Covalent modification of 2′-deoxyuridine with two different molecular switches

Article abstract of DOI:10.1055/s-0031-1290599

Two different molecular switches, a spiropyran and a diarylethene, were attached synthetically to the 5-position of 2-de-oxyuridine. The diarylethene-modified nucleoside can be incorporated synthetically into DNA while preserving its characteristic photochromism. Georg Thieme Verlag Stuttgart · New York.

Full text of DOI:10.1055/s-0031-1290599

LETTER
711
Covalent Modification of 2¢-Deoxyuridine with Two Different Molecular
Switches
Covalent
M
od
e
ification of
b
2
¢
-
Deoxyuri
a
Karlsruhe Institute of Technology, Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
Fax +49(721)60844825; E-mail: Wagenknecht@kit.edu
Received 14 December 2011
ified 2¢-deoxyuridine 1 and the corresponding dia-
rylethene-modified nucleoside 2 and their photoswitching
behavior. With respect to several disadvantages of spiro-
pyrans as covalent labels in DNA we incorporated only
the diarylethene 2 into one representative oligonucleotide
using automated phosphoramidite chemistry, and charac-
terized its photochromism in DNA1 preliminarily.
Abstract: Two different molecular switches, a spiropyran and a di-
arylethene, were attached synthetically to the 5-position of 2¢-de-
oxyuridine. The diarylethene-modified nucleoside can be
incorporated synthetically into DNA while preserving its character-
istic photochromism.
Key words: oligonucleotide, palladium, DNA, photochromism,
phosphoramidite
The synthesis of the spiropyrane 1 (Scheme 1) applied our
previously improved protocol for the preparation of
spirobenzopyrans by ultrasonic irradiation.19 With this
protocol, typically good yields were obtained, and the re-
action time is significantly reduced compared to standard
reaction conditions. Accordingly, the reaction of freshly
distilled Fischer base 319 with 419 under ultrasonic irradi-
ation conditions in EtOH for one hour gave the corre-
sponding N-methyl spirobenzopyran 520 in 76% yield.
The 6-bromo compound 821 was prepared from the indo-
lium iodide 619 and 719 with addition of excess triethyl-
amine under ultrasonic conditions in EtOH and obtained
as a pale pink solid in 77% yield. With the spirobenzopy-
rans 5 and 8 in hand, the Sonogashira cross-coupling was
performed subsequently in two different ways. First, com-
mercially available 5-iodo-2¢-deoxyuridine (9) and
spirobenzopyran 5 were heated at 55 °C for three hours in
Et3N in the presence of Pd(PPh3)2Cl2 (3 mol%) and CuI (5
mol%) as catalysts to provide nucleoside 1 in a yield of
27%. The similarly performed reaction of nucleoside 1022
with the spirobenzopyran 8 gave product 1 in comparable
low yield (24%). Interestingly, a better cross-coupling ef-
ficiency was observed with increased amounts of cata-
lysts: 5 and 9 were dissolved in a mixture of DMF and
Et3N with a relatively high amount of Pd(dppf)Cl2 (17
mol%) and CuI (22 mol%), and the reaction was carried
out at room temperature for 26 hours. Under these opti-
mized reaction conditions, the desired nucleoside 123 was
isolated in 67% yield.
Switching optical properties by light represents an impor-
tant task for the development of new photoreactive nano-
structured materials including those that are based on
nucleic acids. Especially diazobenzenes, spirobenzopyr-
ans and diarylethenes1–3 were prepared and applied as mo-
lecular switches for all kinds of biomolecules.4–13 With
respect to nucleic acids mainly diazobenzene derivatives
were developed as artificial and photoswitchable nucleo-
sides that are suitable to control a variety of different func-
tions in DNA.6–8 Both alternatives, spiropyrans and
diarylethenes, remain rather unexplored as covalent pho-
tochromic labels for nucleic acids, despite their great po-
tential as molecular switches.
In contrast to simple cis-trans switching of diazobenzenes
the ring opening of spiropyrans to merocyanines repre-
sents not only a major structural change but includes also
a large change in polarity.3 In fact, studies with spiropyr-
ans as non-covalently acting DNA and RNA binders have
revealed that strong ground state interactions occur only
between the merocyanine form and the DNA base
stack.14,15 The description of covalent attachment of spiro-
pyran to DNA can be found only very rarely in the
literature12,13 and includes our approach to incorporate
synthetically the spiropyran chromophore as an artificial
DNA base into oligonucleotides.16
The second alternative, diarylethenes, are applied in the
context of switching binding properties of proteins and
peptides17 but are still nearly completely unexplored with
respect to nucleic acids. There is only one recent report on
how to combine 7-deazaadenosine with thiophene to ob-
tain a nucleosidic diarylethene switch.18 Other examples
include simpler stilbene-like switches that do not exhibit
the good photochromic performance of diarylethenes.
Herein, we present the synthesis of the spiropyrane-mod-
The photoswitching properties of the synthesized
spirobenzopyran-modified nucleoside 1 were studied by
UV/Vis spectroscopy (Figure 1). Upon irradiation with
UV light (l = 312 nm) for one minute an increase in the
visible range was observed. The formation of the merocy-
anine form with the characteristic absorption at l = 589
nm was also observable by eye, since the former colorless
solution turned magenta-red. Further irradiation of the
sample for one more minute did not give any further in-
crease; obviously the photostationary equilibrium be-
tween the spiropyran and the merocyanine isomers was
SYNLETT 2012, 23, 711–716
x
x.
x
x.
2
0
1
2
Advanced online publication: 28.02.2012
DOI: 10.1055/s-0031-1290599; Art ID: B77211ST
© Georg Thieme Verlag Stuttgart · New York

712
S. Barrois et al.
LETTER
N+
N
3
6
Me
Me
Br
+
+
O
O
HO
HO
4
7
53 min
76%
2 h
EtOH, )))
EtOH, )))
77%
Figure 1 UV/Vis absorption of spiropyran (closed) form of 1 and
interconversion into merocyanine (open) form, in MeOH (100 mM 1)
at r.t.: after 2 min irradiation with l = 312 nm (red), after thermal re-
closing (blue). Inset shows the time dependence of absorption change
at l = 589 nm due to thermal interconversion of 1 from the mero-
cyanine to the spiropyran form at r.t.
N
O
Br
N
O
Me
Me
8
5
Pd(dppf)Cl2
CuI
DMF, Et3N
Pd(PPh3)4Cl2
CuI
O
N
O
Et3N
I
NH
NH
r.t., 26 h
67%
60 °C, 3 h
24%
available 5-bromo benzothiazole (11) that was methylated
by methyl iodide after deprotonation with LDA to obtain
1225 in quantitative yield. A double Friedel–Crafts-type
acylation using glutaryl chloride linked together two ben-
zothiazoles 12 to compound 1326 in 74% yield. Subse-
quently the central cyclopentene group of 1427 was built
by a double McMurry-type reaction, that meant treatment
of 13 with Zn and TiCl4. The ethynyl linker was attached
by TMS-protected acetylene in a Pd-catalyzed cross-cou-
pling reaction. Although the yield of 1528 was only mod-
erate (43%), attempts to improve it failed. The
competitively formed double substituted by-product
could not be avoided. Thus the potentially usable amount
of TMS-protected acetylene decreased. The synthesis of
the diarylethene building block 1629 was concluded by re-
moval of the TMS protecting group of 15 under standard
conditions using K2CO3 in MeOH. Finally, diarylethene
16 was coupled to 5-iodo-2¢-deoxyuridine by the already
mentioned Sonogashira-type coupling to the diarylethene-
modified nucleoside 2.30
O
N
O
HO
HO
O
O
OH
OH
9
10
N
O
Me
O
NH
N
O
HO
O
OH
1
Scheme 1 Synthesis of the spiropyran-modified nucleoside 1
reached. When the irradiation was abandoned, thermal
reformation of the spiropyran form was observed within
10 minutes at room temperature.
The characteristic absorption bands of the diarylethene
chromophore at l = 242 nm and l = 305 nm are clearly de-
tectable in the UV/Vis spectrum of the modified nucleo-
side 2 if the spectrum is compared with that of 14
(Figure 2). Irradiation of 2 in the UV range, either at l =
242 nm or at l = 310 nm, closed the diarylethene moiety
and the visible absorption band rose at l = 450 nm. The
color of the solution turned yellow. After 30 minutes, the
photostationary state was reached. Irradiation of the sam-
ple at l = 450 nm opened again the chromophore in a few
minutes. In contrast to spiropyrane 1, thermally induced
opening to the diarylethene-modified isomer of 2 was not
observed. The irradiation cycle of closing and subsequent
opening could be repeated several times. The modified
nucleoside 2 stayed similarly stable as the molecular
switch 14. Moreover, the nucleoside 2 shows overall very
similar optical properties as 14. This is a remarkable ob-
servation since the diarylethene chromophore in 2 is con-
Although the spiropyran-modified nucleoside 1 exhibits
promising optical properties, we did not incorporate it into
oligonucleotides for two different reasons: (i) It is report-
ed that spiropyrans decompose in aqueous buffer solu-
tions,24 and (according to our experience) the DNA
environment does not efficiently prevent this decomposi-
tion. (ii) In another study that was performed at the same
time as the part of work presented herein we found out that
the spiropyran chromophore in the DNA environment los-
es its photoswitching abilities.16 Hence, we focused our
efforts on the second alternative which is the diarylethene-
modified nucleoside 2.
The preparation of nucleoside 2 was also based on a
Sonogashira-type cross-coupling as the key step to attach
the photoactive chromophore to the nucleoside
(Scheme 2). The synthesis started with commercially
Synlett 2012, 23, 711–716
© Thieme Stuttgart · New York

LETTER
Covalent Modification of 2¢-Deoxyuridine
713
Br
S
Br
Br
glutaryl
chloride
AlCl3
CH2Cl2
0 °C to r.t., 3 h
O
O
S
S
74%
R
13
11 R = H
THF
–78 to 0 °C, 1 h
Zn, TiCl4
40 °C, 18 h
THF 55 %
THF
–78 °C to r.t., 2 h
99 %
12 R = Me
R
Br
S
S
14 R = Br
THF, reflux, 19 h
43%
TMS
Pd(PPh3)4, CuI,
Et3N
15 R =
TMS
K2CO3
MeOH
40 °C, 18 h
99%
16 R =
O
I
Pd(PPh3)4, CuI
Et3N
NH
N
O
DMF
60 °C, 18 h
HO
O
Figure 2 Top: UV/Vis absorption of open form of 2 and 14 and in-
terconversion into closed form, in acetonitrile (20 mM) at r.t.; after 30
min irradiation with l = 310 nm (red), after 30 min irradiation at l =
450 nm (blue). Inset shows time dependence of absorption change at
l = 450 nm due to the interconversion of 2 and 14 from the open to
the closed form and back to the opened form. Bottom: Absorption
changes at l = 450 nm due to irradiation cycles between the open and
closed form of 2 and 14.
65%
OH
9
S
S
O
N
Br
NH
O
R1O
yields the characteristic absorption of the closed form at l
= 450 nm, and irradiation at the latter wavelength drives
the reaction back to the open form of the switch in DNA1.
It is important to note here that the kinetics for opening
and closing of 2 cannot directly be compared to DNA1
since the solvent in both measurements is different.
DNA1 bearing the open form of the diarylethene switch
exhibited a melting temperature of 60.6 °C. After irradia-
tion at l = 310 nm, the melting temperature decreased sig-
nificantly to 56.8 °C. At the moment this observation
lacks any plausible explanation and needs to be further ex-
plored in the future.
O
OR2
2 R1 = H, R2 = H
pyridine
DMTCl
Et3N
40 °C, 18 h
90%
17 R1 = DMT, R2 = H
N(i-Pr)2
CH2Cl2
r.t., 40 min
99%
P
CN
N(i-Pr)2
Cl
O
P
CN
18 R1 = DMT, R2
=
O
i-PrNEt2
Scheme 2 Synthesis of diarylethene nucleoside 2 and the corre-
sponding DNA building block 18
In conclusion it becomes clear that spiropyrane and dia-
rylethene as well-known molecular switches can be at-
tached covalently to the 5-position of 2¢-deoxyuridine.
Sonogashira-type cross-couplings represent the key steps
in the syntheses of the modified nucleosides 1 and 2 yield-
ing short ethynyl linkers between chromophore and uri-
dine. The photoactive properties of the molecular
switches are maintained in the corresponding nucleosides
1 and 2. The preliminary investigation of the representa-
tively prepared DNA1 shows clearly that diarylethene-
modified 2¢-deoxyuridine can be switched from the open
to closed form and backwards by irradiation in the DNA
environment. The latter result represents one important
jugated with the uracil aromatic system via the acetylene
bridge.
The preparation of the DNA building block 18 follows
standard procedures, including the protection of the 5¢-
OH group of 2 by DMT and subsequent phosphitylation
of the intermediate 1731 to phosphoramidite 18.32 We pre-
pared one representative oligonucleotide33 in order to re-
port preliminarily the optical properties of 2 in double-
stranded DNA1. It is remarkable to observe that the pho-
toswitching behavior of 2 is maintained in the DNA envi-
ronment (Figure 3). Irradiation of DNA1 with l = 310 nm
© Thieme Stuttgart · New York
Synlett 2012, 23, 711–716

714
S. Barrois et al.
LETTER
(8) Liang, X.; Asanuma, H.; Komiyama, M. J. Am. Chem. Soc.
2002, 124, 1877.
(9) Sakata, T.; Yan, Y.; Marriott, G. J. Org. Chem. 2005, 70,
2009.
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Liang, X.; Komiyama, M. Chem. Lett. 2001, 30, 108.
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Chem. Soc. 2008, 130, 11836.
(15) Young, D.; Deiters, A. ChemBioChem 2008, 9, 1225.
(16) Beyer, C.; Wagenknecht, H.-A. Synlett 2010, 1371.
(17) Vomasta, D.; Hogner, C.; Branda, N.; König, B. Angew.
Chem. 2008, 47, 7644.
(18) Singer, M.; Jäschke, A. J. Am. Chem. Soc. 2010, 132, 8372.
(19) Beyer, C.; Wagenknecht, H.-A. J. Org. Chem. 2010, 75,
2752.
(20) Compound 5: Compound 419 (490 mg, 3.35 mmol) was
dissolved in anhyd EtOH (50 mL), freshly distilled 319 (0.59
mL, 3.33 mmol) was added in one portion, and the reaction
mixture was sonicated at 35 kHz under Ar. After 53 min the
solvent was removed under reduced pressure. The crude
product was purified by gradient flash chromatography on
silica gel (hexane–THF, 70:1 → 50:1) yielding 5 (762 mg,
76%) as a pale blue foam; Rf 0.36 (hexane–THF, 50:1). 1H
NMR (600 MHz, CDCl3): d = 7.15–7.27 (m, 2 H, ArH), 7.20
(dt, 1 H, J = 1.2, 7.7 Hz, ArH), 7.09 (d, 1 H, J = 7.2 Hz, ArH),
6.87 (t, 1 H, J = 7.4 Hz, ArH), 6.83 (d, 1 H, J = 10.3 Hz,
ArH), 6.67 (d, 1 H, J = 8.3 Hz, ArH), 6.55 (d, 1 H, J = 7.7
Hz, ArH), 5.74 (d, 1 H, J = 10.2 Hz, ArH), 2.98 (s, 1 H,
C≡CH), 2.74 (s, 3 H, NMe), 1.31 (s, 3 H, Me), 1.18 (s, 3 H,
Me). 13C NMR (150 MHz, CDCl3): d = 155.0, 148.1, 136.6,
133.7, 130.5, 128.8, 127.6, 121.5, 120.3, 119.3, 118.8,
115.2, 113.5, 106.9, 104.8, 83.6, 75.5, 51.9, 28.9, 25.9, 20.1.
MS (CI, NH3): m/z (%) = 302.1 (100) [MH+]. HRMS (EI–
MS): m/z [M+] calcd for C21H19NO: 301.1467; found:
301.1465.
Figure 3 Top: UV/Vis absorption spectra of open form of DNA1
and interconversion into closed form (20 mM in 50 mM Na-Pi buffer,
pH 7, 250 mM NaCl, pH 7) at r.t.; after 30 min irradiation with l =
310 nm (red), after 30 min irradiation at l = 450 nm (blue). Inset
shows time dependence of absorption change at l = 450 nm due to the
interconversion of DNA1 from the open to the closed form and back
to the opened form. Bottom: Sequence of DNA1.
step further in the preparation of photoreactive nanostruc-
tures that are based on nucleic acids as structural scaffold.
(21) Compound 8: Compound 619 (335 mg, 1.11 mmol) was
dissolved in freshly distilled EtOH (10 mL) and anhyd Et3N
(200 mL, 1.43 mmol). Compound 719 (220 mg, 1.09 mmol)
was added and the reaction mixture was sonicated at 35 kHz
under Ar. After 2 h the solvent was removed under reduced
pressure, the residue was dissolved in CH2Cl2 and dried over
anhyd Na2SO4. The solvent was evaporated under reduced
pressure, and the residue was dried in vacuo and purified by
gradient flash chromatography on silica gel (hexane–EtOAc,
30:1 → 15:1) to yield 8 (300 mg, 77%) as a pale pink solid;
Rf 0.49 (hexane–EtOAc, 19:1). 1H NMR (300 MHz, CDCl3):
d = 7.15–7.27 (m, 3 H, ArH), 7.09 (d, 1 H, J = 7.2 Hz, ArH),
6.87 (t, 1 H, J = 7.4 Hz, ArH), 6.80 (d, 1 H, J = 10.3 Hz,
ArH), 6.61 (d, 1 H, J = 9.2 Hz, ArH), 6.55 (d, 1 H, J = 7.7
Hz, ArH), 5.74 (d, 1 H, J = 10.2 Hz, ArH), 2.74 (s, 3 H,
NMe), 1.32 (s, 3 H, 3-Me), 1.18 (s, 3 H, 3-Me). 13C NMR (75
MHz, CDCl3): d = 153.6 (Cquat), 148.0 (Cquat), 136.5 (Cquat),
132.2 (+, CH), 129.1 (+, CH), 128.4 (+, CH), 127.7 (+, CH),
121.5 (+, CH), 120.7 (+, CH), 120.6 (Cquat), 119.3 (+, CH),
116.9 (+, CH), 111.8 (Cquat), 106.9 (+, CH), 104.5 (Cquat),
51.9 (Cquat), 28.9 (+, Me), 25.9 (+, Me), 20.1 (+, Me). MS
(EI, 70 eV): m/z (%) = 357.0(100) [M+·], 339.9 (47) [M+ –
Me.]. HRMS (EI–MS): m/z [M+] calcd for C19H18BrNO:
355.0572; found: 355.0570.
Acknowledgment
Financial support by the Deutsche Forschungsgemeinschaft, the
University of Regensburg and KIT is gratefully acknowledged.
References and Notes
(1) For reviews, see: (a) Raymo, F. M.; Tomasulo, M. Chem.
Eur. J. 2006, 12, 3186. (b) Pischel, U. Angew. Chem. Int.
Ed. 2007, 46, 4026.
(2) For a review, see: Cusido, J.; Deniz, E.; Raymo, F. M. Eur.
J. Org. Chem. 2009, 2031.
(3) For a review, see: Berkovic, G.; Krongauz, V.; Weiss, V.
Chem. Rev. 2000, 100, 1741.
(4) For a review, see: Mayer, G.; Heckel, A. Angew. Chem. Int.
Ed. 2006, 45, 4900.
(5) For a review, see: Moroder, L.; Renner, C. ChemBioChem
2006, 7, 868.
(6) (a) Asanuma, H.; Liang, X.; Komiyama, M. ChemBioChem
2001, 2, 39. (b) Nishioka, H.; Liang, X.; Asanuma, H.
Chem. Commun. 2007, 4354. (c) Liang, X.; Takenaka, N.;
Nishioka, H.; Asanuma, H. Chem. Asian J. 2008, 3, 553.
(7) Yamazawa, A.; Liang, X.; Asanuma, H.; Komiyama, M.
Angew. Chem. Int. Ed. 2000, 39, 2356.
(22) Chung-Shan, Y.; Oberdorfer, F. Synlett 2010, 86.
Synlett 2012, 23, 711–716
© Thieme Stuttgart · New York

LETTER
Covalent Modification of 2¢-Deoxyuridine
715
(23) Compound 1: Compound 5 (53 mg, 0.176 mmol), 9 (50 mg,
0.141 mmol), CuI (6 mg, 0.0315 mmol) and Pd(dppf)Cl2 (20
mg, 0.0245 mmol) were dissolved in anhyd DMF (2.0 mL)
and anhyd Et3N (100 mL, 0.717 mmol). The mixture was
degassed and stirred at r.t. for 26 h. Then all was poured into
an EtOAc–H2O mixture (20 mL, 1:1). After separation, the
aqueous phase was extracted with CH2Cl2, and the combined
organic layers were dried over anhyd Na2SO4 and the solvent
was evaporated under reduced pressure. The residue was
dried in vacuo and purified by gradient flash
7.0 Hz, CH2). 13C NMR (75 MHz, CDCl3): d = 168.6 (CO),
146.1 (Cquat), 142.9 (Cquat), 140.5 (Cquat), 136.5 (Cquat), 127.2
(Carom), 125.0 (Carom), 123.4 (Carom), 118.8 (Carom), 28.6
(CH2), 19.6 (CH2), 15.3 (Me). MS (EI, 70 eV): m/z (%) =
549.9 (14) [M+].
(27) Compound 14: To a suspension of zinc dust (301 mg, 4.6
mmol, stabilized, grading <63 mm) in anhyd THF (50 mL)
TiCl4 (0.26 mL, 2.3 mmol) was added under argon
atmosphere dropwise at 0 °C. The suspension was heated to
40 °C and stirred for 1 h. Compound 13 (631 mg, 1.1 mmol)
was added and the mixture was stirred for 18 h. After cooling
to r.t. the reaction mixture was poured through a silica gel
pallet and rinsed with hexanes. The solvent was removed
under reduced pressure and the residue was dried in vacuo
and purified by flash chromatography on silica gel(hexanes)
to yield 14 (328 mg, 55%) as a white solid; Rf 0.25 (hexanes).
1H NMR (300 MHz, CDCl3): d = 7.64 (s, 2 H, ArH), 7.46 (d,
2 H, J = 8.4 Hz, ArH), 7.24 (s, 2 H, ArH), 2.88–3.02 (m, 4
H, CH2), 2.28 (quin, 2 H, J = 7.22 Hz, CH2), 2.12 (s, 6 H,
Me). 13C NMR (75 MHz, CDCl3): d = 140.9 (Cquat), 137.0
(Cquat), 136.8 (Cquat), 129.72 (Carom), 126.5 (Carom), 125.1
(Carom), 123.3 (Carom), 118.1 (Carom), 37.8 (CH2), 24.1 (CH2),
15.2 (Me). MS (EI, 70 eV): m/z (%) = 517.9 (100) [M+].
(28) Compound 15: Compound 14 (131 mg, 0.25 mmol),
trimethylsilylacetylene (72 mL, 0.51 mmol), anhyd Et3N (41
mL, 0.51 mmol), Pd(PPh3)4 (30 mg, 0.03 mmol) and CuI (5
mg, 0.03 mmol) were dissolved in anhyd THF (3 mL) under
argon. The mixture was degassed and refluxed for 19 h.
After cooling to r.t. the solvent was removed under reduced
pressure, the residue was dried in vacuo and purified by flash
chromatography on silica gel(hexanes) to yield 15 (58 mg,
43%) as a white solid; Rf 0.26 (hexanes). 1H NMR (300
MHz, CDCl3): d = 7.67 (s, 2 H, ArH), 7.54 (d, 1 H, J = 8.2
Hz, ArH), 7.47 (d, 1 H, J = 8.0 Hz, ArH), 7.29 (s, 2 H, ArH),
2.83–3.12 (m, 4 H, CH2), 2.28 (quin, 2 H, J = 7.8 Hz, CH2),
2.04 (s, 6 H, Me), 0.29 (s, 9 H, SiMe3). 13C NMR (75 MHz,
CDCl3): d = 139.1 (Cquat), 138.6 (Cquat), 137.3 (Cquat), 136.7
(Cquat), 127.1 (Carom), 126.4 (Carom), 125.9 (Carom), 125.1
(Carom), 123.3 (Carom), 121.9 (Carom), 118.0 (Carom), 105.9
(C≡C), 37.9 (CH2), 29.9 (C≡C), 24.2 (CH2), 15.3 (Me), 0.3
(SiMe3). MS (EI, 70 eV): m/z (%) = 536.0(100) [M+].
(29) Compound 16: Compound 15 (35 mg, 0.07 mmol) was
dissolved in anhyd MeOH (3 mL) and K2CO3 (27 mg, 0.19
mmol) was added. The reaction mixture was stirred for 18 h
at 40 °C. After cooling to r.t. MeOH was removed under
reduced pressure. The residue was dried in vacuo and
purified by flash chromatography on silica gel (hexanes) to
yield 16 (30 mg, 99%) as a white solid; Rf 0.65 (hexanes–
EtOAc, 20:1) 1H NMR (300 MHz, CDCl3): d = 7.71 (s, 2 H,
ArH), 7.57 (d, 2 H, J = 8.0 Hz, ArH), 7.46 (d, 1 H, J = 7.5
Hz, ArH), 7.28 (s, 1 H, ArH), 3.07 (s, 1 H, C≡CH), 2.84–3.01
(m, 4 H, CH2), 2.28 (quin, 2 H, J = 8.0 Hz, CH2), 2.02 (s, 6
H, Me). 13C NMR (75 MHz, CDCl3): d = 146.8 (Cquat), 139.2
(Cquat), 137.2 (Cquat), 136.9 (Cquat), 126.9 (Carom), 126.4
(Carom), 125.1 (Carom), 123.3 (Carom), 122.0 (Carom), 118.1
(Carom), 117.6 (Carom), 76.5 (C≡C), 37.8 (CH2), 29.9 (C≡C),
24.1 (CH2), 15.2 (Me). MS (EI, 70 eV): m/z (%) = 461.9
(100) [M+].
chromatography on silica gel (CH2Cl2–MeOH, 10:1 → 5.1)
to yield 1 (50 mg, 67%) as glistening green crystals; Rf 0.29
(CH2Cl2–MeOH, 10:1). 1H NMR (600 MHz, MeOD): d =
8.36 (s, 1 H, H-6), 7.27 (d, 1 H, J = 2.0 Hz), 7.23 (dd, 1 H,
J = 8.4 Hz), 7.10 (dt, 1 H, J = 7.6 Hz), 7.03 (d, 1 H, J = 7.2
Hz), 6.92 (d, 1 H, J = 10.3 Hz), 6.78 (t, 1 H, J = 7.1 Hz), 6.61
(d, 1 H, J = 8.4 Hz), 6.52 (d, 1 H, J = 7.8 Hz), 6.26 (t, 1 H,
J = 6.6 Hz, H-1¢), 5.80 (d, 1 H, J = 10.3 Hz), 4.40–4.43 (m,
1 H, H-3¢), 3.94 (q, 1 H, J = 3.3 Hz, H-4¢), 3.83 (dd, 1 H, J =
3.0, 12.0 Hz, H-5¢), 3.75 (dd, 1 H, J = 3.4, 12.0 Hz, H-5¢),
2.70 (s, 3 H, NMe), 2.29–2.34 (m, 1 H, H-2¢), 2.22–2.28 (m,
1 H, H-2¢), 1.26 (s, 3 H, MeC), 1.14 (s, 3 H, Me). 13C NMR
(150 MHz, MeOD): d = 164.4, 156.2, 151.2, 149.5, 144.5
(C6), 137.8, 134.2, 131.1, 130.0, 128.6, 122.4, 121.4, 120.5,
120.4, 116.0, 107.9, 106.3, 100.9, 93.9, 89.1 (C-4¢), 87.0 (C-
1¢), 80.1, 72.0 (C-3¢), 62.6 (C-5¢), 52.9, 41.8 (C-2¢), 29.2
(NMe), 26.3 (Me), 20.4 (Me), 9.3. MS (ESI): m/z (%) =
528.2 (100) [MH+].
(24) Stafforst, T.; Hilvert, D. Chem. Commun. 2009, 287.
(25) Compound 12: Compound 11 (2.50 g, 11.7 mmol) was
dissolved under argon atmosphere in anhyd THF (30 mL)
and cooled to –78 °C. A 2 M lithium diisopropylamide
solution in THF–heptane–ethylbenzene (8.79 mL, 17.6
mmol) was added dropwise and the mixture was stirred for 1
h at 0 °C. After cooling down to –78 °C, MeI (1.10 mL, 17.6
mmol) was added dropwise. The mixture was stirred for 2
additional hours. Then H2O (30 mL) was added, the phases
were separated and the aqueous phase was extracted with
EtOAc. The combined organic layers were dried over anhyd
Na2SO4 and the solvent was evaporated under reduced
pressure. The residue was dried in vacuo and purified by
flash chromatography on silica gel(hexanes) to yield 12
(2.66 g, 99%) as a white solid; Rf 0.57 (hexanes). 1H NMR
(300 MHz, CDCl3): d = 7.78 (d, 1 H, J = 1.9 Hz, ArH), 7.59
(d, 1 H, J = 8.5 Hz, ArH), 7.34 (dd, 1 H, J = 8.5, 1.9 Hz,
ArH), 6.90 (s, 1 H, ArH), 2.59 (d, 3 H, J = 1.2 Hz, Me).
13C NMR (75 MHz, CDCl3): d = 143.1 (Cquat), 142.2 (Cquat),
138.4 (Cquat), 126.5 (Carom), 125.3 (Carom), 123.4 (Carom),
121.0 (Carom), 118.2 (Carom), 16.3 (Me). MS (EI, 70 eV):
m/z (%) = 228.0(100) [M+], 147.1 (24) [M – Me].
(26) Compound 13: Compound 12 (969 mg, 4.3 mmol) and
glutaryl chloride (0.27 mL, 2.1 mmol) were dissolved under
argon atmosphere in anhyd CH2Cl2 (20 mL) and the solution
was cooled to 0 °C. Then AlCl3 (626 mg 4.7 mmol) was
added and the reaction mixture was stirred for 3 h at r.t. After
completion of the reaction, a mixture of ice and 1 M aq HCl
was added. The solution was let to be warmed to r.t., the
phases were separated and the aqueous phase was extracted
with EtOAc. The combined organic layers were dried over
anhyd Na2SO4 and the solvent was evaporated under
reduced pressure. The residue was dried in vacuo and
purified by flash chromatography on silica gel (hexanes–
EtOAc, 10:1) to yield 13 (896 mg, 74%) as a white solid;
Rf 0.31 (hexanes–EtOAc, 10:1). 1H NMR (400 MHz,
CDCl3): d = 8.36 (d, 2 H, J = 1.8 Hz, ArH), 7.57 (d, 2 H, J =
8.5 Hz, ArH), 7.42 (dd, 2 H, J = 8.5, 1.8 Hz, ArH), 3.06 (t, 4
H, J = 6.9 Hz, CH2), 2.77 (s, 6 H, Me), 2.27 (quin, 2 H, J =
(30) Compound 2: Compound 16 (126 mg, 0.27 mmol), 9 (97 mg,
0.27 mmol), anhyd Et3N (45 mL, 0.54 mmol), Pd(PPh3)4 (63
mg, 0.05 mmol) und CuI (11 mg, 0.05 mmol) were dissolved
in anhyd DMF (10 mL). The mixture was degassed and
stirred for 18 h at 60 °C. After cooling to r.t. the solvent was
removed under reduced pressure, the residue was dried in
vacuo and purified by flash chromatography on silica gel
(CH2Cl2–MeOH, 25:1) to yield 2 (121 mg, 65%) as a light
yellow foam; Rf 0.40 (CH2Cl2–MeOH, 10:1). 1H NMR (300
© Thieme Stuttgart · New York
Synlett 2012, 23, 711–716

716
S. Barrois et al.
LETTER
MHz, MeOD): d = 8.37 (s, 1 H, NH), 7.72 (s, 2 H, ArH),
7.58–7.68 (m, 1 H, C=CH), 7.55 (d, 1 H, J = 8.2 Hz, ArH),
7.46 (d, 1 H, J = 6.8 Hz, ArH), 6.95–7.29 (m, 2 H, ArH), 6.26
(t, 1 H, J = 6.2 Hz, 1¢-H), 4.28–4.50 (m, 1 H, 3¢-H), 3.88–
4.03 (m, 1 H, 4¢-H), 3.78–3.87 (m, 1 H, 5¢-H), 3.66–3.78 (m,
1 H, 5¢-H), 2.19–2.61 (m, 4 H, CH2), 2.00–2.48 (m, 9 H, 2¢-
H, CH2, Me), 1.95 (s, 1 H, 2¢-H). 13C NMR (75 MHz,
MeOD): d = 151.2 (CO), 144.7 (C=C), 140.4 (CO), 139.8
(Cquat), 138.6 (Cquat), 138.5 (Cquat), 138.1 (Cquat), 131.3
(Cquat), 127.3 (Carom), 126.0 (Carom), 124.3 (Carom), 122.9
(Carom), 118.9 (Carom), 94.5 (C≡C), 89.2 (4¢-C), 87.1 (1¢-C),
72.1 (3¢-C), 62.6 (5¢-C), 41.8 (2¢-C), 38.6 (CH2), 25.0 (CH2),
15.1 (Me). MS (FAB): m/z (%) = 689.1 (6) [M+]. HRMS
(ESI): m/z [M + H+] calcd for C34H30BrN2O5S2: 691.0759;
found: 691.0766.
H, ArHDMT), 6.16 (t, 1 H, J = 6.7 Hz, 1¢-H), 4.26–4.34 (m, 1
H, 3¢-H), 3.93–398 (m, 1 H, 4¢-H), 3.66–3.80 (m, 2 H, 5¢-H),
3.61 (d, 6 H, J = 2.5 Hz, CH3,DMT), 2.79–2.93 (m, 4 H, CH2),
2.06–2.37 (m, 9 H, 2¢-H, CH2, Me), 1.95–2.03 (m, 1 H, 2¢-
H). 13C NMR (75 MHz, acetone): d = 163.9 (Cquat), 161.9
(Cquat), 159.6 (Cquat), 157.7 (Cquat), 150.4 (CO), 146.0 (Cquat),
143.1 (C=C), 140.3 (CO), 139.0 (Cquat), 138.1 (Cquat), 137.9
(Cquat), 136.6 (Cquat), 131.0 (Carom), 128.9 (Carom), 127.6
(Carom), 127.1 (Carom), 126.0 (Carom), 122.7 (Carom), 114.1
(C≡C), 87.7 (4¢-C), 86.6 (1¢-C), 64.8 (5¢-C), 58.4 (3¢-C), 55.4
(2¢-C), 46.4 (5¢-C), 41.9 (s), 38.3 (CH2), 24.4 (CH2), 15.4
(Me), 8.9 (Me). MS (ESI): m/z (%) = 1015.2 (4)[(M + Na)+].
(32) Compound 18: Compound 17 (62 mg, 0.06 mmol),
diisopropylethylamine (36 mL, 0.16 mmol) and 2-cyano-
ethyldiisopropylphosphoramidite (27 mL, 0.16 mmol) were
dissolved in anhyd CH2Cl2 (3 mL). The solution was stirred
at r.t. for 40 min. The product was purified by flash
chromatography on silica gel (CH2Cl2–MeOH, 100:4 + 0.1%
Et3N) and additionally lyophilized out of benzene to yield 18
(74 mg, 99%) as a light yellow foam; Rf 0.85, 0.91 (CH2Cl2–
MeOH, 25:1). 31P NMR (101 MHz, DMSO): d = 150.6
[P(III), 37%], 16.3 [P(V), 63%]. MS (MALDI): m/z (%) =
1191.3 (28) [M+].
(31) Compound 17: Compound 2 (50 mg, 0.07 mmol),
dimethoxytrityl chloride (37 mg, 0.11 mmol) and anhyd
Et3N (10 mL, 0.12 mmol) were dissolved in anhyd pyridine
(2 mL) under argon atmosphere. The solution was stirred for
18 h at 40 °C. The solvent was removed, the residue was
dried in vacuo and purified by flash chromatography on
silica gel (CH2Cl2–MeOH, 100:3 + 0.1% Et3N) to yield 17
(62 mg, 90%) as a light yellow foam; Rf 0.61 (CH2Cl2–
MeOH, 10:1). 1H NMR (300 MHz, DMSO): d = 8.05 (s, 1
H, NH), 7.70 (d, 2 H, J = 8.2 Hz, ArHbt), 7.63 (s, 1 H,
C=CH), 7.43 (d, 2 H, J =7.4 Hz, ArHbt), 7.18–7.37 (m, 8 H,
ArHDMT), 7.14 (d, 2 H, J = 7.3 Hz, ArHbt), 6.75–6.96 (m, 5
(33) DNA 1: MS (MALDI): m/z (%) = 5950.0(100) [(M +
DMT)+], 5647.9 (38) [M+], 2974.6 (17) [(M + DMT)2+/2],
2823.6 (7) [M2+/2].
Synlett 2012, 23, 711–716
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