Computational Modeling of Photoexcitation in DNA Single and Double Strands

Abstract

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

UV‐inducedDNADamage: The Role of Electronic Excited States

“…On one hand, the improvement of time-resolved techniques has allowed scientists to study their fate over a large time domain, starting from the femtosecond scale; this is achieved by detecting either nucleic acids' absorption in the UV/visible or IR spectral domains or their fluorescence emission (4)(5)(6)(7)(8)(9)(10)(11). On the other hand, with the development of advanced computational methods, it is now possible to include in the calculation of the excited states factors that are crucial for biological systems, such as water molecules, metal cations or even conformational motions of the phosphodeoxyribose backbone (12)(13)(14)(15)(16)(17)(18). The general picture emerging from all these studies is that electronic interactions operating among the bases due to their close proximity within DNA strands play a key role in the properties of the excited states.…”

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer

“…Despite these important advances in the experimental techniques, theoretical modeling is essential to understand the photochemistry of DNA. ,, Due to the complexity of this problem, most of the theoretical studies have focused on the analysis of the photochemical reaction for simpler systems such as two nucleobases in the gas phase − or thymine dinucleoside monophosphate (TpT) in water, , using accurate quantum chemistry or density functional theory (DFT) methods. In these studies, the reaction takes place via a nonadiabatic mechanism on a barrierless singlet excited-state (S 1 ) pathway to a conical intersection , between the S 1 and S 0 potential energy surfaces (PESs), which is the funnel for ultrafast decay into the ground state (S 0 ), leading to the photolesion.…”

High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes

“…Before further discussing the high-energy long-lived excited states of the examined duplexes, we briefly recall the main findings regarding their excited states, reported in the literature. Several theoretical studies have rationalized the Franck–Condon excited states of small A n ●T n duplexes ( n ≤ 10) and showed the existence of Frenkel excitons delocalized over a few bases [ 35 , 36 , 37 , 38 , 39 , 40 , 41 ]. Due to conformational disorder, modelled via molecular dynamics simulations, the steady-state absorption spectrum of these systems was found to be an envelope of a huge number of electronic transitions, each one characterized by its own oscillator strength and polarization, as exemplified in Figure 4 of reference [ 42 ].…”