Asian Journal of Spectroscopy, 14, 1-2, 2010, 47-56

Study on experimental and theoretical vibrational spectra of novel Anti AIDS Drug: Zidovudine- Iron metal complex derived from 3'-Azido-2'deoxythymidine
Y.P.Singha*, Arvind Singh Tomarb and S.K.Vijayc
a

Department of Physics, Govt. Womens Polytechnic College, Sagar (MP), INDIA 470001.E-mail: Y_P_S_2k@Yahoo.com b Department of Physics, S.V.Polytechnic College, Bhopal (MP), INDIA, c Department of Physics, Govt. Geetanjali Girls P.G.College, Bhopal (MP), INDIA

Abstract

A combined experimental and theoretical study on molecular and vibrational structure metal complex of 3'-Azido-2'-deoxythymidine (Zidovudine AZT) with Fe(III) have been reported. The Fourier transform infrared spectra of was recorded in the solid phase, in the region of 2500400 cm-1. Assuming Cs point symmetry, vibrational assignments for the observed frequencies have been proposed and energies of this molecule have also been calculated by means of quantum chemical calculations using density functional theory and HartreeFock method with 6-311++G** basis sets. An assignment of normal modes of vibration to the observed frequencies has been based on these calculations. The theoretical wavenumbers showed very good agreement with the experimental values. A detailed interpretation of the infrared also is reported. The theoretical FT-IR spectra of the title molecule have also been constructed.
Keywords 3'-Azido-2'-deoxythymidine, AZT, Zidovudine, Fe(III), Metal complex, FTIR Spectra, Anti AIDS drug, Hartree-Fock, DFT, MOPAC.

Introduction

There are a number of drugs that have been considered as to be anti HIV. The

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.

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 the solid state AZT forms a hydrogen bond network4. Iron is present on the earth in some or other form, wherever respiration occurs. It is essential for the elementary metabolic process in cells. An extensive survey of the historical uses of iron with many original references has been given by Fairbanks et al5. Most of the iron found in the body is associated with two types of proteins (a) haemoprotein and (b) iron storage or transport protein. Cytochrome C is an example of respiratory enzyme in which iron is complexed in a porphyrin ring system which is in turn covalently bonded to the protein portion of the molecule. Spectroscopic studies of antiAIDS drug have made a significant contribution of this noble endeavor of striving to eliminate the fear of this dreadful disease. The calculation of vibrational frequencies by computational methods is becoming increasingly important in many areas6. Infra red and Raman spectra of molecules in their ground electronic states were predicted by molecular orbital theory7. Density functional (DFT) calculations are reported to provide excellent vibrational frequencies for organic compounds if the calculated frequencies are scaled to compensate for the approximate treatment of electron correlation, basis set deficiencies and for anharmonicity effects 14-19. Conformational analysis of AZT structure and other related drugs have been previously reported at semi

empirical and ab initio levels of theory 10-12 . Hernndez13 at al reported an ab initio HF and DFT study of the dipole polarizability of AZT drug. A comprehensive description of the geometrical and electronic properties implied in such complex appears as important to gain some knowledge about the mechanisms of complex formation. For this purpose, the Density Functional Theory (DFT) was used to identify various possible types of complexations and to obtain the force field parameters from vibrational spectra in order to perform further molecular dynamical studies. 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 HartreeFock, Density Functional Theory (DFT) and MOPAC method.
O 17

H 18
N2

H 21

H 22

C1

C8

C7
N4

H 23

O 19
H 30
O 15
H 31

C3

C5

H 29

H 20

C 13
H 24

O9 H 2 5H 2 8 C 12
N 14
N 16

C6
H 26
N + 32

H 27

F e (III)

3'-Azido-2'-deoxythymidine-Fe(III)complex or Zidovudine-Fe(III) complex

Fig 1 Structure of Zidovudine-Fe(III) complex

Experimental All the chemicals used to prepare experimental sets were of Analar /BDH grade. Zidovudine was purchased from Cipla India Ltd.

Iron and drug solution were mixed in 1:1 molar ratio. The solution was transferred in a beaker and kept over water bath for an appropriate time so that the volume was reduced to one fourth or less of the initial volume. The mixture was kept standing overnight. Precipitate so obtain was filtered, washed and dried over P4O10. I.R. Spectrum has been recorded using KBr disc in solid phase in the range 400-4000cm-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 finely ground mixture was than pressed under very high pressure in a press (about 10/cm2) to form a small pallet ( about 12 mm thick and 1cm in diameter). The accuracy of the measurements was estimated to be within 3cm-1 and the resolution was better than 2cm-1 through the entire spectra. Computational Methods The AM1 and PM3 semi empirical approaches were performed as implemented in MOPAC program 19 and the PRECISE keywords were used. Hartree Fock and DFT calculations were performed using Spartan' 06 program 20 at the B3LYP 10 levels of theory with 6311++G** basis sets 21 . The vibrational IR spectra were calculated at the HF/6311++G** levels of theory then starts from MMFF conformer and AM1 geometry. We have transformed the harmonic force fields, determined initially in the Cartesian coordinates, were transformed to the force fields in the internal local coordinates.

Results and Discussions Molecular Geometry: The geometry parameters optimized at AM1, MP2 and B3LYP levels of theory for Zidovudine are presented in Table 1 and 2. The final optimized geometry displays a C1 molecular point group symmetry with the Fe atom located at the inversion center. Results indicate that bond distances and bond angles, important to describe geometric features of AZT, are very close to those reported from Xray structure14. As, AZT-FeIII is dominated by three fragments, the thymine ring, the Furancose ring and the Azide one, which is coordinately bonded to FeIII. Our results also show that the Azide- FeIII group lies in a nonlinear conformation, where N14N32N16 bond angle range from 71.284 at PM3 to the value of 72.112 , whereas Azide alone ranges from 70.058 to 69.367 at B3LYP level and is attached in trans position to the C6C12 bond of Furancose ring. This may be due to strong coordinate bonding. The Azide- FeIII group also has an anti conformation with respect to both, the hydroxyl group and the thymine ring. The bond length of N32-Fe(III) comes out to be 2.089 and calculated bond lengths are 2.067, 2.082, 2.053 , which agrees well with 2.089 which was reported by Jos M. Domnguez-Vera et al22 . There is much difference between the bond angles reported by Jos M. Domnguez-Vera et al22 and us. A linear fit for bond distances between the calculated and experimental values shows a correlation coefficient of 0.8314, 0.9932 and 0.9787 at AM1, PM3 and B3LYP levels, respectively. A statistical analysis shows a mean values

of 1.522 , 1.546 and 1.522 and standard deviations of 0.2395 0.05227 , 0.2423 0.05288 and 0.2429 0.05301 for the differences between calculated and experimental distances using AM1, PM3 and B3LYP methods. There is some difference between experimental and calculated bond lengths in C-O of thymine and Furancose ring and N-N of Azide ring. This difference is due to electron withdrawing property of oxygen23 and that of nitrogen. Similarly, bond angles, as shown in table 2, have a mean value of 111.5, 112.4 and 114.6 and standard deviation of 14.033.137, 13.132.936, and 9.5212.129 at AM1, PM3 and B3LYP approach. Computed total dipole moments, energy, area and volume are also presented table 3. The exploration of molecular volume and surface is essential for the understanding of drug action since short range dispersion forces play a major role in the binding of drug molecules to receptors. The surfaces of interacting molecules also need to be of complementary character, i.e., they should both be hydrophobic or hydrophilic which will in practice represent their ability to form hydrogen bonds. The net charge on the interacting surfaces also needs to be complementary for strong bonding. Since, AZT-Fe (III) has high value of dipole moment, so it is a polar molecule and has net charge. Vibrational assignments: According to the theoretical calculations, 3'-Azido2'-deoxythymidine (AZT)-Fe(III) complex has a planar structure of Cs point group symmetry. The molecule has 33 atoms so that it has 93 normal modes of fundamental vibrations which span the irreducible representations: 62 a and

31 a. All the calculated modes are numbered from the largest to the smallest frequency within each fundamental wave number. The observed FTIR frequencies for various modes of vibrations are presented in Table 4. Comparison of the frequencies calculated at HF and DFT with the experimental values (Table 4) reveals the overestimation of the calculated vibrational modes due to neglect of anharmonicity in real system. Vibrational frequencies calculated at 6 311++G** basis level were scaled by 0.91, and those calculated at HF level were scaled by 0.79. The calculated frequencies are slightly higher than the observed values for the majority of the normal modes. This may be due to discrepancies between the experimental and computed value, which is related to the fact that the experimental value is an anharmonic frequency while the calculated value is harmonic frequency. While anharmonicity is the main factor of the discrepancies in the case of vibrations related to the CH, NH, Fe(III)-N or OH bonds, for other vibrations most of the discrepancies come from the approximate nature of the used computational technique, and probably also from the lattice effects in the substance, studied as a solid. Normal modes related to Fe (III) complex: A critical comparison of the IR spectrum of Zidovudine with that of its Fe(III) complex showed that the band due to N3 (Azide group) at 2170 in the spectrum of pure drug is shifted to 2150 cm-1 in the spectrum of Fe(III) complex. However, the bands at 1750 cm-1 and 1725 cm-1 are observed at the same frequencies in the IR spectrum of both Zidovudine and its metal complex.

The stretching vibration due to N-H group also occupies the similar position i.e.1680 cm-1 in both the spectra. Thus confirming the involvement of the nitrogen atom of Azide group of the ligand in the complex formation with Fe (III). The Fe-N torsion modes are predicted in the 30-130 cm-1 range in agreement with the corresponding values obtained for the Fe(III) complexes . HF and DFT calculated mode is at 27.908 cm-1 and 28.943 cm-1 . Calculated bands corresponding to the in plane bending (N-Fe-N) normal mode are predicted to occur at 205.007 cm-1 and 178.194 cm-1 by DFT method and HF method it occurs at 204.680 cm-1 and 172.784 cm-1 In a similar way, the stretching (Fe(II)-N) motion is predicted at 414.087 cm-1 by DFT method and 408.867 cm-1 by HF method. Conclusion Attempts have been made in the present work for the proper frequency assignments for the 3'-Azido-2'deoxythymidine- Fe (III) complex from the FT-IR spectra. Any discrepancy noted between the observed and the calculated frequencies may be due to the fact that the calculations have been actually done on single molecules in the gaseous state contrary to the

experimental values recorded in the presence of intermolecular interactions. Also, difference is attributed due to neglect of anharmonicity and incomplete inclusion of electronic correlation effects. Therefore, the assignments made at higher levels of theory with only reasonable deviations from the experimental values, seem to be correct. A generally good agreement between all methods was observed. Further calculations are in progress to apply this force field for Molecular Dynamics which would permit to follow the complex formation and its evolution along physicochemical constraints (pH, temperature, counter-ions or external competitive ligands) keeping in mind the biochemical importance of iron releasing in organisms. For further agreement between computed and experimental frequencies, the computed frequencies are often scaled by some specific factor. Acknowledgements The author is grateful to Department of Technical Education, Govt. of Madhya Pradesh, India and Head and Department of Physics and Chemistry, Dr. H.S.Gour University, Sagar (MP), India ; and Wave function Inc, USA for Spartan'06.

Table 1. Optimized bond distances (in Angstrom ), bond angles and torsion angles (in degrees )of AZT. Bond length ( A AM1 AZT 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 1.511 1.591 1.483 1.492 1.316 1.245 1.729 AZT- e(III) 1.471 1.471 1.471 1.471 1.471 1.531 1.227 1.531 1.096 1.012 1.227 1.096 1.471 1.410 1.531 2.300 1.531 1.410 1.531 1.410 1.471 1.449 1.449 1.589 2.067
0

) PM3 AZT 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 1.549 1.612 1.506 1.507 1.359 1.281 1.937 AZT-Fe(III) 1.471 1.471 1.471 1.471 1.471 1.531 1.289 1.576 1.128 1.047 1.257 1.097 1.493 1.424 1.578 2.352 1.601 1.418 1.568 1.499 1.502 1.472 1.450 1.611 2.082 AZT 1.389 1.379 1.382 1.390 1.347 1.381 1.168 1.502 1.597 1.101 1.205 1.116 1.456 1.404 1.551 1.568 1.999 1.421 1.523 1.476 1.473 1.246 1.108 1.827 B3LYP AZT-Fe(III) 1.485 1.485 1.485 1.485 1.485 1.485 1.296 1.589 1.132 1.059 1.287 1.210 1.483 1.436 1.579 2.387 1.682 1.423 1.524 1.491 1.509 1.491 1.463 1.672 2.053

Bond

Experimental AZT AZT-Fe(III) 1.423 1.421 1.423 1.422 1.462 1.397 1.124 1.539 1.221 1.472 1.402 1.598 2.394 1.489 1.595 1.406 1.511 1.579 1.563 1.624 2.089

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 C11-O9 C11-C13 C13-O15 C12-N14 N14-N16 N16-N32 N32-N14 N32-Fe(III)

1.384 1.368 1.372 1.386 1.332 1.197 1.503 1.201 1.463 1.391 1.535 1.529 1.414 1.515 1.405 1.467 1.231 1.100

Table 2: Optimized bond angles (in degree) of AZT and AZT-Fe(III) metal complex. ) Bond Angle ( A AM1 PM3 AZTFe(III) 120.000 120.000 120.000 120.000 120.000 109.470 109.470 127.840 120.000 109.470 109.470 109.470 105.000 86.430 109.470 109.470 AZT
0

Bond Angle

Experimental AZT

24

AM1 AZT

PM3 AZTFe(III) 120.000 120.000 120.000 120.000 120.000 109.110 109.130 127.960 120.000 110.870 109.970 109.850 106.520 91.360 110.214 110.021

AZTFeIII 132.6 122.8 119.9 119.5 118.4 119.2 108.6 111.3 99.9 103.9

B3LYP (6311++G**) AZT

B3LYP (6311++G**) AZT-Fe(III)

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

130.4 123.1 119.1

117.9 107.8 110.2 98.8 104.7

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

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

121.364 121.620 120.072 120.095 120.012 77.289 70.362 120.00 118.168 120.035 107.984 77.568 110.489 99.008 106.687 104.842

121.00 121.00 121.00 121.00 121.00 110.350 110.698 127.630 121.035 110.954 110.389 108.64 107.521 90.894 111.023 111.687

C11-C12-C6 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 N14-N32-FeIII N16-N32-FeIII

105.6 113.5 111.1 120.0 120.0 120.4 162.3

105.8 114.9 111.9 120.4 120.1 120.1 110.9

113.0

113.0 130.0 110.8

105.995 114.382 141.357 39.462 113.346 121.634 119.924 120.996 160.534 57.165 69.378 56.00 110.0

70.220 109.470 105.000 109.470 116.630 106.410 120.000 109.470 109.470 60.3350 71.284 57.024 112.587 137.171 111.475

104.367 115.216 140.581 40.421 114.624 120.347 120.068 120.624 159.458 58.619 70.58 55.0274 111.621

72.573 110.980 106.842 109.350 117.896 107.421 120.000 110.036 110.021 61.573 72.421 58.342 112.524 136.891 112.024

105.996 113.859 141.887 39.564 112.549 120.006 120.068 120.001 162.547 57.245 69.367 560894 112.895

104.987 113.569 142.531 113.640 118.057 107.569 120.00 112.357 110.257 62.387 72.112 59.467 112.347 137.423 112.925

Table 3: Molecular Properties of AZT S.N. Property Value Zidovudine 1. 2. 3. 4. 5. Energy Dipole Moment Weight Area Volume -149.720422 KJ/mol 20.34 debye 267.245 amu 269.89 A
02

Zidovudine- Fe(III) Complex 1715.07968 KJ/mol 18.16 debye 323.092 amu 299.53 A02 261.79 A03

241.58 A03

Table 4: Principal IR Signals (cm-1) and their Assignments for Zidovudine and its Fe (III) complex S.N. Assignments Zidovudine Exp24 1. 2 3 4. 5. 6. 7. 8. 9. -N3 stretching >C=O Stretching (5mem) >C=O Stretching (6mem) >N-H Stretching Aromatic Vibrations Primary OH Stretching Fe(III)-N Stretching Fe(III)-N in-planebending Fe(III)-N Torsion 2170 1750 1725 1680 1600 700 1100 ---HF 2189.387 1801.985 1739.245 1688.231 1611.254 711.424 1121.826 ---Wave numbers (in cm-1) Fe(III)- complex DFT (B3LYP) 2178.88 1774.118 1734.464 1687.467 1609.378 705.491 1119.381 ----Exp24 2150 1750 1725 1680 1600 700 1100 ---HF 2260.741 1783.123 1741.628 1689.734 1616.154 704.381 1123.002 414.087 204.680 27.908 B3LYP (6-311++G**) 2167.768 1784.638 1732.216 1685.354 1604.328 701.467 1110.307 408.867 205.007 28.943

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

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

Fig 4: Theoretical I. R. Spectra of 3'-Azido-2'-deoxythymidine/ Zidovudine (AZT) - Fe (III) Complex

References

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