An International Peer Reviewed Research Journal
Frequency : Monthly,
ISSN : 0971 – 3093
Editor-In-Chief (Hon.) :
Dr. V.K. Rastogi
e-mail:[email protected]
[email protected]

AJP ISSN : 0971 – 3093
Vol 26, No 11-12, November-December, 2017

Journal of Physics

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

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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


Asian Journal of Physics Vol. 26 No 11 & 12 (2017) 353-357

Electro-optic investigations on ferroelectric and silica nanoparticles doped ferroelectric liquid crystal mixtures 
Rajbir Singh
1Department of Physics, Meerut College, Meerut-250 001, India

Dispersed liquid crystal composites have attracted significant interest among scientific community due to their practical and technological applications in various fields including displays. In this work, a ferroelectric liquid crystal and silica nanoparticles doped ferroelectric liquid crystal composites are studied in SmC* phase. The effect of doping and temperature on the spontaneous polarization, switching time and viscosity of FLC are investigated in thin planar sample cell of thickness 9 µm. The doping of silica decreases the polarization and increases the switching time. The viscosity of the sample also changes after dispersion of silica nanoparticles. © Anita Publications. All rights reserved.

Keywords: Ferroelectric liquid crystal, Silica nanoparticle, Polarization, Switching time.


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Asian Journal of Physics Vol. 26, Nos 11 & 12 (2017) 359-364

Effect of the presence of 5- Guanidino-4- nitroimidazole on B- DNA structure
Neena Srivastavaa, A Dwivedib, P K Tripathic and K Singhd
aDepartment of Chemistry, Mahila Vidyalaya Degree College, Aminabad, Lucknow-226 018, India
bChemistry Section, Directorate of Geology and Mining U.P., Lucknow-226 001, India
cFood Safety and Drug Administration, Collectorate Campus, Bahjoi (Sambhal)- 244 410, India
dDepartment of Molecular Microbiology and Immunology, Bond Life Science Centre,
University of Missouri, Columbia, MO 65211, USA

5-Guanidino-4-nitroimidazole (GN), derived from the oxidation of guanine by reactive oxygen and nitrogen species, contains an unusual flexible ring-opened structure. In this molecule, the nitro and guanidino groups possess multiple hydrogen bonding capabilities. In vitro primer extension experiments with bacterial and mammalian polymerases have shown that it is incorporated against C as well as A and G, depending on the polymerase. To elucidate structural and thermodynamic properties of the mutagenic GN lesion, we have investigated the structure of the modified base itself and the GN-containing nucleoside with semi-empirical quantum mechanical calculations at PM3 level and have used molecular modelling techniques (SYBYL) to determine its status in B-DNA duplexes, with four partner bases opposite the GN. Our results show that GN adopts a planar structure at the damaged base level. However, in the nucleoside and in DNA duplexes, steric hinderance between the guanidino group and its linked sugar causes GN to be nonplanar. The GN lesion can adopt both syn and anti conformations on the DNA duplex level, with the guanidino group positioned in the DNA major and minor grooves, respectively. On the basis of hydrogen bonding and stacking interactions, groove dimensions, and bending, we noted that the least distorted GN-modified duplex contains partner C. However, hydrogen bonding interactions between GN and partner G or A are also found, which is similar to the geometry as that observed for mismatches.© Anita Publications. All rights reserved.

Keywords: Ferroelectric liquid crystal, Silica nanoparticle, Polarization, Switching time.

Peer Review Information
Method: Single- anonymous; Screened for Plagiarism? Yes
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[Received: 29.01.2017; revised recd: 01.06.2017; accepted: 01.08.2017]