Chemically Fueled Transient Geometry Changes in Diphenic Acids

Article abstract of DOI:10.1021/acs.orglett.0c02757

Transient changes in molecular geometry are key to the function of many important biochemical systems. Here, we show that diphenic acids undergo out-of-equilibrium changes in dihedral angle when reacted with a carbodiimide chemical fuel. Treatment of appropriately functionalized diphenic acids with EDC (N-(3-(dimethylamino)propyl)-N′-ethylcarbodiimide hydrochloride) yields the corresponding diphenic anhydrides, reducing the torsional angle about the biaryl bond by ～45°, regardless of substitution. In the absence of steric resistance, the reaction is well-described by a simple mechanism; the resulting kinetic parameters can be used to derive important properties of the system, such as yields and lifetimes. The reaction tolerates steric hindrance ortho to the biaryl bond, although the competing formation of (transient) byproducts complicates quantitative analysis.

Full text of DOI:10.1021/acs.orglett.0c02757

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Letter
Chemically Fueled Transient Geometry Changes in Diphenic Acids
Isuru M. Jayalath, Hehe Wang, Georgia Mantel, Lasith S. Kariyawasam, and C. Scott Hartley*
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ABSTRACT: Transient changes in molecular geometry are key to the
function of many important biochemical systems. Here, we show that
diphenic acids undergo out-of-equilibrium changes in dihedral angle when
reacted with a carbodiimide chemical fuel. Treatment of appropriately
functionalized diphenic acids with EDC (N-(3-(dimethylamino)propyl)-
N′-ethylcarbodiimide hydrochloride) yields the corresponding diphenic
anhydrides, reducing the torsional angle about the biaryl bond by ∼45°,
regardless of substitution. In the absence of steric resistance, the reaction
is well-described by a simple mechanism; the resulting kinetic parameters
can be used to derive important properties of the system, such as yields
and lifetimes. The reaction tolerates steric hindrance ortho to the biaryl
bond, although the competing formation of (transient) byproducts complicates quantitative analysis.
any biochemical systems operate in out-of-equilibrium
Mstates that require a continuous supply of energy to
maintain function.1,2 This “dissipative” behavior3,4 imparts
properties, such as temporal control, that cannot be achieved at
thermodynamic equilibrium.5 Out-of-equilibrium geometry
changes play a vital role in this context.6−8 For example,
geometry changes are fundamental to the operation of ATP-
fueled molecular motor proteins;6,7 these changes are
associated with multiple cell functions, including intracellular
trafficking,6 active transport,8 cell division,9 signal trans-
duction,10 and protein translocation.10
Inspired by Nature’s example, nonbiological out-of-equili-
brium behavior driven by chemical fuels has recently attracted
considerable attention.11−13 Recent work from Boekhoven,14,15
our group,16,17 Das,18,19 and other researchers20,21 has shown
that carbodiimides, typically EDC (N-(3-(dimethylamino)-
propyl)-N′-ethylcarbodiimide hydrochloride), are useful fuels
for abiotic nonequilibrium behavior. In a typical system,
aqueous carboxylic acids react with carbodiimides to form
carboxylic anhydrides, which subsequently undergo hydrolysis
to regenerate the original carboxylic acids.
Unlike other chemical fuels (e.g., alkylating agents11),
carbodiimides form a transient bond between two independent
components. Consequently, they can be used to form
intramolecular bonds,22 a potentially useful tool for inducing
changes in geometry. Here, we demonstrate a simple system
that undergoes significant changes in the twist about a single
bond on treatment with a chemical fuel.23 Our focus is the
water-soluble diphenic acids shown in Figure 1a. Anhydride
bond formation was expected to lead to a substantial decrease
in the dihedral angle about the biaryl axis. The system acts as a
sort of molecular clamp, distinct from other systems that
undergo nonequilibrium conformational switching.24 Of
Figure 1. (a) Transient anhydride formation in the diphenic acids
used in this work. (b) Model acid and anhydride geometries (R = H,
OHxg removed) optimized at the B97-D3(BJ)/TZV(2d,2p) level and
viewed down the biaryl axis.
Received: August 17, 2020
https://dx.doi.org/10.1021/acs.orglett.0c02757
© XXXX American Chemical Society
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A

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course, this unaggregated, single-molecule system is much
simpler than the ATP-fueled biological systems that serve as its
inspiration, but the fundamental concept is similar.
Scheme 1. Syntheses of Diphenic Acids (a) DP-Ac1 and (b)
DP-Ac2/DP-Ac3
Diphenic acid derivatives DP-Ac1−DP-Ac3 were designed
to include hexaglyme groups for water solubility and a small
selection of R groups to test the ability of the chemistry to
work against steric resistance. DFT geometry optimizations
(B97-D3(BJ)/TZV(2d,2p), gas phase, Figure 1b) show that
the dihedral angle about the biaryl bond in diphenic acid
(ϕacid) is almost orthogonal, as shown in Table 1. Bridging via
Table 1. Biaryl Dihedral Angles of Diphenic Acids and
Their Anhydrides Calculated at the B97-D3(BJ)/
TZV(2d,2p) Level
R
ϕacid (deg)
ϕanhydride (deg)
Δϕ (deg)
H
CCH
CH2CH3
82
91
91
37
44
50
45
47
41
anhydride formation reduces the twist (ϕanhydride), with a net
change Δϕ of 45°. Ethynyl and ethyl substituents ortho to the
biaryl bond increase both ϕacid and ϕanhydride, but the net
change is predicted to be similar in all three cases.
The syntheses of the target compounds began with
commercially available diphenic acid 1, as shown in Scheme
1. The synthesis of DP-Ac1 was straightforward from
compound 4 (Scheme 1a), which was synthesized following
a known procedure.25 The key intermediate for the syntheses
of DP-Ac2 and DP-Ac3, dimethyl 6-bromo-4,4′-dinitro-2,2′-
biphenyldicarboxylate 6, was obtained from the monobromi-
nation of known25 compound 2, using NBS (Scheme 1b). It
was reduced, diazotized, and hydrolyzed to form intermediate
8. Sonogashira coupling with TMS-acetylene introduced the
acetyl group in 9. This intermediate was converted to DP-Ac2
by alkylation, giving 10 (deprotection of the TMS group
occurs simultaneously), followed by saponification. This same
intermediate (10) was subjected to catalytic hydrogenation
and saponification to give DP-Ac3.
The formation of anhydride DP-An1 from DP-Ac1 was first
monitored by in situ infrared (IR) spectroscopy. Treatment of
an aqueous solution of DP-Ac1 with 0.5 equiv of EDC resulted
in the appearance of two peaks at 1775 and 1738 cm−1 (see
Figure S1 in the Supporting Information), which are
characteristic of the symmetric and asymmetric carbonyl
stretching modes of diphenic anhydrides.26 These experiments
were performed at relatively low temperature (278 K) to
decrease the rate of anhydride hydrolysis. Monitoring of the
reaction in D2O by 1H NMR spectroscopy was also consistent
with the effective formation of the anhydride (see Figures S6−
S8 in the Supporting Information). To further confirm that the
transient species is indeed the anhydride, an authentic sample
of DP-An1 was synthesized, fully characterized, and compared
with the experimental results (see the Supporting Informa-
tion). It is evident that formation of the intramolecular
anhydride is dominant under these conditions, presumably
because cyclization is favored at these relatively low
concentrations and steric hindrance disfavors intermolecular
coupling.
We later found water:acetone mixtures to be better solvents
for DP-Ac2 and DP-Ac3 (see discussion below). Accordingly,
the remaining experiments for DP-Ac1 were performed in 7:3
D2O:acetone-d6 at 276 K. A typical reaction of 25 mM DP-Ac1
1
with 40 mM EDC at 276 K, as monitored by H NMR
spectroscopy, is shown in Figure 2a. The DP-Ac1 is rapidly
consumed with the associated appearance of signals assigned to
DP-An1. The EDC was concomitantly converted to EDU (not
shown). The anhydride DP-An1 cleanly hydrolyzes back to its
parent acid DP-Ac1 over the course of minutes. The full time
course of the experiment is shown in Figure 2b.
In previous work, the addition of pyridine was necessary to
avoid unproductive rearrangements of the O-acylisourea
intermediate to the N-acylurea.27,28 For the diphenic acids,
no additives were necessary, as intramolecular ring closure is
presumably fast enough to outcompete the rearrangement. The
system can be “refueled” with additional EDC, with three
cycles shown in Figure S2 in the Supporting Information.
To better understand the mechanism, four kinetic runs were
performed, varying the initial concentration of EDC ([EDC]0).
The data was then fit to a simple kinetic model29−31 that
describes the broad features of the system but lacks some
mechanistic details, such as the pH dependence of the rate
constants and EDC speciation.32 Initial reaction of one
B
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k2
(4)
An → DA
The differential equations describing this mechanism were
fit numerically to the complete dataset for DP-Ac1 (see the
Supporting Information). A representative example of the fit is
shown in Figure 2b. Uncertainties (95% confidence interval)
for the regression were estimated by applying a nonparametric
bootstrapping method27 and were reasonable (see the shaded
area in Figure 2b). The resulting apparent rate constants for
+0.39
the DP-Ac1 system under these conditions are k1 = (8.77
−0.37
× 10−2) mM−1 min−1, k2 = (2.576
× 10−1) min−1, and α =
+0.069
−0.071
+0.08
−0.14
1.13
× 10−1. Confidence contour plots were generated to
confirm the independence of the parameters (see the
Supporting Information).33
While these kinetic parameters fully describe the system, it
can be helpful to translate them into terms that are more
intuitive,27 such as the peak anhydride concentration
([An]max), the acid recovery time (τ99, the time required for
the DP-Ac1 to return to 99% of its starting value), and the
anhydride yield (the net quantity of anhydride produced
relative to the amount of EDC added). For this mechanism,
the yield is dependent on the partitioning of I between the
anhydride (eq 2) and direct hydrolysis (eq 3), and is therefore
a simple function of α (yield = 1/(1 + α)). The DP-Ac1
+2
−6
system is very efficient, with a yield of 90 %.
The peak anhydride concentration and the lifetime are both
dependent on the starting concentrations of acid and
carbodiimide but can be simulated from the parameters. The
results of simulations of the reaction of DP-Ac1 (25 mM) with
variable amounts of starting EDC ([EDC]0) are shown in
Figure 3. As expected, [An]max increases rapidly as [EDC]0
Figure 2. (a) 1H NMR spectroscopy of DP-An1 formation upon the
treatment of DP-Ac1 (25 mM) with EDC (40 mM) in D2O:acetone-
d6 at 276 K. (b) Concentration versus time for the DP-Ac1/DP-An1
system (D2O:acetone-d6, 7:3, 276 K) with the addition of 40 mM
EDC to 25 mM DP-Ac1. Solid lines represent the fits to the kinetic
model and the shaded areas represent 95% confidence intervals for
the fits (in some cases, the CIs are narrow enough to be difficult to
distinguish from the line). Note that the fits were generated by fitting
to all four experiments simultaneously.
Figure 3. Simulated behavior of the DP-Ac1 (25 mM) system with
variable addition of EDC: (a) peak anhydride concentration [An]max
vs [EDC]0 and (b) time to recover 99% of the starting acid (τ99) vs
[EDC]0.
carboxylic acid group in diphenic acid (DA) with EDC is
expected to generate an O-acylisourea intermediate (I) (eq 1).
This intermediate can either react with the remaining acid
group to form the anhydride (and EDU, eq 2), or it can
undergo unproductive decomposition to reform the starting
acid (and EDU, eq 3). The anhydride then hydrolyzes back to
the starting acid (eq 4). A steady-state was assumed in I, which
simplifies the parameters with α = kDi A/kiAn.
increases, approaching a limit near the starting acid
concentration (Figure 3a). Because hydrolysis is relatively
slow compared to activation, it takes relatively little EDC to
push the system to high conversion. The recovery time (τ99)
shows a sharp increase initially with increasing EDC, but then
increases only slowly (see Figure 3b).
We then turned to substituted derivatives DP-Ac2 and DP-
Ac3 to determine the ability of this chemistry to act against
steric resistance, which will affect its usefulness in functional
systems. Upon treatment of both diacids with EDC, we again
k1
(1)
DA + EDC → I
1
observe the formation of new species by H NMR spectros-
kiAn
copy. These were confirmed to be the expected anhydrides
DP-An2 and DP-An3 by comparison with independently
synthesized samples (see the Supporting Information). A data
plot of concentration versus time is shown in Figure 4 (and
(2)
I ⎯⎯⎯→⎯ An + EDU
kiDA
(3)
I ⎯⎯⎯⎯→ DA + EDU
C
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ASSOCIATED CONTENT
* Supporting Information
■
sı
The Supporting Information is available free of charge at
https://pubs.acs.org/doi/10.1021/acs.orglett.0c02757.
Experimental procedures, IR spectra, computational
chemistry details, NMR spectra, details on kinetics
analysis (PDF)
Python program used to analyze kinetics (ZIP)
Computational geometries (TXT)
Concentration versus time data (TXT)
AUTHOR INFORMATION
Corresponding Author
■
C. Scott Hartley − Department of Chemistry & Biochemistry,
Miami University, Oxford, Ohio 45056, United States;
orcid.org/0000-0002-5997-6169; Email: scott.hartley@
miamioh.edu
Figure 4. Representative examples of transient anhydride formation
from substituted diphenic acids (D2O:acetone-d6, 7:3, 276 K): (a)
DP-Ac2 with the addition of 2 equiv EDC and (b) DP-Ac3 with the
addition of 2 equiv of EDC. Note that the initial concentration of
EDC cannot be measured in these systems as its consumption begins
immediately upon mixing outside of the NMR spectrometer.
Authors
Isuru M. Jayalath − Department of Chemistry & Biochemistry,
Miami University, Oxford, Ohio 45056, United States
Hehe Wang − Department of Chemistry & Biochemistry, Miami
University, Oxford, Ohio 45056, United States
Georgia Mantel − Department of Chemistry & Biochemistry,
Miami University, Oxford, Ohio 45056, United States
Lasith S. Kariyawasam − Department of Chemistry &
Biochemistry, Miami University, Oxford, Ohio 45056, United
States; orcid.org/0000-0002-8358-5643
Figures S16 and S17 in the Supporting Information). The
chemistry clearly works effectively: the corresponding anhy-
drides form and decay as expected. The overall time scales of
the reactions are longer, particularly for DP-Ac3. Curiously,
the data obtained for DP-Ac2 and DP-Ac3 indicate that the
hydration of EDC seems to go through two phases: faster very
early but then slowing significantly. This is possibly due to the
changing pD during the reactions as the starting acids are
consumed, although it is not immediately obvious why the
effect is more pronounced for these systems compared to DP-
Ac1.
Complete contact information is available at:
https://pubs.acs.org/10.1021/acs.orglett.0c02757
Author Contributions
The manuscript was written through contributions of all
authors. All authors have given approval to the final version of
the manuscript.
Unfortunately, the NMR data for the substituted derivatives
failed to yield good fits to the simple mechanism described
above. Even after treatment with relatively large amounts of
EDC, the maximum conversion peaks at ∼50%, in contrast to
the unsubstituted system (compare Figures 4 and 2b). There is
evidence that the formation of byproducts, likely intermo-
lecular anhydrides, becomes significant with higher concen-
trations of EDC: some broad unassigned peaks appear and
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This work was supported by the U.S. Department of Energy,
Office of Science, Basic Energy Sciences, under Award No. DE-
SC0018645. The purchase of the 400 MHz NMR
spectrometer was supported by the National Science
Foundation (No. CHE-1919850).
1
disappear during the H NMR experiments in the substituted
systems (see Figure S9 in the Supporting Information), and
more time is needed to fully recover the starting acids DP-Ac2
and DP-Ac3. We believe that these byproducts are the result of
intermolecular oligomerization, because steric hindrance in
DP-Ac2 and DP-Ac3 disfavors cyclization. Unfortunately,
these species could not be characterized or quantified. We are
currently working toward experimental conditions that will
yield cleaner data for these systems. Nevertheless, it is
noteworthy that substantial amounts of anhydride are formed,
even for these more-demanding diacids, which bodes well for
integrating these units within more-complex systems.
Our findings demonstrate that intramolecular anhydrides
can be formed from substituted diphenic acids using EDC as a
chemical fuel, leading to a transient change in the geometry of
the molecule. This provides a simple platform to mimic the
conformational changes observed in biological systems. More
work on optimizing the reaction conditions to better quantify
the behavior of substituted diphenic acids, and the study of
other substituted derivatives, is underway.
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