Synthesis of a bicyclic double-headed nucleoside

Article abstract of DOI:10.1016/j.tet.2013.12.013

An attempt of preparing a carbocyclic LNA-analogue using different RCM-methods failed. However, a compound with a hemiacetal linker between the C2′ and the C4′-positions was isolated and found to be a suitable substrate for making a conformationally restricted double-headed nucleoside. This contains two uracil nucleobases organized on a bicyclic skeleton and is locked in an N-type conformation.

Full text of DOI:10.1016/j.tet.2013.12.013

Tetrahedron 70 (2014) 583e589
Contents lists available at ScienceDirect
Tetrahedron
journal homepage: www.elsevier.com/locate/tet
Synthesis of a bicyclic double-headed nucleoside
y
*
Surender Kumar , Signe Inglev Steffansen, Nanna Albæk, Poul Nielsen
Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
a r t i c l e i n f o
a b s t r a c t
Article history:
An attempt of preparing a carbocyclic LNA-analogue using different RCM-methods failed. However,
a compound with a hemiacetal linker between the C20 and the C40-positions was isolated and found to be
a suitable substrate for making a conformationally restricted double-headed nucleoside. This contains
two uracil nucleobases organized on a bicyclic skeleton and is locked in an N-type conformation.
Ó 2013 Elsevier Ltd. All rights reserved.
Received 26 September 2013
Received in revised form 21 November 2013
Accepted 2 December 2013
Available online 7 December 2013
Keywords:
Ring-closing metathesis
Bicyclic nucleosides
Double-headed nucleosides
€
Vorbruggen coupling
1. Introduction
carbocyclic LNA-analogues based on radical cyclizations.4 Hence,
a series of analogues of both 3 and of the carba-LNA monomer 4
Chemically modified nucleotide analogues are essential for the
design of therapeutically active nucleic acids.1e3 A large number of
modifications have been prepared leading to oligonucleotides that
are both physiologically stable and recognize complementary DNA
and RNA with high affinity and selectivity.1e4 Bicyclic nucleoside
monomers, which covalently bridge the C20 with the C40-position
(Fig. 1), have gained particular interest as these are locked in the
C30-endo conformation and preorganised for forming thermally
very strong duplexes.4e6 As the first and prime example, the
monomer 1 is the building block in LNA (locked nucleic acid),7e10
which is now a well-established nucleic acid analogue for numer-
ous applications.11 A number of close analogues of LNA have been
investigated,4e6,12 for instance the 20-amino-LNA, 2, which has
been used to introduce various groups into nucleic acids via the
amino-group leading to interesting components in DNA nano-
technology.13e15 Recently, carbocyclic analogues of LNA have
gained some interest.4,16e21 As the first of these, we introduced the
monomer 3 (B¼U),16 and later some analogues of this,17 which all
contain an all-carbon C20eC40 linker, which is one atom longer than
the oxymethylene linker in LNA (1). The synthesis of 3 was based on
ring-closing metathesis (RCM)22e24 as the key step and was per-
formed in 13 steps and 7% overall yield from uridine.16 Chatto-
padhyaya and co-workers have later developed a general method to
with various substituents at the C20eC40 linker have been ob-
tained.4,18,19 The unsubstituted nucleoside 4 (B¼T) was obtained in
20 steps starting from D
-allose.19 Herein, we present our attempts of
making 4 (B¼U) from a shorter route based on the RCM-strategy.
This was absolutely unsuccessful but led to the development of
a hemiacetal bicyclic nucleoside structure 5 (in a protected form),
that is, a potentially very useful precursor for other analogues, for
instance for placing various entities in the DNA duplex in a similar
* Corresponding author. Tel.: þ45 6550 2565; fax: þ45 6615 8780; e-mail ad-
dress: pouln@sdu.dk (P. Nielsen).
y
Present address: Department of Chemistry, University College, Kurukshetra
University, 136119, India.
Fig. 1. Bicyclic and double-headed nucleosides. B¼any nucleobase, U¼uracil-1-yl.
0040-4020/$ e see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tet.2013.12.013

584
S. Kumar et al. / Tetrahedron 70 (2014) 583e589
way as from amino-LNA. Analogues made from
5
will be
steps.16 Benzoylation and subsequent silylation gave 10, deben-
zoylation afforded 11, and an oxidation/Wittig sequence gave the
nucleoside 12.16 With its two terminal alkenes this constituted
a perfect substrate for an RCM-reaction, which proceeded in 96%
yield affording after hydrogenation and deprotection the bicyclic
nucleoside 3.16 We envisioned that a similar strategy might also
afford the one atom shorter analogue 4 even though ring-closing
metathesis might have its limitation in the formation of very con-
strained ring-systems.24 Nevertheless, it was relatively straight-
forward to convert 12 into a substrate for this using a modified ene-
reaction.37 Hence, treatment of 12 with a triazolinedione afforded
compound 13 as exclusively the E-isomer in a reasonable yield,
whereas treatment with RhCl3 mediated a rearrangement of the
allyl group38 and 50-deprotection to afford 14 as an E/Z-mixture.
However, neither 13 nor 14 worked as substrates for an RCM re-
action using Grubbs second generation catalyst. The problem could
be the problematic combination of a sterically hindered terminal
alkene in the 40-position and internal alkenes in the 20-position. In
a former study on cyclic dinucleotides, we found a dinucleotide
with two 40-C-vinyl groups to be unreactive towards RCM, whereas
cyclizations between a 40-C-vinyl group and a more reactive 50-allyl
group were possible.39 Therefore, we could either introduce a ter-
minal alkene (a vinyl group) at the 20-C-position, where it is ex-
pected to be less sterically hindered, or attempt the so-called relay-
RCM method.40,41 The latter strategy was followed by first rear-
ranging the alkene of compound 11 to give 15 (this time optimized
substituted analogues of 6, which was originally studied by Wang
and co-workers.25 We decided to use 5 as a precursor for a double-
headed nucleoside 7.
Double-headed nucleosides are defined as nucleoside analogues
bearing two nucleobases. We26e33 and others34e36 have recently
studied these as building blocks for oligonucleotides that can either
target nucleic acid secondary structures, form interesting new
nucleic acid motifs or potentially transfer molecular information in
new ways. Recently, the double-headed nucleosides 8 (B¼T/A)
were synthesized and found to form base-pairs in the core of
a duplex hereby extending the duplex with an additional base
pair.31,32 The bicyclic analogue 7 is a conformationally restricted
analogue of 8, but, whereas 8 is preferring a C20-endo conforma-
tion,31 7 would be conformationally locked in a C30-endo confor-
mation. It is of great interest to study how the restriction itself and
the different positioning of the additional nucleobase will influence
the properties in forming artificial nucleic acid motifs and targeting
other nucleic acids.
2. Results and discussion
2.1. Chemical synthesis
In the original synthesis of the bicyclic nucleoside 3, the key
intermediate 9 (Scheme 1) was first prepared from uridine in six
Scheme 1. Reagents and conditions. (a) Ref. 16; (b) 4-methyl-1,2,4-triazoline-3,5-dione, CH2Cl2 (65%) or RhCl3$xH2O, EtOH; (c) Grubbs second generation catalyst, CH2Cl2; (d)
RhCl3$xH2O, K2CO3, EtOH, MW, 80 ꢀC, 61%; (e) i. DMP, CH2Cl2; ii. CH2]CH(CH2)4PPh3Br, n-BuLi, Et2O; (f) i. 4-methyl-1,2,4-triazolidine-3,5-dione, CH2Cl2, (47%); ii. O3, MeOH, ꢁ70 ꢀC;
iii. MeOH, NaBH4, 60% (2 steps); (g) NaOCH3, MeOH, 64%; (h) DMP, CH2Cl2; (i) i. OsO4, NMO, acetone, H2O; ii. NaIO4, dioxane, H2O, 52%; (j) BzCl, pyridine, 85%; (k) RhCl3$xH2O, K2CO3,
EtOH, MW, 75 ꢀC, 55%; (l) i. OsO4, NMO, acetone, H2O; ii. NaIO4, dioxane, H2O, 62%; (m) BzCl, pyridine, 65%; (n) Uracil, BSA, TMS-OTf, CH3CN, 58%; (o) i. NH3, CH3OH; ii. TBAF, THF,
72%. NMO¼N-methylmorpholine-N-oxide, DMP¼DesseMartin periodinane, TBS¼tert-butyldimethylsilyl.

S. Kumar et al. / Tetrahedron 70 (2014) 583e589
585
with K2CO3 to avoid desilylation)42 and then in an oxidation/Wittig
sequence using the hex-5-ene-1-yltriphenylphosphonium bro-
mide43 to make the substrate 16 as a mixture of E/Z-isomers. Here
the idea is that the RCM starts with excluding cyclopentene and
then continues on the hereby activated 40-C substituent to perform
the cyclisation. However, also this attempt failed to give any ring-
closed product. In a last attempt to form a carba-LNA-analogue
using RCM-methodology, we converted compound 10 to the 20-
hydroxymethyl analogue 17 in first an ene reaction and then an
ozonolysis/reduction sequence.37 Deprotection afforded the 20,40-
bis-C-(hydroxy-methyl) nucleoside 18. Nevertheless, any attempt
of converting this into the 20,40-bis-C-formyl (to be an intermediate
towards a 20,40-bis-C-vinylnucleoside or a substrate for a McMurry
coupling) failed probably due to the 20-C-formyl nucleoside being
prone to elimination of the uracil. However, in an attempt to make
a sequential oxidation, compound 15 was cleaved in a dihydrox-
ylation/oxidation sequence to give what was found to be the
hemiacetal 19 as an almost equimolar mixture of epimers. Trapping
the hemiacetal as its benzoic ester afforded, surprisingly, 20 as only
one epimer.
a mutual contact between one of the H60-signals to only one of the
H10/H80-signals and a mutual contact between the other 60-proton
and the other H10/H80-signal proved the 80(R)-configuration. Thus,
the opposite 80(S)-configuration would have shown that one of the
H60-signals would see a contact with both H10/H80-signals and the
other to none of the H10/H80-signals. Next, this information was
used in the assignment of the two different H60-signals (hereafter
called H60a and H60b), the two different uracils and the two different
singlet signals representing H10 and H80 (Fig. 2). Thus, one of the
H60-signals showed a mutual contact to one of the H6-signals. With
an 80(R)-configuration, this is only possible with this being the H60
in the pro-R-position (H60b) and the H6 from the uracil in the 80-
position (H6b), respectively. Finally, these assignments and the
overall configuration was confirmed by mutual contacts between
H6a and H30, between H6a and H10, as well as between H6b and both
H10 and H80. All these conclusive contacts are indicated in Fig. 2,
whereas all other expected contacts though found in the ROESY
spectrum are omitted for the clarity of the Figure.
2.2. Discussion
We envisioned compound 20 to be a substrate for various cou-
pling reactions, for instance with nucleobases to afford double-
headed nucleosides, but with this new target we decided first to
avoid some unnecessary protecting steps. Hence, the nucleoside 9
with two primary alcohols was subjected to a RhCl3 mediated allyl
rearrangement42 to give compound 21 as a mixture of E/Z-isomers.
The same oxidative cleavage as before gave the hemiacetal bicyclic
nucleoside 22 as a mixture of epimers in a 1:5 ratio. Again the
subsequent benzoylation traps the hemiacetal as it benzoic ester 23
It is clear from the present study that the carbocyclic LNA-
analogue 4 and analogues thereof cannot be prepared from an
RCM-strategy. The bicyclic ring-system is too constrained, and the
radical strategy introduced by Chattopahyaya and co-workers is
better for the purpose although the number of steps is significantly
larger. Nevertheless, our attempts on RCM were worth the effort as
they build mainly on intermediates already prepared in our syn-
thesis of compound 3, and as the study adds to the general un-
derstanding of the scope of the RCM-reaction.
€
as only a single epimer in a good yield. A Vorbruggen coupling with
thymine gave a complicated mixture apparently due to some ex-
change of the original uracil of 23 with thymine. However, a cou-
pling of 23 with uracil afforded a pure epimeric mixture of double-
headed nucleosides 24, which after deprotection gave the target
compound 7 as a mixture of epimers in a 2:3 ratio. In a small
An appealing result of the study is, however, that the 20-C-for-
myl-40-C-hydroxymethyl nucleosides obtained from the double-
bond cleavage of either 15 or 21 readily equilibrates to the hemi-
acetal analogues 19 or 22. This shows again that six-membered
rings connecting C20 and C40 are much easier formed than five-
membered rings and less constrained. The benzoic ester of this
amount, the major epimer was isolated for
characterization.
a full NMR
€
hemiacetal, 23, was a good substrate for a Vorbruggen coupling and
First of all, the two signals from H10 and H80 are both singlets in
probably also for other glycosidation reactions. However, this will
be a balance of not also exchanging the uracil of 23, but with the
right optimization, we expect other combinations of nucleobases
on the same skeleton as 7 as well as bicyclic nucleoside analogues
with other groups attached to the C80-postion to be obtainable from
the key compound 23.
1
the H NMR spectrum (with H80 defined as shown in Scheme 1).
This indicates the expected locked C30-endo conformation as well as
both the H10eC10eC20eH20 and the H20eC20eC80eH80 dihedral
angles being restricted in close to 90ꢀ. However, this information is
not conclusive for the 80-configuration. A ROESY spectrum was
hereafter deduced to fully assign the signals and to prove the C80-
configuration to be an (R)-configuration (Fig. 2). First of all,
Both 80-epimers of the bicyclic double-headed nucleoside 7 are
interesting for their potential incorporation into oligonucleotides.
The strong conformational restriction, however, will most probably
give completely different properties as compared to oligonucleo-
tides containing the native analogue 8 (Fig. 1). Hence, the bicyclic
structure will in both epimers prohibit the two nucleobases from
the parallel orientation, which is central for 8 in forming two par-
allel base-pairs in the same duplex.32 On the other hand, oligonu-
cleotides with a central incorporation of
7 can form other
secondary structures and might for instance lead to stable three-
way junctions and hereby a tool in the targeting of other second-
ary structures, as seen before for related double-headed nucleotide
analogues.26,30 They might also be promising building blocks in
evolving nucleic acid aptamers.
3. Conclusion
A bicyclic double-headed nucleoside has been synthesized from
uridine based on the unexpected formation of a bicyclic hemiacetal
structure. This hemiacetal can be an interesting building block for
new derivatives, for instance new therapeutically useful LNA-ana-
logues. Furthermore, the bicyclic double-headed nucleosides can
constitute a promising new series of nucleic acid analogues with
Fig. 2. The conclusive ROESY contacts of the major 80(R)-epimer of 7. Other contacts
are omitted for clarity.

586
S. Kumar et al. / Tetrahedron 70 (2014) 583e589
the ability of forming new nucleic acid motifs, and targeting RNA-
secondary structures. Ring-closing metathesis cannot form the
bicyclo[2.2.1] skeleton of carba-LNA.
(34 mg, 0.06 mmol) and stirred in a microwave reactor at 80 ꢀC for
3 h. The mixture was then concentrated under reduced pressure
and the residue was added brine (3 mL). The aqueous phase was
extracted by EtOAc (2ꢂ5 mL). The organic phase was dried (Na2SO4)
and concentrated under reduced pressure. The residue was purified
by silica gel column chromatography (EtOAc/petroleum ether, 1:4
v/v) to give the product 15 (230 mg as an E/Z-mixture, 7:1, 58%) as
a white foam; Rf 0.50 (EtOAc/petroleum ether, 1:1 v/v); 1H NMR
4. Experimental section
4.1. General
Reactions were performed under an atmosphere of nitrogen
when anhydrous solvents were used. Column chromatography was
carried out on glass columns using silica gel 60 (0.040e0.063 mm).
HRMALDI and ESI mass spectra were recorded in positive-ion
mode. NMR spectra were recorded at 300 or 400 MHz for 1H
(400 MHz, CDCl3)
d
8.85 (br s, 1H, NH), 7.76 (d, 1H, J¼8.0 Hz, H-6),
7.67 (d, 1H, J¼8.0 Hz, H-6), 6.21 (d, 1H, J¼9.6 Hz, H-10), 5.70 (dd, 1H,
J¼2.0, 8.0 Hz, H-5), 5.51e5.38 (m, 2H, CH]CHCH3), 4.38 (d, 1H,
J¼6.0 Hz, H-30), 4.35 (d, 1H, J¼5.6 Hz, H-30), 3.88 (dd, 1H, J¼3.2,
11.6 Hz, H-500), 3.78, 3.68 (AB, 2H, J¼10.4 Hz, H-50), 3.51 (dd, 1H,
J¼10.4, 11.6 Hz, H-500), 2.87 (m, 1H, H-20), 2.16 (m, 1H, OH), 1.65 (d,
3H, J¼5.6 Hz, CH]CHCH3), 1.51 (dd, 3H, J¼0.8, 6.8 Hz, CH]CHCH3),
0.93 (s, 18H, SiC(CH3)3), 0.11 (s, 6H, SiCH3), 0.05 (s, 3H, SiCH3), 0.03
NMR and 75 or 100 MHz for 13C NMR. The
d values are in parts per
million relative to tetramethylsilane as internal standard. Assign-
ments of NMR spectra are based on 2D spectra and follow standard
carbohydrate and nucleoside style; i.e., the carbon atom next to
a nucleobase is assigned C-10, etc. Compound names for the bicyclic
compounds are given according to the von Baeyer nomenclature.
(s, 3H, SiCH3); 13C NMR (100 MHz, CDCl3)
d (major isomer) 163.1 (C-
4), 150.5 (C-2), 140.0 (C-6), 131.2, 123.9 (CH]CHCH3), 102.9 (C-5),
88.9, 86.8 (C-40, C-10), 77.2 (C-30), 65.8 (C-50), 64.0 (C-500), 54.8 (C-20),
25.9, 25.9 (SiC(CH3)3), 18.4, 18.3 (SiC(CH3)3), 13.5 (CH3), ꢁ4.3, ꢁ4.6,
ꢁ5.3, ꢁ5.5 (SiCH3); HRESI MS m/z (549.2783 [MþNa]þ,
4.2. 30,50-Di-O-(tert-butyldimethylsilyl)-20-deoxy-20-[(4-
methyl-3,5-dioxo-1,2,4-triazolidin-1-yl)prop-1-en-1-yl]-40-C-
vinyluridine (13)
C
25H46N2O6Si2eNaþ calcd 549.2787).
4.5. 30,50-Di-O-(tert-butyldi-methyl-silyl)-20-deoxy-40-C-
A solution of nucleoside 12 (40 mg, 0.086 mmol) in CH2Cl2 (2 mL)
was added 4-methyl-1,2,4-trazoline-3,5-dione (10 mg, 0.09 mmol)
and stirred for 24 h at room temperature. An additional amount of 4-
methyl-1,2,4-trazoline-3,5-dione (7 mg, 0.06 mmol) was added and
the mixture was stirred for another 24 h. The mixture was concen-
trated under reduced pressure and the residue was purified by silica
gel column chromatography (25e100% EtOAc in petrol ether) to give
(hepta-1,6-dienyl)-20-(prop-1-en-1-yl)uridine (16)
A degassed solution of 15 (122 mg, 0.23 mmol) in CH2Cl2
(4 mL) was added DesseMartin periodinane (135 mg, 0.32 mmol)
and the mixture was stirred for 1 h at room temperature. Et2O
was added and the mixture was filtered through a layer of Celite.
The filter was washed with EtOAc and the combined organic
phase was washed with a mixture of a saturated aqueous solu-
tion of NaHCO3 and a 5% aqueous solution of Na2S2O3 (1:1 v/v),
dried (MgSO4) and concentrated under reduced pressure to give
the crude intermediate aldehyde (121 mg, quant). To a stirred
solution of (hex-5-en-1yl)triphenyl-phosphonium bromide43
(259 mg, 0.61 mmol) in anhydrous Et2O (2 mL) at 0 ꢀC was
added a solution of n-BuLi in hexane (0.45 mL, 0.50 mmol) and
the mixture was stirred at 0 ꢀC for 15 min. A solution of the al-
dehyde (155 mg, 0.30 mmol) in anhydrous Et2O (1 mL) was
added, and the mixture was stirred at room temperature for 24 h
and then diluted with Et2O (15 mL). The mixture was filtered and
washed with a saturated aqueous solution of NaHCO3 (5 mL) and
dried (MgSO4). The mixture was concentrated under reduced
pressure and the residue was purified by silica gel column
chromatography (20% EtOAc in petrol ether) to give the product
16 (63 mg, 38%, mixture of E/Z-diastereomers) as a white foam,
which was used without further purification in the next step; Rf
0.75 (EtOAc/petrol ether, 1:1 v/v); HRMALDI MS m/z (613.3458
[MþNa]þ, C31H54N2O5Si2eNaþ calcd 613.3464).
the product 13 (32 mg, 65%) as an oil; 1H NMR (300 MHz, CDCl3)
d 9.9
(br s, 1H, NH), 7.91 (d, 2H, J¼8.2 Hz, H-6), 6.11 (d, 1H, J¼7.5 Hz, H-10),
5.94 (dd, 1H, J¼10.8, 15.3 Hz, CH]CH2), 5.80 (dd, 1H, J¼10.8,
17.2 Hz, CH]CHCH2), 5.74 (d, 1H, J¼8.2 Hz, H-5), 5.54e5.42 (m, 2H,
CH]CHCH2, CH]CH2), 5.25 (1H, dd, J¼1.5, 10.0 Hz, CH]CH2), 4.40
(d,1H, J¼6.5 Hz, H-30), 4.28 (dd,1H, J¼4.6,14.7 Hz, CH]CHCH2), 3.86
(dd,1H, J¼8.2,14.7 Hz, CH]CHCH2), 3.67e3.58 (2H, m, H-50), 3.04 (s,
3H, CH3), 2.93 (m, 1H, H-20), 0.92 (s, 9H, SiC(CH3)3), 0.89 (s, 9H,
SiC(CH3)3), 0.11 (s, 6H, SiCH3), 0.05 (s, 3H, SiCH3), 0.01 (s, 3H, SiCH3);
13C NMR (75 MHz, CDCl3)
d 163.1 (C-4),154.9,154.4 (CO) 151.6 (C-2),
139.4 (C-6),134.4,131.6,126.7,116.2 (C]C),103.2 (C-5), 90.7, 87.9 (C-
40, C-10), 75.3 (C-30), 66.8 (C-50), 55.3 (CH]CHCH2), 48.2 (C-20), 25.8,
25.7 (SiC(CH3)3), 25.3 (CH3), 18.3, 18.1 (SiC(CH3)3), ꢁ4.1, ꢁ4.6, ꢁ5.5,
ꢁ5.6 (SiCH3).
4.3. 30-O-(tert-Butyldimethylsilyl)-20-deoxy-20-(prop-1-en-1-
yl)-40-C-vinyluridine (14)
A solution of nucleoside 12 (56 mg, 0.11 mmol) in EtOH (99.9%,
2 mL) was degassed with N2 for 20 min and added RhCl3$xH2O
(4 mg, 0.07 mmol). The mixture was stirred at reflux for 1 h. The
mixture was then concentrated under reduced pressure and the
residue was purified by silica gel column chromatography (EtOAc/
petroleum ether, 1:4 v/v) to give the product 14 (21 mg as a E/Z-
mixture, 48%) as an oil, which was used without further purifica-
4.6. 40-C-Benzoyloxymethyl-30,50-di-O-(tert-butyldime-
thylsilyl)-20-deoxy-20-hydroxymethyluridine (17)
A solution of nucleoside 10 (540 mg, 0.86 mmol) in CH2Cl2
(5 mL) was added 4-methyl-1,2,4-trazoline-3,5-dione (116 mg,
1.03 mmol) and stirred for 14 h at room temperature. The
mixture was concentrated under reduced pressure and the res-
idue was purified by silica gel column chromatography (0e3%
CH3OH in CH2Cl2) to give the intermediate 40-C-benzoylox-
ymethyl-30,50-di-O-(tert-butyldimethylsilyl)-20-deoxy-20-[(4-
methyl-3,5-dioxo-1,2,4-triazolidin-1-yl)-prop-1-en-1-yl]uridine
(297 mg, 47%) as well as unreacted starting material 10 (177 mg,
33%); Rf 0.60 (CH3OH/dichloromethane, 7.5:92.5 v/v); 1H NMR
tion in the next step; 13C NMR (100 MHz, CDCl3)
d (major isomer)
163.2 (C-4), 150.2 (C-2), 142.0 (C-6), 135.0, 130.8, 125.2, 115.6 (C]C),
102.7 (C-5), 90.9, 89.9 (C-40, C-10), 75.3 (C-30), 66.2 (C-50), 52.7 (C-
20), 25.7 (SiC(CH3)3), 18.1 (SiC(CH3)3), 13.5 (CH3), ꢁ4.6, ꢁ4.8 (SiCH3).
4.4. 30,50-Di-O-(tert-butyldimethyl-silyl)-20-deoxy-40-C-hy-
droxymethyl-20-(prop-1-en-1-yl)uridine (15)
A solution of nucleoside 11 (400 mg, 0.76 mmol) in EtOH (99.9%,
4 mL) was added anhydrous K2CO3 (40 mg, 0.29 mmol), RhCl3$xH2O
(300 MHz, CDCl3)
7.71 (d, 1H, J¼8.1 Hz, H-6), 7.59e7.54 (m, 1H, Ar), 7.47e7.42 (m,
d
9.79 (br s, 2H, NH), 8.01 (d, 2H, J¼7.5 Hz, Ar),

S. Kumar et al. / Tetrahedron 70 (2014) 583e589
587
2H, Ar), 6.25 (d, 1H, J¼8.7 Hz, H-10), 5.98 (dd, 1H, J¼9.3,
4.8. (1R,4R/S,5R,6R,8S)-8-(tert-Butyldimethylsilyloxy)-1-(tert-
butyldimethylsilyloxymethyl)-4-hydroxy-6-(uracil-1-yl)-3,7-
dioxabicyclo[3.2.1]octane (19)
15.9 Hz, CH]CHCH2), 5.75 (d, 1H, J¼8.1 Hz, H-5), 5.60e5.52 (m,
1H, CH]CHCH2), 4.56, 4.39 (AB, 2H, J¼12.0 Hz), 4.46 (d, 1H,
J¼5.7 Hz, H-30), 4.27 (dd, 1H, J¼4.5, 14.7 Hz, CH]CHCH2),
3.95e3.82 (m, 3H, CH]CHCH2), 3.04 (s, 3H, CH3), 2.96e2.88 (m,
1H, H-20), 0.95 (s, 9H, SiC(CH3)3), 0.92 (s, 9H, SiC(CH3)3), 0.12 (s,
3H, SiCH3), 0.11 (s, 3H, SiCH3), 0.10 (s, 3H, SiCH3), 0.04 (s, 3H,
To a solution of nucleoside 15 (590 mg, 1.12 mmol) in aqueous
acetone (1:1, 15 mL) was added a 2.5% w/v solution of OsO4 in
tert-butyl alcohol (1.82 mL, 0.18 mmol) and N-methylmorpho-
line-N-oxide (164 mg, 1.40 mmol). The reaction mixture was
stirred for 17 h at room temperature. A 5% aqueous solution of
Na2S2O3 (10 mL) and then EtOAc (10 mL) were added. The mix-
ture was concentrated under reduced pressure to approximately
half of the volume and added EtOAc (12 mL). The mixture was
washed with a saturated aqueous solution of NaHCO3 (10 mL)
and brine (10 mL). The organic phase was dried (Na2SO4) and
concentrated under reduced pressure. The crude diol was dis-
solved in aqueous dioxane (20 mL, 1:1), and NaIO4 (1.20 g,
5.61 mmol) was added. The reaction mixture was stirred for 6 h
at room temperature. The mixture was added EtOAc (15 mL) and
washed with a saturated aqueous solution of NaHCO3 (2ꢂ15 mL)
and brine (15 mL). The organic phase was dried (Na2SO4) and
concentrated under reduced pressure. The residue was purified
by silica gel column chromatography (0e3% CH3OH in CH2Cl2) to
give the hemiacetal product 19 (as an epimeric mixture 1:0.9,
300 mg, 52%); Rf 0.50 (CH3OH/dichloromethane 1:9 v/v); 1H NMR
SiCH3); 13C NMR (75 MHz, CDCl3)
d 166.3, 162.9, 155.0, 154.7,
151.7 (CO, C-4, C-2), 139.1 (C-6), 133.3, 129.8, 129.7, 128.6 (Ar),
130.5 (CH]CHCH2), 127.4 (CH]CHCH2), 103.5 (C-5), 88.7, 87.9
(C-40, C-10), 76.5, 65.2, 65.2 (C-30, C-50, C-500), 55.0 (C-20), 48.4
(CH]CHCH2), 25.9, 25.8 (SiC(CH3)3), 25.3 (CH3), 18.3, 18.3
(SiC(CH3)3), ꢁ4.1, ꢁ4.6, ꢁ5.3, ꢁ5.4 (SiCH3); HRMALDI MS m/z
(766.3254 [MþNa]þ, C35H53N5O9Si2eNaþ calcd 766.3274). A so-
lution of this intermediate (600 mg, 0.81 mmol) in MeOH (6 mL)
was bubbled with ozone at ꢁ70 ꢀC for 5 min. The stirred solu-
tion was allowed to come to room temperature and then poured
into water (5 mL). The organic layer was washed with a satu-
rated aqueous solution of NaHCO3 (5 mL) and brine (5 mL), dried
(Na2SO4) and then concentrated under reduced pressure. The
resulting ozonide was dissolved in MeOH (10 mL) and added
NaBH4 (245 mg, 6.45 mmol), and the reaction mixture was
stirred for 10 min at room temperature. The organic layer was
washed with a saturated aqueous solution of NaHCO3 (2ꢂ5 mL)
and brine (2ꢂ5 mL), and then dried (Na2SO4) and concentrated
under reduced pressure. The residue was purified by silica gel
column chromatography (CH3OH (0e3.0%) in CH2Cl2) to give the
product 17 (299 mg, 60%); Rf 0.70 (CH3OH/CH2Cl2, 1:9 v/v); 1H
(400 MHz, CDCl3)
d 9.52 (br s, 1H, NH), 9.38 (br s, 1H, NH), 8.09
(d, 1H, J¼8.4 Hz, H-6), 8.08 (d, 1H, J¼8.0 Hz, H-6), 6.21 (s, 1H, H-
10), 5.84 (s, 1H, H-10), 5.70e5.67 (m, 2H, H-5), 5.51 (d, 1H,
J¼11.6 Hz, OH), 5.39 (d, 1H, J¼7.6 Hz, H-80), 5.32e5.29 (m, 1H, H-
80), 4.44 (d, 1H, J¼4.8 Hz, H-30), 4.40 (d, 1H, J¼5.6 Hz, H-30), 4.05,
3.33 (AB, 2H, J¼11.6 Hz), 3.94, 3.46 (AB, 2H, J¼11.2 Hz), 3.77, 3.56
(AB, 2H, J¼11.6 Hz), 3.75, 3.52 (AB, 2H, J¼11.2 Hz), 2.59 (dd, 1H,
J¼2.8, 5.2 Hz, H-20), 2.49 (d, 1H, J¼6.0 Hz, H-20), 0.95 (s, 9H,
SiC(CH3)3), 0.93 (s, 9H, SiC(CH3)3), 0.93 (s, 9H, SiC(CH3)3), 0.90 (s,
9H, SiC(CH3)3), 0.19 (s, 3H, SiCH3), 0.17 (s, 3H, SiCH3), 0.14 (s, 3H,
SiCH3), 0.12 (s, 3H, SiCH3), 0.12 (s, 3H, SiCH3), 0.10 (s, 3H, SiCH3),
0.10 (s, 3H, SiCH3), 0.09 (s, 3H, SiCH3); 13C NMR (100 MHz, CDCl3)
NMR (300 MHz, CDCl3)
d 9.35 (br s, 1H, NH), 8.02 (d, 2H,
J¼7.2 Hz, Ar), 7.67 (d, 1H, J¼8.1 Hz, H-6), 7.55 (m, 1H, Ar),
7.46e7.41 (m, 2H, Ar), 6.29 (d, 1H, J¼8.4 Hz, H-10), 5.73 (d, 1H,
J¼8.1 Hz, H-5), 4.66 (d, 1H, J¼6.6 Hz, H-30), 4.55, 4.35 (AB, 2H,
J¼12.0 Hz), 3.90 (m, 2H), 3.83 (m, 2H), 2.52 (m, 1H, H-20), 0.95 (s,
9H, SiC(CH3)3), 0.91 (s, 9H, SiC(CH3)3), 0.15 (s, 3H, SiCH3), 0.14 (s,
3H, SiCH3), 0.11 (s, 3H, SiCH3), 0.09 (s, 3H, SiCH3); 13C NMR
(75 MHz, CDCl3)
d 166.4 (CO), 163.4 (C-4), 151.0 (C-2), 140.1 (C-6),
133.2, 129.9, 129.7, 128.5 (Ar), 103.0 (C-5), 88.0, 87.7 (C-40, C-10),
74.4 (C-30), 64.9, 64.5, 59.3 (C-50, C-500, CH2OH), 52.1 (C-20), 25.9,
25.8 (SiC(CH3)3), 18.4, 18.2 (SiC(CH3)3), ꢁ4.3, ꢁ4.4, ꢁ5.3, ꢁ5.4
d 163.8 (C-4), 150.2, 150.1 (C-2), 139.8, 139.5 (C-6), 101.6, 101.4 (C-
5), 94.8, 91.0 (C-80), 85.0, 83.3, 83.3 (C-10, C-40), 67.1, 66.4 (C-30),
65.1, 60.6, 59.8, 59.4 (C-50, C-60), 51.3, 46.9 (C-20), 26.1, 26.0, 25.7,
25.6 (SiC(CH3)3), 18.6, 18.4, 18.0, 17.9 (SiC(CH3)3), ꢁ4.3, ꢁ4.8, ꢁ4.9,
ꢁ5.0, ꢁ5.1, ꢁ5.3, ꢁ5.3, ꢁ5.4 (SiCH3); HRMALDI MS m/z (537.2446
[MþNa]þ, C23H42N2O7Si2eNaþ calcd 537.2423).
(SiCH3);
HRMALDI
MS
m/z
(643.2838
[MþNa]þ,
C
30H48N2O8Si2eNaþ calcd 643.2841).
4.7. 30,50-Di-O-(tert-butyldimethylsilyl)-20-deoxy-20,40-di-C-
(hydroxymethyl)uridine (18)
4.9. (1R,4R/S,5R,6R,8S)-4-Benzoyloxy-8-(tert-butyldimethyl
silyloxy)-1-(tert-butyldimethylsilyloxymethyl)-6-(uracil-1-yl)-
3,7-dioxabicyclo[3.2.1]octane (20)
To a stirred solution of compound 17 (100 mg, 0.16 mmol) in
anhydrous CH3OH (1 mL) was added NaOCH3 (52 mg, 0.96 mmol)
and the reaction mixture was stirred for 7 h at room temperature.
The reaction was quenched by the addition of 80% CH3COOH (1 mL)
and then extracted with CH2Cl2 (2ꢂ4 mL). The combined extracts
were washed with a saturated aqueous solution of NaHCO3 (5 mL),
dried (Na2SO4), and concentrated under reduced pressure. The
residue was purified by silica gel column chromatography (0e5%
CH3OH in CH2Cl2) to give the product 18 (53 mg, 64%) as a white
foam; Rf 0.50 (CH3OH-dichloromethane, 7.5:92.5 v/v); 1H NMR
To a solution of the hemiacetal 19 (415 mg, 0.81 mmol) in an-
hydrous pyridine (2 mL) was added benzoyl chloride (112
mL,
0.97 mmol) dropwise, and the reaction mixture was stirred at room
temperature for 1 h and then concentrated under reduced pressure.
The residue was partitioned between EtOAc (4 mL) and H2O (4 mL)
and the organic phase was washed with a saturated aqueous so-
lution of NaHCO3 (2ꢂ3 mL), dried (Na2SO4) and concentrated under
reduced pressure. The residue was purified by silica gel column
chromatography (0e3% CH3OH in CH2Cl2) to give the product 20
(425 mg, 85%) as a white foam; Rf 0.70 (CH3OH/dichloromethane
(300 MHz, CDCl3)
d
9.22 (br s, 1H, NH), 7.88 (d, 1H, J¼8.1 Hz, H-6),
6.34 (d,1H, J¼9.0 Hz, H-10), 5.69 (dd,1H, J¼3.9, 8.1 Hz, H-5), 4.48 (m,
1H, H-30), 3.92 (m, 2H), 3.85e3.79 (m, 2H), 3.69e3.65 (m, 2H), 3.61
(d, 1H, J¼10.2 Hz), 2.84 (s, 1H, OH), 2.50 (m, 1H, H-20), 0.90 (s, 9H,
SiC(CH3)3), 0.89 (s, 9H, SiC(CH3)3), 0.11 (s, 3H, SiCH3), 0.10 (s, 3H,
SiCH3), 0.09 (s, 3H, SiCH3), 0.07 (s, 3H, SiCH3); 13C NMR (75 MHz,
1:9 v/v); 1H NMR (400 MHz, CDCl3)
d 9.08 (s, 1H, NH), 8.23 (dd, 2H,
J¼5.2, 7.2 Hz, Ar), 8.18 (d, 1H, J¼8.4 Hz, H-6), 7.57e7.53 (m, 1H, Ar),
7.47e7.43 (m, 2H, Ar), 6.49, 6.44 (s, 2H, H-10, H-80), 5.70 (dd, 1H,
J¼2.0, 8.4 Hz, H-5), 4.51 (d, 1H, J¼5.6 Hz, H-30), 4.10, 3.52 (AB, 2H,
J¼11.2 Hz), 3.80, 3.58 (AB, 2H, J¼11.6 Hz), 2.66 (d, 1H, J¼5.6 Hz, H-
20), 0.95 (s, 9H, SiC(CH3)3), 0.94 (s, 9H, SiC(CH3)3), 0.15 (s, 3H, SiCH3),
0.14 (s, 3H, SiCH3), 0.13 (s, 3H, SiCH3), 0.13 (s, 3H, SiCH3); 13C NMR
CDCl3)
d 163.3 (C-4), 150.9 (C-2), 140.2 (C-6), 102.9 (C-5), 89.1, 86.8
(C-40, C-10), 75.9 (C-30), 66.6, 64.1, 58.4 (C-50, C-500, CH2OH), 52.3
(C-20), 25.9, 25.8 (SiC(CH3)3), 18.4, 18.1 (SiC(CH3)3), ꢁ5.4, ꢁ5.4, ꢁ5.5,
ꢁ5.5 (SiCH3); HRMALDI MS m/z (539.2564 [MþNa]þ,
(100 MHz, CDCl3)
d 164.9 (CO), 163.6 (C-4), 149.8 (C-2), 139.9 (C-6),
C
23H44N2O7Si2eNaþ calcd 539.2579).
133.6, 130.3, 129.3, 128.6 (Ar), 101.5 (C-5), 90.3, 83.7, 83.4 (C-10, C-40,

588
S. Kumar et al. / Tetrahedron 70 (2014) 583e589
C-80), 66.1 (C-30), 66.0, 59.3 (C-50, C-60), 49.6 (C-20), 26.0, 25.7
(SiC(CH3)3), 18.5, 18.0 (SiC(CH3)3), ꢁ4.4, ꢁ4.9, ꢁ5.3, ꢁ5.4 (SiCH3);
HRMALDI MS m/z (641.2699 [MþNa]þ, C30H46N2O8Si2eNaþ
calcd 641.2685).
4.12. (1R,4R/S,5R,6R,8S)-4-Benzoyloxy-1-(benzoyloxymethyl)-
8-(tert-butyldimethylsilyloxy)-6-(uracil-1-yl)-3,7-dioxabicyclo
[3.2.1] octane (23)
A stirred solution of hemiacetal 22 (400 mg, 1.0 mmol) in an-
hydrous pyridine (3 mL) was added benzoyl chloride (0.29 mL,
2.5 mmol) dropwise and then stirred at room temperature for
45 min. The reaction mixture was concentrated under reduced
pressure and the residue was purified by silica gel column chro-
matography (0e2.5% CH3OH in CH2Cl2) to give 23 (398 mg, 65%) as
a white foam; Rf 0.40 (CH3OH/dichloromethane 1:19 v/v); 1H NMR
4.10. 30-O-(tert-Butyldimethylsilyl)-20-deoxy-40-C-hydrox-
ymethyl-20-(prop-1-en-1-yl)uridine (21)
To a stirred solution of nucleoside 9 (923 mg, 2.24 mmol) in
EtOH (99.9%,
7 mL) was added anhydrous K2CO3 (62 mg,
0.45 mmol), RhCl3$xH2O (132 mg, 0.22 mmol) and the reaction
mixture was stirred at 75 ꢀC for 7 days. The mixture was con-
centrated under reduced pressure and the residue was dissolved
in brine. The aqueous phase was extracted by EtOAc (2ꢂ8 mL),
and the organic phase was dried (Na2SO4) and concentrated
under reduced pressure. The residue was purified by silica gel
column chromatography (0e6% CH3OH in CH2Cl2) to give the
product 21 (511 mg, 55%); Rf 0.60 (CH3OH/dichloromethane 1:9
(400 MHz, CDCl3)
d
9.13 (br s, 1H, NH), 8.22 (dd, 2H, J¼1.2, 8.8 Hz,
Ar), 8.01 (dd, 2H, J¼1.2, 8.4 Hz, Ar), 7.88 (d, 1H, J¼8.4 Hz, H-6), 7.65
(t, 1H, J¼7.6 Hz, Ar), 7.59e7.44 (m, 5H, Ar), 6.54, 6.42 (s, 2H, H-10, H-
80), 5.50 (dd, 1H, J¼2.0, 8.4 Hz, H-5), 4.58, 4.36 (AB, 2H, J¼12.8 Hz),
4.53 (d, 1H, J¼5.6 Hz, H-30), 4.26, 3.78 (AB, 2H, J¼11.2 Hz), 2.81 (d,
1H, J¼5.6 Hz, H-20), 0.94 (s, 9H, SiC(CH3)3), 0.15 (s, 3H, SiCH3), 0.09
(s, 3H, SiCH3); 13C NMR (100 MHz, CDCl3)
d 165.7, 164.8, 163.5 (CO,
C-4), 149.7 (C-2), 139.1 (C-6), 134.0, 133.7, 130.3, 129.5, 129.2, 129.2,
129.0, 128.7 (Ar), 101.7 (C-5), 90.3, 84.4 (C-10, C-80), 81.9 (C-40), 67.7
(C-30), 65.7, 60.6 (C-50, C-60), 49.2 (C-20), 25.7 (SiC(CH3)3), 18.0
(SiC(CH3)3), ꢁ4.5, ꢁ5.1 (SiCH3); HRESI MS m/z (631.2093 [MþNa]þ,
v/v); 1H NMR (400 MHz, CDCl3)
d 9.39 (br s, 1H, NH), 7.45 (d,
1H, J¼8.0 Hz, H-6), 5.96 (d, 1H, J¼9.2 Hz, H-10), 5.74e5.70
(m, 1H, H-5), 5.53e5.50 (m, 1H, CH]CHCH3), 5.43e5.39 (m, 1H,
CH]CHCH3), 4.47 (d, 1H, J¼6.4 Hz, H-30), 3.94e3.89 (m, 1H,
CH2OH), 3.79e3.76 (m, 2H, CH2OH), 3.70e3.66 (m, 1H, CH2OH),
3.63e3.56 (m, 2H, CH2OH), 3.18e3.12 (m, 1H, H-20), 1.67 (d, 3H,
J¼6.0 Hz, CH]CHCH3), 0.93 (s, 9H, SiC(CH3)3), 0.08 (s, 3H, SiCH3),
C
31H36N2O9SieNaþ calcd 631.2082).
4.13. (1R,4R/S,5R,6R,8S)-1-(Benzoyloxymethyl)-8-(tert-butyl-
dimethylsilyloxy)-4,6-di-(uracil-1-yl)-3,7-dioxabicyclo[3.2.1]
octane (24)
0.04 (s, 3H, SiCH3); 13C NMR (100 MHz, CDCl3)
d (major isomer)
163.5 (C-4), 150.7 (C-2), 141.6 (C-6), 131.6 (CH]CHCH3), 124.0
(CH]CHCH3), 102.9 (C-5), 90.2 (C-40), 89.0 (C-10), 76.7 (C-30),
64.5, 63.9 (C-50, C-500), 52.5 (C-20), 25.9 (SiC(CH3)3), 18.2
(SiC(CH3)3), ꢁ4.5, ꢁ4.7 (SiCH3); HRESI MS m/z (435.1935
[MþNa]þ, C19H32N2O6SieNaþ calcd 435.1922).
To a stirred solution of 23 (412 mg, 0.68 mmol) and uracil
(228 mg, 2.03 mmol) in anhydrous CH3CN (5 mL) was added N,O-
bis(trimethylsilyl)acetamide (1.16 mL, 4.74 mmol). The reaction
mixture was stirred for 30 min at room temperature and then at
0
ꢀC. Trimethylsilyl triflate (0.6 mL, 3.39 mmol) was added drop-
4.11. (1R,4R/S,5R,6R,8S)-8-(tert-Butyldimethylsilyloxy)-4-
hydroxy-1-hydroxymethyl-6-(uracil-1-yl)-3,7-dioxabicyclo
[3.2.1] octane (22)
wise, and the solution was stirred for 4 days at 60 ꢀC. After cooling
to room temperature, the reaction mixture was diluted with EtOAc
(15 mL) and washed with a saturated aqueous solution of NaHCO3
(2ꢂ10 mL). The combined organic phase was dried (Na2SO4) and
concentrated under reduced pressure. The residue was purified by
silica gel column chromatography (0e5% CH3OH in CH2Cl2) to give
product 24 (as a diastereomeric mixture 1:0.70, 233 mg, 58%) as
a white foam; Rf 0.35 (CH3OH/dichloromethane 7.5:92.5 v/v); 1H
To a stirred solution of nucleoside 21 (525 mg, 1.27 mmol) in
aqueous acetone (1:1, 12 mL) was added a 2.5% w/v solution of
OsO4 in tert-butyl alcohol (2.59 mL, 0.25 mmol) and N-methyl-
morpholine-N-oxide (186 mg, 1.59 mmol). The reaction mixture
was stirred for 17 h at room temperature and then added a 5%
aqueous solution of Na2S2O3 (10 mL) and EtOAc (10 mL). The
mixture was concentrated under reduced pressure to approxi-
mately half of the volume, added EtOAc (12 mL) and then washed
with a saturated aqueous solution of NaHCO3 (10 mL) and brine
(10 mL). The organic phase was dried (Na2SO4) and concentrated
under reduced pressure. The crude diol was dissolved in aqueous
dioxane (18 mL, 1:1) and NaIO4 (1.36 g, 6.37 mmol) was added.
The reaction mixture was stirred for 6 h at room temperature and
then added EtOAc (15 mL). The mixture was washed with a sat-
urated aqueous solution of NaHCO3 (2ꢂ15 mL) and brine (15 mL),
dried (Na2SO4) and concentrated under reduced pressure. The
residue was purified by silica gel column chromatography
(0e7.5% CH3OH in CH2Cl2) to give the product 22 (as a mixture of
epimers 5:1, 314 mg, 62%); Rf 0.60 (CH3OH/dichloromethane 1:4
NMR (400 MHz, CDCl3)
d 10.15 (br s, 2H, NH), 9.69 (br s, 2H, NH),
8.01e7.98 (m, 4H, Ar), 7.77e7.74 (m, 2H, H-6, Ar), 7.68 (d, 1H,
J¼8.0 Hz, H-6), 7.65e7.62 (m, 2H, H-6, Ar), 7.53e7.48 (m, 4H, Ar),
7.41 (d, 1H, J¼8.0 Hz, H-6), 6.08, 5.99 (s, 2H, H-10, H-80), 5.76 (dd, 2H,
J¼2.0, 8.0 Hz, H-5), 5.70 (s, 1H, H-10, H-80), 5.47 (dd, 2H, J¼2.0,
8.0 Hz, H-5), 4.60 (d, 1H, J¼12.0 Hz), 4.55 (d, 1H, J¼12.0 Hz), 4.46 (d,
1H, J¼8.0 Hz, H-30), 4.40 (d, 1H, J¼4.0 Hz, H-30), 4.35e4.25 (m, 4H),
3.96 (d, 1H, J¼12.0 Hz), 3.92 (d, 1H, J¼12.0 Hz), 3.69 (d, 1H, J¼4.0 Hz,
H-20), 3.29 (d,1H, J¼8.0 Hz, H-20), 0.93 (s, 9H, SiC(CH3)3), 0.80 (s, 9H,
SiC(CH3)3), 0.23 (s, 3H, SiCH3), 0.09 (s, 3H, SiCH3), 0.04 (s, 3H,
SiCH3), ꢁ0.05 (s, 3H, SiCH3); 13C NMR (100 MHz, CDCl3)
d 165.7,
163.9, 163.7, 163.6, 163.3 (CO, C-4), 150.6, 150.5, 150.2, 149.9 (C-2),
139.2, 138.1 (Ar), 139.9, 139.2, 138.4, 138.1 (C-6), 134.2, 134.1, 129.6,
129.5, 129.1, 129.0, 128.9 (Ar), 102.1, 102.0, 101.7, 100.1 (C-5), 87.0,
84.3, 83.7, 82.2, 81.6, 79.6 (C-10, C-40, C-80), 67.2, 66.1 (C-30), 66.8,
65.2, 61.2, 60.6 (C-50, C-60), 47.1, 45.4 (C-20), 26.0, 25.7 (SiC(CH3)3),
18.2, 18.0 (SiC(CH3)3), ꢁ4.5, ꢁ4.6,ꢁ5.2, ꢁ5.3 (SiCH3); HRESI MS m/z
(621.1984 [MþNa]þ, C28H34N4O9SieNaþ calcd 621.1987).
v/v); 1H NMR (400 MHz, CD3OD)
d (major isomer) 8.21 (d, 1H,
J¼8.0 Hz, H-6), 6.19, 5.40 (s, 2H, H-10, H-80), 5.68 (d, 1H, J¼8.0 Hz,
H-5), 4.51 (d, 1H, J¼4.8 Hz, H-30), 3.92, 3.43 (AB, 2H, J¼11.2 Hz),
3.68, 3.50 (AB, 2H, J¼12.0 Hz), 2.47 (d, 1H, J¼5.2 Hz, H-20), 0.94 (s,
9H, SiC(CH3)3), 0.14 (s, 3H, SiCH3), 0.13 (s, 3H, SiCH3); 13C NMR
4.14. (1R,4R/S,5R,6R,8S)-8-Hydroxy-1-hydroxymethyl-4,6-di-
(100 MHz, CD3OD)
d
(major isomer) 166.4 (C-4), 151.7 (C-2), 142.4
(uracil-1-yl)-3,7-dioxabicyclo[3.2.1]octane (7)
(C-6), 101.6 (C-5), 91.6, 84.9, 84.3 (C-10, C-40, C-80), 68.3 (C-30),
65.8, 59.2 (C-50, C-60), 52.0 (C-20), 26.1 (SiC(CH3)3), 18.8
(SiC(CH3)3), ꢁ4.7, ꢁ5.1 (SiCH3); HRESI MS m/z (423.1562
[MþNa]þ, C17H28N2O7SieNaþ calcd 423.1559).
To a stirred solution of nucleoside 24 (229 mg, 0.38 mmol) in
anhydrous THF (3 mL) was added a 1 M solution of TBAF in anhy-
drous THF (0.57 mL, 0.57 mmol), and the mixture was stirred at

S. Kumar et al. / Tetrahedron 70 (2014) 583e589
589
6. Obika, S.; Rahman, S. M. A.; Fujisaka, A.; Kawada, Y.; Baba, T.; Imanishi, T.
Heterocycles 2010, 81, 1347e1392.
7. Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem. Commun. 1998,
room temperature for 1 h and then concentrated under reduced
pressure. The residue was dissolved in saturated methanolic NH3
(5 mL), and the reaction mixture was stirred at room temperature
for 4 h and concentrated under reduced pressure. The residue was
purified by silica gel column chromatography (0e7.5% CH3OH in
CH2Cl2) to give the product 7 (as an epimeric mixture 1:0.70,
105 mg, 72%) as a white foam; Rf 0.40 (CH3OH/dichloromethane
455e456.
8. Koshkin, A. A.; Singh, S. K.; Nielsen, P.; Rajwanshi, V. K.; Kumar, R.; Meldgaard,
M.; Olsen, C. E.; Wengel, J. Tetrahedron 1998, 54, 3607e3630.
9. Obika, S.; Nanbu, D.; Hari, Y.; Morio, K.; In, Y.; Ishida, T.; Imanishi, T. Tetrahedron
Lett. 1997, 38, 8735e8738.
10. Obika, S.; Nanbu, D.; Hari, Y.; Andoh, J.; Morio, K.; Doi, T.; Imanishi, T. Tetra-
hedron Lett. 1998, 39, 5401e5404.
11. Veedu, R. N.; Wengel, J. Chem. Biodiversity 2010, 7, 536e542.
12. Hari, Y.; Morikawa, T.; Osawa, T.; Obika, S. Org. Lett. 2013, 15, 3702e3705.
13. Singh, S. K.; Kumar, R.; Wengel, J. J. Org. Chem. 1998, 63, 10035e10039.
14. Hrdlicka, P. J.; Babu, B. R.; Sørense, M. D.; Harrit, N.; Wengel, J. J. Am. Chem. Soc.
2005, 127, 13293e13299.
15. Astakhova, I. K.; Pasternak, K.; Campbell, M. A.; Gupta, P.; Wengel, J. J. Am. Chem.
Soc. 2013, 135, 2423e2426.
16. Albæk, N.; Petersen, M.; Nielsen, P. J. Org. Chem. 2006, 71, 7731e7740.
17. Kumar, S.; Hansen, M. H.; Albæk, N.; Steffansen, S. I.; Petersen, M.; Nielsen, P. J.
Org. Chem. 2009, 74, 6756e6769.
18. Srivastava, P.; Barman, J.; Pathmasiri, W.; Plashkevytch, O.; Wenska, M.; Chat-
topadhyaya, J. J. Am. Chem. Soc. 2007, 129, 8362e8379.
19. Xu, J.; Dupouy, C.; Chattopadhyaya, J. J. Org. Chem. 2009, 74, 6534e6554.
20. Seth, P. P.; Allerson, C. R.; Berdeja, A.; Siwkowski, A.; Pallan, P. S.; Gaus, H.;
Prakash, T. P.; Watt, A. T.; Egli, M.; Swayze, E. E. J. Am. Chem. Soc. 2010, 132,
14942e14950.
21. Seth, P. P.; Pallan, P. S.; Swayze, E. E.; Egli, M. ChemBioChem 2013, 14, 58e62.
22. Grubbs, R. H.; Chang, S. Tetrahedron 1998, 54, 4413e4450.
23. McReynolds, M. D.; Dougherty, J. M.; Hanson, P. R. Chem. Rev. 2004, 104,
2239e2258.
24. Amblard, F.; Nolam, S. P.; Agrofoglio, L. A. Tetrahedron 2005, 61, 7067e7080.
25. Wang, G.; Girardet, J.-L.; Gunic, E. Tetrahedron 1999, 55, 7707e7724.
26. Pedersen, S. L.; Nielsen, P. Org. Biomol. Chem. 2005, 3, 3570e3575.
27. Christensen, M. S.; Madsen, C. M.; Nielsen, P. Org. Biomol. Chem. 2007, 5,
1586e1594.
15:85 v/v); 1H NMR (400 MHz, DMSO-d6)
d 11.29 (br s, 4H, NH), 8.08
(d, 1H, J¼8.0 Hz, H-6), 7.97 (d, 1H, J¼8.4 Hz, H-6), 7.87 (d, 1H,
J¼8.4 Hz, H-6), 7.58 (d, 1H, J¼8.0 Hz, H-6), 6.18 (s, 1H, OH), 5.98,
5.86, 5.75, 5.67 (s, 4H, H-10, H-80), 5.59e5.56 (m, 3H, H-5), 5.50 (d,
1H, J¼8.0 Hz, H-5), 4.24 (d, 1H, J¼5.6 Hz, H-30), 4.17e4.14 (m, 2H, H-
30, H-60), 4.0, 3.70 (AB, 2H, J¼11.2 Hz, H-60), 3.66 (d,1H, J¼11.2 Hz, H-
60), 3.61e3.58 (m, 2H, H-50), 3.50 (dd, 2H, J¼5.2, 12.8 Hz, H-50), 3.10
(dd, 1H, J¼1.2, 4.8 Hz, H-20), 2.70 (d, 1H, J¼5.6 Hz, H-20); HRESI MS
m/z (403.0860 [MþNa]þ, C15H16N4O8eNaþ calcd 403.0861). A small
amount was separated in a new chromatography to give the pure
epimer (1R,4R,5R,6R,8S)-8-hydroxy-1-hydroxymethyl-4,6-di-(ura-
cil-1-yl)-3,7-dioxabicyclo[3.2.1]octane; 1H NMR (400 MHz, DMSO-
d6)
d
11.32 (s, 1H, NH), 11.26 (s, 1H, NH), 7.97 (d, 1H, J¼8.8 Hz, H-6a),
7.87 (d, 1H, J¼8.4 Hz, H-6b), 6.10 (d, 1H, J¼4.4 Hz, 30-OH), 5.98 (s, 1H,
H-80), 5.67 (s, 1H, H-10), 5.58 (d, 1H, J¼8.8 Hz, H-5a), 5.57 (d, 1H,
J¼8.4 Hz, H-5b), 5.27 (t, 1H, J¼5.2 Hz, 50-OH), 4.24 (t, 1H, J¼5.2 Hz,
H-30), 4.01 (d, 1H, J¼10.8 Hz, H-60a), 3.71 (d, 1H, J¼10.8 Hz, H-60b),
3.61 (dd, 2H, J¼5.2, 12.4 Hz, H-50), 3.51 (dd, 2H, J¼5.6, 12.4 Hz, H-50),
2.71 (d, 1H, J¼5.2 Hz, H-20); 13C NMR (100 MHz, DMSO-d6)
d 163.3,
163.1 (C-4), 150.0, 149.9 (C-2), 140.1, 139.2 (C-6), 100.9, 100.5 (C-5),
83.2, 82.2, 78.4 (C-10, C-40, C-80), 66.5 (C-30), 64.3, 57.7 (C-50, C-60),
47.3 (C-20).
28. Christensen, M. S.; Bond, A.; Nielsen, A. Org. Biomol. Chem. 2008, 6, 81e91.
29. Shaikh, K. I.; Madsen, C. S.; Nielsen, L. J.; Jørgensen, A. S.; Nielsen, H.; Petersen,
M.; Nielsen, P. Chem.dEur. J. 2010, 16, 12904e12919.
30. Jørgensen, A. S.; Shaikh, K. I.; Enderlin, G.; Ivarsen, E.; Kumar, S.; Nielsen, P. Org.
Biomol. Chem. 2011, 9, 1381e1388.
31. Madsen, C. S.; Witzke, S.; Kumar, P.; Negi, K.; Sharma, P. K.; Petersen, M.;
Nielsen, P. Chem.dEur. J. 2012, 18, 7434e7442.
Acknowledgements
32. Kumar, P.; Sharma, P. K.; Madsen, C. S.; Petersen, M.; Nielsen, P. ChemBioChem
2013, 14, 1072e1074.
33. Madsen, C. S.; Nielsen, L. J.; Pedersen, N. S.; Lauritsen, A.; Nielsen, P. RSC Adv.
2013, 3, 10696e10706.
The project was supported by The Danish National Research
Foundation, The Danish Council for Independent Research Natural
Sciences (FNU) and Technology and Production Sciences (FTP) and
Villum Kann Rasmussen Fonden.
34. Wu, T.; Froeyen, M.; Schepers, G.; Mullens, K.; Rozenski, J.; Busson, R.; Van
Aershot, A.; Herdewijn, P. Org. Lett. 2004, 6, 51e54.
35. Wu, T.; Nauwelaerts, K.; Van Aershot, A.; Froeyen, M.; Lescrinier, E.; Herdewijn,
P. J. Org. Chem. 2006, 71, 5423e5431.
Supplementary data
36. Umemoto, T.; Wengel, J.; Madsen, A. S. Org. Biomol. Chem. 2009, 7, 1793e1797.
37. Pavey, J. B. J.; Lawrence, A. J.; Potter, A. J.; Cosstick, R.; O’Niel, I. A. Tetrahedron
Lett. 1998, 39, 6967e6970.
38. Warmerdam, E.; Tranoy, I.; Renoux, B.; Gesson, J.-P. Tetrahedron 1998, 39,
8077e8080.
39. Kirchhoff, C.; Nielsen, P. Tetrahedron Lett. 2003, 44, 6475e6478.
40. Hoye, T. R.; Jeffrey, C. S.; Tennakoon, M. A.; Wang, J.; Zhao, H. J. Am. Chem. Soc.
2004, 126, 10210e10211.
Selected NMR spectra can be found in the online version. Sup-
plementary data related to this article can be found at http://
dx.doi.org/10.1016/j.tet.2013.12.013.
References and notes
41. Wallace, D. J. Angew. Chem., Int. Ed. 2005, 55, 1912e1915.
42. Mikkelsen, L. M.; Skrydstrup, T. J. Org. Chem. 2003, 68, 2123e2128.
43. Hauser, C. F.; Brooks, T. W.; Miles, M. L.; Raymond, M. A.; Butler, G. B. J. Org.
Chem. 1963, 28, 372e379.
1. Kurreck, J. Eur. J. Biochem. 2003, 270, 1628e1644.
2. Bell, N. M.; Micklefield, J. ChemBioChem 2009, 10, 2691e2703.
3. Lennox, K. A.; Behlke, M. A. Gene Ther. 2011, 18, 1111e1120.
4. Zhou, C.; Chattopadhyaya, J. Chem. Rev. 2012, 112, 3808e3832.
5. Lebreton, J.; Escudier, J.-M.; Arzel, L.; Len, C. Chem. Rev. 2010, 110, 3371e3418.