Ultrafast processes in light-absorbing proteins have been implicated in the primary step in the light-to-energy conversion and the initialization of photoresponsive biological functions. Theory and computations have played an instrumental role in understanding the molecular mechanism of such processes, as they provide a molecular-level insight of structural and electronic changes at ultrafast time scales that often are very difficult or impossible to obtain from experiments alone. Among theoretical strategies, the application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important approach that has reached an evident degree of maturity, resulting in several important contributions to the field. This review presents an overview of state-of-the-art computational studies on subnanosecond events in rhodopsins, photoactive yellow proteins, phytochromes, and some other photoresponsive proteins where photoinduced double-bond isomerization occurs. The review also discusses current limitations that need to be solved in future developments.

When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model with which the effect of the light-matter coupling on the molecular dynamics can be predicted accurately. Here we present a multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons. Using this model we have performed simulations with up to 1600 Rhodamine molecules in a cavity. The results of these simulations reveal that the contributions of the molecules to the polariton are time-dependent due to thermal fluctuations that break symmetry. Furthermore, the simulations suggest that in addition to the cavity quality factor, also the Stokes shift and number of molecules control the lifetime of the polariton. Because large numbers of molecules interacting with confined light can now be simulated in atomic detail, we anticipate that our method will lead to a better understanding of the effects of strong coupling on chemical reactivity. Ultimately the method may even be used to systematically design cavities to control photochemistry.

We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.

The photochemistry of 2-naphthoyl azide was studied in various solvents by femtosecond time-resolved transient absorption spectroscopy with IR and UV-vis detection. The experimental findings were interpreted with the aid of computational studies. Using polar and nonpolar solvents, the formation and decay of the first singlet excited state (S(1)) was observed by both time-resolved techniques. Three processes are involved in the decay of the S(1) excited state of 2-naphthoyl azide: intersystem crossing, singlet nitrene formation, and isocyanate formation. The lifetime of the S(1) state decreases significantly as the solvent polarity increases. In all solvents studied, isocyanate formation correlates with the decay of the azide S(1) state. Nitrene formation correlates with the decay of the relaxed S(1) state only upon 350 nm excitation (S(0) → S(1) excitation). When S(n) (n ≥ 2) states are populated upon excitation (λ(ex) = 270 nm), most nitrene formation takes place within a few picoseconds through the hot S(1) and higher singlet excited states (S(n)) of 2-naphthoyl azide. The data correlate with the results of electron density difference calculations that predict nitrene formation from the higher-energy singlet excited states, in addition to the S(1) state. For all of these experiments, no recovery of the ground state was observed up to 3 ns after photolysis, which indicates that both internal conversion and fluorescence have very low efficiencies.

The photochemistry of three carbonyl azides was studied by ultrafast time-resolved IR spectroscopy. Benzoyl, 2-naphthoyl, and pivavoyl azides are promoted to upper excited states S(n) with 270 nm excitation in chloroform. The S(n) states decay in 300 fs to form both the carbonylnitrenes and the S(1) excited states. The decay of the S(1) states of the carbonyl azides correlates with the growth of isocyanates. Formation of carbonylnitrene from S(1) is at most a minor process if it happens at all. The quantum yields of azide decomposition of these azides with 270 nm light are close to unity in chloroform.