Complementary double helix formation through template synthesis

Article abstract of DOI:10.1039/c002170a

The dimerization of carboxylic acid derivatives bearing an amino or a formyl group at one end was significantly enhanced in benzene in the presence of an optically active amidine dimer to afford a complementary double helix stabilized with salt bridges.

Full text of DOI:10.1039/c002170a

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Complementary double helix formation through template synthesisw
Hidekazu Yamada,a Yoshio Furusho,*ab Hiroshi Itob and Eiji Yashima*ab
Received 2nd February 2010, Accepted 14th April 2010
First published as an Advance Article on the web 23rd April 2010
DOI: 10.1039/c002170a
The dimerization of carboxylic acid derivatives bearing an
amino or a formyl group at one end was significantly enhanced
in benzene in the presence of an optically active amidine dimer to
afford a complementary double helix stabilized with salt bridges.
group at one end, respectively (Scheme 1). The optically active
dimeric amidine with an azobenzene linker, T,6d was chosen as
the template strand (Scheme 1), because T is compatible in
length to 3. A restricted Hartree–Fock calculation study
suggested that 3 and T could form the hetero-stranded double
helix without any stress or strain (Fig. S5w). The optically
active monomeric amidine, A,6a was also employed for the
control experiments to evaluate the template effect of T on the
complementary duplex formation.
An artificial self-replicating system is the ultimate goal for
synthetic chemists, who have continued to determine and to
identify the principal mechanism of biological systems and to
translate it into synthetic molecular systems.1 Since von
Kiedrowski’s ground-breaking report of the first artificial
self-replicating system,2 several examples of chemical self-
replicating systems have been reported over the last three
decades, although it has not yet been completely achieved.
They involve oligonucleotide analogues,2,3 peptides,4 and
small abiotic organic molecules5 as templates. One of the
key factors necessary for a self-replicating system is a
complementary interaction, which enables the recognition
and transfer of molecular information. Recently, we reported
the rational design and synthesis of artificial hetero-stranded
double helices that consist of complementary molecular
strands intertwined through amidinium-carboxylate salt
bridges.6 Owing to the well-defined geometry and high
association constants of the salt bridges, the double helices
have a significant possibility for further designs and various
types of multiple-stranded helices have already been
successfully prepared. In addition, the helicity of the double
helices is controlled by the optically active substituents on the
amidine groups. As a preliminary step toward truly artificial
self-replication systems, we have started a program to investigate
the effectiveness of the complementary double helical structure
as a replicating field utilizing the salt bridge-based double
helices. In this study, we have synthesized an achiral carboxylic
acid dimer by linking through the imine-bond formation in the
presence of its complementary, optically active dimeric
amidine strand (Fig. 1), and have observed an acceleration
of the imine-bond formation during the complementary
duplex formation. We chose the imine-bond forming reaction
for this study, since it does not necessarily require catalysts
and is well established in modern organic chemistry to form
sophisticated nanostructures.7,8
The imine-bond forming reactions between 1 and 2 in the
presence of T or A were conducted in benzene-d6 at 30 and
50 1C. The reaction progress was first monitored by 1H NMR
spectroscopy (Fig. 2, S1w, and S2w). The 1H NMR (500 MHz,
benzene-d6, 30 1C) spectra of the mixtures of 1 and 2 (0.5 mM)
in the presence of T (0.5 mM) or A (1.0 mM) showed the
resonances of the NH protons in the low magnetic field of ca.
14.5 ppm, indicating the salt bridge formation (Figs. S1w and
S2w). The peak intensity of the aldehyde proton (Ha) decreased
with time, while the benzyl proton peaks (Hb and Hc) newly
appeared and increased with time, both suggesting the
formation of the imine-bond, that is, the complex 3ꢀT and
3ꢀA2, respectively. The formation of the complex 3ꢀT was also
supported by the negative-mode electron-spray ionization
mass (ESI-MS) spectra, which exhibited a molecular ionic
peak at m/z = 2573.4 corresponding to [3ꢀTꢁH]ꢁ (Fig. S3w).
Unfortunately, the peaks derived from the resulting imine
proton of the complex 3ꢀT or 3ꢀA2 overlapped with the
aromatic protons. The benzyl protons (Hb and Hc in Fig. 2)
of the complex 3ꢀA2 appeared as a singlet peak (ca. 4.5 ppm),
indicating that they are virtually chemically and magnetically
equivalent because of the free rotation at the imine-bond
linker of 3. In contrast, the benzylic proton signals of the
complex 3ꢀT appeared as a pair of doublets (ca. 4.3–4.5 ppm).
The non-equivalency of these protons of 3ꢀT is attributed to
the formation of the double helical structure that produces the
chiral environment as well as restricting the rotation at the
linkers.
Time-dependent circular dichroism (CD) and absorption
measurements were then performed to monitor the reaction
We designed and prepared the two achiral carboxylic acid
monomers, 1w and 2w, bearing an aldehyde and an amino
a Department of Molecular Design and Engineering, Graduate School
of Engineering, Nagoya University, Nagoya 464-8603, Japan
b Yashima Super-structured Helix Project, Exploratory Research for
Advanced Technology (ERATO), Japan Science and Technology
Agency (JST), Japan. E-mail: furusho@apchem.nagoya-u.ac.jp,
yashima@apchem.nagoya-u.ac.jp; Fax: +81-52-789-3185
w Electronic supplementary information (ESI) available: Details of
the synthesis, structures, and characterization of compounds 1 and 2.
See DOI: 10.1039/c002170a
Fig. 1 Schematic illustration of an artificial replication system
through complementary double helix formation.
ꢂc
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double helical structure (Fig. S5w). The conversions to 3ꢀT
and 3ꢀA2 at 30 1C were plotted versus the reaction time, as
shown in Fig. 4a. The conversions were estimated by the
changes in the intensities of the CD and absorption spectra,
which were normalized by the CD, absorption, and 1H NMR
spectra of the reference materials.9 As apparent from Fig. 4a,
the imine-bond formation in the presence of the template T
reached equilibrium much faster than that in the presence of A.
Moreover, the template T shifted the equilibrium states to the
imine-bond formation arising from the entropic factors of the
template. Second-order kinetics was assumed as the most
probable mechanism for the present reactions during the
initial stages,10 because the concentration of 1 is equal to that
of 2. The experimental data were fitted to a second-order
kinetic model using eqn (1),
1/C ꢁ 1/C0 = kt
(1)
where C is the concentration of 1 or 2, t is the reaction time,
and k is the reaction rate constant. The rate constant for the
reaction in the presence ofꢁT1 at 30 1C was estimated to be
s , while that in the presence of A
(1.56 ꢃ 0.04) ꢄ 10ꢁ1 Mꢁ1
was (2.58 ꢃ 0.04) ꢄ 10ꢁ2 Mꢁ1 sꢁ1 by the least-squares curve
fitting method. Thus, the reaction was accelerated 6-fold
(k0(T)/k0(A) = 6.0) in the presence of T. To verify the
assumption that the present reactions follow second-order
kinetics, the initial rate constants (k0) were also calculated
from the slope (a) of the linear initial part of the reaction
profiles in Fig. 4a according to eqn (2),
Scheme 1 The imine-bond forming reaction between 1 and 2 in the
presence of the template strand T and monomeric amidine A.
2
k0 = a/C0
(2)
which is valid when [1] = [2]. The k0 values of the reactions
with T and A at a 10% conversion were calculated at 1.31 ꢄ 10ꢁ1
and 2.28 ꢄ 10ꢁ2 Mꢁ1
s
ꢁ1, respectively, which are in good
agreement with those obtained by the curve fitting method,
thus supporting that the reactions obey second-order kinetics
during the initial stage. Similarly, the reaction progress of the
imine-bond formation in the presence of T or A at 50 1C was
plotted versus the reaction time (Fig. S4cw). Both reaction
mixtures reached equilibrium faster than those conducted at
30 1C, while the equilibrium states did not change very much.
The reaction rates during the initial stages were analyzed
based on the assumption that they obey a pseudo-second-
order kinetics, and were estimated to be 1.27 ꢃ 0.03 and
(2.97 ꢃ 0.11) ꢄ 10ꢁ1 Mꢁ1 sꢁ1 for those in the presence of T
and A, respectively (Fig. S4dw), which correspond to a 4-times
acceleration at 50 1C (k0(T)/k0(A) = 4.3). In addition, the
Eyring analysis of the k0 values obtained at different temperatures
(30–50 1C) was used to determine the thermodynamic parameters
for the reaction in the presence of T: DHz = 82.9 ꢃ
Fig. 2 Partial 1H NMR (500 MHz, benzene-d6, 30 1C) spectra of the
mixtures of 1 and 2 (0.5 mM) in the presence of (a) A (1.0 mM) and
(b) T (0.5 mM) during the initial stage of the reaction (top) and after
reaching equilibrium (bottom).
progress at 30 and 50 1C over a period of 72 and 12 h (Fig. 3
and S4w), respectively. In the presence of A, the absorption
spectra slightly changed with time, accompanied by negligible
changes in their CD spectra. On the other hand, in the
presence of T, the absorption spectra gradually changed with
time, accompanied by the enhancement of the negative Cotton
effect, especially in the absorption region of 280–320 nm,
indicating that 3ꢀT most likely adopted a double helical
structure with a helix-sense bias induced by the chiral amidine
groups of T. The restricted Hartree–Fock calculation results
suggested that 3ꢀT could preferably adopt a right-handed
2.7 kJ molꢁ1, DSz = 12.7 ꢃ 9.1 J molꢁ1
K
ꢁ1, and DGz
=
298
79.1 ꢃ 5.4 kJ molꢁ1 (Fig. S8w). It is noted that the enthalpic
contribution (DHz) is much higher than the entropic component
(DSz). The particularly low entropy of activation indicates
organization of the monomers on the template, that is, the
formation of the ternary complex Tꢀ1ꢀ2 contributes to the
acceleration of the reaction.
Finally, the thermodynamic aspect of the template effects
was further investigated by employing a methyl ester derivative
ꢂc
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strand. We believe that double helix formation by the
combination of salt bridges and an imine-bond used in this
study can be applied to the construction of more sophisticated
replicating systems, which is now underway in our laboratory.
Notes and references
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Fig. 3 Time-dependent CD and absorption spectra of the mixtures of
1 and 2 (0.5 mM) in the presence of (a) A (1.0 mM) and (b) T (0.5 mM)
in benzene-d6 at 30 1C. The CD and absorption spectra of T (0.5 mM,
benzene-d6, 30 1C) are also shown in (b). Cell length = 0.1 mm.
7 For recent examples, see: (a) K. S. Chichak, S. J. Cantrill, A. R. Pease,
S.-H. Chiu, G. W. V. Cave, J. L. Atwood and J. F. Stoddart, Science,
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J. S. Moore, J. Am. Chem. Soc., 2007, 129, 4512–4513.
Fig. 4 Time–conversion relationships (a) and kinetic plots (b) of
the imine-bond forming reaction between 1 and 2 in the presence
of T and A at 30 1C.
8 For some examples of template-directed synthesis of DNA derivatives
utilizing imine-bond formation, see: (a) J. T. Goodwin and
D. G. Lynn, J. Am. Chem. Soc., 1992, 114, 9197–9198; (b) Z.-Y.
J. Zhan and D. G. Lynn, J. Am. Chem. Soc., 1997, 119, 12420–12421.
9 Because of the reversible nature of the imine-bond formation,
we could not obtain 3ꢀT and 3ꢀA2 in pure forms. Hence, we
synthesized 3ꢀT and 3ꢀA2 with relatively high conversions as
reference materials using molecular sieves (MS4A). The conversions
of the reference materials were estimated based on the integral
ratios between the aldehyde protons of 1 and the benzyl peaks
of 3ꢀA2 or 3ꢀT in the 1H NMR spectra (Fig. S6w). The CD and
absorption spectra measurements of the reference materials were
also performed (Fig. S7w).
of 1 (4) as an antagonistic competitor to 1 (Fig. S9w). A
solution of equimolar amounts of 1, 2, T, and 4 in benzene-
d6 was heated at 30 1C and the reaction reached equilibrium
within 1 day. The product distribution was determined by the
1H NMR spectrum, which showed that the carboxylic acid
dimer 3 was formed with a high selectivity of ca. 95% over the
ester-containing strand (5).
In summary, we have constructed the complementary
double helix through template synthesis, of which the formation
was significantly accelerated and stabilized by the template
10 Although the imine-bond formation is a reversible reaction, it is
reasonable to assume that it obeys a pseudo-second-order kinetics
during the initial stage, in which the inverse reaction is negligibly small.
ꢂc
This journal is The Royal Society of Chemistry 2010
Chem. Commun., 2010, 46, 3487–3489 | 3489