The synthesis of π-electron molecular rods with a thiophene or thieno[3,2-b]thiophene core unit and sulfur alligator clips

Article abstract of DOI:10.1016/j.tetlet.2013.03.084

A series of short oligo(p-phenylene-ethynylene)- and oligo(p- phenylenevinylene)-type molecular rods with an electronically rich thiophene or thieno[3,2-b]thiophene core unit and sulfur anchoring groups (AcS-, t-BuS-) at the termini have been synthesised

Full text of DOI:10.1016/j.tetlet.2013.03.084

Tetrahedron Letters 54 (2013) 2795–2798
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
The synthesis of
p
-electron molecular rods with a thiophene
or thieno[3,2-b]thiophene core unit and sulfur alligator clips
a
a,
⇑
Arnošt Seidler , Jirí Svoboda , Václav Dekoj b, Jana Vacek Chocholoušová b, Jaroslav Vacek b,
ˇ
b
b,
⇑
´
Irena G. Stará , Ivo Stary
a Department of Organic Chemistry, Prague Institute of Chemical Technology, Technická 5/1905, CZ-166 28 Prague 6, Czech Republic
b Institute of Organic Chemistry and Biochemistry, v. v. i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of short oligo(p-phenylene-ethynylene)- and oligo(p-phenylenevinylene)-type molecular rods
with an electronically rich thiophene or thieno[3,2-b]thiophene core unit and sulfur anchoring groups
(AcSÀ, t-BuSÀ) at the termini have been synthesised using Sonogashira coupling or Horner–Wads-
worth–Emmons (E)-olefination methodology. The collection of linear/bent, conjugated/cross-conjugated
systems has been characterised by UV–vis and fluorescence spectroscopy, optical/calculated HOMO–
LUMO gaps and calculated excitation energies.
Received 13 January 2013
Revised 7 March 2013
Accepted 13 March 2013
Available online 25 March 2013
Keywords:
Ó 2013 Elsevier Ltd. All rights reserved.
Molecular wires
Thiophene OPE rods
Thiophene OPV rods
UV spectra
HOMO–LUMO gaps
p
-Electron molecules, oligomers and polymers are the subject
measurements owing to, inter alia, their variable structure, reason-
able synthesis and stability. Although the incorporation of a het-
erocyclic unit such as thiophene into the OPE- and OPV-type
molecular wires might result in interestingly altered electronic
and geometrical properties, their single-molecule conductance
has not been studied systematically. There are only a few examples
of molecular wires comprising a single thiophene unit,9 in contrast
to the systems represented by thiophene-based switchable photo-
chromic molecules,10 oligo(2,5-thienylene-ethynylene)11 and oli-
gothiophenes,12 whose derivatives exhibit low band gaps and
high charge mobility.13
Herein, we report on the synthesis of the short OPE- and OPV-
type rods 1a–d and 2a–d, in which the central 1,4-phenylene unit
is displaced by electronically rich 2,5-, 2,4- and 3,4-thienylenes as
well as thieno[3,2-b]thiophene-2,5-diyl counterparts (Fig. 1). For
the sake of comparison of the single-molecule conductance of
these compounds with that of the parent OPE and OPV structures,
the molecular rods 1e and 2e, have also been synthesised based on
published procedures.14,15 All compounds 1a–e and 2a–e are
equipped with sulfur moieties to serve as alligator clips during
the measurement of the single-molecule conductance by the MCBJ
technique.16 The results of these physical experiments will be pub-
lished elsewhere.
of intense research since they can mediate charge transport along
the p
-conjugated pathway.1 This key attribute is characterised by
the conductance of a bulk material or a single molecule.2 In partic-
ular, the latter approach is notably challenging and rewarding, be-
cause it provides ‘neat’ conductance of a single molecular wire or,
better, a triad given by the metallic electrode–molecule–metallic
electrode system3 (provided that the intermolecular interaction
can be neglected).4 Nowadays, there are two experimental tech-
niques most frequently used, which allow for quantifying single-
molecule conductance: mechanically controllable break junction
(MCBJ)5 and scanning tunnelling microscopy-based break junction
(STMBJ).6 In both cases, functional rod-like molecules with anchor-
ing groups at both ends are needed to provide a strong covalent
attachment to the metallic contacts (usually a gold source and
drain electrodes). Accordingly, the thiol moiety and its analogues
are routinely used,7 although they suffer from some drawbacks.8
Various molecular wires have been investigated ranging from al-
kane to carotenoid dithiols,2c but short oligo(p-phenylene-ethynyl-
ene) (OPE) and oligo(p-phenylenevinylidene) (OPV) rod molecules
and their congeners equipped with acetylsulfanyl anchoring
groups at the termini are popular in single-molecule conductivity
The preparation of thiophene- and thieno[3,2-b]thiophene-de-
rived OPE molecular rods 1a–c started from commercially avail-
able 2,5-, 2,4- and 3,4-dibromothiophenes 3a–c (Scheme 1). The
known 2,5-diiodothieno[3,2-b]thiophene (3d),17 which was em-
⇑
Corresponding authors. Tel.: +420 220 444 182; fax: +420 220 444 288 (J.S.);
tel.: +420 220 183 315; fax: +420 220 183 133 (I.S.).
E-mail addresses: Jiri.Svoboda@vscht.cz (J. Svoboda), stary@uochb.cas.cz (I.
Stary´).
0040-4039/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tetlet.2013.03.084

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A. Seidler et al. / Tetrahedron Letters 54 (2013) 2795–2798
a
a
O
O
O
Ar
AcS
SAc
Br
Br
S
S
3a
8a
1a-e
Br
Br
O
SR
Ar
RS
Br
S
S
2a-d R = t-Bu
2e
3b
8b
R = Ac
Br
S
O
O
a
b
a
c
e
Ar =
Ar =
Ar =
b
d
Ar =
Ar =
S
S
S
S
S
S
S
3c
8c
O
S
S
S
O
7
8d
Figure 1.
p-Electron molecular rods 1a–e and 2a–e with a thiophene or thieno[3,2-
b]thiophene core unit and sulfur anchoring groups.
Scheme 2. Formylation of dibromothiophenes 3a–c and thieno[3,2-b]thiophene 7.
Reagents and conditions: (a) n-BuLi (1.1 equiv), THF, À78 °C to 0 °C, 30 min, then
DMF (1.2 equiv), room temperature, 2 h, then t-BuLi (1.3 equiv), THF, À78 °C, 5 min,
then DMF (excess), À78 °C to room temperature, overnight, 42% for 8a, 22% for 8b,
29% for 8c; (b) n-BuLi (2.2 equiv), THF, À78 °C to 0 °C, 2 h then DMF (excess), À78 °C
to room temperature, overnight, 17%.
X
Ar
X
3a-c X = Br
3d
X = I
O
TMS
a or b
Ar
O
8a-d
TMS
TMS
Ar
P(O)(OEt)
2
4a-d
-BuS
t
a
9
c
t-BuS
Ar
Ar
St-Bu
5a-d
2a-d
AcS
I
d or e
a
c
Ar =
Ar =
b
d
Ar =
Ar =
S
S
S
6
S
AcS
SAc
Ar
S
1a-d
Scheme 3. The synthesis of OPV-type molecular rods 2a–d. Reagents and conditions:
(a) diethyl [4-(tert-butylsulfanyl)-benzyl]phosphonate (9) (2.0 equiv), t-BuOK (3.2–
3.8 equiv), THF, room temperature, 12 h, 48% for 4a, 57% for 4b, 38% for 4c, 78% for 4d.
a
c
Ar =
Ar =
b
d
Ar =
S
S
S
S
with 3a–d under Pd(PPh3)2Cl2/CuI catalysis in the presence of
diisopropylamine in THF at room temperature, or Pd(PPh3)4/CuI
catalysis in triethylamine at 75 °C, the silylated bis(ethynyl) deriv-
atives 4a,18 4b,19 4c20 and 4d21 were obtained. We adjusted the
reaction conditions (such as relatively long reaction times at ambi-
ent temperature) to obtain high yields and clean products. On reac-
tion with tetrabutylammonium fluoride, the double desilylation
proceeded smoothly to afford bis(ethynyl) heteroaromatics 5a,18
5b,22 5c22 and 5d21 in good yields. Thus, we performed the final
double Sonogashira coupling with S-(4-iodophenyl)ethanethioate
(6)23 under Pd(PPh3)2Cl2/CuI catalysis in the presence of diisopro-
pylamine in THF at room temperature, or Pd(PPh3)4/CuI catalysis
in triethylamine at 75 °C to afford the thiophene- and thieno[3,2-
b]thiophene-derived OPE molecular rods 1a–d in moderate yields
but in good purities, which were further increased by chromato-
graphic separation. Using the same methodology, we prepared
the parent compound 1e.14 It is worth noting that the alternative
Ar =
S
Scheme 1. The synthesis of the OPE-type molecular rods 1a–d. Reagents and
conditions: (a) TMS–C„CH (3.0 equiv), Pd(PPh3)2Cl2 (10 mol %), CuI (10 mol %), i-
Pr2NH (3.2 equiv), THF, room temperature,
(10.0 equiv), Pd(PPh3)4 (10 mol %), CuI (10 mol %), Et3N, 75 °C, 3 d, 87% for 4b, 78%
for 4c, 51% for 4d; (c) n-Bu4NF (16 equiv), THF, room temperature, 1–3 h, 98% for 5a,
98% for 5b, 99% for 5c, 81% for 5d; (d) 6 (2.0 equiv), Pd(PPh3)2Cl2 (10 mol %), CuI
(10 mol %), i-Pr2NH (1.5 equiv), THF, room temperature, 3 d, 40% for 1a, 27% for 1b,
21% for 1c; (e) 6 (2.0 equiv), Pd(PPh3)4 (10 mol %), CuI (10 mol %), Et3N, 75 °C, 40 h,
32% for 1d.
2 d, 90% for 4a; (b) TMS–C„CH
ployed in the synthesis of 1d, was obtained by iodination of com-
mercially available thieno[3,2-b]thiophene (7) using I2 in the pres-
ence of an Ag(I) salt.
The preparation of 1a–d followed a general synthetic scheme,
which relied on Sonogashira coupling methodology (Scheme 1).
Performing the double cross-couplings of trimethylsilyl acetylene

A. Seidler et al. / Tetrahedron Letters 54 (2013) 2795–2798
2797
Table 1
The optical properties of the molecular rods 1a–e and 2a–e
a
b
c
Compound
kmax,abs (nm)
Calculated kmax,abs (nm)
kmax,em (nm) (excitation k, nm)
1a
1b
1c
1d
1e
2a
2b
2c
2d
2e
356
296
286
375
329
400
318
314
409
365
370
311
300
387
339
396
330
305
413
360
416 (390)
weak fluorescence
weak fluorescence
430 (405)
386 (360)
475 (435)
weak fluorescence
weak fluorescence
483 (430)
429 (400)
a
The maximum absorption wavelength kmax,abs corresponds to the absorption maximum of the longest wavelength band in
the experimental UV–vis spectrum (at concentrations of 0.10–26.9 Â 10À5 mol/L in acetonitrile).
b
The maximum absorption wavelength kmax,abs was calculated by TD-DFT (B2PLYP/cc-pVDZ) on the structures optimised by
DFT (B3LYP/ccpVDZ).
c
The maximum emission wavelength kmax,em corresponds to the emission maximum of the longest wavelength band in the
experimental fluorescence spectrum (at concentrations of 8.4–10.6 Â 10À5 mol/L in acetonitrile).
approach to 1a–e through Sonogashira coupling between 3a–e and
S-(4-ethynylphenyl)ethanethioate11 under Pd0/CuI catalysis led
generally to complex mixtures, from which the model compounds
1a–e were difficult to isolate.
With the aim of synthesising the analogous thiophene- and thie-
no[3,2-b]thiophene-derived OPV molecular rods 2a–d through the
Horner–Wadsworth–Emmons (E)-olefination methodology, we
prepared the corresponding dialdehydes 8a,24 8b,25 8c26 and 8d27
by modification of the literature procedures (Scheme 2). The double
formylation of dibromothiophenes 3a–c was carried out as a two-
step process; the first bromine-to-lithium exchange at À78 °C was
performed using n-butyllithium and, after adding an equivalent
amount of N,N-dimethylformamide, the second lithiation proceeded
in the presence of t-butyllithium at À78 °C, followed by the addition
of an excess of DMF. The dialdehyde 8d was prepared by the double
metallation of 7 with 2 equiv of n-butyllithium at 0 °C, after which
the dilithium intermediate was reacted with an excess of DMF.
The syntheses of 2a–d were completed by the double Horner–
Wadsworth–Emmons reaction of diethyl [4-(tert-butylsulfa-
nyl)benzyl]phosphonate (9)15d with dialdehydes 8a–d to give the
corresponding olefins in moderate or good yield (Scheme 3). Using
the same methodology, we also prepared the parent compound
2e,15 which was obtained from its t-butylsulfanyl analogue by
treatment with acetyl chloride and boron tribromide.15d Although
the protecting group transformation proceeded well in this case,
the same operation with the thiophene- and thieno[3,2-b]thio-
phene-derived OPV molecular rods 2a–d failed since a complex
mixture was generally formed.
The thiophene-based OPE and OPV molecular rods 1a–c and 2a–
c are bent at angles ranging from 68° to 150°. The rods 1d, e and 2d,
e are linear, as a result of which they exhibit the largest distances,
in this series, between the sulfur atoms of the anchoring groups
(19.8–22.1 Å).
Figure 2. The electron probability distributions within the frontier orbitals of
linear-conjugated 1a and cross-conjugated 1b were calculated by DFT (B2PLYP/
ccpVDZ) on the structures optimised by DFT (B3LYP/ccpVDZ).
In the UV–vis spectra of 1a–e and 2a–e, a red shift of the
absorption maxima of the longest wavelength bands can be seen
uniformly when going from the corresponding OPE to OPV deriva-
tives (22–44 nm, Table 1). Interestingly, the kmax values of 2,4- and
3,4-thiophene derivatives 1b, c (296 vs 286 nm) are comparable,
which was also observed with 2b, c (318 vs 314 nm), and the
absorption maxima are shifted to shorter wavelengths. This fact
can be ascribed to weaker conjugation along the backbone of 3,4-
thiophene derivatives 1c and 2c and cross-conjugated 1b and 2b.
Such an effect can be demonstrated by comparison of the electron
probability distribution within the frontier orbitals of linear-conju-
gated 1a and cross-conjugated 1b, as calculated by density func-
tional theory (DFT) methods (Fig. 2). The weak fluorescence of
1b, c and 2b, c (Table 1) was also in accord with the reduced con-
jugation in these rod-shaped compounds. In fact, the fluorescence
emission efficiency corresponds to the
p
-conjugation length in the
-con-
excited singlet state,28 which might be correlated with the
p
jugation length in the ground state. The absorption or fluorescence
spectra allowed calculation of the optical HOMO–LUMO gap of 1a–
e and 2a–e (Table 2). Among both the OPE and OPV series, the thi-
eno[3,2-b]thiophene derivatives 1d and 2d exhibited the largest
red shifts and, accordingly, the smallest optical HOMO–LUMO band
gaps of 3.0 or 2.7 eV, respectively. The parent OPE/OPV rods 1e and
2e with 1,4-phenylene core units absorb at shorter wavelengths
than their electron rich 2,5-thiophene counterparts 1a and 2a,
which results in a narrowing of the gap by about 0.2 eV in favour
of the thiophene derivatives. The magnitudes of the HOMO–LUMO
gaps of 1a–e and 2a–e calculated by DFT methods generally over-

2798
A. Seidler et al. / Tetrahedron Letters 54 (2013) 2795–2798
Table 2
The optical/calculated HOMO–LUMO gaps and calculated excitation energies of the molecular rods 1a–e and 2a–2e
Compound
Optical HOMO–LUMO gapa (eV)
Calculated HOMO–LUMO gapb (eV)
Calculated excitation energyc (eV)
1a
1b
1c
1d
1e
2a
2b
2c
2d
2e
3.1 (3.0)
3.5
3.7
3.0 (2.9)
3.3 (3.2)
2.8 (2.6)
3.1
3.3
2.7 (2.6)
3.0 (2.9)
5.2
5.9
6.4
5.0
5.6
4.9
5.5
6.2
4.7
5.2
3.4
4.0
4.1
3.2
3.7
3.1
3.8
4.1
3.0
3.4
a
The optical HOMO–LUMO gap was calculated from the onset of the longest wavelength band in the experimental UV–vis spectra or
from the wavelength of the maximum emission band in the experimental fluorescence spectra (in parentheses).
b
The HOMO–LUMO gap in the ground state was calculated by DFT (B2PLYP/ccpVDZ) on the structures optimised by DFT (B3LYP/
ccpVDZ).
c
The energy needed for the electron excitation to the first singlet state was calculated by TD-DFT (B2PLYP/cc-pVDZ) on the structures
optimised by DFT (B3LYP/ccpVDZ).
4. Wu, S.; González, M. T.; Huber, R.; Grunder, S.; Mayor, M.; Schönenberger, C.;
estimate the actual excitation energies by 67–88% (Table 2) and,
therefore, the energies needed for the electron excitation to the
first singlet state calculated by the TD-DFT method better approx-
imate the corresponding optical HOMO–LUMO gaps, being overes-
timated now by only 7–24%.
In conclusion, we have prepared a series of oligo(p-phenylene-
ethynylene)- and oligo(p-phenylenevinylene)-type molecular rods
with thiophene or thieno[3,2-b]thiophene core units and end-
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conjugation or cross-conjugation in these molecular rods has led
to hypsochromic shifts of the corresponding kmax in the UV–vis spec-
tra (about 60À86 nm) as well as to weak or no fluorescence, in con-
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and calculated excitation energies have been found. Experiments
to estimate their molecular conductivities by using the mechani-
cally controllable break-junction method are currently underway.
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This research was supported by a Grant from the ASCR (Grant
No. IAA400550919), by the Academy of Sciences of the Czech
Republic (Grant No. M200550914), by the Ministry of Education,
Youth and Sports of the Czech Republic from specific university re-
search (MSMT No. 21/2011), and by the Institute of Organic Chem-
istry and Biochemistry, Academy of Sciences of the Czech Republic
(RVO: 61388963).
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Supplementary data
Supplementary data (the experimental procedures and NMR
spectra of the substrates and products) associated with this article
can be found, in the online version, at http://dx.doi.org/10.1016/
j.tetlet.2013.03.084.
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