Molecular dynamics time based formulation

In the present chapter, we will focus on the simulation of the dynamics of photoexcited nucleobases, in particular on the investigation of radiationless decay dynamics and the determination of associated characteristic time constants. We use a nonadiabatic extension of ab initio molecular dynamics (AIMD) [15, 18, 21, 22] which is formulated entirely within the framework of density functional theory. This approach couples the restricted open-shell Kohn-Sham (ROKS) [26-28] first singlet excited state, Su to the Kohn-Sham ground state, S0, by means of the surface hopping method [15, 18, 94-97], The current implementation employs a plane-wave basis set in combination with periodic boundary conditions and is therefore ideally suited to condensed phase applications. Hence, in addition to gas phase reference simulations, we will also present nonadiabatic AIMD (na-AIMD) simulations of nucleobases and base pairs in aqueous solution. 

Section 2 provides a brief overview of the AIMD methodology mainly in the representation of Car-Parrinello molecular dynamics simulations. Bom-Oppenheimer molecular dynamics (BOMD) simulations (time-independent electronic structure) are introduced in a generalized formulation based on the work by Niklasson [7, 8]. This will be followed (Sect. 3) by some recent methodological advancements which allow for computationally more efficient simulations with better statistical sampling and which use more accurate electronic structure methods. After this, some examples from applied chemistry studied from AIMD will be given in Sect. 4. 

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