Development of a novel nucleoside analogue with S-type sugar conformation: 2′-deoxy-trans-3′,4′-bridged nucleic acids

Article abstract of DOI:10.1016/j.tet.2007.06.040

Two novel trans-3′,4′-bridged nucleic acid (trans-3′,4′-BNA) monomers, one with a 3,5,8-trioxabicyclo[5.3.0]decane structure and the other with a 4,7-dioxabicyclo[4.3.0]nonane structure, were successfully synthesized from thymidine. The locked trans-fused ring structures of the nucleoside analogues were confirmed by X-ray crystallography, which also indicated that their furanose rings had a typical S-type conformation involving C_2′-endo or C_3′-exo sugar puckering, respectively, and the same ring conformation as that observed in the B-type helical structure of the DNA duplex.

Full text of DOI:10.1016/j.tet.2007.06.040

Tetrahedron 63 (2007) 8977–8986
Development of a novel nucleoside analogue with S-type sugar
conformation: 20-deoxy-trans-30,40-bridged nucleic acids
Tomohisa Osaki,a Satoshi Obika,a,b Yasuki Harada,a Yasunori Mitsuoka,a Kensaku Sugaya,a
Mitsuaki Sekiguchi,a Somjing Roongjanga and Takeshi Imanishia,
*
aGraduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
bPRESTO, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
Received 7 April 2007; revised 31 May 2007; accepted 1 June 2007
Available online 19 June 2007
Abstract—Two novel trans-30,40-bridged nucleic acid (trans-30,40-BNA) monomers, one with a 3,5,8-trioxabicyclo[5.3.0]decane structure
and the other with a 4,7-dioxabicyclo[4.3.0]nonane structure, were successfully synthesized from thymidine. The locked trans-fused ring
structures of the nucleoside analogues were confirmed by X-ray crystallography, which also indicated that their furanose rings had a typical
0
0
S-type conformation involving C2 -endo or C3 -exo sugar puckering, respectively, and the same ring conformation as that observed in the
B-type helical structure of the DNA duplex.
Ó 2007 Elsevier Ltd. All rights reserved.
1. Introduction
requirements for stable B-type duplex formation have not
yet been developed, and much work is still being carried
out in this area.
The five-membered furanose ring in nucleosides or nucleo-
tides is conformationally very flexible and exists in an
equilibrium of two major conformers (N- and S-forms).
Pre-organization of the nucleoside sugar conformation in
an appropriate form is very effective in forming a stable du-
plex or triplex with single- or double-stranded nucleic acids.
The recently developed 20-O,40-C-methylene bridged nucleic
acid (20,40-BNA1a–c/LNA2) is an artificial nucleoside with an
additional ring between the O20 and C40 atoms, so that the
sugar moiety is tightly restricted in a typical N-type sugar
conformation.Oligonucleotidescontaining20,40-BNAmono-
mers show significantly enhanced binding affinity not only
toward single-stranded RNA complements but also towards
double-stranded DNA complements. Various other N-type
nucleoside analogues have also been synthesized.1d–f
Previously, we prepared trans-30,40-bridged nucleic acid
(trans-30,40-BNA)monomers1and2, whichhavea4,7-dioxa-
bicyclo[4.3.0]nonane structure and a methoxy group at the
C20 position, as S-type nucleoside analogues (Fig. 1).5a–c
The sugar moiety of these artificial nucleosides is restricted
to the S-type conformation by the presence of an additional
trans-fused ring between the C30 and C40 atoms of the
nucleosides; the additional ring is expected to be positioned
outside the B-type DNA duplex without any steric repulsion.
O
O
H3C
OH
H3C
NH
NH
OH
OCH3
N
N
4'
O
O
O
O
O
O
Several nucleoside analogues with S-type sugar conforma-
tion also have been prepared, and the hybridizing ability of
their oligonucleotide derivatives has been evaluated.3a–i
However, a considerable decrease in duplex stability with
complementary DNA strands was observed in many cases,
probably due to inadequate restriction of the sugar moiety
and/or steric repulsion between added structural components
and neighboring nucleotide residues in the B-type duplex.4
Ideal artificial nucleosides, which fulfill the structural
OCH3
2'
3'
OH
OH
1
2 (ΔTm = ca. -12 °C toward ssDNA)
O
O
H3C
OH
H3C
NH
NH
OH
N
N
O
O
O
O
O
O
O
OH
OH
Keywords: BNA; DNA structure mimic; Conformation; X-ray crystallo-
graphy.
3
4
* Corresponding author. Tel.: +81 6 6879 8200; fax: +81 6 6879 8204;
e-mail: imanishi@phs.osaka-u.ac.jp
Figure 1. Structures of trans-30,40-bridged nucleic acids.
0040–4020/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tet.2007.06.040

8978
T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
The phosphoramidite derivative of arabino-type monomer 2
was successfully synthesized and incorporated into oligonu-
cleotides. The modified oligonucleotides containing mono-
mer 2 were found to show low binding affinity towards
complementary ssDNA and ssRNA in comparison with the
corresponding natural oligonucleotides,5c suggesting that
the methoxy group at the C20 (b) position adversely contacts
neighboring residues during formation of the duplex. In addi-
tion, previous research on artificial nucleosides restricted to
an N-type sugar conformation has shown that the size of
the additional ring and the position of oxygen atom on the
bridged moiety affect duplex stability.1b–f
afforded the corresponding aldehyde 11, followed by aldol
condensation with formaldehyde and reduction with sodium
borohydride to give the diol 12, the precursor of interme-
diate A.
Three possible routes for efficient synthesis of the important
intermediate A (13) were examined as shown in Scheme 3.
In our previous communication, we reported that the 50-hy-
droxyl group in 12 was protected with a benzyl group to give
13 (path A).6 However, selective monobenzylation of the 50-
hydroxyl group did not proceed easily, and the desired prod-
uct 13 was obtained in relatively low yield (49%) along with
its isomer 14 (21%). To improve the yield and selectivity of
this benzylation procedure, we attempted regioselective re-
duction of the corresponding benzylidene acetal 15 (path
B), as described in our previous reports.9 The reduction
was carried out using several reagents (Table 1). Treatment
of 15 with diisobutylaluminum hydride or sodium cyanobor-
ohydride afforded complex mixtures (Runs 1 and 2); in con-
trast, the reaction of 15 with triethylsilane in the presence of
boron trifluoride diethyl etherate or tin(IV) chloride gave the
desired isomer 13, but in low yield (Runs 3 and 4). Finally, it
was found that path C was the most efficient for the prepara-
tion of 13: treatment of 12 with 4,40-dimethoxytrityl chloride
resulted in exclusive tritylation of the hydroxyl group on the
opposite side of the C50 position to give 16. After benzyla-
tion of the remaining 50-hydroxyl group, the dimethoxytrityl
group was efficiently deprotected under mildly acidic condi-
tions to give the desired intermediate 13 in 83% yield over
three steps. We inferred that formation of a hydrogen bond
between the 50-hydroxyl group and the oxygen atom at the
C30 substituent in 12 resulted in the opposite hydroxyl group
becoming more reactive for tritylation with 4,40-dimethoxy-
trityl chloride.
Based on these considerations, we designed de novo two
20-deoxy type trans-30,40-BNA analogues 36 and 4, which
we synthesized from thymidine. One had a 3,5,8-trioxabi-
cyclo[5.3.0]decane structure and the other a 4,7-dioxabi-
cyclo[4.3.0]nonane structure (Fig. 1). The syntheses of 3
and 4 are described below.
2. Results and discussion
2.1. Synthesis of the common intermediate A
In the synthetic strategy for 3 and 4, thymidine is used as
a starting material, and hydroxymethyl groups are intro-
duced at the C30 and C40 positions to give the common inter-
mediate A, as outlined in Scheme 1. The trans-fused
structure of 3 may be obtained by acetalization and that of
4 may be obtained via a nucleophilic reaction.
First, we prepared the precursor 12 of intermediate A as
shown in Scheme 2. The 30-deoxy-30-C-methylenethymidine
derivative 5, prepared from thymidine according to known
procedures,7 was oxidized using a catalytic amount of os-
mium tetroxide to give the diol 6 with high stereoselectivity.
After protection of the thymine nucleobase in 6 using benzyl
chloromethyl ether (BOMCl), the obtained product 7 was
treated with dibutyltindimethoxide and chloromethyl methyl
ether (MOMCl) to give 8 in good yield.8 Protection of the 30-
hydroxyl group in 8 with a benzyl group and subsequent re-
moval of the trityl group at C50 proceeded efficiently to give
the primary alcohol 10 via 9. Dess–Martin oxidation of 10
2.2. Synthesis of 3 from intermediate A (13)
The target nucleoside 3 was synthesized from the intermedi-
ate 13 as shown in Scheme 4. We had already developed
20,40-BNAcoc by construction of a cis-methyleneoxymethyl-
ene (–C–O–C–) linkage between the O20 and C40 atoms.10
The same conditions—treatment with paraformaldehyde
and p-toluenesulfonic acid—were applied for direct con-
struction of the trans-fused ring structure from 13.
O
O
O
R
O
H3C
R
H3C
H3C
N
NH
N
RO
N
N
RO
RO
HO
HO
N
O
O
O
O
O
O
4'
4'
3'
3
3'
O
OR
OR
OH
common intermediate A
(R: protective group)
thymidine
O
O
R
H3C
R
H3C
OH
N
N
RO
N
O
N
O
RO
LO
O
O
O
4
OR
OR
L: leaving group
Scheme 1. Synthetic strategies for 3 and 4 from thymidine.

T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
8979
O
N
O
N
O
H3C
H3C
HO
H3C
NH
NH
NH
O
O
N
O
3 steps
Ref. 7
HO
TrO
TrO
O
ii)
O
i)
O
OH
OH
5
6
thymidine
O
N
O
N
O
BOM
H3C
BOM
O
BOM
H3C
H3C
N
N
N
MOMO
TrO
HO
O
O
MOMO
TrO
N
O
TrO
iii)
iv)
v)
O
O
OH
OBn
9
OH
7
8
O
O
O
BOM
BOM
H3C
MOMO
H3C
BOM
H3C
N
N
N
MOMO
N
O
N
O
MOMO
HO
N
O
HO
O
vi)
O
vii)
O
O
HO
OBn
11
OBn
OBn
10
12
Scheme 2. Reagents and conditions: (i) OsO4, N-methylmorpholine-N-oxide, pyridine/H2O/t-BuOH, 75 ꢀC (65%); (ii) BOMCl, DBU, DMF, 0 ꢀC (89%); (iii)
n-Bu2Sn(OMe)2, i-Pr2NEt, MOMCl, 1,4-dioxane/CH2Cl2, reflux (93%); (iv) NaH, BnBr, n-Bu4NI, DMF, room temperature (84%); (v) (+)-10-camphorsulphonic
acid, CH2Cl2/MeOH, room temperature (90%); (vi) Dess–Martin periodinane, CH2Cl2, room temperature; (vii) 37% H2CO aq, 1 M NaOH aq, THF, 15 ꢀC, then
NaBH4, THF, 0 ꢀC (63% from 10).
O
N
O
N
BOM
O
BOM
O
H3C
MOMO
H3C
MOMO
N
N
5'
O
O
HO
HO
Path B
ii)
O
O
Ph
OBn
15
OBn
12
Path C iv)
i)
Path A
iii)
O
O
O
N
BOM
O
H3C
BOM
O
H3C
MOMO
BnO
HO
BOM
O
N
H3C
MOMO
N
N
MOMO
HO
N
N
O
v), vi)
HO
O
+
O
DMTrO
BnO
OBn
OBn
OBn
14
16
13 (=A)
Scheme 3. Reagents and conditions: (i) NaH, BnBr, 0 ꢀC (49%); (ii) benzaldehyde dimethylacetal, (+)-10-camphorsulphonic acid, CH2Cl2, room temperature
quant; (iii) Et3SiH, BF3/Et2O, CH2Cl2, 0 ꢀC (30%); (iv) DMTrCl, Et3N, CH2Cl2, room temperature; (v) NaH, BnBr, n-Bu4NI, DMF, room temperature; (vi)
(+)-10-camphorsulphonic acid, CH2Cl2/MeOH, room temperature (83% over three steps).
Table 1. Regioselective reduction of 15 for 13
Fortunately, the expected nucleoside 17 was obtained suc-
cessfully in 47% yield. We surmised that after initial
removal of the MOM group in 13 under acidic conditions,
a methylene bridged structure was immediately formed be-
tween two hydroxyl groups by excess paraformaldehyde to
afford 17.11 Deprotection of the two benzyl groups and the
BOM group in 17 using ammonium formate and 20%
Pd(OH)2–C gave the desired nucleoside analogue 3 in
Run Conditions
Yield (%)
13
14
1
2
3
4
DIBAL/H (5 equiv)
NaBH3CN (5 equiv), TiCl4 (5 equiv)
Et3SiH (10 equiv), BF3/Et2O (2 equiv) 30
Complex mixtures
Complex mixtures
—
Et3SiH (10 equiv), SnCl4 (2 equiv)
21
42

8980
T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
moderate yield. All spectral data supported the structure as-
signed to 3, and this structure was conclusively established
by X-ray crystallographic analysis.6
J¼6, 8 Hz for 24 and J¼5, 9 Hz for 17), which confirmed
the successful formation of the trans-fused structure. Sur-
prisingly, treatment of 24 with 20% Pd(OH)2–C and cyclo-
hexene in ethyl acetate gave the single compound 25. The
coupling constants between the C10 proton and C20 protons
of 25 (C10 H: J¼2, 11 Hz) were remarkably different from
those of 3 (C10 H: J¼6, 9 Hz). The cis-fused structure of
the unexpected nucleoside 25 was confirmed by X-ray crys-
tallographic analysis (Fig. 2, top).14,15 A possible mecha-
nism for the formation of 25 is shown in Scheme 6; this
nucleoside is obtained via protonation at the O40 position
of 4 and furanose ring opening followed by formation of
the more stable pyranose ring. Therefore, in order to avoid
protonation of 4, we examined the use of ammonium for-
mate instead of cyclohexene as an H2 source. Fortunately,
synthesis of 4 was accomplished by catalytic hydrogenolysis
over Pd(OH)2–C with ammonium formate in 39% yield. The
structure of 4 was confirmed by spectral data and X-ray crys-
tallographic analysis (Fig. 2, bottom).14 X-ray structure
investigation showed that the furanose rings of 36 and 4
O
H3C
BOM
N
BnO
N
i)
ii)
O
O
13
O
3
O
OBn
17
Scheme 4. Reagents and conditions: (i) p-TsOH$H2O, (CH2O)n,
ClCH2CH2Cl, reflux (47%); (ii) HCOONH4, 20% Pd(OH)2–C, EtOH, reflux
(60%).
2.3. Synthesis of 4 from intermediate A (13)
Another type of trans-30,40-BNA 4, whose structure con-
tained a six-membered additional ring, was also synthesized
from 13 (Scheme 5). After the introduction of a tosyl group
as a leaving group in 13, the MOM group was deprotected by
TMSBr to give the alcohol 19 in good yield. Oxidation of 19
gave the corresponding aldehyde 20, which was subjected to
the Wittig reaction to give the enol ether 21. Treatment of 21
with mercury(II) acetate12 and subsequent reduction13 of the
resulting compound 22 gave the alcohol 23, as expected, in
fair yield. A base-mediated intramolecular SN2 reaction of
23 proceeded smoothly on treatment with NaHMDS to
give 24 in excellent yield. NMR analysis showed that the
values of the coupling constants between the C10 proton
and C20 protons of 24 were similar to those of 17 (C10 H:
0
were restricted to typical S-type sugar conformations, C2 -
ꢀ
ꢀ
0
endo puckering (P¼174 ) and C3 -exo puckering (P¼194 )
respectively. It was also clear that both nucleobases were
in an anti orientation (c:ꢁ126ꢀ for 3 and c:ꢁ129ꢀ for 4),
appropriate for the formation of the B-type duplex.
3. Conclusion
We have successfully synthesized two 20-deoxy-type
trans-30,40-bridged nucleic acid monomers, with a 3,5,8-
O
N
O
BOM
O
BOM
O
H3C
H3C
HO
N
N
MOMO
N
BnO
TsO
BnO
TsO
i)
O
ii)
O
iii)
13
OBn
OBn
19
18
O
N
O
N
O
N
BOM
O
H3C
BOM
H3C
O
BOM
O
H3C
H3CO
N
N
N
O
H
O
O
H
BnO
BnO
TsO
BnO
TsO
v)
O
iv)
vi)
O
TsO
OBn
OBn
OBn
20
21
22
O
H3C
O
O
N
NH
O
O
BOM
O
H3C
OH
O
N
H3C
N
HO
BOM
N
viii)
BnO
OH
N
BnO
TsO
vii)
25
O
O
O
O
OBn
23
ix)
OBn
24
4
Scheme 5. Reagents and conditions: (i) p-TsCl, Et3N, DMAP, CH2Cl2, room temperature quant.; (ii) TMSBr, CH2Cl2, ꢁ30 ꢀC (97%); (iii) Dess–Martin period-
inane, CH2Cl2, room temperature; (iv) Ph3PCH2OMe$Cl, LiHMDS, THF, ꢁ78 ꢀC (66% over two steps); (v) Hg(OAc)2, TBAI, THF/H2O, room temperature;
(vi) NaBH4, THF/H2O, 0 ꢀC (63% over two steps); (vii) NaHMDS, THF, reflux (92%); (viii) cyclohexene, 20% Pd(OH)2–C, AcOEt, reflux (82%) for 25; (ix)
HCOONH4, 20% Pd(OH)2–C, EtOH, reflux (39%) for 4.

T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
8981
13C NMR spectra were recorded on a JEOL EX-270
(1H, 270 MHz; 13C, 67.8 MHz) or a JEOL GX-500 (1H,
500 MHz) spectrometer. IR spectra were recorded on a
JASCO FT/IR-200 spectrometer. Mass spectra were mea-
sured on a JEOL JMS-D300 or JMS-600 mass spectrometer.
Optical rotations were recorded on a JASCO DIP-370 instru-
ment. For column chromatography, a Merck Kieselgel 60
(70–200 mesh) or Fuji Silysia BW-127ZH (100–200 mesh)
was used.
4.1.1. 30-C-Hydroxymethyl-50-O-tritylthymidine (6). To
a stirred solution of 5 (5.7 g, 11.9 mmol) in t-BuOH were
added N-methylmorpholine N-oxide (9.6 g, 82.1 mmol),
pyridine (5.1 mL, 63.1 mmol), H2O (6.7 mL), and OsO4
(0.076 M solution in t-BuOH, 0.6 mL). The mixture was
stirred under N2 at 75 ꢀC for 8 h. The reaction mixture was
cooled to room temperature, and saturated Na2S2O3 solution
was added. The mixture was evaporated and extracted with
AcOEt. The combined organic layers were washed with
H2O and saturated NaCl solution, dried over Na2SO4, and
concentrated under reduced pressure. The resultant residue
was purified by silica gel column chromatography (CHCl3/
MeOH¼20:1) to give 6 (4.0 g, 65%) as a colorless solid.
Mp 112–114 ꢀC. [a]D26 ꢁ17.2 (c 1.0, CHCl3). IR (KBr)
nmax 3423, 3052, 1686, 1474, 1443 cmꢁ1 1H NMR
.
(CDCl3) d 1.36 (3H, d, J¼1 Hz), 2.06 (1H, dd, J¼9,
13 Hz), 2.36 (1H, dd, J¼5, 13 Hz), 3.12 (1H, t, J¼6 Hz),
3.24 (1H, dd, J¼2, 11 Hz), 3.49–3.67 (3H, m), 4.04 (1H,
s), 4.12 (1H, dd, J¼2, 4 Hz), 6.44 (1H, dd, J¼5, 9 Hz),
7.22–7.42 (15H, m), 7.64 (1H, d, J¼1 Hz), 9.50 (1H, s).
13C NMR (CDCl3) d 11.8, 41.6, 62.6, 65.0, 81.3, 84.1,
86.1, 88.1, 111.4, 127.5, 128.5, 135.6, 142.5, 150.5, 163.7.
MS (FAB): m/z 515 (MH+). Anal. Calcd for C30H30N2O6:
C, 70.02; H, 5.88; N, 5.44. Found: C, 70.07; H, 6.01; N, 5.23.
Figure 2. ORTEP drawings of 25 (top) and 4 (bottom).
4.1.2. 3-N-Benzyloxymethyl-30-C-hydroxymethyl-50-O-
tritylthymidine (7). To
a solution of 6 (302 mg,
O
0.59 mmol) in DMF (1 mL) was added DBU (0.11 mL,
0.76 mmol) under N2 with ice-cooling. After stirring for
10 min, BOMCl (0.11 mL, 0.77 mmol) was added, and the
mixture was stirred for 5 h at room temperature. The reaction
mixture was partitioned with H2O, and the mixture was ex-
tracted with AcOEt. The combined organic layers were
washed with H2O and saturated NaCl solution, dried over
Na2SO4, and concentrated under reduced pressure. The re-
sultant residue was purified by silica gel column chromato-
graphy (AcOEt/n-hexane¼1:1) to give 7 (332 mg, 89%) as
a colorless solid. Mp 196–198 ꢀC. [a]D26 ꢁ8.4 (c 0.85,
CHCl3). IR (KBr) nmax 3425, 3028, 2927, 1708, 1661,
H3C
H3C
NH
O
O
HO
O
H
O
4'
OH
N
NH
O
N
25
HO
O
OH
4
OH
Scheme 6. Proposed mechanism for the formation of 25.
trioxabicyclo[5.3.0]decane structure and a 4,7-dioxabicy-
clo[4.3.0]nonane structure, respectively, using a common in-
termediate. It was shown by X-ray crystallography that these
novel nucleosides had a typical S-type sugar conformation,
satisfying the conformational requirements of the B-type
DNA duplex. These nucleosides are strong candidates for
ideal DNA structure mimics, which are required to investi-
gate the properties of oligonucleotides.
1
1465 cmꢁ1. H NMR (CDCl3) d 1.50 (3H, s), 1.95 (1H,
dd, J¼9, 13 Hz), 2.36 (1H, dd, J¼5, 13 Hz), 2.54 (1H, t,
J¼7 Hz), 3.08 (1H, s), 3.29 (1H, dd, J¼2, 11 Hz), 3.49
(1H, dd, J¼7, 11 Hz), 3.54–3.61 (2H, m), 4.10 (1H, dd,
J¼2, 5 Hz), 4.69 (2H, s), 5.48 (2H, s), 6.43 (1H, dd, J¼5,
9 Hz), 7.25–7.42 (20H, m), 7.51 (1H, s). 13C NMR
(CDCl3) d 12.5, 41.4, 62.6, 64.9, 70.6, 72.2, 81.0, 84.8,
86.0, 88.3, 110.6, 127.6, 127.7, 128.1, 128.3, 128.5, 134.2,
137.9, 142.6, 151.0, 163.4. MS (FAB): m/z 657 (M+Na).
Anal. Calcd for C38H38N2O7$1/5H2O: C, 72.45; H, 6.11;
N, 4.29. Found: C, 72.40; H, 6.18; N, 4.29.
4. Experimental
4.1. General
All melting points were measured on a Yanagimoto micro
melting point apparatus and were uncorrected. 1H and
4.1.3. 3-N-Benzyloxymethyl-30-C-methoxymethyloxy-
methyl-50-O-tritylthymidine (8). To a stirred solution of 7

8982
T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
(3.2 g, 5.04 mmol) in 1,4-dioxane (60 mL) was added n-
Bu2Sn(OMe)2 (1.3 mL, 5.54 mmol) under N2. The mixture
was refluxed for 5 h. After evaporation of the solvent, the
products were dissolved in CH2Cl2, and i-Pr2NEt (1.3 mL,
7.56 mmol) and MOMCl (0.6 mL, 7.56 mmol) were added
under ice-cooling. The whole was stirred for 2 h at the
room temperature. After addition of saturated NaHCO3 solu-
tion, the mixture was filtered with Celite, and the crude fil-
trate was extracted with AcOEt. The combined organic
layers were washed with H2O and saturated NaCl solution,
dried over Na2SO4, and concentrated under reduced pres-
sure. The resultant residue was purified by silica gel column
chromatography (CHCl3/AcOEt¼4:1) to give 8 (3.17 g,
93%) as a colorless solid. Mp 59–61 ꢀC. [a]D26 ꢁ9.4 (c
0.75, CHCl3). IR (KBr) nmax 3464, 3015, 2928, 1712,
usual work-up and purification by silica gel column chroma-
tography (AcOEt/n-hexane¼1:2) afforded 10 (739 mg,
90%) as a colorless solid. Mp 90–92 ꢀC. [a]D25 ꢁ5.4 (c
0.72, CHCl3). IR (KBr) nmax 3465, 3065, 3031, 2928,
1
1704, 1650, 1467 cmꢁ1. H NMR (CDCl3) d 1.94 (3H, d,
J¼1 Hz), 2.24 (1H, dd, J¼9, 13 Hz), 2.58 (1H, dd, J¼5,
13 Hz), 2.98 (1H, t, J¼6 Hz), 3.41 (3H, s), 3.84–4.01 (4H,
m), 4.24 (1H, unresolved dd appears as br t, J¼3 Hz), 4.60
(2H, s), 4.70 (4H, s), 5.49 (2H, s), 6.19 (1H, dd, J¼5,
9 Hz), 7.25–7.39 (10H, m), 7.60 (1H, d, J¼1 Hz). 13C
NMR (CDCl3) d 13.4, 38.0, 56.1, 62.1, 65.4, 66.8, 70.5,
72.2, 85.4, 85.6, 86.8, 97.0, 110.2, 127.2, 127.5, 127.6,
127.6, 128.2, 128.4, 135.6, 137.9, 151.0, 163.3. MS
(FAB): m/z 527 (MH+). Anal. Calcd for C28H34N2O8: C,
63.87; H, 6.51; N, 5.32. Found: C, 63.75; H, 6.49; N, 5.23.
1
1665, 1457 cmꢁ1. H NMR (CDCl3) d 1.23 (3H, s), 2.13
(1H, dd, J¼10, 13 Hz), 2.38 (1H, dd, J¼5, 13 Hz), 3.13
(1H, s), 3.23 (3H, s), 3.22–3.24 (1H, m), 3.42, 3.72 (2H,
AB, J¼10 Hz), 3.70–3.72 (1H, m), 4.12 (1H, s), 4.22, 4.38
(2H, AB, J¼7 Hz), 4.72 (2H, s), 5.50 (2H, s), 6.58 (1H,
dd, J¼5, 10 Hz), 7.24–7.40 (20H, m), 7.82 (1H, s). 13C
NMR (CDCl3) d 12.0, 42.3, 55.5, 62.3, 70.6, 71.0, 72.1,
80.2, 84.7, 86.4, 87.9, 96.8, 110.6, 127.6, 127.6, 127.7,
128.0, 128.3, 128.9, 134.7, 138.0, 142.6, 151.1, 163.5. MS
(FAB): m/z 701 (M+Na). Anal. Calcd for C40H42N2O8$1/
4H2O: C, 70.31; H, 6.27; N, 4.10. Found: C, 70.27; H,
6.26; N, 4.06.
4.1.6. 30-O-Benzyl-3-N-benzyloxymethyl-40-C-hydroxy-
methyl-30-C-(methoxymethyloxymethyl)thymidine (12).
A solution of 10 (3.4 g, 6.46 mmol) in CH2Cl2 (40 mL)
was added to a suspension of Dess–Martin periodinane
(3.6 g, 8.39 mmol) in CH2Cl2 (20 mL), and the mixture
was stirred for 1 h at room temperature. The mixed solvent
AcOEt/Et2O (1:1, v/v, 10 mL) and saturated Na2S2O3 solu-
tion were added to the reaction mixture, which was swirled
until the suspension became clear. The mixture was ex-
tracted with the same mixed solvent (1:1 AcOEt/Et2O, v/
v). The combined organic layers were washed with H2O
and saturated NaCl solution, dried over Na2SO4, and con-
centrated under reduced pressure to give the crude 11
(3.6 g). To a stirred solution of 11 (3.6 g) in THF (60 mL)
was added 37% aq formaldehyde (5.3 mL) and 1 M aq
NaOH (3.3 mL) at 15 ꢀC. The mixture was stirred for 2.5 h
at the same temperature. NaBH4 (978 mg, 26 mmol) was
added to the reaction mixture with ice-cooling. After stirring
for 2 h, the reaction mixture was neutralized with 0.5 M aq
KHSO4 and extracted with CHCl3. The usual work-up and
purification by silica gel column chromatography (AcOEt/
n-hexane¼2:1) afforded 12 (2.25 g, 63% from 10) as a color-
less oil. [a]2D3 +5.7 (c 1.32, CHCl3). IR (KBr) nmax 3436,
4.1.4. 30-O-Benzyl-3-N-benzyloxymethyl-30-C-methoxy-
methyloxymethyl-50-O-tritylthymidine (9). A solution of
8 (8.03 g, 11.8 mmol) in DMF (15 mL) was added dropwise
to a stirred solution of 60% NaH (520 mg, 13.0 mmol) in
DMF (10 mL) under N2 and ice-cooling. After stirring for
15 min, BnBr (1.55 mL, 13.0 mmol) and n-Bu4NI
(436 mg, 1.18 mmol) were added to the mixture. After stir-
ring for an additional 6 h at room temperature, the reaction
mixture was partitioned with H2O and extracted with
AcOEt. Work-up as previously described and purification
by silica gel column chromatography (AcOEt/n-hexane¼1:3
to 1:2) afforded 9 (7.60 g, 84%) as a colorless solid. Mp 152–
154 ꢀC. [a]2D6 ꢁ25.3 (c 0.88, CHCl3). IR (KBr) nmax 3061,
1
2929, 1706, 1661, 1464 cmꢁ1. H NMR (CDCl3) d 1.92
(3H, s), 2.30 (1H, dd, J¼9, 13 Hz), 2.50 (1H, dd, J¼5,
14 Hz), 2.86 (1H, br s), 3.27 (1H, br s), 3.38 (3H, s), 3.62
(1H, t, J¼8 Hz), 3.90–4.06 (5H, m), 4.55–4.70 (6H, m),
5.47 (2H, s), 6.08 (1H, dd, J¼5, 9 Hz), 7.24–7.37 (10H,
m), 7.62 (1H, s). 13C NMR (CDCl3) d 13.2, 36.3, 56.2,
63.3, 64.5, 65.0, 65.3, 70.5, 72.2, 86.1, 86.8, 90.6, 96.9,
110.2, 127.1, 127.6, 127.7, 127.8, 128.3, 128.6, 135.8,
137.6, 137.9, 151.1, 163.4. MS (FAB): m/z 557 (MH+).
Anal. Calcd for C29H36N2O9$3/4H2O: C, 61.10; H, 6.63;
N, 4.91. Found: C, 61.09; H, 6.35; N, 4.86.
1
3031, 2927, 2884, 1710, 1668, 1493, 1450 cmꢁ1. H NMR
(CDCl3) d 1.25 (3H, s), 2.08 (1H, dd, J¼10, 13 Hz), 2.69
(1H, dd, J¼5, 13 Hz), 3.20 (3H, s), 3.35 (1H, dd, J¼3,
11 Hz), 3.53, 3.93 (2H, AB, J¼11 Hz), 3.74 (1H, dd, J¼4,
11 Hz), 4.00, 4.26 (2H, AB, J¼7 Hz), 4.33 (1H, unresolved
dd appears as a br t, J¼3 Hz), 4.54, 4.59 (2H, AB, J¼11 Hz),
4.71 (2H, s), 5.49 (2H, s), 6.51 (1H, dd, J¼5, 9 Hz), 7.23–
7.40 (25H, m), 7.82 (1H, d, J¼1 Hz). 13C NMR (CDCl3)
d 12.0, 38.8, 55.6, 62.6, 65.3, 66.9, 70.6, 72.2, 84.6, 84.7,
85.3, 87.9, 96.4, 110.6, 127.3, 127.6, 127.6, 127.7, 128.0,
128.3, 128.4, 129.0, 134.7, 138.0, 138.0, 142.7, 151.1,
163.5. MS (FAB): m/z 791 (M+Na). Anal. Calcd for
C47H48N2O8: C, 73.42; H, 6.29; N, 3.64. Found: C, 73.17;
H, 6.37; N, 3.59.
4.1.7. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-40-C-hy-
droxymethyl-30-C-(methoxymethyloxymethyl)thymidine
(13) and 30-O-benzyl-40-C,3-N-dibenzyloxymethyl-30-C-
(methoxymethyloxymethyl)thymidine (14). A solution of
12 (509 mg, 0.91 mmol) in DMF (8 mL) was added drop-
wise to a stirred solution of 60% NaH (40 mg, 1.01 mmol)
in DMF (5 mL) under ice-cooling. After stirring for
15 min, BnBr (0.12 mL, 1.01 mmol) was added, and the
mixture was stirred for 2.5 h under ice-cooling. After addi-
tion of H2O, the mixture was extracted with AcOEt. The
usual work-up and purification by silica gel column chroma-
tography (AcOEt/n-hexane¼1:2) afforded 13 (291 mg,
4.1.5. 30-O-Benzyl-3-N-benzyloxymethyl-30-C-(methoxy-
methyloxymethyl)thymidine (10). To a stirred solution of
9 (1.20 g, 1.56 mmol) in MeOH/CH2Cl2 (3:2, v/v, 5 mL)
was added (+)-10-camphorsulfonic acid (72 mg,
0.31 mmol) at room temperature. After stirring for 9 h at
the same temperature, the reaction mixture was partitioned
with saturated NaHCO3 and extracted with AcOEt. The

T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
8983
49%) and 14 (122 mg, 21%) as colorless oils. Compound 13:
[a]2D1 +3.1 (c 0.98, CHCl3). IR (KBr) nmax 3479, 2951, 2887,
(1H, dd, J¼2, 11 Hz), 5.50 (2H, s), 5.55 (1H, s), 6.11 (1H,
dd, J¼5, 10 Hz), 7.13 (1H, s), 7.25–7.41 (13H, m), 7.46
(2H, m). 13C NMR (CDCl3) d 13.6, 37.0, 55.8, 66.3, 68.7,
68.9, 70.5, 71.6, 72.2, 79.8, 85.3, 85.8, 96.0, 101.3, 110.3,
126.1, 127.0, 127.4, 127.5, 127.6, 128.2, 128.3, 128.3,
129.0, 133.6, 137.0, 138.3, 150.6, 163.1. MS (FAB): m/z
645 (MH+). Anal. Calcd for C36H40N2O9$1/2H2O: C,
66.14; H, 6.25; N, 4.29. Found: C, 66.15; H, 6.26; N, 4.24.
1
1707, 1664, 1460 cmꢁ1. H NMR (CDCl3) d 1.64 (3H, d,
J¼1 Hz), 2.11 (1H, dd, J¼10, 13 Hz), 2.67 (1H, dd, J¼5,
13 Hz), 2.80 (1H, dd, J¼3, 10 Hz), 3.34 (3H, s), 3.51 (1H,
t, J¼10 Hz), 3.82 (1H, d, J¼11 Hz), 3.88 (1H, d,
J¼11 Hz), 3.99–4.07 (3H, m), 4.50–4.64 (6H, m), 4.67
(2H, s), 5,46 (2H, s), 6.38 (1H, dd, J¼5, 10 Hz), 7.23–7.36
(15H, m), 7.80 (1H, d, J¼1 Hz). 13C NMR (CDCl3)
d 13.0, 37.2, 56.3, 63.5, 64.3, 65.3, 70.4, 72.1, 73.1, 73.9,
84.1, 86.0, 90.2, 96.8, 110.0, 127.0,127.5, 127.6, 127.6,
127.8, 128.1, 128.2, 128.4, 128.6, 134.7, 136.6. MS
(FAB): m/z 647 (MH+). HRMS (FAB): calcd for
C36H43N2O9 (MH+): 647.2969; found: 647.2980. Com-
pound 14: [a]D21 +23.0 (c 0.85, CHCl3). IR (KBr) nmax
4.1.9. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-40-C-hy-
droxymethyl-30-C-(methoxymethyloxymethyl)thymidine
(13). To a solution of 12 (580 mg, 1.04 mmol) in CH2Cl2
(18 mL) were added Et3N (0.29 mL, 2.08 mmol) and 4,40-di-
methoxytrityl chloride (459 mg, 1.36 mmol) at room tem-
perature, and the mixture was stirred for 10 min. After
addition of saturated NaHCO3 solution, the reaction mixture
was extracted with AcOEt. The combined organic layers
were washed with H2O and saturated NaCl solution, dried
over Na2SO4, and concentrated under reduced pressure.
The yellow residue containing 16 was co-evaporated with
toluene. To a suspension of 60% sodium hydride (83 mg,
2.08 mmol) in DMF (3 mL) was added the residue in DMF
(7 mL) with ice-cooling. After stirring for 30 min, benzyl
bromide (0.15 mL, 1.25 mmol) and n-Bu4NI (192 mg,
0.52 mmol) were added and the mixture was stirred for 2 h
at room temperature. After addition of H2O, the mixture
was extracted with Et2O. The organic layer was washed
with H2O and saturated NaCl solution, dried over MgSO4,
and concentrated under reduced pressure. The yellow oily
residue was dissolved without further treatment in CH2Cl2/
MeOH (1:1, v/v, 14 mL), to which (+)-10-camphorsulfonic
acid (73 mg, 0.31 mmol) was added, and the mixture was
stirred for 10 min. After addition of saturated NaHCO3 solu-
tion, the mixture was extracted with AcOEt. The usual work-
up and purification by silica gel column chromatography
(AcOEt/n-hexane¼2:3) afforded 13 (559 mg, 83% over
three steps).
3453, 2935, 1706, 1660, 1461, 1095 cmꢁ1 1H NMR
.
(CDCl3) d 1.94 (3H, d, J¼1 Hz), 2.17 (1H, dd, J¼9,
14 Hz), 2.80 (1H, dd, J¼5, 14 Hz), 3.20 (1H, dd, J¼5,
7 Hz), 3.35 (3H, s), 3.81, 3.96 (2H, AB, J¼11 Hz), 3.84,
3.98 (2H, AB, J¼10 Hz), 3.87 (1H, dd, J¼7, 12 Hz), 4.04
(1H, dd, J¼5, 12 Hz), 4.48 (1H, d, J¼12 Hz), 4.59–4.63
(5H, m), 4.69 (2H, s), 5.49 (2H, s), 6.21 (1H, dd, J¼5,
9 Hz), 7.24–7.38 (15H, m), 7.82 (1H, d, J¼1 Hz). 13C
NMR (CDCl3) d 13.4, 36.9, 56.0, 64.9, 65.0, 66.1, 70.4,
72.2, 72.5, 73.8, 86.1, 86.2, 89.9, 96.8, 109.9, 126.9,
127.4, 127.5, 127.5, 127.6, 128.2, 128.3, 128.3, 135.3,
137.7, 137.8, 137.9. MS (FAB): m/z 647 (MH+). Anal. Calcd
for C36H42N2O9$3/4H2O: C, 65.46; H, 6.37; N, 4.30. Found:
C, 65.49; H, 6.64; N, 4.24.
4.1.8. 30-O-Benzyl-3-N-benzyloxymethyl-40-CH2O,50-O-
benzylidene-30-C-(methoxymethyloxymethyl)thymidine
(15). To a solution of 12 (53 mg, 0.095 mmol) in CH2Cl2
(1 mL) were added benzaldehyde dimethyl acetal (68 mL,
0.48 mmol) and (+)-10-camphorsulfonic acid (4 mg,
0.019 mmol) at room temperature, and the mixture was
stirred for 2 h at the same temperature. After addition of sat-
urated NaHCO3 solution, the mixture was extracted with
AcOEt. The usual work-up and purification by silica gel col-
umn chromatography (AcOEt/n-hexane¼2:3) afforded 15
(48 mg, 74% for R-isomer; 16 mg, 25% for S-isomer) as col-
orless solids. R-Isomer: Mp 54–56 ꢀC. [a]D21 +65.8 (c 1.13,
CHCl3). IR (KBr) nmax 1044, 1078, 1271, 1458, 1660,
4.1.10. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C,40-
C-(2,4-dioxapentamethylene)thymidine (17). To a solution
of 13 (229 mg, 0.35 mmol) in 1,2-dichloroethane (5 mL)
were added paraformaldehyde (229 mg) and p-toluenesul-
fonic acid monohydrate (7 mg, 0.037 mmol), and the mix-
ture was refluxed for 4.5 h. After addition of saturated
NaHCO3 solution, the mixture was extracted with CHCl3.
The usual work-up and purification by silica gel column
chromatography (AcOEt/n-hexane¼1:3 to 1:2) afforded 17
(103 mg, 47%) as a colorless oil. [a]2D6 +0.82 (c 0.50,
CHCl3). IR (KBr) nmax 3064, 3031, 2954, 1957, 1704,
1
1706, 2933 cmꢁ1. H NMR (CDCl3) d 1.88 (1H, dd, J¼8,
15 Hz), 1.92 (3H, s), 3.17 (1H, dd, J¼6, 15 Hz), 3.41 (3H,
s), 3.49, 3.92 (2H, AB, J¼12 Hz), 4.00 (1H, dd, J¼3,
12 Hz), 4.26 (1H, d, J¼12 Hz), 4.33 (1H, d, J¼13 Hz),
4.50 (1H, dd, J¼3, 13 Hz), 4.59 (2H, s), 4.63, 4.67 (2H,
AB, J¼7 Hz), 4.71 (2H, s), 5.49 (2H, s), 5.58 (1H, s), 6.05
(1H, br t, J¼7 Hz), 7.21–7.40 (13H, m), 7.54 (2H, dd,
J¼1, 7 Hz), 7.83 (1H, s). 13C NMR (CDCl3) d 13.5, 38.6,
56.2, 64.6, 65.4, 70.4, 70.9, 72.2, 84.1, 85.1, 86.7, 96.9,
101.2, 109.3, 125.9, 126.7, 127.0, 127.5, 127.6, 127.6,
128.2, 128.2, 128.4, 128.5, 129.0, 134.2, 137.5, 137.5,
137.9, 150.6, 163.4. MS (FAB): m/z 645 (MH+). Anal. Calcd
for C36H40N2O9$1/2H2O: C, 66.14; H, 6.25; N, 4.29. Found:
C, 65.91; H, 6.20; N, 4.25. S-Isomer: Mp 43–45 ꢀC. [a]D21
+24.5 (c 0.76, CHCl3). IR (KBr) nmax 1038, 1098, 1459,
1660 cmꢁ1
.
1H NMR (CDCl3) d 1.71 (3H, d, J¼1 Hz),
2.38 (1H, dd, J¼9, 14 Hz), 2.87 (1H, dd, J¼5, 13 Hz),
3.67 (1H, d, J¼11 Hz), 3.74 (1H, d, J¼13 Hz), 3.96 (1H,
d, J¼11 Hz), 4.26 (1H, d, J¼11 Hz), 4.33 (1H, d,
J¼11 Hz), 4.37 (1H, d, J¼13 Hz), 4.56–4.64 (4H, m), 4.67
(2H, s), 4.90, 5.33 (2H, AB, J¼8 Hz), 5.45 (2H, s), 6.29
(1H, dd, J¼5, 9 Hz), 7.23–7.40 (15H, m), 7.82 (1H, d,
J¼1 Hz). 13C NMR (CDCl3) d 13.0, 37.2, 62.9, 63.7, 66.2,
70.4, 72.1, 73.3, 74.0, 77.2, 87.2, 88.0, 90.9, 93.1, 109.6,
127.4, 127.6, 127. 7, 127.7, 128.0, 128.1, 128.2, 128.6,
128.7, 134.8, 136.7, 137.0, 137.9, 150.9, 163.5. MS
(FAB): m/z 615 (MH+). Anal. Calcd for C35H38N2O8$3/
4H2O: C, 66.92; H, 6.34; N, 4.46. Found: C, 66.99; H,
6.24; N, 4.41.
1
1664, 1706, 2881, 2948 cmꢁ1. H NMR (CDCl3) d 1.97
(3H, s), 2.28 (1H, dd, J¼10, 14 Hz), 3.04 (1H, dd, J¼5,
14 Hz), 3.34 (3H, s), 3.72, 3.91 (2H, AB, J¼12 Hz), 4.13,
4.15 (2H, AB, J¼11 Hz), 4.38 (1H, dd, J¼2, 12 Hz), 4.63
(2H, s), 4.70 (2H, s), 4.78, 4.87 (2H, AB, J¼11 Hz), 4.83

8984
T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
4.1.11. 30-C,40-C-(2,4-Dioxapentamethylene)thymidine
(3). To a solution of 17 (26 mg, 0.053 mmol) in EtOH
(1.5 mL) were added ammonium formate (33 mg,
0.53 mmol) and 20% Pd(OH)2–C (26 mg), and the mixture
was refluxed for 5.5 h. After filtration of the mixture, the fil-
trate was concentrated and purified by silica gel preparative
TLC (CHCl3/MeOH¼10:1) to give 3 (10 mg, 60%) as a col-
orless solid. Mp 244–247 ꢀC. [a]D21 +75.8 (c 0.25, CH3OH).
IR (KBr) nmax 3348, 3167, 3059, 2924, 2889, 2505, 2279,
(1H, dd, J¼6, 7 Hz), 2.41 (3H, s), 2.55 (1H, dd, J¼5,
13 Hz), 3.81, 3.88 (2H, AB, J¼11 Hz), 3.80–3.88 (1H, m),
4.02 (1H, dd, J¼6, 13 Hz), 4.31, 4.40 (2H, AB, J¼11 Hz),
4.52 (2H, s), 4.55, 4.65 (2H, AB, J¼11 Hz), 4.66 (2H, s),
5.44 (2H, s), 6.15 (1H, dd, J¼5, 10 Hz), 7.20–7.38 (17H,
m), 7.41 (1H, d, J¼1 Hz), 7.71–7.74 (2H, m). 13C NMR
(CDCl3) d 13.0, 21.8, 36.3, 60.5, 64.5, 70.4, 70.7, 70.9, 72.2,
74.2, 84.7, 88.0, 88.1, 110.1, 127.0, 127.0, 127.6, 127.6,
127.6, 127.6, 127.8, 127.9, 127.9, 128.2, 128.2, 128.3,
128.5, 128.5, 128.7, 128.7, 129.7, 129.7, 132.3, 134.1,
136.4, 137.2, 137.8, 144.8, 150.7, 163.2. MS (FAB): m/z
757 (MH+). HRMS (FAB): calcd for C41H45N2O10S
(MH+): 757.2795; found: 757.2741.
1
1695, 1470 cmꢁ1. H NMR (CD3OD) d 1.89 (3H, d, J¼
1 Hz), 2.36 (1H, dd, J¼6, 13 Hz), 2.48 (1H, dd, J¼9,
12 Hz), 3.73, 4.15 (2H, AB, J¼11 Hz), 3.81 (1H, d, J¼
12 Hz), 3.91 (1H, d, J¼13 Hz), 4.03 (2H, unresolved dd ap-
pears t, J¼12 Hz), 4.85, 5.55 (2H, AB, J¼8 Hz), 6.32 (1H,
dd, J¼6, 9 Hz), 8.15 (1H, d, J¼1 Hz). 13C NMR (CD3OD)
d 12.6, 44.1, 63.7, 66.2, 70.9, 83.6, 88.5, 92.2, 94.1, 111.1,
138.7, 152.4, 166.6. MS (FAB): m/z 315 (MH+). HRMS
(FAB): calcd for C13H19N2O7 (MH+): 315.1192; found:
315.1216. Anal. Calcd for C13H18N2O7$3/2H2O: C, 45.74;
H, 6.20; N, 8.20. Found: C, 46.08; H, 5.82; N, 8.28.
4.1.14. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C-(2-
methoxyethenyl)-40-C-(p-toluenesulfonyloxymethyl)thy-
midine (21 E/Z). To a suspension of Dess–Martin periodi-
nane (110 mg, 0.26 mmol) in CH2Cl2 (1.5 mL) was added
a solution of compound 19 (151 mg, 0.20 mmol) in
CH2Cl2 (1 mL), and the mixture was stirred for 1 h at
room temperature. After addition of a mixture of saturated
Na2S2O3 and saturated NaHCO3 solutions (1:2, v/v), the re-
action mixture was stirred for a further 20 min and then ex-
tracted with Et2O. The organic layer was washed with
saturated NaHCO3 solution, H2O and saturated NaCl solu-
tion, dried over MgSO4, and concentrated under reduced
pressure to give crude compound 20. To a suspension of
(methoxymethyl)triphenyl phosphonium chloride (171 mg,
0.50 mmol) in THF (2.5 mL) was added LiHMDS (1.07 M
in n-hexane, 0.411 mL, 0.44 mmol) with ice-cooling, and
the mixture was stirred for 20 min at room temperature. To
this mixture was added a solution of 20 in THF (1.5 mL)
at ꢁ78 ꢀC, and the mixture was gradually warmed to room
temperature over 2 h. After addition of H2O, the reaction
mixture was extracted with AcOEt. The usual work-up and
purification by silica gel column chromatography (AcOEt/
n-hexane¼2:5) afforded 21 as a colorless foam (103 mg,
66% in two steps, E:Z¼7:4). IR (KBr) nmax 1092, 1178,
4.1.12. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C-
methoxymethyloxymethyl-40-C-(p-toluenesulfonyloxy-
methyl)thymidine (18). To a solution of 13 (1.19 g,
1.84 mmol) in CH2Cl2 (18 mL) were added Et3N (1.03 mL,
7.38 mmol), p-toluenesulfonyl chloride (527 mg, 2.77 mmol),
and 4-dimethylaminopyridine (113 mg, 0.92 mmol) at
room temperature, and the mixture was stirred for 13 h. After
addition of saturated NaHCO3 solution, the reaction mixture
was extracted with AcOEt. The usual work-up and purifica-
tion by silica gel column chromatography (AcOEt/n-
hexane¼1:2) afforded 18 as a colorless foam (1.49 g, quant).
[a]2D3 ꢁ9.3 (c 1.00, CHCl3). IR (KBr) nmax 1098, 1177, 1268,
1362, 1460, 1658, 1710, 2890 cmꢁ1 1H NMR (CDCl3)
.
d 1.62 (3H, d, J¼2 Hz), 2.06 (1H, dd, J¼10, 13 Hz), 2.40
(3H, s), 2.55 (1H, dd, J¼5, 13 Hz), 3.31 (3H, s), 3.77, 3.95
(2H, AB, J¼11 Hz), 3.84, 3.99 (2H, AB, J¼11 Hz), 4.31,
4.43 (2H, AB, J¼11 Hz), 4.45, 4.51 (2H, AB, J¼6 Hz), 4.49
(2H, s), 4.54, 4.61 (2H, AB, J¼11 Hz), 4.65 (2H, s), 5.44 (2H,
s), 6.22 (1H, dd, J¼5, 10 Hz), 7.19–7.38 (17H, m), 7.66 (1H,
d, J¼2 Hz), 7.71–7.74 (2H, m). 13C NMR (CDCl3) d 13.0,
21.7, 36.9, 56.0, 64.4, 65.8, 70.4, 71.0, 71.8, 72.1, 73.9,
84.7, 86.7, 88.2, 96.8, 109.9, 126.9, 126.9, 127.5, 127.5,
127.6, 127.6, 127.7, 127.7, 128.0, 128.0, 128.1, 128.1,
128.2, 128.2, 128.6, 128.6, 129.6, 129.6, 132.1, 134.6,
136.5, 137.4, 137.4, 137.7, 144.7, 150.8, 163.2. MS (FAB):
m/z 801 (MH+). HRMS (FAB): calcd for C43H49N2O11S
(MH+): 801.3057; found: 801.3093.
1
1356, 1373, 1469, 1669, 1707, 2928, 3069 cmꢁ1. H NMR
(CDCl3) d 1.52 (12/11H, d, J¼1 Hz), 1.64 (21/11H, d,
J¼1 Hz), 2.31 (7/11H, dd, J¼10, 13 Hz), 2.37 (12/11H, s),
2.39 (21/11H, s), 2.54 (4/11H, dd, J¼10, 14 Hz), 2.64 (7/
11H, dd, J¼5, 13 Hz), 2.89 (4/11H, dd, J¼5, 14 Hz), 3.52
(21/11H, s), 3.61, 3.77 (14/11H, AB, J¼10 Hz), 3.63 (12/
11H, s), 3.69, 3.84 (8/11H, AB, J¼11 Hz), 4.16 (4/11H, d,
J¼10 Hz), 4.18 (7/11H, d, J¼10 Hz), 4.33–4.54 (59/11H,
m), 4.65 (2H, s), 4.80 (7/11H, d, J¼13 Hz), 5.44 (2H, s),
6.18 (4/11H, d, J¼7 Hz), 6.25 (1H, dd, J¼5, 10 Hz), 6.54
(7/11H, d, J¼13 Hz), 7.18–7.37 (17H, m), 7.66–7.73 (3H,
m). 13C NMR (CDCl3) d 12.8, 13.0, 21.7, 21.7, 37.5, 39.9,
50.9, 56.4, 60.6, 64.3, 64.7, 69.4, 69.8, 70.4, 71.8, 72.1,
72.1, 73.8, 74.1, 84.8, 84.9, 85.5, 86.1, 88.2, 98.7, 100.1,
110.0, 116.0, 126.9, 127.0, 127.1, 127.3, 127.3, 127.5, 127.5,
127.6, 127.7, 127.9, 128.1, 128.1, 128.2, 128.3, 128.4, 128.6,
129.7, 129.7, 132.1, 134.6, 134.9, 136.8, 137.3, 137.8, 137.8,
138.0, 138.4, 144.8, 144.9, 150.7, 150.9, 150.9, 151.5, 163.3,
163.3. MS (FAB): m/z 783 (MH+). HRMS (FAB): calcd for
C43H47N2O10S (MH+): 783.2951; found: 783.2955.
4.1.13. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C-
hydroxymethyl-40-C-(p-toluenesulfonyloxymethyl)-
thymidine (19). To a solution of 18 (1.26 g, 1.57 mmol) in
CH2Cl2 (16 mL) was added TMSBr (2.49 mL, 18.9 mmol)
at ꢁ30 ꢀC, and the mixture was gradually warmed to 0 ꢀC
over 2 h. The mixture was then stirred for 22 h at 0 ꢀC. After
addition of saturated NaHCO3 solution, the reaction mixture
was extracted with AcOEt. The usual work-up and purifica-
tion by silica gel column chromatography (AcOEt/
n-hexane¼2:3) afforded 19 as a colorless solid (1.15 g,
97%). Mp 60–63 ꢀC. [a]D23 +2.06 (c 0.96, CHCl3). IR
(KBr) nmax 1096, 1176, 1266, 1362, 1455, 1658, 1706,
4.1.15. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C-(2-
hydroxyethyl)-40-C-(p-toluenesulfonyloxymethyl)thymi-
dine (23). To a solution of 21 (528 mg, 0.67 mmol) in THF/
H2O (4:1, v/v, 11 mL) was added mercury(II) acetate
2929, 3428, 3745, 3857, 3921 cmꢁ1
.
1H NMR (CDCl3)
d 1.67 (3H, d, J¼1 Hz), 1.95 (1H, dd, J¼10, 13 Hz), 2.20

T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
8985
(860 mg, 2.70 mmol) at room temperature, and the mixture
was stirred for 17 h. Next, n-Bu4NI (2.50 g, 6.74 mmol)
was added and the reaction mixture was stirred for a further
2 h. After addition of saturated NH4Cl solution, the reaction
mixture was extracted with AcOEt. The organic layer was
washed with H2O and saturated NaCl solution, dried over
Na2SO4, and concentrated under reduced pressure to give
22. To a solution of 22 in THF/H2O (4:1, v/v, 11 mL) was
added NaBH4 (306 mg, 8.09 mmol) with ice-cooling, and
the mixture was stirred for 15 min under the same condi-
tions. After addition of saturated NH4Cl solution, the reac-
tion mixture was extracted with AcOEt. The usual work-
up and purification by silica gel column chromatography
(AcOEt/n-hexane¼2:3) afforded 23 as a colorless foam
(325 mg, 63% in two steps). [a]2D2 ꢁ9.92 (c 0.99, CHCl3).
IR (KBr) nmax 1094, 1177, 1278, 1362, 1456, 1653, 1706,
MeOH¼20:1) to give 25 as a colorless solid (49 mg,
82%). Mp 76–78 ꢀC. [a]2D2 +73.3 (c 0.70, MeOH). IR
(KBr) nmax 1046, 1116, 1264, 1319, 1382, 1474, 1690,
1
3328 cmꢁ1. H NMR (CD3OD) d 1.44 (1H, m), 1.71 (1H,
dd, J¼2, 14 Hz), 1.95 (3H, d, J¼1 Hz), 2.23 (1H, dt, J¼6,
13 Hz), 2.61 (1H, dd, J¼11, 14 Hz), 3.46, 3.94 (2H, AB,
J¼12 Hz), 3.66, 4.10 (2H, AB, J¼13 Hz), 3.75 (1H, ddd,
J¼6, 12, 13 Hz), 3.91 (1H, m), 6.11 (1H, dd, J¼2, 11 Hz),
7.66 (1H, d, J¼1 Hz). 13C NMR (CD3OD) d 12.6, 37.2,
38.1, 66.3, 69.3, 70.3, 70.7, 72.5, 80.9, 112.0, 138.2,
152.2, 166.4. MS (FAB): m/z 299 (MH+). HRMS (FAB):
calcd for C13H19N2O6 (MH+): 299.1243; found: 299.1244.
4.1.18. 30-C,40-C-Ethoxymethylenethymidine (4). To a so-
lution of 24 (49 mg, 0.082 mmol) in EtOH (2.7 mL) were
added 20% Pd(OH)2–C (100 mg) and ammonium formate
(1.03 g, 16.4 mmol) at room temperature. The mixture was
refluxed for 6 h. After filtration of the mixture, the filtrate
was concentrated and purified by silica gel column chroma-
tography (CHCl3/MeOH¼15:1) to give 4 as a colorless solid
(10 mg, 39%). Mp 215–217 ꢀC. [a]2D5 +26.6 (c 0.22, MeOH).
IR (KBr) nmax 1037, 1102, 1267, 1479, 1686, 2540, 2961,
3076, 3327 cmꢁ1. 1H NMR (CD3OD) d 1.75 (1H, dd, J¼3,
13 Hz), 1.86–1.97 (1H, m), 1.89 (3H, d, J¼1 Hz), 2.26
(1H, dd, J¼8, 13 Hz), 2.56 (1H, dd, J¼6, 13 Hz), 3.46
(1H, dd, J¼1, 11 Hz), 3.75 (1H, dd, J¼5, 11 Hz), 3.82
(1H, d, J¼10 Hz), 3.92–4.01 (1H, m), 4.00 (1H, dd, J¼1,
10 Hz), 4.17 (1H, d, J¼11 Hz), 6.18 (1H, dd, J¼6, 8 Hz),
8.17 (1H, d, J¼1 Hz). 13C NMR (CD3OD) d 12.6, 34.0,
44.3, 62.9, 63.2, 65.2, 76.6, 86.2, 88.8, 110.4, 138.8,
152.4, 166.8. MS (FAB): m/z 299 (MH+). HRMS (FAB):
calcd for C13H19N2O6 (MH+): 299.1243; Found: 299.1234.
1
2928, 3481, 3920 cmꢁ1. H NMR (CDCl3) d 1.61 (3H, s),
2.10–2.33 (3H, m), 2.40 (3H, s), 2.75 (1H, dd, J¼5,
14 Hz), 3.69–3.85 (2H, m), 3.83, 3.90 (2H, AB, J¼11 Hz),
4.20, 4.40 (2H, AB, J¼10 Hz), 4.40, 4.51 (2H, AB,
J¼11 Hz), 4.56, 4.61 (2H, AB, J¼12 Hz), 4.65 (2H, s),
5.43 (2H, s), 6.13 (1H, dd, J¼5, 10 Hz), 7.17–7.40 (17H,
m), 7.60 (1H, s), 7.69–7.73 (2H, m). 13C NMR (CDCl3)
d 12.9, 21.7, 33.5, 40.2, 57.9, 64.0, 70.4, 70.5, 71.4, 72.1,
73.9, 83.9, 86.6, 88.5, 109.9, 126.8, 126.8, 127.5, 127.5,
127.5, 127.6, 127.6, 127.9, 127.9, 128.1, 128.1, 128.2,
128.4, 128.4, 128.6, 128.6, 129.7, 129.7, 132.0, 132.0,
134.5, 136.6, 137.0, 137.7, 144.9, 150.8, 163.2. MS
(FAB): m/z 771 (MH+). HRMS (FAB): calcd for
C42H47N2O10S (MH+): 771.2951; found: 771.2944.
4.1.16. 30-O,50-O-Dibenzyl-3-N-benzyloxymethyl-30-C,40-
C-ethoxymethylenethymidine (24). To a solution of 23
(33 mg, 0.043 mmol) in THF (0.8 mL) was added NaHMDS
(1.1 M in THF, 0.086 mL, 0.094 mmol) at room tempera-
ture, and the mixture was refluxed for 3.5 h. After addition
of saturated NaHCO3 solution, the reaction mixture was ex-
tracted with AcOEt. The usual work-up and purification by
silica gel column chromatography (AcOEt/n-hexane¼1:2)
afforded 24 as a colorless foam (24 mg, 92%). [a]2D1 ꢁ17.3
(c 0.89, CHCl3). IR (KBr) nmax 1025, 1095, 1165, 1216,
Acknowledgements
We are very grateful for financial support by a Grant-in-Aid
for Scientific Research from the Japan Society for Promotion
of Science.
1
1277, 1367, 1457, 1657, 1704, 2877, 2955, 3031 cmꢁ1. H
References and notes
NMR (CDCl3) d 1.76 (3H, d, J¼1 Hz), 1.79–1.86 (1H, m),
2.12 (1H, dd, J¼8, 13 Hz), 2.14–2.20 (1H, m), 3.18 (1H,
dd, J¼5, 14 Hz), 3.61, 3.78 (2H, AB, J¼10 Hz), 3.78, 4.02
(2H, AB, J¼10 Hz), 3.84, 4.29 (2H, AB, J¼10 Hz), 4.43,
4.54 (2H, AB, J¼11 Hz), 4.56 (2H, s), 4.69 (2H, s), 5.45,
5.49 (2H, AB, J¼10 Hz), 6.03 (1H, dd, J¼6, 8 Hz), 7.20–
7.38 (15H, m), 7.88 (1H, d, J¼1 Hz). 13C NMR (CDCl3)
d 13.2, 28.3, 38.1, 61.5, 63.3, 64.9, 70.3, 72.1, 72.1, 73.6,
81.0, 85.2, 87.9, 108.6, 127.1, 127.1, 127.2, 127.2, 127.5,
127.5, 127.5, 127.6, 127.8, 128.1, 128.1, 128.4, 128.4,
128.4, 128.4, 134.9, 137.1, 137.4, 137.9, 150.7, 163.4. MS
(FAB): m/z 599 (MH+). HRMS (FAB): calcd for
C35H39N2O7 (MH+): 599.2757; found: 599.2782.
1. (a) Obika, S.; Nanbu, D.; Hari, Y.; Morio, K.; In, Y.; Ishida, T.;
Imanishi, T. Tetrahedron Lett. 1997, 38, 8735–8738; (b)
Imanishi, T.; Obika, S. J. Synth. Org. Chem., Jpn. 1999, 57,
969–980; (c) Imanishi, T.; Obika, S. Chem. Commun. 2002,
1653–1659; (d) Freier, S. M.; Altmann, K.-H. Nucleic Acids
Res. 1997, 25, 4429–4443; (e) Wang, G.; Gunic, E.; Girardet,
J.-L.; Stoisavljevic, V. Bioorg. Med. Chem. Lett. 1999, 9,
1147–1150; (f) Morita, K.; Hasegawa, C.; Kaneko, M.;
Tsutsumi, S.; Sone, J.; Ishikawa, T.; Imanishi, T.; Koizumi,
M. Bioorg. Med. Chem. Lett. 2002, 12, 73–76.
2. The 20,40-BNA is also called ‘LNA’ by Wengel, J. et al. See: (a)
Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem.
Commun. 1998, 455–456; (b) Vester, B.; Wengel, J.
Biochemistry 2004, 43, 13233–13241.
4.1.17. 1-(20-Deoxy-30-C,40-C-ethoxymethylene-b-D-ribo-
pyranosyl)thymine (25). To a solution of 24 (120 mg,
0.20 mmol) in AcOEt (2.0 mL) were added 20%
Pd(OH)2–C (120 mg) and cyclohexene (1.5 mL, 15.0 mmol)
at room temperature. The mixture was refluxed for 14 h.
After filtration of the mixture, the filtrate was concentrated
and purified by silica gel column chromatography (CHCl3/
€
3. (a) Tarkoy, M.; Bolli, M.; Schweizer, B.; Leumann, C. Helv.
Chim. Acta 1993, 76, 481–510; (b) Tarkoy, M.; Bolli, M.;
€
Leumann, C. Helv. Chim. Acta 1994, 77, 716–744; (c) Bolli,
M.; Trafelet, H. U.; Leumann, C. Nucleic Acids Res. 1996,
24, 4660–4667; (d) Steffens, R.; Leumann, C. J. Am. Chem.
Soc. 1997, 119, 11548–11549; (e) Steffens, R.; Leumann, C.

8986
T. Osaki et al. / Tetrahedron 63 (2007) 8977–8986
Helv. Chim. Acta 1997, 80, 2426–2439; (f) Steffens, R.;
8. Martinelli, M. J.; Vaidyanathan, R.; Khau, V. V. Tetrahedron
Lett. 2000, 41, 3773–3776.
9. (a) See Ref. 1a; (b) Hari, Y.; Obika, S.; Sakaki, M.; Morio,
K.; Yamagata, Y.; Imanishi, T. Tetrahedron 2002, 58, 3051–
3063.
10. (a) Hari, Y.; Osaki, T.; Eguchi, K.; Obika, S.; Imanishi, T.
Nucleic Acids Res. Suppl. 2002, 2, 147–148; (b) Hari, Y.;
Obika, S.; Ohnishi, R.; Eguchi, K.; Osaki, T.; Ohishi, H.;
Imanishi, T. Bioorg. Med. Chem. 2006, 14, 1029–1038.
11. Compound 17 was not obtained on treatment of 13 with p-tol-
uenesulfonic acid in the absence of paraformaldehyde.6 See
also: Nouguier, R.; Gras, J.-L.; Mchich, M. Tetrahedron
1988, 44, 2943–2950.
12. Sawada, D.; Kanai, M.; Shibasaki, M. J. Am. Chem. Soc. 2000,
122, 10521–10532.
13. Jennings, B. M.; Liu, M. T. H. J. Am. Chem. Soc. 1976, 98,
6417–6418.
14. Crystallographic data (excluding structure factors) for the
structures in this paper have been deposited with the
Cambridge Crystallographic Data Center as supplementary
publication numbers CCDC637463 and CCDC637464 for 4
and 25, respectively. Copies of the data can be obtained, free
of charge, on application to CCDC, 12 Union Road,
Cambridge, CB2 1EZ, UK [fax: +44 (0) 1223 336033 or
e-mail: deposit@ccdc.cam.ac.uk].
Leumann, C. J. Am. Chem. Soc. 1999, 121, 3249–3255; (g)
Nielsen, P.; Pfundheller, H. M.; Olsen, C. E.; Wengel, J.
J. Chem. Soc., Perkin Trans. 1 1997, 3423–3433; (h) Ravn,
J.; Thorup, N.; Nielsen, P. J. Chem. Soc., Perkin Trans. 1
2001, 1855–1861; (i) Vijgen, S.; Nauwelaerts, K.; Wang, J.;
Aerschot, A. V.; Lagoja, I.; Herdewijn, P. J. Org. Chem.
2005, 70, 4591–4597.
4. Leumann’s group has synthesized the novel nucleosides,
namely bicyclo-DNA and tricyclo-DNA. Oligonucleotides
containing the nucleosides showed slightly enhanced duplex
stability in limited sequences. See Ref. 3c,d.
5. (a) Obika, S.; Sekiguchi, M.; Osaki, T.; Shibata, N.; Masaki,
M.; Hari, Y.; Imanishi, T. Tetrahedron Lett. 2002, 43, 4365–
4368. P. Nielsen’s group also reported the synthesis of 1
independently, and reference to Chem. Commun. 2002, 1888–
1889; (b) Sekiguchi, M.; Osaki, T.; Harada, Y.; Obika, S.;
Imanishi, T. Nucleic Acids Res. Suppl. 2003, 3, 111–112; (c)
Sekiguchi, M.; Obika, S.; Harada, Y.; Osaki, T.; Somjing, R.;
Mitsuoka, Y.; Shibata, Y.; Masaki, M.; Imanishi, T. J. Org.
Chem. 2006, 71, 1306–1316.
6. Preliminary results for the synthesis of 3 have been reported:
Obika, S.; Osaki, T.; Sekiguchi, M.; Somjing, R.; Harada, Y.;
Imanishi, T. Tetrahedron Lett. 2004, 45, 4801–4804.
7. (a) Froehlich, M. L.; Swartling, D. J.; Lind, R. E.; Mott, A. W.;
Bergstrom, D. E. Nucleosides Nucleotides 1989, 8, 1529–1535;
(b) Sharma, M.; Bobek, M. Tetrahedron Lett. 1990, 31, 5839–
5842.
15. It has been reported that a furanosyl to pyranosyl ring-isomer-
ization was observed under basic conditions. See: Ueda, T.;
Shuto, S. Nucleosides Nucleotides 1984, 3, 295–302.