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.
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