Synthesis and photophysical properties of 7-deaza-2′-deoxyadenosines bearing bipyridine ligands and their Ru(ii)-complexes in position 7

Article abstract of DOI:10.1039/b805632c

The synthesis of the title 7-deazaadenine 2′-deoxyribonucleosides bearing bipyridine, phenanthroline or terpyridine ligands linked to position 7 via an acetylene or phenylene spacer is reported based on aqueous cross-coupling reactions of unprotected 7-io

Full text of DOI:10.1039/b805632c

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Synthesis and photophysical properties of 7-deaza-2ꢀ-deoxyadenosines bearing
bipyridine ligands and their Ru(II)-complexes in position 7†
Milan Vra´bel,a Radek Pohl,a Ivan Votruba,a Mohsen Sajadi,b Sergey A. Kovalenko,b Nikolaus P. Ernstingb and
Michal Hocek*a
Received 3rd April 2008, Accepted 13th May 2008
First published as an Advance Article on the web 16th June 2008
DOI: 10.1039/b805632c
The synthesis of the title 7-deazaadenine 2ꢀ-deoxyribonucleosides bearing bipyridine, phenanthroline or
terpyridine ligands linked to position 7 via an acetylene or phenylene spacer is reported based on
aqueous cross-coupling reactions of unprotected 7-iodo-7-deaza-2ꢀ-deoxyadenosine with
ligand-functionalized acetylenes or boronic acids. The aqueous cross-coupling with acetylene or
boronate building blocks containing the Ru(bpy)3-type of complex gave the corresponding
Ru-containing nucleosides. Photophysical and electrochemical properties were studied and the most
efficient type of complex was selected for future luminescent and redox labelling of DNA. The title
nucleosides also showed some cytostatic and anti-HCV activities.
nucleoside triphosphates (dNTPs).7 It can be even combined with
cross-coupling reactions of dNTPs, and we have recently used this
Introduction
novel approach8 for the synthesis of DNA bearing amino acids,9
ferrocenes10 and amino- and nitrophenyl groups.11 However, we9
and others7c have shown that 8-substituted purine dNTPs are
poor substrates for DNA polymerases (presumably due to their
preference for syn-conformation and steric hindrance between the
substituent and DNA backbone) and should be replaced by 7-
substituted 7-deazapurine dNTPs.
In order to be able to proceed to polymerase incorporation
of purines bearing bipyridine ligands and their Ru complexes,
we had to first develop the synthetic methodology for the
introduction of the bipyridine and phenanthroline ligands linked
via acetylene or phenylene, as well as the corresponding Ru(II)-
complexes, to position 7 of 7-deaza-2ꢀ-deoxyadenosine and study
the electrochemical and photophysical properties of the resulting
labeled nucleosides and this is the topic of the present paper.
Complexes of bipyridine and phenanthroline ligands with tran-
sition metals possess1 unique electrochemical and photophysical
properties and thus could be used for electrochemical or lumi-
nescent labeling of biomolecules. Some of the phenanthroline
complexes, which are efficient DNA intercalators, have been
extensively used as luminescent and electroactive DNA labels.2
Attachment of probes based on metal complexes directly to
the nucleobase via conjugate linkers should increase efficiency
of the charge transfer and thus enhance sensitivity. Covalently
bound conjugates of pyrimidine nucleotides and phenanthroline
complexes of Ru and Os have been studied as luminescence probes
for DNA hybridization and charge transfer through DNA.3 The
corresponding labeling of purine bases has not been studied
until recently, when we have reported4 on the synthesis and
electrochemistry of model 9-benzyladenine derivatives bearing
oligopyridine ligands or their Ru or Os complexes linked to
position 8 via conjugate phenylene or acetylene tethers that are
designed to transmit electronic changes on the nucleobase to
the electroactive label. Later on, we reported5 the synthesis of
a 2ꢀ-deoxyadenosine nucleoside bearing bipyridine ligands and
the corresponding Ru complexes in position 8. However, our
follow-up study on chemical incorporation of the correspond-
ing protected 8-substituted 2ꢀ-deoxyadenosine phosphoramidites
on solid support was unsuccessful due to very low coupling
yields.6
Results and discussion
Synthesis of 7-deaza-2ꢀ-deoxyadenosine conjugates
In order to attach bipyridine-type ligands linked via an
acetylene or phenylene linker to position 7 of 7-deaza-2ꢀ-
deoxyadenosine,12 we have followed our previous study5 on 8-
substituted-2ꢀ-deoxyadenosines and utilized aqueous-phase cross-
coupling reactions.13 The Sonogashira cross-coupling reactions
of ethynyl oligopyridines 2a and 2b with 7-iodo-7-deaza 2ꢀ-
deoxyadenosine (1) were performed in DMF (rather than in H2O–
CH3CN which caused problems in the 8-substituted adenosine
series5) in the presence of Pd(OAc)2, water soluble ligand P(Ph-
SO3Na)3 (TPPTS), CuI and Et3N to afford the desired ethynyl
conjugates 4a,b in excellent yields of 91 and 82% respectively
(Scheme 1, Table 1). The aqueous-phase Suzuki–Miyaura cross-
coupling reaction of boronates 3a,c,d with 1 also proceeded well.
Using a mixture of H2O–CH3CN (2 : 1) as solvent, in the presence
of Pd(OAc)2, TPPTS and Cs2CO3 as a base, the phenylene-bridged
conjugates 5a,c,d were prepared in excellent yields (Scheme 1,
An alternative method for the construction of functionalized nu-
cleic acids is based on polymerase incorporations of base-modified
aInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of
the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam.
2, CZ-16610, Prague 6, Czech Republic. E-mail: hocek@uochb.cas.cz;
Fax: +420 220183559; Tel: +420 220183324
bInstitut fu¨r Chemie, Humboldt Universita¨t zu Berlin, Brook-Taylor-Str. 2,
D-12489, Berlin, Germany
† Electronic supplementary information (ESI) available: Complete exper-
imental section, characterization data, copies of NMR spectra. See DOI:
10.1039/b805632c
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All the cross-coupling reactions of Ru-containing acetylenes and
boronates were performed in a mixture of H2O–CH3CN in
order to be further applicable for labeling of nucleoside triphos-
phates (dNTPs). The Sonogashira reaction of Ru(II)-containing
acetylenes 6a,b with the nucleoside 1, using Pd(OAc)2–TPPTS, CuI
and Et3N, gave the corresponding nucleoside Ru-complexes 8a,b
in moderate yields of 47 and 59% respectively (Scheme 2, Table 2).
Scheme 1 Synthesis of 7-deaza 2ꢀ-deoxyadenosine conjugates. Reagents
and conditions: i) Pd(OAc)2 (5 mol%), TPPTS (2.5 equiv. to Pd), Et3N
(10 equiv.), CuI (10 mol%), DMF; ii) Pd(OAc)2 (5 ;mol%), TPPTS
(2.5 equiv. to Pd), Cs2CO3 (3 equiv.), H2O–CH3CN = 2 : 1.
Table 1 Synthesis of 7-deaza 2ꢀ-deoxyadenosine conjugates
Entry
Reagent
Product
Yield (%)
1
2
3
4
5
2a
2b
3a
3c
3d
4a
4b
5a
5c
5d
91
82
95
96
78
Scheme 2 Synthesis of 7-deazaadenine nucleosides bearing Ru(II) com-
plexes. Reagents and conditions: i) Pd(OAc)2 (5 mol%), TPPTS (2.5 equiv.
to Pd), Et3N (10 equiv.), CuI (10 mol%), H2O–CH3CN = 2 : 1; ii) Pd(OAc)2
(5 mol%), TPPTS (2.5 equiv. to Pd), Cs2CO3 (3 equiv.), H2O–CH3CN =
2 : 1.
Table 1). The yields of all these reactions were substantially better
than in the case of 8-substituted adenosines.5 We have shown
that a catalytic system consisting of Pd(OAc)2 and TPPTS is
applicable for efficient protection-free attachment of oligopyridine
type ligands to position 7 of 7-deaza-2ꢀ-deoxyadenosine.
Table 2 Synthesis of 7-deazaadenine nucleosides bearing Ru(II)
complexes
Synthesis of 7-deazaadenine nucleosides bearing Ru(II) complexes
Entry
Reagent
Product
Yield (%)
The next goal of our study was to prepare the corresponding Ru(II)
complexes of the 7-deazapurine nucleosides. In analogy to our
previous results, we have applied the direct aqueous-phase cross-
coupling reactions of Ru-containing acetylene 6 and boronate
7 building blocks4 with 7-iodo-7-deaza-2ꢀ-deoxyadenosine (1).
1
2
3
4
5
6a
6b
7a
7c
7d
8a
8b
9a
9c
9d
47
59
95
73
76
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Table 3 Photophysical properties of the 7-bipyridine-derivatives of 7-
In both cases some byproducts were formed, probably due to the
decomposition of the starting materials. However, the reactions
still proceeded much better when compared to 8-substituted-2ꢀ-
deoxyadenosine analogs (16% for 6a and 0% for 6b). On the other
hand, the aqueous-phase Suzuki–Miyaura cross-coupling reaction
of Ru-containing boronic acids proceeded relatively cleanly in
accord with our previous results.5
deazaadenine nucleosides
UV-Vis,
Entry
Compd
4a
k/nm, (e)a
Excitation/nmb
Emission/nmb
1
2
3
4
5
282 (2.8),
321 (2.4)
285 (3.5),
336 (2.5)
291 (3.1),
325 (3.0)
283 (5.1),
322 (4.5)
253 (4.7),
284 (5.4)
351
368
340
330
343
406
427
395
424
425
4b
Reactions of the boronates 7a,c,d with 7-iodo-7-deaza-2ꢀ-
deoxyadenosine (1) in the presence of Pd(OAc)2–TPPTS and
Cs2CO3, gave the corresponding complexes 9a,c,d in good yields
(Scheme 2, Table 2). The Ru(II)-containing complexes were
isolated by column chromatography using a mixture of H2O–
CH3CN–sat. KNO3 as eluent. The only exception was the isolation
of complex 9c where even repeated column chromatography did
not give pure compound and, therefore, it had to be isolated
by preparative loose layer TLC using the same eluent. Final
re-precipitation by saturated aqueous solution of NH4PF6 gave
5a
5c
5d
a In CHCl3, 1.6 × 10−5 M solutions, extinction coefficients e × 104 in
M−1.cm−1
;
b 1.6 × 10−4 M solutions in CHCl3.
−
the desired Ru(II) complexes as PF6 salts. Due to the chirality
of the Ru-complexes, the nucleosides 8 and 9 were isolated
as inseparable (chromatographically homogeneous) mixtures of
diastereoisomers (1 : 1).
7-deazaadenosine conjugates 4 and 5 exhibit intense overlapping
p–p* transitions of the aromatic diimine ligands14 at 280 nm. The
excitation of a chloroform solution of this nucleoside conjugates
at absorption maxima exhibited intensive emissions centered at
415 nm (Fig. 1, Table 3).
Photophysical and redox properties of the 7-substituted
7-deazaadenine nucleosides
The emission spectra of the Ru complexes (both nucleosides
8 and 9 and parent starting acetylenes 6 and boronates 7) are
summarized in Table 4 and one example is given in Fig. 2.
The intense 288 nm band indicates a p→p* (LC) transition in
In order to characterize the new modified 7-deazaadenine nucleo-
sides and to explore their potential applications in DNA labeling,
we have examined their photophysical and redox properties. First
we measured UV-Vis spectra. As shown in Fig. 1 the bipyridine
the bipyridine ligands, and the 450 nm band corresponds to a
2+ 15
d→p* (1MLCT) transition in analogy with Ru(bpy)3
. On the
other hand, the Ru(II) complexes of nucleosides 8 and 9 showed
unexpectedly weak red luminescence. Creation of the 1MLCT
state is followed immediately, in <100 fs, by intersystem crossing
to the lowest MLCT state with near-unit quantum yield.16 The
3
lowest triplet is responsible for the weak emission around 650 nm
and photochemical redox reactions; it has an oxidized Ru(III)
core while the corresponding electron is localized on one of the
ligands.17 Fluorescence is expected before electron localisation, but
this period is still under hot debate.18
Emission quantum yields Uem in acetonitrile are summarized
in Table 4 where the Ru(II) complexes of acetylenes and phenyl-
boronates, are compared to the corresponding Ru-complexes of 7-
deazaadenosine. Standard errors refer to absolute yields (note that
a comparison between a complex and its conjugate is significantly
more accurate than the cited errors imply). Three kinds of behavior
are observed. (1) 6b and 8b have a quantum yield between 2–3%,
2+ 15
comparable to Ru(bpy)3
.
Therefore, nucleoside 8b may be in
principle used for optical labeling of DNA strands. (2) Coupling
of the Ru complex 6a to form 8a leads to a significant decrease of
Uem from 18.8 to 2. 1 ×10−4. (3) For the remaining pairs, Uem is
very low in the pure Ru(II) complex but increases slightly upon
coupling to 7-deazaadenine. Thus, the emission enhancement
which is observed upon intercalation into duplex DNA19 is already
incipient when the nucleoside is attached. Therefore it can be
concluded that only the complex 8b (where Ru(bpy)3 is linked
through the 3-position of bipyridine via acetylene to position
7 of 7-deazaadenine) is promising for luminescent labelling of
DNA, while the other types of linkages (attachment of acetylene
or phenylene to the 2-position of bipyridine or phenanthroline or
to 4ꢀꢀ-position of terpyridine) are not efficient.
Fig. 1 UV/Vis and emission spectra of 7-deazaadenine nucleoside
conjugates.
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Table 4 Photophysical and redox properties of the Ru-complexes and Ru-containing 7-deazaadenine nucleosides
Entry
Compd
UV-VIS, k/nm, (e)a
Emission/nmb
Uem/10−4c
Eox (V)d
1
2
3
4
5
6
7
8
9
6a
6b
7c
7d
8a
8b
9a
9c
9d
243 (3.5), 287 (8.2), 448 (1.8)
246 (3.9), 287 (9.8), 451 (1.8)
268 (9.6), 287 (10.8), 448 (2.7)
272 (9.0), 307 (10.9), 481 (3.3)
288 (8.2), 448 (1.4)
254 (3.6), 287 (9.8), 384 (2.6)
245 (3.3), 289 (7.3), 450 (1.2)
287 (7.1), 448 (1.0)
637
664
654
18.8 1.3
228 15
3.5 0.3
0.9 0.3
2.1 0.3
289 20
1.9 0.3
4.3 0.4
2.4 0.4
—
1.175e
1.165e
—
∼ 715
639
1.205
1.200
1.200
1.210
1.200
665
667
648
633
273 (5.1), 308 (6.4), 485 (2.3)
a Compounds 4 and 5 in CHCl3, 8 and 9 in acetonitrile, all 1.6 × 10−5 M solutions, extinction coefficients e × 104 in M−1 cm−1
.
b From a lognormal fit to
the emission band. c With standard errors. d Oxidation potentials of Ru(II)/Ru(III) on PGE. e taken from ref. 4
The oxidation of the Ru(II) complexes 8 and 9 on PGE
(pyrolitic graphite electrode) showed the peak at around +1.2 V
against Ag/AgCl/3 M KCl electrode, due to oxidation of the
Ru atom in the complexes (Table 4). Compared to unsubstituted
[Ru(bpy)3]2+ (1.095 V) and acetylene 6b or boronate 7c (1.075 and
1.065, respectively), the apparent redox potentials of the Ru(II)
nucleosides were significantly more positive as a result of electron-
withdrawing effect of the deazaadenine moiety, in agreement
with our previous results with 9-Bn-adenine model compounds.4
The different oligopyridine ligands (bpy, phen or tpy) in these
complexes do not show any significant influence on the redox
potential values.
Biological activity
Although the main goal was to develop electrochemical and
luminescent DNA labelling, any novel nucleosides can also
possess biological effects and there were previous precedents22 of
interesting biological activities of some Ru complexes. Therefore,
all the compounds prepared within this study were also subjected
to biological activity screening (Table 5). The cytostatic activity
in vitro (inhibition of cell growth) was studied on the following
cell cultures: (i) mouse leukemia L1210 cells (ATCC CCL 219);
(ii) human promyelocytic leukemia HL60 cells (ATCC CCL 240);
(iii) human cervix carcinoma HeLaS3 cells (ATCC CCL 2.2) and
(iv) human T lymphoblastoid CCRF-CEM cell line (ATCC CCL
119).23 Terpyridine nucleoside 5d showed the most significant
cytostatic effect in all the cell-lines studied, while bipyridine
nucleosides 4b and 5c were less effective. All the other compounds,
including the Ru complexes were entirely inactive. This is in accord
with our previous report5 on 8-substituted 2ꢀ-deoxyadenosine,
where the terpyridine derivative was the most active.
The title modified nucleosides were also tested up to 100 lM
for antiviral activity in the HCV genotype 1b replicon.24,25 Again,
the terpyridine nucleoside 5d showed a very strong effect but,
unfortunately, the compound is toxic at the same concentration.
Most of the other bipyridine nucleosides showed activities at low
lM concentrations but, again, accompanied by toxicity in Huh-7
and/or MT-4 cells. The Ru complexes were much less effective.
Fig.
2
Absorption and emission spectra of the labelled deaza-
-deoxyadenosine 8b (blue and red lines). The absorption of the Ru(II)
complex 6b is shown for comparison (gray). Dashed lines repeat the
absorption spectra, but scaled by 0.2. The solvent was acetonitrile
throughout.
Transient absorption spectra are shown in Fig. 3 for 9d (the
other investigated conjugates are in the ESI†). Excitation was
performed with 40 fs pump pulses at 403 nm on the blue side
of the 1MLCT band. Ground-state bleaching and excited-state ab-
sorption (ESA) is observed immediately. Stimulated emission S1 →
S0 is not resolved, indicating that the triplet manifold is reached
on a timescale < 20 fs, in agreement with recent fluorescence-
upconversion results.18 Transient spectra for the Ru(tpy)2-7-deaza-
adenosine 9d may be compared with those for 7d alone, which has
a lifetime of 120 ps in acetonitrile.20 In the present case, phenyl
extension of a tpy ligand leads to an increase of ESA in the range
k ≥ 530 nm, and the lifetime is increased to 720 ps. A characteristic
feature of 9d is a rise of ESA on a 10 ps time scale, an effect
which has been attributed to structural relaxation of the extended
ligand until the reduced-ligand delocalization is complete.21 With
the phenyl-linked complexes 9a and 9c a picosecond ESA rise is
not observed. Small changes with a 5 ps time constant are found
for all compounds studied across the entire spectral range; they
are attributed to vibrational relaxation of the 3MLCT state.
Conclusions
The synthesis of 7-deazaadenine 2ꢀ-deoxyribonucleosides bearing
bipyridine-type ligands in position 7 by direct cross-coupling
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reactions proceeded much better than in the previously reported
8-substituted adenosine series. The title nucleosides are promis-
ing building blocks for the labelling of DNA and, therefore,
their photophysical and redox properties have been studied.
All the bipyridine-ligand containing 7-deaza-2ꢀ-deoxyadenosine
nucleosides show strong blue fluorescence. On the other hand,
the Ru-complexes show only very weak red luminescence with
very low quantum yields. The only exception is compound 8b
(where Ru(bpy)3 is linked through the 3-position of bipyridine
via acetylene to position 7 of 7-deazaadenine) which gives a
moderate (but still useful) quantum yield of 0.03 and, therefore, it is
promising for luminescent labelling of DNA. All the Ru complexes
gave electrochemical oxidation at ca. 1.2 V and thus could be used
for electrochemical DNA labelling. The follow-up studies on the
preparation of modified dNTPs bearing Ru and Os complexes of
7-[(bipyridin-3-yl)ethynyl]-2ꢀ-deoxyadenosine triphosphates and
other related modified dNTPs, their incorporation to DNA and
applications in bioanalysis are under way and will be published
separately.
Experimental section
All cross-coupling reactions were performed under argon atmo-
sphere. Et3N was degassed in vacuo and stored over molecular
sieves under argon. Compounds 1,9 2a,b, 3a,c,d, 6a,b, 7a,c,d,4 were
prepared according to the literature procedures. Other chemicals
were purchased from commercial suppliers and used as received.
Typical experimental procedures and representative examples of
characterization of compounds are given below. The complete
detailed experimental section including characterization data for
all compounds is in the Electronic Supplementary Information
(ESI)†.
General procedure for Sonogashira cross-coupling reaction of
7-iodo-7-deaza-2ꢀ-deoxyadenosine (1) with ligands 2a,b
DMF (2.5 ml) and Et3N (0.35 ml, 2.5 mmol, 10 equiv.)
were added to an argon-purged flask containing nucleoside 1
(94 mg, 0.25 mmol), an alkyne 2a,b (0.375 mmol, 1.5 equiv.)
and CuI (4.8 mg, 0.025 mmol, 10 mol%). In a separate flask,
Pd(OAc)2 (2.8 mg, 0.0125 mmol, 5 mol%), P(Ph-SO3Na)3 (18 mg,
0.0313 mmol, 2.5 equiv. to Pd) were combined, evacuated and
purged with argon followed by addition of DMF (0.5 ml). This
solution of catalyst was added through a syringe to the reaction
mixture which was then stirred at 75 ◦C until complete consump-
tion of the starting material. The solvent was evaporated in vacuo.
The products were purified by silica gel column chromatography
using CHCl3 and MeOH (1% to 10%) as eluent.
Fig. 3 Transient absorption spectra (top) and kinetics (below) of 9d
in acetonitrile upon 403 nm excitation. Only the bleached absorption
band and ESA are seen. Stimulated emission S1 → S0 is not resolved,
indicating that the triplet manifold is reached on a timescale < 20 fs.
Vertical arrows show signal evolution. The band integral 550–684 nm
(right) rises before 20 ps, followed by uniform decay with a 720 ps time
constant.
7-Deaza-7-[(2ꢀꢀ,2ꢀꢀꢀ-bipyridin-6ꢀꢀ-yl)ethynyl]-2ꢀ-deoxyadenosine (4a)
The ◦product was isolated as white powder 97 mg (91%). Mp 115–
1
reactions of bipiridine-linked boronic acids and acetylenes with
unprotected 7-iodo-7-deaza-2ꢀ-deoxyadenosine in the presence
of the Pd(OAc)2–TPPTS catalytic system, in H2O–acetonitrile
or in DMF was developed. Analogous aqueous-phase cross-
coupling reactions were also used for the attachment of the
corresponding Ru-complexes of bipyridine ligands through cross-
coupling reactions of the unprotected nucleoside with boronic
acid or acetylene derivatives of Ru-complexes. In general, the
120 C. H NMR (600 MHz, DMSO-d6): 2.24 (ddd, 1H, Jgem
=
13.2, J2 b,1 = 6.0, J2 b,3 = 2.8, H-2ꢀb); 2.53 (ddd, 1H, Jgem = 13.2,
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
J2 a,1 = 8.0, J2 a,3 = 5.8, H-2 a); 3.55 (ddd, 1H, Jgem = 11.7, J5 b,OH
=
5.9, J5 b,4 = 4.4, H-5ꢀb); 3.61 (ddd, 1H, Jgem = 11.7, J5 a,OH = 5.2,
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ ꢀ
J5 a,4 = 4.6, H-5 a); 3.86 (ddd, 1H, J4 ,5 = 4.6, 4.4, J4 ,3 = 2.5, H-4 );
4.39 (m, 1H, J3 ,2 = 5.8, 2.8, J3 ,OH = 4.1, J3 ,4 = 2.5, H-3ꢀ); 5.12
ꢀ
ꢀ
ꢀ
ꢀ ꢀ
(dd, 1H, JOH,5 = 5.9, 5.2, OH-5ꢀ); 5.32 (d, 1H, JOH,3 = 4.1, OH-3ꢀ);
ꢀ
ꢀ
6.54 (dd, 1H, J1 ,2 = 8.0, 6.0, H-1ꢀ); 6.93 (bs, 2H, NH2); 7.50 (ddd,
ꢀ
ꢀ
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Table 5 Cytostatic and antiviral activity of nucleosides
Cytostatic activity IC50/lMa
HCV antiviral activity/lM
Compd
HeLa S3
HL60
CCRF-CEM
EC50 repliconb
CC50 Huh7c (MT-4)d
4a
4b
5a
5c
5d
8a
8b
9a
9c
9d
n.a.
13.18 0.81
n.a.
6.77 0.37
3.29 0.22
n.a.
n.a.
n.a.
n.a.
n.a.
n.a.
n.a.
n.a.
8.98 1.30
2.54 0.51
n.a.
n.a.
n.a.
n.a.
4.15 0.06
n.a.
1.77 0.05
0.57 0.07
n.a.
n.a.
n.a.
n.a.
n.a.
13
1
16
>100 (7)
2
>100 (1)
1
1
0.15
32
> 100
23
0.66
>100
>100
>100
>100 (19)
>100
n.a.
n.a.
12
23
a Concentration of a compound needed to reduce population growth by 50% in vitro (XTT test). b Antiviral activity in HCV-Con1 replicon (N = 2).
c MTT measurement of cellular toxicity in Huh-7 cells harboring con-1 replicon (N = 2). d Cellular toxicity in MT-4 cells (N = 2).
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀ
ꢀ
ꢀ
ꢀ
1H, J5
= 7.4, J5
= 4.7, J5
= 1.2, H-5ꢀꢀꢀ); 7.75 (dd, 1H,
J5 b,4 = 4.3, H-5ꢀb); 3.60 (dd, 1H, Jgem = 11.7, J5 a,4 = 4.5, H-
,4
,6
,3
ꢀꢀ
5ꢀa); 3.86 (ddd, 1H, J4 ,5 = 4.5, 4.3, J4 ,3 = 2.5, H-4ꢀ); 4.39 (bm,
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀ
ꢀ
ꢀ ꢀ
J5 = 7.7, J5 = 1.1, H-5 ); 7.98 (ddd, 1H, J4
= 8.0, J4
=
,4
,3
,3
,5
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀ ꢀꢀ
,3
ꢀꢀ ꢀꢀ
7.4, J4
= 1.8, H-4ꢀꢀꢀ); 8.01 (dd, 1H, J4 = 8.0, J4 = 7.7, H-
1H, H-3ꢀ); 5.10 (bs, 1H, OH-5ꢀ); 5.31 (bs, 1H, OH-3ꢀ); 6.35 (bs,
,6
,5
4ꢀꢀ); 8.04 (s, 1H, H-6); 8.19 (s, 1H, H-2); 8.378 (dd, 1H, J3
=
=
2H, NH2); 6.62 (dd, 1H, J1 ,2 = 8.2, 6.1, H-1ꢀ); 7.50 (ddd, 1H,
ꢀꢀ ꢀꢀ
ꢀ ꢀ
,4
8.0, J3
= 1.1, H-3ꢀꢀ); 8.383 (ddd, 1H, J3
= 8.0, J3
J5
= 7.4, J5
= 4.7, J5
= 1.1, H-5ꢀꢀꢀ); 7.65 (m, 2H, H-o-
ꢀꢀ ꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,3
,5
,4
,5
,4
,6
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,5
1.2, J3
= 0.9, H-3ꢀꢀꢀ); 8.71 (ddd, 1H, J6
= 4.7, J6
= 1.8,
phenylene); 7.67 (s, 1H, H-6); 8.02 (ddd, 1H, J4
= 8.0, J4
=
,6
,5
,4
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
J6
= 0.9, H-6ꢀꢀꢀ).13C NMR (151 MHz, DMSO-d6): 40.16 (CH2–
7.4, J4
= 1.8, H-4ꢀꢀꢀ); 8.06 (dd, 1H, J4
=,37.9, J4
= 7.7,
,3
,6
,5
,3
2ꢀ); 62.07 (CH2-5ꢀ); 71.16 (CH-3ꢀ); 83.11 (bpy-C≡C); 83.59 (CH-
1ꢀ); 87.88 (CH-4ꢀ); 91.76 (bpy-C≡C); 93.97 (C-5); 102.51 (C-4a);
120.06 (CH-3ꢀꢀ); 120.89 (CH-3ꢀꢀꢀ); 124.84 (CH-5ꢀꢀꢀ); 126.97 (CH-
5ꢀꢀ); 127.94 (CH-6); 137.78 (CH-4ꢀꢀꢀ); 138.24 (CH-4ꢀꢀ); 142.38 (C-
6ꢀꢀ); 149.62 (CH-6ꢀꢀꢀ); 149.80 (C-7a); 153.25 (CH-2); 154.66 (C-2ꢀꢀꢀ);
155.92 (C-2ꢀꢀ); 157.86 (C-4). ESI MS: m/z (%) 451.1 (100) [M+ +
Na], 429.1 (93) [M+ +H], 313.3 (70) [M+ − dRf]. C23H20N6O3·2H2O
(428.44) calcd. C 59.48, H 5.21, N 18.09; found C 59.73, H 4.57,
N 17.94%. IR (KBr): 3437, 2211, 1631, 1569, 1427, 1094 cm−1.
UV/Vis (CH2Cl2) kmax (e) 282 (27724). Fluorescence (CH2Cl2):
excitation at 351 nm gave emission at 406 nm.
H-4ꢀꢀ); 8.11 (dd, 1H, J5
= 7.9, J5
= 1.0, H-5ꢀꢀ); 8.19 (s, 1H,
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,4
H-2); 8.36 (dd, 1H, J3
= 7.7, J3 ,3 = 1.0, H-3ꢀꢀ); 8.37 (m, 2H,
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,4
,5
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,6
H-m-phenylene); 8.63 (ddd, 1H, J3
= 8.0, J3
= 1.1, J3
=
0.9, H-3ꢀꢀꢀ); 8.72 (ddd, 1H, J6
= ,44 .7, J6
=,51.8, J6
= 0.9,
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,5
,4
,3
H-6ꢀꢀꢀ). 13C NMR (151 MHz, DMSO-d6): 39.84 (CH2–2ꢀ); 62.19
(CH2-5ꢀ); 71.29 (CH-3ꢀ); 83.27 (CH-1ꢀ); 87.66 (CH-4ꢀ); 100.45 (C-
4a); 116.39 (C-5); 119.32 (CH-3ꢀꢀ); 120.59 (CH-5ꢀꢀ); 120.94 (CH-
3ꢀꢀꢀ); 121.44 (CH-6); 124.59 (CH-5ꢀꢀꢀ); 127.45 (CH-m-phenylene);
129.02 (CH-o-phenylene); 135.55 (C-i-phenylene); 136.97 (C-p-
phenylene); 137.69 (CH-4ꢀꢀꢀ); 138.75 (CH-4ꢀꢀ); 149.55 (CH-6ꢀꢀꢀ);
150.75 (C-7a); 151.62 (CH-2); 155.24 (C-2ꢀꢀ); 155.33 (C-6ꢀꢀ); 155.52
(C-2ꢀꢀꢀ); 157.31 (C-4). ESI MS: m/z (%) 365.4 (100) [M+ − dRf],
481.2 (70) [M+], 503.2 (40) [M+ + Na]; C27H24N6O3·H2O (480.2)
calcd. C 65.05, H 5.26, N 16.86; found C 64.95, H 5.12, N 16.77. IR
(KBr): 3470, 3393, 1616, 1582, 1430, 1098 cm−1. UV/Vis (CH2Cl2)
kmax (e) 291 (30685). Fluorescence (CH2Cl2): excitation at 340 nm
gave emission at 395 nm.
General procedure for Suzuki–Miyaura cross-coupling reactions of
7-deaza-7-iodo-2ꢀ-deoxyadenosine (1) with ligands 3a,c,d
A mixture of H2O–CH3CN = 2 : 1 (2.5 ml) was added to an
argon-purged flask containing nucleoside 1 (94 mg, 0.25 mmol),
a boronate 3a,c,d (0.3 mmol, 1.2 equiv.) and Cs2CO3 (247 mg,
0.75 mmol, 3 equiv.). In a separate flask, Pd(OAc)2 (2.8 mg,
0.0125 mmol, 5 mol%) and P(Ph-SO3Na)3 (18 mg, 0.0313 mmol,
2.5 equiv. to Pd) were combined, evacuated and purged with argon
followed by addition of H2O–CH3CN = 2 : 1 (0.5 ml). The catalyst
mixture was then injected to the reaction mixture and the reaction
General procedure for Sonogashira cross-coupling reactions of
Ru(II) building blocks 6a,b
A mixture of H2O–CH3CN = 2 : 1 (1 ml) was added to an argon-
purged flask containing nucleoside 1 (47 mg, 0.125 mmol), an
alkyne 6a,b (0.188 mmol, 1.5 equiv.), CuI (2.4 mg, 0.0125 mmol,
10 mol%) and Et3N (0.175 ml, 1.25 mmol, 10 equiv.). In a separate
flask, Pd(OAc)2 (1.4 mg, 0.00625 mmol, 5 mol%) and P(Ph-
SO3Na)3 (9 mg, 0.0156 mmol, 2.5 equiv. to Pd) were combined,
evacuated and purged with argon followed by an addition of
H2O–CH3CN = 2 : 1 (0.5 ml). This catalyst solution was then
injected to the reaction mixture which was further stirred at 75 ◦C
until complete consumption of the starting material. The solvent
was evaporated in vacuo. The products were purified by silica gel
column chromatography using a mixture of CH3CN–H2O–sat.
◦
mixture was stirred at 80 C until complete consumption of the
starting material. The solvent was evaporated in vacuo. Products
were purified by silica gel column chromatography using CHCl3
and MeOH (1% to 10%) as eluent.
7-Deaza-7-[(2ꢀꢀ,2ꢀꢀꢀ-bipyridin-6ꢀꢀ-yl)phenyl]-2ꢀ-deoxyadenosine (5a)
The prod◦uct was isolated as a white powder 114 mg (95%). Mp
1
135–137 C. H NMR (600 MHz, DMSO-d6): 2.23 (ddd, 1H,
Jgem = 13.2, J2 b,1 = 6.1, J2 b,3 = 2.7, H-2ꢀb); 2.60 (ddd, 1H, Jgem
=
ꢀ
ꢀ
ꢀ
ꢀ
−
13.2, J2 a,1 = 8.2, J2 a,3 = 5.9, H-2ꢀa); 3.53 (dd, 1H, Jgem = 11.7,
KNO3 = 10 : 1 : 0.1 as eluent. The products were isolated as PF6
ꢀ
ꢀ
ꢀ
ꢀ
This journal is
The Royal Society of Chemistry 2008
Org. Biomol. Chem., 2008, 6, 2852–2860 | 2857
©

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salts by precipitation from a water solution by addition of sat.
NH4PF6.
which was then stirred at 80 ◦C until complete consumption of
the starting material. The solvent was evaporated in vacuo. The
products 9a,c,d were purified by silica gel column chromatography
using a mixture of CH3CN–H2O–sat. KNO3 = 10 : 1 : 0.1 as eluent.
The products were isolated as PF6− salt by precipitation from water
solution by addition of sat. NH4PF6.
Complex 8a
The product was isolated as red powder 66 mg (47%). Mp > 300
◦C. 1 : 1 mixture of diastereoisomers 1H NMR (500 MHz, acetone-
d6): 2.46 (ddd, 2H, Jgem = 13.3, J2 b,1 = 6.0, J2 b,3 = 2.8, H-2ꢀb);
ꢀ
ꢀ
ꢀ
ꢀ
Complex 9a
ꢀ
ꢀ
ꢀ
ꢀ
2.61 and 2.62 (2 × ddd, 2 × 1H, Jgem = 13.3, J2 a,1 = 7.9, J2 a,3
=
=
5.6, H-2ꢀa); 3.77, 3.81, 3.84 and 3.89 (4 × dd, 4 × 1H, Jgem
The ◦product was isolated as red powder 140 mg (95%). Mp 244–
12.0, J5 ,4 = 3.2, H-5ꢀ); 4.07 and 4.10 (2 × td, 2 × 1H, J4 ,5 = 3.2,
ꢀ
ꢀ
ꢀ ꢀ
1
249 C. H NMR (500 MHz, acetone-d6): 2.534 and 2.536 (2 ×
J4 ,3 = 2.5, H-4ꢀ); 4.61 (ddd, 2H, J3 ,2 = 5.6, 2.8, J3 ,2 a = 2.5, H-3ꢀ);
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ ꢀ
ddd, 2 × 1H, Jgem = 13.4, J2 b,1 = 6.2, J2 b,3 = 3.2, H-2ꢀb); 2.71
ꢀ
ꢀ
ꢀ
ꢀ
6.59 and 6.62 (2 × dd, 2 × 1H, J1 ,2 = 7.9, 6.0, H-1ꢀ); 6.87 and
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
and 2.74 (2 × ddd, 2 × 1H, Jgem = 13.4, J2 a,1 = 7.5, J2 a,3 = 5.7,
6.93 (2 × ddd, 2 × 1H, J5,4 = 7.5, J5,6 = 5.7, J5,3 = 1.4, H-5-bpy);
H-2ꢀa); 3.88–3.98 (m, 4H, H-5ꢀ); 4.13 and 4.14 (2 × q, 2 × 1H,
7.328 and 7.333 (2 × ddd, 2 × 1H, J4,3 = 8.2, J4,5 = 7.5, J4,6
=
J4 ,5 = J4 ,3 = 3.0, H-4ꢀ); 4.73 (m, 2H, H-3ꢀ); 6.30 (bm, 2H, H-m-
ꢀ
ꢀ
ꢀ ꢀ
1.5, H-4-bpy); 7.48 (ddd, 2H, J5,4 = 7.5, J5,6 = 5.7, J5,3 = 1.4,
phenylene); 6.81 and 6.82 (2 × dd, 2 × 1H, J1 ,2 = 7.5, 6.2, H-1ꢀ);
ꢀ
ꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,3
H-5-bpy); 7.53 (ddd, 2H, J5
= 7.5, J5
= 5.7, J5
= 1.4,
,4
,6
6.98 (ddd, 1H, J5,4 = 7.6, J5,6 = 5.6, J5,3 = 1.3, H-5-bpy); 7.02 (bm,
H-5ꢀꢀꢀ); 7.555, 7.560, 7.67 and 7.68 (4 × ddd, 4 × 1H, J5,4 = 7.6,
2H, H-o-phenylene); 7.09 (ddd, 1H, J5,4 = 7.6, J5,6 = 5.6, J5,3
=
J5,6 = 5.6, J5,3 = 1.3, H-5-bpy); 7.728 and 7.731 (2 × s, 2 × 1H,
1.3, H-5-bpy); 7.28 (bm, 2H, H-o-phenylene); 7.37 and 7.38 (2 ×
ddd, 2 × 1H, J6,5 = 5.6, J6,4 = 1.5, J6,3 = 0.7, H-6-bpy); 7.41 and
7.43 (2 × ddd, 2 × 1H, J5,4 = 7.6, J5,6 = 5.6, J5,3 = 1.3, H-5-bpy);
H-6); 7.81 and 7.82 (2 × ddd, 2 × 1H, J6,5 = 5.7, J6,4 = 1.5, J6,3
=
=
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,3
0.7, H-6-bpy); 7.89 (ddd, 2H, J6
= 5.7, J6
= 1.5, J6
,5
,4
0.7, H-6ꢀꢀꢀ); 7.91 (dd, 1H, J5 = 7.8, J5 = 1.4, H-5ꢀꢀ); 7.92, 7.93,
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,4
7.95 and 7.96 (4 × ddd, 4 × 1H, J6,5 =,35.7, J6,4 = 1.5, J6,3 = 0.7,
H-6-bpy); 8.15 (ddd, 2H, J4,3 = 8.2, J4,5 = 7.5, J4,6 = 1.5, H-4-
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,3
7.51 and 7.52 (2 × ddd, 2 × 1H, J5
= 7.6, J5
= 5.6, J5
=
,4
,6
1.3, H-5ꢀꢀꢀ); 7.53 (dd, 1H, J5 = 7.7, J5 = 1.4, H-5ꢀꢀ); 7.615 and
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,4
,3
7.616 (2 × ddd, 2 × 1H, J5,4 = 7.6, J5,6 = 5.6, J5,3 = 1.3, H-5-bpy);
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
bpy); 8.20 (ddd, 2H, J4
= 8.2, J4
= 7.5, J4
= 1.5, H-4ꢀꢀꢀ);
,3
,5
8.22–8.27 (m, 4H, H-4-bpy); 8.29 (dd, 2H, J4 ,6 = 8.3, J4
=
7.67–7.72 (m, 4H, H-5,6-bpy); 7.78 (ddd, 2H, J4,3 = 8.4, J4,5
=
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,5
7.8, H-4ꢀꢀ); 8.39 (bs, 2H, H-2); 8.40 (ddd, 2H, J6,5,3 = 5.7, J6,4 = 1.5,
J6,3 = 0.7, H-6-bpy); 8.45, 8.47, 8.73, 8.74, 8.79 and 8.80 (6 × ddd,
6 × 1 H, J3,4 = 8.2, J3,5 = 1.4, J3,6 = 0.7, H-3-bpy); 8.86 (ddd,
7.6, J4,6 = 1.5, H-4-bpy); 7.90 (s, 1H, H-6); 7.91 (m, 2H, H-6ꢀꢀꢀ);
7.95 (s, 1H, H-6); 8.078 and 8.082 (2 × ddd, 2 × 1H, J4,3 = 8.4,
J4,5 = 7.6, J4,6 = 1.5, H-4-bpy); 8.157 and 8.162 (2 × ddd, 2 ×
1H, J6,5 = 5.6, J6,4 = 1.5, J6,3 = 0.7, H-6-bpy); 8.19–8.29 (m, 6H,
H-4ꢀꢀꢀ and H-3,4-bpy); 8.33 and 8.34 (2 × ddd, 2 × 1H, J6,5 = 5.6,
J6,4 = 1.5, J6,3 = 0.7, H-6-bpy); 8.343 and 8.345 (2 × dd, 2 × 1H,
= 0.7, H-3ꢀꢀꢀ); 8.87 (dd, 2H,
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,6
2H, J3
ꢀꢀ ꢀꢀ
= 8.2, J3
= 1.4, J3
,5
J3 = ,84 .3, J3 = 1.4, H-3ꢀꢀ); 8.94 and 8.95 (2 × bddd, 2 × 1H,
ꢀꢀ ꢀꢀ
,5
J3,4,4= 8.2, J3,5 = 1.4, J3,6 = 0.7, H-3-bpy). 13C NMR (125.7 MHz,
acetone-d6): 41.90 and 41.98 (CH2–2ꢀ); 63.08 and 63.13 (CH2-
5ꢀ); 72.53 (CH-3ꢀ); 85.96 and 86.30 (CH-1ꢀ); 89.48 (CH-4ꢀ); 89.86
(bpy-C≡C-); 90.11 and 90.24 (bpy-C≡C-); 95.80 and 85.88 (C-5);
102.98 and 103.11 (C-4a); 124.54 and 124.72 (CH-3-bpy), 124.87
(CH-3ꢀꢀ); 125.33, 125.43 and 125.72 (CH-3-bpy); 125.97 (CH-3ꢀꢀꢀ);
127.62, 127.91, 128.30, 128.57, 128.89 and 129.03 (CH-5ꢀꢀꢀ, CH-
5-bpy); 131.03 and 131.11 (CH-6); 135.47 and 135.50 (CH-5ꢀꢀ);
136.51 and 136.57 (CH-4-bpy); 138.88, 138.98, 139.12 and 139.24
(CH-4ꢀꢀ,4ꢀꢀꢀ, CH-4-bpy); 147.91 (CH-2); 148.50 and 148.61 (C-7a);
149.26 and 149.30 (C-6ꢀꢀ); 152.07, 152.14, 152.31, 152.35, 152.57,
153.73 and 153.76 (CH-6ꢀꢀꢀ and CH-6-bpy); 154.11 (C-4); 157.81,
157.99, 158.01, 158.27, 158.74 and 158.80 (C-2ꢀꢀꢀ, C-2-bpy); 158.98
(C-2ꢀꢀ). ESI MS: m/z (%) 987.1 (100) [M+ − PF6−], HR MS (TOF
ES MS+) calc. 987.1657 found. 987.1691. UV/Vis (CH3CN) kmax
(e) = 288 (81880), k (e) = 448 (14150).
= 7.7, H-4ꢀꢀ); 8.36 (ddd, 1H, J3,4 = 8.4, J3,5
=
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
,5
J4
= 8.3, J4
,3
1.3, J3,6 = 0.7, H-3-bpy); 8.501 and 8.503 (2 × s, 2 × 1H, H-2);
8.637, 8.642, 8.69, 8.716 and 8.722 (5 × ddd, 6H, J3,4 = 8.4, J3,5
=
=
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀꢀ ꢀꢀꢀ
,5
1.3, J3,6 = 0.7, H-3-bpy); 8.90 (ddd, 2H, J3
= 8.4, J3
,4
= 0.7, H-3ꢀꢀꢀ); 8.94 (dd, 2H, J3
= 8.3, J3
= 1.4,
ꢀꢀꢀ ꢀꢀꢀ
ꢀꢀ ꢀꢀ
ꢀꢀ ꢀꢀ
1.3, J3
,6
,4
,5
H-3ꢀꢀ). 13C NMR (125.7 MHz, acetone-d6): 42.24 and 42.38 (CH2-
2ꢀ); 62.96 and 63.07 (CH2-5ꢀ); 72.35 and 72.44 (CH-3ꢀ); 85.50 and
85.52 (CH-1ꢀ); 89.25 and 89.37 (CH-4ꢀ); 100.29 and 100.33 (C-4a);
119.50 and 119.51 (C-5); 124.24 and 124.34 (CH-3-bpy), 124.62
(CH-3ꢀꢀ); 124.87 and 124.95 (CH-6); 125.05, 125.14, 125.18, 125.48
and 125.51 (CH-3-bpy); 125.95 (CH-3ꢀꢀꢀ); 127.37, 127.53, 128.16,
128.32 and 128.98 (CH-5ꢀꢀꢀ, CH-5-bpy); 129.10, 129.24, 129.42 and
130.30 (CH-o,m-phenylene); 130.62 and 130.64 (CH-5ꢀꢀ); 133.90
and 133.93 (C-i-phenylene); 136.99 (CH-4-bpy); 138.95, 139.08
and 139.27 (CH-4ꢀꢀ,4ꢀꢀꢀ, CH-4-bpy); 139.31 (C-p-phenylene); 143.44
(CH-2); 148.81 (C-7a); 151.90 (CH-6-bpy); 152.50 (C-4); 152.57,
152.84, 152.88, 152.91 and 153.64 (CH-6ꢀꢀꢀ and CH-6-bpy); 157.62,
157.64, 158.09, 158.22, 158.72, 158.74, 158.93 and 159.03 (C-2ꢀꢀ,
C-2ꢀꢀꢀ and C-2-bpy); 167.16 (C-6ꢀꢀ).ESI MS: m/z (%) 1039.1 (100)
[M+ − PF6−], HR MS (TOF ES MS+) calc. 1039.1970 found.
1039.1986. UV/Vis (CH3CN) kmax (e) = 289 (72812), k (e) = 450
(12178).
General procedure for Suzuki–Miyaura cross-coupling reactions of
Ru(II) building blocks 7a,c,d
A mixture of H2O–CH3CN = 2 : 1 (1 ml) was added to an
argon-purged flask containing nucleoside 1 (47 mg, 0.125 mmol),
a boronate 7a,c,d (0.15 mmol, 1.2 equiv.) and Cs2CO3 (122 mg,
0.375 mmol, 3 equiv.). In a separate flask, Pd(OAc)2 (1.4 mg,
0.00625 mmol, 5 mol%) and P(Ph-SO3Na)3 (9 mg, 0.0156 mmol,
2.5 equiv. to Pd) were combined evacuated and purged with argon
followed by an addition of H2O–CH3CN = 2 : 1 (0.5 ml). The
solution of this catalyst was injected to the reaction mixture
UV/Vis spectra
The UV-Vis spectra were measured on a Varian CARY 100 Bio
Spectrophotometer at room temperature. Compounds 4 and 5
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were measured as 1.6 × 10−5 M solutions in CHCl3. Compounds
8 and 9 were measured as 1.6 × 10−5 M solutions in CH3CN.
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4 M. Vra´bel, M. Hocek, L. Havran, M. Fojta, I. Votruba, B. Kepeta´rˇova´,
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R. Mackman, Eur. J. Inorg. Chem., 2007, 1752–1769.
Fluorescence measurements
The fluorescence measurements of compounds 4 and 5 were
performed on an Aminco Bowman Series 2 Spectrofluorometer
with 220–850 nm range, Xenon source, excitation and emission
wavelength scans, spectral bandwidth 1–16 nm, PMT detector,
scan rate 3–6000 nm min−1, Saya-Namioka grating monochroma-
tor. Compounds 4 and 5 were measured as 1.6 × 10−4 M solutions
in CHCl3.
Stationary absorption and emission spectra of Ru-complexes in
acetonitrile (Merck Uvasol) were obtained with a Cary 300 and
Spex Fluorolog 212, respectively. For measurement of quantum
yields, the emission was excited at 430 nm and compared to that
from the dye DCM. The fluorescence band of DCM in acetonitrile
(Uem = 0.60 0.04)26 is similar to the emission spectrum of the
Ru(II) complexes studied here.
5 M. Vra´bel, R. Pohl, B. Klepeta´rˇova´, I. Votruba and M. Hocek, Org.
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6 M. Vra´bel, M. Hocek, I. Rosenberg, unpublished results.
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Transient absorption spectra were recorded upon excitation
at 403 nm with 40 fs pump pulses. After a variable delay, the
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measured in a dual-beam arrangement.27 The time resolution was
80 fs (fwhm of temporal apparatus function).
8 Recent review: M. Hocek and M. Fojta, Org. Biomol. Chem., 2008, 6,
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ˇ
9 P. Capek, H. Cahova´, R. Pohl, M. Hocek, C. Gloeckner and A. Marx,
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Electrochemistry
12 (a) Recent examples of synthesis and incorporation of 7-alkynyl-7-
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Voltammetric measurements were performed with an Autolab
analyzer (Eco Chemie, The Netherlands) in connection with VA-
Stand 663 (Metrohm, Switzerland). Pyrrolitic graphite electrode
(PGE) was used as a working electrode (prepared and pretreated
as described),28 Then the electrode was rinsed with deionized water
and was placed into the electrochemical cell. Electrochemical
responses were measured in a conventional in situ mode (with
the analyte dissolved in background electrolyte) initial potential
−1.0 V, final potential +1.5 V, pulse amplitude 25 mV, frequency
200 Hz, potential step 5 mV. The measurements were performed
at ambient temperature in 0.1M Tris, 0.2M NaCl, pH 7.3 by
using an Autolab analyzer (EcoChemie, The Netherlands) in
a three-electrode setup (with the PGE as working electrode,
Ag/AgCl/3 M KCl as reference, and platinum wire as counter-
electrode). The voltammograms were baseline corrected by means
of a moving average algorithm (GPES 4 software, EcoChemie).
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Acknowledgements
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This work is a part of the research project Z4 055 0506. It was
supported by the Ministry of Education (LC512) and by Gilead
Sciences, Inc. (Foster City, CA, USA). Antiviral activity was
studied by E. Mabery and Dr I. Shih and R. Mackman (Gilead).
The contribution of these scientists is gratefully acknowledged.
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