Mix and match recognition modules for the formation of H-bonded duplexes

Article abstract of DOI:10.1039/c6sc01884j

Oligomeric molecules equipped with complementary H-bond recognition sites form stable duplexes in non-polar solvents. The use of a single H-bond between a good H-bond donor and a good H-bond acceptor as the recognition motif appended to a non-polar backbone leads to an architecture with interchangeable recognition alphabets. The interactions of three different families of H-bond acceptor oligomers (pyridine, pyridine N-oxide or phosphine oxide recognition module) with a family of H-bond donor oligomers (phenol recognition module) are compared. All three donor-acceptor combinations form stable duplexes, where the stability of the 1:1 complex increases with increasing numbers of recognition modules. The effective molarity for formation of intramolecular H-bonds that lead to zipping up of the duplex (EM) increases with decreasing flexibility of the recognition modules: 14 mM for the phosphine oxides which are connected to the backbone via a flexible linker; 40 mM for the pyridine N-oxides which have three fewer degrees of torsional freedom, and 80 mM for the pyridines where the geometry of the H-bond is more directional. However, the pyridine-phenol H-bond is an order of magnitude weaker than the other two types of H-bond, so overall the pyridine N-oxides form the most stable duplexes with the highest degree of cooperativity. The results show that it is possible to use different recognition motifs with the same duplex architecture, and this makes it possible to tune overall stabilities of the complexes by varying the components.

Full text of DOI:10.1039/c6sc01884j

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Mix and match recognition modules for the
formation of H-bonded duplexes†
Cite this: DOI: 10.1039/c6sc01884j
*
Alexander E. Stross, Giulia Iadevaia and Christopher A. Hunter
Oligomeric molecules equipped with complementary H-bond recognition sites form stable duplexes in
non-polar solvents. The use of a single H-bond between a good H-bond donor and a good H-bond
acceptor as the recognition motif appended to a non-polar backbone leads to an architecture with
interchangeable recognition alphabets. The interactions of three different families of H-bond acceptor
oligomers (pyridine, pyridine N-oxide or phosphine oxide recognition module) with a family of H-bond
donor oligomers (phenol recognition module) are compared. All three donor–acceptor combinations
form stable duplexes, where the stability of the 1 : 1 complex increases with increasing numbers of
recognition modules. The effective molarity for formation of intramolecular H-bonds that lead to zipping
up of the duplex (EM) increases with decreasing flexibility of the recognition modules: 14 mM for the
phosphine oxides which are connected to the backbone via a flexible linker; 40 mM for the pyridine
N-oxides which have three fewer degrees of torsional freedom, and 80 mM for the pyridines where the
geometry of the H-bond is more directional. However, the pyridine–phenol H-bond is an order of
magnitude weaker than the other two types of H-bond, so overall the pyridine N-oxides form the most
stable duplexes with the highest degree of cooperativity. The results show that it is possible to use
different recognition motifs with the same duplex architecture, and this makes it possible to tune overall
stabilities of the complexes by varying the components.
Received 29th April 2016
Accepted 24th May 2016
DOI: 10.1039/c6sc01884j
www.rsc.org/chemicalscience
Fig. 1(b) shows the structure of a duplex designed using this
blueprint. The oligomers were prepared using reductive ami-
Introduction
nation chemistry to generate a relatively non-polar backbone:
there are no H-bond donors on the backbone, and the aniline
nitrogen and aryl ether oxygen sites are very poor H-bond
acceptors (b z 4 and 3 respectively compared with 10 for the
phosphine oxide).4 The recognition module is a single H-bond
between a good H-bond donor (phenol, D), and a very good
H-bond acceptor (phosphine oxide, A), which ensures efficient
formation of duplexes with an increase of an order of magni-
tude in the association constant for every recognition unit
added. We have recently shown that the three different back-
bone modules illustrated in Fig. 1(b) can be used interchange-
ably to form duplexes of comparable stability.5
Fig. 2 illustrates the stepwise equilibria involved in assembly
of a duplex. The efficiency of duplex formation is quantied by
the parameter K EM, where K is the association constant for
formation of an intermolecular A$D H-bond, and EM is the
effective molarity for formation of an intramolecular H-bond.6
Cooperative formation of a duplex occurs if the product K EM is
greater than one, because under these conditions, the intra-
molecular assembly channel shown in Fig. 2 is more favourable
than the intermolecular channel that would lead to ill-dened
aggregates (assuming the operating concentration c is less
than EM). The values of EM for the six possible combinations
of the three backbones shown in Fig. 1(b) are all in the range
Synthetic oligomeric molecules equipped with a sequence of
complementary recognition sites are capable of forming duplex
structures reminiscent of the DNA double helix. Many different
examples have been reported using metal ligand coordination,
salt bridges, aromatic stacking interactions and H-bonding as
the recognition sites.1 In most cases, these recognition sites are
built into the backbone of the oligomer and are xed by the
chemistry used to synthesise the molecules. We recently re-
ported a different architecture, which is based on the nucleic
acid blueprint in Fig. 1(a).2 If the recognition sites are appended
as side chains on the backbone, it is possible to vary these
functional groups independently of the rest of the molecule.
Indeed a range of variants on nucleic acids have been prepared
using the same backbone found in DNA but different types of
base-pair.3 This approach therefore offers the potential for
independent optimisation of the backbone, synthesis and
recognition modules highlighted in Fig. 1(a).
Department of Chemistry, University of Cambridge, Lenseld Road, Cambridge CB2
1EW, UK. E-mail: herchelsmith.orgchem@ch.cam.ac.uk
† Electronic supplementary information (ESI) available: Detailed experimental
procedures with spectroscopic characterization data, NMR titration protocols,
titration spectra and results of tting the data to a 1 : 1 binding isotherm. See
DOI: 10.1039/c6sc01884j
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Fig. 1 (a) Blueprint for a duplex-forming molecule. The key design components are the covalent chemistry used for synthesis (red), the non-
covalent chemistry used for recognition (blue), the backbone linker that determines the geometric complementarity of the two chains (black). (b)
The duplex formed by a phenol 4-mer (DDDD) and a phosphine oxide 4-mer (AAAA). Three possible backbone modules are shown. R is
a 2-ethylhexoxy group that provides solubility in toluene. The antiparallel duplex is shown, but the parallel arrangement is also possible.
Fig. 2 Stepwise assembly of a duplex from two complementary oligomers. There is an intermolecular channel that leads to cross-linked
polymeric networks and an intramolecular channel that leads to duplex formation. K is the association constant for formation of an intermo-
lecular interaction between two complementary H-bonding sites (blue bars), EM is the effective molarity for formation of an intramolecular
interaction.
7–20 mM, and the value of K for the phenol–phosphine oxide H-
Results and discussion
Synthesis
bond in toluene is about 300 Mꢀ1, so K EM is greater than one
for all of these systems.2,4,5 Thus duplex formation appears to be
rather insensitive to the conformational properties of the
backbone, provided it has sufficient exibility to accommodate
simultaneous formation of H-bonds at multiple sites.
Synthesis of the H-bond donor oligomers, DD, DDD and DDDD,
has been reported previously (Fig. 3).2 The monomer units used
for synthesis of the H-bond acceptor oligomers were prepared
by coupling the relevant benzaldehyde derivative with aniline 1
(Scheme 1). The pyridine monomer 2 was prepared by reducing
In this paper, we investigate the effects of changing the
recognition module on duplex formation. The oligomers in
Fig. 1(b) use a two-letter recognition alphabet, H-bond donor (D)
and H-bond acceptor (A), and recognition is based on a single
A$D H-bond. These oligomers should therefore be promiscuous:
a H-bond donor oligomer can form a duplex with a variety of
different H-bond acceptor oligomers. Here we compare the
interactions of a family of H-bond donor oligomers with three
different families of H-bond acceptor oligomer based on phos-
phine oxide, pyridine and pyridine N-oxide recognition modules.
the imine formed between
1
and 4-nicotinaldehyde
using NaBH4. The pyridine N-oxide monomer 3 was made by
reductive amination of 1 and 4-formylpyridine-N-oxide using
NaBH(OAc)3.7
The synthesis of 4 has been previously described, and here it
was used as the starting point for growing the H-bond acceptor
oligomer chains (Scheme 2).2 Iterative reductive amination and
acetal deprotection steps were used to synthesise the three
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Scheme 3 (i) 3, NaBH(OAc)3; (ii) HCl.
Fig. 3 Structures of H-bond donor oligomers.
and alcohols are all much weaker H-bond acceptors than pyri-
dine N-oxides, so differences in the nature of the terminal
functional groups in the pyridine N-oxide oligomers do not
signicantly affect the duplex assembly properties of these
systems.
NMR binding studies
The association constants of length-complementary duplexes
were measured by tting 1H NMR titration data in toluene-d8 to
a 1 : 1 binding isotherm (see ESI for details†). Association
constants for the corresponding 1-mer complexes, A$D, were
measured by titrating 4-methylpyridine or 4-methylpyridine
N-oxide into 4-methylphenol in toluene-d8. The association
constants for duplex formation are provided in Table 1, along
with values of EM and K EM calculated using eqn (1).
Scheme 1 (i) Heat; (ii) NaBH4; (iii) NaBH(OAc)3.
pyridine oligomers shown in Scheme 2 (6, 7 and 8). Similarly,
the pyridine N-oxide oligomers 2-mer and 3-mer were syn-
thesised by sequential deprotection and coupling steps (Scheme
3). The pyridine N-oxide 3-mer was isolated as the aldehyde
rather than the acetal (11). The pyridine N-oxide 4-mer proved
difficult to obtain by this route and was therefore prepared by
direct oligomerisation of compound 12 (Scheme 4). Reverse
phase chromatography was used to separate the mixture of
oligomers obtained under reductive amination conditions.
Compound 13 was isolated from this mixture, and reductive
amination with 4 gave the pyridine N-oxide 4-mer with an
alcohol as the terminal functional group (14). Acetals, aldehydes
KN ¼ 2KNEMNꢀ1
(1)
where KN is the association constant for a duplex with N
recognition units, K is the association constant for the A$D
complex that makes a single H-bond, and EM is the effective
molarity for formation of intramolecular H-bonds in the duplex
(assuming that all stepwise intramolecular interactions shown
in Fig. 2 have the same EM).
For both the pyridine and pyridine N-oxide systems, there is
a uniform increase in the stabilities of the complexes with
increasing numbers of recognition units, which is indicative of
Scheme 2 (i) 2, NaBH(OAc)3; (ii) HCl.
Scheme 4 (i) aq. HCl; (ii) NaBH(AcO)3; (iii) NaBH4; (iv) 4, NaBH(AcO)3.
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Table 1 Association constants (KN) and effective molarities (EM) for
formation of 1 : 1 duplexes measured using 1H NMR titrations in
toluene at 298 Ka
Complex
log KN/Mꢀ1
EM/mM
K EM
Pyridine oligomers
A$D
AA$DD
AAA$DDD
AAAA$DDDD
1.5 ꢁ 0.1
2.1 ꢁ 0.1
2.7 ꢁ 0.1
3.6 ꢁ 0.3
—
—
57 ꢁ 8
82 ꢁ 6
110 ꢁ 30
2 ꢁ 1
3 ꢁ 1
4 ꢁ 1
Pyridine N-oxide oligomers
A$D
AA$DD
AAA$DDD
AAAA$DDDD
2.5 ꢁ 0.1
—
—
3.7 ꢁ 0.1
5.0 ꢁ 0.2
6.6 ꢁ 0.2
30 ꢁ 10
40 ꢁ 10
60 ꢁ 10
8 ꢁ 4
12 ꢁ 5
18 ꢁ 6
Fig. 4 Relationship between the association constant for duplex
formation (log KN) and the number of recognition modules in an
oligomer (N). The H-bond acceptor modules are pyridine N-oxide
(red), pyridine (blue) and phosphine oxide (black). The lines of best fit
are shown for each type of duplex: pyridine N-oxide, log KN ¼ 1.4N +
1.1; pyridine, log KN ¼ 0.7N + 0.8; phosphine oxide, log KN ¼ 1.0N +
1.5.
a
Each titration was repeated twice and the average value is reported
with errors at the 95% condence limit.
cooperative H-bonding along the oligomers and fully assembled
duplex formation. This conclusion is consistent with the values
of K EM, which are greater than one in all cases, indicating that
intramolecular H-bonding is favoured over the intermolecular
interactions that would lead to higher order complexes. The
values of EM are almost independent of the length of the olig-
omer for both types of H-bond acceptor, which implies that there
is good geometric complementarity between the two strands of
the duplex in both systems. Although the limiting complexation-
induced changes in 1H NMR chemical shi are small, there are
similar patterns of chemical shi change within the two families
of duplex, which suggests that they have similar structures (see
ESI†). For example, the signals due to the pyridine alpha protons
all show an upeld shi about 0.2 ppm on duplex formation,
and the signals due to the CH2 groups of the nitrobenzyl moie-
ties all show a small downeld shi of about 0.05 ppm.
Fig. 4 compares the properties of pyridine and pyridine N-
oxide duplexes with the phosphine oxide duplexes previously
reported.2 For all three systems, the logarithm of the association
constant for duplex formation (log KN) increases linearly with
the number of recognition units, N. For the phosphine oxide
system, the association constant increases by an order of
magnitude for each additional H-bond (the slope of the corre-
lation in Fig. 4 is 1.0). The slope of the correlation in Fig. 4 is
signicantly larger for the pyridine N-oxide duplexes (1.4) and
signicantly lower for the pyridine duplexes (0.7).
EM for the pyridine duplexes is even higher (80 mM). Although
the pyridine and pyridine N-oxide recognition modules share
the same basic scaffold, the phenol–pyridine H-bond is more
directional than the phenol–pyridine N-oxide H-bond, which in
effect has an additional degree of freedom through variation in
the H-bond geometry. Fig. 5 shows the distribution of phenol–
pyridine N-oxide and phenol–pyridine H-bonding interactions
found in small molecule X-ray crystal structures in the Cam-
bridge Structural Database (CSD).10 The interactions with pyri-
dine all occur at a very well-dened location along the nitrogen
lone pair direction (Fig. 5(b)). In contrast, the interactions with
pyridine N-oxide sample a wide variety of different geometries
(Fig. 5(a)).
Thus the pyridine duplexes are the most highly organised
complexes and have the largest EM, but the intrinsic strength of
the pyridine–phenol H-bond is an order of magnitude weaker
than the H-bonds in the other two types of duplex (log K ¼ 1.5),
and so the overall increase in stability with N is smaller for the
There are two factors that contribute to the relationship
between log KN and N: the value of EM for formation of intra-
molecular H-bonds, and the intrinsic strength of the H-bonding
interactions, which is quantied by the value of K for the 1-mer
A$D complex. The phosphine oxide and pyridine N-oxide olig-
omers make H-bonds of a similar strength (log K ¼ 2.5), but the
average EM for formation of the pyridine N-oxide duplexes
(40 mM) is signicantly larger than the average EM for forma-
tion of the phosphine oxide duplexes (14 mM). This result can
be explained by the fact that the phosphine oxide recognition
modules have more conformational degrees of freedom than
the pyridine N-oxide modules. In general, more rigid and pre-
organised structures lead to higher values of EM.8,9 The average
Fig. 5 Distribution of phenol OH groups around (a) pyridine N-oxide
H-bond acceptors and (b) pyridine H-bond acceptors in the CSD. Data
from IsoStar 2.2.3 for contacts that are closer than the sum of the van
der Waals radii and plotted using the symmetry-expanded display. For
the phenol–pyridine system, there are a small number of examples
cases (right) that do not correspond to H-bonding interactions.
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pyridine duplexes: the average K EM is 3 compared with 5 and
13 for the phosphine oxide and pyridine N-oxide duplexes
respectively. For all three types of duplex, there is a small but
consistent increase in EM with N, which might suggest some
additional cooperativity due to nucleation of a more highly
organised duplex structure as the chains grow longer. However,
the increases in EM are close to the error margins, so it is
difficult to draw any denite conclusions.
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Conclusions
If two oligomeric chains are functionalised with complementary
recognition sites, they will interact to form a duplex provided
the product K EM is greater than one: K is the association
constant for a single intermolecular interaction between two
complementary recognition sites and depends on the nature of
the functional groups involved; EM is the effective molarity for
intramolecular interactions that lead to zipping up of the
duplex and depends on the geometric complementarity and
complementarity of the backbone chains. In previous work, we
have shown that duplex formation is tolerant of changes in the
backbone, which lead to rather small variations in EM (7–20
mM). In this paper, we have investigated changes in the
recognition modules. H-Bond donor oligomers bearing phenol
recognition groups form stable duplexes with three different
types of H-bond acceptor oligomer bearing phosphine oxide,
pyridine or pyridine N-oxide recognition groups. In all three
cases, the stability of the duplexes increase with increasing
numbers of recognition sites in the oligomers indicating
cooperative duplex assembly. However, the different recogni-
tion modules are found to affect EM as well as K. Phenol–pyri-
dine N-oxide and phenol–phosphine oxide H-bonds are both an
order of magnitude stronger than phenol–pyridine H-bonds in
toluene, and the stronger interactions lead to more stable
duplexes. Due to differences in conformational exibility, the
EM for duplex assembly is greater for the pyridine oligomers (80
mM) than for the pyridine N-oxide oligomers (40 mM), which in
turn have a greater EM than the phosphine oxide oligomers (14
mM). As a result, the pyridine N-oxide oligomers form the most
stable duplexes, due a combination of high K and high EM.
These systems demonstrate that it is possible mix and match
both the backbone and the recognition modules in synthetic H-
bonded duplexes making them particularly versatile and robust
supramolecular assembly motifs. The use of a single donor–
acceptor H-bond as the recognition element provides these
systems an unusual degree of promiscuity making it possible to
switch between different donor–acceptor recognition alphabets.
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Acknowledgements
We thank the EPSRC and ERC for funding.
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