DNA Base Pair Mediated Vibrational Coupling: An Adenine‐Thymine Base Pair Study

ABSTRACT Hydrogen bonding and vibrational coupling in nucleobases are central to the structural stability and spectroscopic behavior of DNA. In this study, we combine density functional theory (DFT) calculations and molecular dynamics simulations to investigate the vibrational interactions between the carbonyl (C═O) mode of thymine and the C═C modes of adenine in isolated nucleobases as well as in Watson–Crick and Hoogsteen base pairs across solvents of varying polarity. DFT results reveal that while the C═O stretching frequency of thymine is highly solvent‐sensitive, the C═C remains largely invariant. Base pairing markedly enhances vibrational coupling between the C═O group of thymine and the C═C bond of adenine, particularly in Hoogsteen configurations, as increasing solvent polarity gradually narrows the frequency gap. Coupling constants, calculated based on the second‐order derivative of DFT‐based potential energy, are consistent with this observation. Mode‐resolved molecular dynamics analyses further demonstrate that Hoogsteen pairs exhibit stronger intramolecular and intermolecular couplings, with periodic energy exchange within 10 ps timescale. In contrast, isolated thymine exhibits weak C═C and C═O coupling because increasing solvent polarity widens the frequency gap. These findings reveal how hydrogen bonding, base‐pair geometry, and solvent environment govern vibrational energy flow in DNA, clarifying its spectroscopic signatures.