[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 …

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

AV Solov'yov, AV Verkhovtsev, NJ Mason… - Chemical …, 2024 - ACS Publications
This roadmap reviews the new, highly interdisciplinary research field studying the behavior
of condensed matter systems exposed to radiation. The Review highlights several recent …

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 …

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 …

Taming the third order cumulant approximation to linear optical spectroscopy

L Allan, TJ Zuehlsdorff - The Journal of Chemical Physics, 2024 - pubs.aip.org
The second order cumulant method offers a promising pathway to predicting optical
properties in condensed phase systems. It allows for the computation of linear absorption …

Importance of Polarizable Embedding for Computing Optical Rotation: The Case of Camphor in Ethanol

M Nottoli, E Vanich, L Cupellini… - The Journal of …, 2024 - ACS Publications
Solvation effects on optical rotation are notoriously challenging to model for computational
chemistry, as the specific rotatory power of a molecule can vary wildly going from apolar to …

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 …

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP

J Nochebuena, AC Simmonett… - The Journal of Chemical …, 2024 - pubs.aip.org
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an
essential tool in computational chemistry, particularly for analyzing complex biological and …

Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies

S Gómez, P Lafiosca, T Giovannini - Molecules, 2024 - mdpi.com
We present a comprehensive computational study of UV/Vis absorption spectra of significant
food colorants, specifically anthocyanins and curcumin tautomers, dissolved in polar protic …