Detailed Mechanism for Photoinduced Cytosine Dimerization: A Semiclassical Dynamics Simulation

Abstract

Semiclassical dynamics simulation is used to study dimerization of two stacked cytosine molecules following excitation by ultrashort laser pulses (25 fs fwhm, Gaussian, 4.1 eV photon energy). The initial excited state was found to form an ultrashort exciton state, which eventually leads to the formation of an excimer state by charge transfer. When the interbase distance, defined as an average value of C(5)-C(5)' and C(6)-C(6)', becomes less than 3 Å, charge recombination occurs due to strong intermolecular interaction, eventually leading to an avoided crossing within 20-30 fs. Geometries at the avoided crossing, with average intermolecular distance of about 2.1 Å, are in accord with CASSCF/CASPT2 calculations. Results indicate that the C(2)-N(1)-C(6)-C(5) and C(2)'-N(1)'-C(6)'-C(5)' dihedral angles' bending vibrations play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to a nonadiabatic transition to the electronic ground state.

Detailed Photoisomerization Dynamics of a Green Fluorescent Protein Chromophore Based Molecular Switch

“…The results of [14,[35][36][37][38][39][40][41][42][43][44] calculated with SERID method have provided a clear demonstration of the following features of simulations based on Ehrenfest dynamics: (1) electronic transitions are automatically observed at an avoided crossing near a conical intersection in configuration space predicted by Teller [45,46], with energy released to molecular vibrations; (2) these transitions occur rapidly, over a time interval of ∼2 femtosecond, during which the nuclei do not move appreciably. In the present work, we have made a little change in the procedure that should lead to better results for the quantum yields.…”

Effect of Initial Orientation on the Laser-Induced Cycloaddition Reaction of Benzene and Ethylene

“…Specifically, we investigated the effect of the stacking orientation at the moment of laser excitation of the benzene molecule on the subsequent dynamics. Previous studies on stacked DNA base molecules have shown that the initial orientation of reactant molecules affects the excited state dynamics [7][8][9][10]. Our simulations provide detailed dynamics features from photon excitation to the formation of product.…”

“…The SERID method has been used in biologically relevant studies such as photoinduced dimerization of thymine [9] and cytosine [10] via [2 + 2] photocycloaddition reaction. All the results were found to be consistent with experimental observations.…”

Computational Modeling of Photoexcitation in DNA Single and Double Strands

“…2) involving a barrier and charge transfer from the 5 0 -end to the 3 0 -end, without excluding monomeric decay pathways in loosely stacked bases. Dou and coworkers [327] observed in their semiclassical dynamics simulations that cyclization takes place after the excimer decays to the ground state through the S 0 / S 1 conical intersection and that the two cyclobutane bonds (C5-C5 0 and C6-C6 0 ) between two stacked thymines are then formed one by one within~110 fs.…”