Formation and Repair of Cyclobutane Pyrimidine Dimers

Thymine dimer PESDiverse mechanisms of formation and repair of CPDs with different charge, excitation, and multiplicity states are mapped using high-level ab initio methods.

Cyclobutane pyrimidine dimers (CPD) are deeply related to mutagenesis and carcinogenesis. It happens when UV radiation induces dimerization of adjacent pyrimidine nucleobases:

thymine_dimer

To understand how the dimerization and the repair process happens, I built a benchmark of computational results based on different methods. For these simulations, I used a thymidine-dimer model in the gas phase and I explored the ground and excited potential energy surfaces of neutral (singlet and triplet), cation, and anion species. These surfaces, computed along the two dimerization coordinates C5-C5′ and C6-C6′, look like the figure below.

Thymine dimer PES

Potential energy surface and charge distribution in the ground state of neutral and charged thymine dimers.

The analysis of such surfaces allowed me to describe several reaction pathways for dimerization and repair, some of them completely unknown so far. The movie below is an animation of one of those paths. It shows the sequential bond breaking of the dimer on the anion surface.

Important: This video above isn’t dynamics simulation. It is only linear interpolation between stationary structures (minima and transition states). I built the movie using the time lags measured by Liu et al.

Reference

M. Barbatti, Computational reference data for photochemistry of cyclobutane pyrimidine dimers; ChemPhysChem, doi:10.1002/cphc.201402302 (2014). doi:10.1002/cphc.201402302

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