Excitation of Nucleobases from a Computational Perspective II: Dynamics

  • Sebastian Mai
  • Martin Richter
  • Philipp Marquetand
  • Leticia GonzálezEmail author
Part of the Topics in Current Chemistry book series (TOPCURRCHEM, volume 355)


This chapter is devoted to unravel the relaxation processes taking place after photoexcitation of isolated DNA/RNA nucleobases in gas phase from a time-dependent perspective. To this aim, several methods are at hand, ranging from full quantum dynamics to various flavours of semiclassical or ab initio molecular dynamics, each with its advantages and its limitations. As this contribution shows, the most common approach employed up to date to learn about the deactivation of nucleobases in gas phase is a combination of the Tully surface hopping algorithm with on-the-fly CASSCF calculations. Different dynamics methods or, even more dramatically, different electronic structure methods can provide different dynamics. A comprehensive review of the different mechanisms suggested for each nucleobase is provided and compared to available experimental time scales. The results are discussed in a general context involving the effects of the different applied electronic structure and dynamics methods. Mechanistic similarities and differences between the two groups of nucleobases – the purine derivatives (adenine and guanine) and the pyrimidine derivatives (thymine, uracil, and cytosine) – are elucidated. Finally, a perspective on the future of dynamics simulations in the context of nucleobase relaxation is given.


DNA photochemistry Ultrafast radiationless decay Non-adiabatic dynamics Excited-state lifetimes Conical Intersections 





Ab initio molecular dynamics


Ab initio multiple spawning


(Semi-empirical) Austin model 1




Complete active space second-order perturbation theory


Complete active space self-consistent field


Configuration interaction


Conical intersection


Car–Parrinello molecular dynamics


Closed shell


Density functional theory


Density functional-based tight binding


Deoxyribonucleic acid


Degree of freedom




Full multiple spawning




Ground state


Internal conversion


Intersystem crossing


Molecular Coulomb Hamiltonian


Multi-configurational time-dependent Hartree


Molecular dynamics


Multi-reference configuration interaction


Multi-reference configuration interaction with single excitations


Non-adiabatic coupling


(Semi-empirical) Orthogonalization model 2


Potential energy hypersurface


(Semi-empirical) Parametrized model 3


Quantum dynamics


Ribonucleic acid


Restricted open-shell Kohn–Sham


Surface hopping including arbitrary couplings


Spin-orbit coupling




Time-dependent density functional theory


Time-dependent density functional-based tight binding


Time-dependent Schrödinger equation


Time-resolved photo-electron spectroscopy


Tully’s surface hopping


Tully’s surface hopping coupled to Car–Parrinello dynamics







Financial support from the Austrian Science Fond (FWF), Project No. P25827 is gratefully acknowledged. Furthermore, we would like to thank Jesus González-Vázquez and Tom Weinacht for their always insightful discussions. Special thanks go to Tom for sharing his unpublished results on enol cytosine with us. The Vienna Scientific Cluster (VSC) is also thanked for generous allocation of computer time.


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© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Sebastian Mai
    • 1
  • Martin Richter
    • 1
  • Philipp Marquetand
    • 1
  • Leticia González
    • 1
    Email author
  1. 1.Institute of Theoretical ChemistryUniversity of ViennaViennaAustria

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