Synthesis and reactivity of enediyne-nucleobase hybrids: Effect of intramolecular π-stacking

Article abstract of DOI:10.1016/j.tet.2012.07.093

Three distinct classes of nucleobase-containing enediynes 1-9 with varying nature of the linker have been synthesized to explore the effect of π-stacking interaction in accelerating the rate of Bergman cyclization (BC). Chemical reactivity study, both experimental and computations demonstrated the important role that aromatic π-stacking interactions between the appended nucleobases within an enediyne frame play in lowering the activation barrier of Bergman cyclization.

Full text of DOI:10.1016/j.tet.2012.07.093

Tetrahedron 68 (2012) 8600e8611
Contents lists available at SciVerse ScienceDirect
Tetrahedron
journal homepage: www.elsevier.com/locate/tet
Synthesis and reactivity of enediyneenucleobase hybrids: effect of intramolecular
p
-stacking
,
Snigdha Roya, Subhendu Sekhar Bag b, Amit Basak a
*
a Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
b Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 12 June 2012
Received in revised form 24 July 2012
Accepted 27 July 2012
Available online 4 August 2012
Three distinct classes of nucleobase-containing enediynes 1e9 with varying nature of the linker have
been synthesized to explore the effect of -stacking interaction in accelerating the rate of Bergman
cyclization (BC). Chemical reactivity study, both experimental and computations demonstrated the im-
portant role that aromatic -stacking interactions between the appended nucleobases within an ene-
diyne frame play in lowering the activation barrier of Bergman cyclization.
Ó 2012 Elsevier Ltd. All rights reserved.
p
p
1. Introduction
synthesis along with chemical reactivity and detailed structural
analysis are reported in this paper.
Bergman cyclization1 of enediyne to the 1,4-benzene diradical2
and related reactions have remained a research area of contem-
porary interest. Many artificial synthetic structural motifs have
been explored till date to affect the Bergman cyclization kinetics
through intramolecular non-covalent interactions,3 such as hy-
2. Results and discussions
The synthesis of class A molecules with a methylene linker was
done via double N-alkylation. For the AA or TT enediynes, the
double N-alkylation was carried out in a single step on the bromide
2c using A or T (Scheme 2). For the synthesis of 1 with different
bases, alkylation was done in two steps (Scheme 1). The first al-
kylation was carried out on the monobromide 1d with bis-Boc
protected adenine to provide 1f. Conversion to the bromide 1h
followed by alkylation with Boc-thymine to provide the tris-Boc
hybrid 1i, which was deprotected with TFA to furnish 1. Protected
bases had to be employed because of competing intramolecular N-
alkylation. Similarly, class B and C compounds were prepared by
using slightly modified protocol. For class B molecules, the dibro-
moacetyl enediyne 5b was employed for the synthesis of AA or TT
enediynes (5 and 6) (Scheme 4) while stepwise alkylation starting
from mono bromoacylated enediyne 4f was used for the synthesis
of 4 with both A and T (Scheme 3). First alkylation was carried out
with bis-Boc protected adenine. The product was deprotected and
coupled directly with carboxymethyl thymine using EDC$HCl and
HOBt. The triazole based enediynes belonging to class C were
prepared via click reaction as shown in Schemes 5 and 6. Final
compounds 1e9 were characterized by NMR and mass spectrom-
etry, in which structures of 1i and 3a were unambiguously con-
firmed by X-ray crystallography study (Fig. 2).12
drogen bonding,4 stacking,5 electrostatic6 and charge transfer
pep
interactions.7 One important natural component, namely the pu-
rine and pyrimidine bases present in the beautifully self-assembled
DNA,8 can show these weak interactions and hence are attractive
motifs for enediynes in perturbing the kinetics of BC. In DNA, the
two helical strands are connected to each other through weak hy-
drogen bonding interactions, though the stability of this complex
molecular aggregation is mainly attributed to comparatively strong
non-covalent pep stacking interaction between aromatic bases of
the two parallel helices.9 According to Nicolaou’s distance theory,10
the spatial distance (d) between the terminals of two acetylenic
arms of enediyne can dictate its reactivity. The value of d should
11
ꢀ
range from 3.20 to 3.31 A for smooth cyclization at ambient
temperature. If two different nucleobases are attached to the two
acetylenic arms of the enediyne moiety through a spacer, they may
show the complementary base pairing via hydrogen bonding and/
or p-stacking interaction, depending on the conformation adopted.
For identical nucleobases attached to the enediyne terminals,
stacking interactions are mainly expected. In order to find out
which interactions (H-bonding or
have synthesized three distinct classes of nucleobase-containing
enediynes 1e9 with varying nature of the linker (Fig. 1). Their
p stacking) are predominant, we
With the target compounds in hand, their thermal reactivity
was studied, specifically to identify the BC products, if any. We
were disappointed in not isolating any distinct product from the
solution phase reactions (heating in DMSO within 150e180 ꢀC for
* Corresponding author. Fax: þ91 3222 83300; e-mail address: absk@chem.-
iitkgp.ernet.in (A. Basak).
0040-4020/$ e see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tet.2012.07.093

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8601
Fig. 1. Design of enediyneenucleobase hybrids.
N
N
N
N
N
N
N
Br
Br
NH2
N(Boc)2
j
N
N
O
O
N
N
N
1i
1
H
Boc
a-d
O
O
i
N
N
N
N
Br
N
N
N(Boc)2
g,h
e,f
OTHP
N(Boc)2
N
N
OH
1d
Br
1h
1f
Reagents and conditions: (a) THP-protected propargyl alcohol, Pd(PPh3)4, n-BuNH2, 80 °C to 85 °C, 3 h (82%);
(b) Propargyl alcohol, Pd(PPh3)4, n-BuNH2, 80 °C to 85 °C, 14 h (80%); (c) MsCl, Et3N, DCM, 0 °C, 15 min
(92%); (d) LiBr, THF, r.t., 8 h (72%); (e) Bis-Boc-adenine, Cs2CO3, CH3CN, r.t., 7 h (60%); (f) PPTS, EtOH, r.t., 6
3
h (78%); (g) MsCl, Et3N, DCM, 0 °C, 15 min (80%); (h) LiBr, THF, r.t., 10 h (80%); (i) N -Boc-thymine, Cs2CO3,
CH3CN, r.t., 7 h (54%); (j) TFA, DCM, 0 °C to r.t., 4 h (45%).
Scheme 1. Synthesis of compound 1 of class A.
O
N
NBoc
N
Br
Br
N
N
N
O
e
c
N(Boc)2
N(Boc)2
N
N
O
NBoc
O
N
2c
3a
2d
N
N
b
f
d
O
N
2b, R = OMs
N
NH
NH
N
O
O
N
N
a
NH2
NH2
R
R
N
N
O
N
2
3
N
N
2a, R = OH
Reagents and conditions: (a) MsCl, Et3N, DCM, 0 °C, 15 min (85%); (b) LiBr, THF, r.t., 10 h (72%); (c)
3
Bis-Boc-adenine, Cs2CO3, CH3CN, r.t., 8 h (58%); (d) TFA, DCM, 0 °C to r.t., 4 h (52%); (e) N -Boc-
thymine, Cs2CO3, CH3CN, r.t., 6 h (60%); (f) TFA, DCM, 0 °C to r.t., 4 h (54%).
Scheme 2. Synthesis of compound 2 and 3 of class A.

8602
S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
N
O
N
NH2
O
NH2
N
O
NH
N
NH
I
I
N
N
i
N
N
O
NH2
NH
N
NH
4h
a,b
4
O
g,h
O
Br
NHBoc
OH
N
H
NHBoc
c,d
e,f
NHBoc
N3
4b
4f
4d
Reagents and conditions: (a) N-Boc-propargylamine, Pd(PPh3)4, CuI, Et3N, r.t., 8 h (54%); (b) Propargyl
alcohol, Pd(PPh3)4, CuI, Et3N, r.t., 6 h (65%); (c) MsCl, Et3N, DCM, 0 °C, 10 min (90%); (d) NaN3, DMF,
r.t., 6 h (70%); (e) PPh3, THF, H2O, r.t., 6 h (78%); (f) bromoacetyl chloride, Et3N, DCM, 0 °C, 15 min
(65%); (g) Bis-Boc-adenine, Cs2CO3, CH3CN, r.t., 6 h (56%); (h) TFA, DCM, 0 °C to r.t., 3 h (50%); (i) 1-
(carboxymethyl)thymine, EDC.HCl, HOBt, DCM, DMF, 0 °C to r.t., 10 h (52%).
Scheme 3. Synthesis of compound 4 of class B.
15e30 h) although there was disappearance of the starting ene-
diynes. It appeared that the compounds underwent de-
composition with formation of polymeric products.13 1H NMR of
the polymer indicated appearance of new peaks in the aromatic
region thus pointing out the occurrence of BC. Also, the diradical
mediated polymerization was confirmed by the MALDI mass
analysis14b of the resultant DMSO solution of enediy-
neenucleobase hybrids. The mass spectrum of compound 3 clearly
showed the formation of different oligomers, dimer, trimer, tet-
ramer etc. by exhibiting their corresponding m/z signals at 829
(with an added Naþ), 1231 (with an added Naþ), 1609, respectively
(Fig. 3). The building block of all these oligomeric species was the
intermediate 1,4-diradical.14a Solution phase kinetic experiment
was performed with class A enediynes (1e3) maintaining the
concentration of each compound at w4ꢁ10ꢂ3 M in DMSO solvent
using naphthalene15 as inert internal standard. The solutions were
heated at 170 ꢀC and the rate of disappearance of the substrates
was measured by recording the HPLC profile of aliquots at different
time points (Zorbax SB C-18 column, 9.4 mmꢁ25 cm, Solvent
system¼a mixture of methanol and water (85:15, v/v), Flow
rate¼1 mL/min). It showed a pseudo first order kinetics and the
corresponding kinetic graph plots are shown in Fig. 4. The rate
constants (kobs) as mentioned in Table 1 showed the following
order: AeA system 2>AeT system 1zTeT system 3.
The solid state reactivity was next studied by recording the
onset temperatures for BC using the Differential Scanning Calori-
metric measurements (DSC)16 under neat conditions (DSC curves,
vide SI, Fig. S3). The various onset temperatures as shown in Table 2
revealed that the reactivity of the enediynes depends not only on
the nature of base pairs but also on the type of spacers. However,
like the solution phase kinetics, a definite trend in reactivity could
be observed. For example, in all the three classes of enediynes, the
reactivity of the AeA pairs (2, 5 and 8) turned out to be highest (as
revealed by their corresponding lower onset temperatures for BC)
followed by the AeT pairs (1, 4 and 7) with the TeT pairs (3, 6 and 9)
showing the lowest reactivity (Table 2). Thus the solid phase re-
activity is similar to what has been observed for class A molecules
in solution phase.
O
Br
N
d,e
b,c
H
H
N
N
Br
NH2
5b
H
N
O
O
N
O
O
a
O
N
N
N
NH
NH
NHBoc
NHBoc
O
H
N
H
N
N
N
NH
N
5
6
O
O
5a
O
N
NH2
N
Reagents and conditions: (a) i) TFA, DCM, 0 °C to r.t., 3 h; ii) bromoacetyl chloride, Et3N, DCM, 0
°C, 10 min (67%); (b) Bis-Boc-adenine, Cs2CO3, CH3CN, r.t., 10 h (58%); (c) TFA, DCM, 0 °C to r.t.,
3
5 h (60%); (d) N -Boc-thymine, Cs2CO3, CH3CN, r.t., 8 h (62%); (e) TFA, DCM, 0 °C to r.t., 5 h (65%).
Scheme 4. Synthesis of compound 5 and 6 of class B.

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8603
N
N
N
N
H
N
N
N
O
N
N3
NH2
e
N
O
N
N
N
N
N
N
O
N
N3
OTHP
7
7e
7a
NH
c,d
O
a
H
N
H
N
N
O
O
N
N
N
N
N
O
O
b
N
N
R
OTHP
7c, R = OH
7d, R = OMs
7b
1
t
Reagents and conditions: (a) N -Propargyl thymine, CuSO4.5H2O, sodium ascorbate, BuOH, H2O, r.t.,
10 h (65%); (b) PPTS, EtOH, r.t., 8 h (86%); (c) MsCl, Et3N, DCM, 0 °C, 15 min (85%); (d) NaN3, DMF,
9
t
r.t., 6 h (78%); (e) N -propargyl adenine, CuSO4.5H2O, sodium ascorbate, BuOH, H2O, r.t., 14 h (52%).
Scheme 5. Synthesis of compound 7 of class C.
Regarding the role of spacer, it can be seen that the reactivity for
AeA pairs 2, 5 and 8 increased as the spacer is changed from
a simple methylene to a methylene amido methylene and ulti-
mately to a bis-methylene triazole moiety. There was substantial
reduction of onset temperature for BC. Similar trend was observed
for the AeT pairs (1, 4 and 7). However, the effect of change of
spacer on the reactivity in case of the TeT pairs (3, 6 and 9) was not
so significant.
Interestingly, the chemical shift of A-2H, A-8H, T-Me and T-6H
also showed some degree of temperature dependence, which is an
indication17b of existence of
p
-stacking interaction between the
nucleobases. It has earlier been shown19 that the
-stacking be-
tween the nucleobases follows the order AeA>AeT>TeT. Since
p
p
-
stacking can be expected to bring the acetylenic arms to come
closer, which should result in increase in reactivity towards BC, the
reactivity should also follow the same order as of the
p-in-
To find out which factor, namely the
p
e
p
stacking or intra-
teractions. This is indeed the case in all the classes of enediynes.
Regarding the dependence of reactivity on the nature of spacer,
the following explanation seems reasonable. In class B and C, ad-
ditional intramolecular stabilization forces were operative. For class
B, the amide NH has a temperature coefficient close to the Kessler
limit and thus showing a strong intramolecular H-bond between
the amide carbonyl and the amide NH of opposing strands. The
formation of H-bonded network between the amide carbonyl and
the amide NH of opposing strands is also evident from the transi-
tion state optimized geometries of all the compounds of class B. For
class C, the two triazole moieties in the opposite strands have ad-
molecular H-bonding, is playing a more important role on the ob-
served reactivity pattern, variable temperature NMR (between
30 ꢀC and 65 ꢀC) were recorded as this is a well-known method to
elucidate the intramolecular hydrogen bonding as well as the
p-
stacking interactions in solution phase (SI, Figs. S5e14).17 The var-
iations of different chemical shifts, as determined at concentration
below 1 mM (to avoid intermolecular associations) are shown in
Table 3. The Dd/DT values of A-NH2 and T-NH for all compounds
were beyond the Kessler limit,18 thus proving the absence of any
significant intramolecular hydrogen bonding between the bases
under this condition.
ditional
p-stacking interaction as is evident from the temperature
N3
b
a
N3
8a
N
N
N
N
N
O
N
N
N
NH2
N
N
NH
O
N
O
N
N
N
N
N
N
N
N
8
9
NH
N
N
O
N
NH2
9
Reagents and conditions: (a) N -Propargyl adenine, CuSO4.5H2O, sodium ascorbate,
t
1
BuOH, H2O, r.t., 24 h (54%); (b) N -propargyl thymine, CuSO4.5H2O, sodium ascorbate,
t
BuOH, H2O, r.t., 20 h (70%).
Scheme 6. Synthesis of compound 8 and 9 of class C.

8604
S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
Fig. 2. ORTEP diagram of compound 1i and 3a with the thermal ellipsoids shown at 50% probability.
dependent chemical shift of the triazole-H. The cooperative effect
of additional interstrand forces between the spacers along with the
transition states and products for the formation of naphthalene
biradical derivatives were obtained using semi-empirical theory
(PM3) for class A and the density functional theory (DFT) with the
B3LYP exchange correlation functional and the 6-31G (d) basis set
for both class A and B.22 A restricted approach was used in the
computational analysis for the closed-shell structure while for the
transition state and the product biradical optimization, an un-
restricted broken-symmetry approach has been used.23 Optimiza-
tion of all the structures at DFT level of theory was done using
B3LYP method with the same basis set. The nature of stationary
p
-stacking between the base pairs enhanced the reactivity of
enediynes with amide and triazole linkers.20
3. Computational study
We have also carried out theoretical calculations on molecules
belonging to class A and B using Gaussian 03 program package.21
Thus, a gas phase optimized geometries of the starting enediynes,
Fig. 3. MALDI mass spectrum of compound 3 heated at 170 ꢀC in DMSO for 22 h.

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8605
Slope = K = 8 x 10-2 h-1
R = 0.99
Slope = K = 18 x 10-2 h-1
Slope = K = 10 x 10-2 h-1
R = 0.99
0.0
-0.1
-0.2
-0.3
-0.4
0.0
0.0
-0.1
-0.2
-0.3
-0.4
R = 0.99
-0.2
-0.4
-0.6
-0.8
-1.0
0
1
2
3
4
5
0
1
2
3
4
5
0
1
2
3
4
Time (h)
Time (h)
Time (h)
Compound 1
Compound 2
Compound 3
Fig. 4. Solution phase kinetic plots for class A enediynes.
Table 1
Solution phase (DMSO) reactivity of enediyneenucleobase hybrids of class Aa
class A are calculated to be 68, 67 and 70 kcal/mol, respectively, at
PM3 level of theory, which supported the observed reactivity order
AeA>AeT>TeT. At the B3LYP/6-31G (d) level of theory, the acti-
vation barrier also follows the same trend. Enediyne 5 of class B
with two A bases appended at the two arm via short amide linkage,
the energy barrier for the formation of product biradical 5p from 5
is calculated as 33.7 kcal/mol at the B3LYP/6-31G* level of theory.
The corresponding values for the other two compounds 4 and 6
were found to be higher. While the energy barrier (39.3 kcal/mol)
for formation of product biradical 4p from enediyne 4 is found to be
higher than 5p, it is almost similar in reactivity as that of 6p whose
activation barrier of formation from 6 is 38.4 kcal/mol.24 The re-
action profiles for class A and B molecules are shown in Fig. 7. Thus,
computational results are more or less in agreement with the ex-
perimental observations. From the computations, it is clear that the
activation barrier for the enediynes of class B with amide spacer is
somewhat lower than that of the enediyne class A. This is again
Compound no.
Compound 1
10ꢁ10ꢂ2
Compound 2
18ꢁ10ꢂ2
Compound 3
8ꢁ10ꢂ2
Solution phase kinetic
rate constant (hꢂ1
)
a
Experimental error is within ꢃ5%.
Table 2
Solid state reactivity of enediyneenucleobase hybrids
Enediynee
DSC onset temperature (ꢀC)
nucleobase
AeT pair
AeA pair
TeT pair
Class A
Class B
Class C
230
207
235
(for compound 1)
177
(for compound 4)
161
(for compound 2)
165
(for compound 5)
151
(for compound 3)
240
(for compound 6)
195
(for compound 7)
(for compound 8)
(for compound 9)
because of
p-stacking as well as H-bonding interactions both of
which are playing an important role in accelerating the reactivity of
class B enediynes compared to that of the class A enediynes and
thus supporting our experimental observation.
In conclusion, we have for the first time synthesized enediy-
neenucleobase hybrids. Solution and solid phase studies indicated
some degree of influence of the nucleobase pair on the reactivity of
points was characterized by vibrational frequency calculations.
There are no imaginary frequencies in frequency analysis of all the
starting enediynes and product biradicals, therefore each calcu-
lated structure is a local energy minimum and for all the transition
states we observed a single imaginary frequency in the frequency
analysis.
the enediynes towards BC. This influence originated from the
p-
stacking interactions between the base pairs, confirmed by VT-
NMR studies. Interestingly, contrary to expectations, no signifi-
cant intramolecular H-bonds are present between the base pairs.
Current studies are aimed towards design of similar hybrids with
reactivity profile under ambient conditions.
The relative energy profiles at all levels of theory for class A and
B molecules (along with their imaginary frequencies in the
parentheses) are shown in Figs. 5 and 6, respectively. Thus, the
activation barriers for the cyclization step of enediyne 1, 2 and 3 of
Table 3
Temperature coefficients (Dd
/D
Tꢁ103) of chemical shift of different hydrogensa
4. Experimental
4.1. General
Compound no.
A-NH2
T-NH
A-8H
A-2H
T-6H
T-Me
1
4
7
ꢂ7.99
ꢂ6.74
ꢂ6.50
ꢂ7.40
ꢂ6.07
ꢂ5.50
ꢂ1.13
þ0.52
ꢂ0.94
þ0.33
ꢂ0.47
ꢂ1.45
ꢂ1.56
ꢂ1.22
ꢂ1.73
þ0.57
þ0.67
þ0.50
All reactions were conducted with oven-dried glassware under
an atmosphere of argon (Ar) or nitrogen (N2). All common reagents
were commercial grade reagents and used without further purifi-
cation. The solvents were dried by standard methods and purified
by distillation before use. All crude products were purified by silica-
gel column chromatography (60e120 mesh) with petroleum ether/
ethyl acetate (P.E/E.A) as eluent and characterized by IR, NMR and
mass spectrometry unless otherwise mentioned. 1H and 13C NMR
spectroscopes of all compounds were recorded in 400 and
100 MHz, respectively, using CDCl3 solvent unless otherwise noted.
Infrared (FTIR) spectra were recorded as thin films on potassium
bromide plates (solid sample), or in chloroform solvent (liquid
sample) using Perkin Elmer Spectrum Rx1 spectrometer and are
Compound no.
A-NH2
A-8H
A-2H
Amide NHb
Triazole CHc
2
5
8
ꢂ7.25
ꢂ5.36
ꢂ6.68
ꢂ1.73
þ0.34
ꢂ1.13
No change
ꢂ0.54
d
d
ꢂ3.86
d
d
ꢂ1.40
þ0.35
Compound no.
T-NH
T-6H
T-Me
Amide NH
Triazole CH
3
6
9
a
ꢂ6.19
ꢂ6.32
ꢂ5.99
ꢂ1.28
ꢂ1.40
ꢂ1.84
þ0.55
þ0.61
þ0.51
d
d
ꢂ4.87
d
d
ꢂ1.17
Concentration of each compound was 5ꢁ10ꢂ3 M in DMSO-d6.
b
Temperature coefficients of chemical shift of two amide eNH of compound 4
are¼ꢂ3.56 and ꢂ3.89ꢁ10ꢂ3 ppm/K.
c
Temperature coefficients of two triazole CH of compound 7 are¼ꢂ1.17 and
þ2.97ꢁ10ꢂ3 ppm/K.

8606
S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
atoms were fixed at calculated positions and refined using a riding
model.
A
T
A
T
A
T
4.2. General procedure for Sonogashira coupling of bromo-
benzene derivative (1a, 1b and 2a)
1
1TS
1P
Rel. E = 0.0(0)
Rel. E = 0.0(0)
68.3(1)
67.1(0)----PM3
41.6(0)----DFT
In an oven-dried flask dry n-butyl amine (10e20 mL) was taken
and enough nitrogen gas was purged to degasify the solvent. Tetrakis-
(triphenylphosphine) palladium (0) [Pd(PPh3)4] (0.03 equiv) catalyst
was added carefully under nitrogen atmosphere. After 10 min of
stirring, dibromobenzene/1a (3.36 mmol) and propargyl alcohol/
THP-protected propargyl alcohol (1.1 equiv) were added successively.
The reaction mixturewasrefluxed at 80e85ꢀC for 3e10 h (depending
on mono or di coupling) under inert atmosphere. Progress of the re-
action was monitored by TLC checking. On completion, it was
quenched with water and extracted with EtOAc (3ꢁ15 mL). The
combined organic layers were washed with a HCl solution (0.05 N,
25 mL), water and brine and then dried over Na2SO4 and concen-
trated. The compounds 1a25c and 2a3c are reported compounds and
their spectral data are in agreement with those reported in literature.
43.8(1)
A
A
A
A
A
A
2
2TS
2P
Rel. E = 0.0(0)
67.0(1)
66.5(0)----PM3
Rel. E = 0.0(0)
38.2(1)
36.2(0)----DFT
T
T
T
T
T
T
3
3TS
3P
4.2.1. 3-{2-[3-(Tetrahydro-pyran-2-yloxy)-prop-1-ynyl]-phenyl}-
prop-2-yn-1-ol (1b). Yellow viscous oil; Rf (P.E/E.A¼3:1) 0.50; yield
80%; dH (200 MHz): 7.39e7.33 (m, 2H), 7.21e7.16 (m, 2H), 5.12 (br s,
1H), 4.49 (s, 2H), 4.45 (s, 2H), 3.86e3.74 (m, 1H), 3.57e3.52 (m, 1H),
1.76e1.51 (m, 6H); dC (50 MHz): 131.7, 131.5, 128.2, 128.0, 125.9,
125.3, 95.6, 92.2, 88.8, 85.1, 83.7, 61.5, 54.5, 51.2, 30.0, 25.4, 18.5.
Rel. E = 0.0(0)
Rel. E = 0.0(0)
70.4(1)
39.6(1)
68.5(0)----PM3
37.3(0)----DFT
Fig. 5. Relative energies and the number of imaginary frequencies (in parentheses) at
PM3 and B3LYP/6-31G* level of theories for the enediyne class A.
expressed as %-transmission (cmꢂ1). ESI-MS and HRMS were
recorded using a Waters LCT mass spectrometer. The single crystal
data was collected on Bruker APEX-2 CCD X-ray diffractometer that
4.3. General procedure for Sonogashira coupling of iodo-
benzene derivative (4a, 4b and 5a)
ꢀ
uses graphite monochromated MoK
a
radiation (
l
¼0.71073 A) by
hemisphere method. The structures are solved by direct methods
and refined by least square methods on F2 using SHELX-97.
Non-hydrogen atoms were refined anisotropically and hydrogen
Pd(PPh3)4 (0.03 equiv) was added to degasified triethylamine
(15 mL) followed by the addition of diiodobenzene/4a (3.06 mmol).
After 15 min of stirring, copper iodide (0.10 equiv) and N-tert-
O
O
O
A
A
N
H
A
N
N
H
H
H
N
H
N
H
T
N
T
T
A
O
4
4TS
4P
O
O
O
Rel. E = 0.0(0)
39.3(1)
38.3(0)----DFT
O
O
A
A
A
A
N
H
N
H
N
H
H
H
H
N
N
N
A
O
O
O
5
5TS
5P
Rel. E = 0.0(0)
33.7(1)
30.3(0)----DFT
O
O
O
T
T
T
N
H
T
T
N
N
H
H
N
H
H
N
H
N
T
O
O
O
6
6TS
6P
Rel. E = 0.0(0)
38.4(1)
34.9(0)----DFT
Fig. 6. Relative energies and the number of imaginary frequencies (in parentheses) at B3LYP/6-31G* level of theory for the enediyne class B.

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8607
a
b
60.0
60.0
1TS
3TS
2TS
1P
4TS
6TS
3P
40.0
40.0
4P
2P
6P
5TS
5P
20.0
0.0
20.0
0.0
1, 2,
3
4, 5,
6
Reaction Coordinate
Reaction Coordinate
Fig. 7. Relative energy wise graphical representation of the enediynes reactants, transition states and product biradicals of class A and B enediynes.
butoxycarbonylprop-2-ynylamine (1.1 or 2.0 equiv, depending on
mono or di coupling)/propargyl alcohol were added to it with 5 min
interval and stirred for 8e12 h at room temperature. The reaction
mixture was quenched with saturated aqueous solution of NH4Cl
(15 mL), and extracted with EtOAc (3ꢁ10 mL), dried over Na2SO4 and
concentrated. The compound 4a25b and 4b25b are reported earlier and
their spectral data are in agreement with those reported in literature.
phenyl)-prop-2-ynyl ester (7d). Yellow oil; Rf (3% MeOH in DCM as
eluent) 0.25; yield 85%; dH (200 MHz): 10.03 (s, 1H), 8.04 (s, 1H),
7.45e7.38 (m, 2H), 7.33e7.27 (m, 3H), 5.42 (s, 2H), 5.10 (s, 2H), 4.95
(s, 2H), 3.11 (s, 3H), 1.83 (s, 3H); dC (50 MHz): 164.6, 151.2, 142.5,
140.4, 132.4, 132.3, 129.2, 129.0, 124.5, 124.2, 123.8, 111.2, 87.2, 85.3,
85.0, 84.7, 58.3, 43.0, 40.8, 39.0, 12.2; HRMS: found 454.1183.
C21H19N5O5SþHþ requires 454.1185.
4.3.1. {3-[2-(3-tert-Butoxycarbonylamino-prop-1-ynyl)-phenyl]-
prop-2-ynyl}-carbamic acid tert-butyl ester (5a). Brown gummy
liquid; Rf (Purification, P.E/E.A¼5:1) 0.40; yield 60%; dH (200 MHz):
7.39e7.35 (m, 2H), 7.25e7.19 (m, 2H), 5.20 (br s, 2H), 4.18e4.15 (m,
4H), 1.46 (br s, 18H); dC (50 MHz): 155.7, 131.9, 128.1, 125.8, 90.0,
81.8, 80.2, 31.6, 28.6.
4.5. General procedure for the synthesis of bromide
(1d, 1h and 2c)
To a dry THF (10e20 mL) solution of mesylate (1c/1g/2b)
(2.11 mmol) LiBr (1.5 and 3 equiv for mono and di substitution, re-
spectively), dissolving in another fraction of dry THF (5 mL), was added
dropwise for 5 min at 0 ꢀC and stirred for 8e10 h. On completion,
whole reaction mixture was poured into a saturated solution of
NaHCO3 (10 mL) and extracted with EtOAc (3ꢁ10 mL). The combined
organic layers were washed with water and brine, dried over Na2SO4,
concentrated. The bromo derivative 2c3c is reported compound and its
spectral data is in agreement with that reported in literature.
4.4. General procedure for mesylation (1c, 1g, 2b, 4c and 7d)
Primary alcohol (1b/1f/2a/4b/7c) (2.52 mmol) was dissolved in
dry DCM (10e20 mL) and cooled to 0 ꢀC. Mesyl chloride (1.1 equiv)
and triethylamine (1.5 equiv) were successively added to it dropwise
and stirred for 15 min and monitored by TLC. On completion, checked
by TLC, the reaction mixture was washed with brine solution, dried
over Na2SO4 and concentrated. The compounds 1c, 1g, 2b, 4c, 7d
were synthesized according to the above general procedure among
which the compounds 2b3c and 4c25b are reported compounds and
their spectral data are in agreement with those reported in literature.
Full characterization data of unknown compounds are listed here.
4.5.1. 2-{3-[2-(3-Bromo-prop-1-ynyl)-phenyl]-prop-2-ynyloxy}-tet-
rahydro-pyran (1d). Yellow oil; Rf (Purification, P.E/E.A¼10:1)
0.40; yield 72%; dH (200 MHz): 7.41e7.36 (m, 2H), 7.24e7.17 (m,
2H), 4.96 (s, 1H), 4.52 (s, 2H), 4.17 (s, 2H), 3.90e3.79 (m, 1H),
3.56e3.50 (m, 1H), 1.89e1.53 (m, 6H); dC (50 MHz): 132.0, 128.5,
128.1, 125.7, 124.8, 96.5, 89.6, 88.2, 85.3, 84.1, 61.8, 54.6, 30.3, 25.4,
19.0, 15.2.
4.4.1. Methanesulfonic acid 3-{2-[3-(tetrahydro-pyran-2-yloxy)-prop-
1-ynyl]-phenyl}-prop-2-ynyl ester (1c). Yellow oil; Rf (Purification,
P.E/E.A¼3:1) 0.45; yield 92%; dH (200 MHz): 7.43e7.37 (m, 2H),
2.27e7.21 (m, 2H), 5.07 (s, 2H), 4.89e4.87 (m,1H), 4.47e4.45 (m, 2H),
3.86e3.75 (m, 1H), 3.55e3.47 (m,1H), 3.15 (s, 3H),1.77e1.51 (m, 6H);
dC (50 MHz): 132.3, 132.2, 129.1, 128.3, 125.7, 123.8, 96.7, 89.8, 87.8,
84.6, 83.9, 61.9, 58.4, 54.5, 39.2, 30.2, 25.3, 18.9.
4.5.2. Compound 1h. Yellow viscous oil; Rf (P.E/E.A¼2:1) 0.40; yield
80%; dH (200 MHz): 8.79e8.78 (m,1H), 8.44e8.43 (m,1H), 7.33e7.30
(m, 2H), 7.20e7.16 (m, 2H), 5.24e5.23 (m, 2H), 4.06e4.05 (m, 2H),
1.35e1.34 (m, 18H); dC (50 MHz): 152.8, 152.1, 150.4, 150.3, 144.3,
132.1, 131.9, 128.9, 128.7, 128.6, 125.0, 124.1, 88.6, 85.3, 84.9, 84.7,
83.7, 34.4, 27.7, 14.9; HRMS: found 566.1402. C27H28BrN5O4þHþ
requires 566.1403.
4.4.2. Compound 1g. Yellow oil; Rf (P.E/E.A¼1:1) 0.50; yield 80%; dH
(200 MHz): 8.76 (s, 1H), 8.38 (s, 1H), 7.33e7.29 (m, 2H), 7.19e7.15
(m, 2H), 5.23 (s, 2H), 4.95 (s, 2H), 3.04 (s, 3H), 1.31 (s, 18H); dC
(50 MHz): 152.8, 152.1, 150.5, 150.1, 132.3, 132.1, 129.2, 128.9, 128.6,
124.4, 124.0, 87.2, 85.4, 85.2, 84.5, 83.7, 58.1, 38.8, 34.2, 27.7; HRMS:
found 582.2020. C28H31N5O7SþHþ requires 582.2023.
4.6. General procedure for the synthesis of Boc-protected
nucleobase attached enediyne (1e, 1i, 2d, 3a, 4g, 5c and 6a)
To a dry CH3CN (15e20 mL) solution of bis-Boc-adenine/N3-Boc
thymine (1.0 or 2.0 equiv, depending on mono or di substitution)
caesium carbonate (1 equiv or 2 equiv) was added and stirred for
0.5 h at room temperature. A colourless solution was obtained to
which the bromide (1d/1h/2c/4f/5b) (0.50 mmol) dissolving in
4.4.3. Methanesulfonic acid 3-(2-{3-[4-(5-methyl-2,4-dioxo-3,4-
dihydro-2H-pyrimidin-1-ylmethyl)-[1,2,3]triazol-1-yl]-prop-1-ynyl}-

8608
S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
5 mL dry CH3CN solvent, was added dropwise and stirred for next
6e10 h at room temperature. Progress of the reaction was checked
by TLC and on completion it was diluted with water and extracted
with EtOAc (3ꢁ10 mL). Afterwards the combined organic layers
were washed with water and brine, dried over Na2SO4 followed by
evaporation in vacuum.
140.6, 131.6, 128.2, 125.4, 110.7, 88.6, 87.0, 81.5, 50.5, 30.2, 27.4,
12.2; nmax (KBr, cmꢂ1):
n 3448, 2090, 1782, 1662, 1534, 1447, 1371,
1241, 1147; HRMS: found 717.2885. C36H40N6O10þHþ requires
717.2884.
4.7. General procedure for the synthesis of azide (4d, 7a, 7e
and 8a)
4.6.1. Compound 1e. Yellow gummy oil; Rf (P.E/E.A¼2:1) 0.50; yield
60%; dH (200 MHz): 8.88 (s, 1H), 8.54 (s, 1H), 7.50e7.42 (m, 2H),
7.35e7.27 (m, 2H), 5.32 (s, 2H), 5.00e5.98 (m, 1H), 4.54e4.53 (m,
2H), 3.92e3.80 (m, 1H), 3.59e3.49 (m, 1H), 1.86e1.62 (m, 5H), 1.45
(s, 19H); dC (50 MHz): 152.7, 151.9, 150.3, 150.1, 144.4, 132.1, 131.8,
128.7,128.6,128.2,125.5,124.0, 96.4, 89.6, 85.4, 84.4, 84.1, 83.4, 61.5,
54.4, 34.2, 30.1, 27.6, 25.2, 18.7; HRMS: found 588.2820.
C32H37N5O6þHþ requires 588.2822.
To a dry DMF (10e15 mL) solution of the mesylate (4c/1c/7d/2b)
(0.32 mmol) sodium azide (1.5 or 3.0 equiv, depending on mono or
di substitution) was added and stirred for 6e8 h at room temper-
ature. Afterwards, it was quenched by water and extracted with
EtOAc (3ꢁ10 mL). The combined organic layers were washed with
water and brine, dried over Na2SO4 and concentrated under vac-
uum. The compounds 4d25b and 8a25a are reported compounds and
their spectral data are in agreement with those reported in
literature.
4.6.2. Compound 1i. Colourless crystal; Rf (with 2% MeOH in DCM
as eluent) 0.30; yield 54%; mp 98e100 ꢀC; dH: 8.90 (s, 1H), 8.53 (s,
1H), 7.48e7.44 (m, 2H), 7.33e7.31 (m, 2H), 7.26 (s, 1H), 5.34 (m, 2H),
4.71 (m, 2H), 1.94 (s, 3H), 1.59 (s, 9H), 1.46 (s, 18H); dC: 161.5, 152.8,
152.2, 150.5, 150.3, 148.5, 147.9, 144.3, 138.5, 132.5, 132.0, 128.9,
128.8, 128.6, 124.5, 124.3, 111.1, 86.9, 85.7, 85.1, 84.8, 84.2, 83.8, 38.2,
4.7.1. 2-{3-[2-(3-Azido-prop-1-ynyl)-phenyl]-prop-2-ynyloxy}-tetra-
hydro-pyran (7a). Yellow oil; Rf (Purification, P.E/E.A¼10:1) 0.55;
yield 82%; dH (200 MHz): 7.49e7.45 (m, 2H), 7.30e7.25 (m, 2H),
4.99e4.98 (m, 1H), 4.55 (s, 2H), 4.19 (s, 2H), 3.95e3.83 (m, 1H),
3.62e3.54 (m, 1H), 1.91e1.60 (m, 6H); dC (50 MHz): 132.2, 128.5,
128.1, 125.6, 124.6, 99.6, 89.7, 85.8, 85.0, 84.1, 61.8, 54.7, 40.6, 30.3,
25.4, 19.0.
34.2, 27.7, 27.4, 12.4; nmax (KBr, cmꢂ1):
n 2926, 2854, 2344, 1784,
1717, 1667, 1602, 1581, 1457, 1371, 1338, 1258, 1146; HRMS: found
712.3096. C37H41N7O8þHþ requires 712.3095.
4.6.3. Compound 2d. Yellow oil; Rf (Flash column with silica-gel,
230e400 mesh using 1% MeOH in DCM as eluent) 0.25; yield 58%;
dH: 8.93 (s, 2H), 8.52 (s, 2H), 7.48e7.45 (m, 2H), 7.35e7.33 (m, 2H),
5.31 (s, 4H), 1.47 (s, 36H); dC (50 MHz): 152.9, 152.3, 150.6, 150.4,
144.3, 132.2, 129.0, 128.7, 124.2, 85.1, 85.0, 83.8, 34.3, 27.8; nmax (KBr,
4.7.2. 1-(1-{3-[2-(3-Azido-prop-1-ynyl)-phenyl]-prop-2-ynyl}-1H-
[1,2,3]triazol-4-ylmethyl)-5-methyl-1H-pyrimidine-2,4-dione
(7e). Yellow gummy oil; Rf (2% MeOH in DCM as eluent) 0.30; yield
78%; dH (200 MHz): 9.88 (s, 1H), 8.02 (s, 1H), 7.46e7.41 (m, 2H),
7.33e7.26 (m, 3H), 5.41 (s, 2H), 4.95 (s, 2H), 4.18 (s, 2H), 1.85 (s, 3H);
dC (50 MHz): 164.5, 151.1, 142.4, 140.2, 132.4, 132.3, 129.0, 128.6,
124.9, 124.0, 123.6, 111.3, 85.6, 85.5, 85.4, 84.0, 42.8, 40.9, 40.6, 12.2;
HRMS: found 401.1471. C20H16N8O2þHþ requires 401.1475.
cmꢂ1):
n 2982, 2931, 2854, 2345, 2234, 1748, 1602, 1501, 1481, 1455,
1409, 1394, 1255, 1145; HRMS: found 821.3738. C42H48N10O8þHþ
requires 821.3735.
4.6.4. Compound 3a. Colourless crystalline solid; Rf (P.E/E.A¼1:2)
0.45; yield 60%; mp 138e140 ꢀC; dH: 7.46e7.44 (m, 2H), 7.33e7.30
(m, 4H), 4.78 (s, 4H), 1.96 (s, 6H), 1.59 (s, 18H); dC (50 MHz): 161.6,
148.7, 148.0, 138.6, 132.3, 128.9, 124.8, 111.2, 86.9, 85.8, 84.3, 38.2,
4.8. General procedure for THP-deprotection (1f and 7c)
THP-protected alcohol (1e/7b) (0.37 mmol) was dissolved in
commercial grade EtOH (10e20 mL) and pyridinium p-toluene
sulfonate (PPTS) (0.1 equiv) was added. Resulting reaction mixture
was stirred for 6 h at room temperature. The solvent was removed
under vacuum and the crude product was subjected to column
chromatography without any further washing.
27.5, 12.4; nmax (KBr, cmꢂ1):
n 3439, 2092, 1781, 1709, 1659, 1443,
1371, 1235, 1145; HRMS: found 603.2454. C32H34N4O8þHþ requires
603.2455.
4.6.5. Compound 4g. Yellow oil; Rf (4% MeOH in DCM as eluent)
0.40; yield 56%; dH (200 MHz): 8.81 (s, 1H), 8.27 (s, 1H), 7.90 (br
s, 1H), 7.34 (m, 2H), 7.23e7.21 (m, 2H), 5.42 (br s, 1H), 5.07 (s,
2H), 4.34e4.32 (m, 2H), 4.17e4.14 (m, 2H), 1.46 (s, 9H), 1.40 (s,
18H); dC (50 MHz): 165.6, 156.3, 153.5, 152.0, 150.4, 150.3, 145.9,
131.5, 128.4, 128.1, 125.6, 90.0, 88.4, 83.8, 82.1, 80.5, 45.8, 30.3,
28.4, 27.8; HRMS: found 660.3145. C34H41N7O7þHþ requires
660.3146.
4.8.1. Compound 1f. Pale yellow gummy oil; Rf (P.E/E.A¼1:1) 0.60;
yield 78%; dH (200 MHz): 8.81e8.80 (m, 1H), 8.67e8.66 (m, 1H),
7.30e7.28 (m, 2H), 7.15 (m, 2H), 5.21 (s, 2H), 4.40 (s, 2H), 1.37 (s,
18H); dC (50 MHz): 152.7, 152.1, 150.5, 150.2, 145.1, 132.2, 131.6,
128.8, 128.6, 128.1, 125.7, 123.8, 92.7, 86.0, 84.3, 84.0, 83.2, 50.8,
34.6, 27.7; HRMS: found 504.2248. C27H29N5O5þHþ requires
504.2247.
4.6.6. Compound 5c. Yellow oil; Rf (Flash column with silica-gel,
230e400 mesh using 2% MeOH in DCM as eluent) 0.30; yield
58%; dH (200 MHz): 8.76 (s, 2H), 8.25 (s, 2H), 7.96 (br s, 2H),
7.35e7.30 (m, 2H), 7.21e7.17 (m, 2H), 4.91 (s, 4H), 4.23 (d,
J¼6.0 Hz, 4H), 1.41 (s, 36H); dC (50 MHz): 166.2, 153.7, 152.0,
150.6, 149.9, 146.3, 131.6, 128.3, 128.1, 125.5, 88.7, 84.1, 81.5, 45.5,
4.8.2. 1-(1-{3-[2-(3-Hydroxy-prop-1-ynyl)-phenyl]-prop-2-ynyl}-
1H-[1,2,3]triazol-4-ylmethyl)-1H-pyrimidine-2,4-dione (7c). White
solid; Rf (3% MeOH in DCM as eluent) 0.20; yield 86%; mp 165 ꢀC; dH
(200 MHz, CDCl3 and DMSO-d6): 10.84 (s, 1H), 8.08 (s, 1H), 7.29 (m,
2H), 7.26 (s, 1H), 7.20e7.16 (m, 2H), 5.36 (s, 2H), 4.85 (s, 2H), 4.34 (s,
2H), 1.72 (s, 3H); dC (50 MHz, CDCl3 and DMSO-d6): 169.5, 156.0,
147.4, 145.0, 136.7, 133.7, 132.8, 130.6, 128.6, 128.5, 115.4, 98.2, 90.4,
31.5, 27.7; nmax (KBr, cmꢂ1):
n 2982, 2293, 1787, 1611, 1584, 1457,
1395, 1371, 1251, 1112; HRMS: found 935.4167. C46H54N12O10þHþ
89.0, 87.3, 55.3, 47.4, 34.3, 17.0; nmax (KBr, cmꢂ1):
n 2931, 2264, 1672,
requires 935.4164.
1479, 1431, 1388, 1364, 1253, 1123; HRMS: found 376.1412.
C20H17N5O3þHþ requires 376.1410.
4.6.7. Compound 6a. Colourless gummy oil; Rf (P.E/E.A¼1:2) 0.45;
yield 62%; dH (200 MHz): 7.67e7.64 (m, 2H), 7.35e7.30 (m, 2H),
7.24e7.17 (m, 2H), 7.06 (s, 2H), 4.39 (s, 4H), 4.24 (d, J¼6.0 Hz, 4H),
1.87 (s, 6H), 1.55 (s, 18H); dC (50 MHz): 166.8, 161.6, 149.4, 148.1,
4.8.3. {3-[2-(3-Amino-prop-1-ynyl)-phenyl]-prop-2-ynyl}-carbamic
acid tert-butyl ester (4e). {3-[2-(3-Azido-prop-1-ynyl)-phenyl]-
prop-2-ynyl}-carbamic acid tert-butyl ester (4d) (700 mg,

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8609
2.26 mmol) was dissolved in THF (25 mL). 3e4 drops water and
triphenylphosphine (1.18 g, 4.51 mmol) were added to the solution.
The reaction mixture was stirred for 6 h at room temperature and
then concentrated. The crude product was purified by column
chromatography (10% MeOH in DCM as eluent).
88.4, 82.2, 37.2, 12.0; nmax (KBr, cmꢂ1):
n
2953, 2843, 2080, 1774,
1654, 1528, 1450, 1422, 1355, 1245, 1016, 759; HRMS: found
403.1400. C22H18N4O4þHþ requires 403.1406.
4.10.4. 2-(6-Amino-purin-9-yl)-N-[3-(2-(6-amino-purin-9-yl)-ace-
tylamino]-prop-1-ynyl}-phenyl)-prop-2-ynyl]-acetamide (5). White
solid; Rf (Flash column with silica-gel, 230e400 mesh using 15%
MeOH in DCM as eluent) 0.35; yield 60%; mp 250 ꢀC (dec); dH
(DMSO-d6): 8.85 (br s, 2H), 8.08e8.06 (m, 4H), 7.44e7.43 (br s, 2H),
7.37e7.36 (br s, 2H), 7.19 (br s, 4H), 4.88 (s, 4H), 4.23e4.22 (m, 4H);
DEPT-135 (DMSO-d6): 152.3 (CH), 141.6 (CH), 131.7 (CH), 128.5 (CH),
4.9. General procedure for bromoacylation of amine
(4f and 5b)
Primary amine (4e/bis-Boc-protected diamine 5a after Boc
deprotection with TFA) was dissolved in dry DCM (30 mL) at 0 ꢀC
under nitrogen atmosphere. Bromoacetyl chloride (1.2 and 2.2 equiv
for mono and di substitution, respectively) and triethylamine (1.4 or
2.5 equiv) were successively added and stirred for next 10e15 min
maintaining 0 ꢀC temp. On completion, it was quenched with water
and extracted with DCM (2ꢁ15 mL). The combined organic layers
were washed with water and brine, dried over Na2SO4 and con-
centrated. It is to be noted that rapid quenching of the reaction
mixture can diminish the formation of unwanted side products.
44.7 (CH2), 28.8 (CH2); nmax (KBr, cmꢂ1):
n 3461, 2078, 1734, 1718,
1654, 1542, 1474, 1208; HRMS: found 535.2065. C26H22N12O2þHþ
requires 535.2067.
4.10.5. 2-(5-Methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-N-
[3-(2-{3-[2-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-
acetylamino]-prop-1-ynyl}-phenyl)-prop-2-ynyl]-acetamide
(6). White solid; Rf (Flash column with silica-gel, 230e400 mesh
using 10% MeOH in DCM as eluent) 0.25; yield 65%; mp 270 ꢀC
(dec); dH (DMSO-d6): 11.26 (s, 2H), 8.69e8.67 (m, 2H), 7.42 (br s,
4H), 7.36e7.34 (m, 2H), 4.31 (s, 4H), 4.21e4.20 (m, 4H), 1.72 (s, 6H);
dC (DMSO-d6): 166.9, 164.5, 151.0, 142.3, 131.8, 128.6, 124.7, 108.1,
4.9.1. 2-Bromo-N-(3-{2-[3-(2-bromo-acetylamino)-prop-1-ynyl]-
phenyl}-prop-2-ynyl)-acetamide (5b). Brown liquid; Rf (Purifica-
tion, P.E/E.A¼1:1) 0.45; yield 67%; dH (200 MHz): 7.43e7.39 (m, 2H),
7.29e7.24 (m, 2H), 4.36e4.34 (m, 4H), 3.95 (s, 4H); dC (50 MHz):
166.2, 132.0, 128.5, 125.6, 88.3, 82.2, 31.1, 28.9.
90.6, 80.3, 49.3, 28.8, 11.9; nmax (KBr, cmꢂ1):
n 3432, 2922, 2378,
1720, 1710, 1678, 1550, 1474, 1435, 1310, 1268, 1212; HRMS: found
517.1832. C26H24N6O6þHþ requires 517.1836.
4.10. General procedure for Boc deprotection (1, 2, 3, 5 and 6)
4.11. Synthesis of 2-(6-amino-purin-9-yl)-N-[3-(2-{3-[2-(2,4-
dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-acetylamino]-prop-1-
ynyl}-phenyl)-prop-2-ynyl]-acetamide (4)
To an ice cold dry DCM (10e20 mL) solution of N-Boc protected
enediynyl amine (5a)/N-Boc protected nucleobase-linked enediyne
(1i/2d/3a/4g/5c/6a) (0.20 mmol) trifluoroacetic acid (TFA)
(25e50 equiv) was added dropwise. The whole reaction mixture
was stirred for 2 h at 0 ꢀC and for another 2 h at room temperature
for complete deprotection. After that the reaction mixture was
concentrated under reduced pressure by liquid nitrogen while the
excess TFA was evaporated out. Resulting gummy mass was washed
by dry benzene (3ꢁ10 mL) and subjected to column chromatog-
raphy (silica-gel, 60e120 mesh, MeOH in DCM as eluent) to get free
amine in pure form.
1-(Carboxymethyl) thymine (50 mg, 0.29 mmol) was taken in
a mixture of dry DCM (15 mL) and dry DMF (3 mL) solution for the
uniform solubility. It was cooled to 0 ꢀC followed by the addition of
EDC$HCl (67 mg, 0.35 mmol) and HOBt (48 mg, 0.35 mmol) under
N2 atmosphere. After 1 h of stirring, the free amine 4h (0.30 mmol)
and DMAP (15 mg, 0.12 mmol) were successively added and con-
tinued the stirring for 10 h at room temperature. On completion, it
was extracted with EtOAc (3ꢁ15 mL), washed with water and brine,
dried over Na2SO4 and concentrated under vacuum. The crude
product was purified by flash column chromatography.
4.10.1. 1-(3-{2-[3-(6-Amino-purin-9-yl)-prop-1-ynyl]-phenyl}-prop-
2-ynyl)-5-methyl-1H-pyrimidine-2,4-dione (1). White solid; Rf
(Flash column with silica-gel, 230e400 mesh using 15% MeOH in
DCM as eluent) 0.35; yield 45%; mp 250 ꢀC (decomposition); dH
(DMSO-d6): 11.42 (s,1H), 8.28 (s,1H), 8.18 (s,1H), 7.57 (s,1H), 7.48 (br
s, 2H), 7.38e7.37 (br s, 2H), 7.27 (s, 2H), 5.29 (s, 2H), 4.71 (s, 2H), 1.75
(s, 3H); dC (DMSO-d6): 164.2, 156.0, 152.8, 150.5, 149.1, 140.2, 140.0,
132.0, 131.9, 129.1, 129.0, 124.2, 124.1, 118.5, 109.6, 88.3, 88.0, 82.4,
4.11.1. 2-(6-Amino-purin-9-yl)-N-[3-(2-{3-[2-(2,4-dioxo-3,4-
dihydro-2H-pyrimidin-1-yl)-acetylamino]-prop-1-ynyl}-phenyl)-
prop-2-ynyl]-acetamide (4). White solid; Rf (230e400 mesh, 8%
MeOH in DCM as eluent) 0.40; yield 52%; mp 230 ꢀC (dec); dH
(DMSO-d6): 11.27 (s, 1H), 8.98 (br s, 1H), 8.81 (br s, 1H), 8.08e8.07
(m, 2H), 7.43 (m, 3H), 7.36e7.35 (m, 2H), 7.18 (s, 1H), 4.91 (s, 2H),
4.32 (s, 2H), 4.22 (m, 4H), 1.70 (s, 3H); DEPT-135 (DMSO-d6): 152.3
(CH), 142.1 (CH), 141.6 (CH), 131.7 (CH), 128.5 (CH), 49.2 (CH2), 44.7
82.2, 37.2, 33.0,12.0; nmax (KBr, cmꢂ1):
n 3363, 3216, 2922, 2851, 2363,
1673, 1604, 1475, 1387, 1332, 1294; MS: m/z¼434.39 [MNaþ], 412.39
[MHþ]; HRMS: found 412.1518. C22H17N7O2þHþ requires 412.1522.
(CH2), 28.8 (CH2), 28.6 (CH2), 11.7 (CH3); nmax (KBr, cmꢂ1):
n 3412,
2922, 2346, 1723, 1710, 1680, 1638, 1550, 1474, 1310, 1268; HRMS:
4.10.2. Compound 2. Light brown solid; Rf (Flash column with sil-
ica-gel, 230e400 mesh using 15% MeOH in DCM as eluent) 0.35;
yield 52%; mp 270 ꢀC (dec); dH (DMSO-d6): 8.31 (br s, 2H), 8.20 (br s,
2H), 7.48e7.46 (m, 2H), 7.38e7.34 (m, 2H), 7.28 (s, 4H), 5.26 (s, 4H);
dC (DMSO-d6): 156.5, 153.3, 149.6, 140.7, 132.5, 129.6, 124.5, 119.0,
found 512.1791. C25H21N9O4þHþ requires 512.1795.
4.12. General procedure of click reaction (7b, 7, 8 and 9)
In
a degassed aqueous (10 mL) solution of CuSO4.H2O
88.4, 82.9, 33.5; nmax (KBr, cmꢂ1):
n
2921, 2851, 2365, 1687, 1638,
(10 mol %) sodium ascorbate (20 mol %) was added and stirred for
10 min followed by the addition of N1-propargyl thymine/N9-
propargyl adenine (0.48 mmol) under inert condition. Another
degassed solution of azide (7a/7e/8a) (1.1 equiv) in tBuOH (10 mL)
was added to this solution after 10 min and stirred for 10e24 h at
room temperature. On completion, it was quenched with satu-
rated NH4Cl solution (15 mL) and extracted with EtOAc (3ꢁ10 mL),
washed with water, brine, dried over Na2SO4 and concentrated
under vacuum.
1578, 1474, 1420, 1384, 1332; MS: m/z¼443.38 [MNaþ], 421.41
[MHþ]; HRMS: found 421.1632. C22H16N10þHþ requires 421.1638.
4.10.3. Compound 3. Light brown solid; Rf (Flash column with sil-
ica-gel, 230e400 mesh using 6% MeOH in DCM as eluent) 0.30;
yield 54%; mp 230 ꢀC (dec); dH (DMSO-d6): 11.4 (s, 2H), 8.35 (s, 2H),
7.66 (s, 2H), 7.49e7.47 (m, 2H), 7.39e7.36 (m, 2H), 4.75 (s, 4H), 1.76
(s, 3H); dC (DMSO-d6): 164.2, 150.5, 140.2, 132.0, 129.1, 124.3, 109.5,

8610
S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
2. (a) Mayer, J.; Sondheimer, F. J. Am. Chem. Soc. 1966, 88, 602; (b) Wong, H. N. C.;
Sondheimer, F. Tetrahedron Lett. 1980, 21, 217.
3. (a) Shetty, A. S.; Zhang, J.; Moore, J. S. J. Am. Chem. Soc. 1996, 118, 1019; (b) Basak,
A.; Mandal, S.; Bag, S. S. Chem. Rev. 2003, 103, 4077; (c) Basak, A.; Bag, S. S.;
Majumder, P. A.; Das, A. K.; Bertolasi, V. J. Org. Chem. 2004, 69, 6927; (d) Gre-
4.12.1. 5-Methyl-1-[1-(3-{2-[3-(tetrahydro-pyran-2-yloxy)-prop-1-
ynyl]-phenyl}-prop-2-ynyl)-1H-[1,2,3]triazol-4-ylmethyl]-1H-pyrim-
idine-2,4-dione (7b). White solid; Rf (P.E/E.A¼1:3) 0.38; yield 65%;
mp 157 ꢀC; dH (200 MHz): 10.03 (s, 1H), 8.05 (s, 1H), 7.43e7.36 (m,
2H), 7.32 (s, 1H), 7.26e7.21 (m, 2H), 5.40 (s, 2H), 4.94e4.92 (s, 2H),
4.49e4.48 (s, 2H), 3.85e3.74 (m, 1H), 3.52e3.47 (m, 1H), 1.65e1.49
(m, 6H); dC (50 MHz): 164.6, 151.1, 140.2, 132.2, 132.1, 128.9, 128.2,
125.7, 123.9, 123.6, 111.1, 96.5, 89.7, 85.9, 84.1, 83.6, 61.8, 54.6, 42.7,
40.9, 30.2, 25.3, 18.9, 12.2; HRMS: found 460.1983. C25H25N5O4þHþ
requires 460.1985.
ꢁ
ꢂ
ꢂ
dicak, M.; Matanovic, I.; Zimmermann, B.; Jeric, I. J. Org. Chem. 2010, 75, 6219.
4. Xu, J.; Egger, A.; Bernet, B.; Vasella, A. Helv. Chim. Acta 1966, 79, 2004.
5. (a) Hirsivaara, L.; Haukka, M.; Pursiainen, J. Eur. J. Inorg. Chem. 2001, 2255; (b)
ꢂ
ꢂ
Fustero, S.; Navarro, A.; Pina, B.; Soler, J. G.; Bartolome, A.; Asensio, A.; Simon, A.;
Bravo, P.; Fronza, G.; Volonterio, A.; Zanda, M. Org. Lett. 2001, 3, 2621; (c) Basak,
A.; Bag, S. S.; Das, A. K. Eur. J. Org. Chem. 2005, 1239; (d) Schmittel, M.; Morbach,
G.; Schenk, W. A.; Hagel, M. J. Chem. Crystallogr. 2005, 35, 373; (e) García Ruano,
ꢂ
J. L.; Parra, A.; Marcos, V.; Pozo, C.; Catalan, S.; Monteagudo, S.; Fustero, S.; Po-
veda, A., __. J. Am. Chem. Soc. 2009, 131, 9432; (f) Catak, S.; D’hooghe, M.; Kimpe,
N. D.; Waroquier, M.; Speybroeck, V. V. J. Org. Chem. 2010, 75, 885.
6. Alabugin, I. V.; Manoharan, M.; Kovalenko, S. V. Org. Lett. 2002, 4, 1119.
7. Kost, D.; Peor, N.; Sod-Moriah, G.; Sharabi, Y.; Durocher, D. T.; Raban, M. J. Org.
Chem. 2002, 67, 6938.
4.12.2. 1-{1-[3-(2-{3-[4-(6-Amino-purin-9-ylmethyl)-[1,2,3]triazol-
1-yl]-prop-1-ynyl}-phenyl)-prop-2-ynyl]-1H-[1,2,3]triazol-4-
ylmethyl}-5-methyl-1H-pyrimidine-2,4-dione (7). Brown solid; Rf
(10% MeOH in DCM as eluent) 0.40; yield 52%; mp 135 ꢀC (dec); dH
(DMSO-d6) 11.31 (s,1H), 8.24 (s, 2H), 8.19 (s, 2H), 8.14 (s, 2H), 7.62 (s,
1H), 7.53e7.46 (m, 2H), 7.42e7.40 (m, 4H), 5.60 (s, 4H), 5.47 (s, 2H),
4.91 (s, 2H), 1.71 (s, 3H); dC (DMSO-d6): 164.3, 155.9, 152.5, 150.8,
149.3, 143.0, 142.9, 141.3, 140.8, 132.1, 129.4, 123.9, 123.7, 118.6,
8. Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737.
9. (a) Sponer, J.; Leszczynski, J.; Hobza, P. J. Biomol. Struct. Dyn. 1996, 14, 117; (b)
Yakovchuk, P.; Protozanova, E.; Frank-Kamenetskii, M. D. Nucleic Acids Res.
2006, 34, 564.
10. Nicolaou, K. C.; Ogawa, Y.; Zuccarello, G.; Schweiger, E. J.; Kumazawa, T. J. Am.
Chem. Soc. 1988, 110, 4866.
11. Schreiner, P. R. J. Am. Chem. Soc. 1998, 120, 4184.
12. The crystal structure has been deposited at the Cambridge Crystallographic
Data Centre and allocated the deposition number CCDC 871969 and 872945 for
1i and 3a, respectively. The difference in c, d-distance is also reflected in their
thermal reactivity.
13. Kinetic experiment in presence of 1,4-CHD also did not produce any well de-
fined cyclized product except a polymeric mixture.
14. (a) John, J. A.; Tour, J. M. J. Am. Chem. Soc. 1994, 116, 5011; (b) Schriemer, D. C.; Li,
L. Anal. Chem. 1997, 69, 4169.
15. Kim, C.-S.; Russel, K. C. J. Org. Chem. 1998, 63, 8229.
109.0, 86.9, 83.4, 42.3, 39.8, 38.0, 12.0; nmax (KBr, cmꢂ1):
n 2925,
2298, 1680, 1654, 1580, 1474, 1412, 1310; HRMS: found 574.2175.
C28H23N13O2þHþ requires 574.2176.
4.12.3. Compound 8. Brown solid; Rf (10% MeOH in DCM as eluent)
0.35; yield 54%; mp 125 ꢀC (dec); dH (DMSO-d6): 8.25 (s, 2H), 8.23 (s,
2H), 8.12 (s, 2H), 7.51e7.49 (m, 2H), 7.42e7.39 (m, 2H), 7.30 (br s,
4H), 5.59 (s, 4H), 5.47 (s, 4H); dC (DMSO-d6): 155.7, 152.3, 149.3,
142.9, 140.9, 132.0, 129.3, 123.9, 123.7, 118.6, 86.9, 83.4, 39.8, 38.0;
16. Konig, B.; Rutters, H. Tetrahedron Lett. 1994, 35, 3501.
17. (a) Gellman, S. H.; Dado, G. P.; Liang, G.-B.; Adam, B. R. J. Am. Chem. Soc. 1991,
113, 1164; (b) Itahara, T. Nucleosides, Nucleotides Nucleic Acids 2003, 22, 309.
18. Kessler, H. Angew. Chem., Int. Ed. Engl. 1982, 21, 512.
nmax (KBr, cmꢂ1):
n 3335, 2925, 2853, 2362, 1686, 1654, 1604, 1578,
19. (a) Browne, D. T.; Eisinger, J.; Leonard, N. J. J. Am. Chem. Soc. 1968, 7302; (b)
Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Sheils, C. J.; Tahmassebi, D. C.;
Kool, E. T. J. Am. Chem. Soc. 2000, 122, 2213.
1479, 1420, 1384, 1303, 1245, 1129, 1053; HRMS: found 583.2290.
C28H22N16þHþ requires 583.2292.
20. In order to clarify our doubt arising out of the assumption that decomposition
of triazole moiety might cause the decrease in the resultant onset temperatures
for triazole spacer containing enediyneenucleobase hybrids (7e9), compound
10 was separately prepared. The onset temperature of compound 10 was found
to be 165 ꢀC whereas that of compounds 7e9 varied from 161e195 ꢀC. Thus the
considerable difference in onset temperatures between enediyneenucleobase
derivatives and compound 10 clearly proves the existence of some interstrand
effect induced by the appended nucleobases on BC. DSC curve of compound 10
is included in SI, Fig. S3.
4.12.4. Compound 9. White solid; Rf (6% MeOH in DCM as eluent)
0.38; yield 70%; mp 155e158 ꢀC; dH (DMSO-d6): 11.28 (s, 2H), 8.19
(s, 2H), 7.62 (s, 2H), 7.53e7.51 (m, 2H), 7.42e7.40 (m, 2H), 5.59 (s,
4H), 4.92 (s, 4H), 1.72 (s, 6H); dC (DMSO-d6): 164.3, 150.8, 142.9,
141.3, 132.1, 129.4, 123.9, 123.7, 108.9, 86.9, 83.4, 42.3, 39.8, 12.0;
nmax (KBr, cmꢂ1): 3356, 2924, 2354, 1686, 1650, 1612, 1594, 1468,
1356, 1324; HRMS: found 565.2058. C28H24N10O4þHþ requires
565.2060.
N
N
Acknowledgements
N
N
DST is acknowledged for an SERC grant to A.B. and for a JC Bose
Fellowship which supported this research. S.R. is grateful to CSIR,
Government of India for a research fellowship. The NMR and X-ray
facility have been provided at IIT, Kharagpur by DST under the
IRPHA and FIST programmes, respectively. The author S.R. is
showing her gratitude to Mr. Dibakar Deb for crystal structure
analysis.
10
21. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;
Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.;
Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.;
Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.;
Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao,
O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken,
V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A.
J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G.
A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.;
Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman,
J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.;
Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.;
Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.;
Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Re-
vision C.02; Gaussian: Wallingford, CT, 2004.
Supplementary data
Crystallographic data and crystallographic information files
(CIFs) for compound 1i and 3a, DSC graphs, solution phase kinetics
plots, VT NMRs for all compounds, Cartesian coordinates for all
optimized geometries, copies of 1H and 13C NMR spectra. Supple-
mentary data associated with this article can be found, in the online
version, at http://dx.doi.org/10.1016/j.tet.2012.07.093.
22. (a) Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200; (b) Lee, C.; Yang,
W.; Parr, R. G. Phys. Rev. B: Condens. Matter 1988, 37, 785; (c) Becke, A. D. Phys.
Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098; (d) Stephens, P. J.; Devlin, F. J.;
Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623; (e) Becke, A. D. J.
Chem. Phys. 1996, 104, 1040.
References and notes
23. (a) Hehre, W.; Radom, L.; Schleyer, P. v. R.; Popple, J. A. Ab Initio Molecular
Orbital Theory; Wiley: New York, NY, 1986; (b) Grafenstein, J.; Kraka, E.; Filatov,
M.; Cremer, D. Int. J. Mol. Sci. 2002, 3, 360; (c) Schreiner, P. R.; Vazquez, A. N.;
Prall, M. Acc. Chem. Res. 2005, 38, 29; (d) Zeidan, T. A.; Manoharan, M.; Ala-
bugin, I. V. J. Org. Chem. 2006, 71, 954; (e) Pickard, F. C., IV; Shepherd, R. L.;
1. (a) Bergman, R. G. Acc. Chem. Res. 1973, 6, 25; (b) Lockhart, T. P.; Comita, P. B.;
Bergman, R. G. J. Am. Chem. Soc. 1981, 103, 4082; (c) Kar, M.; Basak, A. Chem. Rev.
2007, 107, 2861; (d) Roy, S.; Anoop, A.; Biradha, K.; Basak, A. Angew. Chem., Int.
Ed. 2011, 50, 8316.

S. Roy et al. / Tetrahedron 68 (2012) 8600e8611
8611
Gillis, A. E.; Dunn, M. E.; Feldgus, S.; Kirschner, K. N.; Shields, G. C.; Manoharan,
M.; Alabugin, I. V. J. Phys. Chem. A 2006, 110, 2517.
24. While the DSC onset temperature deals with the solid state aggregation of the
crystal, the DFT calculation deals with the gas phase. Therefore, it may be
possible that the reactivity may slightly differ due to differences in molecular
association between these two states. Thus, we observed a difference of 0.
9 kcal/mol in activation energy for compound 4 and 6 in our gas phase cal-
culation [(vide Ref. Zeidan, T. A.; Kovalenko, S. V.; Manoharan, M.; Alabugin, I.
V. J. Org. Chem. 2006, 71, 962)].
25. (a) Basak, A.; Rudra, K. R. Tetrahedron Lett. 2000, 41, 7231; (b) Roy, S.; Basak, A.
Chem. Commun. 2010, 2283; (c) Chandra, K.; Dutta, D.; Mitra, A.; Das, A. K.;
Basak, A. Bioorg. Med. Chem. 2011, 19, 3274.