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We describe the development, implementation, and application of a polarizable QM/MM strategy, based on the AMOEBA polarizable force field, for calculating molecular properties and performing dynamics of molecular systems embedded in complex matrices. We show that polarizable QM/MM is a well‐understood, mature technology that can be deployed using a state‐of‐the‐art implementation that combines efficient numerical methods and linear scaling techniques. Thanks to these numerical advances and to the availability of parameters for a wide manifold of systems in the AMOEBA force field, polarizable QM/AMOEBA can be used for advanced production applications, that range from the prediction of spectroscopies to ground‐ and excited‐state multiscale ab initio molecular dynamics simulations. This article is categorized under:Electronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Combined QM/MM Methods [ABSTRACT FROM AUTHOR]

Hybrid TDDFT/MM approaches are very popular methods for describing electronic transitions of molecules in solution or embedded in more complex (bio)matrices. However, when combined with a polarisable force field some problems can appear depending on the type of environment response scheme that is used. In particular, specific a posteriori corrections are generally needed to accurately describe charge-transfer states implying a large reorganisation of the electron density in the excited state. Here, we present a possible strategy to solve this issue by introducing a ΔSCF formulation. As the ΔSCF strategy has the advantage of being intrinsically state specific, its coupling to a polarisable model is expected to be particularly suited to describe all cases where the standard, linear response, formulation of a polarisable TDDFT/MM approach is not sufficient. [ABSTRACT FROM AUTHOR]

Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes. [ABSTRACT FROM AUTHOR]

We present a polarisable QM/MM investigation of NMR chemical shifts of a photoreceptor protein belonging to the Blue Light-Using Flavin family. Two different structures have been proposed for this photoreceptor which show a large variability in terms of the position and orientation of the protein residues around the flavin chromophore. Here, the two structures have been investigated with our multiscale approach using both DFT and MP2 level of theory. The picture that comes out comparing the 1 H chemical shifts of the flavin and the most strongly interacting protein residues with the available experimental data, indicates a different behaviour of the two structures, with one showing a better correlation with NMR measurements. This shows that hybrid quantum chemical-classical simulations of NMR chemical shifts can indeed become a valuable tool to investigate the structure of complex biosystems. [ABSTRACT FROM AUTHOR]

Quantitative models of light harvesting in photosynthetic antenna complexes depend sensitively on the challenging determination of the relative site energies of the pigments. Herein we analyze the basis of the light harvesting properties of four antennae from cryptophyte algae, phycocyanines PC577, PC612, PC630 and PC645, by comparing two alternative theoretical strategies to derive the excitonic Hamiltonian. The first is based on molecular dynamics simulations and subsequent polarizable quantum/molecular mechanics (QM/MMPol) calculations, whereas the second is based on three‐layer QM/MMPol/ddCOSMO calculations performed on optimized geometries of the pigments, where the water solvent is described using the ddCOSMO continuum model. We find the latter approach to be remarkably accurate, suggesting that these four phycobiliproteins share a common energetic ordering PCB82 < PCB158 < DBV51/61 for pigments located in the highly‐conserved β chains, whereas bilins in the more divergent α chains cause their spectral differences. In addition, we predict a strong screening of the coupling among central dihydrobiliverdins (DBVs) in "open" form complexes PC577 and PC612 compared to "closed" form ones, which together with the increased interpigment separation explains the attenuation of coherence beatings observed for these complexes. [ABSTRACT FROM AUTHOR]

[Display omitted] • Integrated molecular dynamics and QM/MM strategy to characterize the dark state. • Investigation of the photochemical process via (non)adiabatic dynamics simulations. • MD and enhanced sampling to simulate the evolution towards the active state. • Illustrative examples of application to specific photoreceptors. In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein. [ABSTRACT FROM AUTHOR]