Unravelling the Working Mechanisms of Fluorescent Molecular Rotors for Bioimaging

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The overall aim of the thesis will be to gain a detailed understanding of the working mechanism of fluorescent molecular rotors, in particular those based on BODIPY. These rotors can be used as probes to evaluate the local viscosity in cell membranes and lipid bilayers. Our goal will be achieved by a combination of multiscale atomistic simulations in combination with advanced fluorescence imaging. The insight gained will allow to optimise the use of fluorescent molecular rotors as rapid and reliable viscosity sensors in fluorescence microscopy, and other biotechnologically relevant viscosity-sensing and imaging assays.The first stage of my project can be summarised by three questions: Is it possible to accurately characterise the potential energy surface of a prototypical BODIPY-based rotor (BODIPY-Phe)? What can we learn about its excited state characteristics? Which simulation methods are the most efficient and effective tools for studying BODIPY-Phe? The aim of this stage of work is, therefore, to refine and compare the simulation techniques which will likely be needed for detailed future studies of the rotor, whilst gaining a qualitative insight into the radiative decay mechanisms that control its photophysical properties.The second stage of the project will build on the first by performing more complex molecular dynamics simulations, both in vacuo and in solvents. These will be done in conjunction with experimental absorption, emission and anisotropy measurements of the BODIPY rotor in solvents of varying viscosities. The aim of these tasks is to gain a more validated understanding of the behaviour of the molecule in real environments. This will all be complemented by computational characterisation of the ground and excited state of two other molecular rotors: DCVJ and ThT. These rotors are thought to have different working mechanisms to BODIPY, so should be good comparative tools.