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Within the CLiC Research Training Network, the following projects are pursued:

A1.1: Simulation and optimization of VIPER uncaging

In collaboration with the Bredenbeck group (A4) and the Heckel group (A2), this PhD thesis will systematically contribute to a cycle of theoretical prediction, spectroscopic investigation, and synthesis, in order to optimize novel uncaging strategies. The PhD student of this project will focus upon the Vibrationally Promoted Electronic Resonance (VIPER) experiment pioneered by the Bredenbeck group (A4) that potentially offers an ideal tool for orthogonal uncaging, due to highly selective excitation in the mid-IR range, followed by a UV-Vis pulse.

On the theory side, the PhD student will establish a simulation protocol for the VIPER experiment in order to assist in its interpretation and optimisation, as well as the prediction of optimal orthogonal cages. Several steps are involved in the analysis, including (i) the calculation of vibronic spectra as a function of vibrational excitation in the electronic ground state, (ii) the analysis of the influence of intramolecular vibrational redistribution (IVR) on the selectivity of the experiment, and (iii) the full simulation of the two-dimensional 2D-IR-UV/Vis experiment. State-of-the-art multidimensional wavepacket propagation techniques will be employed, in particular the Multicon­figuration Time-Dependent Hartree (MCTDH) method.

The PhD student will actively interact with her/his colleagues of project A4.1 (orthogonal uncaging strategies based on the VIPER pulse sequence) and project A2.1 (synthesis of novel caging groups). At an international level, the project involves a collaboration with Prof. Fabrizio Santoro (University of Pisa).

A1.2: Computational modeling and optimization of uncaging platforms

This project will focus upon molecular dynamics simulations and Markov State modeling, along with selected electronic structure calculations and hybrid quantum mechanics/molecular mechanics approaches. The objective is to develop molecular-level descriptions and kinetic models for uncaging-induced RNA and DNA folding including the effects of conformational flexibility of the caged structures. Collaborations with several experimental groups within the CLiC Research Training Group will be actively pursued. For details, see here.

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