Templated dynamic synthesis of a [3]catenane

Article abstract of DOI:10.1002/anie.201106885

Three rings: The self-assembly of a water-soluble [3]catenane from a library composed of two linear building blocks, both terminated by cysteine components, is promoted either by a high salt concentration or by the presence of spermine. The spermine-templ

Full text of DOI:10.1002/anie.201106885

Angewandte
Chemie
DOI: 10.1002/anie.201106885
Catenanes
Templated Dynamic Synthesis of a [3]Catenane**
Fabien B. L. Cougnon, Nicholas A. Jenkins, G. Dan Pantos¸,* and Jeremy K. M. Sanders*
We present herein the unprece-
dented and efficient formation
of a donor–acceptor [3]cate-
nane from an aqueous dynamic
combinatorial system contain-
ing only linear building blocks
and NaNO3 (1m). Even more
remarkably, the synthesis is
improved if the salt, which
raises the ionic strength and
presumably encourages hydro-
phobic association, is replaced
by a sub-millimolar concentra-
tion of spermine acting as a
template (Scheme 1).
Although of potential inter-
est in the context of nano-
science,[1]
donor–acceptor
[3]catenanes have remained rel-
atively unexplored because of
their challenging synthesis.
Stoddart
and
co-workers
showed that donor–acceptor
interactions could be efficiently
used to reversibly assemble pre-
formed macrocycles into the
thermodynamically
stable
more
This
[3]catenane.[2]
approach is not trivial: careful
design of the size and geometry
of the rings is necessary and,
while the assembly of the cate-
nane is nearly quantitative, the
synthesis of each of the rings
involves a series of delicate
Scheme 1. Synthesis of a [3]catenane in water, templated by the presence of spermine.
steps, ultimately leading to an overall low yield. Apart from
a few variations and improvements to the method developed
by the Stoddart group, these constraints have made examples
of donor–acceptor [3]catenanes rare in the literature.[2–4]
We previously showed that dynamic combinatorial
chemistry[5] led to an unexpected variety of [2]catenanes.[6,7]
To investigate the possibility of forming higher-order inter-
locked structures by applying methods of dynamic combina-
torial chemistry, we designed building block A (acceptor),[8]
composed of two large hydrophobic electron-deficient p sys-
tems (1,4,5,8-naphthalenediimide) connected through a flex-
ible aliphatic chain (Scheme 1). Building block A is termi-
nated by two cysteine components, which provide both the
thiol necessary for disulfide exchange and carboxylate anions
for water solubility. The objective was to explore the behavior
of A in the presence of the electron-rich 2,6-dialkoxynaph-
thalene building block D (donor), which has already been
studied in detail in aqueous libraries.[6]
[*] F. B. L. Cougnon, N. A. Jenkins, Dr. G. D. Panto¸s,[+]
Prof. J. K. M. Sanders
University Chemical Laboratory, University of Cambridge
Lensfield Road, CB2 1EW, Cambridge (UK)
E-mail: jkms@cam.ac.uk
[+] Present address: Department of Chemistry, University of Bath
Bath, BA2 7AY (UK)
E-mail: g.d.pantos@bath.ac.uk
[**] We are grateful to EPSRC (F.B.L.C., J.K.M.S.); Pembroke College,
Cambridge and the University of Bath (G.D.P.) for financial support.
We thank Dr. Artur R. Stefankiewicz for helpful discussions,
Nandhini Ponnuswamy for help with NMR spectroscopy, and Dr.
Ana Belenguer for maintaining the LC–MS facility.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201106885.
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The first library was prepared by dissolving A and D to
give a total concentration of 5 mm (1:2 molar ratio) in water at
pH 8 in the presence of NaNO3 (1m), because the formation
of catenanes is known to be promoted upon addition of
salt.[6,9] The library was stirred for four hours in air in capped
vials to allow oxidation of the thiol building blocks. LC–MS
analysis revealed that the fully oxidized library contains a
relatively small number of significant components, which is
far from the diversity expected from such flexible building
blocks. The only detectable members of this library are the
closed monomer D, the dimers D2 and A2, as well as two
catenanes composed of one and two donor dimers interlocked
with an acceptor dimer, [2]Cat and [3]Cat, respectively
(Figure 1c).
[3]catenane, with the loss of one or both rings producing the
intermediate [2]Cat (m/z 1271.6, doubly charged), dimers A2
(m/z 1583.5) and D2 (m/z 958.9), and smaller fragments.
The presence of [2]Cat along with remaining non-inter-
locked dimers suggested that the library is fully oxidized
before thermodynamic equilibrium is reached. This hypoth-
esis is consistent with previous observations[6a] and was
confirmed by a series of kinetic analyses. To compare the
rates of oxidation of building blocks A and D, we prepared a
library in a 1:1 molar ratio, which showed that the acceptor A
oxidizes faster than donor D (Figure 3b), rapidly forming the
acceptor dimer A2. Although the rate of oxidation of the
thiols should be similar for the two building blocks, it is
perhaps not surprising that favorable hydrophobic and p–p
interactions[10] make the formation of A2 a pseudo-intra-
molecular process and therefore faster than the formation of
the electron-rich and hence unfavorable dimer D2. Strikingly,
the two building blocks do not form any mixed macrocycles,
which may be rationalized by their difference in size and the
likely templation of A2 by D and of D2 by A through donor–
acceptor interactions. The kinetic profiles of the formation of
A2, [2]Cat, and [3]Cat (Figure 3c) show that the acceptor
dimer A2 is threaded by two open donor dimers consecutively,
thereby forming [2]Cat and [3]Cat successively (Figure 3).
From this study, we concluded that the formation of the
[3]catenane appears to be a stepwise process, and the library
evolves until all the donor building block is fully oxidized,
preventing thermodynamic equilibrium from being reach-
ed.[6a] If the disulfide exchange were to occur for a longer
period of time to allow the system to reach thermodynamic
equilibrium, the unthreaded residues should be recycled into
[3]Cat, which is a kinetic trap and may also be the
thermodynamic product in this library. Consequently, the
formation of the [3]catenane is limited both by the fast rate of
thiol oxidation, which prevents the library from reaching
thermodynamic equilibrium, and by the kinetic competition
between the formation of the unthreaded and the threaded
macrocycles.
To test this supposition, we investigated the effect of
successive additions of the fresh thiol D, which reinitiates the
reversible process and favors threading by providing a high
acceptor/donor ratio. Two equivalents of D were added in
aliquots of 0.5 equivalents every two hours to a library
containing the acceptor A. As expected, the yield of the
[3]catenane increased from 33 (one-pot procedure, Figure 1c)
up to 55% (stepwise additions, Figure 1d) with the final ratio
between the building blocks being equal in both cases. These
yields were evaluated by HPLC from the peak areas.
Unfortunately, further increasing the number of successive
additions (0.25 equivalents added every two hours) or chang-
ing the time between the additions did not lead to any
improvement of the [3]catenane yield, most likely owing to
the low overall concentration of free thiols slowing the
exchange kinetics.
Figure 1. HPLC analysis of an aqueous library composed of A and D
(1:2 molar ratio, 5 mm total concentration), prepared a,b) in the
absence of NaNO3, recorded at a) 260 nm and b) 383 nm. The same
library was prepared in presence of 1m of NaNO3, c) in one pot
(383 nm) or d) after stepwise addition of D (383 nm). e) The library
was also prepared in the presence of 0.5 mm of spermine (383 nm).
Note that the closed monomer D and dimer D2 can only be detected
at 260 nm.
Both catenanes were unambiguously identified by tandem
ESI-MS and MS/MS. The [3]catenane displays doubly and
triply charged molecular ions (m/z 1752.5 and 1167.8),
corresponding to a species composed of two acceptor and
four donor building blocks (Figure 2). The fragmentation
pattern of [3]Cat is characteristic of that expected for a
All the significant library members have been isolated and
characterized by 1H NMR spectroscopy (500 MHz, 298 K,
D2O). Whereas A2 and [2]Cat display the very broad
resonances characteristic of flexible macrocycles,[11] the
[3]catenane exhibits a spectrum with sharp signals, in which
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the resonances for a single
asymmetric conformation can
be clearly identified: two sets
of signals were assigned to the
outer (d = 8.1–8.6 ppm) and
inner
(d = 6.9–7.8 ppm)
acceptor units and similarly,
two sets of signals were
observed for the outer (d =
6.4–7.15 ppm) and inner (d =
4.7–6.3 ppm) donor units (Fig-
ure 4a). NOE correlations
between the outer donor pro-
tons and the protons of the
aliphatic chain suggest that the
most likely conformation of
[3]Cat is the one drawn in
Figure 4.
The catenane synthesis de-
scribed above appears to rely
on the increased polarity of the
reaction medium (1m NaNO3
versus pure water, Fig-
ure 1b,c) to promote the bury-
ing of solvent-exposed hydro-
phobic surfaces.[6,9] In a salt-
free reaction, [3]Cat is formed
only in trace amounts, and the
library is dominated by the
homodimers A2 and D2. Of all
Figure 2. Tandem a) MS and b) MS/MS fragmentation of [3]Cat. For clarity, only the cyclic fragments are
shown; however the MS/MS signals may also correspond to the linear species. The gray cartoon dots
represent the sulfur atoms of the cysteine residues.
Figure 3. a) Proposed mechanism for the synthesis of [3]Cat, involving
the successive formation of A2, [2]Cat, and finally [3]Cat. Kinetic profile
~
*
of b) the consumption of building blocks A ( ) and D ( ) and c) of
~
^
the formation of A2 ( ), [2]Cat (&), and [3]Cat ( ), in a library
composed of A and D (5 mm total concentration, 1:1 molar ratio) in
water pH 8, in the presence of NaNO3 (1m). The concentrations were
evaluated from the HPLC peak areas.
Figure 4. 1H NMR spectrum (D2O, 295 K, 500 MHz) of [3]Cat a) in the
absence and b) in the presence of one equivalent of spermine.
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the library members observed in this system, the [3]catenane
possesses the highest density of carboxylate groups, thus
raising the question of whether a suitable polycation might act
as a template.
using building blocks containing more than one acceptor and/
or donor unit. This work is considered as being the first step
towards the self-assembly of more complex polycatenanes.
In nature, polyamines such as spermine bind to the array
of negative charges of the DNA backbone and play an Experimental Section
important role in many cellular processes,[12] thus prompting
the development of artificial spermine binders.[13] To our
delight, addition of merely 0.5 mm spermine promoted the
amplification of [3]Cat to 60% yield (Figure 1e), suggesting a
strong interaction between the [3]catenane and spermine.
Increasing the concentration of template does not further
increase the yield of [3]catenane. It is well-documented and
understood, but counterintuitive, that adding too much
template can lead to amplification of smaller, weaker binding
receptors.[14] No amplification was observed in the presence of
up to 1m NH4Cl, implying 1) that the interaction between
[3]Cat and spermine results from more than the sum of
random carboxylate–ammonium interactions and 2) that the
effect of metal salts such as NaNO3 may be due to more than
purely ionic-strength effects. The geometrical distribution,
hydrophobicity, and number of ammonium centers present in
the polyamine are crucial for an efficient recognition, as
demonstrated by libraries templated by the shorter spermi-
dine and putrescine, in which [3]Cat was amplified to lesser
extent (see the Supporting Information).
The [3]Cat binds spermine with an association constant of
(1.1 Æ 0.01) ꢀ 105 mÀ1 as determined by 1H NMR spectroscopy
titration experiments, thus confirming the strong interaction
between the two species (Figure 4b). Modeling[15] suggests
that the aromatic moieties of the [3]catenane are too closely
packed to accommodate a cavity large enough for spermine.
Therefore we believe that the template binds to the solvent-
accessible surface of the catenane, interacting with the
arrayed carboxylate ions in a manner reminiscent of sper-
mine’s interactions with the phosphate groups of double
helical DNA.
Preparation of a “one-pot” library: Stock solutions (5 mm) of A and
D were prepared by dissolving the building blocks in aqueous NaOH
(10 mm) and subsequent titration with NaOH (100 mm) to pH 8. The
stock solutions were mixed in the relevant ratio to obtain the library.
When necessary, salt (NaNO3) was added directly in solid form to
produce a 1m solution. The final library solutions (0.5 mL) were
stirred in close-capped vials for at least four hours before LC–MS
analysis.
Preparation of a “templated” library: Stock solutions (7 mm) of A
and D were prepared by dissolving the building blocks in aqueous
NaOH (10 mm) and subsequent titration with NaOH (100 mm) to
pH 8. The stock solutions were mixed in the relevant ratio to obtain
the library and diluted with a concentrated aqueous stock solution of
template to reach a total concentration in building blocks of 5 mm and
adequate concentration of the template. The final library solutions
(0.5 mL) were stirred in close-capped vials for at least four hours
before LC–MS analysis.
Preparation of a “stepwise addition” library: A stock solution of
A (5 mm, 0.2 mL) was prepared by dissolving the building block in
aqueous NaOH (10 mm) and subsequent titration with NaOH
(100 mm) to pH 8. NaNO3 was added directly in solid form to give a
1m solution. Every two hours, a freshly prepared aqueous stock
solution of D (50 mL, 5 mm, 1m NaNO3, pH 8) was added. The
addition was repeated four times before LC–MS analysis.
Received: September 28, 2011
Revised: October 27, 2011
Published online: December 30, 2011
Keywords: catenanes · molecular recognition · self-assembly ·
.
supramolecular chemistry · template synthesis
[1] From Non-Covalent Assemblies to Molecular Machines (Eds.:
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ˇ
To conclude, we have shown for the first time that acyclic
units can spontaneously self-assemble into a donor–acceptor
[3]catenane, either in a high-polarity medium or in the
presence of spermine. The amplification of the [3]catenane in
the presence of spermine highlights the importance of small
template molecules in the controlled assembly of large
complex structures through a multitude of seemingly weak
interactions in a highly competitive medium. This work brings
a new insight into the mechanism of donor–acceptor self-
assembly and provides an alternative route to the efficient
synthesis of [3]catenanes. The formation of this catenane is
not fully under thermodynamic control, so kinetic parameters
also play a role in this process. To limit the formation of
competing species, we have therefore developed a stepwise
dynamic approach, moving away from pure dynamic combi-
natorial chemistry, in which the exchange occurs continuously.
This approach involves the idea of an evolutionary process
with iterated cycles of selection and amplification, which is
closer than pure dynamic combinatorial systems to the
phenomena observed in biological systems.[5]
´
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