A Synthetic Replicator Drives a Propagating Reaction-Diffusion Front

Article abstract of DOI:10.1021/jacs.6b03372

A simple synthetic autocatalytic replicator is capable of establishing and driving the propagation of a reaction-diffusion front within a 50 μL syringe. This replicator templates its own synthesis through a 1,3-dipolar cycloaddition reaction between a nit

Full text of DOI:10.1021/jacs.6b03372

Communication
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A Synthetic Replicator Drives a Propagating Reaction−Diffusion
Front
Ilaria Bottero, Jurgen Huck, Tamara Kosikova, and Douglas Philp*
̈
School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K.
S
* Supporting Information
extent, in general, they have been studied under well-stirred
ABSTRACT: A simple synthetic autocatalytic replicator is
capable of establishing and driving the propagation of a
reaction−diffusion front within a 50 μL syringe. This
replicator templates its own synthesis through a 1,3-dipolar
cycloaddition reaction between a nitrone component,
equipped with a 9-ethynylanthracene optical tag, and a
maleimide. Kinetic studies using NMR and UV−vis
spectroscopies confirm that the replicator forms efficiently
and with high diastereoselectivity, and this replication
process brings about a dramatic change in optical
properties of the samplea change in the color of the
fluorescence in the sample from yellow to blue. The
addition of a small amount of the preformed replicator at a
specific location within a microsyringe, filled with the
reaction building blocks, results in the initiation and
propagation of a reaction−diffusion front. The realization
of a replicator capable of initiating a reaction−diffusion
front provides a platform for the examination of
interconnected replicating networks under out-of-equili-
brium conditions involving diffusion processes.
batch reactor conditions. The consequence of this reaction
format places a fundamental limit on the level of complexity
and emergence that can be generated by such systems. In order
to create diverse emergent behavior, there is a need to study
self-replicating systems under out-of-equilibrium conditions,
and propagating reaction−diffusion fronts could provide an
ideal vehicle for such studies. Here, we report the design and
implementation of a molecular replicating system capable of
generating and sustaining a propagating reaction−diffusion
front.
Previously, we described11 an efficient synthetic replicator
based on the general design shown in Figure 1a. Reaction of
nitrone 1a with maleimide 2 in CDCl3 at −10 °C results in the
rapid, autocatalytic formation of the cycloadduct 3a. Cyclo-
adduct 3a is a very efficient template for its own formationit
is capable of accelerating the reaction between 1a and 2 up to
125× through a ternary complex [1a·2·3a], and the structure of
this complex ensures that only the trans diastereoisomer of 3a is
formed during this process. Conventionally, we have monitored
the kinetics of replication processes by NMR spectroscopy. In a
reaction−diffusion format, this reaction requires an alternative
method to monitor the progress12 of the reaction. Ideally, we
desired an optical signature of replication. Therefore, we
designed nitrone 1b, bearing a 9-ethynylanthracene tag. RM1
calculations (Figure 1b) indicated that this nitrone, in
partnership with maleimide 2, was capable of furnishing
template 3b through a ternary complex, [1b·2·3b]. This
complex should permit the formation of only the trans
diastereoisomer of 3b. TD-DFT calculations (see Supporting
Information) indicated that a significant change in the 350−400
nm region of the UV−vis spectrum could be expected on
conversion of nitrone 1b to cycloadduct 3b as a result of the
presence of the 9-ethynylanthracene unit. We synthesized
nitrone 1b using standard methods; this compound forms
yellow-colored solutions in CDCl3, which exhibit an intense
yellow fluorescence (Figure 1a). Pleasingly, the conversion of
1b into 3b resulted in a very significant color changethe
yellow fluorescence of 1b was replaced (Figure 1a) by the blue
fluorescence of 3b.
he spontaneous generation of stationary patterns and
1
Tpropagating fronts in chemical systems
has intrigued
scientists for generations. Such phenomena are ubiquitous in
nature,2 and the physical processes behind their appearance and
stability have been studied extensively3 and are now relatively
well understood. Propagating reaction−diffusion fronts have
received significant attention in this respect. Frequently, one or
more oscillatory or autocatalytic processes are found at the core
of these systems. Front generation is initiated when an
autocatalyst is added at a discrete location in an expanse of
reactant, initially at uniform concentration, and the ensuing
reaction generates wave fronts, which propagate outward from
the initial reaction zone. In almost all4 of the examples reported
to date, the autocatalysis is based on inorganic chemistry,
although, more recently, a small number of examples based on
RNA5 and DNA6 have been described. Self-replication7
represents a niche of autocatalytic behavior in which a
structurally complex template is capable of recognizing the
building blocks necessary for its own formation and catalyzing
their reaction to form an exact copy of itself. We, and others,
have described the use of such systems in instructable
networks,8 as tools for dynamic systemic resolution,9 and in
the construction10 of mechanically interlocked molecules.
Although all of these systems display the nonlinear kinetic
characteristics of autocatalytic systems to a greater or lesser
Next, we conducted a series of kinetic experiments involving
the reaction of 1b and 2 in CDCl3 at 0 and 20 °C, monitoring
1
the production of cycloadduct 3b by 500 MHz H NMR
spectroscopy. The results of these experiments and subsequent
fitting of the experimental data at 20 °C to the appropriate
Received: April 1, 2016
© XXXX American Chemical Society
A
DOI: 10.1021/jacs.6b03372
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Journal of the American Chemical Society
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Figure 2. (a) Concentration (red circles) and rate (black dotted line)
vs time profile for the formation of 3b from nitrone 1b and maleimide
2, as determined by 500 MHz 1H NMR spectroscopy ([1b] = [2] = 10
mM, 20 °C, CDCl3). The red line shows the fit of the appropriate
kinetic model to these data (see Supporting Information). (b)
Appearance of the resonance associated with the formation of the
trans-3b cycloadduct over time in the 500 MHz 1H NMR spectrum of
a reaction mixture containing 1b and 2 ([1b] = [2] = 10 mM, 20 °C,
CDCl3). (c) Selected UV−vis spectra recorded during the reaction of
1b and 2 ([1b] = [2] = 10 mM, 20 °C, CDCl3), showing the
disappearance of nitrone 1b (346 nm band) and simultaneous
appearance of cycloadduct 3b (297 nm band). (d) Comparison of
absorbance at 297 nm vs time. The blue circles show data determined
experimentally from the spectra in panel c. The red line shows the
absorbance at 297 nm computed using the concentrations of 3b
determined from the best fit of the appropriate kinetic model to the
NMR data in panel a.
Figure 1. (a) Self-replicating template 3a is constructed by the
reaction of nitrone 1a with maleimide 2 through the catalytically active
[1a·2·3a] ternary complex. Replacement of the substituent R affords
replicator 3b, which incorporates a 9-ethynylanthracene optical tag,
derived from nitrone 1b. The formation of cycloadduct 3b, mediated
by ternary complex [1b·2·3b], is now associated with a change in
fluorescence from yellow (1b) to blue (3b). (b) Calculated (RM1)
structure of the transition state leading to 3b from the ternary complex
[1b·2·3b].
during the reaction show the disappearance of a band
corresponding to nitrone 1b at 346 nm, with the concomitant
appearance of a band at 297 nm corresponding to cycloadduct
3. In order to relate these data to the kinetic data derived from
NMR spectroscopy, we reconstructed the reaction profile at
297 nm by computing the expected absorbance at this
wavelength from the concentrations of the components of
the reaction mixture determined from the best fit our kinetic
model to the NMR data. The excellent agreement (Figure 2d)
between the calculated and observed reaction profiles provides
compelling evidence that the color change observed during this
reaction is indeed the signature of the replication of 3b.
Normally, propagating reaction−diffusion fronts are ob-
served in reactions that are initiated on flat plates or within
capillary tubes. Since CDCl3 is a relatively volatile solvent, we
chose to investigate whether 3b was capable of supporting a
propagating reaction−diffusion front within a 50 μL gastight
syringe of internal diameter 1.03 mm. Figure 3 illustrates our
experimental setup. Two syringes were placed side-by-side in a
specially constructed stand housed within a controlled
environment where the temperature was regulated at 20 °C.
One syringe was filled with a 5 mM solution of nitrone 1b and
kinetic model are shown in Figure 2a,b. These kinetic
experiments reveal that replicator 3b is an excellent template
for its own formationthe ternary complex [1b·2·3b]
generates an effective molarity13 (EM) of 16.2 M for the
cycloaddition reaction (for details, see Supporting Informa-
tion). This value for the ternary complex EM is broadly similar
to those determined previously9e,10b,11 for similar replicators
and indicates that the incorporation of the 9-ethynylanthracene
optical probe has essentially no effect on the functioning of the
replicator.
Having established that 3b was indeed capable of templating
its own formation, we next sought to establish that the color
change observed during this reaction is a signature of the
autocatalytic replication processes. Accordingly, we monitored
the formation of 3b using UV−vis spectroscopy (Figure 2c)
under conditions identical to those employed in the NMR
kinetic experiments. As expected, the UV−vis spectra recorded
B
DOI: 10.1021/jacs.6b03372
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Journal of the American Chemical Society
Communication
Figure 3. (a) Graphical representation and (b) photograph of the
experimental setup employed for investigation of the propagating
reaction−diffusion front initiated by replicator 3b in two 50 μL
gastight syringes. The upper syringe in each case represents the control
experiment comprising the nitrone 1b and maleimide 2 only ([1b] =
[2] = 5 mM, 20 °C, CDCl3). The lower syringe is seeded with ca. 2 μL
of a solution of 3b ([1b] = [2] = 5 mM, [3b] = 10 mM, 20 °C,
CDCl3).
Figure 4. (a) Processed grayscale images, acquired over time, with the
syringes illuminated using a 365 nm UV lamp, of the template-initiated
reaction−diffusion experiment (+3b, left column) and the control
experiment (−3b, right column). (b) Smoothed profiles of the
grayscale images from the reaction−diffusion experiment (+3b)
showing the progression of the reaction diffusion front over 20 min.
maleimide 2 in CDCl3. The second syringe was prepared
identically with the exception that approximately 2 μL of a 10
mM solution of replicator 3b was drawn into the end of the
syringe after it was filled with the solution of 1b and 2.
We envisaged that the syringe containing only 1b and 2
would change color uniformly as replicator 3b was formed. In
the other syringe, the presence of 3b would initiate the
replication process, and the diffusion of the replicator thus
formed would establish a reaction−diffusion front that would
propagate along the syringe, being observed as the progression
of a blue band along the initially yellow syringe.
throughout the syringe as a result of the background rate of the
cycloaddition reaction forming 3b being significant on the time
scale of the experiment.
Here, we have described the first example of a propagating
reaction−diffusion front that is initiated and driven by a
synthetic replicator. The work reported here represents a proof-
of-principle. The successful implementation of a replicator-
driven reaction−diffusion front, mediated by an autocatalytic
replicator of defined structure and with specific interactions and
catalytic relationships with other similar replicators, opens up15
a number of exciting possibilities. This reaction format will
allow us to explore networks8a of replicators under conditions
and outcomes that lie far from the constraints16 imposed by
well-stirred batch reactors. These studies are currently under-
way in our laboratory.
The syringes were illuminated using a 365 nm UV lamp, and
a color image was captured every 2 min using a digital camera.
Processing of these images (see Supporting Information)
afforded the data shown in Figure 4a. It is evident from these
images that replicator 3b has established (Figure 4a, +3b) a
propagating reaction−diffusion front within the syringe to
which it was added initially. By contrast, no such feature is
evident within the control syringe (Figure 4a, −3b). As an
additional control, we examined the diffusion of 3b in the
absence of an autocatalytic reaction. Approximately 2 μL of a
10 mM solution of replicator 3b was drawn into the end of a
syringe filled with a 5 mM solution of nitrone 1b only in
CDCl3. In this case, the blue color of replicator 3b disappears as
a result of diffusion processes within the syringe, leaving the
syringe visually indistinguishable from one that had been filled
with nitrone 1b only. No optical signature of a propagating
reaction−diffusion front is observed in this case. Selected
images were processed further (see Supporting Information) to
compute the profile (Figure 4b) of the propagating front at a
sequence of time points. These data clearly show the
progression of the reaction−diffusion front mediated by
replicator 3b along the syringe. In many cases, reaction−
diffusion fronts propagate at constant linear or radial velocity.
However, in this case, the progression14 of the front slows and
will eventually stall as nitrone 1b and maleimide 2 are depleted
ASSOCIATED CONTENT
■
S
* Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/jacs.6b03372. The
research data supporting this publication can be accessed at
http://dx.doi.org/10.17630/b05bac27-f50d-485b-966a-
6b2246716481.
Experimental procedures, details of kinetic measure-
ments and fitting, computational modeling of UV
spectra, details of UV−vis and fluorescence analyses,
and methods and analyses for the reaction−diffusion
experiments (PDF)
C
DOI: 10.1021/jacs.6b03372
J. Am. Chem. Soc. XXXX, XXX, XXX−XXX

Journal of the American Chemical Society
Communication
(10) (a) Vidonne, A.; Kosikova, T.; Philp, D. Chem. Sci. 2016, 7,
2592. (b) Kosikova, T.; Hassan, N. I.; Cordes, D. B.; Slawin, A. M. Z.;
Philp, D. J. Am. Chem. Soc. 2015, 137, 16074. (c) Vidonne, A.; Philp,
D. Tetrahedron 2008, 64, 8464.
AUTHOR INFORMATION
■
Corresponding Author
*d.philp@st-andrews.ac.uk
(11) Kassianidis, E.; Philp, D. Angew. Chem., Int. Ed. 2006, 45, 6344.
(12) For an example of an optical readout amplified by autocatalysis,
see: Mohapatra, H.; Schmid, K. M.; Phillips, S. T. Chem. Commun.
2012, 48, 3018.
Notes
The authors declare no competing financial interest.
(13) (a) Page, M. I.; Jencks, W. P. Proc. Natl. Acad. Sci. U. S. A. 1971,
68, 1678. (b) Page, M. I. Chem. Soc. Rev. 1973, 2, 295. (c) Kirby, A. J.
Adv. Phys. Org. Chem. 1980, 17, 183.
(14) In certain cases, convection can affect wave front propagation.
For a discussion of convective effects on chemical waves, see: Pojman,
J. A.; Epstein, I. R. J. Phys. Chem. 1990, 94, 4966.
ACKNOWLEDGMENTS
■
We thank EPSRC for postgraduate studentship awards to J.H.
(EP/E017851/1) and T.K. (EP/K503162/1).
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DOI: 10.1021/jacs.6b03372
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