Abstract :

Chlorophylls play a central role in harnessing light energy during photosynthesis. The aim of this thesis is to understand electronic and vibrational properties of chlorophylls.

To this end, we focus on the interpretation of recent gas phase experimental data through advanced computational approaches. The structural and photophysical properties of chlorophyll a and pheophytin a, in their neutral and anionic states.

We first introduce the quantum chemistry methods used to study molecular structures, for both static and dynamic cases: auxiliary density functional theory (DFT) for ground and excited states, and two semi-empirical methods, namely third order tight-binding DFT and PM6 (parametrized model) with dispersion and hydrogen bonding corrections.

Conformational sampling techniques based on classical molecular dynamics (MD) and parallel tempering are also introduced. The second part of the chapter 1 deals with clustering methods (K-means, HDBSCAN, Yacare).

In Chapter 1, we carried out a conformational analysis of the neutral forms, explicitly including the phytyl chain, which plays a key structuring role through intramolecular interactions. Deprotonation energies are calculated and the most favorable deprotonation sites are identified, while the regioselective addition of a methanol molecule to the anion is also investigated, both complementing experimental mass spectrometry data. We concluded that the most stable deprotonation site lies on the macrocycle, and that in the presence of methanol, it preferentially binds to the beginning of the phytyl chain, following the rupture of a double bond, specifically at the most branched carbon, without proton migration.

Chapter 2 focuses on the conformations of anionic chlorophyll A. Conformations are sampled from MD trajectories and expressed in spherical coordinates. Clustering methods enabled the identification of several typical conformations: a total of 26 structural groups was obtained using the Yacare algorithm. UV-Vis spectroscopy calculations using time-dependent-DFT were performed on each representative structure. The resulting spectra were compared with experimental observations of band broadening as a function of conformation, and the observed fine structure was interpreted as being dependent on the position of the phytyl chain. An orbital analysis of the transitions revealed how variations in intensity and band position are governed by the molecular geometry. We correlate these spectral variations with the position of the chain relative to the macrocycle, as well as with its folding and torsions. This demonstrates that the phytyl chain has a significant impact on the electronic excitations of the molecule.

We also contributed to a collaborative study on CO binding to two molecules structurally related to chlorophyll, namely heme and a sufonate substituted heme, a mechanism of importance in iron transport in heme proteins.

The final chapter deals with a new implementation of electronic circular dichroism (ECD). A dedicated implementation based on electric and magnetic dipole transition moments was developed within the framework of auxiliary DFT. A preliminary application is proposed to explore the relationship between ECD signals and molecular conformation. To this end, we combined MD and ECD simulations to generate time-evolving spectra and analyze structural dynamics along a trajectory.

This thesis thus proposes an integrated approach combining molecular dynamics, data analysis, and theoretical spectroscopy to connect the structures and optical properties of chlorophylls. It highlights the importance of conformational effects in gas-phase spectral broadening, in the absence of solvent interactions.