Water-soluble, electroactive, and photoluminescent quaterthiophene- dinucleotide conjugates

Article abstract of DOI:10.1002/chem.200700950

Quaterthiophene-dinucleotide conjugates ^5′TA ^3′-t4-^3′ AT^5′, ^5′AA^3′-t4-^3′ AA ^5′, and ^5′TT^3′-t4- ^3′TT^5′ (TA: thymidine-adenosine, AA: adenosine-adenosine, TT: thymidine-thymidine) were synthesized and analyzed by a combination of spectroscopy and microscopy, electrical characterization, and theoretical calculations. Circular dichroism (CD) experiments demonstrated a transfer of chirality from the dinucleotides to quaterthiophene at high ionic strength and in cast films. The films were photoluminescent and electroactive. CD and photoluminescence spectra and current density/voltage plots (measured under dynamic vacuum) displayed significant variation on changing the dinucleotide scaffold. Molecular mechanics and molecular dynamics calculations indicated that the conformation and packing modes of the conjugates are the result of a balance between intra- and intermolecular nucleobase-thiophene stacking interactions and intramolecular hydrogen bonding between the nucleobases.

Full text of DOI:10.1002/chem.200700950

FULL PAPER
DOI: 10.1002/chem.200700950
Water-Soluble, Electroactive, andPhotoluminescent Quaterthiophene–
Dinucleotide Conjugates
Silvia Alesi, Giorgia Brancolini, Manuela Melucci, Massimo Luigi Capobianco,
Alessandro Venturini, Nadia Camaioni, and Giovanna Barbarella*[a]
Abstract: Quaterthiophene–dinucleo-
tide conjugates 5’TA3’-t4-3’AT5’, 5’AA3’-
t4-3’AA5’, and 5’TT3’-t4-3’TT5’ (TA: thy-
midine–adenosine, AA: adenosine–ad-
enosine, TT: thymidine–thymidine)
were synthesized and analyzed by a
combination of spectroscopy and mi-
croscopy, electrical characterization,
and theoretical calculations. Circular
dichroism (CD) experiments demon-
strated a transfer of chirality from the
dinucleotides to quaterthiophene at
high ionic strength and in cast films.
The films were photoluminescent and
electroactive. CDand photolumines-
cence spectra and current density/volt-
age plots (measured under dynamic
vacuum) displayed significant variation
on changing the dinucleotide scaffold.
Molecular mechanics and molecular
dynamics calculations indicated that
the conformation and packing modes
of the conjugates are the result of a
balance between intra- and intermolec-
ular nucleobase–thiophene stacking in-
teractions and intramolecular hydrogen
bonding between the nucleobases.
Keywords: charge mobility · circu-
lar dichroism · oligonucleotides ·
photoluminescence · thiophene
Introduction
ready read-out modalities and high sensitivity, fluorescence
detection is the most employed technique for biosensors
based on cationic polythiophenes.[2–3b]
Thiophene oligomers and polymers are among the most in-
vestigated semiconductor materials for organic electronics.[1]
Generally, to make them soluble in organic solvents, alkyl
chains, aryl groups, and a variety of other substituents are
grafted onto the aromatic backbone. A few polythiophenes
with charged-pendant groups, which make them soluble in
water, have also been described and used as optical trans-
ducers in biosensors for the detection of DNA mismatches
in pathological samples.[2] Water-soluble conjugated poly-
electrolytes offer many opportunities to reveal chemical and
biochemical events through changes in absorption or photo-
luminescence signals, electrical conductivity, or redox poten-
tials.[2–3] The methodologies that employ cationic polythio-
phene transducers to detect biomolecules have been demon-
strated to be very sensitive and specific.[2] As a result of the
On these grounds, we focused our attention on the use of
oligonucleotides—readily available and easy to graft onto
organic molecules by means of known methodologies—as
scaffolds to prepare water-soluble functional molecules ca-
pable, on one hand, to recognize the presence of relevant
biomolecules in physiological/pathological processes and, on
the other, to self-assemble over different length scales in
thin films through biomolecular recognition. We aimed, in
particular, at developing theoretical and experimental tools
to understand the interactions of thiophene derivatives with
DNA components by means of the synthesis of oligothio-
phene–oligonucleotide hybrid structures and to study the
way they interact and organize in solution and thin film.
“Biohybrid” materials made of organic and bio-organic seg-
ments are an emerging research area in the field of materi-
als science.[4] However, so far, very few compounds combin-
ing thiophene-based segments with DNA components
(mainly nucleosides) have been reported.[5]
[a] Dr. S. Alesi, Dr. G. Brancolini, Dr. M. Melucci,
Dr. M. L. Capobianco, Dr. A. Venturini, Dr. N. Camaioni,
Dr. G. Barbarella
Consiglio Nazionale Ricerche
CNR-ISOF, Via P. Gobetti 101
40129 Bologna (Italy)
Fax : (+39)051-639-8349
E-mail: barbarella@isof.cnr.it
We report herein an investigation concerning the synthe-
sis and characterization of a structurally homogeneous set of
quaterthiophene–dinucleotide conjugates, in which the thio-
phene oligomer is linked to thymidine–adenosine (TA), ade-
nosine–adenosine (AA), and thymidine–thymidine (TT) di-
nucleotides at both terminal positions (Scheme 1).
Supporting information for this article is available on the WWW
under http://www.chemeurj.org/ or from the author.
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513

assistance in steps (a) and (b)
for the preparation of the
parent quaterthiophene.[7] Qua-
terthiophene 3 with protected
alcoholic groups was obtained
in 87% yield in 5 min through
the solvent-free, microwave-as-
sisted coupling of diiodo deriv-
ative 2 with boronic ester 1
using [PdCl2ACHTER(UNG dppf)]/KF and
Al2O3/KOH (10% aq.) as a
catalytic system. After depro-
tection under microwave acti-
vation, the oligomer was treat-
ed with an excess of 5’-protect-
ed (4,4’-dimethoxytrityl)deoxy
dinucleotides 4a–c previously
phosphorylated with 2-chloro-
phenyl-O,O-bis-(1-benzotriazo-
lyl)phosphate in pyridine as
the solvent. After removal of
the 5’-dimethoxytrityl group
Scheme 1. The molecular structure of the building blocks of conjugates 5’TA3’-t4-3’AT5’, 5’AA3’-t4-3’AA5’, and
5’TT3’-t4-3’TT5’.
Quaterthiophene is one of the most investigated thio-
phene derivatives for its semiconductor[6a] and photolumi-
nescent properties.[6b] TA, AA,
and TT dinucleotides were
linked to the quaterthiophene
backbone through an ethylene
spacer to confer conformation-
al flexibility to the structure.
with benzenesulfonic acid, the detritylated compound was
treated with N1,N1,N3,N3-tetramethylguanidine and syn-pyri-
By means of a combination
of spectroscopic methods, fluo-
rescence microscopy, electrical
characterization, and theoreti-
cal calculations, we demon-
strate that the bioconjugates
are photoluminescent and
electroactive compounds and
that their conformational pref-
erences and packing modalities
originate from a critical bal-
ance between intra- and inter-
molecular
nucleobase–thio-
phene stacking interactions
and intramolecular hydrogen
bonds formed by the nucleo-
bases.
Results andDiscussion
Synthesis: Conjugates 5’TA3’-
t4-3’AT5’, 5’AA3’-t4-3’AA5’, and
5’TT3’-t4-3’TT5’ were prepared
following the synthetic pattern
shown in Scheme 2, thus
taking advantage of microwave
Scheme 2. a) KF, [PdCl2ACHTRE(UNG dppf)], Al2O3/KOH (10% aq.), MW, 5 min; b) HCl (0.2N), THF, MW, 5 min; c) 5, py,
2 h, RT; d) benzenesulfonic acid, MeOH/CH2Cl2, 0.5 h, RT; e) py, 16 h, RT; NH3 (30% aq.), 24 h, 508C. BT=
benzotriazolyl, DMTr=4,4’-dimethoxytrityl, dppf=1,1’-bis(diphenylphosphino)ferrocene, MW=microwave,
py=pyridine, THP=tetrahydropyran, TEA=triethylamine.
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Photophysical Characterization of Dinucleotide Scaffolds
FULL PAPER
dine-2-carboaldoxime and then with aqueous ammonia. The
target compounds 8a–c were obtained from the crude mix-
ture after reversed-phase chromatography and characterized
folds remain unchanged. Instead, the PL signals of 8a–c in
cast films are remarkably sharpened with respect to the so-
lution, well separated from each other, and red-shifted by 70
to nearly 100 nm. This behavior recalls that shown in the
formation of H-type aggregates, such as those described, for
example, for trans-stilbene in Langmuir–Blodgett films[8a] or
for supramolecular assemblies of chiral oligothiophenes[8b]
and indicates that the t4 components form orientationally
ordered domains in the film.[8c] However, further studies are
required to fully elucidate the relationship between the ag-
gregation modalities of 8a–c and their photophysical proper-
ties. Investigations in this direction are currently under way.
Circular dichroism (CD) experiments demonstrated a
transfer of chirality from the dinucleotide substituents to the
quaterthiophene moiety at high ionic strength and in films.
The CDspectra of the bioconjugates in 10 À5 m solution in
aqueous buffer (pH 7.4), aqueous buffer containing 1m
NaCl, and in cast films from solutions in water are shown in
Figure 2. The detailed CDdata of 8a–c are reported in the
Supporting Information.
1
by mass spectrometry, H and 31P NMR spectroscopy, UV/
Vis spectroscopy, and photoluminescence (PL) (further syn-
thetic and characterization details are given in the Support-
ing Information).
Optical properties (UV, PL, andCD) : Conjugates 8a–c are
photoluminescent compounds in solution in water and in
cast films. The UV/Vis and PL spectra in water and in films
cast from 10À3 m solutions in water are shown in Figure 1a
Figure 2. CDspectra of a) conjugates 5’TA3’-t4-3’AT5’, 5’AA3’-t4-3’AA5’, and
5’TT3’-t4-3’TT5 (8a–c) in aqueous buffer (pH 7.4; dotted line) and aqueous
buffer with 1m NaCl (solid line) and b) cast film from 10À3 m solutions in
water.
Figure 1. UV/Vis and PL spectra (lexc =410 nm) of conjugates 5’TA3’-
t4-3’AT5’, 5’AA3’-t4-3’AA5’, and 5’TT3’-t4-3’TT5 (8a–c) in a) water and
b) films cast from a 10À3 m water solution.
and 1b, respectively, while the absorption and PL wave-
lengths are reported in the Supporting Information. The
UV/Vis spectra in solution consist of signals around 260 nm,
from the oligonucleotide moiety, and 400 nm, from the qua-
terthiophene t4. The PL spectra in solution, which arise
from the t4 moieties, consist of a main signal split into two
bands near 500 nm and two red-shifted shoulders in the
region 550–600 nm. These spectra are very similar to those
of “free” quaterthiophene and, in general, to those spectra
of thiophene oligomers in solution.[7] The UV/Vis signals of
the conjugates in cast films are almost superimposable and
are blue-shifted by 10–17 nm with respect to those in solu-
tion, whereas the signals pertaining to the dinucleotide scaf-
The spectra consist of two regions: one with a bisignated
signal at 250–280 nm assigned to the TA, AA, and TT dinu-
cleotides and the other with a signal around 400 nm that cor-
responds to the p–p* absorption region of t4 and is related
to long-range electronic interactions between the t4 moiet-
ies. Upon increasing the ionic strength of the solutions of
8a–c by the addition of NaCl, which increases molecular ag-
gregation, the dinucleotide signals display only minor varia-
tions, while the t4 signals show changes both in intensity and
shape. Conjugate 8a shows a very weak positive signal at
437 nm in aqueous buffer, but the chirality factor g increases
in intensity by more than two orders of magnitude following
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G. Barbarella et al.
the addition of NaCl (see the Supporting Information). Con-
jugate 8b shows a weak positive signal at 410 nm with the
g value increasing sixfold upon addition of NaCl. In this
case, the increase in the g value of the signal at 410 nm is ac-
companied by the appearance of a further weak positive
signal near 450 nm. Conjugate 8c shows a negative and
broad signal around 387 nm in aqueous buffer, which upon
addition of NaCl gives rise to a nonsymmetric bisignated
signal with a stronger negative component at 384 nm and a
weaker positive component at 443 nm with zero crossing at
420 nm. The bisignated signal is characteristic of an exciton
coupling between chromophores in a chiral orientation.[9] In
this specific case, it indicates a right-handed helical arrange-
ment of interacting t4 moieties. In cast film, 8c shows the
same bisignated signal displayed in solution at high ionic
strength with the zero crossing wavelength blue-shifted to
407 nm. Conjugate 8a in cast film shows an inverted, nega-
tive signal blue-shifted to 400 nm. The behavior of conjugate
8b in cast film is more complex. The bisignated signal that
pertains to the oligonucleotide scaffold becomes broad and
there is the appearance of an exciton couplet in the region
of t4, which is composed of a negative band at 367 nm and a
positive band at 407 nm (zero crossing at 383 nm). This be-
havior indicates that the interacting t4 moieties are organ-
ized in a helical left-handed fashion.[9] The spectrum also
shows some signals in the region around 450 nm, thus over-
lapping with the negative part of the bisignated signal.
CDspectroscopy is one of the most sensitive techniques
available for the analysis of aggregation modalities in p–p
conjugated systems.[9,10] In the present case, CDspectra indi-
cate fine variations in aggregation modalities of the conju-
gates on changing the oligonucleotide scaffold. In cast film,
the interplay between molecule–molecule and molecule–
substrate interactions governs the aggregation process.
When molecule–molecule interactions are weak, the interac-
tion of the molecules with the surface drives the formation
of the supramolecular aggregate. Sign inversions in the CD
spectra from solution to film are also commonly observed in
the case of the oligothiophenes.[8b,d] The fact that the shape
of the spectrum does not change for 8c from solution to cast
film is an indication that the aggregate formed by this conju-
gate is intrinsically more stable than those formed by 8a
and 8b.
the length of which could reach up to a 100 m depending on
the rate of solvent evaporation and the hydrophilicity of the
surface employed (glass, glass covered with amylose, SiO2,
and mica were tested). The samples were prepared in a sol-
vent-saturated environment at room temperature to obtain
the deposition under quasi-equilibrium conditions: a 50 mL
aliquot of a 1 mg/200 mL solution in water was cast on glass
and after complete solvent evaporation (ꢀ12 h) was ana-
lyzed under ambient conditions by optical, fluorescence, and
atomic force microscopy (AFM; see the AFM image report-
ed in the Supporting Information). No rod-like aggregates
were observed when the solvent was quickly removed under
vacuum. The longest rods were obtained by employing a sur-
face made of amylose deposited on glass. Upon UV irradia-
tion all the films displayed intense yellow–orange fluores-
cence emission. Figure 3 shows the fluorescence microscopy
Figure 3. Fluorescence microscopy image of rod-like aggregates formed
by the deposition of 5’AA3’-t4-3’AA5’ (8b) on a glass substrate covered
with a thick layer of amylose.
5’
image of a cast film of AA3’-t4-3’AA5’ (8b; 40 mL, 1 mgmLÀ
solution in H2O; the corresponding optical microscopy
image is given in the Supporting Information) deposited at
room temperature on a glass substrate covered with an amy-
lose layer (50 mL, 2 mgmLÀ solution in dimethyl sulfoxide
(DMSO)), therefore showing the formation of rod-like ag-
gregates up to 100 m in length. Amylose, a linear polymer of
a-1,4-linked glucose,[12] has a helical structure and once cast
on glass forms a chiral surface. Thus, it cannot be excluded
that chiral–chiral interactions between the chiral surface and
the chiral conjugates contribute to the formation of the lon-
gest rods. However, since the formation of rod-like aggre-
gates, such as those shown in Figure 3, has never been ob-
served with oligothiophenes, including those made amphi-
philic by the presence of ethylene oxide chains,[8b] it is rea-
sonable to ascribe their formation to the orienting effect of
the dinucleotide scaffolds in 8a–c.
Shape of the aggregates: Conjugates 8a–c are amphiphilic
molecules with hydrophobic (i.e., t4) and hydrophilic (i.e.,
TA, AA, and TT) moieties. As is typical of amphiphilic
compounds,[11] the casting of 8a–c from water leads to the
formation of spherical, globular, or even dendritic aggre-
gates depending on the experimental conditions. However,
under carefully controlled deposition conditions, we ob-
served the formation of rod-like aggregates for all the conju-
gates, thus showing that despite the very different intimate
nature of the 8a–c aggregates on surfaces as revealed by
CDspectroscopy, their morphological habit in cast film was
always the same. This morphology consisted of an amor-
phous matrix containing numerous randomly oriented rods,
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Photophysical Characterization of Dinucleotide Scaffolds
FULL PAPER
Electrical characterization: The cast films of the conjugates
were electroactive. We present the electrical characteristics
of 8b and 8c, for which cast films of suitable and compara-
ble thickness under controlled conditions could be obtained.
For comparison, the data relative to the precursor quater-
thiophene 3a (t4-OTHP; see the Supporting Information for
the molecular structure) are also given. Cast films of 8b, 8c,
and the precursor quaterthiophene were deposited onto sub-
strates consisting of two interdigitated Au electrodes fabri-
cated by evaporating gold onto oxidized silicon wafers and
patterned with photolithography (see the Experimental Sec-
tion and Supporting Information). The electrical characteri-
zations were performed at ambient temperature in a home-
made chamber both in air and under dynamic vacuum. The
procedure was repeated twice with samples from different
preparations to ensure reproducibility of the results. When
the electrical characterization was performed in air, a dra-
matic dependence of the current on the environment was
observed for conjugates 8b and 8c (but not for 3a). As an
example, Figure 4a shows the current density/time (J–t)
pumping (curve 3). In this case, much lower currents were
measured, but the J–t curve still showed decreasing behavior
with time. These findings suggest a space–charge polariza-
tion effect of the sample, as a result of ionic currents, likely
promoted by moisture and leading to increasing resistivity
with time.[13] To avoid ionic conduction, the samples were
left in the measurement chamber for several hours under
dynamic vacuum, until a constant current with time was ob-
served under constant DC applied voltage. Figure 4b shows
the current density/voltage (J–V) curves for 8b, 8c, and 3a
measured at ambient temperature under a dynamic vacuum
of 10À4 mbar. The figure shows that the reference compound
t4-OTHP displays the highest currents, those of 8b and 8c
are smaller by four and three orders of magnitude, respec-
tively. It should be noted that the samples considered herein
are only hole-transporting samples because gold acts as a
hole-injecting contact, for which the work function (5.2 eV)
is energetically matched to the highest occupied molecular-
orbital energy levels of the investigated materials[6a] and pre-
vents electron injection from the negatively biased elec-
trode. We observed that for all samples the current density
has a good quadratic dependence on the voltage in the high-
field region, as better shown in Figure 4b.
This behavior is typical of space–charge limited current
(SCLC,[14] given by j=(9/8)e0ermV2LÀ3 in the trap-free
regime, where e0 is the vacuum permittivity, er is the relative
dielectric constant of the material, m is the charge carrier
mobility, and L is the electrode separation). By setting er to
3, hole mobilities mh of 1.7”10À4, 2.4”10À8, and 2.0”
10À7 cm2 VÀ1 sÀ1 were estimated for t4-OHP, 8b, and 8c, re-
spectively, from the slope of the linear portion of the J–V2
curves (Figure 4c). These values are reasonable as the esti-
mated hole mobility for t4-OHP is the same order of magni-
tude as the field-effect-transistor (FET; a three-electrode
device) hole mobility measured for cast films of quaterthio-
phene,[6b] while those of 8b and 8c are of the same order as
the FET hole mobilities recently measured for cast films of
oligo(p-phenylene vinylene) functionalized with ureido-s-tri-
azine groups.[15] Of course, a more precise evaluation of the
hole mobilities of conjugates 8a and 8c must wait for FET
measurements to be carried out. However, what is signifi-
cant in the present context is that a change in the dinucleo-
tide scaffold leads to almost one order of magnitude differ-
ence in the measured currents of 8b and 8c. Moreover, it is
tempting to make a correlation with CDdata and ascribe
the higher current measured for 8c to its more ordered mo-
lecular organization. A more detailed description of the
electrical behavior of conjugates 8b and 8c, including impe-
dance spectroscopy measurements at different degrees of
humidity, will be reported elsewhere.
Figure 4. a) Current density versus time for a sample of 8c at an applied
voltage of 100 V: 1) in air, 2) while turning on the rotary pump after
150 s in air, 3) at a pressure of 10À3 mbar after 2 h of pumping. b) J–V
characteristics of t4-OTHP (circles), 8c (squares), and 8b (triangles)
measured at ambient temperature and under a dynamic vacuum of
10À4 mbar. Current density versus V2 for samples of c) t4-OTHP (3c),
d) 8c, and e) 8b. The lines represent the linear fit to the experimental
data. The measurements were carried out at ambient temperature and
under a dynamic vacuum of 10À4 mbar.
curves obtained for 8c at a constant applied voltage (100 V)
under three different conditions. First, the current was mea-
sured in air and decreasing values with time at a constant
DC voltage were observed (curve 1). Soon after, the current
was measured again in air (first portion of curve 2 in Fig-
ure 4a) and lower values were obtained, thus indicating that
the behavior of the sample is affected by its past treatment.
Then the rotary pump was turned on and an abrupt fall in
the current was observed (curve 2). Finally, the current was
measured at a pressure of 10À3 mbar after two hours of
Molecular modeling: Theoretical calculations helped to shed
light on the molecular mechanism of the self-assembly of
conjugates 8a–c. Conformational preferences and the ability
to form stable supramolecular aggregates in solution with
water were investigated by molecular mechanics and molec-
ular dynamics calculations. The search of minimum-energy
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G. Barbarella et al.
conformations for monomers and dimers was carried out by
using simulated annealing protocols in the gas phase and in
the presence of the solvent.[16a] The calculations were per-
formed within the AMBER force field.[16b] Furthermore, an
implicit solvent model was used to simulate the presence of
water and decreased charges on the phosphate groups to ac-
count for the presence of the counterions.[16c]
For the monomeric conjugates, two main conformations
were found, with syn and anti oligonucleotide arms with re-
spect to the mean plane of nearly planar t4 (Figure 6). For
all systems, the syn form was energetically favored over the
anti form (i.e., by a few kJmolÀ1; Figure 5). In the syn con-
formation, the dinucleotide arms were folded over the t4
backbone, were aligned at stacking distance, and formed in-
tramolecularly hydrogen-bonded pairs of A···A or T···T. The
distance between the p system of t4 and the adjacent base
pair falls in the range of 3.3–3.5 Š, as in the b form of
DNA[17] and close to that found in stilbene–oligonucleotide
conjugates,[18] but shorter than the distance calculated for
the stacks of chiral oligothiophenes (3.7 Š).[8b]
The most favored syn conformations and stacking distan-
ces of the conjugates are reported in Figure 6, which shows
that the preferred conformation is made of a hydrophobic
core surrounded by phosphate groups. The calculated
energy differences between the syn and anti forms and the
base pairs formed in the favored syn conformations are
shown in the Supporting Information, together with a sketch
of the orientation of the ethylene linkers in the different
conformations.
During the aggregation process, the syn and anti mono-
meric conformations give rise to different supramolecular
systems. The free energies of both types of aggregates were
calculated using the equation DG298 =E(MM)ÀRTlnQ,
where E(MM) is the energy derived from the molecular
modeling and Q is the partition function. For all the conju-
gates, the aggregate of the syn form is more stable than the
Figure 6. Most favored syn conformations and stacking distances of con-
jugates 8a–c.
of conjugates 8a–c are reported in the Supporting Informa-
tion, together with the electrostatic, van der Waals, and sol-
vation contributions to the total energy. The calculated free
energies indicate that the aggregation process is not driven
by differences in entropy, as the entropic contribution is
very similar for both aggregates.
Figure 7 displays the geometry of the dimers of the fa-
vored syn forms of 8a–c, together with the corresponding
top views that show the relative orientation of the two t4
moieties. The corresponding dimers of the anti form and the
orientation of the base pairs in these dimers are shown in
the Supporting Information.
aggregate of the anti form. The largest difference of DG298
=
À50.16 kJmolÀ1 is for the 8c conjugate, and the smallest dif-
ference of DG298 =À20.9 kJmolÀ1 is for the 8a conjugate,
probably as a result of a greater stabilization of the aggre-
gate of the anti form since base pairing occurs between self-
complementary bases. The calculated free energies and a
sketch of the dimers formed by the syn and anti conformers
The calculations show that the formation of the dimers of
the favored syn form is driven by the stacking interactions
between the upper base pairs at 5’ of the first monomer and
the quaterthiophene unit of
the second monomer to maxi-
mize the intermolecular stack-
ing interactions during the ag-
gregation process. Even in 8a
with self-complementary TA
ends—because of which there
was the possibility that 8a
would form intermolecularly
connected A···T Watson and
Crick base pairs—the stacking
interactions impose the same
Figure 5. Sketch of the syn and anti forms of conjugates 8a–c and the calculated energy differences (kJmolÀ1).
Grey=t4, black=oligonucleotide arms.
conformation and aggregation
modalities as in the other con-
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Photophysical Characterization of Dinucleotide Scaffolds
FULL PAPER
tion dipoles are perpendicu-
lar,[9,18] as indicated by the cal-
culations for 8a,b. In agree-
ment with this expectation, no
exciton coupling is displayed
by the CDspectra of these
compounds in solution.
The calculations also offer a
clue to the understanding of
the formation of rod-shaped
supramolecular structures in
cast films of 8a–c prepared
under quasiequilibrium condi-
tions. The shape and dimension
of the aggregates suggest that
they are formed through a self-
assembly process that starts
with syn-8a–c moieties that
pile up in columns. Then side-
to-side aggregation of the col-
umns takes place through elec-
trostatic interactions between
negatively charged phosphate
Figure 7. Most stable dimers of conjugates 8a–c and the corresponding top views showing the relative orienta-
tion of the t4 backbones. In 8a and 8b, the adjacent t4 units form a nearly perpendicular dihedral angle, while
in 8c they form a dihedral angle of about 108.
jugates with the formation of intramolecularly connected
A···A and T···T base pairs.
groups and positively charged counterions that lead to the
formation of 2Dand 3Drods.
The dihedral angle that the quaterthiophene unit of the
second monomer forms with the quaterthiophene unit of the
first monomer is determined by the orientation of the upper
base pair in the single monomer. As a consequence, the t4
moieties within the dimers are rotated with respect to each
other by an angle that depends on the nature of the dinucle-
otide ends. While in the dimers of 8a and 8b, the quater-
thiophene moieties are almost perpendicular, in the dimer
of 8c they form a dihedral angle of about 108 (Figure 7).
Finally, our calculations (not reported) show that on in-
creasing the number of aggregated molecules the energy dif-
ference between the aggregates of the syn and anti forms in-
creases, with the former becoming more and more favored
as a result of the electrostatic contributions to the total
energy.
The calculations offer a key to the interpretation of the
CDspectra. Besides the intrinsic molecular chirality as a
result of the presence of the chiral nucleotide scaffolds,
there is an additional supramolecular chirality that arises
from the way the molecules pile up during the aggregation
process, as indicated by the presence of a CDsignal in the
region that pertains to the p–p transition of t4. Assuming, as
is reasonable, that the quaterthiophene transition dipoles
are polarized along the long molecular axis, the presence of
an exciton coupling in 8c in solution at high ionic strength
(with a À/+ pattern indicative of a right-handed helical or-
ganization) is in agreement with the value of 108 calculated
for the dihedral angle between adjacent t4 units.[9,18] A col-
umnar helical aggregate is formed in which adjacent t4 moi-
eties are progressively staggered by 108 in the same direc-
tion; the aggregate is stable enough to be frozen as such in
cast film. No exciton coupling is expected when the transi-
Conclusion
In conclusion, we have demonstrated that the quaterthio-
phene–dinucleotide hybrid systems described herein lead to
the formation of chiral supramolecular assemblies and
afford cast films that are photoluminescent and electroac-
tive. Thiophene–nucleobase stacking interactions orient the
molecular conformation towards the form with syn dinucleo-
tide ends and the self-assembly modalities towards the for-
mation of columnar aggregates. The films show fine changes
in optical and electrical properties on changing the dinucleo-
tide scaffold. These results pave the way to the synthesis of
oligothiophene–oligonucleotide hybrid structures in which
different competing intra- and intermolecular interactions
(thiophene–nucleobase stacking interactions, hydrogen-
bonding interactions between nucleobases, oligothiophene–
oligothiophene van der Waals interactions, and so forth) can
be exploited by varying the oligonucleotide length, substitu-
tion pattern, and oligothiophene size to build supramolec-
ular assemblies with programmed functional properties.
Experimental Section
Synthesis: 2-(2-Thienyl)ethanol, 3,4-dihydro-2H-pyran, para-toluenesul-
fonic acid, 2,2 diiodobithiophene (2), 2-isopropoxy-4,4,5,5-tetramethyl-
1,3,2-dioxaborolane, n-butyllithium (2.5m in hexane), and [1,1’-bis(diphe-
nylphosphino)ferrocene]dichloropalladium are commercially available.
The synthesis of compounds 4a–c[19]and 5[20] has been reported elsewhere.
The synthesis of compounds 1, 3a, 3, 6a–c, and 7a–c is reported in the
Supporting Information.
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G. Barbarella et al.
General procedure for the synthesis of a,w-bis(dinucleotide)–quaterthio-
phenes 8a–c: Compounds 7a, 7b, or 7c were dissolved in dry pyridine
(3 mL) and treated with N1,N1,N3,N3-tetramethylguanidine (0.6 mL) and
syn-pyridine-2-carboxaldoxime (730 mg) for 16 h at room temperature.
The reaction mixture was then added to 30% aqueous ammonia (10 mL)
and kept in a sealed flask at 508C for 24 h. The crude products thus ob-
tained were purified by reversed-phase chromatography on a column of
C-18 eluting with a linear gradient of triethylammonium acetate (TEAA)
0.1m in H2O from 0 to 80% of CH3CN (300 mL). Compounds 8a--c were
isolated as brown solids after lyophilization in 65–70% yield. 8a: ESI-
MS: calcd for 1652.2; found 1651.7; 8b: ESI-MS: calcd for 1670.0; found:
669.3. 8c: ESI-MS: calcd for 1634.0; found: 1633.4.
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Elmer Lambda 20 spectrometer in aqueous solution (5·10À6 m, pH 7.4)
and in cast film on quartz (100 mL, 10À3 m solution) after solvent evapora-
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CD spectroscopy: Spectra were recorded with
a spectropolarimeter
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Fluorescence microscopy: Nikon Eclipse 80i optical microscope was used
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color camera Nikon Digital Sight DS-2mv. The glass substrates were fur-
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on glass substrates and the solvent was evaporated under a saturated at-
mosphere.
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Electrical characterization: Substrates consisted of two interdigitated
comb-like gold electrodes (13 pairs of electrode fingers, see the Support-
ing Information) deposited onto a layer of silicon dioxide thermally
grown on silicon plates. The thickness of the oxide was 1 mm and the
metal layer was 0.6 mm. The gaps between the interdigitated electrodes
and the width of the Au electrodes were 20 and 40 mm, respectively. The
length of the Au fingers was 3.0 mm. The surface configuration was
chosen to avoid metal diffusion through the organic layer, a common
problem of evaporated electrodes onto sandwich-type structures. The or-
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CHCl3 (5 mL) for t4-OTHP or a solution in water (5 mL) for 8b and 8c to
completely cover the interdigitated area. The concentration of the solu-
tions was 25 gLÀ1, thus leading to films with thicknesses of 0.7–1.0 mm
greater than that of the electrodes layer, as measured by a Tencor Alpha-
step 200 profilometer. The samples were dried under ambient conditions.
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a home-made chamber both in air and under dynamic vacuum. The char-
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pumping. The current–voltage and current–time measurements were car-
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Acknowledgements
This study was partially funded by the FIRB RBNE03S7XZ 005 (SYN-
ERGY) project. We thank Prof. Paolo Biscarini (University of Bologna)
for helpful discussions and Prof. Duncan Macquarrie (University of
York) for the gift of a sample of amylose. We are grateful to Dr. Massi-
miliano Cavallini (CNR-INSM-Section Bo) for the AFM image reported
in the Supporting Information.
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Received: June 21, 2007
Revised: August 29, 2007
Published online: October 12, 2007
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