Double Suzuki cross-coupling reaction of pyrimidine boronic acid: Synthesis of new versatile dielectrophile

Article abstract of DOI:10.1002/aoc.2865

The double Suzuki cross-coupling reaction has successfully been applied for the synthesis of 5,5'-(5-butoxy-1,3-phenylene)bis(2-chloropyrimidine) with two reactive chloro groups and an alkoxy side chain starting from 2-chloropyrimidin-5-ylboronic acid and 1,3-dibromo-5-butoxybenzene. The reactivity of this dielectrophile was tested by reaction with aniline and phenol, a nitrogen and oxygen nucleophile, respectively. The new dielectrophile would further provide an ideal platform for the construction of large hetero-atom bridged macrocycles for desired properties and functions in supramolecular and material chemistry. Copyright

Full text of DOI:10.1002/aoc.2865

Full Paper
Received: 27 February 2012
Revised: 28 March 2012
Accepted: 28 March 2012
Published online in Wiley Online Library
(wileyonlinelibrary.com) DOI 10.1002/aoc.2865
Double Suzuki cross-coupling reaction of
pyrimidine boronic acid: synthesis of new
versatile dielectrophile
Muhammad Moazzam Naseer* and Shahid Hameed
The double Suzuki cross-coupling reaction has successfully been applied for the synthesis of 5,5′-(5-butoxy-1,3-phenylene)bis
(2-chloropyrimidine) with two reactive chloro groups and an alkoxy side chain starting from 2-chloropyrimidin-5-ylboronic
acid and 1,3-dibromo-5-butoxybenzene. The reactivity of this dielectrophile was tested by reaction with aniline and phenol,
a nitrogen and oxygen nucleophile, respectively. The new dielectrophile would further provide an ideal platform for the
construction of large hetero-atom bridged macrocycles for desired properties and functions in supramolecular and material
chemistry. Copyright © 2012 John Wiley & Sons, Ltd.
Keywords: pyrimidine boronic acid; double coupling reaction; dielectrophile; substitution
cross-coupling reaction of 2-chloropyrimidin-5-ylboronic acid
and 1,3-dibromo-5-butoxybenzene to obtain a unique and versa-
Introduction
Dielectrophiles are important building blocks for the construction
of various macrocycles used in host–guest chemistry.[1,2] For
example, dielectrophiles and dinucleophiles react together to
form hetero-atom bridged calixarenes,[3–10] whereas dielectro-
philes and trinucleophiles react to produce molecular cages.[11–15]
The size of these electrophiles and nucleophiles determines the
cavity size of the macrocycles and the cavity size in turn is very
important for their applications. Recently, extensive utilization of
giant macrocycles in the field of supramolecular[16–20] and material
chemistry[21–25] has opened up a need for the synthesis of large,
rigid and reactive dielectrophilic fragments.
In the past two decades, the palladium-catalyzed Suzuki cross-
coupling reaction has evolved into one of the most widely
employed, powerful and versatile tools for carbon–carbon
bond-forming processes.[26–35] This cross-coupling reaction has
gained importance due to the growing availability of the boronic
acids, their stability to moisture and air, and their excellent
compatibility with a large variety of functional groups. Its impact
on organic synthesis is largely recognized due to the fact that
it provides a general, convenient and applicable method for
the formation of biaryls, which are found in many biologically
active compounds,[36–38] polymers,[39] ligands,[40] and other useful
materials.[41]
tile dielectrophile which was further reacted with nitrogen and
oxygen nucleophiles to certify its reactivity for its further utility
in the field of supramolecular, material and medicinal chemistry.
Results and Discussion
We initiated our study with the synthesis of 1,3-phenylenebisboronic
acid (1),[49,50] from 1,3-dibromo-5-butoxybenzene, which was
then treated with 5-bromo-2-chloropyrimidine (2) to obtain our
desired dielectrophile (3). Two different Suzuki cross-coupling
reaction conditions were used for this purpose (Scheme 1).[51,52]
Thin-layer chromatographic analysis gave a clear indication of
some product formation in both cases. However, we were unable
to take that product from the flask in pure form, which led us to
think about the solubility of the product. Fortunately, a small
amount of the pure product was obtained when the reaction
scale was enlarged. As we were thinking, the solubility of the
compound 3 was very poor in almost all of the solvents and the
pure product was indeed difficult to isolate from the reaction
mixture. Nevertheless, we were able to identify the structure of
1
compound 3 by H NMR spectroscopy and electrospray ioniza-
tion (ESI) mass spectrometry.
Aiming to obtain dielectrophile with reasonable solubility for
its further applications, 1,3-dibromo-5-butoxybenzene[53,54] (5)
was prepared by reacting 1,3,5-tribromobenzene with sodium
n-butoxide. When the same strategy as for the synthesis of 1,3-
phenylenebisboronic acid (1) from 1,3-dibromobenzene was
In spite of the enormous progress, limitations of this method
include its inability to maintain the efficiency displayed in simple
aryl–aryl bond formation when nitrogen heterocycles are
employed as one or both of the coupling partners.[42,43] Nitrogen-
based heterocycles are an important component of most of
the biologically active compounds, but usually insertion of these
heterocyclic motifs are detrimental to catalytic activity of
palladium-catalyzed reactions.[36–38] Although there are few
reports available in the literature where heteroarylboronic acids
are used as one of the coupling partner,[44–48] to best of our
knowledge no one has reported double Suzuki cross-coupling
of heteroarylboronic acids. Herein we report the double Suzuki
*
Correspondence to: Muhammad Moazzam Naseer, Department of Chemistry,
Quaid-i-Azam University, Islamabad-45320, Pakistan. E-mail: moazzam@
qau.edu.pk
Department of Chemistry, Quaid-i-Azam University, Islamabad-45320, Pakistan
Appl. Organometal. Chem. 2012, 26, 330–334
Copyright © 2012 John Wiley & Sons, Ltd.

Double Suzuki reaction and dielectrophile
Br
Cl
B(OH)2
+
Pd catalyst
N
N
N
2
N
Base
Solvent
Cl
N
N
Cl
3
B(OH)2
1
Scheme 1. Synthesis of dielectrophile from 1,3-phenylenebisboronic acid and 5-bromo-2- chloropyrimidine: (a) Pd(PPh3)4, Na2CO3, H2O, dioxane,
reflux, 20 h; (b) Pd(PPh3)2Cl2, Na2CO3, dioxane, reflux, 25 h
applied to 1,3-dibromo-5-butoxybenzene (5) for the synthesis
of 5-butoxy-1,3-phenylenebisboronic acid (6) (Scheme 2), it
unfortunately failed and no boronic acid product was isolated.
Interestingly, almost all the starting material was recovered,
suggesting the poor reactivity of 1,3-dibromo-5-butoxybenzene
(5) towards magnesium metal for the formation of Grignard
reagent. Lithiation reaction of compound 5 was then attempted.
Surprisingly, all our attempts again failed to obtain bisboronic (6)
acid of compound 5. However, a small quantity of monoboronic
acid (7) was isolated and identified in almost all cases (Scheme 2).
After failing to obtain bisboronic acid of compound 5, an
alternative route for approaching the target dielecrophile was
designed (Scheme 3). Lithium–halogen exchange of compound
2 with n-BuLi in THF/toluene mixture in the presence of tri-
isopropylborate, followed by an aqueous acid workup, gave pure
compound 8 in 70% yield (Scheme 3). Sequential addition of tri-
isopropyl borate after the lithiation gave compound 8 in only 7%
yield. It is an established fact that successful preparation of
certain heteroarylboronic acids need a specific order of addition
of reagents.[45]
Double Suzuki cross-coupling reaction of compound 8 with
1,3-dibromo-5-butoxybenzene (5) was carried out under a variety
of reaction conditions including different solvents, bases and
catalysts (Table 1). To check the efficiency of different bases,
THF was used as a solvent and Pd(PPh3)4 as a catalyst. When
Na2CO3, K2CO3 and Cs2CO3 were used as bases, the reaction
produced 1%, 4% and 5%, respectively, of mono-coupled
product (9), whereas no bis-coupled product (10) was isolated
(Table 1, entries 1–3). When K3PO4 was used as a base under
similar conditions, it afforded 3% of compound 10 along with
8% of 9 (Table 1, entry 4). However, use of KF as a base
diminished the yields of both compound 9 and compound 10
to 6% and 1%, respectively (Table 1, entry 5). After screening
the bases, different solvents were checked for their reaction
efficiency. 1,4-Dioxane, Dimethoxyethane (DME), and toluene
gave similar results, yielding both mono- and bis-coupled pro-
ducts. It is important to note here that a mixture of 1,4-dioxane
with water resulted in a little increase in the yield of either mono
and bis-coupled products (Table 1, entry 9). Toluene–water (1:1.3)
mixture produced 9% of compound 9 and 7% of compound 10,
respectively (Table 1, entry 10). After getting unsatisfactory
results with Pd(PPh3)4 as a catalyst, it was decided to screen dif-
ferent catalysts in a 1,4-dioxane–water system using K3PO4 as a
base (Table 1, entries 11–17). By using Pd(OAc)2/PCy3 as a catalyst
system, compound 9 was obtained in 52% yield with 14% of
compound 10. To our delight, when Pd2(dba)3/PCy3 was used
as catalyst, 50% yield of compound 10 and 15% of (9) were
isolated. Increase of catalyst quantity from 2 to 5 mol% resulted
in an increase of bis-coupled product (10) to 72% and a decrease
of mono-coupled product (9) to 2% (Table 1, entries 15 and 16).
However, a further increase in the amount of catalyst to 6 mol
% decreased the amount of both compounds 9 and 10 to 0%
and 59%, respectively. It should be noted here that by applying
different reaction conditions both mono- and bis-coupled pro-
ducts could be obtained as major products. Mono-coupled
product (9) may further be reacted with other boronic acids to
produce unsymmetrical dielectrophiles with a larger difference
in their reactivity for desired applications.
After successful synthesis of dielectrophile 10, it was then
reacted with aniline and phenol to test its reactivity with both
nitrogen and oxygen nucleophiles (Scheme 4). In the presence
of K2CO3 in DMSO solvent, both nucleophiles underwent a
rapid aromatic nucleophilic substitution reaction with chloro-
pyrimidines of compound 10 at 80ꢀC to afford amino and oxy-
substituted compounds 12a and 12b with yields of 82% and
87%, respectively.
O
i) Mg, I2, Dry THF
ii) B(OCH3)3, Ether
Br
(HO)2B
B(OH)2
O
6
ONa
DMF, 80 oC
Br
Br
Br
Br
4
5
O
i) n-BuLi, Dry THF
ii) B(OCH3)3, Ether
(HO)2B
Br
7
Scheme 2. Preparation of 5-butoxy-1,3-phenylenebisboronic acid
Appl. Organometal. Chem. 2012, 26, 330–334
Copyright © 2012 John Wiley & Sons, Ltd.
wileyonlinelibrary.com/journal/aoc

M. M. Naseer and S. Hameed
O
O
9
Br
B(OH)2
N
n-BuLi, [(CH3)2CHO]3B
THF/Toluene, -78oC
5
+
N
N
N
N
N
Br
N
Solvent, Base
Catalyst
(70%)
Cl
N
N
Cl
Cl
2
Cl
N
Cl
8
10
Scheme 3. Synthesis of dielectrophile with alkoxy side chain and reactive chloro substituents
Table 1. Optimization of base, solvent and catalyst for double Suzuki cross-coupling reaction
No.
Solvent
Temp. (ꢀC)
Time (h)
Base
Catalyst
9 (%)d
10 (%)d
1
THF
THF
THF
THF
THF
Reflux
Reflux
Reflux
Reflux
Reflux
100
24
24
24
24
24
24
24
24
24
13
10
11
12
10
08
06
05
Na2CO3
K2CO3
Cs2CO3
K3PO4
KF
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)4
Pd(PPh3)2Cl2
PdCl2dppf
1
4
0
0
2
3
5
0
4
8
3
5
6
1
6
1,4-Dioxane
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
K3PO4
8
4
7
DME
Reflux
100
7
3
8
Toluene
8
3
9
1,4-Dioxane/H2O
Toluene/H2O
100
10
9
8
10
11
12
13
14
15a
16b
17c
100
7
1,4-Dioxane/H2O
1,4-Dioxane/H2O
1,4-Dioxane/H2O
1,4-Dioxane/H2O
1,4-Dioxane/H2O
1,4-Dioxane/H2O
1,4-Dioxane/H2O
100
6
9
100
7
10
14
50
63
72
59
100
Pd(OAc)2/PCy3
Pd2(dba)3/PCy3
Pd2(dba)3/PCy3
Pd2(dba)3/PCy3
Pd2(dba)3/PCy3
52
15
7
100
100
100
2
100
0
Entries 1–14; catalyst = 2 mol%.
aCatalyst = 3 mol%.
bCatalyst = 5 mol%.
cCatalyst = 6 mol%.
dIsolated yields, 2-chloro-5-pyrimidylboronic acid (6) (2.2 equiv.), 1,3-dibromo-5-butoxybenzene (5) (1equiv.), base (3.4 equiv.).
O
O
XH
N
N
11
N
N
K2CO3, DMSO
80oC
X
N
N
X
10
Cl
N
N
Cl
12a, X = O
12b, X = NH
Scheme 4. Nucleophilic substitution reaction of dielectrophile with oxygen and nitrogen nucleophiles
and material chemistry. In addition, the presence of two pyrimi-
dine moieties and reactivity towards different kinds of nucleo-
philes will allow us to prepare derivatives for various medicinal
applications.
Conclusion
We have demonstrated the double Suzuki cross-coupling reaction
of 2-chloropyrimidin-5-ylboronic acid (2) with 1,3-dibromo-
5-butoxybenzene (5) to achieve the synthesis of 5,5′-(5-butoxy-
1,3-phenylene)bis(2-chloropyrimidine) (10) as dielectrophile in
good yield. We have also shown the ability of this dielectrophile
to undergo nucleophilic substitution reaction with oxygen and
nitrogen nucleophiles with the production of desired products
in excellent yield. This method of dielectrophile formation with
the installation of alkyl chain will provide a route to the construc-
tion of giant macromolecules for application in supramolecular
Experimental
General
NMR spectra were recorded at 300 MHz (Bruker) and chemical
shifts are reported in ppm versus tetramethylsilane with either
wileyonlinelibrary.com/journal/aoc
Copyright © 2012 John Wiley & Sons, Ltd.
Appl. Organometal. Chem. 2012, 26, 330–334

Double Suzuki reaction and dielectrophile
tetramethylsilane or the residual solvent resonance used as an
internal standard. Melting points are uncorrected. Solvents were
dried according to standard procedures prior to use. All other
major chemicals were obtained from commercial sources and
used without further purification.
9: m.p. 195–196ꢀC;1H NMR (300 MHz, CDCl3) d = 8.71 (s, 2H,
pyrimidinyl), 7.18–7.15 (m, 1H, phenyl), 7.09–7.05 (m, 1H, phenyl),
6.92–6.89 (m, 1H, phenyl), 3.94 (t, J = 6.4 Hz, 1H, CH2), 1.83–1.66
(m, 1H, CH2), 1.51–1.34 (m, 1H, CH2), 0.92 (t, J = 7.4 Hz, 2H, CH3).
13C NMR (75 MHz, CDCl3) d = 160.7, 160.6, 157.4 (pyrimidinyl),
135.6 (C5-phenyl), 131.8 (C1-phenyl), 124.0 (C3-phenyl), 121.9
(C2-phenyl), 118.0 (C4-phenyl), 112.7 (C6-phenyl), 68.3 (CH2-butyl),
31.1 (CH2-butyl), 19.1 (CH2-butyl), 13.7 (CH3-butyl); MS (ESI) m/z 341.0
[M + H] (100%), 343.1 (96), 345.0 (4). Anal. Calcd for C14H14BrClN2O:
C, 49.22; H, 4.13; N, 8.20. Found: C, 49.01; H, 4.08; N, 8.34.
Synthesis of 1,3-dibromo-5-butoxybenzene (5)
Sodium n-butoxide (1.92 g, 20 mmol) was added to a solution of
1,3,5-tribromobenzene (4) (4.72 g, 15 mmol) in DMF (50 ml). The
reaction mixture was stirred at 80ꢀC for 10 h, quenched with a
10% aqueous HCl solution (25 ml) and extracted with CHCl3
(3 Â 40 ml). The combined organic layers were washed with brine
(50 ml), dried with magnesium sulfate and the solvents evapo-
rated. The crude product was purified by column chromatogra-
phy using petroleum ether as mobile phase to afford compound
5 (3.64 g, 79%) as a colourless oil. It was characterized by compar-
General Procedure for the Synthesis of 12
To a solution of 10 (0.19 g, 0.5 mmol) in DMSO (5 ml) at 80ꢀC
was added K2CO3 (finely ground) (0.14g, 1 mmol) and respective
nucleophile 11 (1.1 mmol) with constant stirring. Stirring was con-
tinued further for 24 h. The reaction mixture was then partitioned
between ethyl acetate (60 ml) and water (50 ml), the resulting
mixture separated, and the aqueous layer extracted twice with
ethyl acetate (15 ml). The combined organics were washed with
brine (60 ml), dried over anhydrous MgSO4, filtered, and concen-
trated. The residue was chromatographed on a silica gel column
(100–200) with a mixture of petroleum ether and acetone as the
mobile phase (3:1) to give pure products 12a, 12b as white solids.
1
ing its H and 13C NMR spectra with those of the literature.[53,54]
Synthesis of 2-chloro-5-pyrimidylboronic acid (8)
To a solution of 5-bromo-2- chloropyrimidine (2) (2.5 g, 13.0 mmol)
and triisopropyl borate (4.2 ml, 18.2 mmol) in anhydrous THF
(20 ml) and toluene (5 ml) at À78ꢀC was added nBuLi (2.5 M in
hexane, 6.2 ml, 15.6 mmol) dropwise. The reaction mixture was
stirred for 4 h at À78ꢀC; it was then quenched with water
(40 ml) and warmed to room temperature with stirring overnight.
The organic solvent was evaporated in vacuo, and the remaining
aqueous layer was washed with diethyl ether (3 Â 10 ml) to
remove unreacted starting material. The aqueous layer was then
acidified to pH 5 (with 48% aqueous HBr) to precipitate 8 as a
white solid (1.44 g, 70%). It was characterized by comparing its
1H and 13C NMR spectra with those of the literature.[45]
1
12a (0.20 g, 82%): m.p. 225–226ꢀC; H NMR (300 MHz, CDCl3)
d = 8.57 (s, 4H, pyrimidinyl), 7.26–7.23 (m, 2H, phenyl), 7.43–7.32
(m, 3H, phenyl), 7.12 (t, J = 1.4 Hz, 1H, phenyl), 7.05 (d, J = 1.4 Hz,
2H, phenyl), 7.04–7.00 (m, 1H, phenyl), 4.02 (t, J = 6.4 Hz, 1H,
CH2), 1.85–1.70 (m, 1H, CH2), 1.53–1.36 (m, 1H, CH2), 0.93
(t, J = 7.4 Hz, 1H, CH3); 13C NMR (75 MHz, CDCl3) d = 168.6, 168.5,
156.3 (pyrimidinyl), 153.2 (C5-phenyl), 134.7 (C1-phenoxy), 131.2
(C1, C3-phenyl), 125.3 (C3, C5-phenoxy), 120.5 (C4-phenoxy), 118.7
(C2, C6-phenoxy), 116.3 (C2-phenyl), 112.8 (C4, C6-phenyl), 66.2
(CH2-butyl), 30.9 (CH2-butyl), 18.2 (CH2-butyl),12.9 (CH3-butyl);
MS (ESI) m/z 491.3 [M + H] (100%), 492.2 (33), 493.3 (7). Anal. Calcd
for C30H26N4O3: C, 73.45; H, 5.34; N, 11.42. Found: C, 73.58; H, 5.26;
N, 11.40.
Synthesis of dielectrophile (10)
2-Chloropyrimidin-5-ylboronic acid (8) (0.70 g, 4.40 mmol), 1,3-
dibromo-5-butoxybenzene (5) (0.62 g, 2 mmol), [Pd2(dba)3]
(92 mg, 0.1 mmol), and PCy3 (67 mg, 0.24 mmol) were added to
a 50 ml round-bottom flask equipped with a stirring bar. The flask
was evacuated and refilled with argon three times. 1,4-Dioxane
(10 ml) and aqueous K3PO4 (1.30 M, 13 ml, 17 mmol) were then
added by syringe and heated the mixture at 100ꢀC for 6 h with
continuous stirring. The reaction mixture was then filtered and
washed thoroughly with chloroform. The filtrate obtained was
concentrated under reduced pressure, and the remaining aqueous
residue was extracted with CHCl3 (5 Â 25 ml). The combined
extracts were dried over anhydrous Na2SO4, filtered, and concen-
trated. The residue was chromatographed on a silica gel column
(100–200) with a mixture of petroleum ether and CHCl3 as the
mobile phase (5:1) to give pure 10 (0.54 g, 72%) as a white solid:
m.p. 252–253ꢀC; 1H NMR (300 MHz, CDCl3) d = 8.78 (s, 4H, pyrimidinyl),
7.15 (t, J = 1.4 Hz, 1H, phenyl), 7.07 (d, J = 1.4 Hz, 2H, phenyl), 4.03
(t, J = 6.4 Hz, 2H, CH2), 1.85–1.70 (m, 2H, CH2), 1.54–1.37 (m, 2H,
CH2), 0.94 (t, J = 7.4 Hz, 3H, CH3); 13C NMR (75 MHz, CDCl3)
d = 160.9, 160.8, 157.5 (pyrimidinyl), 135.8 (C5-phenyl), 132.3
(C1, C3-phenyl), 117.6 (C2-phenyl), 113.9 (C4, C6-phenyl), 68.3
(CH2- butyl), 31.1 (CH2-butyl), 19.26 (CH2-butyl),13.8 (CH3-butyl);
MS (ESI) m/z 375.1 [M+ H] (100%), 377.2 (62), 379.1 (9). Anal. Calcd
for C18H16Cl2N4O: C, 57.61; H, 4.30; N, 14.93. Found: C, 57.68; H, 4.28;
N, 14.85. Compound 9 (0.013 g, 2%) was also isolated as a white
solid from column chromatography. When Pd(OAc)2/PCy3 was
used as catalyst, the reaction gave mono-coupled product 9
(0.35 g, 52%) and bis-coupled product 10 (0.11 g, 14%).
1
12b (0.21 g, 87%): m.p. 269–271ꢀC; H NMR (300 MHz, CDCl3)
d = 8.66 (s, 4H, pyrimidinyl), 7.62–7.60 (m, 2H, phenyl), 7.35–7.24
(m, 3H, phenyl), 7.13 (t, J = 1.4 Hz, 1H, phenyl), 7.06 (d, J = 1.4 Hz,
2H, phenyl), 7.04–7.00 (m, 1H, phenyl), 4.02 (t, J = 6.4 Hz, 1H,
CH2), 1.85–1.70 (m, 1H, CH2), 1.53–1.36 (m, 1H, CH2), 0.93
(t, J = 7.4 Hz, 1H, CH3); 13C NMR (75 MHz, CDCl3) d = 163.4, 163.3,
158.1 (pyrimidinyl), 152.1 (C5-phenyl), 138.6 (C1-N-phenyl), 132.1
(C1, C3-phenyl), 124.3 (C3, C5-N-phenyl), 120.5 (C4-N-phenyl),
118.6 (C2, C6-N-phenyl), 116.1 (C2-phenyl), 112.5 (C4, C6-phenyl),
66.1 (CH2-butyl), 30.8 (CH2-butyl), 18.1 (CH2-butyl),12.7 (CH3-butyl);
MS (ESI) m/z 489.3 [M + H] (100%), 490.3 (36), 491.2 (5). Anal. Calcd
for C30H28N6O: C, 73.75; H, 5.78; N, 17.20. Found: C, 73.83; H, 5.86;
N, 16.96.
Acknowledgements
We are highly grateful to the higher education commission (HEC),
Government of Pakistan for financial support.
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