Indian Drugs, 45(1), 2008, 16-25

Spectroscopic and Inter Molecular Studies of Anti AIDS Drug: 3'Azido-2'-deoxythymidine

Y.P.Singha * and Ratnesh Dasb
a

Department of Physics, Govt. Womens Polytechnic College , Sagar (MP) 470001

INDIA,.E-mail: Y_P_S_2k@Yahoo.com
b
Department of Chemistry, Dr. H.S.Gour University, Sagar (MP), INDIA, 470001,
E-mail: ratnesh_das@breakthru.com

ABSTRACT

The vibrational absorption spectra of 3'-Azido-2'-deoxythymidine (Zidovudine) have

been studied. The spectra were analysed based on semi-empirical quantum mechanical (AM1)
and (PM3) calculations. Assuming Cs point symmetry, vibrational assignments for the observed
frequencies have been proposed. The spectra exhibit distinct features originating from low
frequency vibrational modes caused by inter-molecular motion. Normal modes have been
calculated and an assignment of the observed spectra has been proposed.
Keywords : Zidovudine, FTIR Spectra, Anti aids drug, HIV, AM1 and MP2 calculations

INTRODUCTION
There are a number of drugs that have
AIDS has ceased to be a mere health
problem and has now acquired dimensions
which perhaps have very few parallels in the
history of mankind. In reality AIDS1 is , not a
disease but a collection of seventy or more
conditions which result from the damage done to
the immune system and other parts of the body
as a result of infection by HIV.

_________________________________
Address for correspondence:
Yogendra P. Singh, PhD, Department of Physics,
Govt. Polytechnic College, Sagar (MP), INDIA; Tel.:
91-7582-237187; Fax: 91-7582-237470; E-mail:
y_p_s_2k@yahoo.com.

been considered as to be anti HIV. The drugs

like 3'-Azido-2'-deoxythymidine (AZT) and
ribavirin appear most promising because both
cross the blood-brain barrier and can be taken
orally, and in early traities they do not cause
serious side effects.
AZT Zidovudine, was the first drug
approved for the treatment of AIDS and HIV
infection. Jerome Horowitz first synthesized
AZT in 19642. The crystal structure of AZT was
reported by Alan Howie3 in 1988. In the solid
state AZT forms a hydrogen bond network4.

The study of drug complexes have

reporting experimental frequencies

with AM1

assumed much importance, the chemistry of life

and PM3 calculated frequencies because we had

involves, in an essential and indispensible way

surveyed lot of literature but we found nothing.

5, 6

many of the chemical elements

. The word

O 17

AIDS inspires fear, widespread diffusion of

H18
N2

H30

persued all over the world with a view for

O 15
H31

achievimg better understanding of AIDS, its

causes,

symptoms,

diagnostic

mode

treatment

and

of

C13
H24

dreadful disease.

C5

H20

H27

H26
N32

Empirical Formula C10H13N5O4

calculation
by

C6

H23

3'-Azido-2'-deoxythymidine or
Zidovudine

endeavor of striving to eliminate the fear of this

frequencies

C12

N16

Spectroscopis studies of anti-AIDS drug have

The

N4

O9
H 2 5H 28

N14

cure.

made a significant contribution of this noble

C7

H29

spreading,

possible

C3

O19

medicinal and biological sciences are being

C8

C1

information about this disease has made people

aware of its lethal effects. Todal research in the

H22

H21

of

computational

vibrational
methods

Molecular Weight 267.24

is

becoming increasingly important in many areas7.

Infra red and Raman spetra of molecules in their

Fig 1 Structure and Formula of Zidovudine

ground electronic states were predicted by

molecular orbital theory8.
Conformational analysis of AZT structure and

EXPERIMENTAL

other related drugs have been previously

reported at semiempirical and ab initio levels
of theory

7-9

. Hernndez10 at al reported an ab

initio HF and DFT study of the dipole

polarizability of AZT drug.
Thus the present study has been
undertaken with a view to understand the
spectroscopy of this drug and we compared
experimental results with calculated frequencies
using force matrix method and MOPAC method.
Probably, this is the first time when we are

All the chemicals used to prepare

experimental sets were of Analar/BDH grade.
Zidovudine was purchased from Cipla India Ltd.
I.R. Spectrum has been recorded using
KBr disc in solid phase in the range 4004000cm-1 on Perkin-Elmer spectrometer Model
397.
Preparation of KBr Pallets: A small
amount of finally grounded solid sample was
intimately mixed with about 100 times or more

than its weight of Potassium bromide powder.

The vibrational infrared frequencies

The finely ground mixture was than pressed

were also calculated on the basis of AM1 and

under very high pressure in a press (about

PM3 precise set of MOPAC as shown in table 3.

10/cm ) to form a small pallet (about 1-2 mm

3'-Azido-2'-deoxythymidine contains 32 atoms

thick and 1cm in diameter).

so that it has 90 normal modes. The calculated

The accuracy of the measurements was

-1

estimated to be within 3cm and the resolution

normal modes are distributed among 60 a and

30 a species of Cs symmetry group.

-1

was better than 2cm through the entire spectra.

The table 3 also shows that PED

contributions for 90 normal modes. These
assignments are partly based on the calculated
frequencies. As the table 3 is self-explanatory,

RESULTS and DISCUSSIONS

we shall discuss here only some important

Zidovudine is one of the complex
structured drugs. The infra red spectrum of this
drug is presented in figure 2.
spectra is of practical importance for the
of

known

and

unknown

compounds, and has become an important part

of spectro-chemical and quantum chemical
investigations11.
We

can

Only the frequencies from 300cm-1 to

2200cm-1 have been taken into consideration.

The theoretical prediction of vibrational

identification

points.

The experimental bands are shown in figure 2.

All spectra exhibit fine structures. Experimental
O-H stretching bands are not shown; only
theoretically calculated frequencies are taken
into account.
Figure 3 and 4 shows agreement

get

information

from

computational vibrational spectra only when we

compare it with experimental spectrum. The
values of bond angle in angstroms, bond angles

between the experimental and calculated wave

numbers (AM1 and PM3). The graph is linear
which shows that theoretical and experimental
results are in good agreement.

in degrees and Cartesian coordinates are

presented in Table 1. The experimental results
are compared with those obtained by AM1 and

CONCLUSIONS
Theoretical

semi-empirical

quantum

PM3 method. These calculations are done on the

mechanical AM1 and PM3 calculations of the

basis of precise set. The calculated bond

geometry and vibrational frequencies of the

distances and bond angles comes out to be in

AZT drug are presented in this paper and

agreement with the experimental one as reported

compared with infrared spectra. The calculated

12

by Roey et al .

geometries and frequencies agree well with the

experimental

ones,

but

there

are

some

differences between frequencies mainly due to

ACKNOWLEDGEMENTS

intermolecular interactions, anharmonicity and

computational basis set.

The authors are grateful to Director,

Directorate of Technical Education-Madhya
Pradesh, Bhopal and Head, Department of
Chemistry, Dr. H.S.Gour University, Sagar
(MP), India.

Fig 2: I. R. Spectra of 3'-Azido-2'-deoxythymidine/ Zidovudine (AZT)

Table 1. Optimized bond distances (in Angstrom ), bond angles and torsion angles
(in degrees )of AZT.
Bond Angle ( Degree )

Bond
C1-N2
N2-C3
C3-N4
C5-N4
C5-C7
C7-C1
C1-O17
C7-C8
C8-H21
N2-H18
C3-O19
C5-H20
N4-C10
C10-O9
C10-C6
C6-C12
C12-C11

Bond length ( A )
Experime AM1
ntal14
Calculation
1.384
1.368
1.372
1.386
1.332
1.197
1.503
1.201
1.463
1.391
1.535
1.529

1.391
1.391
1.391
1.391
1.391
1.391
1.107
1.542
1.694
1.095
1.095
1.095
1.456
1.401
1.598
1.581
1.946

PM3
Calculation
1.391
1.391
1.391
1.391
1.391
1.391
1.113
1.557
1.703
1.109
1.116
1.115
1.498
1.451
1.603
1.608
1.993

Bond Angle
C1-N2-C3
C1-N2-H18
N2-C1-O17
N2-C3-O19
C3-N4-C5
C7-C8-H21
H21-C8-H22
C7-C5-H20
C5-N4-C10
N4-C10-H27
N4-C10-O9
H27-C10-C6
C11-O9-C10
C10-C6-C12
C10-C6-H26
O9-C11-C12
C11-C12-C6

Experime
ntal14

AM1
Calculation

PM3
Calculation

130.4

120.000
120.000
120.000
120.000
120.000
77.245
69.517
120.000
118.953
120.269
108.329
77.519
111.538
99.157
106.681
103.184
105.995

120.000
120.000
120.010
120.00
120.060
78.058
70.349
121.658
119.359
121.647
109.264
76.927
112.327
100.062
106.992
104.194
104.367

123.1
119.1

117.9
107.8
110.2
98.8
104.7
105.6

C11-O9
C11-C13
C13-O15
C12-N14
N14-N16
N16-N32
N32-N14

1.414
1.515
1.405
1.467
1.231
1.100

1.511
1.591
1.483
1.492
1.316
1.245
1.729

1.549
1.612
1.506
1.507
1.359
1.281
1.937

C11-C13-O15
C13-O15-H31
H30-C13-O15
C6-C12-N14
C5-C7-C1
C5-C7-C8
C13-C11-O9
N4-C10-C6
N14-N16-N32
N16-N32-N14
N32-N14-N16
N2-C3-N4

114.382
141.357
39.462
113.346
121.634
119.924
120.996
160.534
57.165
69.378
56.00
110.0

113.5
111.1
120.0
120.0
120.4
162.3

113.0

Table 2: Cartesian Coordinates

AM1
NO.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

ATOM
C
N
C
N
C
C
C
C
O
C
C
C
C
N
O
N
O
H
O
H
H
H
H
H
H
H
H
H
H
H
H
N

.0000
1.4008
2.1006
1.4002
.0010
4.2036
-.6994
-1.8025
4.7145
5.0983
6.2287
6.3343
5.8960
7.2137
6.5882
6.4851
-.5515
1.9522
3.2037
-.5504
-2.3927
-2.9386
-2.7141
7.1433
5.8477
5.1078
5.2926
3.6686
5.1802
4.9213
7.9281
5.0070

PM3
Y

.0000
.0000
1.2117
2.4246
2.4250
2.5236
1.2119
1.2121
1.1446
3.5291
1.3673
2.7396
.0270
4.1369
-1.0034
5.2408
-.9553
-.9554
1.2117
3.3804
.3261
1.4685
2.1686
1.6133
2.2723
2.5105
4.3952
3.8305
-.8574
.2590
-1.6039
6.0841

Z
.0000
.0000
.0000
.0000
.0000
.7786
.0000
.0000
1.2160
1.5247
1.3141
1.9949
1.3141
1.9949
1.3141
1.9949
.0000
.0000
.0000
.0000
.0000
.0000
.0000
1.3141
.3594
.3594
1.5247
.7786
1.3141
1.3141
1.3141
1.9949

NO.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32

ATOM
C
N
C
N
C
C
C
C
O
C
C
C
C
N
O
N
N
O
H
O
H
H
H
H
H
H
H
H
H
H
H
H

X
.0000
1.4008
2.1006
1.4002
.0010
2.2467
-.6994
-1.8025
2.8323
3.4668
4.1331
4.6962
4.5736
5.3458
5.5266
5.1056
4.5477
-.5515
1.9522
2.7078
-.5504
-1.7139
-2.3664
-2.0873
4.7343
3.9969
3.0875
3.8512
2.6679
3.7636
5.2904
6.4823

Y
.0000
.0000
1.2117
2.4246
2.4250
3.4319
1.2119
1.2121
2.2889
4.2561
1.9632
3.3511
1.1318
3.6474
.6188
4.8577
4.4753
-.9553
-.9554
1.1640
3.3804
-.0315
.4990
1.9235
2.5012
2.8504
3.5391
4.6240
3.9207
.7315
1.4621
.6999

Z
.0000
.0000
.0000
.0000
.0000
.8402
.0000
.0000
1.6796
.3927
.9355
.5971
.9355
.5971
.9355
.5971
.5971
.0000
.0000
.0000
.0000
.0000
.0000
.0000
.9355
.5971
.2340
.3927
.8402
.9355
.9355
.9355

115.216
140.581
40.421
114.624
120.347
120.068
120.624
159.458
58.619
70.058
55.0274
111.621

Table 3

Experimental, Calculated Frequencies and Potential Distribution in Zidovudine

(AZT)

Assignment

Experimental
Frequencies
(in cm

MOPAC Calculated Frequencies (in cm

AM1

PM3

Potential Energy
Distributionb

Atom Pair /
Energy
Contribution
(in %)a

Species a
1
2
3
4
5

3468.99
3451.41
3331.98
3190.12
3143.81

3485.70
3356.85
3294.36
3166.24
3087.32

6
7
8

3142.39
3094.79
3084.79

3077.40
3073.82
3069.05

9
10

3072.90
3055.24

2993.62
2988.79

11

3039.39

2907.71

12

3020.78

2805.41

13

3015.48

2639.90

14

2512.86

2622.94

O15- H31 (99.5)

N2-H18 (99.3)
015-H31 (99.5)
C10-H27 (97.7)
C8-H22 (32.9)
C8-H21 (29.2)
C8-H23 (24.7)

s (Hydroxyl Group)
a (Thymine Ring)
a (Hydroxyl Group)
a (Azide Ring)

C5 H20 (86.0)
C11-H24 (54.9)
C6-H26 (70.1)
C6-H28 (28.4)
C13-H29 (92.1)
C8-H22 (55.8)
C8-H21 (39.2)
C8-H23 (66.4)
C8-H21 (26.5)
C11-H24 (38.8)

s (Thymine Ring)
s
s (Furancose Ring)

C6-H28 (68.4)
C6-H26 (29.8)
N16-N32 (71.7)
N14-N16 (28.0)
C12-N14 (23.6)
C10-H27(42.2)
C12-N14 (16.7)
C11-C12 (15.5)

s (Thymine Ring)

s (Hydroxyl Group)
s (Thymine Ring)
a (Thymine Ring)
a (Furancose Ring)
a (Furancose Ring)
a (Azide Ring)

15
16

2170
1887

2162.78
1842.68

2163.94
1949.16

17

1801

1811.70

1894.66

C5-C7 (21.7)
C3-C5 (15.7)
C3-N4 (10.7)

s + s + s
(Thymine Ring)

18

1725

1728.36

1720.75

19

1623

1653.82

1605.83

C3-N4 (19)
C3-O19 (14.1)
C3-N4 (14.8)
C3-O19 (18.1)

20

1552.48

1543.15

21

1549.01

1532.50

s + s
(Thymine Ring)
a + a
(Thymine Ring)
s + s
(Thymine Ring)
s + s + s

22
23

1483

1539.82

1500.53

1479.92

1472.42

N4-C5 (24.1)
C5-C7 (15.6)
O15-H31 (50.3)
C13-H29 (11.5)
C13-O15 (11.1)
C12-N14 (35.3)
N14-N16 (29.4)
C13-O15 (22.6)
C11-C13 (18.4)
C13-H29 (15.5)

s (Furancose Ring)
s + s + s
(Furancose Ring)

(Hydroxyl Group)

s + s

(Azide Ring)

a + a + a

(Hydroxyl Group)

24

1476.10

25

1460.51

1469.10

1451.15

26

1437.58

1425.70

27
28

1436.61
1412.89

1419.17
1429.43

1414

29

1395.64

1382.55

30
31
32

1384.84
1377.14
1376.39

1377.64
1370.14
1364.90

1372.71
1320.69

1360.08
1330.35

1318.57

1316.84

33
34

1324

35

36

1286.42

1280.66

37

1281.31

1278.95

38

1275.97

1269.91

39

1172.30

1174.33

1171.21

1169.71

1118.52

1112.05

1103.83

1110.50

43

1072.51

1062.79

44

1058.95

1049.28

45

1050.84

1034.86

1012.02

1006.45

40

1151

41
42

46

47
48
49
50

1106

1013

1001
927

966.26
922.03
854.58
694.90

976.38
931.15
863.26
715.21

C7-C8 (25.7)
C1-C7 (15.0)
C5-C7 (13.2)
C6-H26 (20.1)
C6-C10 (16.8)
C6-H28 (15.8)
N2-H18 (29.2)
N2-C3 (10.4)
C11-C12 (21.5)
C1-C7 (13.1)
C8-H22 (10.7)
N2-H18 (10.6)
C6-H28 (12.5)
C6-H26 (12.4)
C11-H24 (17.9)
C11-H24 (14.9)
C8-H22 (34.9)
C8-H23 (21.5)
C3-O19 (11.5)
C13-H29 (25.1)
C11-C13 (13.8)
C1-N2 (30.0)
C1-O17 (13.3)
C1-C7 (12.6)
C5-H20 (28.1)
N2-C3 (12.7)
N4-C5 (11.7)
C13-H29 (17.6)
C12-N14 (14.2)
C6-H28 (23.8)
C13-H29 (22.6)
C13-H29 (19.6)
C6-H28 (10.0)
C11-H24 (16.9)
C11-C13 (14.0)
C11-C13 (18.9)
C11-H24 (17.8)
C5-H20 (22.5)
C1-N2 (14.4)
C3-N4 (14.3)
C8-H23 (36.6)
C8-H21 (21.0)
C8-H22 (17.3)
C8-H23 (11.5)
C8-H21 (24.7)
C8-H22 (26.8)
C6-C10 (19.5)
C10-H27 (10.6)
C6-C10 (18.6)
C6-H26 (17.2)
C6-H28 (15.9)
C11-H24 (24.1)
C11-C12 (19.2)
C1-C7 (12.9)
C5-C7 (13.6)
C6-C10 (11.0)

s + s+ s

(Thymine Ring)

s+ s + s

(Furancose Ring)

s+ s

(Thymine Ring)

s (Furancose Ring)
s + s+ s
(Thymine Ring)

s+ s

(Furancose Ring)

s (Furancose Ring)
a (Furancose Ring)
U (Thymine Ring

s (Thymine Ring)
s + s
(Hydroxyl Group)
s + s+ s
(Thymine Ring)

s + s+ s

(Thymine Ring)

s (Hydroxyl Group)
s (Azide Ring)
s (Furancose Ring)
s (Hydroxyl Group)
a (Furancose Ring)
a (Hydroxyl Group)
s (Furancose Ring)
s (Hydroxyl Group)
a (Hydroxyl Group)
a (Furancose Ring)
s+ s + s
(Thymine Ring)
s + s+ s
(Thymine Ring)
a + a+ a
(Thymine Ring)
s + s

(Furancose Ring)

s+ s+ s

(Furancose Ring)

s+ s

(Furancose Ring)

s (Thymine Ring)
a (Thymine Ring)
s (Furancose Ring)

51

574

574.24

562.87

52
53
54
55
56
57

482

490.62
456.07
417.19
367.44
322.41
305.67

450.83
417.07
402.02
354.55
362.60
317.91

311

58

236.18

225.89

59

144.79

15.47

60

112.24

77.84

Assignment

Experimental
Frequencies
(in cm

C13-O15 (18.7)
C11-C13 (16.2)
C1-C7 (10.5)
O15-H31 (22.4)
N14-N16 (11.8)
C3-015 (37.0)
N14-N16 (21.9)
C6-C10 (14.5)
C6-H28 (21.1)
C6-H26 (18.9)
C6-C10 (24.5)
C6-H28 (20.1)
C6-H26 (19.9)
C6-C10 (13.4)
C10-H27 (13.0)
C7-C8 (24.5)
C8-H21 (21.2)
C8-H22 (20.5)

MOPAC Calculated Frequencies (in cm

AM1

PM3

rocking
(Hydroxyl Group)

s (Thymine Ring)
s (Hydroxyl Group)
s (Azide Group)
s (Hydroxyl Group)
a (Azide Group)
s + s+ s
(Furancose Ring)

a + a+ a

(Furancose Ring)

s+ s

(Furancose Ring)

a+ a

(Thymine Ring)

Potential Energy
Distribution

Atom Pair / Energy

Contribution (in %)

Species a
1

1387

1381.07

1373.55

1191

1213.16

1206.15

5
6
7

914
817

944.84
857.71
815.85

981.27
885.26
813.62

741

752.51

797.30

696.64

699.38

696.22
624.34

671.40
647.93

12

563.95

562.70

C8-H21 (47.9)
C8-H23 (35.4)
C6-H28 (17.3)
C6-H26 (15.0)
C13-H29 (54.1)
O15-H31 (12.7)
C6-H26 (27.1)
C10-H27 (11.8)
C13-H29 (11.8)
C5-H20 (65.0)
C6-C10 (11.9)
C10-H27 (24.8)
C6-H26 (13.9)
C6-H28 (13.7)
C1-C7 (31.7)
C1-N2 (21.6)
C1-O17 (21.5)
C3-N4 (27.3)
N2-C3 (21.3)
C3-O19 (20.8)
N2-H18 (80.2)
C1-N2 (21.1)
N2-C3 (14.8)
C1-C7 (13.8)
C3-C5 (14.5)

1350.60

1363.73

1246.77

1274.74

13
14

537.38
486.23

555.47
489.36

C6-C10 (11.6)
C11-H24 (11.3)

15

461.91

453.46

C12-N14 (12.0)
C11-C12 (10.2)

9
10
11

607

s (Thymine Ring)
s (Furancose Ring)
s + s (Hydroxyl
Group)
a (Furancose Ring)
a (Hydroxyl Group)
s (Thymine Group)
s (Furancose Ring)
s (Furancose ring)
s (Thymine Group)
s (Thymine Group)
s (Thymine Group)
a (Thymine Group)
Rocking (Thymine
Ring)
a (Furancose Ring)
s Scissoring
(Furancose Ring)
a Scissoring
(Furancose Ring)

16

441

448.37

432.65

17

406

427.19

412.02

18

355

344.89

394.32

19

337.41

377.95

20

180.47

191.89

21

167.09

183.81

22

106.61

116.5

23
24

81.07
50.97

71.33
47.41

25

38.55

33.11

26

29.21

27.21

27

28.56

26.8

28

17.86

18.42

29
30

12.50
10.10

13.6
10.8

N16-N32 (52.0)
N14-N16 (41.6)
N14-N16 (11.8)
O15-H31 (21.8)
N14-N16(13.2)
C7-C8 (20.5)
N4-C5 (13.0)
O9-C110 (12.1)
O9-C11 ( 11.4)
C1-N2 (20.3)
N2-C3 (20.0)
N2-H18 (17.7)
C11-C12 (21.4)
C11-C13 (20.6)
C11-H24 (18.8)
C3-O19 (13.6)
C13-O15 (19.0)
C11-C13 (16.2)
O15-H31 (11.9)
C13-O15 (17.5)
C11-C13 (12.9)
C7-C1 ( 19.8)
C7-C5 (17.3)
C7-C8 (12.6)
C10-O9 (18.6)
C10-C6 (16.5)
C10-H27 (12.9)
C8-H21(15.6)
C8-H23 (14.9)
C8-C7 (11.60

s Scissoring
(Azide Ring)
a Scissoring
(Azide Ring)
s (Hydroxyl Group)
s (Azide Ring)
s (Thymine Ring)
s (Furancose Ring)
a (Thymine Ring)
s (Furancose Ring)
s (Thymine Ring)
a ( Hydroxyl Group)
Rocking
(Hydroxyl Group)
Rocking
(Thymine Ring)
Rocking
(Azide Ring)
Rocking
(Thymine Ring)
Twisting
Twisting

Calculated
Wavenumbers (cm-1)

Only contributions > 10% are listed

b = stretching,= in-plane bending, =out-of-plane bending, s= symmetric,
a= asymmetric

2500
2000
1500
1000
500
0
0

500

1000

1500

2000

2500

Experimental Wavenumbers (cm-1)

Fig 3: Correlation Diagram for Experimental Vs Calculated Frequencies (AM1 method)

Calculated
Wavenumbers (cm-1)

2500
2000
1500
1000
500
0
0

500

1000

1500

2000

2500

Experimental Wavenumbers (cm-1)

Fig :4 Correlation Diagram for Experimental Vs Calculated Frequencies (PM3 method)

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