DNA strongly absorbs UV light and this can trigger harmful processes causing alteration of the genetic code and cellular death. However, DNA and its components, the nucleobases, have an intrinsic capability to dissipate the excess electronic energy into heat thanks to a combination of intra-molecular and inter-molecular non-radiative processes, which strongly reduce the risk of potentially dangerous photo reactions. Although deeply studied in literature, many aspects of these mechanisms remain to be clarified. DNA can also be seen as a prototype of many multichromophoric systems so the interest in its photophysics goes beyond its biological relevance. This thesis is devoted to a computational study of DNA photophysics with dynamical approaches. The ultra-fast decays in DNA occur through non-radiative transitions triggered by the coupling between electrons and nuclei motions. These are intrinsically quantum phenomena and therefore we chose to tackle them with fully quantum dynamical approaches. More specifically, in this thesis, we have proposed and applied a computational protocol based on the parameterization with time-dependent density functional theory of Linear Vibronic Coupling models able to describe the competition between intra-base and inter-base decay mechanisms, combined with non-radiative propagations of vibronic wavepackets with advanced multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) approaches. With this strategy we have tackled the study of the ultra-fast light-activated dynamics (∼ 100 fs) of DNA components of growing complexity, starting from isolated nucleobases and their derivatives up to double-stranded tetrads.

Quantum Dynamics of Decay Processes in Photoexcited Nucleobases and Small Oligomers

YAGHOUBI JOUYBARI, MARTHA
2022

Abstract

DNA strongly absorbs UV light and this can trigger harmful processes causing alteration of the genetic code and cellular death. However, DNA and its components, the nucleobases, have an intrinsic capability to dissipate the excess electronic energy into heat thanks to a combination of intra-molecular and inter-molecular non-radiative processes, which strongly reduce the risk of potentially dangerous photo reactions. Although deeply studied in literature, many aspects of these mechanisms remain to be clarified. DNA can also be seen as a prototype of many multichromophoric systems so the interest in its photophysics goes beyond its biological relevance. This thesis is devoted to a computational study of DNA photophysics with dynamical approaches. The ultra-fast decays in DNA occur through non-radiative transitions triggered by the coupling between electrons and nuclei motions. These are intrinsically quantum phenomena and therefore we chose to tackle them with fully quantum dynamical approaches. More specifically, in this thesis, we have proposed and applied a computational protocol based on the parameterization with time-dependent density functional theory of Linear Vibronic Coupling models able to describe the competition between intra-base and inter-base decay mechanisms, combined with non-radiative propagations of vibronic wavepackets with advanced multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) approaches. With this strategy we have tackled the study of the ultra-fast light-activated dynamics (∼ 100 fs) of DNA components of growing complexity, starting from isolated nucleobases and their derivatives up to double-stranded tetrads.
21-nov-2022
Italiano
DNA
photo-excitation
quantum dynamics
ultra-fast decay
Santoro, Fabrizio
Degano, Ilaria
Garavelli, Marco
Pastore, Mariachiara
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.14242/216008
Il codice NBN di questa tesi è URN:NBN:IT:UNIPI-216008