Star-shaped ethynylpyrimidine with long alkoxyl side chains: synthesis, fluorescence and 2D self-assembling

Article abstract of DOI:10.1016/j.tetlet.2009.09.169

In this contribution, we describe the synthesis of a star shaped ethynylpyrimidine having long alkoxyl side chains using Suzuki cross-coupling reactions. This compound presents interesting blue light emission fluorescence as well as self-assembling proper

Full text of DOI:10.1016/j.tetlet.2009.09.169

Tetrahedron Letters 50 (2009) 7055–7058
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Star-shaped ethynylpyrimidine with long alkoxyl side chains: synthesis,
fluorescence and 2D self-assembling
b
b
c
c
Sylvain Achelle a, Nelly Plé a, , David Kreher , André-Jean Attias , Imad Arfaoui , Fabrice Charra
*
a Institut de Chimie Organique Fine (IRCOF) UMR-CNRS 6014, INSA et Université de Rouen, BP08 76131 Mont-Saint-Aignan Cedex, France
b Laboratoire de Chimie des Polymères (LCP), Université Pierre et Marie Curie, CNRS-UMR 7610, 4 Place Jussieu, Case 185, 75252 Paris Cedex 05, France
c Service de Physique et Chimie des Surfaces et Interfaces, Commissariat à l’Energie Atomique, Centre de Saclay, 91191 Gif-sur-Yvette Cedex, France
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 14 July 2009
Revised 28 September 2009
Accepted 29 September 2009
Available online 2 October 2009
In this contribution, we describe the synthesis of a star shaped ethynylpyrimidine having long alkoxyl
side chains using Suzuki cross-coupling reactions. This compound presents interesting blue light emis-
sion fluorescence as well as self-assembling properties on graphite: a chiral system is obtained starting
from a nonchiral molecule. This preliminary work indicates that pyrimidine derivatives could be good
candidates for the development of novel functional organic materials.
Ó 2009 Elsevier Ltd. All rights reserved.
Keywords:
Pyrimidine
Cross-coupling reactions
Fluorescence
Self-assembling
1. Introduction
The marking mechanism consists just in the minimal substitution
of one carbon atom by a nitrogen atom in the central conjugated
Introducing heteroaryl moieties into
p
-extended systems is a
core.10
way to modify and sometimes enhance useful properties of ad-
vanced ‘electro-optic’ materials,1 heteroaromatics being particu-
larly useful where electron transport is necessary.
Consequently, it is interesting to compare the 2D self-assem-
bling properties of an equivalent star-shaped molecule with a
pyrimidine core. The two nitrogen atoms of the pyrimidine ring
are expected to alter the chemical affinity of the final host system
for specific guest molecules.
As a first step towards the above molecular designs (e.g., such as
compound A), 2,4,6-tris(phenylethynyl)pyrimidine substituted by
long alkoxyl chains (compound 1, Fig. 1), which offers a possible
route towards the synthesis of the compound A, through reduction
of the C–C triple bond shows interesting electronic and self-organi-
zation properties by itself. The aim of this Letter is to describe the
synthesis, fluorescence and self-assembling properties of 2,4,6-
tris(phenylethynyl)pyrimidine substituted by long alkoxyl chains.
In this context, over the past decade, the synthesis of pyrimi-
dine derivatives has received intensive research interest with
applications as organic materials in various fields such as calamit-
ic2 and discotic3 liquid crystals, n-type semi-conductors4, fluores-
cence5 or organic light emitting devices (OLEDs) for display and
lighting.6 Indeed, due to its aromaticity, to its strong electron-with-
drawing character, to its high dipolar interaction and to its pH sen-
sibility, pyrimidine presents the requested characteristics in order
to be incorporated in organic material in view of such applications.
On one hand, and in addition to their liquid crystal 3D self-
assembling, judiciously substituted pyrimidine star-shaped deriva-
tives could present also 2D self-assembling properties.7 On the
other hand, similar systems based on specific benzene, pyridine
or triazine cored stilbenoid compounds were described8 and pres-
ent promising applications as molecular sieves.9 In this latter
example, the authors devised a marking/tracking procedure to
achieve direct visual discrimination of individual molecules in a
self-assembled layer based on respective carbon/nitrogen contrast
in high resolution scanning tunneling microscopy (STM) imaging.
2. Results and discussion
The best method for the synthesis of 2,4,6-trialkynylpyrimidine
consists in carrying out Suzuki cross-coupling reaction with potas-
sium alkynyltrifluoroborates on 2,4,6-trichloropyrimidine.11 For
the synthesis of the arm of the molecule, we have chosen to start
from commercially available 3,4-dihydroxybenzaldehyde, and the
ethynyl part will be introduced by the Corey–Fuchs method.12
The first step consists in a Williamson reaction to form the long
alkoxy chains, the second step is the action of carbon tetrabromide
with triphenylphosphine on the aldehyde to access to dibromoal-
* Corresponding author. Tel.: +33 235 522 902; fax: +33 235 522 962.
E-mail address: nelly.ple@insa-rouen.fr (N. Plé).
0040-4039/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2009.09.169

7056
S. Achelle et al. / Tetrahedron Letters 50 (2009) 7055–7058
OC10H21
OC10H21
OC10H21
OC10H21
N
N
N
N
C10H21
O
C10H21O
C10H21
O
OC10H21
OC10H21
OC10H21
OC10H21
OC10H21
A
1
Figure 1.
cene 3. Then 2 equiv of n-BuLi are added leading to the alkyne 4.
The corresponding potassium phenylalkynyltrifluoroborate 5 was
obtained by metallation of 4 with n-BuLi followed by the action
of triisopropyl borate and subsequent treatment with KHF2
(Scheme 1).13
the solution-solid interface: indeed this technique permits to ob-
tain direct-space information on the structures of spontaneously-
formed self-assembled organic monolayers with a submolecular
resolution.16 Such typical in situ room temperature STM images
are presented in Figure 3.
The potassium alkynyltrifluoroborate 5 was then used in cross-
coupling reaction with 2,4,6-trichloropyrimidine. It should be
noted that the tricoupled product cannot be obtained in one step.
Indeed, when 5 equiv of 5 were used, only the dicoupled product
6 was obtained, which could be probably due to the steric hin-
drance induced by the long alkoxy chains. However, when a further
coupling reaction was performed with 6 and five other equivalents
of 5, the expected trisubstituted product 1 is obtained with a mod-
erate yield (Scheme 2).14
The UV absorption and fluorescence emission spectra of 1 are
given in Figure 2. Compound 1 exhibits an absorption maximum
at 377 nm and a structureless emission peak at 476 nm. The rela-
tive fluorescence quantum yield (UF) of 1 was measured to be
0.25 using Harmane (b-carboline derivative) as a reference.15
Based on the peak position on the UV spectrum, chemically sta-
ble compound 1 appears well suited for emission of blue light with
a relatively high quantum yield.
Compound 1, compared to 1,3,5-tris[(E)-2-(3,5-didecyloxyphe-
nyl)-ethenyl]benzene (compound B) as a reference material9 pre-
sents essentially C–C triple bonds instead of double bonds at the
same location. Compound B is constituted of three specific molec-
ular units designed to act as functional linking groups able to form
strong surface-assisted intermolecular ‘clips’ which by interdigita-
tion, strictly mimic the atomically precise organization of n-al-
kanes on HOPG. The ‘clip concept’ is described in details
elsewere.17 The structural difference in case of compound 1 com-
pared with compound B increases the distance between alkyl
chains which become less suited to form the so-called ‘clips’ of
interdigitated alkyl chains. This also prevents the formation of an
arrangement in exact registry with graphite. Consistently, no
stable honeycomb 2D self-organization is observed for 1: Indeed
our ‘host’ system could not compensate the energetic cost of the
formation of empty cavity as initially envisaged. Yet, a different
2D-self-assembly is observed, which consists in formation of di-
mers arranged as single domains: Dimer formation may be ex-
plained by the formation of only one clip per molecule. This may
The self-organization on highly ordered pyrolytic graphite
(HOPG) of compound 1 has been studied as well, using STM at
OC10H21
OC10H21
OC10H21
OH
OC10H21
OH
(ii)
(i)
Br
CHO
CHO
Br
2
3
OC10H21
OC10H21
OC10H21
OC10H21 (iii)
(iv)
BF3K
H
5
4
Scheme 1. Reagents and conditions: (i) BrC10H21, K2CO3, DMF, 150 °C, 2 h, 73%; (ii) CBr4, PPh3, CH2Cl2, 15 min, 0 °C, 79%; (iii) n-BuLi, THF, ꢀ78 °C 1 h, 88%; (iv) 1° n-BuLi, THF,
78 °C 1 h, 2° B(OiPr)3, ꢀ78 °C to ꢀ20 °C, 2 h , 3° KHF2, H2O, ꢀ20 °C to rt, 2 h, 80%.

S. Achelle et al. / Tetrahedron Letters 50 (2009) 7055–7058
7057
Cl
Cl
(i)
N
N
N
N
Cl
Cl
OC10H21
OC10H21
C10H21
O
6
40%
OC10H21
(i)
OC10H21
OC10H21
N
N
OC10H21
OC10H21
C10H21
O
OC10H21
1
31%
Scheme 2. Reagents: (i) 5, PdCl2(dppf), CH2Cl2, Cs2CO3, THF, H2O, d, 12 h.
Figure 2. UV–vis absorption (blue) and fluorescence spectra (red) of 1 (excitation
k = 366 nm) in CHCl3.
be made possible here through an ad-hoc orientation of two 3,4-
substituted arms in order to exhibit two parallel alkyl chains dis-
tant of 4–5 Å. The molecular structure allows only one such pattern
per molecule, which explains the formation of one single clip and
then the dimer organization.
We move now to the longer-range organization of the dimers
themselves as independent entities. On the Figure 3, six different
orientations in two groups of three oriented at 60° one of the other
are observed. Thus, there is epitaxy on the graphite probably due to
the adsorption of the clipped parallel alkyl chains mentioned above
in registry with the substrate. The axes of the domains are tilted
with respect to those of graphite: two chiral domain types, enan-
tiomer one of the other, are then observed. This phenomenon has
already been reported with discotic liquid crystals18 and rod-
shaped molecules.19 The molecule is then in ‘pro-chiral’ configura-
tion, both molecules of dimer being posed on the same face.
In summary, we have synthesized a new star shaped molecule
with a pyrimidine core by Suzuki cross-coupling reaction. This
molecule presents interesting fluorescence properties. Interesting
self-organization properties on HOPG have also been observed by
STM and interpreted based on previous observation. These preli-
minary results confirm the clip concept proposed previously with
a different molecular design.17 Moreover, with a minor modifica-
tion of the molecular design of the arms of molecule 1, the fabrica-
Figure 3. STM images of the monolayer of 1 on HOPG at the interface with a
ꢁ10ꢀ2 mol/L solution in phenyloctane. Scan sizes: 100 ꢂ 100 nm (a), 50 ꢂ 50 nm (b)
and 25 ꢂ 25 nm (c) recorded in the current (i.e., constant height) mode with a
scanning rate of 40 ms per line, a sample bias of ꢀ1000 mV and a set point of 10 pA.
(d) Two excerpts from image b showing the presence of mirror-symmetric domains.
The symmetry line must corresponds to a mirror symmetry axis of HOPG, either
h1 0 0i or h1 1 0i.
tion of a honeycomb-like host matrix can be reasonably envisaged
with two nitrogen atoms oriented toward the cavity, the affinity of
these cavities being then modified which allows to expect a mod-
ulation of the molecular sieve properties. The next step in this ser-
ies of studies will be the synthesis of compound A.

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S. Achelle et al. / Tetrahedron Letters 50 (2009) 7055–7058
concentrated in vacuo. The residue was purified by column chromatography
References and notes
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as a yellow oil. 1H NMR (CDCl3, 300 MHz) : d 0.91 (t, J = 6.8 Hz, 6H, 2 ꢂ CH3),
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0
1.48–1.30 (m, 28H, 14 ꢂ CH2), 1.85–1.78 (m, 4H, 2 ꢂ CH2), 3.00 (s, 1H, H1 ),
4.01–3.96 (m, 4H, 2 ꢂ OCH2), 6.79 (d, J = 7.8 Hz, 1H, H6), 7.01 (d, J = 1.7 Hz, 1H,
H2), 7.07 (dd, J = 7.8 Hz, J = 1.7 Hz, 1H, H5) 13C NMR (CDCl3, 75 MHz): 14.5, 23.1,
23.7, 26.4, 29.6 (2C), 29.8 (2C), 30.0, 30.1, 32.3, 32.4, 69.4, 69.5, 75.9, 84.3,
113.4, 114.5, 117.4, 125.9, 149.0, 150.4 Anal. Calcd for C28H46O2 (414.35): C,
81.10; H, 11.18. Found C, 81.13; H, 11.18. Compound 5: a solution of alkyne
(1.22 g, 2.94 mmol) in 50 mL of dry THF was cooled to ꢀ78 °C under nitrogen.
n-BuLi (1.6 M, 1 equiv) was added dropwise, and the solution was stirred for
1 h at this temperature. Triisopropylborate (1.5 equiv) was then added
dropwise at ꢀ78 °C. The solution was stirred at this temperature for 1 h after
which it was allowed to warm to ꢀ20 °C for 1 h. A saturated aqueous solution
of potassium hydrogen difluoride (6.0 equiv) was added to the vigorously
stirred solution. The resulting mixture was stirred for 1 h at ꢀ20 °C after which
it was warmed to room temperature for 1 h. The solvent was removed under
reduced pressure, and the resulting white solid was dried under high vacuum
to remove all water. The solid was then washed with acetone and with hot
acetone. The resulting organic solution was evaporated to give 1.22 g (80%) of 5
as a colorless solid. Mp >250 °C 1H NMR (DMSO-d6, 300 MHz): d 0.91 (t,
J = 6.8 Hz, 6H, 2 ꢂ CH3), 1.49–1.32 (m, 28H, 14 ꢂ CH2), 1.82–1.72 (m, 4H,
2 ꢂ CH2), 4.00–3.97 (m, 4H, 2 ꢂ OCH2), 6.92–6.86 (m, 3H, H2,5,6
)
13C NMR
(DMSO-d6, 75 MHz) d 14.3, 22.5, 26.0, 26.3, 28.4, 29.1, 29.2, 29.3, 29.5, 31.7,
68.5, 68.6, 90.0, 113.7, 116.5, 118.3, 124.1, 148.2, 148.4 19F NMR (DMSO-d6,
282.5 MHz) ꢀ131.9. IR (KBr, cmꢀ1) 2919, 2851, 2184, 1515, 1239, 1046.
14. Compound 6: 2,4,6-trichloropyrimidine (183 mg, 1.00 mmol),
5 (2.60 g,
5.4 mmol), PdCl2(dppf), CH2Cl2 (216 mg, 0.26 mmol) and Cs2CO3 (5.27 g,
16.2 mmol) were mixed with THF and degassed water under Nitrogen (20:1
THF to water ratio). The solution was heated at reflux for 12 h. Then the
mixture was cooled, and 10 mL of water was added to the flask. The resulting
solution was then extracted with diethyl ether. The combined organic extracts
were washed with 1 M HCl and brine and then dried over MgSO4. After filtering
off the solid, the solvent was removed under reduced pressure to give 375 mg
(40%) of 6 as a pale yellow solid. mp = 58 °C. 1H NMR (CDCl3, 300 MHz): d 0.90
(t, 12H, 4 ꢂ CH3), 1.49–1.18 (m, 56H, 28 ꢂ CH3), 1.89–1.81 (m, 8H, 4 ꢂ CH2)
4.08–4.01 (m, 8H, 4 ꢂ OCH2) 6.84 (d, J = 8.1 Hz, 2H, HPh), 7.12 (s, 2H, HPh), 7.21
(d, J = 8.1 Hz, 2H, HPh), 7.45 (s, 1H, H5) 13C NMR (CDCl3, 75 MHz): d 13.1, 21.7,
25.0, 28.1(2C), 28.4, 28.6, 28.7, 30.9, 68.0, 68.2, 84.1, 96.8, 111.2, 111.7, 116.0,
122.0, 125.6, 147.7, 150.5, 152.1, 160.3. IR (KBr, cmꢀ1) 2818, 2850, 2212, 1557,
1514, 1469, 1268, 1243, 1128. Anal. Calcd for C60H91ClN2O4 (939.83): C, 76.68;
H, 9.76; N, 2.98. Found C, 76.81; H, 9.83; N, 2.81. Compound 1: this compound
was prepared by similar procedure described for compound 6 using 6 instead
of 2,4,6-trichloropyrimidine.yellow solid. mp <50 °C. 1H NMR (CDCl3,
300 MHz): d 0.91 (t, 18H, 6 ꢂ CH3), 1.49–1.18 (m, 84H, 42 ꢂ CH3), 1.89–1.81
(m, 12H, 6 ꢂ CH2) 4.08–4.01 (m, 12H, 6 ꢂ OCH2) 6.90–6.85 (m, 3H, HPh), 7.15
(s, 3H, HPh), 7.24–7.21 (m, 3H, HPh), 7.48 (s, 1H, H5) 13C NMR (CDCl3, 75 MHz): d
13.1, 21.7, 25.0, 28.1, 28.4 (2C), 28.6 (4C), 28.7, 30.9, 68.1, 68.2, 84.6, 85.9, 88.3,
95.0, 111.7, 111.8, 112.0, 116.0, 116.3, 121.9, 125.3, 125.4, 147.5, 147.7, 149.8,
150.2, 152.7. IR (KBr, cmꢀ1) 2924, 2854, 2208, 1555, 1513, 1264, 1247. Anal.
Calcd for C88H136N2O6 (1318.03): C, 80.19; H, 10.40; N, 2.13. Found C, 80.51; H,
10.78; N, 1.89.
12. (a) Corey, E. J.; Fuchs, P. L. Tetrahedron Lett. 1972, 13, 3769–3772; (b) Van Hijfte,
L.; Kolb, M.; Witz, P. Tetrahedron Lett. 1989, 30, 3655–3656.
13. Compound 3: triphenylphosphine (1.37 g, 5.25 mmol) was added to CBr4
(792 mg, 2.39 mmol) in anhydrous CH2Cl2 (17 mL) at 0 °C. Compound 2 (1.00 g,
2.39 mmol) was added and the resulting mixture was stirred at 0 °C for 10 min
before the addition of H2O (6 mL). The organic phase was separated, dried
(MgSO4) and concentrated in vacuo. The yellow slurry obtained was triturated
with hexane and then Et2O to remove Ph3PO. The organic washings were dried
(MgSO4) and concentrated in vacuo. The residue was purified by column
chromatography (silica gel, eluent petroleum ether/ethyl acetate (9:1)) to give
1.08 g (79%) of 3 as a colorless solid mp <50 °C. 1H NMR (CDCl3, 300 MHz): d
0.91–0.86 (m, 6H, 2 ꢂ CH3), 1.47–1.28 (m, 28H, 14 ꢂ CH2), 1.83–1.78 (m, 4H,
2 ꢂ CH2), 4.00–3.96 (m, 4H, 2 ꢂ OCH2), 6.80 (d, J = 7.8 Hz, 1H, H6), 7.06–7.02
15. (a) Fery-Forgues, S.; Lavabre, D. J. Chem. Educ. 1999, 76, 1260–1265; (b) Pardo,
A.; Reyman, D.; Poyato, J. M. L.; Medina, F. J. Lumin. 1992, 51, 269–274.
16. Abdel-Mottaleb, M. M. S.; De Feyter, S.; Gesquière, M.; Sieffert, M.; Klapper, M.;
Müllen, K.; De Schryver, F. C. Nano Lett. 2001, 1, 353–359.
(m, 1H, H5), 7.19 (d, J = 1.7 Hz, 1H, H2), 7.35 (s, 1H, H1 ). 13C NMR (CDCl3,
0
17. (a) Bléger, D.; Kreher, D.; Mathevet, F.; Attias, A.-J.; Schull, G.; Huard, A.;
Douillard, L.; Fiorini-Debuischert, C.; Charra, F. Angew. Chem., Int. Ed. 2007, 46,
7404–7407; (b) Bléger, D.; Kreher, D.; Mathevet, F.; Attias, A.-J.; Arfaoui, I.;
Metgé, G.; Douillard, L.; Fiorini-Debuisschert, C.; Charra, F. Angew. Chem., Int.
Ed. 2008, 47, 8412–8415.
75 MHz): d 14.6, 23.2, 26.5, 29.7, 29.8, 29.9 (2C), 30.1 (2C), 32,4, 69.4, 69.7,
87.3, 113.2, 114.0, 122.4, 128.2, 136.9, 149.0, 150.0. IR (KBr, cmꢀ1) 2919, 2850,
1597, 1517, 1469, 1278, 1281, 1235, 1148, 1138. Anal. Calcd for C28H46Br2O2
(512.19): C, 58.54; H, 8.07. Found: C, 58.49; H, 8.03. Compound 4: n-BuLi
(1.6 M, 9.66 mL, 14 mmol) was added slowly (over 1 h) to 3 (4.06 g, 7 mmol) in
anhydrous THF (90 mL) cooled to ꢀ78 °C. The resulting brown solution was
stirred at ꢀ78 °C for 1 h then warmed slowly to rt and stirred for a further 1 h.
Saturated NH4Cl (50 mL) was added and the mixture extracted with ether
(3 ꢂ 50 mL). The combined etheral extracts were dried (MgSO4) and
18. (a) Charra, F.; Cousty, J. Phys. Rev. Lett. 1998, 80, 1682–1685; (b) Li, C.; Zeng, Q.;
Wu, P.; Xu, S.; Wang, C.; Qiao, Y.; Wan, L.; Bai, C. J. Phys. Chem. B 2002, 106,
13262–13267.
19. Viswanathan, R.; Zasadzinski, J. A.; Schwartz, D. K. Nature 1994, 368, 440–444.