An International Peer Reviewed Research Journal

Vol. 26 No 11 & 12, 2017

AJP

SSN : 0971 - 3093

Vol 26, No 8-10, November-December, 2017


Asian Journal of Physics                                                                                                    Vol. 26 No 11 & 12, 2017, 325-335


The anti-HIV Nucleoside analogue d4T (Stavudine): Solid state simulation by

DFT methods of the FT-IR and FT-Raman spectra


M Alcolea Palafoxa,b, D Kattana,b, and A Nils Kristiana

aNofima AS - the Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, 1430 Ås, Norway

bDepartamento de Química-Física I, Facultad de Ciencias Químicas,Universidad Complutense, Madrid-28040, Spain

___________________________________________________________________________________________________________________________________

The theoretical and experimental vibrational study of the anti-HIV d4T (stavudine or Zerit or 3′-deoxy-2,3´-didehydro thymidine) Nucleoside Analogue was carried out. The calculated spectra were scaled by using the linear scaling equation procedure (LSE). The d4T monomer and dimers were simulated by using DFT methods. The IR spectrum was recorded in the solid state in the region 400-4000 cm-1 and the Raman spectrum was recorded in the region 0-3500 cm-1. The vibrational bands were analyzed and assigned to different normal modes of vibration by comparison with the scaled values of the different dimer forms. Thus, through this comparison, we were able to confirm that the solid state sample corresponds to dimer V. © Anita Publications. All rights reserved.

Keywords: d4T, Stavudine, anti-HIV, IR spectrum, Raman spectrum, DFT

References
1.  Taisheng L, Fuping G, Yijia L, Chengda Z, Yang H, Wei L, Yun H, Hongzhou L, Jing X, Aiqiong H, Yanling L, Xiaoping T, Hui W, Tong Z, Guiju G,  Junkang

     L, Xiaoying Z, Xinhua W, Yongtao S, Jinsong B, Ling L,  Huanling W, Chinese Med J, 127(2014)59-65.
2.  Li T, Dai Y, Kuang J, Jiang J, Han Y, Qiu Z, Jing Xie, Zuo L, Li Y, PLoSONE 3, e3918 (2008); doi.org/10.1371
3.  van Oosterhout J J, Mallewa J, Kaunda S, Chagoma N, Njalale Y, E. Kampira E, Mukaka M, Heyderman R S, PLoSONE 7, e42029(2012); doi.org/10.1371

     /journal.pone.0042029
4.  Phanuphak N, Ananworanich J, Teeratakulpisarn N, Jadwattanakul T, Kerr S J, Chomchey N, Hongchookiat P, Mathajittiphun P, Pinyakorn S, Rungrojrat P, 

     Praihirunyakit P,  Gerschenson M, Phanuphak P,  Valcour V, Kim J H, Cecilia S,  Antivir Ther, 17(2012)1521-1531.
5.  Palafox M A, Iza N, J Molec Struct, 1028(2012)181-195.
6.  Palafox M A, Talaya J, J Phys Chem B, 114(2010)15199-15211.
7.  Zhao Y, Truhlar D G, J Chem Phys, 125(2006)194101; doi:10.1063/1.2370993.
8.  Frisch M J, Trucks G W, Schlegel H B, Scuseria G E, Robb M A, Cheeseman J R, Scalmani G, Barone V,  Mennucci B, Petersson G A, Nakatsuji H, Caricato

     M, Li X, Hratchian H P, Izmaylov A F, Bloino J, Zheng G, Sonnenberg J L, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda

     Y, Kitao O, Nakai H, , Vreven T,  Montgomery J A(Jr), Peralta J E, Ogliaro F, Bearpark M, Heyd J J,  Brothers E, Kudin K N, Staroverov V N, Kobayashi R,

     Normand J, Raghavachari K, Rendell A, Burant J C, Iyengar S S, Tomasi J, Cossi M, Rega N, Millam J M,  Klene M, Knox J E, Cross J B, Bakken V, Adamo C,

     Jaramillo J, Gomperts R, Stratmann R E, Yazyev O,  Austin A J, Cammi R, Pomelli C,  Ochterski J W, Martin R L, Morokuma K, Zakrzewski V G, Voth G A,

     Salvador P, Dannenberg J J, Dapprich S, Daniels A D, Farkas Ö, Foresman J B, Ortiz J V, Cioslowski J, Fox D J, Gaussian 09, Revision D.01, Inc., Wallingford

     CT, 2009.
9.     Palafox M A, Rastogi R, Anupama, Alam M J, Bhat D, Rastogi V K, Asian J Phys, 25(2016)189-219.
10.   El-Sayed A A, Molina A M, Álvarez-Ros M C, Palafox M A, J Biomol.Struct & Dyn, 33(2015)723-748.
11.   Palafox M A, Chem Informatics, 1(2015)1-13.
12.   Palafox M A, Posada-Moreno P, Villarino-Marín A L, Martinez-Rincon C, Ortuño-Soriano I, Zaragoza-García I, J Computer-Aided Molec Design,

        25(2011)145-161.
13.   Palafox M A, Iza N, Struct Chem, 24(2013)967-980.
14.   Yurenko Y P, Zhurakivsky R O, Ghomi M, Samijlenko S P, Hovorun D M, J Phys Chem B, 111(2007)6263-6271.
15.   Palafox M A, Rastogi V K, Spectrochim Acta A, 58 (2002)411-440.
16.   Choi Y, George C, Comin M J (Jr). Barchi J J, Kim H S, Jacobson K A, Balzarini J, Mitsuya H, Boyer P L, Hughes S H, MarquezV E, J Med Chem,

        46(2003)3292-3299.
17.   (a) Palafox M A, Int  J Quantum Chem, 77(2000)661-684.
        (b) Palafox M A, Rastogi V K, in Perspectives in Modern Optics and Optical Instrumentation,  (eds), Jobi J, Sharma A, Rastogi  V K, (Anita Publications,

        FF-43, Mangal Bazar, Laxminagar, Delhi), 2002, pp 91-98
        (c) Palafox M A, Nunez J L, Gill M, Rastogi V K, in Perspectives in Engg Optics,, (eds) Singh K, Rastogi V K, (Anita Publications, FF-43, Mangal Bazar,

         Laxminagar, Delhi), 2003, pp 356-391.
         (d) Palafox M A, Nunez J L, Gill M, Rastogi V K, Mittal L, Sharma R, Int J Quantum Chem, 103(2005)394-421.
         (e) Palafox M A, Asian Chem Letts, 7(1998)785-816.
18.    Palafox M A, Iza N, Gil M, J Mol Struct (Theochem), 585(2002)69-92.
19.    Rastogi V K, Singhal S, Palafox M A, Rao G R, Ind J Phys, 84 (2010)151-165.
20.    Carpenter J E, Weinhold F, J Molec Struct, (Theochem) 169(1988)41-62.
21.    Alvarez-Ros M C, Palafox M A, Pharmaceuticals, 7(2014)695-722.
22.    Palafox M A, Struct.Chem, 25(2014)53-69.
23.    Palafox M A, J Biomol.Struct & Dyn, 32(2014)831-851.
24.    Alvarez-Ros M C, Palafox M A, J Molec Struct, 1047(2013)358-371.
25.    Gauss View 5.1 Gaussian Inc., Wallingford CT, (2009).
26.    Saenger W, Principles of Nucleic Acid Structure, (Springer Verlag Publishers: New York),1984, pp 556.
27.    Mirmehrabi M, Rohani S, Jennings M C, Acta Cryst, C61(2005)o695-o698; doi.org/10.1107/S01082701050345918   
28.    Gurskaya G V, Tsapkina E N, Abstracts of the twelfth European Crystallographic Meeting, Moscow, vol. 2, p 380(1989).
29.    Tsapkina E N, Dissertation for Doctorate I Chemical Sciences, Institute of Molecular Biology, Moscow, (1989).
30.    Harte W E (Jr), Starret J E (Jr), Martin J C, Mansuri M M, Biochem Biophys Res Comm, 175(1991)298-304.
31.    Gurskaya G V, Bochkarev A V,  Zhdanov A S, Dyatkina N B, Kraevskii A A, Mol Biol., 25(2),401 (1991).
32.    Rastogi V K, Singh C, Jain V, Palafox M A, J Raman Spectrosc, 31(2000)1005-1012.
33.    C J Cramer, Essentials of Comput. Chem.;( John Wiley & Sons: Chinchester, England), 265 (2002).
34.    Palafox M A, Iza N, Gil M, J Molec Struct (Theochem), 585(2002)69-92.
35.    Colarusso P, Zhang K, Guo B, Bernath P F, Chem Phys Lett, 269(1997)39-48.

___________________________________________________________________________________________________________________________________


Asian Journal of Physics                                                                                                    Vol. 26 No 11 & 12, 2017, 337-351

 

2-Thiouracil: Influence of water in the first hydration shell and Effect of the
Sulfur Atom on the Base Pairs 2-Thiouridine-Adenosine


M Alcolea Palafox1,V K Rastogi2,3, S P Singh4 and S K Rathor3

1Departamento de Química-Fisica1. Facultad de Ciencias Químicas. Universidad Complutense. Madrid- 28040. Spain.

2R D Foundation Group of Institutions, NH-58, Kadrabad, Modinagar (Ghaziabad), India

3Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad-201 002, India

4Department of Physics, Dr B R Ambedkar Govt Degree College, Mainpuri, India

___________________________________________________________________________________________________________________________________

The crystal unit cell of 2-thiouracil (2TU) in the solid state was simulated through a tetramer form using DFT methods. The first and second hydration shells were simulated by explicit number of water molecules surrounding 2TU up to 30. The calculated spectra were compared to the experimental ones. A linear scaling procedure (LSE) was used for this task. The effect of the hydration on different parameters of the molecular structure of 2TU was analyzed. The total atomic charges were discussed. The effect of the sulfur atom on the Watson-Crick (WC) and reverse WC base pair uridine-adenosine was estimated, and the CP corrected interaction energies were calculated. A microhelix RNA:DNA was simulated with two nucleotides base pairs © Anita Publications. All rights reserved.

Keywords: 2-thiouracil, interaction energies, DFT, hydration, scaling, 2-thiouridine, uridine

Total Refs : 37

___________________________________________________________________________________________________________________________________

© ANITA PUBLICATIONS

All rights reserved

Designed & Maintained by

Manoj Kumar