Mazzeo Patrizia

Contacts:
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Supervisor(s):
Prof. Benedetta Mennucci and Dr. Lorenzo Cupellini

Title of the PhD project:
Novel approaches to simulate Proton-Coupled Electron Transfer processes in biological systems.

Abstract of the PhD project:
Photoreceptors are protein domains in which light-sensitive small molecules, called chromophores, are embedded through a tight network of diverse interactions. Their main function is to convert light signals into biological information, often using conformational changes of the protein. Such photoactivation may involve electron and proton transfer, through a mechanism called Proton-Coupled Electron Transfer (PCET). In PCET, electron and proton transfers may be concerted, or they may occur in multiple steps; they can have the same donor and acceptor, or they can exploit electron tunneling over long distances to create a sequence of proton transfers along the system, facilitated by the spatial arrangement of involved residues.
Molecular dynamics (MD) is a powerful tool to study complex biological systems. In particular, composite techniques in which MD is coupled to quantum mechanics/molecular mechanics (QM/MM) multiscale models are essential to describe light-induced phenomena in such complex 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 characterized by a limited computational cost while keeping a high accuracy of the description. These new techniques will be applied to the investigation of PCET-activated photoreceptors such as Flavin containing proteins.

Publications:

• 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, 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, 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.

Other achievements:

DCCI|UNIPI
Dipartimento di Chimica e Chimica Industriale
Department of Chemistry and Industrial Chemistry
Via G. Moruzzi, 13 - Pisa, Italy
DSCM
Corso di Dottorato in Scienze Chimiche e dei Materiali
Doctoral School in Chemistry and Material Science
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