Solvent-controlled regioselective protection of 5′-O-protected thymidine

Article abstract of DOI:10.1016/j.carres.2008.04.026

This paper describes an efficient procedure for selective 3′-O- or 3-N-protection of 5′-O-tert-butyldimethylsilylthymidine, depending on the use of aprotic polar solvents with low or high dielectric constant, respectively. These syntheses were activated by either ultrasound or microwaves. Several alkyl bromides offer a convenient route to prepare 3′-O- or 3-N-protected and functionalized thymidine derivatives.

Full text of DOI:10.1016/j.carres.2008.04.026

Available online at www.sciencedirect.com
Carbohydrate Research 343 (2008) 1490–1495
Note
Solvent-controlled regioselective protection
of 50-O-protected thymidine
K. Teste,a L. Colombeau,a A. Hadj-Bouazza,a R. Lucas,a R. Zerrouki,a,*
P. Krausza and Y. Champavierb
aLaboratoire de Chimie des Substances Naturelles EA1069, Faculte´ des Sciences et Techniques,
123 Avenue Albert Thomas, F-87060 Limoges, France
bUniversite´ de Limoges, Service Commun de RMN, Faculte´ de Pharmacie, 2 rue du Dr Marcland, F-87025 Limoges, France
Received 18 February 2008; received in revised form 16 April 2008; accepted 17 April 2008
Available online 25 April 2008
Abstract—This paper describes an efficient procedure for selective 30-O- or 3-N-protection of 50-O-tert-butyldimethylsilylthymidine,
depending on the use of aprotic polar solvents with low or high dielectric constant, respectively. These syntheses were activated by
either ultrasound or microwaves. Several alkyl bromides offer a convenient route to prepare 30-O- or 3-N-protected and function-
alized thymidine derivatives.
Ó 2008 Elsevier Ltd. All rights reserved.
Keywords: Regioselective protection; Nucleoside; Solvent effect; Ultrasound activation; Microwave activation
Thymidine is a key biological compound. A large num-
ber of applications in the field of molecular biology rely
on the use of thymidine or thymidine derivatives.1 Inser-
tion of these molecules into polymers or oligomers such
as oligonucleotides requires selective protection and
functionalization procedures. The latter can be allevi-
ated by the use of regioselective reactions such as those
described in this article.
We recently published the dimerization of thymidine
using cross-metathesis. As part of this program, we be-
came interested in the preparation of 50-protected thymi-
dine2 with an allyl group on the 30-position (Scheme 1).
We first allylated the 30-hydroxy group using Chat-
topadhyaya’s method3 with NaH (2.5 equiv) and allyl
bromide (2.5 equiv) in THF under ultrasound activa-
tion. The 30-O-alkylated product was obtained in 95%
Scheme 1. O- and N-Alkylation of 50-O-protected thymidine.
yield after purification. To our surprise, the same reac-
Reagents and conditions: (i) (a) NaH, THF, ultrasound (20 min), (b)
tion when performed in DMF did not lead to O-alkyl-
allyl bromide, ultrasound (45 min); (ii) (a) NaH, DMF, ultrasound
(20 min), (b) allyl bromide, ultrasound (20 min).
ation but produced the 30-O, 3-N-dialkylated product
instead. The use of 1.2 equiv of NaH and 1.2 equiv of
allyl bromide in DMF resulted in the complete reversion
of regioselectivity in favor of the N-alkylated product
(95%). Structures of allyl-protected thymidines were
*
Corresponding author. Tel.: +33 5 55 45 72 24; fax: +33 5 55 45 72
02; e-mail: rachida.zerrouki@unilim.fr
0008-6215/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.carres.2008.04.026

K. Teste et al. / Carbohydrate Research 343 (2008) 1490–1495
1491
elucidated by NMR analysis (1H, 13C, HMQC, and
HMBC). O- and N-Alkylation were demonstrated firstly
by long-range coupling observed in HMBC experiments
between C-30/H-30 and H-a/C-a and between H-a and
C-2/C-4 (Tables 1 and 2) and secondly by the disappear-
ance of the OH and NH groups, respectively. In addi-
tion, the 1H NMR spectra in DMSO-d6 displayed
signals of the NH and OH hydrogens of compounds 1
and 2, respectively (Fig. 1).
Table 1. NMR data of compound 1 in DMSO-d6 (400 MHz for 1H,
100 MHz for 13C)
1
Position
dC
83.9
dH (mult; J in Hz)
HMBC
Figure 1. Comparison of H NMR spectra of compounds 1 (top) and
2.
10
20
6.12 (dd; 8.5, 5.8)
2.10 (ddd; 13.7, 8.5, 6.0)
2.26 (ddd; 13.7, 5.8, 1.8)
4.07 (m)
C-2, 30, 6
C-10, 30, 40
C-10, 30, 40
C-10, 40, 50, a
C-30, 50
C-30, 40
C-30, 40
C-a, c
36.3
30
40
50
78.6
84.1
63.3
The allylation reaction was also carried out in diox-
ane, dichloromethane, 1,2-dichloroethane, and dimethyl
sulfoxide for comparison. In every case, the reaction was
checked by TLC and stopped when there was no more
production of product.
3.98 (m)
3.74 (dd; 11.3, 3.9)
3.78 (dd; 11.3, 4.1)
0.08 (s)
a
ꢀ5.5
0.09 (s)
C-a, c
In view of these results, it seems that regioselectivity
and dielectric constant of solvents are closely linked. In-
deed for solvents whose dielectric constant is lower than
10, the O-alkylated product is exclusively obtained, even
in the presence of excess sodium hydride and allyl
bromide (Table 3). Quasi-stoichiometric conditions
(1.2 equiv) lead to a dramatic decrease in yield. How-
ever, in the case of higher dielectric constant (DMSO,
DMF) and in presence of 1.2 equiv of each reagent, only
N-alkylation is observed. An excess of both base and
bromide results in the formation of dialkylated thym-
idine. Finally, a slow alkylation was observed in dichlo-
roethane, with selective formation of the O-alkylated
product.
b
c
2
NH
4
5
6
d
a
25.7
18.0
150.4
—
163.6
109.5
135.4
12.2
0.89 br s
—
—
C-b, c
—
—
C-2, 4
—
—
C-10, 2, 4, 5, d
C-4, 5, 6
C-30, b, c
C-a
C-a, b
C-a, b
11.36 (br s)
—
—
7.49 (d; 0.7)
1.78 (br s)
4.01 (d; 5.3)
5.90 (ddd; 17.1, 10.4, 5.3)
5.17 (dd; 10.4, 1.6)
5.28 (dd; 17.1, 1.6)
69.1
134.9
116.6
b
c
Table 2. NMR data of compound 2 in DMSO-d6 (400 MHz for 1H,
100 MHz for 13C)
Microwave irradiation was then used to establish a
comparison with ultrasound. Indeed the microwave acti-
vation presents some advantages, such as a remarkable
decrease in reaction times and in some cases, cleaner
reactions and a good selectivity.4
Position
dC
84.9
dH (mult, J in Hz)
HMBC
10
20
6.20 (dd; 7.5, 6.3)
2.08 (ddd; 13.3, 7.5, 6.0)
2.15 (ddd; 13.3, 6.3, 3.1)
4.21 (m)
C-2, 30, 6
C-10, 30, 40
C-10, 30, 40
C-10
39.6
30
70.3
—
86.9
63.1
In a typical procedure, a solution of TBDMS-thymi-
dine with sodium hydride (1.2 equiv) in aprotic solvent
was irradiated for 2 min, then allyl bromide (1.2 equiv)
was added, and the mixture was irradiated again for
4 min (Table 4, entry 2) or for 6 min (Table 4, entry
1). In THF compound 1 was obtained in 99% yield
(Table 4, entry 1), although in DMF compound 2 was
obtained in 96% yield (Table 4, entry 2). We observed
the same regioselectivity using either microwave irradia-
tion or ultrasound activation. In order to evaluate to
what extent this method can be generalized, we tested
different alkyl bromides. The results, summarized in
Table 4, show that this methodology permits one to
selectively protect in high yields either the 3 or 30-posi-
tion of thymidine (entries 5–8) with whichever alkyl
OH
40
50
5.31 (br s)
—
3.84 (br dd; 6.3, 3.2)
3.73 (dd; 11.3, 3.7)
3.80 (dd; 11.3, 3.1)
0.07 (s)
0.08 (s)
0.88 (br s)
—
—
—
—
7.56 (d; 1.0)
1.83 (d; 0.7)
4.40 (br d; 5.4)
5.81 (ddd; 17.2, 10.5, 5.4)
5.05 (dd; 17.2, 1.5)
5.09 (dd; 10.5, 1.5)
C-30, 50
C-30, 40
C-30, 40
C-a, c
C-a, c
C-b, c
—
a
ꢀ5.5
b
c
25.7
17.9
2
4
5
6
d
a
b
c
150.0
162.2
108.4
134.2
12.8
42.4
132.3
116.5
—
—
—
C-10, 2, 4, 5, d
C-4, 5, 6
C-2, 4, b, c
C-a
C-a, b
C-a, b

1492
K. Teste et al. / Carbohydrate Research 343 (2008) 1490–1495
Table 3. Selected results of regioselective allylation (ultrasound activation)
Entry Solvent (er) NaH (equiv) R–Br (equiv) Activation time O-Alkylated 1 (%) N-Alkylated 2 (%) O,N-Dialkylated (%)
First Second
1
2
3
4
5
6
7
Dioxane (2.21)
THF (7.58)
CH2Cl2 (8.93)
ClCH2CH2Cl (10.56) 2.5
DMF (37)
2.5
2.5
2.5
2.5
2.5
2.5
2.5
2.5
1.2
1.2
20 min 45 min 83
20 min 45 min 95
0
0
0
0
0
0
3
80
0
20 min 1 h 30
20 min 3 h
20 min 20 min
20 min 20 min
20 min 20 min
87
35
0
0
2.5
1.2
1.2
10
95
96
DMF (37)
DMSO (46.7)
0
0
0
Table 4. Synthesis of 30-O- and N-alkylated 50-O-tert-butyldimethylsilylthymidine
Entry Solvent Bromide Product Second
activationa (min) yield (%) (m/z)
Isolated
HRESIMS
12
THF
6
99
Calcd for C19H32N2NaO5Si [M+Na]+:
419.1973, found: 419.1977.
2
DMF
THF
DMF
THF
4
96
99
90
82
Calcd for C19H32N2NaO5Si [M+Na]+:
419.1973, found: 419.1974.
35
6
Calcd for C19H30N2NaO5Si [M+Na]+:
417.1816, found: 417.1818.
4
4
Calcd for C19H30N2NaO5Si [M+Na]+:
417.1816, found: 417.1819.
5
15
Calcd for C23H34N2NaO5Si [M+Na]+:
469.2129, found: 469.2133.

K. Teste et al. / Carbohydrate Research 343 (2008) 1490–1495
1493
Table 4 (continued)
Entry Solvent Bromide
Product
Second
Isolated HRESIMS
activationa (min) yield (%) (m/z)
Calcd for C23H34N2NaO5Si [M+Na]+:
469.2129, found: 469.2135.
6
7
8
DMF
4
90
92
82
THF
18
Calcd for C24H36N2NaO6Si [M+Na]+:
499.2235, found: 499.2240.
DMF
4
Calcd for C24H36N2NaO6Si [M+Na]+:
499.2235, found: 499.2240.
a First activation with NaH: 2 min, 200 W, 40 °C.
bromide is used, for example, allyl or propargyl. It is
worth noting that chloride derivatives were not used
since they proved unreactive even after several hours
of microwave or ultrasound activation. Tables 5 and 6
summarize the NMR data for compounds 3–8.
In conclusion, a fast and efficient regioselective pro-
tection method for generation of N- and 30-O-substi-
tuted thymidine was developed. Microwave irradiation
decreases reaction time, but conserves the same regio-
selectivity as sonication. This new product bank could
be of great interest in organic synthesis in order to insert
thymidine into complex compounds or to generate
synthetic oligomers.5
Ethos 1600 MicroSynth reactor from Milestone. The
temperature was measured with a fiberoptic thermo-
meter (ATC-FO)/Ethos. 1H NMR spectra were
recorded at 400.13 MHz with a Bruker DPX spectro-
meter. Chemical shifts (d) are expressed in ppm with
Me4Si as the internal standard (d = 0). Data are
reported as follows: chemical shift, multiplicity (s, sin-
glet; d, doublet; t, triplet; q, quartet; m, multiplet, and
br, broad), coupling constants (Hz), and assignment.
1.2. General method for ultrasound activation: example
with O-allylation (Table 3)
To 50-O-tert-butyldimethylsilylthymidine (2.32 g, 6.52
mmol) in dry THF (30 mL) was added NaH (60%,
652 mg, 2.5 equiv, 16.3 mmol), and the mixture was acti-
vated by ultrasound activation (20 min). Allyl bromide
(1.410 mL, 2.5 equiv, 16.3 mmol) was then added, and
the mixture was activated by ultrasound (20 min). After
workup (NH4Cl–H2O) and purification by chromato-
graphy (CHCl3 as eluent) 1 was obtained: 2.45 g (95%).
1. Experimental
1.1. General methods
All solvents and chemicals were commercially available,
and unless otherwise stated, were used as received. Reac-
tions were monitored by thin-layer chromatography
(TLC) on precoated 0.2-mm Silica Gel 60 F254 (E.
Merck) plates and visualized in two ways: (1) with an
ultraviolet light source at 254 nm, or (2) by spraying
with sulfuric acid (6 N) and heating to 200 °C. Micro-
wave irradiations were performed by the means of an
1.3. General method for microwave activation: example
with O-allylation (Table 4)
To a solution of 50-O-tert-butyldimethylsilylthymidine
(1.27 g, 3.57 mmol) in dry THF (15 mL) was added

1494
K. Teste et al. / Carbohydrate Research 343 (2008) 1490–1495
Table 5. 1H NMR chemical shifts of alkyl compounds 3–8
Position
3
4
5
6
7
8
10
20
6.10 dd 5.7, 8.6
2.10 ddd 6.0,
8.7, 13.7
2.29 ddd 1.6,
5.7, 13.7
4.24 m
3.99 br d 3.7, 5.6
3.74 dd 3.8, 11.2
3.78 dd 4.0, 11.2
—
6.20 dd 6.5, 7.2
2.09 ddd 6.5,
7.4, 13.3
2.16 ddd 3.1,
6.2, 13.3
4.21 m
3.85 br d 3.0, 6.0
3.73 dd 3.8, 11.4
3.80 dd 3.0, 11.4
5.30 d 4.2
0.07 s
6.15 dd 5.7, 8.6
2.12 ddd 6.0,
8.6, 13.5
2.33 ddd 1.7,
5.7, 13.5
4.12 dd 2.0, 3.7, 5.8
4.06 br dd 3.7, 5.8
3.72 dd 3.8, 11.2
3.78 dd 4.2, 11.2
—
6.20 dd 6.5, 7.2
2.09 ddd 6.3,
7.4, 13.2
2.16 ddd 3.2,
6.1, 13.3
4.21 m
3.84 br 3.1, 6.2
3.73 dd 3.8, 11.4
3.80 dd 3.1, 11.4
5.30 d 4.1
0.07 s
6.15 dd 5.8, 8.4
2.11 ddd 6.0,
8.4, 13.6
2.32 ddd 1.6,
5.7, 13.6
6.21 dd 6.5, 7.1
2.10 ddd 6.1,
7.4, 13.3
2.16 ddd 3.3,
6.2, 13.3
30
40
50
4.10 m
4.21 m
4.05 dd 3.6, 5.6
3.72 dd 3.7, 11.3
3.77 dd 4.1, 11.3
—
0.04 s and 0.05 s
0.86 s
3.84 dd 3.2, 6.2
3.73 dd 3.8, 11.4
3.80 dd 3.1, 11.4
5.29 d 4.1
0.07 s
30-OH
a
0.09 s
0.89 s
0.05 s and 0.06 s
0.86 s
b
0.88 s
0.88 s
0.88 s
3-NH
11.35 s
—
11.36 s
—
11.34 s
—
6
d
a
7.48 d 0.7
1.78 br s
4.20 dd 2.2, 16.0
4.25 dd 2.2, 16.0
3.47 t 2.3
—
—
—
—
—
7.57 d 0.6
1.84 br s
4.51 dd 2.4, 15.6
4.55 dd 2.4, 15.6
3.10 t 2.3
—
—
—
—
—
7.49 d 0.8
1.78 br s
4.53 d 14.0
4.56 d 14.0
—
7.35 m
7.37 m
7.31 m
7.37 m
7.58 br s
1.84 br s
4.90 d 14.5
4.94 d 14.5
—
7.36 m
7.37 m
7.30 m
7.37 m
7.47 d 0.7
1.77 br s
7.58 br s
1.85 br s
4.94 d 14.6
4.98 d 14.6
—
6.81 br s
—
6.81 m
4.50 d 14.4
4.53 d 14.3
—
6.90 br d 1.0
—
6.86 br dd 1.5, 7.7
7.27 br t 7.7, 8.2
6.91 br dd 1.0, 8.0
3.75 s
c
Ar-2
Ar-3
Ar-4
Ar-5
Ar-6
3-OCH3
7.21 dd 7.5, 8.9
6.80 br d 7.8
3.72 s
7.35 m
—
7.36 m
—
—
—
Table 6. 13C NMR chemical shifts of alkyl compounds 3–8
Position
3
4
5
6
7
8
10
83.8
35.9
78.2
83.8
63.1
ꢀ5.6
25.7
17.9
12.1
150.3
163.5
109.5
135.2
55.7
79.9
77.3
—
85.1
39.6
70.4
87.0
63.2
ꢀ5.5
25.8
18.0
12.8
149.6
161.7
108.5
134.6
30.0
79.0
73.0
—
83.9
36.2
78.5
84.0
63.2
85.0
39.6
70.4
87.0
63.1
ꢀ5.5
25.7
18.0
12.8
150.0
162.3
108.5
134.5
42.5
—
84.0
36.3
78.6
84.1
63.3
85.0
39.5
70.3
86.9
63.1
20
30
40
50
a
ꢀ5.6
ꢀ5.5
ꢀ5.5
b
25.7
25.7
25.7
c
17.9
12.1
17.9
12.2
17.9
12.8
d
2
150.3
163.5
109.4
135.3
70.0
150.4
163.6
109.5
135.4
69.9
150.3
162.5
108.5
134.4
43.5
4
5
6
a
b
c
—
—
—
—
—
—
—
Ar-1
Ar-2
Ar-3
Ar-4
Ar-5
Ar-6
3-OCH3
137.9
127.5
128.2
127.4
128.2
127.5
—
137.5
127.1
128.5
127.0
128.5
127.1
—
139.6
113.1
159.3
113.0
129.4
119.7
55.0
138.5
113.6
159.1
112.2
129.3
119.5
54.9
—
—
—
—
—
—
—
—
—
—
—
—
NaH (60%, 326 mg, 2.5 equiv, 8.15 mmol), and the mix-
ture was activated by microwave irradiation (2 min,
200 W, 40 °C). Allyl bromide (705 lL, 2.5 equiv,
8.15 mmol) was then added, and the mixture was acti-
vated by microwave irradiation (6 min, 200 W, 40 °C).
After workup (NH4Cl–H2O) and purification by chro-
matography (CHCl3 as eluent) 1 was obtained: 1.28 g
(99%).
Acknowledgments
´
Financial support from the ‘Conseil Regional du Lim-
ousin’ is gratefully acknowledged. The authors are
grateful to Dr. Michel Guilloton for useful comments
on the manuscript. We also thank Dr. Denis Lesage
for HRMS experiments.

K. Teste et al. / Carbohydrate Research 343 (2008) 1490–1495
1495
2. (a) Colombeau, L.; Zerrouki, R.; Krausz, P.; Champavier,
Y. Lett. Org. Chem. 2005, 2, 613–615; (b) Roy, V.;
Zerrouki, R.; Krausz, P. Nucleosides, Nucleotides, Nucleic
Acids 2005, 24, 289–301.
3. Wu, J. C.; Xi, Z.; Gioeli, C.; Chattopadhyaya, J. Tetra-
hedron 1991, 47, 2237–2254.
Supplementary data
Supplementary data (spectra for compounds 1,2) associ-
ated with this article can be found, in the online version,
at doi:10.1016/j.carres.2008.04.026.
4. Thanh, G. V.; Loupy, A. Tetrahedron Lett. 2003, 44, 9091–
9094.
5. (a) Lucas, R.; Neto, V.; Hadj Bouazza, A.; Zerrouki, R.;
Granet, R.; Krausz, P.; Champavier, Y. Tetrahedron Lett.
2008, 49, 1004–1007; (b) Lucas, R.; Zerrouki, R.; Granet,
R.; Krausz, P.; Champavier, Y. Tetrahedron 2008, 64,
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