Contacts:
Supervisor(s):
Prof. Benedetta Mennucci and Dr. Lorenzo Cupellini
Title of the PhD project:
Novel approaches to simulate proton and electron transfer processes in complex system.
Abstract of the PhD project:
Electron and proton transfers act a pivotal role in various chemical and biochemical processes. These transfers can take place in the ground or excited state and typically occur in condensed phases, where the surrounding environment significantly influences the reactions. Additionally, electron and proton transfers work together in the photoactivation of many photoreceptors through a mechanism called proton-coupled electron transfer (PCET).
Molecular dynamics (MD) is a powerful tool to study complex systems. In particular, composite techniques in which MD is coupled to quantum mechanics/molecular mechanics (QM/MM) models are essential to describe light-induced phenomena in such systems. However, these accurate techniques cannot be used to obtain statistically relevant data on realistic systems, due to their high computational cost. The aim of the project is to develop new multiscale techniques of limited computational cost while keeping a high accuracy of the description and to apply them to the investigation photoinduced processes that involves electrons and protons transfers.
Publications:
• G. Londi, G. Salvadori, P. Mazzeo, L. Cupellini and B. Mennucci, Protein-driven electron transfer process in a fatty acid photodecarboxylase, (2024), https://doi.org/10.26434/chemrxiv-2024-c0shc
• P. Mazzeo, E. Cignoni, A. Arcidiacono, L. Cupellini and B. Mennucci, Electrostatic Embedding Machine Learning for Ground and Excited State Molecular Dynamics of Solvated Molecules, (2024), RSC Digit. Discov., accepted, https://doi.org/10.1039/D4DD00295D
• A. Arcidiacono, E. Cignoni, P. Mazzeo, L. Cupellini and B. Mennucci, Predicting Solvatochromism of Chromophores in Proteins through QM/MM and Machine Learning, (2024) J. Phys. Chem. A, 128, 18, 3646-3658, https://doi.org/10.1021/acs.jpca.4c00249
• G. Salvadori, P. Mazzeo, D. Accomasso, L. Cupellini and B. Mennucci, Deciphering photoreceptors through atomistic modeling from light absorption to conformational response, (2023), J. Mol. Biol., 168358, https://doi.org/10.1016/j.jmb.2023.168358
• F. Pes, É. Polack, P. Mazzeo, G. Dusson, B. Stamm and F. Lipparini, A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics, (2023), J. Phys. Chem. Lett., 14, 43, 9720–9726, https://doi.org/10.1021/acs.jpclett.3c02098
• M. Nottoli, M. Bondanza, P. Mazzeo, L. Cupellini, C. Curutchet, D. Loco, L. Lagardère, J. P. Piquemal, B. Mennucci and F. Lipparini, QM/AMOEBA description of properties and dynamics of embedded molecules, (2023), Wiley Interdiscip. Rev. Comput. Mol. Sci. 13, e1674, https://doi.org/10.1002/wcms.1674
• P. Mazzeo, S. Hashem, F. Lipparini, L. Cupellini and B. Mennucci, Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor, (2023), J. Phys. Chem. Lett., 14, 5, 1222–1229, https://doi.org/10.1021/acs.jpclett.2c03797
• M. Nottoli, P. Mazzeo, F. Lipparini, L. Cupellini and B. Mennucci, A ΔSCF model for excited states within a polarisable embedding, (2022), Mol. Phys., https://doi.org/10.1080/00268976.2022.2089605
Oral communications at conferences
• P. Mazzeo, S. Hashem, F. Lipparini, L. Cupellini and B. Mennucci, Excited-state SCF Dynamics in Complex Systems: Unraveling the Photoactivation of a Blue-Light Using Flavin Photoreceptor, Tinker Developers Workshop 2024: New Trends in Modeling, Le Benedettine University of Pisa’s conference center, Pisa (Italy), 29-31 May 2024.
• P. Mazzeo, S. Hashem, M. Nottoli, F. Lipparini, L. Cupellini and B. Mennucci, A Fast Method for Polarizable QM/MM Excited-State Dynamics in Complex Systems, DCTC 2023-VIII Congresso Nazionale della Divisione di Chimica Teorica e Computazionale della SCI, Scuola Normale Superiore, Pisa (Italy), 20-22 September 2023.
Poster communications at conferences:
• P. Mazzeo, E. Cignoni, A. Arcidiacono, L. Cupellini and B. Mennucci, Exploring Intramolecular Proton Transfer Dynamics with Machine Learning Multiscale Simulations, Chemistry for the future 2024, Dipartimento di Chimica e Chimica Industriale, Università di Pisa (Italy), 3-5 July 2024.
• P. Mazzeo, S. Hashem, Michele Nottoli, F. Lipparini, L. Cupellini and B. Mennucci, A Fast Method for Polarizable QM/MM Excited-State Dynamics in Complex Systems, 1st ViRAPID Workshop 2024, University of Vienna, Austria, 26-29 February 2024.
• P. Mazzeo, S. Hashem, F. Lipparini, L. Cupellini and B. Mennucci, Unraveling the Photoactivation of a Blue-Light Using Flavin Photoreceptor through Excited-State SCF Dynamics, Chemistry for the Future 2023, Dipartimento di Chimica e Chimica Industriale, Università di Pisa (Italy), 28-30 June 2023.
• P. Mazzeo, S. Hashem, F. Lipparini, L. Cupellini and B. Mennucci, Unraveling the Photoactivation of a Blue-Light Using Flavin Photoreceptor through Excited-State SCF Dynamics, EuChemS CompChem 2023, Thessaloniki (Greece), 27-31 August 2023.
