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Haloselectivity of Heterocycles
Haloselectivity of Heterocycles
Polysubstituted heterocycles represent some of the most important compounds in the realm of
pharmaceutical and material sciences. New and more efficient ways to selectively produce these
molecules are of great importance and one approach is though the use of polyhalo heterocycles.
Consider:
Ar3
CO2Me
Ar1
3 Suzuki Couplings
N
H
Ar3
CO2Me
Ar1
N
H
Ar3
CO2Me
Ar1
NH3(l), 90%
NH2
NH
N
CO2Me
NH
N
H
Cross Coupling
CO2Me
Virtually all types of cross coupling have been utilized in regioselective cross coupling reactions:
Kumada, Negishi, Sonogashira, Stille, Suzuki, Hiyama, etc.
In all of these examples, the oxidative addition of the metal to the heterocycle is the selectivity
determining steps and is frequently considered to be irreversible. This addition highly resembles a
nucleophilic substitution and it frequently follows similar regioselectivities in traditional SNAr reactions.
The regioselectivity of cross coupling reaction in polyhalo heterocycles do not always follow the BDE's
of the corresponding C-X bonds.
Nu
Nu
N
Nu
2nd
Meisenheimer Complex
1st
Br
83.2
SN(EA)
via:
NaNH2, t-BuONa
pyrrolidine
87.3
THF, 40C
OMe
Nu
HetX
Het
OK
HetNu
N
N
+ Nu
Cl
h!, NH3(l)
88%
+ HetX
HetNu
HetX
88.9
88.9
Br
1st
Merlic and Houk have determined that the oxidative addition in palladium catalyzed cross coupling
reactions is determined by the distortion energy of the C-X bond (related to BDE) and the interaction of
the LUMO of the heterocycle to the HOMO of the Pd species.
HetX
Br
HetX + Nu
2nd
Br
Het
NH2
H
SNAr or SN(AE)
NH2
- Br
Nucleophilic Substitution
Br
N
NH2
N
H
Ar2
Br
Br
NaNH2
CO2Me
Ar2
1 Triple Halogenation
N
H
Br
N
Ar2
3 Halogenations
N
H
Will Gutekunst
Haloselectivity of Heterocycles
Will Gutekunst
Pyrroles can also be selectively monoarylated at C-2 under C-H activation conditions.
Ph2I+BF45% IMesPd(OAc)2
N
Me
Ph
N
Me
Indole
Pyrroles
2nd
7.55
7.00
- Due to the electron rich nature, SNAr reactions do not readily take place
without strong EWGs.
- Cross coupling reactions occur fastest at the 2/5 positions, in accord with
chemical shift prediction.
- Monocoupling in 2,5 dihalo substrates is difficult, but 3,4 dihalo
substrates can be easily controlled on steric grounds.
-
2nd
6.22
6.68
1st
N
H
(CDCl3)
6.45
7.08
N
H
7.40
last
7.27
1st
(Acetone)
Br
O
Cl
Cl
2.5 eq EtSH
TEA, DMSO
86%
EtS
H
N
Me
Cl
S
N
TBS
N
TBS
10% Pd(PPh3)4
Na2CO3, Tol/H2O
reflux, 8 hrs
78%
H
N
Me
Br
Br
B(OH)2
Br
N
Me
Br
Cl
Br
Br
B(OH)2
N
Me
6% Pd(PPh3)4
K3PO4, Tol/H2O
90C, 12 hrs
71%
t-BuLi, MeI
Br
Br
N
TBS
Br
-78 C, THF
81%
N
TBS
Cl
The C-H activation conditions for pyrrole are also successful on indole and tolerates aryl bromides
MeO
MeO
OMOM
MeO
B(OH)2
MeO
MeO
TfO
MeO2C
OTf
N
R
CO2Me
B(OH)2
2% Pd(PPh3)4
8% Pd(PPh3)4
MeO
OMe
Br
Ph2I+BF45% IMesPd(OAc)2
MeO
OMOM
MeO2C
N
R
CO2Me
N
H
60 C, AcOH, 74%
Br
N
H
Ph
Haloselectivity of Heterocycles
Will Gutekunst
Much like the dibromo indole, after the first Negishi coupling, the lithium halogen exchange
at C-3 is favored.
Furan
- Not as resistant as pyrrole, but SNAr reactions still do not readily take place
without strong EWGs.
- Cross coupling reactions occur fastest at the 2/5 positions, in accord with
chemical shift prediction.
- Halogenated furans have general stability problems, making cross couplings
sometimes troublesome.
2nd
6.24
7.29
1st
(CDCl3)
t-BuLi, MeI
-78C, THF
OMe
OMe
OMe
Br
OMe
54%
Br
MeO2C
Br
Br
Br
4% Pd(PPH3)4
DMA, 90C, 79%
MeO2C
Thiophene
SnMe4
5% [PdCl2(Po-Tol3)2]
Br
Bu3Sn
O
7.18
1st
(CDCl3)
2 steps
MeO2C
64%
- A better substrate for SNAr than furan and two orders of magnitude more
reactive than benzene, but not many examples of haloselective reactions.
- Cross coupling reactions occur fastest at the 2/5 positions and the 3/4
much slower. Selectivity on 2,5 dihalothiophenes is scarcely obtained
though some success has been seen with Sonogashira reaction and cases
with substrate bias.
2nd
6.99
Br
rosefuran
Br
46%
Br
BnNHCH3
NBnMe
O
BnMeN
Br
4:1
H
OMe
O
H
Ph
Br
Br
7.63
7.23
6.76
last
7.30
7.51
2.5% [PdCl2(dppf)]
Et2O 63%
Two more
S
Br cross-couplings
54%
7.78
st
(acetone) 1
ClZn
Br
BnZnBr
Pd(PPh3)4
Br
Br
quant
52 - 57%
p-TolMgCl
NiCl2(dppp)
Br
OMe
Br
Benzofuran
2nd
Br
Br
ZnCl
OMe
MgBr
Br
MeZnCl
THF, reflux, 93%
OMe
O
Br
Br
Thiophenes, pg 693
Br
nBuLi, Et2O
-78C; H2O
79%
Br
Haloselectivity of Heterocycles
7.72
7.26
7.22
last
7.24
7.33
7.79
Will Gutekunst
Attempts to displace the second chloride leads to mixtures with ring opened products.
- SNAr occurs readily on benzothiophenes, but they have some strange
reactions with nucleophiles.
- Cross coupling also mimics indole: first at C-2, with C-4 to C-7 reacting
before C-3.
7.70
7.56
Cl
MeS
S
N
NC
1st
1) 2 eq Na2S
(CCl4)
S
NC
2) MeI
Cl
MeS
SMe
7.58
NC
CN
Isoquinolin
7.85
SMe
NH
Br
Pyrazole shows similar reactivity, with a bromide being displaces before an iodide.
Br
Br
106C
200C
73%
N
Me
N
N
Br
MeO
OMe
MeO
S
EtO2C
Br
Br
Ethyl bromoacetate, rt
80%
Me
N
N
MeO
B(OH)2
B(OH)2
EtO2C
Ph
3% Pd(PPh3)4
5% Pd(PPh3)4
Na2CO3, EtOH/DME Ba(OH)2, H2O/DME
95%
71%
Br
Ph
Ph
Br
4% PdCl2(PPh3)2
CuI, TEA/MeCN, rt
56%
Br
Ph
Br
Br
The remaining two bromides were unreactive in further Sonogashira couplings, even at higher temps
1,2-Azoles
1st
Me
N
N
7.45
8.39
3rd
6.20
Ph
S
7.26
8.14
8.54
2nd
Isothiazole (CCl4)
Isoxazole (CS2)
- Selective SNAr reactions are only known with EWGs on the 4-position, but strongly favors substitution
at the 5-position over the 3. This can be rationalized by both innate electronics (seen by NMR) and
conjugation to the EWG.
- Cross coupling also follows Handy rules: first at C-5, then at C-2 and lastly C-3.
Br
EtO
S
NC
N
Cl
EtOH (xs)
94%
N
N
S
NC
2% PdCl2(PPh3)2
4% PdCl2(PPh3)2
CuI, TEA/MeCN, rt CuI, TEA/MeCN, 50C
45% (also 45% deiodo)
42%
MeO
Br
Cl
N
Cl
Ph
MeO
S
N
N
6.28
7.31
8.72
Br
Br
n-BuLi, -78C;
Bu3SnCl
77%
Bu3Sn
N
N
Br
Br
S
N
Br
Haloselectivity of Heterocycles
1st
7.69
7.41
7.98
2.5% Pd(OAc)2
2.5% Xantphos
O
I
Thiazole (CDCl3)
Oxazole (CCl4)
10%
8.88
3rd
7.95
7.09
7.01
Workers at Merck recently disclosed specific ligands to override and reinforce substrate bias in
the 1,3-azoles in a screen of ~200 achiral phosphines.
2nd
Me
N
6.86
Will Gutekunst
Ph
- SNAr reactions occur readily at C-2, though not very well at C-4/5 without assistance, and trends are
not general among the series.
- Cross coupling also does not follow the Handy rules, with usual order of cross coupling being 2>5>4,
Also note that the relative order chemical shifts switches in oxazole.
K3PO4, PhB(OH)2
THF, 64%
KCN, DMSO
18-crown-6
N
Br
N
O2N
Br
O2N
NaH, PhSH
THF
PhS
rt, 75%
O2N
80C, 85%
Br
Br
OMe
PhB(OH)2
10% Pd(PPh3)4, Na2CO3 10% Pd(PPh3)4, Na2CO3
PhH/MeOH/H2O
94%
MOM
N
MeOH/NaOMe
O2N
reflux, 40%
MeO
Br
Br
Br
N
N
SH
EtO2C
Br
N I
n-BuLi, THF
33%
X
OH
Br
K2CO3, DMF
125-180C w
51-84%
Br
N
H
PhBr
PdCl2(PPh3)2
CuI, TEA, THF
80C, 53-89%
Ph
N
X
HN
O
Br
Me2N
O
X
Br
MOM
OMe
EtO2C
i-PrMgCl, THF
-78C, 66%
Ph
N
PhH/MeOH/H2O
71%
Br
Br
Br
Br
Br
EtO2C
B(OH)2
Br
O2N
Ph
I
Similar or better results were obtained for imidazoles, but selective C-4/C-5 over C-2 Suzuki
couplings of dihalo thiophenes was not observed in any cases. No C-4 vs C-5 studies were
undertaken.
CN
CN
K3PO4, PhB(OH)2
THF, 55%
5% Pd(OAc)2
I
I
O
N
MeO
OMe
N
Ph
N
5% Pd(OAc)2
Ph
CuI, DMF, 140C
76%
JOC 2005, 70, 3997, Eur. JOC 2006, 1379
MeO
5% Pd(OAc)2
AsPh3, DMF, CsF MeO
140C, 46%
N
N
Ph
Haloselectivity of Heterocycles
Will Gutekunst
For
EtO-
at 20C
Cl
Cl
Cl
N
Cl
1.7x102
7.3x103
Cl
5.3x104
>
X
4 Cl
5.4x104
Cl
>
BnHN
Ph
2nd
7.16
3rd
1st
(C6D6)
- Pyridines readily undergo SNAr, usually faster at C-4 than C-2/6, but highly
dependent on nucleophile and conditions. C-3/5 react much slower.
- Cross coupling reactions occur fastest at the 2/6 positions followed by C-4
and C-3/5 much slower, much in accord with the Handy predictions. Mono
substitution can usually be acheived with 2,6-dihalo and 3,5-dihalo
pyridines.
Cl
OAr
OH
OR
Cl
Cl
NH2
5% PdCl2(PPH3)2
CuI, TEA, 80C
90%
Cl
N
Ph
soft nucleophiles
F
Br
OAr
NaH, DMSO
Cl
130C, 85%
Cl
Cl
1:6
1:3
hard nuclephiles
Br
cross coupling
In, 4% Pd(PPh3)4
LiI, DMF, 100C
Br
61%
Cl
NaH, THF
Br , then
Br
OR
Br
OH
Cl
NH
OH
1) o-tolMgCl
2) DDQ
KOt-Bu, CuI, py
120C, 61%
Cl
NHtBu
98%
KOt-Bu, DMA
THF, 120C, 84%
Cl
MeN
NHtBu
Cl
O
NHtBu
100C, 97%
N
N
MeN
Ph
Br
OH
7.55
Cl
Ph
NH2
Pyridine
8.52
R = CH2CH2OPh
>
N
NHR
140C, 93%
Cl
>
BnNH2
NHR
K2CO3, THF
reflux, 61%
Cl
>
OL 2003, 5, 3131
1.3x108
5.8x10
>
X
N
Cl
PhB(OH)2
5% PXPd2
NHR
Cl
PhB(OH)2
5% Pd(PPh3)4
K2CO3, THF
reflux
O
OMe
Ph
Cl
Cl
5:1
Usefully, Li-Halogen exchange is slow at 2/6 positions due to lone pair repulsion
OMe
Ph
n-BuLi, -100C;
Br
N
Br
D2SO4, 85%
D
N
Br
Haloselectivity of Heterocycles
Pyridazine/Pyrazine
2nd
8.05
7.46
7.65
8.05
Will Gutekunst
7.56
8.82
7.58
1st
1st
7.5
7.70
7.31
N
9.11
9.17
2nd
1st
Isoquinoline (CCl4)
7.85
Quinoline (CCl4)
7.52
8.45
- SNAr reactions occur readily at all of the positions. All sites are degenerate on pyrazine, and the
4-position is most activated for nucleophilic attack, despite NMR chemical shift.
- Selective cross coupling reactions have not been well studied on pyridazine, but modest selectivity
can be obtained from 3,6-dichloro compounds.
Cl
Cl
MeO2C
MeO2C
HO
ZnBr
LiCl, DMF, rt
83%
Cl
Cl
Cl
aq. Me2NH
EtOH, reflux
I
N N
Cl
Cl
I
N N
99%
Cl
Cl
B(OH)2
N
N
SnBu3
N
Cl
N N
Br
B(OH)2
3% Pd(PPh3)4
CsF, DME
87%
N N
OEt
5% PdCl2(PPh3)2
80C, DMF
54%
5% PdCl2(PPh3)2
80C, DMF
77%
Cl
Cl
N N
4% [Pd(dba)2]PPh3
Tol reflux
80%
S
Me2N
OEt
SnBu3
SnBu3
SnBu3
OMe
OEt
N
Me2N
Cl
Cl
MeOH, NaOMe
60%
DMA, Na2CO3
74%
Pd(PPh3)4 THF
60C, 80%
Cl
Cl
N
CO2Me
N
NH
Cl
Cl
HO
Cl
MeO2C
ZnBr
Pyrazine (C6D6)
Pyridazine (C6D6)
- SNAr reactions of quinoline mimic pyridine largely, with C-4>C-2 generally preferred, but usually
dependent on reaction conditions. Isoquinoline reacts fastest at C-1 followed by C-3 in SNAr.
- Cross coupling reactions in quinoline strongly favor the 2 position followed by 4. Regioselection
between the other positions has not been well investigated. Preference of 1 vs 3 is well established
in isoquinolines, but other positions not as well.
8.6
4% Pd(PPh3)4
DMF, 100C
61%
Br
OMe
Br
Br
N
TBS
10% Pd(PPh3)4
Na2CO3, MeOH/PhH
52%
N
N
OMe
NTBS
Br
Haloselectivity of Heterocycles
Benzannelated Diazines
1st
8.78
7.36
9.26
2nd
Pyrimidine (C6D6)
- Pyrimidines readily undergo SNAr at the 2 and 4/6 positions. 4/6 being
generally more reactive, but is very sensitive to reaction conditions. The 3position is greatly deactivated relative to the others.
- Cross coupling reactions occur fastest at the 4/6 positions followed by C-2
and C-5 much slower, in direct contrast to the Handy predictions.
N
N
H
N
Cl
HN
Cl
86%
7.95
8.44
OH
Cl
TMS
-68C,-rt, 90%
Cl
PhB(OH)2
5% Pd(PPh3)4
Ph
Cl
K2CO3, Tol/DMF
Cl
w, 185C
10 min, 58%
Cl
PhB(OH)2
5% Pd(Pt-Bu3)2
Ph
Cl
K2CO3, Tol/DMF
Cl
w, 185C
10 min, 65%
OTHP
Bu
Br
N
N
Cl
2% PdCl2(PPH3)2
CuI, TEA, rt
67%
O
Cl
Et2O, -40C;
then DDQ, 92%
N
N
Cl
EtOH, NaOEt
70C, 81%
Me2N
Et2O, -40C;
then DDQ, 72%%
Me2N
N
N
Me2N
OTHP
Bu
Li
SH
K2CO3, Tol/DMF
Ph
w, 185C
10 min, 70%
Lithium reagents can directly add into C-4/6, which can be oxidized back to aromaticity easily
Me2N
SMe
Cl
Li
Cl
Br
N
N
Cl
HN
MeCN, 130C
84%
SMe
PhB(OH)2
5% Pd(PPh3)4
2nd
9.35
Quinazoline (CDCl3)
Chem. Soc. Perkin 2 1989, 1499; J. Het. Chem. 1994, 31, 989
Cl
8.06
Quinoxaline (CDCl3)
NH2
OMe
rt, 90%
7.67
N
SMe
MeOH
NaOMe
9.91
7.93
8.84
Phthalazine (acetone)
n-BuLi, THF
Cl
7.93
TMS
8.11
9.60
8.00
9.29
HN
Cl
8.13
2nd
7.86
7.77
- SNAr reactions occur readily at all of the heterocyclic positions. Behavior seems to be similar to the
diazine counterparts, ie C-4 more reactive than C-2 in quinazolines, C-4>C-3 in cinnoline.
- Cross coupling reactions have not been well studied on these systems, but the few examples mimic
the corresponding diazines well.
NH
THF, -10 C to rt
92%
Cl
1st
1st
8.01 8.18
Cinnoline (CDCl3)
4.2 eq
Cl
Will Gutekunst
N
N
Cl
Haloselectivity of Heterocycles
3rd
8.72
Misc Examples
1st
- Purines can participate in SNAr reactions at all carbon centers. For 9-H
purines, the order of reactivity is 6>8>2. For substitution at 9, reactivity
changes to 8>6>2.
- Cross coupling reactions usually occur fastest at the 6 position, though
C-8 becomes competitive in some cases. C-2 is slowest.
8.5
N
H
2nd
Purine (D2O)
Ph
TEA, MeCN
95%
RHN
5% PdCl2(PPh3)2
DCE, 75C
63%
N
THP
120C, 89%
N
H
N
N
CN
NHBn
N
Sug
MeS
BnNH2
N
N
50C, 95%
MeS
Cl
N
DCM, Et2Ni-Pr
91%
SnBu3
HN
KCN, DMSO
SMe
UK-371,104
DCM, Et2Ni-Pr
86%
Cl
NH2
Cl
HN
CO, THF
N
Sug
NH2
N
HN
Ph
N
N
Cl
Ph
Ph
Cl
N
Sug
Ph
Ph
NH2
Cl
H2N
Will Gutekunst
OEt
Cl
N
THP
SNAr, Sonogashira
Stille and Suzuki
Cl
OEt
N
N
N
Single regioisomer
(no yields reported)
Cl
N
N
Cl
N
Cl
MeMgCl
Fe(acac)3
PhB(OH)2
5% Pd(PPh3)4
72%
K2CO3, Tol
100C
N
Bn
5% Pd(OAc)2
CuI, Cs2CO3
DMF, 160C
79% (two steps)
Ph
N
Bn
Cl
B(OH)2
S
PhB(OH)2
5% Pd(PPh3)4 5% Pd(PPh3)4
Cl
Ph
OL 2007, 9, 4673
OL 2006, 8, 5389
OH
Cl
MeMgCl
30% Fe(acac)3
Cl
N
N
THP
NMP/THF
37%
OH
Cl
O
O
N
N
THP
Br
N
N
Br
Ar
NaHMDS
THF, -10C
78%
OH
Br
OH
Br
OH
O
N
N
LiHMDS
THF, -40C
60%
HO
N
N
Ar
Haloselectivity of Heterocycles
Conclusions
Selective reactions of polyhaloheterocycles has proven to be a very powerful method for synthesis of
functionalized heterocycles. Frequently cross-coupling and SNAr are complementary methods, with
C-H functionalization rapidly growing. While the prediction of regioselectivity is difficult to rationalize
at times, common trends are seen in certain heterocyclic motifs and can be extrapolated to more
complex situations, though, screening seems to still be needed for many cases. Future directions
are in the ligand controlled cross coupling and further development of C-H activation reactions.
Key References
Cross coupling reviews:
Tetrahedron 2005, 61, 2245
Chem. Soc. Rev. 2007, 36, 1036
Synthesis 2009, 9, 1405
Computational Analysis of Polyhalo Heterocycles
JACS, 2007, 129, 12664
JACS, 2009, 131, 6632
Handy Predictions
Chem. Comm. 2006, 299
Will Gutekunst