arXiv subjects

Jishnu Narayanan S J

Publications and source records attributed to Jishnu Narayanan S J.

6 recordsLinked to original sources

arXiv2026

Role of Native and Zwitterionic Glycine in Electron Attachment to DNA: From Dipole-Bound to Solvent-Bound Doorway States

Electron attachment to DNA is strongly influenced by its molecular environment, yet the role of amino acids under physiologically relevant conditions remains poorly understood. Here, we investigate the effect of native and zwitterionic glycine on electron attachment to thymine using high-level electron-affinity calculations and QM/MM molecular dynamics simulations. Under micro-solvated conditions, electron attachment occurs through a dipole-bound doorway state that evolves into a valence-bound anion via nonadiabatic coupling. The zwitterionic form of glycine strengthens stabilization of the diffuse electron owing to its larger internal charge separation, whereas the stability of the valence-bound anion is determined by the hydrogen-bonding geometry. Barrier-free proton transfer is observed only for specific binding motifs and substantially stabilizes the thymine-centered anion. In bulk solution, the doorway mechanism persists, with a solvent-bound state replacing the dipole-bound state as the initial electron-trapping state. The larger electrostatic field of zwitterionic glycine delays electron localization on thymine, while permanent proton transfer is observed only in selected native glycine trajectories and is absent throughout the present simulations of zwitterionic glycine. Despite these differences in electron-transfer dynamics, both amino acid forms provide similar stabilization of the thymine-centered anion after solvent reorganization. Our results establish the solvent-bound state as the condensed-phase analogue of the dipole-bound doorway state and reveal how amino acid environments modulate electron attachment pathways in realistic DNA systems.

physics.chem-ph↗

arXiv2026

Do Water Molecules Always Stabilize Resonances? Microhydration Effects on Thymine Shape Resonances

We investigate microhydration effects on the three low-lying π* shape resonances of thymine using the Resonance via Padé approach in combination with the DLPNO-EA-EOM-CCSD method. For isolated thymine, the calculated resonance positions are benchmarked against projected CAP-EA-EOM-CCSD calculations and compared with available theoretical and experimental data. Upon hydration, the 1π* and 2π* resonances undergo systematic stabilization accompanied by significant increases in their lifetimes, whereas the 3π* resonance exhibits a more complex behavior. In particular, the lifetime of the lowest resonance increases from 39 fs in isolated thymine to 110 fs in the thymine(H2O)3 cluster. Detailed analysis reveals that the observed resonance shifts arise from competing contributions involving hydrogen bonding, electrostatic interactions, microsolvation-induced geometric distortion, and finite-basis-set effects. Ghost-atom calculations demonstrate that diffuse basis functions associated with nearby water molecules contribute appreciably to the apparent stabilization, while explicit inclusion of water molecules leads to genuine physical stabilization of the resonance states. Furthermore, calculations on multiple conformers of the monohydrated cluster show that resonance positions and lifetimes depend strongly on the local hydrogen-bonding arrangement and microsolvation geometry. These findings demonstrate that resonance stabilization in microhydrated nucleobases is governed by a subtle interplay between geometry, basis-set effects, and intermolecular interactions.

physics.chem-ph↗

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↗

arXiv2022

Electron Attachment to Wobble Base Pairs

We have analyzed the low-energy electron attachment to wobble base pairs using the equation motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.

physics.chem-ph↗

arXiv2021

A Doorway mechanism for Electron Attachment Induced DNA Strand Break

We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ* type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism explains the relative rates of electron attachment induced bond cleavages in genetic materials.

physics.chem-ph↗