New methods for the synthesis of N-benzoylated uridine and thymidine derivatives; a convenient method for N-debenzoylation

Article abstract of DOI:10.1016/S0008-6215(01)00325-1

An improved procedure for the synthesis of N-benzoyl-2′,3′-O-isopropylidene uridine via one-step selective N-benzoylation of 2′,3′-O-isopropylidene uridine has been developed. An efficient synthetic route to N-benzoyl thymidine via initial tribenzoylation, followed by selective hydrolysis of the benzoates is also described. De-N-benzoylation of N-benzoylated thymidine and uridine derivatives can be conveniently effected under neutral conditions, by heating with benzyl alcohol.

Full text of DOI:10.1016/S0008-6215(01)00325-1

Carbohydrate Research 337 (2002) 369–372
www.elsevier.com/locate/carres
Note
New methods for the synthesis of N-benzoylated uridine and
thymidine derivatives; a convenient method for N-debenzoylation
Anita R. Maguire,* Isabelle Hladezuk, Alan Ford
Department of Chemistry, Uni6ersity College Cork, Cork, Ireland
Received 11 June 2001; received in revised form 15 October 2001; accepted 10 December 2001
Abstract
An improved procedure for the synthesis of N-benzoyl-2%,3%-O-isopropylidene uridine via one-step selective N-benzoylation of
2%,3%-O-isopropylidene uridine has been developed. An efficient synthetic route to N-benzoyl thymidine via initial tribenzoylation,
followed by selective hydrolysis of the benzoates is also described. De-N-benzoylation of N-benzoylated thymidine and uridine
derivatives can be conveniently effected under neutral conditions, by heating with benzyl alcohol. © 2002 Elsevier Science Ltd.
All rights reserved.
Keywords: Selective protection and deprotection; N-Benzoyl uridine and thymidine
Since the introduction of the chemical synthesis of
oligonucleosides, a myriad of protecting groups for
nucleosides has been developed.1 Among the protecting
groups which have been explored for the bases in
uridine and thymidine, the benzoyl group has emerged
as the most important and commonly employed.2,3
While this group provides a number of significant ad-
vantages as a means of N3 protection, such as ease of
introduction and stability towards many commonly
encountered reaction conditions, deprotection is usually
performed under basic conditions and the concentrated
NH4OH–methanol procedure3 is perhaps the most use-
ful. Notably, Ko¨ster and co-workers4 have reported
interesting data concerning the stability of N-acyl
groups towards a potent deacylating system (0.2 M
NaOH–MeOH).
ditions. For practical purposes, efficient synthetic
routes to the N-benzoylated key intermediates were
sought. This paper describes an improved procedure for
the synthesis of N-benzoyl-2%,3%-O-isopropylidene
uridine (2) via one-step selective N-benzoylation of
2%,3%-O-isopropylidene uridine (1), two new synthetic
methods for N-benzoyl thymidine 5 and a convenient
method for N-debenzoylation of the N-benzoylated
nucleoside derivatives under neutral conditions.
Despite the relatively simple structure of N-benzoyl-
2%,3%-O-isopropylidene uridine (2), which can be envis-
aged as a useful synthetic intermediate, we were unable
to find any reference to its synthesis. Synthesis of
N-benzoyl uridine from uridine by trimethylsilylation,
treatment with benzoyl chloride and hydrolysis has
been described.2b Direct reaction of 2%,3%-O-isopropyli-
dene uridine (1) with benzoyl chloride and pyridine was
reported to produce the 5%-O-benzoyl derivative.5 N-
Benzoylation of uridine under phase transfer conditions
was also conducted on the precursor protected at the 3%-
and 5%-OH groups by silylation.6 Thus direct N-benzoy-
lation of uridine in the presence of the unprotected
primary 5%-OH group poses a challenge.
During a recent study, we required N-benzoylated
pyrimidine derivatives as precursors, but due to the
base sensitivity of our final products, we needed to
conduct the subsequent deprotection under neutral con-
* Corresponding author. Tel.: +353-21-4902125; fax:
+353-21-4274097.
E-mail address: a.r.maguire@ucc.ie (A.R. Maguire).
We undertook an extensive investigation of the influ-
ence of reaction conditions, and especially the nature of
0008-6215/02/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0008-6215(01)00325-1

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A.R. Maguire et al. / Carbohydrate Research 337 (2002) 369–372
transfer conditions, using KOH, benzyltriethylammo-
nium chloride (TEBAC) and benzoyl chloride in
dichloromethane for 8 h. This intermediate was sub-
jected to selective de-O-acylation, which could be per-
formed quantitatively under alkaline treatment using 1
M NaOH (2.2 equiv) in pyridine overnight. After neu-
tralisation with Amberlite resin IR-120(H), the desired
product 5 was obtained in 92% yield (Scheme 2).
Interestingly, when thymidine 3 was reacted under
the conditions employed for the direct N-benzoylation
of 2%,3%-O-isopropylidene uridine (1), i.e., benzoyl chlo-
ride, triethylamine in dichloromethane, selective N-pro-
tection was not achieved; instead 3%,5%-dibenzoyl
thymidine 610,11 was obtained in 24% yield and the
tribenzoyl derivative 4 was obtained in 3% yield.
Having achieved efficient synthetic routes to the N-
benzoylated pyrimidine derivatives 2 and 5, our atten-
tion focused on developing a method for N-de-
benzoylation under neutral conditions. While this de-
protection is usually conducted under basic conditions
as outlined above, Ishido and co-workers developed
specific N-debenzoylation of a series of perbenzoylated
adenosine and cytidine derivatives by treatment with a
series of phenols and aliphatic alcohols to give the
corresponding benzoates with free amino groups in
high yields.12
These results prompted us to investigate deprotection
of the N-benzoylated thymidine and uridine derivatives
2 and 5 on treatment with alcohols; use of benzyl
alcohol proved successful, although it was not among
the alcohols described in the earlier report.12 The N-
benzoyl uridine derivative 2 was dissolved in benzyl
alcohol and after stirring at 90 °C for 30 h, the expected
product 1 was obtained in good yield (85%, Scheme 1).
This method has been also applied to the compound 5,
and under the same conditions described above, the
N-deprotection to thymidine 3 was effected in 82%
yield (Scheme 2).
Scheme 1. (i) BzCl (1.1 equiv), Et3N (1.1 equiv), CH2Cl2, rt,
6 h, 56%; (ii) BnOH, 90 °C, 30 h, 85%.
Scheme 2. (i) BzCl (3.6 equiv), DMAPcat, pyridine, rt, 9 h,
89%; (ii) BzCl (3.3 equiv), KOH (3.3 equiv), TEBACcat
,
CH2Cl2, rt, 8 h, 83%; (iii) NaOH 1 M (2.2 equiv), pyridine, rt,
overnight, 92%; (iv) BnOH, 90 °C, 30 h, 82%.
the base, on the regioselectivity of the benzoylation.
When 1, prepared following a literature procedure,7
was treated with benzoyl chloride (1.1 equiv) in the
presence of triethylamine (1.1 equiv) in dichloro-
methane at room temperature for 6 h, selective N-ben-
zoylation of 2%,3%-O-isopropylidene uridine (1) was ob-
served producing N-benzoyl-2%,3%-O-isopropylidene
uridine 2 in 56% yield (Scheme 1). The product was
fully characterised spectroscopically and by elemental
analysis. Use of other bases such as DMAP (4-N,N-
dimethylaminopyridine) under the same conditions
gave 5%-O-benzoyl-2%,3%-O-isopropylidene uridine, con-
sistent with the literature precedent for preferential
reaction at the 5%-OH group,5 highlighting the signifi-
cance of the selective N-benzoylation achieved using
triethylamine as base. The reason for the difference in
behaviour depending on the base employed is not clear.
Synthesis of N-benzoyl thymidine 5 was previously
reported by Sekine and co-workers.8 Protection of the
3%- and 5%-OH groups by silylation prior to N-benzoyla-
tion and subsequent O-deprotection, was conducted,3
reminiscent of the literature approaches developed for
N-benzoyl uridine outlined above. However, a synthetic
route to N-benzoyl deoxycytidine by Khorana and
co-workers9 caught our attention—they had reported
initial conversion of deoxy cytidine to the N, 3%,5%-
tribenzoyl derivative followed by selective ester hydrol-
ysis. This strategy appeared attractive as an efficient
route to N-benzoyl thymidine 5, obviating the necessity
for intermediate silyl protection.
In conclusion, the present paper describes efficient
methods for the synthesis of N-benzoyl uridine and
thymidine derivatives, and a practical solution for the
N-debenzoylation of these protected nucleosides under
very mild, neutral conditions and in good yields. The
selective N-benzoylation of 2%,3%-O-isopropylidene
uridine (1) is notable. The use of these intermediates in
the synthesis of multifunctionalised nucleosides is under
investigation in our laboratory and will be reported in
due course.
1. Experimental
Treatment of thymidine 3 with 3.6 equiv of benzoyl
chloride in the presence of a catalytic amount of
DMAP in pyridine for 9 h gave the N, 3%,5%-tribenzoyl
derivative 4 in 89% yield. Alternatively, benzoylation of
thymidine was also effected in 83% yield under phase
1H and 13C NMR spectra were recorded on a JEOL
GSX FT or on a Bruker Avance DPX 300 spectrome-
ter. Chemical shifts (l) are expressed in parts per
million (ppm) and J values are reported in Hz. TMS

A.R. Maguire et al. / Carbohydrate Research 337 (2002) 369–372
371
1
was used as an internal standard for H and 13C NMR.
IR spectra were recorded on a Perkin–Elmer Paragon
1000 FT-IR spectrometer as liquid films or KBr discs.
Thin-layer chromatography was performed on DC-Alu-
foilen Kieselgel 60F254 0.2 mm plates (E. Merck) and
visualised under UV light and stained with phospho-
molybdic acid–aq H2SO4 solution.
CDCl3) 8.18–7.38 (16 H, m, H-6, 3 Ph), 6.49–6.44 (1
H, m, H-1%), 5.68–5.66 (1 H, m, H-3%), 4.83–4.65 (2 H,
m, 2 H-5%), 4.55–4.52 (1 H, m, H-4%), 2.75–2.40 (2 H,
m, 2 H-2%), 1.66 (3 H, s, CH3); lC (75.4 MHz, CDCl3)
168.8, 165.9, 162.8 (3 CO), 162.5 (C-4), 149.2 (C-2),
135.1, 134.6, 134.5, 133.7, 131.5, 130.5, 130.4, 129.7,
129.5, 129.3, 129.0, 128.9, 128.6 (C-6, C-Ar), 111.5
(C-5), 85.1 (C-4%), 82.7 (C-1%), 74.9 (C-3%), 64.2 (C-5%),
37.8 (C-2%), 12.8 (CH3).
Method B. Pulverised KOH (0.15 g, 2.7 mmol, 3.3
equiv), TEBAC (20 mg, 0.08 mmol, 0.1 equiv) and
benzoyl chloride (0.31 mL, 2.7 mmol, 3.3 equiv) were
added to a solution of thymidine 3 (0.2 g, 0.83 mmol) in
CH2Cl2 (10 mL). The mixture was stirred at rt for 8 h,
then extracted twice with water (10 mL). After drying,
the organic phase was evaporated to dryness under
reduced pressure. Flash chromatography on silica gel
(1:1 EtOAc–hexane) afforded N,3%,5%-O-tribenzoyl
thymidine (4, 0.38 g, 83%).
Column chromatography was performed on
Kieselgel 60 (E. Merck) 60–200 mesh. All solvents were
distilled before use: hexane from calcium chloride,
CH2Cl2 and EtOAc from phosphorous pentoxide. Dry
solvents were prepared by refluxing over a drying agent
under an inert atmosphere: THF was dried over
sodium–benzophenone, ether, benzene and toluene
were dried over LiAlH4. DMF was distilled from CaH2
under reduced pressure (ca. 15 mmHg) and stored over
activated molecular sieves. Magnesium sulphate was
used as drying agent.
N3-Benzoyl-2%,3%-O-isopropylidene uridine (2).—Ben-
zoyl chloride (0.55 mL, 4.8 mmol, 1.1 equiv) and tri-
ethylamine (0.67 mL, 4.8 mmol, 1.1 equiv) were added
to a solution of 2%,3%-O-isopropylidene uridine (1, 1.14
g, 4.3 mmol) in CH2Cl2 (30 mL). The mixture was
stirred at rt under nitrogen for 9 h. The solvent was
evaporated. Toluene (20 mL) was introduced and evap-
orated. This operation was repeated twice. Flash chro-
matography on silica gel (1:1 EtOAc–hexane) afforded
the main product 2 (0.95 g, 56%) (Found: C, 56.32; H,
5.32; N, 6.93. C19H20N2O7·H2O requires C, 56.16; H,
5.46; N, 6.89); wmax (KBr)/cm−1 3440 (OH), 1748
(CꢀOBz), 1705, 1670 (CꢀC, CꢀOuracil); lH (300 MHz,
CDCl3) 7.81–7.78, 7.60–7.20 (6 H, m, H-6, Ph), 5.74 (1
H, J5,6 8.1, d, H-5), 5.67–5.65 (1 H, m, H-1%), 4.88–4.86
(1 H, m, H-2%), 4.80–4.76 (1 H, m, H-3%), 4.25–4.23 (1
H, m, H-4%), 3.80–3.63 (2 H, m, CH2-5%), 1.47, 1.25 (6
H, 2s, 2 CH3); lC (75.4 MHz, CDCl3) 167.4 (CO), 161.2
(C-4), 148.3 (C-2), 141.2 (C-6), 134.4, 130.2, 129.5,
128.3 (C-Ar), 113.2 (C(CH3)2), 101.1 (C-5), 94.1 (C-1%),
85.9 (C-2%), 83.2 (C-3%), 79.5 (C-4%), 61.5 (C-5%), 26.2,
24.2 (2CH3); m/z (EI): 43 (98), 59 (74), 77 (80, Ph+),
105 (100, PhCO+), 173 (27), 216 (14), 277 (46), 388
(1%, M+).
N3-Benzoyl thymidine (5)8.—A solution of NaOH
(8.14 mL, 1 M, 8.14 mmol, 2.2 equiv) was added to a
mixture of N3,3%,5%-O-tribenzoyl thymidine (4, 2.04 g,
3.7 mmol) in freshly distilled pyridine (20 mL) and the
mixture was stirred vigorously overnight. (The effi-
ciency of this process is critically dependent on the
quality of the pyridine employed—distilling just before
use is recommended.) The solution was neutralised with
Amberlite resin IR-120(H). The ion exchanger was
washed with CH2Cl2 and flash chromatography on
silica gel (7:3 EtOAc–hexane) afforded N-benzoyl
thymidine 5 as a cream solid (1.17 g, 92%) lH (300
MHz, CDCl3) 7.95–7.30 (6 H, m, H-6, H-Ar), 6.15–
6.06 (1 H, m, H-1%), 4.41–4.32 (1 H, m, H-3%), 3.88–
3.72 (1 H, m, H-4%), 3.72–3.50 (2 H, m, 2 H-5%),
2.28–2.20 (2 H, m, 2 H-2%), 1.85 (3 H, s, CH3); lC (75.4
MHz, CDCl3) 167.5 (CO), 162.5 (C-4), 149.0 (C-2),
135.6, 134.3, 130.3, 129.5, 128.2 (C-Ar, C-6), 110.0
(C-5), 86.0 (C-4%), 85.3 (C-1%), 70.3 (C-3%), 61.2 (C-5%),
39.2 (C-2%), 11.6 (CH3).
General procedure for the debenzoylation.—The com-
pound (1 mmol) was dissolved in 1 mL of benzyl
alcohol and heated at 90 °C for 30 h. The solvent was
evaporated under vacuum and flash chromatography
on silica gel afforded the N-debenzoylated derivative.
Purification conditions and yield of the product are
as follows.
This sample is obtained as a cream solid after drying.
All the attempts to crystallise it from a variety of
solvents failed.
N3,3%,5%-O-Tribenzoyl thymidine (4)10
2%,3%-O-Isopropylidene uridine (1).—Silica gel-column
chromatography (EtOAc) of the crude product of 1
mmol synthesis (0.39 g of 2) afforded 1 (0.24 g, 85%) as
Method A. Benzoyl chloride (1.7 mL, 14.8 mmol, 3.6
equiv) and dimethylaminopyridine DMAP (40 mg)
were added to a solution of thymidine 3 (1 g, 4.1 mmol)
in pyridine (30 mL). The mixture was stirred at rt for 9
h. The solvent was evaporated. Toluene (20 mL) was
introduced and evaporated. This operation was re-
peated twice. Flash chromatography on silica gel (1:1
1
a cream solid. This product showed H and 13C NMR
spectral data identical to those of an authentic sample
of 3.
Thymidine (3).—Silica gel-column chromatography
(20:1 CH2Cl2–EtOH) of the crude product of 1 mmol
synthesis (0.24 g of 5) afforded 3 (0.28 g, 82%) as a
white solid. This product is identical in all respects to
the commercial material.
EtOAc–hexane)
afforded
N,3%,5%-O-tribenzoyl
thymidine (4, 2.04 g, 89%) as a white solid, mp 121–
122 °C (EtOH) (lit,10 mp 124–125 °C) lH (300 MHz,

372
A.R. Maguire et al. / Carbohydrate Research 337 (2002) 369–372
(b) Welch, C. J.; Chattopadhyaya, J. Acta Chem. Scand.
Acknowledgements
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3. For example, see Matsuzaki, J.; Hotoda, H.; Sekine, M.;
Hata, T. Tetrahedron Lett. 1984, 25, 4019–4022.
4. Ko¨ster, H.; Kulikowski, K.; Liese, T.; Heikens, W.;
Kohli, V. Tetrahedron 1981, 37, 363–369.
The authors wish to acknowledge Dr R. Storer for
helpful discussions and Tanaud Ireland for financial
support for this research.
5. Kumar, A.; Walker, R. T. Tetrahedron 1990, 46, 3101–
3110.
6. Sekine, M. J. Org. Chem. 1989, 54, 2321–2326.
7. Tomasz, J. In Nucleic Acid Chemistry; Townsend, L. B.;
Tipson, R. S., Eds.; Wiley: New York, 1978; Vol. 2, p.
765.
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