Photoinduced Thymine Dimerization Studied by Semiclassical Dynamics Simulation

Abstract

Response to ultrashort laser pulses of two stacked thymine molecules has been studied by semiclassical dynamics simulation with laser radiation explicitly incorporated. The laser pulses used to excite the thymine molecule have a 25 (fwhm) fs Gaussian shape with a photon energy of 4.0 eV. Simulation follows two different reaction paths produced by the laser pulses with two different fluences. In one reaction, the stacked thymine molecules form a cyclobutane pyrimidine dimer, which is the main course of photoinduced DNA damage, and the formation of two chemical bonds linking two thymines occurs nonsynchronously after the excimer decays to electronic ground state. In the other reaction, only one bond is formed between the two thymine molecules. In the second reaction, the bond breaks about 50 fs after formation, and then the two molecules move away from each other. This reaction leads to the DNA damage repair. The simulation finds that the deformation of the pyrimidine ring plays an important role in cleaving this bond.

Dynamics of laser-excited stacked adenines: Semiclassical simulations

“…We have previously applied the SERID technique to study the photoisomerization mechanism of azobenzene by n * excitation [35] and isomerization quantum yields [36] for n * and * excitations. The method has also been used in biologically-relevant studies (nonadiabatic decay for adenine [5], photodissociation of cyclobutane thymine dimer [37], and photoinduced dimerization of thymine [38]) and the results were found to be consistent with experimental observations. A limitation of this method is that the simulation trajectory moves along a path produced by averaging over all the terms in the Born-Oppenheimer expansion [39][40][41][42][43], total (Xn, x e , t) = …”

“…Of the 100 trajectories, one representative for each initial geometry, 62 show a noticeable interaction between the stacked adenines and a well-defined decay process. The other (38) trajectories lead to a simple separation of the two adenine molecules and will not be discussed. Of the 62 trajectories, 6 were found to undergo a fast nonradiative deactivation; 37 were found to undergo a slow deactivation process that involve formation of a covalent bond between the stacked adenines and the rest show behavior similar to that discussed in an earlier publication [48] (where an "B-like configuration" was selected as initial geometry).…”

A new photoproduct of 5-methylcytosine and adenine: a theoretical study

“…Law et al predicted thymine dimerization yields through molecular dynamics simulations and the outcomes agreed well with experimental quantum yields [6]. Zhang et al also carried out semi-classical dynamics simulation study on stacked thymine molecules and they found two different reaction paths to create two different products [7]. One pathway results in the formation of cyclobutane pyrimidine dimer and the other returns back to reactants after deactivation.…”

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

“…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.…”