Combined experimental/theoretical study on d-glucosamine promoted regioselective sulfenylation of indoles catalyzed by copper

Article abstract of DOI:10.1039/c7nj02784b

A combined experimental/theoretical investigation on the d-glucosamine promoted sulfenylation of indoles at the C3 position with sodium sulfinates catalyzed by copper is presented. The C3-sulfenylation of indoles shows good functional-group tolerance and yields. The 3-I-indole was identified as a crucial intermediate in the catalytic cycle. The catalytic role of [Cu(DMSO)₂]²⁺ was addressed using quantum chemical calculations. In the interaction of [Cu(DMSO)₂]²⁺ with indole, the [Cu(DMSO)₂]²⁺ complex abstracts a hydrogen from the C3 of indole. The electronic origin for selective C-H bond activation of indole was revealed.

Full text of DOI:10.1039/c7nj02784b

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Jason B. Benedict et al.
The role of atropisomers on the photo-reactivity and fatigue of
diarylethene-based metal–organic frameworks
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Combined Experimental/theoretical Study on D-Glucosamine
Promoted Regioselective Sulfenylation of Indoles Catalyzed by
Copper
a,b
a
a
b
b
b
Xin Ge , Fengli Sun , Xuemin Liu , Xinzhi Chen , Chao Qian * and Shaodong Zhou *
a
School of Chemical and Material Engineering, Jiangnan University, Wuxi, P.R China
b
Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology,
College ofChemical and Biological Engineering, Zhejiang University, Hangzhou, P.R China.
Abstract: A combined experimental/theoretical investigation on the DꢀGlucosamine promoted
sulfenylation of indoles at the C3 position with sodium sulfinates catalyzed by copper is presented.
The C3ꢀsulfenylation of indoles shows good functionalꢀgroup tolerance and yield. The 3ꢀIꢀindole
2+
2
was identified as a crucial intermediate in the catalytic cycle. The catalytic role of [Cu(DMSO) ]
2
+
was addressed using quantum chemical calculations. In the interaction of [Cu(DMSO)2] with
2
+
2
indole, the complex [Cu(DMSO) ] abstracts a hydrogen from C3 of indole. The electronic origin
for selective C–H bond activation of indole was revealed.
Keyword: indole; sodium sulfinates; copper; sulfenylation; DFT
Introduction
Indole is an important privileged structural scaffold which plays a major role in natural and
1
pharmacological compounds . The electronꢀrich nature of indole rings is employed in the CꢀC and
2
ꢀ6
CꢀX bond coupling via direct C–H bond functionalization . Thus, the functionalization of indole,
7
ꢀ10
11ꢀ14
in particular, at C2
or C3
position, have attracted much attention on the background of
developing efficient synthetic strategy. One of these utilities is the synthesis of 3ꢀthioindole via
1
3, 14
construction of CꢀS bond at C3 position of indole ring
including antiꢀHIV, antiꢀcancer and antiꢀbacterial infection, etc.
To date, quite some C–H functionalization
, which has various bioactivities
of
indole
catalyzed
by
*
Corresponding author. Chao Qian, Eꢀmail: qianchao@zju.edu.cn and Shaodong Zhou, Eꢀmail:
shaodong.zhou@campus.tuꢀberlin.de

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9, 15ꢀ20
7, 8, 11, 21ꢀ26
transitionꢀmetalꢀcontaining
or metalꢀfree
species were reported. In particular,
iodineꢀcatalyzed and copperꢀcatalyzed synthetic strategies have been proven to be efficient for
promoting the C–H functionalization of indole. For direct sulfenylation of indole, the electrophilic
23, 25
27
sulfenylating reagents, thiols
, disulfides and sulfenyl halides, are used as the major starting
materials. Nevertheless, these sulfenylating reagents have some wellꢀknown disadvantages, i.e.
strong and repulsive odors of thiols and disulfides, instability of sulfenyl halides. Thus, alternative
13, 15, 21
sulfenylating reagents have been exploited including sulfonyl hydrazides
, arylsulfonyl
16
14
28
chlorides , bunte salts and sulfinic acids . However, the application of these sulfenylating
reagents is still limited due to their expensive, airꢀ or waterꢀsensitive characters as well as the
excessive usage in sulfenylation. Thus, it continues to be challenging and interesting to explore
green and efficient catalytic system for C3ꢀsulfenylation of indole.
Sodium sulfinate is currently attracting much attention as it is inexpensive, odorless and
stable solid, which have been widely used as sulfenylation agent. Recently, iodineꢀcatalyzed
synthetic strategy has been proven to be efficient for the C–H functionalization of indole with
11, 22, 29
22
sodium sulfinates
. For instance, Kuhakarn et al. reported the sulfenylation of indole with
11
sodium sulfinates catalyzed by iodineꢀPPh
3
. Deng et al. described the similar strategy and found
that disulfide was generated from sodium benzenesulfinateꢀparticipated sulfenylation catalyzed by
iodine and diethyl phosphite. However, iodineꢀcatalyzed C3ꢀsulfenylation of indoles still suffers
from low yields. Inspired by our interest in the ligand and catalytic effect of carbohydrates on
30, 31
coupling reaction
, we developed Dꢀglucosamine promoted C3ꢀsulfenylation of indoles with
sodium sulfinates catalyzed by copper catalyst. The DFT calculation complemented experimental
findings will be presented.
Results and Discussion
In an initial attempt of direct C–H functionalization of indole catalyzed by copper,
C3ꢀsulfenylindole was obtained selectively and the structure of product 3q was proved by
singleꢀcrystal Xꢀray diffraction (Fig.1). Next, detailed study on copperꢀcatalyzed C3ꢀsulfenylation
of indoles was implemented. The reaction of indole (1a) and sodium benzenesulfinate (2a) was
selected as the model reaction, and more details on optimization of C3ꢀsulfenylation was shown in
Table 1. We first studied the influence of various ligands on the catalytic activity. Comparison of

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different ligands, i.e. dimethylehylenediamine (DMEDA), tetramethylethylenediamine (TMEDA),
,10ꢀphenanthroline, Glucose, NꢀAcetylꢀDꢀGlucosamine, DꢀGlucosamine, showed that
1
DꢀGlucosamine is the best ligand (Table 1, entries 1ꢀ6). In addition, the yield of the catalytic system
without ligand was 45% (Table 1, entry 7). It was found that monoiodide was necessary for
C3ꢀsulfenylation of indoles (Table 1, entry 8). Therefore, a series of monoiodides were tested
4
(Table 1, entries 8ꢀ11), and NH I exhibits the highest efficiency with 86% yield. More details on the
effect of additive will be discussed later. Next, the various copper sources, i.e. CuI, CuBr, CuCl,
CuSO ·5H O and Cu(OAc) , were examined in this process. While all copper salts initiate this
4
2
2
reaction (Table 1, entries 10, 13ꢀ16), Cu(OAc)
excellent yield was obtained.
2
was found to be best effective catalyst and the
a
Table 1. Optimization of C3ꢀsulfenylation of indoles with sodium sulfinates
b
Entry
Catalyst
CuI
Additive
Ligand
Yield (%)
1
2
3
4
KI
KI
KI
KI
DMEDA
TMEDA
30
43
54
63
CuI
CuI
1,10ꢀphen
CuI
Glucose
NꢀAcetylꢀDꢀGlucos
amine
5
CuI
KI
61
6
7
8
9
CuI
CuI
CuI
CuI
CuI
KI
KI
ꢀ
DꢀGlucosamine
ꢀ
67
45
DꢀGlucosamine
DꢀGlucosamine
DꢀGlucosamine
trace
52
NaI
10
NH
4
I
86

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1
1
CuI
ꢀ
I
2
DꢀGlucosamine
DꢀGlucosamine
DꢀGlucosamine
DꢀGlucosamine
DꢀGlucosamine
DꢀGlucosamine
trace
1
1
1
1
1
2
3
4
5
6
NH
NH
NH
NH
NH
4
I
4
I
4
I
4
I
4
I
trace
72
CuCl
CuBr
83
CuSO
4
·5H
2
O
81
Cu(OAc)
2
91
a
Reaction conditions: 1a (1 mmol), 2a (1.2 mmol), catalyst (0.1 mmol), ligand (0.1 mmol), additive
o
b
(
3 mmol), DMSO (5 mL), 110 C, air, 6 h. Isolated yield.
Fig. 1 Singleꢀcrystal Xꢀray structure of 3q.
Further study focused on testing the scope of above obtained protocal, i.e. Dꢀglucosamine
promoted C3ꢀsulfenylation of indoles with sodium sulfinates catalyzed by copper catalyst, and the
results were summarized in Table 2. Indoles with methyl group in C4, C5, C6 and C7 position, can
couple smoothly with sodium benzenesulfinate (2a) and the desired products were obtained in 93%,
9
7%, 96% and 98% yields, respectively. When the C3 position of indole moisty was occupied by
the Me group, no C2 sulfenylation product was detected. In contrast, when indoles possessed
methyl group in N1 and C2 position, the yields of the reaction decreased to 74% and 73%
2
respectively. If the electronꢀwithdrawing substituents, e.g. Cl, Br, CN, NO were present at the
benzene ring of indole, the yields were lower as compared to the ones with electronꢀdonating
substituents, e.g. Me and OH. Meanwhile, regardless of whether the substituents, e.g. Me and Cl,
located at any optional position of benzene ring, the corresponding yields were not affected

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considerably. Subsequently, the effect of the substitutes at sodium sulfinates was evaluated. The
pꢀtoluenesulfonic acid sodium salts reacted with indole to generate the corresponding product in
excellent yield. Arylsulfinic acid sodium salts with halogen, e.g. F, Cl, substituted at the
paraꢀposition, were well tolerated and the desired products were obtained with 89% and 85% yield,
respectively. To our disappointment, sodium methanesulfinate could not react with indole. It was
speculated that the boiling point of intermediate disulfide is low and its existence in the reaction
system is difficult.
a
Table 2. Reaction of substituted indoles and sodium sulfinates
R2
S
Cu(OAc)2,D-Glucosamine
+
R1
R2SO2Na
R1
N
NH4I, DMSO
N
Z
Z
1
2
3
Z=H, Me
S
S
S
S
N
N
N
H
N
H
H
3a 91%
3b 74%
3d 0%
3c 73%
S
S
S
N
N
H
N
H
H
3
e 93%
3g 96%
3f 97%
S
Cl
S
S
S
Cl
HO
N
H
N
H
j 85%
N
H
N
H
3
3k 83%
3
h 98%
3i 95%
S
S
Br
S
2
O N
NC
N
H
N
N
H
H
3
l 79%
3
m 84%
3n 88%
F
Cl
S
S
S
S
N
H
N
H
o 95%
N
H
p 89%
N
H
3
3q 85%
3r 0%
3
a
2
Reaction Conditions: 1 (1 mmol), 2 (1.2 mmol), catalyst Cu(OAc) (0.1 mmol), ligand
o
DꢀGlucosamine (0.1mmol), additive NH
4
I (3 mmol), DMSO (5 mL), 110 C, air, 6 h.

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To investigate the mechanism of this reaction, various control experiments were carried out
Scheme 1). 3ꢀIꢀindole was detected via a copperꢀcatalyzed aerobic C–H oxidation of indole and
(
isolated during the reaction with 45% yield. It is notable that the formation of 3ꢀIꢀindole was
3
2
kinetically favored, in consistence with the previous report . In presence of NH
benzenesulfinate, diphenyldisulfide and diphenylsulfide were obtained with 89% and 3% yields,
respectively. This means that sodium benzenesulfinate can be reduced by NH I, which is similar to
4
I with sodium
4
24
Ding’s report . Further, the desired product was generated by Ullmann type CꢀS coupling reaction
of 3ꢀIꢀindole and diphenyldisulfide catalyzed by copper(Ⅱ ) and Dꢀglucosamine.
Scheme 1. Control experiments
A plausible mechanism for Dꢀglucosamine promoted regioselective sulfenylation of indoles
Ⅱ
catalyzed by copper is proposed (Scheme 2). Initially, glucosamineꢀligated Cu species (Ⅱ ) is
Ⅱ
31, 33,
generated by the reduction or disproportionation of the Cu precursors ligated to glucosamine
34
.
With the remove of acetate ion, the intervention of arylsulfenyl ion affords the
Ⅱ
glucosamineꢀligated Cu thiolate intermediate (Ⅱ ). In addition, 3ꢀIꢀindole can be synthesized via
copperꢀcatalyzed aerobic C–H oxidation of indole, the mechanism of which will be unraveled later
Ⅱ
by DFT calculation. Then, a threeꢀcenter Cu intermediate (Ⅱ ) is formed via oxidative addition of
intermediate Ⅱ with 3ꢀIꢀindole. Subsequently, intermediated Ⅱ undergo transionization with

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acetate ion to produce intermediate Ⅱ . Finally, the desired product 3a was obtained by reductive
Ⅱ
elimination and the glucosamineꢀligated Cu species (Ⅱ ) is regenerated.
Scheme 2. Proposed mechanism
While the mechanisms of Ullmannꢀtype CꢀS coupling catalyzed by copper catalyst have been
addressed previously, the origin for selective C3ꢀiodization remains unknown. To obtain further
evidence for probing the reaction mechanisms, additional experiments were performed. It turns
out that replacing Cu(OAc)
2 4 2
with CuSO ·5H O does not affect the selective generation of
3
ꢀIꢀindole. However, the presence of DMSO is crucial as alternative solvents such as toluene and
hexane do not bring about the generation of iodized indole (See Table.S1 in the ESI). The crucial
role of DMSO in iodineꢀcatalyzed regioselective sulfenylation of indoles has been revealed
11
previously by Deng et al. that it acts as an oxidant. Alternatively, however, it will be shown later
that in the iodization of indole DMSO serves as the hydrogen abstractor.
Further, as it has been proven experimentally that a twoꢀstep process is responsible for the
formation of sulfides, the iodization of indoles upon selective C–H bond activation is crucial for
the regioselective sulfenylation of indoles. Thus, the iodization of indole (1a) was selected for the
interrogation of reaction mechanisms using quantum mechanical calculation. As described above,
for the iodization of indole the presence of copper and DMSO is indispensable while it does not
matter which copper salt is used. Based on this, we built a DMSOꢀaided CꢀI coupling model. The

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potential energy surfaces (PESs) and selected structural information for the iodization of indole
are presented in Fig. 2. An initial inspection of the possible isomers of iodized indole indicates that
ꢀ1
2
ꢀIꢀindole is less stable than 3ꢀIꢀindole by 6 kJ mol , and as will be shown later kinetics are
involved for the selective generation of 3ꢀIꢀindole.
Fig. 2 Simplified PESs for the generation of 2ꢀIꢀindole and 3ꢀIꢀindole starting from the encounter
complex EC1a/EC1b as calculated at the B97ꢀ1/BSII//B97ꢀ1/BSI level of theory. Zeroꢀpoint
ꢀ1
corrected, relative energies are given in kJ mol and bond lengths in Å; charges are omitted for
the sake of clarity.
2
+
2
The active species addressed in a catalytic cycle of the iodization process is [Cu(DMSO) ] .
As shown in Fig. 2, the transformation starts from the encounter complex EC1a/EC1b in which
two DMSO and one indole molecules ligate with the copper via the CuꢀO and CuꢀC interactions.
By surmounting TS1a/TS1b, the Oꢀatom of one DMSO abstracts a hydrogen from 3ꢀC/2ꢀC of
indole, forming the intermediate IM1a/IM1b. Subsequent barrierless absorption of I‾ and
elimination of C H SOH‾ generate the product complex PC1a/PC1b. Next, by liberating the
2
6

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2
+
product 3ꢀIꢀ/2ꢀIꢀindole the catalyst [Cu(DMSO)
2
]
is regenerated. Note that the eliminated
+
C H SOH‾ has to be consumed upon reaction with NH for the sake of the forward conversion.
2
6
4
According to the calculation, the barrier for the generation of 3ꢀIꢀindole (ꢀG
r
(TS1a)ꢀꢀG
r
(EC1a))
ꢀ1
is lower than that of 2ꢀIꢀindole (ꢀG (TS1b)ꢀꢀG (EC1b)) by 25 kJ mol . This considerable energy
r r
difference makes TS1b bypassed, in line with the selective generation of 3ꢀIꢀindole as observed
experimentally.
2
+
2+
In addition to the [Cu(DMSO)
2
] /indole, the [Cu(DMSO)] /indole model was also
considered. However, according to the calculation, the associated reaction barriers were found to
2
+
be much higher than that for [Cu(DMSO) ] /indole. For more details, see SI.
2
To obtain further insight into the hydrogen transfer process, we examined the correlation of
the deformation energy (ꢀEdef) required to distort the reactants along the reaction coordinate to
‡
ꢀ1
their TSs with the respective gasꢀphase barrier (ꢀE ). The results are: ꢀEdef(TS1a) = 528 kJ mol ,
ꢀ1
‡
ꢀ1
‡
ꢀ1
ꢀ
E (TS1b) = 496 kJ mol ; ꢀE (TS1a) = 118 kJ mol , ꢀE (TS1a) = 131 kJ mol . Clearly, for
def
‡
both processes, ꢀEdef >> ꢀE , that is, the TSs have great stabilizing interactions which lower the
barriers well below the respective deformation energies. Next, Fig. 3 shows the singly occupied
spin natural orbitals (SNOs) for TS1a and TS1b. The contributing orbitals on indole are πꢀtype (or
πꢀlone pair type) orbitals that are perpendicular to the σꢀlobes of the SꢀO orbital of DMSO; this
electronic feature indicates that both pathways are predominantly protonꢀcoupled electron transfer
35
36
(
PCET) processes. Further, as shown in Fig. 4, for both TS1a and TS1b low charges are located
on the Hꢀabstracted indole (QSꢀH) while large degrees of charge have been transferred from indole to
2
+
[
2
Cu(DMSO) ] (QCT). This means that both TSs have a discrete electron transfer (ET) character.
Fig. 3 SNOs in TS1a and TS1b. the hydrogen atoms not in O···H···X moiety are omitted for clarity.

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Fig. 4 Schematic representations of the TSs together with NBO charges (Q) and spin densities (ρ) on
the Hꢀabstracted indole (SꢀH), the charge on the catalyst (Q ), and the amount of charge transferred
CT) from indole to the catalyst.
c
(Q
Thus, the lower relative energy of TS1a as compared to that of TS1b can be explained by the
charges at associated atoms: the charges at C2, C3, 2ꢀH, and 3ꢀH amount to ꢀ0.04, ꢀ0.32, 0.24, and
.25, respectively. A higher negative charge at C3 favors donating electron density to the Cu atom
while a higher positive charge at 3ꢀH is more prone to be protonated. Accordingly, the PCET
process at C3 H is more favored.
0
–
Conclusion
In summary, we have reported a combined experimental/theoretical study on regioselective
sulfenylation of indoles at C3 catalyzed by copper. The reaction is promoted by Dꢀglucosamine
and copper, and the presence of NH I is crucial. The scope of the obtained strategy was examined.
Mechanistic study provided evidence for the formation of 3ꢀIꢀindole. According to the calculation,
4
2
+
[
Cu(DMSO)2] is the active species in the catalytic cycle of the iodization process; next,
activation of the C3ꢀH bond of indole proceeds via PCET and the iodization process was
2 6
accomplished by involvement of I‾ and elimination of C H SOH‾. A higher negative charge at C3
is responsible for the selective generation of 3ꢀIꢀindole.
Acknowledgements
The authors are grateful for the financial support from the Natural Science Foundation of China

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(
21476194, 21606104), the National Key Research and Development Program of China
2016YFB0301800) and China Postdoctoral Science Foundation funded project (2016M590536).
(
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Graphical abstract