Diastereoselective and regioselective synthesis of conformationally restricted thio-dioxa- and oxo-oxathiaphosphorinane dinucleotides featuring noncanonical α/β torsion angle combinations (α,β-CNAs)

Article abstract of DOI:10.1002/ejoc.200601030

Control of the regioselective cyclisation of a stereodefined 5′-C-tosyloxy phosphorothioate dinucleotide unit to provide conformationally restricted dinucleotides of either thio-di-oxa- or oxo-oxathiaphosphorinane types is described. NMR structural analys

Full text of DOI:10.1002/ejoc.200601030

FULL PAPER
DOI: 10.1002/ejoc.200601030
Diastereoselective and Regioselective Synthesis of Conformationally Restricted
Thio-dioxa- and Oxo-oxathiaphosphorinane Dinucleotides Featuring
Noncanonical α/β Torsion Angle Combinations (α,β-CNAs)
Ingrid Le Clézio,[a] Alain Vigroux,[a] and Jean-Marc Escudier*[a]
Keywords: Constrained molecules / Nucleic acids / Phosphorothioate / Cyclisation / Regioselectivity
Control of the regioselective cyclisation of a stereodefined
5Ј-C-tosyloxy phosphorothioate dinucleotide unit to provide
conformationally restricted dinucleotides of either thio-di-
oxa- or oxo-oxathiaphosphorinane types is described. NMR
structural analysis of the newly synthesized building units
showed the α and β torsional angles to be constrained to non-
canonical values {gauche(+), trans} or {anticlinal(–), trans}.
(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim,
Germany, 2007)
structure. One possible approach through which to preorga-
nize single-stranded oligonucleotides is to include one or
more backbone bonds (α–ζ) within a well-defined ring
structure.
Introduction
Conformational restrictions in nucleic acid structures
have been introduced and studied mainly with the goal of
improving the abilities of these analogues to form stable
Watson–Crick (WC) duplexes with complementary nucleic
acid targets.[1–4] It is therefore desirable that chemical modi-
fications made on natural nucleic acids should preserve, as
much as possible, the two major interactions that stabilize
the double-helical structures of nucleic acid duplexes:
namely the WC hydrogen bonds and base stacking interac-
tions. In structural terms, the most promising DNA/RNA
analogues are usually expected to be those in which the
backbone torsion angles closely match the geometries of
torsion angles α–ζ in standard A- or B-type duplexes.
The preparation of well defined structures in nucleic ac-
ids requires control over the backbone torsion angles, still a
particularly challenging task in the field of oligonucleotide
chemistry.[5–6] The capacity to control the α–ζ dihedrals
along the sugar-phosphate backbone would help structural
chemists better understand the complex interrelationship
that underlies these torsions and the overall solution struc-
tures of DNA and RNA, and would also allow the physical,
biochemical and biological properties of various backbone
geometries to be studied, irrespective of the base sequence.
From the concept of structural preorganization,[7] it
could be anticipated that if the conformational states of an
oligonucleotide single strand could be locally reduced to
those that match the geometry of this strand in the target
structure, then an entropic benefit could be expected, and
that this should result in an overall stabilization of the
We have undertaken an experimental program to explore
the chemistry of DNA and RNA analogues containing
modified backbones that might, at least in principle, favour
unusual helical conformations as well as the formation of
structurally well defined non-base-pair states. As an initial
step in this direction, we have already reported on the syn-
thesis of a covalently constrained dinucleotide building unit
in which α and β torsions are locked in a noncanonical
(g+, t) conformation that frequently occurs in protein–DNA
complexes and in bulged regions of nucleic acids.[8] Our ap-
proach is based on the introduction of the neutral 1,3,2-
dioxaphosphorinane ring structure at key positions along
the sugar-phosphate backbone (Figure 1). We reasoned that
the resulting constrained nucleic acids (D-CNAs) could lo-
cally adopt either helical or nonhelical conformations, de-
pending on the spatial arrangements of the dioxaphosphor-
inane systems and on which backbone bonds were included
[a] Laboratoire de Synthèse et Physico-Chimie de Molécules
d’Intérêt Biologique, UMR 5068 CNRS, Université Paul
Sabatier,
Figure 1. Left: the six backbone torsion angles (labelled α to ζ) in
nucleic acids. Right: α,β--CNA units are dinucleotides in which α
and β are stereocontrolled by dioxaphosphorinane ring structures
featuring two new asymmetric centres.
31062 Toulouse Cedex 9, France
E-mail: escudier@chimie.ups-tlse.fr
Eur. J. Org. Chem. 2007, 1935–1941
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
1935

I. Le Clézio, A. Vigroux, J.-M. Escudier
FULL PAPER
in the ring structures. This approach was usefully applied
to prepare α,β-D-CNAs with exceptional binding properties
associated with the introduced constraint, regardless of the
charge reduction[9] and dinucleotide units, with α,β,γ and
δ,ε,ζ possessing noncanonical values (α,β,γ-D-CNA and
δ,ε,ζ-D-CNA).[10]
However, the synthetic route developed for α,β-D-CNA
dinucleotides allowed us to prepare only three out of the
four possible diastereoisomers efficiently.[11] In order to ex-
tend the α,β-torsional angle value set and therefore to pro-
vide access to an additional α,β-CNA dinucleotide unit ex-
hibiting new noncanonical values, we explored a novel syn-
thetic pathway through the cyclisation of stereodefined
phosphorothioate esters.
Results and Discussion
Our previous retrosynthetic approach towards dioxa-
phosphorinane-constrained dinucleotide building blocks
had been based on steric and electronic control in the cyclis-
ation of the 5ЈC-tosyloxy dinucleotide phosphate precursor.
Because of the high selectivity of the pro-R oxygen attack
for the cyclisation of the 5Ј-C(S)-configured dinucleotide
precursor, the (SC,SP) isomer of the α,β-D-CNA cannot be
prepared in a reasonable yield for further investigation.[11]
We therefore anticipated that replacement of one of the
oxygen atoms in the phosphate group by a sulfur might
help to induce the formation of a geometrical analogue of
the previously inaccessible α,β-D-CNA isomer. Note that
in the Cahn–Ingold–Prelog system the same geometries are
designated by (SC,SP) for the α,β-dioxaphosphorinane-
CNA and by (SC,RP) for the α,β-oxo-oxathiaphosphorin-
ane-CNA isomers.
Whereas the attack of the oxygen atom (O-cyclisation)
could give rise to the thio-dioxaphosphorinane (denoted as
II in Scheme 1) with all the substituents in the correct posi-
tions, we expected that the preferred charge localization on
the sulfur atom, despite the unfavourable conformation of
the six-member transition state cycle with the N2 substitu-
ent in the axial position, could be a determining element
(S-cyclisation) for the formation of the desired isomer (de-
noted as I in Scheme 1), if starting from the (SC,RP) isomer
of the acyclic thiophosphate precursor. In contrast, if start-
ing from the (SC,SP) isomer of the acyclic thiophosphate
precursor, the regiochemical outcome of the cyclisation re-
action should be only in favour of the formation of the oxo-
oxathiaphosphorinane (denoted as III in Scheme 1) because
of the nucleophile behaviour of the sulfur atom together
with the favoured transition state cycle substituted with N2
in an equatorial position and ON1 in the axial one.
Scheme 1. Elements for regioselective S- and O-cyclisation. N1 and
N2 stand for the remaining atomic fragments that define the upper
and lower nucleoside units, respectively.
standard procedures from the diastereopure 5Ј-C(S)-tosyl-
oxyethyl thymidine 1 (Scheme 2).[12] They were easily sepa-
rated by silica gel chromatography. The more rapidly eluted
compound was further identified (by its ability to cyclise,
see Scheme 1) as the (SC,RP) isomer 2 (δP = 67.1 ppm) and
so the more slowly eluted compound was the (SC,SP) isomer
3 (δP = 66.9 ppm).
We first removed the cyanoethyl phosphate protective
groups of 2/3 under our previously described conditions
(Et3N, DMF, 90 °C), therefore promoting the formation of
the phosphorinane ring. As planned, 3 underwent cyclis-
ation into a single isomer characterized by 31P NMR spec-
troscopy as the oxo-oxathiaphosphorinane 6 by a chemical
shift of 15.3 ppm. From 2, on the other hand, we observed
the formation of two compounds through the O- and S-
cyclisation pathways in a 1:1 ratio.
The O-cyclisation provided the thio-dioxaphosphorinane
4 (δP = 60.1 ppm), while the attack of the sulfur afforded
the oxo-oxathiaphosphorinane 5 (δP = 24.1 ppm), the geo-
metrical analogue of the inaccessible α,β-D-CNA
(SC,SP).[11] In order to modify the ratio of O- to S-cyclis-
ation, we investigated various sets of reaction conditions
(base, temperature, counterion). The results are summa-
rized in Table 1.
Synthesis of the (SC5Ј,RP)-Thio-dioxa- and (SC5Ј,RP)- or
(SC5Ј,SP)-Oxo-oxathiaphosphorinane Diastereoisomers of
the α,β-CNA TT Dimer
A diastereoisomeric mixture of the thiophosphate dinu-
When the temperature was increased to 150 °C, the S-
cleotides 2 and 3 was prepared in an equimolar ratio by cyclisation pathway became predominant, showing that
1936
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Eur. J. Org. Chem. 2007, 1935–1941

Dinucleotides with Noncanonical α/β Torsion Angle Combinations
FULL PAPER
Scheme 2. Reagents and conditions. a) (i) thymidine phosphoramidite (3 equiv.), tetrazole (15 equiv.), CH3CN, room temp., 45 min. (ii) tol-
uene, Pyr, S8 (4 equiv.). b) NEt3 (4 equiv.), DMF, 90 °C, 2 h.
Table 1. Reaction conditions parameters for the regioselective to S-cycl from 10:90 to 100:0, Entries 7 and 8). To obtain
evidence on the cation effect, we measured 31P chemical
shifts at 54.2, 55.0 and 51.9 ppm, corresponding to the reac-
cyclisation of 2 into the thio-dioxaphosphorinane 4 (O-cycl) or into
the oxo-oxathiaphosphorinane 5 (S-cycl).
Base
T [°C]
Salt
O-cycl vs. S-cycl [%][a]
tion conditions with K2CO3, K2CO3/MgCl2 and K2CO3/
CdCl2, respectively.[14] The displacement from 51.9 to
55.0 ppm is indicative of a change in the strength of the
ionic pair between the phosphorothioate and cadmium or
magnesium. The lower chemical shift observed for cad-
mium shows a tight ionic pair favourable for the O-cyclis-
ation, whereas the weak ionic pair between sulfur and mag-
nesium is characterised by a higher chemical shift showing
a more dissociated ionic pair resulting in the formation of
the oxo-oxathiaphosphorinane as the major compound.
These favourable reaction conditions found for the selec-
tive O-cyclisation of 2, when applied to 3, failed to provide
any thio-dioxophosphorinane formation because of the
highly favourable nature of the S-cyclisation process
(Scheme 1).
1
2
3
4
Et3N
Et3N
Et3N
Et3N
Cs2CO3
K2CO3
K2CO3
K2CO3
90
150
90
90
25
25
25
25
–
–
50:50
15:85
50:50
0:100
57:43
57:43
10:90
100:0
CdCl2
MgCl2
–
5
6
–
7[b]
MgCl2
CdCl2
8[c]
[a] Relative percentages were determined by 31P NMR after quanti-
tative conversion of 2. [b] Reaction time was extended to 15 d.
[c] Reaction time was extended to 18 d.
lowering of the ionic pair strength can increase the selectiv-
ity of the cyclisation process (Table 1, Entry 2). We there-
fore considered changing the counterion of the phos-
phorothiate from triethylammonium to cadmium or magne-
sium. Whereas addition of a cadmium salt did not change
the ratio of the O- to S-cyclisation (Entry 3), the low affin-
ity of magnesium towards sulfur anion provided, as ex-
pected,[13] a loose ionic pair very favourable to the selective
formation of the oxo-oxathiaphosphorinane 5 (4/5 = 0:100,
Structural Assignment of Thio-dioxa- and Oxo-oxathia-
phosphorinane α,β-CNA TT Dimers
In order to obtain solution-state structure determi-
Entry 4). In a same way, the use of Cs2CO3 or K2CO3 as nations of both isomers, independently of protective groups,
base slightly increased the ratio in favour of the O-cyclis- by NMR spectroscopy, we removed the 5Ј-O-dimethoxytri-
ation (Entries 5 and 6). In these cases, the potassium cation tyl and the 3Ј-O-tert-butyldiphenylsilyl groups by standard
can be effectively replaced by cadmium or magnesium with procedures to provide the dinucleotides 7, 8 and 9 from the
dramatic effects on the cyclisation process. The reaction be- corresponding thio-dioxaphosphorinane 4 or oxo-oxathia-
came very slow and highly selective in both cases (O-cycl phosphorinane 5 and 6, respectively (Scheme 3).
Eur. J. Org. Chem. 2007, 1935–1941
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1937

I. Le Clézio, A. Vigroux, J.-M. Escudier
FULL PAPER
Scheme 3. Reagents and conditions. a) nBu4NF (1.1 equiv.), THF, room temp., 1 h. b) 2% TFA/CH2Cl2, room temp., 15 min.
Like that of the dioxaphosphorinane (SC5Ј,RP) isomer,[8] equation established by Lankhorst et al.[16] can be used to
the chair conformation of 7 is clearly established from the determine – from the coupling constants JH3Ј,P (5.9 Hz for
1
1H and H-{31P} NMR spectra, with no detectable coup- 7, 5.8 Hz for 8 and 6.4 Hz for 9) – the values of the tor-
ling constant between the 5Ј-H involved in the thio-diox- sional angles ε (around –160° for all) and therefore the rela-
aphosphorinane system and phosphorus (3JH5Ј,P Ͻ 1 Hz), tive positions of the upper nucleosides in relation to the
which is characteristic of an axial position of this proton.[15] phosphorus triester linkages.
3
The observation of small (1 Hz) and large (24 Hz) JH,P
The puckerings of the 2Ј-deoxyribose moieties of 7, 8 and
coupling constants between the dioxaphosphorinane 7Ј-H 9 in solution were assigned by examination of the sugar
protons and phosphorus are also indicative of axial and ring H/H coupling constants (Table 2). The small JH3Ј,H4Ј
equatorial positions, respectively, for these protons,.
coupling constants measured for 7, 8 and 9 and the values
In contrast, average values of 15.3 and 23.0 Hz were ob- of JH2Ј,H3Ј and JH1Ј,H2Ј are consistent with the standard
3
served for the JH,P coupling constants involving the two C2Ј-endo conformations previously observed in natural 2Ј-
7Ј-H protons of 8, thus suggesting that the oxo-oxathia- deoxyribose units.[17]
phosphorinane structure of this (SC5Ј,RP)-configured iso-
Table 2. H,H coupling constants (Hz) in the 1H NMR spectra
mer (Scheme 1) is in a twist-chair conformation. This “in-
(400 MHz) of α,β-CNA TT dimers 7, 8 and 9 (n.d. = not deter-
between” conformation is probably the result of the involve-
ment of conflicting steric and anomeric effects in either
chair conformation of 8 due to the cis relationship between
the ON1 and N2 groups.
mined).
Coupling constant J (Hz)
J(1Ј,2Ј) J(2Ј,3Ј)
8.7
Nucleoside
J(3Ј,4Ј)
7
8
9
upper
lower
5.6
6.2
5.2
1.7
1.7
2.6
Other important structural information relating to com-
pounds 7, 8 and 9 can be found in the observation of long-
range coupling constants between the 4Ј-H protons of the
lower sugar units and phosphorus (4JH4Ј,P = 4.6, 5.0 and
5.7 Hz for 7, 8 and 9, respectively). These couplings are in-
dicative of typical W-shaped P–O5Ј–C5Ј–C4Ј–H4Ј junc-
tions, which is consistent with gauche(+) conformations of
γ in 7 and 9 and anticlinal(–) conformations of γ in 8. The
W-shaped P–O5Ј–C5Ј–C4Ј–H4Ј junction deduced in the
case of 8 also suggests that the backbone torsion angles α
and β are only slightly affected by the conformational
change involved between the true chair and twist-chair
8.0
n.d.
n.d.
upper
lower
5.7
6.2
8.5
7.6
5.8
6.3
1.9
3.3
1.7
2.9
upper
lower
5.7
7.4
8.6
7.4
6.0
6.0
1.9
3.0
1.9
2.9
Conclusions
Regioselective cyclisations of a stereodefined 5Ј-C-tosy-
forms of 8. Overall, these NMR spectroscopic data allow loxy phosphorothioate dinucleotide unit to provide confor-
us to assign the conformations of the backbone torsion mationally restricted dinucleotides (α,β-CNAs) of either
angles α, β and γ as (α, β, γ) = (g+, t, g+) for 7 and 9 and thio-dioxa- or oxo-oxathiaphosphorinane types has been
(α, β, γ) = (a–, a+/t, a–) for 8. In addition, the empirical described. We have shown that the regiochemical outcome
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Dinucleotides with Noncanonical α/β Torsion Angle Combinations
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144.1, 135.8–111.5, 87.3, 87.2, 84.8, 84.3, 79.8, 74.7, 69.6, 63.1,
62.5, 55.3, 40.0, 38.7, 26.8, 24.5, 21.6, 19.1, 19.0, 12.6, 11.8 ppm.
31P NMR (81 MHz, CDCl3): δ = 67.1 ppm. MS (FAB, MNBA):
1376 [M + Na]+, 1353 [M + H]+.
of the cyclisation process can be controlled by addition of
suitable cations (Mg2+ or Cd2+) to the reaction medium.
Structural analysis by means of NMR spectroscopy indi-
cates that the (SC5Ј,SP) diastereoisomer of the oxo-oxathia-
phosphorinane and the (SC5Ј,RP)-thio-dioxaphosphorinane
Data for 3: TLC, Rf (AcOEt/petroleum ether, 8:2) = 0.30. 1H NMR
have their internucleotide linkages in true chair conforma- (250 MHz, CDCl3): δ = 9.33 and 9.11 (2ϫs, 2 H, NH), 7.73–6.82
tions with α and β locked in the atypical (g+, t) conforma-
(m, 29 H, Ph and 6-H), 6.52 and 6.32 (2ϫm, 2 H, 1Јa-H and 1Јb-
H), 5.29–5.27 (m, 1 H, 3Јa-H), 4.36–3.82 (m, 8 H, 3Јb-H, 4Ј-H, 5Ј-
H and 2ϫCH2), 3.78 (s, 6 H, Me DMTr), 3.35–3.31 (m, 2 H, CH2),
tions frequently found in B-type duplexes in complexation
with proteins or in bulged or loop region of nucleic acids
2.59–2.52 (m, 2 H, CH2), 2.41(s, 3 H, Me Ts), 2.29–2.22 (m, 2 H,
(Table 3). The remaining (SC5Ј,RP)-oxo-oxathiaphosphorin-
CH2), 1.89 and 1.84 (2ϫs, 6 H, 2 Me), 1.47 and 1.25 (2ϫm, 4 H,
ane diastereoisomer is characterized by the very unusual
2ϫCH2), 1.06 (s, 9 H, tBu) ppm. 13C NMR (63 MHz, CDCl3): δ
anticlinal(–) conformation of α and the twist-chair confor-
= 163.8, 158.8, 150.6, 144.9, 144.0, 135.8–111.7, 87.3, 84.5, 79.8,
mation of its phosphorinane linkage. The puckering mode
74.5, 69.4, 63.2, 62.8, 55.3, 39.8, 39.0, 26.9, 24.5, 21.6, 19.2, 19.0,
12.6, 11.8 ppm. 31P NMR (81 MHz, CDCl3): δ = 66.9 ppm. MS
of the 2Ј-deoxyribose units, however, is clearly C2Ј-endo (S-
type), which is characteristic of B-type duplexes.
(FAB, MNBA): 1376 [M + Na]+, 1353 [M + H]+.
Thio-dioxaphosphorinane Derivative (SC,RP)-4: K2CO3 (34 mg,
0.250 mmol) and CdCl2 (20 mg, 0.103 mmol) were added under ar-
gon to compound 2 (20 mg, 0.014 mmol) dissolved in anhydrous
DMF (2 mL). After 18 d of stirring at room temperature, the reac-
tion mixture was diluted with ethyl acetate and washed with water
and brine. The organic layer was then dried with MgSO4 and the
solvent was removed in vacuo to provide compound 4 (15 mg, 95%
Table 3. Summary of the backbone torsion angles α, β and γ in
the oxo-oxathia- and thio-dioxaphosphorinane α,β-CNA dimeric
units.[a]
Diastereoisomer
α
β
γ
thio-dioxa (RC5Ј,SP)
oxo-oxathia (SC5Ј,RP)
oxo-oxathia (SC5Ј,SP)
g+
a–
g+
t
g+
a–
g+
a+/t
t
1
yield). TLC, Rf (AcOEt) = 0.60. H NMR (400 MHz, CDCl3): δ =
9.63 and 9.37 (2ϫs, 2 H, NH), 7.61–6.80 (m, 25 H, Ph, 6a-H and
6b-H), 6.58 (dd, J = 5.6 and 9.1 Hz, 1 H, 1Јb-H), 6.42 (dd, J = 5.2
and 9.6 Hz, 1 H, 1Јa-H), 5.35 (dd, J = 4.6 and JH,P = 9.6 Hz, 1 H,
3Јa-H), 4.28 (m, 1 H, 7Јb-H), 4.24 (d, J = 5.5 Hz, 1 H, 3Јb-H), 4.12
(m, 1 H, 7Јb-H), 4.01 (m, 1 H, 4Јa-H), 3.80 (m, 1 H, 5Јb-H), 3.75
(s, 6 H, MeO), 3.66 (d, J = 5.3 HZ, 1 H, 4Јb-H), 3.35 (m, J = 1.0
and 11.0 Hz, 1 H, 5Јa-H), 3.33 (s, 1 H, 5Јa-H), 2.41 (m, 2 H, 2Јa-
H), 2.23 (m, 2 H, 2Јb-H and 6Јb-H), 1.95 (s, 3 H, Me), 1.84 (m, 1
H, 2Јb-H), 1.31 (m, 1 H, 6Јb-H), 1.42 (s, 3 H, Me), 1.03 (s, 9 H,
tBu) ppm. 13C NMR (100 MHz, CDCl3): δ = 164.0, 158.9, 150.9,
150.8, 144.2, 135.9, 135.7, 135.3, 135.2, 135.1, 133.4, 132.6, 130.6,
130.4, 130.2, 128.3, 128.2, 127.4, 113.6, 112.5, 112.2, 88.0, 87.6,
85.1, 84.7, 84.6, 80.2, 78.9, 74.7, 67.5, 63.7, 55.5, 40.0, 39.2, 27.6,
27.0, 19.1, 12.7, 11.9 ppm. 31P NMR (81 MHz, CDCl3): δ =
60.1 ppm. MS (ESI): 1151.6 [M + Na+]+, 1167.5 [M + K]+.
C59H65N4O13PSSi (1129.30): calcd. C 60.86, H 5.53, N 4.78; found:
C 61.35, H 5.61, N 4.86.
[a] The torsion angle ranges are indicated in parentheses for α–
γ: gauche(+) = 60Ϯ30° (g+), trans = 180Ϯ30° (t), anticlinal(–) =
240Ϯ30° (a–) and anticlinal(+) = 120Ϯ30° (a+).
We therefore have available an increasing number of
building units featuring noncanonical values of the α tor-
sional angles, providing unique opportunities to explore
their capabilities to stabilize unpaired structures of nucleic
acids such as bulges or hairpin loops.
Experimental Section
Cyanoethyl 3Ј-O-(5Ј-O-Dimethoxytrityl)thymidinyl-5Ј-C(S)-tosyl-
oxyethyl-(3Ј-tert-butyldiphenyl silyl)thymidinyl Thiophosphoric Es-
ters (SC,RP)-2 and (SC,SP)-3: 3Ј-O-tert-Butyldiphenylsilyl-5Ј-C(S)-
(tosyloxyethyl)thymidine (1, 500 mg, 0.736 mmol), thymidine O3Ј-
phosphoramidite (1.1 g, 1.47 mmol) and freshly sublimed tetrazole
(515 mg, 7.36 mmol) were dissolved in anhydrous acetonitrile
(10 mL) and the mixture was stirred for 45 min at room tempera-
ture. After addition of pyridine (7.7 mL, 95.3 mmol), the phosphite
was oxidized with S8 (752 mg, 2.94 mmol) and toluene (7 mL). The
reaction mixture was stirred for 1 h and diluted with ethyl acetate
and the organic layer was washed with an aqueous solution satu-
rated with NaHCO3, with water and with brine. The organic layer
was then dried with MgSO4, the solvent was removed in vacuo,
and the crude material was chromatographed on silica gel with
ethyl acetate/petroleum ether (7:3) as eluent. After evaporation of
the solvent, compound 2 and 3 were recovered as white foams
(320 mg of 2 and 325 mg of 3, 68% yield).
Oxo-oxathiaphosphorinane Derivative (SC,RP)-5: Triethylamine
(8 µL, 0.058 mmol) and MgCl2 (5 mg, 0.053 mmol) were added un-
der argon to compound 2 (20 mg, 0.014 mmol) dissolved in anhy-
drous DMF (2 mL). After 2 h of stirring at 95 °C, the reaction
mixture was diluted with ethyl acetate and washed with water and
brine. The organic layer was then dried with MgSO4 and the sol-
vent was removed in vacuo to provide compound 5 (15 mg, 95%
1
yield). TLC, Rf (AcOEt) = 0.44. H NMR (400 MHz, CDCl3): δ =
8.65 and 8.75 (2ϫs, 2 H, NH), 7.60–6.79 (m, 25 H, Ph, 6a-H and
6b-H), 6.49 (dd, J = 5.5 and 8.7 Hz, 1 H, 1Јb-H), 6.22 (t, J =
7.1 Hz, 1 H, 1Јa-H), 5.30 (m, 1 H, 3Јa-H), 3.71 (d, J = 5.7 Hz, 1
H, 3Јb-H), 4.12 (s, 1 H, 4Јa-H), 3.76 (s, 6 H, MeO), 3.75 (m, 1 H,
5Јb-H), 3.71 (m, JH,P = 5.5 Hz, 1 H, 4Јb-H), 3.45 and 3.36 (2ϫm,
J = 10.8, 3.0 and 2.3 Hz, 2 H, 5Јa-H), 2.98 (m, JH,P = 15.3 Hz, 1
H, 7Јb-H), 2.82 (m, JH,P = 23 Hz, 1 H, 7Јb-H), 2.38 (m, 2 H, 2Јa-
H), 2.33 (m, 1 H, 2Јb-H), 2.01 (m, 1 H, 6Јb-H), 1.87 (m, 1 H, 2Јb-
H), 1.83 (s, 3 H, Me), 1.60 (m, 1 H, 6Јb-H), 1.32 (s, 3 H, Me), 1.04
(s, 9 H, tBu) ppm. 13C NMR (100 MHz, CDCl3): δ = 163.6, 158.8,
Data for 2: TLC, Rf (AcOEt/petroleum ether, 8:2) = 0.44. 1H NMR
(250 MHz, CDCl3): δ = 9.36 and 9.20 (2ϫs, 2 H, NH), 7.77–6.82
(m, 29 H, Ph and 6-H), 6.50 and 6.24 (2ϫm, 2 H, 1Јa-H and 1Јb-
H), 5.16–5.12 (m, 1 H, 3Јa-H), 4.39–3.90 (m, 8 H, 3Јb-H, 4Ј-H, 5Ј-
H and 2ϫCH2), 3.79 (s, 6 H, Me DMTr), 3.49–3.33 (m, 2 H, CH2),
2.44 (s, 3 H, Me Ts), 2.30–2.10 (m, 4 H, 2ϫCH2), 1.87 (s, 6 H, 2 150.5, 150.1, 143.9, 135.8–127.3, 113.4, 111.6, 111.4, 88.3, 87.4,
Me), 1.47 and 1.28 (2ϫm, 4 H, 2ϫCH2), 1.06 (s, 9 H, tBu) ppm. 84.3, 84.2, 79.7, 79.3, 74.4, 63.1, 55.2, 40.4, 39.7, 29.7, 27.7, 26.9,
13C NMR (63 MHz, CDCl3): δ = 163.7, 158.8, 150.5, 150.4, 144.9, 19.0, 12.6, 1.6 ppm. 31P NMR (81 MHz, CDCl3): δ = 24.1 ppm.
Eur. J. Org. Chem. 2007, 1935–1941
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
1939

I. Le Clézio, A. Vigroux, J.-M. Escudier
FULL PAPER
MS (ESI) 1167.4 [M + K+]+, 1151.5 [M + Na]+. C59H65N4O13PSSi
(1129.30): calcd. C 60.86, H 5.53, N 4.78; found: C 60.75, H 5.53,
N 4.66.
H), 2.98 and 2.82 (m, JH,P = 15.3 and 23.0 Hz, 2 H, 7Јb-H), 2.64
(A part of an ABX system, J = 8.5, 1.8 and 14.2 Hz, 1 H, 2Јa-H),
2.47 (B part of an ABX system, J = 5.7, 14.2 and JH,P = 1.4 Hz, 1
H, 2Јa-H), 2.28 (m, 1 H, 2Јb-H), 2.01 (m, 1 H, 6Јb-H), 1.92 (brd,
6 H, Me), 1.87 (m, J = 3.3, 7.6 and 14.0 Hz, 1 H, 2Јb-H), 1.60 (m,
1 H, 6Јb-H) ppm. 13C NMR (100 MHz, CD3OD): δ = 166.3, 152.4,
137.8, 137.4, 112.2, 112.0, 89.2, 87.2, 86.2, 86.1, 85.4, 85.3, 79.8,
72.7, 62.5, 40.8, 39.4, 29.5, 28.5, 12.6, 12.5 ppm. 31P NMR
(81 MHz, CD3OD): δ = 20.1 ppm. MS (DCI/NH3): 606.2 [M +
NH4]+, 589.2 [M + H]+.
Data for 9: TLC, Rf (AcOEt/MeOH, 8:2) = 0.4. 1H NMR
(400 MHz, CD3OD): δ = 7.84 (m, J = 1.2 Hz, 1 H, 6a-H), 7.65 (m,
J = 1.2 Hz, 1 H, 6a-H), 6.40 (dd, J = 7.4 and 7.5 Hz, 1 H, 1Јb-H),
6.37 (dd, J = 5.7 and 8.6 Hz, 1 H, 1Јa-H), 5.20 (m, J = 1.9, 1.9,
Oxo-oxathiaphosphorinane Derivative (SC,SP)-6: Triethylamine
(80 µL, 0.58 mmol) was added under argon to compound 3
(200 mg, 0.14 mmol) dissolved in anhydrous DMF (20 mL). After
2 h of stirring at 95 °C, the reaction mixture was diluted with ethyl
acetate and washed with water and brine. The organic layer was
then dried with MgSO4 and the solvent was removed in vacuo to
provide compound 6 (160 mg, 100% yield). TLC, Rf (AcOEt) =
1
0.50. H NMR (400 MHz, CDCl3): δ = 9.85 and 9.43 (2ϫs, 2 H,
NH), 7.62–6.80 (m, 25 H, Ph, 6a-H and 6b-H), 6.61 (dd, J = 5.6
and 9.1 Hz, 1 H, 1Јb-H), 6.46 (dd, J = 5.0 and 9.4 Hz, 1 H, 1Јa-
H), 5.20 (dd, J = 5.0 and JH,P = 8.4 Hz, 1 H, 3Јa-H), 4.30 (d, J =
5.7 Hz, 1 H, 3Јb-H), 4.16 (m, 1 H, 4Јa-H), 3.75 (s, 6 H, MeO), 3.68
(d, J = 6.7 Hz, 1 H, 4Јb-H), 3.45 (m, J = 2.0 and 10.3 Hz, 1 H,
5Јa-H), 3.37 (m, 2 H, 5Јa-H and 5Јb-H), 2.89 (m, 1 H, 7Јb-H), 2.76
(m, 1 H, 7Јb-H), 2.68 (m, 1 H, 2Јa-H), 2.40 (m, 1 H, 2Јa-H), 2.31
(m, 1 H, 2Јb-H), 2.00 (m, 1 H, 6Јb-H), 1.95 (m, 1 H, 2Јb-H), 1.88
(s, 3 H, Me), 1.59 (m, 1 H, 6Јb-H), 1.36 (s, 3 H, Me), 1.04 (s, 9 H,
tBu) ppm. 13C NMR (100 MHz, CDCl3): δ = 164.2, 159.0, 151.1,
150.9, 144.2, 135.9, 135.8, 135.3, 133.4, 132.6, 130.5, 130.3, 130.2,
128.7, 127.5, 113.6, 112.3, 112.1, 88.9, 87.6, 85.2, 84.6, 83.3, 79.4,
74.9, 63.6, 55.4, 40.2, 38.8, 28.2, 27.4, 27.0, 19.2, 12.6, 11.6.) ppm.
31P NMR (81 MHz, CDCl3): δ = 15.4 ppm. MS (ESI): 1167.5 [M
+ K]+, 1151.6 [M + Na]+. C59H65N4O13PSSi (1129.30): calcd. C
60.86, H 5.53, N 4.78; found: C 60.71, H 5.61, N 4.92.
and 6.0 Hz, 1 H, 3Јa-H), 4.88 (m, J = 1.8, 6.0, and 7.8 Hz, JH,P
Ͻ
1 Hz, 1 H, 5Јb-H), 4.49 (m, J = 2.9, 3.0, and 6.0 Hz, 1 H, 3Јb-H),
4.31 (dd, J = 2.0 and 3.0 Hz, 1 H, 4Јa-H), 3.93 (m, J = 1.9, 2.9,
and JH,P = 5.7 Hz, 1 H, 4Јb-H), 3.83 (d, J = 3.0 Hz, 2 H, 5Јa-H),
3.24–3.10 (m, 2 H, 7Јb-H), 2.62 (A part of an ABX system, J =
1.9, 5.7 and 14.1 Hz, 1 H, 2Јa-H), 2.45 (B part of an ABX system,
J = 6.0, 8.6, 14.2 and JH,P = 1.5 Hz, 1 H, 2Јa-H), 2.24 (m, 2 H,
2Јb-H), 2.18 (m, 2 H, 6Јb-H), 1.90 and 1.89 (brd, 6 H, Me) ppm.
13C NMR (100 MHz, CD3OD): δ = 166.1, 153.1, 137.8, 137.2,
111.9, 111.7, 90.0, 86.9, 86.5, 86.0, 85.7, 83.1, 79.3, 73.2, 62.1, 40.5,
40.0, 29.5, 28.4, 12.5 ppm. 31P NMR (81 MHz, CD3OD): δ =
20.3 ppm. MS (DCI/NH3) 606.0 [M + NH4]+, 589.0 [M + H]+.
C22H29N4O11PS (588.52): calcd. C 44.90, H 4.97, N 9.52; found C
44.20, H 5.12, N 8.99.
Thio-dioxaphosphorinane, Oxo-oxathiaphosphorinane, and Oxo-
oxathiaphosphorinane Derivatives (SC,RP)-7, (SC,RP)-8, (SC,SP)-9:
Tetrabutylammonium fluoride (93 µL, 0.039 mmol) was added un-
der argon at room temperature to the dinucleotide 4 (or 5/6)
(30 mg, 0.026 mmol) in anhydrous THF (2 mL). After 15 min,
THF was removed under vacuum. The crude material was treated
with TFA 2%/CH2Cl2 for 5 min, dried under high vacuum. and
chromatographed on silica gel with ethyl acetate/methanol (0 to
20%) as eluent. Compounds 7 (or 8/9) were recovered in 72, 77
and 88% yields, respectively.
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Data for 7: TLC, Rf (AcOEt/MeOH, 8:2) = 0.4. 1H NMR
(400 MHz, CD3OD): δ = 7.84 (m, J = 1.1 Hz, 1 H, 6b-H), 7.68 (m,
J = 1.1 Hz, 1 H, 6a-H), 6.46 (dd, J = 6.2 and 8.0 Hz, 1 H, 1Јb-H),
6.38 (dd, J = 5.6 and 8.7 Hz, 1 H, 1Јa-H), 5.22 (m, J = 1.7, 1.7,
5.3, and JH,P = 5.9 Hz, 1 H, 3Јa-H), 4.88 (m, 1 H, 5Јb-H), 4.60 (m,
1 H, JH,P = 1.0 Hz, 7Јb-H), 4.50 (m, 1 H, 3Јb-H), 4.45 (m, JH,P
=
24 Hz, 1 H, 7Јb-H), 4.32 (m, 1 H, 4Јa-H), 3.93 (m, J = 1.8, 2.6,
and JH,P = 4.6 Hz, 1 H, 4Јb-H), 3.85 (d, J = 3.2 Hz, 2 H, 5Јa-H),
2.60 (A part of an ABX system, J = 5.2, 5.6 and 14.1 Hz, 1 H, 2Јa-
H), 2.45 (B part of an ABX system, J = 1.7, 8.7, 14.1 and JH,P
=
1.0 Hz, 1 H, 2Јa-H), 2.39 (m, 1 H, 6Јb-H), 2.24–2.20 (m, 2 H, 2Јb-
H), 1.98 (brd, 3 H, a-Me), 1.91 (brd, 3 H, b-Me), 1.88 (m, 1 H,
6Јb-H) ppm. 13C NMR (100 MHz, CD3OD): δ = 165.2, 151.3,
136.6, 136.0, 111.4, 110.7, 87.3, 87.4, 85.0, 84.7, 79.6, 79.3, 71.8,
68.0, 61.6, 39.4, 38.1, 27.7, 12.8, 11.5 ppm. 31P NMR (81 MHz,
CD3OD): δ = 61.5 ppm. MS (DCI/NH3): 606.0 [M + NH4]+, 589.0
[M + H]+. C22H29N4O11PS (588.52): calcd. C 44.90, H 4.97, N 9.52;
found: C 45.23, H 4.85, N 9.34.
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Data for 8: TLC, Rf (AcOEt/MeOH, 8:2) = 0.4. 1H NMR
(400 MHz, CD3OD): δ = 7.85 (m, J = 1.2 Hz, 1 H, 6b-H), 7.67 (m,
J = 1.2 Hz, 1 H, 6a-H), 6.42 (dd, J = 6.2 and 7.6 Hz, 1 H, 1Јb-H),
6.38 (dd, J = 5.7 and 8.5 Hz, 1 H, 1Јa-H), 5.22 (m, J = 1.7, 1.9,
and 5.8 Hz, 1 H, 3Јa-H), 4.89 (m, 1 H, 5Јb-H), 4.52 (m, 1 H, 3Јb-
H), 4.33 (dd, J = 3.0 and 5.4 Hz, 1 H, 4Јa-H), 3.95 (m, J = 1.9,
2.8, and JH,P = 5.0 Hz, 1 H, 4Јb-H), 3.84 (d, J = 3.0 Hz, 2 H, 5Јa-
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1940
www.eurjoc.org
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Eur. J. Org. Chem. 2007, 1935–1941

Dinucleotides with Noncanonical α/β Torsion Angle Combinations
FULL PAPER
[15] Typical upper and lower limits observed for the 3JH,P coupling
constants for dioxaphosphorinane structures in chair confor-
mations are 3JHax,P Ͻ ca. 3 Hz and 3JHeq,P Ͼ ca. 20 Hz, respec-
tively. See: D. G. Gorenstein, R. Rowell, J. Findlay, J. Am.
Chem. Soc. 1980, 102, 5077–5081.
ε was determined from the following relationship: ε° = –θ –
120° and θ was calculated with JH3Ј,P = 15.3 cos2(θ) – 6.1 cos
(θ) + 1.6.
[17] D. J. Wood, K. K. Ogilvie, F. E. Hruska, Can. J. Chem. 1975,
53, 2781–2790.
[16] P. P. Lankhorst, C. A. G. Haasnoot, C. Erkelens, C. J. Altona,
J. Biomol. Struct. Dyn. 1984, 1, 1387–1405. The torsional angle
Received: November 29, 2006
Published Online: March 6, 2007
Eur. J. Org. Chem. 2007, 1935–1941
© 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.eurjoc.org
1941