Hydrogen-Bonded Duplexes with Lengthened Linkers

Article abstract of DOI:10.1021/acs.orglett.8b00283

Connecting basic hydrogen-bonding units with lengthened flexible or rigid linkers generates oligoamide strands that carry new H-bonding sequences and association specificity, leading to H-bonded homo- and heteroduplexes with association constants in the 1

Full text of DOI:10.1021/acs.orglett.8b00283

Letter
pubs.acs.org/OrgLett
Cite This: Org. Lett. XXXX, XXX, XXX−XXX
Hydrogen-Bonded Duplexes with Lengthened Linkers
Yukun Zhang,†,‡,⊥ Ruikai Cao,§,⊥ Jie Shen,∥ Cadnel S. F. Detchou,§ Yulong Zhong,§ Heng Wang,†,‡
Sheng Zou,† Qingfei Huang,† Chunxia Lian,† Qiwei Wang,† Jin Zhu,*,† and Bing Gong*,§
†Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
‡Graduate University of Chinese Academy of Sciences, Beijing 100049, China
§Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
∥Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, 138669, Singapore
S
* Supporting Information
ABSTRACT: Connecting basic hydrogen-bonding units with
lengthened flexible or rigid linkers generates oligoamide
strands that carry new H-bonding sequences and association
specificity, leading to H-bonded homo- and heteroduplexes
with association constants in the 104 M−1 range in chloroform.
Computational and experimental studies indicate that in
duplexes with rigid aromatic linkers the oligoamide strands
adopt bent conformations that allow the formation of
interstrand H-bonds and accommodate the introduced
aromatic liners, offering a new series of association units.
he control of molecular association is essential for
Timplementing noncovalent synthesis, i.e., predictably
organizing molecular components into supramolecular assem-
blies.1 Many H-bonded complexes, such as those first studied
by Jorgensen and Zimmerman2 and soon developed by
Zimmerman and Meijer3 and many others,4 are known. The
majority of these complexes are based on heterocycles and have
Figure 1. Examples of known H-bonded duplexes with four
interstrand H-bonds.
evolved from those having limited strength and being
complicated by interconverting tautomers to ones with great
strength and high specificity.4 For example, highly stable H-
bonded complexes5,6 served as association units in constructing
supramolecular polymers1b,f,7 and other molecular architec-
tures.8
association constants (Ka’s) in the 104 M−1 range, while those
with six H-bonds have Ka’s in the 109 M−1 range.
In addition to binding strength, the effectiveness of H-
bonded complexes as association units also depends on their
specificity. Our H-bonded duplexes allow the tuning of
association specificity by combining different types of H-
bonding benzene units;9 or by replacing benzene units with
naphthalene residues.12 With their tunable affinity and
sequence-specificity, our H-bonded duplexes, along with related
systems developed by others, have instructed the formation of
β-sheets,13 supramolecular (noncovalent) block copoly-
mers,1b,f,h,7,14,15 the specification of chemical reactions,16 and
other applications.17
We developed a series of H-bonded duplexes consisting of
linear oligoamide strands.1d,9,10 Basic H-bonding units linked
via glycine residues result in oligoamide strands having H-
bonding sequences defined by arrays of H-bond donors (D)
and acceptors (A). An oligoamide specifically pairs with
another strand carrying a complementary H-bonding sequence,
leading to self-complementary duplexes such as the quadruply
H-bonded 1·1, 2·2, or heterocomplementary duplexes such as
3·4 (Figure 1) and their longer analogues.9
Our H-bonded duplexes are free of tautomerism that
typically accompanies heterocycle-based complexes. Secondary
electrostatic interactions, which accompany most known H-
bonded complexes and result in association strengths that rely
on both the number of H-bonds and the specific H-bonding
sequences,11 are absent in our system. Thus, the stabilities of
our duplexes are proportional to the number of interstrand H-
bonds. In CHCl3, duplexes with four interstrand H-bonds have
Rather than varying the arrangement of H-bond donors and
acceptors to generate new H-bonding sequences, which
requires the incorporation of multiple types of H-bonding
units, such as those derived from naphthalene, that offer limited
Received: January 26, 2018
© XXXX American Chemical Society
A
DOI: 10.1021/acs.orglett.8b00283
Org. Lett. XXXX, XXX, XXX−XXX

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Letter
1
availability, duplexes with new association specificity may be
generated by adjusting the spacing between linked basic H-
bonding units that are readily available. Specifically, replacing
glycine residues with longer linkers will widen the spacing
between adjacent H-bonding units, which will generate new
association specificity, including new sequences.
Table 1. Association Constants Obtained from H NMR
Dilution Experiments
a
complex
K (M−1
)
complex
K (M−1
)
b
5′·5′
25
6·6
7·7
6·7
(2.6 0.4) × 102
(1.8 0.2) × 10
(4.3 0.8) × 104
5a·5a
5b·5b
(3.2 0.1) × 102
(3.0 0.5) × 104
Oligoamide 5a was first designed and examined (Figure 2).
Based on coupling steps we reported before for preparing
a
Measured based on dilution experiments in CDCl3 at room
temperature. Errors are based on values of association constants
b
obtained from triplicate runs. Value from ref 10a.
Our original quadruply H-bonded duplexes have association
constants that are 2 orders of magnitude, i.e., in the 104 M−1
range,10 larger than the dimerization constant of 5a·5a. The low
stability of 5a·5a, which impairs its effectiveness as an
association unit, can be attributed to the linker based on 4-
aminobutyric acid. Compared to glycine, this longer linker
increases the conformational freedom of 5a and thus enhances
the entropic barrier for forming 5a·5a.
To address the low stability of 5a·5a and its analogues,
strands 5b, 6, and 7 were designed by connecting basic H-
bonding units derived from 5-aminosalicylic acid with linkers
based on the readily available m-aminobenzoic acid, isophthalic
acid, and m-phenylenediamine (Figure 4). These rigid linkers
Figure 2. Oligoamide strand 5a and its H-bonded duplex 5a·5a. The
structure of previously reported 5′10a is also shown. Cross-strand
NOEs revealed by the NOESY are shown with double-headed red
arrows.
strands 1 through 4,10 H-bonding units derived from 5-
aminosalicylic acid were connected with a linker derived from
4-aminobutyric acid into 5a (Scheme S1 and the Supporting
Information (SI)). With its ADAD array, strand 5a should
dimerize into H-bonded duplex 5a·5a.
At 10 mM in CDCl3, the 1H NMR signals of amide protons a
(at 9.24 ppm) and c (at 9.76 ppm) of 5a move downfield with
respect to the aniline NH signal (at 7.91 ppm) of 5′ that
undergoes very weak self-association,10a suggesting that protons
a and c engage in enhanced H-bonding interactions. The
involvement of protons a and c in intermolecular H-bonding is
demonstrated by the shifts of their signals with concentrations.
As shown in Figure 3a, from 0.10 to 50 mM, the resonances of
Figure 4. Design of oligoamide strands (a) 5b, and (b) 6, and 7 and
their corresponding H-bonded duplex 5b·5b and 6·7.
should reduce conformational flexibility and also ensure
extended conformations on the oligoamide strands, which
facilitate the pairing of these strands into duplexes. Duplex 5b·
5b, like 5a·5a, shares the same H-bonding sequence (ADAD)
with 1·1 while having association specificity different from 1·1
because of the widened spacing between its two basic H-
bonding units. Another advantage of incorporating the rigid
aromatic linkers is that H-bonding sequences, such as ADDA
and DAAD, of 6 and 7, that cannot be generated with our
previous designs based on glycine linkers, are now available.
A potential problem with 5b·5b and 6·7 is that the two
benzene rings that serve as the linkers in each duplex could
impose steric hindrance that may obstruct the formation of the
duplex. This possible complication was ruled out computation-
ally. The energy-minimized structures of 5b·5b and 6·7,
obtained by calculation at the B3LYP/6-31G(d,p) level of
theory with chloroform as the solvent (Figure 5), indicate that
Figure 3. Concentration-dependent change in the chemical shifts of
protons a, b, c, and d of (a) 5a and (b) 5b. Each of the chemical shift
values is the average of those from triplicate runs.
protons a and c show downfield shifts of 1.3 ppm and ∼0.5
ppm, respectively. In contrast, protons b and d, which form
intramolecular H-bonds, have negligible shifts in the same
concentration range. Nonlinear regression analysis10 of the
concentration-dependent chemical shift values of proton c
yielded a dimerization constant of 322 10 M−1 for 5a (Table
1) that is much larger than that of 5′ (∼25 M−1 in CDCl3).10a
The formation of duplex 5a·5a is confirmed by the NOESY
spectrum of 5a (10 mM) recorded in CDCl3 (Figure S1),
which revealed cross-strand NOEs between protons a and h, c
and i, and g and h, that are consistent with the expected
antiparallel alignment of two strands of 5a (Figure 2).
Figure 5. Energy-minimized structures of (a) duplex 5b·5b and 6·7.
All side and end groups are replaced with methyls. H-bonds are
indicated as dashed green lines.
B
DOI: 10.1021/acs.orglett.8b00283
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Organic Letters
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the two benzene rings of the central linker indeed face each
other, but with one ring being “lifted” and the other being
“pushed down”. This leads to bent conformations for the
individual strands, which accommodate both the interstrand H-
bonds and the stacking of the aromatic linkers. In each duplex,
the benzene rings of the linkers are parallel and within stacking
distance (∼3.8 Å), which may provide additional stability.
Strands 5b, 6, and 7 were synthesized based on procedures
similar to those we reported before10 (Scheme S1 and the SI).
confirms the 1:1 stoichiometry for the association of 6 and 7
and thus the formation of duplex 6·7.
1
In CDCl3, the H resonances of protons a and c (9.86 and
10.01 ppm) of 5b (10 mM) show significant downfield shifts
relative to the aniline NH resonance of compound 5′ (at 10
mM, 7.91 ppm), indicating the involvement of these protons in
intermolecular H-bonding interactions.
Figure 6. Job plot of 6 and 7 in CDCl3. The total concentration of 6
and 7 was kept at 5 mM.
Diluting 5b in CDCl3 (from 50 to 0.16 mM) revealed
significant shifts of amide protons a and c (Figure 3b). In
contrast, the 1H signals of intramolecularly H-bonded protons b
and d exhibit negligible shifts in the same concentration range
(Figure 3b). Nonlinear regression analysis of the concentration-
dependent changes in the chemical shifts of proton c yielded a
The NOESY spectrum of 5b·5b, measured in CDCl3 (10
mM, 400 MHz, 300 K, mixing time = 0.3 s), reveals NOEs
between protons a and f, c and e, and g and h (Figure S2). The
ROESY spectrum of 6·7, measured in CDCl3 (5.5 mM of each
strand, 400 MHz, 298 K, mixing time = 0.3 s), shows ROEs
between protons a and f, a and i, e and f, and g and h (Figure
S3). Since within each single strand the distance between each
pair of protons is too long to give the observed NOE or ROE
cross-peak, the detected cross-peaks must correspond to
interstrand contacts between otherwise remote protons that
are placed into close proximity in the duplexes.
By widening the spacing between basic H-bonding units,
oligoamide strands carrying H-bonding sequences that defined
new association specificity are generated. The limitation of a
linker derived from 4-aminobutyric acid, which results in
lowered stability and thus renders duplex 5a·5a and its
analogues ineffective as association units, is overcome by
incorporating aromatic linkers based on meta-disubstituted
benzene residues. Instead of introducing steric hindrance that
would obstruct the association of the individual strands, the
aromatic linkers, being placed within stacking distances, do not
compromise the formation of H-bonded homoduplexes 5b·5b
and heteroduplex 6·7. The H-bonded duplexes described
herein have expanded the diversity of H-bonded duplexes with
new association specificity or new H-bonding sequences. More
interestingly, this series of duplexes, with their aromatic linkers
that can be further tuned electronically, may provide a platform
for incorporating and specifying noncovalent forces besides H-
bonding, which may lead to the creation of association units
that operate in media in which H-bonding is ineffective.
dimerization constant of (3.0
0.5) × 104 M−1 (Table 1).
Thus, replacing the flexible linker of 5a with a rigid aromatic
one results in strand 5b with a dimerization constant that is in
line with those of quadruply H-bonded duplex 1·1, 2·2, or 3·4.
Upon mixing 6 and 7 (1:1, 2.5 mM/strand) in CDCl3, amide
proton a of 6 moved downfield, from 9.00 ppm for the single
strand to 10.00 ppm for the 1:1 mixture. Proton c of 7 also
showed a downfield shift from 7.27 ppm of the single strand to
9.22 ppm of the 1:1 mixture. In contrast, protons b and d,
which are intramolecularly H-bonded, experienced much
smaller shifts (0.32 and 0.12 ppm) between the single strands
and the 1:1 mixture. These observations demonstrate that 6
and 7 associate via intermolecular H-bonding.
The 1H NMR signal of an aromatic proton located near (≤7
Å) another aromatic ring is known to move upfield18 that
indicates parallel stacking of the two aromatic rings.19 The
resonance of proton e shifts 0.43 ppm upfield, from 7.56 ppm
of single strand 6 to ppm 7.13 of duplex 6·7. Aromatic proton f
of 7 should undergo similar shift upon mixing 6 and 7 although
its signal could not be assigned due to signal overlap. The
upfield shift of proton e demonstrates that the aromatic rings of
the linkers are brought into close proximity, which is consistent
with the optimized structure of 6·7.
The 1:1 mixture of 6 and 7 in CDCl3 was diluted from 40
mM to 0.078 mM, and the concentration-dependent shifts of
amide proton a of 6 was fitted to a 1:1 binding motif,10,20 which
revealed an association constant of (4.3
0.8) × 104 M−1
ASSOCIATED CONTENT
* Supporting Information
■
(Table 1). The self-association of strands 6 or 7 was probed by
diluting a solution of either strand in CDCl3 from 40 mM to
0.156 mM. The concentration-dependent shifts of proton a of 6
and proton c of 7 led to “dimerization” constants of 260 44
M−1 for 6 and 18 2 M−1 for 7 (Table 1). In comparison to
the association constant of 6 and 7, the self-association of 6 or 7
is either much weaker or negligible, and thus has little effect on
the formation of heteroduplex 6·7.
S
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.or-
glett.8b00283.
Synthetic procedures; analytical data; NMR spectra;
computational details (PDF)
The difference in the chemical shifts (Δδ) of amide proton c
of 7 in a series of solutions with different molar fractions of 7
(X7) and that of single strand 7 in CDCl3 was monitored, while
the total molar concentration of the two strands was held
constant at 5 mM. The values of Δδ·X7, which is proportional
to the complex of 6 and 7,21 are plotted against X7 (Figure 6).
The resultant Job plot exhibits a peak with X7 being 0.5, which
AUTHOR INFORMATION
Corresponding Authors
■
*E-mail: bgong@acsu.buffalo.edu.
*E-mail: jinzhu@cioc.ac.cn.
ORCID
Bing Gong: 0000-0002-4155-9965
C
DOI: 10.1021/acs.orglett.8b00283
Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
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Author Contributions
⊥Y.Z. and R.C. contributed equally.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We thank the US National Science Foundation (CBET-
1512164), American Chemical Society-Petroleum Research
Fund (PRF No. 58364-ND7), and Biomedical Research
Council, Agency for Science, Technology and Research of
Singapore, for support.
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D
DOI: 10.1021/acs.orglett.8b00283
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