These data can be obtained
free of charge from The Cambridge Crystallographic Data
Centre via www.ccdc.cam.ac.uk/data_request/cif.
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