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Vimalanandan

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons58784

Lu,  You
Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society;

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Citation

Lu, Y. (2012). Vimalanandan. PhD Thesis, Universitätsbibliothek, Düsseldorf.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000E-EFA2-8
Abstract
The main goal of this work was to probe a wide panorama of excited-state phenomena. The systems studied range from the small cation CH<sub>2</sub>NH<sub>2</sub><sup>+</sub>(6 atoms) via the medium-sized chromophore DMN (26 atoms) and the large fluorophore OVP5 (164 atoms) to solvated DNA oligomers (größer 10<sup>4</sup> atoms). Correspondingly, the applied computational methods covered ab initio theory, semiempirical multi-reference configuration interaction (MRCI), and hybrid quantum mechanical/molecular mechanical (QM/MM) approaches. One aspect of this work was to establish procedures for dealing with the dynamics of a wide variety of excited states, from small molecules in the gas phase toward macromolecules in the solvent phase. The QM/MM investigation of adenine in solvated DNA oligomers was among the most advanced attempts of performing nonadiabatic dynamics simulations for such large biological systems and helped to establish a reliable routine for simulating the photoinduced processes of such complex systems in silico. The tasks in this work included the validation of methodology, the computation of vertical transitions and excited-state geometries, the identification of reaction paths, the simulation of decay dynamics, the search for conical intersections, the construction of potential energy surfaces (PESs), and the prediction of absorption and emission spectra. Major applications were the comprehensive studies of DMN and of adenine in DNA which led to the following results. DMN was investigated in the gas phase at the semiempirical OM2/MRCI level using surface-hopping nonadiabatic dynamics simulations. A lifetime of 1.2 ps was predicted for the S<sub>1</sub> state, in accordance with experimental observation. The reactive coordinate was found to be the C7=C8 double-bond twisting accompanied by pronounced pyramidalization at the C8 atom. The structures of conical intersections were located by full optimizations. The time-resolved fluorescence of DMN was simulated, which compared well with the experimental spectrum. The use of different active spaces in the OM2/MRCI calculations yielded similar results and thus demonstrated their internal consistency. Adenine embedded in solvated DNA oligomers, (dA)<sub>10</sub> and (dA)<sub>10</sub>·(dT)10, was studied at the QM/MM (QM=OM2/MRCI) level using surface-hopping dynamics simulations. Both model systems were found to decay from the S<sub>1</sub> to the S</sub>0</sub> state via different monomeric channels, on account of the strong hydrogen-bonding interactions between the Watson-Crick pair in the double-stranded oligomer. Surprisingly the decay times (~4-6 ps) for the current models were ten times longer than those of 9H-adenine in the gas or aqueous phase (~0.4-0.5 ps), while matching one of the time components observed experimentally. Possible reasons were identified for these longer decay times, with focus on the influence of MM environment on the QM adenine chromophore. Steady-state and time-dependent fluorescence spectra were computed to help understand the experimental observations.