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Photoinduced Phenomena in Nucleic Acids I pp 99–153Cite as

Excitation of Nucleobases from a Computational Perspective II: Dynamics

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Part of the book series: Topics in Current Chemistry ((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.

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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

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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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  1. Institute of Theoretical Chemistry, University of Vienna, Währinger Str. 17, 1090, Vienna, Austria

    Sebastian Mai, Martin Richter, Philipp Marquetand & Leticia González

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  1. Sebastian Mai
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  2. Martin Richter
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  3. Philipp Marquetand
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  4. Leticia González
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Correspondence to Leticia González .

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  1. Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany

    Mario Barbatti

  2. Institute of Chemistry, University of São Paulo, São Paulo, Brazil

    Antonio Carlos Borin

  3. Department of Physics and Astronomy, The University of Georgia, Athens, Georgia, USA

    Susanne Ullrich

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Mai, S., Richter, M., Marquetand, P., González, L. (2014). Excitation of Nucleobases from a Computational Perspective II: Dynamics. In: Barbatti, M., Borin, A., Ullrich, S. (eds) Photoinduced Phenomena in Nucleic Acids I. Topics in Current Chemistry, vol 355. Springer, Cham. https://doi.org/10.1007/128_2014_549

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