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

G Salvadori, P Mazzeo, D Accomasso… - Journal of molecular …, 2024 - 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 …

Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method

P Colinet, F Neese… - Journal of Computational …, 2025 - Wiley Online Library
This paper reports the improvement in the efficiency of embedded‐cluster model (ECM)
calculations in ORCA thanks to the implementation of the fast multipole method. Our …

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 …

Protein-Driven Electron-Transfer Process in a Fatty Acid Photodecarboxylase

G Londi, G Salvadori, P Mazzeo, L Cupellini… - JACS Au, 2024 - ACS Publications
Naturally occurring photoenzymes are rare in nature, but among them, fatty acid
photodecarboxylases derived from Chlorella variabilis (Cv FAPs) have emerged as …

Investigating the Origin of Automatic Rhodopsin Modeling Outliers Using the Microbial Gloeobacter Rhodopsin as Testbed

D Barreiro-Lage, V Ledentu, J D'ascenzi… - The Journal of …, 2024 - ACS Publications
The automatic rhodopsin modeling (ARM) approach is a computational workflow devised for
the automatic buildup of hybrid quantum mechanics/molecular mechanics (QM/MM) models …

First‐principles simulations of the fluorescence modulation of a COX‐2‐specific fluorogenic probe upon protein dimerization for cancer discrimination

Á Pérez‐Sánchez, C Curutchet… - Protein …, 2025 - Wiley Online Library
Abstract Cyclooxygenase‐2 (COX‐2) plays a crucial role in inflammation and has been
implicated in cancer development. Understanding the behavior of COX‐2 in different cellular …