5-Substituted pyrimidine L-2-deoxyribonucleosides: Synthetic, quantum chemical, and NMR studies

Article abstract of DOI:10.1080/15257770.2011.641651

As a part of an ongoing medicinal chemistry, we report here the synthesis and structure evaluation of 1-(2-deoxy-3,5-di-O-acetylpentofuranosyl)-5-[(3- methyl-5-oxo-1-phenyl-4,5-dihydro-4H-pyrazol-4-ylidene) pyrimidine-2,4(1H,3H)- dione 5 and 5-[bis(3-methyl-5-oxo-1-phenyl-4,5-dihydro-4H-pyrazol-4-yl)methyl-1- (2-deoxy-3,5-di-O-acetylpentofuranosyl)pyrimidine-2,4(1H,3H)-dione 6 derived from 3,5-di-O-acetyl-5-formyl-2-deoxy - L-uridine 1. Base hydrolysis of compounds 1 and 6 furnished their deacetylated analogues in good yields, whereas hydrolysis of 5 was troublesome. Structural features of these molecules are discussed by NMR spectra analyses and density functional theory quantum chemical calculations. The newly synthesized L-analogues show no significant activity against vaccinia and cowpox viruses.

Full text of DOI:10.1080/15257770.2011.641651

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5-Substituted Pyrimidine L-2′-
Deoxyribonucleosides: Synthetic,
Quantum Chemical, and NMR Studies
Adel Amer a , Samir Senior a b & Xuesen Fan c
a Department of Chemistry, Faculty of Science, Alexandria
University, Egypt
b Department of Chemistry, College of Sciences and Arts, Rabigh
Campus, King Abdulaziz University, Saudi Arabia
c School of Chemistry and Environmental Sciences, Henan Key
Laboratory for Environmental Pollution Control, Henan Normal
University, Xinxiang, Henan, 453007, P. R. China
Published online: 18 Jan 2012.
To cite this article: Adel Amer , Samir Senior & Xuesen Fan (2012): 5-Substituted Pyrimidine L-2′-
Deoxyribonucleosides: Synthetic, Quantum Chemical, and NMR Studies, Nucleosides, Nucleotides and
Nucleic Acids, 31:1, 42-54
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Nucleosides, Nucleotides and Nucleic Acids, 31:42–54, 2012
Copyright ꢀC ASRT, Egypt
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770.2011.641651
5-SUBSTITUTED PYRIMIDINE L-2ꢀ-DEOXYRIBONUCLEOSIDES:
SYNTHETIC, QUANTUM CHEMICAL, AND NMR STUDIES
Adel Amer,1 Samir Senior,1,2 and Xuesen Fan3
1Department of Chemistry, Faculty of Science, Alexandria University, Egypt
2Department of Chemistry, College of Sciences and Arts, Rabigh Campus, King Abdulaziz
University, Saudi Arabia
3School of Chemistry and Environmental Sciences, Henan Key Laboratory for Environmental
Pollution Control, Henan Normal University, Xinxiang, Henan 453007, P. R. China
As a part of an ongoing medicinal chemistry, we report here the synthesis and structure eval-
2
uation of 1-(2-deoxy-3,5-di-O-acetylpentofuranosyl)-5-[(3-methyl-5-oxo-1-phenyl-4,5-dihydro-4H-
pyrazol-4-ylidene) pyrimidine-2,4(1H,3H)-dione 5 and 5-[bis(3-methyl-5-oxo-1-phenyl-4,5-dihydro-
4H-pyrazol-4-yl)methyl-1-(2-deoxy-3,5-di-O-acetylpentofuranosyl)pyrimidine-2,4(1H,3H)-dione
6
derived from 3 ꢁ,5 ꢁ-di-O-acetyl-5-formyl-2 ꢁ-deoxy-β-L-uridine 1. Base hydrolysis of compounds
1 and 6 furnished their deacetylated analogues in good yields, whereas hydrolysis of 5 was
troublesome. Structural features of these molecules are discussed by NMR spectra analyses and
density functional theory quantum chemical calculations. The newly synthesized L-analogues show
no significant activity against vaccinia and cowpox viruses.
Keywords L-nucleoside; tautomerism; NMR; DFT calculations
INTRODUCTION
Drug discovery in antiviral chemotherapy has provided effective treat-
ments for various viral infections. In particular, nucleoside analogues have
been the cornerstone of antiviral treatments for several decades. In the
search for new, safe, and effective agents within this class, L-nucleoside enan-
tiomers of the natural D-nucleosides represent an immense breakthrough.[1]
As a general feature, these compounds with an unnatural configuration con-
fer in most cases lower toxicity and higher metabolic stability compared with
the natural D-counterparts. As a result of our recent study, which showed
that several novel 5-substituted pyrimidine 2ꢁ-deoxyribonucleosides I have
Received 25 May 2011; accepted 11 November 2011.
Address correspondence to Adel Amer, Department of Chemistry, Faculty of Science, Alexandria
University, Egypt. E-mail: adel.amer@alex-sci.edu.eg
42

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
43
FIGURE 1 Structures of biologically active 5-substituted pyrimidine D-2ꢁ-deoxyribonucleosides I and the
title L-nucleosides II.
potent in vitro antiviral activity against two representative orthopox, vac-
cinia, and cowpox viruses,[2–6] herein we report the synthesis of some of
their L-analogues II (Figure 1).
The building block unit for the present study, namely 3ꢁ,5ꢁ-di-acetyl-
5-formyl-2ꢁ-deoxy-L-uridine 1, was successfully prepared in good yield by
the following protocol: (1) Treating L-thymidine 2 with acetic anhydride
to afford 3ꢁ,5ꢁ-di-O-acety-L-thymidine 3; (2) oxidation of 3 with potassium
peroxysulfate (K2S2O8) in the presence of CuSO4·5H2O and 2,6-lutidine in
aqueous acetonitrile to give 1 (see Scheme 1).
Ph
Ph
Ph
N
Ph
N
N
N
N
O
OH
N
N
OH
O
N
O
O
O
O
OH
N
H3C
N
OH
H3C
N
NH
O
NH
N
HN
O
N
HN
O
Ph
Ph
N
c
Ph
HO
Ph
HO
O
O
c
OA
c
OA
OA
c
O
A
N
N
N
N
N
O
O
O
N
CH3
CH3
c
OA
c
OA
c
OA
6A
6B
E
6
D
c
OA
6
Ph
Ph
N
N
N
O
N
O
O
O
O
N
H3C
N
NH
O
N
HN
O
Ph
O
Ph
O
c
OA
c
O
A
N
N
O
N
CH3
6C
c
OA
c
OA
F
6
SCHEME 1

44
A. Amer et al.
Condensation of 1 with equimolar of 1-phenyl-3-methyl-2-pyrazolin-5-
one 4 afforded a mixture of compounds 5 and 6 in 3:2 mole ratio. Of the four
isomeric forms theoretically possible, the spectral data of 5 indicated that it
exists solely in one form A. Its 13C NMR in chloroform showed 22 signals only,
which correlated well with all its proton signals in the Heteronuclear Multiple
Bond Correlation (HMQC) spectrum. The preferred conformation of 5 was
determined from the nuclear Overhauser effect (NOE) data measurement
and by analysis of the nuclear Overhauser effect spectroscopy (NOESY)
spectrum, which confirmed interactions between the methyl group and the
substituted vinyl proton, as well as the H6 and the methylene protons on
C5ꢁ of sugar moiety. This result is in agreement with the previously reported
result for the D-analogue.
Because an accurate knowledge of the conformational properties of
these nucleosides would be an important help for the interpretation of
drug–target interactions, in the present work, conformational preference
of 5 is supported by molecular modeling using the density functional theory
(DFT) in gas phase and solution.
According to difference on the calculated total energy it is found that
the isomer 5A (anti orientation) is more stable than isomer (syn orientation)
5B by 2.513 kcal/mol (Table 1), and that can be related to the presence of
. . .
. . .
C-H O type of hydrogen bond, namely (C11-H43 O22) (Figure 2). The
calculations show that the H-bond is stronger in isomer 5A relative to isomer
˚
5B because its bond length is shorter by 0.026 A, its bond angle is smaller, and
the O22 atom is more planar (Table 2). Calculation of natural population
analysis (Table 3) shows that the electrons accumulate on O22 in isomer 5A
(−0.663 e−) more than isomer 5B (−0.632 e−) and the H43 was found to
be more deficient in electrons in isomer 5B (0.298 e−) relative to isomer
5A (0.292 e−). A simple calculation of the force of attraction between the
two atoms forming H-bond (H43 and O22) in the two isomers according to
Coulomb’s law shows that the force of attraction between the two atoms in
isomer 5A is more than isomer 5B by 7.128 × 10−11 N. There is also another
. . .
. . .
C-H O H-bond, which is formed in two isomers, namely C11-H45 O12 in
. . .
isomer 5B and C11-H45 O22 in isomer 5A. Although the two H-bonds are
fairly planar, the latter is found to be shorter by 0.134 A.
˚
TABLE 1 B3LYP/6–31G(d,p) calculated total energies of structures 5A–5D
Compound
Total energy (a.u.)
5A
5B
5C
5D
−1749.30928102
−1749.30527692
−1749.28662385
−1749.28693448

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
45
FIGURE 2 B3LYP/6–31G(d,p) optimized geometry for 5A with atom number scheme (Color figure
available online).
In the case of the other two isomers 5D (syn orientation) and 5C (anti
orientation), the DFT calculations show that these are less stable than isomer
. . .
5A or 5B due to lack of H-bond, C11-H43 O22, which is present in isomers
5A and 5B. The isomer 5D is found to be less stable than isomer 5B by
˚
TABLE 2 B3LYP/6–31G(d,p) calculated bond lengths (A), bond angles (degree), and dihedral angles
(degree) concerning the H-bonds formed in structures 5A–5D
Compound
5A
5B
5C
5D
2.360
134.15
166.0
. . .
H43 O22
1.841
1.867
2.370
. . .
H45 O12
. . .
H45 O22
2.236
111.56
. . .
C
C
C
11-H43 O22
149.21
132.55
. . .
14-H45 O12
. . .
14-H45 O22
142.56
179.1
. . .
N6-C11-H43 O22
O27-C14-H45 O12
O27-C14-H45 O22
175.3
168.6
. . .
. . .
119.34

46
A. Amer et al.
TABLE 3 B3LYP/6–31G(d,p) calculated charges using the natural population analysis scheme on
centers concerning the H-bonds formed in the structures 5A–5D
Compound
Center
A
B
C
D
N6
−0.44204
0.11090
−0.43783
0.10738
−0.44986
0.07271
−0.44340
0.07876
C11
O12
C14
O22
O27
H43
H45
−0.59328
−0.15151
−0.66291
−0.55355
0.29152
−0.61116
−0.15922
−0.63250
−0.56188
0.29841
−0.59735
−0.14612
−0.57918
−0.55558
0.25615
−0.61527
−0.15835
−0.57587
−0.56437
0.25791
0.28290
0.27360
0.25772
0.27208
11.510 kcal/mol. The calculations show that isomer 5D is more stable than
isomer 5C by 0.195 kcal/mol. That can be ascribed to the presence of the
. . .
other H-bond, C11-H45 O12 in isomer 5D; in contrast, its analogues C11-
. . .
H45 O22 cannot be formed in isomer 5C. So the net conclusion drawn from
the DFT/B3LYP/6–3-1G (d,p) calculations on isomers is that the order of
stability of the four isomers is 5A > 5B >> 5D > 5C.
On the other hand, the 1H NMR spectrum of 6 in chloroform showed an
isomeric mixture. The presence of two tautomers in solution was confirmed
ꢁ
by the presence of pair-wise CH1 at δ6.17, δ6.35 ppm. These two forms
were assigned as 6A and 6B (syn orientations) and are in 0.33:0.67 ratio (see
experimental part) by combination of 1D COSY and 2D HMQC spectra. This
observation was also supported by DFT calculations, and the rotation of the
nucleobase about the glycosidic bond relative to the sugar moiety was also
considered. According to the total energy of each isomer in the gas phase
calculations it is found that the order of stabilization is 6B > 6A > 6C (syn
orientations). Isomer 6B is more stable than isomer 6A by 0.075 kcal/mol,
and it is more stable than isomer 6C by 1.412 kcal/mol. The stability of
isomer 6B over 6A or 6C can be attributed to the presence of two H-bonds
between the uracil oxygen atom and hydroxyl groups (Figure 3).
The calculation of the population of each isomer shows that in gas
phase using the total energy the population of 6A:6B:6C is 44.65:50.67:4.67.
The population of 6A:6B:6C in chloroform solution was found to be
16.10:83.25:0.65 using the total free energy of solvation calculated using
the CPCM//B3LYP/6–31G(d,p) method and 17.48:81.32:1.20 when using
the total energy in solution.
The same trend of stability was found in the three sets of rotomers
6E > 6D > 6F (antiorientations) with populations of 94.36%, 3.45%,
and 2.19%, respectively, in the gas phase and 99.80%, 0.19%, and 0.01%
in solution using the total free energy of solvation calculated using the

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
47
FIGURE 3 B3LYP/6–31G(d,p) optimized geometry for 6B with atom number scheme (Color figure
available online).
CPCM//B3LYP/6–31G(d,p) method. When using the total energy in solu-
tion, the population was found to be 0.38% of isomer 6D, 99.61% of isomer
6E (Figure 4), and 0.01% of isomer 6F.
It can be seen from the examination of Table 4 that the syn conformers
are more stable than their corresponding antiforms in the gas phase and
in solution. Table 5 shows the intramolecular H-bonds computed at the
B3LYP/6–31G(d,p) level.
Because the deacetylated D-analogues of the above-prepared compounds
were found to be more active biologically, based on our previously reported
TABLE 4 B3LYP/6–31G(d,p) calculated total energies of isomers 6A–6F
Total Energy
(a.u.)
Total energy in
solution (a.u.)
Total free energy in
solvation (a.u.)
Isomer
6A
6D
6B
6E
6C
6F
−2321.696438
−2321.693561
−2321.696558
−2321.696684
−2321.694307
−2321.693131
−2321.733452
−2321.728732
−2321.734904
−2321.733996
−2321.730922
−2321.725440
−2321.696840
−2321.689235
−2321.698391
−2321.695143
−2321.693809
−2321.685592

48
A. Amer et al.
FIGURE 4 B3LYP/6–31G(d,p) optimized geometry for 6E with atom number scheme (Color figure
available online).
work, we have decided to prepare compound 7 using the following approach.
First, the formyl group in 1 was protected as dimethyl acetal 8, which was
then treated with NaOMe/MeOH and AcOH/H2O sequentially to give 7
(see Scheme 4). Also, compound 9 was prepared via mild base hydrolysis
˚
TABLE 5 B3LYP/6–31G(d,p) calculated H-bonds bond lengths (A) formed in isomers 6A–6F
Isomer
6A
6D
6B
6E
6C
6F
. . .
H83 O43
1.770
2.535
. . .
H83 O13
. . .
H77 O22
1.783
2.469
. . .
H77 O13
. . .
H63 O13
1.744
1.765
1.762
1.735
. . .
H78 O13
. . .
CH75 O13
2.127
2.238
. . .
CH60 O43
. . .
CH60 O13
2.225
2.175
2.263
. . .
CH75 O22
. . .
CH50 O12
2.227
2.314
. . .
CH52 O12
2.316
. . .
CH53 O12
2.446
2.440

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
49
TABLE 6 B3LYP/6–31G(d,p) calculated gas phase total energies and solvation-free energies of 9A and
9B isomers
Isomer
Total energy (a.u.)
Total free energy of solvation (a.u.)
9A syn
9B anti
−2016.372897
−2016.370376
−2016.388382
−2016.384524
of its corresponding 6 and its NMR spectra showed that it exists in one
tautomeric form 9A only in dimethyl sulfoxide solution (see Experimental
section). On the other hand, compound 5 was found to be very sensitive to
base hydrolysis and the workup of the reaction mixture was tedious.
According to the total energy of each isomer in the gas phase calcula-
tions, it is found that the order of stabilization is 9A (syn orientation)>9B
(antiorientation) (Table 6). The syn-isomer is more stable than the anti-
isomer by 1.582 kcal/mol. The stability of syn-isomer over anti-isomer can
be attributed to the presence of additional two H-bonds formed in the syn-
isomer. The syn-isomer has a hydroxyl group oriented in a direction suitable
for H-bond formation with the uracil and the sugar ring oxygen atoms
(Figure 5, Table 7). The calculated charges using the natural population
analysis are summarized in Table 8. The calculation of population of each
isomer shows that in gas phase using the total energy, the population will be
6.48% of anti-isomer and 93.52% of syn-isomer. The population in dimethyl
sulfoxide (DMSO) solvent was found to be 1.65% of anti-isomer and 98.35%
of syn-isomer using the total free energy of solvation calculated using the
CPCM//B3LYP/6–31G(d,p) method.
The newly synthesized L-analogues show no significant activity against
vaccinia and cowpox viruses. At this point, it seems that the D-configuration
is crucial for exhibiting the antiviral activity.
FIGURE 5 B3LYP/6–31G(d,p) optimized geometry for 9A and 9B with atom number scheme (Color
figure available online).

50
A. Amer et al.
˚
TABLE 7 B3LYP/6–31G(d,p) calculated bond lengths (A), bond angles (degree), and dihedral angles
(degree) concerning the H-bonds formed in anti- and syn-isomers
9 Isomer
Anti
Syn
. . .
H66 O13
1.737
1.749
1.756
1.738
2.359
2.456
165.74
167.68
135.73
97.88
25.5
. . .
H57 O13
. . .
H72 O12
. . .
H72 O1
. . .
O
22-H57 O13
O37-H66 O13
24-H72 O12
24-H72 O1
C9-O13-H66 O37
C9-O13-H57 O22
C7-O12-H72 O24
165.86
167.13
. . .
. . .
O
O
. . .
. . .
15.9
28.9
. . .
13.0
134.6
. . .
EXPERIMENTAL
Melting points were recorded with a Barnstead 1201D electrothermal
melting point apparatus and are uncorrected. 1H NMR and 13C NMR spectra
were recorded on a Varian 400 MHz spectrometer. The chemical shifts are
reported in parts per million (δ) and signals are quoted as s (singlet, d
(doublet), t (triplet), m (multiplet), dd (doublet of doublets), and ddd
(doublet of doublets of doublets). The mass spectra were performed on a
HP 1100 MSD spectrometer at the HT Laboratories, San Diego. The High
Resolution Mass Spectra (HRMS) were performed on a JEOL HX 110 A
spectrometer at the Department of Chemistry, University of Arizona.
TABLE 8 B3LYP/6–31G(d,p) calculated charges using the natural population analysis scheme on
centers concerning the H-bonds formed in anti- and syn-isomers
Isomer
Gas phase
Solution phase
Center
Anti
Syn
Anti
Syn
O1
C7
−0.59530
0.82970
−0.58411
0.84237
−0.60082
0.84473
−0.60185
0.85261
C9
0.68794
0.69196
0.69020
0.69441
O12
O13
O22
O24
O37
H57
H66
H72
−0.61608
−0.70477
−0.72288
−0.75829
−0.72394
0.52695
−0.63372
−0.69780
−0.72168
−0.75198
−0.72206
0.51847
−0.64738
−0.72414
−0.73073
−0.79251
−0.72704
0.53057
−0.65509
−0.72056
−0.72557
−0.78216
−0.73033
0.52419
0.51968
0.47505
0.52616
0.49285
0.52543
0.51007
0.53006
0.50246

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
3ꢀ-5ꢀ-di-O-Acetyl-β-L-thymidine 3
51
Acetic anhydride (52 mL) was added to a mixture of β-L-thymidine
(4.84 g, 20 mmol) and 4-(dimethylamino)pyridine (0.124 g). The reaction
mixture was stirred for 48 hours at room temperature, then rotary evapo-
rated. The traces of acetic anhydride were removed by adding ethanol 25 ×
3 mL and rotary evaporated. The product was recrystallized from water. m.p.
1
127–128◦C; yield 5.87 g. H NMR (CDCl3) δ: 1.87 (s, 3H, CH3C(5)), 2.06,
2.07 (2s, 6H, 2CH3CO), 2.13 (m, 1H, HaC(2ꢁ)), 2.41 (ddd, J = 1.6, 5.6, 14.4
Hz, 1H, HbC(2ꢁ)), 4.19 (m, 1H, HC(4ꢁ)), 4.28 (dd, J = 3.2, 12.2 Hz, 1H,
HaC(5ꢁ)), 4.32 (dd, J = 4.4, 12.2 Hz, 1H, HbC(5ꢁ)), 5.17 (m, 1H, HC(3ꢁ)),
6.28 (dd, J = 5.6, 8.40 Hz, 1H, HC(1ꢁ)), 7.24 (s, 1H, HC(6)), 9.91 (s, 1H,
NH). FAB HRMS: (MH)+ found m/e 327.1207. C14H18N2O7 requires m/e
327.1192.
3ꢀ,5ꢀ-di-O-Acetyl-5-formyl-2ꢀ-deoxy-β-L-uridine 1
Acetonitrile solution (55 mL) containing 3ꢁ-5ꢁ-di-O-acetyl-β-L-thymidine
(5 g, 15.3 mmol) and 2,6-lutidine (6.1 mL) under Argon atmosphere was
added to a clear blue solution of K2S2O8 (8.3 g, 30.7 mmol) and CuSO4·
5H2O (1.5 g) in water (55 mL) at 65◦C. The mixture was stirred at 65–70◦C
and monitored by TLC (EtOAc: n-C6H14 2:1) until the disappearance of the
starting material (ca ∼3 hours). The mixture was concentrated to half of the
initial volume and the remaining solution was extracted with EtOAc. The
organic layer was washed with water. The aqueous layers were combined and
back-extracted with CHCl3. The organic layers were combined, dried over
anhydrous Na2SO4, and evaporated in vacuum. The residue was purified
by flash chromatography (EtOAc: n-C6H14 2:1) to afford 1; m.p. 140–141◦C
1
(1.58 g). H NMR (CDCl3) δ: 2.12, 2.21 (2s, 6H, 2 CH3CO), 2.26 (m, 1H,
HaC(2ꢁ)), 2.61 (ddd, J = 2.8, 3.2, 14.0 Hz, 1H,, HbC(2ꢁ)), 4.36 (m, 3H,
HC(4ꢁ), and H2C(5ꢁ)), 5.17 (m, 1H, HC(3ꢁ)), 6.33 (t, J = 6.80 Hz, 1H,
HC(1ꢁ)), 8.49 (s, 1H, HC(6)), 9.12 (s, 1H, NH), 10.02 (s, 1H, CHO). 13C NMR
(CDCl3) δ: 20.90, 21.07, 39.01, 63.80, 74.19, 83.33, 86.31, 111.95, 1444.55,
149.38, 161.73, 170.51, 170.71, 185.96. FAB HRMS: (MH)+, found 341.0986.
C14H16N2O8 requires m/e 341.0985.
Reaction of Compound 1 with
3-methyl-1-phenyl-pyridazolin-5-one 4
Solution of 3-methyl-1-phenyl-pyrazolin-5-one (87 mg, 0.50 mmol) was
added drop-wise over a period of 3 hours with stirring to a warm solution of
compound 1 (170 mg, 0.50 mmol) in anhydrous ethanol (3 mL) at 45◦C. The
reaction mixture was left at this temperature for 7 hours, then at room tem-
perature overnight. After evaporation to dryness, the residue was purified

52
A. Amer et al.
by flash chromatography (EtOAc: n-C6H14 4:1) to afford 3ꢁ,5ꢁ-di-O-Acetyl-
5-((3-methyl-5-oxo-1-phenyl-1H-pyrazol-4(5H)-ylidene)methyl)-2ꢁ-deoxy-β-L-
uridine 5; m.p. 238–240◦C (15 mg); 1H NMR (CDCl3) δ: 1.97 (s, 3H, CH3),
2.14, 2.34 (2s, 6H, 2 CH3CO), 2.58 (m, 2H, H2C(2ꢁ)), 4.47 (m, 1H, HC(4ꢁ)),
4.46 (dd, J = 5.4, 11.9 Hz, 1H, HaC(5ꢁ)), 4.54 (dd, J = 4.8, 11.9 Hz, 1H,
HbC(5ꢁ)), 5.39 (m, 1H, HC(3ꢁ)), 6.37 (t, J = 6.0 Hz, 1H, HC(1ꢁ)), 7.19
(tt, J = 1.2, 7.6 Hz, 1H, p-Ph), 7.41 (t, J = 8.0 Hz, 2H, m-Ph), 7.68 (s, 1H,
HC = ), 7.91 (dd, J = 1.2, 8.0 Hz, 2H, o-Ph), 9.27 (s, 1H, HC(6)), 10.92
(s, 1H, NH); 13C NMR (CDCl3) δ: 13.34, 20.92, 21.16, 37.74, 64.01, 74.37,
83.15, 86.64, 109.01, 119.45, 125.38, 126.57, 129.06, 136.27, 138.32, 148.47,
149.37, 151.08, 161.95, 162.70, 170.43, 170.63. FAB HRMS: (MH)+, found
m/e 497.1675. C24H24N4O8 requires m/e 497.1672.
3ꢁ ,5ꢁ -di-O-Acetyl-5-((5-hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)(3-
methyl-5-oxo-1-phenyl-4,5-dihydro-1H-pyrazol-4-yl)methyl)-2ꢁ -deoxy-β-L-
1
uridine 6; m.p. 148–150◦C (15 mg); H NMR (CDCl3) δ: 1.84, 1.95, 2.01,
2.04, 2.06, 2.12, 2.18, 2.25, 2.32, 2.38, 2.55 (s, s, m, s, m, s, s, s, s, m,
m, 14.67 H, CH3 groups of two forms A and B, H2C(2ꢁ) and H2C(2ꢁꢁ)),
3.40 (bs, 0.67H, HC(1ꢁꢁ) form A), 4.10 (m, 2H, H2C(5ꢁ)), 4.33 (m, 0.33H,
HC(4ꢁ) form B), 4.49 (m, 0.67H, HC(4ꢁ) form A), 4.78 (bs, 0.33H, HC(1ꢁꢁ)
form B), 5.15, 5.37 (2m 2:1, 1H, HC(3ꢁ) forms A and B, 6.17, 6.35 (2t
2:1, 1H, HC(1ꢁ)), 7.10–7.91 (m, 11H, ArH and HC(6)), 9.63, 9.80, 10.03,
10.89 (4bs, 2.33H, NH and OHs); 13C NMR (CDCl3) δ: 11.91, 12.13, 13.32,
17.21, 20.74, 20.93, 21.15, 21.11, 26.28, 37.07, 37.70, 43.33, 63.62, 64.06,
74.39, 74.66, 82.52, 83.13, 86.45, 86.77, 108.98, 114.58, 119.18, 119.48,
121.34, 121.48, 125.36, 125.40, 126.32, 126.45, 129.06, 129.11, 129.18,
136.41, 136.94, 137.38, 137.67, 138.18, 138.31, 147.11, 147.35, 148.53, 149.43,
150.23, 151.10, 156.64, 162.05, 162.72, 163.82, 170.40, 170.46, 170.56, 170.73,
170.91; FAB HRMS: (MH)+, found m/e 671.2436. C34H35N6O9 requires
m/e 671.2466.
5-Formyl-2ꢀ-deoxyuridine 7
In the presence of Amberlite IR-120 (200 mg), 3ꢁ,5ꢁ-di-O-acetyl-5-formyl-
2ꢁ-deoxyuridine (1, 510 mg, 1.5 mmol) in 25 mL of anhydrous methanol
were refluxed with stirring for 4 hours. The mixture was filtered to remove
the Amberlite resin and the filtrate was concentrated. The residue was pu-
rified through silica gel column chromatography with a mixture of EtOAc
and Hexane (4:1, v/v) as eluant to give a colorless solid (210 mg). The
intermediate 8 was dissolved in 5 mL of anhydrous methanol, and 3.3 mL
of NaOMe/MeOH solution (0.5 M) was added. The mixture was stirred at
ambient temperature for 3 hours. At completion, the mixture was concen-
trated under reduced pressure. To this residue was added 4 mL of AcOH
and 1.5 mL of water. The mixture was then stirred at 50◦C overnight. At

5-Substituted Pyrimidine L-2 ꢁ-Deoxyribonucleosides
53
completion, the solvent was removed under vacuum. The residue was puri-
fied through column chromatography (chloroform–methanol, 4:1) to give
1
7 (100 mg). m.p. 157∼158◦C; H NMR (DMSO-d6) δ: 2.51∼2.56 (m, 2H,
H2ꢁ), 3.53∼3.63 (m, 2H, H5ꢁ), 383∼3.85 (m, 1H, H4ꢁ), 4.21∼4.24 (m, 1H,
H3ꢁ), 5.23 (bs, 2H, 2OH), 6.08 (t, 1H, H1ꢁ), 8.68 (s, 1H, H6), 9.74 (s, 1H,
CHO). 13C NMR (DMSO-d6) δ: 41.32, 61.40, 70.53, 86.54, 88.62, 111.38,
147.75, 150.46, 162.73, 186.96. FAB HRMS: (MH)+, found m/e 257.0782.
C10H13N2O6 requires m/e 257.0774.
5-((5-Hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)(3-methyl-5-oxo-
1-phenyl-4,5-dihydro-1H-pyrazol-4-yl)methyl)-2ꢀ-deoxy-β-L-uridine
9
A mixture of compound (120 mg, 0.18 mmol) and K2CO3 (74 mg, 0.54
mmole) in anhydrous methanol (5 ml) was stirred at room temperature and
monitored by TLC (CHCl3:MeOH 4:1). After 1 hour the reaction mixture
was filtered off and the solvent was evaporated in vacuum to afford 9 (30
mg). m.p. 181–183◦C; 1H NMR (DMSO-d6) δ: 1.96∼2.13 (m, 2H, H2ꢁ), 2.07,
2.14 (2s, 6H, 2CH3),3.21 (d, 1H, OH3ꢁ), 3.46∼3.55 (m, 2H, H5ꢁ), 3.68∼3.75
(m, 1H, H4ꢁ), 3.79 (bm, 1H, OH5ꢁ), 4.21∼4.35 (m, 1H, H3ꢁ), 4.62 (s, 1H,
CH), 4.85, 5.25 (2bs, 2H, 2OH), 6.15 (t, 1H, H1ꢁ), 7.00∼7.04, 7.26∼7.30,
7.84∼7.91 (3m, 10H, ArH), 8.09 (s, 1H, H6), 11.13 (s, 1H, NH). 13C NMR
(DMSO-d6) δ: 13.68, 26.01, 62.83, 71.38, 84.34, 88.13, 101.71, 102.03, 118.39,
119.83, 119.90, 123.69, 128.92, 128.95, 135.80, 141.26, 141.36, 146.09, 146.53,
150.85, 157.38, 158.23, 163.59. FAB HRMS: (MH)+, found m/e 587.2250.
C30H31N6O7 requires m/e 587.2254.
METHOD OF CALCULATIONS
To estimate the population of the isomers in the mixture at ther-
modynamic equilibrium, each structure of the isomers was optimized at
DFT/B3LYP/6–31G(d,p) level in gas phase using the Gaussian 03 pack-
age.[7]
This method and the basic set were found to give accurate molecular ge-
ometries.[8] The solvated species were calculated with the CPCM continuum
solvation method.[9,10] For each isomer, a single point in the solvent was
done. The total energies and the Gibbs free energies of solvation were cal-
culated. Isomer populations were calculated from the following equations:
ꢀ
ꢁ
ꢀGi
RT
ni = exp −
,
ꢀGi = Gi − Gj ,

54
A. Amer et al.
N = nA + nB + nC ,
ni
N
%i =
× 100,
where ni is the ratio number of isomers of type i and j, ꢀGi is the energy differ-
ence of isomers i and j; j is an isomer chosen arbitrarily; R is the gas constant
(1.987 cal mol−1 K−1), and T is the absolute temperature (289.15 K).
ACKNOWLEDGMENT
This work was financially supported by a collaborative Research ASRT
(Egypt)-NSF (China) Grant. The authors thank Prof. Paul F. Torrence for
his continuous support and encouragement.
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