Thio- and Seleno-Dioxaphosphorinane-Constrained Dinucleotides (D-CNA): Synthesis and Conformational Study

Article abstract of DOI:10.1002/ejoc.201601568

Thio- and seleno-α,β- and α,β,γ-D-CNA (constrained nucleic acid) dinucleotides in which two or three torsion angles of the sugar/phosphate backbone are controlled within a dioxaphosphorinane structure have been prepared. Their structural determination was carried out by means of NMR spectroscopy to show only slight variation on the torsion-angle control in comparison with their oxo analogues. Unexpected selenium migration has been pointed out from selenophosphotriester moiety to phosphoramidite group, but this drawback can be overcome using H-phosphonate chemistry.

Full text of DOI:10.1002/ejoc.201601568

A Journal of
Accepted Article
Title: Thio- and Seleno-Dioxaphosphorinane-Constrained
Dinucleotides (D-CNA), Synthesis and Conformational Study
Authors: Béatrice Gerland, Claudia Addamiano, Brice-Loïc Renard,
Corinne Payrastre, Deshmukh Gopaul, and Jean-Marc
Escudier
This manuscript has been accepted after peer review and appears as an
Accepted Article online prior to editing, proofing, and formal publication
of the final Version of Record (VoR). This work is currently citable by
using the Digital Object Identifier (DOI) given below. The VoR will be
published online in Early View as soon as possible and may be different
to this Accepted Article as a result of editing. Readers should obtain
the VoR from the journal website shown below when it is published
to ensure accuracy of information. The authors are responsible for the
content of this Accepted Article.
To be cited as: Eur. J. Org. Chem. 10.1002/ejoc.201601568
Link to VoR: http://dx.doi.org/10.1002/ejoc.201601568
Supported by

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
Thio- and Seleno-Dioxaphosphorinane-Constrained Dinucleotides
(D-CNA), Synthesis and Conformational Study
Béatrice Gerland,*[a] Claudia Addamiano,[a] Brice-Loïc Renard,[a] Corinne Payrastre,[a] Deshmukh
Gopaul[b] and Jean-Marc Escudier*[a]
Abstract: Thio- and seleno-α,β- and α,β,γ-CNA (Constrained
chain terminators of DNA polymerases.[10] However during the
automated chemical synthesis of the highly modified ONs
involved in these experiments, it appeared that the
dioxaphosphorinane ring could be partially cleaved by the final
and harsh ammonia treatment. Therefore, in order to increase
the stability of the ring structure towards hydrolysis while
maintaining the geometry constrain on the sugar/phosphate
backbone, we have undertaken the synthesis of thio- and
seleno-analogues of D-CNA by replacing the exo and non-
bridging oxygen of the dioxaphosphorinane ring by a sulfur or
selenium atom (Figure 1). Our previous attempts towards thio-
Nucleic Acid) dinucleotides in which two or three torsional angles of
the sugar/phosphate backbone are controlled within
a
dioxaphosphorinane structure have been prepared. Their structural
determination have been carried out by means of NMR to show only
slight variation on the torsional angle control in comparison with their
oxo analogues. Unexpected selenium migration has been pointed
out from seleno-phosphotriester moiety to phosphoramidite group,
but this drawback can be overcome using H-phosphonate chemistry.
α,β-D-CNA analogues, based on
a stereoselective thio-
Introduction
phosphate ring closure suffered from a competition between O-
and S-cyclisation and a low yield of the target compound with
the sulfur at the desired exocyclic location.[11]
Conformationnaly restricted nucleotides have been investigated
for therapeutic purposes to enhance duplex formation and
stability with the target strand once incorporated into synthetic
oligonucleotides.[1] The main success in this approach relies on
bicyclic analogues with furanose ring conformational equilibrium
locked in the C3'-endo form (North).[2] This conformation can
mainly be reached by introduction of a 2'OH-C4' methylene
bridge within the ribose for LNA (Locked Nucleic Acid), by
constrain applied to the C4'-C5' exocyclic bond or by combining
both.[3] Tricylic analogues (tc-DNA) modified with a C3'-C5'
ethylene bridge further rigidified by an additional fused
cyclopropane unit have also been designed.[4] Another approach
by-passes the need of a bicyclic scaffold to lock the sugar
conformation. 2'-Fluorination of the furanose ring induces a
North pucker preference due to strong stereoelectronic effects,[5]
and the introduction of a second fluorine atom definitely rigidifies
the 2',4'-difluoro nucleotides in a pure North conformation.[6]
We recently showed that restricting the sugar phosphate
backbone rotational freedom by means of dioxaphosphorinane
rings can be favorable not only to stabilize duplex[7] but also to
preorganize loops and bulges when those structural elements
Figure 1. Top: the DNA backbone torsion angles (labelled α to ζ). Down left
and middle: Dioxaphosphorinane-Constrained Nucleic Acid dinucleotides in
which either α and β or α, β and γ are stereocontrolled within the ring structure.
Right: structure superimposition of α,β-D-CNA {blue: alpha = gauche(-), beta =
trans, red: alpha = gauche(+), beta = trans} and α,β,γ-D-CNA {green: alpha =
gauche(-), beta = gauche(-), gamma = gauche(-), yellow: alpha = gauche(+),
beta = cis/gauche(+), gamma = gauche(-)/anti(-)} showing the change in
directionality from 3'-end to 5'-end.
feature unusual torsion angles values sets and, as
consequence, become able to stabilize secondary structures
(Figure 1).[8]
Interestingly, oligodeoxynucleotides (ONs) modified with
dioxaphosphorinane constrained nucleic acid dinucleotides (D-
CNA) displaying either the canonical gauche(-) or the non-
canonical gauche(+) value of α (Figure 1), exhibited biological
properties such as supporting RNase H cleavage[9] or acting as
a
Herein, we describe the efficient synthesis of all the possible
isomers of two classes of CNA namely thio- and seleno-α,β-D-
CNA and thio- and seleno-α,β,γ-D-CNA. The structural impact of
replacement of the exocyclic oxygen of the dioxaphosphorinane
ring by a sulfur or selenium atom is evaluated by means of NMR
spectroscopy. These rigid dinucleotides analogues are expected
to be able to describe a large conformational space (Figure 1)
and to act within artificial oligonucleotides as mimics of distorted
transient DNA structures.
[a] Laboratoire de Synthèse et Physico-Chimie de Molécules d’Intérêt
Biologique, UMR CNRS 5068, Université Paul Sabatier
118 route de Narbonne, 31062 Toulouse, France.
E-mail: gerland@chimie.ups-tlse.fr or escudier@chimie.ups-tlse.fr
[b]
Laboratoire de Génomes et Génétique, UMR 3525 Institut Pasteur
25 rue du Docteur Roux, 75015 Paris, France.
Supporting information for this article is given via a link at the end of
the document.((Please delete this text if not appropriate))
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
Results and Discussion
of the silyl ether on the secondary hydroxyl group of the 5'-C-
(R) isomer of 4 can be achieved with potassium carbonate in
methanol at low temperature with a special care in the reaction
time, while the silyl ether on the primary hydroxyl group of
epimeric 4 was removed. Then, 5'-C-(R)-hydroxyethylthymidine
5 was easily separated from the remaining 5'-C-(S)-hydroxyethyl
thymidine 6 still bearing the silyl ether on the 5'-hydroxyl group.
Eventually, 6 can be converted back to 3 in acidic medium
quantitatively.
Our seminal approach of D-CNA synthesis was based on the
steric and electronic control of an intramolecular cyclisation by
attack of a phosphate thio or oxyanion of an activated 4' or 5'-
carbon to displace a tosylate group.[12] In order to install a sulfur
or selenium atom on a common phosphite intermediate for each
D-CNA, we chose to condense a thymidine phosphorodiamidite
on 4'-C-hydroxymethylthymidine 2 (for α,β,γ-D-CNA) and on 5'-
C-hydroxyethylthymidine 3 and 5 (for α,β-D-CNA) (Scheme 1).
Therefore oxidation of the resulting phosphite either by S8 or
KSeCN would provide the target compounds with the hetero
element as a non-bridging atom (Scheme 2 and 3).
Synthesis of thio- and seleno-α,β-D-CNA
The two 5'-C isomers hydroxyethylthymidine 3 and 5 were
independently engaged in a coupling with the freshly prepared
bis(diisopropylamino)phosphodiamidite
of
thymidine
and
Synthesis of thymidine diol precursors
activated with 5-(ethylthio)-1H-tetrazole (Scheme 2).[17]
4'-C-Hydroxymethylthymidine 2 can be obtained in a moderate
yield (45%) from thymine aldehyde 1 and formaldehyde in basic
medium following a previously described method.[13] 5'-C(S)-
Hydroxyethylthymidine 3 was easily accessible in pure form from
thymidine aldehyde 1 in a two steps procedure in good yield
(75%) and high quantity.[14] On the other hand, synthesis of the
5'-C(R) isomer 5 was previously achieved through a fastidious
multi-steps procedure in a modest yield.[15] Therefore, we
engaged a methodology of racemization/separation from 3 to
gain a better access to 5 (Scheme 1).
OH OH
5'
T
O
OTBDPS
3
a) 5-(Ethylthio)-1H-tetrazole,
CH3CN, 2 h
b) S8, pyr or KSeCN, Et3N
38-46%, 2 steps
T
DMTrO
O
O
P[N(iPr2)]2
RO
RO
T
T
O
O
X
+
T
O
P
T
P
O
O
O
O
O
ref11
OH OH
T
T
O
O
O
X
OR'
O
O
5'
OR'
1
3
OTBDPS
ref10
OTBDPS
R
R'
DMTr
a) TBDMS-Cl, Pyr, 12 h
TBDPS
7a (26%), 7b (27%)
9a (quant.), 9b (64%)
8a (20%), 8b (11%)
c) TBAF,
THF, 1 h
b) Dess-Martin Periodinane
DCM, Pyr, 2 h then EtOH,
NaBH4
c) PTSA, MeOH, 1 h
d) TMS-Cl, HMDS,Pyr 2 h
85% overall
10a (quant.), 10b (34%)
12a (93%), 12b (29%)
DMTr
H
H
H
d) TCA 2%,
DCM, 1 h
T
11a (80%), 11b (46%)
HO
HO
O
4'
c)
a: X=S and b: X=Se
OTBDPS
2
TMSO OTMS
T
OH OH
T
O
O
5'
4
OTBDPS
5
OTBDPS
e) K2CO3 (1,5 eq),
MeOH, 0°C, 1 h 30
T
DMTrO
a) 5-(Ethylthio)-1H-tetrazole,
CH3CN, 2 h
O
OH OH
T
OH
OTMS
T
+
b) S8, pyr or KSeCN, Et3N
51-57%, 2 steps
O
O
O
5'
P[N(iPr2)]2
5
OTBDPS
54%
6
OTBDPS
28%
RO
RO
T
T
O
O
X
P
+
O
Scheme 1. Synthesis of diastereoisomeric 4'-C-hydroxymethylthymidine 2 and
5'-C-hydroxylethylthymidine 3 and 5 precursors.
O
O
T
O
P
X
O
O
T
O
O
OR'
OR'
R
R'
The primary hydroxyl group of 3 was selectively protected by a
tert-butyldimethylsilyl ether in anhydrous pyridine in quantitative
yield. Oxidation of the remaining secondary hydroxyl group was
performed with Dess-Martin periodinane[16] and the resulting
ketone was reduced in situ with sodium borohydride. Acidic
removal of the tert-butyldimethylsilyl ether followed by per-
13a (42%), 13b (52%)
DMTr
14a (9%), 14b (5%)
16a (86%), 16b
18a (50%), 18b
TBDPS
c) TBAF,
THF, 1 h
15a (61%), 15b (71%) DMTr
H
H
d) TCA 2%,
DCM, 1 h
H
17a (50%), 17b (56%)
(quant., 2 steps)
a: X=S and b: X=Se
silylation with trimethylsilyl chloride afforded
4 as a 2/1
inseparable diastereoisomeric mixture in favor of the 5'-C(R)
1
isomer as depicted by H NMR. At this stage, a kinetic removal
Scheme 2. Synthesis of thio- and seleno-α,β-CNA dinucleotides.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
The intermediate phosphite can be oxidized either by S8 to
provide 7a/8a or 13a/14a or by KSeCN to install the selenium
atom to obtain 7b/8b or 13b/14b respectively from 3 and 5 in
moderate to good yield. Interestingly, the ratio of the
diastereoisomeric couple 7/8 or 13/14 was 1.6/1 as depicted by
31P NMR indicative of an unexpected diastereoselection when
compare with the 1/1 ratio during formation of larger cycle (13-
membered) following the same methodology with a starting
nucleoside bearing two primary hydroxyl groups.[17a] In the
present case, it could be explained, first by the difference in the
nucleophile involved that exhibits a primary and a secondary
hydroxyl group and secondly by the more favorable formation of
the 6-membered ring phosphite intermediate with all properly
positioned substituents with the upper nucleoside in the apical
position and with the lower nucleoside and the sulfur or selenium
atom in the equatorial position.
Here, because of a precursor with two primary hydroxyl groups,
the ratio of the formed dioxaphosphorinane isomers cis (3'-O of
the upper nucleoside and 4'-O of the lower nucleoside on the
same side of the average plan of the dioxaphosphorinanne ring)
and trans (3'-O of the upper nucleoside and 4'-O of the lower
nucleoside on the opposite sides of the average plan of the
dioxaphosphorinanne ring) was 1/1 for both 19a/20a (P=S) and
19b/20b (P=Se). However, cis and trans isomers 19a/20a and
19b/20b were easily separable by means of silica gel
chromatography whereas theirs D-CNA oxo-analogues required
a tedious reverse phase HPLC separation. Successive removals
of the tert-butyldiphenylsilyl and the dimethoxytrityl protective
groups were accomplished by means of fluoride ion and
trichloroacetic acid respectively in good yields leading to fully
deprotected thio-α,β,γ-D-CNA 23a/24a and seleno-α,β,γ-D-CNA
23b/24b for structural study purpose.
A relative instability appeared for the minor isomers 8b and 14b
(P=Se) that were slowly converted into their phosphoryl
counterparts with formation of elemental selenium upon
standing.[18] Eventually, removal of the tert-butyldiphenylsilyl
protective group by treatment with fluoride ion provided
9a,b/10a,b and 15a,b/16a,b in moderate to good yield. It is
noteworthy that due to its poor stability, 16b was not isolated at
NMR structural assignment of CNA
Sugar puckering
The overall conformation analysis of the newly synthesized thio-
and seleno-α,β- or α,β,γ-CNA was carried out by means of H,
1
this stage and was directly involved in the next deprotection step. 13C, 31P and 2D NMR study.
Acidic conditions allowed dimethoxytrityl group removal in good
yield, giving access to four diastereoisomers of thio-α,β-D-CNA,
11a, 12a, 17a, 18a and four diastereoisomers of seleno-α,β-D-
CNA, 11b, 12b, 17b, 18b.
The sugar puckering of the upper and lower deoxyribose
moieties within each dinucleotide (11a,b, 12a,b, 17a,b, 18a,b,
23a,b and 24a,b) was estimated by the approximation of Altona
and Sundaralingam: % South = [JH1',H2'/(JH1',H2' + JH3',H4')] x 100
(Table 1).[19]
Table 1. H/H coupling constants (Hz) of 2'-deoxyribose moieties in the 1H
NMR spectra of α,β-CNA dinucleotides 11a,b, 12a,b, 17b, 18a (500 MHz) and
17a (400 MHz) and of α,β,γ-CNA dinucleotides 23a,b and 24a,b (500 MHz).
Synthesis of thio- and seleno-α,β,γ-D-CNA
The synthetic pathway towards thio- and seleno-α,β,γ-D-CNA
followed the same steps applied for the thio- and seleno-α,β-D-
CNA approach, and started with the activation by 5-(ethylthio)-
1H-tetrazole of the bis(diisopropylamino)phosphoramidite of
thymidine with 4'-C-hydroxymethyl thymidine 2, in 38-70% yield
(Scheme 3).
Coupling constant J (Hz)
J(2',3')
%
sugar
South
J(1',2')
5.8
J(3',4')
1.9
2.5
1.6
2.7
1.4
2.3
1.3
2.6
2.0
3.0
2.2
3.1
1.8
2.0
2.0
2.0
1.9
-
11a
11b
12a
12b
17a
17b
18a
18b
23a
23b
24a
24b
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
upper
lower
8.8
8.1
8.8
8.2
9.1
8.2
9.1
8.4
8.7
7.5
8.6
7.3
8.4
8.4
9.1
8.4
8.4
7.3
9.4
7.0
8.6
8.6
8.5
8.0
1.8
3.1
1.7
2.9
1.2
2.4
1.2
2.2
1.8
nd
5.7
5.9
5.6
5.6
5.5
6.0
5.5
6.0
6.0
nd
82
76
84
75
87
78
87
76
81
71
80
70
82
81
82
81
82
nd
83
nd
83
nd
85
nd
6.1
5.7
6.3
5.5
6.0
5.5
5.9
5.7
6.6
5.8
6.6
5.5
5.8
6.1
5.9
5.9
6.6
6.0
7.0
5.8
5.9
6.0
6.1
T
HO
4'
O
HO
OTBDPS
2
T
a) 5-(Ethylthio)-1H-tetrazole,
CH3CN, 2 h
DMTrO
O
b) S8, pyr or KSeCN, Et3N
38-70%, 2 steps
O
P[N(iPr2)]2
RO
RO
T
1.7
3.2
1.8
1.9
2.1
2.0
nd
5.8
6.3
5.8
5.9
5.6
5.7
5.8
3.9
6.1
3.4
5.2
6.0
6.0
2.8
T
O
O
O
+
O
OR'
T
P
P
O
O
O
X
X
O
O
O
OR'
T
R
R'
nd
c) TBAF,
THF, 1 h
19a (32%), 19b (16%)
21a (81%), 21b (80%)
TBDPS 20a (38%), 20b (22%)
DMTr
1.8
6.4
nd
1.9
-
22a (60%), 22b (81%)
DMTr
H
H
d) TCA 2%,
DCM, 1 h
23a (quant.), 23b (quant.)
24a (quant.), 24b (quant.)
H
1.7
-
a: X=S and b: X=Se
2.6
1.5
6.0
1.5
-
Scheme 3. Synthesis of thio- and seleno-α,β,γ-CNA dinucleotides.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
With a neutral internucleotidic linkage and with an increasing
atomic radius size coupled with a lower electronegativity of the
non-bridging heteroatom on the phosphorus from oxygen[15, 20] to
sulfur and then to selenium atom, neither the 5'-sugar nor the 3'-
sugar puckering of all CNA dinucleotides exhibited a change in
their South conformation as depicted by the analysis values of
H/H coupling constants (Table 1). The upper nucleoside sugar
puckering was still in all cases, strongly pushed in South (C2'-
endo) conformation due to the loss of the negative charge of the
internucleotidic linkage.[21]
down-stream nucleoside and the phosphorus atom, that was
indicative of
a W-shaped P-O5'-C5'-C4'-H4' junction, only
observable if the nucleoside adopts the equatorial position.
Therefore, all these observations let us to conclude that the
backbone torsional angle values of α and β associated with
these conformations remain unchanged with respect to their
oxo-analogues[15] and are in the (g+,t) and (g-,t) range for 11a,b
and 17a,b, respectively and (t,t) for 12a,b and 18a,b.
Table 2. H/P coupling constants (Hz) within dioxaphosphorinane moieties in the
1H NMR spectra (400 or 500 MHz) and estimated α,β torsional angle values of
α,β-CNA dinucleotides (11a,b, 12a,b, 17a,b and 18a,b).
The downstream nucleosides of α,β-CNAs exhibited H/H
coupling constants and sugar puckering (South, C2'-endo) in
2'-deoxyribonucleosides.[22]
Coupling constant J (Hz)
Torsional anglea
accordance
with
unmodified
Because of the spiro-junction between the sugar and the
dioxaphosphorinane moieties, the Sundaralingam’s rule was not
applicable to the lower nucleosides of α,β,γ-CNAs for
determining the puckering. However, examination of the
remaining J1'/2' and J2'/3' coupling constants in comparison with
those of unmodified thymidine, suggested that the sugar was
also in South conformation.
J(5'/P)
J(7'/P)
J(7''/P)
α
g+
β
11a
11b
12a
12b
17a
17b
18a
18b
1.4
1.4
3.1
2.5
1.6
1.4
2.8
2.8
1.7
23.0
24.3
24.6
25.0
24.3
23.0
23.3
>20
t
2.0
4.1
4.0
2.4
2.6
5.0
4.9
g+
t
t
t
t
t
t
t
t
t
g-
g-
t
Dioxaphosphorinane ring conformation
In the early 80’s Gorenstein showed that dioxaphosphorinane
structure in chair conformation could be characterized by
1
examination of the coupling data in H NMR spectra. Typically,
t
axial protons should exhibit a small H/P coupling constant
(3JHax/P < ca. 3 Hz) together with large coupling constant for
a
The following 6-fold staggered pattern of the torsional angles is used: cis= 0
3
equatorial protons (3JHeq/P > ca. 20 Hz).[23] JH/P coupling
±30° (c), gauche(+)= 60 ±30° (g+), anticlinal(+)= 120 ±30° (a+), trans= 180 ±30°
(t), anticlinal(-)= 240 ±30° (a-), gauche(-)= 300 ±30° (g-). The notation a+/t is
used to designate a torsion angle on the border of anticlinal(+) and trans.
constants values depicted for the newly synthesized CNA are
reported in Table 2 for α,β-CNA dinucleotides and in Table 3 for
α,β,γ-CNA dinucleotides. The coupling constants observed for
dinucleotides 11a,b and 17a,b were very similar and clearly
established that these α,β-CNAs were in chair conformation with
all the substituents around the dioxaphosphorinane ring in
favorable position (apical for the upper nucleoside, equatorial for
the lower nucleoside and for the sulfur or selenium atom).
The dioxaphosphorinane conformation within α,β,γ-CNA can be
readily assigned by examination of the two couples of coupling
constants JH/P exhibited by the methylene protons 5'-H and 5''-H
with the phosphorus atom (Table 3). The chair conformation of
the structure of the cis-thio isomer 23a is clearly established with
a small (3JHax/P ~ 2 Hz) and a large coupling constant (3JHeq/P ~ 25
Hz) for each methylene proton both characteristic of a neat axial
and equatorial position for each of them. In contrast, the trans
isomer 24a adopted a twist-chair conformation suggested by the
3
In contrast, for the minor isomers 12a,b and 18a,b average
3
values around 3, 4 or 5 Hz were observed for the JH/P coupling
constants involving the 5'b- and 7'b-H respectively, thus
suggesting that the dioxaphosphorinane structure of these
isomers was in a slightly twisted chair conformation.
3
average values 11.5 Hz < JH/P < 14.0 Hz observed for the
coupling constants. On the other hand, none of the seleno
1
derivatives 23b or 24b were found to be in chair conformation as
Interestingly, Stec reported that the coupling constant JP/Se
3
between 31P directly bonded with 77Se (the NMR active isotope
with a natural abundance of 7%) could be used for structural
determination on the basis that 1JP/Se(ax) was always lower than
1JP/Se(eq) for diastereoisomeric cyclic phosphoroselenoate
compounds with an exocyclic selenium atom.[24] Indeed, we
observed for 11b and 17b a 1JP/Se coupling constant of 1006 and
1008 Hz respectively, whereas coupling constants of 954 and
974 Hz were depicted for 12b and 18b respectively, which was
indicative of the equatorial position of the selenium atom within
the dioxaphosphorinane structure for 11b and 17b and axial for
12b and 18b. As a consequence, it can be assumed that in all
the α,β-CNAs regardless of the stereochemistry, the lower
nucleoside adopts an equatorial or pseudo-equatorial position
on the dioxaphosphorinane ring.
denoted by the average values 6.2 Hz < JH/P < 9.5 Hz of the
coupling constants observed for the protons involved in the
dioxaphosphorinane ring. But as expected the minor isomer 24b
showed a more pronounced twist-chair conformation than 23b
that sill exhibited large coupling constant for two protons (3JH/P
~
20 Hz) indicative of a pseudo-equatorial position.
1
Moreover, examination of the JP/Se coupling constant showed
only a small difference between the cis and trans isomers with
1009 and 992 Hz, respectively. This could suggest that in both
cases the exocyclic seIenium atom was close to the equatorial
position. In contrast with the cis-oxo- or thio-α,β,γ-CNA, the
dioxaphosphorinane structure within cis-seleno-α,β,γ-CNA 23b
adopting a slightly twisted-chair conformation induced a deviation
of the associated torsional angles from those proposed for the
oxo- or thio-analogues with β shifting to c/g- and γ to g-/a- while α
remained unchanged in g- conformation (Table 3).
This was confirmed by the observation in all cases of a long
range coupling (3.5 Hz < JH/P < 4.5 Hz) between the 4'-H of the
4
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
For each CNA structure, it clearly appeared that increasing the
radius of the atom connected at the phosphorus atom resulted in
an increase of the value of the coupling constant (from around 6
Hz for P=O to around 10 Hz for P=Se) and therefore a strong
variation of ε close to 20°.
Table 3. H/P coupling constants (Hz) within dioxaphosphorinane moieties in the
1H NMR spectra (500 MHz) and estimated α,β,γ torsional angle values of α,β,γ-
CNA dinucleotides (23a,b and 24a,b).
Coupling constant J (Hz)
Torsional anglea
These observations evidenced that the upper nucleoside rotates
above the dioxaphosphorinane ring when the exocyclic hetero
element on the phosphorus atom switched from oxygen (radius
of 0.48 Å) to sulfur (0.88 Å) and then to selenium atom (1.03 Å),
in order to accommodate the increasing steric hindrance.
J(5'/P)
J(5'/P)
J(5''/P)
J(5''/P)
α
β
γ
23a
23b
24a
24b
2.5
25
2.0
25
g-
g-
g-
6.2
20.0
14.0
11.5
6.7
19.0
11.5
14.0
g-
c/ g-
c/ g-
c/ g-
g-/ a-
g-/a-
g-/a-
11.5
8.5
12.5
9.5
a+/g+
a+/g+
The selenium trip around phosphorus atoms
In order to use CNA for the synthesis of conformationaly
constrained ONs by automated supported synthesis according
to the phosphoramidite technology,[26] the thio- and seleno-CNA
dinucleotides must be converted into their corresponding O3'-
phosphoramidite by treatment with N,N-diisopropylamino-
cyanoethyl-phosphonamidic chloride. Whereas the thio-α,β- or
α,β,γ-CNA derivatives can be readily converted into the
appropriate phosphoramidites (data not shown) the seleno-D-
CNA exhibited an unexpected behaviour. As a typical exemple,
seleno-α,β-CNA 9b (31P NMR δ = 64.9 ppm) was treated with
the phosphitylating agent and provided in good yield (85%) a
clean product 25 after purification on silica gel chromatography
(Scheme 4). Surprisingly, while two peaks with 31P NMR
chemical shift around 150 ppm were expected for the
phosphoramidite moiety and two others around 65 ppm for the
seleno-dioxaphosphorinane, 25 exhibited two couples of peaks
at 131.0/130.5 ppm and 74.2/73.7 ppm respectively. It appeared
that 25 was a regioisomer of the desired seleno-α,β-CNA
phosphoramidite, corresponding to a migration of the selenium
atom from the dioxaphosphorinane ring to the newly introduced
phosphoramidate leading to a phosphite triester (131.0/130.5
ppm) and a seleno-phosphoramidate (74.2/73.7 ppm).
a
The following 6-fold staggered pattern of the torsional angles is used: cis= 0
±30° (c), gauche(+)= 60 ±30° (g+), anticlinal(+)= 120 ±30° (a+), trans= 180
±30° (t), anticlinal(-)= 240 ±30° (a-), gauche(-)= 300 ±30° (g-). The notation
a+/g+ is used to designate a torsion angle on the border of anticlinal(+) and
gauche(+).
The trans thio- and seleno isomers geometry was conserved
with respect of the previously described oxo-trans α,β,γ-CNA
conformation with a (α,β,γ) value set of (a+/g+, c/g-, g-/a-).
Finally, an another structural information can be obtained from
the measure of the coupling constant JH3'/P between the 3'-H of
3
the upper nucleoside and the phosphorus atom shown to be
correlated with the torsional angle ε (C4'-C3'-O3'-P) following the
3
rule of Altona: ε = –θ – 120° and θ was calculated with JH3'/P
=
15.3 cos2(θ) – 6.1 cos (θ) + 1.6.[25] The value of ε provides good
information about the position of the upper nucleoside relatively
to the dioxaphosphorinane ring within CNA. Depicted JH3'/P
coupling constants and calculated values for ε torsional angle for
CNAs dinucleotides 11a,b, 12a,b, 17a,b, 18a,b, 23a,b and
24a,b are given in Table 4 with those of their oxo-analogues
(P=O) previously synthesized as reference.
3
Table 4. 3'-H/P coupling constants (Hz) value in the 1H NMR spectra (500
MHz) and calculated ε torsional angle values (°) of α,β-CNA and α,β,γ-CNA
dinucleotides.
DMTrO
DMTrO
ClP(OCE)NiPr2
DIPEA, THF, 2 h
T
T
O
O
85%
T
δP ~ 64.9,
65.2 ppm
δP = 64.3
ppm
O
P
O
P
T
α,β-CNA 5'-C(S)
O
O
O
O
O
O
Se
Se
CNA
RP
11a
11b
SP
12a
12b
OH
O
P=Oa
P=S
P=Se
P=Oa
P=S
P=Se
9b
δP ~ 148.9,
149.7 ppm
P
NiPr2
CEO
3J3'-H/P
6.6
9.1
9.9
nd
nd
8.4
9.0
DMTrO
DMTrO
T
T
ε
-156
-142
-136
-146
-142
O
O
δP = 130.5,
131.0 ppm
δP = -8.1,
-8.0 ppm
α,β-CNA 5'-C(R)
O
P
O
P
T
T
I2/H2O
quant.
CNA
RP
P=Ob
17a
17b
SP
P=Ob
18a
18b
O
O
O
O
O
O
O
P=S
P=Se
P=S
P=Se
O
O
δP = 73.7,
74.2 ppm
NiPr2
δP = 73.5,
74.3 ppm
NiPr2
P
P
Se
Se
26
25
3J3'-H/P
5.8
9.0
9.8
6.4
8.8
9.7
OCE
OCE
ε
-160
-142
-136
-157
-144
-137
α,β,γ-CNA
Scheme 4. Selenium migration during phosphoramidite synthesis.
CNA
cis
23a
23b
trans
24a
24b
P=Oc
P=S
P=Se
P=Oc
P=S
P=Se
The proposed structure for 25 was confirmed by its conversion
by iodine/water oxidation into the α,β-D-CNA derivative 26 with
two 31P NMR chemical shifts at -8.0/8.1 ppm which are
characteristic for the dioxaphosphorinane moiety in chair
conformation[14] and the seleno-phosphoramidate part remained
3J3'-H/P
6.2
8.9
10.0
6.8
8.7
10.0
-135
ε
-158
-143
-135
-155
-145
a
[14]
b
[15] c
The values are taken from ref
values are taken from ref [20]
.
The values are taken from ref
. The
.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
around 74 ppm. Interestingly, this also demonstrated that the
selenium migration/oxidation process occurred with a retention
of the phosphorus configuration as outlined by 31P NMR while
the other isomer should be depicted around -3 ppm.[15]
It seemed that seleno-D-CNA (in between brackets, Scheme 4)
was a source of eletrophilic selenium. The reaction was fast and
occurred readily under mild conditions but only after formation of
the phosphoramidite at 3'-O position. A selenium transfer to the
N,N-diisopropylamino-cyanoethyl-phosphonamidic chloride prior
to the reaction with the free hydroxyl group can be rejected
because two equivalents of the phosphonamidic chloride
derivative were used and therefore 25 would not have been
building oligonucleotide through phosphoramidite technology,
we explored the compatibility of seleno-dioxaphosphorinane with
H-phosphonate chemistry. As an example, seleno-α,β,γ-CNA
19b was converted into its H-phosphonate triethylammonium
salt 29 by reacting diphenyl phosphonate on the 3'-hydroxyl
group of 19b (Scheme 6). 29 exhibited the expected 31P NMR
spectrum with a characteristic signal at 63.9 ppm corresponding
to the seleno-dioxaphosphorinane and another at 2.9 ppm
belonging to the H-phosphonate.
DMTrO
DMTrO
T
T
O
O
isolated in
a 85% yield. Moreover, the putative seleno-
O
P
δP = 63.9 ppm
O
P
a) HPO(OPh)2, pyr
b) H2O, Et3N
T
T
phosphonamidic chloride would present a lower reactivity and an
extra dinucleotide featuring both the phosphite in the ring and
the phosphoramidite moieties should have been detected in 31P
NMR.
O
O
O
O
Se
Se
O
O
88%, 2 steps
OH
O
19b
29
Et3NH+
O
δP = 2.9
ppm
P
O
H
We reproduced a similar synthetic sequence with the major
isomer 15b of seleno-α,β-CNA (Scheme 5). After phosphitylation
and selenium transfer, the intermediate was readily oxidized by
means of S8 in pyridine to produce 27 that exhibited the
expected couples of peaks in 31P NMR around 74 ppm and 60
ppm. Since we observed that the selenium atom migrates from
the phosphorus atom involved in seleno-phosphorinane to the
phosphorus atom of the phosphoramidite group, and similarly to
reported phosphorus-based selenium-transferring reagent,[27] we
postulate that 27 could be a source of electrophilic selenium for
an oxidative migration to hexamethylphosphoramide (HMPA).
Indeed, after treatment with two equivalents of HMPA at room
temperature in acetonitrile, 27 readily transferred its selenium
atom and Se-HMPA was formed as observed in 31P NMR with a
chemical shift of 82.7 ppm.[28]
Scheme 6. Synthesis of seleno-α,β,γ-CNA H-phosphonate 29.
Interestingly, the seleno-dioxaphosphorinane group within 19b
did not behave as a selenium-transferring reagent neither on the
diphenyl phosphonate reactant nor on the H-phosphonate
moiety of 29 whereas this was observed with triphenyl
phosphine selenide.[27] Therefore H-phosphonate chemistry may
be better adapted for the construction of ONs featuring seleno-
phosphorinane-modified nucleotides.
Conclusions
DMTrO
Four diastereoisomers of each thio- and seleno-α,β-CNA and
two isomers of each thio- and seleno-α,β,γ-CNA dinucleotides in
which the α,β or α,β,γ torsional angles of the sugar/phosphate
backbone are controlled within a dioxaphosphorinane structure
with a sulfur or selenium as exocyclic hetero element have been
synthesized and their conformation determined.
DMTrO
T
T
O
O
δP = 64.8
ppm
δP = 60.14,
60.10 ppm
a) ClP(OCE)NiPr2
O
P
O
P
DIPEA,THF, 2 h
b) S8, pyr,
T
T
O
O
O
O
Se
S
O
O
O
ACN, toluene
81%, 2 steps
27
15b OH
NiPr2
It appeared that replacing the exocyclic oxygen of the
dioxaphosphorinane ring either by a sulfur or a selenium atom
did not modified notably the constrain applied to the torsional
angle involved in the cycle. The main 5'-C(R) or 5'-C(S) isomers
of thio- and seleno-α,β-CNA displayed (g-, t) and (g+, t) set of
values for (α, β) respectively. The same trend was observed for
the thio- and seleno-trans-α,β,γ-CNA and for thio-cis-α,β,γ-CNA
as they behave the same as their oxo-counterparts. A slight
variation was observed for the cis-seleno-α,β,γ-CNA in which
while α remained in g- conformation, β moved to (cis/g-) and γ
angle to (g-/a-) conformation due to the selenium atom that
distorted the dioxaphosphorinane chair conformation. Eventually,
in all D-CNA because of the increasing atom size from oxygen to
sulfur and then to selenium atom, ε torsional angle was impacted
resulting in a rotation of the upper nucleoside above the
dioxaphosphorinane ring that reached 20° in seleno-CNA with
respect to the oxo-analogues.
δP = 73.3,
74.0 ppm
P
Se
OCE
DMTrO
T
HMPA
41%
O
Se
P
O
P
δP = 60.13,
60.12 ppm
+
Me2N
NMe2
T
O
O
S
NMe2
δP = 82.7 ppm
O
O
28
NiPr2
δP = 150.0,
148.7 ppm
P
OCE
Scheme 5. Recovering process from seleno-α,β-CNA to thio-α,β-CNA
phosphoramidite by selenium migration over phosphorus.
Thio-α,β-CNA phosphoramidite 28 was isolated and
characterized by 31P NMR with typical chemical shifts of 60.1
ppm for the thio-dioxaphosphorinane and 150.0/148.7 ppm
representative of the recovered phosphoramidite group. On the
other hand, 28 can be straightforwardly obtained from 15a upon
reaction with N,N-diisopropylamino-cyanoethyl- phosphonamidic
chloride in standard conditions.
We observed that selenium atom within seleno-CNA behaves as
an electrophilic specie able to migrate from dioxaphosphorinane
group to oxidize a phosphoramidite moiety that ablates the
synthesis of the corresponding dinucleotide phosphoramidite.
This issue can be overcome by using H-phosphonate chemistry
Eventually, while trying to circumvent the issue of selenium
migration that prevents the use of seleno-CNA derivatives in
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
that allows for the preparation of H-phosphonate derivatives of
seleno-D-CNA.
Hz, 2 H, H6R), 6.59 (dd, J = 5.4, 9.3 Hz, 1 H, H1'S), 6.35 (dd, J = 5.7, 8.7
Hz, 2 H, H1'R), 4.43 (m, 2 H, H3'R), 4.22 (m, 1 H, H3'S), 3.96 (m, 3 H, H4'S
and H4'R), 3.88 (m, 2 H, H5'R), 3.49-3.43 (m, 7 H, H7' and H5'S), 2.24-2.11
(m, 3 H, H2'), 1.84 (m, 9 H, H7), 1.71-1.37 (m, 9 H, H2' and H6'), 1.06 (s,
27 H, tBu), 0.13, 0.07, 0.02 and -0.11 (s, 60 H, SiMe3) ppm.
These newly synthesized CNAs complete our set of constrained
dinucleotides featuring non-canonical conformations, their
behaviour within biologically relevant nucleic acids secondary
structures are under evaluation and will be reported in due
course.
3'-O-tert-Butyldiphenylsilyl-5'-O-trimethylsilyl-5'-oxyethylthymidine
(6): Diastereoisomers 4 (1 g, 1.5 mmol) were submitted to K2CO3 (310
mg, 2.24 mmol) in anhydrous methanol at 0°C for 1.5 h. The reaction
was stopped by addition of a saturated aqueous solution of NH4Cl and
compounds 5 and 6 were extracted with EtOAc. After drying, the organic
layer was concentrated in vacuo and the crude material was submitted to
silica gel chromatography with a mixture of CH2Cl2/EtOAc (1:1) as eluent.
424 mg (54%) of 5 and 250 mg (28%) of 6 (and 161 mg (18%) of a 1/2
mixture of 6 and its 5'-C epimer) were isolated. Data for 5.[15] Data for 6:
1H NMR (300 MHz, CDCl3): δ = 7.77 (bq, J = 1.2 Hz, 1 H, H6), 7.64-7.60
(m, 4 H, Ph), 7.44-7.36 (m, 6 H, Ph), 6.58 (dd, J = 5.4, 9.3 Hz, 1 H, H1'),
4.20 (d, J = 5.4 Hz, 1 H, H3'), 3.92 (s, 1 H, H4’), 3.50 (m, 2 H, H7'), 3.27
(ddd, J = 1.2, 5.2, 7.6 Hz, 1 H, H5'), 2.29 (A part of an ABX syst, J = 5.5,
13.1 Hz, 1 H, H2'), 1.89-1.82 (m, 4 H, H7 and H2'), 1.73-1.57 (m, 2 H, H6'),
-0.08 (s, 9 H, SiMe3) ppm.13C NMR (75 MHz, CDCl3): δ = 164.0, 150.5,
136.0, 135.6, 133.2, 132.9, 129.9, 127.8, 127.7, 110.8, 89.5, 84.5, 84.9,
76.0, 70.0, 58.3, 40.7, 37.0, 26.8, 18.9, 14.4, 0.0 ppm.
Experimental Section
Products were purified by medium pressure liquid chromatography on a
Waters 2545 apparatus by using Amicon 6-35 mm or Merck 15 mm silica
unless stated otherwise. Alternatively, they were purified by high
performance liquid chromatography (HPLC and RP-HPLC) using
a
Waters 2545 Binary Gradient Module (BGM, high-pressure mixing binary
gradient pump) combined to a Waters 2489 UV/Vis detector. HPLC
instrument control, data collection and analysis were performed on a PC
equipped with Microsoft Windows XP, and Acquity software.
NMR spectra were recorded on a Bruker Avance-300, Avance-400 or
Avance 500 spectrometers (300, 400 or 500 MHz for 1H; 75, 100 or 125
MHz for 13C and 121 or 202 MHz for 31P). Chemical shifts for 1H and 13
C
are reported in ppm (δ) relative to an internal standard (solvent residual
peak). Mass spectra were recorded on a Nermag R10-10, on a Perkin-
Elmer API 365 or on a MALDI-TOF Waters Micro MX. All solvents were
distilled and dried before use.
Compounds 1, 2, 7a, 9a and 11a have been previously described,[20] as
compounds 3[14] and 5.[15]
General procedure A for the preparation of protected α,β-thio-D-
CNA and α,β,γ-thio-D-CNA dinucleotides: 4'-C-Hydroxymethyl
thymidine 2 or 5'-C-hydroxyethylthymidine 3 or 5 (1 eq.) and 5-(ethylthio)-
1H-tetrazole (5 eq.) were dissolved in dry acetonitrile (C = 0.5 M) at r.t.
under an argon atmosphere. A solution of 5'-O-dimethoxytrityl thymidine
phosphorodiamidite[17b] (1.2 eq.) in dry acetonitrile (C = 0.5 M) was added
dropwise to the mixture over a period of 15 min. The resulting mixture
was stirred at r.t. until TLC analysis indicated the completion of the
reaction (ca. 2 h). To the reaction mixture were added dry pyridine (24
eq.) and S8 (5 eq.). The yellow suspension was stirred and heated at
60°C for 2 h. The reaction mixture was then allowed to cool down to r.t.
3'-O-tert-Butyldiphenylsilyl-5'-O-trimethylsilyl-5'-(trimethylsilyloxy
ethyl) thymidine (4): To a solution of 3 (1 g, 1.91 mmol) in anhydrous
pyridine (6 mL) was added tert-butyltrimethylsilyl chloride (0.316 g, 2.1
mmol) at room temperature. After 12 h of stirring, the reaction was
stopped by addition of a saturated aqueous solution of NH4Cl. The
silylated intermediate was extracted with EtOAc and dried over MgSO4.
The crude white foam obtained (1.25 g) was directly subjected to the
oxidation/reduction process by addition of Dess-Martin periodinane (1.62
g) in 10 mL of anhydrous dichloromethane and pyridine (80 mL). After 2
h of stirring at room temperature the reaction mixture was diluted with
ethanol (20 mL). After 30 min, NaBH4 was added (432 mg, 11.4 mmol)
and stirring was maintained for 2 h. As TLC control (EP/CH2Cl2/EtOAc,
3:5.6:1.4) showed a single spot corresponding to the starting material,
the reaction was stopped by addition of a saturated aqueous solution of
NH4Cl and the epimeric mixture was extracted with EtOAc and the
organic layer dried over magnesium sulphate. The tert-butyldimethylsilyl
ether was then removed by dilution of the crude product in dry methanol
(20 mL) and p-toluenesulfonic acid (250 mg) was added. After 1 h, the
reaction was stopped by addition of a saturated aqueous solution of
NaHCO3. The methanol was evaporated and the resulting diol was
extracted with ethyl acetate, washed with brine and the organic layer
dried over MgSO4. The crude material was then submitted to persilylation
with hexamethyldisilazane (0.808 mL, 0.381 mmol) and trimethylsilyl
chloride (0.970 mL, 0.381 mmol) in anhydrous pyridine (6 mL). After 2 h
of stirring at room temperature, the reaction was stopped by addition of a
saturated aqueous solution of NH4Cl and compound 4 was extracted with
diethyl ether, the organic layer was washed with water and brine, and
dried over magnesium sulphate. After removal of the solvent, compound
4 (1.08 g, 85% overall yield from 3) was isolated after silica gel
chromatography (CH2Cl2/EtOAc, 4:1) as a 1/2 mixture of 5'-C(S) and 5'-
C(R) diastereoisomers. 1H NMR (300 MHz, CDCl3): δ = 8.20 (m, 3 H, NH),
7.69-7.66 (m, 12 H, Ph), 7.45-7.41 (m, 19 H, Ph and H6S), 7.12 (d, J = 1.2
The suspension was filtered through
a sintered funnel to remove
elemental sulfur and the solvents were evaporated. The residue was then
dissolved in H2O (10 mL) and the resultant solution extracted with EtOAc
(3 × 20 mL). The combined organic layers were washed with H2O (20
mL) and brine (20 mL), dried over MgSO4 and then concentrated in
vacuo. The crude product was purified by silica gel column
chromatography by eluting either with a mixture of EtOAc/DCM/Et3N
(5:5:0.05) to yield protected α,β-thio-D-CNA dinucleotides as white foams
or with
a mixture of EtOAc/petroleum ether/Et3N (1:1:0.05) to
EtOAc/MeOH/Et3N (95:5:0.05) to yield α,β,γ-thio-D-CNA dinucleotides as
white foams.
General procedure B for the preparation of protected α,β-seleno-D-
CNA and α,β,γ-seleno-D-CNA dinucleotides: 4'-C-Hydroxymethyl
thymidine 2 or 5'-C-hydroxyethylthymidine 3 or 5 and 5-(ethylthio)-1H-
tetrazole (5 eq.) were dissolved in dry acetonitrile (C = 0.5 M) at r.t. under
an argon atmosphere.
A solution of 5'-O-dimethoxytritylthymidine
phosphorodiamidite (1.2 eq.)[17b] in dry acetonitrile (2 mL) was added
dropwise to the mixture over a period of 10 min. The resulting mixture
was stirred at r.t. for 2 h until TLC analysis indicated the completion of
the reaction. To the reaction mixture were added dry Et3N (10 eq.) and
potassium selenocyanate (5 eq.). The pink suspension was stirred and
heated at 60°C for 1 h. The reaction mixture was then allowed to cool
down to r.t. over night. After 15 h, the suspension was filtered through a
silica plug and washed with EtOAc to remove toxic KSeCN. The solvents
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
were evaporated and co-evaporated with toluene. The residue was then
dissolved in H2O (10 mL) and the resultant solution extracted with EtOAc
(3 x 20 mL). The combined organic layers were washed with H2O (20
mL) and brine (20 mL), dried over MgSO4 and then concentrated in
vacuo. The crude product was purified by silica gel column
chromatography eluting with a mixture of EtOAc/petroleum ether/Et3N
(5:5:0.05 to 9:1:0.05) to yield protected α,β-seleno-D-CNA and α,β,γ-
seleno-D-CNA as pink solids.
1 H, H4'b), 3.76 (s, 6 H, OMe), 3.65 (d, 3J = 5.1 Hz, 1 H, H5'b), 3.41-3.29
(m, 3 H, H3'a and 2 × H5'a), 2.45-2.21 (m, 4 H, H2'), 1.98 (d, 4J7-6 = 0.9 Hz,
4
3 H, H7), 1.90-1.81 (m, 1 H, H6'b), 1.43 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.40-
1.34 (m, 1 H, H6'b), 1.03 (s, 9 H, tBu) ppm. 13C NMR (75 MHz, CDCl3): δ
= 164.0, 163.9, 158.9, 158.8, 150.9, 150.8, 144.1, 135.8, 135.7, 135.3,
135.2, 135.1, 133.3, 132.5, 130.6, 130.3, 130.2, 130.1, 130.0, 128.2,
128.0, 113.5, 113.4, 112.4, 112.1, 87.8, 87.7, 87.5, 87.2, 85.5, 84.5, 80.9,
78.5, 75.9, 74.5, 63.6, 55.4, 45.6, 45.4, 39.8, 39.1, 23.6, 22.3, 19.0, 12.7,
11.8 ppm. 31P NMR (121 MHz, CDCl3): δ = 64.6 ppm. Data for 8b: 1H
NMR (300 MHz, CDCl3): δ = 8.95 and 8.92 (bs, 2 H, NH), 7.72-7.64 (m, 5
H, Ph), 7.57 (bs, 1 H, H6), 7.50-7.23 (m, 15 H, Ph), 6.85 (bd, 4 H, Ph),
6.54 (dd, 3J = 5.4, 8.4 Hz, 1 H, H1'), 6.32 (t, 3J = 7.2 Hz, 1 H, H1'), 5.71
(dd, 3J = 3.3, 10.2 Hz, 1 H, H3'a), 4.41-4.35 (m, 3 H, H3'b and H7'b), 4.25
(bs, 1 H, H4'b), 4.21-4.09 (m, 1 H, H7'b), 3.89 (bdd, 3J = 2.1 and 11.4 Hz, 1
H, H5'b), 3.81 (s, 6 H, OMe), 3.76 (m, 1 H, H4'a), 3.50 and 3.41 (AB part of
an ABX syst, 3J = 2.1, 2.4, 11.1 Hz, 2 H, H5'a, H5''a), 2.49-2.39 (m, 3 H,
General procedure C for the fluoride ion deprotection of α,β-D-CNA
and α,β,γ-D-CNA dinucleotides: To fully protected D-CNA (1 eq.) in
solution in dry THF (C = 0.1 M) was added TBAF (1 M solution in THF, 1
eq.). The solution was stirred under an argon atmosphere at 0°C. After
TLC analysis showed complete conversion of starting material (40 min –
1 h), the solvent was concentrated under reduced pressure controlling
the temperature of the rotavapor bath (T < 25°C) and the crude was then
purified by silica gel column chromatography eluting with a mixture of
EtOAc/MeOH/Et3N (10:0:0.05 to 9:1:0.05) to give 5'-DMTr dinucleotides
D-CNA as white solids.
4
H2'), 2.27-2.14 (m, 1 H, H2'), 1.94 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.91-1.81
4
(m, 1 H, H6'b), 1.42 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.33-1.23 (m, 1 H, H6'b),
1.11 (s, 9 H, tBu) ppm.13C NMR (75 MHz, CDCl3): δ = 163.7, 163.6,
158.8, 150.4, 150.1, 144.1, 135.9, 135.7, 135.2, 135.0, 134.9, 133.2,
132.7, 130.2, 130.1, 130.0, 128.3, 128.2, 128.1, 128.0, 128.0, 127.2,
113.4, 111.6, 111.5, 87,8, 87.6, 87,4, 85.4, 84.6, 84.2, 81.8, 74.3, 71.4,
67.0, 63.4, 55.3, 40.3, 39.5, 26.9, 25.7, 19.0, 12.9, 11.7 ppm. 31P NMR
(121 MHz, CDCl3): δ = 71.9 ppm.
General procedure D for the detritylation of α,β-D-CNA and α,β,γ-D-
CNA dinucleotides. The 5'-DMTr dinucleotide D-CNA (1 equiv.) was
dissolved in a TCA solution (2% in CH2Cl2, 35 mL/mmol) and stirred at r.t.
and after 30 min, the solution was concentrated and the residue was re-
dissolved in the same volume of the 2% TCA solution for another 30 min.
One drop of a saturated solution of NaHCO3 was added and the solution
concentrated under reduced pressure. The crude was dissolved in the
minimum of eluant EtOAc/MeOH (9:1) and was purified by silica gel
column chromatography eluting with a mixture of EtOAc/MeOH (95:5 to
90:10) to yield to fully deprotected thio-D-CNA dinucleotides as white
solids and fully deprotected seleno-D-CNA dinucleotides as pink solids.
5’-O-Dimethoxytrityl-α,β-thio-D-CNA (SC,SP) (9a) Following the
general procedure C starting from 7a gave product 9a (quantitative, 435
mg).[20]
5’-O-Dimethoxytrityl-α,β-thio-D-CNA (SC,RP) (10a): Following the
general procedure C starting from 8a gave product 10a (quantitative, 356
mg). 1H NMR (300 MHz, CDCl3): δ = 10.02 (br. s, 2 H, 2 × NH), 7.59 (s, 1
H, H6a), 7.45 (s, 1 H, H6b), 7.35-7.19 (m, 9 H, Ph), 6.81 (d, 3J = 9.0 Hz, 4
5'-O-Dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β-thio-D-CNA
(SC,SP) (7a) and 5'-O-dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β-
thio-D-CNA (SC,RP) (8a): Following the general procedure A starting
from 3 gave the products 7a (26%, 550 mg)[11] and 8a (20%, 410 mg).
Data for 8a: 1H NMR (300 MHz, CDCl3): δ = 9.10 (s, 1 H, NH), 9.07 (s, 1
H, NH), 7.65-7.60 (m, 5 H, Ph), 7.53 (d, 4J6-7 = 1.3 Hz, 1 H, H6), 7.49-7.13
3
3
3
H, Ph), 6.38 (dd, J1'b-2'b = 6.1, J1'b-2''b = 8.0 Hz, 1 H, H1'b), 6.22 (dd, J1'a-
3
3
2'a = 5.4, J1'a-2''a = 9.0 Hz, 1 H, H1'a), 5.86 (m, J3'a-P = 1.6 Hz, 1 H, H3'a),
3
3
4.86 (m, J5'b-P = 1.8 Hz, 1 H, H5'b), 4.60 (m, J7'b-P = 0.5 Hz, 1 H, H7'b),
3
3
3
4.49 (m, 1 H, H3'b), 4.39-4.32 (m, J7''b-6''b = 3.2, J7''b-6'b = 5.3, J7''b-7'b
=
11.5, 3J7''b-P = 25.6 Hz, 1 H, H7''b), 4.27 (br. s, 1 H, H4'a), 4.07 (m, 1 H, H4'b),
3.76 (s, 6 H, OMe), 3.41 (br. s, 2 H, 2 × H5'a), 2.65 (dd, 3J2'a-1'a = 5.2, 3J2'a-
2''a = 13.9 Hz, 1 H, H2'a), 2.44-2.39 (m, 3 H, H2'a, H2'b, H6'b), 2.13-2.07 (m,
(m, 15 H, Ph, H6), 6.83-6.79 (m, 4 H, Ph), 6.51 (dd, 3J1'b-2'b = 5.7, 3J1'b-2'b
=
8.9 Hz, 1 H, H1'b), 6.28 (dd, 3J1'b-2'b = 6.1, 3J1'b-2'b = 8.3 Hz, 1 H, H1'a), 5.57
(m, 1 H, H3'a), 4.26-4.10 (m, 3 H, H3'b, 2 × H7'b), 4.02 (br. s, 1 H, H4'a),
3.78 (br. s, 1 H, H3'b), 3.77 (s, 6 H, OMe), 3.71 (d, 3J = 5.4 Hz, 1 H, H4'b),
3.40 (m, 2 H, 2 × H5'a), 2.42-2.36 (m, 2 H, 2 × H2'a), 2.28-2.19 (m, 3 H,
4
1 H, H2'b), 1.89 (d, J7-6 = 0.5 Hz, 3 H, H7b), 1.83 (m, 1 H, H6'b), 1.40 (d,
4J7-6 = 0.5 Hz, 3 H, H7a) ppm. 13C NMR (75 MHz, CDCl3): δ = 164.5 (C4b),
164.5 (C4a), 158.9 (CHPh), 151.1 (C2b), 151.0 (C2a), 144.3 (Cq,Ph), 135.6
(C6b), 135.3 (C6a), 135.2, 135.1 (Cq,Ph), 130.22, 130.20, 128.3, 128.2,
127.4 (CHPh), 113.6 (CHPh), 111.84 (C5b), 111.82 (C5a), 87.6 (Cq,Ph), 87.0
(3J4'b-P = 8.2 Hz, C4'b), 85.7 (C1'b), 84.9 (C1'a), 84.8 (3J4'a-P = 8.6 Hz, C4'a),
81.7 (C3'a), 78.7 (3J5'b-P = 4.6 Hz, C5'b), 72.6 (C3'b), 67.0 (C7'), 63.7 (C5'a),
55.5 (OMe), 40.7 (C2'b), 40.7 (C2'a), 28.3 (C6'), 13.0 (C7b), 12.0 (C7a) ppm.
31P NMR (121 MHz, CDCl3): δ = 66.6 ppm. MS (Malfi Tof): m/z = 913.4
[M+Na]+, 929.4 [M+K]+.
4
H6'b, 2 × H2'b), 1.89 (d, J7-6 = 1.1 Hz, 3 H, H7), 1.90-1.80 (m, 1 H, H6'b),
1.44-1.14 (m, 1 H, H6'b), 1.38 (d, 4J7-6 = 1.0 Hz, 3 H, H7), 1.07 (s, 9 H, tBu)
ppm. 13C NMR (75 MHz, CDCl3): δ = 164.1, 164.0, 158.9, 158.8, 150.6,
150.3, 144.3, 136.0, 135.9, 135.4, 135.24, 135.20, 133.4, 132.9, 130.4,
130.2, 129.3, 128.5, 128.3, 128.2, 128.0, 127.9, 127.3, 113.6, 113.4,
111.8, 111.7, 88.2, 88.0, 87.5, 86.0, 85.6, 81.1, 77.5, 74.4, 66.6, 63.6,
55.5, 40.5, 39.7, 28.5, 27.1, 19.2, 13.0, 11.9 ppm.31P NMR (121 MHz,
CDCl3): δ = 67.6 ppm. MS (Malfi Tof): m/z = 1151.8 [M+Na]+.
5’-O-Dimethoxytrityl-α,β-seleno-D-CNA (SC,SP) (9b): Following the
general procedure C starting from 7b gave the products 9b (64%, 400
mg). As already been observed on previous protected D-CNA, the NMR
spectra were obtained with a very poor resolution for 1H spectra and
without detection of the aliphatic carbons for the 13C spectrum.[20] 1H
NMR (300 MHz, CD3OD): δ = 7.45 (bd, 4J6-7 = 1.2 Hz, H6), 7.34 (bd, 4J6-7
= 1.2 Hz, H6), 7.23-7.05 (m, 9 H, Ph), 6.67 (m, 4 H, Ph), 6.26 (m, 2 H, 2 ×
H1'), 5.30 (dd, 3J = 4.8, 10.2 Hz, H3'a), 4.67 (bd, 3J = 11.4 Hz, H3'b), 4.43-
4.21 (m, 2 H, H7'b), 4.17 (m, 2 H, H4'a, H4'b), 3.61 (s, 6 H, OMe), 3.70 (m, 1
5’-O-Dimethoxytrityl-3’-O-tert-butyldiphenylsilyl-α,β-seleno-D-CNA
(SC,SP) (7b) and 5’-O-dimethoxytrityl-3’-O-tert-butyldiphenylsilyl-α,β-
seleno-D-CNA (SC,RP) (8b): Following the general procedure B starting
from 3 gave the products 7b (27%, 780 mg) and 8b (11%, 310 mg). Data
for 7b: 1H NMR (300 MHz, CDCl3): δ = 9.53 and 9.10 (bs, 2 H, NH), 7.61-
7.46 (m, 6 H, Ph), 7.40-7.21 (m, 15 H, Ph), 6.81 (bd, 4 H, Ph), 6.59 (dd,
3J = 5.1, 9.6 Hz, 1 H, H1'), 6.45 (dd, 3J = 6.0, 9.0 Hz, 1 H, H1'), 5.43 (dd,
3J = 4.2, 10.8 Hz, 1 H, H3'a), 4.25-4.18 (m, 3 H, 2 × H7'b and H4'a), 4.02 (bs,
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
H, H5'b), 3.39 and 3.25 (AB part of an ABX syst, 3J = 2.7, 3.0, 10.8 Hz, 2
H, 2 × H5'a), 2.46-2.26 (m, 2 H, H2' and H6'b), 2.01 and 1.88 (AB part of an
ABX(Y) syst, 3J = 2.4, 5.4, 5.7, 9.0, 13.2 Hz, 2 H, H2'), 1.83 (d, 4J7-6 = 1.2
Hz, 3 H, H7), 1.70 (bd, 3J = 14.4 Hz, 1 H, H6''b), 1.23 (d, 4J7-6 = 1.2 Hz, 3 H,
H7) ppm. 31P NMR (121 MHz, CD3OD): δ = 64.3 ppm. MS (Malfi Tof): m/z
= 961.6 [M+Na]+. HRMS (ESI): calcd for C43H47N4O13PNaSe, 961.1945
[M+Na]+; found 961.1931.
4.40 (dt, 3J3'b-4'b = 2.2, 3J3'b-2'b = 2.4, 3J3'b-2''b = 5.9 Hz, 1 H, H3'b), 4.24 (td,
3J4'a-3'a = 1.4, 3J4'a-5'a = 2.9, 3J4'a-5''a = 2.9 Hz, 1 H, H4'a), 4.00 (ddd, 3J4'b-3'b
2.3, J4'b-5'b = 2.6, 3J4'b-P = 4.4 Hz, 1 H, H4'b), 3.83 and 3.77 (AB part of an
=
3
3
3
ABX syst, J5'a-4'a = 2.9, 3J5''a-4'a = 2.9, J5'a-5''a = 12.0 Hz, 2 H, H5'a, H5''a),
3
3
3
2.39 (ddd, J2'a-3'a = 1.2, J2'a-1'a = 5.5, J2'a-2''a = 14.1 Hz, 1 H, H2'a), 2.36
3
3
3
3
(dddd, J6'b-7''b = 5.0, J6'b-5'b = 11.4, J6'b-7'b = 12.6, J6'b-6''b = 14.5 Hz, 1 H,
3
3
3
H6'b), 2.44 (ddd, J2''a-3'a = 5.5, J2''a-1'a = 8.9, J2''a-2'a = 14.1 Hz, 1 H, H2''a),
3
3
3
2.26 (ddd, J2'b-3'b = 2.4, J2'b-1'b = 6.0, J2'b-2''b = 13.8 Hz, 1 H, H2'b), 2.12
(ddd, 3J2''b-3'b = 6.0, 3J2''b-1'b = 8.3, 3J2''b-2'b = 13.8 Hz, 1 H, H2''b), 1.94 (d, 4J7-
6 = 1.0 Hz, 3 H, H7b), 1.90 (dddd, 3J6''b-7''b = 1.9, 3J6''b-7'b = 2.6, 3J6''b-5'b = 2.6,
5’-O-Dimethoxytrityl-α,β-seleno-D-CNA (SC,RP) (10b): Following the
general procedure C starting from 8b gave the product 10b (34%, 84 mg)
and was engaged immediately in the next detritylation step. As for 9b,
NMR spectra were recorded with a very low resolution. 1H NMR (300
MHz, CD3OD): δ = 7.59 (bd, 4J6-7 = 1.2 Hz, H6), 7.42 (bd, 4J6-7 = 1.2 Hz,
H6), 7.39-7.23 (m, 9 H, Ph), 6.82 (m, 4 H, Ph), 6.38 (m, 3J = 5.7, 7.5 Hz, 1
H, H1'), 6.24 (m, 3J = 5.4, 9.0 Hz, 1 H, H1'), 5.64 (dd, 3J = 5.4, 8.4 Hz,
H3'a), 4.88 (bd, 3J = 10.8 Hz, 1 H, H3'b), 4.62 (m, 1 H, H7'b), 4.48 (m, 2 H,
H4'), 4.37-4.20 (m, 2 H, H7'b and H4'), 4.05 (m, 1 H, H5'b), 3.76 (s, 6 H,
3J6''b-6'b = 14.4 Hz, 1 H, H6''b), 1.87 (d, J7-6 = 1.1 Hz, 3 H, H7a) ppm. 13C
4
NMR (125 MHz, CD3OD): δ = 166.51 (C4b), 166.48 (C4a), 152.5 (C2b),
152.2 (C2a), 137.8 (C6a), 137.4 (C6b), 112.3 (C5b), 111.9 (C5a), 88.8 (3J4'b-P
= 8.7 Hz, C4'b), 87.3 (3J4'a-P = 7.4 Hz, C4'a), 86.8 (C1'b), 86.1 (C1'a), 81.7
(2J3'a-P = 2.9 Hz, C3'a), 80.2 (2J5'b-P = 5.0 Hz, C5'b), 73.3 (C3'b), 68.4 (2J7'b-P
4.8 Hz, C7'), 63.0 (C5'a), 41.2 (C2'b), 40.3 (3J2'a-P = 4.4, C2'a), 29.6 (3J6'b-P
=
=
5.5 Hz, C6'b), 13.1 (C7b), 12.6 (C7a) ppm. 31P NMR (202 MHz, CD3OD): δ
= 66.9 ppm. HRMS (ESI): calcd for C22H30N4O11PS 589.1369 [M+H]+;
found 589.1379.
OMe), 3.43 (m, 2 H, 2 × H5'a), 2.67 (A part of an ABX syst, 3J = 5.4, 14.1
4
Hz, 1 H, H2'), 2.49-2.35 (m, 1 H, H2'), 2.11 (m, 1 H, H6'b), 1.92 (d, J7-6
=
1.0 Hz, 3 H, H7), 1.83 (bd, 3J = 14.4 Hz, H6''b), 1.42 (d, 4J7-6 = 1.0 Hz, 3 H,
H7). 31P NMR (121 MHz, CD3OD): δ = 70.9 ppm. MS (Malfi Tof): m/z =
961.4 [M+Na]+.
α,β-seleno-D-CNA (SC,SP) (11b): Following the general procedure D
starting from 9b gave the product 11b (46%, 11 mg). 1H NMR (500 MHz,
CD3OD): δ = 7.83 (d, 4J6-7 = 1.3 Hz, 1 H, H6a), 7.65 (d, 4J6-7 = 1.2 Hz, 1 H,
α,β-thio-D-CNA (SC,SP) (11a): Following the general procedure
D
H6b), 6.44 (dd, 3J1'b-2'b = 6.3, 3J1'b-2''b = 8.2 Hz, 1 H, H1'b), 6.37 (dd, 3J1'a-2'a
=
5.7, 3J1'a-2''a = 8.8 Hz, 1 H, H1'a), 5.24 (ddt, 3J3'a-4'a = 1.6, 3J3'a-2'a = 1.6, 3J3'a-
2''a = 5.8, 3J3'a-P = 9.9 Hz, 1 H, H3'a), 4.86 (dddd, 3J5'b-4'b = 2.0, 3J5'b-6''b = 2.0,
starting from 9a gave the product 11a (80%, 16 mg). 1H NMR (500 MHz,
CD3OD): δ = 7.80 (d, 4J6-7 = 1.2 Hz, 1 H, H6a), 7.65 (d, 4J6-7 = 1.2 Hz, 1 H,
H6b), 6.43 (dd, 3J1'b-2'b = 6.1, 3J1'b-2''b = 8.1 Hz, 1 H, H1'b), 6.36 (dd, 3J1'a-2'a
5.8, J1'a-2''a = 8.8 Hz, 1 H, H1'a), 5.21 (ddt, 3J3'a-4'a = 1.9, 3J3'a-2'a = 1.6, J3'a-
=
3J5'b-6'b = 11.8, 3J5'b-P = 1.4 Hz, 1 H, H5'b), 4.65 (ddt, 3J7'b-6''b = 2.6, 3J7'b-7''b
11.3, 3J7'b-6'b = 12.7, 3J7'b-P = 2.0 Hz, 1 H, H7'b), 4.48 (dt, J3'b-2'b = 2.7, 3J3'b-
=
3
3
3
2''a = 5.7, 3J3'a-P = 9.1 Hz, 1 H, H3'a), 4.86 (dddd, 3J5'b-4'b = 1.9, 3J5'b-6''b = 1.9,
4'b = 2.7, 3J3'b-2''b = 5.6 Hz, 1 H, H3'b), 4.43 (dddd, 3J7''b-6'b = 1.7, 3J7''b-6'b = 4.7,
3J5'b-6'b = 11.6, J5'b-P = 1.4 Hz, 1 H, H5'b), 4.58 (dddd, J7'b-6''b = 2.1, J7'b-
7''b= 10.8, 3J7'b-6'b = 13.0, 3J7'b-P = 1.7 Hz, 1 H, H7'b), 4.48 (ddd, 3J3'b-2'b = 3.1,
3J3'b-4'b = 2.5, 3J3'b-2''b = 5.8 Hz, 1 H, H3'b), 4.43 (dddd, 3J7''b-6''b = 1.5, 3J7''b-6'b
3J7''b-7'b = 11.1, 3J7''b-P = 24.3 Hz, 1 H, H7''b), 4.33 (td, 3J4'a-3'a = 1.8, 3J4'a-5'a
3.1, 3J4'a-5''a = 3.1 Hz, 1 H, H4'a), 3.93 (ddd, 3J4'b-5'b = 1.8, 3J4'a-3'b = 2.4, 3J4'b-P
=
3
3
3
3
3
= 4.5 Hz, 1 H, H4'b), 3.83 (ABX, J5'a-4'a = 3.2, 3J5''a-4'a = 3.2, J5'a-5''a = 12.1
3
3
3
3
= 4.9, 3J7''b-7'b = 11.1, 3J7''b -P = 23.0 Hz, 1 H, H7''b), 4.30 (td, J4'a-3'a = 1.9,
Hz, 2 H, H5'a, H5''a), 2.60 (ddd, J2'a-3'a = 1.7, J2'a-1'a = 5.7, J2'a-2''a = 14.1
3J4'a-5'a = 3.2, 3J4'a-5''a = 3.2 Hz, 1 H, H4'a), 3.93 (ddd, 3J4'b-5'b = 1.8, 3J4'b-3'b
2.5, 3J4'b-P = 4.5 Hz, 1 H, H4'b), 3.83 (ABX syst, 3J5'a-4'a = 3.1, 3J5''a-4'a = 3.1,
=
Hz, 1 H, H2'a), 2.44 (dddd, J6'b-7''b = 4.8 Hz, J6'b-5'b= 11.8, J6'b-7'b = 12.6,
3J6'b-6''b = 14.7 Hz, 1 H, H6'b), 2.43 (ddd, 3J2''a-3'a = 5.6, 3J2''a-1'a = 8.7, 3J2''a-2'a
= 14.1 Hz, 1 H, H2''a), 2.22 (ddd, 3J2'b-3'b = 2.9, 3J2'b-1'b = 6.0, 3J2'b-2''b = 13.5
3
3
3
3
3
3J5'a-5''a = 12.2 Hz, 2 H, H5'a, H5''a), 2.58 (ddd, J2'a-3'a = 1.8, J2'a-1'a = 5.8,
3J2'a-2''a = 14.1 Hz, 1 H, H2'a), 2.42 (ddd, 3J2''a-3'a = 5.7, 3J2''a-1'a = 8.8, 3J2''a-2'a
Hz, 1 H, H2'b), 2.17 (ddd, J2''b-3'b = 5.6, J2''b-1'b = 8.0, J2'b-2''b = 13.6, 1 H,
H2''b), 1.99 (d, 4J7-6 = 1.2 Hz, 3 H, H7b), 1.95 (dddd, 3J6''b-7''b = 1.7, 3J6''b-7'b
=
3
3
3
3
3
3
= 13.9 Hz, 1 H, H2''a), 2.39 (dddd, J6'b-7''b = 5.0, J6'b-5'b = 11.7, J6'b-7'b
=
=
3
3
3
3
3
3
4
13.0 Hz, J6'b-6''b = 14.3 Hz, 1 H, H6'b), 2.23 (ddd, J2'b-3'b = 3.1, J2''b-1'b
1.9, J6''b-5'b = 1.9, J6''b-6'b = 14.8, J6''b-P = 0.6 Hz, 1 H, H6''b), 1.89 (d, J7-6
= 1.2 Hz, 3 H, H7a) ppm. 13C NMR (125 MHz, CD3OD): δ = 166.5 (C4),
166.4 (C4), 152.60 (C2), 152.56 (C2), 137.9 (C6a), 137.3 (C6b), 112.7 (C5b),
112.1 (C5a), 88.7 (3J4'b-P = 7.5 Hz, C4'b), 87.3 (3J4'a-P = 5.3 Hz, C4'a), 86.4
(C1'a), 86.0 (C1'b), 81.5 (2J3'a-P = 4.0 Hz, C3'a), 80.7 (2J5'b-P = 9.8 Hz, C5'b),
3
3
3
6.1, J2'b-2''b = 13.3 Hz, 1 H, H2'b), 2.18 (ddd, J2''b-3'b = 5.9, J2''b-1'b = 8.0,
3J2''b-2'b = 13.3 Hz, 1 H, H2''b), 1.94 (d, 4J7-6 = 1.1 Hz, 3 H, H7b), 1.89 (d, 4J7-
6 = 1.1 Hz, 3 H, H7a), 1.87 (dddd, 3J6''b-7''b = 1.6, 3J6''b-5'b = 1.9, 3J6''b-7'b = 2.2,
3J6''b-6'b = 14.4 Hz, 1 H, H6''b) ppm.13C NMR (125 MHz, CD3OD): δ = 166.5
(C4a), 166.4 (C4b), 152.6 (C2), 152.5 (C2), 137.9 (C6a), 137.4 (C6b), 112.7
(C5b), 112.1 (C5a), 88.7 (3J4'b-P = 7.7 Hz, C4'b), 87.3 (3J4'a-P = 5.5 Hz, C4'a),
86.5 (C1'a), 86.1 (C1'b), 80.9 (2J5'b-P = 9.1 Hz, C5'b), 80.7 (2J3'a-P = 2.9 Hz,
C3'a), 73.1 (C3'b), 69.4 (2J7'b-P = 9.1 Hz, C7'), 63.0 (C5'a), 40.8 (C2'b), 39.5
(3J2'a-P = 4.8 Hz, C2'a), 29.1 (3J6'b-P = 4.0 Hz, C6'b), 12.8 (C7b), 12.6 (C7a).
31P NMR (202 MHz, CD3OD): δ = 60.3 ppm. HRMS (ESI): calcd for
C22H30N4O11PS 589.1369 [M+H]+; found 589.1379.
73.1 (C3'b), 69.2 (2J7'b-P = 9.8 Hz, C7'), 63.0 (C5'a), 40.7 (C2'b), 39.4 (3J2'a-P
=
4.8 Hz, C2'a), 29.2 (3J6'b-P = 6.3 Hz, C6'b), 13.0 (C7b), 12.6 (C7a) ppm. 31P
NMR (202 MHz, CD3OD): δ = 63.7 (JP-Se = 1006.2 Hz) ppm. MS (ESI) m/z
= 637.1 [M+H]+, 659.1 [M+Na]+. HRMS (ESI): calcd for C22H30N4O11PSe
636.0856 [M+H]+; found 636.0862.
α,β-seleno-D-CNA (SC,RP) (12b): Following the general procedure D
starting from 10b gave the product 12b (29%, 10 mg) which underwent
degradation during purification. 1H NMR (500 MHz, CD3OD): δ = 7.81 (d,
4J6-7 = 1.2 Hz, 1 H, H6a), 7.63 (d, 4J6-7 = 1.2 Hz, 1 H, H6b), 6.38 (dd, 3J1'b-2'b
= 5.9, 3J1'b-2''b = 8.4 Hz, 1 H, H1'b), 6.27 (dd, 3J1'a-2'a = 5.5, 3J1'a-2''a = 9.1 Hz,
α,β-thio-D-CNA (SC,RP) (12a): Following the general procedure D
starting from 10a gave the product 12a (93%, 16 mg). 1H NMR (500 MHz,
CD3OD): δ = 7.81 (d, 4J6-7 = 1.2 Hz, 1 H, H6a), 7.63 (d, 4J6-7 = 1.2 Hz, 1 H,
H6b), 6.38 (dd, 3J1'b-2'b = 6.0, 3J1'b-2''b = 8.3 Hz, 1 H, H1'b), 6.27 (dd, 3J1'a-2'a
=
1 H, H1'a), 5.54 (dddd, 3J3'a-4'a = 1.3, 3J3'a-2'a = 1.3, J3'a-2''a = 5.2, 3J3'a-P = 9.0
3
5.5, 3J1'a-2''a = 9.1 Hz, 1 H, H1'a), 5.44 (ddd 3J3'a-2'a = 1.2, 3J3'a-4'a = 1.6, 3J3'a-
2''a = 5.3, 3J3'a-P = 8.4 Hz, 1 H, H3'a), 4.90 (dddd, 3J5'b-4'b = 2.3, 3J5'b-6'b = 2.6,
3
3
3J5'b-6'b = 11.6, J5'b-P = 3.1 Hz, 1 H, H5'b), 4.66 (dddd, J7'b-6''b = 2.6 Hz,
3
3
3
3J7'b-7''b = 11.7 Hz, J7'b-6'b = 12.4, 3J7'b-P = 4.1 Hz, 1 H, H7'b), 4.45 (dddt,
3J7''b-6'b = 1.9, 3J7''b-6'b = 5.0, 3J7''b-7'b = 11.7 Hz, 3J7''b-P = 24.6 Hz, 1 H, H7''b),
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
3
5''a = 2.9 Hz, 1 H, H4'a), 4.00 (ddd, 3J4'b-5'b = 2.2, J4'a-3'b = 2.6, 3J4'b-P = 4.5
column (5µ, 30 mm × 150 mm) eluting with a mixture of EtOAc/petroleum
ether (6:4). 14b is unstable and was converted partially to its α,β-oxo-D-
CNA counterpart (3%, 38 mg). Data for 13b: 1H NMR (300 MHz, CDCl3):
δ = 9.23 (s, 1 H, NH), 9.10 (s, 1 H, NH), 7.68-7.62 (m, 5 H, Ph), 7.51 (d,
4J6-7 = 1.2 Hz, 1 H, H6), 7.44-7.23 (m, 16 H, H6, Ph), 6.83-6.80 (m, 4 H,
Hz, 1 H, H4'b), 3.82 (ABX syst, J5'a-4'a = 2.9, 3J5''a-4'a = 2.9, J5'a-5''a = 12.0
3
3
Hz, 2 H, H5'a, H5''a), 2.45 (m, 3J2'a-3'a = 1.2, 3J2'a-2''a = 14.3, 3J2'a-1'a = 5.4 Hz,
1 H, H2'a), 2.42 (dddd, 3J6'b-7''b = 5.0, 3J6'b-5'b = 11.5, 3J6'b-7'b = 12.8, 3J6'b-6''b
=
3
3
3
15.8 Hz, 1 H, H6'b), 2.38 (ddd, J2''a-3'a = 5.5, J2''a-1'a = 9.1, J2''a-2'a = 14.3
3
3
3
Hz, 1 H, H2''a), 2.26 (ddd, J2'b-3'b = 2.2, J2'b-1'b = 6.0, J2'b-2''b = 13.8 Hz, 1
Ph), 6.39 (dd, 3J1'b-2'b = 6.5, 3J1'b-2''b = 8.1 Hz, 1 H, H1'b), 6.35 (dd, 3J1'a-2'a
=
3
3
3
3
3
3
H, H2'b), 2.11 (ddd, J2''b-3'b = 6.0, J2''b-1'b = 8.4, J2''b-2'b = 13.9 Hz, 1 H,
H2''b), 1.95 (d, 4J7-6 = 1.1 Hz, 3 H, H7b), 1.95 (dddd, 3J6''b-7''b = 1.6, 3J6''b-7'b
5.4, J1'a-2''a = 9.1 Hz, 1 H, H1'a), 5.46 (dddd, J3'a-2'a = 1.4, J3'a-4'a = 1.6,
3
=
3J3'a-2''a = 5.2, J3'a-P = 10.1 Hz, 1 H, H3'a), 4.58 (m, 2 H, H5'b, H3'b), 4.31
2.4, 3J6''b-5'b = 2.4, 3J6''b-6'b = 15.8 Hz, 1 H, H6''b), 1.87 (d, 4J7-6 = 1.2 Hz, 3 H,
H7a) ppm. 13C NMR (125 MHz, CD3OD): δ = 166.5 (C4), 166.4 (C4), 152.5
(C2b), 152.2 (C2a), 137.7 (C6a), 137.3 (C6b), 112.3 (C5b), 111.9 (C5a), 88.7
(3J4'b-P = 9.1 Hz, C4'b), 87.2 (3J4'a-P = 7.4 Hz, C4'a), 86.8 (C1'b), 86.1 (C1'a),
83.5 (C3'a), 80.3 (2J5'b-P = 5.1 Hz, C5'b), 73.4 (C3'b), 68.5 (2J7'b-P = 4.6 Hz,
C7'), 63.0 (C5'a), 41.2 (C2'b), 40.3 (3J2'a-P = 4.3 Hz, C2'a), 29.7 (3J6'b-P = 5.5
Hz, C6'b), 13.1 (C7b), 12.6 (C7a) ppm. 31P NMR (202 MHz, CD3OD): δ =
70.7 (JP-Se = 954 Hz) ppm. MS (ESI) m/z (%) = 637.08 [M+H]+. HRMS
(ESI): calcd for C22H30N4O11PSe 636.0856 [M+H]+; found 636.0873.
(dddd, J7'b-6''b = 1.9, J7'b-7''b = 10.9, 3J7'b-6'b = 12.8, J7'b-P = 2.6 Hz, 1 H,
H7'b), 4.18 (td, 3J4'a-3'a = 1.5, 3J4'a-5'a = 2.5, 3J4'a-5''a = 2.5 Hz, 1 H, H4'a), 4.05-
3.98 (dddd, 3J7''b-6''b = 1.9, 3J7''b-6'b = 4.4, 3J7''b-7'b = 10.9, 3J7''b-P > 20 Hz, 1 H,
H7''b), 3.90 (ddd, 3J4'b-3'b = 1.6, 3J4'b-5'b = 4.2, 3J4'b-P = 3.0 Hz, 1 H, H4'b), 3.77
(s, 6 H, OMe), 3.44 (A of an ABX syst, 3J5'a-4'a = 2.5, 3J5'a-5''a = 10.8 Hz, 1 H,
3
3
3
3
3
H5'a), 3.35 (B of an ABX syst, J5''a-4'a = 2.5, J5''a-5'a = 10.8 Hz, 1 H, H5''a),
2.39 (dd app, 3J2'a-3'a = 1.4, 3J2'a-1'a = 5.4, 3J2'a-2''a = 13.8 Hz, 1 H, H2'a), 2.28
3
3
3
(ddd, J2''a-3'a = 5.4, J2''a-1'a = 9.2, J2''a-2'a = 13.9 Hz, 1 H, H2''a), 2.20 (ddd,
3J2'b-3'b = 2.3, 3J2'b-1'b = 6.6, 3J2'b-2''b = 14.0 Hz, 1 H, H2'b), 2.16 (ddd, 3J2''b-3'b
= 5.2, 3J2''b-1'b = 8.0, 3J2''b-2'b = 13.6 Hz, 1 H, H2''b), 1.87 (d, 4J7-6 = 0.9 Hz, 3
H, H7), 1.53-1.41 (m, 2 H, 2 × H6'b), 1.41 (d, 4J7-6 = 1.1 Hz, 3 H, H7), 1.06
(s, 9 H, tBu) ppm. 13C NMR (75 MHz, CDCl3): δ = 164.0 (C4), 164.9 (C4),
158.9 (CPh), 150.9 (C2), 150.8 (C2), 144.2 (CPh), 136.1, 136.0 (CPh), 135.3,
135.1, 135.0 (CPh, C6a, C6b), 133.0, 132.9, 130.32, 130.30, 130.2, 128.3,
128.2, 128.4, 127.4, 113.6 (CPh), 112.2 (C5), 111.6 (C5), 88.3 (3J4'b-P = 7.8
Hz, C4'b), 87.5 (CPh), 85.8 (C1'b), 84.7 (3J4'a-P = 5.8 Hz, C4'a), 84.5 (C1'a),
80.8 (2J3'a-P = 2.4 Hz, C3'a), 79.0 (2J5'b-P = 9.7 Hz, C5'b), 72.9 (C3'b), 67.5
5'-O-Dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β-thio-D-CNA
(RC,RP) (13a) and 5'-O-dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-
α,β-thio-D-CNA (RC,SP) (14a): Following the general procedure
A
starting from 5 gave the product 13a (42%, 457 mg) and 14a (9%, 94
mg). Data for 13a: 1H NMR (300 MHz, CDCl3): δ = 8.95 (s, 1 H, NH), 8.87
4
(s, 1 H, NH), 7.68-7.62 (m, 4 H, Ph), 7.50 (bd, J6-7 = 0.9 Hz, 1 H, H6),
7.43-7.22 (m, 16 H, Ph and H6), 6.82 (bd, 4 H, Ph), 6.37 (dd, 3J = 6.3, 8.1
Hz, 1 H, H1'), 6.34 (dd, 3J = 5.4, 9.0 Hz, 1 H, H1'), 5.50 (dd, 3J = 5.1, 9.3
Hz, 1 H, H3'a), 4.58 (m, 1 H, H3'b), 4.52 (ddd, 3J = 2.1, 4.2, 12.3 Hz, 1 H,
H5'b), 4.24 (m, 1 H, H7'b), 4.16 (bq, 3J = 3.0 Hz, 1 H, H4'a), 4.09-3.97 (m, 1
H, H7'b), 3.94 (ddd, 3J = 1.5, 4.2, 9.0 Hz, 1 H, H4'b), 3.41 and 3.35 (AB
part of an ABX syst, J = 2.4, 2.7, 10.8 Hz, 2 H, H5'a), 2.38 (A part of an
ABX syst, 3J = 5.1, 13.8 Hz, 1 H, H2'), 2.30-2.10 (m, 3 H, H2'), 1.86 (d, 4J7-
(2J7'b-P = 10.5 Hz, C7'), 63.6 (C5'a), 55.4 (OMe), 39.6 (C2'b), 38.7 (3J2'a-P
=
3.2 Hz, C2'a), 27.07 (CMe3), 27.01 (C6'b), 19.3 (CMe3) 12.7 (C7b), 11.9
(C7a) ppm. 31P NMR (120 MHz, CDCl3): δ = 64.5 (JP-Se = 1015.3 Hz) ppm.
HRMS (ESI): calcd for C59H65N4O13PNaSeSi 1198.3164 [M+Na]+; found
1198.3181. Data for 14b: 1H NMR (300 MHz, CDCl3): δ = 8.49 (s, 1 H,
NH), 8.39 (s, 1 H, NH), 7.65-7.61 (m, 5 H, Ph), 7.58 (d, 4J6-7 = 0.9 Hz, 1 H,
H6), 7.41-7.17 (m, 19 H, H6, Ph), 6.83-6.80 (m, 4 H, Ph), 6.40 (m, 2 H,
= 0.9 Hz, 3 H, H7), 1.42 (m, 4 H, H7 and H6'b), 1.20 (m, 1 H, H6'b), 1.06
6
3
3
(s, 9 H, tBu) ppm. 13C NMR (75 MHz, CDCl3): δ = 164.1, 158.8, 150.9,
144.1, 136.0, 135.8, 135.2, 135.0, 134.9, 132.9, 132.8, 130.2, 130.0,
128.1, 128.0, 127.3, 113.4, 112.1, 111.5, 88.2, 87.4, 85.6, 84.7, 84.5,
79.7, 79.2, 72.8, 67.7, 63.5, 55.3, 39.6, 38.7, 26.9, 19.1, 12.6, 11.8 ppm.
31P NMR (120 MHz, CDCl3): δ = 59.9 ppm. HRMS (ESI): calcd for
C59H65N4O13PNaSSi 1151.3680 [M+Na]+; found 1151.3698. Data for 14a:
1H NMR (300 MHz, CDCl3): δ = 9.18 (s, 1 H, NH), 9.04 (s, 1 H, NH), 7.67-
7.58 (m, 6 H, Ph and H6), 7.43-7.19 (m, 15 H, Ph and H6), 6.81 (bd, 4 H,
Ph), 6.42 (t, 3J = 4.7 Hz, 1 H, H1'), 6.39 (t, 3J = 4.8 Hz, 1 H, H1'), 5.50 (dd,
3J = 5.7, 9.9 Hz, 1 H, H3'a), 4.60 (qd, 3J = 2.1, 5.7, 11.7 Hz, 1 H, H5'b),
4.47 (d, 3J = 5.4 Hz, 1 H, H3’b), 4.29 (m, 3J = 3.0, 11.4, J7'b-P = 7.5 Hz, 1 H,
H7'b), 4.03-3.95 (m, 1 H, H7’b), 4.03 (bs, 1 H, H4’a), 3.90 (m, 3J = 0.8, 2.4,
3J4'b-P = 4.5 Hz, 1 H, H4’b), 3.76 (s, 6H, OMe), 3.33 (bs, 2 H, H5'a), 2.51 (A
part of an ABX syst, 3J = 5.4, 14.1 Hz, 1 H, H2'), 2.41-2.29 (m, 2 H, H2'),
1.92-1.81 (m, 2 H, H2' and H6'b), 1.71 (d, 4J7-6 = 1.2 Hz, 3 H, H7), 1.40 (d,
H1'a, H1'b), 6.41 (dd, J1'a-2'a = 5.4, J1'a-2''a = 8.4 Hz, 1 H, H1'a), 6.39 (dd,
3J1'b-2'b = 5.3, 3J1'b-2''b = 8.6 Hz, 1 H, H1'b), 5.64 (ddd, 3J = 1.4, 2.5, 5.0, 3J3'a-
2
P = 10.6 Hz, 1 H, H3'a), 4.65 (dq, 3J = 2.7, 2.7, 11.4, J5'b-P = 2.7 Hz, 1 H,
H5'b), 4.47 (dd app, 3J = 1.2, 1.5 Hz, 4.9 Hz, 1 H, H3'b), 4.32 (dddd, 3J7'b-6''b
= 3.2, 3J7'b-P = 5.2, 3J7'b-7''b = 10.9, 3J7'b-6'b = 12.4 Hz, 1 H, H7'b), 4.05 (br dd,
3J4'a-5'a = 1.7, 3J4'a-5''a = 1.7, 3J4'a-3'a = 2.4 Hz, 1 H, H4'a), 4.02-3.92 (m, 1 H,
H7''b), 3.90 (ddd, 3J4'a-3'b = 1.5, 3J4'b-5'b = 2.9, 3J4'b-P = 4.0 Hz, 1 H, H4'b), 3.76
3
3
(s, 6 H, OMe), 3.35 (ABX syst, J5'a-4'a = 2.1, 3J5''a-4'a = 2.1, J5'a-5''a = 10.6
Hz, 2 H, H5'a, H5''a), 2.52 (dd app, 3J2'a-3'a = 1.3, 3J2'a-1'a = 5.4, 3J2'a-2''a = 13.9
3
3
3
Hz, 1 H, H2'a), 2.40 (ddd, J2''a-3'a = 5.3, J2''a-1'a = 8.4, J2''a-2'a = 14.0 Hz, 1
H, H2''a), 2.33 (ddd, 3J2'b-3'b = 1.3, 3J2'b-1'b = 5.3, 3J2'b-2''b = 13.1 Hz, 1 H, H2'b),
3
3
3
1.85 (ddd, J2''b-3'b = 4.4, J2''b-1'b = 8.6, J2''b-2'b = 13.1 Hz, 1 H, H2''b), 1.39
(d, 4J7-6 = 0.9 Hz, 3 H, H7), 1.18-1.10 (m, 2 H, 2 × H6'b), 1.44 (d, 4J7-6 = 0.9
Hz, 3 H, H7), 1.04 (s, 9 H, tBu) ppm. 13C NMR (75 MHz, CDCl3): δ =
166.59 (C4), 166.57 (C4), 159.03, 159.02 (CPh), 150.4 (C2), 152.3 (C2),
144.2 (CPh), 136.1, 136.0 (CPh), 135.5 (C6), 135.4 (C6), 135.2, 135.1,
133.1, 132.8, 130.5, 130.2, 128.34, 128.3, 128.2, 127.5, 113.7 (CPh),
112.0 (C5), 111.6 (C5), 88.3 (3J4'b-P = 8.8 Hz, C4'b), 85.9 (C1'b), 85.3 (3J4'a-P
= 6.2 Hz, C4'a), 84.6 (C1'a), 81.7 (2J3'a-P = 1.2 Hz, C3'a), 79.2 (2J5'b-P = 4.7
Hz, C5'b), 73.0 (C3'b), 66.9 (2J7'b-P = 5.6 Hz, C7'), 63.7 (C5'a), 55.5 (OMe),
40.7 (C2'b), 39.4 (3J2'a-P = 4.7 Hz, C2'a), 27.1 (CMe3, C6'b), 19.3 (CMe3)
4J7-6 = 1.2 Hz, 3 H, H7), 1.18 (m, 1 H, H6'), 1.05 (s, 9 H, tBu) ppm.13
C
NMR (75 MHz, CDCl3): δ = 158.8, 150.7, 150.5, 144.1, 135.9, 135.8,
135.1, 134.9, 130.3, 130.0, 129.2, 128.1, 128.0, 127.8, 111.9, 111, 5,
88.3, 87.4, 86.1, 85.7, 85.1, 84.5, 80.7, 79.1, 72.9, 66.8, 63.5, 55.3, 40.5,
39.3, 26.9, 19.1, 12.5, 11.7 ppm. 31P NMR (121 MHz, CDCl3): δ = 65.2
ppm. HRMS (ESI): calcd for C59H65N4O13PNaSSi 1151.3680 [M+Na]+;
found 1151.3673.
12.7 (C7b), 11.8 (C7a) ppm. 31P NMR (121 MHz, CDCl3): δ = 69.6 (JP-Se
=
972.2 Hz) ppm. HRMS (ESI): calcd for C59H65N4O13PNaSeSi, 1198.3164
[M+Na]+; found 1198.3172.
5'-O-Dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β-seleno-D-CNA
(RC,RP) (13b) and 5'-O-dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-
α,β-seleno-D-CNA (RC,SP) (14b): Following the general procedure B
starting from 5 gave the product 13b (52%, 813 mg) and 14b (5%, 79
mg) after a second purification by direct phase HPLC using a Sunfire C18
5'-O-Dimethoxytrityl-α,β-thio-D-CNA (RC,RP) (15a): Following the
general procedure C starting from 13a gave the product 15a (61%, 93
mg). 1H NMR (300 MHz, MeOD): δ = 7.63 (d, J = 1.2 Hz, 1 H, H6a), 7.58
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
(d, J = 1.2 Hz, 1 H, H6b), 7.44-7.27 (m, 9 H, Ph), 6.87 (d, 3J = 9.0 Hz, 4 H,
Ph), 6.38-6.31 (m, 2 H, H1'b, H1'a), 5.48 (m, 3J = 2.7, 2.7, 6.2, J3'a-P = 8.7
Hz, 1 H, H3'a), 4.89 (m, 1 H, H5'b), 4.60 (ddd, 3J = 3.1, 4.0, 5.9 Hz, 1 H,
H3'b), 4.49 (ddd, 3J7'b-6''b = 2.2, 3J = 12.1, 13.3 Hz, 1 H, H7'b), 4.42-4.34 (m,
1 H, H7''b), 4.30 (dd, 3J = 2.9, 5.5 Hz, 1 H, H4'a), 3.96 (ddd, 3J = 3.2, 3.2,
3J4'b-P = 3.4 Hz, 1 H, H4'b), 3.78 (s, 6 H, OMe), 3.45 (br. t, 3J = 2.4 Hz, 2 H,
111.6 (C5), 87.6 (C4'b), 87.5 (CPh), 85.7 (C1'b), 84.7 (C4'a), 84.6 (C1'a), 80.6
(C3'a), 79.4 (C5'b), 70.8 (C3'b), 63.6 (C7'), 60.6 (C5'a), 55.5 (OMe), 39.5
(C2'b), 38.9 (C2'a), 27.8 (C6'b), 12.8 (C7b), 11.9 (C7a) ppm. 31P NMR (121
MHz, CDCl3): δ = 64.8 (JP-Se= 1007.2 Hz) ppm. HRMS (ESI): calcd for
C43H47N4O13PNaSe, 961.1945 [M+Na]+; found 961.1934.
3
3
3
3
2 × H5'a), 2.23 (ddd, J2'a-3'a = 2.6, J2'a-1'a = 6.0, J2'a-2''a = 14.2 Hz, 1 H,
5'-O-Dimethoxytrityl-α,β-seleno-D-CNA (RC,SP) (16b): Following the
general procedure C starting from 14b (40 mg, 0.034 mmol) gave the
product 16b as a yellow oil. The crude was immediatly engaged in the
next step.
3
3
3
H2'a), 2.06 (ddd, J2''a-3'a = 6.2, J2''a-1'a = 8.0, J2''a-2'a = 14.3 Hz, 1 H, H2''a),
2.32-2.19 (m, 3 H, 2 × H2'b, H6'b), 1.90 (d, 4J7-6 = 1.1 Hz, 3 H, H7b), 1.88 (m,
4
1 H, H6''b), 1.41 (d, J7-6 = 1.1 Hz, 3 H, H7a) ppm. 13C NMR (75 MHz,
MeOD): δ = 166.3 (C4a), 166.2 (C4b), 160.5 (CPh), 152.5 (C2b), 152.3 (C2a),
145.9 (CPh), 137.7 (C6b), 137.3 (C6a), 136.8, 136.7 (CPh), 131.5, 129.5,
129.2, 128.4, (CHPh), 114.5 (CHPh), 112.22 (C5), 112.19 (C5), 88.9 (3J4'b-P
= 8.3 Hz, C4'b), 88.6 (CPh), 86.0 (C1'b, C4'a, C1'a), 81.0 (2J5'b-P = 8.7 Hz, C5'b),
80.1 (2J3'a-P = 4.3 Hz, C3'a), 71.0 (C3'b), 69.6 (2J7'b-P = 8.5 Hz, C7'), 64.5
α,β-thio-D-CNA (RC,RP) (17a): Following the general procedure D
starting from 15a gave the product 17a (50%, 11 mg). 1H NMR (400 MHz,
4
4
CD3OD, 40°C): δ = 7.78 (d, J6-7 = 1.2 Hz, 1 H, H6a), 7.55 (d, J6-7 = 1.2
Hz, 1 H, H6b), 6.35 (m, 3J1'a-2'a= 5.7, 3J1'b-2'b = 6.6, 3J1'b-2''b = 7.5 Hz, 3J1'a-2''a
(C5'a), 55.9 (OMe), 40.8 (C2'b), 39.7 (3J2'a-P = 4.0 Hz, C2'a), 28.7 (3J6'b-P
=
= 8.7 Hz, 2 H, H1'b, H1'a), 5.20 (dddd, 3J3'a-4'a = 2.0, 3J3'a-2'a = 2.0, 3J3'a-2''a
6.0, 3J3'a-P = 9.0 Hz, 1 H, H3'a), 4.88 (dddd, 3J5'b-6''b = 2.2, 3J5'b-4'b = 3.4, 3J5'b-
=
7.1 Hz, C6'b), 13.1 (C7b), 12.3 (C7a) ppm. 31P NMR (121 MHz, CDCl3): δ =
60.7 ppm. MS (Malfi Tof) m/z = 913.5 [M+Na]+.
6'b = 12.0, 3J5'b-P = 1.6 Hz, 1 H, H5'b), 4.61-4.55 (A of ABX(Y) syst, 3J7'b-6'b
=
2.6, J7'b-7''b = 11.7, 3J7'b-6'b = 12.4, 3J7'b-P = 2.4 Hz, 1 H, H7'b), 4.48 (A of
3
3
5'-O-Dimethoxytrityl-α,β-thio-D-CNA (RC,SP) (16a): Following the
general procedure C starting from 14a gave the product 16a (86%, 63
mg). 1H NMR (300 MHz, MeOD): δ = 7.65 (d, J = 1.2 Hz, 1 H, H6a), 7.49
(d, J = 1.2 Hz, 1 H, H6b), 7.43-7.24 (m, 9 H, Ph), 6.88 (d, 3J = 8.6 Hz, 4 H,
AMX(Y) syst, 3J3'b-2'b = 2.3, 3J3'b-4'b = 3.1, J3'b-2''b = 6.0 Hz, 1 H, H3'b), 4.44
3
3
(dddd, J7''b-6''b = 1.6, J7''b-6'b = 4.8, 3J7''b-7'b = 11.3, 3J7''b-P = 24.3 Hz, 1 H,
H7''b), 4.27 (td, 3J4'a-3'a = 2.1, 3J4'a-5'a = 3.1, 3J4'a-5''a = 3.1 Hz, 1 H, H4'a), 3.92
3
(ddd, 3J4'b-3'b = 3.0, J4'b-5'b = 3.5, 3J4'b-P = 3.5 Hz, 1 H, H4'b), 3.82 (ABX,
Ph), 6.33 (dd, 3J1'b-2'b = 6.0, 3J1'b-2'b = 8.1 Hz, 1 H, H1'b), 6.27 (dd, 3J1'a-2'a
5.8, 3J1'a-2''a = 8.4 Hz, 1 H, H1'a), 5.48 (m, 1 H, H3'a), 4.91 (m, 3J = 2.6, 2.9,
=
3J5'a-4'a = 3.0, 3J5''a-4'a = 3.0, J5'a-5''a = 11.9 Hz, 2 H, H5'a, H5''a), 2.56 (ddd,
3
3J2'a-3'a = 1.8, 3J2'a-1'a = 5.7, 3J2'a-2''a = 14.1 Hz, 1 H, H2'a), 2.35 (ddd, 3J2''a-3'a
= 6.0, 3J2''a-1'a = 8.7, 3J2''a-2''b = 14.2 Hz, 1 H, H2''a), 2.31 (m, 1 H, H2'b), 2.25
(m, 1 H, H2''b), 2.23 (dddd, 3J6'b-7''b = 4.9, 3J6'b-7'b = 11.8, 3J6'b-5'b = 11.8, 3J6'b-
3
3
3
11.6 Hz, 1 H, H5'b), 4.59 (m, J7'b-6''b = 3.9, J7'b-7''b = 11.5, J7'b-6'b = 11.5,
3J7'b-P = 5.1 Hz, 1 H, H7'b), 4.47 (ddd, 3J = 1.8, 2.1, 5.9 Hz, 1 H, H3'b), 4.39-
3
3
3
3
3
3
4.32 (m, J7''b-6'b = 2.1, J7''b-6'b = 4.7, J7''b-7'b = 11.2, J7''b-P = 23.7 Hz, 1 H,
H7''b), 4.25 (q, 3J = 2.3 Hz, 1 H, H4'a), 3.96 (dd, 3J = 2.1, 3.2 Hz, 1 H, H4'b),
3.78 (s, 6 H, OMe), 3.43 (br. t, 3J = 2.6 Hz, 2 H, 2 × H5'a), 2.23 (ddd, 3J2'a-
3'a = 2.0, 3J2'a-1'a = 5.9, 3J2'a-2''a = 13.6 Hz, 1 H, H2'a), 2.06 (ddd, 3J2''a-3'a = 6.0,
3J2''a-1'a = 8.4, 3J2''a-2'a = 13.6 Hz, 1 H, H2''a), 2.15-1.90 (m, 4 H, 2 × H2'b, 2 ×
6''b = 14.4 Hz, 1 H, H6'b), 1.96 (m, J6''b-7''b = 1.7, J6''b-6'b= 14.5 Hz, 1 H,
4
4
H6''b), 1.93 (d, J7-6 = 1.2 Hz, 3 H, H7b), 1.88 (d, J7-6 = 1.2 Hz, 3 H, H7a
)
ppm. 13C NMR (125 MHz, CD3OD): δ = 166.43 (C4a), 166.37 (C4b),
152.51 (C2), 152.46 (C2), 138.0 (C6a), 137.7 (C6b), 112.3 (C5b), 112.1
(C5a), 89.1 (3J4'b-P = 8.3 Hz, C4'b), 87.4 (3J4'a-P = 6.3 Hz, C4'a), 86.6 (C1'a),
86.1 (C1'b), 81.1 (2J5'b-P = 9.7 Hz, C5'b), 80.8 (2J3'a-P = 4.4 Hz, C3'a), 71.3
(C3'b), 69.8 (2J7'b-P = 9.2 Hz, C7'), 62.8 (C5'a), 40.7 (C2'b), 39.5 (3J2'a-P = 4.1
Hz, C2'a), 28.7 (3J6'b-P = 6.0 Hz, C6'b), 13.0 (C7b), 12.7 (C7a) ppm. 31P NMR
(202 MHz, CD3OD): δ = 60.4 ppm. HRMS (ESI): calcd for C22H30N4O11PS
589.1369 [M+H]+; found 589.1374.
4
4
H6'b), 1.78 (d, J7-6 = 1.1 Hz, 3 H, H7b), 1.42 (d, J7-6 = 1.1 Hz, 3 H, H7a
)
ppm. 13C NMR (75 MHz, MeOD): δ = 164.1 (C4), 163.9 (C4), 159.0 (CPh),
151.1 (C2), 150.7 (C2), 144.3 (Cq,Ph), 135.4 (C6), 135.4 (C6), 135.3, 135.2
(Cq,Ph), 130.22, 130.19, 128.3, 128.2, 127.5 (CHPh), 113.6 (CHPh), 112.3
(C5), 111.7 (C5), 87.6 (CPh), 87.5 (C4'b), 85.3 (C1'a), 87.4 (C1'b), 87.4 (C4'a),
80.9 (C3'a), 79.5 (C5'b), 71.3 (C3'b), 66.9 (C7'), 63.8 (C5'a), 55.5 (OMe), 40.5
(C2'b), 39.1 (C2'a), 28.1 (C6'), 14.4 (C7b), 12.8 (C7a) ppm. 31P NMR (100
MHz, CDCl3): δ = 62.8 ppm. MS (Malfi Tof) m/z = 913.4 [M+Na]+, 929.4
[M+K]+.
α,β-thio-D-CNA (RC,SP) (18a): Following the general procedure D
starting from 16a gave the product 18a (50%, 13 mg). 1H NMR (500 MHz,
CD3OD): δ = 7.79 (d, 4J6-7 = 1.0 Hz, 1 H, H6a), 7.57 (d, 4J6-7 = 1.0 Hz, 1 H,
3
3
3
3
H6b), 6.31-6.27 (m, J1'a-2'a = 5.5, J1'a-2''a = 8.4, J1'b-2'b = 5.8, J1'b-2''b = 8.4
Hz, 2 H, H1'a, H1'b), 5.34 (ddt, 3J3'a-4'a = 1.8, 3J3'a-2'a = 1.8, 3J3'a-2''a = 5.7, 3J3'a-
P = 8.8 Hz, 1 H, H3'a), 4.94 (dddd, 3J5'b-4'b = 2.8, 3J5'b-6'b = 2.8, 3J5'b-6'b = 11.8,
5'-O-Dimethoxytrityl-α,β-seleno-D-CNA (RC,RP) (15b): Following the
general procedure C starting from 13b gave the product 15b (71%, 463
4
3
3
mg). 1H NMR (300 MHz, CDCl3): δ = 7.56 (d, J6-7 = 0.9 Hz, 1 H, H6),
3J5'b-P = 2.8 Hz, 1 H, H5'b), 4.62 (ddt, J7'b-6'b = 2.8, J7'b-6'b = 11.8, 3J7'b-7''b
=
7.39-7.20 (m, 10 H, H6, Ph), 6.82 (d, 3J = 8.9 Hz, 4 H, Ph), 6.42 (dd, 3J1'b-
2'b = 5.3, 3J1'b-2''b = 9.1 Hz, 1 H, H1'b), 6.14 (t, 3J1'a-2'a = 6.8, 3J1'a-2''a = 6.8 Hz,
1 H, H1'a), 5.51 (ddd, 3J = 0.8, 5.3, 3J3'a-P = 10.2 Hz, 1 H, H3'a), 4.86 (ddd,
11.8, 3J7'b-P = 5.0 Hz, 1 H, H7'b), 4.54 (ddt, 3J3'b-2'b = 2.0, 3J3'b-4'b = 2.0, J3'b-
3
3
3
3
= 5.7 Hz, 1 H, H3'b), 4.49 (dddd, J7''b-6''b = 2.0, J7''b-6'b = 4.9, J7''b-7'b
=
2''b
11.5, 3J7''b-P = 23.3 Hz, 1 H, H7''b), 4.19 (td, 3J4'a-3'a = 1.8, 3J4'a-5'a = 2.9, 3J4'a-
3
3
3J5'b-6''b = 1.6, 3J5'b-4'b = 4.9, 3J5'b-6'b = 11.6, J5'b-P < 1 Hz, 1 H, H5'b), 4.72
5''a = 2.9 Hz, 1 H, H4'a), 4.00 (ddd, 3J4'b-3'b = 2.0, J4'b-5'b = 3.0, 3J4'b-P = 3.5
3
3
3
3
(ddd, 3J = 3.3, 4.4, 7.1 Hz, 1 H, H3'b), 4.55 (dddd, J7'b-6''b = 2.1, J7'b-7''b
=
Hz, 1 H, H4'b), 3.77 (ABX syst, J5'a-4'a = 3.1, 3J5''a-4'a = 3.1, J5'a-5''a = 12.3
11.7, 3J7'b-6'b = 11.7, J7'b-P < 1 Hz, 1 H, H7'b), 4.33 (m, J7''b-6''b = 1.5, J7''b-
Hz, 2 H, H5'a, H5''a), 2.48 (ddd, 3J2'a-3'a = 1.8, 3J2'a-1'a = 5.7, 3J2'a-2''a = 14.1 Hz,
3
3
3
3
3
3
3
3
6'b = 4.1, J7''b-7'b = 11.3, J7''b-P > 20 Hz, 1 H, H7''b), 4.26 (td, J4'a-3'a= 1.5,
3J4'a-5'a = 2.5, 3J4'a-5''a = 2.5 Hz, 1 H, H4'a), 3.88 (ddd, J4'b-3'b = 3.6, 3J4'b-5'b
1 H, H2'a), 2.39 (ddd, J2''a-3'a = 5.8, J2''a-1'a = 8.6, J2''a-2'a = 14.3 Hz, 1 H,
3
3
3
3
=
H2''a), 2.29 (ddd, J2'b-3'b = 1.9, J2'b-1'b = 5.8, J2'b-2''b = 13.6 Hz, 1 H, H2'b),
4.6, 3J4'b-P < 1 Hz, 1 H, H4'b), 3.76 (s, 6 H, OMe), 3.46 (A of an ABX syst,
3J5'a-4'a = 2.6, 3J5'a-5''a = 10.4 Hz, 1 H, H5'a), 3.38 (B of an ABX syst, 3J5''a-4'a
= 2.5, 3J5''a-4'a = 10.4 Hz, 1 H, H5''a), 2.71-2.60 (m, 2 H, 2 × H2'a), 2.51-2.18
2.23 (dddd, J6'b-7''b = 4.9, J6'b-7'b = 11.8, J6'b-5'b = 11.8, J6'b-6''b = 14.4 Hz,
3
3
3
3
3
3
3
1 H, H6'b), 2.14 (ddd, J2''b-3'b = 5.9, J2''b-1'b = 8.4, J2''b-2'b = 13.6 Hz, 1 H,
3
3
3
3
H2''b), 2.01 (dddd, J6''b-7''b = 2.0, J6''b-7'b = 3.0, J6''b-5'b = 3.0, J6''b-6'b = 14.4
Hz, 1 H, H6''b), 1.93 (bs, 3 H, H7b), 1.88 (bs, 3 H, H7a) ppm. 13C NMR (125
MHz, CD3OD): δ = 166.7 (C4), 166.6 (C4), 152.6 (C2a), 152.5 (C2b), 138.0
(C6b), 137.5 (C6a), 112.1 (C5), 112.0 (C5), 89.5 (3J4'b-P = 8.3 Hz, C4'b), 87.4
(3J4'a-P = 6.1 Hz, C4'a), 86.9 (C1'a), 86.4 (C1'b), 81.6 (2J3'a-P = 5.5 Hz, C3'a),
(m, 4 H, 2 × H2'a, 2 × H6'b), 1.89 (d, 4J7-6 = 0.9 Hz, 3 H, H7), 1.42 (d, 4J7-6
=
0.8 Hz, 3 H, H7) ppm. 13C NMR (75 MHz, CDCl3): δ = 164.3 (C4), 164.2
(C4), 158.9 (CPh), 151.2 (C2), 151.1 (C2), 144.3 (CPh), 135.3, 135.2 (CPh),
135.3, 135.1 (C6, C6), 130.2, 128.3, 128.2, 127.4, 113.6 (CPh), 112.1 (C5),
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
80.9 (2J5'b-P = 5.5 Hz, C5'b), 71.9 (C3'b), 68.5 (2J7'b-P = 5.8 Hz, C7'), 62.8
(C5'a), 41.3 (C2'b), 39.8 (3J2'a-P = 4.7 Hz, C2'a), 29.2 (3J6'b-P = 6.5 Hz, C6'b),
12.9 (C7b), 12.6 (C7a). 31P NMR (202 MHz, CD3OD): δ = 64.2 ppm. HRMS
(ESI): calcd for C22H30N4O11PS 589.1369 [M+H]+; found 589.1379.
5'-O-Dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β,γ-thio-D-CNA
cis (19a) and 5'-O-dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β,γ-
thio-D-CNA trans (20a): Following the general procedure A starting from
2 gave the product 19a (32%, 345 mg) and product 20a (38%, 410 mg).
Data for 19a: 1H NMR (300 MHz, CDCl3): δ = 9.51 (bs, 2 H, NH), 7.71-
7.60 (m, 5 H, Ph and H6a), 7.50-7.42 (m, 8 H, Ph), 7.37-7.32 (m, 7 H, Ph),
7.05 (s, 1 H, H6b), 6.90-6.87 (d, 3J = 9.0 Hz, 4 H, Ph), 6.53-6.49 (dd, 3J =
5.7, 8.7 Hz, 1 H, H1'a), 6.08-6.04 (m, 1 H, H1'b), 5.48-5.43 (m, 1 H, H3'a),
4.69-4.63 (m, 1 H, H5''b), 4.58-4.47 (m, 2 H, H3'b and H5''b), 4.28 (m, 1 H,
H4'a), 4.05-3.94 (m, 2 H, H5'b), 3.82 (s, 6 H, OMe), 3.57-3.47 (m, 2 H, H5'a),
2.67-2.61 (m, 1 H, H2'a), 2.57-2.45 (m, 2 H, H2'a and H2'b), 2.43-2.32 (m, 1
α,β-seleno-D-CNA (RC,RP) (17b): Following the general procedure D
starting from 15b gave the product 17b (56%, 13 mg). 1H NMR (500 MHz,
CD3OD): δ = 7.81 (d, 4J6-7 = 1.1 Hz, 1 H, H6a), 7.56 (d, 4J6-7 = 1.1 Hz, 1 H,
H6b), 6.36 (dd, 3J1'b-2'b = 6.6, 3J1'b-2''b = 7.3 Hz, 1 H, H1'b), 6.33 (dd, 3J1'a-2'a
5.8, J1'a-2''a = 8.6 Hz, 1 H, H1'a), 5.25 (dddt, 3J3'a-2'a = 1.8, J3'a-4'a = 2.2,
=
3
3
3J3'a-2''a = 5.8, 3J3'a-P = 9.8 Hz, 1 H, H3'a), 4.95 (dddd, 3J5'b-6''b = 2.3, 3J5'b-4'b
3.3, 3J5'b-6'b = 12.1, 3J5'b-P = 1.4 Hz, 1 H, H5'b), 4.66 (dddd, J7'b-6''b = 2.1,
=
3
H, H2'b), 1.84 (s, 3 H, H7b), 1.50 (s, 3 H, H7a), 1.14 (s, 9 H, tBu) ppm. 13
C
3J7b'-7b'' = 11.4, 3J7'b-6'b = 12.0, 3J7'b-P = 2.6 Hz, 1 H, H7'b), 4.60 (td, 3J3'b-4'b
=
NMR (75 MHz, CDCl3): δ = 164.2 (C4a), 164.0 (C4b), 158.8 (CPh), 150.5
(C2a), 149.7 (C2b), 144.2 (CPh), 138.3 (C6b), 135.9 (C6a), 135.8, 135.3,
135.2, 135.1, 132.4, 132.0, 130.7, 130.5, 130.1, 128.3, 128.2, 128.1,
127.3, 113.5, 113.3 (CPh), 111.7 (C5a), 110.3 (C5b), 88.2 (C1'b), 87.4 (CPh),
84.9 (C4'a), 84.5 (C1'a), 81.1 (C4'b), 79.7 (C3'a), 74.0 (C3’b), 72.3 (C5’b), 70.8
(C5’’b), 63.5 (C5’a), 55.3 (OMe), 39.5 (C2’a), 39.3 (C2'b), 26.9 (CMe3), 19.2
(CMe3), 12.3 (C7b), 11.8 (C7a) ppm. 31P NMR (121 MHz, CDCl3) δ = 60.0
ppm. HRMS (ESI): calcd for C58H62N4O13PSSi 1113.3541 [M-H]-; found
1113.3544. Data for 20a: 1H NMR (300 MHz, CDCl3) δ = 9.61 (bs, 2 H,
3.2, 3J3'b-2'b = 3.2, 3J3'b-2''b = 6.3 Hz, 1 H, H3'b), 4.43 (dddd, J7''b-6'b = 1.4,
3J7''b-6'b = 4.9, 3J7''b-7'b= 11.4 Hz, 3J7''b-P = 23.0 Hz, 1 H, H7''b), 4.29 (q, 3J4'a-3'a
= 2.1, 3J4'a-5'a = 2.7, 3J4'a-5''a = 2.7 Hz, 1 H, H4'a), 3.91 (ddd, 3J4'b-5'b = 3.1,
3
3J4'b-3'b = 3.1, 3J4'b-P = 3.5 Hz, 1 H, H4'b), 3.83 (d, 3J = 3.0 Hz, 2 H, H5'a
,
3
3
3
H5''a), 2.57 (m, J2'a-3'a = 1.7, J2'a-1'a = 5.9, J2'a-2''a = 14.1 Hz, 1 H, H2'a),
3
3
3
2.37 (ddd, J2''a-3'a = 5.8, J2''a-1'a = 8.6, J2''a-2'a = 14.0 Hz, 1 H, H2''a), 2.35-
2.19 (m, 3 H, H2'b, H2''b, H6'b), 2.05 (dddd, 3J6''b-7''b = 1.6, 3J6''b-7'b = 2.4, 3J6''b-
3
4
5'b = 2.4, J6''b-6'b = 14.8 Hz, 1 H, H6''b), 1.95 (d, J7-6 = 1.1 Hz, 3 H, H7b),
1.88 (d, J7-6 = 1.1 Hz, 3 H, H7a) ppm. 13C NMR (125 MHz, CD3OD): δ =
4
4
NH), 7.77-7.71 (m, 4 H, Ph), 7.62 (d, J6-7 = 1.2 Hz, 1 H, H6a), 7.52-7.42
166.42 (C4a), 166.36 (C4b), 152.52 (C2), 152.48 (C2), 137.9 (C6a), 137.6
(m, 8 H, Ph), 7.36-7.27 (m, 7 H, Ph), 6.90-6.87 (m, 5 H, Ph and H6b),
6.53-6.48 (dd, 3J = 5.4, 9.0 Hz, 1 H, H1'a), 6.15-6.10 (m, 1 H, H1'b), 5.59-
5.54 (m, 1 H, H3'a), 4.92-4.84 (dd, 3J = 11.7, 14.7 Hz, 1 H, H5''b), 4.65-4.63
(m, 1 H, H3'b), 4.43-4.19 (m, 4 H, H5''b, 2 × H5'b, H4'a), 3.83 (s, 6 H, OMe),
3.57-3.43 (m, 2 H, H5'a), 2.74-2.68 (m, 3J = 5.4, 11.7 Hz, 1 H, H2'a), 2.51-
2.41 (m, 1 H, H2'a), 2.24-2.06 (m, 2 H, H2'b), 1.84 (s, 3 H, H7b), 1.47 (s, 3
H, H7a), 1.15 (s, 9 H, tBu) ppm.13C NMR (75 MHz, CDCl3): δ = 164.0
(C4a), 163.8 (C4b), 158.8 (CPh), 150.8 (C2a), 150.2 (C2b), 144.3 (CPh),
136.0 (C6b), 135.8 (C6a), 135.3 (CPh), 135.2 (CPh), 135.1 (CPh), 132.9
(CPh), 131.5 (CPh), 130.5 (CPh), 130.4 (CPh), 130.1 (CPh), 128.4 (CPh),
128.2 (CPh), 128.1 (CPh), 127.3 (CPh), 113.5 (CPh), 111.8 (C5a), 111.5
(C5b), 87.3 (CPh), 87.0 (C1'b), 84.8 (C4'a), 84.5 (C1'a), 81.3 (C4'b), 80.3 (C3'a),
74.0 (C3'b), 71.4 (C5'b), 69.0 (C5''b), 63.5 (C5'a), 55.3 (OMe), 39.3 (C2'a),
38.1 (C2'b), 27.0 (CMe3), 19.3 (CMe3), 12.5 (C7b), 11.8 (C7a) ppm. 31P
(C6b), 112.4 (C5b), 112.1 (C5a), 88.9 (3J4'b-P = 8.0 Hz, C4'b), 87.1 (3J4'a-P
=
6.2 Hz, C4'a), 86.4 (C1'a), 86.0 (C1'b), 81.3 (2J3'a-P = 3.9 Hz, C3'a), 80.7 (2J5'b-
P = 9.9 Hz, C5'b), 71.1 (C3'b), 69.3 (2J7'b-P = 10.0 Hz, C7'), 62.8 (C5'a), 40.7
(C2'b), 39.4 (3J2'a-P = 4.1 Hz, C2'a), 28.8 (3J6'b-P = 6.7 Hz, C6'b), 13.1 (C7b),
12.6 (C7a) ppm. 31P NMR (202 MHz, CD3OD): δ = 63.9 (JP-Se = 1008.2
Hz) ppm. HRMS (ESI): calcd for C22H30N4O11PSe 636.0856 [M+H]+;
found 636.0861.
α,β-seleno-D-CNA (RC,SP) (18b): Following the general procedure D
starting from 16b gave the product 18b (quant., 21 mg) over two steps.
1H NMR (500 MHz, CD3OD): δ = 7.81 (d, 4J6-7 = 1.2 Hz, 1 H, H6a), 7.56 (d,
4J6-7 = 1.2 Hz, 1 H, H6b), 6.38 (dd, 3J1'b-2'b = 5.9, 3J1'b-2''b = 8.4 Hz, 1 H, H1'b),
6.27 (dd, 3J1'a-2'a = 6.1, 3J1'a-2''a = 9.1 Hz, 1 H, H1'a), 5.44 (dddt, 3J3'a-4'a = 2.0,
3
3
3J3'a-2'a = 2.1, J3'a-2''a = 5.3, 3J3'a-P = 9.7 Hz, 1 H, H3'a), 4.97 (dq, J5'b-4'b
=
NMR (121 MHz, CDCl3) δ = 62.2 ppm. HRMS (ESI): calcd for
C58H62N4O13PSSi 1113.3541 [M-H]-; found 1113.3546.
2.8, 3J5'b-6''b = 2.8, 3J5'b-6'b = 11.8, J5'b-P = 2.8 Hz, 1 H, H5'b), 4.65 (dddd,
3J7'b-6''b = 2.7, 3J7'b-7''b = 11.4, 3J7'b-6'b = 12.0, 3J7'b-P = 4.9 Hz, 1 H, H7'b), 4.54
(dt, 3J3'b-4'b = 2.1, 3J3'b-2'b = 2.1, 3J3'b-2''b = 5.8 Hz, 1 H, H3'b), 4.43 (dddd,
3
5'-O-Dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β,γ-seleno-D-CNA
cis (19b) and 5'-O-dimethoxytrityl-3'-O-tert-butyldiphenylsilyl-α,β,γ-
seleno-D-CNA trans (20b): Following the general procedure B starting
from 2 gave the product 19b (16%, 454 mg) and product 20b (22%, 624
mg). Data for 19b: 1H NMR (300 MHz, CDCl3) δ = 8.78 and 8.69 (s, 2 H,
3
3J7''b-6'b = 1.6, J7''b-6'b = 4.9, 3J7''b-7'b = 11.4, 3J7''b-P > 20 Hz, 1 H, H7''b), 4.21
(dt, 3J4'a-3'a = 1.8, 3J4'a-5'a = 3.0, 3J4'a-5''a = 3.0 Hz, 1 H, H4'a), 4.01 (ddd, 3J4'b-
3'b = 2.0, 3J4'b-5'b = 2.6, 3J4'b-P = 3.9 Hz, 1 H, H4'b), 3.78 (d, 3J = 3.0 Hz, 2 H,
H5'a, H5''a), 2.49 (m, 3J2'a-3'a = 2.1, 3J2'a-1'a = 6.1, 3J2'a-2''a = 14.2 Hz, 1 H, H2'a),
3
3
3
2.41 (ddd, J2''a-3'a = 5.6, J2''a-1'a = 8.6, J2''a-2'a = 14.1 Hz, 1 H, H2''a), 2.29
NH), 7.65-7.56 (m, 5 H, Ph), 7.44-7.22 (m, 15 H, H6, Ph), 6.94 (d, 4J6-7
=
3
3
3
(ddd, J2'b-3'b = 2.0, J2'b-1'b = 5.9, J2'b-2''b = 13.7, 1 H, H2'b), 2.26 (dddd,
3J6'b-7''b = 4.8, J6'b-5'b = 10.9, J6'b-7'b = 12.0, J6'b-6''b = 14.4, 1 H, H6'b), 2.11
1.2 Hz, 1 H, H6), 6.82 (m, 4 H, Ph), 6.44 (dd, 3J = 5.7, 9.0 Hz, 1 H, H1'a),
6.02 (t, 3J = 6.6 Hz, 1 H, H1'b), 5.50 (dd, 3J = 5.4, 11.5 Hz, 1 H, H3'a), 4.62
(A part of an AB syst, 3J = 9.0, 11.7 Hz, 1 H, H5’b), 4.49-4.39 (m, 2 H, H5''b
and H3'b), 4.24 (m, 1 H, H4'a), 4.03-3.90 (m, 2 H, H5'b and H5''b), 3.77 (s, 6
H, OMe), 3.52 and 3.41 (AB part of an ABX syst, 3J = 2.4, 10.5 Hz, 2 H,
H5'a), 2.55 (A part of an ABX syst, J = 6.4, 15.0 Hz, 1 H, H2'), 2.49-2.36
(m, 2 H, H2'), 2.22 (m, 1 H, H2'), 1.82 (d, 4J7-6 = 0.9 Hz, 3 H, H7), 1.43 (d,
4J7-6 = 0.9 Hz, 3 H, H7), 1.08 (s, 9 H, tBu) ppm. 13C NMR (75 MHz,
CDCl3) δ = 164.3, 164.2, 158.8, 150.5, 149.7, 144.1, 138.8, 135.8, 135.7,
135.2, 130.7, 130.5, 130.1, 128.2, 128.1, 127.3, 113.5, 111.7, 110.1,
88.7, 87.4, 84.7, 84.5, 81.1, 80.5, 74.2, 71.9, 70.4, 63.5, 55.3, 39.2, 33.9,
29.7, 26.9, 25.7, 25.0, 19.2, 12.3, 11.8 ppm. 31P NMR (121 MHz, CDCl3)
3
3
3
(ddd, 3J2''b-3'b = 5.7, 3J2''b-1'b = 8.4, 3J2''b-2'b = 13.7 Hz, 1 H, H2''b), 1.95 (dddd,
3
3
3
3J6''b-7''b = 1.6, J6''b-7'b = 2.4, J6''b-5'b = 2.4, J6''b-6'b = 15.8 Hz, 1 H, H6''b),
4
4
1.93 (d, J7-6 = 1.2 Hz, 3 H, H7b), 1.88 (d, J7-6 = 1.2 Hz, 3 H, H7a) ppm.
13C NMR (125 MHz, CD3OD) δ = 166.5 (C4a), 166.4 (C4b), 152.5 (C2a),
152.4 (C2b), 138.0 (C6a), 137.4 (C6b), 112.1 (C5b), 112.1 (C5a), 89.4 (3J4'b-P
= 8.3 Hz, C4'b), 87.4 (3J4'a-P = 6.2 Hz, C4'a), 86.9 (C1'b), 86.4 (C1'a), 82.1
(2J3'a-P = 5.3 Hz, C3'a), 81.1 (2J5'b-P = 5.4 Hz, C5'b), 71.8 (C3'b), 68.6 (2J7'b-P
=
5.5 Hz, C7'), 62.7 (C5'a), 41.3 (C2'b), 39.8 (3J2'a-P = 4.7 Hz, C2'a), 29.4 (3J6'b-
= 6.4 Hz, C6'b), 13.0 (C7b), 12.6 (C7a) ppm. 31P NMR (202 MHz,
P
CD3OD):
δ = 67.3 (JP-Se= 973.7) ppm. HRMS (ESI): calcd for
C22H30N4O11PSe 636.0856 [M+H]+; found 636.0872.
δ
=
65.5 (JP-Se
C58H62N4O13PSeSi 1161.2985 [M-H]-; found 1161.2989. Data for 20b: 1
NMR (300 MHz, CDCl3): δ = 9.21 and 9.14 (s, 2 H, NH), 7.70-7.63 (m, 5
= 1006.8 Hz) ppm. HRMS (ESI): calcd for
H
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
H, Ph), 7.56 (d, 4J6-7 = 1.2 Hz, 1 H, H6), 7.48-7.25 (m, 15 H, H6, Ph), 6.80
(m, 4 H, Ph), 6.44 (dd, 3J = 5.4, 9.0 Hz, 1 H, H1'a), 6.01 (t, 3J = 6.9 Hz, 1
H, H1'b), 5.63 (dd, 3J = 5.7, 10.2 Hz, 1 H, H3'a), 4.64 (t, 3J = 11.9 Hz, 1 H,
H5'b), 4.51 (m, 1 H, H3’b), 4.35-4.12 (m, 4 H, H5'b, 2 × H5''b and H4'a), 3.77
(s, 6 H, OMe), 3.51 and 3.36 (AB part of an ABX syst, 3J = 2.7, 10.8 Hz,
2 H, 2 × H5'a), 2.64 (A part of an ABX syst, 3J = 5.1, 14.1 Hz, 1 H, H2'),
2.42 (m, 1 H, H2'), 2.16-2.10 (m, 2 H, H2'), 1.79 (d, 4J7-6 = 0.9 Hz, 3 H, H7),
CDCl3): δ = 63.9 ppm. HRMS (ESI): calcd for C42H45N4O13PNaSe
947.1784 [M+Na]+; found 947.1798.
5'-O-Dimethoxytrityl-α,β,γ-seleno-D-CNA trans (22b): Following the
general procedure C starting from 20b gave the product 22b (81%, 400
mg). 1H NMR (300 MHz, CDCl3): δ = 10.06 (bs, 2 H, NH), 7.61 (s, 1 H,
H6), 7.41-7.20 (m, 9 H, Ph), 7.10 (s, 1 H, H6), 6.87 (d, 4 H, Ph), 6.45 (dd,
3J = 6.3, 8.4 Hz, 1 H, H1'a), 6.10 (t, 3J = 6.9 Hz, 1 H, H1'b), 5.60 (dd, 3J =
4.5, 8.4 Hz, 1 H, H3'a), 4.75-4.67 (m, 2 H), 4.51 (t, J = 13.0 Hz, 1 H), 4.42-
4.26 (m, 3 H), 3.78 (s, 6 H, OMe), 3.53 and 3.40 (AB syst, 3J = 9.0 Hz, 2
H, 2 × H5'a), 2.71-2.43 (m, 4 H, H2'), 1.85 (s, 3 H, H7), 1.44 (s, 3 H, H7)
ppm. 13C NMR (75 MHz, CDCl3): δ = 164.4, 164.3, 158.7, 151.0, 150.8,
144.2, 135.3, 135.0, 130.0, 128.2, 128.1, 128.0, 127.3, 113.5, 111.9,
111.3, 87.3, 84.7, 81.5, 81.3, 72.3, 63.8, 60.5, 55.3, 21.1, 14.2, 12.5,
11.8 ppm. 31P NMR (121 MHz, CDCl3): δ = 66.8 ppm. HRMS (ESI):
calcd for C42H45N4O13PNaSe 947.1784 [M+Na]+; found 947.1788.
1.40 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.09 (s, 9 H, tBu) ppm. 13C NMR (75
4
MHz, CDCl3) δ = 164.0, 163.9, 158.8, 150.8, 150.2, 114.2, 136.4, 135.9,
135.8, 135.3, 135.1, 132.8, 131.5, 130.5, 130.1, 128.4, 128.2, 128.1,
127.3, 113.5, 111.8, 111.4, 87.3, 87.1, 84.7, 84.5, 81.2, 81.1, 74.1, 71.5,
69.4, 67.0, 63.5, 39.2, 38.4, 27.0, 19.3, 12.5, 11.8 ppm. 31P NMR (100
MHz, CDCl3): δ = 67.4 (JP-Se = 993.5 Hz) ppm. HRMS (ESI): calcd for
C58H62N4O13PSeSi: 1161.2985 [M-H]-; found 1161.2993.
5’-O-Dimethoxytrityl-α,β,γ-thio-D-CNA cis (21a): Following the
general procedure C starting from 19a gave the product 21a (81%, 200
mg). 1H NMR (300 MHz, CDCl3): δ = 7.59 (s, 1 H, H6a), 7.39-7.37 (m, 2 H,
Ph), 7.32-7.20 (m, 10 H, Ph and H6b), 6.86-6.83 (d, 4 H, Ph), 6.47-6.43
(m, 1 H, H1'a), 6.13-6.08 (m, 1 H, H1'b), 5.40-5.36 (m, 1 H, H3'a), 4.82-4.23
(m, 6 H, 2 × H5''b, H3'b, 2 × H5'b, H4'a), 3.78 (s, 6 H, OMe), 3.54-3.39 (m, 2
α,β,γ-thio-D-CNA cis (23a): Following the general procedure D starting
from 21a gave the product 23a (quant., 65 mg). 1H NMR (500 MHz,
DMSO): δ = 11.36 (s, 2 H, NH), 7.73 (d, 4J6-7 = 1.2 Hz, 1 H, H6a), 7.57 (d,
3
3
4J6-7 = 1.2 Hz, 1 H, H6b), 6.35 (dd, J1'b-2'b = 6.6, J1'b-2''b = 7.3 Hz, 1 H,
3
3
H, 2 × H5'a), 2.70-2.35 (m, 4 H, H2'), 1.89 (s, 3 H, H7b), 1.51 (s, 3 H, H7a
)
H1'b), 6.25 (dd, J1'a-2'a = 5.9, J1'a-2''a = 8.4 Hz, 1 H, H1'a), 5.85 (d, 3J = 4.5
Hz, 1 H, OHb), 5.36 (t, 3J = 5.1 Hz, 1 H, OHa), 5.05 (m, 3J = 1.8, 5.8, JP =
8.9 Hz, 1 H, H3'a), 4.65 (A part of an ABX syst, 3J = 11.7, JP = 2.5 Hz, 1 H,
H5'b), 4.54 (A part of an ABX syst, 3J = 12.0, JP = 2.0 Hz, 1 H, H5''b), 4.36
(m, 3J = 12.0, JP = 25.0 Hz, 2 H, H5'b and H5''b), 4.30 (m, 1 H, H3'b), 4.18
(dd, 3J = 1.9, 3.6 Hz, 1 H, H4'a), 3.65 (t, J = 4.4 Hz, 2 H, H5'a), 2.50 (m, 1
H, H2'a), 2.40 (m, 2 H, H2'a and H2'b), 2.18 (B part of an ABX syst, 3J = 3.9,
ppm. 13C NMR (75 MHz, CDCl3): δ = 164.5 (C4a), 163.9 (C4b), 158.9 (CPh),
151.8 (C2a), 150.9 (C2b), 144.2 (CPh), 136.0 (C6a), 135.2 (C6b), 135.1,
130.1, 128.2, 128.1, 127.3 (CPh), 113.5 (CPh), 112.6 (C5a), 111.3 (C5b),
87.8 (C1'b), 87.5 (CPh), 84.6 (C4'a), 84.5 (C1'a), 81.2 (C4'b), 80.3 (C3'a), 72.7
(C5'b), 71.8 (C5''b), 70.5 (C3'b), 55.4 (OMe), 39.4 (C2'a), 37.4 (C2'b), 12.5
(C7b), 12.0 (C7a) ppm. 31P NMR (121 MHz, CDCl3): δ = 59.4 ppm. HRMS
(ESI): calcd for C42H44N4O13PS 875.2363 [M-H]-; found 875.2333.
4
4
6.6, 13.7 Hz, 1 H, H2'b), 1.81 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.78 (d, J7-6
=
0.9 Hz, 3 H, H7) ppm. 13C NMR (125 MHz, DMSO): δ = 164.13, 164.11,
150.82, 150.78, 136.8, 136.3, 110.5, 110.1, 85.3, 84.2, 84.1, 80.3, 78.9,
73.2, 71.8, 71.3, 61.3, 38.1, 37.6, 12.4, 12.2. 31P NMR (200 MHz,
DMSO): δ = 59.6 ppm. HRMS (ESI): calcd for C21H26N4O11PS 573.1056
[M-H]-; found 573.1057.
5'-O-Dimethoxytrityl-α,β,γ-thio-D-CNA trans (22a): Following the
general procedure C starting from 20a gave the product 22a (60%, 195
mg). 1H NMR (300 MHz, CDCl3): δ = 7.60 (s, 1 H, H6a), 7.40-7.37 (m, 2 H,
Ph), 7.32-7.25 (m, 7 H, Ph), 7.09 (s, 1 H, H6b), 6.86-6.83 (d, 3J = 9.0 Hz,
4 H, Ph), 6.47-6.42 (m, 1 H, H1'a), 6.15-6.10 (m, 1 H, H1'b), 5.50-5.46 (m,
α,β,γ-thio-D-CNA trans (24a): Following the general procedure D
starting from 22a gave the product 24a (quant., 65 mg). 1H NMR (500
1 H, H3'a), 4.73-4.64 (m, 2 H, H5''b, H3'b), 4.50-4.26 (m, 4 H, H5''b, 2 × H5'b
,
4
H4'a), 3.78 (s, 6 H, OMe), 3.53-3.40 (m, 2 H, H5'a), 2.71-2.46 (m, 2 H, H2'a),
2.47-2.43 (m, 2 H, H2'b), 1.84 (s, 3 H, H7b), 1.45 (s, 3 H, H7a) ppm. 13C
NMR (75 MHz, CDCl3): δ = 164.3 (C4a), 164.2 (C4b), 158.8 (CPh), 151.0
(C2a), 150.8 (C2b), 144.2 (CPh), 136.9 (C6a), 135.3 (C6b), 135.1, 130.1,
128.2, 128.0, 127.3 (CPh), 113.5 (CPh), 112.0 (C5a), 111.4 (C5b), 87.7
(C1'b), 87.3 (CPh), 84.7 (C4'a), 84.5 (C1'a), 81.2 (C4'b), 80.5 (C3'a), 72.2 (C3'b),
71.7 (C5'b), 69.3 (C5''b), 63.5 (C5'a), 55.3 (OMe), 39.2 (C2'a), 38.3 (C2'b),
12.5 (C7b), 11.8 (C7a) ppm. 31P NMR (121 MHz, CDCl3): δ = 62.1 ppm.
HRMS (ESI): calcd for C42H44N4O13PS 875.2363 [M-H]-; found 875.2341.
MHz, DMSO): δ = 11.33 (s, 2 H, NH), 7.71 (d, J6-7 = 1.2 Hz, 1 H, H6a),
7.52 (d, 4J6-7 = 1.2 Hz, 1 H, H6b), 6.32 (dd, 3J1'b-2''b = 5.9, 3J1'b-2'b = 8.6 Hz,
1 H, H1'b), 6.21 (dd, 3J1'a-2'a = 5.8, 3J1'a-2''a = 8.6 Hz, 1 H, H1'a), 5.97 (d, 3J =
4.8 Hz, 1 H, OHb), 5.30 (t, 3J = 5.1 Hz, 1 H, OHa), 5.14 (m, 3J = 1.7, 5.2,
3J3'a-P = 8.7 Hz, 1 H, H3'a), 4.57 (A part of an ABX syst, 3J = 11.7, JP =
11.5 Hz, 1 H, H5'b), 4.55 (A part of an ABX syst, 3J = 11.7, JP= 12.5 Hz, 1
H, H5''b), 4.37 (dd, 3J = 2.2, 5.6 Hz, 1 H, H3'b), 4.36 (m, 3J = 11.7, JP = 14.0
Hz, 2 H, H5'b and H5''b), 4.12 (dd, 3J = 1.7, 3.3 Hz, 1 H, H4'a), 3.60 (m, 2 H,
2 × H5'a), 2.48 (m, 1 H, H2'a), 2.37 (m, 1 H, H2'a), 2.27 (m, 1 H, H2'b), 2.16
(B part of an ABX syst, 3J = 2.6, 6.0, 13.5 Hz, 1 H, H2'b), 1.80 (d, 3 H, 4J7-6
4
5'-O-Dimethoxytrityl-α,β,γ-seleno-D-CNA cis (21b): Following the
general procedure C starting from 19b gave the product 21b (80%, 290
mg). Probably due to aggregates formation[20], the NMR specra were
recorded with a very poor resolution for 1H and with a low detection level
of the aliphatic carbon for 13C. 1H NMR (300 MHz, CDCl3): δ = 10.46 (bs,
2 H, NH), 7.60 (s, 1 H, H6), 7.40-7.19 (m, 10 H, H6 and Ph), 6.87 (d, 4 H,
Ph), 6.47 (dd, 3J = 5.1, 8.4 Hz, 1 H, H1'a), 6.08 (t, 3J = 6.3 Hz, 1 H, H1'b),
5.47 (dd, 3J = 3.6, 9.0 Hz, 1 H, H3'a), 4.83-4.70 (m, 3 H), 4.61 (bs, 1 H,
H4'a), 4.48-4.28 (3 H), 3.79 (s, 6 H, OMe), 3.52 and 3.45 (AB syst, J = 9.9
Hz, 2 H, 2 × H5'a), 2.67-2.41 (m, 4 H, H2'), 1.87 (s, 3 H, H7), 1.50 (s, 3 H,
H7) ppm. 13C NMR (75 MHz, CDCl3): δ = 166.1, 165.9, 160.1, 152.4,
151.8, 145.5, 139.4, 136.8, 136.6, 136.5, 131.5, 129.5, 128.6, 114.8,
113.3, 112.0, 89.4, 88.8, 86.2, 85.8, 82.7, 81.9, 73.7, 73.5, 72.2, 72.0,
64.9, 62.0, 56.6, 40.4, 22.3, 15.4, 13.5, 12.9 ppm. 31P NMR (121 MHz,
= 0.9 Hz, H7), 1.76 (d, 3 H, J7-6 = 0.9 Hz, H7) ppm. 13C NMR (125 MHz,
DMSO): δ = 164.06 (C4), 164.05 (C4), 150.8 (C2), 150.7 (C2), 136.4 (C6),
136.2 (C6), 110.5 (C5), 110.1 (C5), 85.4 (3J4'a-P = 4.9 Hz, C4'a), 84.4 (C1'),
84.0 (C1'), 80.41 (C3'a), 80.35 (C4'b), 71.9 (2J5'b-P = 6.8 Hz, C5'b), 70.9 (C3b'),
69.9 (2J5''b-P = 6.9 Hz, C5'b), 61.2 (C5'a), 37.8 (C2'b), 37.7 (3J2'a-P = 3.5 Hz,
C2'a), 12.4 (C7), 12.2 (C7) ppm. 31P NMR (202 MHz, DMSO): δ = 61.9
ppm. HRMS (ESI): calcd for C21H26N4O11PS 573.1056 [M-H]-; found
573.1050.
α,β,γ-seleno-D-CNA cis (23b): Following the general procedure D
starting from 21b gave the product 23b (quant., 9 mg). 1H NMR (500
4
4
MHz, CD3OD): δ = 7.84 (d, J6-7 = 0.9 Hz, 1 H, H6a), 7.51 (d, J6-7 = 0.9
Hz, 1 H, H6b), 6.37 (dd, 3J1'a-2'a = 6.0, 3J1'a-2''a = 9.4 Hz, 1 H, H1'a), 6.28 (dd,
3J1'b-2''b = 7.0, J1'b-2'b = 7.0 Hz, 1 H, H1'b), 5.29 (dddd, J3'a-4'a = 1.9, 3J3'a-2'a
3
3
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
3
= 1.9, J3'a-2''a = 6.1, 3J3'a-P = 10.0 Hz, 1 H, H3'a), 4.70 (A part of an ABX
5'-O-Dimethoxytrityl-3'-O-[(cyanoethyl)(diisopropylamino)-
syst, 3J = 12.0, JP = 6.2 Hz, 1 H, H5'b), 4.66 (A part of an ABX syst, 3J =
11.8, 3JP = 6.7 Hz, 1 H, H5''b), 4.42 (dd, 3J3'b-2''b = 3.4, 3J3'b-2'b = 6.4 Hz, 1 H,
H3'b), 4.39 (B part of an ABX syst, 3J = 2.5, 12.0 Hz, JP = 20 Hz, 1 H, H5'b),
4.35 (B part of an ABX syst, 3J = 2.5, 11.8, JP = 19 Hz, 1 H, H5''b), 4.30 (m,
1 H, H4'a), 3.85 and 3.84 (ABX syst, 3J = 3.0, 3.5, 12.5 Hz, 2 H, 2 × H5'a),
2.58 (A part of an ABX syst, 3J2'a-3'a = 1.8, 3J2'a-1'a = 5.8, 3J2'a-2''a = 14.2 Hz,
selenophosphamide]-α,β-D-CNA (SC,SP) (26): To 9b (5 mg) in a NMR
tube was added a commercially available solution of iodine I2 (0.75 ml,
0.02 M, THF/pyridine/water 70:20:10) used during oligonucleotide
synthesis. 31P NMR spectrum was recorded 5 min after addition. 31P
NMR (121 MHz, no lock): δ = 74.3, 73.5, - 8.00, -8.12 ppm.
1 H, H2'a), 2.52 (A part of an ABX syst, 3J2'b-3'b = 6.4, 3J2'b-1'b = 7.2, 3J2'b-2'b
=
=
=
5'-O-Dimethoxytrityl-3'-O-[(cyanoethyl)(diisopropylamino)-
3
3
14.1 Hz, 1 H, H2'b), 2.42 (B part of an ABX syst, J2''a-3'a = 6.4, J2''a-1'a
selenophosphamide]-thio-α,β-D-CNA (SC,SP) (27): Compound 15b
(328 mg, 0.31 mmol) was dissolved under an argon atmosphere in dry
THF (2 mL) at room temperature. N-Ethyldiisopropylamine (0.21 mL,
1.24 mmol) and then 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite
(146 mg, 0.62 mmol) were added. The reaction mixture was stirred for 2
h, the white precipitate was filtered and the filtrate diluted in EtOAc
saturated with argon. The organic layer was washed with a cold aqueous
solution of potassium carbonate (10%), dried over MgSO4, filtered and
concentrated with care under reduced pressure. The crude was then
dissolved in a mixture of acetonitrile/toluene (1:1, 4 mL) and pyridine (2
mL) and elemental sulfur S8 (290 mg, 1.13 mmol) were added. The
reaction mixture was heated at 60°C for 1 h and was allowed to cool
down to r.t. before the filtration of the residual S8. The filtrate was then
diluted in EtOAc and the organic layer washed with water, dried over
MgSO4, filtered and concentrated to give 27 as a yellow foam (81%, 286
mg, contaminated with inseparable residual H-phosphonate). 31P NMR
(121 MHz, CDCl3): δ = 74.0, 73.3, 60.14, 60.10 ppm.
3
3
8.7, J2''a-2'a = 14.3 Hz, 1 H, H2''a), 2.38 (B part of an ABX syst, J2''b-3'b
3.4, 3J2''b-1'b = 6.7, 3J2''b-2'b = 14.0 Hz, 1 H, H2''b), 1.91 (d, 4J7-6 = 0.9 Hz, 3 H,
H7), 1.89 (d, 4J7-6 = 0.9 Hz, 3 H, H7) ppm. 13C NMR (125 MHz, CD3OD): δ
= 166.3 (C4), 166.3 (C4), 152.5 (C2), 152.3 (C2), 138.7 (C6), 138.1 (C6),
112.1 (C5), 111.9 (C5), 87.9 (C1'a), 87.1 (3J4'a-P = 5.2 Hz, C4'a), 86.4 (C1'b),
82.7 (3J4'b-P = 6.3 Hz, C4'b), 81.5 (2J3'a-P = 4.0 Hz, C3'a), 73.4 (C3'b), 73.4
(C5'b), 72.1 (2J5''b-P = 8.6 Hz, C5''b), 62.9 (C5'a), 40.1 (C2'b), 39.5 (3J2'a-P = 4.5
Hz, C2'a), 12.6 (C7), 12.5 (C7) ppm. 31P NMR (202 MHz, CD3OD): δ = 63.8
(JP-Se
= 1009.3 Hz) ppm. HRMS (ESI): calcd for C21H26N4O11PSe
621.0502 [M-H]-; found 621.0499.
α,β,γ-seleno-D-CNA trans (24b): Following the general procedure D
starting from 22b gave the product 24b (quant., 8 mg). 1H NMR (500
4
4
MHz, CD3OD): δ = 7.81 (d, J6-7 = 0.9 Hz, 1 H, H6a), 7.47 (d, J6-7 = 0.9
Hz, 1 H, H6b), 6.33 (dd, 3J1'b-2''b = 6.1, 3J1'b-2'b = 8.0 Hz, 1 H, H1'b), 6.31 (dd,
3J1'a-2'a = 6.0, J1'a-2''a = 8.5 Hz, 1 H, H1'a), 5.36 (dddd, 1 H, J3'a-4'a = 1.5,
3J3'a-2'a = 1.5, J3'a-2''a = 6.0, 3J3'a-P = 10.0 Hz, H3'a), 4.70 (A part of an ABX
3
3
3
syst, 3J = 12.0, JP = 8.5 Hz, 1 H, H5'b), 4.60 (A part of an ABX syst, 3J =
12.0, JP = 9.5 Hz, 1 H, H5''b), 4.47 (dd, 3J3'b-2''b = 3.0, 3J3'b-2'b = 6.0 Hz, 1 H,
H3'b), 4.38 (B part of an ABX syst, 3J = 1.5, 12.0, JP = 11.5 Hz, 1 H, H5'b),
5'-O-Dimethoxytrityl-3'-O-[(cyanoethyl)(diisopropylamino)-
phosphoramidite]-thio-α,β-D-CNA (SC,SP) (28): Compound 27 (286
mg, 0.25 mmol) was then dissolved in anhydrous acetonitrile (2 mL) and
a solution of P(NMe2)3 (C = 0.5 M, 1 mL, 0.50 mmol) was added. The
reaction mixture was stirred at r.t. for 3 h under an argon atmosphere.
The solution was hydrolyzed with a cold aqueous solution of potassium
carbonate (10%) then diluted in EtOAc saturated with argon. The organic
layer was washed with water and brine, dried over MgSO4, filtered and
concentrated with care under reduced pressure. 31P NMR analysis of the
crude indicated the presence of a signal at 82.7 ppm caracteristic of
SeP(NMe2)3.[28] The crude was then purified by silica gel column
chromatography eluting with a mixture of ether EtOAc/petroleum ether
(7:3) with 10% of Et3N to give 28 (41%, 110 mg) as a white foam. 31P
NMR (121 MHz, CDCl3): δ = 150.0, 148.7, 60.13, 60.12 ppm. HRMS
(ESI): calcd for C52H65N6O14P2S 1091.3755 [M+H]+; found 1091.3730.
4.34 (B part of an ABX syst, 3J = 2.0, 12.0, JP = 14.0 Hz, 1 H, H5''b), 4.26
3
(m, 1 H, H4'a), 3.77 (m, 2 H, H5'a), 2.54 (A part of an ABX syst, J2'b-3'b
=
6.0, 3J2'b-1'b = 8.0, 3J2'b-2'b = 14.1 Hz, 1 H, H2'b), 2.52 (A part of an ABX syst,
3J2'a-3'a = 1.1, 3J2'a-1'a = 5.9, 3J2'a-2''a = 13.9 Hz, 1 H, H2'a), 2.39 (B part of an
ABX syst, 3J2''a-3'a = 6.4, 3J2''a-1'a = 8.0, 3J2''a-2'a = 14.2 Hz, 1 H, H2''a), 2.32 (B
3
3
3
part of an ABX syst, J2''b-3'b = 2.8, J2''b-1'b = 6.0, J2''b-2'b = 13.8 Hz, 1 H,
4
4
H2''b), 1.91 (d, J7-6 = 0.9 Hz, 3 H, H7), 1.88 (d, J7-6 = 0.9 Hz, 3 H, H7)
ppm. 13C NMR (125 MHz, CD3OD): δ = 166.5 (C4), 166.4 (C4), 152.6 (C2),
152.4 (C2), 138.7 (C6b), 138.1 (C6a), 112.3 (C5), 112.0 (C5), 87.4 (C1'b),
87.3 (3J4'a-P = 4.6 Hz, C4'a), 86.4 (C1'a), 82.7 (3J4'b-P = 6.0 Hz, C4'b), 82.2
(2J3'a-P = 6.3 Hz, C3'a), 73.2 (2J5'b-P = 6.8 Hz, C5'b), 72.9 (C3'b), 71.4 (2J5''b-P
= 6.9 Hz, C5''b), 62.8 (C5'a), 39.6 (C2'b, C2'a), 12.6 (C7), 12.5 (C7) ppm. 31
P
NMR (202 MHz, CD3OD): δ = 65.5 (JP-Se= 992.3 Hz) ppm. HRMS (ESI):
calcd for C21H26N4O11PSe 621.0502 [M-H]-; found 621.0500.
Triethylammonium salt of 5'-O-dimethoxytrityl-3'-O-H-phosphonate-
α,β,γ-seleno-D-CNA cis (29): To a solution of 19b (111 mg, 0,12 mmol)
in anhydrous pyridine (600 µL) was added diphenylphosphonate (115 µL,
0.60 mmol). The reaction mixture was stirred at r.t. for 45 min then
cooled to 0°C and H2O (50 µL) and Et3N (50 µL) were added. After 15
min, the reaction mixture was poured into a saturated solution of
NaHCO3 (5 mL) and extracted with CH2Cl2 (3 × 10 mL). The combined
organic layers were dried over MgSO4 and then concentrated in vacuo.
Addition of the minimum volume of EtOAc led to the precipitatation of the
product. After filtration, the solid was further purified by silica gel
5'-O-Dimethoxytrityl-3'-O-[(cyanoethyl)(diisopropylamino)-
selenophosphamide]-α,β-CNA (SC) phosphite (25): Compound 9b
(432 mg, 0.46 mmol) was dissolved under argon in dry THF (3 mL) at
room temperature. N-Ethyldiisopropylamine (0.32 mL, 1.84 mmol) and
then 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite (242 mg, 0.92
mmol) were added. The reaction mixture was stirred for 2 h, the white
precipitate was filtered and the filtrate diluted in EtOAc saturated with
argon. The organic layer was washed with a cold aqueous solution of
potassium carbonate (10%), dried over MgSO4, filtered and concentrated
with care under reduced pressure. The crude was then purified by silica
chromatography, eluting with
a
mixture of EtOAc/MeOH/Et3N
(90:10:0.05) to yield 29 as a white solid (114 mg, 88%). As already
observed for 19b, the NMR spectra were recorded with a very poor
resolution for 1H and with a low detection level of the aliphatic carbon for
13C. 1H NMR (300 MHz, CDCl3): δ = 7.56 (s, 1 H, H6), 7.38-7.16 (m, 10 H,
H6 and Ph), 6.83 (d, 1JH-P = 629.8 Hz, 1 H, H-P), 6.81 (d, 3J = 8.7 Hz, 4 H,
Ph), 6.39 (dd, 3J = 5.6, 8.6 Hz, 1 H, H1'a), 6.11 (t, 3J = 6.2 Hz, 1 H, H1'b),
5.48-5.43 (m, JP = 10.7 Hz, 1 H, H3'a), 4.92 (m, 1 H, H3'b), 4.77 (m, 2 H, 2
gel column chromatography eluting with
a mixture of EtOAc/Et3N
(10:0.02) to give 25 (85%, 443 mg) contaminated with inseparable
residual H-phosphonate) as a white foam. 31P NMR (121 MHz, CD3OD):
δ = 131.0, 130.5, 74.2, 73.7 ppm. MS (ESI): m/z = 1161.3 [M+Na]+.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
[18] A. Skowronska, E. Krawczyk, Synthesis 1983, 509-510.
× H5'b), 4.40-4.13 (m, 3 H, 2 × H5''b, H4'a), 3.75 (s, 6 H, OMe), 3.52 and
3.37 (m, 2 H, 2 × H5'a), 2.97 (m, 6 H), 2.68-2.38 (m, 4 H, H2'), 1.86 (s, 3 H,
H7), 1.36 (s, 3 H, H7), 1.25 (t, 9 H) ppm. 13C NMR (75 MHz, CDCl3): δ =
164.2, 164.1, 158.9, 150.8, 150.4, 144.4, 135.4, 135.3, 130.29, 130.26,
128.8, 127.4, 113.6, 111.8, 111.1, 87.5, 86.9, 84.8, 84.6, 80.5, 73.8, 71.2,
63.7, 55.5, 47.1, 39.2, 38.8, 29.9, 23.3, 22.9, 12.1, 11.9, 9.2 ppm. 31P
NMR (121 MHz, CDCl3): δ = 63.9, 2.9 ppm. HRMS (ESI): calcd for
C42H45N4O15P2Se 987.1527 [M]-; found 987.1541.
[19] C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 1973, 95, 2333-2344.
[20] I. Le Clézio, H. Gornitzka, J.-M. Escudier, A. Vigroux, J. Org. Chem.
2005, 70, 1620-1629.
[21] M. Ikehara, Heterocycles 1984, 21, 75-90.
[22] a) D. J. Wood, F. E. Hruska, K. K. Ogilvie, Can. J. Chem. 1974, 52,
3353-3366; b) D. J. Wood, K. K. Ogilvie, F. E. Hruska, Can. J. Chem.
1975, 53, 2781-2790.
[23] D. G. Gorenstein, R. Rowell, J. Findlay, J. Am. Chem. Soc. 1980, 102,
5077-5081.
[24] W. J. Stec, A. Maciaszek, P. Guga, Phosphorus, Sulfur Silicon Relat.
Elem. 2008, 183, 897-907.
Acknowledgements
[25] P. P. Lankhorst, C. A. G. Haasnoot, C. Erkelens, C. Altona, J. Biomol.
Struct. Dyn. 1984, 1, 1387-1405.
[26] M. H. Caruthers, Acc. Chem. Res. 1991, 24, 278-284.
[27] M. Bollmark, J. Stawinski, Chem. Commun. 2001, 771-772.
[28] S. M. Godfrey, S. L. Jackson, C. A. McAuliffe, R. G. Pritchard, J. Chem.
Soc., Dalton Trans. 1998, 4201-4204.
The authors are grateful to the Agence Nationale de la
Recherche for a postdoctoral grant for B.L.R. and B.G. and for
financial support for the D-CNA project (ANR-11-BS07-0012).
We thank the Integrated Screening Platform of Toulouse (PICT,
IBiSA) for providing access to HPLC equipment and the Service
Commun de Spectroscopie de Masse (Université Paul Sabatier)
for the high resolution mass spectra.
Keywords: Nucleotide • oligonucleotide • structure •
dioxaphosphorinane • selenium
[1]
a) C. J. Leumann, Bioorg. Med. Chem. 2002, 10, 841-854; b) A. J. A.
Cobb, Org. Biomol. Chem. 2007, 5, 3260-3275; c) C. Zhou, J.
Chattopadhyaya, Curr. Opin. Drug Discovery Dev. 2009, 12, 876-898;
d) N. M. Bell, J. Micklefield, ChemBioChem 2009, 10, 2691-2703; e) J.
Lebreton, J.-M. Escudier, L. Arzel, C. Len, Chem. Rev. 2010, 110,
3371-3418; f) T. Yamamoto, M. Nakatani, K. Narukawa, S. Obika,
Future Med. Chem. 2011, 3, 339-365.
[2]
[3]
H. Kaur, B. R. Babu, S. Maiti, Chem. Rev. 2007, 107, 4672-4697.
a) A. Goyenvalle, C. J. Leumann, L. Garcia, J. Neuromuscular
Diseases 2016, 157-167; b) R. D. Giacometti, J. C. Salinas, M. E.
Ostergaard, E. E. Swayze, P. P. Seth, S. Hanessian, Org. Biomol.
Chem. 2016, 14, 2034-2040.
[4]
a) R. Steffens, C. J. Leumann, J. Am. Chem. Soc. 1997, 119, 11548-
11549; b) R. Steffens, C. J. Leumann, J. Am. Chem. Soc. 1999, 121,
3249-3255.
[5]
[6]
R. G. Schultz, S. M. Gryaznov, Nucleic Acids Res. 1996, 24, 2966-2973.
S. Martínez-Montero, G. F. Deleavey, A. Kulkarni, N. Martín-Pintado, P.
Lindovska, M. Thomson, C. González, M. Götte, M. J. Damha, J. Org.
Chem. 2014, 79, 5627-5635.
[7]
[8]
[9]
A. Boissonnet, C. Dupouy, P. Millard, M.-P. Durrieu, N. Tarrat, J.-M.
Escudier, New J. Chem. 2011, 35, 1528-1533.
B. Gerland, P. Millard, C. Dupouy, B.-L. Renard, J.-M. Escudier, RSC
Advances 2014, 4, 48821-48826.
M. E. Østergaard, B. Gerland, J.-M. Escudier, E. E. Swayze, P. P. Seth,
ACS Chem. Biol. 2014, 9, 1975-1979.
[10] O. Martinez, V. Ecochard, S. Mahéo, G. Gross, P. Bodin, J. Teissié, J.-
M. Escudier, L. Paquereau, PLoS One 2011, 6, e25510.
[11] I. Le Clézio, A. Vigroux, J.-M. Escudier, Eur. J. Org. Chem. 2007, 1935-
1941.
[12] D.-A. Catana, B.-L. Renard, M. Maturano, C. Payrastre, N. Tarrat, J.-M.
Escudier, Journal of Nucleic Acids 2012, 215876.
[13] a) R. D. Youssefyeh, J. P. H. Verheyden, J. G. Moffatt, J. Org. Chem.
1979, 44, 1301-1309; b) G. H. Jones, M. Taniguchi, D. Tegg, J. G.
Moffatt, J. Org. Chem. 1979, 44, 1309-1317.
[14] I. Le Clézio, J.-M. Escudier, A. Vigroux, Org. Lett. 2003, 5, 161-164.
[15] C. Dupouy, I. Le Clézio, P. Lavedan, H. Gornitzka, J.-M. Escudier, A.
Vigroux, Eur. J. Org. Chem. 2006, 5515-5525.
[16] D. B. Dess, J. C. Martin, J. Am. Chem. Soc. 1991, 113, 7277-7287.
[17] a) M. Sekine, O. Kurasawa, K.-I. Shohda, K. Seio, T. Wada, J. Org.
Chem. 2000, 65, 6515-6524; b) A. Grajkowski, J. Cieślak, J. S.
Kauffman, R. J. Duff, S. Norris, D. I. Freedberg, S. L. Beaucage,
Bioconjugate Chem. 2008, 19, 1696-1706.
This article is protected by copyright. All rights reserved.

10.1002/ejoc.201601568
European Journal of Organic Chemistry
FULL PAPER
FULL PAPER
We report the synthesis and structural
determination of thio- and seleno-α,β-
and α,β,γ-Constrained Nucleic Acid
Nucleotides
Béatrice Gerland,* Claudia Addamiano,
Brice-Loïc Renard, Corinne Payrastre,
Deshmukh Gopaul and Jean-Marc
Escudier*
HO
HO
T
T
O
O
OH OH
5'
T
O
O
P
T
S
dinucleotides (D-CNA) in which
a
O
*
*
X
P
R
O
O
O
O
T
X
α
O
β
O
OTBDPS
OH
dioxaphosphorinane ring locks two or
three torsional angles of the
sugar/phosphate backbone. For solid
phase synthesis, selono-CNA H-
phoshonates were prepared to
address selenium migration occurring
during the synthesis of seleno-CNA
phosphoramidites.
OH
O
T
5'-C(R) and 5'-C(S)-α,β-D-CNAs
O
X = S, Se
HO
OTBDPS
Page No. – Page No.
HO
T
T
O
O
T
HO
4'
O
P
O
O
OH
Thio and seleno-Dioxaphosphorinane
-Constrained dinucleotides (D-CNA),
synthesis and conformational study
T
P
α
O
HO
O
X
X
OTBDPS
O
γ
O
O
β
O
OH
cis and trans-α,β,γ-D-CNAs
T
12 thio- and seleno-D-CNA dinucleotides
This article is protected by copyright. All rights reserved.