Amine functionalized polythiophenes: Synthesis and formation of chiral, ordered structures on DNA substrates

Article abstract of DOI:10.1016/S0040-4039(00)01918-3

Highly regioregular, head-to-tail coupled, 3-(amino functionalized)-polythiophenes can be synthesized by CuO co-catalyzed Stille coupling. Salts of one example are water soluble, and become helically ordered upon addition of DNA.

Full text of DOI:10.1016/S0040-4039(00)01918-3

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 42 (2001) 155–157
Amine functionalized polythiophenes: synthesis and formation of
chiral, ordered structures on DNA substrates
Paul C. Ewbank,a,c Guido Nuding,a Hikaru Suenaga,b Richard D. McCulloughc,* and
Seiji Shinkaia,*
aChemotransfiguration Project, Japan Science and Technology Corporation, 2432 Aikawa-cho, Kurume, Fukuoka 839, Japan
bBiotechnology and Food Research Institute, Fukuoka Industrial Technology Center, 1465-5, Aikawa-cho, Kurume,
Fukuoka 839, Japan
cDepartment of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Received 29 September 2000; revised 23 October 2000; accepted 24 October 2000
Abstract—Highly regioregular, head-to-tail coupled, 3-(amino functionalized)-polythiophenes can be synthesized by CuO co-cat-
alyzed Stille coupling. Salts of one example are water soluble, and become helically ordered upon addition of DNA. © 2000
Elsevier Science Ltd. All rights reserved.
Polythiophenes (PT) have interesting optical and elec-
tronic properties that are sensitive to perturbations in the
electronic structure, most notably deconjugative twisting
arising from steric interactions.1–3 Head-to-tail (HT)
regioregular PT prepared via cross-coupling have few
coupling defects, a common cause of twisting.2 HTPT
can be combined with environmentally-responsive sub-
stituents so that exposure to various analytes causes
twisting of the polymer backbone, generating a colori-
metric response.1,3,4 We report the synthesis of two highly
regioregular, amine functionalized polythiophenes, one
of which (5a, Scheme 1) was water-soluble and could be
induced to chirally order upon binding to DNA.
Compound 1 was dripped into 8 equivalents of
CH3NH2 in EtOH and stirred for 1 h. The product 25
was extracted into aqueous acid, made basic, re-ex-
tracted into Et2O, then distilled (63°C, 0.34 T) in 60%
yield. Compound 2 was dissolved in dry Et2O, and
2-chlorotetrahydropyran (THP-Cl)6 was added. The so-
lution was stirred for 2 h, extracted with satd aq.
Na2CO3, then compound 37 was distilled (0.005 T,
105–115°C) in 84% yield. LDA was added to a cooled
(−70°C) solution of 3 in THF, stirred for 1 h, then
reacted with Me3SnCl for 1 h. This was partitioned
between Et2O and satd aq. Na2CO3 before compound
48 was distilled (0.005 T, 120°C) in 70% yield.
Scheme 1. Reagents and conditions: (i) CH3NH2, EtOH, 1 h; (ii) THP-Cl, Et2O; (iii) (a) LDA, −70°C, 1 h, (b) Me3SnCl, −70°C,
1 h; (iv) Pd2(dba)3, PPh3, CuO, DMF, 100°C; (v) 3 M HCl; (vi) BOC2O, DMAP; (vii) butyryl chloride.
* Corresponding authors.
0040-4039/01/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(00)01918-3

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P. C. Ewbank et al. / Tetrahedron Letters 42 (2001) 155–157
Polymerization1 of 4 gave an insoluble solid that was
hydrolyzed to 5a. Polymer 5a was soluble in water
solutions (HCl) from pH 1 to 7, while pH 8 or greater
gave a red solid. The UV–vis spectrum (sodium phos-
phate buffer, pH 6.8) exhibited a umax of 383 nm and a
conjugation length of about four thiophene rings.9
Polymer 5a was not highly conjugated and adopted a
twisted conformation. The product was indirectly char-
low thin films, with a UV–vis spectrum identical to that
of the solution.
Compound 5a was designed to interact with DNA in
order to probe the use of polythiophenes as biosensors.
Aqueous solutions of polycationic polythiophenes
could be ideally suited for binding to a polyanionic
template such as DNA. Polymers designed for specific
nucleobase recognition have been described;12,13 how-
ever, unlike these models, 5a could exhibit a non-spe-
cific response to all types of DNA. Non-specific binding
is advantageous when 5a is applied as a ‘probe’ to
detect conformational changes in DNA, e.g. the resul-
tant helical ordering in DNA should be spectroscopi-
cally detectable by a polythiophene sensor. To check
this hypothesis, various DNA samples were added to
the HCl salt of 5a and polymer binding monitored by
changes in CD activity (solutions of 5a exhibit no CD
optical activity). In a typical experiment, 0.2 mg poly-
thiophene 5a was dissolved in aqueous HCl, the solvent
was removed, and the resultant brown solid was re-dis-
solved in 3 mL of 0.001 mol/L Na2HPO4/NaH2PO4
phosphate buffer (pH 6.8). The solution was titrated
with DNA over a range of concentrations from 2×10−5
to 2×10−4 mol/L, and a distinct response associated
with the polymer p–p* absorption was induced. Higher
polymer concentrations could not be assayed because
an aggregate precipitated upon addition of DNA.
1
acterized as the amide 6.10 Integration of the H NMR
a-methylene region of amide 6a indicated at least a 90%
HT coupling ratio. Since the polymer was not easily
fractionated, the isolated polymer shows a broad poly-
dispersity (GPC, Mn=1537, PDI 3.0, DP=12 rings).
This general approach has produced the first amine
derivative of a regioregular polythiophene.
A regioregular polythiophene bearing a long alkyl-
amine substituent, which should have improved solu-
bility and processability, was also prepared. Thus
monomer 7 was prepared analogously to 2, and purified
by chromatography. Polymerization yielded 5b11 which
precipitated from solution as a brown tacky material
(Mn=8769; PDI=1.83; DP=31 rings). Polymer 5b
was soluble in many organic solvents. Solutions of this
material were also yellow (umax=416 nm) indicating a
twisted polymer. Extractions and dialysis to remove
any possible coordinated ions changed neither the solu-
tion or thin-film color nor the film consistency, suggest-
ing that the twisted nature of the polymer is a
consequence of the proximal amine substituent. Thin
films were brown with a broad, optical absorption
centered around 402 nm. The color and breadth of the
absorption suggested a random mixture of ordered
(red) and disordered (yellow) phases. Electrochemical
studies show that an irreversible oxidation leads to dark
films. Attempts to induce self-assembly in polymer films
of 5b by metal ion complexation have been unsuccess-
ful. Protonated 5b (w/CH3COOH) formed tacky, yel-
Mixing calf thymus (CT) DNA with polymer 5a did not
perturb the CD spectral features of the DNA sample in
the 260 nm region, suggesting that there was no confor-
mational reorganization of DNA due to binding of
polythiophene 5a (Fig. 1). However, a new CD absorp-
tion centered at 480 nm was observed indicating that
the highly-disordered polythiophene 5a is chirally or-
dered by the DNA and was dependent upon DNA
Figure 1. Electronic absorption (lower left) and CD (upper left) for CT DNA (B), 5a (A), and CT DNA with 5a (solid lines).
Electronic absorption (lower right) and CD (upper right) for AT DNA (C), 5a (A), and AT DNA with 5a (solid lines).

P. C. Ewbank et al. / Tetrahedron Letters 42 (2001) 155–157
157
concentration. The intensity increased with added DNA
as indicated in Fig. 1. In the visible spectrum, growth of
a corresponding shoulder in the 480 nm region was
noted. This large 100 nm bathochromic shift of the
lambda maximum indicated that association with DNA
had induced a dramatic ordering of PT 5a. Although
distinct absorptions for DNA and DNA complexed PT
were found, a clear isosbestic point could not be
measured.
A.; Elsenbaumer, R. L.; Reynolds, J. R., Eds.; Marcel
Dekker: New York, 1998; p. 225.
3. For a review of conformation related chromatism, see:
LeClerc, M.; Fa¨ıd, K. ibid. 695.
4. Marsella, M. J.; Swager, T. M. J. Am. Chem. Soc. 1993,
115, 12214.
1
5. Compound 2: H NMR (300 MHz, CDCl3) l 2.46 (3H,
s), 3.27 (2H, s), 6.91 (d, J=6.0 Hz), 7.19 (d, J=6.0 Hz).
13C NMR (75 MHz, CDCl3) l 35.8, 49.5, 110.3, 125.6,
128.2, 139.8.
The results were markedly different with weakly H-
bonded poly AT DNA (Fig. 1). Polymer 5a binds to
DNA as evidenced by the absorption in the 480 nm
region. The data show an exciton coupling band indica-
tive of a very interesting bimolecular ordering of PT
chromophores that is being induced by the DNA tem-
plate. The intensity of the CD absorption varied as
indicated with increasing DNA concentration. The
shape and sign were characteristic of a right-handed
helical form of polythiophene first observed by Meier,14
and lead to the conclusion that helically ordered con-
ducting polymer aggregates had formed. The normal
bisignate CD spectrum of DNA near 260 nm disap-
peared. Reorganization of the nucleic acid as a conse-
quence of PT binding had also occurred, and may
reflect expansion of the major groove to accommodate
stacked 5a.
6. Synthesis of 2-chlorotetrahydropyran (THP-Cl): A sam-
ple of 3,4-dihydro-2-H-pyran (10 mL, 190.6 mmol) was
dissolved in anhydrous Et2O and cooled in an ice bath. A
1.0 M solution of HCl in Et2O (Aldrich; 130 mmol) was
added dropwise, and the reaction was stirred for 3 h.
Concentration and distillation (46°C, 0.16 T) afforded a
colorless oil (6.8 g, 56 mmol, 51% yield). This is a
simplification of the procedure first reported by: Eliel, E.
L.; Daignault, R. A. J. Org. Chem. 1965, 30, 2450.
7. Compound 3 is a racemic mixture of chiral THP isomers.
1H NMR (300 MHz, CDCl3) l 1.38–1.53 (3H, m),
1.58–1.70 (2H, m), 1.82–1.91 (H, M), 2.33 (3H, s),
3.35–3.45 (H, m), 3.62–3.79 (2H, m), 3.86–4.02 (2H, m).
13C NMR (75 MHz, CDCl3) l 23.9, 25.9, 29.9, 36.4, 51.0,
67.6, 92.9, 110.5, 125.2, 128.9, 139.5. Calculated: C,
45.52; H, 5.56; Br, 27.53; N, 4.83; Found: C, 45.3; H,
5.58; Br, 27.60; N, 4.86.
8. Compound 4 is a racemic mixture of chiral THP isomers.
1H NMR (300 MHz, CDCl3) l 0.33 (9H, Sn t, J=28.5
Hz), 1.37–1.54 (3H, m), 1.57–1.71 (2H, m), 1.81–1.92
(H, m), 2.34 (3H, s), 3.35–3.46 (H, m), 3.61 (3H, m),
3.85–4.04 (2H, m), 6.98 (H, Sn t, J=13.2 Hz). 13C NMR
(75 MHz, CDCl3) l −8.3 (Sn t, J=707 Hz), 23.8, 25.8,
29.7, 36.4, 50.7, 67.5, 92.8, 115.2, 136.9 (Sn t, J=48.6
Hz), 138.0, 140.3. Calculated: C, 37.12; H, 5.34; Br,
17.64; N, 3.09. Found: C, 37.29; H, 5.15; Br, 17.87; N,
3.18.
In summary, we have demonstrated a synthesis for
amine functionalized polythiophenes. These polymers
do not appear to self-organize, remaining highly twisted
and disordered in solution. However, polythiophene 5a
can be induced to order differentially by different DNA
structures in water, producing a low energy p–p* ab-
sorption that is comparable to that seen in self-assem-
bled PT thin films.2 However, in the AT DNA case, the
dramatic red shift of the absorption maximum, along
with the observed exciton coupling, indicates that the
p-systems on adjacent chains in PT are interacting in an
organized (e.g. stacked) fashion. This is similar to an
observation of DNA templating of dyes by Armitage
and co-workers.15 These preliminary observations
demonstrate the remarkable application of highly re-
gioregular polythiophene as a biological chemosensor.
We expect that continued investigation of the PT/DNA
interaction will allow us to further develop PT
biosensors.
9. For a comparison with HT regioregular oligothiophenes,
see: Bidan, G.; De Nichola, A.; Enee, V.; Guillerez, S.
Chem. Mater. 1998, 10, 1052.
10. Compound 6: 1H NMR (300 MHz, 100°C, TCE-d4) l
0.94–0.99 (3H, m), 1.62–1.72 (2H, m), 2.30–2.37 (2H,
m), 2.91–2.97 (3H, m), 4.50 (non-HT-a-methylene,
0.2H), 4.67 (HT-a-methylene, 1.8H), 7.02 (b, s).
1
11. Compound 5b: H NMR (300 MHz, CDCl3) l 0.85 (3H,
T, J=6.6 Hz), 1.19–1.27 (18H, m), 1.44–1.51 (2H, m),
3.10–3.21 (2H, m), 4.40 (non-HT-a-methylene, 0.4H, b),
4.54 (HT-a-methylene, 1.6H), 6.98.
12. Korri-Youssoufi, K.; Garnier, F.; Srivastava, P.; Godil-
lot, P.; Yassar, A. J. Am. Chem. Soc. 1997, 119, 7388.
13. Bauerle, P.; Emge, A. Adv. Mater. 1998, 3, 324.
14. Langeveld-Voss, B. M. W.; Christiaans, M. P. T.;
Janssen, R. A. J.; Meijer, E. W. Macromolecules 1998, 31,
6702.
References
1. McCullough, R. D.; Ewbank, P. C.; Loewe, R. S. J. Am.
Chem. Soc. 1997, 119, 633.
2. For a review of regioregular polythiophene synthesis and
properties, see: McCullough, R. D.; Ewbank, P. C. In
Handbook of Conducting Polymers, 2nd ed.; Skotheim, T.
15. Seifert, J. L.; Connor, R.; Wang, M.; Kushon, S. A.;
Armitage, B. J. Am. Chem. Soc. 1999, 121, 2987.
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