Modeling pH-dependent biomolecular photochemistry

16 November 2023, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics, using a combination of constant-pH molecular dynamics and semi-classical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena Sensory Rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties such as the isomerization quantum yield or decay rates. We decompose our results in single titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.


Non-adiabatic molecular dynamics
quantum yield

Supplementary materials

Supplementary information
Computational details, analysis of each ensemble of trajectories, BLA and dihedral torsions in the 13C sets, fitting S1 decay time evolution, and residue-based analysis.


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