Journal of the American Chemical Society
Article
The kinetic model allows for extracting the individual
reaction rates that dominate the evolution of the oligomers.
For example, when we analyze the evolution of oligomer 3, we
find three possible pathways to its formation (Figure 2D), i.e.,
the fuel-driven activation (e.g., 1 + 2 yields 3), the
transacylation (e.g., 4 + 2 yields 3 + 3), or the deactivation
of longer oligomers (e.g., 4 yields 3 + 1). Similarly, we find
three possible pathways for the breakdown of oligomer 3, i.e.,
its spontaneous hydrolysis (deactivation), its transacylation
(scrambling), or its activation into a longer oligomer (Figure
2D). In the first few minutes, the fuel-driven activation governs
the formation of 3. However, we were surprised to find that,
within minutes, the formation of 3 is dominated by the
scrambling of other oligomers, e.g., the transacylation of two
dimers 2 resulting in a 3 and a monomer 1 (Figure 2E). Even
more surprising was that the breakdown kinetics of 3 is always
dominated by the kinetics of transacylation as opposed to the
deactivation via hydrolysis (Figure 2F). Specifically, the
reaction that leads to most of the loss of 3 is the transacylation
of 3, with 1 resulting in two molecules of 2. This loss via
transacylation can be explained by the high concentrations of
1. Taken together, our kinetic model can capture the kinetics
of the reaction cycle and reveals that the scrambling via
transacylation plays an important role in the dynamics of our
nonequilibrium system’s chemistry (Figure 2D). Even though
the activation and deactivation kinetics are dictated by
nonequilibrium chemical reactions, the transacylation, which
dominates the dynamics of the library, is an equilibrium
reaction.
Next, we tested the response of the system to larger batch
sizes of fuel, i.e., 75 and 100 mM. We were surprised to find
that the maximum concentrations of the anhydrides did not
decay exponentially with oligomer length as observed before
(Figure 3A). While 2 had by far the highest maximum
concentration, the maximum concentrations of oligomers 3, 4,
5, and 6 were similar at ∼2.5 mM and much higher compared
to the experiment with 50 mM fuel. The difference in the
kinetics of the chemical reaction cycle was likely due to the
oligomer’s ability to self-assemble because the samples
immediately turned turbid after the addition of the larger
batches of fuel (Figure 3B). Moreover, the turbidity was a
transient phenomenon, i.e., it decayed over 130 min, at which
point the original transparency was restored. We imaged the
rapid increase and subsequent decay of turbidity by time-lapse
photography and measured the gray value of the samples with
microscopy with the hydrophobic dye Nile red showed that
micron-sized light-scattering particles were responsible for the
increased turbidity (Figure 3C). Furthermore, cryogenic
transmission electron microscopy (cryo-TEM) revealed a
fibrillar substructure in the irregular micron-sized assemblies
(Figure 3D). We measured the sample scattering rate by
dynamic light scattering (DLS), which is a more sensitive
measure of the presence of assemblies compared to the
turbidity assays. The addition of 75 or 100 mM fuel drastically
increased the scattering rate of our samples, whereas the
addition of 50 mM or less did not, further corroborating that
>50 mM fuel was needed to induce the formation of transient
Figure 3. Response of the dynamic combinatorial library to a large
batch of fuel. (A) Maximum concentrations of the library compounds
2−6, plotted on a logarithmic scale when fueling with 100 mM EDC
(crosses). The data is an average of the maximum yields obtained in
the reaction cycle. The kinetic model was used to fit the maximum
yields (squares). (B) Photographs of 1 at different time points. (C)
Micrograph of 1 and 25 μM Nile red, fueled with 75 mM EDC after 5
min. (D) Cryo-TEM micrograph of 1 fueled with 75 mM EDC after 2
min. (E, F) HPLC data (markers, monitored at 290 nm) of 3 and 6,
respectively, when 1 was fueled with 100 mM EDC. The kinetic
model was used to fit the experimental data (lines). (G) Schematic
representation of the feedback of assemblies on the deoligomerization
reactions and scrambling reactions of the transient dynamic
combinatorial library. Only oligomer 4 is shown in the scheme to
save space.
oligomers in the supernatant and pellet. We found that the
pellet contained mostly oligomers 4−6 (95 mol %) and only
contrast, the supernatant contained only 0.1 mM 4 but no 5 or
6. We conclude that library members 4−6 can assemble when
a larger amount of fuel is added and that assembly can change
the reaction kinetics, resulting in increasing yields of 4−6.
Because of the ill-defined morphology of the assemblies and
the huge polydispersity, we assume that all these library
members randomly coassemble as opposed to self-sorting into
individual assemblies.
We analyzed the evolution of the concentration of fuel and
anhydrides 2−6 when assemblies were present (Figures 3E, S8,
and S9). When 100 mM EDC was added, the fuel was entirely
consumed within 16 min (Figure S9A). The concentrations of
anhydrides 2−6 initially rose and then collapsed (Figures 3E
and F and S9B−D). However, we observed a large difference
in the deactivation kinetics of the oligomers that assembled
(4−6) compared to those that did not (2 and 3, Figure 3E and
F). For 100 mM EDC, we found that 2 and 3 peaked in the
first few minutes and then decayed with first-order kinetics
(Figures 3E and S10B). Moreover, at the time where the most
fuel was consumed, these anhydrides had also mostly decayed.
Surprisingly, 4, 5, and 6 peaked at ∼9 min, which is close to
the point where almost all fuel was depleted. Moreover,
Ten minutes after the addition of fuel, we centrifuged the
reaction solution and measured the concentration of the
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J. Am. Chem. Soc. 2021, 143, 7719−7725