Publications de Leonardo Guidoni

Pivotal role of the redox-active tyrosine in driving the water splitting catalyzed by photosystem II

Photosynthetic water oxidation is catalyzed by the Mn4Ca cluster in photosystem II (PSII). The nearby redox-active tyrosine (Y-Z) serves as a direct electron acceptor of the Mn4Ca cluster and it forms a low-barrier H-bond (LBHB) with a neighboring histidin ...

ROYAL SOC CHEMISTRY2020

On the comparison between differential vibrational spectroscopy spectra and theoretical data in the carboxyl region of photosystem II

Leonardo Guidoni, Daniele Narzi

Understanding the structural modification experienced by the Mn4CaO5 oxygen-evolving complex of photosystem II along the Kok-Joliot's cycle has been a challenge for both theory and experiments since many decades. In particular, differential infrared spectr ...

WILEY2019

Evolution from S-3 to S-4 States of the Oxygen-Evolving Complex in PhotosystemII Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics

Leonardo Guidoni, Daniele Narzi

2018

Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II

Leonardo Guidoni, Marco Manzoli, Daniele Narzi

Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunli ...

Elsevier Science Bv2017

A Spotlight on the Compatibility between XFEL and Ab Initio Structures of the Oxygen Evolving Complex in Photosystem II

Leonardo Guidoni, Daniele Narzi

The Mn4CaO5 cluster of photosystem II promotes a crucial step in the oxygenic photosynthesis, namely, the water-splitting reaction. The structure of such cluster in the S-1 state of the Kok-Joliot's cycle has been recently resolved by femtosecond X-ray fre ...

Wiley-V C H Verlag Gmbh2017

Vibrational fingerprints of the Mn4CaO5 cluster in Photosystem II by mixed quantum-classical molecular dynamics

Leonardo Guidoni, Daniele Narzi

A detailed knowledge of the structures of the catalytic steps along the Kok-Joliot cycle of Photosystem II may help to understand the strategies adopted by this unique enzyme to achieve water oxidation. Vibrational spectroscopy has probed in the last decad ...

Elsevier Science Bv2016

Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics

Denis Bucher, Ursula Röthlisberger, Leonardo Guidoni, Paolo Carloni

Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K+ and Na+ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K+ ions were found to displa ...

Elsevier2010

Developing Improved Charge Sets for the Modeling of the KcsA K+ Channel Using QM/MM Electrostatic Potentials

Denis Bucher, Ursula Röthlisberger, Leonardo Guidoni

The performance of popular molecular mechanics (MM) force fields in treating problems that involve ion-channel interactions is explored. We have used quantum mechanical/molecular mechanical (QM/MM) calculations to compute the electrostatic potential inside ...

2009

Hybrid QM/MM molecular dynamics study of copper binding sites in the C-terminal domain of mouse prion protein

Ursula Röthlisberger, Leonardo Guidoni, Maria Carola Colombo

2008

The protonation state of of the Glu-71/Asp-80 residues in the KcsA Potassium channel: A first-principles QM/MM molecular dynamics study

Denis Bucher, Ursula Röthlisberger, Leonardo Guidoni

2007

Protonation of the chromophore in the photoactive yellow protein

Ursula Röthlisberger, Leonardo Guidoni

2007

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore

Ursula Röthlisberger, Leonardo Guidoni

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol soln., and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid qu ...

2005

Scanning Reactive Pathways with Orbital Biased Molecular Dynamics

Ursula Röthlisberger, Leonardo Guidoni

To accelerate reactive events in mol. dynamics simulations we introduce a general bias potential scheme which depends only on the electronic degrees of freedom of the reactive system. This electronic reaction coordinate, which is expressed in terms of a pe ...

2005

Quantum mechanical/molecular mechanical (QM/MM) Car-Parrinello simulations in excited states

Marc-Etienne Moret, Ursula Röthlisberger, Leonardo Guidoni, Ivano Tavernelli, Enrico Marko Tapavicza

The combination of time-dependent d. functional theory (TDDFT) for the description of excited states with a hybrid quantum mechanics/mol. mechanics (QM/MM) approach enables the study of photochem. processes in complex environments. Here, we present a short ...

2005

Experimental and theoretical study of intramolecular exchange in Ir2Rh2(CO)(12) and Ir-4(CO)(11)(mu-SO2)

Gabor Laurenczy, Raymond Roulet, Zoltan Beni, Ursula Röthlisberger, Leonardo Guidoni

As observed by variable-temperature and -pressure C-13 NMR, intramolecular carbonyl scrambling in Ir2Rh2(CO)(12) and Ir-4(CO)(11)(mu-SO2) proceeds via a 'change of basal face' mechanism. In both cases the site exchange process has a positive activation vol ...

2005