Synthesis of bicyclic 2′-deoxynucleosides with α-L-ribo- And β-D-xylo-configurations and restricted S- and N-type conformations

Article abstract of DOI:10.1021/jo8023472

Two bicyclic 2'′-deoxynucleoside analogues are synthesized in 12 steps each from thymidine. With a six- membered ring fused to the C3'′-C4'′ bond and an α-L-ribo- and a β-D-xylo- configuration, these are conformationally restricted in an S- and an N-type

Full text of DOI:10.1021/jo8023472

Synthesis of Bicyclic 2′-Deoxynucleosides with r-L-ribo- and
ꢀ-D-xylo-Configurations and Restricted S- and N-Type
Conformations
Khalil I. Shaikh,† Surender Kumar,†,§ Lene Lundhus,† Andrew D. Bond,‡
Pawan K. Sharma,§ and Poul Nielsen*,†
Nucleic Acid Center, Department of Physics and Chemistry, UniVersity of Southern Denmark, 5230 Odense M,
Denmark, and Department of Chemistry, Kurukshetra UniVersity, Kurukshetra-136 119, India
pon@chem.sdu.dk
ReceiVed October 21, 2008
Two bicyclic 2′-deoxynucleoside analogues are synthesized in 12 steps each from thymidine. With a six-
membered ring fused to the C3′-C4′ bond and an R-L-ribo- and a ꢀ-D-xylo-configuration, these are
conformationally restricted in an S- and an N-type conformation, respectively. The constitutions were proven
by X-ray crystallography. The ꢀ-D-xylo-configured analogue is successfully converted to a 3′-phosphoramidite
and incorporated into oligodeoxynucleotides, which are found to hybridize to DNA and RNA complements
with decreased affinity.
Introduction
The field of nucleic acid chemistry has developed tremendously
by the introduction of conformationally restricted nucleoside
building blocks.1 Especially, nucleosides with bi- or tricyclic
carbohydrate moieties have led to oligonucleotides with strong
affinities for complementary DNA and RNA.2 As a prime example,
locked nucleic acid (LNA) has been introduced as oligonucleotides
containing one or more of the [2.2.1]bicyclic nucleoside monomer
1, which is conformationally locked in the N-type nucleoside
conformation as a result of the additional 2′,4′-oxymethylene
connection as compared to unmodified 2′-deoxynucleotides (Figure
1).3 The introduction of one or more LNA monomers in an
oligodeoxynucleotide (ODN) secures a conformational steering of
† Nucleic Acid Center, Department of Physics and Chemistry, University of
Southern Denmark. The Nucleic Acid Center is funded by the Danish National
Research Foundation for studies on nucleic acid chemical biology.
‡ Department of Physics and Chemistry, University of Southern Denmark.
§ Kurukshetra University.
(1) (a) Kool, E. T. Chem. ReV. 1997, 97, 1473–1487. (b) Kurreck, J. Eur.
J. Biochem. 2003, 270, 1628–1644.
(2) (a) Meldgaard, M.; Wengel, J. J. Chem. Soc., Perkin Trans. 2000, 1, 3539–
3554. (b) Leumann, C. J. Bioorg. Med. Chem. 2002, 10, 841–854.
(3) (a) Singh, S. K.; Nielsen, P.; Koshkin, A. A.; Wengel, J. Chem. Commun.
1998, 455–456. (b) Koshkin, A. A.; Singh, S. K.; Nielsen, P.; Rajwanshi, V. K.;
Kumar, R.; Meldgaard, M.; Olsen, C. E.; Wengel, J. Tetrahedron 1998, 54, 3607–
3630. (c) Obika, S.; Nanbu, D.; Hari, Y.; Andoh, J.; Morio, K.; Doi, T.; Imanishi,
T. Tetrahedron Lett. 1998, 39, 5401–5404. (d) Koshkin, A. A.; Nielsen, P.;
Meldgaard, M.; Rajwanshi, V. K.; Singh, S. K.; Wengel, J. J. Am. Chem. Soc. 1998,
120, 13252–13253.
FIGURE 1. (a) Low-energy conformations of 2′-deoxynuclesides. (b)
Conformationally restricted ꢀ-D- and R-L-configured bicyclic nucleo-
sides. B ) any nucleobase. T ) thymin-1-yl.
neighboring 2′-deoxynucleotides toward the N-type conformation
and formation of A-type or A-type-like duplexes with comple-
10.1021/jo8023472 CCC: $40.75
Published on Web 01/20/2009
2009 American Chemical Society
J. Org. Chem. 2009, 74, 1557–1566 1557

Shaikh et al.
mentary RNA and DNA, respectively.4 LNA has demonstrated
unprecedented DNA- and RNA-recognition and promising results
as potential antisense therapeutic compounds.5
an ꢀ-D-arabino configuration is conformationally locked in the
E-type conformation and demonstrated in mixmers with 2′-
deoxynucleotides and as fully modified sequences somewhat
increased hybridization to complementary DNA and RNA.14
Also its R-anomer (i.e., R-D-arabino configuration) has been
studied demonstrating the formation of stable parallel duplexes
with RNA complementing the properties of R-D-LNA.15 Many
studies toward the synthesis of a perfect locked S-type mimic
have been performed over the years by us and others,16-20 but
the most obvious solution to the problem, with no unfavorable
steric demand in the duplex core, seems to be the [4.3.0]bicyclic
2′-deoxynucleoside 4 with a four-atom 3′,4′-connection and an
additional six-membered ring forcing the 2′-deoxyribose moiety
into a locked or at least very restricted S-type conformation.18-20
This nucleoside and corresponding ODNs thereof have been
only very recently synthesized, and the hybridization was only
briefly reported to display a decrease in melting temperature of
a DNA:DNA duplex by 3 °C for one modification.18 The two
2′-O-methyl analogues 5 and 6 (with ꢀ-D-ribo- and ꢀ-D-arabino-
configuration, respectively) have also been studied,19,20 but
whereas the incorporation of 5 synthetically failed, 6 led to
significantly decreased hybridization properties, most probably
due to an unfavorable steric influence of the 2′-O-methyl
group.19 The synthesis of 5 and 6 has been accomplished
through a long convergent strategy starting from diacetone-R-
D-glucose with oxidation and a stereoselective Grignard reaction
as the first key step and with the stereoselectivity controlled by
the 1,2-di-O-isopropylidine group.19 Nevertheless, a high num-
ber of functional group transformations including nucleobase
coupling and protection/deprotections were necessary, giving a
synthesis of 5 and 6 in 19 and 21 steps, respectively.18 The
synthesis of 4 by a similar strategy would demand a final 2′-
deoxygenation. However, the preparation of 4 was finally
accomplished through a linear 17-step synthesis from thymi-
dine.18
Among a large number of chemical analogues of LNA, the
stereoisomers of LNA have shown intriguing results.6-10 R-L-
LNA, 2, has shown the same ability of significantly increasing
duplex stability both in fully modified R-L-LNA sequences and
in combination with unmodified naturally ꢀ-D-ribo-configured
2′-deoxynucleotides.6,7 The resulting duplexes, however, are
more B-type-like duplexes with the unmodified 2′-deoxynucle-
otides in S-type conformations.8 Also the two stereoisomers of
LNA with xylo- instead of ribo-configuration (i.e., ꢀ-D-xylo-
LNA and R-L-xylo-LNA corresponding to opposite 3′-config-
urations as compared to 1 and 2, Figure 1) have been synthesized
and studied. Fully modified ꢀ-D-xylo-LNA oligothymidylate
sequences demonstrated an affinity for DNA and RNA that is
increased as compared to unmodified oligodeoxynucleotides but
somewhat decreased as compared to LNA.6,9 Studies of these
four LNA stereoisomers in the “mirror-image world” by mixing
the sequences with ꢀ-L-configured DNA and RNA demonstrated
the features of ꢀ-L-LNA, R-D-LNA, ꢀ-L-xylo-LNA, and R-D-
xylo-LNA.6 Among these, R-D-LNA has also been synthetically
realized,10 and both R-D-LNA and ꢀ-L-LNA form parallel
duplexes with complementary RNA of increased thermal
stability6,10 as compared to the well-known parallel-stranded
duplex formed between R-D-ribo-configured ODNs (R-DNA)
and complementary DNA and RNA.11
The intriguring hybridization properties of the series of LNA
and LNA stereoisomers are based on the locked [2.2.1]bicyclic
structure and the resulting inflexible N-type conformation.12
However, natural nucleosides exist in an equilibrium between
N- and S-type conformations with the E-type conformation as
the transition state conformation.13 Therefore, also bicyclic
nucleosides locked in E- or S-type conformations are interesting
and intensively studied.2 The [3.2.0]bicyclic nucleoside 3 with
In the present study, we decided to investigate the locked
S-type conformation of the [4.3.0]bicyclic skeleton of 4 in
combination with other stereoisomers. With the remarkable
(4) (a) Bondensgaard, K.; Petersen, M.; Singh, S. K.; Rajwanshi, V. K.;
Kumar, R.; Wengel, J.; Jacobsen, J. P. Chem. Eur. J. 2000, 6, 2687–2695. (b)
Nielsen, K. E.; Rasmussen, J.; Kumar, R.; Wengel, J.; Jacobsen, J. P.
Bioconjugate Chem. 2004, 15, 449–457. (c) Petersen, M.; Bondensgaard, K.;
Wengel, J.; Jacobsen, J. P. J. Am. Chem. Soc. 2002, 124, 5974–5982.
(5) (a) Petersen, M.; Wengel, J. Trends Biotechnol. 2003, 21, 74–81. (b)
Jepsen, J. S.; Wengel, J. Curr. Opin. Drug DiscoVery DeV. 2004, 7, 188–194.
(c) Kaur, H.; Babu, B. R.; Maiti, S. Chem. ReV. 2007, 107, 4672–4697.
(6) (a) Rajwanshi, V. K.; Håkansson, A. E.; Sørensen, M. D.; Pitsch, S.;
Singh, S. K.; Kumar, R.; Nielsen, P.; Wengel, J. Angew. Chem., Int. Ed. 2000,
39, 1656–1659. (b) Christensen, N. K.; Bryld, T.; Sørensen, M. D.; Arar, K.;
Wengel, J.; Nielsen, P. Chem. Commun. 2004, 282–283.
(7) Sørensen, M. D.; Kværnø, L.; Bryld, T.; Håkansson, A. E.; Verbeure,
B.; Gaubert, G.; Herdewijn, P.; Wengel, J. J. Am. Chem. Soc. 2002, 124, 2164–
2176.
(8) Petersen, M.; Håkansson, A. E.; Wengel, J.; Jacobsen, J. P. J. Am. Chem.
Soc. 2001, 123, 7431–7432.
(14) (a) Christensen, N. K.; Petersen, M.; Nielsen, P.; Jacobsen, J. P.; Olsen,
C. E.; Wengel, J. J. Am. Chem. Soc. 1998, 120, 5458–5463. (b) Højland, T.;
Kumar, S.; Babu, B. R.; Umemoto, T.; Albæk, N.; Sharma, P. K.; Nielsen, P.;
Wengel, J. Org. Biomol. Chem. 2007, 5, 2375–2379.
(15) Sharma, P. K.; Petersen, M.; Nielsen, P. J. Org. Chem. 2005, 70, 4918–
4928.
(16) (a) Tarko¨y, M.; Bolli, M.; Schweizer, B.; Leumann, C. HelV. Chim.
Acta 1993, 76, 481–510. (b) Altmann, K.-H.; Imwinkelried, R.; Kesselring, R.;
Rihs, G. Tetrahedron Lett. 1994, 35, 7625–7628. (c) Nielsen, P.; Pfundheller,
H. M.; Olsen, C. E.; Wengel, J. J. Chem. Soc., Perkin Trans. 1997, 1, 3423–
3433. (d) Ravn, J.; Thorup, N.; Nielsen, P. J. Chem. Soc., Perkin Trans. 2001,
1, 1855–1861. (e) Renneberg, D.; Leumann, C. J. J. Am. Chem. Soc. 2002, 124,
5993–6002. (f) Albaek, N.; Ravn, J.; Freitag, M.; Thomasen, H.; Christensen,
N. K.; Petersen, M.; Nielsen, P. Nucleosides, Nucleotides Nucleic Acids 2003,
22, 723–725. (g) Freitag, M.; Thomasen, H.; Christensen, N. K.; Petersen, M.;
Nielsen, P. Tetrahedron 2004, 60, 3775–3786. (h) Obika, S.; Osaki, T.; Sekiguchi,
M.; Somjing, R.; Harada, Y.; Imanishi, T. Tetrahedron Lett. 2004, 45, 4801–
4804. (i) Obika, S.; Sekiguchi, M.; Somjing, R.; Imanishi, T. Angew. Chem.,
Int. Ed. 2005, 44, 1944–1947. (j) Stauffiger, A.; Leumann, C. Nucleic Acids
Symp. Ser. 2008, 52, 267–268.
(9) (a) Rajwanshi, V. K.; Håkansson, A. E.; Dahl, B. M.; Wengel, J. Chem.
Commun. 1999, 1395–1396. (b) Rajwanshi, V. K.; Håkansson, A. E.; Kumar,
R.; Wengel, J. Chem. Commun. 1999, 2073–2074.
(10) (a) Nielsen, P.; Dalskov, J. K. Chem. Commun. 2000, 1179–1180. (b)
Nielsen, P.; Christensen, N. K.; Dalskov, J. K. Chem. Eur. J. 2002, 8, 712–722.
(11) (a) Morvan, F.; Rayner, B.; Imbach, J.-L.; Thenet, S.; Bertrand, J.-R.;
Paoletti, J.; Malvy, C.; Paoletti, C. Nucleic Acids Res. 1987, 15, 3421–3437. (b)
Thuong, N. T.; Asseline, U.; Roig, V.; Takasugi, M.; He´le`ne, C. Proc. Natl.
Acad. Sci. U.S.A. 1987, 84, 5129–5133. (c) Gagnor, C.; Bertrand, J.-R.; Thenet,
S.; Lemaˆıtre, M.; Morvan, F.; Rayner, B.; Malvy, C.; Lebleu, B.; Imbach, J.-L.;
Paoletti, C. Nucleic Acid Res. 1987, 15, 10419–10436. (d) Gagnor, C.; Rayner,
B.; Leonetti, J.-P.; Imbach, J.-L.; Lebleu, B. Nucleic Acid Res. 1989, 17, 5107–
5114.
(17) Also an R-D-ribo-configured S-type mimic has been studied: Keller,
B. M.; Leumann, C. J. Synthesis 2002, 789–796.
(18) (a) Sugaya, K.; Harada, Y.; Mitsuoka, Y.; Osaki, T.; Obika, S.; Kodama,
T.; Imanishi, T. Nucleic Acid Symp. Ser. 2007, 51, 155–156. (b) Osaki, T.; Obika,
S.; Harada, Y.; Mitsuoka, Y.; Sugaya, K.; Sekiguchi, M.; Roonjang, S.; Imanishi,
T. Tetrahedron 2007, 63, 8977–8986.
(12) The N-type conformation is defined as the conformation with the 3′-
carbon puckering to the same side as the 5′-carbon. Therefore, we define 1, 2,
and 8 as N-type mimics, whereas 4-7 are defined as S-type mimics.
(13) For definitions and nomenclature regarding nucleoside and nucleic acid
structure and conformations, see: Saenger, W. Principles of Nucleic Acid
Structure; Springer: New York, 1984.
(19) (a) Obika, S.; Sekiguchi, M.; Osaki, T.; Shibata, N.; Masaki, M.; Hari,
Y.; Imanishi, T. Tetrahedron Lett. 2002, 43, 4365–4368. (b) Sekiguchi, M.;
Obika, S.; Harada, Y.; Osaki, T.; Somjing, R.; Mitsuoka, Y.; Shibata, N.; Masaki,
M.; Imanishi, T. J. Org. Chem. 2006, 71, 1306–1316.
(20) Thomasen, H.; Meldgaard, M.; Freitag, M.; Petersen, M.; Wengel, J.;
Nielsen, P. Chem. Commun. 2002, 1888–1889.
1558 J. Org. Chem. Vol. 74, No. 4, 2009

Synthesis of Bicyclic 2′-Deoxynucleosides
SCHEME 1. Preparation of ꢀ-D-xylo-Configured
2′-Deoxynucleoside 8a
FIGURE 2. Retrosynthesis of compound 7. T ) thymin-1-yl. Pg )
protecting group.
properties of R-L-LNA, 2, in mind, the corresponding R-L-ribo-
configured S-type mimic 7 was our primary goal. Hence,
mixmers of 7 with standard 2′-deoxynucleotides might form
improved hybridization properties toward DNA and RNA
complements and/or toward double-stranded DNA in the
formations of triplexes, whereas fully modified sequences might
be even more interesting. In the mirror-image world (meaning
with L-DNA and L-RNA complements), this bicyclic nucleoside
would give immediate information on the R-D-configured
analogue and thereby conclude also the study on the scope of
parallel duplex formation.10,11,15,17 The synthesis is envisioned
to be much simpler than the synthesis of 4 due to the opposite
3′-configuration (see retrosynthesis in Figure 2). Thus, the
reaction of Grignard and organolithium reagents with 5′-O-
protected 3′-ketonucleosides A has been reported to give the
xylo-configured products with a high stereoselectivity due to
the steric influence from the nucleobase.21,22 Hereby, a 3′-
allylcompound B should be easily accessible, and subsequent
standard 5′-oxidation and aldol condensation followed by double
bond cleavage should give C and ring-closure the target R-L-
ribo- configured bicyclic nucleoside 7. As a secondary goal,
also the ꢀ-D-xylo-configured 8 (Figure 1) should be achievable
from the same strategy using the 4′-epimer of C.
a Reagents and conditions: (a) (i) pyridinium dichromate, CH2Cl2, (ii)
AllylMgBr, CeCl3 ·7H2O, THF, -78°C, 41%; (b) NaH, BnBr, THF, -78°C
to rt, 80% 11, 10% 12; (c) (i) 80% aq AcOH, 90°C, (ii) NaOMe, MeOH,
75%; (d) (i) Dess-Martin periodinane, CH2Cl2 or (COCl)2, DMSO, NEt3,
CH2Cl2, (ii) HCHO, NaOH, 57% or 60%; (e) DMT-Cl, pyridine, 59%; (f)
Ms-Cl, CH2Cl2, 2,6-lutidine, 82%; (g) OsO4-NaIO4, then NaBH4, aq THF,
49%; (h) NaH, DMF, 68%; (i) Pd(OH)2/C, EtOH, 86%; (j) DMT-Cl,
pyridine, mw 80°C, 93%; (k) NC(CH2)2OP(Cl)N(iPr)2, EtN(iPr)2, CH2Cl2,
79%. Bn ) benzyl, DMT ) 4,4′-dimethoxytrityl, Ms ) methanesulfunyl.
Results and Discussion
Chemical Synthesis of Bicyclic Nucleosides. As the first
step in the planned linear synthesis, thymidine was converted
to its well-known 5′-tritylated derivative 9 (Scheme 1). Oxida-
tion using PCC and subsequent Grignard reaction with allyl-
magnesium bromide was accomplished with some difficulties
due to the sensitivity of the intermediate ketone to undergo a
ꢀ-elimination of the nucleobase. However, a cerium-assisted
Grignard reaction22 afforded the ꢀ-D-xylo-configured 3′-C-allyl
nucleoside derivative 10 in a reasonable 41% yield over the
two steps. The benzyl group was chosen as a permanent
protecting group for the tertiary alcohol. However, benzylation
performed at room temperature or with slight cooling afforded
the monobenzylated product 11 as well as the dibenzylated
12. The latter can even be obtained in a high yield with a
large excess of benzylbromide (see Supporting Information).
However, this dibenzylation was prevented by lowering the
reaction temperature further, and the reaction was carried
out from -78 °C to room temperature, yielding 11 in 80%.23
Detritylation of 11 by treatment in refluxing 80% aqueous
(21) (a) Koole, L. H.; Buck, H. M.; Vial, J.-M.; Chattopadhyaya, J. Acta
Chem. Scand. 1989, 43, 665–669. (b) Webb, T. R. Tetrahedron Lett. 1988, 29,
3769–3772. (c) Huss, S.; De las Heras, F. G.; Camarasa, M. J. Tetrahedron
1991, 47, 1727–1736. (d) Dupouy, C.; Lavedan, P.; Escudier, J.-M. Tetrahedron
2007, 63, 11235–11243.
(22) (a) Bender, S. L.; Moffett, K. K. J. Org. Chem. 1992, 57, 1646–1647.
(b) Jung, P. M. J.; Burger, A.; Biellmann, J.-F. Tetrahedron Lett. 1995, 36, 1031–
1034. (c) Nielsen, P.; Larsen, K.; Wengel, J. Acta Chem. Scand. 1996, 50, 1030–
1035. (d) Jung, P. M. J.; Burger, A.; Biellmann, J.-F. J. Org. Chem. 1997, 62,
8309–8314.
(23) The cleavage of an N3-benzylthymine-bond has been reported before
using Na-naphthalate as the active reagent: Philips, K. D.; Horwitz, J. P. J. Org.
Chem. 1975, 40, 1856–1858. Therefore, the synthesis of the bicyclic nucleoside
target has also been approached using the N3-benzylated compound 12 in order
to remove both benzyl groups in the last step. All steps were prepared in similar
yields giving finally the N3-benzyl derivative of 8. However, efficient removal
of the N3-benzyl group was not accomplished. See Supporting Information for
details.
J. Org. Chem. Vol. 74, No. 4, 2009 1559

Shaikh et al.
acetic acid gave the target 5′-hydroxy compound 13 as well
as the corresponding 5-acetylated derivative, wherefore the
mixture was treated with sodium methoxide to give 13 as
the only product in 75% yield. Oxidation using Dess-Martin
periodinane and a subsequent standard aldol condensation
followed by Cannizzarro reaction afforded the 4′-C-hydroxym-
ethyl nucleoside 14 in 57% yield. On a slightly smaller scale,
this oxidation was also accomplished on compound 13 using
Swern oxidation conditions, yielding after the aldol/Cannizzarro
reaction 14 in 60% yield. Regioselective differentiation between
the two primary alcohols in different analogues of 14 has been
accomplished before. Nucleosides with ribo-configuration have
been applied,24-26 including 3′-C-substituted analogues,18 and
also xylo-configured nucleosides have been applied.27 In all
cases, the 4′-hydroxymethyl group has been selectively reacted
over the 5′-hydroxyl group. The regioselectivity has been
deduced to steric hindrance from the nucleobase. Among others,
the 4,4′-dimethoxytrityl (DMT) group has been applied,18,25,27
and therefore, compound 14 was treated with DMT-Cl in
pyridine at room temperature to give 15 in 59% yield. No other
products were isolated. However, the stereochemistry of C-4′
was not proved at this stage and, in fact, was opposite of what
was predicted. Mesylation of 15 gave easily 16 in 82%, and
oxidative cleavage of the allyl group and subsequent reduction
of the aldehyde was achieved with OsO4-NaIO4 and NaBH4
to give 17 in 49% yield. The ring closure was accomplished
with a treatment of NaH in DMF to give the bicyclic compound
18 in 68% yield. Different reaction conditions to give the
selective debenzylation and an intact trityl ether was attempted
including the use of ammonium formate, which has been used
before to solve a similar problem in the synthesis of R-L-LNA.9,27
Nevertheless, the best method proved to be a hydrogenation
with palladium hydroxide over carbon to give the fully
deprotected target nucleoside 8 in 86% yield. The NMR spectra
of this compound did not prove the stereochemistry of the
3
bicyclic nucleoside. For instance, the two JH1′H2′ coupling
constants of 2.1 and 8.1 Hz were in accordance with both 7
and 8 expecting a 3′-endo/2′-exo conformation in both cases.
However, the compound was crystallized from methanol, and
the single-crystal X-ray structure (Figure 3) revealed that the
stereochemistry of the C-4′-position was opposite to that of the
expected compound and that the synthetic route resulted in
the 2′-deoxynucleoside 8 with ꢀ-D-xylo-configuration and not
the targeted 2′-deoxynucleoside 7 with R-L-ribo-configuration.
This result proved that the relative reactivity for the two
primary alcohols in 14 were opposite the expected and that the
regioselective protection strategy had to be changed. Therefore,
mesylation was carried out first using mesylchloride, affording
compound 21 as well the dimesylate 22 in 44% and 33% yield,
respectively (Scheme 2). Later, compound 22 was reconverted
into 21 in 25% yield (or 37% based on the recovery of starting
material) by nucleophilic substitution using potassium acetate
and 18-crown-6 and subsequent hydrolysis. The position of the
mesyl group was determined directly by single-crystal X-ray
FIGURE 3. X-ray crystal structures of (a) 7 and (b) 8.
analysis of compound 21, which was crystalized from CH2Cl2
(see Supporting Information). To improve the regioselective
reaction by considering steric effect of the 5′-hydroxyl group,
activation with the tosyl group as an alternative to the mesyl
group was applied. Unfortunately, tosylation by the treatment
of 14 with tosylchloride in CH2Cl2 in the presence of 2,6-lutidine
was very slow and resulted in only 26% yield of the desired
compound 23 (or 86% based on the recovery of 70% starting
material). The 4′-hydroxymethyl group of the two 5′-sulfonic
esters 21 and 23 was blocked with the DMT residue to give 24
and 25 in 75% and 81% yield, respectively. Oxidative cleavage
of the allyl group by OsO4-NaIO4 and subsequent reduction
of the aldehyde with NaBH4 was achieved to give compounds
26 and 27 in 48% and 50% yield, respectively. The ring closure
was accomplished on both compounds using similar condition
as described for 17 (NaH in DMF) to give the bicyclic
compound 28 in a 95% yield in both cases. As in the
deprotection of 18, similar attempts were made for a chemose-
lective debenzylation without detritylation, but hydrogenolysis
with catalytic amount of palladium hydroxide over carbon for
10 h at room temperature resulted only in cleavage of the 5′-
DMT ether to give 29 still containing the benzyl group. The
(24) (a) O-Yang, C.; Wu, H. Y.; Fraser-Smith, E. B.; Walker, K. A. M.
Tetrahedron Lett. 1992, 33, 37–40. (b) Thrane, H.; Fensholdt, J.; Regner, M.;
Wengel, J. Tetrahedron 1995, 51, 10389–10402.
(25) (a) Montembault, M.; Bourgougnon, N.; Lebreton, J. Tetrahedron Lett.
2002, 43, 8091–8094. (b) Le Cle´zio, I.; Gornitzka, H.; Escudier, J.-M.; Vigroux,
A. J. Org. Chem. 2005, 70, 1620–1629.
(26) Albæk, N.; Petersen, M.; Nielsen, P. J. Org. Chem. 2006, 71, 7731–
7740.
(27) Håkansson, A. E.; Koshkin, A. A.; Sørensen, M. D.; Wengel, J. J. Org.
Chem. 2000, 65, 5161–5166.
1560 J. Org. Chem. Vol. 74, No. 4, 2009

Synthesis of Bicyclic 2′-Deoxynucleosides
SCHEME 2. Preparation of r-L-ribo-Configurated
2′-Deoxynucleoside 7a
to give 19 (Scheme 1) and 31 (Scheme 2) in 93% and 97%
yield, respectively. Phosphitylation of compound 19 using
standard conditions was successful, giving the phosphoramidite
20 in 79% yield. On the other hand, similar phosphitylation to
give the target phosphoramidite 32 from 31 was most unfor-
tunately not successful at all. A wide range of conditions were
attempted including 2-cyanoethyl N,N,N′,N′-tetraisopropylphos-
phoramidite as an alternative phosphitylation reagent with
tetrazole or 4,5-dicyanoimidazole as an activator. The reason
for the unsuccesful phosphitylation might be found in a
significant steric hindrance of the tertiary alcohol of 7. Thus, a
similar phosphitylation of compound 5 has also been reported
unsuccessful, whereas the isomer 6 was easily reacted.19 The
pseudoequatorially positioned methylgroup on the R-face of the
ring is most probably sterically hindering the 3′-hydroxyl group
of 5. In the case of 7, the steric problem might be the nucleobase
in proximity to the 3′-hydroxy group in a 1,3-diaxial orientation.
The reason why 8 is more reactive than 7 might be found in
the less constrained bicyclic structure allowing some flexibility
and compensation for this steric hindrance.
The phosphoramidite 20 was incorporated into 9-mer ODN
sequences with either one or three modifications (Table 1). The
same 9-mer sequence as employed in the first study of LNA3
and other nucleic acid analogues7,9,26,28 was employed for easy
comparison. Coupling of 20 proceeded in high yields, and the
composition of the modified oligonucleotides was verified by
MALDI MS. The hybridization of the modified ODNs toward
complementary DNA and RNA sequences was studied by
thermal denaturation experiments, and the melting temperatures
of the formed duplexes were determined and compared with
the unmodified duplexes (Table 1). These experiments show
that a single incorporation of the bicyclic ꢀ-D-xylo-configured
2′-deoxynucleoside 8 led to decreased affinity for both DNA
and RNA, whereas no stable duplexes could be detected in the
case of three modifications.
These results demonstrate clearly that the unnatural xylo-
configuration of 8 is not compatible with natural unmodified
2′-deoxynucleotides in a mixmer sequence concerning the
formation of stable duplexes, although the destabilizing effect
is somewhat less pronounced for a DNA:RNA duplex than for
the DNA:DNA duplex. In the same mixmer sequences, the
unrestricted 2′-deoxy-xylo-DNA thymine monomer has been
found to give only slightly smaller decreases in melting
temperature (∆Tm ) -6 in DNA:DNA and -1 °C in DNA:
RNA).28 The ꢀ-D-xylo-configured LNA-stereoisomer has also
been found to be incompatible with 2′-deoxynucleotides in
mixmers, as large decreases in melting temperature were
observed.9,28 On the other hand, stable duplexes were formed
between fully modified xylo-LNA oligothymidylates and comple-
mentary DNA and RNA.9,28 The xylo-configured analogue 8 is
clearly not as strongly conformationally restricted as the xylo-
LNA monomer (or as 7 or the other bicyclic analogues shown
in Figure 1) due to the syn-fused bicyclic system. The large
hydrophobic ring might contribute significantly to the large
decrease in duplex stability. In the end, the R-L-ribo-configu-
ration has shown more intriguing properties than the ꢀ-D-xylo-
configuration in the locked N-type conformation of R-L-LNA,
2, in both fully modified and mixmer contexts.6,7 Therefore,
the failed preparation of the phosphoramidite of the R-L-ribo-
configured bicyclic target nucleoside 7 with its locked S-type
a Reagents and conditions: (a) MsCl, CH2Cl2, 2,6-lutidine, 44% 21 +
33% 22; (b) DMT-Cl, pyridine, 75% 24, 81% 25; (c) 18-crown-6, KOAc,
CH2Cl2, 100°C, 25%; (d) TsCl, CH2Cl2, 2,6-lutidine, 26%; (e) OsO4-NaIO4,
NaBH4, aq THF, 48% 26, 50% 27; (f) NaH, DMF, 95% from 26, 95%
from 27; (g) Pd(OH)2/C, EtOH, 89%; (h) BCl3, CH2Cl2, 50%; (i) Pd(OH)2/
C, EtOH, 55%; (j) DMT-Cl, pyridine, 97%. Ts ) p-toluenesulfunyl.
bicyclic structure and the position of the benzyl group was
proven by single-crystal X-ray analysis of the compound (see
Supporting Information). The debenzylation was therefore
attempted using a Lewis acid mediated reaction with BCl3, but
both deprotections and a ring opening of the constrained six-
membered ring took place to give compound 30 in 50% yield.
Therefore, slightly harsher hydrogenolysis conditions were
applied for the debenzylation of 28. A large excess of palladium
hydroxide over carbon was used, and hydrogen gas was passed
through the reaction mixture for 5 days to give a fully
deprotected target nucleoside 7 in 55% yield. Some depyrim-
idination was also detected. The fully deprotected target
nucleoside 7 was successfully crystallized (as a hydrate) from
a solution in methanol for the determination of stereochemistry,
and the expected structure was confirmed by single-crystal X-ray
3
analysis (Figure 3). Remarkably, the two JH1′H2′ coupling
1
constants were found from the H NMR spectra to be exactly
the same 2.1 and 8.1 Hz for 7 as for compound 8, indicating
exactly the same 3′-endo puckering defined as S- and N-type
conformations, respectively.12
Synthesis and Evaluation of Oligonucleotides. For the
preparation of oligonucleotides by standard solid-phase chem-
istry using the phosphoramidite approach, the two bicyclic
nucleosides 7 and 8 had to be converted into the 5′-O-DMT-
protected 3′-O-phosphoramidites. As shown above, the 5′-DMT
group was cleaved during hydrogenolysis in the preparation of
both compounds, wherefore a selective retritylation was neces-
sary. This was accomplished in both cases using standard
conditions affording selective protection of the primary alcohols
(28) Babu, B. R.; Raunak; Poopeiko, N. E.; Juhl, M.; Bond, A. D.; Parmar,
V. S.; Wengel, J. Eur. J. Org. Chem. 2005, 2297–2321.
J. Org. Chem. Vol. 74, No. 4, 2009 1561

Shaikh et al.
TABLE 1. Thermal Stability Data of Modified Duplexes
Tm (∆Tm), °Cb
complementary DNA
5′-dGCATATCAC-3′
complementary RNA
5′-rGCAUAUCAC-3′
ODN sequencesa
33
34
35
5′-dGTGATATGC-3′
5′-dGTGAXATGC-3′
5′-dGXGAXAXGC-3′
29.0
21.0 (-8.0)
<10.0 (<-6.0)
26.5
23.5 (-3.0)
<10.0 (<-5.5)
a Oligodeoxynucleotide sequences with X ) 8 (incorporation of 20). b Melting temperatures obtained from the maxima of the first derivatives of the
melting curves (A260 vs temperature) recorded in a buffer containing 5 mM Na2HPO4, 10 mM NaH2PO4, 100 mM NaCl, 0.1 mM EDTA, pH 7.0 using
1.0 µM concentrations of each strand. Values in brackets show the changes in Tm values per modification compared with the reference strand.
(bs, 1H, NH), 7.86 (s, 1H, H-6), 7.47-7.20 (m, 15H, Ar), 6.16
(dd, 1H, J ) 2.7, 8.1 Hz, H-1′), 5.72 (m, 1H, H-2′′), 5.08-4.99
(m, 2H, H-3′′), 3.79 (t, 1H, J ) 3.6 Hz, H-4′), 3.70-3.61 (m, 2H,
H-5′, 3′-OH), 3.48 (dd, 1H, J ) 3.6, 10.8 Hz, H-5′), 2.45 (dd, 1H,
J ) 8.1, 14.7 Hz, H-2′), 2.33-2.08 (m, 3H, H-1′′, H-2′), 1.82 (s,
3H, CH3); 13C NMR (75 MHz, CDCl3) δ 164.2 (C-4), 150.7 (C-2),
143.1 (C-6), 137.4 (Ar), 132.5 (C-2′′), 128.8, 128.3, 127.6 (Ar),
119.6 (C-3′′), 110.3 (C-5), 88.0 (CAr3), 79.0 (C-3′), 84.3, 84.0 (C-
4′, C-1′), 62.1 (C-5′), 45.0 (C-2′), 42.6 (C-1′′), 12.6 (CH3); HR-
MALDI MS m/z (547.2180 [M + Na]+, C32H32N2O5 - Na+ calcd
547.2203).
conformation is, of course, most unfortunate. However, the
synthesis of the nucleoside monomer 7 was in fact very efficient,
and work on alternative ways for its introduction into oligo-
nucleotides is in progress.
Conclusion
The two bicyclic 2′-deoxynucleosides 7 and 8 with R-L-ribo-
and ꢀ-D-xylo-configurations and restricted S- and N-type con-
formations, respectively, were each prepared as planned from
the retrosynthetic analysis in only 12 synthetic steps. This makes
their preparation much more straightforward than the corre-
sponding synthesis of the ꢀ-D-ribo-configured stereoisomer 4.
Only the ꢀ-D-xylo-configured N-type mimic 8 has been incor-
porated into oligodeoxynucleotides leading to decreased hy-
bridization affinity for complementary DNA and RNA.
Preparation of 1-N-(3′-C-Allyl-3′-O-benzyl-5′-O-trityl-2′-deoxy-
ꢀ-D-xylofuranosyl)thymine (11) and 1-N-(3′-C-Allyl-3′-O-benzyl-
5′-O-trityl-2′-deoxy-ꢀ-D-xylofuranosyl)-3-N-benzylthymine (12). A
solution of the allyl derivative 10 (2.5 g, 4.77 mmol) in anhydrous
THF (200 mL) was stirred at -78 °C. Sodium hydride (60% in oil
w/w, 860 mg, 21.50 mmol) was added, and after 1 h of stirring,
benzyl bromide (2 mL, 16.84 mmol) was added dropwise. The
reaction mixture was brought to room temperature in 10 h and
stirred over 5 days at room temperature. The reaction was quenched
by slow addition of a mixture of H2O and a saturated aqueous
solution of NaHCO3 (1:1, v/v, 50 mL), and the mixture was
extracted with EtOAc (3 × 20 mL). The combined organic phase
was washed with H2O (3 × 20 mL), dried (Na2SO4), and
concentrated under reduced pressure. The residue was purified by
column chromatography (methanol (0-2%) in dichloromethane)
affording 11 (2.33 g, 80%) as a white foam as well as 12 (334 mg,
10%). Compound 11: Rf 0.70 (CH2Cl2/MeOH 9:1); 1H NMR (300
MHz, CDCl3) δ 8.43 (bs, 1H, NH), 7.56-7.14 (m, 19H, H-6, Ar),
6.94-6.91 (m, 2H, Ar), 6.09 (t, 1H, J ) 5.1 Hz, H-1′), 5.71 (m,
1H, H-2′′), 5.17-5.04 (m, 2H, H-3′′), 4.38, 4.05 (AB, 2H, J )
11.1 Hz, OCH2Ar), 4.28 (t, 1H, J ) 6.0 Hz, H-4′), 3.54-3.47 (m,
2H, H-5′), 2.62-2.50 (m, 2H, H-1′′), 2.44-2.40 (m, 2H, H-2′),
1.27 (d, 3H, J ) 0.9 Hz, CH3); 13C NMR (75 MHz, CDCl3) δ
163.7 (C-4), 150.3 (C-2), 143.8, 137.4, 136.4 (C-6, Ar), 132.2 (C-
2′′), 128.8, 128.5, 128.0, 127.7, 127.2, 126.9 (Ar), 119.9 (C-3′′),
109.6 (C-5), 87.3, 83.5 (CAr3, C-3′), 86.3 (C-4′), 84.9 (C-1′), 64.4
(OCH2Ar), 62.8 (C-5′), 39.6 (C-2′), 37.3 (C-1′′), 12.0 (CH3); HR-
MALDI MS m/z (637.2670 [M + Na]+, C39H38N2O5 - Na+ calcd
Experimental Section
Assignments of NMR spectra follow standard nucleoside style,
i.e., the carbon atom next to a nucleobase is assigned as C-1′ and
so on. C-1′′, C-2′′, and C-3′′ designate the carbon atoms attached
to the 3′-C branch, and C-5′′ designates the carbon atom attached
to the C-4′ branch.
Preparation of 1-N-(3′-C-Allyl-5′-O-trityl-2′-deoxy-ꢀ-D-xylofura-
nosyl)thymine (10). A slurry of 3Å molecular sieves powder (5.25
g) and pyridiniumdichromate (3.73 g, 9.92 mmol) in anhydrous
CH2Cl2 (50 mL) was stirred. A solution of nucleoside 9 (4.0 g,
8.26 mmol) in anhydrous CH2Cl2 (20 mL) was added. The dark
brown mixture was stirred for 5 h and then filtered through 3Å
molecular sieves powder (deposited as a slurry with anhydrous
CH2Cl2) on a sintered glass filter. The plug was washed with
anhydrous CH2Cl2 (100 mL), and the combined filtrate was
concentrated under reduced pressure to 10 mL. To the brown
mixture was added anhydrous EtOAc (600 mL) causing some of
the chromium salts to precipitate. The mixture was filtered through
3Å moleculer sieves powder (deposited as a slurry with anhydrous
EtOAc) on a sintered glass filter. The residue was washed with
anhydrous EtOAc (150 mL), and the combined filtrate was
concentrated under reduced pressure. CeCl3 ·7H2O (18.0 g, 48.31
mmol) was dried at 190 °C under vacuum for 16 h and then cooled
to room temperature under nitrogen atmosphere. Anhydrous THF
(150 mL) was added, and the slurry was stirred at -78 °C.
AllylMgBr in anhydrous Et2O (1M, 50 mL, 50.0 mmol) was added
dropwise, and the slurry was stirred for 1 h at -78 °C. The crude
nucleoside (3.91 g, 8.12 mmol) was dissolved in anhydrous THF
(50 mL), cooled to -78 °C, and canulated slowly to the slurry.
The reaction mixture was stirred for 16 h at -78 °C. Glacial acetic
acid (10 mL) was added, and the reaction mixture was partitioned
between EtOAc (600 mL) and water (200 mL). The organic phase
was washed with water (2 × 200 mL) and brine (3 × 150 mL),
dried (Na2SO4), and concentrated under reduced pressure. The
residue was purified by column chromatography (methanol (0-5%)
in dichloromethane) affording 10 (1.78 g, 41%) as a white solid.
1
637.2673). Compound 12: Rf 0.80 (CH2Cl2/MeOH 9:1); H NMR
(300 MHz, CDCl3) δ 7.49-7.12 (m, 24H, H-6, Ar), 6.82 (d, 2H,
J ) 7.2 Hz, Ar), 6.08 (dd, 1H, J ) 3.6, 5.7 Hz, H-1′), 5.70 (m,
1H, H-2′′), 5.14-4.98 (m, 4H, H-3′′, NCH2Ar), 4.32, 3.96 (AB,
2H, J ) 11.1 Hz, OCH2Ar), 4.27 (t, 1H, J ) 5.4 Hz, H-4′),
3.53-3.47 (m, 2H, H-5′), 2.58-2.52 (m, 2H, H-1′′), 2.42-2.39
(m, 2H, H-2′), 1.30 (s, 3H, CH3); 13C NMR (75 MHz, CDCl3) δ
163.4 (C-4), 151.0 (C-2), 143.8, 137.4, 137.2, 134.4 (C-6, Ar), 132.2
(C-2′′), 129.2, 128.8, 128.4, 128.4, 127.9, 127.6, 127.2, 126.8 (Ar),
119.8 (C-3′′), 108.9 (C-5), 87.2, 83.4 (CAr3, C-3′), 86.3 (C-4′),
85.6 (C-1′), 64.4 (OCH2Ar), 62.8 (C-5′), 44.2 (NCH2Ar), 39.6 (C-
2′), 37.3 (C-1′′), 12.8 (CH3); HR-MALDI MS m/z (727.3113 [M
+ Na]+, C46H44N2O5 - Na+ calcd 727.3142).
Preparation of 1-N-(3′-C-Allyl-3′-O-benzyl-2′-deoxy-ꢀ-D-xylo-
furanosyl)thymine (13). A solution of compound 11 (7.86 g, 12.80
mmol) in 80% aqueous acetic acid (150 mL) was stirred at 90 °C
for 6 h. The solution was concentrated under reduced pressure, and
1
Rf 0.60 (CH2Cl2/MeOH 9:1); H NMR (300 MHz, CDCl3) δ 8.97
1562 J. Org. Chem. Vol. 74, No. 4, 2009

Synthesis of Bicyclic 2′-Deoxynucleosides
the residue was coevaporated with ethanol (2 × 30 mL) and toluene
(20 mL). The residue was redissolved in anhydrous methanol (100
mL) and added sodium methoxide (692 mg, 12.81 mmol), and the
mixture was stirred for 17 h at room temperature and then
neutralized with dilute aqueous hydrochloric acid. The mixture was
extracted with CH2Cl2 (2 × 50 mL), and the combined organic
phase was washed with a saturated aqueous solution of NaHCO3
(3 × 50 mL), dried (Na2SO4), and concentrated under reduced
pressure. The residue was purified by column chromatography
(methanol (0-5%) in dichloromethane) to give compound 13 as a
white foam (3.57 g, 75%). Rf 0.30 (CH2Cl2/CH3OH 9:1); 1H NMR
(300 MHz, CDCl3) δ 8.96 (bs, 1H, NH), 7.70 (s, 1H, H-6),
7.35-7.16 (m, 5H, Ar), 6.10 (dd, 1H, J ) 3.6, 6.9 Hz, H-1′), 5.84
(m, 1H, H-2′′), 5.27-5.21 (m, 2H, H-3′′), 4.55, 4.18 (AB, 2H, J )
10.5 Hz, OCH2Ar), 4.12-3.98 (m, 3H, H-4′, H-5′), 2.79 (dd, 1H,
J ) 6.6, 15.0 Hz, H-1′′), 2.59-2.41 (m, 3H, H-1′′, H-2′), 1.60 (s,
3H, CH3); 13C NMR (75 MHz, CDCl3) δ 164.0 (C-4), 150.5 (C-2),
136.8 (Ar), 136.2 (C-6), 128.9, 128.3, 127.6 (Ar), 131.6 (C-2′′),
120.3 (C-3′′), 110.2 (C-5), 86.3 (C-4′), 85.1 (C-3′), 84.2 (C-1′),
65.5 (OCH2Ar), 61.8 (C-5′), 40.5 (C-2′), 38.1 (C-1′′), 12.3 (CH3);
HR-MALDI MS m/z (395.1562 [M + Na]+, C20H24N2O5 - Na+
calcd 395.1577).
affording 15 (2.25 g, 59%) as a white foam. Rf 0.60 (CH2Cl2/MeOH
9:1); 1H NMR (300 MHz, CDCl3) δ 8.67 (bs, 1H, NH), 7.45-7.15
(m, 13H, H-6, Ar), 6.92 (dd, 2H, J ) 3.6, 6.9 Hz, Ar), 6.80 (dd,
4H, J ) 0.9, 8.7 Hz, Ar), 6.25 (d, 1H, J ) 6.3 Hz, H-1′), 5.65-5.51
(m, 1H, H-3′′), 5.09 (d, 1H, J ) 5.4 Hz, H-2′′), 4.91 (d, 1H, J )
16.8 Hz, H-3′′), 4.35, 4.01 (AB, 2H, J ) 10.8 Hz), 4.19 (dd, 1H,
J ) 4.5, 11.7 Hz, H-5′′), 3.90 (dd, 1H, J ) 5.1, 11.7 Hz, H-5′′),
3.77-3.73 (m, 7H), 3.44 (d, 1H, J ) 11.1 Hz), 2.78 (dd, 1H, J )
6.3, 16.2 Hz, H-1′′), 2.67-2.35 (m, 3H, H-1′′, H-2′), 1.18 (d, 3H,
J ) 0.9 Hz, CH3); 13C NMR (75 MHz, CDCl3) δ 163.8 (C-4), 158.7
(Ar), 150.5 (C-2), 144.5, 137.2, 136.6, 135.7, 135.6 (C-6, Ar), 132.3
(C-2′′), 130.1, 130.1, 128.4, 128.2, 128.0, 127.7, 127.0, 126.9, 113.3
(Ar), 118.9 (C-3′′), 109.5 (C-5), 93.2, 86.8, 85.7 (CAr3, C-4′, C-3′),
85.3 (C-1′), 65.1, 63.4 (OCH2Ar, C-5′), 64.3 (C-5′′), 55.3 (OCH3),
40.9 (C-2′), 35.1 (C-1′′), 11.9 (CH3); HR-MALDI MS m/z
(727.2992 [M + Na]+, C42H44N2O8 - Na+ calcd 727.2990).
Preparation of 1-N-[3′-C-Allyl-3′-O-benzyl-5′-O-(4,4′-dimethox-
ytrityl)-4′-C-methanesulfonyloxymethyl-2′-deoxy-ꢀ-D-xylofurano-
syl]thymine (16). To a stirred solution of compound 15 (2.21 g,
3.14 mmol) in anhydrous CH2Cl2 (10 mL) at 0 °C were added 2,6-
lutidine (2.5 mL, 21.56 mmol) and methanesulfonyl chloride (0.98
mL, 12.60 mmol), and the mixture was stirred at room temperature
for 10 h. The reaction mixture was cooled to 0 °C, and water (3
mL) was added followed by a saturated aqueous solution of
NaHCO3 (5 mL). The resulting mixture was extracted with CH2Cl2
(3 × 5 mL), and the organic phase was dried (Na2SO4) and
concentrated under reduced pressure. The residue was purified by
column chromatography (methanol (0-2%) in dichloromethane
containing 0.5% pyridine) affording 16 (2.01 g, 82%) as a white
Preparation of 1-N-(3′-C-Allyl-3′-O-benzyl-4′-C-hydroxymethyl-
2′-deoxy-ꢀ-D-xylofuranosyl)thymine (14). Compound 13 (3.55 g,
9.54 mmol) was coevaporated with anhydrous pyridine (2 × 10
mL) and toluene (2 × 10 mL) and then redissolved in anhydrous
CH2Cl2 (50 mL). Dess-Martin periodinane (8.09 g, 19.08 mmol)
was added, and the white and nonclear reaction mixture was stirred
for 5 h at room temperature. The reaction mixture was filtered
through celite (deposited as slurry with CH2Cl2 on a glass filter).
The plug was washed with CH2Cl2 (100 mL), and the resulting
solution was washed with a mixture of a saturated aqueous solution
of Na2S2O3 and a saturated aqueous solution of NaHCO3 (1:1, v/v,
80 mL). The organic phase was dried (Na2SO4) and concentrated
under reduced pressure. The crude aldehyde (quantative) was
dissolved in dioxane (50 mL), an aqueous solution of formaldehyde
(37%, 2.09 mL, 25.77 mmol) was added, and then an aqueous
solution of sodium hydroxide (2 M, 4.77 mL, 9.54 mmol) was added
dropwise. The reaction mixture was stirred at room temperature
for 14 h. The mixture was cooled to 0 °C, sodium borohydride
(363 mg, 9.55 mmol) was added slowly, and the mixture was stirred
at room temperature for 3 h. Then, a mixture of pyridine and glacial
acetic acid (4:1, v/v, 50 mL) was added, and the solvent was
removed under reduced pressure. The resulting residue was purified
by column chromatography (methanol (0-5%) in dichloromethane)
affording 14 (2.19 g, 57%) as a white solid. Rf 0.30 (CH2Cl2/MeOH
1
solid. Rf 0.50 (CH2Cl2/MeOH 19:1); H NMR (300 MHz, CDCl3)
δ 8.72 (bs, 1H, NH), 7.42-7.10 (m, 13H, H-6, Ar), 6.95-6.92
(m, 2H, Ar), 6.80 (d, 4H, J ) 8.7 Hz, Ar), 6.29 (d, 1H, J ) 6.6
Hz, H-1′), 5.52 (m, 1H, H-2′′), 5.19 (d, 1H, J ) 10.2 Hz, H-3′′),
4.98 (d, 2H, J ) 16.8 Hz, H-3′′), 4.79, 4.50 (AB, 2H, J ) 11.1
Hz), 4.36, 4.05 (AB, 2H, J ) 10.8 Hz), 3.79-3.76 (m, 7H), 3.40
(d, 1H, J ) 10.8 Hz), 3.11 (s, 3H, CH3SO2), 2.85 (dd, 1H, J ) 4.5,
15.6 Hz, H-1′′), 2.62-2.44 (m, 3H, H-1′′, H-2′), 1.16 (s, 3H, CH3);
13C NMR (75 MHz, CDCl3) δ 163.7 (C-4), 158.7 (Ar), 150.4 (C-
2), 144.3, 136.7, 136.2, 135.4, 135.3, 131.3 (C-6, Ar), 131.3 (C-
2′′), 130.1, 128.6, 128.2, 128.0, 127.9, 127.1, 126.9, 113.3 (Ar),
119.8 (C-3′′), 109.9 (C-5), 91.6, 86.9, 85.6, 85.5 (CAr3, C-4′, C-3′,
C-1′), 70.3, 64.5, 63.6, (OCH2Ar, C-5′′, C-5′), 55.3 (OCH3), 41.1
(C-2′), 37.5 (CH3SO2), 35.1 (C-1′′), 11.9 (CH3); HR-MALDI MS
m/z (805.2765 [M + Na]+, C43H46N2O10S - Na+ calcd 805.2751).
Preparation of 1-N-[3′-O-Benzyl-5′-O-(4,4′-dimethoxytrityl)-3′-
C-(2-hydroxyethyl)-4′-C-methanesulfonyloxymethyl-2′-deoxy-ꢀ-D-
xylofuranosyl]thymine (17). To a solution of nucleoside 16 (1.94
g, 2.48 mmol) in a mixture of THF (6 mL) and water (6 mL) were
added sodium periodate (1.59 g, 7.46 mmol) and a 2.5% solution
of osmium tetraoxide in tert-butyl alcohol (203 µL, 0.02 mmol).
The reaction was stirred at room temperature for 22 h and the
mixture was extracted with CH2Cl2 (2 × 10 mL). The combined
extract was washed with a saturated aqueous solution of NaHCO3
(2 × 5 mL), dried (Na2SO4), and concentrated under reduced
pressure. The residue was redissolved in a mixture of THF (7.5
mL) and water (7.5 mL), and sodium borohydride (283 mg, 7.45
mmol) was added at 0 °C. The reaction mixture was stirred at room
temperature for 2 h, water (2 mL) was added, and the mixture was
extracted with CH2Cl2 (2 × 10 mL). The combined organic phase
was washed with a saturated aqueous solution of NaHCO3 (2 × 5
mL), dried (Na2SO4) and concentrated under reduced pressure. The
residue was purified by column chromatography (methanol (0-2%)
in dichloromethane containing 0.5% pyridine) affording 17 (960
mg, 49%) as a white foam. Rf 0.40 (CH2Cl2/MeOH 9:1); 1H NMR
(300 MHz, CDCl3) δ 8.74 (bs, 1H, NH), 7.45-7.11 (m, 13H, H-6,
Ar), 6.93-6.90 (m, 2H, Ar), 6.80 (d, 4H, J ) 8.4 Hz, Ar), 6.23 (d,
1H, J ) 6.0 Hz, H-1′), 4.76, 4.71 (AB, 2H, J ) 11.1 Hz), 4.24,
4.01 (AB, 2H, J ) 11.1 Hz), 3.82-3.75 (m, 7H), 3.61-3.52 (m,
2H), 3.08 (s, 3H, CH3SO2), 2.67-2.48 (m, 2H, H-2′), 2.25 (m, 1H,
1
9:1); H NMR (300 MHz, CD3OD) δ 7.65 (d, 1H, J ) 1.2 Hz,
H-6), 7.35-7.23 (m, 5H, Ar), 6.19 (d, 1H, J ) 5.7 Hz, H-1′),
6.10-5.96 (m, 1H, H-2′′), 5.30-5.19 (m, 2H, H-3′′), 4.58, 4.28
(AB, 2H, J ) 10.5 Hz), 4.14, 3.86 (AB, 2H, J ) 12.6 Hz), 3.95,
3.79 (AB, 2H, J ) 12.3 Hz), 2.98 (dd, 1H, J ) 5.7, 15.9 Hz, H-1′′),
2.78-2.59 (m, 3H, H-1′′, H-2′), 1.40 (d, 3H, J ) 1.2 Hz, CH3);
13C NMR (75 MHz, CD3OD) δ 166.5 (C-4), 152.3 (C-2), 139.1
(Ar), 138.6 (C-6), 134.5 (C-2′′), 129.5, 128.7 (Ar), 118.9 (C-3′′),
110.0 (C-5), 94.7, 87.0 (C-4′, C-3′), 86.5 (C-1′), 64.7, 64.1, 63.5
(OCH2Ar, C-5′′, C-5′), 42.7 (C-2′), 36.3 (C-1′′), 12.2 (CH3); HR-
MALDI MS m/z (425.16.81 [M + Na]+, C21H26N2O6 - Na+ calcd
425.1683).
Preparation of 1-N-[3′-C-Allyl-3′-O-benzyl-5′-O-(4,4′-dimethox-
ytrityl)-4′-C-hydroxymethyl-2′-deoxy-ꢀ-D-xylofuranosyl]thymine (15).
Compound 14 (2.16 g, 5.37 mmol) was coevaporated with
anhydrous pyridine (2 × 5 mL) and toluene (2 × 5 mL) and then
redissolved in anhydrous pyridine (15 mL). DMTCl (2.28 g, 6.73
mmol) was added, and the reaction mixture was stirred at room
temperature for 24 h. Water (2 mL) was added, and the reaction
mixture was extracted with CH2Cl2 (2 × 5 mL). The combined
organic phase was dried (Na2SO4) and concentrated under reduced
pressure. The residue was purified by column chromatography
(methanol (0-3%) in dichloromethane containing 0.5% pyridine)
J. Org. Chem. Vol. 74, No. 4, 2009 1563

Shaikh et al.
1
H-2′′), 2.05 (m, 1H, H-2′′), 1.74-1.68 (m, 2H, H-1′′), 1.19 (d, 3H,
J ) 0.9 Hz, CH3); 13C NMR (75 MHz, CDCl3) δ 163.7 (C-4), 158.7
(Ar), 150.4 (C-2), 144.3, 136.7, 136.1, 135.4, 135.3, 130.2, 130.2,
128.6, 128.3, 128.0, 127.9, 127.2, 126.8, 113.3 (C-6, Ar), 109.8
(C-5), 91.8, 87.0, 85.6 (CAr3, C-4′, C-3′), 85.3 (C-1′), 70.6, 63.9,
63.6, 57.5 (OCH2Ar, C-5′′, C-5′, C-2′′), 55.3 (OCH3), 41.4 (C-2′),
37.5 (CH3SO2), 33.4 (C-1′′), 11.9 (CH3); HR-MALDI MS m/z
(809.2715 [M + Na]+, C42H46N2O11S - Na+ calcd 809.2699).
Preparation of (1R,6R,8R)-6-Benzyloxy-1-(4,4′-dimethoxytrity-
loxymethyl)-8-(thymin-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (18). Com-
pound 17 (600 mg, 0.76 mmol) was dissolved in anhydrous DMF
(1.5 mL), and a suspension of sodium hydride (60% in oil, w/w,
92 mg, 2.30 mmol) in anhydrous DMF (0.5 mL) was added
dropwise at 0 °C. The reaction was stirred at room temperature for
3 h and then quenched with water (1 mL). The mixture was
extracted with CH2Cl2 (2 × 5 mL), and the combined organic phase
was washed with a saturated aqueous solution of NaHCO3 (2 × 2
mL), dried (Na2SO4), and concentrated under reduced pressure. The
residue was purified by column chromatography (ethyl acetate
(0-70%) in petroleum ether containing 0.5% pyridine) affording
18 (358 mg, 68%) as a white foam. Rf 0.50 (petroleum ether/EtOAc
1:3); 1H NMR (300 MHz, CDCl3) δ 8.62 (bs, 1H, NH), 7.50-7.09
(m, 13H, H-6, Ar), 6.90 (dd, 2H, J ) 3.3, 7.2 Hz, Ar), 6.84-6.78
(m, 4H, Ar), 6.15 (d, 1H, J ) 6.0 Hz, H-1′), 4.71, 3.13 (AB, 2H,
J ) 12.0 Hz), 4.29 (d, 1H, J ) 11.1 Hz), 4.03-3.95 (m, 2H), 3.76
(s, 6H, OCH3), 3.64, 3.53 (AB, 2H, J ) 11.1 Hz), 3.43 (m, 1H,
H-2′′), 2.76 (dd, 1H, J ) 7.5, 15.6 Hz, H-2′), 2.34 (m, 1H, H-2′),
2.07 (m, 1H, H-1′′), 1.81 (ddd, 1H, J ) 5.7, 12.3, 18.0 Hz, H-1′′),
1.21 (d, 3H, J ) 0.9 Hz, CH3); 13C NMR (75 MHz, CDCl3) δ
163.8 (C-4), 158.5, (Ar), 150.3 (C-2), 144.9, 137.2, 136.5, 136.0,
136.0, 130.3, 130.3, 128.5, 128.3, 128.4, 127.9, 127.7, 126.9, 113.2
(C-6, Ar), 109.4 (C-5), 86.6, 86.4, 81.7 (CAr3, C-4′, C-3′), 85.0
(C-1′), 68.5, 63.1, 62.2 (OCH2Ar, C-5′′, C-5′), 65.1 (C-2′′), 55.2
(OCH3), 37.0 (C-2′′), 30.4 (C-1′′), 11.9 (CH3); HR-MALDI MS
m/z (713.2846 [M + Na]+, C41H42N2O8 - Na+ calcd 713.2833).
Preparation of (1S,6R,8R)-6-Hydroxy-1-hydroxymethyl-8-(thy-
min-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (8). To a stirred solution
of nucleoside 18 (340 mg, 0.49 mmol) in ethanol (5 mL) was added
20% palladium hydroxide over carbon (690 mg, 0.99 mmol). The
mixture was degassed several times with argon and placed under a
hydrogen atmosphere. The reaction mixture was stirred at room
temperature for 7 h and then filtered through celite. The filter was
washed with ethanol (3 × 10 mL), and the combined filterate was
concentrated under reduced pressure. The residue was purified by
column chromatography (methanol (0-8%) in dichloromethane)
affording nucleoside 8 as a white foam (126 mg, 86%). Rf 0.10
CH3OH 9:1); H NMR (300 MHz, CDCl3) δ 8.04 (s, 1H, H-6),
7.45-7.16 (m, 9H, Ar), 6.85 (d, 4H, J ) 9.0 Hz, Ar), 6.24 (dd,
1H, J ) 2.1, 8.1 Hz, H-1′), 4.78 (bs, 1H, 3′-OH), 3.87 (dd, 1H, J
) 5.1, 12.0 Hz, H-2′′), 3.79 (s, 6H, OCH3), 3.71-3.60 (m, 3H),
3.36 (m, 1H, H-2′′), 3.10 (d, 1H, J ) 12.3 Hz), 2.89 (dd, 1H, J )
8.1, 14.7 Hz, H-2′), 2.14 (dd, 1H, J ) 2.1, 14.7 Hz, H-2′), 1.96
(m, 1H, H-1′′), 1.81 (s, 3H, CH3), 1.73 (m, 1H, H-1′′); 13C NMR
(75 MHz, CDCl3) δ 164.0 (C-4), 158.9 (Ar), 150.8 (C-2), 144.0,
137.3, 135.0, 134.7, 130.1, 130.0, 128.3, 128.0, 127.3, 113.5 (C-6,
Ar), 110.5 (C-5), 88.0, 84.5, 77.7 (CAr3, C-4′, C-3′), 83.6 (C-1′),
70.5, 64.7 (C-5′′, C-5′), 65.7 (C-2′′), 55.3 (OCH3), 42.8 (C-2′), 35.0
(C-1′′), 12.6 (CH3); HR-MALDI MS m/z (623.2359 [M + Na]+,
C34H36N2O8 - Na+ calcd 623.2364).
Preparation of (1R,6R,8R)-6-(2-Cyanoethoxy(diisopropylami-
no)phosphinoxy)-1-(4,4′-dimethoxytrityloxymethyl)-8-(thymin-1-
yl)-3,9-dioxabicyclo[4.3.0]nonane (20). The DMT-protected nucle-
oside 19 (63 mg, 0.10 mmol) was coevaporated with anhydrous
CH2Cl2 (2 × 3 mL) and dissolved in anhydrous CH2Cl2 (0.7 mL).
N,N-Diisopropylethylamine (0.11 mL, 0.63 mmol) followed by
2-cyanoethyl-N,N-diisopropylphosphoramidochloridite (94 µL, 0.42
mmol) were added, and the mixture was stirred at room temperature
for 10 h. The reaction was quenched with methanol (0.5 mL) and
the mixture was dissolved in ethyl acetate (2 mL), washed with a
saturated aqueous solution of NaHCO3 (2 × 2 mL) and brine (1
mL), dried (Na2SO4), and concentrated under reduced pressure. The
residue was purified by column chromatography (methanol (0-2%)
in dichloromethane containing 0.5% pyridine) affording 20 as a
white foam (66 mg, 79%). Rf 0.70 (CH2Cl2/MeOH 9:1), 31P NMR
(75 MHz, CDCl3) δ 144.9, 143.0; HR-MALDI MS m/z (823.3474
[M + Na]+, C43H53N4O9P - Na+ calcd 823.3442).
Preparation of 1-N-(3′-C-Allyl-3′-O-benzyl-4′-C-hydroxymethyl-
5′-O-methanesulfonyl-2′-deoxy-ꢀ-D-xylofuranosyl)thymine (21) and
1-N-(3′-C-Allyl-3′-O-benzyl-4′-C-methanesulfonyloxymethyl-5′-O-
methanesulfonyl-2′-deoxy-ꢀ-D-xylofuranosyl)thymine (22). Method
A: To a stirred solution of 14 (1.05 g, 2.61 mmol) in anhydrous
CH2Cl2 (40 mL) at 0 °C were added 2,6-lutidine (345 µL, 2.98
mmol) and methanesulfonyl chloride (230 µL, 2.96 mmol), and
the reaction mixture was stirred at room temperature for 16 h. The
reaction was quenched with water (50 mL) and extracted with
CH2Cl2 (3 × 50 mL). The combined organic phase was washed
with a saturated aqueous solution of NaHCO3 (50 mL), dried
(Na2SO4), and concentrated under reduced pressure. The residue
was purified by column chromatography (acetone (10-30%) in
dichloromethane) affording compound 21 as white foam (554 mg,
44%) as well as the dimesylated compound 22 (493 mg, 33%).
Method B: To a solution of 22 (600 mg, 1.04 mmol) in dioxane
(20 mL) were added potassium acetate (490 mg, 5.0 mmol) and
18-crown-6 (528 mg, 2.0 mmol). The reaction mixture was stirred
at 105 °C for 4 days and then cooled. Water (10 mL) was added,
and the mixture was extracted with CH2Cl2 (2 × 30 mL). The
combined organic phase was dried (Na2SO4) and concentrated under
reduced pressure. The residue was redissolved in a saturated
methanolic solution of NH3 (30 mL), and the solution was stirred
for 20 h at room temperature. The mixture was concentrated under
reduced pressure, and the residue was purified by column chro-
matography (acetone (10-30%) in dichloromethane) affording
compound 21 as a white foam (125 mg, 25%) as well as 30% of
the starting material 22. Compound 21: Rf 0.22 (CH2Cl2/CH3OH
1
(CH2Cl2/CH3OH 9:1); H NMR (300 MHz, CD3OD) δ 8.07 (d,
1H, J ) 1.2 Hz, H-6), 6.13 (dd, 1H, J ) 2.4, 8.1 Hz, H-1′), 4.04
(d, 2H, J ) 12.3 Hz), 3.90-3.80 (m, 2H), 3.51 (ddd, 1H, J ) 3.0,
11.7, 14.7 Hz, H-2′′), 3.11 (d, 1H, J ) 12.3 Hz), 3.01 (dd, 1H, J
) 8.1, 15.0 Hz, H-2′), 2.06 (dd, 1H, J ) 2.4, 15.0 Hz, H-2′),
1.99-1.94 (m, 2H, H-1′′), 1.88 (d, 3H, J ) 1.2 Hz, CH3); 13C NMR
(75 MHz, CD3OD) δ 166.5 (C-4), 152.4 (C-2), 139.4 (C-6), 110.4
(C-5), 86.7, 77.3 (C-4′, C-3′), 85.5 (C-1′), 68.6, 62.3 (C-5′′, C-5′),
66.2 (C-2′′), 44.2 (C-2′), 35.7 (C-1′′), 12.5 (CH3); HR-MALDI MS
m/z (321.1052 [M + Na]+, C13H18N2O6 - Na+ calcd 321.1057).
Preparation of (1R,6R,8R)-1-(4,4′-Dimethoxytrityloxymethyl)-
1-hydroxy-8-(thymin-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (19). The
bicyclic nucleoside 8 (106 mg, 0.36 mmol) was dissolved in
anhydrous pyridine (1.0 mL) and DMTCl (301 mg, 0.89 mmol)
was added in one portion. The mixture was heated in a microwave
vial at 80 °C for 30 min. The reaction was quenched by the addition
of methanol (0.5 mL), and the mixture was concentrated under
reduced pressure. The residue was dissolved in CH2Cl2 (3 mL) and
washed with a saturated aqueous solution of NaHCO3 (2 × 2 mL)
and brine (1 mL), dried (Na2SO4), and concentrated under reduced
pressure. The residue was purified by column chromatography
(methanol (0-3%) in dichloromethane containing 0.5% pyridine)
affording 19 (199 mg, 93%) as a white foam. Rf 0.60 (CH2Cl2/
1
19:1); H NMR (300 MHz, DMSO-d6) δ 11.22 (s, 1H, NH), 7.44
(d, 1H, J ) 0.9 Hz, H-6), 7.36-7.21 (m, 5H, Ar), 6.17 (t, 1H, J )
4.5 Hz, H-1′), 5.93 (m, 1H, H-2′′), 5.40 (t, 1H, J ) 5.1 Hz, 5′′-
OH), 5.26-5.11 (m, 2H, H-3′′), 4.63, 4.41 (AB, 2H, J ) 11.1 Hz),
4.48, 4.29 (AB, 2H, J ) 11.1 Hz), 3.73-3.58 (m, 2H, H-5′′), 3.17
(s, 3H, CH3SO2), 2.94 (dd, J ) 6.3, 15.7 Hz, 1H, H-1′′), 2.66-2.59
(m, 3H, H-1′′, H-2′), 1.35 (d, 3H, J ) 0.9 Hz, CH3); 13C NMR (75
MHz, DMSO-d6) δ 164.6 (C-4), 151.2 (C-2), 138.6 (Ar), 136.7
(C-6), 134.2, 129.2, 128.3, 128.2 (Ar, C-2′′), 119.7 (C-3′′), 109.5
(C-5), 91.3, 85.0, (C-3′, C-4′), 86.7 (C- 1′), 70.5, 63.9 (OCH2Ar,
C-5′), 62.4 (C-5′′), 41.1 (C-2′), 38.0 (CH3SO2), 35.6 C-1′′), 12.7
1564 J. Org. Chem. Vol. 74, No. 4, 2009

Synthesis of Bicyclic 2′-Deoxynucleosides
(CH3); HR-ESI MS m/z 503.1472 ([M + Na]+, C22H28N2O8S -
Na+ calcd 503.1459). Compound 22. Rf 0.40 (CH2Cl2/CH3OH 19:
1); H NMR (300 MHz, CDCl3) δ 8.86 (s, 1H, NH), 7.42 (d, 1H,
91.7 (C-3′), 86.1 (C- 1′), 87.9, 85.9 (CAr3, C- 4′), 69.8, 64.2, 64.0
(OCH2Ar, C-5′′, C-5′), 57.6 (C-2′′), 55.4 (OCH3), 41.8 (C-2′), 38.2
(CH3SO2), 33.1 (C-1′′), 12.1 (CH3); HR-ESI MS m/z (809.2715
[M + Na]+, C42H46N2O11S - Na+ calcd 809.2729).
1
J ) 1.2 Hz, H-6), 7.37-7.16 (m, 5H, Ar), 6.22 (dd, 1H, J ) 2.1,
7.2 Hz, H-1′), 5.84 (m, 1H, H-2′′), 5.40-5.30 (m, 2H, H-3′′), 4.90
(d, 1H, J ) 11.1 Hz), 4.54-4.39 (m, 4H), 4.19 (d, 1H, J ) 10.5
Hz) 3.14 (s, 3H, CH3SO2), 3.07 (s, 3H, CH3SO2), 3.01 (m, 1H,
H-1′′), 2.74-2.51 (m, 3H, H-1′′, H-2′), 1.52 (d, J ) 1.2 Hz, 3H,
CH3); 13C NMR (75 MHz, CDCl3) δ 163.7 (C-4), 150.4 (C-2),
136.1, 135.6 (Ar, C-6), 130.9 (C-2′′), 129.0, 128.5, 127.6 (Ar), 120.6
(C-3′′), 110.7 (C-5), 89.5, 85.6 (C-3′, C-4′), 86.0 (C- 1′), 68.4, 68.0,
64.6 (C-5′, C-5′′, OCH2Ar), 41.0 (C-2′), 38.0, 37.8 (2 × CH3SO2),
35.1 (C-1′′), 12.1 (CH3); HR-ESI MS m/z (581.1225 [M + Na]+,
C23H30N2O10S2 - Na+ calcd 581.1234).
Preparation of (1S,6R,8R)-6-O-Benzyl-1-(4,4′-dimethoxytrity-
loxymethyl)-8-(thymin-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (28).
Method 1: To a stirred suspension of sodium hydride (60% in
oil, w/w, 20 mg, 0.5 mmol) in anhydrous DMF (1 mL) at 0 °C
was slowly added a solution of 26 (115 mg, 0.15 mmol) in
anhydrous DMF (1 mL). The reaction mixture was stirred at
room temperature for 4 h. The reaction was quenched with water
(15 mL) and extracted with CH2Cl2 (3 × 20 mL). The combined
organic phase was dried (Na2SO4) and concentrated under
reduced pressure. The residue was coevaporated with xylene and
purified by column chromatography (methanol (0-3%) in
dichloromethane) affording compound 28 as a white foam (96
mg, 95%). Method 2: The same procedure using compound 27
(200 mg, 0.23 mmol), sodium hydride (60% in oil, w/w, 40 mg,
1.0 mmol), and DMF (4 mL) afforded compound 28 (152 mg,
95%). Rf 0.66 (CH2Cl2/CH3OH 9:1); 1H NMR (300 MHz, CDCl3)
δ 8.68 (s, 1H, NH), 7.41-7.12 (m, 15H, H-6, Ar), 6.77 (d, 4H,
J ) 8.1 Hz, Ar), 6.01 (d, 1H, J ) 7.2 Hz, H-1′), 4.32 (d, 1H, J
) 9.5 Hz), 4.24 (d, 1H, J ) 10.5 Hz), 3.96-3.92 (m, 2H), 3.72
(s, 6H, OCH3), 3.63-3.55 (m, 3H), 3.17 (d, 1H, J ) 10.2 Hz,
H-2′′), 2.46 (m, 1H, H-2′), 2.29 (d, 1H, J ) 14.4 Hz, H-2′),
2.00 (d, 1H, J ) 14.0 Hz, H-1′′), 1.49 (m, 1H, H-1′′), 1.27 (s,
3H, CH3); 13C NMR (75 MHz, CDCl3) δ 163.9 (C-4), 158.6
(Ar), 150.4 (C-2), 144.6, 137.1, 136.8, 135.9, 135.7, 130.2, 130.1,
128.8, 128.2, 128.1, 128.1, 127.6, 127.0, 113.3 (C-6, Ar), 109.1
(C-5), 87.0, 84.6, 79.9 (C-Ar3, C-3′, C-4′), 86.0 (C-1′), 65.9,
63.0, 61.7 (OCH2Ar, C-5′′, C-5′), 64.9 (C-2′′), 55.4 (OCH3),
38.5 (C-2′), 28.2 (C-1′′), 12.0 (CH3); HR-ESI MS m/z (713.2833
[M + Na]+, C41H42N2O8 - Na+ calcd 713.2816).
Preparation of (1R,6R,8R)-6-Hydroxy-1-hydroxymethyl-8-(thy-
min-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (7). To a stirred solution
of 28 (120 mg, 0.17 mmol) in ethanol (3 mL) was added 20%
palladium hydroxide over carbon (243 mg, 0.35 mmol). This
mixture was bubbled with hydrogen for 5 days under stirring.
Methanol (10 mL) was added, the mixture was filtered through
celite, and the filter was washed with methanol (5 × 5 mL).
The combined filtrate was concentrated under reduced pressure,
and the residue was purified by column chromatography
(methanol (0-10%) in dichloromethane) affording nucleoside
7 (28 mg, 55%) as a white solid. Rf 0.18 (CH2Cl2/CH3OH 9:1):
1H NMR (300 MHz, CD3OD) δ 8.03 (s, 1H, H-6), 6.15 (dd,
1H, J ) 2.1, 8.1 Hz, H-1′), 4.09 (d, 1H, J ) 9.3 Hz), 3.98-3.73
(m, 4H), 3.54 (d, 1H, J ) 12.0 Hz), 2.65 (m, 1H, H-2′), 2.02
(m, 1H, H-2′), 1.90-1.76 (m, 5H, H-1′′, CH3); 13C NMR (75
MHz, CD3OD) δ 166.5 (C-4), 152.5 (C-2), 140.0 (C-6), 109.9
(C-5), 86.4 (C-4′), 85.0 (C-1′), 74.6 (C-3′), 65.5, 63.1, 62.4 (C-
5′, C-2′′, C-5′′), 44.8 (C-2′), 34.5 (C-1′′), 12.5 (CH3); HR-
MALDI MS m/z (321.1065 [M + Na]+, C13H18N2O6 - Na+ calcd
321.1057).
Preparation of 1-N-[3′-C-Allyl-3′-O-benzyl-4′-C-(4,4′-dimethox-
ytrityloxymethyl)-5′-O-methanesulfonyl-2′-deoxy-ꢀ-D-xylofurano-
syl]thymine (24). To a stirred solution of 21 (250 mg, 0.52 mmol)
in anhydrous pyridine (6 mL) was added DMT-Cl (300 mg, 0.88
mmol). The reaction was stirred for 24 h at room temperature,
CH2Cl2 (30 mL) was added, and the mixture was washed with a
saturated aqueous solution of NaHCO3 (30 mL). The aqueous layer
was extracted with CH2Cl2 (2 × 30 mL). The combined organic
phase was dried (Na2SO4) and concentrated under reduced pressure.
The residue was purified by column chromatography (acetone
(0-10%) in dichloromethane) affording 24 as a white foam (305
1
mg, 75%). Rf 0.57 (CH2Cl2/acetone 19:1); H NMR (300 MHz,
CDCl3) δ 8.61 (s, 1H, NH), 7.61-7.21 (m, 15H, H-6, Ar),
7.16-7.12 (m, 4H, Ar), 6.48 (d, J ) 6.6 Hz, 1H, H-1′), 5.60 (m,
1H, H-2′′), 5.02 (d, 1H, J ) 12.0 Hz), 4.92 (d, 1H, J ) 10.5 Hz,
H-3′′), 4.46-4.42 (m, 2H, H-3′′, H-5′), 4.21-4.14 (m, 2H), 3.79
(s, 6H, OCH3), 3.69, 3.08 (AB, 2H, J ) 10.8 Hz), 3.04-2.94 (m,
4H, H-2′, CH3SO2), 2.80-2.63 (m, 2H, H-2′, H-1′′), 2.23 (dd, 1H,
J ) 9.6, 15.9 Hz, H-1′′), 1.56 (s, 3H, CH3); 13C NMR (75 MHz,
CDCl3) δ 163.9 (C-4), 158.8 (Ar), 150.4 (C-2), 143.9, 136.4 135.5,
135.0 (C-6, Ar), 131.4 (C-2′′), 130.2, 130.0, 128.8, 128.2, 128.2,
127.6, 127.3 (Ar), 119.8 (C-3′′), 113.5 (Ar), 110.1 (C-5), 91.7 (C-
3′), 88.0 (CAr3), 86.4 (C-1′), 86.1 (C-4′), 70.2, 64.2, 63.7 (OCH2Ar,
C-5′′, C-5′), 55.4 (OCH3), 41.6 (C-2′), 38.4 (CH3SO2), 34.7 (C-
1′′), 12.0 (CH3); HR-ESI MS m/z (805.2752 [M + Na]+,
C43H46N2O10S - Na+ calcd 805.2765).
Preparation of 1-N-[3′-O-Benzyl-4′-C-(4,4′-dimethoxytrityloxy-
methyl)-3′-C-(2-hydroxyethyl)-5′-O-methanesulfonyl-2′-deoxy-ꢀ-D-
xylofuranosyl]thymine (26). To a solution of compound 24 (1.15
g, 1.47 mmol) in a mixture of THF (15 mL) and water (15 mL)
were added sodium periodate (820 mg, 3.83 mmol) and a 2.5%
solution of osmium tetraoxide in tert-butyl alcohol (81.0 µL, 0.008
mmol). The reaction mixture was stirred at room temperature for
24 h. Water (30 mL) was added, and the mixture was extracted
with CH2Cl2 (3 × 50 mL). The combined organic phase was washed
with a saturated aqueous solution of NaHCO3 (50 mL), dried
(Na2SO4), and concentrated under reduced pressure. The residue
was redissolved in a mixture of THF (10 mL) and water (10 mL)
and cooled to 0 °C, and sodium borohydride (380 mg, 10.0 mmol)
was added. The mixture was stirred for 2 h at room temperature,
and water (50 mL) was added. The mixture was extracted with
CH2Cl2 (3 × 50 mL), and the combined organic phase was washed
with a saturated aqueous solution of NaHCO3 (50 mL), dried
(Na2SO4), and concentrated under reduced pressure. The residue
was purified by column chromatography (methanol (0-2%) in
dichloromethane) affording compound 26 as a white foam (560
Preparation of (1S,6R,8R)-1-(4,4′-Dimethoxytrityloxymethyl)-
6-hydroxy-8-(thymin-1-yl)-3,9-dioxabicyclo[4.3.0]nonane (31). Com-
pound 7 (85 mg, 0.28 mmol) was dissolved in anhydrous pyridine
(3.0 mL), and DMT-Cl (120 mg, 0.35 mmol) was added in one
portion. The mixture was stirred at room temperature for 24 h.
Dichloromethane (20 mL) was added, and the mixture was
washed with a saturated aqueous solution of NaHCO3 (20 mL).
The aqueous phase was washed with CH2Cl2 (2 × 20 mL), and
the combined organic phase was dried (Na2SO4) and concentrated
under reduced pressure. The residue was purified by column
chromatography (methanol (0-3%) in dichloromethane contain-
ing 0.5% pyridine) affording the DMT-protected derivative 31
(166 mg, 97%) as a white foam. Rf 0.30 (CH2Cl2/CH3OH 95:5);
1H NMR (300 MHz, CDCl3) δ 8.69 (bs, 1H, NH), 7.46-7.18
(m, 10H, H-6, Ar), 6.83 (d, 4H, J ) 9.0 Hz, Ar), 5.50 (dd, 1H,
J ) 1.8, 7.8 Hz, H-1′), 4.17, 3.99 (AB, 2H, J ) 9.6 Hz), 3.89
1
mg, 48%). Rf 0.49 (CH2Cl2/CH3OH 19:1); H NMR (300 MHz,
CDCl3) δ 8.66 (s, 1H, NH), 7.59-6.85 (m, 19H, H-6, Ar), 6.33 (d,
1H, J ) 6.3 Hz, H-1′), 4.99, 4.52 (AB, 2H, J ) 12.0 Hz), 4.29,
4.07 (AB, 2H, J ) 10.5 Hz), 3.79 (s, 6H, OCH3), 3.58-3.52 (m,
3H), 3.29 (d, 1H, J ) 10.5 Hz), 2.95 (s, 3H, CH3SO2), 2.86-2.63
(m, 2H, H-2′), 2.12 (m, 1H, H-1′′), 1.76 (m, 1H, H-1′′), 1.56 (d,
3H, J ) 1.2 Hz, CH3); 13C NMR (75 MHz, CDCl3) δ 163.8 (C-4),
158.8 (Ar), 150.4 (C-2), 143.9, 136.4, 136.1, 135.2, 135.0, 130.2,
130.1, 128.8, 128.2, 127.4, 127.3, 113.5 (C-6, Ar), 110.2 (C-5),
J. Org. Chem. Vol. 74, No. 4, 2009 1565

Shaikh et al.
(m, 1H), 3.78 (s, 6H, OCH3), 3.75 (s, 1H, 3′-OH), 3.65-3.60
(m, 2H), 3.08 (d, 1H, J ) 9.9 Hz, H-2′′), 2.45 (dd, 1H, J ) 8.1,
14.0 Hz, H-2′), 2.18 (d, 1H, J ) 14.0 Hz, H-2′), 1.88 (s, 3H,
CH3), 1.70-1.56 (m, 2H, H-1′′); 13C NMR (75 MHz, CDCl3) δ
164.4 (C-4), 158.6 (Ar), 151.2 (C-2), 144.5, 138.8, 136.2, 136.0,
130.1, 130.0, 128.4, 128.0, 127.0, 113.3 (C-6, Ar), 108.4 (C-5),
86.8, 85.3, 74.2 (CAr3, C-4′, C-3′), 86.3 (C-1′), 66.4, 62.2 (C-
5′′, C-5′), 64.2 (C-2′′), 55.3 (OCH3), 43.3 (C-2′), 33.8 (C-1′′),
12.6 (CH3); HR-MALDI MS m/z (623.2364 [M + Na]+,
C34H36N2O8 - Na+ calcd 623.2348).
X-ray Crystallography. Single-crystal X-ray analysis of 8, 21,
and 29 was performed at 180(2) K, and 7·H2O was analyzed at
room temperature. In all cases, H atoms bound to C and N atoms
were placed in geometrically idealized positions and allowed to
ride on their parent atoms during subsequent refinement. H atoms
of the OH groups were located in difference Fourier maps and
refined without restraint with isotropic displacement parameters.
In 21, the presence of the S atoms permitted determination of the
absolute structure via refinement of the Flack parameter (refined
value 0.00(5)). In 7·H2O, 8, and 29, the lack of significant
anomalous scattering meant that the absolute structure could not
be determined reliably, and Friedel pairs were merged as equivalent
data prior to the final cycles of refinement. Crystallographic data
for 7·H2O, 8, 21, and 29 have been deposited at the Cambridge
Crystallographic Data Centre (deposition numbers 698429-698432).
Acknowledgment. The project was supported by The Danish
Research Agency′s Programme for Young Researchers, Nucleic
Acid Center and The Danish National Research Foundation,
NAC-DRUG (Nucleic Acid Based Drug Design Training
Center) in the Sixth Framework Programme Marie Curie Host
Fellowships for Early Stage Research Training under contract
no. MEST-CT-2004-504018, The Danish Natural Science
Research Council, and Møllerens Fond. Mrs. Birthe Haack is
thanked for technical assistance. We thank the Danish Natural
Science Research Council and the Carlsberg Foundation for
provision of the X-ray equipment.
Supporting Information Available: General introduction to
the experimental section and the experimental details for the
compounds 23, 25, 27, 29, and 30 as well as the compounds
describing the synthetic steps from 12 toward a bicyclic
nucleoside;23 crystallographic data for 7·H2O, 8, 21, and 29 in
CIF format; experimental details for the preparation and
evaluation of oligonucleotides and selected NMR spectra. This
material is available free of charge via the Internet at
http://pubs.acs.org.
JO8023472
1566 J. Org. Chem. Vol. 74, No. 4, 2009