Diastereoselective synthesis of conformationally restricted dinucleotides featuring canonical and noncanonical α/β torsion angle combinations (α,β-D-CNA)

Article abstract of DOI:10.1002/ejoc.200600593

The synthesis of the four possible diastereoisomers of α,β-D-CNA 5′-XT (X = A, T, G and C) building units of nucleic acids, in which the α and β torsional angles are stereocontrolled by a dioxaphosphorinane ring structure (D-CNA family) is described. The

Full text of DOI:10.1002/ejoc.200600593

FULL PAPER
DOI: 10.1002/ejoc.200600593
Diastereoselective Synthesis of Conformationally Restricted Dinucleotides
Featuring Canonical and Noncanonical α/β Torsion Angle Combinations
(α,β-D-CNA)
Christelle Dupouy,[a] Ingrid Le Clézio,[a] Pierre Lavedan,[b] Heinz Gornitzka,[c]
Jean-Marc Escudier,*[a] and Alain Vigroux*[a]
Keywords: Nucleic acids / Conformation analysis / Dinucleotide / DNA structure
The synthesis of the four possible diastereoisomers of α,β-D-
CNA 5Ј-XT (X = A, T, G and C) building units of nucleic
the α and β torsional angles are restricted to the canonical
{gauche(–),trans} conformation typically observed in DNA
acids, in which the α and β torsional angles are stereocon- duplexes.
trolled by a dioxaphosphorinane ring structure (D-CNA fam-
ily) is described. The crystal structure analysis of the
(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim,
(RC5Ј,SP)-configured α,β-D-CNA TT dimer demonstrates that
Germany, 2006)
Introduction
Oligonucleotide analogues have attracted considerable
attention over the last two decades due to their potential
use in many areas of science including molecular biology,
medicinal chemistry, material science and nanotechnology.
Because most, if not all, of the expected applications of
DNA analogues rely on their ability to form stable and spe-
cific helical complexes to a target nucleic acid, much atten-
tion has been devoted to the design of synthetic analogues
with enhanced binding properties.
According to the concept of preorganization,[1] high af-
finity and high selectivity should, in principle, be achieved
by a single structural modification, which would rigidify a
single-stranded oligonucleotide into a shape that more re-
sembles the shape of this strand in its complexed form.
With regard to duplex formation, an ideal oligonucleotide
analogue should, therefore, have a single-stranded confor-
mational preorganization that fits with the standard A- or
B-form helical structures of nucleic acids; that is, it should
possess torsion angle values and sugar puckers similar to
the values observed in A- or B-form duplexes (Figure 1).
Figure 1. Summary of the average backbone torsion angles α–ζ,
derived from natural DNA. Values are from: B. Schneider, S.
Neidle, H. M. Berman, Biopoly 1997, 42, 113–124. The torsion an-
gle ranges are indicated in parentheses for α–γ: gauche(–) =
300Ϯ30° (g–), gauche(+) = 60Ϯ30° (g+) and trans = 180Ϯ30° (t).
The furanose ring in nucleosides or in single-stranded
nucleic acids is well known to have relatively large confor-
mational flexibility.[2] When a nucleic acid forms a duplex
(or triplex), however, the conformational freedom is drasti-
cally restricted. Thus, one way to efficiently preorganize a
single-stranded oligonucleotide for favourable duplex for-
mation is to strongly restrict its furanose unit into either an
S-type conformation (C2Ј-endo, B-form duplexes) or an N-
type conformation (C3Ј-endo, A-form duplexes). A great
number of conformationally restricted oligonucleotides
have been produced based on this principle.[3–6] It turned
out that constraining the furanose moieties of an oligonu-
[a] Laboratoire de Synthèse et Physico-Chimie de Molécules
d’Intérêt Biologique, UMR 5068 CNRS, Université Paul
Sabatier,
31062 Toulouse Cedex 9, France
E-mail: escudier@chimie.ups-tlse.fr
Vigroux@chimie.ups-tlse.fr
[b] Service Commun de RMN, Université Paul Sabatier,
31062 Toulouse Cedex 9, France
[c] Laboratoire d’Hétérochimie Fondamentale et Appliquée, UMR
5069 CNRS, Université Paul Sabatier,
31062 Toulouse Cedex 9, France
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cleotide into the C3Ј-endo (N-type) conformation is indeed specific canonical or noncanonical backbone conforma-
a very productive way of improving its duplex- and triplex- tions, we have developed dimeric building units, referred to
forming ability.[7–10]
as D-CNA, in which two or three of the backbone torsion
In contrast, very little attention has been devoted to the angles α–ζ are part of a dioxaphosphorinane ring structure
preparation of oligonucleotide analogues with a conforma- (Figure 2).[13,14] We recently reported the synthesis of the
tionally restricted phosphate linkage. Previous studies in- (SC5Ј,RP)-configured α,β-D-CNA TT dimer, in which the α
volving conformational restriction around the phosphate and β torsion angles are locked in a noncanonical
backbone have been mostly concentrated on the stabiliza- {gauche(+),trans} conformation, which frequently occurs in
tion of nonhelical secondary or tertiary structural elements protein-DNA complexes and in bulged regions of nucleic
found especially in RNA.[11,12] For the purpose of con- acids.[13] Herein, we disclose the detailed synthesis and crys-
structing covalently constrained nucleic acids (CNA) with tal structure of its (RC5Ј,SP) stereoisomer, in which α and β
Figure 2. Example of previously described D-CNA dimeric units. D-CNA are oligonucleotides that contain one or more D-CNA dimers,
in which a set of backbone torsion angles α–ζ is stereocontrolled to canonical or noncanonical values by a 1,3,2-dioxaphosphorinane
ring structure. For a given dinucleotide step, there are fourteen possible [β--deoxyribo]-configured D-CNA stereoisomers, which formally
result from the introduction of a methylene/ethylene linker between the nonbridging phosphate oxygen atoms and the 2Ј/4Ј-carbon atoms
(methylene linker, blue arrows) or 3Ј/5Ј-carbon atoms (ethylene linker, red arrows).
Figure 3. Retrosynthetic pathway for the diastereoselective synthesis of the four possible stereoisomers of α,β-D-CNA dimers. N1 and N2
stand for the remaining atomic fragments that define the upper and lower nucleoside units, respectively. The expected gauche(+), gauche-
(–), or trans conformations of α (P–O5Ј) and β (O–C5Ј) are indicated for the hypothetical true chair conformations associated with each
diastereoisomer.
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Conformationally Restricted Dinucleotides
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adopt the canonical {gauche(–),trans} conformation found
in nucleic acid duplexes. The exceptional binding properties
of duplexes involving these two α,β-D-CNA dimers have
been reported recently.[15] We also describe the synthesis
and solution structure of all possible diastereoisomers de-
rived from the α,β-D-CNA GT, CT and AT dimers.
Results and Discussion
Our retrosynthetic analysis for the synthesis of the four
possible stereoisomers of a given α,β-D-CNA dinucleotide
step is summarized in Figure 3. It is based on the very sim-
ple strategy that consists of using both steric and anomeric
effects to stereocontrol the cyclization reaction of a dinucle-
otide precursor in which the pro-(R)- and pro-(S)-phos-
phate oxyanions can attack an electrophilic tosyloxy-substi-
tuted carbon atom. Among the four possible α,β-D-CNA
diastereoisomers, we anticipated that the (SC5Ј,RP) and
(RC5Ј,SP) isomers with the alkoxy group ON1 axial (equato-
rial P=O) and the carbon group N2 equatorial would be
formed preferentially due to the sterically and anomerically
favourable trans relationship between ON1 and N2 in the
corresponding six-membered chair conformations. Actually,
the cyclization reaction from the (5ЈS)-configured acyclic
TT precursor was completely diastereoselective, leading ex-
clusively to the (SC5Ј,RP)-configured dimer with an
{α(g+),β(t)} conformation.[13] As shown in Figure 3, the key
starting material for the preparation of this diastereoisomer
is the diastereopure (5ЈS)-C-tosyloxyethyl-substituted nu-
cleoside, which is obtained by a Mukaiyama-type aldolis-
ation reaction on the corresponding 5Ј-C-aldehyde nucleo-
side.[16] Similarly, the preparation of the (RC5Ј,SP) stereoiso-
mer featuring the canonical {α(g–),β(t)} conformation re-
quires the preparation of the (5ЈR)-C-tosyloxyethyl-substi-
tuted nucleoside.
(RC5Ј,SP)- and (RC5Ј,RP)-Configured α,β-D-CNA TT
Dimers
Our synthesis of the (5ЈR)-C-(tosyloxyethyl)thymidine 3
involves the preparation of the diastereopure (5ЈR)-C-
(hydroxyethyl)thymidine 2 (Scheme 1). The latter com-
pound was obtained in 64% combined yield by a three-step
oxidative cleavage of the double bond of the available (5ЈR)-
C-(hydroxypentenyl)thymidine 1, prepared by a Sakurai al-
Scheme 1. Diastereoselective synthesis of the (RC5Ј,SP)- and
lylation reaction of the 5Ј-C-thymidine aldehyde.[17] Selec- (RC5Ј,RP)-configured α,β-D-CNA TT dimers. Reagents and condi-
tions: (a) i) OsO4 cat., N-methylmorpholine N-oxide, H2O. ii)
tive tosylation of the primary hydroxy group of 2 was
NaIO4, MeOH. iii) NaBH4, EtOH, 64% overall yield. (b) TsCl,
achieved in 77% yield by treating 2 with tosyl chloride in
Pyr, CHCl3, 77%. (c) 5Ј-O-Dimethoxytrityl-3Ј-O-phosphoramidite-
thymidine, tetrazole, CH3CN, then collidine, I2/H2O, 93%. (d)
the presence of pyridine.[18]
(5ЈR)-C-(Tosyloxyethyl)thymidine 3 was then coupled
with the commercially available thymidine phosphoramidite
according to standard phosphoramidite technology[19] to
give two diastereoisomeric dinucleotides 4 in an equimolar
Et3N, DMF, 90 °C, 90%. (e) nBu4NF, THF, 86–90%. (f) 3% TFA
in CH2Cl2, 77–85%.
ratio. Under the reaction conditions used to release the diastereoisomers 5 and 6, respectively, as observed by 31P
charged phosphodiester function of 4 (Et3N, DMF and NMR (δ = –9.1 ppm and –5.9 ppm). The cyclization reac-
90 °C), cyclization occurred in a 90% yield providing a 7:3 tion from the (5ЈR)-configured acyclic phosphate precursor
diastereoisomeric mixture of the (RC5Ј,SP) and (RC5Ј,RP) (70% de) appears, therefore, less diastereoselective than that
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previously observed for the corresponding (5ЈS) isomer 9 also reveals that both sugar rings are in the C2Ј-endo
(100% de).[13] The reason for this difference in diastereo- (south-type) conformation, which is typical of B-DNA,
selectivity is presently unclear. Both diastereoisomers 5 and with pseudorotation phase angles of 160° and 159°
6 were easily separated at this stage by silica gel chromatog- (Table 1).
raphy (∆Rf = 0.3 in AcOEt). Finally, the sequential removal
of the protective groups with fluoride ion and trifluoro-
acetic acid (TFA) provided the final compounds (RC5Ј,SP)-
9 and (RC5Ј,RP)-10 in ca. 21% and 9% overall yields,
respectively, from 1.
The dinucleotide analogues 9 and 10 were fully charac-
terized by elemental analysis and mass spectrometry and by
1H, 13C and 31P NMR spectroscopy. The determination of
the absolute configuration at the C5Ј atom and the newly
created asymmetric P centre of both stereoisomers was
greatly simplified by the X-ray structure of 9, identified as
the (RC5Ј,SP) diastereoisomer (Figure 4). This crystal struc-
ture gives evidence that the dioxaphosphorinane linkage of
the (RC5Ј,SP)-configured dimer is in a true chair conforma-
tion, as expected, with backbone torsion angle values δ(N1)
= 147.1°, δ(N2) = 138.9°, ε = –154.2°, ζ = 176.2°, α =
–69.0°, β = –173.9° and γ = 49.0°. The X-ray structure of
The solid-state structure of 9 agrees with the solution-
state structure obtained by NMR spectroscopy. The chair
conformation of 9 is, like its (SC5Ј,RP) diastereoisomer,[13]
1
clearly established from the H NMR spectra, with no de-
tectable coupling between the 5Ј-H involved in the diox-
aphosphorinane system and P (3JH5Ј/P ≈ 0), which is charac-
teristic of an axial position for this proton.[20] The observa-
3
tion of small (3 Hz) and large (20 Hz) JH/P values between
the dioxaphosphorinane 7Ј-H protons and P are also in-
dicative of an axial and an equatorial position of these pro-
tons, respectively. In contrast, average values of 10.4 Hz and
3
12.4 Hz were observed for the JH/P values involving the
two 7Ј-H protons of 10, suggesting that the dioxaphosphor-
inane structure of this (RC5Ј,RP)-configured isomer (Fig-
ure 3) is in a twist-chair conformation. This “in-between”
conformation probably results from the involvement of con-
flicting steric and anomeric effects in either chair conforma-
tion of 10 due to the cis relationship between the ON1 and
N2 groups.
Additional important structural information relative to
compounds 9 and 10 resides in the observation of a long-
range coupling between the 4Ј-H proton of the lower sugar
unit and P (4JH4Ј/P = 2–3 Hz). This coupling is indicative
of a typical W-shaped P–O5Ј–C5Ј–C4Ј–H4Ј junction (also
observed in the crystal structure of 9), which is consistent
with gauche(+) and anticlinal(–) conformations of γ in 9
and 10, respectively. The W-shaped P–O5Ј–C5Ј–C4Ј–H4Ј
junction deduced in the case of 10 also suggests that the
backbone torsion angles α and β are not significantly affec-
ted by the conformational change involved between the true
chair and twist-chair forms of 10. Overall, these NMR
spectroscopic data allow us to assign the conformation of
the backbone torsion angles α, β, and γ as (α,β,γ) = (g–,t,g+)
for 9 and (α,β,γ) = (t,t,a–) for 10. In addition, the empirical
equation established by Lankhorst et al.[21] can be used to
determine, from the JH3Ј/P value (5.8 Hz for 9 and 6.4 Hz
for 10), the value of the torsional angle ε (–160° for 9 and
–157° for 10) and, therefore, the relative position of the
upper nucleosides toward the dioxaphosphorinane linkage.
The puckering of the 2Ј-deoxyribose moieties of 9 and
10 in solution was determined by examination of the sugar
ring H/H coupling constants (Table 2). The small JH3Ј/H4Ј
values measured for 9 and 10 and the values of JH2Ј/H3Ј and
JH1Ј/H2Ј are consistent with the standard C2Ј-endo confor-
Figure 4. X-ray molecular structure of the (RC5Ј,SP)-configured
α,β-D-CNA TT dimer 9 with the adopted numbering scheme, dis-
playing the chair and C2Ј-endo conformations of the dioxaphos-
phorinane and sugar subunits. For clarity, hydrogen atoms and
cocrystallized solvent molecules are omitted, and thermal ellipsoids
are shown at 40% probability.
Table 1. X-ray crystal values [°] of the glycosyl (χ) and endocyclic (ν0–ν4) torsion angles along with the pseudorotation phase angles (P)
of both sugar units of the (RC5Ј,SP)-configured α,β-D-CNA TT dimer 9.[a]
χ
ν0
ν1
ν2
ν3
ν4
P[b]
Puckering mode[b]
Upper unit (N1)
Lower unit (N2)
–115.9
–126.9
–20.5
–20.3
30.6
30.5
–29.6
–29.1
18.9
18.7
1.3
1.6
160
159
C2Ј-endo (2E)
C2Ј-endo (2E)
[a] Definitions: χ (O4Ј–C1Ј–N1–C2), ν0 (C4Ј–O4Ј–C1Ј–C2Ј), ν1 (O4Ј–C1Ј–C2Ј–C3Ј), ν2 (C1Ј–C2Ј–C3Ј–C4Ј), ν3 (C2Ј–C3Ј–C4Ј–O4Ј) and
ν4 (C3Ј–C4Ј–O4Ј–C1Ј), see Figure 4. [b] For the definition of P and an overview of the terminology used in the description of the sugar
puckering modes, see: C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 1972, 94, 8205–8212.
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mation previously observed in natural 2Ј-deoxyribose (SC5Ј,SP)-, (SC5Ј,RP)-, (RC5Ј,SP)- and (RC5Ј,RP)-Configured
units.[22] On the basis of the structural data collected for 9, α,β-D-CNA TT, GT, CT and AT Dimers
it can be concluded that the puckering mode of the sugar
units of α,β-D-CNA dimers is not dependent on solvation
effects.
Although the synthetic pathway of Scheme 1 gives access
to the diastereopure (5ЈR)-C-(tosyloxyethyl)thymidine 3 in
almost 50% yield from 1, the overall yield from the starting
5Ј-C-thymidine aldehyde is rather low (25%). In an attempt
to increase the overall yield of 3 and to prepare all access-
ible diastereoisomers of the modified 5Ј-XT dimers in a
one-pot procedure, we opted for a more pragmatic strategy
(Scheme 2), which takes advantage of the easier accessibility
of the 5Ј-epimer of 3 (the latter compound, referred to as
11 in Scheme 2, is obtained from the starting aldehyde in
ca. 70% overall yield[13]). Oxidation of the 5Ј-hydroxy func-
tion of 11 with the pyridinium dichromate (PDC),[23] imme-
diately followed by the reduction of the corresponding
Table 2. H/H coupling constants [Hz] in the 1H NMR spectra
(400 MHz) of α,β-D-CNA TT dimers 9 and 10.
J [Hz]
J (2Ј,3Ј)
J (1Ј,2Ј)
J (3Ј,4Ј)
9
upper nucleoside
lower nucleoside
5.7
8.4
7.0
6.7
7.9
5.8
2.2
3.5
2.0
3.2
2.2
3.4
3.2
2.8
7.0
5.7
6.2
6.4
5.6
6.4
10 upper nucleoside
lower nucleoside
Scheme 2. Diastereoselective synthesis of the (RC5Ј,SP)-, (RC5Ј,RP)-, (SC5Ј,RP)- and (SC5Ј,SP)-configured α,β-D-CNA XT dimers (X = T,
G, C and A). Reagents and conditions: (a) PDC (pyridinium dichromate), CH2Cl2, room temp. (b) NaBH4, EtOH, 0 °C, 90%. (c) 5Ј-O-
Dimethoxytrityl-3Ј-O-phosphoramidite-nucleoside (T, G, C and A), tetrazole, CH3CN, then collidine, I2/H2O, 67–92%. (d) K2CO3, DMF,
room temp., 84–95%.
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ketone (with NaBH4) gave a 4:6 diastereoisomeric mixture oxaphosphorinane structure of this isomer is in a twist-
of 11/3 in a 90% combined yield. chair conformation consistent with the conformational set
Thus, according to the synthetic route shown in (α,β) = (t,t). The conformational ranges of α, β and γ (de-
Scheme 2, the tosylated building block 3 was synthesized in duced from NMR spectroscopy) are summarized in Table 3
four steps and in ca. 40% yield (from the starting aldehyde) for each α,β-D-CNA diastereoisomer.
compared with five steps and 25% for the approach de-
Table 3. Summary of the backbone torsion angles α, β and γ of the
scribed in Scheme 1. The diastereoisomeric mixture of 3
four possible diastereoisomers of α,β-D-CNA dimeric units.[a]
and 11 was then treated with the four commercially avail-
Diastereoiso-
mer
able nucleoside phosphoramidites under standard condi-
tions[19] to afford the four expected diastereoisomers of the
5Ј-XT dimers 12a (X = T), 12b (X = G), 12c (X = C) and
12d (X = A). The dioxaphosphorinane ring structure was
directly introduced from the diastereoisomeric mixture 12a–d
in 84–95% yield under milder conditions than those de-
scribed in Scheme 1 (we used K2CO3 at room temperature
in preference to Et3N at 90 °C to avoid any deprotection of
the bases). As previously observed,[13] the (5ЈS)-configured
acyclic 5Ј-TT precursor cyclized with complete diastereo-
selectivity into the (SC5Ј,RP) diastereoisomer 13a. Interest-
ingly, cyclization of the corresponding (5ЈS)-configured 5Ј-
XT 12b–d precursors proceeded in a somewhat less dia-
stereoselective manner (90% de, 95% de and 92.5% de,
respectively) giving access to the previously unknown
(SC5Ј,SP) diastereoisomers 14b–d (in 1%, 0.5% and 0.8%
overall yield from 11, respectively). Cyclization of the (5ЈR)-
configured precursors provided the (RC5Ј,SP) and (RC5Ј,RP)
diastereoisomers (5a–d and 6a–d in Scheme 2) in a more
diastereoselective manner (78% de, 82% de, 83% de and
88% de, respectively) than previously observed for the
(5ЈR)-configured precursor 4 with Et3N/DMF (70% de,
Scheme 1). Although the fully protected dimeric building
blocks 5a–d, 6a–d, 13a–d and 14c could be isolated by silica
gel chromatography, 14b and 14d failed to be separated
from 5b and 13d, respectively. Nevertheless, after treatment
with fluoride (TBAF), the resulting 3Ј-O-deprotected dinu-
cleotides 14Јb and 14Јd could be isolated by reverse-phase
HPLC purification. Finally, the dimers 5a and 6a (referred
to as 5 and 6 in Scheme 1) were obtained from the starting
5Ј-C-thymidine aldehyde in an overall isolated yield of 23%
and 6.5%, respectively, compared with 14% and 6% for the
first procedure (Scheme 1).
α
β
γ
(RC5Ј,SP)
(RC5Ј,RP)
(SC5Ј,RP)
(SC5Ј,SP)
g–
t
t
t
t
t
g+
a–
g+
t
g+
nd
[a] The torsion angle ranges are indicated as defined in Figure 1
with anticlinal(–) = 240Ϯ30° (a–).
Conclusions
Compared with natural dinucleotides, α,β-D-CNA di-
mers contain a neutral dioxaphosphorinane linkage, which
simultaneously locks the backbone torsion angles α and β
of nucleic acids at canonical or noncanonical values. In this
paper, the synthesis of the four possible α,β-D-CNA dia-
stereoisomers has been described, and a new strategy has
been developed for synthesizing all accessible diastereoiso-
mers of 5Ј-XT dimers (X = T, G, C and A) in a one-pot
procedure. Structural analysis including X-ray crystallogra-
phy and NMR spectroscopy indicates that the (RC5Ј,SP)
diastereoisomer has its dioxaphosphorinane linkage in a
true chair conformation with α and β locked in the typical
(g–,t) conformation found in A- and B-type duplexes. The
puckering mode of the 2Ј-deoxyribose units, however, is
clearly C2Ј-endo (S-type), which is characteristic of B-type
duplexes. The dioxaphosphorinane linkage of the (SC5Ј,RP)
diastereoisomer also adopts a true chair conformation but
with α and β locked in the atypical (g+,t) conformation fre-
quently observed in bulged or looped regions of nucleic ac-
ids and in protein-DNA complexes. The remaining
(RC5Ј,RP) and (SC5Ј,SP) diastereoisomers are both charac-
terized by the very unusual trans conformation of α and β
and the twist-chair conformation of their dioxaphosphorin-
ane linkage.
The structure and geometry of the fully protected build-
ing blocks 5a–d, 6a–d, 13a–d and 14c were confirmed by
mass spectrometry, and by 1H, 13C and 31P NMR spec-
Previous studies[15] have revealed the exceptional duplex-
forming ability of oligonucleotides containing canonical D-
CNA dimeric units. The formation of stable triplex (and
quadruplex) structures could, in principle, benefit from
such an approach as well. Several projects are in progress
in our laboratory to evaluate the potential advantages of
using canonical and noncanonical D-CNA dimers as stabi-
lizing components of biologically important nucleic acid
secondary structures.
3
troscopy. The JH5Ј/P values (Ͻ1 Hz) assigned to 5a–d and
13a–d fit reasonably well with the corresponding values as-
signed to the unprotected dimer 9, indicating that the chair
conformation of the dioxaphosphorinane linkage is affected
neither by the presence of the protective groups nor by the
(RC5Ј,SP) or (SC5Ј,RP) configuration. Also, we found that
the conformational range of the backbone torsion angles
α, β and γ assigned for each diastereoisomer of the 5Ј-TT
modified dimers 5a, 6a and 13a remains largely unchanged
in the corresponding 5Ј-GT, 5Ј-CT and 5Ј-AT modified di-
mers.
Experimental Section
As observed for the (RC5Ј,RP)-configured diastereoiso-
3
mers 6a and 10, the value observed for the JH5Ј/P of the
3Ј-O-tert-Butyldiphenylsilyl-5Ј-C(R)-(hydroxyethyl)thymidine
(2):
(SC5Ј,SP) diastereoisomer 14c (4.0 Hz) suggests that the di- To compound 1 (0.5 g, 0.89 mmol), dissolved in acetone (1.5 mL)
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Conformationally Restricted Dinucleotides
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and H2O (0.3 mL), were added N-methylmorpholine N-oxide was removed in vacuo. The crude material was chromatographed
(1.03 mL of a 40% solution in H2O, 10.7 mmol) and osmium te- on silica gel with 9:1 AcOEt/petroleum ether as the eluent. After
troxide (40 µL of a 4% solution in H2O). Stirring was maintained evaporation of the solvent, compound 4 (mixture of diastereoiso-
for 16 h, and the reaction was stopped by the addition of aqueous mers) was recovered as a white foam (1.68 g, 93% yield). TLC: Rf
NaHSO3 (1 , 2 mL) and the mixture diluted with AcOEt. The (AcOEt) = 0.52. 1H NMR (250 MHz, CDCl3): δ = 9.93 (s, 4 H,
organic layer was collected, washed with brine and dried with NH), 9.89 (s, 4 H, NH), 9.87 (s, 4 H, NH), 9.70 (s, 4 H, NH), 7.50–
MgSO4. After removal of the solvent under reduced pressure, the 6.80 (m, 29 H, ph and 6-H), 6.42 (2m, 2 H, 1Ј-H), 6.15 (2m, 2 H,
crude material (530 mg) was dissolved in methanol (7 mL) at 0 °C. 1Ј-H), 5.05 (m, 1 H, 3Ј-H), 4.10 (m, 8 H, 3Ј-H, 4Ј-H, 5Ј-H and 2
Sodium periodate (451 mg, 2.1 mmol) was added, and after stirring CH2), 3.76 (s, 6 H, Me DMTr), 2.67 (m, 2 H), 2.44 (s, 3 H, Me
at 0 °C for 1 h and at room temperature for 2 h, aqueous NaHSO3 Ts), 2.24 (m, 4 H), 1.84 (s, 6 H, 2 Me), 1.25–1.21 (2m, 4 H), 1.41–
(1 , 3 mL) was added to stop the reaction. After removal of the 1.38 (2m, 4 H), 1.04 (s, 9 H, tBu) ppm. 13C NMR (63 MHz,
methanol under reduced pressure, the aqueous layer was extracted CDCl3): δ = 164.5, 164.1, 158.8, 150.9, 150.6, 141.1, 135.8, 135.1,
with AcOEt (3ϫ50 mL), and the organic layer was washed with 132.8, 132.6, 130.2, 130.0, 128.0, 127.3, 121.6, 113.4, 111.4, 87.2,
H2O and brine and dried with MgSO4. Removal of the solvent 86.4, 85.5, 84.4, 80.0, 73.9, 65.8, 62.6, 61.9, 55.4, 55.3, 39.6, 38.3,
provided a white foam (400 mg), which was submitted to sodium 27.8, 26.9, 21.7, 19.5, 19.4, 19.1, 11.7 ppm. 31P NMR (81 MHz,
borohydride (85 mg, 2.28 mmol) in ethanol (3 mL) at 0 °C. After CDCl3): δ = –3.5 and –3.4 ppm. MS (FAB): m/z = 1360 [M +
12 h of stirring at room temperature, aqueous NH4Cl was added Na]+, 1338 [M + H]+, 1036 [M – DMTr+2H]+.
(5 mL), and the ethanol was removed under reduced pressure. After
dilution with AcOEt (50 mL), the organic layer was washed with
H2O and brine and dried with MgSO4. Compound 2 (299 mg,
0.57 mmol, 64% overall yield) was recovered as a white foam after
5Ј-O-Dimethoxytrityl-3Ј-O-tert-butyldiphenylsilyl-α,β-D-CNA TT
(RC,SP) (5) and 5Ј-O-Dimethoxytrityl-3Ј-O-tert-butyldiphenylsilyl-
α,β-D-CNA TT (RC,RP) (6): To a solution of 4 (770 mg, 0.57 mmol)
in anhydrous DMF (20 mL), was added Et3N (319 µL, 2.28 mmol).
silica gel chromatography with 1:1 AcOEt/dichloromethane as the
After 3 h of stirring at 90 °C, the reaction mixture was cooled and
eluent. TLC: Rf (AcOEt/CH2Cl2, 1:1) = 0.35. 1H NMR (250 MHz,
diluted with AcOEt (100 mL) and washed with H2O (3ϫ20 mL)
and brine. The organic layer was dried with MgSO4, and the sol-
CDCl3): δ = 8.49 (s, 1 H, NH), 7.67–7.39 (m, 11 H, ph and 6-H),
6.20 (dd, J = 9.1, 5.8 Hz, 1 H, 1Ј-H), 4.53 (m, 1 H, 3Ј-H), 3.89–
vent was removed in vacuo. The cyclic phosphotriesters 5 and 6
3.86 (m, 2 H, 5Ј-H and 4Ј-H), 3.67 (m, 1 H, 7Ј-H), 2.26–2.15 (m,
were recovered as white foams. Compounds 5 (400 mg, 0.36 mmol)
and 6 (171 mg, 0.15 mmol) were isolated (90% yield) after silica gel
chromatography with AcOEt as the eluent.
4 H, 2Ј-H and 6Ј-H), 1.67 (s, 3 H, Me), 1.07 (s, 9 H, tBu) ppm. 13
C
NMR (63 MHz, CDCl3): δ = 164.1, 150.6, 137.8, 135.9, 135.8,
133.2, 130.1, 130.0, 128.0, 127.9, 127.8, 110.9, 91.2, 73.0, 61.2, 40.1,
33.8, 26.9, 19.1, 12.4 ppm. C28H36N2O6Si (524.68): calcd. C 64.10,
H 6.92, N 5.34; found C 64.05, H 7.01, N 5.31.
Data for 5: TLC: Rf (AcOEt) = 0.50. 1H NMR (250 MHz, CDCl3):
δ = 9.59 (2 s, 2 H, NH), 9.44 (2 s, 2 H, NH), 7.72–6.84 (m, 25 H,
ph, 6a-H and 6b-H), 6.38 (m, 2 H, 1Јb-H and 1Јa-H), 5.21 (m,
JH/P = 5.7 Hz, 1 H, 3Јa-H), 4.58 (m, 1 H, 3Јb-H), 4.49 (ddd, J =
11.7, 4.4 and 2.5 Hz, JH/P Ͻ 1 Hz, 1 H, 5Јb-H), 4.20 (m, 1 H, 4Јa-
H), 4.17 (m, 1 H, 7Јb-H), 4.10 (m, 1 H, 7Јb-H), 4.01 (m, 1 H, 4Јb-
H), 3.81 (s, 6 H, Me DMTr), 3.50 (A part of an ABX system, J =
10.7 and 3.0 Hz, 1 H, 5Јa-H), 3.39 (B part of an ABX system, J =
10.6 and 2.4 Hz, 1 H, 5Јa-H), 2.40 (m, 1 H, 2Јa-H), 2.29 (m, 1 H,
2Јa-H), 2.23 (m, 2 H, 2Јb-H), 1.86 (s, 3 H, Me), 1.51 (2m, 2 H, 6Јb-
H), 1.42 (2m, 2 H, 6Јb-H), 1.38 (s, 3 H, Me), 1.09 (s, 9 H, tBu)
ppm. 13C NMR (63 MHz, CDCl3): δ = 164.2, 159.2, 151.0, 144.4,
143.7, 139.9, 136.6, 136.4, 136.0, 135.4, 135.3, 133.3, 133.1, 131.4,
130.6, 130.5, 128.5, 128.4, 127.7, 113.7, 112.4, 111.6, 88.5, 87.7,
86.4, 84.9, 84.4, 80.4, 79.2, 73.2, 68.5, 63.7, 55.7, 39.8, 39.0, 30.1,
29.8, 27.6, 27.3, 19.5, 13.0, 12.0 ppm. 31P NMR (81 MHz, CDCl3):
δ = –9.1 ppm. C59H65N4O14PSi (1113.24): calcd. C 63.66, H 5.89,
N 5.03; found C 63.27, H 5.81, N 5.13.
3Ј-O-tert-Butyldiphenylsilyl-5Ј-C(R)-(tosyloxyethyl)thymidine (3):
To compound 2 (0.5 g, 0.96 mmol), dissolved in anhydrous pyridine
(1 mL) and chloroform (5.2 mL), tosyl chloride (270 mg, 1.4 mmol)
was added at 0 °C. Stirring was maintained for 12 h, and the reac-
tion mixture was diluted with AcOEt and washed with saturated
aqueous NH4Cl. The organic layer was collected and washed with
H2O and brine and dried with MgSO4. After removal of the solvent
under reduced pressure, the crude product was purified by silica
gel chromatography with 1:1 AcOEt/dichloromethane as the eluent.
Compound 3 was recovered as a white foam (501 mg, 0.74 mmol,
77% yield). TLC: Rf (AcOEt/petroleum ether, 1:1) = 0.25. 1H
NMR (250 MHz, CDCl3): δ = 9.11 (s, 1 H, NH), 7.81–7.61 (m, 6
H, ph), 7.39–7.30 (m, 9 H, ph and 6-H), 6.14 (t, J = 6.1 Hz, 1 H,
1Ј-H), 4.45 (m, 1 H, 3Ј-H), 4.15–3.75 (m, 4 H, 7Ј-H, 5Ј-H and 4Ј-
H), 3.13 (m, 1 H, OH), 2.43 (s, 3 H, MeTs), 2.21 (m, 2 H, 2Ј-H),
1.89 (s, 3 H, Me), 1.63–1.21 (m, 2 H, 6Ј-H), 1.08 (s, 9 H, tBu) ppm.
13C NMR (63 MHz, CDCl3): δ = 164.0, 150.5, 137.7, 135.9, 135.8,
133.0, 132. 7, 130.2, 129.9, 127.9, 111.1, 90.6, 88.0, 72.6, 67.7, 67.4,
39.6, 31.7, 26.9, 19.1, 12.5 ppm. C35H42N2O8SSi (678.87): calcd. C
61.92, H 6.24, N 4.13; found C 62.01, H 6.29, N 4.03.
Data for 6: TLC: Rf (AcOEt) = 0.20. 1H NMR (250 MHz, CDCl3):
δ = 9.38 (2 s, 2 H, NH), 9.27 (2 s, 2 H, NH), 7.69–6.84 (m, 25 H,
ph, 6a-H and 6b-H), 6.44 (dd, J = 9.4 and 5.4 Hz, 1 H, 1Јa-H),
6.35 (dd, J = 8.5 and 5.7 Hz, 1 H, 1Јb-H), 5.20 (m, JH/P = 6.0 Hz,
Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)thymidinyl-5Ј-C(R)-tosyl- 1 H, 3Јa-H), 4.52 (m, 2 H, 3Јb-H and 5Јb-H), 4.32 (m, 1 H, 7Јb-
oxyethyl-3Ј-(tert-butyldiphenylsilyl)thymidinyl Phosphoric Ester H), 4.17 (m, 1 H, 7Јb-H), 4.09 (br. s, 1 H, 4Јa-H), 3.98 (m, 1 H,
(Mixture of Diastereoisomers) (4): Compound
3 (920 mg, 4Јb-H), 3.80 (s, 6 H, Me DMTr), 3.44 (A part of an ABX system,
1.35 mmol), thymidine O3Ј-phosphoramidite (3.02 g, 4.05 mmol) J = 10.6 and 2.1 Hz, 1 H, 5Јa-H), 3.30 (B part of an ABX system,
and freshly sublimed tetrazole (1.11 g, 16.2 mmol) were dissolved J = 11.0 and 2.6 Hz, 1 H, 5Јa-H), 2.56 (m, J = 13.8 and 5.4 Hz, 1
in anhydrous acetonitrile (13 mL) and the mixture was stirred at H, 2Јa -H), 2.39 (m, J = 14.1, 9.3 and 5.1 Hz, 1 H, 2Јa-H), 2.27
room temperature for 20 min. After addition of collidine (1.1 mL, (m, J = 13.3, 5.9 and Ͻ 1 Hz, 1 H, 2Јb-H), 2,03 (m, J = 13.5, 8.4
8.11 mmol), the intermediate phosphite was oxidized with iodine and 5.5 Hz, 1 H, 2Јb-H), 1.82 (d, J = 1.1 Hz, 3 H, b-Me), 1.41 (m,
(0.1 M solution in 2:1 THF/H2O) until the dark brown colour per- 2 H, 6Јb-H), 1.37 (d, J = 1.1 Hz, 3 H, a-Me), 1.09 (s, 9 H, tBu)
sisted. The reaction mixture was diluted with AcOEt and washed ppm. 13C NMR (63 MHz, CDCl3): δ = 164.2, 164.1, 159.2, 151.0,
with aqueous sodium thiosulfate (15%) to remove excess iodine. 150.7, 144.4, 136.2, 136.1, 135.4, 135.3, 133.2, 133.1, 130.7, 130.5,
The organic layer was washed with H2O and brine, and the solvent 128.5, 128.4, 127.8, 113.8, 112.3, 111.9, 88.5, 87.8, 86.7, 85.1, 84.6,
Eur. J. Org. Chem. 2006, 5515–5525
© 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
5521

J.-M. Escudier, A. Vigroux, et al.
FULL PAPER
80.7, 79.8, 73.3, 68.4, 63.9, 55.7, 40.0, 39.0, 27.2, 19.5, 13.0, 12.0
ppm. 31P NMR (81 MHz, CDCl3): δ = –5.9 ppm. C59H65N4O14PSi
(1113.24): calcd. C 63.66, H 5.89, N 5.03; found C 63.11, H 5.71,
N 5.22.
2.0 Hz, 1 H, 6Јb-H], 1.91 (d, 3 H, b-Me), 1.90 (d, 3 H, a-Me) ppm.
13C NMR (100 MHz, CD3OD): δ = 165.1, 165.0, 151.1, 136.6,
110.8, 87.3, 85.9, 85.1, 84.9, 80.7, 78.8, 69.9, 69.0, 61.4, 39.1, 38.2,
27.6, 11.4, 11.3 ppm. 31P NMR (121 MHz, CD3OD): δ = –6.4 ppm.
C22H29N4O12P (572.46): calcd. C 46.26, H 5.11, N 9.79; found C
45.95, H 5.18, N 9.88.
Data for 10: TLC: Rf (20% MeOH/AcOEt) = 0.48. 1H NMR
(400 MHz, CD3OD): δ = 7.79 (d, J = 1.2 Hz, 1 H, 6a-H), 7.52 (d,
J = 1.1 Hz, 1 H, 6b-H), 6.31 (dd, J = 6.7 and 5.7 Hz, 1 H, 1Јa-H),
6.29 (dd, J = 7.9 and 6.2 Hz, 1 H, 1Јb-H), 5.13 (dddd, J = 2.0, 3.2,
5.6 Hz and JH/P = 6.4 Hz, 1 H, 3Јa-H), 4.91 (ddd, J = 2.8, 5.2,
10.8 Hz and JH/P = 4.0 Hz, 1 H, 5Јb-H), 4.61 (m, JH7Јb/P = 10.4 Hz,
JH7Јa/P = 12.4 Hz, 2 H, 7Ј-H), 4.57 (m, 1 H, 3Јb-H), 4.23 (t, J =
5Ј-O-Dimethoxytrityl-α,β-D-CNA TT (RC,SP) (7) and 5Ј-O-Dimeth-
oxytrityl-α,β-D-CNA TT (RC,RP) (8): To compound 5 (0.7 g,
0.63 mmol) or 6 (0.15 g, 0.13 mmol), dissolved in anhydrous THF
(5 mL, 1.5 mL for 6), tetrabutylammonium fluoride (0.7 mL,
0.7 mmol or 0.15 mL for 6) was added at room temperature. Stir-
ring was maintained for 1 h. After removal of the solvent under
reduce pressure, the crude product was purified on a silica gel col-
umn with 95:5 AcOEt/methanol as the eluent. Compound 7 (or 8)
was recovered as a white foam (473 mg, 90% yield or 97 mg, 86%
yield for 8). Probably due to the formation of aggregates in solu-
tion, the NMR spectra were obtained with a very poor resolution
3.2, 3.2 Hz, 1 H, 4Јa-H), 3.99 (ddd, J = 2.8, 5.2 Hz and JH4Јb/P
=
2.4 Hz, 1 H, 4Јb-H), 3.81 and 3.79 (AB part of an ABX system, J =
3.2, 3.2 and 12.0 Hz, 2 H, 5Јa-H), 2.53 (A part of an ABX system, J
= 14.0, 5.6 and 1.6 Hz, 1 H, 2Јa-H), 2.41 (B part of an ABX system,
J = 14.0, 6.7, 5.6 Hz and JH2Јa/P = 1.2 Hz, 1 H, 2Јa-H), 2.29 (m, 2
H, 2Јb-H),2.25 (m, 1 H, 6Јb-H), 2.15 (m, J = 12.0, 2.8 and 2.8 Hz,
1 H, 6Јb-H), 1.91 (d, J = 1.1 Hz, 3 H, b-Me). 1.90 (d, 3 H, J =
1.2 Hz, a-Me) ppm. 13C NMR (100 MHz, CD3OD): δ = 165.1,
165.0, 151.1, 136.7, 136.6, 110.8, 110.7, 87.3, 86.0, 85.9, 85.0, 81.7,
79.8, 70.5, 68.0, 61.4, 39.0, 38.3, 28.7, 11.3, 11.2 ppm. 31P NMR
(121 MHz, CD3OD): δ = –3.8 ppm. C22H29N4O12P (572.46): calcd.
C 46.26, H 5.11, N 9.79; found C 46.81, H 5.07, N 9.80.
1
for H and without detection of the aliphatic carbon atoms in the
13C spectrum. This phenomenon has already been observed with
the (SC,RP)-configured α,β-D-CNA diastereoisomer (see support-
ing information of ref.[13]).
Data for 7: TLC: Rf (5% MeOH/AcOEt) = 0.15. 1H NMR
(250 MHz, CDCl3): δ = 10.15 (s, 2 H, NH), 9.92 (s, 2 H, NH),
7.52–7.19 (m, 11 H, ph and 6-H), 6.80 (m, 4 H, ph), 6.43 (m, 1 H,
1Ј-H), 6.22 (m, 1 H, 1Ј-H), 5.22 (m, 1 H, 3Ј-H), 4.66 (m, 3 H), 4.31
(m, 4 H), 4.22 (m, 4 H), 3.96 (m, 2 H), 3.76 (s, 6 H, MeO), 3.35
(m, 2 H), 2.64 (m, 2 H), 2.35 (m, 2 H), 2.13 (m, 3 H), 1.84 (s, 3 H,
Me), 1.38 (s, 3 H, Me) ppm. 31P NMR (81 MHz, CDCl3): δ = –8.7
ppm. MS (electrospray): m/z = 897.3 [M + Na]+, 919 [M + K]+.
Data for 8: TLC: Rf (5% MeOH/AcOEt) = 0.12. 1H NMR
(250 MHz, CDCl3): δ = 10.10 (s, 2 H, NH), 9.90 (s, 2 H, NH),
7.56–7.20 (m, 11 H, ph and 6-H), 6.82 (m, 4 H, ph), 6.43 (dd, J =
9.1 and 5.2 Hz, 1 H, 1Ј-H), 6.26 (t, J = 6.7 Hz, 1 H, 1Ј-H), 5.11
(m, 1 H, 3Ј-H), 4.62 (m, 4 H), 4.47 (m, 4 H), 4.02 (m, 2 H), 3.77
(s, 6 H, MeO), 3.42 (m, 2 H), 2.62 (m, 2 H), 2.30 (m, 2 H), 2.11
(m, 3 H), 1.84 (s, 3 H, Me), 1.38 (s, 3 H, Me) ppm.31P NMR
(81 MHz, CDCl3): δ = –7.7 ppm. MS (ESI): m/z = 897.3 [M +
Na]+, 919 [M + K]+.
Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)thymidinyl-5Ј-C-tosyloxy-
ethyl-3Ј-(tert-butyldiphenylsilyl)thymidinyl Phosphoric Ester (12a),
Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)-N-isobutylguanidinyl-5Ј-C-
tosyloxyethyl-3Ј-(tert-butyldiphenylsilyl)thymidinyl Phosphoric Ester
(12b), Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)-N-benzoylcytidinyl-
5Ј-C-tosyloxyethyl-3Ј-(tert-butyldiphenylsilyl)thymidinyl Phosphoric
Ester (12c) and Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)-N-benzoyl-
adenidinyl-5Ј-C-tosyloxyethyl-3Ј-(tert-butyldiphenylsilyl)thymidinyl
Phosphoric Ester (12d): Dinucleotides 12a–d were prepared accord-
ing to the protocol described for 4, starting in each case from 0.5 g
of a (5ЈR/S) mixture of 3Ј-O-tert-butyldiphenylsilyl-5Ј-C-(tosyloxy-
ethyl)thymidine and with commercially available phosphoramidite.
After silica gel chromatography, compounds 12a–d were isolated as
white foams in 88%, 78%, 67% and 92% yield, respectively. Since
a mixture of four diastereoisomers is obtained in each case, the
corresponding 1H and 13C NMR spectra are very complicated and
are, therefore, not described.
Data for 12a: TLC: Rf (AcOEt) = 0.55. 31P NMR (121 MHz,
CDCl3): δ = –2.6, –2.7, –3.4, –3.5 ppm. MS (ESI): m/z = 1360 [M
+ Na]+, 1338 [M + H]+, 1036 [M – DMTr + 2 H]+.
Data for 12b: TLC: Rf (AcOEt) = 0.35. 31P NMR (81 MHz,
CDCl3): δ = –2.8, –3.0, –3.1, –3.8 ppm. MS (ESI): m/z = 1434 [M
+ H]+, 1131 [M – DMTr + 2 H]+.
Data for 12c: TLC: Rf (AcOEt) = 0.45. 31P NMR (81 MHz,
CDCl3): δ = –2.8, –3.5, –3.6, –3.7 ppm. MS (ESI): m/z = 1465 [M
+ K]+, 1449 [M + Na]+, 1423 [M + H]+.
Data for 12d: TLC: Rf (AcOEt) = 0.40. 31P NMR (121 MHz,
CDCl3): δ = –2.8, –2.9, –3.4, –3.6 ppm. MS (ESI): m/z = 1473.7
[M + Na]+, 1451.6 [M + H]+, 1149.4 [M – DMTr + 2 H]+.
α,β-D-CNA TT (RC,SP) (9) and α,β-D-CNA TT (RC,RP) (10): Com-
pound 7 (300 mg, 0.34 mmol) or 8 (70 mg, 0.08 mmol) was dis-
solved in TFA/dichloromethane (2%, 7 mL or 2 mL for 8) at room
temperature. After 15 min, the red solution was concentrated to
dryness. The crude material was dissolved in THF and purified by
silica gel chromatography. It was first eluted with AcOEt to remove
the dimethoxytrityl residue and then with 4:1 AcOEt/methanol to
collect the (RC,SP)-configured diastereoisomer 9 [or the (RC,RP)-
configured diastereoisomer 10] obtained as a white foam after
evaporation of the solvent (9: 166 mg, 85% yield, 10: 35 mg, 77%
yield).
Data for 9: TLC: Rf (15% MeOH/AcOEt) = 0.25. 1H NMR
(400 MHz, CD3OD): δ = 7.82 (d, J = 1.2 Hz, 1 H, 6a-H), 7.54 (d,
J = 1.2 Hz, 1 H, 6b-H), 6.35 (dd, J = 5.7 and 8.4 Hz, 1 H, 1Јa-H),
6.31 (t, J = 7.0 Hz, 1 H, 1Јb-H), 5.11 (dddd, J = 2.2, 2.2, 5.8 Hz
and JH/P = 5.9 Hz, 1 H, 3Јa-H), 4.86 (ddd, J = 2.1, 4.2 and 11.5 Hz,
1 H, 5Јb-H), 4.61 (ddd, J = 3.4, 3.5 and 6.6 Hz, 1 H, 3Јb-H), 4.56–
4.54 (m, JH/P = 3.0 and 20 Hz, 2 H, 7Јb-H), 4.27 (dd, J = 2.2 and
3.2 Hz, 1 H, 4Јa-H), 3.93 (ddd, J = 3.3, 4.3 Hz and JH/P = 3.2 Hz,
1 H, 4Јb-H), 3.84 (A part of an ABX system, J = 12.0, and 3.2 Hz,
5Ј-O-Dimethoxytrityl-3Ј-O-tert-butyldimethylsilyl-α,β-D-CNA
1 H, 5Јa-H), 3.82 (B part of an ABX system, J = 12.0, and 3.2 Hz, GiBuT (RC,SP) (5b), (RC,RP) (6b), (SC,RP) (13b) and (SC,SP) (14b),
1 H, 5Јa-H), 2.59 (A part of an ABX system, J = 14.2, 5.8 and
5Ј-O-Dimethoxytrityl-3Ј-O-tert-butyldiphenylsilyl-α,β-D-CNA CBz
T
2.1 Hz, 1 H, 2Јa-H), 2.41 (B part of an ABX system, J = 14.2, 8.4 (RC,SP) (5c), (RC,RP) (6c), (SC,RP) (13c) and (SC,SP) (14c) and 5Ј-
and 5.8 Hz, 1 H, 2Јa-H), 2.37 (m, 1 H, 2Јb-H), 2.27 [B part of an
ABX(Y) system, J = 13.8, 6.4, and 3.5 Hz, 1 H, 2Јb-H], 2.20 (m, 1
O-Dimethoxytrityl-3Ј-O-tert-butyldiphenylsilyl-α,β-D-CNA
(RC,SP) (5d), (RC,RP) (6d), (SC,RP) (13d) and (SC,SP) (14d): The
ABz
T
H, 6Јb-H), 2.04 [B part of an ABX(Y) system, J = 12.4, 2.0, and α,β-D-CNA dimers 5a–d, 6a–d, 13a–d and 14a–d were obtained in
5522 Eur. J. Org. Chem. 2006, 5515–5525
www.eurjoc.org
© 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

Conformationally Restricted Dinucleotides
FULL PAPER
90%, 91%, 95% and 84% yield, respectively, from the correspond-
ing dinucleotides according to the following protocol: to dinucleo-
tide 12a–d (0.5 mmol) in anhydrous DMF (20 mL), was added po-
tassium carbonate (1.1 g, 8 mmol). After 4 h of stirring at 25 °C,
the excess of base was filtered off, and the reaction mixture was
diluted with AcOEt (100 mL) and washed with H2O (3ϫ20 mL)
and brine. The organic layer was dried with MgSO4, and the sol-
vent was removed in vacuo. 5a (identical to 5), 6a (identical to 6)
and 13a were separated by silica gel chromatography with AcOEt
as the eluent. TLC: Rf (AcOEt) = 0.50 (5a), 0.35 (13a) and 0.2 (6a).
Data for 13a are provided in ref.[13] 5b/14b, 6b and 13b were sepa-
rated by reverse-phase chromatography on a Kromasil C18, 7 µm,
100 Å, 250ϫ4.6 mm column for analysis or a 250ϫ20 mm prepa-
ratory scale column with 30:70 H2O/acetonitrile. tr = 29.48 min,
20.18 min and 21.8 min, respectively.
8.7 Hz, 1 H, 1ЈT-H), 6.17 (dd, J = 5.4 and 8.4 Hz, 1 H, 1ЈG-H),
5.38 (m, 1 H, 3ЈG-H), 4.33–4.24 (m, 1 H, 7ЈT-H), 4.29 (m, 1 H, 3ЈT-
H), 4,21 (m, 1 H, 4ЈG-H), 4.13–4.05 (m, 1 H, 7ЈT-H), 3.87 (m,
JH/P Ͻ 1 Hz, 1 H, 5ЈT-H), 3.82 (m, 1 H, 4ЈT-H), 3.74 (2s, 6 H,
MeO), 3.34 (AB part of an ABX syst, J = 2.7, 3.3 and 10.8 Hz, 2
H, 5ЈG-H), 3.17 (AB part of an ABX syst, J = 2.7, 3.3 and 10.8 Hz,
2 H, 5ЈG-H), 3.10 (m, 1 H, 2ЈG-H), 2.56 (B part of an ABX syst, J
= 2.4, 5.7 and 13.2 Hz, 1 H, 2ЈG-H), 2.36–2.16 (m, 3 H, 2ЈT-H and
CH iBu), 1.94 (br. s, 3 H, Me), 1.94–1.82 (m, 1 H, 6ЈT-H), 1.25–
1.22 (m, 1 H, 6ЈT-H), 1.08 (d, J = 6.6 Hz, 3 H, Me iBu), 1.07 (s, 9
H, tBu), 0.94 (d, J = 6.6 Hz, 3 H, Me iBu) ppm. 13C NMR
(100 MHz, CDCl3): δ = 179.6, 164.5, 158.6, 155.6, 150.7, 148.1,
147.9, 144.4, 136.4, 135.8, 135.7, 135.5, 135.4, 133.2, 132.5, 130.3,
130.0, 128.1, 127.9, 127.0, 121.7, 113.2, 111.6, 88.2, 88.1, 86.6, 86.3,
84.7, 84.1, 79.9, 77.8, 74.4, 67.8, 62.9, 60.4, 55.2, 39.8, 38.1, 35.9,
27.5, 26.9, 19.0, 18.9, 18.7, 12.3 ppm. 31P NMR (121 MHz,
CDCl3): δ = –9.0 ppm. MS (ESI): m/z = 1230.7 [M + Na]+, 1208.8
[M + H]+.
Data for 5b: 1H NMR (300 MHz, CDCl3): δ = 10.00 (s, 1 H, NH),
8.82 (s, 1 H, NH), 7.69–7.22 (m, 21 H, ph, 6T-H and 2G-H), 6.82
(B part of AB syst, J = 8.7 Hz, 4 H, DMT), 6.81 (B part of AB
syst, J = 8.7 Hz, 4 H, DMT), 6.50 (t, J = 7.4 Hz, 1 H, 1ЈT-H), 6.13
(dd, J = 5.4 and 9.0 Hz, 1 H, 1ЈG-H), 5.38 (t, J = 5.3 Hz, 1 H, 3ЈG-
H), 4.61 (m, 1 H, 3ЈT-H), 4.37 (br. d, J = 12.3 Hz, JH/P Ͻ 1 Hz, 1
H, 5ЈT-H), 4.15–3.89 (m, 4 H, 7ЈT-H, 4ЈG-H and 4ЈT-H), 3.78 (s, 6
H, MeO), 3.36 (AB part of an ABX syst, J = 3.9, 5.7 and 10.2 Hz,
2 H, 5ЈG-H), 3.23 (AB part of an ABX syst, J = 3.9, 5.7 and
10.2 Hz, 2 H, 5ЈG-H), 2.82 (sept, J = 6.9 Hz, 1 H, CH iBu), 2.73
(A part of an ABX syst, J = 0.9, 5.7 and 13.8 Hz, 1 H, 2ЈG-H),
2.45 (B part of an ABX syst, J = 5.4, 9.0 and 13.8 Hz, 1 H, 2ЈG-
H), 2.34 (m, 2 H, 2ЈT-H), 2.01 (s, 3 H, Me), 1.27–1.15 (m, 1 H, 6ЈT-
H), 1.21 (d, J = 6.9 Hz, 3 H, Me iBu), 1.17 (d, J = 6.6 Hz, 3 H,
Me iBu), 1.08 (s, 9 H, tBu), 1.05–1.02 (m, 1 H, 6ЈT-H) ppm. 13C
NMR (100 MHz, CDCl3): δ = 180.1, 164.7, 158.7, 155.6, 150.6,
148.5, 148.0, 144.3, 136.6, 136.2, 135.9, 135.7, 135.2, 132.8, 132.5,
130.6, 130.0, 128.2, 128.0, 127.1, 121.3, 113.3, 111.2, 88.6, 88.5,
86.9, 85.6, 84.6, 84.5, 83.7, 81.3, 78.3, 72.3, 68.3, 63.1, 60.4, 55.3,
39.2, 38.8, 35.7, 29.3, 26.9, 26.6, 19.2, 19.1, 18.8, 12.7 ppm.31P
NMR (121 MHz, CDCl3): δ = –8.9 ppm. MS (ESI): m/z = 1230.7
[M + Na]+, 1208.8 [M + H]+.
5c, 6c, and 13c/14c were separated by silica gel chromatography
with AcOEt as the eluent. TLC: Rf (AcOEt) = 0.30 (5c), 0.20 (13c/
14c) and 0.15 (6c). 13c was separated from 14c on a Kromasil C18,
7 µm, 100 Å, 250ϫ20 mm column with 90:10 MeOH/H2O as the
eluent. tr = 18.9 min for 14c and 22.4 min for 13c.
1
Data for 5c: H NMR (300 MHz, CDCl3): δ = 8.77 (s, 1 H, NH),
8.36 (s, 1 H, NH), 8.05 (d, J = 7.5 Hz, 1 H, 6C-H), 7.88 (d, J =
7.5 Hz, 2 H, ph), 7.67–7.22 (m, 24 H, ph, 5C-H, and 6T-H), 6.85
(m, 4 H, DMT), 6.37 (t, J = 7.3 Hz, 1 H, 1ЈT-H), 6.25 (t, J =
6.4 Hz, 1 H, 1ЈC-H), 5.11 (m, 1 H, 3ЈC-H), 4.54 (m, 1 H, 3ЈT-H),
4.37 (m, JH/P Ͻ 1 Hz, 1 H, 5ЈT-H), 4.29 (m, 1 H, 4ЈC-H), 4.14–4.05
(m, 2 H, 7ЈT-H), 3.95 (m, 1 H, 4ЈT-H), 3.78 (s, 6 H, MeO), 3.46
(AB part of an ABX syst, J = 3.3, 3.6 and 10.9 Hz, 2 H, 5ЈC-H),
3.40 (AB part of an ABX syst, J = 3.3, 3.6 and 10.9 Hz, 2 H, 5ЈC-
H), 2.65 (m, 1 H, 2ЈC-H), 2.21–2.12 (m, 3 H, 2ЈT-H and 2ЈC-H),
1.83 (br. s, 3 H, Me), 1.60–1.32 (m, 2 H, 6ЈT-H), 1.06 (s, 9 H, tBu)
ppm. 13C NMR (100 MHz, CDCl3): δ = 164.0, 162.8, 158.8, 150.8,
144.1, 143.9, 136.0, 135.8, 135.1, 134.9, 133.1, 132.9, 132.8, 130.2,
130.1, 128.9, 128.1, 128.0, 127.9, 127.3, 113.4, 111.4, 97.0, 88.1,
88.0, 87.3, 86.7, 85.4, 85.0, 84.9, 80.1, 77.6, 72.9, 68.1, 62.6, 55.3,
40.0, 39.4, 27.2, 26.9, 19.1, 12.6 ppm. 31P NMR (121 MHz,
CDCl3): δ = –9.3 ppm. MS (ESI): m/z = 1203.1 [M + H]+.
1
Data for 6b: H NMR (300 MHz, CDCl3): δ = 9.00 (s, 1 H, NH),
8.71 (s, 1 H, NH), 7.72 (s, 1 H, 2G-H), 7.64–7.17 (m, 20 H, ph and
6T-H), 6.78 (B part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.77 (B
part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.11 (t, J = 6.6 Hz, 1 H,
1ЈT-H), 6.08 (dd, J = 5.4 and 8.4 Hz, 1 H, 1ЈG-H), 5.25 (m, 1 H,
3ЈG-H), 4.60 (m, 1 H, 5ЈT-H), 4.51 (m, 1 H, 3ЈT-H), 4.34 (m, 1 H,
7ЈT-H), 4,21 (m, 1 H, 4ЈG-H), 4.20–4.07 (m, 1 H, 7ЈT-H), 4.02 (m,
1 H, 4ЈT-H), 3.77 (2s, 6 H, MeO), 3.33 (AB part of an ABX syst,
J = 3.6, 3.6 and 10.5 Hz, 2 H, 5ЈG-H), 3.19 (AB part of an ABX
syst, J = 3.6, 3.6 and 10.5 Hz, 2 H, 5ЈG-H), 2.86 (m, 1 H, 2ЈG-H),
2.50 (m, 1 H, 2ЈG-H), 2.34 (m, 1 H, 2ЈT-H), 2.22 (sept, J = 6.6 Hz,
1 H, CH iBu), 2.07 (m, 1 H, 2ЈT-H), 1.86 (br. s, 3 H, Me), 1.61–
1.47 (m, 1 H, 6ЈT-H), 1.39–1.32 (m, 1 H, 6ЈT-H), 1.09 (d, J = 6.6 Hz,
Me 3 H, iBu), 1.05 (s, 9 H, tBu), 0.96 (d, J = 6.6 Hz, 3 H, Me iBu)
ppm. 13C NMR (100 MHz, CDCl3): δ = 179.3, 164.2, 158.7, 155.5,
150.2, 148.0, 147.9, 144.4, 136.6, 135.8, 135.7, 135.5, 135.3, 132.8,
132.7, 130.3, 130.1, 128.2, 128.0, 127.2, 121.9, 113.3, 113.0, 111.0,
88.3, 88.2, 87.4, 86.6, 84.5, 84.4, 84.1, 79.6, 78.9, 72.6, 67.2, 63.0,
60.4, 55.2, 40.3, 38.6, 36.0, 26.8, 26.6, 19.1, 18.9, 18.8, 12.4 ppm.31P
NMR (121 MHz, CDCl3): δ = –6.4 ppm. MS (ESI): m/z = 1230.7
[M + Na]+, 1208.8 [M + H]+.
1
Data for 6c: H NMR (300 MHz, CDCl3): δ = 8.74 (s, 1 H, NH),
8.16 (s, 1 H, NH), 8.07 (d, J = 7.5 Hz, 1 H, 6C-H), 7.90 (d, J =
7.5 Hz, 2 H, ph), 7.68–7.21 (m, 23 H, ph, 5C-H), 7.17 (br. d, 1 H,
6T-H), 6.84 (B part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.35 (dd,
J = 5.7 and 8.7 Hz, 1 H, 1ЈT-H), 6.23 (dd, J = 5.4 and 7.5 Hz, 1
H, 1ЈC-H), 5.12 (m, 1 H, 3ЈC-H), 4.55–4.49 (m, 2 H, 3ЈT-H and 5ЈT-
H), 4.34–4.26 (m, 1 H, 7ЈT-H), 4.22 (m, 1 H, 4ЈC-H), 4.19–4.11 (m,
1 H, 7ЈT-H), 3.97 (m, 1 H, 4ЈT-H), 3.79 (s, 6 H, MeO), 3.37 (d, 1
H, 5ЈC-H), 2.86 (m, 1 H, 2ЈC-H), 2.31–2.20 (m, 2 H, 2ЈT-H and 2ЈC-
H), 2.06–1.97 (m, 1 H, 2ЈT-H), 1.83 (br. s, 3 H, Me), 1.47–1.27 (m,
2 H, 6ЈT-H), 1.07 (s, 9 H, tBu) ppm. 13C NMR (100 MHz, CDCl3):
δ = 164.2, 163.2, 158.8, 150.9, 144.1, 143.8, 135.6, 135.1, 135.0,
134.9, 133.2, 133.1, 133.0, 132.5, 130.4, 130.3, 130.0, 128.8, 128.1,
128.0, 127.9, 127.2, 113.4, 112.2, 97.3, 87.7, 87.6, 87.4, 87.2, 85.8,
85.7, 84.6, 79.8, 78.9, 74.4, 67.7, 63.1, 55.2, 40.5, 39.9, 27.5, 26.8,
19.0, 12.3 ppm. 31P NMR (121 MHz, CDCl3): δ = –6.0 ppm. MS
(ESI): m/z = 1203.1 [M + H]+.
1
Data for 13c: H NMR (300 MHz, CDCl3): δ = 8.70 (s, 1 H, NH),
Data for 13b: 1H NMR (300 MHz, CDCl3): δ = 9.14 (s, 1 H, NH),
8.69 (s, 1 H, NH), 7.66 (s, 1 H, 2G-H), 7.65–7.18 (m, 20 H, ph and
6T-H), 6.75 (B part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.72 (B
part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.36 (dd, J = 6.0 and
8.16 (s, 1 H, NH), 7.99 (d, J = 7.2 Hz, 1 H, 6C-H), 7.84 (d, J =
7.5 Hz, 2 H, ph), 7.58–7.22 (m, 20 H, ph, 5C-H, and 6T-H), 7.16
(A part of an AB syst, J = 1.5 and 8.7 Hz, 4 H, DMT), 6.77 (B
part of AB syst, J = 8.7 Hz, 4 H, DMT), 6.61 (dd, J = 5.4 and
Eur. J. Org. Chem. 2006, 5515–5525
© 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
5523

J.-M. Escudier, A. Vigroux, et al.
FULL PAPER
9.3 Hz, 1 H, 1ЈT-H), 6.31 (dd, J = 5.4 and 8.1 Hz, 1 H, 1ЈC-H), 5.09
(t, J = 5.4 Hz, 1 H, 3ЈC-H), 4.42–4.30 (m, 1 H, 7ЈT-H), 4.37 (d, J
= 5.7 Hz, 1 H, 3ЈT-H), 4.30 (s, 1 H, 4ЈC-H), 4.15–4.07 (m, 1 H, 7ЈT-
H), 3.71 (s, 6 H, MeO), 3.70 (m, 1 H, 4ЈT-H), 3.48 (br. d, J =
and 3ЈT-H), 4.41–4.29 (m, 2 H, 7ЈT-H and 4ЈA-H), 4.23–4.10 (m, 1
H, 7ЈT-H), 4.00 (m, 1 H, 4ЈT-H), 3.72 (s, 6 H, MeO), 3.40 (AB part
of an ABX syst, J = 3.9, 3.9 and 10.5 Hz, 2 H, 5ЈA-H), 3.34 (AB
part of an ABX syst, J = 3.9, 3.9 and 10.5 Hz, 2 H, 5ЈA-H), 3.01
11.1 Hz, JH/P Ͻ 1 Hz, 1 H, 5ЈT-H), 3.41 (m, 2 H, 5ЈC-H), 2.86 (m, (m, 1 H, 2ЈA-H), 2.69 (B part of an ABX syst, J = 0.9, 5.4 and
1 H, 2ЈC-H), 2.34–2.17 (m, 3 H, 6ЈT-H, 2ЈT-H and 2ЈC-H), 1.92– 13.8 Hz, 1 H, 2ЈA-H), 2.25 (A part of an ABX syst, J = 1.8, 6.3
1.82 (m, 1 H, 2ЈT-H), 1.94 (br. s, 3 H, Me), 1.32–1.27 (m, 1 H, 6ЈT- and 13.2 Hz, 1 H, 2ЈT-H), 2.03 (m, 1 H, 2ЈT-H), 1.82 (br. s, 3 H,
H), 1.07 (s, 9 H, tBu) ppm. 13C NMR (100 MHz, CDCl3): δ =
163.7, 162.5, 158.8, 150.3, 144.3, 143.9, 135.9, 135.8, 134.9, 133.2,
133.1, 132.8, 132.7, 130.4, 130.3, 130.2, 130.1, 130.0, 129.0, 128.1,
127.7, 127.3, 113.4, 111.5, 97.3, 88.2, 88.1, 87.3, 87.1, 86.2, 85.6,
85.5, 79.5, 79.4, 79.3, 72.9, 67.1, 63.0, 55.3, 40.5, 39.7, 26.9, 26.3,
19.1, 12.5 ppm. 31P NMR (121 MHz, CDCl3): δ = –9.0 ppm. MS
(ESI): m/z = 1203.1 [M + H]+.
Me), 1.62–1.43 (m, 2 H, 6ЈT-H), 1.07 (s, 9 H, tBu) ppm. 13C NMR
(100 MHz, CDCl3): δ = 165.0, 163.8, 158.7, 151.8, 150.4, 149.9,
144.2, 135.9, 135.8, 135.3, 133.5, 132.8, 132.7, 130.3, 130.0, 128.7,
128.2, 128.1, 127.9, 127.1, 123.7, 113.3, 111.6, 88.1, 88.0, 86.8, 86.3,
85.3, 85.2, 84.5, 80.0, 79.3, 79.2, 73.0, 67.2, 67.1, 63.3, 60.4, 55.3,
39.5, 38.8, 26.8, 19.1, 12.5 ppm. 31P NMR (121 MHz, CDCl3): δ
= –6.2 ppm. MS (ESI): m/z = 1248.6 [M + Na]+, 1226.7
[M + H]+.
1
Data for 14c: H NMR (500 MHz, CDCl3): δ = 8.70 (s, 1 H, NH),
Data for 13d: 1H NMR (300 MHz, CDCl3): δ = 9.34 (s, 1 H, NH),
8.89 (s, 1 H, NH), 8.81 (2 s, 2 H, 8A-H and 2A-H), 8.19 (2 s, 2 H,
8A-H and 2A-H), 8.06 (m, 2 H, ph), 7.67–7.22 (m, 23 H, ph), 6.78
(B part of an AB syst, J = 9.0 Hz, 4 H, DMT), 6.62 (dd, J = 5.7
and 9.1 Hz, 1 H, 1ЈT-H), 6.55 (dd, J = 5.4 and 9.3 Hz, 1 H, 1ЈA-
H), 5.21 (t, J = 5.6 Hz, 1 H, 3ЈA-H), 4.43–4.31 (m, 3 H, 7ЈT-H, 3ЈT-
H and 4ЈA-H), 4.15–4.07 (m, 1 H, 7ЈT-H), 3.76 (s, 1 H, 4ЈT-H), 3.72
(s, 6 H, MeO), 3.50 (d, J = 11.4 Hz, JH/P Ͻ 1 Hz, 1 H, 5ЈT-H), 3.41
(AB part of an ABX syst, J = 3.3, 3.6 and 10.5 Hz, 2 H, 5ЈA-H),
3.35 (AB part of an ABX syst, J = 3.3, 3.6 and 10.5 Hz, 2 H, 5ЈA-
H), 2.95 (m, 1 H, 2ЈA-H), 2.74 (B part of an ABX syst, J = 5.4 and
13.8 Hz, 1 H, 2ЈA-H), 2.33–2.17 (m, 2 H, 2ЈT-H and 6ЈT-H), 2.01–
1.94 (m, 4 H, 2ЈT-H and Me), 1.38 (m, 1 H, 6ЈT-H), 1.04 (s, 9 H,
tBu) ppm. 13C NMR (100 MHz, CDCl3): δ = 165.4, 164.2, 158.7,
152.0, 151.1, 150.1, 144.2, 135.9, 135.3, 135.2, 133.4, 132.8, 132.5,
130.4, 130.0, 128.4, 128.2, 128.1, 128.0, 127.1, 123.7, 113.3, 112.4,
87.7, 87.7, 87.0, 85.5, 85.4, 84.7, 84.2, 79.7, 79.6, 79.3, 74.6, 67.5,
63.4, 60.4, 55.3, 39.9, 39.4, 27.6, 26.9, 19.1, 12.4 ppm.31P NMR
(121 MHz, CDCl3): δ = –9.3 ppm. MS (ESI): m/z = 1248.7 [M +
Na]+, 1226.6 [M + H]+.
8.16 (s, 1 H, NH), 8.11 (d, J = 7.5 Hz, 1 H, 6C-H), 7.92 (d, J =
7.5 Hz, 2 H, ph), 7.72–7.26 (m, 24 H, ph, 5C-H, and 6T-H), 6.87
(B part of AB syst, J = 9.0 Hz, 4 H, DMT), 6.53 (dd, J = 5.5 and
9.0 Hz, 1 H, 1ЈT-H), 6.19 (t, J = 6.5 Hz, 1 H, 1ЈC-H), 5.32 (m, 1 H,
3ЈC-H), 4.53 (d, J = 5.8 Hz, 1 H, 3ЈT-H), 4.33–4.19 (m, 2 H, 7ЈT-
H), 4.30 (m, 1 H, 4ЈC-H), 3.82 (s, 6 H, MeO), 3.75 (m, JH/P
≈
4.0 Hz, 1 H, 5ЈT-H), 3.73 (s, 1 H, 4ЈT-H), 3.44 (d, 2 H, 5ЈC-H), 2.82
(m, 1 H, 2ЈC-H), 2.44–2.35 (m, 2 H, 2ЈT-H and 2ЈC-H), 2.22–2.00
(m, 1 H, 2ЈT-H), 2.17 (m, 1 H, 6ЈT-H), 1.87 (br. s, 3 H, Me), 1.41–
1.38 (m, 1 H, 6ЈT-H), 1.12 (s, 9 H, tBu) ppm. 13C NMR (100 MHz,
CDCl3): δ = 163.2, 158.7, 150.2, 143.8, 135.4, 135.3, 135.2, 135.1,
134.8, 133.3, 133.2, 132.5, 130.4, 130.3, 130.2, 130.0, 129.1, 129.0,
128.0, 127.8, 127.6, 127.2, 113.3, 111.3, 87.6, 87.5, 87.3, 86.7, 85.2,
85.0, 84.9, 78.8, 77.9, 77.8, 73.9, 66.7, 62.4, 55.3, 40.8, 40.0, 29.7,
27.8, 19.1, 12.7 ppm. 31P NMR (121 MHz, CDCl3): δ = –2.9 ppm.
MS (ESI): m/z = 1203.1 [M + H]+.
5d, 6d, and 13d/14d were separated by reverse-phase chromato-
graphy on a Kromasil C18, 7 µm, 100 Å, 250ϫ4.6 mm column for
analysis or with a 250ϫ20 mm preparatory scale column with
25:75 H2O/acetonitrile. tr = 17.9 min, 19.0 min, 15.2 min and
21.3 min, respectively. Under these conditions, 14d could not be
isolated in a pure form.
Crystal Data for 9: C23H29.5N4.5O12.5P, M = 599.98, monoclinic,
C2, a = 29.223(6) Å, b = 10.337(2) Å, c = 9.754(2) Å, β =
106.623(5)°, V = 2823.2(10) Å3, Z = 4 and T = 193(2) K. 6267
reflections (3623 independent, Rint = 0.0716) were collected at low
temperatures with an oil-coated shock-cooled crystal using a
Bruker-AXS CCD 1000 diffractometer with Mo-Kα radiation (λ =
0.71073 Å). The structure was solved by direct methods (SHELXS-
97)[24] and all non-hydrogen atoms were refined anisotropically
with the least-squares method on F2.[25] Largest electron density
residue: 0.450 e·Å–3; R1 [for I Ͼ 2σ(I)] = 0.0673 and wR2 = 0.1661
1
Data for 5d: H NMR (300 MHz, CDCl3): δ = 9.22 (s, 1 H, NH),
8.92 (s, 1 H, NH), 8.69 (2 s, 2 H, 8A-H and 2A-H), 8.07 (2 s, 2 H,
8A-H and 2A-H), 8.04 (m, 2 H, ph), 7.69–7.23 (m, 22 H, ph), 7.17
(br. s, 1 H, 6T-H), 6.79 (B part of an AB syst, J = 8.1 Hz, 4 H,
DMT), 6.43 (dd, J = 6.0 and 8.1 Hz, 1 H, 1ЈA-H), 6.38 (dd, J =
6.0 and 8.7 Hz, 1 H, 1ЈT-H), 5.20 (m, 1 H, 3ЈA-H), 4.59 (d, J =
5.4 Hz, 1 H, 3ЈT-H), 4.49 (br. d, J = 12.3 Hz, JH/P Ͻ 1 Hz, 1 H,
5ЈT-H), 4.30 (m, 1 H, 4ЈA-H), 4.12–4.05 (m, 2 H, 7ЈT-H), 3.97 (m,
1 H, 4ЈT-H), 3.71 (s, 6 H, MeO), 3.40 (m, 2 H, 5ЈA-H), 3.05 (m, 1
H, 2ЈA-H), 2.72 (B part of an ABX syst, J = 1.8, 6.0 and 14.4 Hz,
1 H, 2ЈA-H), 2.24 (A part of an ABX syst, J = 1.8, 6.3 and 13.8 Hz,
1 H, 2ЈT-H), 2.14 (m, 1 H, 2ЈT-H), 1.81 (br. s, 3 H, Me), 1.43–1.17
(m, 2 H, 6ЈT-H), 1.08 (s, 9 H, tBu) ppm. 13C NMR (100 MHz,
CDCl3): δ = 165.4, 163.9, 158.7, 151.5, 150.8, 150.1, 144.2, 135.9,
135.8, 135.3, 133.6, 132.8, 132.6, 130.3, 130.0, 128.6, 128.3, 128.1,
127.9, 127.1, 123.5, 113.3, 111.4, 88.0, 87.9, 86.9, 85.3, 85.0, 84.9,
84.5, 80.5, 80.4, 78.6, 72.5, 68.8, 63.0, 60.4, 55.3, 39.6, 37.9, 26.9,
19.1, 12.6 ppm. 31P NMR (121 MHz, CDCl3): δ = –9.1 ppm. MS
(ESI): m/z = 1248.6 [M + Na]+, 1226.7 [M + H]+.
2
2 2
(all data) with R1 = Σ||Fo| – |Fc||/Σ|Fo| and wR2 = [Σw(Fo – Fc ) /
Σw(Fo2)2]0.5. CCDC-614026 contains the supplementary crystallo-
graphic data for this paper. These data can be obtained free of
charge from The Cambridge Crystallographic Data Centre via
www.ccdc.cam.ac.uk/data_request/cif.
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Data for 6d: H NMR (300 MHz, CDCl3): δ = 9.09 (s, 1 H, NH),
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5524
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© 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2006, 5515–5525

Conformationally Restricted Dinucleotides
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Received: July 11, 2006
Published Online: October 19, 2006
Eur. J. Org. Chem. 2006, 5515–5525
© 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
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