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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 …
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
In this review, we discuss the successes and challenges of the atomistic modeling of
photoreceptors. Throughout our presentation, we integrate explanations of the primary …
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
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 …
challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be …
Grassmann extrapolation of density matrices for Born–Oppenheimer molecular dynamics
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 …
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
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 …
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
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 …
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
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 …
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
Naturally occurring photoenzymes are rare in nature, but among them, fatty acid
photodecarboxylases derived from Chlorella variabilis (Cv FAPs) have emerged as …
photodecarboxylases derived from Chlorella variabilis (Cv FAPs) have emerged as …
Difference in the Charge-Separation Energetics between Distinct Conformers in the PixD Photoreceptor
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 …
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 …
(BLUF) photoreceptor domains are connected to the catalytic domains with long coiled-coil …