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Excitation of Nucleobases from a Computational Perspective II: Dynamics

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

Abstract

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.

Keywords

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

Abbreviations

A

Adenine

AIMD

Ab initio molecular dynamics

AIMS

Ab initio multiple spawning

AM1

(Semi-empirical) Austin model 1

C

Cytosine

CASPT2

Complete active space second-order perturbation theory

CASSCF

Complete active space self-consistent field

CI

Configuration interaction

CoIn

Conical intersection

CPMD

Car–Parrinello molecular dynamics

cs

Closed shell

DFT

Density functional theory

DFTB

Density functional-based tight binding

DNA

Deoxyribonucleic acid

DOF

Degree of freedom

FC

Franck–Condon

FMS

Full multiple spawning

G

Guanine

GS

Ground state

IC

Internal conversion

ISC

Intersystem crossing

MCH

Molecular Coulomb Hamiltonian

MCTDH

Multi-configurational time-dependent Hartree

MD

Molecular dynamics

MRCI

Multi-reference configuration interaction

MRCIS

Multi-reference configuration interaction with single excitations

NAC

Non-adiabatic coupling

OM2

(Semi-empirical) Orthogonalization model 2

PEH

Potential energy hypersurface

PM3

(Semi-empirical) Parametrized model 3

QD

Quantum dynamics

RNA

Ribonucleic acid

ROKS

Restricted open-shell Kohn–Sham

Sharc

Surface hopping including arbitrary couplings

SOC

Spin-orbit coupling

T

Thymine

TD-DFT

Time-dependent density functional theory

TD-DFTB

Time-dependent density functional-based tight binding

TDSE

Time-dependent Schrödinger equation

TRPES

Time-resolved photo-electron spectroscopy

TSH

Tully’s surface hopping

TSH-CP

Tully’s surface hopping coupled to Car–Parrinello dynamics

U

Uracil

UV

Ultraviolet

Notes

Acknowledgements

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

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

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