Current Science

Sumit Mittal ¹, Brijesh Kumar Mishra ², N. Sathyamurthy ¹

Affiliations
1 Indian Institute of Science Education and Research Mohali, Manauli 140 306, IN
2 Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, IN

Abstract

The influence of sugar-phosphate backbone on the stacking interaction in the adenine…thymine base-pair dimer (A…T)₂ has been studied using the density functional theoretic method and the dispersion-corrected density functional BLYP-D3 and the triple-zeta quality basis set def2-TZVP. In the absence of the sugar-phosphate backbone, several stacked conform-ers were obtained with a small difference in their stabilization energy values (-20 to -25 kcal/mol). However, the presence of the sugar-phosphate back-bone limits the movement of the two A…T units, and yet the stacking interaction remains significant (-19.4 kcal/mol). Despite the constraints imposed by the backbone, the dimer (A…T)₂ is found to retain its favourable geometry. The influence of sodium ions on the geometry and the interaction energy is found to be negligible.

Keywords

B-DNA Helix Formation, BLYP-D3, Stacking Interaction, Sugar–Phosphate Backbone.

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R. P. S. Abhijith Kumar ¹, Sagarika Dev ¹, Brijesh Kumar Mishra ², N. Sathyamurthy ¹

Affiliations
1 Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140 306, IN
2 Department of Chemistry, Umea University, Umea 90187, SE

Abstract

It is shown by ab initio calculations using secondorder Møller-Plesset perturbation theory and 6-31g, aug-cc-pVDZ and aug-cc-pVTZ basis sets and coupled cluster singles, doubles and perturbative triples method with the 6-31g basis set, that it is possible to stabilize the cage structure of the smallest fullerene C₂₀ by encapsulating small cations like H⁺ and He²⁺. While the latter stabilizes the cage structure by charge transfer, the former prefers to form a covalent linkage with the carbon atoms.

Keywords

Atoms-in-Molecules, Encapsulation of Protons, Fullerene, Natural Bond Orbital, Perturbation Theory

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