Manipulating replication processes within a dynamic covalent framework

Article abstract of DOI:10.1021/ol8018665

(Chemical Equation Presented) The reaction of an amine bearing an amidopyridine recognition site and an aldehyde bearing a carboxylic acid recognition site affords an imine that is capable of directing its own formation through a dynamic covalent replicat

Full text of DOI:10.1021/ol8018665

ORGANIC
LETTERS
2008
Vol. 10, No. 20
4589-4592
Manipulating Replication Processes
within a Dynamic Covalent Framework
Vicente del Amo, Alexandra M. Z. Slawin, and Douglas Philp*
EaStCHEM and Centre for Biomolecular Sciences, School of Chemistry, UniVersity of
St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
d.philp@st-andrews.ac.uk
Received August 11, 2008
ABSTRACT
The reaction of an amine bearing an amidopyridine recognition site and an aldehyde bearing a carboxylic acid recognition site affords an
imine that is capable of directing its own formation through a dynamic covalent replication cycle. Additionally, the amine, formed by reduction
of the replicating imine, is a more efficient catalyst for the formation of the replicating imine than the imine is a catalyst for its own formation.
The fabrication of materials and intelligent devices that
operate on the nanometer scale could be revolutionized by
the development of molecular and supramolecular architec-
tures that can direct their own formation. A fundamental
understanding of the recognition-mediated processes that
allow molecules to function as specific and efficient tem-
plates1 for the formation of themselves will drive the
development of protocols that establish and manage replica-
tion, organization, and evolution within synthetic supramo-
lecular assemblies. This approach to predetermined dynamic
behavior has been termed2 “systems chemistry”. In the
context of our long-term goals, we have been able to exploit
replication to amplify a single structure from a pool of
reagents based on its ability to guide its own formation
through recognition processes. The cycloadditions of male-
imides with N-aryl nitrones or furans have been incorporated
successfully3 into modular self-replicating systems. These
reactions form covalent bonds irreversibly, thus the structures
amplified by virtue of recognition-meditated events are a
result of kinetic selection processes operating within the
reaction networks present in the replicating systems.
Motivated by our interest in the study of complex reaction
networks, we became intrigued by the possibility of intro-
ducing a reversible covalent bond-forming reaction into our
replicating systems, thus marrying the opportunities4,5 of
dynamic combinatorial chemistry (DCC) with those of self-
replicating systems. The condensation reaction between an
aniline derivative and an aromatic aldehyde to form an imine,
(1) For general reviews on replication, see: (a) Patzke, V.; von
Kiedrowski, G. ArkiVoc 2007, 293. (b) Paul, N.; Joyce, G. F. Curr. Opin.
Chem. Biol. 2004, 8, 634. (c) Li, X.; Chmielewski, J. Org. Biomol. Chem.
2003, 1, 901. (d) Robertson, A.; Sinclair, A. J.; Philp, D. Chem. Soc. ReV.
2000, 29, 141. (e) Lee, D. H.; Severin, K.; Ghadiri, M. R. Curr. Opin.
Chem. Biol. 1997, 1, 491.
(2) (a) Kindermann, M.; Stahl, I.; Reimold, M.; Pankau, W. M.; von
Kiedrowski, G. Angew. Chem., Int. Ed. 2005, 44, 6750. (b) Stankiewicz,
J.; Eckardt, L. H. Angew. Chem., Int. Ed. 2006, 45, 342. (c) Corbett, P. T.;
Sanders, J. K. M.; Otto, S. Angew. Chem., Int. Ed. 2007, 46, 8858. (d)
Sarma, R. J.; Nitschke, J. R. Angew. Chem., Int. Ed. 2008, 47, 377. (e)
Ludlow, R. F.; Otto, S. Chem. Soc. ReV. 2008, 37, 101. (f) Dadon, Z.;
Wagner, N.; Ashkenasy, G. Angew. Chem., Int. Ed. 2008, 47, 6128.
(3) (a) Allen, V. C.; Philp, D.; Spencer, N. Org. Lett. 2001, 3, 777. (b)
Quayle, J. M.; Slawin, A. M. Z.; Philp, D. Tetrahedron Lett. 2002, 43,
7229. (c) Pearson, R. J.; Kassianidis, E.; Philp, D. Tetrahedron Lett. 2004,
45, 4777. (d) Kassianidis, E.; Pearson, R. J.; Philp, D. Org. Lett. 2005, 7,
3833. (e) Pearson, R. J.; Kassianidis, E.; Slawin, A. M. Z.; Philp, D.
Chem.sEur. J. 2006, 12, 6829. (f) Kassianidis, E.; Philp, D. Angew. Chem.,
Int. Ed. 2006, 45, 6334.
10.1021/ol8018665 CCC: $40.75
Published on Web 09/25/2008
2008 American Chemical Society

Scheme 1
a well-studied6 reaction in the context of DCC, is central to
number of interesting features that arise from the reversibility
inherent in imine formation. The reaction between 1 and 2
to form imine 3 within the ternary complex is pseudouni-
molecular and, therefore, should proceed at a faster rate than
the bimolecular reaction between the same reagents. How-
ever, since the reverse reaction is still bimolecular, this
acceleration of the forward reaction7 will also affect the
overall stability of imine 3. We also envisaged that amine 4
might act as a crosscatalytic template for the formation of 3
through the catalytic cycle shown in Scheme 1. Here, we
demonstrate that imine 3 is capable of directing its own
formation through the recognition-mediated manipulation of
the dynamic equilibria shown in Scheme 1 and that amine 4
is capable of acting as a crosscatalyst for the formation of
3.
the design (Scheme 1) of our system. Amine 1 and aldehyde
2 can react reversibly through a bimolecular mechanism to
form imine 3 which can potentially act as a template for its
own formation. Imine 3 is capable of recognizing and binding
both 1 and 2 forming the ternary complex [1·2·3]. Reaction
of 1 and 2 within this complex leads to an additional copy
of imine 3 and the formation of the product duplex [3·3]. At
this point, imine 3 has completed a formal replication cycle,
and dissociation of the product duplex [3·3] completes the
autocatalytic cycle. In contrast to previous work on kineti-
cally controlled replication, this autocatalytic cycle has a
(4) For general reviews, see: (a) Lehn, J.-M. Chem.sEur. J. 1999, 5,
2455. (b) Rowan, S. J.; Cantrill, S. J.; Cousins, G. R. L.; Sanders, J. K. M.;
Stoddart, J. F. Angew. Chem., Int. Ed. 2002, 41, 898. (c) Corbett, P. T.;
Leclaire, J.; Vial, L.; West, K. R.; Wietor, J.-L.; Sanders, J. K. M.; Otto, S.
Chem. ReV. 2006, 106, 3652. (d) Otto, S.; Severin, K. Top. Curr. Chem.
2007, 277, 267.
In order to assess the effects of molecular recognition on
this system, aldehyde 5, which is incapable of recognition,
was used as a model for the background bimolecular reaction
between 1 and 2. Initially, we wished to establish the position
of equilibrium under the reaction conditions (dry8 CDCl3,
(5) For a set of imine-based replicating systems which operate in polar
aprotic solvents, see: Terfort, A.; von Kiedrowski, G. Angew. Chem., Int.
Ed. Engl. 1992, 31, 654. For an imine-based self-duplicator, see: Xu, S.;
Giuseppone, N. J. Am. Chem. Soc. 2008, 130, 1826.
(6) For some recent examples, see: (a) Rowan, S. J.; Stoddart, J. F. Org.
Lett. 1999, 1, 1913. (b) Nitschke, J. R.; Lehn, J.-M. Proc. Natl. Acad. Sci.
U.S.A. 2003, 100, 11970. (c) Godoy-Alcantar, C.; Yatsimirsky, A. K.; Lehn,
J.-M. J. Phys. Org. Chem. 2005, 18, 979. (d) Nitschke, J. R. Angew. Chem.,
Int. Ed. 2004, 43, 3073. (e) Giuseppone, N.; Schmitt, J. L.; Schwartz, E.;
Lehn, J.-M. J. Am. Chem. Soc. 2005, 127, 5528. (f) Oh, K.; Jeong, K. S.;
Moore, J. S. Nature 2001, 414, 889. (g) Zhao, D. H.; Moore, J. S. J. Am.
Chem. Soc. 2002, 124, 9996. (h) Hochgurtel, M.; Kroth, H.; Piecha, D.;
Hofmann, M. W.; Nicolau, C.; Krause, S.; Schaaf, O.; Sonnenmoser, G.;
Eliseev, A. V. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 3382. (i) Storm, O.;
Lu¨ning, U. Chem.sEur. J. 2002, 8, 793. (j) Bugaut, A.; Toulme, J. J.;
Rayner, B. Angew. Chem., Int. Ed. 2004, 43, 3144. (k) Schultz, D.; Nitschke,
J. R. Chem.-Eur. J. 2007, 13, 3660. (l) Sarma, R. J.; Otto, S.; Nitschke,
J. R. Chem.-Eur. J. 2007, 13, 9542. (m) Nitschke, J. R. Acc. Chem. Res.
2007, 40, 103.
(7) The reversible formation of [3·3] from [1·2·] is associated with an
equlibrium constant K, which is the equal to kforward/kreverse for this
transformation. The intramolecular nature of [1·2·3] f [3·3] will result in
this process being accelerated with respect to the bimolecular pathway 1 +
2 f 3. The reverse process [3·3] f [1·2·3] is still bimolecular, and thus,
one would envisage that this rate is close to that for 3 f 1 + 2. The net
effect is therefore to increase K for the recognition-mediated process making
the formation of 3 from [1·2·3] more favorable.
(8) CDCl3 (99.8% atom D) was purchased from Aldrich as 100 g bottles.
Bottles were opened under a positive pressure of Ar, and the contents were
stored over preactivated 4 Å molecular sieves. The water content was
determined to be 14 ppm using Karl-Fischer titration (Mettler Toledo DL32
coulometer).
4590
Org. Lett., Vol. 10, No. 20, 2008

25 °C) in the absence of recognition. We therefore measured9
(Figure 1a, green diamonds) the rate of reaction between 1
reaching more than 50% conversion after 16 h, and the
concentration vs time profile for the formation of 3 is clearly
sigmoidal. Additionally, the rate vs time profile (Figure 1b,
red line) for the reaction between 1 and 2 shows the
characteristic rate maximum for an autocatalytic reaction with
the maximum rate of formation of 3 (0.79 mM h-1) being
achieved after 3 h. Taken together, these data suggest that
imine 3 is capable of replication. In order to confirm this
hypothesis, we performed two additional experiments. The
role of hydrogen bonding in the formation of imine 3 was
confirmed by performing the reaction between 1 and 2 in
the presence of the competitive inhibitor 7. Amide 7 disrupts
the association between the carboxylic acid present in 2 and
amidopyridine-bearing species present in the autocatalytic
cycle (Scheme 1). Thus, reaction between 1 and 2 in the
presence of 7 ([1] ) [2] ) 15 mM, [7] ) 7.5 mM, dry
CDCl3, 25 °C) results in a significant decrease11 in the rate
of reaction. This result demonstrates that the formation of
imine 3 is recognition-mediated. Critically, we were able to
demonstrate that imine 3 is capable of accelerating its own
formation. The addition of substoichiometric amounts of 3
at the start of the reaction between 1 and 2 should result in
a significant increase in the initial rate of formation of 3.
Thus, reaction of 1 and 2 under conditions identical to those
described previously, in the presence of 15 mol % of imine
3, results (Figure 1, blue data) in a disappearance of the lag
period for the formation of imine 3 and a maximum rate of
1.36 mM h-1 was reached at the beginning of the reaction (t
) 0) as expected.
Figure 1. (a) Concentration vs time profiles for the formation of 6
From these data, it is clear that imine 3 is capable of
directing its own formation through the autocatalytic cycle
presented in Scheme 1. It is also clear that the recognition-
mediated reaction processes operating in this system affect
both the rate of formation of 3 and the equilibrium
concentration of 3. We turned to kinetic simulation and fitting
in order to gain further insight into the changes in the rate
and equilibrium constants for this system engendered by
molecular recognition. Fitting of the experimental concentra-
tion vs time data to a simple bimolecular model (Figure 1a,
green line) affords an equilibrium constant of 0.30 for the
formation of 6 from 1 and 5. The bimolecular rate constant
for the forward reaction between 1 and 2 is 4.54 × 10-4
M-1 s-1. Fitting of the experimental concentration vs time
data for the formation of 3 from 1 and 2 to our standard
kinetic model for replicating systems3a,d-f gives excellent
fits (Figure 1a, red and blue lines, see the Supporting
Information for details). From these fits, a number of
interesting thermodynamic and kinetic parameters can be
extracted. The unimolecular rate constant for the formation
3 in the [1·2·3] ternary complex is is 8.14 × 10-3 s-1
revealing that this complex generates a kinetic effective
molarity12 of 17.9 M and a thermodynamic effective molarity
of 15.0 M. The best fit association constant for the product
duplex [3·3] is 65000 M-1, corresponding to a connection
from 1 and 5 (green diamonds), 3 from 1 and 2 (red diamonds),
and 3 from 1 and 2 in the presence of 15 mol % 3 at the start of
the experiment (blue diamonds). The data for the reaction in the
presence of added 3 is corrected for the initial concentration of 3
and, thus, represents new imine 3 formed during the experiment.
All experiments were conducted in CDCl3 at 25 °C from starting
concentrations of the appropriate reagents (1 and 2 or 1 and 5) of
15 mM. In each case, the solid line represents the best fit of the
experimental data to the appropriate kinetic model (see the text
and Supporting Information). (b) Rate vs time profiles derived from
the concentration-time data in (a). Formation of 6 from 1 and 5
(green line), 3 from 1 and 2 (red line) and 3 from 1 and 2 in the
presence of 15 mol % 3 at the start of the experiment (blue line).
and 5 in dry CDCl3 at 25 °C ([1] ) [5] ) 15 mM,
[4-bromophenylacetic acid]10 ) 15 mM). After 16 h, the
conversion of 1 and 5 to imine 6 was only around 9%. Next,
we assessed the effect of introducing recognition into the
reagents on both the reaction rate and the position of
equilibrium. We therefore measured the rate of reaction
between 1 and 2 in dry CDCl3 at 25 °C ([1] ) [2] ) 15
mM). In this case, the recognition-mediated reaction (Figure
1a, red diamonds) between 1 and 2 was significantly faster,
(9) The time course of each reaction was followed by 500 MHz 1H NMR
spectroscopy. The disappearance of the resonances arising from the aldehyde
protons in 2 and 5 (δ ) 9.95-10.05) and the simultaneous appearance of
resonances arising from the imine protons in 3 and 6 (δ ) 8.42-8.47)
were monitored. Concentration vs time profiles were constructed by
deconvolution of these resonances.
(11) See the Supporting Information for the concentration vs time profile
for this experiment.
(10) 4-Bromophenylacetic acid (1 equiv) was added to the control
reaction between 1 and 5 to ensure that the acid concentration was the same
as in reactions involving aldehyde 2.
(12) (a) Kirby, A. J. AdV. Phys. Org. Chem. 1980, 17, 183. (b) Mandolini,
L. AdV. Phys. Org. Chem. 1986, 22, 1. (c) Cacciapaglia, R.; Di Stefano, S.;
Mandolini, L. Acc. Chem. Res. 2004, 37, 113.
Org. Lett., Vol. 10, No. 20, 2008
4591

free energy (∆Gs) of -8.08 kJ mol-1. Given the single point
association of carboxylic acid 2 and amidopyridine 7 has an
association constant of 50 M-1, this result indicates that the
formation of the product duplex from two separate binding
events is significantly positively cooperative. Some evidence
for the stability of the [3·3] duplex comes from the fact that
this species could be crystallized intact from CDCl3 solution
and its structure determined (Figure 2a) by single crystal
consumption of starting materials. The reduction of imines
to “freeze” dynamic libraries has been reported14 widely.
The methods employed for reduction make use of an excess
of borane or borohydride reagents in nonprotic solvents.
The structural similarity of the [4·4] duplex, as determined
by single crystal X-ray diffraction (Figure 2b), to that of the
[3·3] duplex intrigued us. We reasoned that the [1·2·4] ternary
complex should have significant stability, thus opening up
the crosscatalytic cycle shown in Scheme 1. Accordingly,
we performed condensation reactions between 1 and 2 in
the presence of 5 mol %15 of 4 ([1] ) [2] ) 15 mM, [4] )
0.75 mM dry CDCl3, 25 °C). The maximum rate of formation
of imine 3 was found to be 1.22 mM h-1, indicating that 4
is a better crosscatalyst for the formation of imine 3 than
imine 3 is an autocatalyst for the formation itself. Although
we have investigated the condensation reaction between
amine 1 and aldehyde 2 and the in situ reduction of imine 3
in CDCl3 (at t ) 0, [1] ) [2] ) 15 mM, [NaBH(OAc)3] )
45 mM; 25 °C), precipitation of the reduced product 4
(presumably as its Na salt) prevented us from recording
adequate kinetic data.
In summary, we have demonstrated that it is possible to
design and implement an efficient replicating system based
on reversible imine formation in a nonpolar solvent. The
ultimate efficiency of this replicator is, however, hampered
by the fully dynamic nature of the system. We have
demonstrated that a simple functional group transformation
(reduction) can convert the autocatalytic, but dynamic, imine
into a static crosscatalyst for the formation of imine 3, namely
amine 4. We are currently developing the use of this
methodology in more complex reaction networks.
Figure 2. Ball and stick representations of the structures of (a)
[3·3] and (b) [4·4] as determined by single-crystal X-ray diffraction.
Carbon atoms are colored dark gray, nitrogen atoms are colored
blue, oxygen atoms are colored red, and hydrogen atoms are colored
light gray. Most hydrogen atoms have been omitted for clarity.
Dashed lines represent hydrogen bonds.
We thank the EPSRC for financial support (Grant No. EP/
E017851/1). We thank Prof. G. von Kiedrowski (Ruhr-
Universita¨t Bochum, Germany) for providing us with his
SimFit program.
X-ray diffraction. The overall equilibrium constant for the
formation of 3 from 1 and 2 is now 3.59. Thus, the net effect
of all of the recognition events within this system is to
stabilize 3 by 6.19 kJ mol-1 with respect to the situation in
the absence of recognition and to dramatically shorten the
time taken for the system to reach equilibrium.
Supporting Information Available: Synthetic procedures
and characterization for compounds 1, 2, 3, 4. and 7.
Experimental details of kinetic experiments and kinetic
simulation and fitting. Details of solid state structures of [3·3]
and [4·4] determined by single-crystal X-ray diffraction. This
material is available free of charge via the Internet at
http://pubs.acs.org.
It is clear, however, that, despite the efficient recognition-
mediated processes that operate within this system, there is
a fundamental limit to the formation of imine 3 that cannot
be breached. We have observed13 this phenomenon previ-
ously in small dynamic libraries, and it is manifest in the
template-directed experiment performed here (blue line,
Figure 1a) s the initial addition of template 3 limits the
amount of new template 3 that can be formed and this
amount diminishes as the amount of template added at the
start of the experiment increases. It is therefore clear that in
order to breach the limit imposed by the fully dynamic nature
of the system, an irreversible reaction step must be incor-
porated within the reaction network. Reduction of imine 3
to amine 4 in situ should, in principle, drive the reversible
condensation reaction between 1 and 2 toward the full
OL8018665
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