QM/AMOEBA description of properties and dynamics of embedded molecules

M Nottoli, M Bondanza, P Mazzeo… - Wiley …, 2023 - Wiley Online Library
We describe the development, implementation, and application of a polarizable QM/MM
strategy, based on the AMOEBA polarizable force field, for calculating molecular properties …

[HTML][HTML] Hybrid QM/classical models: Methodological advances and new applications

F Lipparini, B Mennucci - Chemical Physics Reviews, 2021 - pubs.aip.org
Hybrid methods that combine quantum mechanical descriptions with classical models are
very popular in molecular modeling. Such a large diffusion reflects their effectiveness, which …

Fast method for excited-state dynamics in complex systems and its application to the photoactivation of a blue light using flavin photoreceptor

P Mazzeo, S Hashem, F Lipparini… - The journal of …, 2023 - ACS Publications
The excited-state dynamics of molecules embedded in complex (bio) matrices is still a
challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be …

Multiscale models for light-driven processes

M Nottoli, L Cupellini, F Lipparini… - Annual Review of …, 2021 - annualreviews.org
Multiscale models combining quantum mechanical and classical descriptions are a very
popular strategy to simulate properties and processes of complex systems. Many alternative …

Trajectory surface hopping for a polarizable embedding QM/MM formulation

M Bondanza, B Demoulin, F Lipparini… - The Journal of …, 2022 - ACS Publications
We present the implementation of trajectory surface-hopping nonadiabatic dynamics for a
polarizable embedding QM/MM formulation. Time-dependent density functional theory was …

[HTML][HTML] Data-driven many-body potentials from density functional theory for aqueous phase chemistry

E Palos, S Dasgupta, E Lambros… - Chemical Physics …, 2023 - pubs.aip.org
Density functional theory (DFT) has been applied to modeling molecular interactions in
water for over three decades. The ubiquity of water in chemical and biological processes …

A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born–Oppenheimer Molecular Dynamics

F Pes, É Polack, P Mazzeo, G Dusson… - The Journal of …, 2023 - ACS Publications
This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann
extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in …

Grassmann extrapolation of density matrices for Born–Oppenheimer molecular dynamics

E Polack, G Dusson, B Stamm… - Journal of Chemical …, 2021 - ACS Publications
Born–Oppenheimer molecular dynamics (BOMD) is a powerful but expensive technique.
The main bottleneck in a density functional theory BOMD calculation is the solution to the …

[HTML][HTML] Deciphering photoreceptors through atomistic modeling from light absorption to conformational response

G Salvadori, P Mazzeo, D Accomasso… - Journal of Molecular …, 2023 - Elsevier
In this review, we discuss the successes and challenges of the atomistic modeling of
photoreceptors. Throughout our presentation, we integrate explanations of the primary …

Analytic gradient for time-dependent density functional theory combined with the fragment molecular orbital method

H Nakata, DG Fedorov - Journal of Chemical Theory and …, 2023 - ACS Publications
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the
fragment molecular orbital (FMO) method combined with time-dependent density functional …