Study of optical absorption cross-section spectra and high-order harmonic generation of thymine, thymine glycol, and thymine dimer molecules.

Abstract

The last two decades have witnessed advances in femtosecond and sub-femtosecond physics which have made accessible the study of phenomena with atomic and subatomic resolution. In particular, developments in laser physics and high-order harmonic generation have enabled tracking and investigating molecular reaction dynamics and the actual dynamics of electrons in chemical reactions, as well as investigating the structure of molecules. High-order harmonic generation has proved to be an ideal means for generating autosecond pulses. Time-dependent density functional theory provides an invaluable tool for the theoretical study of high-order harmonic generation. In this article, an exact study of the optical absorption cross-section spectra and high-order harmonic generation of thymine and its damage forms (thymine glycol and thymine dimer) has been performed using the time dependent density functional theory via the octopus code. The spectra have been characterized with the aim of distinguishing thymine from its damaged forms. The discrepancies in the optical absorption spectra of thymine and its damaged forms have been elucidated. The effects of laser pulse intensity and pulse profile on the high-order harmonic spectra of these molecules has been investigated, showing the possibility to distinguish between thymine and its damaged forms using high-order harmonic generation. In particular, it is demonstrated that high-order harmonic generation corresponding to a laser pulse with a cosinusoidal envelope and intensity [Formula: see text] clearly differentiates thymine from its damaged forms. This laser could potentially be applied to discern damage in more complex DNA material.