Synthesis and Conformation of Pentopyranoside Nucleoside Phosphonates

Article abstract of DOI:10.1021/acs.joc.8b03178

In contrast to natural nucleosides, where the nucleobase is positioned at the anomeric center, we report the synthesis of pentopyranoside nucleosides with a phosphonate functionality at the 1′-anomeric oxygen. Starting from l-arabinose, key functionalized l-glycero- A nd l-erythro-pentopyranose carbohydrate synthons were prepared and further elaborated into the final six-membered ring nucleosides via nucleobase incorporation and phosphonomethylation reactions. NMR analysis demonstrated that these nucleoside phosphonates exist in solution as conformers predominantly adopting a chair structure in which the base moiety is equatorially positioned. Such conformation prevents unfavorable 1,3-diaxial steric and electronic interactions. Notably, the stereochemical outcome of the Vorbrüggen glycosylation step utilized en route to the thymine analogue clearly suggests the absence of anchimeric assistance, as opposed to what is usually observed during nucleoside synthesis using protected furanose precursors. The finding that the diphosphates of the compounds developed in this study are recognized by DNA polymerases is important in view of the future selection of artificial genetic systems and dedicated polymerases as well as applications in therapy.

Full text of DOI:10.1021/acs.joc.8b03178

Subscriber access provided by UNIV AUTONOMA DE COAHUILA UADEC
Article
Synthesis and conformation of Pentopyranoside Nucleoside Phosphonates
Xiao-Chen Li, Shrinivas G. Dumbre, Eveline Lescrinier, Elisabetta Groaz, and Piet Herdewijn
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.8b03178 • Publication Date (Web): 03 May 2019
Downloaded from http://pubs.acs.org on May 3, 2019
Just Accepted
“Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted
online prior to technical editing, formatting for publication and author proofing. The American Chemical
Society provides “Just Accepted” as a service to the research community to expedite the dissemination
of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in
full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully
peer reviewed, but should not be considered the official version of record. They are citable by the
Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore,
the “Just Accepted” Web site may not include all articles that will be published in the journal. After
a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web
site and published as an ASAP article. Note that technical editing may introduce minor changes
to the manuscript text and/or graphics which could affect content, and all legal disclaimers and
ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or
consequences arising from the use of information contained in these “Just Accepted” manuscripts.
is published by the American Chemical Society. 1155 Sixteenth Street N.W.,
Washington, DC 20036
Published by American Chemical Society. Copyright © American Chemical Society.
However, no copyright claim is made to original U.S. Government works, or works
produced by employees of any Commonwealth realm Crown government in the
course of their duties.

Page 1 of 32
The Journal of Organic Chemistry
1
2
3
4
5
Synthesis and Conformation of Pentopyranoside Nucleoside Phosphonates
6
7
8
9
Xiaochen Li, Shrinivas Dumbre, Eveline Lescrinier, Elisabetta Groaz, and Piet Herdewijn*
Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, Bus 1041, 3000 Leuven,
Belgium
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
GRAPHICAL ABSTRACT
OH
R1
HO P O
1,4-syn
H
O
R2
L-Arabinose
H
O
OH
H
H
O
B
H
R1 = OAc, R2 = Thymine
OH
H
or
R1 = -OCH2PO(OiPr)2, R2 = NH2
B = Thymine and Adenine
ABSTRACT
In contrast to natural nucleosides, where the nucleobase is positioned at the anomeric center, we report the
synthesis of pentopyranoside nucleosides with a phosphonate functionality at the 1ʹ-anomeric oxygen.
Starting from L-arabinose, key functionalized L-glycero- and L-erythro-pentopyranose carbohydrate
synthons were prepared and further elaborated into the final six-membered ring nucleosides via nucleobase
incorporation and phosphonomethylation reactions. NMR analysis demonstrated that these nucleoside
phosphonates exist in solution as conformers predominantly adopting a chair structure in which the base
moiety is equatorially positioned. Such conformation prevents unfavorable 1,3-diaxial steric and electronic
interactions. Notably, the stereochemical outcome of the Vorbrüggen glycosylation step utilized en route
to the thymine analogue clearly suggests the absence of anchimeric assistance, as opposed to what is usually
observed during nucleoside synthesis using protected furanose precursors. The finding that the
diphosphates of the compounds developed in this study are recognized by DNA polymerases is important
in view of the future selection of artificial genetic systems and dedicated polymerases as well as applications
in therapy.
1
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 2 of 32
1
2
3
4
INTRODUCTION
5
6
7
8
9
Advances in the application of nucleosides and oligonucleotides as antiviral/anticancer therapeutics as well
as gene silencing and editing tools largely depend on the systematic exploration of related chemical space
through nucleobase and/or backbone modifications.1-4 In DNA and RNA, the hydrophobic nitrogenous
nucleobases encode information and ensure genetic fidelity through the formation of Watson-Crick pairs,
while the furanose sugar and phosphate backbone moieties define the structure and stability of the genetic
material. Chemical variations at the sugar moiety have been frequently exploited to modulate the biological
and physicochemical properties of these molecules by inducing changes in nucleoside conformation
without interfering with the accuracy of base pairing. This strategy has proven highly effective in altering
enzyme recognition and activation by kinases and polymerases as well as binding affinity towards RNA or
DNA targets.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Our group previously prepared nucleoside analogues comprising a hexopyranose sugar mimic, i.e., 1,5-
anhydro-2,3-dideoxy-β-D-arabinohexitol, linked to the nucleobase at C2ʹ rather than the anomeric position.5
In contrast to pyranosyl nucleosides, anhydrohexitol derivatives were found to preferentially adopt a
slightly distorted chair conformation with an axial orientation of the nucleobase [1a, Figure 1(A)] instead
of the usual equatorial position [1a’, Figure 1(A)].5-6 This is presumably a consequence of the sterically
unfavorable 1,3-diaxial repulsive interactions in the six-membered chair. Such an atypical sugar
conformation resulted in both distinguishing biological activities and physicochemical properties at the
monomer and oligonucleotide level, respectively. For example, hexitol nucleosides proved to be potent and
highly selective inhibitors of herpes simplex virus type 1 and 2 (HSV-1 and HSV-2).5 With regard to the
corresponding oligomers, hexitol nucleic acid (HNA) sequences demonstrated the ability to fold into helical
structures7 as well as form stable hybrids with natural counterparts,8 by reproducing the A-type form of
dsRNA.9 HNA has been also proven to act as xenobiotic genetic material (XNA) capable of evolution in
vitro,10-11 while directing DNA synthesis in E. coli.12
However, while HNA oligonucleotides are resistant against cellular nucleases,7 their phosphorylated
nucleoside precursors might be dephosphorylated by phosphatases in a cellular environment. On the other
hand, HNA nucleosides are phosphorylated only in herpes virus infected cells by the viral thymidine kinase
and not in non-infected cells. One important approach to obtain nucleoside phosphate mimics is to replace
the natural P-O-C bond with a phosphonate (P-C-O) linkage.13-14 The phosphonate moiety is a bioisostere
of the phosphate group with similar polar and electronic properties, which may function just like its natural
counterpart within an artificial information system. The improved stability of phosphonate mimics may
also lead to prolonged intracellular half-lives.
2
ACS Paragon Plus Environment

Page 3 of 32
The Journal of Organic Chemistry
1
2
3
4
5
(A)
NH2
NH2
N
N
N
HO
N
N
6
7
8
9
N
5'
N
H
O
H
N
H
O
2' H
2'
4'
HO
5'
OH
H
OH
H
1a
1a'
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
(B)
O
5'
4'
O
1'
2'
5'
4'
3'
1'
2'
3'
O
P
O
B
O
B
HO
O
HO
P
HO
HO
OH
OH
B = T, 2a
B = A, 2b
1
Figure 1. (A) Conformational preference of a hexitol nucleoside; (B) Structural diversity between hexitol nucleoside
monophosphates (1) and target D-threo-pentopyranoside nucleoside phosphonates 2a and 2b.
A number of methods are available in the literature for the preparation of five-membered cyclic as well as
acyclic nucleoside phosphonates,13-15 however in the case of six-membered ring analogues the synthesis is
complicated by the greater conformational diversity arising from the pyranosyl moiety. A general method
to generate these derivatives has not yet been described and reported properties of the corresponding
monomers/oligomers have therefore been limited.16-20 In this context, we set out to investigate plausible
synthetic pathways that would enable the construction of a suitably functionalized pentopyranoside scaffold
as key intermediate for further nucleobase incorporation and glycosylation reactions.
Herein, we report the results of our synthetic studies that ultimately led to phosphonomethyl D-threo
pentopyranoside nucleoside analogues 2a and 2b [Figure 1(B)] bearing a 4ʹ-nucleobase, which differ from
hexitol nucleoside monophosphates [1, Figure 1(B)] by the presence of an O-C-P bond at the anomeric
position, along with their conformational analysis and preliminary biological data.
RESULTS AND DISCUSSION
Nucleoside phosphonates are usually synthesized either by initial insertion of the nucleobase on the glycone
moiety followed by phosphonomethylation (SN2 or glycosylation reaction) or vice versa. The key
disconnections in our retrosynthetic analysis of target D-threo-pentopyranoside nucleoside phosphonates
2a,b are shown in Figure 2. For both proposed routes A and B, it was envisaged that the synthesis of a
suitably functionalized L-glycero-pentopyranose (II) or L-erythro-pentopyranose (IV) synthon could begin
from a five carbon L-sugar; thus, L-arabinose 3 was chosen as common starting material.
3
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 4 of 32
1
2
3
4
Route A
O
5
6
7
8
O
Nucleobase
Incorporation
HO
HO
R
O
O
Glycosylation
O
P
O
O
B
BnO
O
B
O
PO
HO
2a b
,
I
II
9
R
Route B
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Nucleobase
Sugar
Modification
Incorporation
iPrO
O
O
Sugar
Modification
O
O
O
R
P
Glycosylation
iPrO
O
O
R'
O
O
R'
HO
OH
OH
O
O
HO
IV
III
R
R
L-Arabinose, 3
P = protecting group
R = Ph or Me
R' = functional group used for nucleobase incorporation
Figure 2. Retrosynthetic analysis of planned D-threo-pentopyranoside nucleoside phosphonates 2a and 2b.
Since the glycosidic linkage between the anomeric OH and the phosphonate functionality might be
susceptible to epimerization during other synthetic manipulations that need to be performed along the
overall synthetic path, route A in Figure 2, which entails the introduction of this group towards the end of
the synthetic sequence, was initially pursued in order to minimize this possibility. Thus, benzyl
isopropylidene arabinoside 4 was readily synthesized from L-arabinose 3 in four steps and used without
need of chromatographic purification (Scheme 1).21 The key step entailed the inversion of configuration of
the 2-hydroxyl group via TEMPO-mediated oxidation, followed by reduction of the resultant 2-ketone.
Given that the glycosylation step for the introduction of the phosphonomethyl moiety usually requires the
anchimeric assistance from a neighboring 2-O-acyl group, the 2-hydroxyl of compound 4 was protected as
an acetate, affording 5 in excellent yield. While initial attempts to hydrolyze the isopropylidene acetal of 5
in the presence of p-toluenesulfonic acid resulted in the concurrent cleavage of the 2-O-acetyl group, the
use of 80% aq. acetic acid was found to allow for selective cleavage of the acetal functionality to afford
diol 6. The next step in the synthesis entailed the regioselective protection of the equatorially oriented 4-
hydroxy group, however only an inseparable mixture of products was obtained in the presence of
TBDMSCl due to concurrent silylation at different positions of the sugar ring. To minimize 3-O-silylation,
a bulkier reagent such as TBDPSCl was employed, which successfully led to the highly predominant
formation of the desired compound 7. Subsequently, 3-hydroxy glycoside 7 was subjected to Barton-
McCombie deoxygenation, however no desired product (8) was formed upon reaction with a variety of
sulfur reagents such as CS2 MeI, 1,1ʹ-dithiocarbonydiimidazole (TCDI), and O-phenyl chlorothionoformate.
This result may be attributed to the axial orientation as well as the increased steric hindrance of the bulky
4-OTBDPS moiety, which might prevent the formation of the corresponding O-thiocarbonyl intermediate
8. Alternatively, compound 7 was converted to 3-O-triflate derivative 9, which underwent successive SN2
iodination and radical reduction to furnish fully protected sugar synthon 11. Later, desilylation at the 4-
4
ACS Paragon Plus Environment

Page 5 of 32
The Journal of Organic Chemistry
1
2
3
4
5
position afforded coupling partner 12 required for the construction of 1ʹ-O-phosphonomethyl-D-threo-
pentapyranosides carrying a nucleobase at the 4ʹ-position.
6
7
8
Scheme 1. Initial Routes for the Preparation of Functionalized L-Glycero-pentopyranoside Scaffolds
12, 14a-c, and 16.a
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
O
O
O
O
BnO
OTBDPS
S
a to d
f
BnO
O
HO
OH
OH
BnO
OR1
AcO
O
RO
O
HO
AcO
OH
R1 = H
R2
4
5
6
7
R = H
e
g
3
8
R = Ac
R1 = TBDPS
N
R2 =
h
, PhO, SMe
N
O
O
O
n
i
BnO
BnO
OTBDPS
BnO
OTBDPS
O
AcO
16
AcO
I
AcO
OTf
10
9
j
O
O
O
O
m
l
BnO
OR4
BnO
Thy
BnO
OR3
BnO
AcO
AcO
15
AcO
AcO
13
14a,
14b,
R4 = Ms
R4 = Ts
11
12
R3 = TBDPS
R3 = H
k
aReagents and conditions: (a) BnOH, AcCl, 75%; (b) DMP, CSA, DMF, 96%; (c) TEMPO, NaClO, KBr, DCM, H2O,
90%; (d) NaBH4, CH3OH, 90%; (e) Ac2O, Et3N, DMAP, DCM, 93%; (f) 80% aq. AcOH, 83%; (g) TBDPSCl,
imidazole, DCM, 71%; (h) Tf2O, pyridine, DCM, 95%; (i) NaI, DMF, 96%; (j) Bu3SnH, AIBN, toluene, 94%; (k)
TBAF, THF, 87%; (l) thymine or N3-benzoylthymine, PPH3, DIAD or DEAD, THF or dioxane, rt; (m) MsCl or TsCl,
Et3N/pyridine, DCM; (n) TBAF, THF, 95%.
However, all attempts to introduce thymine or N3-benzoyl protected thymine as nucleobase by reacting 12
under Mitsunobu conditions5 resulted in the formation of E2 elimination product 13 rather than the desired
nucleoside, most likely due to the axial orientation of the 4-hydroxyl group (for detailed conditions, see
Experimental Section). Further efforts to achieve the nucleophilic substitution of 4-OTs and 4-OMs
substituted analogues 14a,b by thymine in the presence of different bases such as DBU, NaH, Cs2CO3, and
K2CO3 alone or in combination with a variety of crown ethers were also unsuccessful. Moreover, the
conversion of the 4-OH of 12 into a better leaving group using triflic anhydride did not provide the expected
activated product, but rather led to a 3,4-elimination reaction (13) and nucleophilic substitution with
pyridine at the 4-position. Therefore, another option for the introduction of the nucleobase was investigated
focusing on the preparation of a 3,4-epoxy sugar, which could in principle undergo a ring-opening reaction
upon nucleophilic attack of a heterocyclic nitrogen. Initially, the envisaged epoxide 16 was directly
obtained in one step from 3-iodo derivative 10 upon removal of the 4-O-silyl protecting group (Scheme 1).
It was found that the basic conditions due to the deprotecting reagent TBAF favored efficient epoxide
formation once the 4-hydroxyl group was unmasked. However, when epoxide 16 was reacted with thymine
under basic (DBU) and high temperature (110 °C) conditions, conversion to the desired nucleoside occurred
5
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 6 of 32
1
2
3
4
5
concomitantly with the migration and hydrolysis of the 2ʹ-acetyl group leading to a complex mixture of
products.
6
7
8
9
This problem was addressed by adopting an alternative synthetic strategy that would allow to generate a
differently substituted key sugar intermediate with higher stability under base-sugar coupling conditions
(Scheme 2). In particular, a Corey-Winter olefination was employed to install the alkene at the 3,4-position
to obtain the L-glycero-pentopyranose ring. Treatment of 6 with TCDI afforded cyclic thionocarbonate 17,
which subsequently underwent a syn-elimination in the presence of triethyl phosphite to furnish 3,4-
unsaturated pentose 13 in good yield (84% over two steps). It should be noted that in this case the standard
use of trimethyl phosphite was ineffective to promote the desulfurization step. Epoxidation of 13 using
either m-CPBA or H2O2 did not proceed stereoselectively, while resulting in a mixture of diastereomeric
epoxides. Hydrolysis of the 2-O-acetyl group of 13 prior to epoxidation was therefore necessary, in order
for the corresponding free hydroxyl moiety to establish a hydrogen bonding interaction with the oxidizing
agent that allowed for the reaction to selectively take place from the same side of the 2-hydroxy group.
Thus, epoxide 19 was obtained in good yield, and successively subjected to MEM protection, epoxide ring
opening with thymine, and Barton deoxygenation to yield 4ʹ-thymidylated sugar 22. The MEM protecting
group was then removed under acidic conditions affording a 15:1 mixture of - and -anomers 23a and
23b, which were characterized after column chromatography separation, and further benzoylated at the 2ʹ
position to furnish 24a and 24b in an overall 92% yield. While the Pd/C-catalyzed hydrogenolysis of the
anomeric OBn functionality proceeded sluggishly in either methanol or acetic acid (3 days), a significant
enhancement of the reaction rate was observed when the debenzylation was conducted in THF as solvent
(8 h). Later, we found that treatment of a mixture of 24a and 24b under transfer hydrogenation conditions
(cyclohexene in ethanol) produced the desired glycone 25 in 88% yield.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
For the final glycosylation step, glycone 25 was first activated at the anomeric position either as a N-
phenyltrifluoroacetimidate (PTFAI, 26a), trichloroacetimidate (TCAI, 26b), or acetate (26c), while
diisopropyl phosphonomethanol was used as glycosyl acceptor. A variety of standard conditions for the
formation of the O-C-P bond were screened and are summarized in Table 1. Glycosylated product 27 could
not be isolated as a pure compound by silica gel column chromatography at this stage due to
diisopropylphosphonomethanol contamination, thus it was used as such in the following debenzoylation
step, and product characterization was carried out at the level of compound 28. Surprisingly, glycosyl
donors 26a and 26b yielded either starting material 25 (entries 1 and 3, Table 1) or a product with undesired
stereochemistry at the anomeric center (-28, entries 2 and 4, Table 1). The formation of -28 suggests the
non-participation of the 2ʹ-O-acyl moiety, with the aglycone acceptor approaching the oxocarbenium
intermediate from the -face to form the 1,4-anti conformer. In contrast, 1ʹ-acetylated nucleoside donor 26c
furnished the desired -28 isomer as major compound (-28:-28 = 2:1) in the presence of a strong Lewis
acid (TMSOTf) at room temperature. It can be postulated that at low temperature (-78 ºC) the presence of
aglycone moieties with an increased leaving group ability as those in 26a and 26b support the formation of
product -28 as a result of the absence of neighboring group assistance, whereas in the case of 26c bearing
a poorer leaving group the reaction favors isomer -28. Final removal of the diisopropyl ester
6
ACS Paragon Plus Environment

Page 7 of 32
The Journal of Organic Chemistry
1
2
3
4
5
functionalities under standard conditions afforded nucleoside phosphonate 2a in 40% yield (0.98% overall
yield).
6
7
Scheme 2. Synthesis of Thymine α-D-Threo-pentopyranoside Nucleoside Phosphonate 2a.a
8
9
O
O
O
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
a
b
BnO
OH
OH
BnO
O
BnO
S
AcO
AcO
O
RO
6
17
13
18
R = Ac
R = H
c
d
O
O
O
g,h
f
BnO
BnO
Thy
BnO
Thy
O
R1O
MEMO
i
MEMO
OH
22
21
19
20
R1 = H
R1 = MEM
e
O
O
O
O
O
BnO
Thy
iPrO P
m
k
R3O
Thy
Thy
OiPr
R2O
BzO
R4O
25
R3 = H
23
24
27
28
R2 = H
R2 = Bz
R4 = Bz
R4 = H
j
n
l
C
NH
CCl3
26a
R3 =
o
Ph
26b
R3
=
C N
CF3
O
O
O
HO P
OH
Thy
26c
R3 = Ac
HO
2a
aReagents and conditions: (a) TCDI, DCM, 83%; (b) triethylphosphite, 140 °C, 85%; (c) MeONa, methanol, 91%; (d)
m-CPBA, DCM, 89%; (e) 2-Methoxyethoxymethyl chloride (MEMCl), DCM, 91%; (f) thymine, DBU, DMF, 85%;
(g) TCDI, DMAP, DCM; (h) Bu3SnH, AIBN, toluene, 83% over two steps; (i) 1M HCl in dioxane, 75% for α-25 and
5% for β-25; (j) BzCl, pyridine, 0 °C, 92%; (k) Pd/C, cyclohexene, ethanol, 88%; (l) Ac2O, pyridine, 85%; (m)
TMSOTf, hydroxymethyl phosphonic acid diisopropyl ester, CH2Cl2; (n) 7 M NH3 in methanol, 20% over two steps;
(o) TMSBr, 2,6-lutidine, acetonitrile, 40%.
7
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 8 of 32
1
2
3
4
Table 1. Optimization of the Phosphonylation Step
5
6
7
8
entry
glycosyl donor
Lewis acid and T (°C)
TMSOTf, -78 °C
BF3.Et2O, -78 °C
TMSOTf, -78 °C
BF3.Et2O, -78 °C
TMSOTf, rt
product (yield%)
25
1
2
3
4
5
6
26ab
-28 (30%)a
25
9
26bb
26c
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
-28 (40%)a
-28/-28 (20/10%)a
-28 (traces)a
BF3.Et2O, rt
Thy
O
O
O P O
OH
O
O
O
P
O
H
O
Thy
H
O
OH
H
28
-
28

aYields refer to the glycosylated product isolated after the following debenzoylation step.
bExperimental procedures for the phosphonylation of 26a and 26b are detailed in the Supporting Information
(S192-S193).
By analogy to early work towards thymine D-threo-pentopyranoside phosphonate 2a, we initially
investigated the nucleophilic substitution of 4-sulfonate activated sugars 14a-c as well as ring opening
reactions of epoxide 20 with 6-chloropurine and N6-benzoyl protected adenine (Scheme S1, in Supporting
Information). However, all attempts to directly introduce the purine ring at the 4-position by changing the
base or using various additives failed.
Therefore, we opted for the construction of the purine ring via a linear approach. As shown in Scheme 3,
radical deoxygenation of previously synthesized thionocarbonate derivative 17 afforded 3-deoxy
compound 12 in 60% yield along with small amounts of the undesired 4-deoxy product (10%), under high
dilution reaction conditions (0.02 mol/L). It should be noted that when the reaction was conducted at a
concentration of 0.10 mol/L, the reduction of the C=S bond to a methylene moiety (-CH2) took place instead
of the desired deoxygenation reaction at the 3-position. Mesylation and subsequent azidation of the 4-
hydroxyl group occurred smoothly to afford 4-azido compound 29 in good yield. After deacetylation at the
2-position, compound 30 was reacted under Staudinger conditions to give 4-amino-D-threo-
pentopyranoside 31. Next, a literature procedure was employed for the construction of the purine ring
starting from precursor 31 and 4,6-dichloro-5-formamidopyrimidine.22 The initially formed pyrimidine
nucleoside intermediate underwent in situ cyclization under basic conditions to smoothly provide 6-
chloropurine pyranoside 32. Subsequent amination at the 6-position of purine in 32 yielded adenine
analogue 33 in excellent yield (95%), whose further reaction with an excess of benzoyl chloride furnished
8
ACS Paragon Plus Environment

Page 9 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
fully protected derivative 34. Following attempts to achieve the removal of the 1ʹ-OBn group along with
mono-debenzoylation at the primary amino group of 34 under different hydrogenation conditions in the
presence of a range of Pd catalysts (10% Pd/C, 20% Pd(OH)2/C, Pd(OAc)2, and Pd-black) did not deliver
chemoselectively glycone 35, due to the contamination of the desired compound with other fully and
partially N-debenzoylated by-products. However, the use of a Lewis-acid such as boron trichloride enabled
benzyl removal with the exclusive formation of the desired anomeric hydroxyl glycone 35 in good yield.
After acetylation of the anomeric 1ʹ-OH, the resulting glycosyl donor 36 was reacted with diisopropyl
phosphonomethanol under conditions similar to those developed earlier for the phosphomethylation of
thymine analogue 2a (Table 1, entry 5). To our dismay, none of these conditions provided the desired target
phosphonate glycoside 37 and similar attempts to prepare a 6-chloropurine containing nucleoside starting
from 32 through a similar sequence of steps also met with failure.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Scheme 3. Building of the Purine Ring on 4-Amino-D-Threo-pentopyranoside Sugar 31.
O
O
O
BnO
N3
BnO
O
a
BnO
OR
c
R1O
S
AcO
O
AcO
R = H
R = Ms
R
1 = Ac
12
14a
29
30
17
34
35
b
d
R
1 = H
e
NBz2
N
R2
N
N
N
N
N
O
N
h
f
BnO
NH2
O
O
N
BnO
BnO
HO
BzO
HO
R
R
2 = Cl
2 = NH2
31
32
33
g
i
NHBz
NHBz
NHBz
N
N
N
N
N
N
N
N
N
N
j
k
O
P
O
O
O
N
N
O
HO
AcO
O
O
BzO
BzO
BzO
36
37
aReagents and conditions: (a) Bu3SnH, AIBN, toluene; (b) MsCl, TEA, DMAP, DCM, 54% over two steps; (c) NaN3,
DMF, 91%; (d) MeONa, MeOH, 95%; (e) triphenyl phosphine, THF then water, 92%; (f) 4,6-dichloro-5-
formamidopyrimidine, DIPEA, BuOH, 75%; (g) NH3 in ethanol, 95%; (h) BzCl, pyridine, 88%; (i) 1 M BCl3, DCM,
-78 to 0 °C, 80%; (j) Ac2O, pyridine, 78%; (k) TMSOTf, hydroxymethyl phosphonic acid diisopropyl ester, CH2Cl2.
In view of these results, we therefore decided to turn to route B in our retrosynthetic plan (Figure 2). As
illustrated in Scheme 4, the amino moiety of sugar scaffold 31 was first protected with a trifluoroacetyl
group to yield 38, whose benzyl group was later cleaved by Pd/C catalytic hydrogenation. Diol 39 was then
transformed into 1,2-diacetyl glycosyl donor 40, which underwent smooth glycosylation with diisopropyl
9
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 10 of 32
1
2
3
4
5
6
7
8
9
phosphonomethanol at the 1-position affording 41.23 Subsequent trifluoroacetyl deprotection under basic
conditions provided key amino sugar intermediate 42, which served as synthon for the stepwise
construction of the purine nucleobase. The final adenine nucleoside phosphonate 2b was successfully
obtained in 40% yield (0.78%, overall yield) following the cleavage of the diisopropyl esters with TMSBr
in the presence of lutidine. It is worth mentioning that 1-O-diisopropylphosphonomethyl-3,4-dideoxy-4-
amino-α-D-threo-pentopyranoside 42 might constitute a versatile intermediate for the construction of a
variety of purine or pyrimidine nucleobases.22
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Scheme 4. Synthesis of Adenine α-D-threo-pentopyranoside Nucleoside Phosphonate 2b.
O
O
O
O
O
a
b
BnO
NH2
BnO
NHCCF3
HO
NHCCF3
HO
HO
HO
31
38
39
c
R2
N
O
N
N
O
O
O
N
NHR
iPrO
P
OiPr
O
f
d
AcO
NHCCF3
O
P
O
O
R3O
R1O
AcO
OR3
HO
R = Cl, R = iPr
40
43
44
2b
R = COCF , R = Ac
2
3
g
h
41
42
3
1
e
R = NH , R = iPr
R = H, R = H
2
2
3
1
R = NH , R = H
2
2
3
aReagents and conditions: (a) ethyl trifluoroacetate, TEA, methanol, 91%; (b) Pd/C, H2, methanol, 82%; (c) Ac2O,
pyridine, 80%; (d) hydroxymethyl phosphonic acid diisopropyl ester, TMSOTf, DCM, rt; (e) 7 M NH3 in methanol,
40% over two steps; (f) 4,6-dichloro-5-formamidopyrimidine, DIPEA, BuOH, 75%; (g) NH3 in ethanol, 92%; (h)
TMSBr, acetronitrile, 40%.
A detailed solution conformational analysis of the final phosphonate products 2a and 2b was carried out
using NMR spectroscopy. A preference for a 1,4-syn substitution pattern (Figure 3) was established for
both pyrimidine and purine derivatives 2a and 2b following complete assignment using 1D and 2D NMR
experiments and based on the values of the coupling constants observed in the 1H NMR spectra. Table 2
summarizes the proton NMR spectroscopic data acquired for thymine derivative 2a. The corresponding
data obtained for adenine containing nucleoside phosphonate 2b can be found in the Supporting Information
(Table S2) together with all relevant spectra.
10
ACS Paragon Plus Environment

Page 11 of 32
The Journal of Organic Chemistry
1
2
3
O
4
5
6
7
8
9
1,3 diaxial
HN
1,3 diaxial
O
NOE
H
O
O
N
P
opposite
dipole
parallel dipole
HO
H
5'
H
H
H
O
HO
5'
H
1'
H
H
O
4'
O
O
N
H
H
H
O
HO
P
NH
2'
3'
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
3J =
2'
2.2Hz
4'
1'
HO
H
OH
OH
O
H
H
H
3J =
10.8Hz
Figure 3. Schematic representation of the solution phase preferential conformation of 1ʹ-phosphonate D-threo-
pentopyranose nucleoside bearing thymine as base (2a) as determined by NMR studies. Dashed lines indicate the
observed NOE interaction between the H6 of thymine and the axially positioned H3ʹ and H5ʹ.
As shown in the 1H NMR spectrum of 2a (see Supporting Information), H1ʹ ( 4.68) and H2ʹ ( 4.04)
appear as a doublet and triplet of doublets, respectively, with a small 3J1ʹ,2ʹ diequatorial coupling constant,
which is consistent with a chair conformation with both phosphonomethyl group and 2ʹ-OH occupying an
axial orientation. The td pattern of H2’ with the largest splitting equal to 3.6 Hz is characteristic of an
equatorial position of this proton. Furthermore, the H4ʹ signal at  4.79 consists of a triplet of triplets arising
from the coupling with the protons at C3ʹ and C5ʹ; notably, the observed 3J4ʹ,3ʹ and 3J4ʹ,5ʹ values of 12.1 and
10.8 Hz between H4ʹ and H3ʹa and H5’a, respectively, support an equatorial orientation of the nucleobase
at the 4ʹ-position. This chair conformation of the pyranose ring was further confirmed by the presence of a
clear NOE correlation between the H6 of thymine and the axially positioned H3ʹ and H5ʹ.
Such 1,4-syn-relationship is similar to that previously reported between the heterocyclic base and either the
5′-hydroxymethyl to be phosphorylated in 1,5-anhydrohexitol nucleosides5 or the 4ʹ-O-phosphonomethyl
moiety in 2ʹ,3ʹ-dideoxy-2ʹ,3ʹ-didehydro-pentopyranosyl16 nucleoside phosphonates. However, nucleoside
phosphonates 2a,b differ in their conformational behavior from 1 by the orientation of the nucleobase,
which is equatorial rather than axial, with both the hydroxymethyl and secondary OH groups at the 1ʹ- and
2ʹ-positions axially positioned. Thus, it can be assumed that the preferred conformation in 2a,b is sterically
enforced in order to avoid the 1,3-diaxial steric interactions among bulky substituents and/or between the
lone pairs of the ring oxygen and the anomeric oxygen, along with the opposite direction of the dipole
moment.
For comparison, the -anomer of compound 2a (-S2a) was obtained upon deprotection of -28 and fully
characterized by 1D and 2D NMR experiments (for details, see Table S3 and Figure S3 in the Supporting
Information). Accordingly, the analysis of these NMR data indicated that the preferred chair conformation
of the pyranose ring in -S2a adjusts to a 1,4-trans-diaxial orientation of the bulky substituents.
It is noteworthy that the conformation of such nucleoside analogues is expected to easily adapt to external
conditions such as those required by enzyme binding24 or insertion within a nucleic acid chain,25 thus
influencing oligonucleotides properties in a variable way.
11
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 12 of 32
1
2
3
4
5
6
7
8
9
Table 2. 1H NMR Analysis of the Sugar Skeleton of Thymine D-Threo-pentopyranoside
Nucleoside Phosphonate 2a(600 MHz, D2O).
bond orientationa
multiplicity J (Hz) (D2O) 3J connection
 (ppm)
4.68
C-H1ʹ
C-H2ʹ
e
e
d
2.2
H1ʹe-H2ʹe
H2ʹe-H1ʹe
H2ʹe-H3ʹe
H2ʹe-H3ʹa
H3ʹa-H2ʹe
H3ʹa-H4ʹa
H3ʹa-H3ʹe
H3ʹe-H2ʹe
H3ʹe-H4ʹa
H3ʹe-H3ʹa
H4ʹa-H3ʹa
H4ʹa-H5ʹa
H4ʹa-H3ʹe
H4ʹa-H5ʹe
H5ʹa-H5ʹe
H5ʹa-H4ʹa
H5ʹe-H3ʹeb
H5ʹe-H4ʹa
H5ʹe-H5ʹa
4.04
td
2.2–3.0
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
3.6
3.0
C-H3ʹ
C-H3ʹʹ
C-H4ʹ
a
e
a
2.38
1.93
4.79
ddd
dtd
tt
12.1
13.8
1.2
3.9
13.1
10.8
4.8
C-H5ʹ
C-H5ʹʹ
a
e
3.91
3.73
t
10.7
ddd
1.4
4.7
11.2
ae stands for equatorial, a for axial. bW proton-proton coupling (4JHH).
In order to define whether D-threo-pentopyranoside nucleoside phosphonates are still recognized by
enzymes involved in nucleoside and nucleotide metabolism, compounds 2a,b were at first evaluated for
their antiviral activity against different herpesviruses (varicella zoster virus (VZV), HSV-1, and HSV-2).
Contrary to the results obtained for 15 as well as known furanose nucleoside phosphonates,26 these studies
revealed that 2a,b exerted poor inhibitory activity of DNA viral replication. This could be due to a lack of
cell penetration (the negatively charged phosphonate moiety is very polar) as well as inefficient intracellular
enzymatic phosphorylation. Specifically, the very high EC50 values determined for 2a,b (Table S4, in the
Supporting Information) suggest that these issues cannot be overcome by synthesizing the corresponding
prodrugs.
Furthermore, aiming to gain knowledge about the potential utility of these synthetic analogues for the
selection of artificial information systems, the adenine containing nucleoside phosphonate 2b was
converted to its corresponding diphosphate 45 using a known phosphorylation procedure (Scheme 5).27
Compound 45 was assessed for its ability to be accepted as substrate by DNA polymerases in an enzymatic
primer extension assay where a primer-template duplex with a seven 5’-dT overhang was used. Enzymes
lacking 3ʹ,5ʹ-proofreading activity such as Klenow fragment (exo-) and Vent (exo-) were tested in the
presence or absence of Mn2+ ions and shown to be able to use 45 as substrate, although only the formation
12
ACS Paragon Plus Environment

Page 13 of 32
The Journal of Organic Chemistry
1
2
3
4
5
of P+1 or P+2 products was detected, as exemplified in Figure 4 (for a complete account of used conditions
and results, see Supporting information, Figure S1 and S2).
6
7
8
Scheme 5. Phosphorylation of Adenine α-D-Threo-pentopyranoside Phosphonate 2b.a
9
NH2
NH2
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
N
N
N
N
N
a
O
O
O
O
P
O
O
P
P
P
HO
O
O
HO
O
O
N
N
OH
OH
OH
OH
HO
2b
HO
45
aReagents and conditions: (a) (i) 1,1′-carbonyldiimidazole, DMF; (ii) (HNBu3)2H2P2O7, (ii) TEAB buffer, 30%.
Figure 4. Primer extension of compound 45 in the presence of Vent polymerase (exo-) and Mn2+ ions. The positions
were 45 has to be incorporated opposite the template oligonucleotide are in bold. dA stands for 2′-deoxyadenosine
triphosphate (positive control), while Neg for negative control.
CONCLUSION
In summary, D-threo-pentopyranoside nucleoside analogues bearing a phosphonate functionality rather than
a nucleobase (i.e., in natural nucleosides) at the anomeric center have been synthetized starting from L-
arabinose. Specifically, stereocontrolled routes to suitably functionalized key carbohydrate scaffolds have
been established and optimized. Such intermediates were further assembled and elaborated into the final
six-membered ring nucleosides using two main strategies entailing the initial insertion of the nucleobase
on the glycone moiety followed by phosphonomethylation or by inverting this reaction sequence. Notably,
when a thymine containing pentopyranose glycosyl donor was subjected to Vorbrüggen glycosylation
conditions, the reaction proceeded without neighboring group participation, in contrast to the usual behavior
of protected furanose nucleoside precursors. The synthesis of the adenine analogue relied on a linear
approach for building the purine base on a phosphonometylated 4-amino pentopyranoside synthon. This
method allowed for an improved stereoselectivity and could potentially be extended to the stepwise
construction of other purine as well as pyrimidine bases. According to NMR studies, the solution
13
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 14 of 32
1
2
3
4
5
6
7
8
9
conformation of such pentopyranoside nucleoside phosphonates prefers an equatorial orientation of the
nucleobase that circumvents unfavorable 1,3-diaxial interactions, in contrast to HNA nucleosides.
Preliminary primer incorporation reactions using a mesophilic and thermophilic polymerase revealed that
the compounds synthesized by these pathways constitute potentially useful monomers for medicinal and
biotechnological applications.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
EXPERIMENTAL SECTION
General Information. All reagents and solvents were purchased from commercial sources and used as
obtained. Moisture sensitive reactions were performed using oven-dried glassware under a nitrogen or
argon atmosphere. NMR spectra were recorded on a Bruker Advance 300 MHz (1H NMR, 300 MHz; 13C
NMR, 75 MHz; 31P NMR, 121 MHz), 500 MHz (1H NMR, 500 MHz; 13C NMR, 125 MHz; 31P NMR, 202
MHz), or 600 MHz (1H NMR, 600 MHz; 13C NMR, 150 MHz) spectrometer with tetramethylsilane as
internal standard or referenced to the residual solvent signal, and 85% H3PO4 for 31P NMR. All
intermediates and final compounds were characterized by using 2D NMR (1H-COSY, HSQC, NOESY, and
HMBC) spectroscopic techniques. For NMR assignment of sugar protons and carbons, prime numbering is
used. High-resolution mass spectra [HRMS (ESI)] were obtained on a quadruple orthogonal acceleration
time-of-flight mass spectrometer (Synapt G2 HDMS, Waters, Milford, MA). Samples were infused at 3
μL/min and spectra were obtained in positive (or in negative) ionization mode with a resolution of 15000
(fwhm) using leucine enkephalin as lock mass. Precoated aluminum sheets (254 nm) were used for TLC.
Products were purified by column chromatography on silica gel (60 Å, 0.035−0.070 mm, Acros Organics).
Preparative RP-HPLC purifications were carried out on a Phenomenex Gemini 110A column (C18, 10 μm,
21.2 mm × 250 mm) using CH3CN/0.05 M TEAB buffer or H2O/ CH3CN as eluent gradient.
Benzyl 2-O-acetyl-3,4-O-isopropylidene-β-L-ribopyranoside (5). Benzyl 3,4-O-isopropylidene-β-L-
ribopyranoside 4 was prepared in 4 steps from L-arabinose 3 following a literature procedure that did not
require column chromatography purification.21 Next, to a stirred solution of 4 (34.7 g, 123.8 mmol), DMAP
(0.76 g, 6 mmol) and triethylamine (69.0 mL, 495.2 mmol) in DCM (500 mL), acetic anhydride (23.4 mL,
247.6 mmol) was added dropwise at 0 ºC. The reaction mixture was slowly warmed to room temperature
and stirred for 2 h. After completion of the reaction, the mixture was cooled to 0 ºC and quenched with
saturated aq. NaHCO3. The organic layer was washed with brine (200 mL), dried over Na2SO4, and
concentrated in vacuo. The resulting residue was purified by column chromatography on silica gel (10:1,
1
hexane/EtOAc, Rf = 0.3) to afford 5 (37.3 g, 93% yield) as a white solid. H NMR (300 MHz, CDCl3) δ
7.38–7.26 (m, 5H, Ph), 5.00 (dd, J = 6.1, 3.3 Hz, 1H, H-2), 4.93 (d, J = 6.2 Hz, 1H, H-1), 4.80 (d, J = 12.3
Hz, 1H, CH2Ph), 4.80 (d, J = 12.3 Hz, 1H, CH2Ph), 4.57 (dd, J = 7.0, 3.2 Hz, 1H, H-3), 4.56 (d, J = 12.2
Hz, 1H, CH2Ph), 4.32 (dt, J = 7.0, 1.9 Hz, 1H, H-4), 3.87 (dd, J = 13.1, 2.5 Hz, 1H, H-5), 3.71 (dd, J =
13.1, 1.6 Hz, 1H, H-5′), 2.13 (s, 3H, CH3CO), 1.53 (s, 3H, [C(CH3)2]), 1.33 (s, 3H, [C(CH3)2]); 13C NMR
(75 MHz, CDCl3) δ 170.3 (CH3CO), 137.6, 128.5, 127.8, 127.7 (Ph), 110.4 [C(CH3)2], 96.9 (C-1), 73.6 (C-
2), 71.8 (CH2Ph), 70.3 (C-3), 69.5 (C-4), 62.5 (C-5), 26.5 [C(CH3)2], 25.3 [C(CH3)2], 21.2 (CH3CO); HRMS
(ESI-TOF) m/z: [M+Na]+ calcd for C17H22O6Na 345.1309; Found 345.1308.
14
ACS Paragon Plus Environment

Page 15 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
Benzyl 2-O-acetyl-β-L-ribopyranoside (6). A solution of 5 (20.0 g, 62.04 mmol) in 80% aq. acetic acid
(400 mL) was stirred at 60 ºC for 2 h. After removal of all the volatiles under reduced pressure, the residue
was partitioned between water (200 mL) and EtOAc (300 mL). The water layer was extracted with EtOAc
(1 × 200 mL). The combined organic layers were washed with brine, dried over Na2SO4 and concentrated
in vacuo. The resulting residue was purified by column chromatography on silica gel (100:5 DCM/methanol,
Rf = 0.25) to afford 6 (14.6 g, 83%) as a white solid. 1H NMR (500 MHz, DMSO-d6) δ 7.41–7.18 (m, 5H,
Ph), 5.10 (d, J = 4.7 Hz, 1H, OH-3), 4.76 (d, J = 7.0 Hz, 1H, H-1), 4.73 (d, J = 12.4 Hz, 1H, CH2Ph), 4.67
(d, J = 7.0 Hz, 1H, OH-4), 4.55 (dd, J = 6.8, 2.9 Hz, 1H, H-2), 4.54 (d, J = 12.3 Hz, 1H, CH2Ph), 3.96 (dt,
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
13
J = 4.3, 2.6 Hz, 1H, H-3), 3.69–3.55 (m, 3H, H-4, H-5 and H-5′), 2.11 (s, 3H, CH3CO); C NMR (125
MHz, DMSO-d6) δ 169.6 (CH3CO), 137.8, 128.3, 127.5, 127.4 (Ph), 97.1 (C-1), 72.0 (C-2), 69.5 (CH2Ph),
67.8 (C-3), 66.7 (C-4), 63.5 (C-5), 20.9 (CH3CO); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C14H18O6Na
305.0996; Found 305.0998.
Benzyl 2-O-acetyl-4-O-tert-butyldiphenylsilyl-β-L-ribopyranoside (7). To a stirred solution of 6 (10.0 g,
35.41 mmol) and imidazole (6.03 g, 88.5 mmol) in dry acetonitrile (300 mL) at 0 °C, a solution of tert-
butyldiphenylchlorosilane (10.1 mL, 38.9 mmol) in anhydrous acetonitrile (50 mL) was added dropwise.
The reaction mixture was stirred at room temperature for 8 h. After removal of all the volatiles under
reduced pressure, the resulting residue was partitioned between water (100 mL) and EtOAc (200 mL). The
water layer was extracted with EtOAc (1 × 200 mL). The combined organic layers were washed with brine
(150 mL), dried over Na2SO4, and concentrated in vacuo. The residue was purified by column
chromatography on silica gel (10:1 hexane/EtOAc, Rf = 0.3) to afford 7 (13.0 g, 71% yield) as a colorless
oil. 1H NMR (300 MHz, CDCl3) δ 7.75–7.62 (m, 4H, Ph), 7.47–7.36 (m, 6H, Ph), 7.32–7.22 (m, 5H, Ph),
4.92 (d, J = 5.2 Hz, 1H, H-1), 4.82 (dd, J = 5.1, 3.6 Hz, 1H, H-2), 4.71 (d, J = 12.0 Hz, 1H, CH2Ph), 4.50
(d, J = 12.0 Hz, 1H, CH2Ph), 4.10 (t, J = 3.3 Hz, 1H, H-3), 3.92 (dt, J = 5.9, 3.9 Hz, 1H, H-4), 3.63–3.49
(m, 2H, H-5 and H-5′), 2.12 (s, 3H, CH3CO), 1.09 (s, 9H, [C(CH3)3] ); 13C NMR (75 MHz, CDCl3) δ 170.4
(CH3CO), 137.3, 135.8, 135.75, 133.2, 132.5, 130.3, 130.2, 128.5, 128.1, 128.0, 127.8 , 127.6 (Ph), 97.3
(C-1), 71.3 (C-2), 70.1 (CH2Ph), 69.1 (C-4), 67.6 (C-3), 63.1 (C-5), 27.0 [C(CH3)3], 21.2 (CH3CO), 19.4
[C(CH3)3]; HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C30H36O6SiNa 543.2174; Found 543.2167.
Benzyl 2-O-acetyl-4-O-tert-butyldiphenylsilyl-3-O-trifluoromethanesulfonyl-β-L-ribopyranoside (9).
To a stirred solution of 7 (10.0 g, 19.22 mmol) and pyridine (4.8 mL, 57.7 mmol) in dry DCM (300 mL) at
0 °C, triflic anhydride (6.5 mL, 38.44 mmol) was added dropwise. The reaction mixture was stirred at room
temperature for 1 h. After completion of the reaction, the mixture was cooled to 0 ºC and quenched with
saturated aq. NaHCO3. The reaction mixture was further washed with saturated aq. NaHCO3 (100 mL) and
brine (100 mL). The organic layer was dried over Na2SO4 and concentrated in vacuo. The resulting residue
was purified by silica gel column chromatography (silica gel was presoaked with 0.5% of triethylamine in
hexane; chromatography was performed using 15:1 hexane/EtOAc, Rf = 0.2) to afford 9 (11.9 g, 95% yield)
as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.79–7.58 (m, 4H, Ph), 7.54–7.15 (m, 11H, Ph), 5.31 (dd,
J = 2.4, 2.2 Hz, 1H, H-2), 4.82 (dd, J = 7.3, 2.4 Hz, 1H, H-3), 4.74 (d, J = 12.0 Hz, 1H, CH2Ph), 4.72 (d, J
= 7.2 Hz, 1H, H-1),4.50 (d, J = 12.0 Hz, 1H, CH2Ph), 3.94 (ddd, J = 9.4, 5.8, 2.3 Hz, 1H, H-4), 3.56 (dd, J
= 11.6, 9.5 Hz, 1H, H-5), 3.39 (dd, J = 11.6, 4.8 Hz, 1H, H-5′), 2.08 (s, 3H, CH3CO), 1.08 (s, 9H, [C(CH3)3]);
15
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 16 of 32
1
2
3
4
5
6
7
8
13C NMR (75 MHz, CDCl3) δ 169.6 (CH3CO), 135.9, 135.85, 133.0, 130.6, 130.5, 128.6, 128.3, 128.1,
127.7 (Ph), 120.8 (CF3), 97.2 (C-1), 86.0 (C-3), 70.9 (C-2), 68.7 (CH2Ph), 67.3 (C-4), 63.7 (C-5), 26.8
[C(CH3)3], 20.7 (CH3CO), 19.2 [C(CH3)3]; HRMS (ESI-TOF) m/z: [M+NH4]+ calcd for C31H39NF3O8SSi
670.2118; Found 670.2119.
9
Benzyl 2-O-acetyl-4-O-tert-butyldiphenylsilyl-3-deoxy-3-iodo-β-L-xylopyranoside (10). A suspension
of 9 (4.00 g, 6.12 mmol) and NaI (2.76 g, 18.38 mmol) in THF (70 mL) was stirred at room temperature
for 12 h. After removal of all the volatiles under reduced pressure, the resulting residue was separated
between EtOAc (100 mL) and saturated aq. NaHCO3 (50 mL). The water layer was extracted with EtOAc
(50 mL) once. The combined organic layers were washed with brine (50 mL), dried over Na2SO4, and
concentrated in vacuo. The residue was purified by column chromatography on silica gel (15:1
hexane/EtOAc) to afford 10 (3.71 g, 96% yield) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.94–7.62
(m, 4H, Ph), 7.56–7.10 (m, 11H, Ph), 5.06 (dd, J = 10.5, 7.2 Hz, 1H, H-2), 4.76 (d, J = 12.4 Hz, 1H, CH2Ph),
4.49 (d, J = 12.4 Hz, 1H, CH2Ph), 4.29 (d, J = 7.2 Hz, 1H, H-1), 4.14–3.87 (m, 2H, H-3 and H-4), 3.64 (dd,
J = 11.6, 4.4 Hz, 1H, H-5), 3.28–3.03 (m, 1H, , H-5′), 2.07 (s, 3H, CH3CO), 1.09 (s, 9H, [C(CH3)3]); 13C
NMR (75 MHz, CDCl3) δ 169.0 (CH3CO), 136.3, 135.9, 130.3, 130.1, 128.5, 128.0, 127.9, 127.8, 127.7
(Ph), 100.4 (C-1), 73.7 (C-2), 73.1 (C-4), 70.4 (CH2Ph), 68.2 (C-5), 33.5 (C-3), 27.2 [C(CH3)3], 21.0
(CH3CO), 19.7 [C(CH3)3]; HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C30H35IO5SiNa 653.1193; Found
653.1196.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 2-O-acetyl-4-O-tert-butyldiphenylsilyl-3-deoxy-β-L-erythro-pentopyranoside (11). To a stirred
solution of 10 (2.00 g, 3.17 mmol) and AIBN (0.26 g, 1.59 mmol) in toluene (100 mL), tributyltin hydride
(1.7 mL, 6.34 mmol) was added dropwise. The reaction mixture was heated at 110 °C for 1 h. After removal
of all the volatiles under reduced pressure, the resulting crude residue was purified by column
chromatography on silica gel (15:1 hexane/EtOAc, Rf = 0.2) to afford 11 (1.5 g, 94% yield) as a colorless
oil. 1H NMR (300 MHz, CDCl3) δ 7.70–7.60 (m, 4H, Ph), 7.45–7.34 (m, 6H, Ph), 7.33–7.25 (m, 5H, Ph),
4.75 (d, J = 12.2 Hz, 1H, CH2Ph), 4.72–4.65 (m, 1H, H-2), 4.56 (d, J = 5.3 Hz, 1H, H-1), 4.52 (d, J = 12.2
Hz, 1H, CH2Ph), 3.88–3.78 (m, 1H, H-4), 3.74 (ddd, J = 11.4, 3.7, 1.2 Hz, 1H, H-5a), 3.32 (dd, J = 11.4,
6.3 Hz, 1H, H-5e), 2.21 (dtd, J = 13.2, 4.6,1.2 Hz, 1H, H-3e), 2.04 (s, 3H, CH3CO), 1.77 (dt, J = 13.2, 7.6
Hz, 1H, H-3a), 1.06 (s, 9H, [C(CH3)3]); 13C NMR (75 MHz, CDCl3) δ 170.2 (CH3CO), 137.6, 135.8, 133.9,
133.6, 123.0, 128.5, 127.9, 127.8 (Ph), 99.2 (C-1), 69.7 (CH2Ph), 68.6 (C-2), 67.4 (C-5), 65.5 (C-4), 34.3
(C-3), 27.0 [C(CH3)3], 21.3 (CH3CO), 19.3 [C(CH3)3]; HRMS (ESI-TOF) m/z: [M+Na]+ calcd for
C30H36O5SiNa 527.2224; Found 527.2216.
Benzyl 2-O-acetyl-3-deoxy-β-L-erythro-pentopyranoside (12). To a stirred solution of 11 (1.00 g, 1.98
mmol) in THF (40 mL) at 0 °C, TBAF (1 M in THF, 3.96 mL, 3.96 mmol) was added dropwise. The
reaction mixture was slowly warmed to room temperature and stirred for 5 h. After completion of the
reaction, all volatiles were removed in vacuo. The resulting residue was separated between EtOAc (40 mL)
and saturated aq. NaHCO3 (20 mL). The water layer was extracted with EtOAc (30 mL) once. The
combined organic layers were washed with brine (20 mL), dried over Na2SO4, and concentrated in vacuo.
The residue was purified by column chromatography on silica gel (gradient hexane/EtOAc, 5:1, v/v; 1:1,
v/v) affording 12 (0.46 g, 87%) as a colorless oil. 1H NMR (600 MHz, CDCl3) δ 7.41–7.30 (m, 5H, Ph),
16
ACS Paragon Plus Environment

Page 17 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
4.90 (dt, J = 3.2, 2.3 Hz, 1H, H-2), 4.78 (bs, 1H, H-1e), 4.77 ( d, J = 11.6 Hz, 1H, CH2Ph), 4.56 (d, J = 11.6
Hz, 1H, CH2Ph), 4.01 (dd, J = 12.0, 1.8 Hz, 1H, H-5a), 3.75 (dq, J = 2.7, 2.4 Hz, 1H, H-4e), 3.67 (dt, J =
11.9, 2.3 Hz, 1H, H-5e), 2.22 (td, J = 15.0, 3.7 Hz, 1H, H-3a), 2.1 (s, 3H, CH3CO), 1.96 (ddtd, J = 15.0,
3.2, 2.4, 0.93 Hz, 1H, H-3e); 13C NMR (151 MHz, CDCl3) δ 169.5 (CH3CO), 137.0, 128.5, 127.9, 127.8
(Ph), 95.8 (C-1), 69.3 (CH2Ph), 68.5 (C-2), 64.5 (C-5), 64.2 (C-4), 29.3 (C-3), 21.2 (CH3CO); HRMS (ESI-
TOF) m/z: [M+Na]+ calcd for C14H19O5Na 289.1046; Found 289.1045.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 2-O-acetyl--L-glycero-pent-3-enopyranoside (13). This compound was first obtained as a side
product during the Mitsunobu reaction (see Scheme 1), and it was later synthesized by using the triethyl
phosphite method.
Mitsunobu conditions: To a stirred suspension of 12 (1 eq), thymine or Bz-thymine (2 eq), and
triphenylphosphine (2.2 eq) in anhydrous dioxane or THF, a solution of DEAD or DIAD in 2 mL of THF
or dioxane was slowly added. The mixture was stirred until disappearance of starting material 12. After
removal of all the volatiles under reduced pressure, the resulting residue was separated between EtOAc and
saturated aq. NaHCO3. The water layer was extracted with EtOAc. The combined organic layers were
washed with brine, dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by
flash column chromatography on silica gel using 15:1(v/v) hexane/ EtOAc. The reaction was conducted at
different temperatures (-78, -20, 0 °C, and rt), however only the elimination product 13 was formed instead
of the desired nucleoside.
Triethyl phosphite conditions: A stirring solution of 17 (8.00 g, 24.7 mmol) in triethylphosphite (250 mL)
was maintained at 140 ºC for 14 h and the reaction was monitored by TLC for completion. After removal
of all the volatiles under reduced pressure, the crude residue was subjected to column chromatography on
silica gel (15:1 hexane/EtOAc) to give 13 (5.20 g, 85% yield) as a colorless oil. 1H NMR (300 MHz, CDCl3)
δ 7.40–7.27 (m, 5H, Ph), 6.08 (td, J = 10.3, 2.4 Hz, 1H, H-3), 5.95–5.71 (m, 1H, H-4), 5.11–4.94 (m, 1H,
H-2), 4.90 (bs, 1H, H-1), 4.81 (d, J = 12.0 Hz, 1H, CH2Ph), 4.62 (d, J = 12.0 Hz, 1H, CH2Ph), 4.37–4.09
(m, 2H, H-5 and H-5′), 2.07 (s, 3H, CH3CO); 13C NMR (75 MHz, CDCl3) δ 170.4 (CH3CO), 137.4, 131.3,
128.6, 128.0 (Ph), 127.9 (C-3), 120.4 (C-4), 96.8 (C-1), 69.9 (C-2), 66.1 (CH2Ph), 59.7 (C-5), 21.2 (CH3CO);
HRMS (ESI-TOF) m/z: [M+H]+ calcd for C14H17O4 249.1121; Found 249.1123.
General procedure for the synthesis of benzyl 2-O-acetyl-3-deoxy-4-sulfonate-β-L-erythro-
pentopyranosides 14a-c. To a stirred solution of 12 (0.2 g, 0.75 mmol) and pyridine (0.18 mL, 2.25 mmol)
in DCM (10 mL) at 0 °C, a solution of a sulfonyl chloride in DCM (2 mL) was added dropwise. The
progress of the reaction was monitored by TLC, and 0.5 mL of saturated aq. NaHCO3 was added to quench
the reaction at 0 °C. The reaction mixture was washed with saturated aq. NaHCO3 (5 mL) and brine (5 mL).
The organic layer was dried over Na2SO4 and concentrated in vacuo. The crude mesylate or tosylate was
purified by column chromatography on silica gel to afford the desired sulfonate, after prewashing the
column with 0.1% of triethylamine in hexane.
Mesylate (14a). Following the general procedure in the presence of mesyl chloride (0.12 mL, 1.5 mmol), a
crude product was obtained, which was purified by column chromatography using 5:1 hexane/EtOAc as
eluent to afford 14a (0.23 g, 87% yield) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.39–7.27 (m, 5H,
Ph), 4.84–4.70 (m, H-1, H-2, H-4 and CH2Ph), 4.54 (d, J = 12.1 Hz, 1H, CH2Ph), 4.03 (dd, J = 13.0, 1.8
17
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 18 of 32
1
2
3
4
5
6
7
8
Hz, 1H, H-5), 3.82 (d, J = 13.0 Hz, 1H, H-5′), 3.01 (s, 3H, CH3 SO2), 2.29–2.21 (bs, 2H, H-3 and H-3′),
2.07 (s, 3H, CH3CO); 13C NMR (75 MHz, CDCl3) δ 179.9 (CH3CO), 136.7, 128.3, 127.8, 127.7 (Ph), 95.9
(C-1), 72.5 (C-2), 69.2 (CH2Ph), 66.2 (C-4), 61.5 (C-5), 38.4 (CH3 Ms), 27.8 (C-3), 20.8 (CH3CO); HRMS
(ESI-TOF) m/z: [M+Na]+ calcd for C15H20O7S1Na 367.0822; Found 367.0816.
9
Tosylate (14b). Following the general procedure in the presence of tosyl chloride (0.29 g, 1.5 mmol), a
crude product was obtained, which was purified by column chromatography using 10:1 hexane/EtOAc to
afford 14b (0.267 g, 85% yield) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.79 (d, J = 8.1 Hz, 2H,
Ph), 7.45–7.18 (m, 7H, Ph), 4.84–4.66 (m, 3H, H-1, H-2 and CH2Ph ), 4.61– 4.56 (m, 2H, H-4 and CH2Ph),
3.95 (d, J = 12.8 Hz, 1H, H-5), 3.68 (d, J = 12.8 Hz, 1H, H-5′), 2.45 (s, 3H, CH3 Ts), 2.24–2.06 (m, 2H,
H-3 and H-3′), 2.04 (s, 3H, CH3CO); 13C NMR (75 MHz, CDCl3) δ 170.3 (CH3CO), 145.0, 137.0, 134.2,
130.0, 128.6, 128.1, 128.0, 127.8 (Ph), 96.3 (C-1), 73.0 (C-2), 69.6 (CH2Ph), 66.6 (C-4), 61.9 (C-5), 28.0
(C-3), 21.7 (CH3 Ts), 21.2 (CH3CO); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C21H24O7S1Na 443.1135;
Found 443.1135.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 2-O-acetyl-3,4-anhydro-β-L-ribopyranoside (16). Following a similar procedure as that used for
the synthesis of 12, epoxide 16 was obtained starting from 10 (0.57 g, 0.32 mmol), TBAF (0.63 mL, 0.63
mmol, 1 M in THF) in THF (10 mL). The crude residue was purified by column chromatography using
hexane/EtOAc (8:1, v/v; 3:1 v/v) to give 16 as a white solid (0.2 g, 95%). 1H NMR (300 MHz, CDCl3) δ
7.51–7.24 (m, 5H, Ph), 4.95 (dd, J = 4.7, 3.2 Hz, 1H, H-2), 4.74 (d, J = 12.0 Hz, 1H, CH2Ph), 4.65 (d, J =
3.0 Hz, 1H, H-1), 4.52 (d, J = 12.0 Hz, 1H, CH2Ph), 4.08 (dd, J = 13.3, 1.6 Hz, 1H, H-5), 3.98 (d, J = 13.3
Hz, 1H, H-5′), 3.59 (appt, J = 4.0 Hz, 1H, H-3), 3.34 (dd, J = 3.9, 1.2 Hz, 1H, H-4), 2.14 (s, 3H, CH3CO);
13C NMR (75 MHz, CDCl3) δ 170.3 (CH3CO), 137.0, 128.6, 128.1, 127.9 (Ph), 95.8 (C-1), 69.9 (C-2), 68.3
(CH2Ph), 58.7 (C-5), 51.2 (C-3), 49.8 (C-4), 20.9 (CH3CO); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for
C14H16O5Na 287.0890; Found 287.0894.
Benzyl 2-O-acetyl-3,4-O-thiocarbonyl-β-L-ribopyranoside (17). A solution of 6 (10.0 g, 35.42 mmol)
and TCDI (12.6 g, 70.9 mmol) in anhydrous DCM (500 mL) was stirred at room temperature for 10 h. The
reaction mixture was washed with saturated aq. NaHCO3 (200 mL). The organic layer was separated, and
the aqueous layer was extracted with DCM. The combined organic layers were washed with brine and dried
over Na2SO4. After removal of all the volatiles under reduced pressure, the crude residue was purified by
column chromatography (3:1 DCM/hexane) to afford 17 (9.60 g, 83% yield) as a white solid. 1H NMR (300
MHz, CDCl3) δ 7.43–7.30 (m, 5H, Ph), 5.22 (dd, J = 7.7, 4.0 Hz, 1H, H-4), 5.11 (appt, J = 4.2 Hz, 1H, H-
2), 5.00 (d, J = 4.6 Hz, 1H, H-1), 4.98 (dd, J = 7.8, 1.2 Hz, 1H, H-3), 4.78 (d, J = 11.9 Hz, 1H, CH2Ph),
4.60 (d, J = 11.9 Hz,, 1H, CH2Ph), 4.10 (dd, J = 14.1, 0.7 Hz, 1H, H-5), 4.01 (dd, J = 14.1, 2.0 Hz, 1H, H-
5′), 2.15 (s, 3H, CH3CO); 13C NMR (75 MHz, CDCl3) δ 191.2 (CS), 169.9 (CH3CO), 136.5, 128.7, 128.4,
128.1 (Ph), 96.1 (C-1), 78.4 (C-4), 75.6 (C-3), 70.1 (CH2Ph), 66.7 (C-2), 58.6 (C-5), 20.8 (CH3CO); HRMS
(ESI-TOF) m/z: [M+H]+ calcd for C15H17O6S1 325.0740; Found 325.0740.
Benzyl -L-glycero-pent-3-enopyranoside (18). To a stirred solution of 13 (3.75 g, 15.1 mmol) in
methanol (150 mL) at 0 °C, a 30% NaOMe solution in MeOH (5.59 mL, 30.2 mmol) was added dropwise.
The reaction mixture was stirred at room temperature for 2 h. After completion of the reaction, all the
volatiles were removed in vacuo. The remaining residue was partitioned between EtOAc (100 mL) and
18
ACS Paragon Plus Environment

Page 19 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
saturated aq. NaHCO3 (100 mL). The water layer was extracted with EtOAc (1 × 50 mL). The combined
organic layers were washed with brine (50 mL), dried over Na2SO4, and concentrated in vacuo. The crude
residue was purified by column chromatography on silica gel (4:1 hexane/EtOAc) to give 18 (2.86 g, 91%
yield) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.56–7.24 (m, 5H, Ph), 6.08–5.78 (m, 2H, H-3 and
H-4), 4.80 (d, J = 11.8 Hz, 1H, CH2Ph ), 4.77 (d, J = 2.6 Hz, 1H, H-1), 4.58 (d, J = 11.8 Hz, 1H, CH2Ph),
4.27–4.03 (m, 2H, H-5 and H-5′), 3.89 (bs, 1H, H-2), 2.61 (s, 1H, OH); 13C NMR (75 MHz, CDCl3) δ 137.4,
128.7, 128.5, 128.0 (Ph), 127.9 (C-3), 124.6 (C-4), 99.9 (C-1), 70.0 (CH2Ph), 64.8 (C-2), 60.8 (C-5); HRMS
(ESI-TOF) m/z: [M+H]+ calcd for C12H15O3 229.08353; Found 229.0842.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 3,4-anhydro-β-L-ribopyranoside (19). A solution of m-chloroperbenzoic acid (mCPBA, 77%,
4.12 g, 9.46 mmol) in DCM (5 mL) was added dropwise to a stirring solution of 18 (2.60 g, 12.6 mmol) in
dry DCM (120 mL) at 0 °C. After the addition was completed, the reaction mixture was stirred at 8-9 °C
for 24 h. It was then cooled to 0 °C and 20% aq. Na2S2O3 (25 mL) was added, and the stirring was continued
for 2 h. The organic layer was separated and successively washed with saturated aq. NaHCO3 and brine,
dried over Na2SO4, and concentrated in vacuo. The residue was purified by silica gel column
chromatography (3:1 hexane/EtOAc) to afford 19 (2.50 g, 89% yield) as a white solid. 1H NMR (300 MHz,
CDCl3) δ 7.46–7.22 (m, 5H, Ph), 4.72 (d, J = 11.8 Hz, 1H, CH2Ph), 4.58 (d, J = 2.3 Hz, 1H, H-1), 4.49 (d,
J = 11.8 Hz, 1H, CH2Ph), 4.01 (dd, J = 13.4, 1.5 Hz, 1H, H-5), 3.93 (d, J = 13.4 Hz, 1H, H-5′), 3.82 (dd, J
13
= 4.5, 2.4 Hz, 1H, H-2), 3.50 (appt, J = 4.5 Hz, 1H, H-3), 3.33 (ddd, J = 4.2, 1.5, 0.6 Hz, 1H, H-4); C
NMR (75 MHz, CDCl3) δ 137.0, 128.6, 128.1, 128.0 (Ph), 97.9 (C-1), 69.7 (CH2Ph), 64.7 (C-2), 58.0 (C-
5), 51.8 (C-3), 51.4 (C-4); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C12H14O4Na 245.0785; Found
245.0791.
Benzyl 3,4-anhydro-2-O-methoxyethoxymethyl-β-L-ribopyranoside (20). To a stirred solution of 19
(2.10 g, 9.45 mmol) and DIPEA (4.90 mL, 28.4 mmol) in dry DCM (50 mL) at 0 °C was added MEMCl
(2.16 mL, 18.9 mmol). After the addition was completed, the reaction mixture was stirred at room
tempearture for 1 h, and later at 40 ºC for 8 h. The reaction mixture was washed with saturated aq. NaHCO3
and brine. The organic layer was dried over Na2SO4 and concentrated in vacuo. The remaining residue was
purified by column chromatography on silica gel (15:1 hexane/EtOAc) to afford 20 (2.68 g, 91% yield) as
1
a colorless oil. H NMR (300 MHz, CDCl3) δ 7.39–7.20 (m, 5H, Ph), 4.89 (s, 2H, OCH2O), 4.75 (d, J =
11.9 Hz, 1H, CH2Ph), 4.61 (d, J = 4.0 Hz, 1H, H-1), 4.50 (d, J = 11.8 Hz, 1H, CH2Ph), 4.07 (dd, J = 13.4,
2.3 Hz, 1H, H-5), 3.92 (d, J = 13.4 Hz, 1H, H-5′), 3.92–3.79 (m, 2H, H-2 and OCH2CH2O), 3.76–3.63 (m,
1H, OCH2CH2O), 3.56–3.47 (m, 3H, H-3 and OCH2CH2O), 3.39–3.31 (m, 1H, H-4), 3.35 (s, 3H, OCH3);
13C NMR (75 MHz, CDCl3) δ 137.1, 128.3, 127.7, 127.7 (Ph), 97.6 (OCH2O), 95.1 (C-1), 71.7 (C-2), 71.6
(OCH2CH2O), 69.9 (CH2Ph), 67.1 (OCH2CH2O), 59.9 (C-5), 58.8 (OCH3), 51.9 (C-3), 51.7 (C-4); [M+Na]+
calcd for C16H22O6Na 333.1309; Found 333.1317.
Benzyl 4-deoxy-2-O-(2-methoxyethoxymethyl)-4-(thymid-1-yl)-α-D-lyxopyranoside (21). To a stirred
suspension of 20 (1.90 g, 6.12 mmol) and thymine (2.32 g, 18.4 mmol) in dry DMF (50 mL) at 0 °C was
slowly added DBU (3 mL, 18.87 mmol). The suspension was stirred at room temperature for 30 min until
all the solid dissolved and then heated at 80 °C for 8 h. After removal of all the volatiles under reduced
pressure, the remaining syrup was dissolved in EtOAc and washed with saturated aq. NaHCO3. The organic
19
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 20 of 32
1
2
3
4
5
phase was collected, dried over Na2SO4 and concentrated in vacuo. The product was purified by silica gel
1
column chromatography (100:2 DCM/Methanol) to afford 21 (2.27 g, 85% yield) as a colorless oil. H
6
7
8
9
NMR (500 MHz, CDCl3) δ 9.74 (s, 1H, NH), 7.35 (m, 5H, Ph), 7.03 (s, 1H, H-6), 5.02 (d, J = 1.5 Hz, 1H,
H-1′), 4.87 (d, J = 7.2 Hz, 1H, OCH2O), 4.80 (d, J = 7.2 Hz, 1H, OCH2O), 4.76 (d, J = 11.7 Hz, 1H, CH2Ph),
4.54 (d, J = 11.7 Hz, 1H, CH2Ph), 4.28 (appt, J = 7.9 Hz, 1H, H-3′), 3.98 (appt, J = 2.4 Hz, 1H, H-2′), 3.89–
3.66 (m, 4H, H-5′, H-5′ and OCH2CH2O), 3.51 (s, 2H, OCH2CH2O), 3.34 (s, 3H, OCH3), 1.88 (s, 3H, T
CH3); 13C NMR (126 MHz, CDCl3) δ 163.9 (C-4), 151.8 (C-2), 137.1 (C-6), 137.0, 128.6, 128.1, 127.9
(Ph), 111.0 (C-5), 98.3 (C-1′), 96.7 (OCH2O), 78.9 (C-2′), 71.5 (OCH2CH2O), 69.4 (CH2Ph), 67.8
(OCH2CH2O), 65.9 (C-3′), 60.2 (C-5′), 58.9 (OCH3), 54.7 (C-4′), 12.5 (T CH3); HRMS (ESI-TOF) m/z:
[M+Na]+ calcd for C21H28N2O8Na 459.1738; Found 459.1731.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 3,4-dideoxy-2-O-(2-methoxyethoxymethyl)-4-(thymid-1-yl)-α-D-threo-pentopyranoside (22).
To a solution of 21 (1.40 g, 2.6 mmol) and DMAP (100 mg, 0.8 mmol) in anhydrous DCM (30 mL) was
added TCDI (940 mg, 5.20 mmol) at room temperature. The reaction mixture was stirred at 40 °C overnight.
It was then washed with brine, dried over Na2SO4, and concentrated under reduced pressure. The resulting
residue was dissolved in toluene (50 mL), and AIBN (170 mg, 1.10 mmol) was added followed by
tributyltin hydride (1.70 mL, 4.20 mmol). The reaction mixture was refluxed for 1 h. After removal of all
the volatiles under reduced pressure, the crude residue was purified by column chromatography on silica
gel (gradient CH2Cl2/MeOH, 100:0, v/v; 100:2, v/v; 30:1, v/v) to afford 22 (1.10 g, 83% yield over two
steps) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 9.95 (s, 1H, NH), 7.47–7.19 (m, 5H, Ph), 7.06 (s,
1H, H-6), 5.10–4.89 (m, 1H, H-4′), 4.80 (m, 4H, OCH2O, CH2Ph and H-1′), 4.59 (d, J = 11.1 Hz, 1H,
CH2Ph), 3.93 (bs, 1H, H-2′), 3.85–3.64 (m, 4H, H-5′, H-5′, OCH2CH2O), 3.51 (dd, J = 5.4, 3.6 Hz, 2H,
OCH2CH2O), 3.34 (s, 3H, OCH3), 2.30 (td, J = 12.7, 2.8 Hz, 1H, H-3′), 2.03 (dt, J = 12.6, 3.1 Hz, 1H, H-
3′′), 1.90 (s, 3H, T CH3); 13C NMR (75 MHz, CDCl3) δ 164.3 (C-4), 151.4 (C-2), 137.5 (C-6), 137.0, 128.8,
128.20, 128.25 (Ph), 111.2 (C-5), 96.7 (OCH2O), 95.2 (C-1′), 73.0 (C-2′), 71.9 (OCH2CH2O), 69.5 (CH2Ph),
67.5 (OCH2CH2O), 61.3 (C-5′), 59.2 (OCH3), 47.6 (C-4′), 29.2 (C-3′), 12.8 (T CH3); HRMS (ESI-TOF)
m/z: [M+H]+ calcd for C21H29N2O7 421.1969; Found 421.1964.
Benzyl 3,4-dideoxy-4-(thymid-1-yl)-α/β-D-threo-pentopyranoside (23). Hydrochloric acid in 1,4-
dioxane (4 M, 8 mL) was added dropwise to a solution of 22 (1.20 g, 2.86 mmol) in 1,4-dioxane (24 mL),
and the reaction mixture was stirred at room temperature for 8 h. After removal of all the volatiles under
reduced pressure, the remaining syrup was co-evaporated with triethylamine (5 mL) once and then
subjected to column chromatography on silica gel to give α/β-23. Data for the α-23: (0.72 g, 75% yield);
1H NMR (600 MHz, CDCl3) δ 9.96 (s, 1H, NH), 7.46–7.29 (m, 5H, Ph), 7.12 (d, J = 1.1 Hz, 1H, H-6),
5.13–4.97 (m, 1H, H-4′), 4.80 (d, J = 11.9 Hz, 1H, CH2Ph), 4.71 (d, J = 2.4 Hz, 1H, H-1′), 4.57 (d, J = 11.9
Hz, 1H, CH2Ph), 3.96 (bs, 1H, H-2′), 3.82 (m, 2H, H-5′ and H-5′′), 3.67 (d, J = 6.1 Hz, 1H, OH), 2.27 (appt
d, J = 13.0, 3.3 Hz, 1H, H-3′), 2.01 (d appt, J = 13.3, 4.3 Hz, 1H, H-3′), 1.88 (d, J = 1.1 Hz, 3H, T CH3);
13C NMR (151 MHz, CDCl3) δ 163.8 (C-4), 151.3 (C-2), 137.0 (C-6), 136.6, 128.5, 128.0, 128.0 (Ph),
111.0 (C-5), 98.3 (C-1′), 69.5 (CH2Ph), 67.0 (C-2′), 61.4 (C-5′), 46.8 (C-4′), 30.8 (C-3′), 12.5 (T CH3);
HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H21N2O5 333.1445; Found 333.1443.
Data for the -23: (48 mg, 5% yield); 1H NMR (500 MHz, CDCl3) δ 9.52 (s, 1H, NH), 7.61 (d, J = 1.2 Hz,
20
ACS Paragon Plus Environment

Page 21 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
1H, H-6), 7.42–7.29 (m, 5H, Ph), 4.92 (d, J = 2.9 Hz, 1H, H-1′), 4.84 (d, J = 11.9 Hz, 1H, CH2Ph), 4.76–
4.52 (m, 2H, CH2Ph, H-4′), 4.13 (dd, J = 13.0, 3.9 Hz, 1H, H-5′), 3.94–3.73 (m, 2H, H-5′, H-2′), 2.48 (d, J
= 8.3 Hz, 1H, OH), 2.21– 2.17 (dT, J = 12.9, 3.8 Hz, 1H, H-3′), 2.15– 2.09 (m, 1H, H-3′′), 1.95–1.86 (d, J
= 1.2 Hz, 3H, T CH3); 13C NMR (126 MHz, CDCl3) δ 164.0 (C-4), 150.9 (C-2), 138.2, 136.4 (C-6), 128.5,
128.1, 128.0 (Ph), 110.6 (C-5), 97.3 (C-1′), 69.9 (CH2Ph), 64.4 (C-2′), 61.1 (C-5′), 51.2 (C-4′), 31.1 (C-3′),
12.5 (T CH3).
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 2-O-benzoyl-3,4-dideoxy-4-(thymid-1-yl)-α/β-D-threo-pentopyranoside (24). To a solution of
α/β-23 (400 mg, 1.20 mmol) in pyridine (15 mL) at 0 °C, benzoyl chloride (0.24 mL, 1.81 mmol) was added
dropwise. The reaction mixture was stirred at 0 °C for 2 h. After removal of all the volatiles under reduced
pressure, the remaining residue was partitioned between DCM (30 mL) and saturated aq. NaHCO3 (20 mL).
The aqueous layer was extracted again with DCM (20 mL). The combined organic layers were washed with
saturated aq. NaHCO3 and brine, dried over Na2SO4, and concentrated in vacuo. The residue was purified
by silica gel column chromatography (3:1 hexane/EtOAc) to afford α/β-24 (483 mg, 92% yield) as a
colorless oil.
Data for α-24: 1H NMR (600 MHz, CDCl3) δ 9.17 (s, 1H, NH), 8.09 (m, 2H, Ph), 7.64–7.30 (m, 8H, Ph),
7.04 (d, J = 1.2 Hz, 1H, H-6), 5.31 (td, J = 3.5, 3.2 Hz, 1H, H-2′), 5.09 (tt, J = 11.7, 5.0 1H, H-4′), 4.92 (d,
J = 1.6 Hz, 1H, H-1′), 4.82 (d, J = 11.9 Hz, 1H, CH2Ph), 4.62 (d, J = 11.9 Hz, 1H, CH2Ph), 3.87 (appt, J =
10.8 Hz, 1H, H-5′), 3.81 (ddd, J = 10.7, 5.0, 1.9 Hz, 1H, H-5′), 2.49 (td, J = 13.2, 3.2 Hz, 1H, H-3′), 2.26–
2.04 (dt, J = 13.8, 3.6 Hz, 1H, H-3′′), 1.92 (d, J = 1.2 Hz, 3H, T CH3); 13C NMR (151 MHz, CDCl3) δ 165.5
(PhCO), 163.5 (C-4), 150.8 (C-2), 136.8, 136.1 (C-6), 133.4, 129.8, 129.4(Ar-C), 128.6, 128.5, 128.3, 128.1,
127.9 (Ph), 111.3 (C-5), 95.0 (C-1′), 69.5 (CH2Ph), 69.1 (C-2′), 60.7 (C-5′), 47.0 (C-4′), 28.2 (C-3′), 12.5
(T CH3); HRMS (ESI-TOF) m/z: [M+H]+ calcd for C24H25N2O6 437.1707; Found 437.1700.
Data for β-24: 1H NMR (300 MHz, CDCl3) δ 9.36 (s, 1H, NH), 8.18–7.72 (m, 2H, Ph), 7.46 (m, 3H, Ph),
7.19 (m, 5H, Ph), 5.29 (dd, J = 6.9, 9.9 Hz, 1H, H-2′), 5.01 (td, J = 5.9, 10.9 Hz, 1H, H-4′), 4.85 (d, J =
12.4 Hz, 1H, CH2Ph), 4.63 (d, J = 12.4 Hz, 1H, CH2Ph), 4.58 (d, J = 7.4 Hz, 1H, H-1′), 4.11 (dd, J = 3.7,
11.1 Hz, 1H, H-5′), 3.60 (appt, J = 11.0 Hz, 1H, H-5′′), 2.18–1.74 (m, 5H, , H-3′, , H-3′′ and T CH3); 13C
NMR (75 MHz, CDCl3) δ 165.4 (PhCO), 163.6 (C-4), 151.4 (C-2), 136.8 , 136.0 (C-6), 133.5, 130.0, 129.0,
128.5, 128.4, 127.9, 127.9 (Ph), 111.7 (C-5), 100.6 (C-1′), 71.1 (C-2′), 70.3 (CH2Ph), 62.6 (C-5′), 54.0 (C-
4′), 30.8 (C-3′), 12.7 (T CH3).
2-O-Benzoyl-3,4-dideoxy-4-(thymid-1-yl)-α-D-threo-pentopyranose (25). To a solution of α/β-24 (300
mg, 0.69 mmol) in ethanol (10 mL), Pd/C (366 mg, 0.34 mmol) and cyclohexene (1.39 mL, 13.8 mmol)
were added. The reaction mixture was stirred at 80 ºC for 6 h. It was then cooled and filtered through a pad
of Celite to give 25 (209 mg, 88%) as a white solid. 1H NMR (600 MHz, DMSO-d6) δ 11.3 (s, 1H, NH),
8.01 (m, 2H, Ph), 7.72–7.68 (m, 1H, Ph), 7.65 (d, J = 1.2 Hz, 1H, H-6), 7.59–7.56 (m, 2H, Ph), 7.00 (d, J
= 4.7 Hz, 1H, OH), 5.04 (td, J = 4.7, 3.6 Hz, 1H, H-2′), 5.01 (dd, J = 4.7, 1.4 Hz, 1H, H-1′), 4.79 (tt, J =
10.7, 4.3 Hz, 1H, H-4′), 4.03 (appt, J = 10.8 Hz, 1H, H-5′), 3.59 (ddd, J = 10.5, 4.4, 1.7 Hz, 1H, H-5′′), 2.59
(td, J = 13.4, 3.1 Hz, 1H, H-3′), 2.01 (dt, J = 13.4, 4.5 Hz, 1H, H-3′), 1.79 (d, J = 0.9 Hz, 3H, T CH3); 13C
NMR (151 MHz, DMSO-d6) δ 165.0 (PhCO), 163.8 (C-4), 151.0 (C-2), 138.0, 133.7 (C-6), 129.7, 129.4,
129.3, 128.9, 128.8 (Ph), 109.2 (C-5), 89.7 (C-1′), 70.9 (C-2′), 59.8 (C-5′), 47.3 (C-4′), 27.3 (C-3′), 12.1 (T
21
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 22 of 32
1
2
3
4
CH3); HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H19N2O6 347.1238; Found 347.1241.
5
6
7
8
General procedure for the synthesis of trichloroacetimidate and N-phenyltrifluoroacetimidate
glycosylation donors 26a and 26b. To a stirred solution of 25 (100 mg, 0.29 mmol) and K2CO3 (44 mg,
0.32 mmol) in acetone (3 mL) at 0 ºC, N-aryltrifluoroacetimidoyl chloride (120 mg, 0.58 mmol) or
trichloroacetonitrile (0.06 mL, 0.58 mmol) was added dropwise. The reaction was monitored by TLC for
completion. The reaction mixture was then filtered through a pad of Celite and concentrated under reduce
pressure to afford the corresponding crude donor.
Data for 26a: 1H NMR (300 MHz, (CD3)2CO) δ 9.27 (s, 1H, NH), 8.00–7.97 (m, 2H, Ph), 7.59–7.50 (m,
1H, Ph), 7.42 (m, 2H, Ph), 7.31 (s, 1H, H-6), 6.21 (bs, 1H, H-1′ ), 5.31 (bs, 1H, H-2′), 4.89 (m, 1H, H-4′),
4.14 (t, J = 10.8 Hz, 1H, H-5′), 3.88 (m, 1H, H-5′′), 2.76 (t, J = 13.3 Hz, 1H, H-3′), 2.29 (d, J = 13.6 Hz,
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
13
1H, H-3′), 1.68 (s, 3H, T CH3), C NMR (75 MHz, (CD3)2CO) δ 165.8 (C-4), 151.8 (C-2), 138.6, 134.4
(C-6), 130.5, 129.5 (Ph), 110.9 (C-5), 93.9 (C-1′), 69.4 (C-2′), 63.1 (C-5′), 49.2 (C-4′), 28.5 (C-3′), 12.4 (T
CH3).
Data for 26b: 1H NMR (300 MHz, CDCl3) δ 8.18–8.00 (m, 2H, Ph), 7.61 (m, 1H, Ph), 7.48 (m, Ph), 7.32
(m, 2H, Ph), 7.13 (m, 1H, Ph), 6.96 (bs, 1H, H-6), 6.88 (d, J = 7.7 Hz, 2H, Ph), 6.27 (bs, 1H, H-1′), 5.46
(bs, 1H, H-2′), 5.12 (m, 1H, H-4′), 3.95 (bs, 2H, H-5′, H-5′), 2.54 (m, 1H, H-3′), 2.31 (m, 1H, H-3′), 1.96
13
(d, J = 1.0 Hz, 3H, T CH3); C NMR (75 MHz, CDCl3) δ 165.4, 163.1 (C-4), 150.7(C-2), 143.2, 135.9,
133.9 (C-3), 130.1, 129.2, 129.0, 128.8, 124.9 (Ph), 119.7 (CF3), 111.9 (C-5), 92.4 (C-1′), 67.9 (C-2′), 62.4
(C-5′), 47.0 (C-4′), 28.3 (C-3′), 12.7 (T CH3); [M+Na]+ calcd for C25H22F3N3O6Na 540.1353; Found
540.1362.
Acetyl 2-O-benzoyl-3,4-dideoxy-4-(thymid-1-yl)-α-D-threo-pentopyranoside (26c). To a solution of 25
(150 mg, 0.43 mmol) in pyridine (5 mL) at 0 °C, acetic anhydride (0.082 mL, 0.87 mmol) was added
dropwise. The reaction mixture was slowly warmed to room temperature and left stirring for 2 h. After
removal of all the volatiles under reduced pressure, the remaining residue was taken up with DCM (10 mL),
and 10 mL of saturated aq. NaHCO3 was added. The aqueous layer was then extracted with DCM (2 × 10
mL). The combined organic layers were washed with saturated aq. NaHCO3 (5 mL) and brine (5 mL), dried
over Na2SO4, and concentrated in vacuo. The residue was purified by silica gel column chromatography
(2:1 hexane/EtOAc) to give 26c (142.8 mg, 85%) as a colorless oil. 1H NMR (600 MHz, CDCl3) δ 9.26 (s,
1H, NH), 8.17–8.01 (m, 2H, Ph), 7.63–7.54 (m, 1H, Ph), 7.53–7.40 (m, 2H, Ph), 7.08 (d, J = 1.2 Hz, 1H,
H-6), 6.10 (d, J = 1.9 Hz, 1H, H-1′), 5.28 (td, J = 3.4, 1.9 Hz, 1H, H-2′), 4.93 (tt, J = 10.4, 4.3 Hz, 1H, H-
4′), 4.02 (appt, J = 10.8 Hz, 1H, H-5′), 3.92 (ddd, J = 11.0, 4.7, 1.8 Hz, 1H, H-5′′), 2.61 (ddd, J = 13.6, 12.3,
3.3 Hz, 1H, H-3′), 2.27 (dt, J = 13.6, 3.7 Hz, 1H, H-3′′), 2.21 (s, 3H, CH3CO), 1.95 (d, J = 1.1 Hz, 3H, T
CH3); 13C NMR (151 MHz, CDCl3) δ 168.8 (CH3CO), 165.4 (PhCO), 163.7 (C-4), 150.9 (C-2), 136.9 (C-
6), 133.8, 130.0, 129.2, 128.7 (Ph), 111.6 (C-5), 89.6 (C-1′), 68.3 (C-2′), 62.5 (C-5′), 48.7 (C-4′), 28.5 (C-
3′), 21.1 (CH3CO)), 12.7 (T CH3); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C19H20N2O7Na 411.1163;
Found 411.1157.
Diisopopylphosphonomethyl 2-O-benzoyl-3,4-dideoxy-4-(thymid-1-yl)-α-D-threo-pentopyranoside
(27). To a stirred solution of 26c (120 mg, 0.31 mmol) and diisopropylphosphonomethanol (121 mg, 0.62
mmol) in dry DCM (3 mL) was added 4 Å molecular sieves, and the mixture was stirred for 30 min at room
22
ACS Paragon Plus Environment

Page 23 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
temperature. The reaction mixture was cooled to 0 ºC and TMSOTf (0.073 mL, 0.40 mmol) was added.
The mixture was warmed to room temperature and stirred for 10 h. The reaction was quenched by addition
of saturated aq. NaHCO3 at 0 ºC. It was then diluted with DCM (10 mL) and saturated aq. NaHCO3 (10
mL). The aqueous layer was extracted with DCM (2 × 10 mL). The combined organic layers were washed
with saturated aq. NaHCO3 and brine, dried over Na2SO4, and concentrated in vacuo. The residue was
purified by silica gel column chromatography to afford 27 as a mixture of ɑ and β isomers, along with
residual diisopropylphosphonomethanol. This material was used in the next step without further
purification. HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C24H33N2O9P1Na 547.1816; Found 547.1801.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Diisopopylphosphonomethyl 3,4-dideoxy-4-(thymid-1-yl)-α/β-D-threo-pentopyranoside (28).
A
solution of crude 27 in 7 N NH3 in MeOH (5 mL) was stirred at room temperature for 2 h. The mixture was
concentrated under reduced pressure and the resultant residue was purified by silica gel column
chromatography (20:1 CH2Cl2/MeOH) to give α/β-28 as a white foam.
Data for α-28: 25 mg, 20% over two steps; 1H NMR (500 MHz, CDCl3) δ 9.69 (s, 1H, NH), 7.24 (s, 1H,
H-6), 5.01 (tt, J = 10.3, 4.0 Hz, 1H, H-4′), 4.84–4.73 (m, 2H, [CH(CH3)2]), 4.68 (d, J = 2.6 Hz, 1H, H-1′),
4.05–3.93 (m, 2H, PCH2 and H-2′), 3.86 (td, J =10.8, 4.2 Hz, 1H, H-5′), 3.80–3.70 (m, 2H, H-5′′ and PCH2),
2.27 (ddd, J = 12.8, 3.7, 1.2 Hz, 1H, H-3′), 2.05–1.97 (dt, J = 13.2, 4.3 Hz,1H, H-3′′), 1.91 (d, J = 1.1 Hz,
13
3H, T CH3), 1.41–1.29 (m, 12H, [CH(CH3)2]); C NMR (126 MHz, CDCl3) δ 163.9 (C-4), 151.3 (C-2),
137.0 (C-6), 111.2 (C-5), 100.4 (d, 3JP,C = 11.1 Hz, C-1′), 71.6 [CH(CH3)2], 66.5 (C-2′), 61.9 (C-5′), 61.8
(d, 1JP,C = 171.8Hz, PCH2), 47.0 (C-4′), 31.0 (C-3′), 24.2 [CH(CH3)2], 12.6 (T CH3); 31P NMR (121 MHz,
CDCl3) δ 20.0; HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H30N2O8P1 421.1734; Found 421.1735.
Data for β-28: 13 mg, 10% over two steps; 1H NMR (500 MHz, CDCl3) δ 9.24 (s, 1H, NH), 7.64 (d, J =
1.2 Hz, 1H, H-6), 4.94 (d, J = 2.6 Hz, 1H, H-1′), 4.79 (tdd, J = 12.4, 6.2, 1.3 Hz, 2H, [CH(CH3)2]), 4.62 (tt,
J = 4.4, 3.7 Hz, 1H, H-4′), 4.17 (dd, J = 13.2, 3.9 Hz, 1H, H-5′), 4.03 (dd, J = 13.8, 9.4 Hz, 1H, PCH2),
3.90–3.67 (m, 3H, H-5′′, PCH2 and H-2′ ), 2.19–2.16 (dt, J = 13.8, 4.9 Hz, 1H, H-3′), 2.19–2.06 (ddd, J =
13.8, 9.8, 3.9 Hz, 1H, H-3′′), 1.93 (d, J = 1.1 Hz, 3H, T CH3), 1.34 (m, 12H, [CH(CH3)2]); 13C NMR (126
MHz, CDCl3) δ 163.9 (C-4), 151.0 (C-2), 138.2 (C-6), 110.8 (C-5), 99.8 (d, 3JP,C = 9.9 Hz, C-1′), 71.8, 71.7
(d, 2JP,C = 6.6 Hz, [CH(CH3)2]), 64.3 (C-2′), 62.6 (d, 1JP,C = 171.0Hz, PCH2), 61.2 (C-5′), 51.2 (C-4′), 30.9
(C-3′), 24.2 [CH(CH3)2], 12.8 (T CH3); 31P NMR (121 MHz, CDCl3) δ 20.0.
Phosphonomethyl 3,4-dideoxy-4-(thymid-1-yl)-α-D-threo-pentopyranoside (2a). To a solution of -28
(20 mg, 0.048 mmol) and 2,6-lutidine (0.04 mL, 0.38 mmol) in dry CH3CN (2 mL) was added
bromotrimethylsilane (0.05 mL, 0.38 mmol) at 0 °C. The reaction mixture was stirred at room tempearture
overnight and quenched with 1.0 M aq. TEAB solution (1 mL). After removal of all the volatiles under
reduced pressure, the remaining residue was partitioned between water and EtOAc/ether (1:1) and the water
layer was lyophilized. The crude residue was first purified by silica gel column chromatography (10:1:0 to
10:5:1, CH2Cl2/MeOH/1 M aq. TEAB) and then by preparative reverse phase HPLC with a gradient of
CH3CN in 0.05 M aq. TEAB ranging from 2 to 30% to give 2a (2a·0.67 Et3N salt, 8.3 mg, 40%) as a white
foam. 267 = 9.7 103 (M−1 cm−1) in water; 1H NMR (600 MHz, D2O) δ 7.66 (s, 1H, H-6), 4.79 (tt, J = 10.8,
4.8 Hz, 1H, H-4′), 4.68 (d, J = 2.2 Hz, 1H, H-1′), 4.04 (td, J = 3.0, 3.6 Hz, 1H, H-2′), 3.91 (appt t, J = 10.7
Hz, 1H, H-5′), 3.87 (dd, J = 13.1, 9.3 Hz, 1H, PCH2), 3.73 (ddd, J = 11.2, 4.7, 1.4 Hz, 1H, H-5′′), 3.63 (dd,
23
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 24 of 32
1
2
3
4
5
6
7
8
9
J = 13.2, 9.3 Hz,1H, PCH2), 3.18 (q, J = 7.4 Hz, 4H, CH2CH3), 2.38 (ddd, J = 13.8, 12.1, 3.0 Hz, 1H, H-
3′), 1.93 (dtd, J = 13.1, 3.9, 1.2 Hz, 1H, H-3′), 1.88 (s, 3H, T CH3), 1.26 (t, J = 7.3 Hz, 6H, CH2CH3); 13C
NMR (151 MHz, D2O) δ 166.1 (C-4), 151.9 (C-2), 139.1 (C-6), 110.7 (C-5), 99.3 (d, 3JP,C = 12.0 Hz, C-
1′), 99.3 (C-1′), 65.7 (C-2′), 62.9 (d, 1JP,C = 156.6 Hz, PCH2), 60.4 (C-5′), 46.7 (C-4′), 29.2 (C-3′), 11.0 (T
CH3); 31P NMR (121 MHz, D2O) δ 15.7; HRMS (ESI-): [M-H]- calcd for C11H16N2O8P1 335.0650; Found
335.0654.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Benzyl 2-O-acetyl-3-deoxy-β-L-erythro-pentopyranoside (12). A solution of 17 (2.00 g, 6.20 mmol) and
AIBN (306 mg, 1.86 mmol) in toluene (310 mL) was heated at 100 °C until complete dissolution of the
reagents. To this solution, Bu3SnH (3.34 mL, 12.4 mmol) was added and the mixture was stirred for 30 min
at 100 °C under an argon atmosphere. After removal of all the volatiles under reduced pressure, the
remaining residue was directly subjected to silica gel column chromatography to afford a mixture of 3′-
deoxy (60%) and 4′-deoxy (10%) products, which were separated after the next mesylation step.
Benzyl 2-O-acetyl-4-azido-3,4-dideoxy-α-D-threo-pentopyranoside (29). A suspension of 14a (5.60 g,
16.3 mmol) and sodium azide (2.11 g, 32.52 mmol) in DMF (150 mL) was stirred at 90 °C for 8 h. After
removal of all the volatiles under reduced pressure, the resulting residue was taken up with DCM (150 mL),
and 100 mL of saturated aq. NaHCO3 was added. The aqueous layer was extracted with DCM (2 × 75 mL).
The combined organic layers were washed with brine, dried over Na2SO4 and concentrated in vacuo. The
crude residue was purified by silica gel column chromatography (15:1 hexane/EtOAc) to give 29 (4.30 g,
91%) as a colorless oil. 1H NMR (500 MHz, CDCl3) δ 7.44–7.21 (m, 5H, Ph), 4.94 (dt, J = 3.3, 2.9 Hz, 1H,
H-2), 4.72 (d, J = 11.9 Hz, 1H, CH2Ph), 4.69 (d, J = 1.6 Hz, 1H, H-1), 4.49 (d, J = 11.9 Hz, 1H, CH2Ph),
3.77 (tt, J = 11.1, 5.5 Hz, 1H, H-4), 3.70 (ddd, J = 10.7, 4.9, 1.9 Hz, 1H, H-5), 3.60 (appt, J = 10.8 Hz, 1H,
H-5′), 2.21–1.90 (m, 5H, H-3, H-3′, CH3CO); 13C NMR (126 MHz, CDCl3) δ 169.7 (CH3CO), 136.9, 128.4,
127.8, 127.7 (Ph), 94.8 (C-1), 69.0 (CH2Ph), 68.6 (C-2), 61.4 (C-5), 52.1 (C-4), 29.1 (C-3), 20.9 (CH3CO);
HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C14H17N3O4Na 314.1111; Found 314.1113.
Note: Concentrating azide-containing reaction mixtures and products through rotary evaporation have
caused documented explosions. NaN3 is known to decopose violently causing explosing at 275 °C
Benzyl 4-azido-3,4-dideoxy-α-D-threo-pentopyranoside (30). A methanolic solution of NaOMe (5.4 M,
5.09 mL, 27.5 mmol) was added dropwise to a solution of 29 (4.00 g, 13.73 mmol) in methanol (150 mL).
The reaction was stirred at room temperature for 3 h. After removal of all the volatiles under reduced
pressure, the resulting residue was taken up with DCM (100 mL), and 50 mL of saturated aq. NaHCO3 was
added. The aqueous layer was extracted again with DCM (50 mL). The combined organic layers were
washed with saturated aq. NaHCO3 and brine, dried over Na2SO4, and concentrated in vacuo. The residue
was purified by silica gel column chromatography (10:1 hexane/EtOAc) give 30 (3.25 g, 95%) as a colorless
oil. 1H NMR (500 MHz, CDCl3) δ 7.41–7.25 (m, 5H, Ph), 4.79 (d, J = 11.8 Hz, 1H, CH2Ph), 4.50 (d, J =
11.9 Hz, 1H, CH2Ph), 4.47 (d, J = 4.2 Hz, 1H, H-1), 3.80 (td, J = 5.3, 2.0 Hz, 1H, H-2), 3.76 (m, 1H, H-4),
3.74–3.69 (dd, J = 7.3, 11.2 Hz, 1H, H-5), 3.63 (ddd, J = 11.0, 3.8, 1.2 Hz, 1H, H-5′), 2.68 (d, J = 3.0 Hz,
1H, OH), 2.06–1.97 (dddd, J = 13.5, 8.9, 3.7, 1.0 Hz,, 1H, H-3), 1.90 (dddd, J = 13.5, 6.3, 4.2, 1.1 Hz, 1H,
H-3′); 13C NMR (126 MHz, CDCl3) δ 137.0, 128.4, 128.3, 127.9 (Ph), 99.6 (C-1), 69.5 (CH2Ph), 66.5 (C-
2), 63.4 (C-5), 53.4 (C-4), 32.1 (C-3); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C12H15N3O3Na 272.1006;
24
ACS Paragon Plus Environment

Page 25 of 32
The Journal of Organic Chemistry
1
2
3
4
Found 272.1003.
5
6
7
8
Benzyl 4-amino-3,4-dideoxy-α-D-threo-pentopyranoside (31). To a solution of 30 (2.00 g, 8.02 mmol) in
dry THF (80 mL) was added Ph3P (0.46 g, 1.75 mmol). The mixture was stirred at room temperature for 1
h. Water (2 mL) was added and the mixture was stirred at 50 ºC for 6 h. It was then evaporated, and the
resulting residue was purified by silica gel column chromatography (100/15 DCM/MeOH) to give 31 (1.65
g, 92%) as a colorless oil. 1H NMR (500 MHz, CDCl3) δ 7.46–7.28 (m, 5H, Ph), 4.80 (d, J = 11.8 Hz, 1H,
CH2Ph), 4.52 (d, J = 11.8 Hz, 1H, CH2Ph), 4.50 (d, J = 3.3 Hz, 1H, H-1), 3.80 (dt, J = 5.9, 3.5 Hz, 1H, H-
2), 3.60 (ddd, J = 11.0, 4.1, 1.3 Hz, 1H, H-5), 3.50 (dd, J = 11.0, 8.0 Hz, 1H, H-5), 3.15 (tt, J = 12.7, 4.2
Hz, 1H, H-4), 2.05–1.53 (m, 5H, H-3, H-3, OH, NH2); 13C NMR (126 MHz, CDCl3) δ 137.3, 128.4, 127.9,
127.8 (Ph), 99.7 (C-1), 69.4 (CH2Ph), 67.6 (C-5), 66.9 (C-2), 43.6 (C-4), 36.4 (C-3); HRMS (ESI-TOF)
m/z: [M+H]+ calcd for C12H18N1O3 224.1281; Found 224.1283.
9
10
11
12
13
14
15
16
17
18
19
Benzyl
4-(6-chloropurine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside
(32).
4,6-Dichloro-5-
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
formamidopyrimidine (860 mg, 4.48 mmol) and DIPEA (1.17 mL, 6.72 mmol) were added to a solution of
pentopyranoside 31 (500 mg, 2.24 mmol) in n-butanol (25 mL). The reaction mixture was stirred for 2 h at
100 °C, the temperature was then raised to 140 °C and maintained at this temperature for 10 h. After removal
of all the volatiles under reduced pressure, the remaining residue was purified by silica gel column
chromatography (gradient CH2Cl2/MeOH, 100:0, v/v; 99:1, v/v; 20:1, v/v) to give 32 (605 mg, 75%) as a
1
colorless oil. H NMR (600 MHz, DMSO-d6) δ 8.25 (s, 1H, H-8), 8.16 (s, 1H, H-2), 7.45–7.25 (m, 5H,
Ph), 5.34 (d, J = 3.9 Hz, 1H, OH), 4.92 (tt, J = 11.1, 4.2 Hz, 1H, H-4′), 4.76 (d, J = 12.2 Hz, 1H, CH2Ph),
4.66 (d, J = 1.8 Hz, 1H, H-1′), 4.54 (d, J = 12.2 Hz, 1H, CH2Ph), 4.10 (appt, J = 10.6 Hz, 1H, H-5′), 3.82
(dt, J = 6.0, 3.3 Hz, 1H, H-2′), 3.76 (ddd, J = 10.6, 4.4, 1.6 Hz, 1H, H-5′), 2.71 (td, J = 12.6, 3.0 Hz, 1H,
H-3′), 1.99 (dt, J = 12.8, 3.8 Hz, 1H, H-3′); 13C NMR (150 MHz, DMSO-d6) δ 156.2 (C-6), 152.4 (C-2),
149.6 (C-4), 139.6 (C-8), 137.9, 128.4, 127.9, 127.7 (Ph), 119.1 (C-5), 98.1 (C-1′), 68.2 (CH2Ph), 65.7 (C-
2′), 61.7 (C-5′), 46.7 (C-4′), 31.6 (C-3′); HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H18Cl1N4O3 361.1061;
Found 361.1056.
Benzyl 4-(adenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside (33). A solution of 32 (300 mg, 0.83
mmol) in saturated ammonia in ethanol (10 mL) was stirred in a sealed flask at 60 ºC for 8 h. After removal
of all the volatiles under reduced pressure, the resulting residue was purified by silica gel column
chromatography (CH2Cl2/MeOH, 15:1) to give 33 (269 mg, 95%) as a colorless oil. 1H NMR (500 MHz,
DMSO-d6) δ 8.82 (s, 1H, H-8), 8.79 (s, 1H, H-2), 7.46–7.29 (m, 5H, Ph), 5.38 (d, J = 4.0 Hz, 1H, OH),
5.07 (tt, J = 11.5, 4.3 Hz, 1H, H-4′), 4.76 (d, J = 12.2 Hz, 1H, CH2Ph), 4.67 (d, J = 1.8 Hz, 1H, H-1′), 4.55
(d, J = 12.2 Hz, 1H, CH2Ph), 4.16 (appt, J = 10.6 Hz, 1H, H-5′), 3.99–3.74 (m, 2H, H-5′ and H-2′), 2.76
(td, J = 12.5, 3.0 Hz, 1H, H-3′), 2.06 (ddd, J = 12.7, 5.2, 2.8 Hz, 1H, H-3′′); 13C NMR (126 MHz, DMSO-
d6) δ 152.0 (C-4), 151.4 (C-2), 149.2 (C-6), 146.4 (C-8), 137.8, 131.2 (C-5), 128.4, 127.8, 127.6 (Ph), 98.0
(C-1′), 68.3 (CH2Ph), 65.6 (C-2′), 61.2 (C-5′), 47.9 (C-4′), 31.4 (C-3′); HRMS (ESI-TOF) m/z: [M+H]+
calcd for C17H20N5O3 342.1561; Found 342.1566.
Benzyl 2-O-benzoyl-4-(N6,N6-dibenzoyladenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside (34). To
a solution of 33 (200 mg, 0.59 mmol) in dry pyridine (6 mL) at 0 ºC was added benzoyl chloride (0.46 mL,
3.52 mmol), and the reaction mixture was warmed to room temperature and stirred for 3 h. After removal
25
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 26 of 32
1
2
3
4
5
6
7
8
9
of all the volatiles under reduced pressure, the resulting residue was partitioned between saturated aq.
NaHCO3 (10 mL) and DCM (20 mL). The water layer was further extracted with DCM (1 × 10 mL). The
combined organic layers were washed with brine (10 mL), dried over Na2SO4, and concentrated in vacuo.
The crude residue was purified by silica gel column chromatography (gradient hexane/EtOAc, 10:1, v/v;
3:1) to give 34 (282 mg, 88%) as a white solid. 1H NMR (500 MHz, CDCl3) δ 8.67 (s, 1H, H-2), 8.21–8.04
(m, 3H, H-8, Ph), 8.00–7.74 (m, 4H, Ph), 7.65–7.53 (m, 1H, Ph), 7.51–7.27 (m, 14H, Ph), 5.36 (td, J = 4.2,
1.5 Hz, 1H, H-2′), 5.15 (tt, J = 11.7, 4.3 Hz, 1H, H-4′), 5.01 (d, J = 1.3 Hz, 1H, H-1′), 4.86 (d, J = 11.9 Hz,
1H, CH2Ph), 4.64 (d, J = 11.9 Hz, 1H, CH2Ph), 4.24 (appt, J = 10.9 Hz, 1H, H-5′), 4.03 (ddd, J = 10.4, 5.1,
1.8 Hz 1H, H-5′), 3.01 (td, J = 13.3, 3.1 Hz, 1H, H-3′), 2.44 (dt, J = 13.2, 5.2 Hz, 1H, H-3′); 13C NMR (126
MHz, CDCl3) δ 172.2 (PhCO), 165.4 (PhCO), 153.1 (C-4), 152.0 (C-2), 152.0 (C-6), 142.8 (C-8), 136.8,
134.1, 133.5, 132.9, 129.8, 129.4, 128.7, 128.6, 128.5, 128.1, 127.9(Ph), 127.4 (C-5), 95.1 (C-1′), 69.5
(CH2Ph), 68.9 (C-2′), 61.5 (C-5′), 47.8 (C-4′), 29.0 (C-3′); HRMS (ESI-TOF) m/z: [M+H]+ calcd for
C38H32N5O6 654.2346; Found 654.2358.
2-O-Benzoyl-4-(N6-benzoyladenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranose (35). To a stirred
solution of 34 (140 mg, 0.25 mmol) in anhydrous CH2Cl2 (4 mL) was added 1 M BCl3 (0.76 mL, 0.76
mmol) at -78 °C. Then, the reaction mixture was slowly warmed to 0 °C over 2.5 h and stirred at this
temperature for 30 min. After completion of the reaction, the mixture was cooled to -20 °C and quenched
by dropwise addition of saturated aq. NaHCO3 (10 mL). The aqueous layer was extracted with CH2Cl2 (3
× 5 mL). The combined organic layers were washed with brine (10 mL) and dried over Na2SO4, filtered,
and concentrated in vacuo. The resulting residue was filtered through a pad of silica gel to give crude 35 as
a colorless oil, which was used as such in the following step. HRMS (ESI-TOF) m/z: [M+H]+ calcd for
C24H22N5O5 460.1615; Found 460.1617.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Acetyl
2-O-benzoyl-4-(N6-benzoyladenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside
(36).
Compound 36 was prepared using a similar procedure as that described for 26c starting from 35 (117 mg,
0.25 mmol), pyridine (5 mL), and acetic anhydride (0.048 mL, 0.5 mmol), and obtained after silica gel
column chromatography (gradient hexane/EtOAc, 8:1, v/v; 3:1, v/v;) as a colorless sticky oil (99 mg, 78%).
1H NMR (500 MHz, CDCl3) δ 8.76 (s, 1H, H-2), 8.19–8.05 (m, 3H, H-8, Ph), 8.02 (d, J = 7.4 Hz, 2H, Ph),
7.63–7.53 (m, 2H, Ph), 7.49 (td, J = 7.9, 2.1 Hz, 4H, Ph), 6.19 (d, J = 1.8 Hz, 1H, H-1′), 5.33 (td, J = 5.3,
1.8 Hz, 1H, H-2′), 5.14 (tt, J = 11.0, 4.3 Hz, 1H, H-4′), 4.34 (appt, J = 10.8 Hz, 1H, H-5′), 4.12 (ddd, J =
11.1, 4.7, 1.8 Hz, 1H, H-5′′), 3.04 (ddd, J = 14.3, 12.1, 3.2 Hz, 1H, , H-3′), 2.51 (dt, J = 14.2, 4.7 Hz, 1H,
H-3′′), 2.24 (s, 3H, CH3CO); 13C NMR (126 MHz, CDCl3) δ 168.8 (CH3CO), 165.3 (PhCO), 152.6 (C-2),
152.2 (C-4), 150.0 (C-6), 141.3(C-8), 133.8, 133.6, 132.9, 123.0, 129.2, 128.9, 128.7, 128.1 (Ph), 123.5 (C-
5), 89.6 (C-1′), 68.0 (C-2′), 63.3 (C-5′), 47.9 (C-4′), 29.3 (C-3′), 21.1 (CH3CO); HRMS (ESI-TOF) m/z:
[M+H]+ calcd for C26H24N5O6 502.1721; Found 502.1723.
Benzyl 3,4-dideoxy-4-trifluoroacetylamino-α-D-threo-pentopyranoside (38). To a mixture of 31 (1 g,
4.48 mmol) and triethylamine (1.87 mL, 13.44mmol) in methanol (50 mL), ethyl trifluoroacetate (1.07 mL,
8.96 mmol) was added dropwise. The mixture was stirred at room temperature for 2 h. After removal of all
the volatiles under reduced pressure, the resulting residue was purified by silica gel column chromatography
(hexane/EtOAc, 3:1) to give 38 (1.3g, 91%) as a colorless oil. 1H NMR (300 MHz, CDCl3) δ 7.55–7.16 (m,
26
ACS Paragon Plus Environment

Page 27 of 32
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
5H, Ph), 6.91 (d, J = 7.9 Hz, 1H, NH), 4.80 (d, J = 11.6 Hz, 1H, CH2Ph), 4.53 (d, J = 11.6 Hz, 1H, CH2Ph),
4.45 (d, J = 4.8 Hz, 1H, H-1), 4.27 (m, 1H, H-2), 3.80–3.61 (m, 3H, H-5, H-5′ and OH), 3.01 (d, J = 3.8
Hz, 1H, H-4), 2.17–1.98 (ddd, J = 13.5, 6.7, 4.0 Hz, 1H, H-3), 1.88–1.69 (ddd, J = 13.5, 7.4, 4.1 Hz, 1H,
H-3′); 13C NMR (75 MHz, CDCl3) δ 157.0 (q, 2JF,C = 37.8 Hz, COCF3), 137.0, 128.64, 128.20 (Ph), 115.8
(q, 1JF,C = 288.9 Hz, CF3), 101.3 (C-1), 70.3 (C-2), 66.6 (CH2Ph), 64.6 (C-5), 44.4 (C-4), 32.8 (C-3); HRMS
(ESI-TOF) m/z: [M+Na]+ calcd for C14H16F3N1O4Na 342.0924; Found 342.0916.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
3,4-dideoxy-4-trifluoroacetylamino-α/β-D-threo-pentopyranose (39). To a solution of 38 (1.00 g, 3.13
mmol) in methanol (50 mL) was added 10% Pd/C (1 g, 0.94 mmol), and evacuation-replacement cycles
were carried out using a hydrogen baloon (3×). The reaction mixture was stirred at room temperature for
20 h under an atmospheric pressure of hydrogen. After completion of the reaction, the catalyst was removed
by filtration through a pad of Celite and washed with methanol. The filtrate was concentrated under reduced
pressure to afford 39 (590 mg, 82%) as a colorless foam without further purification.1H NMR (600 MHz,
DMSO-d6) δ 9.32 (d, J = 6.7 Hz, 0.16 H, NHβ), 9.26 (d, J = 7.9 Hz, 1H, NHα), 6.34 (d, J = 4.0 Hz, 1H,
OH-1α), 6.29 (d, J = 4.3 Hz, 0.16 H, OH-1β), , 4.94 (bs, 1H, OH-2α), 4.85–4.77 (m, 0.22H, OH-2β), 4.69
(dd, J = 4.8, 2.0 Hz, 0.18 H, H-1β), 4.68 (dd, J = 3.3, 2.2 Hz, 1H, H-1α), 4.17–4.08 (m, 1H, H-4α), 4.07–
4.00 (m, 0.2 H, H-4β), 3.80 (ddd, J = 11.5, 3.6, 0.9 Hz, 0.18 H, H-5β), 3.66 (t, J = 10.2 Hz, 1H, H-5α), 3.56
(bs, 1.14 H, H-2α), 3.43 (ddd, J = 10.6, 4.6, 1.6 Hz, 1 H, H-5′α and H-2β), 3.30 (dd, J = 11.1, 6.6 Hz, 0.3
H, H-5′β), 1.96 (ddd, J = 13.1, 10.9, 3.2 Hz, 1H, H-3α), 1.88 (dddd, J = 13.3, 7.3, 4.3, 0.9 Hz, 0.2 H, H-
3β), 1.65 (dtd, J = 13.1, 4.8, 1.4 Hz, 1H, H-3′α), 1.42 (ddd, J = 13.3, 7.8, 3.7 Hz, 0.14 H, H-3′β); 13C NMR
(151 MHz, DMSO-d6) δ 156.2 (q, 2JF,C = 38 Hz, COCF3), 115.9 (q, 1JF,C = 289 Hz, CF3), 93.7 (C-1β), 93.4
(C-1α), 68.1(C-2β), 66.4 (C-2α), 62.8 (C-5β), 60.8 (C-5α), 44.3 (C-4β), 42.6 (C-4α), 32.2 (C-3β), 31.3 (C-
3α); HRMS (ESI-TOF) m/z: [M+Na]+ calcd for C7H10F3N1O4Na 252.0454; Found 252.0448.
1,2-Di-O-acetyl-3,4-dideoxy-4-trifluoroacetylamino-α-D-threo-pentopyranoside
(40).
1O,2O-
Diacetylated compound 40 was prepared using a similar procedure as that described for 26c starting from
39 (500 mg, 2.18 mmol), Ac2O (0.62 mL, 6.55 mmol), and pyridine (25 mL), and obtained after silica gel
column chromatography (gradient hexane/EtOAc, 6:1, v/v; 2:1, v/v) as a colorless sticky oil (550 mg, 80%),
1H NMR (600 MHz, CDCl3) δ 6.78 (d, J = 7.9 Hz, 1H, NH), 5.88 (d, J = 2.8 Hz, 1H, H-1), 4.93 (td, J =
6.1, 3.8 Hz, 1H, H-2), 4.37 (dtt, J = 17.6, 7.9, 4.6 Hz, 1H, H-4), 3.88 (ddd, J = 11.4, 4.2, 1.5 Hz,1H, H-5),
3.66 (dd, J = 11.0, 9.7 Hz, 1H, H-5′), 2.17–2.09 (m, 8H, CH3CO, CH3CO, H-3, H-3); 13C NMR (151 MHz,
CDCl3) δ 170.0 (CH3CO), 168.9 (CH3CO), 157.0 (q, 2JF,C = 38 Hz, COCF3), 115.5 (q, 1JF,C = 289 Hz, CF3),
89.8 (C-1), 67.1 (C-2), 63.4 (C-5), 42.5 (C-4), 29.5 (C-3), 21.0 (CH3CO), 20.9 (CH3CO); HRMS (ESI-
TOF) m/z: [M+Na]+ calcd for C11H14F3N1O6Na 336.0666; Found 336.0660.
Diisopropylphosphonomethyl
2-O-acetyl-3,4-dideoxy-4-trifluoroacetylamino-α-D-threo-
pentopyranoside (41). Phosphonomethylated compound 41 was prepared using a similar procedure as that
described for 27 starting from 40 (300 mg, 0.96 mmol), TMSOTf (0.35 mL, 1.92 mmol),
diisopropylphosphonomethanol (564 mg, 2.87 mmol) in dry DCM (15 mL). Purification by silica gel
column chromatography (gradient CH2Cl2/MeOH, 99:1, v/v; 49:1, v/v; 24:1, v/v) afforded 41 as a colorless
sticky oil, which was still contaminated with diisopropylphosphonomethanol. 1H NMR (600 MHz, CDCl3)
δ 7.45 (d, J = 8.3 Hz, 1H, NH), 4.91 (td, J = 4.7, 2.2 Hz, 1H, H-2), 4.83–4.69 (m, 2H, [CH(CH3)2]), 4.69
27
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 28 of 32
1
2
3
4
5
6
7
8
9
(d, J = 1.8 Hz, 1H, H-1), 4.45–4.34 (m, 1H，H-4), 3.92 (dd, J = 13.2, 10.0 Hz, 1H, PCH2), 3.79–3.72 (ddd,
J = 10.9, 5.1, 1.7 Hz, 1H, H-5), 3.72–3.66 (m, 1H, PCH2), 3.64 (appt, J = 10.7 Hz, 1H, H-5′), 2.12 (s, 3H,
CH3CO), 2.11–2.08 (m, 1H, H-3), 2.07–1.99 (dt, J = 13.7, 4.2 Hz, 1H, H-3′), 1.38–1.30 (m, 12H,
[CH(CH3)2]); 13C NMR (151 MHz, CDCl3) δ 170.2 (CH3CO), 157.1 (q, 2JF,C = 37.0 Hz, COCF3), 115.8 (q,
1JF,C = 288.9 Hz, CF3), 96.4 (d, 3JP,C = 11.1Hz, C-1), 71.8, 71.7 (d, 2JP,C = 6.2 Hz, [CH(CH3)2]), 68.0 (C-2),
60.9 (d, 1JP,C = 171.7 Hz, PCH2), 61.4 (C-5), 41.8 (C-4), 29.0 (C-3), 24.0 [CH(CH3)2]; 31P NMR (121 MHz,
CDCl3) δ 19.0; HRMS (ESI-TOF) m/z: [M+H]+ calcd for C16H28F3N1O8P1 450.1499; Found 450.1497.
Diisopropylphosphonomethyl 4-amino-3,4-dideoxy-α-D-threo-pentopyranoside (42). Compound 42
was prepared using a similar procedure as that described for 28 starting from crude 41 and 7 M NH3 in
MeOH (15 mL), and obtained after silica gel column chromatography (gradient CH2Cl2/MeOH, 50:1, v/v;
25:1, v/v; 6:1, v/v) as a colorless sticky oil (121 mg, 40% over two steps), 1H NMR (600 MHz, CDCl3) δ
4.81–4.67 (m, 2H, [CH(CH3)2]), 4.54 (d, J = 3.0 Hz, 1H, H-1), 3.99 (dd, J = 13.6, 9.1 Hz, 1H, PCH2), 3.91
(m, 1H, H-2), 3.76–3.68 (m, 2H, H-5 and PCH2), 3.65 (appt, J = 9.5 Hz, 1H, H-5′), 3.49–3.42 (m, 1H, H-
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
13
4), 2.06–2.01 (m, 1H, H-3), 1.96 (td, J = 11.2, 3.2 Hz, 1H, H-3′), 1.37–1.29 (m, 12H, [CH(CH3)2]); C
NMR (151 MHz, CDCl3) δ 101.2 (d, 3JP,C = 10.4 Hz, C-1′), 71.7, 71.5 (d, 2JP,C = 5.6 Hz, [CH(CH3)2]), 65.7
(C-2), 64.7 (C-5), 61.6 (d, 1JP,C = 170.9 Hz, PCH2), 43.6 (C-4), 33.6 (C-3), 24.0 [CH(CH3)2]; 31P NMR (121
MHz, CDCl3) δ 19.3; HRMS (ESI-TOF) m/z: [M+H]+ calcd for C12H27N1O6P1 312.1570; Found 312.1570
Diisopropylphosphonomethyl 4-(6-chloropurine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside (43).
Compound 43 was prepared using a similar procedure as that described for 32 starting from 42 (120 mg,
0.39 mmol), 4,6-dichloro-5-formamidopyrimidine (96 mg, 0.5 mmol), and DIPEA (0.2 mL, 1.16 mmol) in
n-butanol (5 mL), and obtained after silica gel column chromatography (gradient CH2Cl2/MeOH, 99:1, v/v;
1
49:1, v/v; 24:1, v/v) as a colorless sticky oil (130 mg, 75%). H NMR (600 MHz, CDCl3) δ 8.75 (s, 1H,
H-2), 8.37 (s, 1H, H-8), 5.14 (tt, J = 12.6, 4.1 Hz, 1H, H-4′), 4.80 (tt, J = 12.4, 6.2 Hz, 2H, [CH(CH3)2]),
4.74 (d, J = 3.8 Hz, 1H, H-1′), 4.29 (dd, J = 11.5, 7.7 Hz, 1H, H-5′), 4.09 (dd, J = 13.8, 9.4 Hz, 1H, PCH2),
3.98 (dd, J = 11.7, 3.8 Hz, 1H, H-5′), 3.98 (td, J = 7.0, 3.8 Hz, 1H, H-2′), 3.84 (dd, J = 13.8, 8.3 Hz, 1H,
PCH2), 2.71 (ddd, J = 13.0, 9.1, 3.6 Hz, 1H, H-3′), 2.20 (dt, J = 13.2, 4.8 Hz, 1H, H-3′), 1.40–1.32 (m, 12H,
[CH(CH3)2]); 13C NMR (151 MHz, CDCl3) δ 152.0 (C-2), 151.9 (C-4), 151.4 (C-6), 144.0 (C-8), 131.8 (C-
5), 102.2 (d, 3JP,C = 11.1 Hz, C-1′), 71.9, 71.7 (d, 2JP,C = 6.2 Hz, [CH(CH3)2]), 66.0 (C-2′), 63.8 (C-5′), 62.1
(d, 1JP,C = 171.1 Hz, PCH2), 48.8 (C-4′), 32.7 (C-3′), 24.2 [CH(CH3)2]; 31P NMR (121 MHz, CDCl3) δ 19.6;
HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H27Cl1N4O6P1 449.1351; Found 449.1349.
Diisopropylphosphonomethyl
4-(adenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside
(44).
Compound 44 was prepared using a similar procedure as that described for 37 starting from 43 (100 mg,
0.22 mmol) in a mixture of aq. NH3 (25%)/1,4-dioxane = 1:1(10mL), and obtained after silica gel column
chromatography (gradient CH2Cl2/MeOH, 50:1, v/v; 25:1, v/v; 15:1, v/v) as a colorless sticky oil (88 mg,
92%). 1H NMR (600 MHz, methanol-d4) δ 8.23 (s, 1H, H-8), 8.19 (s, 1H, H-2), 5.08–4.97 (tt, J = 10.7, 3.7
Hz,1H, H-4′), 4.82–4.75 (m, 2H, [CH(CH3)2]), 4.74 (d, J = 2.3 Hz, 1H, H-1′), 4.14 (appt, J = 10.5 Hz, 1H,
H-5′), 4.10–4.05 (dd, J = 14.0, 9.2 Hz, 1H, PCH2), 3.95–3.89 (m, 2H, H-2′ and H-5′′), 3.88 (dd, J = 14.0,
9.2 Hz, 1H, PCH2), 2.70 (ddd, J = 14.6, 11.1, 3.0 Hz,1H, H-3′), 2.19–2.14 (m, 1H, H-3′), 1.40–1.34 (dd, J
= 6.2, 1.9 Hz, 12H, [CH(CH3)2]); 13C NMR (151 MHz, methanol-d4) δ 157.3 (C-6), 153.7 (C-2), 150.8 (C-
28
ACS Paragon Plus Environment

Page 29 of 32
The Journal of Organic Chemistry
1
2
3
4
5
4), 140.9 (C-8), 120.1 (C-5), 101.7 (d, 3JP,C = 11.6 Hz, C-1′), 73.4, 73.3 [CH(CH3)2], 67.2 (C-2′), 63.6 (C-
1
5′), 62.2 (d, JP,C = 170.9 Hz, PCH2), 48.5 (C-4′), 32.9 (C-3′), 24.3 [CH(CH3)2]; 31P NMR (121 MHz,
6
7
8
9
methanol-d4) δ 20.0; HRMS (ESI-TOF) m/z: [M+H]+ calcd for C17H29N5O6P1 430.1850; Found 430.1848.
Phosphonomethyl 4-(adenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside (2b). Compound 2b was
prepared using a similar procedure as that described for 2a starting from 44 (70 mg, 0.16 mmol), 2,6-
lutidine (0.15 mL, 1.3 mmol), and TMSBr (0.17 mL, 0.16 mmol) in dry acetonitrile (2 mL) and obtained
as a colorless sticky oil (2b·1Et3N salt, 22 mg, 40%). 259 =    (M−1cm−1) in water; 1H NMR (600
MHz, D2O) δ 8.22 (s, 1H, H-8), 8.05 (s, 1H, H-2), 4.72 (m, 1H, H-4′), 4.71 (d, J = 3.3 Hz, 1H, H-1′), 4.09
(dd, J = 11.4, 8.7 Hz, 1H, H-5′), 3.97 (td, J = 4.8, 3.3 Hz, 1H, H-2′), 3.92 (dd, J = 11.4, 4.0 Hz, 1H, H-5′),
3.90 (dd, J = 13.2, 9.3 Hz, 1H, PCH2), 3.64 (dd, J = 13.0, 9.5 Hz, 1H, PCH2), 3.16 (q, J = 7.4 Hz, 6H,
CH2CH3), 2.56 (ddd, J = 13.4, 10.1, 3.4 Hz, 1H, H-3′), 2.15 (dt, J = 13.3, 4.3 Hz, 1H, H-3′′), 1.23 (t, J = 7.3
Hz, 9H, CH2CH3); 13C NMR (151 MHz, D2O) δ 156.5(C-6), 153.3(C-2), 149.8 (C-4), 141.7 (C-8), 119.4
(C-5), 102.4 (d, 3JP,C = 11.8 Hz, C-1′), 67.1 (C-2′), 65.3 (d, 1JP,C = 158.5 Hz, PCH2), 64.1 (C-5′), 48.7 (C-
4′), 32.6 (C-3′); 31P NMR (121 MHz, D2O) δ 15.2; HRMS (ESI-TOF) m/z: [M-H]+ calcd for C11H15N5O6P1
344.0765; Found 344.0760.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Diphosphorylphosphonomethyl
4-(adenine-9-yl)-3,4-dideoxy-α-D-threo-pentopyranoside
(45).
Adenine α-D-threo-pentopyranoside nucleoside phosphonic acid 2b (30 mg, 0.087 mmol) was dissolved in
anhydrous DMF (1 mL) and carbonyldiimidazole (70.4 mg, 0.434 mmol) was added. The mixture was
stirred for 30 min at room temperature, and then a solution of pyrophosphate (333 mg, 0.608 mmol) in dry
DMF (2 ml) was added and the stirring was continued overnight. An excess of 25% aq. ammonia (1 mL)
was added and the mixture was concentrated in vacuo. The resulting residue was purified by
chromatography on a DEAE-cellulose column (gradient: 0.1 to 1 M TEAB (v/v); 1/0, 1/0.2, 1/0.5, 1/1).
Further purification was performed by RP-HPLC to afford diphosphate(phosphonomethyl) 3-deoxy-4-
deoxy-4-(adenine-9-yl)-α-D-threo-pentopyranoside triethylammonium salt 45 as a white solid (30% yield).
1H NMR (600 MHz, D2O): δ 8.38 (s, 1H, H-2), 8.23 (s, 1H, H-8), 4.91 (tt, J = 9.3, 4.1 Hz, 1H, H-4′), 4.82
(d, J = 3.2 Hz, 1H, H-1′), 4.19 (dd, J = 12.0, 8.6 Hz, 1H, H-5′), 4.08–4.03 (m, 2H, PCH2 and H-2′), 3.99
(dd, J = 12.0, 4.1 Hz, 1H, H-5′′), 4.19 (dd, J = 13.2, 9.8 Hz, 1H, PCH2), 2.63 (ddd, J = 13.5, 9.9, 3.1 Hz,
1H, H-3′), 2.15 (dt, J = 13.2, 5.1 Hz, 1H, H-3′′); 13C NMR (150 MHz, D2O): δ 157.0 (C-6), 153.7 (C-2),
150.3 (C-4), 142.1 (C-8), 119.8 (C-5), 102.6 (d, 3JP, C = 9.8 Hz, C-1′), 67.0 (C-2′), 65.2 (d, 1JP, C = 167.1
Hz, PCH2), 60.3 (C-5′), 48.7 (C-4′), 32.6 (C-3ʹ); 31P NMR (121 MHz, D2O): δ 7.6 (d, J = 23.1 Hz, Pα), -
6.4 (d, J = 18.9 Hz, Pγ), -22.7 (t, J = 21.4 Hz, Pβ); HRMS (ESI-TOF) m/z: [M-H]- calcd for C11H17N5O12P3,
504.0092; found 504.0096.
ASSOCIATED CONTENT
Supporting Information
NMR spectra, supplementary NMR data, procedures, scheme, and figures.
AUTHOR INFORMATION
Corresponding author
29
ACS Paragon Plus Environment