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 …

Time-resolved infrared absorption spectroscopy applied to photoinduced reactions: how and why

A Mezzetti, J Schnee, A Lapini, M Di Donato - … & Photobiological Sciences, 2022 - Springer
Time-resolved infrared (IR) spectroscopy is a widely used technique in the investigation of
photoinduced reactions, given its capabilities of providing structural information about the …

Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine

D Moscato, G Mandelli, M Bondanza… - Journal of the …, 2024 - ACS Publications
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying
the solvation process of molecules in water at the nuclear quantum mechanical level with …

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 …

[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 …

Vibrational spectroscopy simulation of solvation effects on a G-quadruplex

D Moscato, F Gabas, R Conte… - Journal of Biomolecular …, 2023 - Taylor & Francis
It is commonly believed that solvation effects on the vibrational properties of a solute are
easily accounted for by simple rules of thumbs, that is, solvating a polar molecule in a polar …

Recent progress in atomistic modeling of light-harvesting complexes: A mini review

S Maity, U Kleinekathöfer - Photosynthesis Research, 2023 - Springer
In this mini review, we focus on recent advances in the atomistic modeling of biological light-
harvesting (LH) complexes. Because of their size and sophisticated electronic structures …

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

J Guan, Y Lu, K Sen, J Abdul Nasir… - … of the Royal …, 2023 - royalsocietypublishing.org
Vibrational spectroscopy is one of the most well-established and important techniques for
characterizing chemical systems. To aid the interpretation of experimental infrared and …

The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics

M Bondanza, T Nottoli, M Nottoli, L Cupellini… - The Journal of …, 2024 - pubs.aip.org
We present a new library designed to provide a simple and straightforward way to
implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular …

[引用][C] Molecular Dynamics Simulations and Vibrational Spectroscopy

A Amadei, M Aschi - 2024 - Elsevier