Dynamics of model biomolecular systems in the ground and exited electronic states

Novak, Jurica (2015) Dynamics of model biomolecular systems in the ground and exited electronic states. Doctoral thesis, Faculty of Science > Department of Chemistry.

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Abstract

This dissertation contributes to the fundamental understanding of photochemical processes of complex systems on the boundary of chemistry, physics and biology. Implementation of theoretical procedures enables us to investigate the dynamics of the system of interest on the molecular level. Nonadiabatic dynamics in the framework of the time dependent density functional theory is used to simulate in vacuo relaxation of two conformers of formic acid monomers and dimers. By establishing hydrogen bonds, fragmentation dynamics of monomer changes to dissociative dynamics of dimers. Quantum - mechanical anharmonic frequency calculations confirmed the existence of two types of aggregates between protonated all-trans n-butylamine Schiff base of retinal (nSBR+) and the hydrogen bonded trifluoroacetic acid counterion. Using nonadiabatic dynamics simulations of the chromophore-counterion pairs in the dichloromethane, it is shown that the relaxation processes that set in after photo-excitation involve a formation of an inter-molecular charge transfer as a decisive step. In solution, this leads to dissociation of the chromophore-counterion pair and abortion of the photoisomerization, but constraining the distance of a counterion results in increasing biologically active C13=C14 bond length. Simulations of solvated nSBR+ reveal rotations around formally single bonds as a non-reactive channel.

Item Type: Thesis (Doctoral thesis)
Keywords: TDDFT, nonadiabatic dynamics, formic acid, retinal, charge transfer state
Supervisor: Došlić, Nađa
Date: 2015
Number of Pages: 164
Subjects: NATURAL SCIENCES > Chemistry
Divisions: Faculty of Science > Department of Chemistry
Depositing User: Branka Maravic
Date Deposited: 01 Jul 2015 11:46
Last Modified: 01 Jul 2015 11:46
URI: http://digre.pmf.unizg.hr/id/eprint/4083

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