Phosphorus pentachloride promoted gem-dichlorination of 2′- and 3′-deoxynucleosides

Article abstract of DOI:10.3390/molecules23061457

Halogen substitution at various positions of canonical nucleosides has generated a number of bioactive structural variants. Herein, the synthesis of two unique series of sugar modified nucleosides bearing a gem-dichloro group is presented. The synthetic plan entails the controlled addition of phosphorus pentachloride to suitably protected 2′- or 3′-ketodeoxynucleoside intermediates as the key step, facilitating the rapid construction of such functionalized molecules. Under the same reaction conditions, the highest chemoselectivity was observed for the formation of 2′,2′-dichloro-2′,3′-dideoxynucleosides, while a competing 2′,3′-elimination process occurred in the case of the 3′,3′-dichloro counterparts.

Full text of DOI:10.3390/molecules23061457

molecules
Article
Phosphorus Pentachloride Promoted
gem-Dichlorination of 20- and 30-Deoxynucleosides
ID
ID
Fabio da Paixao Soares ID , Elisabetta Groaz and Piet Herdewijn *
Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
fabio.dapaixaosoares@student.kuleuven.be (F.d.P.S.); elisabetta.groaz@kuleuven.be (E.G.)
* Correspondence: piet.herdewijn@kuleuven.be; Tel.: +32-16-322-657
Academic Editor: Christian Ducho
ꢀꢁꢂꢀꢃꢄꢅꢆꢇ
ꢀꢁꢂꢃꢄꢅꢆ
Received: 29 May 2018; Accepted: 11 June 2018; Published: 15 June 2018
Abstract: Halogen substitution at various positions of canonical nucleosides has generated
a number of bioactive structural variants. Herein, the synthesis of two unique series of sugar
modified nucleosides bearing a gem-dichloro group is presented. The synthetic plan entails the
controlled addition of phosphorus pentachloride to suitably protected 20- or 30-ketodeoxynucleoside
intermediates as the key step, facilitating the rapid construction of such functionalized molecules.
Under the same reaction conditions, the highest chemoselectivity was observed for the formation of
20,20-dichloro-20,30-dideoxynucleosides, while a competing 20,30-elimination process occurred in the
case of the 30,30-dichloro counterparts.
Keywords: emphgem-dichlorination; modified nucleosides; halogenated nucleosides; phosphorus
pentachloride
1. Introduction
One promising way to impart biologically favorable properties to natural nucleosides consists in
the introduction of one or more halogen substituents into their sugar ring moiety [
the replacement of an H atom or OH group by a more electronegative chlorine atom can
affect inter and/or intramolecular forces, allowing for instance additional dipolar interactions [ ].
This, in combination with the potential conformational changes induced in the parent molecule by
the increased atomic size of chlorine [ ], may influence the binding of ligands, thus modulating the
inhibition of specific targets [ ]. Furthermore, the high polarizability associated with chlorine can give
1,2]. In particular,
3
4
5
rise to London dispersion and consequently lipophilic properties, which may increase the passive
diffusion of chlorinated nucleoside derivatives across the cell membrane. In general, chlorine has
been widely employed as a bioisostere in drug development to provide a large number of therapeutic
agents with a remarkable safety profile for the treatment of a variety of diseases [
to date the investigation of such structural variation in the field of nucleosides remains underexplored.
Recently, phosphoramidate prodrugs of
-D-20-deoxy-20,20-dichlorouridine, which were obtained
upon 20-C-modification of uridine with a gem-dichloro (CCl2) functionality, have been shown to have
inhibitory activity against hepatitis C virus (HCV) replication (Figure 1, ) [ ]. Additionally, Zhou et al.
6]. However,
β
1
7
reported that the substitution of the 20-methyl group in sofosbuvir with a chlorine atom generated
20-chloro-20-fluoro ribonucleotide prodrugs with pan-genotypic anti-HCV activity (Figure 1, 2) [8].
Various protocols have been reported for the preparation of monochlorinated sugar modified
nucleosides. Chlorine has been introduced starting from anhydro nucleosides by using either
HCl-Py or HCl-dioxane in the synthesis of seven-membered ring nucleoside analogues [
well as 30- and 20-chlorinated thymidine derivatives [10
11], respectively. Alternatively, milder
conditions have been employed including either a mixture of SOCl2 and hexamethylphosphoramide
9] as
,
Molecules 2018, 23, 1457; doi:10.3390/molecules23061457
www.mdpi.com/journal/molecules

Molecules 2018, 23, 1457
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to achieve the regioselective chlorination at the 50-position of ribonucleosides [12
,13] or lithium
chloride via nucleophilic displacement of sulfonyl ester derivatives as in the synthesis of
40-chloromethyl-20-deoxy-30,50-di-O-isobutyryl-20-fluorocytidine, a respiratory syncytial virus
(RSV) polymerase inhibitor [14
tris(2,4,6-tribromophenoxy) dichlorophosphorane (BDCP) [16] and CCl4/PPh3
,
15]. Other reagents that have been successfully used are
17]. However,
[
most of these methods require multistep protecting group strategies that make them time-consuming,
expensive, and low yielding. On the other hand, few efforts have been devoted to the preparation
of halogenated nucleosides by condensing the base moiety with a chlorinated carbohydrate.
Watanabe et al.
described the synthesis of several 20-halo-5-substituted-arabinofuranosyl
derivatives upon coupling of trimethylsilylated pyrimidines with suitably protected
2-fluoro-, 2-chloro-, or 2-bromoarabinosyl bromides in good yields [18]. The glycosylation of
2-deoxy-2,2-dichlorofuranose 1-chloride with N4-Bz-cytosine has also been reported towards the
synthesis of
were prepared from a
β
-D-20-deoxy-20,20-dichlorouridine [
-2-chloro-
7 β α
-20-Chloro- -20-fluororibonucleoside derivatives
].
α-2-fluororibofuranose intermediate, which was in turn obtained
β
from 2-deoxy-D-ribose in five steps using N-chlorosuccinimide (NCS) in the presence of lithium
bis(trimethylsilyl)amide (LiHMDS) in the chlorination step [8].
Herein, we describe the unprecedented synthesis of 30,30-gem-dichloro- (Figure 1,
3) and
20,20-gem-dichloro-20,30-dideoxynucleoside analogues (Figure 1,
4) bearing both purines and
pyrimidines as nucleobases by using PCl5 as a powerful chlorinating agent. In addition, all synthesized
compounds were further evaluated for their antiviral activity against human immunodeficiency virus
(HIV) type 1 (IIIB strain) and type 2 (ROD) in MT-4 cell cultures.
Figure 1. Selected biologically active (1–2) and targeted (3–4) sugar chlorinated nucleos(t)ide analogues.
2. Results and Discussion
At the start of our synthetic endeavor towards the preparation of compounds of type
we initially considered the preparation of suitably protected 3,3-gem-dichloro-20,30-dideoxyribose
as common synthon for further base condensation reactions (Scheme 1). The known 5-silylated
1-methoxy-2-deoxyribofuranose , prepared in two-steps from 2-deoxy-D-ribose 19 21], was easily
oxidized using Dess-Martin periodinane (DMP) to provide protected 3-ketoribofuranose as
was reacted under a range of
3 (Figure 1),
8
6
5
[
–
7
a stable compound in excellent yield. However, when
standard chlorination conditions including PCl5/PCl3
7
[
22], Appel reaction [23,24], and the
N-chlorosuccinimide/chlorodiphenylphosphine system [25], gem-dichloro sugar
Interestingly, the desired product could be obtained when the reaction was conducted in the presence
of PCl5 at low temperature ( was purified by column chromatography using
78 ◦C). Compound
8 could not be formed.
−
8
neutralized silica gel, nonetheless it underwent extensive degradation and could only be isolated
in a disappointing 13% yield. This is presumably due to its proclivity towards aromatization
following elimination of a molecule of methanol and HCl under acid or basic conditions. In addition,
the chlorinated sugar could not be converted to its acetylated derivative, while suffering further
decomposition under Vorbrüggen glycosylation conditions.
Due to the chemical instability of 3,3-dichloro-2,3-dideoxyribofuranose
8, this route
was thus discontinued in favor of an alternative synthetic approach directly starting from
20-deoxy-ribonucleosides. As shown in Scheme 2, 20-deoxythymidine
9 was regioselectively silylated
at the 50-position using tert-butyldimethylsilyl (TBSCl) and the remaining hydroxyl functionality was
then oxidized to give compound 10 in good yield. In agreement with the aforementioned results,

Molecules 2018, 23, 1457
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when a variety of chlorinating conditions were screened, only the use of PCl5 at low temperature
78 ◦C) enabled the formation of 30,30-gem-dichloro thymidine derivative 12. However, while the
(
−
gem-dichlorination was found to be possible, it was observed that under the employed conditions
only a modest yield (22%) of the desired compound was obtained. The starting 30-ketonucleoside
10 was in fact mainly converted to compounds 14 and 15 resulting from perchlorination reactions,
which occurred after in situ deprotection of the 50-TBS group. A small amount (8%) of an additional
0
0
0
side product, i.e., 3 -chloro-vinyl derivative 13, was also isolated owing to the 2 ,3 -elimination of HCl
from 12. In order to improve the observed chemoselectivity, it was reasoned that the replacement
of the protecting group at the 50-position with a relatively less reactive moiety could suppress the
perchlorination pathways. 50-TBDPS-30-ketonucleoside 11 was therefore synthesized, which led
to an improved yield of the corresponding thymidine gem-dichloride 16 (30%) when subjected to
the chlorination conditions. Although an exclusive 30-dichlorination was ultimately not realized,
compound 16 could be easily separated by column chromatography from the monochlorinated
derivative 17 (ratio 16
tetra-n-butylammonium fluoride (TBAF) at
18 in good yields. TBAF was added at low temperature in order to avoid fast decomposition of the
starting material, which was observed when the addition was performed either at room temperature
or 0 ◦C.
:
17 was approximately 1:1). Both compounds were readily deprotected with
−
50 ◦C to afford the corresponding nucleosides 3a and
Scheme 1. Initial attempted route towards the preparation of gem-dichlorinated nucleosides.
0
0
0
0
0
0
Scheme 2. Synthesis of 3 ,3 -gem-dicloro and 2 ,3 -vinyl-3 -chloro 2 -deoxythymidine analogues.

Molecules 2018, 23, 1457
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In a similar fashion, 30-keto-200-deoxyribonucleoside derivative 19 bearing uracil as nucleobase
was synthetized in two steps from 2 -deoxyuridine (see Materials and Methods). After the chlorination
step, a 1.2:1 mixture of di- (20) and monochlorinated (21) derivatives was formed, which were
isolated by subsequent chromatrographic purification and additionally submitted to pyrimidine base
interconversion under standard conditions (Scheme 3). However, when the transformation into of the
corresponding triazolyl intermediates (for example compound 22) was conducted at room temperature,
only poor product yields were observed due to the formation of side products originating from the
nucleobase elimination. Pleasingly, it was found that by premixing 20 (and analogously 21) with POCl3
in dry acetonitrile at low temperature (
50 ◦C) prior to the slow addition of triethylamine, followed
−
by an acetonitrile solution containing 1,2,4-triazole and triethylamine, no degradation was observed.
After desilylation and substitution at the 4-position, gem-dichloro compound 3b was obtained in good
yield (72%) over two steps, while compound 23 was also synthesized in 3 steps from 21 with an overall
yield of 54%.
0
0
0
0
0
0
Scheme 3. Synthesis of 3 ,3 -gem-dicloro and 2 ,3 -vinyl-3 -chloro 2 -deoxycytidine analogues.
Next, the previously synthesized triazolyl derivative 22 was subjected to a transglycosylation
reaction [26], as depicted in Scheme 4. Thus, compound 22 was reacted with silylated 6-chloropurine
in the presence of trimethylsilyl trifluoromethanosulfonate as catalyst to afford nucleoside 24 as
an anomeric mixture, which could be separated by column chromatography to afford 57% and 43%
of the
α and β anomer, respectively. The β anomer was then reacted with TBAF to accomplish the
removal of the TBDPS group, followed by displacement of the chlorine atom with NH3 in MeOH.
The desired 30,30-gem-dichloro-20,30-dideoxyadenosine derivative 3c was obtained in poor yield (14%),
together with side products 25 and 26.
0
0
0
Scheme 4. Synthesis of 3 ,3 -gem-dichloro 2 -deoxyadenosine analogue 3c.

Molecules 2018, 23, 1457
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In order to access the corresponding structural nucleoside analogues bearing a gem-dichloro
moiety at the 20-position (
, Figure 1), we envisioned an analogous sequence of reactions. In this
4
case, the synthesis plan involved the initial preparation of a suitably protected 3-deoxyribofuranose
synthon (Scheme 5). Thus, 1,2-O-isopropylidene-D-xylofuranose was obtained from D-(+)-xylose
over two steps in one pot and multigram scale according to a previously reported procedure [27],
and further protected at the 5-position to afford 5-O-o-toluoyl-1,2-isopropylidene-D-xylofuranose 27
.
Subsequently, this compound was transformed into its 3-thiocarbonylimidazole derivative and
subjected to Barton-McCombie deoxygenation conditions to give a 3-deoxyribofuranose intermediate,
which was diacetylated using a mixture of acetic anhydride and acetic acid in the presence of a catalytic
amount of sulfuric acid to furnish glycosyl donor 28 in 51% yield over 3 steps. Alternatively,
TFA could also be used as catalyst to provide acetylated 30-deoxyribofuranose 28 in higher yield
(90%), but a longer reaction time was required. The ortho-toluoyl protecting group at the 5-position was
preferred over the previously employed TBDPS functionality after that initial attempts to introduce
the thiocarbonyldimidazole at the sterically hindered 3-position in the presence of such silyl group
were unsuccessful.
0
0
Scheme 5. Synthesis of 2 -keto-3 -deoxynucleoside precursors.
3-Deoxyribofuranose 28 was reacted with thymine, N4-benzoylcytosine, and 6-chloropurine
under Vorbrüggen glycosylation conditions to provide the corresponding 50-O-o-toluoyl-20-O-acetyl-
30-deoxynucleosides 29a
–
c
. Upon coupling with thymine, the corresponding
analogue 29a was exclusively formed in quantitative yield. However, in the case of N4-benzoyl-cytosine
and 6-chloropurine, 10% of the -anomer (
ratio of 1:9) and 7% of the N7-alkylated regioisomer
were also formed, together with other side products that were not isolated (<5%), respectively, leading
to relatively lower yields of compounds 29b and 29c. The assignment of the -glycosidic bond
β-anomeric nucleoside
α
α:β
β
of the 30-deoxynucleoside analogues was carried out by 2D-NOESY experiments. The presence of
a significant NOE effect between H-40 and H-10, and the absence of any NOE interaction between
H-10 and H-50 at the level of the sugar moiety corroborated the stereoselectivity of the reaction for
purine and pyrimidine nucleobases. In addition, the coupling constants for the anomeric protons of
the synthesized 30-deoxynucleosides were found to be in agreement with previous reports [28
After standard protecting group manipulation, compounds 29a (B = T) and 29b (B = CBz) were
,29].

Molecules 2018, 23, 1457
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converted to 50-TBDPS-30-deoxynucleosides 30a and 30b. 6-Chloropurine 30-deoxynucleoside 29c
could either undergo displacement of the chlorine atom by a methoxide functionality or be transformed
into the corresponding adenine containing derivative, depending on the reaction conditions, to afford
0
after further silylation compounds 30c and 30d, respectively. Silylated 3 -deoxynucleoside derivatives
30a (B = T) and 30c (B = 6-OMe-purine) were then oxidized using DMP in dry DCM at 0 ◦C to give
the desired 50-O-TBDPS-20-ketonucleosides 33a and 33b in quantitative yield, which could be easily
purified by column chromatography.
In order to obtain the corresponding cytosine- and adenine-containing nucleoside derivatives,
compounds 30b (B = C) and 30d (B = A) were fully protected at the 20-OH and exocyclic amino group
using o-toluoyl chloride in the presence of pyridine. The resulting compounds 31a and 31b were then
◦
reacted with one equivalent of potassium tert-butoxide at
−
78 C in dry THF. In the case of the cytosine
derivative, regioselective deprotection at the 20-position led to the desired nucleoside intermediate,
which was readily oxidized to the corresponding ketone 33c. In contrast, under similar conditions,
0
0
adenine derivative 31b underwent complete detoluylation reverting to 5 -O-TBDPS-3 -deoxyadenosine
30d. However, we found that the desired transformation could be efficiently achieved after replacement
of the 50-TBDPS with a 50-o-Tol group. Thus, compound 29c was transformed into 30-deoxyadenosine
(
30-dA), toluoylated to 32, which subsequently could be selectively deprotected at the 20-position
and further oxidized to give the desired 50-O-o-toluolyl-20-keto-6-N-o-toluoyl adenine containing
nucleoside 33d in 55% yield over two steps.
Subsequently, all suitably protected 20-keto nucleosides 33a
–d were subjected to the chlorination
reaction in the presence of PCl5 to furnish thymine and 6-OMe-purine containing 20,20-gem-dichloro
nucleosides 4a and 4b as well as protected nucleosides 34 and 35, which upon final removal of the
toluoyl moieties with ethanolic ammonia provided the desired 20,20-dichloro-20,30-dideoxycytidine
and adenosine derivatives 4c and 4d (Scheme 6). Although this transformation could also suffer from
a concomitant elimination reaction, we did not notice any side product formation with the exception
of the thymine derivative. In this case, 50-O-TBDPS-20-chloro-20,30-vinyl-20,30-dideoxythymidine
derivative (19%) was readily isolated from the reaction mixture after column chromatography
and characterized.
0
0
0
0
Scheme 6. Synthesis of 2 ,2 -gem-dichloro-2 ,3 -dideoxynucleosides.
The confirmation of the structure of all intermediates and final compounds was carried out by
1D and 2D NMR spectroscopic analysis. Furthermore, mass spectroscopy in positive mode further
proved the structure of the chlorinated nucleosides. The presence of chlorine atoms in the target
compounds was confirmed by the intensity ratios of the isotopes of the protonated molecular ions
(see Supplementary Materials). In the case of the dichloride derivatives, the molecular ions consisted
of three peaks spaced by two mass units, while for monochlorinated nucleoside derivatives two
peaks were observed. AQS for biological activity, unfortunately, none of the synthesized chlorinated
nucleoside analogues showed any activity against HIV-1 and HIV-2 in MT-4 cell cultures.

Molecules 2018, 23, 1457
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3. Materials and Methods
3.1. General Information
All reagents and solvents were purchased from commercial sources and used as obtained.
Moisture sensitive reactions were carried out in oven-dried glassware under a nitrogen or argon
1
atmosphere unless otherwise stated. H- and 13C-NMR spectra were recorded on an Avance 300, 500,
or 600 MHz spectrometer (Bruker BioSpin, Billerica, MA, USA) using tetramethylsilane as internal
standard or referenced to the residual solvent signal. Chemical shifts (δ) are expressed in parts per
million (ppm), while coupling constants in Hz (Hertz). High-resolution mass spectra (HRMS) were
acquired on a quadruple orthogonal acceleration time-of-flight mass spectrometer (Synapt G2 HDMS,
Waters, Milford, MA, USA). Samples were infused at 3 µL/min, and spectra were obtained in positive
(or in negative) ionization mode with a resolution of 15,000 (FWHM) using leucine enkephalin as
lock mass. Thin layer chromatography (TLC) was performed on silica gel Alugram (aluminum foil)
pre-coated sheets (254 nm, Macherey-Nagel, Düren, Germany). Products were purified by column
chromatography on silica gel (60 Å, 0.035
RP-HPLC purification was performed on a Gemini 110A column (C18, 10
Phenomenex, Utrecht, Belgium) using H2O/CH3CN as eluent gradient. Purities of all the tested
compounds were verified to be >95% by HPLC analysis.
−
0.070 mm, Acros Organics, Geel, Belgium). Preparative
m, 21.2 mm 250 mm,
µ
×
3.2. General Oxidation Procedure
A stirred solution of 20- or 30-deoxynucleoside (1.0 equiv.) in CH2Cl2 (15 mL/mmol) was cooled
in an ice bath, and then Dess-Martin periodinane (DMP) (1.0 equiv.) was added under an inert
atmosphere. The reaction mixture was allowed to warm to room temperature and stirred for 4 h.
It was then diluted with EtOAc (50 mL/mmol) and washed successively with saturated aq. NaHCO3,
water, and brine. The organic layer was dried over Na2SO4, filtered, and evaporated in vacuo to give a
crude residue, which was purified by silica gel column chromatography to afford the title compound.
3.3. General Chlorination Procedure
To a stirred solution of 30- or 20-ketonucleoside (1 equiv.) in dry CH2Cl2 (20.0 mL/mmol) at
−
78 ◦C was added PCl5 (3.8 equiv.) under an inert atmosphere. The reaction mixture was allowed to
warm to
−
50 ◦C and stirred for 4 h. It was then diluted with EtOAc (200.0 mL/mmol) and quenched
with a K2HPO4/KH2PO4 buffer (pH = 7, 200.0 mL/mmol). Subsequently, the organic layer was
separated and washed with cold water and brine. The organic layer was dried over Na2SO4, filtered,
and concentrated in vacuo to give a crude residue that was purified by column chromatography to
afford the title compound.
3.4. General Desilylation Procedure
To a stirred solution of 50-O-TBDPS chlorinated nucleoside (1 equiv.) in dry THF at
−
50 ◦C was
added a 1M TBAF solution in THF (1.5 equiv.). The reaction mixture was allowed to slowly warm to
room temperature over 2 h. After completion of the reaction, the mixture was diluted with EtOAc and
washed with water. The organic layer was dried over Na2SO4, filtered, and concentrated in vacuo to
give a crude residue that was purified by column chromatography to afford the title compound.
3.5. General Procedure for Sugar-Base Condensation
To a solution of nucleobase (1 equiv.) in dry CH3CN, was added N,O-bis(trimethylsilyl)acetamide
(2.5 equiv.) and the resulting mixture was stirred for 20 min at room temperature. A solution◦of
28 (0.8 equiv.) in dry CH3CN was then added and the reaction mixture was cooled to
−
20 C.
Next, trimethylsilyl trifluoromethanesulfonate (TMSOTf) (1.05 equiv.) was added dropwise and the
◦
mixture was allowed to slowly warm to room temperature over 1 h, heated to 70 C, and further

Molecules 2018, 23, 1457
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stirred for 1 h. It was then diluted with EtOAc and washed with saturated aq. NaHCO3, water, and
brine. The organic layer was dried over Na2SO4, filtered, and evaporated in vacuo to give a crude
residue, which was purified by silica gel column chromatography to afford the tile compound.
50-O-(tert-Butyldiphenylsilyl)-30-keto-20-deoxythymidine (11). To a solution of 20-deoxythymidine
(1.15 g, 4.78 mmol) and imidazole (0.650 g, 9.56 mmol) in anhydrous DMF (50 mL) was added
tert-butyldiphenylsilyl chloride(TBDPSCl) (1.38 g, 5.00 mmol) at
50 ◦C. The reaction mixture was
9
−
allowed to warm to room temperature and stirred for 4 h. It was then diluted with EtOAc (200 mL) and
washed with water and brine. The organic layer was dried over Na2SO4, filtered, and evaporated in
0
0
1
vacuo to give 5 -O-(tert-butyldiphenylsilyl)-2 -deoxythymidine in quantitative yield (2.28 g). H-NMR
(500 MHz, CDCl3): 8.95 (s, 1H, NH), 7.68–7.66 (m, 4H, ArH), 7.54 (d, 1H, J = 1.1 Hz, H-6), 7.41–7.34
(m, 6H, ArH), 6.48 (dd, 1H, J = 8.2, 5.7 Hz, H-1 ), 4.61 (br s, 1H, OH), 4.27–4.26 (m, 1H, H-3 ), 4.10–4.08
δ
0
0
0
0
(m, 1H, H-4 ), 4.00 (dd, 1H, J = 11.4, 2.2 Hz, H-5 ), 3.88 (dd, 1H, J = 11.4, 2.2 Hz, H-5”), 2.49–2.47 (m, 1H,
H-2 ), 2.21–2.19 (m, 1H, H-2”), 1.58 (d, J = 1.1 Hz, 3H, CH3), 1.09 (s, 9H, 3
0
×
CH3); 13C-NMR (125 MHz,
CDCl3):
129.8 (ArC), 129.7 (ArC), 127.7 (ArC), 127.6 (ArC), 110.8 (5-C), 87.1 (10-CH), 84.5 (40-CH), 71.3 (30-CH),
64.0 (50-CH2), 40.7 (20-CH2), 31.3 (-C(CH3)3), 26.7 (3
CH3), 11.8 (5-CH3). Following the general
δ 164.2 (C=O), 150.6 (C=O), 135.3 (ArC), 135.2 (ArC), 135.0 (6-C), 132.8 (ArC), 132.1 (ArC),
×
0
0
oxidation procedure, 5 -O-(tert-butyldiphenylsilyl)-2 -deoxythymidine (1.54 g, 3.00 mmol) was reacted
with DMP (1.70 g, 4.00 mmol) in CH2Cl2 (100 mL). After work-up, the resulting crude residue was
then recrystallized from CHCl3 to provide 11 as a white solid (1.14 g, 80%, over two steps), which
was used in the next step without any further purification. HRMS: C26H30N2O5 [M + Na+]+ Calc.:
501.1816, found: 501.1886.
0
0
0
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-3 ,3 -gem-dichloro-3 -deoxythymidine (16) and 5 -O-(tert-butyldiphenylsilyl)-3 -
0
0
0
chloro-2 ,3 -didehydro-3 -deoxythymidine (17). Following the general chlorination procedure, a solution of
compound 11 (0.500 g, 1.04 mmol) in dry CH2Cl2 (20 mL) was reacted with PCl5 (0.822 g, 3.95 mmol)
at
−
78 ◦C under an inert atmosphere. After work-up, the resulting crude residue was purified by
column chromatography (hexane: EtOAc 4:1) to give 16 (0.165 g, 30%) and 17 (0.180 g, 35%) as pale
1
yellow solids. Data for 16: H-NMR (500 MHz, CDCl3):
δ 10.3 (s, 1H, NH), 7.68–7.66 (m, 4H, ArH),
7.54 (d, 1H, J = 1.1 Hz, H-6), 7.41–7.35 (m, 6H, ArH), 6.48 (dd, 1H, J = 8.2, 5.7 Hz, H-10), 4.10 (dd,
1H, J = 4.7, 2.2 Hz, H-40), 3.99 (dd, 1H, J = 11.5, 2.2 Hz, H-50), 3.88 (dd, 1H, J = 11.5, 4.7 Hz, H-5”),
0
3.79 (dd, 1H, J = 11.5, 5.7 Hz, H-2 ), 3.35 (dd, 1H, J = 11.5, 8.2 Hz, H-2”), 1.54 (s, 3H, 5-CH3), 0.97 (s, 9H,
3
×
CH3); 13C-NMR (150 MHz, CDCl3):
δ
163.7 (C=O), 150.2 (C=O), 135.4 (6-C), 135.4 (ArC), 135.3 (ArC),
135.3 (ArC), 135.1 (ArC), 129.7 (ArC), 129.6 (ArC), 127.6 (ArC), 127.5 (ArC), 110.8 (5-C), 87.5 (40-CH),
85.0 (30-C(Cl)2), 84.5 (10-CH), 63.7 (50-CH2), 41.0 (20-CH2), 26.6 (3
×
CH3), 19.0 (C(CH3)), 11.6 (5-CH3);
HRMS: C26H30N2O4SiCl2 [M + H+]+ Calc.: 533.1424, found: 533.1442. Data for 17: H-NMR (500 MHz,
1
CDCl3):
ArH, H-6), 7.02 (dd, 1H, J = 4.0, 1.3 Hz, H-10), 5.93 (t, 1H, J = 1.3 Hz, H-20), 4.78–4.77 (m, 1H, H-40),
4.09–4.08 (m, 2H, H-50, H-5”), 1.17 (s, 3H, 5-CH3), 1.09 (s, 9H, 3 CH3); 13C-NMR (125 MHz, CDCl3):
163.7 (C=O), 150.7 (C=O), 136.3 (6-C), (30-C(Cl)), 135.3 (ArC), 135.2 (ArC), 133.5 (ArC), 132.6 (ArC),
130.1 (ArC), 129.9 (ArC), 127.9 (ArC), 127.8 (ArC), 121.2 (20-CH), 111.6 (5-C), 87.5 (40-CH), 86.5 (10-CH),
62.1 (50-CH2), 27.1 (3 CH3), 19.6 (C(CH3)), 11.3 (5-CH3); HRMS: C26H29N2O4SiCl [M + Na+]+ Calc.:
δ 9.00 (s, 1H, NH), 7.67 (d, 2H, J = 6.7 Hz, ArH), 7.62 (d, 2H, J = 6.7 Hz, ArH), 7.43–7.25 (m, 7H,
×
δ
×
519.14775, found: 519.1468.
30,30-gem-Dichloro-30-deoxythymidine (3a). Following the general desilylation procedure, a solution
of compound 16 (0.143 g, 0.27 mmol) in dry THF (2.0 mL) was reacted with TBAF (1 mL, 2 mmol)
◦
at
−
50 C. After work-up, the resulting crude residue was purified by column chromatography
1
(EtOAc) to give 3a as a yellow solid (76 mg, 89%). H-NMR (600 MHz, DMSO-d6):
δ 11.4 (s, 1H, NH),
7.70 (d, 1H, J = 1.2 Hz, H-6), 6.27 (dd, 1H, J = 7.0, 6.3 Hz, H-10), 5.34 (t, J = 5.0 Hz, 1H, OH), 4.38 (dd,
1H, J = 5.1, 3.1 Hz, 40-H), 3.82 (ddd, 1H, J = 12.1, 5.1, 3.1 Hz, H-50), 3.78 (ddd, 1H, J = 12.1, 5.0, 3.1 Hz,
H-5”), 3.21 (dd, J = 14.7, 6.3 Hz, 1H, H-20), 3.03 (dd, J = 14.6, 7.0 Hz, 1H, H-2”), 1.78 (d, 3H, J = 1.2
Hz, 5-CH3); 13C-NMR (150 MHz, DMSO):
δ 163.7 (C=O), 150.5 (C=O), 135.6 (6-C), 109.8 (5-C), 89.0

Molecules 2018, 23, 1457
9 of 22
0
0
0
0
0
(4 -CH), 86.9 (3 -C(Cl)2), 81.8 (1 -CH), 60.7 (5 -CH2), 50.4 (2 -CH2), 12.4 (5-CH3); HRMS: C10H12Cl2N2O4
[M + H+]+ Calc.: 317.0066, found: 317.0074.
0
0
0
0
3 -Chloro-2 ,3 -didehydro-3 -deoxythymidine (18). Following the general desilylation procedure, a solution
of compound 17 (0.124 g, 0.25 mmol) in dry THF (2.0 mL) was reacted with TBAF (1 mL, 2 mmol) at
−
50 ◦C. After work-up, the resulting crude residue was purified by column chromatography (EtOAc)
1
to give 18 (62.6 mg, 88%) as a yellow solid. H-NMR (600 MHz, CDCl3):
δ 8.87 (s, 1H, NH), 7.72 (d, 1H,
J = 1.4 Hz, H-6), 7.01 (dd, 1H, J = 4.7, 1.7 Hz, H-10), 5.96 (t, 1H, J = 1.7 Hz, H-20), 5.30 (s, 1H, OH),
5.00–4.99 (m, 1H, 40-H), 3.93 (dd, 1H, J = 15.5, 3.0 Hz, H-50), 3.89 (dd, 1H, J = 15.5, 3.0 Hz, H-5”),
1.91 (d, 3H, J = 1.4 Hz, CH3); 13C-NMR (150 MHz, CDCl3):
0
δ 163.5 (C=O), 150.7 (C=O), 135.9 (3 -C(Cl)),
135.7 (6-C), 122.9 (20-C), 111.9 (5-C), 87.5 (40-CH), 84.1 (10-CH), 44.1 (50-CH2), 12.4 (5-CH3); HRMS:
C10H11Cl1N2O4 [M + H+]+ Calc.: 259.0480, found: 259.0489.
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-3 -keto-2 -deoxyuridine (19). To a solution of uridine (1.09 g, 4.78 mmol) and
imidazole (0.650 g, 9.56 mmol) in anhydrous DMF (50 mL) was added TBDPSCl (1.38 g, 5.00 mmol)
◦
at
−
50 C. The reaction mixture was allowed to warm to room temperature and stirred for 4 h.
It was then diluted with EtOAc (200 mL) and washed with water and brine. The organic layer was
dried over Na2SO4, filtered, and evaporated in vacuo to give 50-O-(tert-butyldiphenylsilyl) uridine
1
in quantitative yield (2.21 g). H-NMR (500 MHz, CDCl3):
δ 10.1 (s, 1H, NH), 7.83 (d, 1H, J = 8.1 Hz,
H-6), 7.66–7.63 (m, 4H, ArH), 7.42–7.37 (m, 6H, ArH), 6.37 (t, 1H, J = 6.4 Hz, H-10), 5.43 (d, 1H, J = 8.1
Hz, H-5), 4.56 (br s, 1H, OH), 4.11–4.10 (m, 1H, H-30), 4.03–4.02 (m, 1H, H-40), 3.98 (dd, 1H, J = 11.4,
2.3 Hz, H-50), 3.85 (dd, 1H, J = 11.4, 2.9 Hz, H-5”), 2.49–2.44 (m, 1H, H-20), 2.24–2.18 (m, 1H, H-2”),
1.07 (s, 9H, 3
135.1 (ArC), 132.6 (ArC), 132.1 (ArC), 129.8 (ArC), 129.8 (ArC), 127.7 (ArC), 127.7 (ArC), 102.0 (5-C),
87.0 (10-CH), 84.8 (40-CH), 70.8 (30-CH), 63.6 (50-CH2), 41.0 (20-CH2), 31.3 (-C(CH3)3), 26.7 (3
CH3);
×
CH3); 13C-NMR (125 MHz, CDCl3):
δ 163.7 (C=O), 150.4 (C=O), 140.0 (6-C), 135.4 (ArC),
×
HRMS for C25H30N2O4Si1 [M + Na]+ Calc.: 489.1816, found: 489.1816. Following the general oxidation
procedure, 50-O-(tert-butyldiphenylsilyl) uridine (1.39 g, 3.00 mmol) was reacted with DMP (1.70 g,
4.00 mmol) in CHCl3 (100 mL). After work-up, the resulting crude residue was recrystallized from
CHCl3 to provide 19 as a white solid (1.23 g, 87% over two steps), which was used in the next step
without any further purification. HRMS: C25H28N2O5 [M + Na+]+ Calc.: 487.1659 found: 487.1686.
50-O-(tert-Butyldiphenylsilyl)-30,30-gem-dichloro-20,30-dideoxyuridine (20) and 50-O-(tert-butyldiphenyl-
silyl)-30-chloro-20,30-didehydro-20,30-dideoxyuridine (21). Following the general chlorination procedure,
a solution of compound 19 (0.482 g, 1.04 mmol) in dry CH2Cl2 (20 mL) was reacted with PCl5 (0.822 g,
3.95 mmol) at
−
78 ◦C under an inert atmosphere. After work-up, the resulting crude residue was
purified by column chromatography (hexane:EtOAc 4:1) to give 20 (0.227 g, 44%) and 21 (0.175 g,
1
35%) as yellow pale solids. Data for 20: H-NMR (500 MHz, CDCl3):
δ 9.57 (s, 1H, NH), 7.70–7.66
(m, 4H, ArH), 7.56 (d, 1H, J = 8.2 Hz, H-6), 7.47–7.38 (m, 6H0, ArH), 6.23 (dd, 1H, J = 6.8, 4.9 Hz, H-10),
0
5.51 (d, 1H, J = 8.2 Hz, H-5), 4.43 (dd, 1H, J = 5.1, 3.0 Hz, H-4 ), 4.15 (dd, 1H, J = 11.8, 3.0 Hz, H-5 ), 4.03
0
(dd, 1H, J = 11.8, 5.2 Hz, H-5”), 3.23 (dd, 1H, J = 14.8, 6.9 Hz, H-2 ), 2.96 (dd, 1H, J = 14.8, 4.8 Hz, H-2”),
1.08 (s, 9H, 3
×
CH3); 13C-NMR (125 MHz, CDCl3):
δ 163.2 (C=O), 150.2 (C=O), 139.4 (6-C), 135.7 (ArC),
135.4 (0ArC), 132.7 (ArC), 132.2 (ArC), 130.0 (ArC), 130.0 (ArC), 127.9 (ArC), 127.8 (ArC), 102.1 (5-C),
0
0
0
0
89.9 (4 -CH), 84.5 (3 -C(Cl)2), 83.3 (1 -CH), 63.1 (5 -CH2), 52.7 (2 -CH2), 29.6 (-C(CH3)3), 26.8 (3
×
CH3);
HRMS: C25H28Cl2N2O4Si [M + H+]+ Calc.: 519.1268, found: 519.1290. Data for 21: H-NMR (600 MHz,
1
CDCl3):
δ 8.44 (s, 1H, NH), 7.81 (d, 1H, J = 8.2 Hz, 6-H), 7.66–7.64 (m, 3H, ArH), 7.57–7.55 (m, 2H,
ArH), 7.44–7.35 (m, 5H, ArH), 7.03 (dd, 1H, J = 3.8, 1.5 Hz, H-10), 5.9 (t, 1H, J = 1.5 Hz, H-20), 4.86
(d, 1H, J = 8.2 Hz, 5-H), 4.80 (dddd, 1H, J = 3.8, 2.7, 1.5, 1.3 Hz, H-40), 4.07 (dd, 1H, J = 12.3, 1.3 Hz,
H-50), 4.07 (dd, 1H, J = 12.3, 2.7 Hz, H-5”), 1.10 (s, 9H, 3
×
CH3); 13C-NMR (150 MHz, CDCl3):
δ 158.9
(C=O), 149.7 (C=O), 136.9 (6-C), 136.5 (30-C(Cl)), 136.5 (ArC), 135.5 (ArC), 135.2 (ArC), 132.9 (ArC),
132.3 (ArC), 130.0 (ArC), 129.9 (ArC), 127.8 (ArC), 127.7 (ArC), 121.7 (20-CH), 109.9 (5-C), 88.3 (40-CH),
86.9 (10-CH), 62.9 (50-CH2), 29.6 (C(CH3), 27.1 (3
505.1321, found: 505.1321.
×
-CH3); HRMS: C25H27ClN2O4Si [M + Na+]+ Calc.:

Molecules 2018, 23, 1457
10 of 22
50-O-(tert-Butyldiphenylsilyl)-30,30-dichloro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine (22). To a stirred
◦
solution of 20 (1.04 g, 2.00 mmol) in dry CH3CN (10 mL) was added POCl3 (0.28 mL, 3 mmol) at
−
50 C.
Triethylamine (0.7 mL, 5.00 mmol) was then added dropwise over 10 min, followed by a solution of
1,2,4-triazole (0.414 g, 6.00 mmol) and triethylamine (0.8 mL, 6.00 mmol) in dry CH3CN (15 mL) over
30 min. The reaction mixture was stirred at room temperature for two days. It was then diluted with
EtOAc (200.0 mL) and quenched with a NaH2PO4/Na2HPO4 buffer (pH = 7, 150.0 mL). The organic
layer was washed with water and brine, dried over Na2SO4, and evaporated in vacuo to give a crude
residue, which was purified by column chromatography (EtOAc:hexane 7:3) to afford compound 22
1
as a white solid (0. 967 mg, 85%). H-NMR (300 MHz, CDCl3):
δ 9.19 (s, 1H, N-CH=N), 8.06 (s, 1H,
N-CH=N), 7.98 (d, 1H, J = 7.3 Hz, H-6), 7.68–7.62 (m, 4H, ArH), 7.43–7.42 (m, 6H, ArH), 6.81 (d, 1H,
J = 7.3 Hz, H-5), 6.10 (dd, 1H, J = 7.3, 3.0 Hz, H-10), 4.49 (dd, 1H, J = 6.0, 3.0 Hz, H-40), 4.19 (dd, 1H,
J = 11.8, 3.0 Hz, H-50), 4.01 (dd, 1H, J = 11.8, 6.0 Hz, H-5”), 3.38 (dd, 1H, J = 15.3, 7.3 Hz, H-20),
3.05 (dd, 1H, J = 15.3, 3.0 Hz, H-2”), 1.03 (s, 9H, 3
×
CH3); 13C-NMR (75 MHz, CDCl3):
δ 159.8 (C=O),
154.4 (4-CN), 146.6 (N-CH=N), 143.6 (N-CH=N), 136.1 (6-C), 136.0 (ArC), 135.8 (ArC), 132.9 (ArC),
132.7 (ArC), 130.4 (ArC), 130.3 (ArC), 128.2 (ArC), 128.1 (ArC), 94.4 (5-C), 90.9 (40-CH), 86.4 (10-CH),
84.3 (30-C(Cl)2), 63.2 (50-CH2), 53.3 (20-CH2), 30.0 (C(CH3)3), 27.1 (3
×
CH3); HRMS: C27H29Cl2N5O3Si
[M + H+]+ Calc.: 570.1489, found: 570.1489.
30,30-gem-Dichloro-20,30-dideoxycytidine (3b). Following the general desilylation procedure, 22 (0.142 g,
0.25 mmol) was reacted with a solution of TBAF in THF (0.4 mL, 0.375 mmol) in dry THF (2.0 mL).
After work-up, the resulting crude residue was purified by column chromatography (EtOAc) to
give 30,30-gem-dichloro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine as a yellow solid (66 mg, 80%).
1H-NMR (500 MHz, DMSO-d6):
δ
9.44 (s, 1H, N-CH=N), 8.61 (d, 1H, J = 7.3 Hz, H-6), 8.41 (s, 1H,
0
N-CH=N), 7.03 (d, 1H, J = 7.3 Hz, H-5), 6.15 (dd, 1H, J = 7.4, 3.6 Hz, H-1 ), 5.35 (s, 1H, OH), 4.56 (dd, 1H,
J = 5.9, 3.1 Hz, H-40), 3.91 (dd, 1H, J = 12.3, 3.1 Hz, H-50), 3.88 (dd, 1H, J = 12.3, 5.8 Hz, H-5”), 3.50 (dd,
J = 14.9, 7.4 Hz, 1H, H-20), 3.06 (dd, J = 14.9, 3.6 Hz, 1H, H-2”); 13C-NMR (125 MHz, DMSO-d6):
δ
159.9 (2-C=O), 154.2 (4-CN), 153.5 (N-CH=N), 148.1 (N-CH=N), 143.8 (6-C), 140.1 (5-C), 93.8 (40-CH),
90.0 (10-CH), 85.9 (30-C(Cl)2), 60.3 (50-CH2), 51.7 (20-CH2); HRMS: C11H11Cl2N5O3 [M + Na+]+ Calc.:
354.0131, found: 354.0132. To a stirred solution of the above compound (0.100 g, 0.30 mmol,) in
EtOH (3 mL) at
−
20 ◦C was added a solution of NH3 in EtOH, and then the reaction was allowed
to warm to room temperature. After stirring for 4 h, the volatiles were removed in vacuo, and the
crude residue was purified by column chromatography (EtOAc:EtOH 75:25) to give 3b as a pale green
1
solid (0.753 g, 90%). H-NMR (600 MHz, DMSO-d6):
δ 7.78 (d, 1H, J = 7.5 Hz, H-6), 7.34 (s, 1H, NH2),
0
7.19 (s, 1H, NH2), 6.19 (dd, 1H, J = 7.1, 5.2 Hz, H-1 ), 5.78 (d, 1H, J = 7.5 Hz, H-5), 5.32 (t, 1H, J = 5.3 Hz,
OH), 4.37 (dd, 1H, J = 5.0, 3.0 Hz, H-40), 3.83 (ddd, 1H, J = 12.1, 5.3, 3.0 Hz, H-50), 3.77 (ddd, 1H,
J = 12.1, 5.3, 5.0 Hz, H-5”), 3.25 (dd, 1H, J = 14.7, 7.2 Hz, H-20), 2.87 (dd, 1H, J = 14.6, 5.2 Hz, H-2”);
13C-NMR (150 MHz, DMSO-d6):
δ
165.7 (4-C-NH2), 154.9 (2-C=O), 140.65 (6-C), 94.2 (5-C), 89.1 (40-C),
86.80 (30-C(Cl)2), 83.1 (10-CH), 60.6 (50-CH2), 51.6 (20-CH2); HRMS: C9H10Cl1N3O3 [M + H+]+ Calc.:
280.0250, found: 280.0250.
30-Chloro-20,30-didehydro-20,30-dideoxycytidine (23). To a stirred solution◦of 21 (0.95 g, 2.00 mmol)
in dry CH3CN (10 mL) was added POCl3 (0.28 mL, 3 mmol) at
−
50 C. Triethylamine (0.7 mL,
5.00 mmol) was then added dropwise over 10 min, followed by a solution of 1,2,4-triazole (0.414 g,
6.00 mmol) and triethylamine (0.8 mL, 6.00 mmol) in dry CH3CN over 30 min. The reaction
mixture was stirred at room temperature for two days. It was then diluted with ethyl acetate
(200 mL) and quenched with a NaH2PO4/Na2HPO4 buffer (pH = 7, 150.0 mL). The organic
layer was washed with water and brine, dried over Na2SO4, and evaporated in vacuo to give
a crude residue, which was purified by column chromatography (EtOAc:hexane 7:3) to give
50-O-(tert-butyldiphenylsilyl)-30-chloro-20,30-didehydro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine
1
as a white solid (0.884 mg, 80%). H-NMR (300 MHz, CDCl3):
δ 9.24 (s, 1H, N-CH=N), 8.55 (d, 1H,
J = 7.25 Hz, H-6), 8.07 (s, 1H, N-CH=N), 8.07–7.08 (m, 10H, ArH), 7.09 (dd, 1H, J = 3.3, 1.5 Hz, H-10),

Molecules 2018, 23, 1457
11 of 22
6.28 (d, 1H, J = 7.25 Hz, H-5), 6.16 (t, 1H, J = 1.5 Hz, H-20), 4.89–4.87 (m, 1H, H-40), 4.13 (dd, 1H,
J = 12.2, 1.6 Hz, H-50), 4.11 (dd, 1H, J = 12.2, 2.0 Hz, H-5”), 1.11 (s, 9H, 3 CH3); 13C-NMR (75 MHz,
CDCl3):
154.0 (C=O), 147.8 (4-CN), 147.6 (N-CH=N), (6-C) 143.2, 141.8 (N-CH=N), 136.3 (30-C(Cl)),
135.5 (ArC), 135.0 (ArC), 130.5 (ArC), 130.4 (ArC), 128.3 (ArC), 128.2 (ArC), 123.0 (20-C), 94.9 (5-C),
×
δ
90.3 (40-CH), 87.5 (10-CH), 62.5 (50-CH2), 29.9 (C(CH3)3), 27.3 (3
×
CH3); HRMS: C27H28ClN5O3Si
[M + H+]+ Calc.: 534.1722, found: 534.1718. Following the general desilylation procedure, a solution of
50-O-(tert-butyldiphenylsilyl)-30-chloro-20,30-didehydro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine
(0.53 g, 1.00 mmol) in dry THF (2.00 mL) was reacted with TBAF (1.5 mL, 1.5 mmol) at
After work-up, the resulting crude residue was purified by column chromatography (EtOAc)
to give 30-chloro-20,30-didehydro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine as a white solid
◦
−
50 C.
(0.221 mg, 75%). 1H-NMR (500 MHz, MeOD):
δ 9.38 (s, 1H, N-CH=N), 8.87 (d, 1H, J = 7.2 Hz,
H-6), 8.24 (s, 1H, N-CH=N), 7.12 (d, 1H, J = 7.2 Hz, H-5), 7.02 (dd, 1H, J = 2.5, 1.5 Hz, H-10),
6.19 (t, 1H, J = 1.5 Hz, H-20), 4.89 (br s, 1H, H-40), 3.89 (dq, 2H, J = 12.8, 1.5 Hz, H-50, H-5”);
13C-NMR (125 MHz, DMSO):
δ 161.1 (4-C=N), 157.1 (2-C=O), 154.8 (N-CH=N), 150.5 (N-CH=N),
144.7 (6-C), 137.7 (30-C(Cl)), 123.3 (20-CH) 96.0 (5-C), 92.0 (40-CH), 89.3 (10-CH), 62.9 (50-CH2);
HRMS: C11H10ClN5O3 [M + H+]+ Calc.: 296.0544, found: 296.0542. To a stirred solution of
30-chloro-20,30-didehydro-20,30-dideoxy-4-(1H-1,2,4-triazol-1-yl)uridine (0.295 g 0.01 mmol,) in EtOH
◦
(3.00 mL) at
−
20 C was added a solution of NH3 in EtOH. The reaction mixture was allowed to warm
to room temperature and stirred for 4 h. After removal of all the volatiles in vacuo, the crude residue
was purified by column chromatography (EtOAc:EtOH 75:25) to give 23 as a pale green solid (0.194 g,
1
80%). H-NMR (600 MHz, MeOD):
δ
8.12 (d, 1H, J = 7.5 Hz, H-6), 7.01 (dd, 1H, J = 3.3, 1.5 Hz, H-10),
0
0
6.06 (t, 1H, J = 1.5, H-2 ), 5.93 (d, 1H, J = 7.5 Hz, H-5), 4.87–4.77 (m, 1H, H-4 ), 3.86 (dq, 2H, J = 12.8, 2.0
Hz, H-50, H-5”); 13C-NMR (150 MHz, MeOD): 166.7 (4-C), 157.1 (C=O), 144.2 (6-C), 137.1 (30-CCl),
δ
123.7 (20-C), 96.0 (5-C), 90.2 (10-C), 88.4 (40-CH), 61.2 (50-CH2); HRMS: C9H10Cl1N3O3 [M + Na+]+
Calc.: 266.0303, found: 266.0308.
50-O-(tert-Butyldiphenylsilyl)-30,30-gem-dichloro-20,30-dideoxy-6-chloropurine (24). To a stirred solution of
6-chloropurine (0.616 g, 4.00 mmol) in dry CH3CN (10 mL), N,O-bistrimeth◦ylsilylacetamide (1.09 mL,
4.50 mmol) was added, and then the reaction mixture was heated at 78 C for 1 h. After cooling
to room temperature, a solution of compound 22 (0.569 g, 1.00 mmol) in dry CH3CN (15 mL) was
◦
added. The reaction mixture was then cooled to
−
20 C and TMSOTf (0.92 mL, 5.00 mmol) was added.
The mixture was allowed to slowly warm to 20 ◦C and it was then heated at 78 ◦C and stirred for 5 h.
It was then diluted with ethyl acetate and washed with saturated aq. NaHCO3 (50 mL), water (50 mL),
and brine (50 mL). The organic layer was dried over Na2SO4, filtered, and concentrated in vacuo.
The crude residue was purified by column chromatography (hexane:EtOAc 8.5:1.5 to 7:3) to give 24 as
an anomeric mixture (0.448 g, 80%). This mixture was further purified by column chromatography to
give 57% of 24a
(
α
-anomer) and 43% of 24b
(
β
-anomer). The unreacted excess of 6-chloropurine was
1
recovered. Data for 24b: H-NMR (300 MHz, CDCl3):
δ
8.71 (s, 1H, H-2), 8.28 (s, 1H, H-8), 7.69–7.26
(m, 10H, ArH), 6.54 (dd, 1H, J = 6.3, 5.3 Hz, H-10), 4.55 (dd, 1H, J = 5.5, 3.4 Hz, H-40), 4.20 (dd, 1H,
J = 11.7, 3.3 Hz, H-50), 4.09 (dd, 1H, J = 11.7, 5.5 Hz, H-5”), 3.44–3.42 (m, 2H, H-20, H-2”), 1.06 (s, 9H,
3
×
CH3); 13C-NMR (75 MHz, CDCl3):
δ 152.4 (6-C), 151.8 (2-C), 151.3 (4-C), 144.0 (5-C), 135.9 (ArC),
0
0
135.8 (ArC), 133.0 (ArC), 132.9 (ArC), 130.2 (8-C), 128.0 (ArC), 128.0 (ArC), 90.1 (4 -CH), 85.5 (3 -C(Cl2)),
84.4 (10-CH), 63.5 (50-CH2), 52.3 (20-CH2), 29.9 (C(CH3)3), 27.0 (3
×
CH3); HRMS: C26H27Cl3N4O2Si
[M + H+]+ Calc.: 561.1041, found: 561.1046.
0
0
0
0
3 ,3 -gem-Dichloro-2 ,3 -dideoxyadenosine (3c). Following the general desilylation procedure, 24b (0.028 g,
0.05 mmol) was reacted with a solution of TBAF in THF (0.5 mL, 0.5 mmol) in dry THF (5 mL).
◦
After work-up, the resulting crude material was dissolved in dry MeOH (5 mL) and cooled to
−
20 C.
A saturated solution of NH3 in H2O (10 mL, 25%) was then added; the reaction mixture was allowed to
warm to room temperature and stirred overnight. After removal of all the volatiles in vacuo, the crude
residue was purified by column chromatography (MeOH:EtOAc 0:10 to 2.5:7.5) to give 3c as a pale

Molecules 2018, 23, 1457
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yellow solid (4 mg, 14%). Compounds 25 and 26 were also isolated as an oil (11%) and white solid
1
(15%), respectively. Data for 3c: H-NMR (600 MHz, DMSO-d6):
δ 8.33 (s, 1H, H-2), 8.16 (s, 1H, H-8),
7.38 (s, 2H, NH2), 6.47 (t, 1H, J = 6.8 Hz, H-10), 5.48 (t, 1H, J = 5.3 Hz, OH), 4.46 (dd, 1H, J = 5.0,
3.3 Hz, H-40), 3.83 (ddd, 1H, J = 10.4, 5.0, 3.3 Hz, H-50), 3.79 (ddd, 1H, J = 10.4, 5.3, 5.0 Hz, H-5”),
0
3.65 (dd, 1H, J = 14.6, 6.8 Hz, H-2 ), 3.42 (dd, 1H, J = 14.6, 6.8 Hz, H-2”); 13C-NMR (150 MHz, DMSO-d6):
0 0 0
δ
156.2 (6-C), 152.8 (2-C), 149.2 (4-C), 139.1 (8-C), 118.9 (5-CH), 89.7 (4 -CH), 87.0 (3 -C(Cl2)), 81.2 (1 -CH),
61.2 (50-CH2), 49.9 (20-CH2); HRMS: C10H11Cl2N5O2 [M + H+]+ Calc.: 304.0362, found: 304.0357.
1
Data for 25:0 H-NMR (600 MHz, DMSO-d6):
δ
8.56 (s, 1H, H-2), 8.55 (s, 1H, H-8), 6.57 (dd, 1H, J = 7.1,
0
6.2 Hz, H-1 ), 5.32 (t, 1H, J = 4.9 Hz, OH), 4.48 (dd, 1H, J = 5.3, 3.4 Hz, 1H, H-4 ), 3.84 (ddd, 1H, J = 12.2,
5.0, 3.4 Hz, H-50), 3.80 (ddd, 1H, J = 12.2, 5.3, 5.0 Hz, H-5”), 3.66 (dd, 1H, J = 14.6, 6.2 Hz, H-20), 3.48
(dd, 1H, J = 14.6, 7.1 Hz, H-2”); 13C-NMR (150 MHz, DMSO-d6):
δ
160.10(6-C), 152.0 (2-C), 151.8 (4-C),
0
0
0
0
141.7 (8-C), 120.9 (5-CH), 89.7 (1 -CH), 86.7 (3 -C(Cl2)), 81.4 (4 -CH), 60.9 (5 -CH2), 50.0 (2 -CH2). Data for
26: H-NMR (300 MHz, DMSO-d6):
1
δ 8.23 (s, 1H, H-2), 8.15 (s, 1H, H-8), 7.29 (s, 2H, NH2), 6.96 (dd, 1H,
0
0
0
J = 5.1, 1.6 Hz, H-1 ), 6.37 (t, 1H, J = 1.6 Hz, H-2 ), 5.06–5.03 (m, 1H, H-4 ), 3.71 (dd, 1H, J = 12.7, 1.9 Hz,
H-5”), 3.59 (dd, 1H, J = 12.7, 3.0 Hz, H-50);013C-NMR (75 MHz, DMSO-d6):
δ 156.1 (6-C), 152.9 (2-C),
0
0
0
0
149.2 (4-C), 139.1 (8-C), 134.8 (3 -C), 122.0 (2 -CH), 119.0 (5-CH), 87.1 (1 -CH), 87.0 (4 -CH), 60.4 (5 -CH2);
HRMS: C10H10ClN5O2 [M + H+]+ Calc.: 268.0595, found: 268.0587.
5-O-(o-Toluoyl)-1,2-isopropylidene-α-D-xylofuranose (27). D-xylose (10.0 g, 0.067 mol) was dissolved
in acetone (260 mL) containing H2SO4 (0.66 M, 10.0 mL) and the solution was stirred for 30 min.
A solution of Na2CO3 (13.0 g, 0.123 mol) in water (112 mL) was carefully added to the above cooled
mixture, which was then stirred for further 2.5 h at 20 ◦C. Then, solid Na2CO3 (7.00 g, 0.066 mol) was
added, Na2SO4 (22.3 g) was filtered off and washed with acetone, and the filtrate was evaporated
in vacuo to afford a crude residue (14 g). This residue was resolubilized in a 9:1 mixture of EtOAc
(270 mL) and methanol (30 mL), filtered, and evaporated in vacuo to give a yellow oil (12 g, 96%).
This residue was dissolved in dry DMF (150 mL) under an inert atmosphere, cooled in an ice bath,
and then o-toluoyl chloride (9.85 g, 8.31 mL, 0.064 mol) was added, followed by imidazole (4.35 g,
0.064 mol). The reaction mixture was allowed to warm to room temperature and stirred for 5 h. It was
then diluted with EtOAc (300 mL) and washed with water (300 mL) and brine (100 mL). The organic
layer was dried over Na2SO4, filtered, and evaporated in vacuo to give a crude residue, which was
purified by column chromatography (hexane:EtOAc 7:3) to afford compound 27 (16.5 g, 84%) as
1
a colorless oil. H-NMR (300 MHz, CDCl3):
δ 7.92 (dd, 1H, J = 8.2, 1.6 Hz, ArH), 7.41–7.20 (m, 3H,
ArH), 5.97 (d, J = 3.6 Hz, 1H, H-10), 4.69 (dd, 1H, J = 13.4, 8.4 Hz, H-50), 4.57 (d, 1H, J = 3.6 Hz, H-20),
4.43 (dd, 1H, J = 13.4, 6.0 Hz, H-5”), 4.42 (ddd, 1H, J = 8.4, 6.0, 2.1 Hz, H-40), 4.24 (d, 1H, J = 2.1, H-30),
3.73 (s, 1H, OH), 2.57 (s, 3H, CH3), 1.49 (s, 3H, CH3), 1.30 (s, 3H, CH3); 13C-NMR (75 MHz, CDCl3):
δ
168.2 (CO), 140.7 (ArC), 132.7 (ArC), 132.0 (ArC), 131.1 (ArC), 129.0 (ArC), 126.0 (ArC), 112.0 (OCO)
105.1 (10-C), 85.4 (40-C), 78.8 (30-CH), 74.8 (20-CH), 62.0 (50-CH2), 27.0 (CH3), 26.4 (CH3), 22.0 (CH3);
HRMS for C16H20O6 [M + Na+]+ Calc.: 331.1152, found: 331.1156.
5-O-(o-Toluoyl)-1,2-diacetyl-3-deoxyxylofuranose (28). Compound 27 (1.00 g, 3.10 mmol) and N,N-
thiocarbonyldiimidazole (0.55 g, 3.10 mmol) were dissolved in dry DMF (20 mL) and then imidazole
(0.034 g, 0.50 mmol) was added under a nitrogen atmosphere. The reaction mixture was stirred
overnight, and it was then diluted with EtOAc (100 mL) and washed with water (100 mL) and
brine (500 mL). The organic layer was dried over Na2SO4, filtered, and evaporated in vacuo
to give a crude residue which was purified by column chromatography (hexane:EtOAc 7:3) to
afford 5-O-(o-toluoyl)-3-O-imidazolylthiocarbonyl-1,2-isopropylidene-D-xylofuranose (1.10 g, 89%)
as a pale yellow oil. 1H-NMR (300 MHz, CDCl3):
δ 8.32 (s, 1H, NCH) 7.88–7.01 (m, 6H,
ArH, NCH), 6.06 (d, 1H, J = 3.8 Hz, H-10), 5.99 (d, 1H, J = 2.9, H-30), 4.81–4.76 (m, 1H, H-40),
4.78 (d, 1H, J = 3.9 Hz, H-20), 4.59–4.56 (m, 2H, H-50, H-5”), 2.53 (s, 3H, ArCH3), 1.57 (s, 3H,
CH3), 1.35 (s, 3H, CH3); 13C-NMR (75 MHz, CDCl3):
δ
182.2 (CS), 168.8 (CO), 140.7 (C=N),
137.2 (C=N), 132.6 (ArC), 131.9 (ArC), 131.5 (ArC), 130.9 (ArC), 126.0 (ArC), 117.9 (ArC), 112.9 (OCO),

Molecules 2018, 23, 1457
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105.1 (10-C), 84.5 (40-C), 83.0 (30-CH), 76.9 (20-CH), 61.1 (50-CH2), 26.8 (CH3), 26.4 (CH3), 21.9 (CH3).
5-O-(o-Toluoyl)-3-O-imidazolylthiocarbonyl-1,2-isopropylidene- -D-xylofuranose (1.05 g, 2.50 mmol)
α
and AIBN (0.254 g, 1.50 mmol) were solubilized in toluene (50 mL). The resulting solution was stirred
◦
at 105 C for 25 min, and then tri-n-butyltin hydride (0.87 mL, 3.00 mmol) was added dropwise over 1
◦
h under a nitrogen atmosphere. The reaction mixture was stirred for an additional 2.5 h at 105 C, and
then it was cooled to room temperature and evaporated in vacuo. The crude residue was dissolved in
EtOAc (200 mL) and washed with water (200 mL) and brine (100 mL). The organic layer was dried
over Na2SO4, filtered, and evaporated in vacuo to give a crude product that was purified by column
chromatography (hexane:EtOAc 4:1) to afford 5-O-(o-toluoyl)-1,2-isopropylidene-3-deoxyxylofuranose
(0.50 g, 60%) as a colorless oil. 1H-NMR (300 MHz, CDCl3):
δ 7.95–7.92 (m, 2H, ArH), 7.42–7.37
(m, 2H, ArH), 7.26–7.21 (m, 4H, ArH), 5.96 (d, 1H, J = 3.8 Hz, H-10), 5.87 (d, 1H, J = 3.7 Hz, H-10),
4.79–4.76 (m, 1H, H-20), 4.59 (dd, 1H, J = 10.5, 4.1 Hz, H-50), 4.79–4.45 (m, 5H, H-40, H-40, H-50,
H-5”, H-5”), 2.21–2.15 (m, 1H, H-30), 1.77 (ddd, 1H, J = 13.1, 10.7, 4.9 Hz, H-3”), 2.60 (s, 3H, ArCH3),
2.59 (s, 3H, ArCH3), 1.54 (s, 3H, CH3), 1.50 (s, 3H, CH3), 1.33 (s, 6H, 2
×
CH3); 13C-NMR (75 MHz,
CDCl3): 167.5 (CO), 140.5 (ArC), 132.4 (ArC), 132.3 (ArC), 131.9 (ArC), 131.0 (ArC), 125.9 (ArC),
δ
112.0 (OCO), 105.5 (10-C), 84.6 (40-C), 76.0 (20-CH), 62.5 (50-CH2), 35.7 (30-CH), 27.0 (CH3), 26.5 (CH3),
22.0 (CH3); HRMS for C16H20O5 [M + Na+]+ Calc.: 315.1203, found: 315.1195. To a round-bottom
flask containing 5-O-(o-toluoyl)-1,2-isopropylidene-3-deoxyxylofuranose (0.292 g, 1.00 mmol) were
added acetic acid (5.0 mL) and acetic anhydride (3.0 mL). The reaction mixture was then cooled to
0 ◦C and then H2SO4 (0.5 mL) was added the stirring was continued overnight. The reaction mixture
was then diluted with EtOAc (50 mL) and washed with a saturated solution of NaHCO3 (200 mL),
water (50 mL), and brine (50 mL). The organic layer was dried over Na2SO4, filtered, and evaporated
in vacuo to give a crude residue that was purified by column chromatography (hexane:EtOAc 7:3)
1
to afford compound 28 (0.32 g, 95%) as a colorless oil and anomeric mixture. H-NMR (300 MHz,
CDCl3):
δ 7.95 (d, 1H, J = 8.0 Hz, ArH), 7.43–7.38 (m, 1H, ArH), 7.27–7.21 (m, 2H, ArH), 6.19 (s, 1H,
H-10), 5.23 (dd, 1H, J = 4.2, 1.5 Hz, H-20), 4.73–4.67 (m, 1H, H-40), 4.47 (dd, 1H, J = 11.8, 3.9 Hz, H-50),
4.33 (dd, 1H, J = 11.8, 5.6 Hz, H-5”), 2.61 (s, 3H, ArCH3), 2.25–2.20 (m, 2H, H-30, H-3”), 2.09 (s, 3H,
CH3), 1.96 (s, 3H, CH3); 13C-NMR (75 MHz, CDCl3):
δ
170.2 (ArCO), 169.5 (10-CO), 167.3 (20-CO),
140.7 (ArC), 132.5 (ArC), 132.0 (ArC), 130.9 (ArC), 125.9 (ArC), 121.6 (ArC), 99.6 (10-CH), 78.9 (40-CH),
76.9 (20-CH), 66.1.0 (50-CH2), 31.9 (30-CH2), 22.0 (ArCH3), 21.3 (COCH3), 21.1 (COCH3); HRMS for
C17H20O7 [M − H]− Calc.: 335.1136, found: 335.1121.
50-O-(o-Toluoyl)-20-O-acetyl-30-deoxythymidine (29a). Following the general procedure for sugar-base
condensation, a solution of thymine (0.302 g, 2.40 mmol) in dry CH3CN (10 mL) was reacted with
N,O-bis(trimethylsilyl)acetamide (1.46 mL, 6.00 mmol), a solution of 28 (0.672 g, 2.00 mmol) in dry
CH3CN (10 mL), and TMSOTf (0.46 mL, 2.50 mmol). After work-up, the crude residue was purified by
silica gel column chromatography (hexane:EtOAc 3:2) to afford compound 29a (0.803 g) as a white
1
solid in quantitative yield. H-NMR (300 MHz, CDCl3):
δ 8.76 (s, 1H, NH), 7.92–7.14 (m, 1H, ArH),
7.45–7.40 (m, 1H, ArH), 7.28–7.22 (m0, 2H, ArH), 7.14 (d, 1H, J = 1.2 Hz, 0H-6), 5.85 (d, 1H, J = 2.3 Hz,
0
H-1 ), 5.35 (dt, 1H, J = 9.5, 2.3 Hz, H-2 ), 4.65 (dd, J = 12.6, 2.7 Hz, 1H, H-5 ), 4.60 (dddd, J = 6.6, 5.6, 5.0,
2.7 Hz, 1H, H-40), 4.47 (dd, 1H, J = 12.8, 5.0 Hz, H-5”), 2.60 (s, 3H, CH3), 2.40 (ddd, 1H, J = 14.0, 9.5,
0
6.6 Hz, H-3 ), 2.19 (ddd, 1H, J = 14.0, 5.6, 2.2 Hz, H-3”), 2.12 (s, 3H, CH3), 1.65 (d, J = 1.1 Hz, 3H, 6-CH3);
13C-NMR (75 MHz, CDCl3):
132.7 (ArC), 132.5 (ArC), 130.5 (ArC), 126.2 (ArC), 111.5 (5-CH), 91.3 (1 -CH), 77.9 (4 -CH), 77.6 (2 -CH),
64.6 (50-CH2), 33.1 (30-CH), 21.9 (CH3), 21.1 (CH3), 12.1 (6-CH3); HRMS for C20H22N2O7 [M + H+]+
Calc.: 403.1499, found: 403.1495.
δ 170.3 (CO), 167.2 (CO), 163.7 (4-C), 150.2 (2-C), 140.8 (6-C), 135.8 (ArC),
0
0
0
50-O-(o-Toluoyl)-20-O-acetyl-30-deoxy-4-N-benzoylcytidine (29b). Following the general procedure for
sugar-base condensation, a solution of N4-benzoylcytosine (0.538 g, 2.40 mmol) in dry CH3CN (10 mL)
was reacted with N,O-bis(trimethylsilyl)acetamide (0.73 mL, 3.00 mmol), a solution of 28 (0.672 g,
2.00 mmol) in dry CH3CN (10 mL), and TMSOTf (0.46 mL, 2.50 mmol). After work-up, the crude

Molecules 2018, 23, 1457
14 of 22
residue was purified by silica gel column chromatography (hexane:EtOAc 1:1) to afford product 29b
(0.677 g) as a white solid in 69% yield. The corresponding
α
-anomer was also isolated as a white
1
solid (0.098 g, 10%). H-NMR (300 MHz, CDCl3):
δ 8.00–7.99 (m, 1H, ArH), 7.90–7.89 (m, 2H, ArH),
7.79 (d, J = 7.8 Hz, 1H, H-6), 7.64–7.62 (m, 1H, ArH), 7.54–7.52 (m, 2H, ArH), 7.36–7.20 (m, 3H, ArH),
6.38 (d, 1H, J = 7.8 Hz, H-5), 5.58–5.55 (m, 1H, H-40), 5.51 (d, 1H, J = 4.7 Hz, H-10), 4.42–4.40 (m,
1H, H-20), 4.56 (dd, 1H, J = 12.0, 4.2 Hz, H-50), 4.40 (dd, 1H, J = 12.0, 6.2 Hz, H-5”), 2.23–2.17 (m,
1H, H-30), 2.10–2.06 (m, 1H, H-3”), 2.57 (s, 3H, CH3), 2.28 (s, 3H, CH3); 13C-NMR (75 MHz, CDCl3):
δ
186.4 (NHCO), 167.7 (ArCO), 166.6 (CH3CO), 162.2 (4-CN), 145.5 (2-CO), 140.6 (6-C), 133.3 (ArC),
132.3 (ArC), 131.7 (ArC), 130.5 (ArC), 129.1 (ArC), 128.5 (ArC), 127.5 (ArC), 125.8 (ArC), 97.3 (5-C),
92.0 (10-CH), 73.8 (40-C), 70.3 (20-C), 62.2 (50-CH2), 36.5 (30-CH2), 21.9 (CH3), 21.7 (CH3); HRMS for
C26H25N3O7 [M + H+]+ Calc.: 492.1765, found: 492.1763.
0
0
0
5 -O-(o-Toluoyl)-2 -O-acetyl-3 -deoxy-6-chloropurine (29c). Following the general procedure for sugar-base
condensation, a solution of 6-chloropurine (0.371 g, 2.40 mmol) in dry CH3CN (10 mL) was reacted
with N,O-bis(trimethylsilyl)acetamide (1.46 mL, 6.00 mmol), a solution of 28 (0.672 g, 2.00 mmol) in
dry CH3CN (10 mL), and TMSOTf (0.46 mL, 2.50 mmol) After work-up, the crude residue was purified
by silica gel column chromatography (hexane:EtOAc 3:2) to afford product 29c (0.473 g) as a white
1
solid in 55% yield. H-NMR (300 MHz, CDCl3):
δ 8.65 (s, 1H, H-2), 8.24 (s, 1H, H-8), 7.78–7.16 (m, 4H,
ArH), 6.10 (d, 1H, J = 1.3 Hz, H-10), 5.84 (dt, 1H, J = 6.1, 1.3 Hz, H-20), 4.78 (dddd, 1H, J = 10.4, 5.6, 5.3,
3.1 Hz, H-40), 4.66 (dd, 1H, J = 12.2, 3.1 Hz, H-50), 4.50 (dd, 1H, J = 12.2, 5.3 Hz, H-5”), 2.85 (ddd, 1H,
J = 14.0, 10.4, 6.2 Hz, H-30), 2.54 (s, 3H, CH3), 2.34 (ddd, 1H, J = 14.0, 5.6, 1.3 Hz, H-3”), 2.16 (s, 3H,
CH3); 13C-NMR (75 MHz, CDCl3):
δ 170.4 (ArCO), 167.1 (CO), 152.3 (6-C), 151.6 (2-C), 151.0 (4-C),
144.4 (8-C), 140.7 (ArC), 132.7 (ArC), 132.6 (ArC), 132.1 (ArC), 130.6 (ArC), 128.8 (ArC), 126.0 (5-CH),
90.9 (10-CH), 79.4 (40-CH), 78.0 (20-CH), 64.6 (50-CH2), 33.3 (30-CH2), 21.9 (CH3), 21.1 (CH3); HRMS for
C20H19Cl1N4O5 [M + H+]+ Calc.: 431.1116, found: 431.1115.
50-O-(tert-Butyldiphenylsilyl)-30-deoxythymidine (30a). To a solution of 29a (0.402 g, 1.00 mmol) in dry
MeOH (20 mL) was added K2CO3 (0.276 g, 2.00 mmol) and the reaction mixture was stirred at
room temperature for 4 h. The solvent was then removed in vacuo and the resulting crude residue
was purified by silica gel column chromatography (CH2Cl2:MeOH 9:1) to give 30-deoxythymidine
(0.241 g) as a white solid in quantitative yield. 1H-NMR (500 MHz, MeOD):
δ 7.97 (d, 1H, J = 1.1
Hz, H-6), 5.68 (d, 1H, J = 1.8 Hz, H-10), 4.41 (dddd, 1H, J = 9.9, 3.2, 2.6, 2.5 Hz, H-40), 4.33–4.32 (dt,
1H, J = 5.6, 1.8 Hz, H-20), 3.93 (dd, 1H, J = 12.4, 2.6 Hz, H-50), 3.67 (dd, 1H, J = 12.4, 3.2 Hz, H-5”),
2.13 (ddd, 1H, J = 13.4, 9.9, 5.6 Hz, H-30), 1.87 (ddd, 1H, J = 13.4, 5.6, 2.5 Hz, H-3”), 1.86 (d, 3H, J = 1.1
0
Hz, CH3); 13C-NMR (125 MHz, MeOD):
δ 166.5 (4-C), 152.4 (2-C), 138.2 (6-C), 110.6 (5-CH), 93.6 (1 -CH),
0
0
0
0
82.5 (4 -CH), 77.0 (2 -CH), 63.1 (5 -CH2), 34.0 (3 -CH), 12.3 (6-CH3); HRMS for C10H14N2O5 [M + Na+]+
Calc.: 265.0795, found: 265.0796. To a stirred solution of 30-deoxythymidine (0.242 g, 1.00 mmol) and
imidazole (0.070 g, 1.00 mmol) in dry DMF (5.0 mL) was added TBDPSCl (0.275 g, 1.00 mmol) at
−
50 ◦C. The reaction mixture was allowed to warm to room temperature and stirred for 4 h. It was
then diluted with EtOAc (100 mL) and washed with saturated aq. NaHCO3 (100 mL), water, and brine.
The organic layer was dried over Na2SO4, filtered, and concentrated in vacuo. The crude residue was
purified by silica gel column chromatography (hexane:EtOAc 3:2) to give product 30a (0.456 g) as
1
1
a white solid in 95% yield. H-NMR (600 MHz, CDCl3): H-NMR (600 MHz, CDCl3):
δ 9.08 (s, 1H,
NH), 7.66–7.64 (m, 4H, ArH), 7.60 (d, 1H, J = 1.2 Hz, H-6), 7.45–7.37 (m, 6H, ArH), 5.68 (d, 1H, J = 2.1 Hz,
0
0
0
0
H-1 ), 4.54–4.51 (m, 1H, H-4 ), 4.46–4.44 (m, 1H, H-2 ), 4.10 (dd, 1H, J = 11.8, 2.5 Hz, H-5 ), 3.75 (dd, 1H,
J = 11.8, 3.4 Hz, H-5”), 2.20 (ddd, 1H, J = 13.2, 8.6, 6.4 Hz, H-30), 1.99 (ddd, 1H, J = 13.2, 6.1, 3.3 Hz,
H-30), 1.62 (d, J = 1.2 Hz, 3H, CH3), 1.08 (s, 9H, 3
×
CH3); 13C-NMR (150 MHz, CDCl3):
δ 163.7 (4-C),
150.9 (2-C), 135.5 (ArC), 135.4 (ArC), 135.1 (6-C), 133.0 (ArC), 132.6 (ArC), 130.0 (ArC), 130.0 (ArC), 127.9
(ArC), 127.9 (ArC), 110.3 (5-CH), 93.6 (10-CH), 82.5 (40-CH), 77.0 (20-CH), 63.1 (50-CH2), 34.0 (30-CH),
29.6 (C(CH3)3), 26.9 (3
found: 481.2154.
×
CH3), 12.2 (6-CH3); HRMS for C26H32N2O5Si1 [M + H+]+ Calc.: 481.2153,

Molecules 2018, 23, 1457
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50-O-(tert-Butyldiphenylsilyl)-30-deoxycytidine (30b). To a solution of 29b (0.491 g, 1.00 mmol) in dry
MeOH (20 mL) was added K2CO3 (0.415 g, 3.00 mmol) and the reaction mixture was stirred at room
temperature for 4 h. The solvent was then removed in vacuo and the resulting crude residue was
purified by silica gel column chromatography (CH2Cl2:MeOH 9:1) to give 30-deoxycytidine (0.225 g)
1
as a white solid in quantitative yield. H-NMR (500 MHz, MeOD):
δ 8.16 (d, 1H, J = 7.5 Hz, H-6),
5.86 (d, 1H, J = 7.5 Hz, H-5), 5.75 (s, 1H, H-10), 4.45 (dddd, 1H, J = 10.7, 5.4, 3.4, 2.7 Hz, H-40),
4.28 (dd, 1H, J = 5.2, 1.6 Hz, H-20), 3.97 (dd, 1H, J = 12.4, 2.7 Hz, H-50), 3.71 (dd, 1H, J = 12.4, 3.4
Hz, H-50), 2.02 (ddd, 1H, J = 13.3, 10.7, 5.2 Hz, H-30), 1.85 (ddd, 1H, J = 13.3, 5.4, 1.6 Hz, H-3”);
13C-NMR (150 MHz, MeOD):
δ
167.8 (4-C), 158.4 (2-C), 142.6 (6-C), 118.6 (5-CH), 94.9 (10-CH), 83.1
(40-CH), 77.6 (20-CH), 63.0 (50-CH2), 33.5 (30-CH2); HRMS for C9H13N3O4 [M + H+]+ Calc.: 228.0978,
found: 228.0988. To a stirred solution of 30-deoxycytidine (0.227 g, 1.00 mmol) and imidazole (0.070 g,
1.00 mmol) in dry DMF (5.0 mL) was added TBDPSCl (0.275 g, 1.00 mmol) at
−
50 ◦C. The reaction
mixture was allowed to warm to room temperature and stirred for 4 h. It was then diluted with EtOAc
(100 mL) and washed with saturated aq. NaHCO3 (100 mL), water, and brine. The organic layer was
dried over Na2SO4, filtered, and concentrated in vacuo. The crude residue was purified by silica gel
column chromatography (CH2Cl2:MeOH 9:1) to give compound 30b (0.432 g) as a white solid in 93%
1
yield. H-NMR (600 MHz, DMSO-d6):
δ 7.80 (d, 1H, J = 7.4 Hz, H-6), 7.73–7.72 (m, 1H, ArH), 7.65–7.62
(m, 3H, ArH), 7.49–7.44 (m, 3H, ArH), 7.35–7.33 (m, 1H, ArH), 7.23–7.21 (m, 2H, ArH), 7.01 (s, 2H,
NH2), 5.72 (d, 1H, J = 1.1 Hz, H-10), 5.51 (d, 1H, J = 7.4 Hz, H-5), 4.36 (dddd, 1H, J = 10.5, 3.5, 2.6,
1.5 Hz, H-40), 4.12 (dt, 1H, J = 5.1, 1.1 Hz, H-20), 4.02 (dd, 1H, J = 11.7, 2.6 0Hz, H-50), 3.72 (dd, 1H,
J = 11.8, 3.5 Hz, H-5”), 3.50 (s, 1H, OH), 2.01 (ddd, 1H, J = 12.9, 5.2, 1.5 Hz, H-3 ), 1.75 (ddd, 1H, J = 12.9,
10.5, 5.2 Hz, H-3”), 1.02 (s, 9H, 3
140.3 (6-C), 138.0 (ArC), 135.2 (ArC), 135.0 (ArC), 132.7 (ArC), 132.4 (ArC), 131.1 (ArC), 130.4 (ArC),
130.1 (ArC), 130.0 (ArC), 129.7 (ArC), 128.0 (ArC), 125.5 (5-CH), 92.2 (1 -CH), 80.2 (4 -CH), 75.4 (2 -CH),
64.4 (50-CH2), 33.1 (30-CH), 29.6 (C(CH3)3), 26.7 (CH3); HRMS for C25H31N3O4Si1 [M + Na+]+ Calc.:
488.1976, found: 488.1976.
×
CH3); 13C-NMR (150 MHz, DMSO-d6):
δ 165.6 (4-C), 155.2 (2-C),
0
0
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-3 -deoxy-6-methoxy-adenosine (30c). To a solution of 29c (0.430 g, 1.00 mmol)
in dry MeOH (20 mL) was added K2CO3 (0.415 g, 3.00 mmol) and the reaction mixture was stirred
at room temperature for 4 h. The solvent was then removed in vacuo and the resulting crude
residue was purified by silica gel column chromatography (CH2Cl2/MeOH 9:1) to give product
30-deoxy-6-methoxy-adenosine (0.260 g) as a white solid in quantitative yield. H-NMR (500 MHz,
1
MeOD):
δ
8.62 (s, 1H, H-2), 8.52 (s, 1H, H-8), 6.08 (d, 1H, J = 2.2 Hz, H-10), 4.74 (ddt, 1H, J = 5.8, 3.2,
2.2 Hz, H-20), 4.56 (dddd, 1H, J = 8.7, 6.4, 3.5, 2.7 Hz, H-40), 4.19 (s, 3H, OCH3), 3.95 (dd, J = 12.4,
2.7 Hz, 1H, H-50), 3.70 (dd, 1H, J = 12.4, 3.5 Hz, H-5”), 2.40 (ddd, 1H, J = 13.4, 8.7, 5.8 Hz, H-30),
2.07 (ddd, 1H, J = 13.4, 6.4, 3.2 Hz, H-3”)0; 13C-NMR (0125 MHz, MeOD):
δ
152.8 (6-C), 143.7 (2-C),
0
0
142.8 (4-C), 133.7 (8-C), 113.1 (5-CH), 84.2 (1 -CH), 73.4 (4 -CH), 67.4 (2 -CH), 54.5 (OCH3), 45.4 (5 -CH2),
45.4 (3 -CH2); HRMS for C11H14N4O4 [M + H+]+ Calc.: 267.1087, found: 267.1092. To a stirred mixture
0
0
of 3 -deoxy-6-methoxy-adenosine (0.266 g, 1.00 mmol) and imidazole (0.070 g, 1.00 mmol) in dry DMF
(5.0 mL) was added TBDPSCl (0.275 g, 1.00 mmol) at
warm to room temperature and stirred for 4 h. It was then diluted with EtOAc (100 mL), and then
washed with water and brine. The organic layer was dried over Na2SO4, filtered, and concentrated in
vacuo. The crude residue was purified by silica gel column chromatography (hexane:EtOAc 7:3) to
−
50 ◦C. The reaction mixture was allowed to
1
give compound 30c (0.463 g) as a white solid in 92% yield. H-NMR (300 MHz, CDCl3): δ 8.50 (s, 1H,
H-2), 8.31 (s, 1H, H-8), 7.66–7.600(m, 4H, ArH), 7.45–7.302 (m, 6H, ArH), 5.98 (d, 1H, J = 2.7 Hz, H-10),
5.13 (s, 1H, OH), 4.72 (m, 1H, H-2 ), 4.64–4.59 (m, 1H, H-4 ), 4.19 (s, 3H, OCH3), 4.00 (dd, 1H, J = 11.5, 3.1
Hz, H-50), 3.73 (dd, 1H, J = 11.5, 3.5 Hz, H-5”), 2.39 (ddd, 1H, J = 13.1, 7.2, 5.7 Hz, H-30), 2.13 (ddd, 1H,
J = 13.1, 6.6, 4.5 Hz, H-3”), 1.02 (s, 9H, 3
×
CH3); 13C-NMR (150 MHz, CDCl3):
δ 161.4 (6-C), 152.0 (2-C),
151.0 (4-C), 140.5 (8-C), 135.8 (ArC), 135.8 (ArC), 133.0 (ArC), 133.0 (ArC), 130.1 (ArC), 128.1 (ArC), 128.0
(ArC), 115.5 (5-CH), 93.2 (10-CH), 81.7 (40-CH), 76.7 (20-CH), 65.2 (50-CH2), 54.6 (OCH3), 33.4 (30-CH2),
29.9 (C(CH3)3), 27.1 (CH3); HRMS: C27H32N4O4Si [M + H+]+ Calc.: 505.2265, found: 505.2269.

Molecules 2018, 23, 1457
16 of 22
0
0
5 -O-(tert-Butyldiphenylsilyl)-3 -deoxy-adenosine (30d). A 50 mL round-bottomed flask was charged with
◦
29c (0.430 g, 1.00 mmol) and dry EtOH (10 mL) and the mixture was cooled to
of NH3 in MeOH (10 mL, 7 N) was added and the mixture was stirred for 48 h. After removal
of all the volatiles in vacuo, the resulting crude residue was purified by silica gel chromatography
−
20 C. Then, a solution
0
CH2Cl2/MeOH (7:3) to afford product 3 -deoxyadenosine (0.250 g) as a white solid in quantitative yield.
0
1H-NMR (600 MHz, D2O):
δ 8.26 (s, 1H, H-2), 8.14 (s, 1H, H-8), 6.01 (d, 1H, J = 2.2 Hz, H-1 ), 4.76 (m, 2H,
H-20, H-40), 3.91 (dd, 2H, J = 12.6, 2.7 Hz, H-50), 3.71 (dd, 1H, J = 12.6, 4.5 Hz, H-5”), 2.28 (ddd, 1H,
J = 13.6, 8.7, 5.7 Hz, H-30), 2.20 (ddd, 1H, J = 13.6, 6.6, 3.2 Hz, H-3”); 13C-NMR (150MHz, D2O):
δ
155.3 (6-C), 152.3 (2-C), 148.0 (4-C), 139.6 (8-C), 118.6 (5-CH), 90.8 (10-CH), 81.1 (40-CH), 74.8 (20-CH),
62.6 (50-CH2), 32.9 (30-CH2); HRMS for C10H13N5O3 [M + H+]+ Calc.: 252.1091, found: 252.1085.
To a stirred mixture of 30-deoxyadenosine (0.05 g, 0.25 mmol) and imidazole (0.070 g, 1.0 mmol) in
anhydrous DMF (5 mL) was added TBDPSCl (0.275 g, 1.0 mmol) at
allowed to warm to room temperature and stirred for 4 h. It was then diluted with EtOAc (100 mL) and
washed with water and brine. The organic layer was dried over Na2SO4, filtered, and concentrated
−
50 ◦C. The reaction mixture was
in vacuo. The crude residue was then purified by silica gel column chromatography (EtOAc) to
1
afford compound 30d (0.112 g, 92%) as a white solid. H-NMR (600 MHz, MeOD):
δ 8.32 (s, 1H, H-2),
8.18 (s, 1H, H-8), 7.67–7.32 (m, 10H, ArH), 6.02 (d, 1H, J = 1.5 Hz, H-10), 4.71 (dt, 1H, J = 5.5, 1.6 Hz,
H-20), 4.57 (dddd, 1H, J = 8.9, 3.9, 2.8, 2.1 Hz, H-40), 4.05 (dd, 1H, J = 11.6, 2.8 Hz, H-50), 3.78 (dd, 1H,
0
J = 11.7, 3.9 Hz, H-5”), 2.46 (ddd, 1H, J = 14.4, 8.9, 5.5 Hz, H-3 ), 2.01 (ddd, 1H, J = 14.4, 5.6, 2.1 Hz, H-3”),
1.28 (s, 9H, 3
×
CH3); 13C-NMR (150 MHz, MeOD):
δ 157.3 (6-C), 153.8 (2-C), 150.0 (4-C), 140.3 (8-C),
136.7 (ArC), 136.6 (ArC), 134.2 (ArC), 134.0 (ArC), 131.0 (ArC), 131.0 (ArC), 128.8 (ArC), 120.4 (5-CH),
93.2 (10-CH), 82.7 (40-CH), 77.0 (20-CH), 66.0 (50-CH2), 34.4 (30-CH2), 31.6 (CCH3)3), 27.4 (CH3); HRMS
for C26H31N5O3Si1 [M + H+]+ Calc.: 490.2268, found: 490.2273.
50-O-(tert-Butyldiphenylsilyl)-20-O-o-toluoyl-4-N-o-toluoyl-30-deoxycytidine (31a). To a stirred solution of
30b (0.93 g, 2.00 mmol) in dry DMF (30 mL), ortho-toluoyl chloride (0.386 g, 0.325 mL, 2.50 mmol)
was added at 0 ◦C under an inert atmosphere. Next, imidazole (0.17 g, 2.50 mmol) was added and
the mixture was stirred at room temperature for 3 h. It was then diluted with EtOAc (100 mL) and
washed with water (100 mL) and brine (100 mL). The organic layer was dried over Na2SO4, filtered,
and concentrated in vacuo. The crude residue was purified by silica gel column chromatography
1
(hexane:EtOAc 7:3) to afford compound 31a as a colorless oil (1.17 g, 84%). H-NMR (300 MHz, CDCl3):
δ
8.52 (d, 1H, J = 7.5 Hz, H-6), 8.01–7.14 (m, 18H, ArH), 6.26 (s, 1H, H-10), 5.58 (d, 1H, J = 7.5 Hz,
H-5), 5.27 (s, 1H, H-20), 4.56–4.51 (m, 1H, H-40), 4.27 (dd, 1H, J = 12.0, 2.0 Hz, H-50), 3.79 (dd, 1H,
J = 12.0, 2.5 Hz, H-5”), 2.62 (s, 3H, CH3) 2.51 (s, 3H, CH3) 2.14 (dd, 1H, J = 14.0, 4.9 Hz, H-30), 2.13 (dd,
J = 14.0, 4.9 Hz, 1H, H-3”), 1.15 (s, 9H, 3
×
CH3); 13C-NMR (75 MHz, CDCl3):
δ 171.1 (CO), 166.7 (CO),
163.2 (4-C), 154.9 (2-C), 145.0 (6-C), 138.3 (ArC), 137.7 ArC), 135.8 (ArC), 135.7 (ArC), 132.1 (ArC),
131.7 (ArC), 131.2 (ArC), 128.5 (ArC), 128.3 (ArC), 126.1 (ArC), 125.8 (ArC), 117.6 (5-CH), 91.3 (10-CH),
82.0 (40-CH), 79.2 (20-CH), 63.6 (50-CH2), 31.1 (30-CH2), 29.9 (C(CH3)3), 27.2 (3
×
CH3), 22.1 (ArCH3),
22.1 (ArCH3); HRMS: C41H43N3O6Si [M + Na+]+ Calc.: 724.2813, found: 724.2947.
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-2 -O-o-toluoyl-6-N-O-o-toluoyl-3 -deoxyadenosine (31b). To a stirred solution
of 30d (0.489 g, 1.00 mmol) in dry pyridine (30 mL), ortho-toluoyl chloride (0.386 g, 0.325 mL, 2.5 mmol)
◦
was added at 0 C under an inert atmosphere. The mixture was stirred at room temperature overnight.
It was diluted with EtOAc (100 mL) and washed with water (100 mL) and brine (100 mL). The organic
layer was dried over Na2SO4, filtered, and concentrated in vacuo. The crude residue was purified by
silica gel column chromatography (hexane:EtOAc 7:3) to give compound 31b as a colorless oil (0.580 g,
80%). 1H-NMR (600 MHz, CDCl3):
δ 8.74 (s, 1H, H-2), 8.41 (s, 1H, H-8), 7.73–7.09 (m, 18H, ArH),
5.96 (d, 1H, J = 3.1 Hz, H-10), 4.78 (ddd, 1H, J = 5.8, 3.1, 2.4 Hz, H-20), 4.62 (ddt, 1H, J = 6.9, 3.9, 3.5 Hz,
H-40), 3.95 (dd, 1H, J = 11.5, 3.5 Hz, H-50), 3.73 (dd, 1H, J = 11.5, 3.9 Hz, H-5”), 2.49 (s, 6H, ArCH3),
0
2.38 (ddd, 1H, J = 13.1, 6.9, 5.8 Hz, H-3 ), 2.17 (ddd, 1H, J = 13.1, 6.9, 2.4 Hz, H-3”), 1.02 (s, 9H, 3
×
CH3);
13C-NMR (150 MHz, CDCl3):
δ 172.3 (CO), 152.2 (6-C), 151.8 (2-C), 151.6 (4-C), 143.1 (8-C), 139.2 (ArC),

Molecules 2018, 23, 1457
17 of 22
135.5 (ArC), 134.9 (ArC), 132.7 (ArC), 132.7 (ArC), 131.3 (ArC), 131.30(ArC), 129.90(ArC), 129.30(ArC),
0
128.2 (ArC), 127.7 (ArC), 127.7 (ArC), 125.4 (5-CH), 93.0 (1 -CH), 81.3 (4 -CH), 76.1 (2 -CH), 65.1 (5 -CH2),
0
33.5 (3 -CH2), 29.6 (C(CH3)3), 26.8 (3
×
CH3), 19.9 (CH3), 19.1 (CH3); HRMS: C42H43N5O5Si [M + H+]+
Calc.: 726.3106, found: 726.3123.
30,50-Bis-O-o-toluoyl-6-N-O-o-toluoyl-30-deoxyadenosine (32). To a stirred solution of 30-deoxyadenosine
(0.251 g, 1.00 mmol) in dry pyridine (30 mL), o-toluoyl chloride (0.539 g, 0.453 mL, 3.50 mmol) was
added at 0 ◦C under an inert atmosphere and stirred overnight at room temperature. The mixture
was diluted with EtOAc (100 mL) and washed with water (100 mL) and brine (100 mL). The organic
layer was dried over Na2SO4, filtered, and evaporated in vacuo. The crude residue was purified by
1
column chromatography (EtOAc:hexane 3:7) to afford 32 as a colorless oil (0.600 g, 99%). H-NMR
(600 MHz, CDCl3):
δ 8.49 (s, 1H, H-2), 8.10 (s, 1H, H-8), 7.99–7.19 (m, 12H, ArH), 6.26 (d, 1H, J = 1.3 Hz,
H-10), 6.07 (dt, 1H, J = 6.0, 1.3 Hz, H-20), 4.85 (dddd, 1H, J = 9.2, 5.6, 5.4, 3.1 Hz, H-40), 4.68 (dd, 1H,
J = 12.1, 3.1 Hz, H-50), 4.53 (dd, 1H, J = 12.1, 5.4 Hz, H-5”), 3.18 (s, 3H, ArCH3), 2.98 (ddd, 1H,
J = 12.9, 9.2, 6.0 Hz, H-30), 2.60 (s, 3H, ArCH3), 2.56 (s, 3H, ArCH3), 2.46 (ddd, 1H, J = 12.9, 5.6, 1.3 Hz,
H-3”); 13C-NMR (150 MHz, CDCl3):
δ 171.1 (NHCO), 166.9 (CO), 166.3 (CO), 161.0 (6-C), 152.2 (2-C),
151.0 (4-C), 141.1 (8-C), 140.8 (ArC), 140.4 (ArC), 132.7 (ArC), 131.9 (ArC), 131.7 (ArC), 130.8 (ArC),
130.4 (ArC), 128.6 (ArC), 128.0 (ArC), 125.8 (ArC), 125.7 (ArC), 122.1 (5-CH), 90.4 (10-CH), 78.9 (40-CH),
78.1 (20-CH), 64.6 (50-CH2), 33.4 (30-CH2), 21.9 (CH3), 21.8 (CH3), 21.6 (CH3).
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-2 -keto-3 -deoxythymidine (33a). Following the general oxidation procedure,
a solution of 30a (0.480 g, 1.00 mmol) in CH2Cl2 (15 mL) was reacted with DMP (0.425 g, 1.00 mmol).
After work-up, the crude residue was purified by silica gel column chromatography (hexane:EtOAc
1
7:3) to afford compound 33a (0.476 g, 100%) as a white solid in quantitative yield. H-NMR (300 MHz,
CDCl3):
δ
10.2 (s, 1H, NH), 8.45–7.96 (m, 11H, ArH, H-6), 6.02 (s, 1H, H-10), 5.10 (dddd, 1H, J = 8.4,
7.3, 4.8, 3.6 Hz, H-40), 4.67 (dd, 1H, J = 11.3, 3.6 Hz, H-50), 4.59 (dd, 1H, J = 11.2, 4.8 Hz, H-5”),
3.60 (dd, 1H, J = 18.8, 8.4 Hz, H-30), 3.22 (dd, 1H, J = 18.7, 7.3 Hz, H-3”), 2.44 (d, 3H, J = 1.0 Hz,
CH3), 1.77 (s, 9H, 3 × CH3); 13C-NMR (75 MHz, CDCl3):
δ
207.0 (20-CO), 163.9 (4-C), 150.3 (2-C),
138.4 (6-C), 135.8 (ArC), 135.7 (ArC), 133.2 (ArC), 133.2 (ArC), 130.1 (ArC), 128.0 (ArC), 112.0 (5-CH),
85.9 (10-CH), 76.2 (40-CH), 65.4 (50-CH2), 36.6 (30-CH), 29.9 (C(CH3)), 27.1 (6-CH3) 12.3 (6-CH3); HRMS
for C26H30N2O5Si1 [M + Na+]+ Calc.: 501.1816, found: 501.1817.
0
0
0
5 -O-(tert-Butyldiphenylsilyl)-2 -keto-3 -deoxy-6-methoxy-adenosine (33b). Following the general oxidation
procedure, a solution of 30c (0.504 g, 1.00 mmol) in CH2Cl2 (15 mL) was reacted with DMP (0.425 g,
1.00 mmol). After work-up, the crude residue was purified by silica gel column chromatography
(hexane:EtOAc 7:3) to afford compound 33b (0.500 g, 99%) as a white solid in quantitative yield.
1H-NMR (300 MHz, CDCl3):
δ 8.40 (s, 1H, H-2), 7.96 (s, 1H, H-8), 7.62–7.29 (m, 10H, ArH), 5.92 (s, 1H,
H-10), 4.61 (dddd, 1H, J = 8.7, 6.7, 4.4, 3.9 Hz, H-40), 4.18 (s, 3H, OCH3), 4.03 (dd, 1H, J = 11.3, 3.9 Hz,
H-50), 3.90 (dd, 1H, J = 11.3, 4.4 Hz, H-5”), 3.24 (dd, 1H, J = 18.7, 8.7 Hz, H-30), 2.79 (dd, 1H, J = 18.7,
0
6.7 Hz, H-3”), 1.03 (s, 9H, 3
×
CH3); 13C-NMR (75 MHz, CDCl3):
δ
206.9 (2 -CO), 161.4 (6-C), 152.7 (2-C),
151.7 (4-C), 141.5 (8-C), 135.8 (ArC), 135.7 (ArC), 133.0 (ArC), 130.1 (ArC), 128.0 (ArC), 127.9 (ArC),
122.0.0 (5-CH), 82.3 (10-CH), 76.5 (40-CH), 65.1 (50-CH2), 54.6 (OCH3), 37.5 (30-CH), 29.9 (C(CH3)),
27.0 (3 × CH3); HRMS for C27H30N4O4Si1 [M + H+]+ Calc.: 503.2108, found: 503.2102.
50-O-(tert-Butyldiphenylsilyl)-20-keto-4◦-N-o-toluoyl-30-deoxycytidine (33c). To a solution of 31a (0.701 g,
1.00 mmol) in dry THF (30 mL) at
−
78 C under an inert atmosphere was added potassium tert-butoxide
(0.112 g, 1.00 mmol), and the mixture was stirred for 1 h. It was then diluted with EtOAc (100 mL) and
washed with water (100 mL) and brine (100 mL). The organic layer was dried over Na2SO4, filtered,
and concentrated in vacuo. The crude residue was purified by silica gel column chromatography
(EtOAc:hexane 1:1) to afford 5 -O-(tert-butyldiphenylsilyl)-4-N-o-toluoyl-3 -deoxycytidine as a colorless
oil (0.466 g, 80%). 1H-NMR (300 MHz, CDCl3):
8.42 (d, 1H, J = 7.3 Hz, H-6), 7.66–7.26 (m, 14H,
ArH), 5.77 (s, 1H, H-10), 4.59 (d, 1H, J = 7.3 Hz, H-5), 4.59 (m, 1H, H-20), 4.45 (br s, 1H, OH), 4.15–4.08
0
0
δ

Molecules 2018, 23, 1457
18 of 22
(m, 2H, H-40, H-50), 3.73 (d, 1H, J = 9.9 Hz, H-5”), 2.31–2.17 (m, 2H, H-30,H-3”), 2.50 (s, 3H, CH3),
1.25 (s, 9H, 3 168.9 (CO), 162.7 (4-C), 156.2 (2-C), 144.8 (6-C), 137.6
CH3); 13C-NMR (75 MHz, CDCl3):
×
δ
(ArC), 135.8 (ArC), 135.7 (ArC), 135.7 (ArC), 134.4 (ArC), 133.0 (ArC), 132.8 (ArC), 131.9 (ArC), 131.7
(ArC), 130.3 (ArC), 128.2 (Ar0C), 127.4 (ArC), 126.3 (ArC), 96.5 (5-CH), 95.5 (10-CH), 82.5 (40-CH), 77.5
0
0
(2 -CH), 64.4 (5 -CH2), 32.7 (3 -CH2), 29.9 (C(CH3)3), 27.2 (3
×
CH3), 20.3 (CH3); HRMS: C33H37N3O5Si
[M + H+]+ Calc.: 584.2575, found: 584.2586. Following the general oxidation procedure, a solution of
50-O-(tert-butyldiphenylsilyl)-4-N-o-toluoyl-30-deoxycytidine (0.466 g, 0.80 mmol) in CH2Cl2 (15 mL)
was reacted with DMP (0.425 g, 1.00 mmol). After work-up, the crude residue was purified by silica gel
column chromatography (hexane:EtOAc 7:3) to afford compound 33c (0.46 g, 100%) as a white solid in
quantitative yield. H-NMR (300 MHz, CDC0l3): 7.66–7.26 (m, 16H, ArH, H-5, H-6), 5.40 (s, 1H, H-10),
1
0
0
4.57–4.51 (m, 1H, H-4 ), 3.99–3.97 (m, 2H, H-5 , H-5”), 3.03 (dd, 1H, J = 18.6, 8.1 Hz, H-3 ), 2.63 (dd, 1H,
J = 18.6, 7.6 Hz, H-3”), 2.51 (s, 3H, CH3), 1.25 (s, 9H, 3
×
CH3); 13C-NMR (75 MHz, CDCl3):
δ 206.0
(20-CO), 163.6 (4-C), 154.6 (2-C), 148.2 (6-C), 137.9 (ArC), 135.8 (ArC), 135.8 (ArC), 133.3 (ArC), 132.0
(ArC), 131.9 (ArC), 130.1 (ArC), 128.0 (ArC), 128.0 (ArC), 127.4 (ArC), 126.4 (ArC), 117.7 (5-CH), 97.4
(10-CH), 87.7 (40-CH), 66.0 (50-CH2), 37.0 (30-CH2), 29.9 (C(CH3)3), 27.1 (3
×
CH3), 20.4 (CH3); HRMS:
C33H35N3O5Si [M + H+]+ Calc.: 582.2418, found: 582.2429.
50-O-o-Toluoyl-20-keto-6-N-o-toluoyl-30-deoxyadenosine (33d). To a stirred suspension of 32 (0.302 g,
0.50 mmol) in dry THF (10 mL) at
78 ◦C under an inert atmosphere was added potassium
−
tert-butoxide (0.112 g, 1.00 mmol) and the mixture was stirred for 1 h. It was then diluted
with EtOAc (100 mL) and washed with water (100 mL) and brine (100 mL). After work-up, the
crude residue was purified by silica gel column chromatography (hexane:EtOAc 1:1) to afford
1
50-O-o-toluoyl-6-N-o-toluoyl-30-deoxyadenosine as a colorless oil (0.133 g, 55%). H-NMR (600 MHz,
CDCl3):
5.01 (m), 1H, H-40), 4.75 (m, 1H, H-20), 4.64 (m, 2H, H-50, H-5”), 3.65–3.55 (m, 1H, H-30), 3.43–3.37 (m,
1H, H-3”), 3.27 (s, 3H, ArCH3), 3.11 (s, 3H, ArCH3); 13C-NMR (75 MHz, CDCl3):
172.5 (NHCO),
δ
9.34 (s, 1H, H-2), 8.94 (s, 1H, H-8), 8.61–7.73 (m, 8H, ArH), 6.42 (d, 1H, J = 5.8 Hz, H-10),
δ
166.8 (CO), 153.1 (6-C), 152.6 (2-C), 151.8 (4-C), 143.2 (8-C), 140.8 (ArC), 139.5 (ArC), 135.9 (ArC),
135.8 (ArC), 133.0 (ArC), 131.6 (ArC), 130.2 (ArC), 128.5 (ArC), 128.2 (ArC), 125.7 (5-CH), 85.8 (10-CH),
84.8 (40-CH), 75.1 (20-CH), 64.2 (50-CH2), 38.6 (30-CH2), 27.2 (CH3), 20.2 (CH3). Following the general
0
0
oxidation procedure, a solution of 5 -O-o-toluoyl-6-N-o-toluoyl-3 -deoxyadenosine (0.097 g, 0.20 mmol)
in CH2Cl2 (10 mL) was reacted with DMP (0.106 g, 0.25 mmol). After work-up, the crude residue was
purified by silica gel column chromatography (hexane:EtOAc 3:2) to afford compound 33d (0.077 g,
1
80%) as a white solid. H-NMR (300 MHz, CDCl3):
δ
8.40 (s, 1H, H-2),07.94 (s, 1H, H-8), 8.05–7.18 (m,
0
8H, ArH), 5.88 (s, 1H, H-1 ), 4.89 (dddd, 1H, J = 9.2, 6.7, 5.4, 3.3 Hz, H-4 ), 4.72 (dd, 1H, J = 12.0, 3.3 Hz,
H-50), 4.60 (dd, 1H, J = 12.1, 5.4 Hz, H-5”), 3.31 (dd, 1H, J = 18.5, 9.2 Hz, H-30), 2.94 (dd, 1H, J = 18.6,
6.7 Hz, H-3”), 2.55 (s, 6H, CH3); 13C-NMR (75 MHz, CDCl3):
δ
206.8 (20-CO), 167.1 (CO), 161.5 (CO),
152.7 (6-C), 151.5 (2-C), 142.0 (4-C), 141.8 (8-C), 140.9 (ArC), 132.7 (ArC), 132.1 (ArC), 130.9 (ArC), 126.0
(ArC), 122.0 (5-CH), 82.4 (10-CH), 74.2 (40-CH), 65.2 (50-CH2), 37.9 (30-CH2), 21.9 (CH3), 21.8 (CH3).
20,20-gem-Dichloro-30-deoxythymidine (4a). Following the general chlorination procedure, a solution
of compound 33a (0.500 g, 1.04 mmol) in dry CH2Cl2 (20 mL) was reacted with PCl5
(0.822 g, 3.95 mmol) at
−
78 ◦C under an inert atmosphere. After work-up, the resulting
crude residue was purified by column chromatography (hexane:EtOAc 4:1) to give 50-O-(tert-
butyldiphenylsilyl)-20,20-gem-dichloro-30-deoxythymidine (0.283 g, 51%) as a major compound and
50-O-(tert-butyldiphenylsilyl)-20-chloro-20,30-didehydro-30-deoxythymidine as a minor side product
1
(0.049 g, 10%). H-NMR (500 MHz, CDCl3):
δ 8.91 (s, 1H, NH), 7.66–7.37 (m, 11H, ArH, H-6), 6.55
(s, 1H, H-10), 4.37 (dddd, 1H, J = 12.4, 6.0, 3.2, 2.8 Hz, H-40), 4.15 (dd, 1H, J = 14.3, 3.2 Hz, H-50), 3.84
(dd, 1H, J = 14.3, 2.8 Hz, H-5”), 2.90 (dd, 1H, J = 16.7, 12.4 Hz, H-30), 2.82 (dd, 1H, J = 16.7, 6.0 Hz,
H-3”), 1.61 (s, 3H, CH3), 1.11 (s, 9H, 3
×
CH3); 13C-NMR (125 MHz, CDCl3):
δ 163.4 (4-C), 150.3 (2-C),
135.4 (6-C), 135.2 (ArC), 134.2 (ArC), 132.7 (ArC), 132.3 (ArC), 130.1 (ArC), 131.1 (ArC), 128.0 (ArC),
111.0 (5-CH), 92.8 (10-CH), 89.2 (20-C(Cl)2), 78.5 (40-CH), 62.8 (50-CH2), 47.2 (30-CH), 29.6 (C(CH3)), 26.9

Molecules 2018, 23, 1457
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(3
×
CH3) 12.0 (6-CH3); HRMS: C26H30N2O4SiCl2 [M + H+]+ Calc.: 533.1424, found: 533.1428. Data
1
for 50-O-(tert-butyldiphenylsilyl)-20-chloro-20,30-didehydro-30-deoxythymidine: H-NMR (300 MHz,
CDCl3):
δ
8.23 (s, 1H, NH), 7.66–7.600(m, 4H, ArH), 7.46–7.344 (m, 6H, ArH), 7.06 (d, 1H0, J = 1.3 Hz,
0
H-6), 6.89 (dd, 1H, J = 3.8, 1.7 Hz, H-1 ), 6.30 (t, 1H, J = 1.7 Hz, H-3 ), 4.95–4.93 (m, 1H, H-4 ), 3.90–3.89
(m, 2H, H-50, H-5”),1.46 (d, 3H, J = 1.3 Hz, CH3), 1.09 (s, 9H, 3
×
CH3);HRMS: C26H29N2O4SiCl
[M + Na+]+ Calc.: 519.1477, found: 519.1477. Following the general desilylation procedure, a solution
0
0
0
0
of 5 -O-(tert-butyldiphenylsilyl)-2 ,2 -gem-dichloro-3 -deoxythymidine (0.266 g, 0.50 mmol) in dry THF
(10 mL) was reacted with TBAF (0.75 mL, 0.75 mmol). After work-up, the resulting crude residue
1
was purified by column chromatography (EtOAc) to give 4a as a white solid (0.132 g, 90%). H-NMR
(600 MHz, MeOD):
δ
8.18 (d, 1H, J = 2.4 Hz, H-6), 6.51 (s, 1H, H-10), 4.44 (ddt, 1H, J = 10.8, 5.5, 2.4,
Hz,0H-40), 4.06 (dd, 1H, J = 12.8, 2.4 Hz, H-50), 3.76 (dd, 1H, J = 12.8, 2.4 Hz, H-5”), 2.86–2.85 (m, 2H,
H-3 , H-3”), 1.88 (d, 3H, J = 2.3 Hz, CH3); 13C-NMR (150 MHz, MeOD):
δ
166.1 (4-C), 152.5 (2-C), 136.8
0
0
0
0
0
(6-C), 111.4 (5-CH), 93.9 (1 -CH), 91.2 (2 -C(Cl)2), 81.6 (4 -CH), 61.1 (5 -CH2), 46.4 (3 -CH), 12.4 (6-CH3);
HRMS: C10H12Cl2N2O4 [M + H+]+ Calc.: 295.0246, found: 295.0244.
0
0
0
0
2 ,2 -gem-Dichloro-2 ,3 -dideoxy-6-methoxy-adenosine (4b). Following the general chlorination procedure,
a solution of compound 33b (0.500 g, 1.00 mmol) in dry CH2Cl2 (20 mL) was reacted
with PCl5 (0.790 g, 3.80 mmol) at
−
78 ◦C under an inert atmosphere. After work-up, the
resulting crude residue was purified by column chromatography (hexane:EtOAc 4:1) to give
50-O-(tert-butyldiphenylsilyl)-20,20-gem-dichloro-20,30-dideoxy-6-methoxy-adenosine (0.359 g, 65%) as
a pale yellow solid. 1H-NMR (300 MHz, CDCl3):
δ 8.55 (s, 1H, H-2), 8.47 (s, 1H, H-8), 7.70–7.38
(m, 10H, ArH), 6.67 (s, 1H, H-10), 4.55 (dddd, 1H, J = 10.0, 5.3, 4.8, 3.2 Hz, H-40), 4.20 (s, 3H,
OCH3), 4.13 (dd, 1H, J = 11.9, 3.2 Hz, H-50), 3.87 (dd, 1H, J = 8.5, 4.8 Hz, H-5”), 3.24 (dd, 1H,
J = 13.9, 10.0 Hz, H-30), 2.86 (dd, 1H, J = 13.9, 5.3 Hz, H-3”), 1.13 (s, 9H, 3
×
CH3); 13C-NMR
(75 MHz, CDCl3):
(ArC), 130.3 (ArC), 128.2 (ArC), 128.0 (ArC), 121.9 (5-CH), 93.0 (10-CH), 89.0 (20-C(Cl)2), 80.0 (40-CH),
63.7 (50-CH2), 54.5 (OCH3), 45.9 (30-CH), 29.9 (C(CH3)), 27.0 (3
CH3); HRMS: C27H30N4O3SiCl2
δ 161.4 (6-C), 152.7 (2-C), 149.2 (4-C), 140.2 (8-C), 135.8 (ArC), 135.7 (ArC), 132.6
×
[M + H+]+ Calc.: 557.1536, found: 557.1219. Following the general desilylation procedure,
a solution of 50-O-(tert-butyldiphenylsilyl)-20,20-gem-dichloro-20,30-dideoxy-6-methoxy-adenosine
(0.278 g, 0.50 mmol) in dry THF (10 mL) was reacted with TBAF (0.75 mL, 0.75 mmol). After work-up,
the resulting crude residue was purified by column chromatography (EtOAc) to give compound 4b
as a white solid (151 mg, 95%). 1H-NMR (600 MHz, MeOD):
δ 8.95 (s, 1H, H-2), 8.58 (s, 1H, H-8),
6.77 (s, 1H, H-10), 4.62 (dddd, 1H, J = 10.5, 5.1, 2.9, 2.6 Hz, H-40), 4.21 (s, 3H, OCH3), 4.09 (dd, 1H,
J = 12.6, 2.6 Hz, H-50), 3.87 (dd, 1H, J = 12.6, 2.9 Hz, H-5”), 3.20 (dd, 1H, J = 14.1, 10.5 Hz, H-30), 2.98
(dd, 1H, J = 14.1, 5.1 Hz, H-3”); 13C-NMR (150 MHz, MeOD):
δ 162.4 (6-C), 153.7 (2-C), 153.1 (4-C),
142.4 (8-C), 121.8 (5-CH), 94.2 (10-CH), 90.2 (20-C(Cl)2), 82.4 (40-CH), 61.7 (50-CH2), 54.9 (OCH3), 45.7
(30-CH); HRMS: C11H12Cl2N4O3 [M + H+]+ Calc.: 319.0359, found: 319.0361.
0
0
0
0
2 ,2 -gem-Dichloro-4-N-o-toluoyl-2 ,3 -dideoxycytidine (34). Following the general chlorination procedure,
a solution of compound 33c (0.46 g, 0.80 mmol) in dry CH2Cl2 (20 mL) was reacted with
PCl5 (0.632 g, 3.04 mmol) at
−
78 ◦C under an inert atmosphere.
After work-up, the
resulting crude residue was purified by column chromatography (hexane:EtOAc 4:1) to give
50-O-(tert-butyldiphenylsilyl)-20,20-gem-dichloro-4-N-o-toluoyl-20,30-dideoxycytidine (0.350 g, 69%)
as a pale yellow solid. 1H-NMR (300 MHz, CDCl3): 8.40 (d, 1H, J = 7.5 Hz, H-6), 7.68–7.26
(m, 15H, ArH, H-5), 6.67 (s, 1H, H-10), 4.45 (ddt, 1H, J = 10.8, 4.7, 2.3 Hz, H-40), 4.24 (dd, 1H,
J = 12.2, 2.3 Hz, H-50), 3.80 (dd, 1H, J = 12.2, 2.3 Hz, H-5”), 2.94 (dd, 1H, J = 13.4, 10.8 Hz,
H-30), 2.76 (dd, 1H, J = 13.4, 4.7 Hz, H-3”), 2.52 (s, 3H, CH3), 1.15 (s, 9H, 3
(75 MHz, CDCl3): 162.7 (4-C), 155.3 (2-C), 144.1 (6-C), 137.7 (ArC), 135.8 (ArC), 135.6 (ArC),
×
CH3); 13C-NMR
δ
134.3 (ArC), 132.6 (ArC), 132.3 (ArC), 132.0 (ArC), 131.8 (ArC), 130.6 (ArC), 130.5 (ArC), 128.4
(ArC), 128.3 (ArC), 127.2 (ArC), 126.4 (ArC), 96.8 (5-CH), 93.4 (10-CH), 89.0 (20-C(Cl)2), 79.7 (40-CH),
62.7 (50-CH2), 46.0 (30-CH2), 29.5 (C(CH3)3), 27.2 (3
×
CH3), 20.4 (CH3); HRMS: C33H35Cl2N3O4Si

Molecules 2018, 23, 1457
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[M + H+]+ Calc.: 636.1846, found: 636.1848. Following the general desilylation procedure,
a solution of 50-O-(tert-butyldiphenylsilyl)-20,20-gem-dichloro-4-N-o-toluoyl-20,30-dideoxycytidine
(0.350 g, 0.55 mmol) in dry THF (10 mL) was reacted with TBAF (0.82 mL, 0.82 mmol). After work-up,
the resulting crude residue was purified by column chromatography (EtOAc) to give compound 34 as
1
a white solid (0.217 g, 100%). H-NMR (600 MHz, MeOD): 8.76 (d, 1H, J = 7.5 Hz, H-6), 7.59 (d, 1H,
J = 7.5 Hz, H-5), 7.53–7.29 (m, 4H, ArH), 6.67 (s, 1H, H-10), 4.53 (ddt, 1H, J = 9.7, 6.2, 2.5, Hz, H-40),
4.06 (dd, 1H, J = 12.8, 2.5 Hz, H-50), 3.79 (dd, 1H, J = 12.8, 2.5 Hz, H-5”), 2.88–2.86 (m, 2H, H-30, H-30),
2.46 (s, 3H, CH3); 13C-NMR (150 MHz, MeOD):
δ 171.7 (CO), 165.0 (4-C), 158.0 (2-C), 145.7 (6-C), 138.0
(ArC), 136.2 (ArC), 132.2 (ArC), 132.2 (ArC), 128.6 (ArC), 126.9 (ArC), 98.3 (5-CH), 94.8 (10-CH), 90.6
(20-C(Cl)2), 82.0 (40-CH), 61.1 (50-CH2), 46.4 (30-CH2), 19.9 (CH3); HRMS: C17H17Cl2N3O4 [M + H+]+
Calc.: 398.0668, found: 398.0665.
50-O-o-Toluoyl-20,20-gem-dichloro-6-N-o-toluoyl-20,30-dideoxyadenosine (35). Following the general
chlorination procedure, a solution of compound 33d (0.048 g, 0.10 mmol) in dry CH2Cl2 (5 mL)
◦
was reacted with PCl5 (0.079 g, 0.38 mmol) at
−
78 C under an inert atmosphere. After work-up,
the resulting crude residue was purified by column chromatography (hexane:EtOAc 7.5:2.5) to give
1
compound 35 (0.037 g, 70%) as a pale yellow solid. H-NMR (600 MHz, MeOD):
δ
9.08 (s, 1H, H-2), 8.76
(s, 1H, H-8), 7.67–7.08 (m, 8H, ArH), 6.76 (s, 1H, H-10), 4.60 (dddd, 1H, J = 10.5, 5.2, 3.0, 2.7 Hz, H-40),
4.06 (dd, 1H, J = 12.6, 2.7 Hz, H-50), 3.84 (dd, 1H, J = 12.6, 3.0 Hz, H-5”), 3.14 (dd, 1H, J = 14.2, 10.5 Hz,
H-30), 2.95 (dd, 1H, J = 14.2, 5.2 Hz, H-3”), 2.45 (s, 6H, 2
×
CH3); 13C-NMR (150 MHz, MeOD):
δ 173.5
(NHCO), 170.2 (CO), 154.6 (6-C), 153.5 (2-C), 152.5 (4-C), 145.5 (8-C), 140.1 (ArC), 136.1 (ArC), 132.6
(ArC), 132.3 (ArC), 129.9 (ArC), 129.1 (ArC), 126.5 (ArC), 126.5 (5-CH), 94.2 (10-CH), 90.6 (20- C(Cl)2),
82.5 (40-CH), 61.5 (50-CH2), 45.7 (30-CH2), 20.1 (CH3), 14.4 (CH3); HRMS: C26H23Cl2N5O4 [M + H+]+
Calc.: 540.1199, found: 540.1211.
20,20-gem-Dichloro-20,30-dideoxycytidine (4c). To a stirred solution of 34 (0.050 g, 0.125 mmol) in EtOH
(3.0 mL) at
−
20 ◦C was added a saturated solution of NH3 in EtOH. The reaction mixture was then
stirred for 2 days at room temperature. After removal of all the volatiles in vacuo, the crude residue
was purified by silica gel column chromatography (EtOAc:MeOH 7.5:2.5) to give 4c as a white solid
0
(0.031 g, 89%). HRMS: 1H-NMR (600 MHz, MeOD): 8.21 (d, 1H, J = 7.6 Hz, H-6), 6.63 (s, 1H, H-1 ), 5.91
(d, 1H, J = 7.6 Hz, H-5), 4.43 (ddt, 1H, J = 10.4, 5.1, 2.6 Hz, H-40), 4.02 (dd, 1H, J = 12.8, 2.6 Hz, H-50),
3.76 (dd, 1H, J = 12.7, 2.7 Hz, H-5”), 2.84 (dd, 1H, J = 13.7, 10.4 Hz, H-30), 2.79 (dd, 1H, J = 13.8, 5.1 Hz,
H-30); 13C-NMR (150 MHz, MeOD):
δ
167.6 (4-C), 158.2 (2-C), 141.7 (6-C), 96.1 (5-CH), 94.5 (10-CH),
91.2 (20-(CCl)2), 81.2 (40-CH), 61.3 (50-CH2), 46.7 (30-CH2); C9H11Cl2N3O3 [M + H+]+ Calc.: 280.0250,
found: 280.0250.
20,20-gem-Dichloro-20,30-dideoxyadenosine (4d). To a stirred solution of 35 (0.037 g, 0.068 mmol) in
dry MeOH (5.0 mL) was added K2CO3 (0.138 g, 0.10 mmol), and then the reaction mixture was
stirred for 48 h. After removal of all the volatiles, the crude residue was purified by silica gel column
1
chromatography (MeOH:CHCl3 1.5:8.5 to 2.5:7.5) to give 4d as a white solid (0.0092 mg, 45%). H-NMR
(300 MHz, DMSO-d6):
δ
8.88 (s, 1H, H-2), 8.62 (s, 1H, H-8), 6.70 (s, 1H, H-10), 5.52 (s, 1H, OH), 4.51
(dddd, 1H, J = 8.7, 7.7, 3.9, 3.2, H-40), 3.92 (dd, 1H, J = 12.5, 8.7 Hz, H-50), 3.76 (dd, 1H, J = 12.5,
3.2 Hz, H-50), 3.17 (dd, 1H, J = 11.1, 7.7 Hz, H-30), 3.06 (dd, 1H, J = 11.1, 3.9 Hz, H-3”); 13C-NMR
(75 MHz, DMSO-d6):
δ
160.6 (6-C), 152.3 (2-C), 151.9 (4-C), 141.0 (8-C), 120.7 (5-CH), 92.1 (10-CH), 89.8
(20-C(CCl)2), 81.0 (40-CH), 60.5 (50-CH2), 44.4 (30-CH2); HRMS: C10H11Cl2N5O2 [M + NH4+]+ Calc.:
321.0395, found: 321.0328.
4. Conclusions
In this study, a new method for the preparation of two different sets of sugar chlorinated
nucleosides starting from 20-and 30-ketonucleoside intermediates was developed. The reaction
of 30-keto-20,30-dideoxynucleosides in the presence of phosphorus pentachloride afforded the
0
0
corresponding 3 ,3 -gem-dichloride derivatives in moderate yields. An elimination reaction was found

Molecules 2018, 23, 1457
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to be a significant side process leading to the concomitant formation of vinyl 30-monochlorinated
products. The method was extended to the chemoselective formation of 20,20-gem-dichloro-20,30-
dideoxynucleosides in good yields under the same reaction conditions. This work contributes to
the development of general synthetic strategies for the synthesis of modified nucleosides as well as
structure-activity relationship studies on such compounds as potential antiviral agents.
Supplementary Materials: The following are available online. Physical and spectroscopic data of the
relevant compounds.
Author Contributions: P.H. conceived the study; F.d.P.S., E.G. and P.H. designed the experiments and analyzed
the data; F.d.P.S. performed the experiments; P.H. contributed reagents/materials/analysis tools; E.G. with the
assistance of F.d.P.S wrote the paper.
Funding: This research received no external funding.
Acknowledgments: The authors are grateful to Jef Rozenski, Eveline Lescrinier, and Luc Baudemprez for
recording the HRMS and NMR spectra. We would like to thank Christophe Pannecouque and Kristien Erven for
carrying out the antiviral screening.
Conflicts of Interest: The authors declare no conflict of interest.
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Sample Availability: Samples of the compounds are available from the authors.
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