Exploring proton-coupled electron transfer at multiple scales

S Hammes-Schiffer - Nature computational science, 2023 - nature.com
The coupling of electron and proton transfer is critical for chemical and biological processes
spanning a wide range of length and time scales and often occurring in complex …

[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 …

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 …

Grassmann extrapolation of density matrices for Born–Oppenheimer molecular dynamics

É 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 …

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 …

Nanocellulose composites as smart devices with chassis, light-directed DNA storage, engineered electronic properties, and chip integration

E Bencurova, S Shityakov, D Schaack… - … in Bioengineering and …, 2022 - frontiersin.org
The rapid development of green and sustainable materials opens up new possibilities in the
field of applied research. Such materials include nanocellulose composites that can …

Integrated computational study of the light-activated structure of the appa bluf domain and its spectral signatures

S Hashem, GB Alteri, L Cupellini… - The Journal of Physical …, 2023 - ACS Publications
We apply an integrated approach combining microsecond MD simulations and (polarizable)
QM/MM calculations of NMR, FTIR, and UV–vis spectra to validate the structure of the light …

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 …

Difference in the Charge-Separation Energetics between Distinct Conformers in the PixD Photoreceptor

T Noji, H Tamura, H Ishikita, K Saito - The Journal of Physical …, 2023 - ACS Publications
Blue light using flavin (BLUF) domain proteins are photoreceptors in various organisms. The
PixD BLUF domain can adopt two conformations, W91out and W91in, with Trp91 either …

Unveiling the Photoactivation Mechanism of BLUF Photoreceptor Protein through Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Calculation

M Taguchi, S Sakuraba, J Chan… - ACS Physical Chemistry …, 2024 - ACS Publications
OaPAC is a photoactivated enzyme that forms a homodimer. The two blue-light using flavin
(BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil …