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Coherent control and quantum dynamics in complex chemical and biological environments
Coherent control and quantum dynamics in complex chemical and biological environments
In ultrafast molecular sciences, short laser pulses are used to initiate and interrogate chemical and physical phenomena. This thesis presents simulations on different molecular examples within this framework, where the specific goal ranges from the design of ultrafast experiments, over their interpretation and to feasibility assessments for future applications. Additionally, simulation protocols are developed to consider the influence of complex environments on the studied processes, as this is essential for the aspired experimental connection and often very challenging. The first topic deals with the initiation of a synthetically relevant reaction with shaped laser pulses. The model system is a methyl transfer between cyclohexanone and trimethylaluminium, which includes a carbon-carbon bond formation as the key step in many pharmaceutical syntheses. The surrounding molecules of the chemical solution are found to considerably affect the one-dimensional model reaction coordinate describing the methyl transfer. Quantum control studies are performed by optimizing laser pulses, selectively steering a nuclear wavepacket toward the methyl transfer pathway. A simulation protocol based on multi-target Optimal Control Theory is employed to overcome the environmental complexities and excite the molecules in various different static solvent cages simultaneously. In combination with statistical estimates, it is found that theoretically the population yield in the target level can be considerable. Going beyond the static inclusion of solvent cages, the temporal evolution of the environmental influence is revealed along five different classical trajectories of 2.5~picoseconds each. The affected vibrational levels of the target molecule are found to fluctuate on the femtosecond time scale, i.e. the environmental influence can switch between extreme cases several times during the time where the controlling laser pulse is active. Optimized laser pulses can also be efficient in scenarios which they were not optimized for, which has several implications for practical applications. The second topic revolves around photoexcited phenomena in nucleic acids. The RNA-nucleobase uracil is investigated with respect to its photostability. One reason for the canonical nucleobases being extraordinarily stable towards UV absorption is their ultrafast relaxation back to the electronic ground state. Besides presenting the first full quantum dynamical simulations on this process for uracil, quantum control optimizations are used to trap the wave packet and prevent relaxation. This artificially prepares the elusive state which can be a precursor for photodamage, as delayed relaxation has been directly connected with the formation of harmful lesions before. The optimized laser pulse is surprisingly smooth and within the accessibility of modern experimental setups, which renders this study a tangible instruction for possible spectroscopic experiments. Besides the artificial trap on isolated uracil, wavepacket simulations within its natural RNA environment reveal that this influence can also lead to trapping in the photoexcited state. Sampling over 10 different neighboring base sequences and a total of 275 environmental snapshots, this mechanism is found to be base-independent. In this connection, the third study goes from the formation of photodamage to its repair. An experimentally observed repair mechanism of the frequently occurring cyclobutane pyrimidine dimer - formed by two thymines in DNA - is investigated with quantum chemistry. The excited states of the neighboring guanine adenine sequence are characterized to distinguish between local and charge transfer excitation, validating the initial step of the experimentally suggested mechanism.
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Keefer, Daniel
2019
English
Universitätsbibliothek der Ludwig-Maximilians-Universität München
Keefer, Daniel (2019): Coherent control and quantum dynamics in complex chemical and biological environments. Dissertation, LMU München: Faculty of Chemistry and Pharmacy
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Abstract

In ultrafast molecular sciences, short laser pulses are used to initiate and interrogate chemical and physical phenomena. This thesis presents simulations on different molecular examples within this framework, where the specific goal ranges from the design of ultrafast experiments, over their interpretation and to feasibility assessments for future applications. Additionally, simulation protocols are developed to consider the influence of complex environments on the studied processes, as this is essential for the aspired experimental connection and often very challenging. The first topic deals with the initiation of a synthetically relevant reaction with shaped laser pulses. The model system is a methyl transfer between cyclohexanone and trimethylaluminium, which includes a carbon-carbon bond formation as the key step in many pharmaceutical syntheses. The surrounding molecules of the chemical solution are found to considerably affect the one-dimensional model reaction coordinate describing the methyl transfer. Quantum control studies are performed by optimizing laser pulses, selectively steering a nuclear wavepacket toward the methyl transfer pathway. A simulation protocol based on multi-target Optimal Control Theory is employed to overcome the environmental complexities and excite the molecules in various different static solvent cages simultaneously. In combination with statistical estimates, it is found that theoretically the population yield in the target level can be considerable. Going beyond the static inclusion of solvent cages, the temporal evolution of the environmental influence is revealed along five different classical trajectories of 2.5~picoseconds each. The affected vibrational levels of the target molecule are found to fluctuate on the femtosecond time scale, i.e. the environmental influence can switch between extreme cases several times during the time where the controlling laser pulse is active. Optimized laser pulses can also be efficient in scenarios which they were not optimized for, which has several implications for practical applications. The second topic revolves around photoexcited phenomena in nucleic acids. The RNA-nucleobase uracil is investigated with respect to its photostability. One reason for the canonical nucleobases being extraordinarily stable towards UV absorption is their ultrafast relaxation back to the electronic ground state. Besides presenting the first full quantum dynamical simulations on this process for uracil, quantum control optimizations are used to trap the wave packet and prevent relaxation. This artificially prepares the elusive state which can be a precursor for photodamage, as delayed relaxation has been directly connected with the formation of harmful lesions before. The optimized laser pulse is surprisingly smooth and within the accessibility of modern experimental setups, which renders this study a tangible instruction for possible spectroscopic experiments. Besides the artificial trap on isolated uracil, wavepacket simulations within its natural RNA environment reveal that this influence can also lead to trapping in the photoexcited state. Sampling over 10 different neighboring base sequences and a total of 275 environmental snapshots, this mechanism is found to be base-independent. In this connection, the third study goes from the formation of photodamage to its repair. An experimentally observed repair mechanism of the frequently occurring cyclobutane pyrimidine dimer - formed by two thymines in DNA - is investigated with quantum chemistry. The excited states of the neighboring guanine adenine sequence are characterized to distinguish between local and charge transfer excitation, validating the initial step of the experimentally suggested mechanism.