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In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties., (© 2022. The Author(s).)

The results of new and recently reported CASSCF/6-31G* photoisomerization path computations of a series of models of the 11-cis retinal chromophore of the visual pigment rhodopsin are discussed. The results indicate that, with respect to the chromophore in vacuo, certain structural, intramolecular and environmental factors are capable of speeding up the excited-state decay associated with the cis --> trans isomerization motion. Using suitable protonated Schiff-base models, it is shown that three structural factors can potentially speed up the isomerization: (i) reducing the length of the conjugated chain, (ii) twisting of the hydrocarbon end of the conjugated chain with respect to the protonated Schiff-base end and (iii) ring locking of the conjugated chain with an eight-membered ring. All these factors operate through increasing the slope of the excited-state energy surface and enhancing the coupling between stretching and torsional modes. We argue that the protein catalysis seen in rhodopsin may, at least partly, exploit the same principles.