First zipper-featured molecular duplexes driven by cooperative donor-acceptor interaction

Article abstract of DOI:10.1021/ol034549p

(Matrix presented) The first class of zipper-shaped artificial duplexes, which are driven by multiple donor-acceptor interactions between electron-rich 1,5-dioxynaphthalene or 1,4-dioxybenzene and electron-deficient pyromellitic dimide units, have been st

Full text of DOI:10.1021/ol034549p

ORGANIC
LETTERS
2003
Vol. 5, No. 11
1955-1958
First Zipper-Featured Molecular
Duplexes Driven by Cooperative
Donor−Acceptor Interaction
Qi-Zhong Zhou,† Xi-Kui Jiang,† Xue-Bin Shao,† Guang-Ju Chen,‡ Mu-Xin Jia,‡ and
,†
Zhan-Ting Li*
Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences,
354 Fenglin Lu, Shanghai 200032, China, and Department of Chemistry,
Beijing Normal UniVersity, Beijing 100875, China
ztli@pub.sioc.ac.cn
Received March 29, 2003
ABSTRACT
The first class of zipper-shaped artificial duplexes, which are driven by multiple donor−acceptor interactions between electron-rich 1,5-
dioxynaphthalene or 1,4-dioxybenzene and electron-deficient pyromellitic dimide units, have been studied in organic media by 1H NMR, UV−
vis, and vapor pressure osmometry. 1H NMR binding investigations reveal substantial cooperativity of the donor−acceptor interaction in the
duplexes.
Self-assembly of linear molecules into double, triple, and
higher order multistranded complexes is a common structural
motif in biological systems. Biological zipper motif is of
fundamental importance for self-replication, fiber behavior,
and formation of functional multicomponent complexes.1 In
the past decade, synthetic zipper systems have received
increasing attention for mimicking biological structures and
self-assembly of functional supramolecular structures. Metal
ion-ligand coordination,2,3 electrostatic interaction,4 and
intermolecular hydrogen bonds5,6 have been successfully
utilized to construct a number of discrete bimolecular zippers.
However, to our knowledge, no stable linear synthetic
duplexes, induced by donor-acceptor interaction, have ever
been reported. We describe here the first class of donor-
acceptor interaction-driven duplexes with a zipper-like bind-
ing motif.
It has been well-established that electron-rich 1,5-dialkoxy-
naphthalene and electron-deficient pyromellitic dimide (PDI)
(4) (a) Schmuck, C.; Heil, M. Org. Lett. 2001, 3, 1253. (b) Sanchez-
Quesada, J.; Seel, C.; Prados, P.; de Mendoza, J.; Dalcol, I.; Giralt, E. J.
Am. Chem. Soc. 1996, 118, 277.
(5) (a) Carver, F. J.; Hunter, C. A.; Jones, P. S.; Livingstone, D. J.;
McCabe, J. F.; Seward, E. M.; Tiger, P.; Spey, S. E. Chem. Eur. J. 2001,
7, 4854. (b) Bisson, A. P.; Carver, F. J.; Eggleston, D. S.; Haltimanger, R.
C.; Hunter, C. A.; Livingstone, D. L.; McCabe, J. F.; Rotger, C.; Rowan,
A. E. J. Am. Chem. Soc. 2000, 122, 8856.
(6) (a) Corbin, P. S.; Zimmerman, S. C.; Thiessen, P. A.; Hawryluk, N.
A.; Murray, T. J. J. Am. Chem. Soc. 2001, 123, 10475. (b) Gong, B.; Yang,
Y.; Zeng, H.; Skrzypczak-Jankunn, E.; Kim, Y. W.; Zhu, J.; Ickes, H. J.
Am. Chem. Soc. 1999, 121, 5607. (c) Beijer, F. H.; Sijbesma, R. P.;
Kooijman, H.; Spek, A. L.; Meijer, E. W. J. Am. Chem. Soc. 1998, 120,
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† Shanghai Institute of Organic Chemistry.
‡ Beijing Normal University.
(1) Horton, R. H.; Moran, L. A.; Ochs, R. S.; Rawn, D. J.; Scrimgeour,
G. K. Principles of Biochemistry; Prentice Hall Internaltional, Inc.: London,
UK, 1992.
(2) (a) Fatin-Rouge, N.; Blanc, S.; Pfeil, A.; Rigault, A.; Albrecht-Gary,
A.-M.; Lehn, J.-M. HelV. Chim. Acta 2001, 84, 1694. (b) Berl, V.; Huc, I.;
Khoury, R. G.; Lehn, J.-M. Chem. Eur. J. 2001, 7, 2810.
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10.1021/ol034549p CCC: $25.00 © 2003 American Chemical Society
Published on Web 05/02/2003

could form a donor-acceptor complex.7 In recent years, this
kind of noncovalent interaction has been utilized to self-
assemble neutral [2]catenanes by using macrocyclic crown
ether, incorporated with two 1,5-dioxynaphthalene units, as
a template.8,9 We envisioned that structurally matched linear
molecules incorporated with multiple electronic donor or
acceptor units might also be used to generate new stable
dimers through multisite binding. Therefore, compounds 1
and 2 were designed.
Scheme 1. The Synthesis of Monomers 1 and 2
The synthesis of 1 and 2 is outlined in Scheme 1.
Compound 3 was first alkylated to afford 4, which reacted
with ethyl bromoacetate to produce ester 5. Subsequent
hydrolysis followed by treatment of the resulting acid with
oxalyl chloride produced intermediate 6. Compound 6 reacted
with butylamine or diol 7 in the presence of triethylamine
in chloroform to afford the desired naphthalene derivatives
1a and 1b-d, respectively. The synthesis of 2 proceeded
with acyl chloride 10 as the key intermediate. Compound 8
first reacted with n-dodecylamine and glycine in refluxing
DMF10 to afford acid 9, which was readily converted to 10
with oxalyl chloride. Compound 10 reacted with butylamine
or diol 7 under the conditions described for the synthesis of
1, leading to the formation of 2a or 2b-d, respectively. The
introduction of the long dodecyl groups to compounds 1b-d
and 2b-d provides them good solubility in common organic
solvents such as chloroform and dichloromethane, making
both series of monomers ideal for 1H NMR binding analysis.
1H NMR dilution experiments in CDCl3 from ca. 40 mM
to ca. 0.3 mM were first performed for compounds 1 and 2,
which revealed no pronounced chemical shifts (e0.03 ppm)
for the aromatic protons. These observations indicate that
these compounds do not self-aggregate substantially in
chloroform.11 Quantitative binding studies were then carried
out in CDCl3 solutions by titrating acceptors 2a-d with
1a-d and observing the changes in the chemical shifts of
H-1 or H-2 of 2a-d.12 These protons exhibited sharp signals
within the investigated concentration range. In contrast, the
signals of the naphthalene protons in compounds 1a-d
overlapped each other, and were not suitable for titration
analysis. Figure 1 shows as an example the titration curve
for the H-1 signal of 2c (0.5 mmol) during titration with 1c
(from 0.1 to 40 mmol). The association constants (Kassoc
)
for complexes 1‚2 in CDCl3 were calculated by the fitting a
function containing Kassoc as a variable parameter to the
(7) (a) Hamilton, D. G.; Lynch, D. E.; Byriel, K. A.; Kennard, C. H. L.;
Sanders, J. K. M. Aust. J. Chem. 1998, 51, 441. (b) Hamilton, D. G.; Lynch,
D. E.; Byriel, K. A.; Kennard, C. H. L. Aust. J. Chem. 1997, 50, 439. (c)
Peover, M. E. Trans. Faraday Soc. 1962, 58, 2370.
(8) (a) Hamilton, D. G.; Feeder, N.; Prodi, L.; Teat, S. J.; Clegg, W.;
Sanders, J. K. M. J. Am. Chem. Soc. 1998, 120, 1096. (b) Hamilton, D. G.;
Davies, J. E.; Prodi, L.; Sanders, J. K. M. Chem. Eur. J. 1998, 4, 608. (c)
Hamilton, D. G.; Sanders, J. K. M.; Davies, J. E.; Clegg, W.; Teat, S. J.
Chem. Commun. 1997, 897.
(9) (a) Philp, D.; Stoddart, J. F. Angew. Chem., Int. Ed. Engl. 1996, 35,
1154. (b) Amabilino, D. B.; Stoddart, J. F. Chem. ReV. 1995, 95, 2725.
(10) (a) Nagata, T. Bull. Chem. Soc. Jpn. 1991, 64, 4; 3005. (b) Hunter,
C. A.; Sanders, J., K. M.; Beddard, G. S.; Evans, S. J. Chem. Soc., Chem.
Commun. 1989, 1765.
(11) (a) Tobe, Y.; Utsumi, N.; Kawabata, K.; Nagano, A.; Adachi, K.;
Araki, S.; Sonoda, M.; Hirose, K.; Naemura, K. J. Am. Chem. Soc. 2002,
124, 5350. (b) Cubberley, M. S.; Iverson, B. L. J. Am. Chem. Soc. 2001,
123, 7560.
(12) The H-1 and H-2 signals of 2c could be easily assigned by comparing
their 1H NMR integral intensities, while the two sharp Ar-H signals of 2d
could not be differentiated by 1H NMR and one of them was used for
titration analysis.
(13) (a) Conners, K. A. Binding Constants: The Measurement of
Molecular Complex Stability; Wiley: New York, 1987. (b) Wilcox, C. S.
In Frontiers in Supramolecular Organic Chemistry and Photochemistry;
Schneider, H.-J., Du¨rr, H., Eds.; VCH: New York, 1991; p 123.
1956
Org. Lett., Vol. 5, No. 11, 2003

It was envisioned that replacing the PDI unit in 2 with
the naphthalene-1,8:4,5-tetracarboxydiimide (NDI) unit,16
a
more electron-deficient acceptor than PDI, should lead to
the construction of heterodimers of similar binding motif but
with higher binding stability. Therefore, compounds with the
skeletons of 2b-d but incorporating two to four NDI units
have also been prepared. However, these compounds were
found to be insoluble in organic solvents such as chloroform
and DMSO and a quantitative binding study with compounds
1 could not be performed.
Then, another four donor molecules 11a, 11b, 16a, and
16b were prepared, as outlined in Scheme 2, to investigate
Scheme 2. The Synthesis of Monomers 11 and 16
Figure 1. 1H NMR titration curves of 2c with 1c (b) and 11b (9)
(vide infra) in CDCl3 at room temperature.
experimental data and are summarized in Table 1.13,14 The
1:1 binding stoichiometry of the complexes was proved by
the Job’s plot of the probe signals vs the mole fraction of 1
in the mixture solution, in which the maximum chemical
shift change was observed at 0.5 mol fraction.15 The Kassoc
values of complex 1b‚2c in solvents of higher polarity were
also obtained and are provided in Table 1.
Several important features can be found for the new class
of heterodimers from Table 1: (1) The association constants
increase substantially with the increase of the number of the
aromatic units in both 1 and 2. (2) For complexes with a
totally identical number of aromatic units, the complexes
consisting of longer 1 and shorter 2 are usually more stable
than those consisting of shorter 1 and longer 2. For example,
the Kassoc of complex 1c‚2b is considerably larger than that
of complex 1b‚2c. (3) The stability of the complexes is
reduced with the addition of solvents of high polarity, such
as methanol-d, acetone-d6, and DMSO-d6. This observation
suggests that the formation of the new complexes is mainly
driven by the intermolecular donor-acceptor interaction but
not by the possible solvophobic interaction, although Iverson
et al. had demonstrated that solvophobic interaction was the
major driving force for a similar, simpler dimeric system.11b
Table 1. Association Constants (Kassoc) of Novel
Donor-Acceptor Interaction-Driven Artificial Heterodimers 1·2
in CDCl3 at Room Temperaturea
the diversity of the new binding motif. In brief, treatment of
amines 10a and 10b with 6 and base afforded 11a and 11b,
respectively, while 16a and 16b were prepared starting from
1217 with use of the methods described for the synthesis of
1. Both compounds 11 and 16 are soluble in chloroform.
complex
K
assoc (M-1
)
complex
Kassoc (M-1
)
1a ‚2a
1b‚2a
1c‚2b
1c‚2b
1c‚2b
1c‚2b
1c‚2c
1c‚2d
10
40
670
450b
360c
380f
1200
3100
1a ‚2b
1b‚2b
1b‚2c
1c‚2b
1c‚2b
1c‚2b
1d ‚2c
1d ‚2d
25
130
290
500d
290g
410e
4200
8800
(14) Table 1 lists the association constants of the 1:1 complexes, which
consist of 1 and 2 incorporating the same number of aromatic units, or
with one more or less aromatic units compared to each other. The
complexing behavior of 1 toward 2 with more or less than one number of
aromatic units was also investigated in CDCl3. Although an important
change of the chemical shifts of the H-1 of 2 was also exhibited, no good
results of association constants could be derived by fitting to a nonlinear
binding equation appropriate for a 1:1 or 1:2 binding model, revealing that
more complicated binding models might exist.
a With an error e20%. b With 10% CD3OD (v/v). c With 20% CD3OD
(v/v). d With 10% CD3COCD3 (v/v). e With 20% CD3OD (v/v). f With 10%
CD3SOCD3 (v/v).). g With 20% CD3SOCD3 (v/v).
(15) Job, P. Ann. Chim. Ser. 10 1928, 9, 113.
Org. Lett., Vol. 5, No. 11, 2003
1957

The binding study of 11 and 16 toward 2b-d in CDCl3
was then carried out by 1H NMR titration of 2b-d with 11
and 16. The corresponding association constants Kassoc are
derived by nonlinear regression for a 1:1 binding model and
provided in Table 2. It can be found that 11a and 11b exhibit
Table 3. Molar Extinction Coefficients (ꢀ) of the 1:1
Complexes in Chloroform at [Monomer] ) 0.016 M at Room
Temperature
ꢀ
λmax
ꢀ
λmax
complex
(M-1 cm-1
)
(nm) complex (nm) (M-1 cm-1
)
1a ‚2a a,19
1c‚2c
11a ‚2c
16a ‚2c
11b‚2d b
12
118
155
65
441
452
450
430
451
1b‚2b
1d ‚2d
11b‚2d
16b‚2d
30
225
260
110
449
440
445
433
Table 2. Association Constants (Kassoc) of Donor-Acceptor
Interaction-Driven Heterodimers 11·2 and 16·2 in CDCl3
a
complex
K
assoc (M-1
)
complex
Kassoc (M-1
)
180
11a ‚2b
11a ‚2c
11a ‚2d
16b‚2c
16b‚2d
700
1800
3300
260
11b‚2c
11b‚2d
16a ‚2b
16a ‚2c
16a ‚2d
4300
11000
90
210
350
a Obtained at [monomer] ) 0.05 M. b Obtained at [monmomer] ) 3.0
× 10-3 M.
are shown in Table 3. It can be found that the ꢀ values are
increased substantially with increasing monomer length. This
observation also supports that important cooperative donor-
acceptor interaction exists within the complexes.
All the above binding studies suggest that the new kind
of duplexe may adopt a multisite zipper-like binding motif,
as shown in Figure 2 with 1d‚2d as an example, which
facilitates multisite donor-acceptor interactions and conse-
quently promotes the stability of dimers consisting of long
monomers.20
420
a Performed at 25 °C with an error e20%.
similar binding ability toward acceptors 2 compared to
compounds 1b and 1c, respectively, suggesting that the
possible intra- and intermolecular hydrogen bonds produced
by the two peripheral amide groups have no substantial effect
on the formation of the donor-acceptor interaction-driven
heterodimers. In contrast, 16 exhibits significantly lower
complexing ability than those of 1 or 11 with the same num-
ber of donor units. These results are not unexpected con-
sidering that 1,5-dioxynaphthalene-incorporating macrocyclic
ether is a much more effective template than the 1,4-
dioxybenzene-incorporated analogue for donor-acceptor
interaction-induced self-assembly and molecular recogni-
tion.18 NOESY experiments were also performed for the most
strong complexes 1d‚2d and 11b‚2d in CDCl3, which did
not reveal intermolecular NOEs for the aromatic protons.
An average molecular mass of 3100 ( 400 u was
determined with vapor pressure osmometry (VPO) in chloro-
form-toluene (60:40 v:v) at 30 °C for complex 1d‚2d. The
result is consistent with that calculated for the 1:1 binding
motif (3468 u) of the complex.
Figure 2. The proposed binding motif for duplex 1d‚2d.
All the complexes display pale to dark orange color in
chloroform, depending on their stability and concentration.
Consistently, UV-vis investigations also reveal broad
electron-transfer absorbance between 400 and 600 nm for
the new complexes. The corresponding molar extinction
coefficients (ꢀ) obtained in chloroform at room temperature
In conclusion, donor-acceptor interaction has been, for
the first time, successfully utilized for the formation of a
new class of stable duplexes from readily available linear
molecules. By modifying the molecular skeletons and
introducing new, more electron deficient units into the
acceptor molecules, more stable binding motifs are expected
to be generated. Further applications of the new binding motif
in self-assembly of a new generation of supramolecular
species are also under investigation.
(16) (a) Zych, A. J.; Iverson, B. L. J. Am. Chem. Soc. 2000, 122, 8898.
(b) Hamilton, D. G.; Montalti, M.; Prodi, L.; Fontani, M.; Zanello, P.;
Sanders, J. K. M. Chem. Eur. J. 2000, 6, 608. (c) Lokey, R. S.; Iverson, B.
L. J. Am. Chem. Soc. 1999, 121, 2639.
(17) Berdague, P.; Perez, F.; Courtieu, J.; Bayle, J. P. Bull. Soc. Chim.
Fr. 1993, 130, 475.
Acknowledgment. We thank the Ministry of Science and
Technology (G2000078101) and the Natural Science Foun-
dation (No. 20172069) of China for financial support.
(18) (a) Li, Z.-T.; Stein, P. C.; Becher, J.; Jensen, D.; Mørk, P.; Svenstrup,
N. Chem. Eur. J. 1996, 2, 624. (b) Amabilino, D. B.; Ashton, P. R.; Reder,
A. S.; Spencer, N.; Stoddart, J. F. Angew. Chem., Int. Ed. Engl. 1994, 33,
1286. (c) Ashton, P. R.; Brown, C. L.; Chrystal, E. J. T.; Goodnow, T.;
Kaifer, A. E.; Parry, K. P.; Philp, D.; Slawin, A. M. Z.; Spencer, N.;
Stoddart, J. F.; Williams, D. J. J. Chem. Soc., Chem. Commun. 1991, 634.
(19) No detectable absorbance was exhibited in the visible range at [1a]
()[2a]) ) 0.016 M.
(20) This binding pattern requires a folding conformation for the
monomers. Simple monomers such as 1b and 2b might also form complexes
through linear, unfolded conformation, which, however, possess less donor-
acceptor interaction sites than the proposed zipper-featured motif.
Supporting Information Available: The synthesis and
1
characterizations of all new compounds, H NMR titration
method, and UV-vis spectra of complexes 1b‚2b, 1c‚2c,
and 1d‚2d. This material is available free of charge via the
Internet at http://pubs.acs.org.
OL034549P
1958
Org. Lett., Vol. 5, No. 11, 2003