Pd(II)-catalyzed regioselective direct arylation of uracil via oxidative Heck reaction using arylboronic acids

Article abstract of DOI:10.1016/j.tetlet.2013.12.092

A palladium catalyzed regioselective synthesis of 6-aryl uracils via oxidative Heck reaction (C-H bond functionalization) of uracils and arylboronic acids is reported. The method is simple, atom-economical, and high yielding.

Full text of DOI:10.1016/j.tetlet.2013.12.092

Tetrahedron Letters 55 (2014) 1077–1081
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Pd(II)-catalyzed regioselective direct arylation of uracil via oxidative
Heck reaction using arylboronic acids
⇑
Biplab Mondal, Somjit Hazra, B. Roy
Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
a r t i c l e i n f o
a b s t r a c t
Article history:
A palladium catalyzed regioselective synthesis of 6-aryl uracils via oxidative Heck reaction (C–H bond
functionalization) of uracils and arylboronic acids is reported. The method is simple, atom-economical,
and high yielding.
Received 25 September 2013
Revised 23 December 2013
Accepted 25 December 2013
Available online 3 January 2014
Ó 2014 Elsevier Ltd. All rights reserved.
Keywords:
Oxidative Heck reaction
C–H bond functionalization
Uracil
Direct arylation
Catalysis
O
C-Aryl pyrimidines exhibit a wide range of bioactivities.1 5-Aryl
uracil is used as biosensor2 and in labeling of nucleotides as well as
DNA.3 Likewise, 6-aryl uracils also attract the biochemists due to
their various potential bioactivities (Fig. 1).4
For example, 6-aryl uracil derivatives (I and II) are two classes
of sirtuin inhibitors which show antitumor activity.1c 5-Halo-6-
phenyl pyrimidines (III and IV) demonstrate cardioregulatory
and anti-inflammatory activities.4d Various 6-aryl thiouracils are
also impending therapeutics such as antiviral, anticancer, and anti-
microbial agents.4e 6-Aryl-5-cyano thiouracil quinoxaline hybrid V
shows strong inhibitory effect on EBV-EA activation without
cytotoxicity on Raji cells.5 VI possesses inhibitory property against
hepatitis C viral NS5B RNA-dependent RNA polymerase.6
R3
R4
HO
O
N
R2
N
N
HN
X
R1
N
R1
III R1 = R3 = H; R4 = Br or I
R2 = COCH3 or COCH2CH2COOH
IV R1 =R2 = H; R4 = Br or I
R3 = methyl or allyl group
R2
I
R1 = R2 = H; X = S cambinol
II R1 = R2 = H; X = O
O
NC
NH
O
NC
NH N
N
S
N
N
S
Br
VI
Cl
C-Aryl uracils are usually synthesized by heterocyclic cycliza-
tion,7 cross coupling of halouracil with arylboronic acid, or via met-
allated uracil which couples with aryl halides.8 Though there are
many available methodologies for the synthesis of 5-aryl uracils,
known methodologies for the synthesis of 6-aryl uracils are scanty
due to inaccessibility of 6-halouracil. In recent years, a range of di-
rect arylation by C–H bond functionalization reactions has been
developed to synthesize C-arylated heterocycles with high effi-
ciency.9 In 2009, Hocek et al. reported that N-substituted uracil
could be arylated at C-6 position with aryl iodides using Pd(OAc)2
as catalyst in the presence of CuI.10 In 2012 Kim et al. described an-
other methodology for the generation of C-6 aryl uracil via double
V
NS5B RNA dependent
RNA polymerase
Figure 1. Some examples of pharmaceutically active C-6 aryl pyrimidines.
C–H activation between 1,3-dimethyluracil (1,3-DMU) and arenes,
which were used as solvent, in the presence of catalytic amount of
Pd(TFA)2.11 But they isolated 5-arylated uracil and dimeric byprod-
ucts also together with the 6-arylated uracil in the reaction condi-
tion. Organoboron-mediated oxidative Heck type reactions for C–C
bond formation have received much attention in the past few
years. The commercial accessibility, functional group tolerance,
low toxicity, and general applicability of boron reagent increase
its importance in industrial research.12 In 2013, Cheng et al. re-
ported Cu(I)-mediated C-6 arylation of uracil using 4 equiv of
LiOtBu in DMF with aryl iodides, but this reaction shuts down
⇑
Corresponding author. Tel.: +91 3325828750; fax: +91 3325828282.
E-mail addresses: broy@klyuniv.ac.in, broybsku@gmail.com (B. Roy).
0040-4039/$ - see front matter Ó 2014 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tetlet.2013.12.092

1078
B. Mondal et al. / Tetrahedron Letters 55 (2014) 1077–1081
Table 1
Optimization of the reaction condition for direct C–H arylation
O
O
OH
B
catalyst, ligand,
solvent,
N
N
+
N
OH
O
N
temperature,
O
time
3a
1a
2a
Entry
Catalyst
Ligand
Solvent
Temperature (°C)
Conversion (%)
Yielda (%)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
Cu(OTf)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
PdCl2
Pd(PPh3)2Cl2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
—
—
Toluene
DMF
DMF
DMF
DMF
DMF
DMF
DMF
Toluene
DMSO
DMA
DCE
CH3CN
DMF
DMF
DMF
DMF
DMF
DMF
DMF
DMF
DMF
DMF
110
rt-100
rt
0
0
0
0b
5
30
10
25
70
N.D
N.R
5
TMEDA
TMEDA
DMEDA
DMAP
Phen
L-Proline
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
Phen
20
54
25
45
90
100
0
20
80
50
100
55
64
100
100
75
100
60
80
0
60
60
60
60
60
60
60
60
60
60
60
60
90
110
90
90
90
90
90
90
50
20
N.D
15
20
82
65
60c
80d
50e
65f
0g
0
0h
Reactions condition: 1,3-DMU 1a (1 equiv), phenylboronic acid 2a (3 equiv), Pd catalyst (10 mol %), ligand (15 mol %), O2 balloon in the mentioned solvent (10 ml) heated for
16 h.
Bold line indicates the optimized condition.
a
Yields were calculated after flash chromatography.
Na2CO3 (2 equiv) used as base.
Catalyst used 5 mol %.
Catalyst used 15 mol %.
Reaction continued for 8 h.
Reaction continued for 12 h.
b
c
d
e
f
g
Reaction performed under N2 atmosphere.
Reaction performed under open air. Phen = 1,10-Phenanthroline; TMEDA = N,N,N0,N0-tetramethylethylenediamine DMEDA = N,N0-dimethylethylenediamie. N.D = no
h
desired product (complicated result). N.R = no reaction (conversion of starting material is zero).
when arylboronic acid was used as coupling partner.13 Very re-
cently, we developed a route for the synthesis pyrrolo[3, 2-
d]pyrimidine derivatives that involves activation of uracil C6-H
bond.14 In this context, we opted to explore an alternative way
for uracil C6-H bond functionalization via boronic acid-mediated
oxidative Heck reaction. Herein, we report the synthesis of 6-aryl
uracil through organoboron-mediated oxidative Heck reaction
and to the best of our awareness, this is the first Letter of C-6 ary-
lation of uracil by Pd(II)-catalyzed organoboron-mediated oxida-
tive Heck reaction.
yields, respectively. A significant improvement was observed with
1,10-phenanthroline which afforded 70% yield of 3a (Table 1, entry
7), but in case of L-proline no arylated product was found (Table 1,
entry 8). The above results showed that ligand played an important
role and 1,10-phenonthroline ligand appeared to be the best. The
solvent effect for this coupling reaction was also tested. No product
was obtained with toluene and acetonitrile (Table 1, entry 9, 13). A
poor to moderate yield of 3a was observed for the solvents DMSO,
DMA, and DCE (Table 1, entry 10–12). DMF gave the most satisfac-
tory result and it was selected as the preferred solvent. The maxi-
mum yield (82%) of 6-phenyl-1,3-DMU 3a was isolated when the
temperature was increased to 90 °C and the reaction continued
for 16 h (Table 1, entry 16). A further increase in temperature re-
sulted in lowering of the desired product 3a, (Table 1, entry 17).
With PdCl2 and Pd(PPh3)2Cl2 as catalyst, the yield of 3a was inad-
equately low (Table 1, entry 14, 15). When we changed the reac-
tion atmosphere from oxygen to nitrogen or open air no reaction
took place (Table 1, entry 22, 23). This finding indicated that
molecular oxygen played an important role in this reaction. After
the survey of different reaction conditions a combination of
10 mol % Pd(OAc)2 as catalyst, 15 mol % 1,10-phenonthroline as
ligand in DMF under oxygen atmosphere at 90 °C (Table 1, entry
16) temperature was found to be optimal.
Taking a clue from our previous work,14 we carried out a preli-
minary experiment where 1,3-dimethyluracil (1,3-DMU) (1a) and
phenylboronic acid (2a) in toluene were refluxed in the presence
of 20 mol % of Cu(OTf)2 for 12 h (Table 1, entry 1). But we failed
to obtain any product. On changing the catalyst to Pd(OAc)2
(10 mol %) and introducing Na2CO3 (2 equiv) as base12b in DMF at
room temperature under oxygen atmosphere (Table 1, entry 2),
we obtained the same result. A sign of progress was recorded when
we used a ligand (20 mol % of TMEDA) at room temperature
(Table 1, entry 3) and a further improvement was observed at
60 °C (Table 1, entry 4), as the reaction afforded 30% yield of only
C-6 arylated product (after 16 h). This result prompted us to
optimize this oxidative Heck reaction.
At first we decided to explore various ligands in the initial reac-
tion condition. By changing the ligand to DMEDA and DMAP, the 6-
arylated product was isolated (table-1, entry-5, 6) in 10% and 25%
Encouraged by these results, we next investigated the applica-
bility of this methodology to several uracil derivatives (Table 2).
The result indicates that N-substitution has some effect on the

B. Mondal et al. / Tetrahedron Letters 55 (2014) 1077–1081
1079
Table 2
Palladium-catalyzed direct C-6 arylation of different uracil derivatives 1 with different boronic acids 2a
Entry
Starting
Product
Yield (%)
Entry
Starting
Product
Yield (%)
O
O
O
O
Me
Et
N
O
Me
Et
N
N
N
N
N
N
N
O
N
O
N
1
82
7
70
64
56*
69
0
O
N
N
Me
3a
O
Et
Me
Et
3g
1g
1a
O
O
O
Me
Et
Et
Me
Et
N
N
N
N
N
O
N
O
N
2
3
4
5
70
78
82
78
8
9
O
N
O
N
Me
nPr
3h
O
Me
1b
O
nPr
3b
1h
O
O
Me
Me
Et
N
O
N
O
N
Bn
3i
O
N
O
N
Me
Me
Bn
3c
1c
1i
O
O
O
O
Me
Me
Me
Me
N
N
N
N
O
N
O
N
10
11
O
N
O
N
Me
3d
O
OMe
OMe
Me
3j
O
Cl
Me
Me
1d
1j
O
O
Me
H
Me
H
N
N
O
N
Me
3e
O
N
H
O
N
O
N
H
Me
1e
3k
1k
O
O
O
O
Et
Me
Et
Me
N
N
N
N
O
N
Me
3f
O
N
O
N
O
N
Me
OAc
OAc
O
O
6
75
12
0
OAc
OAc
1f
OAc
OAc
3l
1l
a
Reaction condition: Uracil 1 (1 equiv), aryl boronic acid 2 (3 equiv), Pd(OAc)2 (10 mol %), 1,10-phenthroline (15 mol %), O2 balloon in 10 ml dry DMF heated in a round
bottom flask at 90 °C for 16 h; yields were calculated after flash chromatography.
*
32% of Michael addition product was also isolated.
yield of the arylated product. We found maximum yield 82% for
1,3-DMU (Table 2, entry 1) and lowest yield 56% for 1-benzyl-3-
ethyluracil (Table 2, entry 9). It seems that the steric factor might
have played some role in the formation of desired 6-arylated prod-
uct. We also tested 3-methyl-20,30,50-triacetyluridine (Table 2, en-
try 12), but it remained unchanged, i.e., no arylated product was
found. 1-Methyl-3-ethyl and 1,3-diethyluracils also gave good
yields of the products, in 75% and 70%, respectively (Table 2, entry
6, 7). For simple uracil (Table 2, entry 11) no arylated product was
isolated and total recovery of stating material was observed. On
the other hand, 1-benzyl-3-ethyluracil afforded moderate yield
(56%) of 6-arylated product along with the Michael addition prod-
uct 4 in 32% yield.
Furthermore, we studied the oxidative Heck reaction of
1,3-DMU with different types of arylboronic acids. The substituted
arylboronic acids containing methyl or methoxy group also under-
went the reaction smoothly under the same condition to give the
corresponding 6-arylated product in good to high yield. For
2-methyl phenylboronic acid (Table 2, entry 2) the yield was some-
what lower indicating again that steric effect might have some
influence on the fate of the reaction. The chloro group was also
well tolerated in this reaction condition and offered 69% yield of
3j (Table 2, entry 10). We also explored the reactivity of boronic es-
ter and hetero arylboronic acids in this oxidative Heck process.
When dimethyl phenyl boronate was treated with compound 1a,
the compound 3a was obtained in comparatively lower yield of
40%. On the other hand when we tried heteroaromatic boronic
acids (5-methoxypyridin-2-ylboronic acid, thiophen-2-ylboronic
acid) the starting precursor remained unchanged.
A possible mechanistic pathway for the oxidative Heck reaction
of arylboronic acid (2) with uracil (1) is shown in Scheme 1. Palla-
dium phenanthroline complex15 (A) takes part in a metal insertion
step to form the complex B which subsequently adds to C–C double
bond of uracil in syn fashion.16 This palladated uracil (C) in turn,
may afford the target compound 3 in two possible pathways; (i)
base-catalyzed b-elimination via an E2-like mechanism or by (ii)
syn-elimination via palladotropic shift.17 Our failure to obtain the
desired product in the base catalyzed condition (Table 1, entry 2)
indicates that the reaction is most probably not going through
anti-elimination mode.12b So this eliminates the possibility of path-
way (i). We hypothesize that a palladotropic shift helps C to remain
in equilibrium with E via the intermediacy of D. Now E would
likely afford the desired product 3 via syn-elimination. In this reac-
tion molecular oxygen plays an important role to complete the cat-
alytic cycle by reoxidizing Pd(0) to Pd(II). When N-1 position is
substituted by the benzyl group, it gets very difficult for the elim-
inating groups to come in syn-periplanar position, required for the
elimination, due to steric reason with the phenyl ring at C-6 posi-
tion. As a result, we obtained the product 4 in substantial amount
along with the product 3i.12b These findings rule out the base

1080
B. Mondal et al. / Tetrahedron Letters 55 (2014) 1077–1081
II
N
N
OAc
OAc
A
Pd
ArB(OH)2
2
A
cOB(OH)2
ArB(OH)2
II
N
N
O
O
2
HOAc
II
O
N
N
Ar
II
Pd
N
Ar
Pd
R1
O
Pd
OOB(OH)2
N
OAc
N
G
O2
H
syn-
HOOB(OH)2
B
addition
N
R2
1
N
N
N
N
Pd(0)
O
N
O
N
Pd
path (i)
R1
OAc
R1
HOAc
II
N
N
N
base promoted
anti-elimination
O
Ar
O
Ar
R2
R2
3
N
N
C
II
Pd
OAc
H
palladotropic
shift
F
path (ii)
syn-elimination
N
N
N
N
Pd
O
N
O
O
II
II OAc
Pd
R1
O
R1
R1
O
OAc
N
R1 = Et,
R2 = Bn,
Ar = Ph
H
N
Ar
O
N
Ar
N
Ar
R2
R2
R2
4
Michael
D
E
addition product
Scheme 1. Proposed mechanism for the oxidative Heck reaction.
2. (a) Fukuda, M.; Nakamura, M.; Takada, T.; Yamana, K. Tetrahedron Lett. 2010,
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assisted b-elimination and give strong indications toward a ligand-
assisted syn-elimination for this oxidative Heck12b type reaction.
Thus, the function of phenanthroline, we conclude, in this reaction
is as a ligand, not as a base.
In conclusion, we have developed an efficient, regioselective,
and atom economical ligand assisted and base-free protocol for
the synthesis of 6-aryl uracils via palladium-catalyzed oxidative
Heck reaction of N-substituted uracils and arylboronic acids. This
methodology provides a clear-cut route to biologically appealing
6-aryl uracils via regioselective direct arylation without
prefunctionalization.
Acknowledgments
We thank DST (New Delhi) for financial assistance through DST-
PURSE programme and DST fast track scheme. Two of us, (B.M. &
S.H.) are thankful to CSIR (New Delhi) and University of Kalyani
respectively for research fellowships. We also thank DST (New
Delhi) for providing FT-IR, NMR spectrometer (400 MHz) and
CHN analyzer.
5. Galal, S. A.; Abdelsamie, A. S.; Tokuda, H.; Suzuki, N.; Lida, A.; El-Hefnawi, M.
M.; Ramadan, R. A.; Atta, M. H. E.; El Diwani, H. I. Eur. J. Med. Chem. 2011, 46,
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Supplementary data
8. (a) Nencka, R.; Votruba, I.; Hrebabecky´, H.; Jansa, P.; Tloust’ová, E.; Horská, K.;
´
Masojídková, M.; Holy, A. J. Med. Chem. 2007, 50, 6016; (b) Kusturin, C.;
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Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.tetlet.2013 . 12
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