A convenient synthesis of N,N'-dibenzyl-2,4-diaminopyrimidine-2'- deoxyribonucleoside and 1-Methyl-2'-deoxypseudoisocytidine

Article abstract of DOI:10.1080/15257770902946090

The syntheses of N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deoxyribonucleoside and 1-methyl-2'-deoxypseudoisocytidine via Heck coupling are described. A survey of the attempts to use the Heck coupling to synthesize N,N'-dibenzyl-2,4-diaminopyrimidine-2'-deox

Full text of DOI:10.1080/15257770902946090

Nucleosides, Nucleotides and Nucleic Acids, 28:275–291, 2009
Copyright ꢀC Taylor & Francis Group, LLC
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770902946090
A CONVENIENT SYNTHESIS OF N,Nꢀ-DIBENZYL-2,4-
DIAMINOPYRIMIDINE-2ꢀ-DEOXYRIBONUCLEOSIDE
AND 1-METHYL-2ꢀ-DEOXYPSEUDOISOCYTIDINE
Kevin W. Wellington,1 Hua Chee Ooi,2 and Steven A. Benner3
1CSIR Biosciences, Pinelands, Modderfontein, South Africa
2Seattle Genetics, Bothell, Washington, USA
3Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and
Technology, Gainesville, Florida, USA
The syntheses of N,Nꢁ-dibenzyl-2,4-diaminopyrimidine-2 ꢁ-deoxyribonucleoside and 1-methyl-2 ꢁ-
2
deoxypseudoisocytidine via Heck coupling are described. A survey of the attempts to use the Heck
coupling to synthesize N,N ꢁ-dibenzyl-2,4-diaminopyrimidine-2 ꢁ-deoxyribonucleoside is provided,
indicating a remarkable diversity in outcome depending on the specific heterocyclic partner used.
Keywords Synthesis; Heck coupling; hydrogen bonding patterns; synthetic biology;
artificial genetic systems
INTRODUCTION
Some time ago, we showed that it was possible to create mutually ex-
clusive nucleobase pairs that maintained the same geometry as the Watson-
Crick base pairs, but which possessed different hydrogen bonding patterns.
This not only allowed for the introduction of extra letters into the genetic
alphabet,[1] but also initiated the emerging field of synthetic biology,
where investigators in many laboratories are attempting to create artificial
genetic systems.[2–5] In this regard, C-glycosides have been of particular
interest to our work since they are robust with respect to chemical degra-
dation and analogs of natural nucleotides (e.g., formycin A for adenosine,
Received 30 September 2008; accepted 20 March 2009.
We are grateful for financial support from the National Institutes of Health. This work was partly
supported by R01GM08152 and R01HG004647.
Address correspondence to Steven A. Benner, Foundation for Applied Molecular Evolution and
The Westheimer Institute for Science and Technology, 1115 NW 4th Street, Gainesville, FL, 32601, USA.
E-mail: sbenner@ffame.org
275

276
K. W. Wellington et al.
FIGURE 1 C-Glycosides are used to implement three nonstandard hydrogen bonding patterns in an
artificially expanded genetic information system (AEGIS).[13–15]
pseudothymidine for thymidine) could be utilized to create more
stable DNA structures. C-glycosides have also been successfully implemented
in strategies that do not maintain a Watson-Crick geometry to expand the
genetic alphabet.[6–8] In addition, C-glycosides are potentially useful in
architectures to detect, amplify, quantitate, and sequence DNA and RNA.[9]
They can not only be used in binding studies, but also in dynamic assay
architectures where oligonucleotides incorporating multiple C-glycosides
are both copied and synthesized by polymerases.
In N -glycosides, the heterocycle is joined to the sugar through a
carbon-nitrogen bond. Isocytidine (Figure 1) is an example of a six-
membered heterocyclic N -glycoside with a nonstandard acceptor-acceptor-
donor hydrogen bonding pattern. It is currently being used in the
‘branched DNA’ diagnostic assay developed at Chiron and Bayer. Hav-
ing now obtained FDA approval, this diagnostic helps manage the care
of some 400,000 patients annually infected with the HIV, hepatitis B
and hepatitis C viruses.[10–12] Other nonstandard hydrogen bonding pat-
terns, however, require their six-membered heterocycle to be attached
to their sugar by a carbon-carbon bond. This has led to many non-
standard hydrogen-bonding patterns being implemented on C-glycosides
(Figure 1).

Diaminopyrimidine and Pseudoisocytidine Derivatives
277
As part of our work, we required protected forms of a nonstan-
dard nucleoside that bears a heterocycle that presents a “donor-acceptor-
donor” (pyDAD) hydrogen bonding pattern on a pyrimidine skeleton such
as kappa (Figure 1, bottom left). This should form a nucleobase pair
having normal Watson-Crick geometry with purines and purine analogs
that present an “acceptor-donor-acceptor” pattern, including xanthosine
7-deazaxanthosine, and 5-aza-7-deazaxanthosine[15] (Figure 1, bottom left).
While these and other purine analogs are readily available, the 2,4-
diaminopyrimidine-2ꢁ-deoxyribonucleoside that presents a “donor-acceptor-
donor” hydrogen bonding pattern was available only by a long procedure
that began with D-ribose.[16] This has always limited the access to protected
2,4-diaminopyrimidine-2ꢁ-deoxyribonucleoside derivatives.
The synthesis of the nonstandard 1-methyl-2ꢁ-deoxypseudoisocytidine
having a “donor-acceptor-acceptor” (pyDAA) hydrogen bonding pattern on
a pyrimidine skeleton has also been of interest to us since this would be
the C-glycoside equivalent of cytidine (Figure 1, top left). This nucleoside
should form a normal Watson-Crick nucleobase pair with purine or purine
analogs having an “acceptor-donor-donor” hydrogen bonding pattern.
The Heck coupling is, in principle, an elegant way to synthesize
such molecules by making use of a protected derivative of 5-iodo-2,4-
diaminopyrimidine or 5-iodo-1-methyl-isocytosine. We report here an ex-
perimental procedure that yields the 2,4-diaminopyrimidine-2ꢁ-deoxy-
ribonucleoside in the N,N’-dibenzylated form and also another that yields
unprotected 1-methyl-2ꢁ-deoxypseudoisocytidine.
RESULTS AND DISCUSSION
A
retrosynthesis of 2,4-diaminopyrimidine-2ꢁ-deoxyribonucleoside,
kappa, is shown in Scheme 1. The resulting components, the aglycon
4 and protected glycals 1 and 2 are substrates for the Heck coupling
reaction.
SCHEME 1

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K. W. Wellington et al.
Procedures for the synthesis of these glycals have been reported in the
literature.[17–19] Glycal 1 was synthesized in five steps while 2 was synthesized
in two steps from thymidine following procedures reported by Cameron
et al.[19] There are several reports in the literature of Heck coupling
reactions that were successful without protection of the exocyclic primary
amines of the aglycon.[20–24] The reports inspired the investigation of the
Heck coupling of the aglycon 4 with each of the glycals 1 and 2 to produce
5 and 6, respectively.
The aglycon 4 was prepared from commercially available 2,4-
diaminopyrimidine 3 by reacting it with iodine under acidic conditions. The
Heck coupling reaction was then attempted with the unprotected aglycon
4 and glycals 1 and 2 (Scheme 2). The coupling conditions that were
attempted are shown in Table 1.
SCHEME 2
The coupling reactions were conducted at two different tem-
perature ranges (60–65◦C and 85–90◦C) using two different bases
[triethylamine (Et3N) and diisopropylethylamine (DIEA)], two dif-
ferent palladium sources [palladium (II) acetate (Pd(OAc)2) and
bis(dibenzylideneacetone)palladium (Pd(dba)2)], two different ligands
[triphenylarsine (AsPh3) and 1,3-(diphenylphosphino)propane (dppp)]
and two different solvents [dimethylformamide (DMF) and acetonitrile
(MeCN)]. In entry 6 silver carbonate was added to the reaction mixture
because it increases conversion rates in analogous processes. Despite the
variations in reaction conditions the desired coupled products 5 and 6
were not obtained. These unsuccessful attempts may be attributed to
coordination of the palladium with the nitrogen atoms of the aglycon. In
the light of these results, it was decided to protect the primary amines of
the aglycon. For this purpose, the benzyl group was chosen as a protecting
group. The synthesis of the benzylated pyrimidine 8a was reported by
Vorbru¨ggen and Krolikiewicz when they investigated silylation-amination

Diaminopyrimidine and Pseudoisocytidine Derivatives
279
TABLE 1 Reactions conditions used for attempted coupling of glycals 1 and 2 with aglycon 4
Base and
salt
Solvent and
temperature
Reaction
time
Entry Aglycon Glycal
Pd source
Ligand
Result
1
2
3
4
5
6
4
4
4
4
4
4
2
2
1
1
1
1
Et3N
DIEA
DIEA
DIEA
DIEA
Et3N,
Ag2CO3
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(dba) 2
Pd(dba) 2
AsPh3
AsPh3
AsPh3
AsPh3
AsPh3
dppp
DMF, 85–90◦C
MeCN, 85–90◦C
DMF, 85–90◦C
DMF, 60–65◦C
DMF, 60–65◦C
MeCN, 60–65◦C
1h
1h
1.5h
23.5h
72h
72h
—
—
—
—
—
—
of hydroxy N -heterocycles.[25] This procedure was successfully employed to
synthesize 8a as well as 8b and 8c.
Treatment of 8a–c with N -iodosuccinnimide (NIS) afforded the iodi-
nated heterocycles 9a–c as depicted in Scheme 3. It was envisaged that the
Heck products 10a–c and 11a–c could be obtained by coupling each of the
aglycons 9a–c with glycals 1 and 2, respectively (Scheme 4).
SCHEME 3
The conditions used for each of the Heck coupling reactions are listed
in Table 2. For entries 1–9 in Table 2, 10 mol% of the palladium source
was used. For entry 7 a yield of 22% was obtained for 10a at 65–70◦C
when 10 mol% of the Pd(dba)2 was used. The Heck reaction for 10a was
then optimized by using 20 mol% of Pd(dba)2 and afforded a 60% yield
(entry 10). For these reactions, the bulky TBDPS group at the 3-position
directs addition of the aglycon to the β-face and results in the formation
of the β-anomer as the only isomer. Triethylamine was used as the base
for these reactions since it was easier to remove during purification and
1.5 equivalents of glycal was found to be sufficient. Desilylation of 10a
was achieved by reacting with TBAF at 0◦C and afforded the ketone 12.
The free 5ꢁ-hydroxyl leads to stereospecific reduction of ketone 12 by
complexation with NaBH(OAc)3 and affords the benzylated nucleoside 13

280
K. W. Wellington et al.
SCHEME 4
in 31% yield (Scheme 5). Attempted debenzylation of 13 by catalytic transfer
hydrogenation using 10% Pd-C and ammonium formate in methanol
was unsuccessful.[26] The debenzylation of 13 using Pd black and 1,4-
cyclohexadiene in glacial acetic acid was also attempted.[27] Pd black is sup-
posedly a more efficient catalyst than 10% Pd-C and glacial acetic acid has
been reported to be a better solvent for performing debenzylations under
TABLE 2 Reagents and conditions employed in the Heck coupling reaction
Solvent and
temperature
Reaction
time
Entry Aglycon Glycal
Base
Pd source
Ligand
Result
1
2
3
4
5
6
7
9a
9b
9c
9a
9a
9b
9a
1
1
1
2
2
2
1
Et3N
Et3N
Et3N
Bu3N
Bu3N
Bu3N
DIEA
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(OAc)2
Pd(dba) 2
Pd(dba) 2
Pd(dba)2
AsPh3
AsPh3
AsPh3
AsPh3
AsPh3
AsPh3
AsPh3
DMF, 85–90◦C
DMF, 85–90◦C
DMF, 85–90◦C
DMF, 60–65◦C
MeCN, 60–65◦C
MeCN, 60–65◦C
DMF, 65–70◦C
1 h
1 h
—
—
—
—
—
—
10a
(22%)
1.5 h
23.5 h
72 h
72 h
7.5 h
8
9
10
9b
9c
9a
1
1
1
DIEA
DIEA
Et3N
Pd(dba)2
Pd(dba)2
∗Pd(dba)2
AsPh3
AsPh3
AsPh3
DMF, 65–70◦C
DMF, 65–70◦C
DMF, 65–70◦C
8 h
11 h
4 h
∗10a
(60%)
∗20 mol% Pd(dba)2.

Diaminopyrimidine and Pseudoisocytidine Derivatives
281
SCHEME 5
catalytic transfer hydrogenation conditions. This attempt was, however, also
unsuccessful.
The synthesis of nucleoside 21, which possesses a donor-acceptor-
acceptor hydrogen bonding pattern, was achieved from isocytosine 14, as
outlined in Scheme 6. The heterocycle 15 was obtained in quantitative yield
(99%) after reaction with NIS in DMF. Reaction of 15 with HMDS in the
presence of ammonium sulfate, followed by treatment with a large excess of
methyl iodide gave the methylated heterocycle 16 as the sole product in 51%
yield. Methylation of N -1 was performed to avoid unwanted tautomerization
(Figure 2) that would result in an unwanted “donor-donor-acceptor” hy-
drogen bonding pattern in the desired nucleoside. The structure of 16 was
confirmed by an HMBC experiment that showed a long range correlation
between the aromatic proton and the methyl carbon on N -1. If methylation
had occurred on N -3, no correlation would have been observed.
Due to the difficulties associated with coupling the unprotected aglycon
4 with glycal 1, it was decided to protect the exocyclic amine of 16 with
a pivaloyl group prior to Heck coupling. This was achieved by reacting 16
with pivaloyl chloride in the presence of DMAP in pyridine and afforded
aglycon 17 in high yield (72%).
The Heck coupling reaction was successfully conducted using palla-
dium acetate and triphenylarsine in the presence of tri-n-butylamine and
afforded the desired Heck product 18 in moderate yield (44%) after
3 days. Subsequent deprotection of 18 was achieved using TBAF at 0◦C and
stereoselective reduction of the resulting ketone 19 was achieved by using
NaBH(OAc)3 to afford 20 in good yield (62%). Removal of the pivaloyl
group of 20 was achieved by treatment with methanolic ammonia and
afforded the desired nucleoside 21 in moderate yield (46%).

282
K. W. Wellington et al.
SCHEME 6
FIGURE 2 Tautomeric forms of the iodinated heterocycle 15.

Diaminopyrimidine and Pseudoisocytidine Derivatives
CONCLUSION
283
The Heck coupling is an extremely useful reaction for the coupling
of a variety of iodopyrimidinones to glycals, including those that gener-
ate 2ꢁ-deoxypseudouridine.[7] Our work here has uncovered a peculiar
set of limitations on the Heck glycal coupling strategy. From a purely
practical perspective, we have found the coupling quite useful to prepare
large amounts of pseudothymidine[28] for conversion to triphosphates and
phosphoramidites. A variety of explanations can be suggested to explain
why some coupling reactions are successful, while others are not. We
have not been able to generate a single explanatory set of rules that
account for all of the data that we have collected. Perhaps the most
curious pair of coupling experiments are those that successfully couple
2,4-N,N ꢁ-dibenzylamino-5-iodopyrimidine 9a to the glycal 1, but fail to
couple 2,4-diamino-5-iodopyrimidine 4 to the same glycal 1. Regardless of
the explanation, this manuscript offers a convenient route to the dibenzyl
protected derivative of the 2,4-diaminopyrimidine-2ꢁ-deoxyribonucleoside
13 as well as to 1-methyl-2ꢁ-deoxypseudoisocytidine 21.
EXPERIMENTAL
1
Anhydrous solvents were used for water sensitive reactions. NMR: H
at 300 MHz and 13C at 75 MHz; δ in ppm; calibration to SiMe4 (1H) or
residual solvent peak (13C). Melting points were determined by using an
Electrotherm Mel-Temp apparatus and are uncorrected.
2,4-Diamino-5-iodopyrimidine 4
2,4-Diaminopyrimidine (3.00 g, 27.2 mmol) was dissolved with stirring
in a mixture of 15 mL of H2O and 100 mL of glacial acetic acid, followed by
iodine (8.63 g, 68 mmol) and H5IO6 (8.07 g, 35.4 mmol). The mixture was
treated dropwise with concentated H2SO4 (1.0 mL), stirred for 5.5 hours
and then allowed to cool to room temperature. The solution, which was
placed on ice, was treated with solid KOH until a suspension formed. The
mixture solidified. The solids were recovered by filtration and washed with
water (450 mL). The filtrate was treated with KOH to create solids which
were recovered by filtration, dried in air, and then dried under high vacuum
to afford a light brown powder (1.65 g, 26%). The remaining solid material
was added to water (400 mL), stirred overnight and the suspension filtered
off and dried on the high vacuum pump to afford a brown powder (4.55 g,
71%). The combined yields afforded the product in a total yield of 6.20 g
(97%) m.p. 222–225◦C Rf = 0.45 (DCM-MeOH, 10:1). 1H NMR (DMSO-d6,
300 MHz): δ6.10 (NH2, s, 2H), 6.40 (NH2, br s, 2H) and 7.92 (ArH, s, 1H).
13C NMR (DMSO-d6, 75 MHz): δ162.0 and 2 × 162.8. HRMS-ESI: [MH+]
MS calcd for C4H5IN4 236.9632, found 236.9630.

284
K. W. Wellington et al.
N2,N4-Dibenzyl-pyrimidine-2,4-diamine 8a
Benzylamine 7a (13.12 mL, 100 mmol) was added to a hot, stirred
mixture of p-toluene sulfonic acid monohydrate (0.96 g, 5.2 mmol) and
uracil (4.48 g, 40 mmol) in HMDS under Ar. The resulting reaction mixture
was heated at 118◦C for 29 hours and then the solvent was removed on
the rotary evaporator at 50◦C. MeOH (50 mL) was added to the residue
and the mixture was allowed to stand overnight. The solvent was then
removed on the rotary evaporator and the crude material purified by flash
chromatography (silica: EtOAc-hexane, 1:1) to afford the product as a
brown oil (9.73 g, 84%) that solidified upon standing. m.p. 62–64◦C (lit.[25]
68–70◦C) Rf = 0.42 (DCM-MeOH, 10:1). 1H NMR (CDCl3, 300 MHz): δ4.45
(CH2, d, 2H, J = 5.7 Hz), 4.55 (CH2, d, 2H, J = 6 Hz), 5.20 (NH, br s, 1H),
5.53 (NH, br s, 1H), 5.67 (ArH, d, 1H, J = 5.7 Hz), 7.18–7.38 (ArH, m,
10H) and 7.75 (ArH, d, 1H, J = 6 Hz). 13C NMR (CDCl3, 75 MHz): δ45.3
(2 × CH2), 126.9, 127.3, 127.4, 128.4, 128.6, 139.8, 156.4, 162.2 and 162.9.
HRMS-ESI: [MH+] MS calcd for C18H18N4 291.1604, found 291.1600.
N2,N4-Bis-(4-methyl-benzyl)-pyrimidine-2,4-diamine 8b
Following the procedure described for the synthesis of 8a, 4-
methylbenzylamine 7b (15.16 mL, 120 mmol), p-toluenesulfonic acid mono-
hydrate (0.96 g, 5.2 mmol) and uracil (4.48 g, 40 mmol) were heated at
118◦C in HMDS for 38.5 hours while stirring under Ar. The solvent was
removed on the rotary evaporator at 50◦C and the residue purified by
flash chromatography (silica: EtOAc-hexanes, 1:2) to afford a light-brown
powder (8.08 g, 63%). m.p. 78–80◦C Rf = 0.44 (DCM-MeOH, 10:1). 1H NMR
(CDCl3, 300 MHz): δ2.33 (2 × CH3, m, 6H), 4.42 (CH2, d, 2H, J = 6 Hz),
4.53 (CH2, d, 2H, J = 6 Hz), 5.08 (NH, br s, 1H), 5.33 (NH, br s, 1H), 5.67
(ArH, d, 1H, J = 3 Hz), 7.05–7.30 (ArH, m, 8H) and 7.75 (ArH, 1H, d, J =
6 Hz). 13C NMR (CDCl3, 75 MHz): δ21.1 (2 × CH3), 45.0 (2 × CH2), 127.4,
129.1, 129.3, 136.5, 136.6, 137.0, 147.2, 156.3, 162.1 and 162.9. HRMS-ESI:
[MH+] MS calcd for C20H22N4 319.1917, found 319.1912.
N2,N4-Bis-(4-methoxy-benzyl)-pyrimidine-2,4-diamine 8c
4-Methoxybenzylamine 7c (15.64 mL, 120 mmol), p-toluene sulfonic
acid monohydrate (0.96 g, 5.2 mmol), and uracil (4.48 g, 40 mmol) were
heated at 118◦C in HMDS for 24 hours while stirring under Ar following
the procedure described for 8a. The solvent was removed on the rotary
evaporator at 50◦C and the residue purified by flash chromatography (silica:
EtOAc-hexanes, 1:3; EtOAc) to afford a light-brown powder (9.32 g, 66%).
m.p. 115–117◦C Rf = 0.44 (DCM-MeOH, 10:1). 1H NMR (CDCl3, 300 MHz):
δ3.72–3.88 (2 × OCH3, m, 6H), 4.40 (CH2, d, 2H, J = 5.1 Hz), 4.49 (CH2,
d, 2H, J = 6 Hz), 5.11 (NH, br s, 1H), 5.37 (NH, br s, 1H), 5.68 (ArH, d, 1H,

Diaminopyrimidine and Pseudoisocytidine Derivatives
285
J = 5.7 Hz), 6.7–6.91 (ArH, m, 4H), 7.16–7.32 (ArH, m, 4H) and 7.77 (ArH,
1H, d, J = 5.4 Hz). 13C NMR (CDCl3, 75 MHz): δ44.7 (2 × OCH3), 55.1
(CH2), 55.2 (CH2), 113.8, 114.0, 128.6, 128.7, 131.8, 156.2, 158.6, 158.8,
162.0 and 162.9. HRMS-ESI: [MH+] MS calcd for C20H22N4O2 351.1816,
found 351.1809.
N2,N4-Dibenzyl-5-iodo-pyrimidine-2,4-diamine 9a
N -Iodosuccinimide (5.74 g, 26 mmol) was added to a stirred solution of
the heterocycle 8a (5.00 g, 17 mmol) in MeOH (50 mL) and the resulting
reaction mixture was stirred at room temperature for 3 hours. The reaction
was monitored by TLC (silica: EtOAc-hexanes, 1:1) and upon completion
the solvent was removed on the rotary evaporator. The crude material
was purified by flash chromatography (silica: EtOAc-hexanes, 1:1; 2:1) to
afford a cream-yellow powder (4.00 g, 57%). m.p. 123–124◦C Rf = 0.36
1
(DCM-MeOH, 20:1) H NMR (CDCl3, 300 MHz): δ4.54 (CH2, d, 2H, J =
5.7 Hz), 4.61 (CH2, d, 2H, J = 6 Hz), 5.40 (NH, br s, 1H), 7.20–7.40 (ArH,
m, 10H) and 7.98 (ArH, 1H, m). 13C NMR (CDCl3, 75 MHz): δ45.1 (CH2),
45.6 (CH2), 127.1, 127.5, 128.5, 128.6, 138.6, 161.5 and 161.9. HRMS-ESI:
[MH+] MS calcd for C18H17IN4 417.0571, found 417.0563.
5-Iodo-N2,N4-Bis-(4-methyl-benzyl)-pyrimidine-2,4-diamine 9b
Following the procedure described for the synthesis of 9a, N -
iodosuccinimide (2.47 g, 11 mmol) was added to a stirred solution of the
heterocycle 8b (3.50 g, 11 mmol) in MeOH (50 mL) and the resulting
reaction mixture was stirred at room temperature. Upon completion the
solvent was removed on the rotary evaporator. The crude material was
purified by flash chromatography (silica: EtOAc-hexanes, 1:3; 1:2) to afford
a yellow powder (3.74 g, 77%). m.p. 130–132◦C Rf = 0.44 (DCM-MeOH,
1
20:1) H NMR (CDCl3, 300 MHz): δ2.33 (2 × CH3, m, 6H), 4.50 (CH2, d,
J = 6 Hz, 2H), 4.56 (2H, d, J = 5.7 Hz, CH2), 5.34 (2H, br s, NH), 7.06–7.24
(8H, m, ArH) and 7.95 (ArH, s, 1H). 13C NMR (CDCl3, 75 MHz): δ21.1 (2 ×
CH3) 44.9 (CH2), 45.3 (CH2), 127.5, 127.6, 129.2, 129.3, 135.6, 136.7, 137.0,
159.7, 161.5, 161.9 and 174.2. HRMS-ESI: [MH+] MS calcd for C20H21IN4
445.0884, found 445.0877.
5-Iodo-N2,N4-Bis-(4-methoxy-benzyl)-pyrimidine-2,4-diamine 9c
N -Iodosuccinimide (2.25 g, 10 mmol) was added to a stirred solution
of the heterocycle 8c (3.50 g, 10 mmol) in DMF (10 mL) and the resulting
reaction mixture was stirred at room temperature. The reaction was moni-
tored by TLC (silica: DCM-MeOH, 9:1) and upon completion the reaction
mixture was added to H2O (300 mL) and stirred overnight. The resulting
precipitate was filtered off and dried on the high vacuum pump to afford a

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K. W. Wellington et al.
light-brown powder (4.17 g, 88%). m.p. 114–115◦C Rf = 0.42 (DCM-MeOH,
1
20:1) H NMR (CDCl3, 300 MHz): δ3.79 (2 × OCH3, m, 6H), 4.48 (CH2,
d, 2H, J = 5.7 Hz), 4.54 (CH2, d, 2H, J = 5.7 Hz), 5.33 (NH, br s, 1H),
6.78–6.94 (ArH, m, 4H), 7.16–7.32 (ArH, m, 4H) and 7.97 (ArH, m, 1H).
13C NMR (CDCl3, 75 MHz): δ44.6 (OCH3), 45.0 (OCH3), 55.2 (2 × CH2),
113.8, 114.0, 128.7, 128.8, 130.6, 131.5, 158.6, 158.9, 159.6, 161.4 and 161.8.
HRMS-ESI: [MH+] MS calcd for C20H21IN4O2 477.0782, found 445.0777.
General Heck Coupling Procedure for Entries 1–6 in Table 1 and
Entries 1–9 in Table 2
A mixture of the palladium source (0.05 mmol) and triphenylarsine
(0.10 mmol) in dry DMF (2.0 mL) was stirred under argon at room
temperature for 20–40 minutes. This mixture was then transferred by
syringe to a solution of the aglycon (0.5 mmol), glycal 1 or 2 (0.8 mmol) and
base (0.22 mL, 1.6 mmol) in dry DMF (1.5 mL). The resulting orange-brown
solution was stirred under argon at 65–70◦C. The reaction mixture was
then filtered through celite and the volatiles were removed on the rotary
evaporator. The residue was purified by flash chromatography.
[5-(2,4-Bis-benzylamino-pyrimidin-5-yl)-3-(tert-butyl-diphenyl-
silanyloxy)-2,5-dihydro-furan-2-yl]-methanol 10a
A mixture of bis(dibenzylideneacetone)-palladium(0) (0.80 g, 1 mmol)
and triphenylarsine (0.80 g, 2 mmol) in dry DMF (1.5 mL) was stirred
under argon at room temperature for 40 minutes. This mixture was
then transferred by syringe to a solution of the iodinated heterocy-
cle 9a (2.10 g, 5 mmol), Daves’ sugar (1,4-anhydro-2-deoxy-3-O-[(1,1-
dimethylethyl)diphenylsilyl]-D-erythro-pent-1-enitol) 1 (2.80 g, 8 mmol) and
triethylamine (2.09 mL, 15 mmol) in dry DMF (3.00 mL) also under argon.
The resulting orange-brown solution was heated under argon at 65–70◦C.
After 2 hours of heating more triethylamine (2.09 mL, 15 mmol) was
added and the reaction monitored by TLC (silica: MeOH-DCM, 1:20). After
5 hours the reaction was complete and the reaction mixture was then
filtered through celite and the volatiles removed on a rotary evaporator.
The resulting crude material was purified by flash chromatography (silica:
DCM-MeOH, 280:1, 140:1, 100:1, 50:1) and afforded a brown powder (1.91
g, 60%). Rf = 0.31 (silica: MeOH-DCM, 1:20). 1H NMR (CDCl3, 300 MHz):
δ3.78–4.02 (CH2OH, m, 2H), 4.22 (s,1H), 4.47 (CH2, d, J = 5.7 Hz, 2H),
4.52–4.70 (m, 3H), 5.27 (m, 1H), 7.18–7.31 (10H, m, ArH), 7.32–7.54
(7H, m, ArH) and 7.63–7.76 (4H, m, ArH). 13C NMR (CDCl3, 75 MHz):
δ19.2, 19.3, 26.4, 26.6, 44.36, 2 × 45.1, 61.7, 62.7, 81.4, 82.8, 83.6, 101.3,
127.0, 127.4, 127.7, 128.0, 2 × 128.4, 128.5, 130.4, 130.6, 130.7, 134.8, 135.3
and 135.4. HRMS-ESI: [MH+] MS calcd for C39H43N403Si 643.3099, found
643.3067.

Diaminopyrimidine and Pseudoisocytidine Derivatives
287
[5-(2,4-Bis-benzylamino-pyrimidin-5-yl)-2-hydroxymethyl-
tetrahydro-furan-3-ol 13
The ketone 12 (0.60 g, 1.5 mmoL) was added to a mixture of acetonitrile
(8 mL) and glacial acetic acid (3 mL) and the resulting mixture cooled to
0◦C. Sodium triacetoxyborohydride (0.44 g, 2.1 mmol) was then added and
the reaction monitored by TLC (silica: DCM-MeOH, 10:1). After 35 minutes
stirring was stopped and the solvent removed on the rotary evaporator to
afford a brown crude material. This was purified by flash chromatography
(silica: DCM-MeOH, 40:1, 20:1, 10:1, 10:3) to afford a light brown material
(0.19 g, 31%). Rf = 0.15 (DCM-MeOH, 10:1). 1H NMR (CD3OD, 300 MHz):
δ1.81–1.86 (m, 1H), 2.23–2.40 (m, 1H), 3.71 (t, J = 2.4 and 2.1 Hz, 2H),
3.92 (m, 1H), 4.38 (d, J = 6.6 Hz, 1H), 4.42–4.63 (m, 4H), 4.88 (m, 1H),
7.12–7.26 (ArH, m, 10H) and 7.55 (ArH, s, 1H). 13C NMR (CD3OD, 75
MHz): δ40.9, 44.6, 45.8, 48.7, 63.1, 74.7, 80.1, 80.2, 89.3, 106.6, 2 × 127.6,
128.2, 129.2, 129.3, 141.5141.8, 153.6, 161.9 and 162.7. HRMS-ESI: [MH+]
MS calcd for C23H27N403 407.2078, found 407.2073.
5-Iodo-isocytosine 15
DMF (50 mL) was added to a mixture of isocytosine 14 (8.33 g, 75 mmol)
and N -iodosuccinimide (18.56 g, 82.5 mmol) under an Ar atmosphere. The
reaction vessel was covered in foil and ultrasonicated for 30 minutes to break
up the solid mass at the bottom of the reaction vessel (the reaction mixture
was, however, still heterogeneous). The heterogeneous mixture was then
stirred for an additional 12 hours before adding it to water (150 mL). The
insoluble material was collected by filtration, washed with additional water
and dried over P2O5 to give the desired material as a pale tan solid (17.70 g,
99%). The material was used without further purification. 1H NMR (DMSO-
d6, 300 MHz): δ6.70 (NH2, br s, 2H), 7.94 (ArH, s, 1H), 11.26 (NH, br s,
1H).
5-Iodo-1-methyl-isocytosine 16
HMDS (20 mL) was added to a mixture of 5-iodo-isocytosine 15 (3.56 g,
15 mmol) and powdered ammonium sulfate (0.08 g) under an Ar atmo-
sphere. The reaction mixture was stirred and heated to reflux for 6.5 hours.
After this time it was removed from the heat, allowed to cool, and the
solvent removed under reduced pressure (high vacuum pump) to afford
a brown oil. The oil was dissolved in acetonitrile (20 mL) and methyl iodide
(9.34 mL, 150 mmol) added under an Ar atmosphere. The reaction mixture
was stirred for 1 day and the crude product was collected by filtration.
Recrystallization from water, decolorizing with charcoal gave the desired
material as a pale yellow crystalline solid (1.91 g, 51%). The filtrate was
concentrated, which on cooling, gave an additional batch of material, also

288
K. W. Wellington et al.
1
as a pale yellow solid (0.26 g, 7%). H NMR (DMSO-d6, 300 MHz) δ3.37
(3H, s, N-Me), 7.75 (1H, br s, NH), 8.15 (1H, s, ArH). 13C NMR (DMSO-
d6, 75 MHz) δ 38.3, 75.7, 149.7, 154.2, 162.7. HRMS (EI +ve) calcd for
C5H6N3OI 250.9560 (M+), found 250.9560.
5-Iodo-1-methyl-2-pivaloylamino-4-pyrimidinone 17
Pivaloyl chloride (15.8 mL, 128.3 mmol) was added in one lot to a stirred
mixture of 5-iodo-1-methyl-isocytosine 16 (2.01 g, 8 mmol) and DMAP
(1.96 g, 16 mmol) in anhydrous pyridine (32 mL) under an Ar atmosphere.
The reaction was stirred for 18 hours, and triethylamine (16 mL) was added.
The reaction vessel was cooled in an ice/water bath, and ethanol (32 mL)
was cautiously added to the reaction mixture. The reaction mixture was con-
centrated under reduced pressure and the resulting solid was partitioned
between dichloromethane (50 mL) and water (50 mL). After removing
the aqueous phase, the organic solution was washed with additional water
(2 × 50 mL), dried (MgSO4), filtered, and the filtrate concentrated under
reduced pressure to give the crude material as a pink solid. Purification by
flash chromatography (1:3 ethyl acetate:hexane) gave the desired material
as a pale yellow solid (1.94 g, 72%). 1H NMR (DMSO-d6, 300 MHz,) δ 1.15
(t-Bu, s, 9H), 3.43 (N-Me, s, 3H), 8.44 (ArH, s, 1H), 13.10 (NH, br s, 1H).
13C NMR (CDCl3, 75 MHz) δ27.7, 38.2, 42.5, 71.0, 149.7, 153.2, 157.8, 193.6.
MS (EI +ve) 335 (5%, M+), 279 (15), 278 (100), 152 (13), 123 (13),
83 (29). HRMS (EI +ve) calcd for C10 H14N3O2I 335.0130 (M+), found
335.0120.
N-{5-[4-(tert-Butyl-dimethyl-silanyloxy)-5-hydroxymethyl-2,5-
dihydro-furan-2-yl]-1-methyl-4-oxo-1,2,3,4-tetrahydro-pyrimidin-2-
yl}-2,2-dimethyl-propionamide 18
DMF (20 mL) was added to a mixture of palladium acetate (0.10 g,
0.44 mmol) and triphenyl arsine (0.34 g, 1.11 mmol) under an Ar at-
mosphere. The reaction mixture was stirred, and the initially clear yellow
solution became cloudy within approximately one minute. After 20 minutes
a solution of the iodoheterocycle 17 (1.85 g, 5.53 mmol), the glycal 1 (2.35 g,
6.64 mmol) and tri-n-butylamine (2.04 mL, 8.58 mmol) in DMF (10 mL)
(prepared in a different flask under an Ar atmosphere) was added by syringe
in one lot. This flask was washed with additional DMF (2 × 5 mL), and
the washings also added to the reaction mixture, which was now a clear
orange solution. The reaction mixture was heated to 60◦C. After 3 days,
TLC (silica: ethyl acetate:hexane, 1:3) showed that there was no starting
material remaining. The reaction mixture was removed from the heat,
allowed to cool, and the solvent removed under reduced pressure (high

Diaminopyrimidine and Pseudoisocytidine Derivatives
289
vacuum pump) without the use of a heat source. The resulting dark brown
oil was dissolved in methanol, adsorbed onto silica, and purified by flash
chromatography (silica: ethyl acetate:hexane, 2:5) to give an impure sample
of the desired product (1.64 g), as well as some dehalogenated heterocycle
(0.23 g, 20%). The impure material was dissolved in a small volume of
1:3 ethyl acetate:hexane, and within approximately one minute, some of
the desired material crystallized from solution as a white solid (0.62 g).
The filtrate was concentrated under reduced pressure to dryness, and this
was repeated to give an additional crop of material (0.15 g). The filtrate
was again concentrated under reduced pressure to dryness and the solid
dissolved in a small amount of 1:5 ethyl acetate:hexane, which gave more
material (0.30 g). This filtrate was concentrated to dryness, and purified
by flash chromatography (silica: ethyl acetate:hexane, 1:3) to give more of
1
the desired product (0.28 g). Total yield: 1.35 g, (44%). H NMR (CDCl3,
500 MHz) δ1.06 (s, 9H, C(CH3)3,), 1.18 (s, 9H, C(CH3)3), 2.20 (dd, J =
7.7, 5.1 Hz, 1H, 5ꢁ-OH), 3.33 (s, 3H, N-CH3), 3.85 (ddd, J = 12.0, 5.1, 2.6,
1H, H5ꢁa), 3.89 (ddd, J = 12.0, 7.0, 2.6 Hz, 1H, H5ꢁb), 4.30 (s br, 1H, H2ꢁ),
4.71 (dq, J = 3.7, 2.6 Hz, 1H, H4ꢁ), 5.52 (dd, J = 3.7, 1.2 Hz, 1H, H1ꢁ),
7.02 (s, 1H, H6), 7.38–7.49 (m, 6H, ArH), 7.72 (dd, J = 7.9, 1.4 Hz, 2H,
ArH) and 12.93 (br s, 1H, NH). 13C NMR (CDCl3, 75 MHz) δ19.4, 26.5,
27.8, 38.1, 42.3, 62.3, 78.2, 83.6, 101.3, 117.7, 128.0, 128.2, 130.4, 130.5, 2 ×
131.4, 135.5, 136.0, 143.4, 150.9, 153.0, 160.0 and 193.1. HRMS (FAB) calcd
for C31H40N3O5Si 562.2731 (MH+), found 562.2737.
N-{5-[5-hydroxymethyl-4-oxo-tetrahydro-furan-2-yl]-1-methyl-4-
oxo-1,4-dihydro-pyrimidin-2-yl}-2,2-dimethyl-propionamide 19
A solution of TBAF in THF (3.00 mL, 1.0 M, 3.00 mmol) was added
to a solution of the coupled product 18 (1.124 g, 2.00 mmol) in THF
(4 mL) which was cooled in an ice/water bath under an Ar atmosphere.
The reaction mixture immediately became yellow, and after 1 minute TLC
(silica: ethyl acetate:hexane, 1:1) showed that there was no starting material
remaining. The reaction was quenched by addition of methanol (2 mL)
and the reaction mixture was concentrated under reduced pressure. The
resulting yellow oil was purified twice by flash chromatography (silica: ethyl
acetate:hexanes, 3:1) to give the desired product as a pale yellow foam (0.58
1
g, 90%). H NMR (CDCl3, 500 MHz) δ1.22 (s, 9H, C(CH3)3,), 2.70 (dd,
J = 18.2, 10.8 Hz, 1H, H2ꢁa), 2.85 (dd, J = 18.2, 6.8 Hz, 1H, H2ꢁb), 2.97
(br t, J = 6.2 Hz, 1H, 5ꢁOH), 3.54 (s, 3H, NCH3), 3.90–3.94 (m, 2H, H5ꢁa,
H5ꢁb), 4.03 (t, J = 2.8 Hz, 1H, H4ꢁ), 5.00 (d, J = 10.8, 6.8 Hz, 1H, H1ꢁ), 7.49
(s, 1H, ArH) and 13.18 (br s, 1H, NH). 13C NMR (CDCl3, 75 MHz) δ27.8,
38.4, 42.4, 42.6, 62.1, 73.1, 82.2, 115.3, 143.2, 153.0, 160.0, 193.6 and 213.3.
HRMS (FAB) calcd for C15H22N3O5 324.1559 (MH+), found 324.1549.

290
K. W. Wellington et al.
Pivaloylated 1-Methyl-2ꢁ-deoxypseudoisocytidine 20
Sodium triacetoxyborohydride (0.55 g, 2.48 mmol) was added in one
lot to a solution of the hydroxyketone 19 (0.53 g, 1.65 mmol) in acetonitrile
(8.00 mL) and acetic acid (4.00 mL) under an Ar atmosphere. TLC (silica:
ethyl acetate) indicated that there was no starting material after 12 minutes.
The reaction was quenched by the addition of acetone, and the reaction
mixture concentrated under reduced pressure. The resulting pale yellow
gum was dissolved in methanol, adsorbed onto silica, and purified by flash
chromatography (silica: ethyl acetate) to give the desired material as a white
1
solid (0.40 g, 62%). H NMR (CDCl3, 300 MHz) δ1.21 (s, 9H, C(CH3)3,),
1.95 (d, J = 3.5 Hz, 1H, 3ꢁ-OH), 2.10 (ddd, J = 13.2, 5.6, 1.4 Hz, 1H, H2ꢁa),
2.41 (ddd, J = 13.2 10.5, 5.6 Hz, 1H, H2ꢁb), 3.51 (s, 3H, NCH3), 3.57 (dd,
J = 9.5, 2.9 Hz, 1H, 5ꢁ-OH), 3.69 (ddd, J = 11.9, 9.5, 2.7 Hz, 1H, H5ꢁa), 3.82
(ddd, J = 11.9, 2.9, 2.7 Hz, 1H, H5ꢁb), 4.03 (dt, J = 4.7, 2.7 Hz, 1H, H4ꢁ),
4.52–4.57 (m, 1H, H3ꢁ), 4.89 (dd, J = 10.5, 5.6 Hz, 1H, H1ꢁ), 7.69 (d, J = 0.5
Hz, 1H, ArH) and 13.12 (br s, 1H, NH). 13C NMR (CDCl3, 75 MHz) δ27.8,
38.3, 40.9, 42.3, 63.5, 74.0, 88.0, 116.2, 143.2, 153.0, 160.4 and 193.6. HRMS
(FAB) calcd for C15H22N3O5 324.1559 (MH+), found 324.1549.
1-Methyl-2ꢁ-deoxypseudoisocytidine 21
The protected nucleoside 20 (0.03 g, 0.1 mmol) was dissolved in a solu-
tion of saturated methanolic ammonia (25 mL), stoppered and the reaction
mixture stirred for 5 days. The reaction mixture was then concentrated
under reduced pressure and the resulting film was dissolved in water (5 mL)
and washed with dichloromethane (6 × 10 mL). The aqueous solution was
filtered to remove particulate matter and the filtrate freeze dried to give the
1
desired product as a white solid (0.01 g, 46%). H NMR (D2O, 500 MHz)
δ1.95 (ddd, J = 13.5, 10.1, 6.0 Hz, 1H, H2ꢁa), 2.15 (ddd, J = 13.5, 5.9, 2.1
Hz, 1H, H2ꢁb), 3.39 (s, 3H, NCH3), 3.55 (dd, J = 12.2, 5.1 Hz, 1H, H5ꢁa),
3.63 (dd, J = 12.2, 4.1 Hz, 1H, H5ꢁb), 3.90 (ddd, J = 5.1, 4.1, 2.8 Hz, 1H,
H4ꢁ), 4.27 (dddd, J = 6.0, 2.8, 2.1, 0.6 Hz, 1H, H3ꢁ), 4.92 (dddd, J = 10.1,
5.9, 0.9, 0.6 Hz, 1H, H1ꢁ) and 7.47 (d, J = 0.9 Hz, 1H, ArH). 13C NMR
(D2O, 75 MHz) δ38.7, 39.8, 62.3, 72.9, 74.9, 86.6, 117.3, 142.8, 155.9 and
171.3. HRMS (EI) calcd for C10H15N3O4 241.1063, found 241.1055.
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