Contacts:
Mail:
Supervisors:
Dr. Filippo Lipparini
Prof. Benedetta Mennucci
Title:
Development of new methods for quantum/classical molecular dynamics simulations
Abstract:
The computational modeling of processes of molecules embedded in complex (bio)matrices requires the use of molecular dynamics simulations coupled with a hybrid quantum/classical description of the system.
Hybrid quantum/classical methods are used to describe accurately the interesting region of the system while accounting for the surrounding environment in a computationally cheap way. These methods can be classified in at least two categories depending on the classical description of the environment; this can be molecular mechanics giving rise to the so called QM/MM methods, or it can be further simplified to a continuum medium as in the polarizable continuum models (PCM).
The project aims to provide a completely new tool for the study of dynamical processes in complex systems. The new tool consists in a software able to run quantum/classical dynamics of ground and excited states of molecules embedded in (bio)matrices. This requires putting together existing models, deriving new ones and finally implementing the theory in an efficient computer code.
The new method will be then applied to the modeling of photoinduced processes.
Journal articles:
M. Nottoli, S. Jurinovich, L. Cupellini, A. T. Gardiner, R. Cogdell, B. Mennucci,
The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria, Photosynth. Res., 2018, DOI:10.1007/s11120-018-0492-1
Publications:
• S. Hashem, V. Macaluso, M. Nottoli, F. Lipparini, L. Cupellini, B. Mennucci; From Crystallographic Data to Solution Structure of Photoreceptors: The Case of AppA BLUF Domain 2021, 10.26434/chemrxiv.14731980.v1
• M. Nottoli, M. Bondanza, F. Lipparini, B. Mennucci; An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone, J. Chem. Phys. 2021, 154, 18, 184107, 10.1063/5.0046844,
• M. Nottoli, L. Cupellini, F. Lipparini, G. Granucci, B. Mennucci; Multiscale Models for Light-Driven Processes, Annu. Rev. Phys. Chem. 2021, 72, 1, 489-513, 10.1146/annurev-physchem-090419-104031
• M. Nottoli, F. Lipparini; General formulation of polarizable embedding models and of their coupling, J. Chem. Phys. 2020, 153, 22, 224108, 10.1063/5.0035165
• M. Nottoli, B. Mennucci, F. Lipparini; Excited state Born-Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA, Phys. Chem. Chem. Phys. 2020, 22, 35, 19532-19541, 10.1039/d0cp03688a
• M. Bondanza, M. Nottoli, L. Cupellini, F. Lipparini, B. Mennucci; Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?, Phys. Chem. Chem. Phys. 2020, 22, 26, 14433-14448, 10.1039/d0cp02119a
• F. Cardoso Ramos, M. Nottoli, L. Cupellini, B. Mennucci; The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling, Chem. Sci. 2019, 10, 42, 9650-9662, 10.1039/c9sc02886b
• L. Cupellini, M. Bondanza, M. Nottoli, B. Mennucci; Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation, Biochim. Biophys. Acta - Bioenergetics 2020, 1861, 4, 148049, 10.1016/j.bbabio.2019.07.004
• M. Nottoli, B. Stamm, G. Scalmani, F. Lipparini; Quantum Calculations in Solution of Energies, Structures, and Properties with a Domain Decomposition Polarizable Continuum Model, J. Chem. Theory Comput. 2019, 15, 11, 6061-6073, 10.1021/acs.jctc.9b00640
• M. Nottoli, S. Jurinovich, L. Cupellini, A. T. Gardiner, R. Cogdell, B. Mennucci; The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria, Photosynth. Res., 2018, 137, 2, 215--226, 10.1007/s11120-018-0492-1
Oral communications at conferences:
• M. Nottoli, B. Mennucci, F. Lipparini; Development of new methods for quantum/classical molecular dynamics simulations; CFF 2021 - Chemistry for the Future International Conference; Università di Pisa; Pisa, June 30 July 1-2, 2021
• M. Nottoli (invited), B. Mennucci, F. Lipparini; Adiabatic excited state dynamics in a polarizable embedding; VIRTUAL WORKSHOP – Many-Body Interactions: From Quantum Mechanics to Force Fields; Telluride Science Research Center; June 8-12 2020
• M. Nottoli (invited), F. Cardoso Ramos, L. Cupellini, B. Mennucci; The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling; 2019 ESP Congress - Molecular • Modelling and Simulation in Photobiological Systems; European Society for Photobiology; Barcelona, August 25-30 2019
• M. Nottoli (invited), B. Stamm, F. Lipparini Quantum calculations in solution of energy, structures and properties with a domain decomposition polarizable continuum model; The Mathematics of Finite Elements and Applications 2019 - Numerical Methods for Continuum Solvation; Brunel University; London, June 18-21 2019
Poster communications at congress:
• M. Nottoli, F. Lipparini; General formulation of polarizable embedding models and of their coupling; Virtual Symposium on Chemical Theory and Computation (VS-CTC) 2020; Società Chimica Italiana; December 21 2020
• M. Nottoli, B. Mennucci, F. Lipparini; Excited State Born-Oppenheimer Molecular Dynamics with a Polarizable Embedding: Implementation of QM/AMOEBA Gradients for TD-DFT; Modelling Photoinduced Processes in Molecular Systems; Imperial College; London, February 6-8 2020
• M. Nottoli, B. Stamm, F. Lipparini Quantum calculations in solution of energy, structures and properties with a domain decomposition polarizable continuum model; CFF 2019 - Chemistry for the Future International Conference; Università di Pisa; Pisa, July 3-5, 2019
