Visibly Emitting Thiazolyl-Uridine Analogues as Promising Fluorescent Probes

Article abstract of DOI:10.1021/acs.joc.9b03208

Microenvironment-sensitive fluorescent (ESF) nucleosides are powerful tools for nucleic acid research. The new 5-substituted uridine analogues are synthesized, which comprise a 4H-cyclopenta[d]thiazole ring obtained by the Hantzsch synthesis reaction of 5-thioamide-uridine with aromatic α-bromocarbonyl compounds. The emission maximum of new compounds is in the visible region. They exhibit strong solvent- A nd pH-dependent fluorescent properties, indicating their promising ability to be fluorescent probes.

Full text of DOI:10.1021/acs.joc.9b03208

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Article
Visibly Emitting Thiazolyl-uridine
Analogues as promising fluorescent probes
Jinsi Li, Xuerong Fang, and Xin Ming
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.9b03208 • Publication Date (Web): 10 Mar 2020
Downloaded from pubs.acs.org on March 10, 2020
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Visibly Emitting Thiazolyl-uridine Analogues as promising
fluorescent probes
Jinsi Li, Xuerong Fang, Xin Ming*
Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue,
Chengdu, Sichuan, 610500, P. R. China
mingxin@cmc.edu.cn
Abstract: Microenvironment sensitive fluorescent (ESF) nucleosides are powerful
tools for nucleic acids research. The new 5-substituted uridine analogues are
synthesized, which comprise a 4H-cyclopenta[d]thiazole ring obtained by Hantzsch
synthesis reaction of 5-thioamide-uridine with aromatic α-bromocarbonyl
compounds. The emission maximum of new compounds is in the visible region.
They exhibit strong solvent and pH dependent fluorescent properties, indicating their
promising ability to be fluorescent probes.
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Introduction
RNA displays a wide range of functions, including gene regulation, protein
1
2
3
synthesis and reaction catalysts. The functional diversity of RNAs originates from
their ability to fold into a number of secondary and tertiary structure elements, which
are crucial for a variety of binding events with other biomolecules .4-7 Several
biophysical methods, such as NMR, electron paramagnetic resonance (EPR) and
fluorescence combined with circular dichroism (CD) have been developed to
understand structures and functions of RNAs.8-10 Among them, Fluorescent
spectroscopy are widely utilized in nucleic acids research with many advantages, such
as high sensitivity, low cost, easy detection, etc.11-13 As nature nucleic acids are
almost nonemissive, numerous fluorescent nucleoside derivatives are used to explore
nucleic acid conformation, recognition, sequence and interactions of nucleic acid and
protein.14-17 An attractive feature of emissive nucleobase analogues with similar shape
to canonical nucleobases is that they do not perturb DNA structure and retain
nucleobase recognition. In particular, the microenvironment sensitive fluorescent
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(ESF) nucleosides are powerful tools for nucleic acids research. Among the
monomeric uridine analogues are 5-(furan-2-yl)-uridine, 5-(thiophen-2-yl)-uridine, 5-
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(benzo[b]thiophen-2-yl)-uridine and 5-(benzofuran-2-yl)-uridine (Figure 1). The
research has shown that 5-benzo[b]thiophen-2-yl-uridine 2b displays remarkable
solvent dependent fluorescence with emission maximum in the visible region. T7
RNA polymerase can incorporate its corresponding triphosphate into RNA
oligonucleotides. The fluorescence quantum yield of 2b is not remarkably quenched
when placed within a complementary duplex or an ssRNA.18c However, its quantum
yield is not satisfied. We try to synthesize new fluorescent ribonucleoside analogues
whose expected favorable photophysical properties would be useful for promising
fluorescence probe.
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O
O
N
X
NH
X
NH
N
O
O
O
O
HO
HO
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HO
OH
HO
OH
1
1
a: X = O
b: X = S
2a: X = O
2b: X = S
Figure 1. The emissive 5-conjugated uridine analogues.
There are three categories for fluorescent pyrimidine analogues: extended
fluorescent scaffolds by use of linkers; modified pyrimidine substituents and ring-
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fused pyrimidine ring systems. Among the three approaches, linking a fluorophore
to the pyrimidine framework is an important approach to generate a fluorescent
pyrimidine nucleoside. To date, most extensions on the pyrimidine ring take place at
the 5 position to make use of the conjugation with the N1 nitrogen and 5, 6 double
19
bond and to avoid perturbing base pairing. Previous researches have shown that the
heterocycle moiety attached to the 5 position of uridine may enhance the π
conjugation and impart better photophysical properties to the nucleobase.18b,19-21 This
manuscript reports on Hantzsch synthesis reaction of 5-thioamide-uridine with
aromatic α-bromocarbonyl compounds to generate thiazol-conjugated fluorescent
uridine analogues.
Results and discussion.
The first two thiazol-conjugated 2'-deoxyuridine analogues have been synthesized
via palladium-catalyzed coupling reaction of 2-tributylstannylthiazoles with 3',5'-di-
2
2
O-p-toluyl-IdU. Later, Matsuda and co-workers have synthesized substituted 5-
(
benzothiazol-2-yl)-2'-deoxyuridine by 2-aminobenzenethiol and 5-furyl-2'-
2
3
deoxyuridine. To avoid the toxic heteroarylstannanes and expand the diversity of
uridine analogues, we report a new method to synthesize thiazol-conjugated uridine
analogues with 5-thioamide-uridine and aromatic α-bromocarbonyl compounds. 5-
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thioamide-uridine can be achieved from 5-cyano-uridine. Bleackl group has firstly
reported the synthesis of 5-cyano-2'-deoxyuridine from 5-iodo-2'-deoxyuridine, using
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hexamethyldisilazane and CuCN, with 5% yield. Later, Terrence and coworkers
have used protected 5-bromo-uridine and NaCN to get protected 5-cyano-uridine,
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with yield of 35%. Because CuCN is safer and easier to be accessible than NaCN,
we use CuCN to prepare 5-cyano-uridine. As 5-cyano-uridine is a high polar molecule
and difficult to be purified, the 2',3',5'-tri-actyl-5-iodo-uridine (3) is used as starting
material and is silylated with hexamethyldisilazane at 130 °C for 10 hours. The
silylated intermediate is reacted with CuCN in pyridine at 120 °C for 8 h under
nitrogen, providing protected 5-cyano-uridine (4) in improved yield (83%) over two
steps (Scheme 1).
O
O
S
O
N
I
NC
NH
NH
H N
2
NH
1. HMDS, 130 °C, 10 h
P2S5, EtOH
N
O
N
O
O
2
. Py, CuCN, 120 °C, 8 h
85 °C, 7 h
O
O
O
AcO
AcO
AcO
AcO
OAc
AcO
OAc
HO
OAc
4
5
3
Scheme 1. The synthesis route of key intermediate 5.
The first protocol for conversion of cyano function to a thioamide group has been
26
reported by Herdewijn and coworkers. They have saturated the solution of protected
5
-cyano-2'-deoxyuridine in DMF with H S, which is stored at room temperature for
2
24 h. Here, we report a new protocol of the conversion of non-fluorescent compound
4 to the intermediate 5-thioamide-uridine analogue (5) by treatment with phosphorus
pentasulfide. The compound 4 and P S are reacted at 85 °C for 7 h to afford
2
5
compound 5 which was partially deprotected at 3'-OH as major product (65%)
(Scheme 1). The mechanism of partial deprotection is not clear. The reaction product
is purified by flash column chromatography and identified by using ESI-TOF mass
spectra and NMR spectra. The reaction enables mild and safe conditions to convert
the cyano function to a thioamide group compared to using hydrogen sulfide.
For the desirable fluorescent nucleobases, they exhibit emission wavelength in the
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visible region. Incorporating heteroatoms and extending π-systems can make optical
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profiles redshifted. Here, we incorporate N and S heteroatoms and extended π-
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systems by classic Hantzsch synthesis reaction. The non-fluorescent 5-thioamide-
uridine (5) is allowed to react with a series of non-fluorescent aromatic α-haloketones
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(
6a-m) in EtOH (6k in DMF) and deprotected in 0.05 M K CO in MeOH to afford
2 3
the target uridine analogues 7a-m, in yields 40%-80% (Scheme 2). The reaction
mechanism of fluorescent uridine analogues is shown in Figure 2.
.
Figure 2. Reaction mechanism of fluorescent uridine analogues
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o
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i) EtOH, 85 C
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NH2
NH
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OH
O
7a: 81%
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O
AcO
Ar
S
O
N
Ar
Br
N
HO
OAc
NH
5
6b-m
O
o
(
i) EtOH, 85 C
O
(
ii) 0.05M K CO /MeOH
HO
2
3
HO
OH
7b - m
F
O
S
S
S
S
O
N
N
N
N
7
b: 80%
7c: 82%
7d: 76%
7e: 75%
O
O
S
S
S
O
S
N
N
N
N
7f: 65%
7g: 80%
7h: 75%
7i: 40%
S
O
S
S
S
S
S
N
N
N
N
N
7j: 41%
7k: 44%
7l: 52%
7m: 50%
Scheme 2. Transformation of the intermediate 5 to the nucleosides 7a-m.
The photophysical properties of new pyrimidine analogues 7a–m are investigated
and shown in table 1. All thiazol-conjugated uridine analogues are fluorescent. The
absorbance maxima are in 350-400 nm and the emission maxima rang from ca. 450 to
5
60 nm, in the visible region. Especially for 7i, its emission max is 557 nm in water.
1
8
Compared to the known fluorescent 5-modified uridines 2 and 3, the newly
synthesized compounds show red-shifted absorption and emission spectra. All
−1
derivatives display rather large Stokes shifts (>5000 cm ), especially for compound
i (>10000 cm−1).
7
Increasing the electron-rich character of the moiety, such as methoxyphenyl,
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dimethoxyphenyl, thienyl, furanyl and so on, combination with a 4H-
cyclopenta[d]thiazole ring leads to a red shift for both absorption and emission
maxima. This illustrates the impact of the combined moiety on both the ground and
excited state. For most of fluorescent nucleosides, their highest quantum yield is in
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organic solvent . But interestingly, for nucleosides 7a and 7j, they have highest
relative quantum yields in water.
Next, the photophysical properties of 7a–m in various solvents are examined. We
observed that the absorption and emission properties of 7a–m have been significantly
affected by the solvent polarity (Figure 3 and S1-13). A red shift of λem max is seen for
all the new compounds when solvent polarity is increased. The plot of the Stokes shift
29
determined in solvents vs Reichardts’ microscopic solvent polarity parameter E (30)
T
shows a very good linear correlation, which quantifies this effect.
The observed emission intensity in various solvents is in accordance with the
relative quantum yield in different solvents (Table 1), which further ascertains the
responsiveness of the fluorescent nucleosides 7a-m to microenvironmental changes
(Figure S1-13).
Table 1. Photophysical Properties of Fluorescent Nucleosides 7a-ma
Brightness
Stokes shift
abs-λem cm (nm)
Compound
solvent
λ
abs,max (nm)
εb
λ
em (nm)
Φc
3
-1
ε x Φ x10
0.56
0.66
1.21
4.01
6.43
1.52
1.70
4.03
0.74
4.70
0.59
0.11
1.27
1.68
0.13
3.23
0.01
＜0.01
1.46
0.21
0.02
0.93
0.43
0.02
0.12
0.12
0.02
λ
7a
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
350
345
345
359
355
355
363
358
359
373
370
371
355
358
360
373
371
370
365
364
374
372
370
412
350
348
350
21.6
21.2
16.6
24.3
22.9
13.0
13.8
13.7
10.2
14.2
13.5
10.7
15.5
9.7
422
452
472
439
460
484
442
456
489
464
502
507
442
468
499
493
530
539
455
491
508
461
495
522
549
549
557
0.026
0.031
0.073
0.165
0.317
0.117
0.123
0.294
0.072
0.331
0.04
5946 (72)
6862 (107)
7572 (127)
5076 (80)
6430 (105)
7550 (129)
4924 (79)
6003 (98)
7405 (130)
5257 (91)
7107 (132)
7230 (136)
5544 (87)
6565 (113)
7737 (139)
6526 (120)
8080 (159)
8508 (169)
5419 (90)
7106 (127)
7787 (134)
5190 (90)
6825 (125)
5115 (110)
10356 (199)
10521 (201)
10628 (207)
7
b
7
c
7
d
0.014
0.082
0.153
0.014
0.276
0.001
7
e
9.0
7f
12.1
12.1
7.5
15.0
11.2
8.6
13.1
12.9
8.0
30.0
29.3
22.4
＜10-
0.097
0.019
0.002
0.071
0.033
0.003
0.004
0.004
0.001
3
7
g
7h
7
i
dioxane
methanol
water
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4
4
4
4
4
4
4
4
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5
5
5
5
5
5
5
5
5
6
7j
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
dioxane
methanol
water
354
347
347
369
371
372
363
363
364
370
367
356
15.6
13.1
14.8
12.4
11.4
9.6
10.5
10.0
8.6
420
428
447
468
502
535
457
486
513
464
497
485
0.082
0.112
0.161
0.039
0.040
0.002
0.091
0.175
0.005
0.126
0.069
0.005
1.28
1.47
2.38
0.48
0.46
0.02
0.96
1.75
0.04
1.45
0.79
0.05
4439 (66)
5454 (81)
6447 (100)
5733 (99)
7034 (131)
8190 (163)
5666 (90)
6972 (123)
7979 (149)
5475 (94)
7127 (130)
7471 (129)
7
k
7l
0
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9
0
7
m
10.4
11.5
10.4
aAbsorption and steady-state emission spectroscopy were measured using samples from a concentrated
b
3
-1
-1
c
DMSO stock solution. ε In [ 10 M cm ]. The fluorescence quantum yields (ϕ) were calculated using
quinine sulfate in 0.5 M H SO (ϕ = 0.55) as the standard .
2
4
Figure 3. (a) Absorption (30 μM, dash) and emission (5.0 μM, solid) spectra of compound 7b in
different solvents. (b) Correlating Stokes shift vs E (30) values obtained from respective
solvents for 7b.
T
Since uridine is a pH sensitive molecule and its N3 can be deprotonated at
basic condition, the properties of 7a-m under a variety of pH conditions are
invesigated. As the thiazole system is prone to degradation, the stability of the
compounds is examined in harsh condition. The compounds are treated at pH 1 and
pH 13 at room temperature for 3 h separately and the reaction is examined by
RP18-HPLC. After 3h treatment, almost no change is observed (S14-17). We
observe that the fluorescence of newly synthesized nucleosides exhibit a high pH-
dependency (Figure 4). In basic conditions (from pH 7.0-10.0), absorption and
emission spectra of most compounds reveal a strong influence of pH on the
intensity and maximum. The electron properties of the combined moiety to a 4H-
cyclopenta[d]thiazole impact the changes of absorption and emission properties in
basic conditions. The electron-donating character of the combined moiety to a 4H-
cyclopenta[d]thiazole, such as methoxyphenyl, thienyl, furanyl and so on, results in
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increase of both absorption and emission intensity, while the electron-withdrawing
character of the combined moiety, such as Pyridyl (7j), decreases the intensity of
emission and increases the intensity of absorption. The pH-dependent fluorescence
(
except 7f, it is difficult to dissolve in buffer) is used to determine the pK value of
a
1
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deprotonation (Figure 4 and S18-28). As shown in Table 2, compared to uridine, the
pK values of the compounds changes result from the electron-withdrawing
a
character of the thiozole groups making deprotonation more favourable. It is almost
30
identical to the pK value obtained by using UV spectrophotometry (Figure 4 and
a
S18-28). The possible pyrimidine nucleoside tautomers and suggested pKa values
corresponding to possible deprotonation sites are shown in Figure 5.
Figure 4. pH-Dependent UV spectra and fluorescence spectra of 7c measured in 0.1 M sodium
phosphate buffer with (a) UV-spectra at pH values from 1.99 to 12.03 (b) Emission spectra at
pH values from 1.99 to 12.03. (c) Graph of the absorption (abs) maxima against pH value
(black line) and its first derivative (red line) using data from (a). (d) Graph of the emission (em)
maxima against pH value (black line) and its first derivative (red lines) using data from (b).
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Table 2. pK values of uridine and its derivatives
a
Compound
U31, 32
7a
7b
7c
7d
7e
7g
7h
7j
7k
7l 7m
pK
a
(abs)
9.20-9.25 8.66 8.40 8.36 8.30 8.32 8.91 7.74 8.41 8.04 8.32 8.86
pK
a
(em)
8.62 8.51 7.94 8.21 8.08 8.46 8.15 8.73 8.31 8.19 8.43
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8
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0
1
2
3
4
5
6
7
8
9
0
Figure 5. Schematic representation of possible pyrimidine
nucleoside tautomers with labelled nitrogen atoms (red) and suggested
pKa values (blue) corresponding to possible deprotonation sites.
Conclusion
In conclusion, the new fluorescent uridine analogues whose emission maximum
is in the visible region are obtained. They exhibit remarkable solvent and pH
dependent fluorescence, indicating their promising ability to be fluorescent probes.
We have also described a novel protocol for the preparation of 5-thioamide-uridine, a
valuable intermediate for polyaromatic heterocycle. Further studies on the application
of new uridine analogues are currently underway in our laboratory.
Experimental Section
General Experimental Methods. All materials and solvents were of laboratory grade as obtained
from commercial suppliers (Energy Chemical, Leyan, Tianjin ZhiYuan Reagent Co. Ltd) and were
used without further purification. Thin-layer chromatography (TLC) was covered with silica gel 60
1
F254 (0.2 mm). Flash column chromatography (FC): silica gel (40−60 μM) at 0.4 bar. H NMR spectra
were recorded on 400 MHz spectrometers (Bruker). The J values are given in Hz, and δ values are in
ppm relative to Me
4
Si as internal standard residual solvent peaks were used as internal standards:
H
13
DMSO (quint, δ = 2.50 ppm). C-NMR spectra were recorded on 100 MHz spectrometers (Bruker); δ
relative to DMSO (δ 40.5 ppm).The following abbreviations were used to explain the multiplicities: s =
singlet, d = doublet, t = triplet, q = quartet, quint = quintet, sext = sextet, m = multiplet, dd = doublet-
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doublet, ddd = doublet- doublet -doublet, dt = doublet-triplet, dq =doubletquartet, br = broad. Mass
spectra were obtained on a quadrupole ion trap instrument equipped with an atmospheric pressure ion
source (Agilent 6230B).
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Photophysics. For all photophysical experiments, fluorescent nucleosides 7a-m were prepared as 20
mM DMSO stock solutions and stored at -20 °C. Measurements were performed with
2
spectrophotometric grade 1, 4-dioxane, DMSO, ethanol, methanol and deionized H O. For all values
reported, final DMSO concentrations after dilution were always less than 0.1%. Absorption spectra
were measured on a UV spectrophotometer (Speco5d50 Plus, Analytik Jena AG, Germany) with 1 nm
resolution and corrected for the blank. Fluorescence spectra were recorded on a fluorescence
spectrophotometer (F-4500, Hitachi, Japan) with a 1 nm resolution. Molar extinction coefficient
measurements were conducted in deionized H
absorbance. Quantum yield measurements were performed with optical densities adjusted to 0.1 ± 0.05
at the indicated λabs of each nucleoside and corresponding standard quinine sulfate in 0.5 M H SO
0.55) was used as the standard for all compounds 7a-m. The relative quantum yields of each
compound were determined using the formula: Φref =Φ × (A
2), Here Φ, A, I.
and n stand for quantum yield, integrated emission intensity, optical density at λex and refractive index
2
O using Beer’s Law plots of concentration versus
2
4
(Φfl
3
3
=
s
s s s
/Aref) × (Iref/I
) × (nref2/n
(nwater = 1.333, ndioxane = 1.417, nmethanol = 1.326, nethanol = 1.361, nDMSO = 1.480), respectively. Sample
and reference are denoted by s and ref, respectively. 34
5
-Cyano-1-[(2ʹ,3ʹ,5ʹ-O-tri-acetyl)-β-D-ribofuranosyl)]-uracil (4).
5
-Iodouridine35 (15.0 g, 40.5 mmol) was dissolved in pyridine (80 mL) and Ac
O (17.0 g, 162.0
2
mmol, 5 eq.) was added. The mixture was stirred at at room temperature overnight. When the
reaction was completed, the solvent was removed in vacuo. The resultant mixture was extracted
with CH
2
Cl
2
(80 mL × 3). The combined organic layers were washed with brine (100 mL × 3)
. The solvent was removed in vacuum and the residue was suspended in
and dried over MgSO
4
HMDS (100 mL) and heated at 130 °C for 10 h on an oil bath. The excess of HMDS was
removed under reduced pressure and the resulting clear colourless oil was dissolved in dry
pyridine (200 mL). Cuprous cyanide (25.4 g, 283.5 mmol, 7 eq.) was added and the solution
heated under argon for 8 h at 120 °C on an oil bath. Pyridine was removed under reduced
pressure and 200 mL of ethyl acetate was added .The solution was filtered through a pad of
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celite and extensively washed with ethyl acetate. The filtrate was washed by water (100 mL × 3)
2 4
and the organic layers were combined and dried with Na SO and concentrated on a rotary
evaporator. The residue was purified by column chromatography on silica gel (Petroleum
ether/EtOAc, 2:1 to 1:1) to give the compound 4 as light yellow foam (13.0 g, 83%). TLC (silica
0
1
2
3
4
5
6
7
8
9
0
1
2
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1
gel, CH
2
Cl
2
/MeOH, 20:1) R
f
0.50; H NMR (400 MHz, DMSO-d
6
) δ 12.15 (br s, 1H, NH), 8.67
(
s, 1H), 5.88 (d, J = 4.0 Hz, 1H), 5.50 (dd, J = 6.3Hz, 4.0 Hz, 1H), 5.36 (dd, J = 6.2 Hz, 1H),
1
4
1
.42 – 4.21 (m, 3H), 2.14 – 1.99 (m, 9H); 13C{ H} NMR (100 MHz, DMSO-d
6
) δ 170.0, 169.2,
59.9, 150.5, 148.9, 114.0, 89.2, 88.9, 79.2, 72.5, 68.8, 62.5, 20.5, 20.2, 20.2; HR-ESI MS
-
(
m/z): [M - H] calcd for C16
H
16
N
3
O
9
394.0892, found 394.0915.
5
-Carbothioamide-1-[(2ʹ,3ʹ-O-di-acetyl-β-D-ribofuranosyl)]-uracil (5).
(4.9 g, 11.1 mmol, 2 eq.) in EtOH (80 mL) was stirred at rt. for 1 h. 5-Cyano-
2ʹ, 3ʹ, 5ʹ-triaceyl)-Uridine (2.2 g, 5.6 mmol) was added and the resulting solution was stirred at
2 5
A solution of P S
(
85 °C for 7 h on an oil bath. The mixture was concentrated in vacuo and purified by a silica gel
column (methanol/ dichloromethane 1:80) to give the compound 5 as a yellow solid (1.4 g,
1
65%). TLC (silica gel, CH
2
Cl
2
/MeOH, 20:1) R
f
0.45; H NMR (400 MHz, DMSO-d
6
) δ 12.05 (s,
1H), 10.14 (d, J = 4.4 Hz, 1H), 9.90 (d, J = 4.4 Hz, 1H), 9.30 (s, 1H), 6.06 (d, J = 5.5 Hz, 1H),
5.46 (t, J = 5.5 Hz, 1H), 5.35 (dd, J = 5.6 Hz, 3.7 Hz, 1H), 4.25 – 4.21 (m, 1H), 4.02 – 3.91(m,
1
1
1
H), 3.67 (t, J = 3.6 Hz, 2H), 2.10 (s, 3H), 2.04 (s, 3H); 13C{ H} NMR (100 MHz, DMSO-d
6
) δ
91.3, 169.4, 169.3, 162.4, 150.2, 149.2, 110.3, 87.5, 83.6, 73.3, 71.3, 71.1, 60.8, 20.4, 20.3;
+
HR-ESI MS (m/z): [M + H] calcd for C14
H
18
N
3
O
8
S 388.0809, found 388.0778.
The synthesis of 2-bromo 1-indanones (6c, 6e – m):
To a solution of indanones (2 mmol) in ethyl acetate (15 mL) was added with copper (II) bromide (4
mmol, 2eq.) and refluxed on an oil bath until the reaction completed (monitored by TLC), The
solution was filtered and concentrated. The resultant mixture was extracted with ethyl acetate (10
mL × 3). The combined organic layers were washed with brine (30 mL × 3) and dried over
4
MgSO and removed in vacuo. The residue was purified by FC (silica gel; petroleum ether /
ethyl acetate, 25:1). The compound 6f was purified by recrystallization from ethanol. The
compound 6j was used in the next step without further purification because it was easy to
decompose.
2
-bromo-5-fluoro-2,3-dihydro-1H-inden-1-one (6c)
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Compound 6c (360 mg, 78%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
1
7
1
2
0:1) R
f
0.52; H NMR (400 MHz, DMSO-d
6
) δ 7.82 (dd, J = 8.5 Hz, 5.4 Hz, 1H), 7.47 – 7.42 (m, 1H),
.37 – 7.30 (m, 1H), 5.03 (dd, J = 7.4 Hz, 2.9 Hz, 1H), 3.89 (dd, J = 18.5, 7.4 Hz, 1H), 3.32 (dd, J =
8.6 Hz, 2.8 Hz, 1H). The NMR data are identical to earlier reported literature values.36
-bromo-6-methoxy-2,3-dihydro-1H-inden-1-one (6e)
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
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0
Compound 6e (400 mg, 83%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
5
1
1
:1) R
f
0.50; H NMR (400 MHz, DMSO-d
6
) δ 7.49 (d, J = 8.4 Hz, 1H), 7.35 (dd, J = 8.4 Hz, 2.6 Hz,
H), 7.19 (d, J = 2.6 Hz, 1H), 5.03 (dd, J = 7.2 Hz, 2.9 Hz, 1H), 3.86 – 3.79 (m, 7H), 3.80 – 3.76 (m,
H), 3.23 (dd, J = 17.9 Hz, 2.7 Hz, 1H). The NMR data are identical to earlier reported literature
values.37
2
-bromo-5,6-dimethoxy-2,3-dihydro-1H-inden-1-one (6f)
Compound 6f (440 mg, 81%) was obtained as a yellow solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
1:1) R
f
0.53; H NMR (400 MHz, DMSO-d
6
) δ 7.14 (d, J = 9.7 Hz, 2H), 4.96 (dd, J = 7.2 Hz, 2.7 Hz,
1H), 3.89 (s, 3H), 3.82 (s, 3H), 3.80 – 3.73 (m, 1H), 3.21 (dd, J = 18.1 Hz, 2.5 Hz, 1H). The NMR
data are identical to earlier reported literature values.38
6-bromo-2,3,5,6-tetrahydro-7H-indeno[5,6-b]furan-7-one (6g)
Compound 6g (430 mg, 85%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
5:1) R
f
0.54; H NMR (400 MHz, DMSO-d
6
) δ 7.41 (s, 1H), 6.95 (s, 1H), 5.00 (dd, J = 7.2 Hz, 2.8 Hz,
1H), 4.61 (t, J = 8.7 Hz), 3.77 (dd, J = 17.8 Hz, 7.2 Hz, 1H), 3.28 (t, J = 8.6 Hz, 2H), 3.20 (dd, J = 17.6
Hz, 2.6 Hz, 1H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 198.6, 160.08, 145.1, 138.9, 133.1, 123.1,
6
+
1
2
02.0, 71.6, 46.2, 37.0, 29.3; HR-ESI MS (m/z): [M + H] calcd for C12
H
7
BrO 252.9859 found
52.9861.
2
-bromo-2,3-dihydro-1H-cyclopenta[a]naphthalen-1-one (6h)
Compound 6h (460 mg, 88%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
1
0:1) R
f
0.54; H NMR (400 MHz, DMSO-d
6
) δ 8.93 (d, J = 8.3 Hz, 1H), 8.32 (d, J = 8.4 Hz, 1H), 8.09
(d, J = 8.1 Hz, 1H), 7.74 – 7.79 (m, 1H), 7.66 (t, J = 7.6 Hz, 2H), 5.11 (dd, J = 7.1 Hz, 2.6 Hz, 1H),
1
3
.99 (dd, J = 18.6 Hz, 7.1 Hz, 1H), 3.45 (dd, J = 18.7 Hz, 2.6 Hz, 1H); 13C{ H} NMR (100 MHz,
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5
5
5
5
6
DMSO-d
6
) δ 199.9, 155.4, 137.2, 132.4, 129.5, 128.8, 128.6, 127.1, 126.8, 124.1, 122.7, 45.9, 37.8;
+
HR-ESI MS (m/z): [M + H] calcd for C13
H
9
BrO 260.9910 found 260.9911.
2
-bromoacenaphthylen-1(2H)-one (6i)
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
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8
9
0
Compound 6i (440 mg, 91%) was obtained as a yellow solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
1
f 6
5:1) R 0.45; H NMR (400 MHz, DMSO-d ) δ 8.38 (d, J = 8.1 Hz, 1H), 8.08 (d, J = 7.3 Hz, 2H), 7.89
(dd, J = 8.1 Hz, 7.0 Hz, 1H), 7.83 – 7.74 (m, 2H), 6.20 (s, 1H). The NMR data are identical to earlier
reported literature values.39
5-bromo-5,6-dihydro-4H-cyclopenta[b]thiophen-4-one (6k)
Compound 6k (380 mg, 87%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
10:1) R
f
0.52; H NMR (400 MHz, DMSO-d
6
) δ 7.77 (d, J = 5.1 Hz, 1H), 7.24 (d, J = 5.1 Hz, 1H), 5.22
(dd, J = 6.7 Hz, 2.4 Hz, 1H), 3.99 (dd, J = 18.5 Hz, 6.7 Hz, 1H), 3.42 (dd, J = 18.5 Hz, 2.1 Hz, 1H);
1
3
1
C{ H} NMR (100 MHz, DMSO-d
6
) δ 191.1, 168.0, 141.4, 133.5, 119.4, 119.4, 49.4, 36.3; HR-ESI
+
MS (m/z): [M + H] calcd for C
7
H
5
BrOS 216.9317 found 216.9320.
5
-bromo-4,5-dihydro-6H-cyclopenta[b]thiophen-6-one (6l)
Compound 6l (375 mg, 85%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
1
0:1) R
f
0.52; H NMR (400 MHz, DMSO-d6) δ 8.46 (d, J = 4.7 Hz, 1H), 7.26 (d, J = 4.8 Hz, 1H), 5.23
(dd, J = 6.7 Hz, 2.4 Hz, 1H), 3.82 (dd, J = 18.1 Hz, 6.7 Hz, 1H), 3.24 (dd, J = 18.1 Hz, 2.4 Hz, 1H);
1
3
1
C{ H} NMR (100 MHz, DMSO-d6) δ 190.15, 166.10, 143.99, 136.50, 124.74, 49.35, 36.10; HR-ESI
+
MS (m/z): [M + H] calcd for C
7
H
5
BrOS 215.9244 found 216.9320.
5
-bromo-5,6-dihydro-4H-cyclopenta[b]thiophen-4-one (6m)
Compound 6m (375 mg, 85%) was obtained as a white solid. TLC (silica gel, n-Hexane / ethyl acetate,
1
10:1) R
f
0.52; H NMR (400 MHz, DMSO-d
6
) δ 8.06 (d, J = 2.0 Hz, 1H), 6.80 (d, J = 2.0 Hz, 1H), 5.19
(dd, J = 6.5 Hz, 2.1 Hz, 1H), 3.85 (dd, J = 18.4 Hz, 6.5 Hz, 1H), 3.29 (dd, J = 18.5, 1.9 Hz, 1H);
1
3
1
C{ H} NMR (100 MHz, DMSO-d
6
) δ 188.6, 179.7, 151.8, 124.2, 105.4, 50.1, 34.3. HR-ESI MS
+
(m/z): [M + H] calcd for C
7
H
5
BrO
2
200.9546, found 200.9561.
The synthesie of compounds (7a - m):
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Compounds 6a - l (1.2 mmol, 1.1 eq.) were added to a solution of mixture of compound 5 (300 mg,
0
.77 mmol) in 20 mL of ethanol. The reaction mixture was stirred for 3 h at 85 °C on an oil bath.
After the mixture was cooled to room temperature and concentrated in vacuo. The residue was
treated with 0.05 M K CO (in methanol, 20 mL) and the mixture was refluxed for 10 mins to
2
3
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1
2
3
4
5
6
7
8
9
0
remove the protecting groups. The organic solvent was neutralized with a solution of HCl (1N)
and evaporated to dryness. The residue was purified by column chromatography (silica gel,
CH
RediSepRf 43 g column, 10–25% acetonitrile in water for 30 min).
-(4,5-Diphenylthiazole-2-yl)-1-(β-D-ribofuranosyl)–uracil (7a).
Compound 7a (300 mg, 81%) was obtained as a white solid. TLC (silica gel, CH
2 2
Cl /MeOH, 10:1) or flash chromatography using a C18 reverse phase column (C18
5
2
Cl
) δ 12.06 (br s, 1H), 9.07 (s,
H), 7.69 – 7.48 (m, 2H), 7.46 – 7.24 (m, 8H,), 5.94 (d, J = 4.7 Hz, 1H), 5.52 (d, J = 5.4 Hz, 1H,),
2 f
/MeOH, 5:1) R
1
0
.64; UV (MeOH): λmax 343 nm (22000); H NMR (400 MHz, DMSO-d
6
1
5.23 – 5.12 (m, 2H), 4.21 (dd, J = 10.0 Hz, 4.8 Hz, 1H), 4.08 (dd, J = 10.0 Hz, 5.0 Hz, 1H), 4.00 – 3.93
(m, 1H), 3.78 – 3.63 (m, 2H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 159.9, 161.4, 155.9, 149.6,
6
147.8, 139.0, 134.5, 132.3, 129.2, 129.0, 128.5, 128.3, 127.7, 107.6, 88.9, 85.1,74.2, 69.8, 60.6;
+
HR-ESI MS (m/z): [M + H] calcd for C24
H
22
N
3
O
6
S 480.1224, found 480.1248.
5-(8H-indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)–uracil (7b).
2 2
Compound 7b (297 mg, 80%) was obtained as a light yellow solid. TLC (silica gel, CH Cl /MeOH,
1
5
9
1
4
3
1
:1) R
f
0.59; UV (MeOH): λmax 355 nm (22900); H NMR (400 MHz, DMSO-d
6
) δ 11.99 (br s, 1H),
.12 (s, 1H), 7.77 (d, J = 7.3 Hz, 1H), 7.57 (d, J = 7.4 Hz, 1H), 7.39 (t, J = 7.4 Hz, 1H), 7.31 – 7.22 (m,
H), 5.91 (d, J = 4.6 Hz,1H), 5.50 (d, J = 5.3 Hz, 1H), 5.25 (t, J = 4.5 Hz,1H), 5.16 (d, J = 5.3 Hz, 1H),
.20 (dd, J = 9.9 Hz, 4.9 Hz, 1H), 4.07 (dd, J = 9.9 Hz, 4.9 Hz, 1H), 3.99 – 3.97 (m, 1H), 3.92 (s, 2H),
.82 – 3.74, 3.72 – 3.64 (2m, 2H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 166.0, 159.3,155.5,
6
46.4, 137.6, 137.2, 136.2, 126.7, 125.1, 124.7, 118.2, 108.0, 89.1, 84.59,7.78, 70.1, 61.3, 31.9;
+
HR-ESI MS (m/z): [M + H] calcd for C19
H
18
N
3
O
6
S 416.0911, found 416.0911.
5
-(6-Fluoro-8H-indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)–uracil (7c).
Compound 7c (275 mg, 82%) was obtained as a white solid. TLC (silica gel, CH2Cl2/MeOH, 5:1)
1
R
f
0.54; UV (MeOH): λmax 358 nm (13400); H NMR (400 MHz, DMSO-d
6
) δ 11.98 (br s, 1H),
9
.14 (s, 1H), 7.75 (dd, J = 8.3 Hz, 5.3 Hz, 1H), 7.45 (dd, J = 9.2 Hz, 2.4 Hz, 1H), 7.29 – 7.19
(
m, 1H), 5.92 (d, J = 4.5 Hz, 1H), 5.52 (br s, 1H), 5.27 (br s, 1H), 5.16 (br s, 1H), 4.20 (t, J =
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.7 Hz, 1H), 4.08 (t, J = 4.8 Hz, 1H), 3.98 (d, J = 7.5 Hz, 3H), 3.79 (d, J = 11.7 Hz), 3.68 (d, J
12.3 Hz, 1H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 162.4, 162.0, 161.3, 159.6, 159.0,
=
6
1
1
49.6, 148.9, 148.8, 139.1, 136.6, 136.6, 133.1, 133.0, 119.5, 119.4, 113.6, 113.41, 113.1,
12.9, 108.1, 88.9, 84.9, 74.3, 69.7, 60.5, 32.4; HR-ESI MS (m/z): [M + H]+ calcd for
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
C
19
H
17FN
3
O
6
S 434.0817, found 434.0840.
5
-(6-Methoxy-8H-indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)–uracil (7d).
Compound 7d (258 mg, 75%) was obtained as a light yellow solid. TLC (silica gel, CH
2
Cl
2
/MeOH,
1
5
1
:1) R
f
0.54; UV (MeOH): λmax 351 nm (15100); H NMR (400 MHz, DMSO-d
6
) δ 11.98 (br s,
H), 9.08 (s, 1H), 7.65 (d, J = 8.3 Hz, 1H), 7.20 (d, J = 2.3 Hz, 1H), 6.96 (dd, J = 8.3 Hz, 2.4
Hz, 1H), 5.92 (d, J = 4.7 Hz, 1H), 5.51 (br s, 1H), 5.26 (t, J = 4.5 Hz, 1H), 5.17 (br s, 1H), 4.20
(
d, J = 5.1 Hz, 1H), 4.08 (t, J = 4.8 Hz, 1H), 3.98 (dd, J = 4.8 Hz, 2.8 Hz, 1H), 3.90 (s, 2H),
3 6
.83 – 3.74 (m, 4H, CH ) δ 161.8,
), 3.72 – 3.64 (m, 1H); 13C{ H} NMR (100 MHz, DMSO-d
1
3
161.19, 159.9, 157.9, 149.5, 148.3, 138.7, 134.8, 129.6, 119.1, 112.3, 111. 7, 108.3, 88.8, 84.9,
+
74.2, 69.8, 60.6, 55.3, 32.2; HR-ESI MS (m/z): [M + H] calcd for C20
H
20
N
3
O
7
S 446.1016,
found 446.1029.
5-(5-Methoxy-8H-indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)–uracil (7e).
Compound 7e (265 mg, 77%) was obtained as a white solid. TLC (silica gel, CH
2
Cl
2 f
/MeOH, 5:1) R
1
0
9
1
.59; UV (MeOH): λmax 358 nm (12000); H NMR (400 MHz, DMSO-d
6
) δ 12.00 (br s, 1H),
.13 (s, 1H), 7.45 (d, J = 8.3 Hz, 1H), 7.33 (d, J = 2.5 Hz, 1H), 6.83 (dd, J = 8.3 Hz, 2.5 Hz,
H), 5.93 (d, J = 4.7 Hz, 1H), 5.52 (br s, 1H), 5.31 (t, J = 4.3 Hz, 1H), 5.17 (br s, 1H), 4.22 (t, J
=
3 2
4.8 Hz, 1H), 4.09 (t, J = 4.8 Hz, 1H), 4.01 – 3.95 (m, 1H), 3.90 – 3.75 (m, 6H, CH , CH ),
.72 – 3.65 (m, 1H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 162.1, 161.3, 159.8, 158.8, 149.6,
3
1
3
5
6
39.0, 138.3, 138.2, 137.78, 125.7, 110.837, 108.2, 104.7, 88.8, 84.9, 74.2, 69.7, 60.5, 55.3,
+
1.4; HR-ESI MS (m/z): [M + H] calcd for C20
H
20
N
3
O
7
S 446.1016, found 446.1032.
-(5,6-Dimethoxy-8H-indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)-uracil (7f).
Compound 7f (240 mg, 65%) was obtained as a bright yellow solid. TLC (silica gel,
1
CH
2
Cl
2
/MeOH, 5:1) R
f
0.54; UV (MeOH): λmax 371 nm (21200); H NMR (400 MHz, DMSO-
d
6
) δ 11.99 (br s, 1H), 9.08 (s, 1H), 7.34 (s, 1H), 7.25 (s, 1H), 5.92 (d, J = 4.9 Hz, 1H), 5.51 (d,
J = 5.4 Hz, 1H), 5.29 (t, J = 4.4 Hz, 1H), 5.16 (d, J = 5.3 Hz, 1H), 4.22 (dd, J = 10.1 Hz, 5.0 Hz,
1
H), 4.09 (dd, J = 9.8 Hz, 4.9 Hz, 1H), 4.00 – 4.95 (m, 1H), 3.86 (s, 3H), 3.84 (s, 2H), 3.81 (s,
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9
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3
1
6
H), 3.80 – 3.75, 3.72 – 3.64 (2m, 2H); 13C{ H} NMR (100 MHz, DMSO-d
6
) δ 161.6, 161.9,
60.3, 149.5, 148.3, 147.5, 138.7, 138.7, 135.4, 129.3, 110.0, 108.4, 103.2, 88.8, 84.9, 74.0,
+
9.8, 60.5, 55.9, 55.8, 31.9; HR-ESI MS (m/z): [M + H] calcd for C21
H
22
N
3
O
8
S 476.1122,
found 476.1123.
-(7,9-Dihydro-6H-furo[3',2':5,6]indeno[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)-uracil
7g).
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
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3
3
3
3
3
3
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5
5
5
5
5
5
5
5
5
6
0
1
2
3
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5
6
7
8
9
0
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5
6
7
8
9
0
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7
8
9
0
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5
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7
8
9
0
1
2
3
4
5
6
7
8
9
0
5
(
2 2 f
Compound 7g (265 mg, 75%) was obtained as a white solid. TLC (silica gel, CH Cl /MeOH, 5:1) R
1
0
1
1
1
1
.65; UV (MeOH): λmax 364 nm (11200); H NMR (400 MHz, DMSO-d
6
) δ 8.63 (s, 1H, H-6), 7.27 (s,
H), 7.05 (s, 1H), 5.99 (d, J = 5.4 Hz, 1H), 5.23 (br s, 1H), 4.66 – 4.50 (m, 2H), 4.20 (t, J = 5.4 Hz,
H), 4.06 (t, J = 4.7 Hz, 1H), 3.93 (dd, J = 7.5 Hz, 3.7 Hz 1H), 3.75 – 3.63 (m, 2H), 3.52 – 3.41 (m,
H), 3.25 – 3.16 (t, J = 8.9 Hz, 2H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 168.8, 165.4, 159.1,
6
59.0, 155.7, 138.4, 137.5, 137.1, 136.4, 123.7, 121.6, 108.1, 99.6, 88.8, 84.6, 73.9, 71.1, 70.1, 61.2,
+
31.2, 29.1; HR-ESI MS (m/z): [M + H] calcd for C21
H
20
N
3
O
7
S 458.1016, found. 458.0948.
5-(7H-benzo[6,7]indeno[1,2-d]thiazol-9-yl)-1-(β-D-ribofuranosyl)-uracil (7h).
2 2
Compound 7h (288 mg, 80%) was obtained as a light green solid. TLC (silica gel, CH Cl /MeOH,
1
5:1) R
f
0.65; UV (MeOH): λmax 370 nm (12900); H NMR (400 MHz, DMSO-d
6
) δ 9.19 (d, J = 8.2 Hz,
1H), 8.75 (s, 1H), 8.00 (d, J = 8.2 Hz, 1H), 7.76 (d, J = 8.3 Hz, 1H), 7.72 – 7.64 (m, 1H), 7.57 (t, J =
7
4
1
1
.4 Hz, 1H), 7.49 (d, J = 8.3 Hz, 1H), 6.11 (d, J = 5.6 Hz, 1H), 5.31 (br s, 2H), 4.37 (t, J = 5.4 Hz, 1H),
.17 (t, J = 4.3 Hz, 1H), 4.05 – 3.95 (m, 1H), 3.81 (s, 2H), 3.69 (d, J = 22.4 Hz, 1H), 3.30 – 3.15 (m,
H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ 169.8, 166.0, 159.9, 156.6, 143.7, 137.4, 136.2, 132.6,
6
32.3, 127.8, 126.4, 125.9, 125.4, 125.1, 124.3, 123.5, 108.2, 88.7, 85.2, 74.0, 70.7, 61.9, 32.3; HR-ESI
+
MS (m/z): [M + H] calcd for Chemical Formula: C23
H
20
N
3
O
6
S 466.1067 found. 466.1083.
5
-(Acenaphtho[1,2-d]thiazol-8-yl)–1-(β-D-ribofuranosyl)-uracil (7i).
The residue was purified by flash chromatography using a C18 reverse phase column (C18
RediSepRf 43 g column, 10-20% acetonitrile in water for 30 min) to afford the compound 7i (185
2 2 f
mg, 53%) as a bright yellow solid. TLC (silica gel, CH Cl /MeOH, 5:1) R 0.13; UV (MeOH):
1
λ
max 348 nm (29300); H NMR (400 MHz, DMSO-d
6
) δ 12.02 (br s, 1H), 9.21 (s, 1H), 8.09 (d, J
=
6.8 Hz, 1H), 8.03 – 7.90 (m, 3H), 7.68 (ddd, J = 19.9, 8.3, 6.9 Hz, 2H), 5.94 (d, J = 4.5 Hz,
1
1
H), 5.55 (br s,1H), 5.31(br s, 1H), 5.20 (br s, 1H), 4.24 (t, J = 4.7 Hz, 1H), 4.12 (t, J = 4.9 Hz,
H), 4.04 – 3.9 8 (m, 1H), 3.88 – 3.78, 3.77 – 3.67 (2m, 2H); 13C{ H} NMR (100 MHz, DMSO-
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5
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6
d
6
) δ 161.8, 161.5, 159.6, 149.6, 139.3, 134.1, 131.6, 130.4, 128.8, 128.2, 127.9, 127.6, 127.3,
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22.7, 121.6, 108.1, 89.0, 84.9, 74.3, 69.7, 60.5; HR-ESI MS (m/z): [M + H]+ calcd for
S 452.0911, found. 452.0909.
-(8H-thiazolo[5',4':4,5]cyclopenta[1,2-b]pyridin-2-yl)-1-(β-D-ribofuranosyl)-uracil (7j).
22 18 3 6
C H N O
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0
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2
3
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7
8
9
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1
2
3
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5
6
7
8
9
0
The residue was purified by flash chromatography using a C18 reverse phase column (C18
column, 10-30% acetonitrile in water for 30 min) to afford compound 7j (132 mg, 41%) as a gray
1
solid .TLC (silica gel, CH
MHz, DMSO-d
.92 (d, J = 5.7 Hz, 1H), 5.12 (br s, 2H), 4.14 (t, J = 5.6 Hz, 1H), 3.99 (t, J = 4.8 Hz, 1H), 3.92 – 3.80
2
Cl
2
/MeOH, 5:1) R
f
0.65; UV (MeOH): λmax 346 nm (13100); H NMR (400
6
) δ 8.51 – 8.40 (m, 2H), 7.85 (d, J = 7.1 Hz, 1H), 7.18 (dd, J = 7.5 Hz, 5.0 Hz, 1H),
5
m, 3H), 3,66 – 3.56 (m, 2H); 13C{ H} NMR (100 MHz, DMSO-d
1
(
6
) δ 169.4, 166.8, 158.5, 156.2,
1
55.6, 147.2, 141.7, 140.3, 137.6, 132.0, 119.3, 108.0, 88.5, 84.9, 73.5, 70.3, 61.7, 29.8; HR-ESI MS
+
17 4 6
(m/z): [M + H] calcd for C18H N O S 417.0863, found. 417.0867.
5-(7H-thieno[3',2':4,5]cyclopenta[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)-uracil (7k).
Compound 7k (143 mg, 44%) was obtained as a bright yellow solid.TLC (silica gel,
1
CH
2
Cl
2
/MeOH, 5:1) R
f
0.65; UV (MeOH): λmax 371 nm (11400); H NMR (400 MHz, DMSO-
6
d ) δ 12.03 (br s, 1H), 8.91 (s, 1H), 7.53 (d, J = 4.8 Hz, 1H), 7.23 (d, J = 4.8 Hz, 1H), 5.91 (d, J
= 5.2 Hz, 1H), 5.49 (d, J = 5.5 Hz, 1H), 5.23 – 5.11 (m, 2H), 4.21 (dd, J = 10.3 Hz, 5.2 Hz, 1H),
.05 – 4.20 (m, 1H), 3.96 – 3.90 (m, 1H), 3.84 (s, 2H), 3.73 – 3.60 (m, 2H); 13C{ H} NMR (100
1
4
MHz, DMSO-d
6
) δ 161.3, 161.2, 156.0, 150.7, 149.5, 138.6, 137.5, 136.1, 126.1, 123.5, 108.3,
8
4
5
8.6, 85.1, 73.8, 69.8, 60.8, 30.6; HR-ESI MS (m/z): [M + H]+ calcd for C17
16 3 6 2
H N O S
22.0475, found 422.0475.
-(4H-thieno[2',3':4,5]cyclopenta[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)-uracil (7l).
Compound 7l (170 mg, 52%) was obtained as a bright yellow solid. TLC (silica gel,
1
CH
2
Cl
2
/MeOH, 5:1) R
f
0.59; UV (MeOH): λmax 363 nm (10000); H NMR (400 MHz, DMSO-
d
6
) δ 11.99 (br s, 1H), 9.02 (s, 1H), 7.63 (d, J = 5.0 Hz, 1H), 7.35 (d, J = 5.0 Hz, 1H), 5.91 (d, J
4.9 Hz, 1H), 5.51 (d, J = 5.4 Hz, 1H), 5.21 (t, J = 4.4 Hz, 1H), 5.17 (d, J = 5.2 Hz, 1H), 4.25 –
=
4
.16 (m, 1H), 4.10 – 4.03 (m, 1H), 4.05 – 3.90 (m, 3H), 3.80 – 3.71, 3.69 – 3.61 (2m, 2H);
13
1
C{ H} NMR (100 MHz, DMSO-d
6
) δ 161.2, 160.7, 157.1, 149.5, 145.5, 141.7, 138.5, 137.0,
+
1
29.0, 117.8, 108.4, 88.7, 84.9, 74.0, 69.8, 60.6, 31.1; HR-ESI MS (m/z): [M + H] calcd for
17 16 3 6 2
C H N O S 422.0475, found 422.0478.
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5
-(4H-furo[2',3':4, 5]cyclopenta[1,2-d]thiazol-2-yl)-1-(β-D-ribofuranosyl)-uracil (7m).
Compound (6m) (1.2 mmol, 1.1 eq.) was added to a solution of mixture of compound 5 (300 mg,
.77 mmol) in 10 mL of DMF. The reaction mixture was stirred for 6 h at 105 °C on an oil bath.
After the mixture was cooled to room temperature and concentrated in vacuo. The residue was
treated with 0.05 M K CO (in methanol, 20 mL) and the mixture was refluxed for 10 mins to
0
1
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5
5
6
0
1
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9
0
1
2
3
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5
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7
8
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0
1
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7
8
9
0
1
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6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
2
3
remove the protecting groups. The organic solvent was neutralized with a solution of HCl (1N)
and evaporated to dryness. The residue purified flash chromatography using a C18 reverse phase
column (C18 RediSepRf 43 g column, 10–25% acetonitrile in water for 30 min) to afford
compound 7m (160 mg, 51%) as a light yellow solid. TLC (silica gel, CH
2
Cl
) δ 8.74 (s, 1H), 7.78 (d, J = 1.9 Hz,
H), 6.79 (d, J = 2.0 Hz, 1H), 5.92 (d, J = 5.4 Hz, 1H), 4.18 (t, J = 5.3 Hz, 1H), 4.05 (t, J = 4.7 Hz,
2 f
/MeOH, 5:1) R 0.54;
1
UV (MeOH): λmax 365 nm (11300); H NMR (400 MHz, DMSO-d
6
1
1H), 3.94 – 3.89 (m, 1H), 3.85 (s, 2H), 3.72 – 3.60 (m, 2H); 13C{ H} NMR (100 MHz, DMSO-d
1
) δ
6
164.1, 163.0, 160.8, 153.8, 151.9, 146.8, 137.7, 130.7, 123.3, 108.4, 104.8, 88.7, 84.8, 73.7, 69.9, 61.0,
+
28.5; HR-ESI MS (m/z): [M + H] calcd for C17
H
16
N
3
O
7
S 406.0703 found 406.0681.
ASSOCIATED CONTENT
Supporting Information
The Supporting Information is available free of charge on the ACS Publications
website. Description of new compound’s sensitivity to polarity and pH, LC
chromatograms of compound 7b, 7c, 7e and 7l at pH 1, 7 and 13 and NMR
spectra of new and known compounds.
Acknowledgements
This work was financially supported by The Scientific Research Foundation for the
Returned Overseas Chinese Scholars, State Education Ministry of China.
References
(1) Morris, K. V. Role of RNA in the regulation of gene expression. Nutr. Rev. 2008, 66, 31–32.
(2) Choi, Y. S.; Patena, W.; Leavitt, A. D.; McManus, M. T. Widespread RNA 3'-end oligouridylation
in mammals. RNA 2012, 18, 394–401.
(3) Fica, S. M.; Tuttle, N.; Novak, T.; Li, N. S.; Lu, J.; Koodathingal, P.; Dai, Q.; P. Staley, J.;
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 20 of 23
1
2
3
4
5
6
7
8
9
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
Piccirilli, J. A. RNA catalyses nuclear pre-mRNA splicing. Nature 2013, 503, 229–234.
4) Nagai, K., RNA—protein complexes. Curr. Opin. Struct. Biol. 1996, 6, 53-61.
(
(
5) Hermann, T.; Patel, D. J., RNA bulges as architectural and recognition motifs. Structure 2000, 8,
R47-R54.
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
(
(
(
6) Jones, S.; Daley, D. T. A.; Luscombe, N. M.; Berman, H. M.; Thornton, J. M., Protein–RNA
interactions: a structural analysis. Nucleic Acids Res. 2001, 29, 943-954.
7) Srivatsan, S. G.; Sawant, A. A., Fluorescent ribonucleoside analogues as probes for investigating
RNA structure and function. Pure Appl. Chem. 2010, 83, 213-232.
8) Manna, S.; Srivatsan, S. G., Fluorescence-based tools to probe G-quadruplexes in cell-free and
cellular environments. RSC Adv. 2018, 8, 25673-25694.
(
9) (a) Giassa, I.-C.; Rynes, J.; Fessl, T.; Foldynova-Trantirkova, S.; Trantirek, L., Advances in the
cellular structural biology of nucleic acids. FEBS Lett.s 2018, 592, 1997-2011. (b) Azarkh, M.;
Singh, V.; Okle, O.; Dietrich, D. R.; Hartig, J. S.; Drescher, M. Intracellular conformations of
human telomeric quadruplexes studied by electron paramagnetic resonance spectroscopy.
ChemPhysChem 2012, 13: 1444–1447.
(10) Vorlíčková, M.; Kejnovská, I.; Sagi, J.; Renčiuk, D.; Bednářová, K.; Motlová, J.; Kypr, J.
Circular dichroism and guanine quadruplexes. Methods 2012, 57, 64-75.
(11) Lakowicz, J. R., Principles of fluorescence spectroscopy. Springer Science & Business Media
2
013.
(
12) Haller, A.; Souliere, M., Soulie re, MF and Micura, R. The dynamic nature of RNA as key to
understanding riboswitch mechanisms. Acc. Chem. Res. 2011, 44, 1339-1348.
(
13) Zheng, C.; Zhai, W.; Hong, J.; Zhang, X.; Zhu, Z.; Wang, L., Synthesis of two 6-aza-uridines
modified by benzoheterocycle as environmentally sensitive fluorescent nucleosides. Tetra. Lett.
2
017, 58, 3008-3013.
(14) Sinkeldam, R. W.; Greco, N. J.; Tor, Y., Fluorescent analogs of biomolecular building blocks:
design, properties, and applications. Chemi. Rev. 2010, 110, 2579-2619.
(15) Tanpure, A. A.; Pawar, M. G.; Srivatsan, S. G. Fluorescent nucleoside analogs: probes for
investigating nucleic acid structure and function. Isr. J. Chem. 2013, 53, 366 – 378.
(16) (a) Börjesson, K.; Preus, S.; El-Sagheer, A. H.; Brown, T.; Albinsson, B.; Wilhelmsson, L. M.
Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid
ACS Paragon Plus Environment

Page 21 of 23
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
containing systems. J. Am. Chem. Soc. 2009, 131, 4288–4293. (b) Rovira, A. R.; Fin, A.; Tor, Y.
Chemical mutagenesis of an emissive RNA alphabet. J. Am. Chem. Soc. 2015, 137, 14602–14605.
(c) Mata, G.; Schmidta, O. P.; Luedtke, N. W. A fluorescent surrogate of thymidine in duplex
DNA. Chem. Comm. 2016, 52, 4718– 4721. (d) McCoy, L. S.; Shin, D.; Tor, Y. Isomorphic
emissive GTP surrogate facilitates initiation and elongation of in vitro transcription reactions. J.
Am. Chem. Soc. 2014, 136, 15176–15184. (e) Beharry, A. A.; Lacoste, S.; O’Connor, T. R.; Kool,
E. T. Fluorescence monitoring of the oxidative repair of DNA alkylation damage by ALKBH3, a
prostate cancer marker. J. Am. Chem. Soc. 2016, 138, 3647–3650.
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
(
17) (a) Tokugawa, M.; Masaki, Y.; Canggadibrata, J. C.; Kaneko, K.; Shiozawa, T.; Kanamori, T.;
Grotli, M.; Wilhelmsson, L. M.; Sekine, M.; Seio, K. 7-(Benzofuran-2-yl)- 7-deazadeoxyguanosine
as a fluorescence turn-on probe for single-strand DNA binding protein. Chem. Commun. 2016, 52,
3
809–3812. (b) Suzuki, A.; Yanaba, T.; Saito, I.; Saito, Y. Molecular design of an environmentally
sensitive fluorescent nucleoside, 3-deaza-2ʹ -deoxyadenosine derivative: distinguishing thymine by
probing the DNA minor groove. ChemBioChem 2014, 15, 1638–1644. (c) Wilson, D. L.; Beharry,
A. A.; Srivastava, A.; O’Connor, T. R.; Kool, E. T. Fluorescence probes of ALKBH2 measure
DNA alkylation repair and drug resistance responses. Angew. Chem., Int. Ed. Engl. 2018, 57,
12896–12900. (d) Cservenyi, T. Z.; Van Riesen, A. J.; Berger, F. D.; Desoky, A.; Manderville, R.
A. A simple molecular rotor for defining nucleoside environment within a DNA aptamer–protein
complex. ACS Chem.Biol. 2016, 11, 2576–2582.
(
18) (a) Srivatsan, S. G.; Tor, Y. Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic
incorporation, and utilization. J. Am. Chem. Soc. 2007, 129, 2044–2053. (b) Srivatsan, S. G.; Tor, Y.
Enzymatic incorporation of emissive pyrimidine ribonucleotides. Chem. Asian J. 2009, 4, 419–427.
(
c) Pawar, M. G.; Srivatsan, S. G. Synthesis, photophysical characterization, and enzymatic
incorporation of a microenvironment-sensitive fluorescent uridine analog. Org. Let. 2011, 13, 1114–
117. (d) Tanpure A. A.; Srivatsan S. G. A microenvironment-sensitive fluorescent pyrimidine
1
ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA
abasic Site. Chem. Eur. J. 2011, 17, 12820–12827. (e) Sinkeldam, R. W.; Hopkins, P. A.; Tor, Y.
ChemPhysChem, 2012, 13, 3350–3356.
(
19) Xu, W.; Chan, K. M.; Kool, E.T. Fluorescent nucleobases as tools for studying DNA and RNA.
Nat. Chem. 2017, 9, 1043–1055.
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 22 of 23
1
2
3
4
5
6
7
8
9
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
(
20) Pawar, M. G.; Nuthanakanti, A.; Srivatsan, S. G. Heavy atom containing fluorescent
ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjugate
Chem. 2013, 24, 1367–1377.
(
21) Greco, N. J.; Tor, Y. Simple fluorescent pyrimidine analogues detect the presence of DNA abasic
sites. J. Am. Chem. Soc. 2005, 127, 10784–10785.
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
(
22) Gutierrez, A. J.; Matteucci, M. D.; Grant, D.; Matsumura, S.; Wagner, R. W.; Froehler, B. C.
Antisense gene inhibition by C-5-substituted deoxyuridine-containing oligodeoxynucleotides.
Biochemistry, 1997, 36, 743-748.
(23) (a) Hirose, W.; Sato, K.; Matsuda, A. Selective detection of 5-formyl-2’-deoxyuridine, an
oxidative lesion of thymidine, in DNA by a fluorogenic reagent. Angew. Chem. Int. Ed. 2010, 49,
8
392–8394. (b) Hirose, W.; Sato, K.; Matsuda, A. Fluorescence properties of 5-(5,6-
dimethoxybenzothiazol-2-yl)- 2’-deoxyuridine (dbtU) and oligodeoxyribonucleotides containing
dbtU. Eur. J. Org. Chem. 2011, 6206–62176206
(24) Bleackley, R. C.; Jones, A. S.; Walker, R. T. The preparation of 5-cyanouracil and 5-cyano-2'-
deoxyuridine from the corresponding 5-iodo derivative and cuprous cyanide. Nucleic Acids Res.
1975, 5, 683–690.
(25) Terrence, P. F.; Bhooshan, B. Improved synthesis and in vitro antiviral activities of 5-cyanouridine
and 5-cyano-2ʹ-deoxyuridine. J. Med. Chem.1977, 20, 974–976.
(
(
(
26) Wigerinck, P.; Snoeck, R.; Claes, P.; Clercq, E. D.; Herdewijn, P. Synthesis and antiviral activity
of 5-heteroaryl-substituted 2ʹ-deoxyuridines. J. Med. Chem. 1991, 46, 1767–1834.
27) Vernin, G. In thiazole and its derivatives; Metzger, J. V. Ed.; John Wiley & Sons: New York,
1
979; Vol. 34, pp 165–335.
28) (a) Hopkins, P. A.; Sinkeldam, R. W.; Tor Y. Visibly emissive and responsive extended 6‑aza-
uridines. Org. Lett. 2014, 16, 5290−5293. (b) Bag, S. S.; Gogoi H. Design of “Click” Fluorescent
Labeled 2ʹ -deoxyuridines via C5-[4-(2-Propynyl(methyl)amino)]phenyl Acetylene as a Universal
Linker: Synthesis, Photophysical Properties, and Interaction with BSA. J. Org. Chem. 2018, 83,
7
606−7621. (c) Mata, G.; Luedtke, N. W. Synthesis and solvatochromic fluorescence of biaryl
pyrimidine nucleosides. Org. Lett. 2013, 15, 2462-2465.
(
29) Christian, R. Solvatochromic dyes as solvent polarity indicators. Chem. Rev. 1994, 94, 2319–2358.
30) Thibaudeau, C.; Plavec, J.; Chattopadhyaya, J. Quantitation of the pH dependent thermodynamics
(
ACS Paragon Plus Environment

Page 23 of 23
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
of the N ⇄ S pseudorotational equilibrium of the pentofuranose moiety in nucleosides gives a direct
a
measurement of the strength of the tunable anomeric effect and the pK of the nucleobase. Org.
Chem. 1996, 61, 266–286.
(
(
(
(
31) Simpson, R. B. Association constants of methylmercuric and mercuric ions with nucleosides. J.
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
4
4
4
4
4
4
5
5
5
5
5
5
5
5
5
5
6
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
Am. Chem. Soc. 1964, 86, 2059−2065.
32) Luyten, I.; Pankiewicz, K. W.; Watanabe, K. A.; Chattopadhyaya, J. Determination of the
tautomeric equlibrium of Ψ-uridine in the basic solution. J.Org. Chem. 1998, 63, 1033−1040.
33) Du, H.; Fuh, R.-C. A.; Li, J.; Corkan, L. A.; Lindsey, J. S. PhotochemCAD‡: A computer-aided
design and research tool in photochemistry. Photochem. Photobiol. 1998, 68, 141–142.
34) Du, H.; Fuh, R.-C. A.; Li, J.; Corkan, L. A.; Lindsey, J. S. Are fluorescence quantum yields so
tricky to measure? A demonstration using familiar stationery products. J. Chem. Educ. 1999, 76,
1
260–1264.
(35) Prusoff, W. H. Synthesis and biological activities of iododeoxyuridine, an analog of thymidine.
Biochim. Biophys. Acta 1959, 32, 295–296.
(36) Joncour, A.; Desroy, N.; Housseman, C.; Bock, X.; Bienvenu, N.; Cherel, L.; Labeguere. V.;
Peixoto, C.; Annoot, D.; Lepissier, L.; Heiermann, J.; Hengeveld, W. J.; Pilzak, G.; Monjardet, A.;
Wakselman, E.; Roncoroni, V.; Tallec, S. L.; Galien, R.; David, C.; Vandervoort, N.; Christophe,
T.; Conrath, K.; Jans, M.; Wohlkonig, A.; Soror, S.; Steyaert, J.; Touitou, R.; Fleury, D.;
Vercheval, L.; Mollat, P.; Triballeau, N.; Aar, E.; Brys, R.; Heckmann, B. Discovery, structure–
activity relationship, and binding mode of an imidazo[1,2-a]pyridine series of autotaxin inhibitors.
J. Med. Chem. 2017, 60, 7371–7392.
(
37) House, H. O.; McDaniel, W. C. Perhydroindan derivatives. 18. The use of indenone ketals as
dienophiles. J. Org. Chem. 1977, 42, 2155–2160.
(
38) Greunen, D. G.; Westhuizen, C. J.; Cordier, W.; Nell, M.; Stander, A.; Steenkamp, V.; Panayides,
J-L.; Riley, D. L. Novel N-benzylpiperidine carboxamide derivatives as potential cholinesterase
inhibitors for the treatment of alzheimer's disease. Eur. J. Med. Chem. 2019, 179, 680–693.
39) Iglesias, B.; Peña, D.; Pérez, D.; Guitián, E.; Castedo, L. Palladium-catalyzed trimerization of
strained cycloalkynes: synthesis of decacyclene. Synlett 2002, 3, 486–488.
(
ACS Paragon Plus Environment