Oligonucleotide analogues with integrated bases and backbones. Part 25: Structural effects on the gelation of self-complementary A*[s]U dinucleosides

Article abstract of DOI:10.1002/hlca.201000050

The ability of A*[s]U dinucleosides to gel organic solvents and water is modulated by changing the nature of the substituents at O-C(2′) and O-C(3′), as evidenced by comparing the gelation of the dinucleosides 7-9 and the properties of the gels. A mere ex

Full text of DOI:10.1002/hlca.201000050

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Helvetica Chimica Acta – Vol. 93 (2010)
Oligonucleotide Analogues with Integrated Bases and Backbones
Part 25
Structural Effects on the Gelation of Self-Complementary A*[s]U Dinucleosides
by Nicolas Bogliotti and Andrea Vasella*
Laboratorium fꢀr Organische Chemie, ETH Zꢀrich, Wolfgang-Pauli Strasse 10, CH-8093 Zꢀrich
(e-mail: vasella@org.chem.ethz.ch)
The ability of A*[s]U dinucleosides to gel organic solvents and water is modulated by changing the
nature of the substituents at OꢀC(2’) and OꢀC(3’), as evidenced by comparing the gelation of the
dinucleosides 7 – 9 and the properties of the gels. A mere extension of the hydrophobic moiety, by
replacing the isopropylidene groups of 2 by cyclohexylidene groups, as in 7, has a small effect, while
changing the conformation of the ribose ring and reducing the size of the hydrophobic moiety, as in 8, has
a strong effect on the scope of gelation, the minimum gelation concentration, as low as 0.07% for
pentanol and decanol, and the properties of the gel. The fully deprotected dinucleoside 9 gels water at a
minimal gelation concentration of 0.6%. A TEM of the corresponding xerogel shows the formation of
fibers with a diameter of ca. 30 to 90 nm.
Introduction. – The A*[s]U1) silyl ether 1 in CHCl3 solution forms an equilibrium
of the monoplex and linear associates [1], whereas the A*[s]U(*) alcohols 2 and 5 form
gels with organic solvents involving their self-association to build a network by H-
bonding, as evidenced by the absence of gelation by the deaminated HA*[s]U
dinucleoside 3 [2]. Also the corresponding N-Me analogue MeA*[s]U 4 of 2 and the
deoxygenated A*[s]HU* analogue 6 of 5 do not form gels, further evidencing that
gelation requires the formation of linear associates that are cross-linked by H-bonding
involving the nucleobase and/or HOCH2ꢀC(6/I) [3]. The synthesis and the evaluation
of the gelation properties of these dinucleosides identified some of the structural
elements involved in the formation of gels. Other structural aspects of these
dinucleosides that may affect gelation involve the dimethyl-dioxolane rings, viz., the
size of this hydrophobic moiety and the conformational restriction resulting from its
annulation. To investigate their effect, we planned to synthesize the cyclohexylidene-
1
)
Conventions for abbreviated notation: The substitution at C(6) of pyrimidines and C(8) of purines is
denoted by an asterisk (*); for example, A* and U* for hydroxymethylated adenosine and uridine
derivatives, respectively. U(*) represents both unsubstituted and hydroxymethylated uridine
derivatives. The replacement of the amino group at C(6) of adenosine by a N6-methylamino group
and the replacement of the HOCH2 group of uridine by an H-atom are denoted by ꢂMeꢃ in
superscript (Me) and ꢂ Hꢃ in superscript (H), respectively; for example, MeA and HU represent N6-
methyladenosine and C(6)-methyluridine derivatives, respectively. The moiety x linking C(8)ꢀCH2
of unit II and C(5’) of unit I is indicated in square brackets, i.e., [s] for a S-atom.
ꢁ 2010 Verlag Helvetica Chimica Acta AG, Zꢀrich

Helvetica Chimica Acta – Vol. 93 (2010)
889
protected A*[s]U dinucleoside 7, the 2’,3’-di-O-methyl ether 8, and the unprotected
dinucleoside 9, and to evaluate their ability to form gels with different solvents.
Results and Discussion. – We envisaged to prepare the dinucleosides 7 and 8 by
coupling the 2’,3’-O-cyclohexylidene monomers 13 and 20, and the 2’,3’-di-O-methyl
monomers 18 and 25, respectively, according to a previously established procedure [1]
(cf. Scheme 3). The deprotected pentol 9 should be obtained in one step from the
known isopropylidene-protected A*[s]U dinucleoside 28 [1].
Synthesis of the Adenosine Intermediates. A one-pot 5’-O-silylation and N(6)-
benzoylation of the known cyclohexylidene-adenosine 10 [4] provided the fully
protected adenosine 11 (80%; Scheme 1). It was hydroxymethylated at C(8) by
deprotonation with LDA [5], formylation with DMF, hydrolysis, and reduction of the
resulting aldehyde [6], to yield 81% of the alcohol 12. Treatment of this alcohol with
MsCl provided the chloromethyl derivative 13 (72%); the initially formed methane-
sulfonate was not isolated. To synthesize the chloromethylated 2’,3’-di-O-methylade-
nosine 18, we methylated the OH groups of the ditrityl-protected adenosine 14 [7] with
MeI and NaH in THF, and detritylated the crude product by heating in aqueous AcOH
to yield 67% of the known 2’,3’-O-dimethyladenosine (15) which had been obtained by
unselective methylation of adenosines [8 – 10]. Similarly as for the preparation of the
cyclohexylidenated chloromethyl-adenosine 13, the 2’,3’-O-dimethyl derivative 15 was
silylated and benzoylated to 16 (83%) that was hydroxymethylated to 17 (74%).
Mesylation of 17, followed by addition of LiCl, afforded 95% of the chloride 18.

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Scheme 1
a) TDSCl, pyridine, then BzCl; 80% of 11; 83% of 16. b) 1. LDA (¼ lithium diisopropylamide), THF,
ꢀ 788, then DMF; 2. NaBH4, AcOH, EtOH; 81% of 12; 95% of 17. c) MsCl, EtN(i-Pr)2, CH2Cl2; 72%.
d) 1. NaH, THF, then MeI; 2. AcOH/H2O 4 :1, 1008; 67%. e) MsCl, EtN(i-Pr)2, CH2Cl2, then LiCl; 95%.
Synthesis of the Uridine Intermediates. Tosylation of 2’,3’-O-cyclohexylideneuridine
(19) [11], followed by substitution with AcSK, afforded the thioacetate 20 (77%;
Scheme 2). The analogous 2’,3’-O-dimethyl derivative 25 was prepared via 2’,3’-O-
dimethyluridine (24) [12] that was obtained from the 4-O-methyluridine (21) [12] by
continuous addition over 2 d of excess CH2N2, followed by hydrolysis of the
methoxyimino group at C(4) [12]. A safer and more convenient access to 24 was
realized by silylation of the OH group at C(5’) of 21 with thexyl(dimethyl)silyl chloride
(TDSCl) to the silyl ether 22 that was directly O-methylated with MeI and Ag2O to 23.
This 2’,3’-O-dimethyl derivative was treated with Amberlite resin (Hþ form) in aqueous
MeOH to yield 40% (from 21) of crystalline 2’,3’-di-O-methyluridine (24). Tosylation,
followed by substitution with AcSK, afforded 47% of the thioacetate 25.
Synthesis of the Dinucleosides. The cyclohexylidenated A*[s]U thioether 26 was
obtained in 91% yield by nucleophilic substitution of the chloromethylated adenosine
13 by the thiolate that was formed in situ by treating the thioacetate 20 with MeONa in
degassed dry MeOH [1] (Scheme 3). Desilylation of the dinucleoside 26 with (HF)3 ·
Et3N yielded 88% of the alcohol 7. The methylated A*[s]U dinucleoside 27 was

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Scheme 2
a) 1. TsCl, pyridine; 2. AcSK, DMF, 758; 77% of 20; 47% of 25. b) TDSCl, 1H-imidazole, DMF. c) MeI,
Ag2O, acetone. d) Amberlite IR-120 (Hþ form), MeOH/H2O 1:5; 40% from 21.
prepared similarly to 26, by treating a mixture of the chloromethylated 18 and the
thioacetate 25 with MeONa to yield 86% of 27. This dinucleoside was desilylated to the
alcohol 8 (98%). Acid-catalyzed hydrolysis of the isopropylidenated thioether 28 [1]
gave the fully deprotected dinucleoside 9 (98%). Of these dinucleosides, only 26 and 27
are soluble in CHCl3, and allowed determining the mode of association in the standard
way [1]. The dinucleosides 7 – 9 are not sufficiently soluble in CHCl3. Of these, 7 and 8
form organogels, while 8 and 9 form a hydrogel, as will be discussed after describing the
conformation of the mono- and dinucleosides, and the association of 26 and 27.
Conformation of the Adenosine Mononucleosides. Replacing the isopropylidene by
a cyclohexylidene group did not significantly affect the conformation of the adenosine
monomers in CDCl3 solution. As previously observed for the corresponding
isopropylidene-adenosine derivative [1], the fully protected 11 adopts an anti-
conformation, as revealed by the chemical shift of 5.31 ppm for HꢀC(2’) (Table 5 in
the Exper. Part). The J(1’,2’)/J(3’,4’) ratio of 1.1 reflects a slight preference for the (S)-
conformation. A gg/tg/gt rotamer distribution of 50 :25 :25 is evidenced by J(4’,5’a) and
J(4’,5’b) values of 4.2 and 4.4 Hz, respectively2). The C(8)-chloromethylated
2
)
See [1] for the calculation of the rotamer distribution.

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Scheme 3
a) MeONa, MeOH; 91% of 26; 86% of 27. b) Et3N · 3 HF, THF; 88% of 7; 98% of 8. c) F3CCOOH
(TFA)/H2O 4 :1; 98%.
adenosine 13 adopts a syn-conformation (d(HꢀC(2’)) ¼ 5.83 ppm). HꢀC(2’) of the
C(8)-hydroxymethylated 12 resonates slightly upfield (d ¼ 5.71 ppm). An assumed
d(HꢀC(2’)) of 5.20 ppm for the anti-conformer of 12 (cf. [1]) suggests a ca. 4 :1 syn/
anti-equilibrium and the stabilization of the anti-conformer by an intramolecular H-
bond between HOCH2ꢀC(8) (br. s at 5.59 ppm) and OꢀC(5’) (see [1 – 3]). Both 12
and 13 show a preference for the (N)-conformation (J(1’,2’)/J(3’,4’) ¼ 0.7) and a similar
gg/gt/tg rotamer distribution (17:36 :47 and 17:38 :45, resp.), as deduced from J(4’,5’a)
and J(4’,5’b) values ranging from 5.8 to 6.1 Hz.

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The exchange of the isopropylidene and cyclohexylidene protecting group by two
Me groups allows a stronger puckering of the furanose ring and leads to an upfield shift
of the HꢀC(2’) and HꢀC(3’) signals, but is expected to only moderately affect the syn/
anti-equilibrium. The d values of 5.22 and 5.26 ppm for HꢀC(2’) of the 8-substituted 17
and 18, respectively, evidence a similar syn-conformation (Table 5 in the Exper. Part).
A strong upfield shift for HꢀC(2’) of the 8-unsubstituted 16 (Dd ꢁ 0.85 ppm relative to
17 and 18) evidences a complete anti-conformation. These data suggest that chemical
shifts of 5.20 – 5.30 and 4.40 ppm are characteristic for syn- and anti-configured 2’,3’-di-
O-methyladenosines in CDCl3, respectively3). The orientation of the nucleobase has a
strong influence upon the furanose ring conformation and the orientation of the side
chain at C(4’). Thus, the anti-configured 16 prefers a (N)-conformation and gg-
orientation of the side chain (gg/gt/tg 78 :8 :14), whereas the syn-configured 17 and 18
adopt an (S)-conformation and show a reduced preference for the gg-orientation (gg/
gt/tg 43 :15 :42).
In CDCl3, the alcohol 15 shows a persistent intramolecular H-bond from
HOꢀC(5’) to N(3), resulting in a syn-conformation, as revealed by the exclusive
population of the gg-rotamer (J(4’,5’a) ¼ 1.5 and J(4’,5’b) ¼ 1.6 Hz), the strong
preference for the (S)-conformation (J(1’,2’)/J(3’,4’) > 5.3), the downfield shift of
HOꢀC(5’) (6.81 ppm), and typical J(5’,OH) values of 1.9 and 12.0 Hz (see [1 –
3][14][15]). As the consequence of the intramolecular H-bond, one observes a
characteristic upfield shift of the HꢀC(2’) signal ((Dd ¼ 0.5 ppm, relative to 17 and 18).
Conformation of the Uridine Mononucleosides. The cyclohexylidenated thioacetate
20 in CDCl3 adopts the same conformation as the isopropylidenated analogue [1], as
1
revealed by similar H-NMR chemical shifts (Dd ꢂ 0.07 ppm) and coupling constants
(DJ ꢂ 0.02 Hz; Table 7 in the Exper. Part). It forms a ca. 3 :1 syn/anti-equilibrium,
prefers a (N)-conformation, and avoids the gg-orientation of the AcSCH2 moiety (gg/
gt/tg 16 :42 :42).
The expectation that the silyl ether 23 prefers an anti-conformation, similarly to the
corresponding isopropylidene acetal [1], is confirmed by the exclusive gg-orientation of
the (silyloxy)methyl group of 23 (J(4’,5’a) þ J(4’,5’b) ¼ 3.1 Hz (see [16]; Table 7 in the
Exper. Part). The anti-conformation is confirmed by the shift value for HꢀC(2’) of
4
3.90 ppm. The small J(1’,2’) < 1.0 and the large J(3’,4’) ¼ 9.2 Hz of 23 evidence a E-
conformation (an extreme (N)-type). The downfield shift for HꢀC(2’) of the
thioacetate 25 (4.00 ppm) evidences a syn/anti-equilibrium, but the proportion of the
syn-conformer must be distinctly smaller than the 75% found for the isopropylidene
and cyclohexylidene acetals (see above), as indicated by a weaker downfield shift for
HꢀC(2’) of the thioacetate 25 (Dd ¼ 0.12 relative to the silyl ether 23 as compared to
Dd ¼ 0.28 ppm for the corresponding pair of isopropylidene acetals) and also by a
weaker upfield shift for HꢀC(1’) (Dd ¼ 0.16 vs. 0.40 ppm). The smaller proportion of
the syn-conformer of 25 than of 20 is corroborated by a higher gg proportion (gg/gt/tg
32 :45 :23 vs. 16 :42 :42). Both 25 and 20 show a similar preference for the (N)-
conformation.
3
)
HꢀC(2’) of 2’,3’-di-O-methyl-5’-O-trityladenosines resonates in CDCl3 solution at 4.60 – 4.63 ppm
[13].

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The downfield shift for HꢀC(2’) of the alcohol 24 in D2O (4.20 ppm) is due to the
change of the solvent rather than to a syn/anti-equilibrium. The (N)-conformation and
a large proportion of the gg-conformer (gg/gt/tg 66 :25 :9) agree well with an anti-
oriented uracil moiety.
Conformation of the A*[s]U Dinucleosides. The analysis is restricted to the silyl
ethers 26 and 27 that are soluble in CDCl3. The NMR data of the dinucleosides 7 – 9
were recorded of solutions in DMSO, i.e., of solvated monoplexes. HꢀC(2’/I) of 26 and
27 in CDCl3 resonates at 4.99 and 3.90 ppm, respectively (Table 9 in the Exper. Part),
suggesting a ca. 3 :2 syn/anti-equilibrium for 26 and an anti-conformation for 27. In
agreement with this result, a lower proportion of the gg-rotamer is found for 26 (gg/gt/tg
26 :44 :30) than for 27 (gg/gt/tg 53 :33 :14). Both 26 and 27 show a similar preference
for the (N)-conformation of unit I. According to these observations, 26 (but not 27)
could form cyclic duplexes.
Association of the A*[s]U Dinucleosides in CHCl3. The self-association of the
silylated dinucleosides 26 and 27 in CDCl3 was investigated by analyzing the
concentration dependence of the chemical shift for HꢀN(3/I) resulting in shift/
concentration curves (SCCs) and by temperature-dependent circular dichroism. The
dinucleosides 7 – 9 form gels in several solvents (see below). Their solubility in CHCl3
was too low to analyse their self-association.
The SCCs of 26 and 27 show a flattening above ca. 40 mm without reaching a
plateau and a rather low value for d(HꢀN(3)) at the lowest practical concentration.
They resemble strongly the SCC of corresponding isopropylidene-protected analogue 1
[1] and reflect an equilibrium between monoplexes and linear associates (Fig. 1).
Somewhat surprising is the rather steep ascent of the SCCs at lower concentrations,
suggesting the facile formation of longer linear associates. The SCCs of 26 and 27 were
analysed numerically by the method proposed by Gutowsky and Saika [17] including a
value of 7.70 ppm for a 0.0001 mm solution [1]. The extrapolated chemical shift for the
Fig. 1. Shift/concentration curves (SCCs) of the silyl ethers 26 and 27 in CDCl3 solution (including a value
of 7.70 ppm for a 0.0001 mm soln.).

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Table 1. Association Constants Kass from the Concentration Dependence of d(HN(3/I)) in CDCl3 at 295 K
for the A*[s]U Dinucleotides 26 and 27 (including a value of 7.70 ppm for a 0.0001 mm soln.),
Extrapolated Chemical Shifts of the Monoplexes and Duplexes, and DG295 Values
Dimer
Kass [mꢀ1
]
dmonoplexa) [ppm]
dduplexb) [ppm]
DG295 [kcal/mol]
26
27
282
145
7.73
7.82
12.26
12.31
ꢀ 3.3
ꢀ 2.9
a) Extrapolated for 0 mm. b) Extrapolated for infinite concentration.
duplexes of 26 (12.26 ppm; Table 1) and 27 (12.31 ppm) hints at a ca. 1:1 mixture of
Watson – Crick- and Hoogsteen-type base-paired associates (cf. [14]).
The association constant for the cyclohexenylidenated 26 (Kass ¼ 282 mꢀ1; Table 1) is
slightly higher than that for its isopropylidene-protected analogue (Kass ¼ 225 mꢀ1 [1]),
while the methylated 27 associates more weakly (Kass ¼ 145 mꢀ1), evidencing the
influence of the substituent at C(2’) and C(3’) on duplex formation, presumably mostly
by affecting the conformation of the ribose ring of unit I (see below). The Kass values
agree well with an equilibrium between monoplex and linear associates.
The temperature-dependent CD spectra of 1 mm CHCl3 solutions of 26 and 27
show a stronger variation of the ellipticity (Fig. 2) than the spectra of the corresponding
isopropylidene acetal 1 (see [1]), evidencing more extensive p-stacking of the
nucleobases. Remarkably, the change of the ellipticity of 26 is asymmetric, concerning
only the part of the maximum at higher wavelength, while the ellipticity of the complete
maximum of 27 is diminished, and the change also affects the minimum at lower
wavelength. This may be rationalized by assuming that only the conformation of one of
the units of 26 is strongly affected by the temperature change, presumably the (C(6)-
unsubsituted) uridine moiety. The molar ellipticity ([q]) of 26 and 27, between ca. ꢀ 2 ·
104 and þ 3 · 104 deg · cm2/dmol, compares well with the one of 1 (ca. ꢀ 1 · 104 to þ 2 ·
104 deg · cm2/dmol [1]4)).
Characterization of the Gels. 1. Solvents. We determined the ability of the
dinucleosides 7 – 9 to form gels with a selection of 33 solvents, based on classification
of Chastrette et al. [18], at a concentration of 1% (w/v), as reported in [2][3]. The
monoalcohols 7 and 8 were insoluble in apolar and in most electron-pair donor solvents,
and soluble in highly dipolar solvents and in 2,2,2-trifluoroethanol (Table 2). Turbid or
partial gels5) were obtained from aprotic dipolar and H-bonding solvents. Surprisingly,
the tetramethyl ether 8 gelates also H2O (ꢂambidextrous gelatorꢃ) and proved largely
superior to the other gelators tested (2 and 5; see [1]) when considering the scope of
gelated solvents. The pentol 9 formed a gel in H2O. As expected, it is insoluble in all
solvents tested, with the exception of the highly dipolar DMF, DMSO, sulfolane, and
2,2,2-trifluoroethanol.
Gel – Sol Transition Temperature and Minimum Gelation Concentration. As
previously observed for the A*[s]U(*) gelators 2 and 5 [2], the gel – sol (melting)
4
)
For the sake of comparison, the ellipticity values (q, [mdeg]) reported in [1] were converted to [q]
[deg · cm2/dmol].
See [2] for a definition and evaluation of partial gels.
5
)

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Helvetica Chimica Acta – Vol. 93 (2010)
Fig. 2. Temperature-dependent CD spectra (in 108 steps from 0 to 508) of 1 mm solutions in CHCl3 of the
silyl ethers 26 and 27
temperature (Tm) and minimum gelation concentration (MGC) depend on both the
gelator and the solvent. The Tm values for the 1% (w/v) gels of 7 and 9 are sharp, and
range between 56 and 768, except for gels with MeCN and AcOEt that melt between
57 – 678 and 64 – 748, respectively (Table 3). In linear alcohols (MeOH to decan-1-ol),
Tm of the gels of 7 increases from 48 to 768 with increasing chain length (decreasing
solvent polarity), evidencing the formation of a network of gelator molecules linked by
H-bonds [2][3]. Most of the gels formed by the tetra-O-methyl derivative 8 show a
broad Tm (47 to 808), and do not clearly reveal the relation between solvent polarity
(chain length of linear alcohols) and gel – sol transition temperature. The different
behaviour exhibited by 8, as compared to 7 and 9, further illustrates the effect of the
structure of the gelator on the properties of the gel.
The MGC for the gels of 7 ranges between 0.2% (w/v) (decan-1-ol) and 0.8%
(butan-2-one and t-BuOH), while 9 gelates H2O at a concentration of 0.6% (Table 4).
The lowest MGC for 8 is obtained with pentan-1-ol and decan-1-ol (0.07%), and the
highest one with THF (0.9%). As expected for compounds associating by H-bonds, the
MGC observed for 7 and 8 in linear alcohols decreases with decreasing solvent polarity,
from 0.5% (EtOH) to 0.2% (decan-1-ol) and from 0.5% (in MeOH) to 0.07% (pentan-
1-ol and decan-1-ol), respectively. The efficiency of 7 and 9 is similar to that of other
nucleobase-derived gelators, ranging from ca. 0.3 to 0.8% [2][19][20]. The remarkable
efficiency of 8 in pentan-1-ol and decan-1-ol (MGC 0.07%) allows a comparison with
ꢂsupergelatorsꢃ such as benzylidene acetals of pyranosides [21], or trehalose esters [22]
that form gels in cyclohexane and AcOEt, respectively, at a concentration of 0.04%.
Circular Dichroism. The supramolecular structure of the gels of 7 – 9 in different
solvents was also studied by temperature-dependent circular dichroism (CD). At 08,
the CD spectrum of the 1% (w/v) gel of 7 and MeCN shows a minimum and a
maximum at ca. 285 and 305 nm, respectively (Fig. 3). As the temperature increases to
508, the minimum shifts to ca. 280 nm, and its intensity increases significantly, while the
maximum shifts to ca. 300 nm and becomes slightly more intense. At 608, the CD
spectrum still shows intense signals (minimum and maximum at ca. 280 and 300 nm,

Helvetica Chimica Acta – Vol. 93 (2010)
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Table 2. Solubility of the Dinucleosides 7 – 9 in Selected Solvents and Properties of the Gelsa)
Class
Solvent
7
8
9
Aliphatic, apolarb)
Pentaneb)
Hexanec)
Id) Id)
–
I
–
–
I
I
I
I
I
I
Cyclohexanec)
c
CCl4
)
Aromatic, apolar
Benzene
Toluene
I
I
I
I
–
I
Aromatic, relatively polar
Electron-pair donor
Acetophenone
S
TG
I
Et2O
Id) Id)
I
I
S
–
–
–
I
(i-Pr)2O
I
I
PG
t-BuOMeb)
1,4-Dioxane
Aprotic, dipolar
CH2Cl2
PG PGd)
PG TG
TG PG
TG TG
TG PG
TG PG
I
I
–
–
–
I
Acetone
ClCH2CH2Cl
Butan-2-one
MeCN
AcOEt
Aprotic, highly dipolar
DMF
DMSO
S
S
Sd)
Sd)
Sd)
Sd)
Aprotic, highly dipolar, and highly polarisable H-Bonding Sulfolane
2,2,2-Trifluoroethanol
S
S
S
S
Sd)
S
Sd)
TG
MeOH
EtOH
PrOH
BuOH
Pentan-1-ol
Decan-1-olb)
i-PrOH
Ie)
I
TG TG
TG TG
TG TG
TG TG
TG TG
TG TG
TG TG
I
–
–
–
I
–
t-BuOH
H-Bonding, strongly associated
Miscellaneous
H2O
I
TG
TG
TG
CHCl3
S
I
I
–
1,2-Dimethoxyethanec) Sd) TG
THFc)
Sd) TG
a) [gelator] ¼ 1% (w/v), I: insoluble, S: soluble, PG: partial gel, TG: turbid gel. b) Missing in Chastretteꢃs
original classification [18]. c) Reclassified solvent. d) At 258. e) Soluble at 708.
resp.) although most gel – sol transitions occur at about this temperature (Tm 57 – 678),
suggesting that a significant proportion of the gelator is still highly organized. The CD
spectra of the gels of 7 in AcOEt, EtOH, and decan-1-ol show similar trends, with a
maximum around 290 nm and a broad tail-shaped negative band centered at ca.
310 nm. The intensity of both bands decreases with increasing temperature, while a
negative band appears around 280 nm. Melting of the gel is associated with a significant
loss of band intensity.

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Table 3. Gel – Sol Transition Temperature (Tm [8]) of 1% (w/v) Gels of the Dinucleosides 7 – 9
Class
Solvent
7
8
9
Aromatic, relatively polar
Aprotic, dipolar
Acetophenone
–
63
–
Acetone
–
56
64
57 – 67
64 – 74
60 – 65
–
61 – 63
–
–
–
–
–
–
–
ClCH2CH2Cl
Butan-2-one
MeCN
AcOEt
H-Bonding
MeOH
EtOH
PrOH
BuOH
Pentan-1-ol
Decan-1-ol
i-PrOH
t-BuOH
–
47 – 53
63 – 65
63
62 – 63
65 – 67
64 – 80
55 – 60
49
–
–
–
–
–
–
–
–
48
52
56
57
76
55
50
H-bonding, strongly associated
Miscellaneous
H2O
–
60 – 70
42
CHCl3
1,2-Dimethoxyethane
THF
–
–
–
55 – 59
60 – 62
50 – 55
–
–
–
Table 4. Minimum Gelation Concentration (MGC [% (w/v)]) of the Gels of the Dinucleosides 7 – 9
Class
Solvent
7
8
9
Aromatic, relatively polar
Aprotic, dipolar
Acetophenone
–
0.2
–
Acetone
–
0.4
0.5
0.3
–
–
–
–
–
–
ClCH2CH2Cl
Butan-2-one
MeCN
0.4
0.8
0.6
0.5
AcOEt
–
H-Bonding
MeOH
EtOH
PrOH
BuOH
Pentan-1-ol
Decan-1-ol
i-PrOH
t-BuOH
–
0.5
0.4
0.3
–
–
–
–
–
–
–
–
0.5
0.4
0.4
0.3
0.2
0.3
0.8
0.2
0.07
0.07
0.2
0.4
H-Bonding, strongly associated
Miscellaneous
H2O
–
0.5
0.6
CHCl3
1,2-Dimethoxyethane
THF
–
–
–
0.4
0.5
0.9
–
–
–
The CD spectra recorded for the gel of 7 compare well with those of the analogous
isopropylidene A*[s]U gelator 2 in the same solvents [2], suggesting a similar
conformation and mode of association in the gel state.

Helvetica Chimica Acta – Vol. 93 (2010)
899
Fig. 3. Temperature-dependent CD spectra (in 108 steps from 0 to 608) of the cyclohexylidenated alcohol 7
for 1% (w/v) gels in MeCN, AcOEt, EtOH, and decan-1-ol
The 1% (w/v) gels of 8 in CHCl3 and in decan-1-ol did not lead to satisfactory CD
spectra, presumably because of their high turbidity. The problem was avoided by
decreasing the amount of gelator. At 08, the CD curve of the 0.5% (w/v) gel of 8 in
CHCl3 exhibits a minimum and a maximum around 280 and 300 nm, respectively
(Fig. 4). Their intensity decreases by increasing the temperature up to 508. The signals
disappeared at 608 with melting of the gel. The CD spectra of the 0.1% (w/v) gel of 8 in
decan-1-ol (at 208) and of the 1% (w/v) gel of 9 in H2O (at 108) show a strong maximum
at ca. 265 and 285 nm, respectively, and a negative tail-shaped band centered at 310 nm.
The intensity of these bands decreased by increasing the temperature to 40 and 608 for
9 and 8, respectively, where the gel melted. As previously observed and discussed in
detail [2], most of the CD spectra of the gels derived from A*[s]U dinucleosides show
strong bands with long tails above 300 nm. This feature is ascribed to the formation of a
compact network of gelators and a concomitant desolvation of the nucleobases upon
gelation.
Scanning Electron Microscopy. The morphology of the 1% (w/v) hydrogel of 9 was
studied by scanning electron microscopy (SEM) of the dried gel, revealing a tertiary
and secondary structure formed by a self-assembled network of fibers with a diameter
of ca. 30 to 90 nm and several mm in length, typical for hydrogels [23] (Fig. 5,a).

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Helvetica Chimica Acta – Vol. 93 (2010)
Fig. 4. Temperature-dependent CD spectra (in 108 steps from 0 to 508) of the tetramethyl ether 8 for a
0.5% (w/v) gel in CHCl3 and a 0.1% (w/v) gel in decan-1-ol, and of the pentol 9 for a 1% (w/v) gel in H2O
Fig. 5. Scanning-electron microscopy pictures of the dried a) 1% (w/v) gel and b) 0.4% (w/v) solution of
the pentan-1-ol 9 in H2O
Although the primary structure is not directly accessible by this technique, one can
reasonably assume that the assembly at the molecular level occurs by reticulation of
linear associates by H-bonding involving the nucleobases, as previously evidenced for

Helvetica Chimica Acta – Vol. 93 (2010)
901
A*[s]U dimers [3]. Interestingly, the 0.4% (w/v) solution of 9 in H2O (Fig. 5,b),
showed fibrous aggregates with a diameter of several mm, which presumably result from
the precipitation of a self-assembled fibrillar network from solution rather than from its
entrapment [23].
´
We thank Dr. Severine Hebbe for exploratory studies of 9, Dr. Michael Stalder, Laboratory of
Inorganic Chemistry, ETH Zꢀrich, for recording the SEM pictures, and Dr. Bruno Bernet for his
contribution to the conformational analysis and for checking the experimental part.
Experimental Part
General. See [2].
N6-Benzoyl-2’,3’-O-cyclohexylidene-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]adenosine (11). A
soln. of 10 [4] (8.00 g, 23.0 mmol) in dry pyridine at 08 was treated with thexyl(dimethyl)silyl chloride
(TDSCl; 6.3 ml, 32.2 mmol), stirred at 258 for 48 h, cooled to 08, treated with BzCl (13.3 ml,
114.6 mmol), and stirred at 258 for 72 h. The mixture was cooled to 08, treated with H2O (26 ml) and 25%
NH3 · H2O soln. (53 ml), and stirred for 30 min at 08. After evaporation, a soln. of the residue in toluene
was evaporated. A soln. of the residue in AcOEt was washed twice with 0.01m aq. HCl and twice with sat.
aq. NH4Cl soln., dried (Na2SO4), and evaporated. FC (cyclohexane/AcOEt 4 :1 ! 2 :1 ! 1:1) gave 11
(10.91 g, 80%). White solid. Rf (cyclohexane/AcOEt 1:1) 0.55. M.p. 958 (sintering from 658). [a]D25
¼
ꢀ51.0 (c ¼ 1.05, CHCl3). UV (CHCl3): 281 (22000). IR (ATR): 3240w (br.), 3200w (br.), 2936m,
2854w, 1696m, 1607m, 1580m, 1510m, 1485m, 1452s, 1407w, 1367w, 1330m, 1287m, 1248s, 1215m, 1162m,
1090s, 1028m, 1000w, 968w, 939w, 927w, 909w, 875w, 827s. 1H-NMR (300 MHz, CDCl3): see Table 5;
additionally, 9.12 (br. s, NH); 8.02 – 7.98 (m, 2 arom. H); 7.62 – 7.46 (m, 3 arom. H); 1.87 – 1.82 (m, 2 H);
1.71 – 1.50 (m, 6 H); 1.55 (sept., J ¼ 6.8, Me2CH); 1.44 – 1.38 (m, 2 H); 0.82 (d, J ¼ 6.8, Me2CH); 0.78 (s,
Me2CSi); 0.04 (s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 6; additionally, 164.50 (s, C¼O); 133.72
(s); 132.72 (d); 128.84 (2d); 127.83 (2d); 115.07 (s, (CH2)2C); 37.22, 34.93 (2t); 34.17 (d, Me2CH); 25.45 (s,
Table 5. Selected 1H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the Adenosines 11 – 13
and 15 – 18 in CDCl3
11
8.80
8.21
–
12
8.69
13
8.79
15a)
16
8.77
8.38
–
17
8.77
18
8.77
HꢀC(2)
HꢀC(8)
CHa – C(8)
CHb – C(8)
HꢀC(1’)
HꢀC(2’)
HꢀC(3’)
HꢀC(4’)
Ha – C(5’)
Hb – C(5’)
J(Ha,Hb)
J(1’,2’)
J(2’,3’)
J(3’,4’)
J(4’,5’a)
J(4’,5’b)
J(5’a,5’b)
8.33
7.82
–
–
–
–
–
4.93
4.93
6.26
5.71
5.04
4.22
3.67
3.58
4.93
4.87
6.30
5.83
5.10
4.29
3.74
3.63
12.6
2.5
6.3
3.4
5.9
4.98
4.94
6.07
5.22
4.20
4.16
3.91
3.74
15.7
5.8
5.1
4.0
5.7
4.91
4.87
6.17
5.26
4.27
4.17
3.92
3.74
12.6
5.4
5.1
4.4
5.6
–
–
–
6.20
5.31
4.95
4.41
3.84
3.75
–
2.8
6.2
2.6
4.2
4.4
5.87
4.73
4.16
4.39
4.02
3.70
–
8.0
4.9
< 1.5
6.22
4.38
4.04
4.22
4.02
3.81
–
3.7
4.6
5.8
3.4
2.8
b
)
2.4
6.4
3.5
6.1
5.8
10.8
1.5
1.6
13.0
5.9
10.8
4.1
11.2
4.1
11.2
11.2
11.6
a) J(5’a,OH) ¼ 1.9, J(5’b,OH) ¼ 12.0 Hz. b) Not assigned.

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Helvetica Chimica Acta – Vol. 93 (2010)
Table 6. Selected 13C-NMR Chemical Shifts [ppm] of the Adenosines 11 – 13 and 15 – 18 in CDCl3
11
12
13
15
16
17
18
C(2)
C(4)
C(5)
C(6)
152.77
149.47
123.38
151.24
141.79
–
91.56
84.26
81.18
87.42
63.38
152.53
149.08
121.34
152.28
154.72
57.71
90.05
82.77
81.18
153.05
149.61
121.97
152.17
150.04
36.72
90.44
82.56
81.24
152.28
148.33
121.18
156.17
140.82
–
89.82
81.92
79.54
85.51
63.78
152.76
149.57
123.67
151.43
141.66
–
87.03
82.08
77.35
82.64
61.97
152.54
149.25
121.97
153.00
155.16
57.85
87.45
79.51
78.29
83.04
62.33
153.03
149.76
122.37
152.69
150.65
36.73
87.75
79.51
78.21
82.90
C(8)
CH2ꢀC(8)
C(1’)
C(2’)
C(3’)
C(4’)
C(5’)
87.55
62.80
87.68
62.87
62.15
Me2CSi); 25.15, 24.22, 23.87 (3t); 20.47, 20.42 (2q, Me2CSi); 18.64 (q, Me2CH); ꢀ 3.16, ꢀ 3.28 (2q,
Me2Si). HR-MALDI-MS: 594.3100 ([M þ H]þ, C31H44N5O5Siþ; calc. 594.3112).
N6-Benzoyl-2’,3’-O-cyclohexylidene-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-8-(hydroxymethyl)-
adenosine (12). A soln. of (i-Pr)2NH (9.9 ml, 75.7 mmol) in dry THF (38 ml) at 08 was treated dropwise
with 1.6m BuLi in hexane (47.3 ml, 75.7 mmol), stirred for 40 min at 08, cooled to ꢀ 788, treated dropwise
with a soln. of 11 (8.989 g, 15.14 mmol) in dry THF (38 ml), stirred for 2 h at ꢀ 788, treated dropwise
with DMF (29 ml, 375 mmol), stirred for 3 h, treated with AcOH (29 ml), and allowed to warm to 258.
The mixture was diluted with EtOH (38 ml), cooled to 08, treated portionwise with NaBH4 (1.72 g,
45.4 mmol), stirred for 30 min at 08, diluted with sat. aq. NH4Cl soln. (100 ml) and H2O, and extracted
three times with AcOEt. The combined org. layers were washed three times with sat. aq. NH4Cl soln.,
dried (Na2SO4), and evaporated. FC (cyclohexane/AcOEt 2 :1 ! 1:1 ! AcOEt) gave 12 (7.691 g, 81%).
Slightly yellow solid. Rf (cyclohexane/AcOEt 1:1) 0.45. M.p. 1158 (sintering from 858). [a]2D5 ¼ ꢀ23.0
(c ¼ 0.95, CHCl3). UV (CHCl3): 283 (21720). IR (ATR): 3407w (br.), 3266w (br.), 2936m, 2864w,
1698m, 1611m, 1584m, 1531w, 1502w, 1484m, 1461m, 1448m, 1430m, 1356m, 1330m, 1249s, 1163m, 1092s,
1
1047s, 1000m, 969m, 939m, 927m, 909m, 897m, 875m, 828s. H-NMR (300 MHz, CDCl3): see Table 5;
additionally, 9.43 (br. s, NH); 8.02 – 7.98 (m, 2 arom. H); 7.57 – 7.42 (m, 3 arom. H); 5.59 (br. s, OH);
1.83 – 1.80 (m, 2 H); 1.71 – 1.49 (m, 6 H); 1.56 (sept., J ¼ 6.8, Me2CH); 1.46 – 1.38 (m, 2 H); 0.81 (d, J ¼
6.8, Me2CH); 0.77, 0.76 (2s, Me2CSi); ꢀ 0.04 (s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 6;
additionally, 165.03 (s, C¼O); 133.72 (s); 132.80 (d); 128.83 (2d); 128.00 (2d); 115.20 (s, (CH2)2C); 37.07,
34.91 (2t); 34.16 (d, Me2CH); 25.34 (s, Me2CSi); 25.11, 24.12, 23.76 (3t); 20.37, 20.34 (2q, Me2CSi); 18.55,
18.53 (2q, Me2CH); ꢀ 3.40 (q, Me2Si). HR-MALDI-MS: 624.3206 ([M þ H]þ, C32H46N5O6Siþ; calc.
624.3217).
N6-Benzoyl-8-(chloromethyl)-2’,3’-O-cyclohexylidene-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-
adenosine (13). A soln. of 12 (5.410 g, 8.67 mmol) in dry CH2Cl2 (43 ml) at 08 was treated with EtN(i-Pr)2
(2.27 ml, 13.01 mmol) and MsCl (738 ml, 9.54 mmol), stirred at 258 for 20 h, and evaporated. FC
(cyclohexane/AcOEt 4 :1 ! 1:1) gave 13 (4.013 g, 72%). White solid. Rf (cyclohexane/AcOEt 1:4) 0.18.
M.p. 908 (sintering from 678). [a]2D5 ¼ ꢀ18.0 (c ¼ 0.9, CHCl3). UV (CHCl3): 285 (22370). IR (ATR):
3249w (br.), 2936m, 2864w, 1697m, 1607m, 1580m, 1525m, 1498m, 1483m, 1463m, 1448m, 1429m, 1357m,
1344m, 1328m, 1248s, 1163m, 1142m, 1091s, 1028m, 1000m, 968w, 939m, 926m, 911m, 875m, 827s.
1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 9.00 (br. s, NH); 8.01 – 7.98 (m, 2 arom. H); 7.63 –
7.49 (m, 3 arom. H); 1.86 – 1.82 (m, 2 H); 1.73 – 1.52 (m, 6 H); 1.56 (sept., J ¼ 6.8, Me2CH); 1.45 – 1.41 (m,
2 H); 0.83 (d, J ¼ 6.8, Me2CH); 0.79, 0.78 (2s, Me2CSi); ꢀ 0.01, ꢀ 0.03 (2s, Me2Si). 13C-NMR (75 MHz,
CDCl3): see Table 6; additionally, 164.36 (s, C¼O); 133.60 (s); 132.86 (d); 128.92 (2d); 127.81 (2d); 115.12
(s, (CH2)2C); 37.25, 35.05 (2t); 34.28 (d, Me2CH); 25.45 (s, Me2CSi); 25.22, 24.23, 23.84 (3t); 20.51, 20.48
(2q, Me2CSi); 18.70, 18.68 (2q, Me2CH); ꢀ 3.21 (q, Me2Si). HR-MALDI-MS: 642.2885 ([M þ H]þ,
C32H45ClN5O5Siþ; calc. 642.2878).

Helvetica Chimica Acta – Vol. 93 (2010)
903
2’,3’-Di-O-methyladenosine (15) [8 – 10]. A suspension of 60% NaH in oil (1.159 g, 28.98 mmol) in
THF (20 ml) was cooled to 08, treated with a soln. of 14 [7] (6.226 g, 8.28 mmol) in THF (20 ml), and
stirred at 258 for 2.5 h. The mixture was cooled to 08, treated with MeI (1.55 ml, 24.8 mmol), stirred at 258
for 3 h, treated with sat. aq. NH4Cl soln., diluted with H2O, and extracted three times with AcOEt. The
combined org. layers were dried (Na2SO4) and evaporated. The residue was treated with AcOH/H2O 4 :1
(50 ml), stirred for 30 min at 1008, and evaporated. FC (AcOEt/MeOH 9 :1) and recrystallization in
EtOH gave 15 (1.627 g, 67%). White solid. Rf (AcOEt/MeOH 9 :1) 0.13. M.p. 1818 ([8]: 1778). [a]D25
¼
ꢀ120.5 (c ¼ 0.55, CHCl3; [8]: ꢀ 49). UV (CHCl3): 261 (14680). IR (ATR): 3362m, 3264m, 3230m,
3108m, 2988w, 2921m, 2832w, 2747w, 2692w, 1683s, 1611s, 1567m, 1514w, 1475m, 1422m, 1387m, 1343m,
1325w, 1289s, 1216m, 1186m, 1173w, 1114s, 1095s, 1076s, 1048s, 1021m, 977m, 952m, 911w, 879w, 815w.
1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 6.81 (dd, J ¼ 12.0, 1.9, HOꢀC(5’)); 5.74 (br. s,
NH2); 3.54, 3.33 (2s, 2 MeO). 13C-NMR (75 MHz, CDCl3): see Table 6; additionally, 58.60, 58.04 (2q,
2 MeO). HR-MALDI-MS: 296.1353 ([M þ H]þ, C12H18N5O4þ ; calc. 296.1359). Anal. calc. for
C12H17N5O4 (295.30): C 48.81, H 5.80, N 23.72; found: C 48.84, H 5.81, N 23.42.
N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-di-O-methyladenosine (16). A soln. of
15 (2.879 g, 9.75 mmol) in pyridine (45 ml) at 08 was treated with TDSCl (2.49 ml, 12.68 mmol), stirred at
258 for 7.5 h, and treated with two additional portions of TDSCl (2 ꢃ 1.3 ml, 13.2 mmol) over 24 h. The
soln. was cooled to 08, treated with BzCl (5.7 ml, 48.8 mmol), and stirred at 258 for 13 h. The mixture was
cooled to 08, treated with H2O (20 ml) and 25% NH3 · H2O soln. (40 ml), stirred for 30 min at 08, and
evaporated. A soln. of the residue in AcOEt was washed with aq. 0.01m HCl and sat. aq. NaHCO3 soln.
The org. layer was dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 95 :5) gave 16 (4.399 g, 83%).
White solid. Rf (CH2Cl2/MeOH 95 :5) 0.38. M.p. 608 (sintering from 458). [a]2D5 ¼ ꢀ13.6 (c ¼ 0.9, CHCl3).
UV (CHCl3): 280 (21670). IR (ATR): 3252w, 3125w, 3059w, 2955m, 2865w, 2830w, 1698m, 1608s, 1580s,
1509m, 1482m, 1451s, 1405w, 1390w, 1377w, 1326m, 1290m, 1248s, 1220s, 1189m, 1124s, 1094s, 1074s,
1048m, 1030m, 998m, 983m, 876m, 824m. 1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 9.20 (br.
s, NH); 8.00 – 7.98 (m, 2 arom. H); 7.59 – 7.46 (m, 3 arom. H); 3.57, 3.44 (2s, 2 MeO); 1.64 (sept., J ¼ 6.8,
Me2CH); 0.88 (d, J ¼ 6.8, Me2CH); 0.88 (s, Me2CSi); 0.16, 0.15 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3):
see Table 6; additionally, 164.77 (s, C¼O); 133.89 (s); 132.76 (d); 128.89 (2d); 127.94 (2d); 58.70, 58.19
(2q, 2 MeO); 34.15 (d, Me2CH); 25.53 (s, Me2CSi); 20.48, 20.40 (2q, Me2CSi); 18.64, 18.56 (2q, Me2CH);
ꢀ 3.24, ꢀ 3.46 (2q, Me2Si). HR-MALDI-MS: 542.2800 ([M þ H]þ, C27H40N5O5Siþ; calc. 542.2799).
N6-Benzoyl-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-8-(hydroxymethyl)-2’,3’-di-O-methyladeno-
sine (17). A soln. of (i-Pr)2NH (4.85 ml, 37.0 mmol) in THF (25 ml) at 08 was treated dropwise with 1.6m
BuLi in hexane (23.1 ml, 37.0 mmol), stirred for 40 min at 08, cooled to ꢀ 788, treated dropwise with a
soln. of 16 (4.006 g, 7.40 mmol) in THF (25 ml), stirred for 2 h at ꢀ 788, treated dropwise with DMF
(14.3 ml, 185 mmol), stirred for 3 h, treated with AcOH (6.4 ml, 111 mmol), and allowed to warm to 258.
The mixture was diluted with EtOH (30 ml), cooled to 08, treated portionwise with NaBH4 (840 mg,
22.2 mmol), stirred for 30 min at 08, treated with sat. aq. NH4Cl soln. and H2O, and extracted three times
with AcOEt. The combined org. layers were washed three times with sat. aq. NH4Cl soln., dried
(Na2SO4), and evaporated. FC (CH2Cl2/MeOH 95 :5) gave 17 (3.134 g, 74%). A sample for analysis was
recrystallized in MeCN. White solid. Rf (CH2Cl2/MeOH 95 :5) 0.23. M.p. 1478. [a]2D5 ¼ ꢀ34.9 (c ¼ 0.8,
CHCl3). UV (CHCl3): 283 (21380). IR (ATR): 3410w (sh.), 3233w, 3204w, 2955m, 2933m, 2868w, 2831w,
1698s, 1614s, 1583m, 1527m, 1505m, 1488m, 1461m, 1438m, 1344m (sh.), 1330m, 1301w, 1249s, 1209w,
1121s, 1071s, 998m, 986m, 966w, 937w, 899w, 875w, 828s. 1H-NMR (300 MHz, CDCl3): see Table 5;
additionally, 9.12 (br. s, NH); 8.04 – 8.02 (m, 2 arom. H); 7.62 – 7.50 (m, 3 arom. H); 4.24 (t, J ¼ 6.3, OH);
3.52, 3.43 (2s, 2 MeO); 1.59 (sept., J ¼ 6.9, Me2CH); 0.85 (d, J ¼ 6.9, Me2CH); 0.81 (s, Me2CSi); 0.08, 0.06
(2s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 6; additionally, 164.88 (s, C¼O); 133.88 (s); 132.84
(d); 128.96 (2d); 128.02 (2d); 58.58, 58.14 (2q, 2 MeO); 34.23 (d, Me2CH); 25.37 (s, Me2CSi); 20.38, 20.34
(2q, Me2CSi); 18.61 (q, Me2CH); ꢀ 3.37, ꢀ 3.42 (2q, Me2Si). HR-MALDI-MS: 572.2904 ([M þ H]þ,
C28H42N5O6Siþ; calc. 572.2897). Anal. calc. for C28H41N5O6Si (571.75): C 58.82, H 7.23, N 12.25; found: C
58.91, H 7.04, N 12.12.
N6-Benzoyl-8-(chloromethyl)-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-di-O-methyladenosine
(18). A soln. of 17 (1.892 g, 3.31 mmol) in CH2Cl2 (16 ml) at 08 was treated with EtN(i-Pr)2 (866 ml,
4.97 mmol) and MsCl (256 ml, 3.31 mmol), stirred at 258 for 24 h, treated with LiCl (140 mg, 3.31 mmol),

904
Helvetica Chimica Acta – Vol. 93 (2010)
and stirred for 7 h. The mixture was diluted with H2O and extracted three times with CH2Cl2. The
combined org. layers were dried (Na2SO4) and evaporated. FC (cyclohexane/AcOEt 1:1) gave 18
(1.847 g, 95%). White solid. Rf (cyclohexane/AcOEt 1:1) 0.45. M.p. 658 (sintering from 458). [a]D25
¼
ꢀ30.9 (c ¼ 0.7, CHCl3). UV (CHCl3): 286 (22630). IR (ATR): 3411w, 3253w, 2955m, 2929m, 2868w,
2831w, 1697m, 1608s, 1581m, 1525w, 1484m, 1461m, 1422m, 1352m, 1326m, 1247s, 1210w, 1190w, 1172w,
1125w, 1072w, 999w, 945w, 875w, 827s. 1H-NMR (300 MHz, CDCl3): see Table 5; additionally, 9.03 (br. s,
NH); 8.00 – 7.98 (m, 2 arom. H); 7.60 – 7.48 (m, 3 arom. H); 3.53, 3.45 (2s, 2 MeO); 1.56 (sept., J ¼ 6.9,
Me2CH); 0.83 (d, J ¼ 6.9, Me2CH); 0.79 (s, Me2CSi); 0.08, 0.03 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3):
see Table 6; additionally, 164.56 (s, C¼O); 133.78 (s); 132.87 (d); 128.96 (2d); 127.91 (2d); 58.59, 58.15
(2q, 2 MeO); 34.18 (d, Me2CH); 25.33 (s, Me2CSi); 20.34, 20.30 (2q, Me2CSi); 18.56 (q, Me2CH); ꢀ 3.40,
ꢀ 3.44 (2q, Me2Si). HR-MALDI-MS: 590.2561 ([M þ H]þ, C28H41ClN5O5Siþ; calc. 590.2565).
5’-S-Acetyl-2’,3’-O-cyclohexylidene-5’-thiouridine (20). A soln. of 19 [11] (869 mg, 2.68 mmol) in dry
pyridine (13 ml) at 08 was treated with TsCl (842 mg, 4.42 mmol), allowed to warm to 258, stirred for
20 h, and evaporated. A soln. of the residue in dry DMF (4 ml) was treated with AcSK (775 mg,
6.79 mmol) and heated to 758 for 2 h. After evaporating DMF, a soln. of the residue in AcOEt was
washed three times with sat. aq. NH4Cl soln. The combined org. layers were dried (Na2SO4) and
evaporated. FC (cyclohexane/AcOEt 4 :1 ! 1:1 ! AcOEt) gave 20 (792 mg, 77%). Slightly yellow solid.
Rf (cyclohexane/AcOEt 1:1) 0.40. M.p. 958 (sintering from 758). [a]2D5 ¼ þ10.3 (c ¼ 0.7, CHCl3). UV
(CHCl3): 259 (10190). IR (ATR): 3188w (br.), 3099w, 3062w, 2935w, 2860w, 1682s, 1631m, 1450m, 1423w,
1376m, 1356w, 1262m, 1229w, 1162m, 1087s, 1048m, 1008m, 964w, 939m, 927m, 909m, 869w, 846m, 808m.
1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 9.67 (br. s, NH); 2.37 (s, AcS); 1.77 – 1.72 (m,
2 H); 1.69 – 1.50 (m, 6 H); 1.45 – 1.32 (m, 2 H). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally,
194.74 (s, SC¼O); 115.45 (s, (CH2)2C); 37.00, 34.80 (2t); 30.71 (q, MeC¼O); 25.00, 24.03, 23.67 (3t). HR-
MALDI-MS: 405.1080 ([M þ Na]þ, C17H22N2NaO6Sþ; calc. 405.1096).
1
Table 7. Selected H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the Uridines 20 and
22 – 25 in CDCl3
20
22
5.92
8.18
5.82
4.14 – 4.24
4.14 – 4.24
4.29
3.94
3.78
23
24a)
25
5.78
HꢀC(5)
HꢀC(6)
HꢀC(1’)
HꢀC(2’)
HꢀC(3’)
HꢀC(4’)
HaꢀC(5’)
HbꢀC(5’)
J(5,6)
5.76
7.25
5.59
5.02
4.73
4.21
3.29
3.29
8.1
5.81
8.34
5.94
3.88
3.74
4.13
4.09
3.78
7.4
5.87
7.90
5.97
4.20
4.02
4.16
3.92
3.78
8.1
7.48
5.78
4.00
3.54
4.18
3.31
3.27
8.1
7.4
–
b
b
J(5,NH)
J(1’,2’)
J(2’,3’)
2.0
–
)
)
2.0
6.5
4.0
6.5
2.8
)
2.4
2.2
2.1
11.8
< 1.0
4.7
9.2
1.7
1.4
3.5
5.2
6.3
2.9
4.0
3.0
5.1
6.5
5.1
6.5
14.2
c
J(3’,4’)
J(4’,5’a)
J(4’,5’b)
J(5’a,5’b)
6.5
b
)
11.8
12.9
a) In D2O. b) Not assigned.
1-{5-O-[Dimethyl(1,1,2-trimethylpropyl)silyl]-b-d-ribofuranosyl}-4-methoxypyrimidin-2(1H)-one
(22). A soln. of 21 [12] (3.522 g, 13.64 mmol) and 1H-imidazole (1.207 g, 17.73 mmol) in DMF (38 ml) at
08 was treated with TDSCl (2.68 ml, 13.64 mmol), stirred at 258 for 18 h, treated with 1H-imidazole

Helvetica Chimica Acta – Vol. 93 (2010)
905
Table 8. Selected 13C-NMR Chemical Shifts [ppm] of the Uridines 20 and 22 – 25 in CDCl3
20
22
23
24a)
25
C(2)
C(4)
C(5)
C(6)
C(1’)
C(2’)
C(3’)
C(4’)
C(5’)
150.10
163.66
102.81
142.92
95.36
84.13
83.05
86.57
31.46
157.40
172.15
95.66
142.58
92.82
77.11
71.40
86.89
62.62
155.61
171.83
94.99
151.07
165.84
101.97
141.34
87.67
80.92
76.81
82.11
60.33
150.15
163.60
102.68
140.28
89.72
80.53
80.23
81.27
142.89
88.83
81.41b)
75.33
81.78b)
60.53
31.05
a) In D2O. b) Assignments may be interchanged.
(281 mg, 4.13 mmol), cooled to 08, treated with TDSCl (536 ml, 2.73 mmol), and stirred at 258 for 30 h.
After evaporation, a soln. of the residue in AcOEt was washed three times with sat. aq. NH4Cl soln. and
once with sat. aq. NaHCO3 soln. The org. layer was dried (Na2SO4) and evaporated to give crude 22
(5.069 g, ca. 93%), suitable for the next step without further purification. Colourless paste. Rf (AcOEt/
MeOH 9 :1) 0.67. 1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 4.75 (br. s, exchange with D2O,
OH); 3.95 (s, MeO); 3.74 (br. s, exchange with D2O, OH); 1.58 (sept., J ¼ 6.8, Me2CH); 0.84 (d, J ¼ 6.8,
Me2CH); 0.81 (s, Me2CSi); 0.11 (s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 54.79
(q, MeO); 34.10 (d, Me2CH); 25.49 (s, Me2CSi); 20.47, 20.35 (2q, Me2CSi); 18.66, 18.62 (2q, Me2CH);
ꢀ 3.19, ꢀ 3.29 (2q, Me2Si). HR-MALDI-MS: 423.1919 ([M þ Na]þ, C18H32N2NaO6Siþ; calc. 423.1927).
1-{5-O-[Dimethyl(1,1,2-trimethylpropyl)silyl]-2,3-di-O-methyl-b-d-ribofuranosyl}-4-methoxypyrimi-
din-2(1H)-one (23). A soln. of crude 22 (5.019 g, 12.53 mmol) in acetone (63 ml) was treated with Ag2O
(8.710 g, 37.59 mmol) and MeI (3.12 ml, 50.12 mmol), and stirred at 258 for 72 h. Filtration through Celite
and evaporation gave crude 23 (5.368 g, quant.), suitable for the next step without further purification.
Colourless paste. Rf (AcOEt) 0.63. 1H-NMR (300 MHz, CDCl3): see Table 7; additionally, 3.93 (s,
MeOꢀC(4)); 3.70, 3.34 (2s, 2 MeO); 1.63 (sept., J ¼ 6.8, Me2CH); 0.87 (d, J ¼ 6.8, Me2CH); 0.86 (s,
Me2CSi); 0.14 (s, Me2Si). 13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 58.67, 58.14 (2q,
2 MeO); 54.48 (q, MeOꢀC(4)); 34.11 (d, Me2CH); 25.63 (s, Me2CSi); 20.48, 20.43 (2q, Me2CSi); 18.65 (q,
Me2CH); ꢀ 3.12, ꢀ 3.35 (2q, Me2Si). HR-MALDI-MS: 429.2419 ([M þ H]þ, C20H37N2O6Siþ; calc.
429.2421).
2’,3’-Di-O-methyluridine (24) [12]. A soln. of crude 23 (5.312 g, 12.39 mmol) in MeOH/H2O 1:5
(68 ml) was treated with Amberlite IR-120 (Hþ form, 20 ml), stirred at 258 for 19 h, and filtered.
Evaporation, FC (AcOEt/MeOH 9 :1), and recrystallization in EtOH gave 24 (1.477 g, 40% from 21).
White solid. Rf (AcOEt/MeOH 9 :1) 0.43. M.p. 170 – 1728 ([12]: 176 – 1778). [a]2D5 ¼ þ66.4 (c ¼ 1.3,
1
MeOH) ([12]: [a]D25 ¼ þ74.7 (c ¼ 1.3, MeOH)). H-NMR (300 MHz, D2O): see Table 7; additionally,
3.51, 3.44 (2s, 2 MeO). 13C-NMR (75 MHz, D2O): see Table 8; additionally, 57.85, 57.51 (2q, 2 MeO).
5’-S-Acetyl-2’,3’-di-O-methyl-5’-thiouridine (25). A soln. of 24 (1.351 g, 4.96 mmol) in pyridine
(25 ml) at 08 was treated with TsCl (1.418 g, 7.44 mmol), stirred at 258 for 4 h, treated with two additional
portions of TsCl (2 ꢃ 709 mg, 3.72 mmol), added over 3 h, and stirred at 258 for 16 h. The mixture was
diluted with CH2Cl2, washed with 0.1m H2SO4, sat. aq. NaHCO3 soln., and brine. The combined org.
layers were dried (Na2SO4) and evaporated. A soln. of the residue in DMF (12.4 ml) was treated with
AcSK (1.416 g, 12.4 mmol), heated to 758 for 2 h, and evaporated. A soln. of the residue in AcOEt was
washed three times with sat. aq. NH4Cl soln. The combined org. layers were dried (Na2SO4) and
evaporated. FC (cyclohexane/AcOEt 4 :1 ! AcOEt ! AcOEt/MeOH 9 :1) gave 25 (763 mg, 47%).
Slightly red solid. Rf (cyclohexane/AcOEt 1:4) 0.24. M.p. 1038. [a]2D5 ¼ þ82.6 (c ¼ 0.8, CHCl3). UV
(CHCl3): 262 (10010). IR (ATR): 3145w, 3004w, 2917w, 2826w, 1770w, 1676s, 1627m, 1461w, 1383m,
1
1356w, 1319w, 1273m, 1258s, 1217m, 1192w, 1125s, 1106m, 1061s, 1010m, 963s, 870m, 819m. H-NMR
(300 MHz, CDCl3): see Table 7; additionally, 9.76 (br. s, NH); 3.53, 3.41 (2s, 2 MeO); 2.38 (s, AcS).

906
Helvetica Chimica Acta – Vol. 93 (2010)
13C-NMR (75 MHz, CDCl3): see Table 8; additionally, 194.63 (s, MeC¼O); 58.72, 58.36 (2q, 2 MeO);
30.69 (q, MeC¼O). HR-MALDI-MS: 353.0778 ([M þ Na]þ, C13H18N2NaO6Sþ; calc. 353.0783).
2’,3’-O-Cyclohexylidene-5’-O-[dimethyl(1,1,2-trimethylpropyl)silyl]adenosine-8-methyl-(81 ! 5’-S)-
2’,3’-O-cyclohexylidene-5’-thiouridine (26). A soln. of 20 (607 mg, 1.59 mmol) and 13 (1.019 g,
1.59 mmol) in dry degassed MeOH (3.2 ml) at 08 was treated with a freshly prepared 1.99m soln. of
MeONa in MeOH (3.2 ml, 6.36 mmol), and stirred at 258 for 17 h. The mixture was cooled to 08, diluted
with sat. aq. NH4Cl soln. and H2O, and extracted four times with AcOEt. The combined org. layers were
dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 95 :5) gave 26 (1.219 g, 91%). White solid. Rf
(CH2Cl2/MeOH 95 :5) 0.28. M.p. 1708 (sintering from 1408). [a]2D5 ¼ ꢀ79.0 (c ¼ 1.0, CHCl3). UV
(CHCl3): 263 (23060). IR (ATR): 3484w (sh.), 3330w (br.), 3188w, 2935m, 2863w, 1692s, 1634m, 1603m,
1577w, 1461w, 1446m, 1368m, 1330w, 1251m, 1231w, 1162w, 1144w, 1087s, 1051m, 968w, 938m, 927m,
909m, 874w, 828s. 1H-NMR (300 MHz, CDCl3; assignments based on a DQF-COSY and a HSQC
spectrum): see Table 9; additionally, 7.28 (d, J ¼ 8.1, HꢀC(6/I)); 5.73 (d, J ¼ 8.1, HꢀC(5/I)); 1.85 – 1.81
(m, 2 H); 1.74 – 1.35 (m, 18 H); 1.59 (sept., J ¼ 6.9, Me2CH); 0.82 (d, J ¼ 6.9, Me2CH); 0.77, 0.76 (2s,
Me2CSi); ꢀ 0.03, ꢀ 0.06 (2s, Me2Si). 13C-NMR (75 MHz, CDCl3; assignments based on a DQF-COSY
and a HSQC spectrum): see Table 10; additionally, 115.25, 114.45 (2s, 2 (CH2)2C); 37.18, 37.07, 35.07, 34.83
(4t); 34.31 (d, Me2CH); 25.38 (s, Me2CSi); 25.30, 25.11, 24.27, 24.16, 23.90, 23.77 (6t); 20.51 (q, Me2CSi);
18.70 (q, Me2CH); ꢀ 3.19 (q, Me2Si). HR-MALDI-MS: 842.3939 ([M þ H]þ, C40H60N7O9SSiþ; calc.
842.3942).
2’,3’-O-Cyclohexylideneadenosine-8-methyl-(81 ! 5’-S)-2’,3’-O-cyclohexylidene-5’-thiouridine (7). In
a polyethylene flask, a soln. of 26 (533 mg, 0.63 mmol) in dry THF (4 ml) at 258 was treated with a soln.
of Et3N · 3 HF (1.04 ml, 19 mmol) and stirred at 258 for 49 h. The mixture was cooled to 08, treated with
1m aq. NaOH soln. until the pH reached ca. 9, and extracted once with CH2Cl2/MeOH 9 :1 and four times
with CH2Cl2. The combined org. layers were dried (Na2SO4) and evaporated. FC (CH2Cl2/MeOH 9 :1)
gave 7 (392 mg, 88%). White solid. Rf (CH2Cl2/MeOH 9 :1) 0.45. M.p. 165 – 1758. [a]2D5 ¼ ꢀ74.5 (c ¼ 0.74,
CHCl3/MeOH 7:1). UV (CHCl3/MeOH 7:1): 264 (25010). IR (ATR): 3331w, 3194w, 2933m, 2859w,
1690s, 1635s, 1603m, 1579m, 1447m, 1369m, 1332m, 1262m, 1230m, 1162m, 1145w, 1089s, 1053s, 967m,
1
936s, 926s, 909m, 847m. H-NMR (400 MHz, (D6)DMSO; assignments based on a DQF-COSY and a
HSQC spectrum): see Table 9; additionally, 7.69 (d, J ¼ 8.1, HꢀC(6/I)); 5.63 (dd, J ¼ 8.1, 2.1, HꢀC(5/I));
5.26 (dd, J ¼ 6.5, 5.1, HOꢀC(5’/II); 1.81 – 1.78 (m, 2 H); 1.62 – 1.29 (m, 18 H). 13C-NMR (100 MHz,
(D6)DMSO; assignments based on a DQF-COSY and a HSQC spectrum): see Table 10; additionally,
113.90, 113.76 (2s, 2 (CH2)2C); 36.68, 36.42, 34.43, 34.19 (4t); 24.48, 24.43, 23.67, 23.56, 23.25, 23.16 (6t).
HR-MALDI-MS: 700.2760 ([M þ H]þ, C32H42N7O9Sþ; calc. 700.2765).
5’-O-[Dimethyl(1,1,2-trimethylpropyl)silyl]-2’,3’-di-O-methyladenosine-8-methyl-(81 ! 5’-S)-2’,3’-di-
O-methyl-5’-thiouridine (27). A soln. of 18 (1.152 g, 1.95 mmol) and 25 (645 mg, 1.95 mmol) in degassed
MeOH (6 ml) at 08 was treated with a freshly prepared 1.95m soln. of MeONa in MeOH (4.0 ml,
7.8 mmol) and stirred at 258 for 18 h. The mixture was cooled to 08, treated with sat. aq. NH4Cl soln. and
H2O, and extracted four times with AcOEt. The combined org. layers were dried (Na2SO4) and
evaporated. FC (CH2Cl2/MeOH 9 :1) gave 27 (1.242 g, 86%). White solid. Rf (CH2Cl2/MeOH 9 :1) 0.39.
M.p. 110 – 1188. [a]2D5 ¼ ꢀ11.6 (c ¼ 0.7, CHCl3). UV (CHCl3): 264 (27090). IR (ATR): 3328w, 3194w,
2933m, 2830w, 1690s, 1635s, 1603m, 1576w, 1442m, 1368m, 1329w, 1298w, 1257m, 1207w, 1128s, 1067s,
1018m, 990m, 875w, 828s. 1H-NMR (400 MHz, CDCl3; assignments based on a DQF-COSYand a HSQC
spectrum): see Table 9; additionally, 7.56 (d, J ¼ 8.1, HꢀC(6/I)); 5.74 (d, J ¼ 8.1, HꢀC(5/I)); 3.52, 3.48,
3.42, 3.33 (4s, 4 MeO); 1.56 (sept., J ¼ 6.9, Me2CH); 0.83 (d, J ¼ 6.9, Me2CH); 0.78 (s, Me2CSi); 0.04, 0.03
(2s, Me2Si). 13C-NMR (100 MHz, CDCl3; assignments based on a DQF-COSY and a HSQC spectrum):
see Table 10; additionally, 58.58, 58.52, 58.07, 58.01 (4q, 4 MeO); 34.23 (d, Me2CH); 25.27 (s, Me2CSi);
20.36, 20.34 (2q, Me2CSi); 18.60 (q, Me2CH); ꢀ 3.39, ꢀ 3.40 (2q, Me2Si). HR-MALDI-MS: 738.3298
([M þ H]þ, C32H52N7O9SSiþ; calc. 738.3316).
2’,3’-Di-O-methyladenosine-8-methyl-(81 ! 5’-S)-2’,3’-di-O-methyl-5’-thiouridine (8). In a polyethy-
lene flask, a soln. of 27 (683 mg, 0.93 mmol) in THF (6.2 ml) at 258 was treated with a soln. of (HF)3 ·
Et3N (1.52 ml, 27.8 mmol) and stirred at 258 for 48 h. The mixture was diluted with THF, treated with
1m aq. NaOH soln. until the pH reached ca. 10, and extracted four times with CH2Cl2/MeOH 9 :1. The
combined org. layers were evaporated. FC (CH2Cl2/MeOH 95 :5 ! 90 :10) gave 8 (540 mg, 98%). White

Helvetica Chimica Acta – Vol. 93 (2010)
907
Table 9. Selected 1H-NMR Chemical Shifts [ppm] and Coupling Constants [Hz] of the A*[s]U
Dinucleotides: 26 and 27 in CDCl3, and 7 – 9 in (D6)DMSO Solutiona)
26
27
7
8
9
60 mm
101 mm
130 mm
120 mm
37 mm
Uridine unit (I)
HꢀN(3/I)
HꢀC(1’/I)
HꢀC(2’/I)
HꢀC(3’/I)
HꢀC(4’/I)
HaꢀC(5’/I)
HbꢀC(5’/I)
J(1’,2’/I)
11.78
5.57
4.99
4.73
4.22 – 4.28
3.00
2.95
1.8
11.59
5.87
3.90
3.67
4.23 – 4.28
3.03
2.96
3.5
11.41
5.78
4.97
4.60
4.08
2.92
2.92
2.4
11.41
5.83
4.07 – 4.09
3.73
4.07 – 4.09
3.00
2.93
11.34
5.78
4.12
3.90
3.97 – 4.02
2.96
2.87
5.5
5.4
J(2’,3’/I)
6.5
5.3
6.5
4.7
5.6
J(3’,4’/I)
4.0
6.2
4.0
4.7
4.7
J(4’,5’a/I)
J(4’,5’b/I)
J(5’a,5’b/I)
6.5
5.6
13.3
5.2
4.8
14.4
6.7
6.0
6.3
14.1
5.2
6.7
13.9
6.7
b
)
Adenosine unit (II)
H2NꢀC(6/II)
HꢀC(2/II)
CHaꢀC(8/II)
CHbꢀC(8/II)
HꢀC(1’/II)
HꢀC(2’/II)
HꢀC(3’/II)
HꢀC(4’/II)
HaꢀC(5’/II)
HbꢀC(5’/II)
J(Ha,Hb/II)
J(1’,2’/II)
6.99
8.32
4.18
4.10
6.32
5.93
5.09
4.22 – 4.28
3.64
3.52
14.6
1.9
6.51
8.31
4.26
4.11
6.05
5.45
4.23 – 4.28
4.14
3.93
3.68
14.4
5.8
7.34
8.12
4.16
4.08
6.19
5.61
5.02
4.17
3.55
3.47
14.4
3.2
7.64
8.18
4.13
4.13
6.01
4.90
4.16
4.12 – 4.14
3.69
7.37
8.08
4.14
4.03
5.92
4.81
4.17
3.97 – 4.02
3.69
3.55
14.3
7.2
3.56
b
)
7.1
5.1
J(2’,3’/II)
6.2
5.5
6.2
5.3
J(3’,4’/II)
2.9
3.6
2.9
2.3
2.0
J(4’,5’a/II)
6.9
6.8
4.8
3.8
3.1
J(4’,5’b/II)
6.4
4.5
4.8
3.5
3.1
J(5’a,5’b/II)
10.5
11.0
11.7
12.2
12.4
a) Assignments based on a DQF-COSY and a HSQC spectrum. b) Not assigned.
solid. Rf (CH2Cl2/MeOH 9 :1) 0.36. M.p. 137 – 1488. [a]2D5 ¼ ꢀ56.2 (c ¼ 0.9, DMSO). UV (MeOH): 264
(24220). IR (ATR): 3386w, 3327w, 3193m, 3063w, 2988w, 2927w, 2829w, 1704s, 1693s, 1655s, 1633s, 1575w,
1446m, 1372m, 1333m, 1306w, 1275s, 1261s, 1221w, 1200w, 1127m, 1092s, 1065s, 1019m, 985m, 918w, 883w,
859w, 828w. 1H-NMR (400 MHz, (D6)DMSO; assignments based on a DQF-COSY and a HSQC
spectrum): see Table 9; additionally, 7.65 (d, J ¼ 8.1, HꢀC(6/I)); 6.2 – 5.5 (br. s, HOꢀC(5’/II)); 5.66 (dd,
J ¼ 8.1, 2.1, HꢀC(5/I)); 3.42, 3.30, 3.27, 3.26 (4s, 4 MeO). 13C-NMR (100 MHz, (D6)DMSO; assignments
based on a DQF-COSY and a HSQC spectrum): see Table 10; additionally, 57.56, 57.40, 57.26, 57.11 (4q,
4 MeO). HR-MALDI-MS: 596.2133 ([M þ H]þ, C24H34N7O9Sþ; calc. 596.2139).
Adenosine-8-methyl-(81 ! 5’-S)-5’-thiouridine (9). A suspension of 28 [1] (426 mg, 0.69 mmol) in
H2O (1.4 ml) at 08 was treated with TFA (5.6 ml), vigorously stirred at 258 for 45 min, and evaporated at
258. A soln. of the residue in H2O was treated with Amberlite IRA-68 (free base form) until the pH

908
Helvetica Chimica Acta – Vol. 93 (2010)
Table 10. Selected 13C-NMR Chemical Shifts [ppm] of the A*[s]U Dinucleotides: 26 and 27 in CDCl3,
and 7 – 9 in (D6)DMSO Solutiona)
26
27
7
8
9
Uridine unit (I)
C(2/I)
C(4/I)
C(5/I)
C(6/I)
C(1’/I)
C(2’/I)
C(3’/I)
C(4’/I)
150.97
163.75
103.14
142.72
95.63
84.13
83.35
90.31
34.78
151.12
164.09
102.99
140.39
89.22
81.42
79.76
81.00
33.67
150.24
163.12
102.03
142.64
91.74
82.97
82.29
85.22
33.41
150.43
162.88
102.31
140.45
86.63
80.67
79.29
79.84
33.36
150.70
162.97
102.17
140.94
88.25
72.49
72.12
82.73
35.51
C(5’/I)
Adenosine unit (II)
C(2/II)
C(4/II)
C(5/II)
C(6/II)
152.58
150.97
118.40
155.41
149.37
28.99
88.14
82.51
82.00
87.10
152.66
150.77
118.82
155.46
150.04
28.71
152.30
149.77
117.94
155.66
148.13
27.73
89.43
81.81
151.16
149.80
118.09
154.96
148.95
27.93
86.72
79.95
78.17
83.89
61.86
151.85
149.66
118.24
155.79
148.48
27.91
88.70
72.35
70.88
86.79
62.15
C(8/II)
CH2ꢀC(8/II)
C(1’/II)
87.53
C(2’/II)
C(3’/II)
C(4’/II)
C(5’/II)
78.82b)
78.77b)
82.84
80.95
86.35
61.51
63.09
62.33
a) Assignment based on a DQF-COSY and a HSQC spectrum. b) Assignment may be interchanged.
reached 7. Filtration (washing with H2O and MeOH), evaporation, and FC (AcOEt/MeOH/H2O
7:2 :0.5 ! 7:2 :1) gave 9 (364 mg, 98%). White solid. Rf (AcOEt/MeOH/H2O 7:2 :1) 0.41. M.p. 1858
(dec.). [a]2D5 ¼ ꢀ40.3 (c ¼ 0.5, DMSO). UV (MeOH): 265 (19280). IR (ATR): 3327m, 3195m, 2931w,
1671s, 1645s, 1577m, 1449m, 1378m, 1334m, 1309w, 1261m, 1201m, 1123s, 1080s, 1044s, 987m, 913w, 886w.
1H-NMR (400 MHz, (D6)DMSO; assignments based on a DQF-COSY and a HSQC spectrum): see
Table 9; additionally, 7.64 (d, J ¼ 8.1, HꢀC(6/I)); 5.93 (dd, J ¼ 9.4, 3.1, HOꢀC(5’/II)); 5.62 (d, J ¼ 8.1,
HꢀC(5/I)); 5.46 (d, J ¼ 5.7, HOꢀC(2’/I)); 5.33 (d, J ¼ 7.6, HOꢀC(2’/II)); 5.30 (d, J ¼ 4.3, HOꢀC(3’/II));
5.23 (d, J ¼ 5.5, HOꢀC(3’/I)). 13C-NMR (100 MHz, (D6)DMSO; assignments based on a DQF-COSY
and a HSQC spectrum): see Table 10. HR-MALDI-MS: 540.1502 ([M þ H]þ, C20H25N7O9Sþ; calc.
540.1513).
CD Spectra of the Gels. The CD measurements were performed according to [2], except for the gel of
8 in decan-1-ol: 2.0-nm band width, 1-s response, low sensitivity, 0.1 nm data pitch, and 200-nm/min
scanning speed.
REFERENCES
[1] A. Ritter, D. Egli, B. Bernet, A. Vasella, Helv. Chim. Acta 2008, 91, 673.
[2] N. Bogliotti, A. Ritter, S. Hebbe, A. Vasella, Helv. Chim. Acta 2008, 91, 2181.
[3] N. Bogliotti, A. Vasella, Helv. Chim. Acta 2009, 92, 1167.
[4] M. Thiel, K. Stach, W. Schaumann, K. Dietmann, US Pat. 3,412,082, 1968.
[5] H. Hayakawa, K. Haraguchi, H. Tanaka, T. Miyasaka, Chem. Pharm. Bull. 1987, 35, 72.
[6] W. Czechtizky, A. Vasella, Helv. Chim. Acta 2001, 84, 594.

Helvetica Chimica Acta – Vol. 93 (2010)
909
[7] C. D. Anderson, L. Goodman, B. R. Baker, J. Am. Chem. Soc. 1959, 81, 3967.
[8] J. B. Gin, C. A. Dekker, Biochemistry 1968, 7, 1413.
[9] Z. Kazimierczuk, E. Darz˙ynkiewicz, D. Shugar, Biochemistry 1976, 15, 2735.
[10] K. Yamauchi, M. Kinoshita, J. Chem. Soc., Perkin Trans. 1 1978, 762; K. Yamauchi, T. Nakagima, M.
Kinoshita, J. Chem. Soc., Perkin Trans. 1 1980, 2787; K. Yamauchi, T. Nakagima, M. Kinoshita, J.
Org. Chem. 1980, 45, 3865; K. Yamauchi, K. Hattori, M. Kinoshita, J. Chem. Soc., Perkin Trans. 1
1985, 1327.
´
[11] S. Chladek, J. Smrt, Collect. Czech. Chem. Commun. 1963, 28, 1301.
[12] M. J. Robins, S. R. Naik, Biochemistry 1971, 10, 3591.
[13] M. Prashad, K. Prasad, O. Repic, Nucleosides, Nucleotides Nucleic Acids 1994, 13, 945.
[14] X. Zhang, B. Bernet, A. Vasella, Helv. Chim. Acta 2006, 89, 2861.
[15] H. Gunji, A. Vasella, Helv. Chim. Acta 2000, 83, 1331.
[16] D. B. Davies, Prog. Nucl. Magn. Reson. Spectrosc. 1978, 12, 135.
[17] H. S. Gutowsky, A. Saika, J. Chem. Phys. 1953, 21, 1688.
[18] M. Chastrette, M. Rajzmann, M. Chanon, K. F. Purcell, J. Am. Chem. Soc. 1985, 107, 1.
[19] E. Snip, K. Koumoto, S. Shinkai, Tetrahedron 2002, 58, 8863.
[20] I. Yoshikawa, S. Yanagi, Y. Yamaji, K. Araki, Tetrahedron 2007, 63, 7474.
[21] R. Luboradzki, O. Gronwald, A. Ikeda, S. Shinkai, Chem. Lett. 2000, 1148.
[22] G. John, G. Zhu, J. Li, J. S. Dordick, Angew. Chem., Int. Ed. 2006, 45, 4772.
[23] L. A. Estroff, A. D. Hamilton, in ꢂMolecular Gels: Materials with Self-Assembled Fibrillar
Networksꢃ, Eds. R. G. Weiss, P. Terech, Springer-Verlag, Dordrecht, 2006, pp. 721 – 742.
Received February 8, 2010