We address the investigation of the thermodynamics and kinetics of charge transfer (CT) reactions in biomolecular systems as redox-active proteins, enzymes and photoactive proteins. We use to this aim a hybrid quantum classical approach, namely the Perturbed Matrix Method, that we contributed to develop. This approach allows us to obtain the quantum properties of a reaction site interacting with systems with large configurational complexity. We also extended the approach to investigate the same processes for biomolecules interacting with inorganic surfaces and nanoparticles.
We can obtain macroscopic properties such as redox potentials, deprotonation free energies and kinetic rates to be directly compared to experimental measurements. This allows us to understand the molecular mechanisms underlying the thermodynamics and kinetics of CT reactions. Among other applications, we computed the redox potential of cytochrome c bound to a gold electrode, we studied the photoinduced electron transfer in a flavoprotein and the thermodynamics of the catalytic proton transfer reaction in Sars-CoV-2 main protease.
| People | Stefano Corni, Laura Zanetti Polzi* |
| Keywords | Electron transfer, proton transfer, light-induced charge transfer, redox proteins, photoreceptors |
| Methods, techniques | Hybrid quantum/classical computational approaches, all-atoms molecular dynamics simulations |
| Collaborations | University of L’Aquila, University of Rome “Tor Vergata”, RMIT University (Australia), Oak Ridge National Laboratories (USA). |
| Publications | |
| L Zanetti-Polzi, MD Smith, C Chipot, JC Gumbart, DL Lynch, A Pavlova, JC Smith, I Daidone Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design J Phys Chem Lett 2021 | |
| L Zanetti-Polzi, I Daidone, A Amadei Fully Atomistic Multiscale Approach for pKa Prediction J Phys Chem B 2020 | |
| L Zanetti-Polzi, I Daidone, S Corni Evidence of a Thermodynamic Ramp for Hole Hopping to Protect a Redox Enzyme from Oxidative Damage J Phys Chem Lett 2019 | |
| L Zanetti-Polzi, M Aschi, A Amadei, I Daidone Alternative Electron-Transfer Channels Ensure Ultrafast Deactivation of Light-Induced Excited States in Riboflavin Binding Protein J Phys Chem Lett 2017 | |
| L Zanetti-Polzi, I Daidone, CA Bortolotti, S Corni Surface Packing Determines the Redox Potential Shift of Cytochrome c Adsorbed on Gold J Am Chem Soc 2014 |