Searcharxiv⌕ Search

arXiv subjects

Amitava Adhikary

Publications and source records attributed to Amitava Adhikary.

2 recordsLinked to original sources
arXiv2026

The Effect of Base-Pairing on the Shape Resonances of Nucleobases

In this work, we have studied the effect of base-pairing on the shape resonances of guanine and cytosine nucleobases. Among the seven π* resonances we identified in the guanine-cytosine (GC) anion radical, three were centered on cytosine, and the remaining were guanine-centered. Relative to the isolated bases, upon base pair formation, the cytosine resonances were red shifted, while the guanine-centered states showed an opposite trend - where their energy was blue shifted. In addition to the electronic interactions, geometric distortion and basis set superposition error plays a crucial role in the resonance positions and widths of the GC radical anion. The electronic interaction from the complementary base seems to have a larger effect on the stabilization of the anionic resonances than the surrounding environment.

physics.chem-ph↗
arXiv2025

Effect of Protein Environment on the Shape Resonances of RNA Nucleobases: Insights From a Model System

In this work, the effect of amino acid environment on the nucleobase-centered anion radical shape resonances is investigated by employing uracil as a model system for pyrimidine base in RNA. Anionic uracil-glycine complexes have been used to model the RNA-protein interactions. The resonance positions and widths of these complexes have been simulated using the equation of motion coupled cluster method coupled with resonance via Padé approach. Our work shows that in the transient negative ion (TNI, or, the anion radical of glycine:uracil complex), glycine stabilizes the nucleobase-centered resonances through hydrogen bonding, increasing the lifetime of TNI. At the same time, a glycine-centered resonance shows the ability of amino acids to capture the electron density and move it away from the uracil nucleobase. At the micro-solvation level, this modeling indicates that amino acids would have more influence on nucleobase-centered resonances in the TNI than that displayed by the corresponding aqueous environment.

physics.chem-ph↗