Molecolab Pisa

Structural and Spectroscopic Basis of Excitation Energy Transfer in Microbial Rhodopsins Binding Xanthophylls Carotenoids are essential for light harvesting in certain microbial rhodopsins, with xanthorhodopsins that bind salinaxanthin being the most well-known example. But how do carotenoids that lack the ty...

Carotenoid antennas 📡 for rhodopsins? Laura's new work reveals the structural origin of Carotenoid to Retinal energy transfer in the proton-pumping rhodopsin Kin4B8.

See the full news molecolab.dcci.unipi.it/eet-rhodopsi...

#openaccess doi.org/10.1039/D5SC...

MolecoLab at the 21st Congress of European Society for Photobiology, ESP-2025 MolecoLab was proudly represented at the 21st Congress of European Society for Photobiology last week in Bari (Italy), with three members contributing to key symposia on cutting-edge re...

Molecolab members at #ESPCongress2025 @photobiologyeurope.bsky.social !

molecolab.dcci.unipi.it/molecolab-es...

Lorenzo @lcupellini.bsky.social Laura and Piermarco

An Efficient and Robust Implementation of CASSCF Linear Response Theory We present a robust and efficient implementation of linear response theory for a Complete Active Space─Self-Consistent Field wave function. Our approach relies on the Cholesky Decomposition of the two-electron integrals, enabling the routine treatment of large molecular systems on standard hardware. It allows for the computation of both absorption energies and transition properties, as well as frequency-dependent molecular response functions. For both classes of properties, numerically stable and efficient algorithms have been developed. The capabilities of our implementation are demonstrated through the calculation of absorption spectra and molecular response properties of large systems with extended basis sets.

New work is out!
We implemented linear response CASSCF in CFour, powered by the open-source Diaglib solver: we are now able to access absorption spectra & frequency-dependent properties on standard hardware.

doi.org/10.1021/acs....

#compchem #molecolab #casscf @tommasonottoli.bsky.social

Multiscale Simulation of Photoinduced Electron Transfer in Cryptochrome 4 from European Robin and Pigeon Indicates a Conserved Dynamics Cryptochrome 4 (Cry4) is a leading candidate for mediating magnetoreception in birds. Upon photoexcitation of its flavin adenine dinucleotide (FAD) cofactor, Cry4 initiates an electron transfer (ET) c...

Our work combines AlphaFold modeling, MD simulations, polarizable QM/MM calculations, and electron transfer modeling, to provide an unprecedented insight into the electron transfer cascade at the basis of birds’ magnetoreception. doi.org/10.1021/acs.jpclett.5c01814

Mariastella's work on the electron transfer in the cryptochrome of birds has been selected as the front cover of today’s issue of
JPC Letters! @pubs.acs.org #MyACSCover doi.org/10.1021/acs.jpclett.5c01814 @lcupellini.bsky.social

Last week I had the opportunity to present my poster at WATOC2025✨

It was a valuable occasion to share my work and engage with researchers in the field.

Many thanks to the organizers and participants for the stimulating event.

#WATOC2025 #computationalchemistry #machinelearning

Patrizia is back—and she brought cake! That's how you make a comeback. Thanks, @pamazzeo.bsky.social !

Electrostatic embedding machine learning for ground and excited state molecular dynamics of solvated molecules The application of quantum mechanics (QM)/molecular mechanics (MM) models for studying dynamics in complex systems is nowadays well established. However, their significant limitation is the high compu...

Want to know more? Have a look at Patrizia's paper in Digital Discovery doi.org/10.1039/D4DD...

Patrizia's talk at the 2025 SIMPLAIX @simplaix.bsky.social workshop explaining ML/MM methods for solvent-dependent excited-state dymamics
#machinelearning #ML #compchem

A Computational Approach to Modeling Excitation Energy Transfer and Quenching in Light-Harvesting Complexes Light-harvesting complexes (LHCs) play a critical role in modulating energy flux within photosynthetic organisms in response to fluctuating light. Under high light conditions, they activate quenching ...

Take a look at our new computational protocol presented in #JPCB to model excited-state lifetimes of Light-harvesting complexes!

doi.org/10.1021/acs....

Congrats to Chris for her first paper at Molecolab!

#compchem #theoreticalchemistry #photochemistry

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 (CvFAPs) have emerged as promising photobiocatalysts capable of performing the redox-neutral, light-induced decarboxylation of free fatty acids (FAs) into C1-shortened n-alka(e)nes. Using a hybrid QM/MM approach combined with a polarizable embedding scheme, we identify the structural changes of the active site and determine the energetic landscape of the forward electron transfer (fET) from the FA substrate to the excited flavin adenine dinucleotide. We obtain a charge-transfer diradical structure where a water molecule rearranges spontaneously to form a H-bond interaction with the excited flavin, while the FA’s carboxylate group twists and migrates away from it. Together, these structural modifications provide the driving force necessary for the fET to proceed in a downhill direction. Moreover, by examining the R451K mutant where the FA substrate is farther from the flavin core, we show that the marked reduction of the electronic coupling is counterbalanced by an increased driving force, resulting in a fET lifetime similar to the WT, thereby suggesting a resilience of the process to this mutation. Finally, through QM/MM molecular dynamic simulations, we reveal that, following fET, the decarboxylation of the FA radical occurs within tens of picoseconds, overcoming an energy barrier of ∼0.1 eV. Overall, by providing an atomistic characterization of the photoactivation of CvFAP, this work can be used for future protein engineering.

Our computational study on a fatty acid photodecarboxylase is out in JACS Au #openaccess.

Check out what drives the electron transfer and decarboxylation in this exciting #photoenzyme!

pubs.acs.org/doi/10.1021/...

#QMMM #compchem #photobiocatalysis

Congrats to Giacomo and all authors!