A straightforward diphenylmethyl protection method and deprotection of some pyrimidine nucleosides

Article abstract of DOI:10.3390/molecules18078524

Benzhydryl protection of primary and secondary alcohols has been reported previously via reaction with metal alcoholates. Our aim was to find generally useful and very mild conditions for the alcoholic protection and deprotection of nucleosides with the diphenylmethyl group. This was accomplished for some pyrimidine nucleosides using PdCl2 as the transition metal catalyst, and with optimization yields of 70-90% have been achieved. A lack of solubility of other nucleosides hampers its more general use.

Full text of DOI:10.3390/molecules18078524

Molecules 2013, 18, 8524-8534; doi:10.3390/molecules18078524
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
A Straightforward Diphenylmethyl Protection Method and
Deprotection of Some Pyrimidine Nucleosides
Milind Saudi and Arthur van Aerschot *
Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10,
Leuven 3000, Belgium; E-Mail: milind.saudi@rega.kuleuven.be
* Author to whom correspondence should be addressed; E-Mail: arthur.vanaerschot@rega.kuleuven.be;
Tel.: +32-16-337-388; Fax: +32-16-337-340.
Received: 31 May 2013; in revised form: 10 July 2013 / Accepted: 16 July 2013 /
Published: 18 July 2013
Abstract: Benzhydryl protection of primary and secondary alcohols has been reported
previously via reaction with metal alcoholates. Our aim was to find generally useful and
very mild conditions for the alcoholic protection and deprotection of nucleosides with the
diphenylmethyl group. This was accomplished for some pyrimidine nucleosides using
PdCl2 as the transition metal catalyst, and with optimization yields of 70–90% have been
achieved. A lack of solubility of other nucleosides hampers its more general use.
Keywords: hydroxyl protecting group; palladium catalyst; nucleoside; diphenyl methyl
1. Introduction
Nucleoside and nucleotide chemistry generally involves multistep synthesis protocols, where
selective and efficient protection and deprotection reactions have always played a central role. The
criteria involved in the choice of protecting groups are based on high yielding protection and
deprotection steps, chemoselectivity and orthogonality with other protecting and functional groups. For
example, various acyl, benzyl, trityl, triethylsilyl [1], and tert-butyldimethylsilyl ethers [2] have found
common use for selective protection of primary/secondary alcohols, particularly in carbohydrate and
nucleoside/nucleotide chemistry. To our knowledge, only very few specific reviews for nucleoside
protection are available [3,4]. For a complete overview of alcohol protecting groups readers may
consult Greene and Wuts [5].

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Due to their orthogonality regarding deprotection conditions, the 5′-, 3′- and 2′-hydroxyl groups of
nucleosides are usually temporarily acylated or converted to either silyl or alkyl ethers for protection,
of which the benzyl and trityl groups represent the most popular ethers [6]. The trityl moiety can be
readily introduced even on a secondary alcohol under neutral conditions in presence of a hydrogen
chloride scavenger like pyridine or triethylamine. In contrast, O-alkylation with a benzyl or diphenyl
methyl group generally requires increased activity of the alcohol via deprotonation [7], or activation of
the benzyl moiety as a trichloroacetimidate combined with acidic reaction conditions [8]. In some
instances, robust protection is mandatory as with a benzyl moiety. The latter however requires
hydrogenation conditions for its removal. An alternative protecting strategy therefore is warranted.
Hence, we now want to report on metal-catalyzed conditions for protection and deprotection of
nucleoside analogues using the diphenylmethyl (DPM) ether group.
Synthesis of DPM ethers using many different strategies has been previously reported, but this
protecting group is not very common. As for most benzyl-type ethers, its introduction usually involves
nucleophilic substitution of chloro- or bromodiphenylmethane using sodium hydride-generated
alkoxides [9]. However, diphenylmethanol in the presence of either a Brønsted acid, Lewis acid, or
supported acids likewise has been shown to form DPM ethers. Mechanistically the reaction occurs
either via intimate ion-molecule pairs, via solvent separated ion-molecule pairs or via benzhydryl
carbocations [10]. A few other methods can nevertheless be found in the literature. These include reagents
such as diphenyl-methylphosphate–trifluoroacetic acid [11], diphenylmethyldiazomethane [12,13],
or the use of orthoformates [14] at high temperature.
Many other strategies involve metal-catalysed reactions. Ishii, in 2003, reported the first use of
Yb(OTf)3, Sc(OTf)3 and Hf(OTf)3 as Lewis acids for the direct reaction of alcohols. Quite interestingly,
Ishii found that phenylethanol is in equilibrium with its diether during the reaction with La(OTf)3 as
catalyst [15]. Pale and co-workers reported the use of palladium (II) chloride as a catalyst [16,17].
Later they reported CuBr2 to be an even better catalyst [18]. Recently, an effective method for the
allylation of heteroarenes has also been catalysed by PdCl2 [19]. Baba and his co-workers reported the
use of InCl3 in the direct substitution of allylic alcohols, benzylic alcohols and benzhydrylic alcohols
with nucleophiles. Mechanistic investigation showed that the ether was obtained by the action of In
(III) salts [20]. Highly regioselective catalytic amination of Baylis-Hillman adduct with aromatic
amines has been promoted by the Lewis acid In(OTf)3 [21].
As for any benzyl-type ether, deprotection of DPM ethers is mostly achieved under hydrogenation
conditions [22], but many other protocols have been reported, including acidolysis [23] and electrolytic
reduction [24]. Our research focused on finding a simpler and environmentally acceptable procedure
for protection and deprotection of DPM ethers specifically for nucleoside chemistry. We therefore
adopted a strategy using transition metals as the catalyst with preference for Pd salts.
2. Results and Discussion
In search for the best catalyst, we allowed thymidine (1) at a scale of 100 mg to react with
diphenylmethanol (DPM-OH) in dichloroethane (DCE) in presence of 0.2 equivalents (eq) of various
metal salts. Initially, as the rate of reaction was too low at room temperature, we decided to heat the
reaction to 85 °C. As shown in Scheme 1, we expected three different products, the mono- and

Molecules 2013, 18
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di-O-protected thymidines 3a and 3b, and ether 4, resulting from dimerization of diphenylmethanol.
However, using 2.5 eq of DPM-OH and following heating overnight, thymidine 1 was cleanly
converted to its protected form 3b in 87% yield with only trace formation of the unwanted ether 4
(Table 1). Likewise formation of benzophenone was not observed. This result indicated that there is
complex formation by coordination between the Pd catalyst and diphenylmethanol in which the Lewis
acid character of the Pd-complex outbalances the β-elimination pathway (Scheme 2).
Scheme 1. Protection of both hydroxyl groups of thymidine as diphenylmethyl ether.
Table 1. Comparison of catalyst effectiveness for formation of bis-benzhydryl thymidine (3b).
Exp.
Catalyst
PdCl2
Recovered 1 (%)
Recovered 2 (%)
Yield 3b (%) a
Yield 4 (%)
1
2
3
4
5
6
-
6
94
0
87
Trace
-
NiCl2
95
43
10
90
32
2
CuCl2·2H2O
Pd(OAc)2
Ni(OAc)2
Cu(OAc)2
55 (24 h)
Trace
-
0
65
0
0
Trace
-
45
Trace
a Reactions on 100 mg scale were run in refluxing DCE for 16 h with 0.2 eq of the metal catalyst and 2.5 eq of DPM-OH.
Scheme 2. Mechanism for diphenylmethyl ether protection.
As we wanted to favor the Lewis acid pathway, we further evaluated catalysts which can form more
acidic salt complexes, e.g., nickel being located in the same column as palladium in the Mendeleev
periodic table. Unfortunately, when NiCl2 was used we did not obtain the expected product, and even
after 48 h 95% of the starting material was recovered. Reaction in presence of CuCl2·2H2O offered the

Molecules 2013, 18
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desired product, albeit in low yield. This metal salt screening showed that PdCl2 was the most effective
catalyst for protection of both hydroxyl groups in 1 as their diphenylmethyl ethers, affording almost
quantitative yields of the desired product (Table 1).
We also evaluated the effectiveness of metal-catalysed DPM protection in different solvents with
thymidine as substrate. As expected, non-polar solvents like dichloroethane, being non-coordinating,
proved to be the best and reactions looked very clean on TLC. Formation of diphenylmethanol dimer
remained below 5%. On the other hand, polar solvents like DMF led to messy reactions in which the
desired product could not be isolated (Table 2). Finally, when carried out on a 2 mmol scale in DCE,
70% of the desired 3b was isolated.
Table 2. Solvent influence on DPM ether formation at either 85 °C or boiling temperature.
Entry
Solvent
DCE
Time (h)
Yield 3b (%)
1
2
3
4
5
16
48
48
16
16
87
47
Acetonitrile
THF
42
Dioxane
DMF
Degradation
Degradation
Having optimized the conditions for DPM protection for 1, we decided to evaluate this reaction for
other nucleosides under similar conditions. Using 2.5 eq of DPM-OH, both 2′-deoxyuridine and
5-fluoro-2′-deoxyuridine reacted cleanly to afford the ethers 6b and 7b in 88% and 85% yield,
respectively. Moreover selective protection of the 5′ primary alcohol proved feasible for
2′-deoxynucleosides using only 1.2 eq of DPM-OH with heating at 85 °C, and afforded around 65% for
each of the mono-O-alkylated analogues 3a, 6a and 7a (Table 3) with likewise 67% yield for 3a on a
2 mmol scale. Only trace amounts of the bis-diphenylmethyl ether analogues were isolated.
Unfortunately, reaction of the ribonucleosides uridine and 5-fluorouridine with 1.2 eq of DPM-OH
only afforded a trace of the desired 5′-O-protected nucleoside (Table 3, experiments 7 and 10,
respectively). Using 2.5 eq of DPM-OH on both uridine analogues, more than 80% of the bisalkylated
derivatives were obtained as a mixture of the 2′,5′- and 3′,5′-O-alkylated conformers (Table 3,
experiments 8 and 11, respectively). Finally, per-O-alkylation of ribonucleosides in about 80% yield
proved feasible by increasing the incoming DPM-OH ratio to 3.7 eq. This proves much more difficult
with the sterically more demanding trityl moieties [25]. Separation of both bis-diphenylmethyl ethers
(2′,5′- and 3′,5′-derivative) was cumbersome, but was achieved by using appropriate solvent polarity
during column chromatography. The correct position of the diphenylmethyl moiety was determined
using 2D-NMR techniques (COSY, HSQC), with the 2′,5′-analogue proving slightly more lipophilic
than the 3′,5′-analogue.
As reported before [17], the reaction is believed to occur via formation of the latter benzhydryl
carbocation. As shown in Scheme 2, coordination of the hydroxyl oxygen atom to the mild Lewis acid
PdII is highly likely. Following coordination, there may be transfer of the hydroxyl group to the
palladium affording the benzhydryl carbocation.

Molecules 2013, 18
8528
As shown in Scheme 3, deprotection of synthesized 3′,5′-di-O-benzhydryl-thymidine 3b was
successfully achieved by only changing solvent. Following heating of 3b in ethanol at 85 °C with
catalytic PdCl2 (0.2 eq) for 16 h, it was cleanly converted to thymidine.
Table 3. Synthesis of different benzhydryl protected nucleosides.
Eq
Entry
Substrate
Product
Yield (%)
DPM-OH
1.2
1
2
3
4
thymidine
5′-O-benzhydryl-thymidine 3a
3′,5′-di-O-benzhydryl-thymidine 3b
5′-O-benzhydryl-2′-deoxyuridine 6a
3′,5′-di-O-benzhydryl-2′-deoxyuridine 6b
67
87
65
88
2.5
2′-deoxyuridine
1.2
2.5
5-fluoro-2′-
5
6
1.2
2.5
5′-O-benzhydryl-5-fluoro-2′-deoxyuridine 7a
64
85
deoxyuridine
3′,5′-di-O-benzhydryl-5-fluoro-2′-
deoxyuridine 7b
7
8
uridine
1.2
2.5
5′-O-benzhydryl-uridine 8a
Trace
54
2′,5′-di-O-benzhydryl-uridine 8b
3′,5′-di-O-benzhydryl-uridine 8c
2′,3′,5′-tris-O-benzhydryl-uridine 8d
5′-O-benzhydryl-5-fluorouridine 9a
2′,5′-di-O-benzhydryl-5-fluorouridine 9b
3′,5′-di-O-benzhydryl-5-fluorouridine 9c
2′,3′,5′-tris-O-benzhydryl-5-fluorouridine 9d
32
9
3.7
1.2
2.5
81
10
11
5-fluorouridine
Trace
59
23
12
3.7
79
The resulting byproduct ethoxydiphenylmethane 5 was also isolated and characterized by 1H-NMR
showing a singlet at 5.44δ, a quartet at 3.61δ and a triplet at 1.35δ. Deprotection was also attempted
using CuBr2 in catalytic amounts, but even after refluxing for 16 h, presence of the starting material
was still observed along with some degraded material (Table 4). The use of CuBr2 however has been
reported before for clean cleavage of bis-(methoxyphenyl)methyl ether moieties [18]. The latter are
much more prone to cleavage in agreement with the strongly reduced acid stability of dimethoxytrityl
ether in comparison with trityl moieties.
Scheme 3. Deprotection of the DPM ether moiety in refluxing ethanol.

Molecules 2013, 18
8529
Table 4. Deprotection of DPM ethers in ethanol at 85 °C.
Entry
Catalyst
PdCl2
Time (h)
Yield of 1 (%) a
1
2
16
16
85
43
CuBr2
a Reaction on 100 mg scale in refluxing ethanol for 16 h with 0.2 eq of metal catalyst.
As reported before [16], introduction of DPM ether is compatible with the presence of different
protecting groups like acyl groups, silyl and benzyl ethers or ester moieties. In our hands, following
overnight treatment of 3b with conc. ammonia:MeOH (1:1) or 2M NaOH:dioxane (1:1) no reaction
was observed. The compounds likewise proved relatively stable in acidic conditions showing no
reaction at RT in 80% acetic acid with overnight treatment, but starting to degrade after heating for 4 h
at 80 °C. Finally, a 3% trichloroacetic acid solution in DCE afforded deprotection only after 15 h of
reaction, with 50% benzhydryl cleavage after 6 h. Unfortunately, use of the DPM group seems limited
to a small series of pyrimidine nucleosides. When evaluating cytidine, adenosine or guanosine
nucleosides, the lack of solubility of the starting compounds prevented reaction in DCE while in more
polar solvents, degradation was noticed with time. In an attempt to remediate the problem, prior
persilylation with bis(trimethylsilyl)acetamide afforded soluble substrates for 2′-deoxycytidine and
guanosine, but upon addition of DPM-OH and PdCl2, rapid precipitation occurred and no alkylated
nucleosides could be obtained. Finally, adding small amounts of polar solvents like NMP to improve
the solubility in DCE prevented reaction as of likely complexation of the PdCl2. In conclusion,
straightforward introduction and ease of removal of the DPM ether on uridine analogues, promised to
make a nice addition to the nucleosidic protecting group repertoire, but unfortunately, the lack of
solubility of other nucleosides hampers its general use.
3. Experimental
3.1. General
Reagents and solvents were purchased from commercial suppliers (Acros, Sigma-Aldrich, Bachem,
Novabiochem) and used as provided, unless indicated otherwise. All the solvents were of analytical
grade and were stored over 4Å molecular sieves. Reactions were carried out in oven-dried glassware
under a nitrogen atmosphere with stirring at 85 °C.
1H and 13C-NMR spectra of the compounds dissolved in CDCl3, MeOD or DMSO-d6 were recorded
on a Bruker UltraShield Avance 300 MHz or 600 MHz spectrometer. The chemical shifts are
expressed as δ values in parts per million (ppm), using the residual solvent peaks (CDCl3: 1H, 7.26 ppm;
13C, 77.16 ppm; MeOD: 1H, 3.31 ppm; 13C, 49.00 ppm) as a reference. Coupling constants are given in
Hertz (Hz). The peak patterns are indicated by the following abbreviations: bs = broad singlet,
d = doublet, m = multiplet, q = quadruplet, s = singlet and t = triplet. High resolution mass spectra
were recorded on a quadrupole time-of-flight mass spectrometer (Q-Tof-2, Micromass, Manchester, UK)
equipped with a standard ESI interface; samples were infused in 2-propanol/H2O (1:1) at 3 µL min−1.
For TLC, precoated aluminium sheets were used (Merck, Silica gel 60 F254). The spots were
visualized by UV light at 254 nm. Column chromatography was performed on ICN silica gel 60A°
40–60 µM.

Molecules 2013, 18
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3.2. General Procedure for Protection
To a solution of the respective nucleoside (100 mg) and diphenylmethanol in dichloroethane
(5 mL/mmol) was added palladium chloride (0.2 eq). The reaction mixture was heated at 85 °C under
an argon atmosphere for 16 h or until disappearance of the starting materials as monitored by TLC.
The solvent was removed in vacuo and the crude mixture obtained was purified by column
chromatography to afford the desired compound.
5′-O-Benzhydryl-thymidine (3a). White solid; TLC (DCM/MeOH 9:1): Rf = 0.70. 1H-NMR (300 MHz,
CDCl3): δ 8.96 (bs, 1H, NH), 7.55 (s, 1H), 7.54–7.28 (m, 10H), 6.50–6.45 (m, 1H, H-1′), 5.44 (s, 1H,
CH), 4.63 (s, 1H), 4.14–4.13 (m, 1H), 3.80–3.76 (m, 1H, H-5′/H-5′′), 3.68–3.63 (m, 1H, H-5′/H-5′′),
2.79 (bs, 1H, OH), 2.46–2.39 (m, 1H, H-2′/H-2′′), 2.36–2.27 (m, 1H, H-2′/H-2′′), 1.41 (s, 3H).
13C-NMR (75 MHz, CDCl3) δ: 163.4, 150.2, 141.2, 141.0, 135.4, 128.4, 127.7, 127.5, 126.6, 126.0,
111.0, 85.8, 84.6, 84.5, 72.5, 68.8, 40.7, 11.4. HRMS calcd for C23H24N2O5 [M+Na]+: 431.1577;
found:431.1576.
1
3′,5′-di-O-Benzhydryl-thymidine (3b). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.70. H-NMR
(300 MHz, CDCl3): δ 9.28 (bs, 1H, NH), 7.50 (s, 1H), 7.49–7.19 (m, 20H), 6.53–6.48 (m, 1H, H-1′),
5.47 (s, 1H, CH), 5.37 (s, 1H, CH), 4.43–4.39 (m, 1H), 4.33–4.30 (m, 1H), 3.77–3.72 (m, 1H, H-5′/H-5′′),
3.53–3.49 (m, 1H, H-5′/H-5′′), 2.62–2.54 (m, 1H, H-2′/H-2′′), 2.24–2.15 (m, 1H, H-2′/H-2′′), 1.42 (s,
13
3H). C-NMR (75 MHz, CDCl3): δ 163.6, 150.2, 141.3, 141.2, 141.1, 141.0, 135.2, 128.4, 128.3,
128.3, 128.2, 127.6, 127.5, 127.5, 126.8, 126.7, 126.5, 126.1, 110.9, 84.8, 84.3, 83.8, 82.1, 77.2, 77.2
68.7, 38.3, 11.4. HRMS calcd for C36H34N2O5 [M+H]+: 575.2540; found: 575.2540.
5′-O-Benzhydryl-2′-deoxyuridine (6a). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.30. 1H-NMR
(600 MHz, CDCl3): δ 8.35 (bs, 1H, NH), 7.77 (d, 1H, J = 7.8 Hz), 7.36–7.26 (m, 10H), 6.39 (t, 1H,
H-1′, J = 6.6 Hz), 5.39 (s, 1H, CH), 5.21–5.19 (m, 1H), 4.64–4.62 (m, 1H), 4.10 (s, 1H), 3.81–3.78 (m,
1H, H-5′/H-5′′), 3.72–3.70 (m, 1H, H-5′/H-5′′), 2.41–2.38 (m, 1H, H-2′/H-2′′), 2.29–2.24 (m, 1H,
H-2′/H-2′′), 2.05 (d, 1H, OH, J = 3.6 Hz). 13C-NMR (150 MHz, CDCl3): δ 162.7, 150.0, 141.2, 140.9,
140.3, 128.7, 128.7, 128.1, 128.0, 126.8, 126.7, 102.1, 86.0, 85.1, 85.0, 72.3, 68.9, 59.5, 41.3. HRMS
calcd for C22H22N2O5 [M+Na]+: 417.1421; found: 417.1421.
3′,5′-di-O-Benzhydryl-2′-deoxyuridine (6b). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.70.
1H-NMR (600 MHz, CDCl3): δ 8.32 (bs, 1H, NH), 7.70 (d, 1H, J =8.4 Hz), 7.36–7.18 (m, 20H), 6.41
(t, 1H, H-1′, J =6.3 Hz), 5.44 (s, 1H, CH), 5.31 (s, 1H, CH), 5.19–5.15 (m, 1H), 4.39–4.36 (m, 1H),
4.31–4.28 (m,1H), 3.77–3.73 (m, 1H, H-5′/H-5′′), 3.57–3.53 (m, 1H, H-5′/H-5′′), 2.56–2.50 (m, 1H,
H-2′/H-2′′), 2.16–2.07 (m, 1H, H-2′/H-2′′). 13C-NMR (150 MHz, CDCl3): δ 162.8, 150.0, 141.4, 141.3,
141.2, 140.8, 140.2, 128.7, 128.6, 128.5, 128.0, 127.9, 127.8, 127.1, 127.0, 126.7, 126.6, 102.1, 85.3,
84.9, 84.3, 82.4, 69.0, 38.8. HRMS calcd for C35H32N2O5 [M+H]+: 561.2383; found: 561.2377.
5′-O-Benzhydryl-5-fluoro-2′-deoxyuridine (7a). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.20.
1H-NMR (300 MHz, CDCl3): δ 8.39 (bs, 1H, NH), 7.95 (d, 1H, J = 6.3 Hz), 7.37–7.28 (m, 10H),
6.40–6.35 (m, 1H, H-1′), 5.43(s, 1H, CH), 4.64–4.62 (m, 1H), 4.15–4.13 (m, 1H), 3.87–3.82 (m, 1H,

Molecules 2013, 18
8531
H-5′/H-5′′), 3.70–3.66 (m, 1H, H-5′/H-5′′), 2.48–2.40 (m, 1H, H-2′/H-2′′), 2.31–2.22 (m, 1H, H-2′/H-2′′),
13
1.95 (bs, 1H, OH). C-NMR (75 MHz, CDCl3): δ 156.6, 156.4, 148.5, 141.2, 141.0, 140.8, 139.6,
128.8, 128.1, 128.0, 126.8, 126.6, 124.3, 124.1, 86.3, 85.6, 85.3, 72.6, 69.0, 41.3. HRMS calcd for
C22H21FN2O5 [M+Na]+: 435.1327; found: 435.1328.
3′,5′-di-O-Benzhydryl-5-fluoro-2′-deoxyuridine (7b). White solid; TLC (ethyl acetate/hexane 1:1):
1
Rf = 0.70. H-NMR (600 MHz, CDCl3): δ 8.42 (bs, 1H, NH), 7.86 (d, 1H, J= 6Hz), 7.34–7.15
(m, 20H), 6.37–6.34 (m, 1H, H-1′), 5.40(s, 1H, CH), 5.29 (s, 1H, CH), 4.33–4.28 (m, 2H), 3.75–3.73
(m, 1H, H-5′/H-5′′), 3.48–3.46 (m, 1H, H-5′/H-5′′), 2.56–2.52 (m, 1H, H-2′/H-2′′), 2.09–2.04 (m, 1H,
13
H-2′/H-2′′). C-NMR (150 MHz, CDCl3): δ 156.6, 156.4, 141.4, 141.3, 141.2, 140.9, 139.6, 128.7,
128.6, 128.5, 128.5, 128.0, 127.9, 127.8, 127.1, 127.0, 124.3, 124.1, 85.8, 85.1, 84.5, 82.5, 76.8, 69.0,
38.7. HRMS calcd for C35H31FN2O5 [M+Na]+: 601.2109; found: 601.2098.
1
2′,5′-di-O-Benzhydryl-uridine (8b). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.60. H-NMR
(600 MHz, CDCl3): δ 8.78 (bs, 1H, NH), 7.65 (d, 1H, J = 8.2 Hz), 7.37–7.19 (m, 20H), 6.22 (d, 1H,
H-1′, J = 4.2 Hz), 5.80 (s, 1H, CH), 5.37 (s, 1H, CH), 4.93–4.91 (m, 1H), 4.37–4.34 (m, 1H), 4.23–4.21
(m, 1H), 4.15 (t, 1H, J = 4.8 Hz), 3.85–3.83 (m, 1H, H-5′/H-5′′), 3.71–3.69 (m, 1H, H-5′/H-5′′), 2.75
13
(d, 1H, OH, J = 6 Hz). C-NMR (150 MHz, CDCl3): δ 162.7, 149.9, 140.9, 140.6, 140.4, 139.9,
139.6, 128.5, 128.4, 128.3, 127.9, 127.7, 126.9, 126.6, 126.6, 126.4, 101.7, 86.6, 84.8, 83.7, 82.6, 79.5,
69.2, 67.7. HRMS calcd for C35H32N2O6 [M+H]+: 577.2333; found : 577.2336.
3′,5′-ditri-O-Benzhydryl-uridine (8c). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.40. 1H-NMR
(600 MHz, CDCl3): δ 8.39 (bs, 1H, NH), 7.63 (d, 1H, J = 8.2 Hz), 7.39–7.17 (m, 20H), 6.02 (d, 1H,
H-1′, J = 4.2 Hz), 5.52 (s, 1H, CH), 5.26 (s, 1H, CH), 5.13–5.11 (m, 1H), 4.27–4.25 (m, 2H), 4.20–4.17
(m, 1H), 3.72–3.70 (m, 1H, H-5′/H-5′′), 3.41–3.39 (m, 1H, H-5′/H-5′′), 2.95 (d, 1H, OH, J = 7.2 Hz).
13C-NMR (150 MHz, CDCl3): δ 162.4, 150.0, 140.7, 140.4, 140.2, 139.7, 128.5, 128.4, 128.3, 127.9,
127.9, 127.8, 127.6, 126.8, 126.6, 126.4, 126.3, 101.9, 89.0, 84.6, 83.6, 81.5, 75.9, 74.0, 67.8. HRMS
calcd for C35H32N2O6 [M+H]+: 577.2333; found: 577.2330.
2′,3′,5′-tri-O-Benzhydryl-uridine (8d): White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.80. 1H-NMR
(600 MHz, CDCl3): δ 8.63 (bs, 1H, NH), 7.63 (d, 1H, J = 8.4 Hz), 7.27–7.03 (m, 30H), 6.23 (d, 1H,
H-1′, J = 3 Hz), 5.75(s, 1H, CH), 5.25 (s, 1H, CH), 5.21 (s, 1H, CH), 4.78–4.76 (m, 1H), 4.46 (d, 1H,
J = 6 Hz), 4.14 (t, 1H, J = 5.4 Hz), 4.06–4.04 (m, 1H), 3.78–3.76 (m, 1H, H-5′/H-5′′), 3.56–3.54 (m,
1H, H-5′/H-5′′). 13C-NMR (150 MHz, CDCl3): δ 162.5, 149.5, 141.3, 140.7, 140.6, 140.5, 139.6,
128.5, 128.4, 128.3, 128.2, 128.1, 128.0, 127.9, 127.7, 127.6, 127.6, 127.5, 127.4, 127.3, 127.2, 127.1,
126.5, 126.4, 126.4, 126.3, 101.3, 87.4, 84.5, 81.8, 81.8, 77.7, 72.4, 67.0. HRMS calcd for C48H42N2O6
[M+H]+: 743.3115; found: 743.3107.
2′,5′-di-O-Benzhydryl-5-fluorouridine (9b). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.60.
1H-NMR (600 MHz, CDCl3): δ 8.61 (bs, 1H, NH), 7.68 (d, 1H, J = 12.6 Hz), 7.36–7.22 (m, 20H),
6.21–6.20 (m, 1H, H-1′), 5.67 (s, 1H, CH), 5.38 (s, 1H, CH), 4.33–4.31 (m, 1H), 4.24–4.22 (m, 1H),
4.17–4.15 (m, 1H), 3.86–3.83 (m, 1H, H-5′/H-5′′), 3.65–3.62 (m, 1H, H-5′/H-5′′), 2.75 (d, 1H, OH,
13
J = 5.4 Hz). C-NMR (150 MHz, CDCl3): δ 148.6, 140.9, 140.6, 140.4, 140.3, 139.9, 139.0, 128.5,

Molecules 2013, 18
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128.4, 128.3, 127.9, 127.7, 126.8, 126.6, 126.5, 126.3, 123.5, 123.3, 86.6, 85.2, 83.9, 83.2, 79.4, 69.5,
68.1. HRMS calcd for C35H31FN2O6 [M+Na]+: 617.2058; found: 617.2062.
3′,5′-ditri-O-Benzhydryl-5-fluorouridine (9c): White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.40.
1H-NMR (600 MHz, CDCl3): δ 8.38 (bs, 1H, NH), 7.78 (d, 1H, J = 7.2 Hz), 7.36–7.16 (m, 20H),
6.02–6.00 (m, 1H, H-1′), 5.50 (s, 1H, CH), 5.27 (s, 1H, CH), 4.25–4.23 (m, 2H), 4.20–4.17 (m, 1H),
3.73–3.70 (m, 1H, H-5′/H-5′′), 3.32–3.30 (m, 1H, H-5′/H-5′′), 2.94 (d, 1H, OH, J = 9.6 Hz). 13C-NMR
(150 MHz, CDCl3): δ 156.2, 155.9, 148.5, 141.2, 140.4, 140.3, 140.1, 139.3, 128.5, 128.4, 128.3,
128.0, 127.9, 127.8, 127.6, 126.8, 126.6, 126.5, 126.4, 123.8, 123.5, 89.0, 84.8, 83.8, 81.9, 76.3, 74.1,
67.9. HRMS calcd for C35H31FN2O6 [M+Na]+: 617.2058; found: 617.2061.
2′,3′,5′-tri-O-Benzhydryl-5-fluorouridine (9d). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.80.
1H-NMR (600 MHz, CDCl3): δ 8.55 (d, 1H, NH, J = 5.4 Hz), 7.64 (d, 1H, J = 7.2 Hz), 7.37–7.06 (m,
30H), 6.23 (m, 1H, H-1′), 5.60 (s, 1H, CH), 5.34 (s, 1H, CH), 5.23 (s, 1H, CH), 4.43–4.41 (m, 1H),
4.16–4.13 (m, 1H), 4.08–4.05 (m, 1H), 3.79–3.76 (m, 1H, H-5′/H-5′′), 3.46–3.44 (m, 1H, H-5′/H-5′′).
13C-NMR (150 MHz, CDCl3): δ 156.7, 148.6, 141.5, 141.1, 141.0, 140.9, 140.8, 140.6, 139.1, 128.6,
128.5, 128.4, 128.3, 128.0, 127.9, 127.8, 127.7, 127.5, 127.3, 127.2, 127.0, 126.9, 126.8, 126.7, 123.8,
123.5, 87.4, 85.1, 82.7, 82.5, 82.4, 78.3, 73.2.4, 67.9. HRMS calcd for C48H41FN2O6 [M+H]+:
761.3021; found: 761.3037.
3.3. General Procedure for Deprotection
To a solution of 3′,5′-di-O-benzhydryl-thymidine 3b (100 mg) in ethanol (5 mL/mmol) was added
palladium chloride (0.2 eq). The reaction mixture was heated at 85 °C for 16 h until disappearance of
the starting material monitoring by TLC. The solvent was removed in vacuo and the crude mixture
obtained was purified by column chromatography affording compound 5 and recovered 1 in 85% yield.
Ethoxydiphenylmethane (5). White solid; TLC (ethyl acetate/hexane 1:1): Rf = 0.90. 1H-NMR (300 MHz,
CDCl3): δ 7.46–7.28 (m, 10H), 5.44 (s,1H), 3.61 (q, 2H, J =6.9 Hz), 1.35 (t, 3H, J =6.9 Hz). 13C-NMR
(75 MHz, CDCl3): δ 142.3, 128.1, 127.1, 126.7, 83.2, 64.3, 15.1.
Recovered Thymidine (1). White solid; TLC (DCM/MeOH 9:1): Rf = 0.40. 1H-NMR (300 MHz, CD3OD):
δ 7.2 (bs, 1H, NH), 6.29 (t, 1H, H-1′, J = 6.6 Hz), 4.43–4.39 (m, 1H), 3.94–3.90 (m, 1H), 3.84–3.71
13
(m, 2H), 2.27–2.22 (m, 2H), 1.89 (s, 3H, CH3). C-NMR (75 MHz, CD3OD): δ 164.7, 150.6, 136.5,
109.8, 87.1, 84.5, 70.5, 61.1, 39.5, 10.7.
4. Conclusions
A convenient and effective method for the protection of hydroxyl groups of nucleosides as the
corresponding diphenylmethyl ether has been developed with the aid of a transition metal catalyst. In
addition, only by changing the solvent, the corresponding diphenylmethyl ethers can be deprotected
under similar conditions using palladium (II) chloride as catalyst. With both protection and
deprotection reactions proceeding under mild conditions and with nice selectivity, this high yielding
strategy can be useful for the synthesis of complex nucleosides and nucleotides.

Molecules 2013, 18
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Supplementary Materials
A supplementary file with scanned spectra is provided. Supplementary materials can be accessed at:
http://www.mdpi.com/1420-3049/18/7/8524/s1.
Acknowledgments
We would like to acknowledge Erasmus Mundus External Cooperation Window lot 13 for their
financial support. Mass spectrometry was done by Jef Rozenski and made possible by the support of
the Hercules Foundation of the Flemish Government (grant 20100225–7). The chemistry part
was supported by the Rega Foundation. Our thanks also go to Luc Baudemprez for the help with
NMR acquisition.
Conflict of Interest
The authors declare no conflict of interest.
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Sample Availability: Samples of the compounds are available from the authors.
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