Linearized approximations for condensed phase non-adiabatic dynamics: Multi-layered baths and Brownian dynamics implementation

Computational elucidations on the role of vibrations in energy transfer processes of photosynthetic complexes

Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes.

Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case

We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.

Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems

In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.

A theoretical-computational procedure, based on Molecular Dynamics simulations, is proposed for modelling the kinetics of non-adiabatic processes in very complex systems.

Single Molecule Spectroscopy of Monomeric LHCII: Experiment and Theory

We derive approximate equations of motion for excited state dynamics of a multilevel open quantum system weakly interacting with light to describe fluorescence-detected single molecule spectra. Based on the Frenkel exciton theory, we construct a model for the chlorophyll part of the LHCII complex of higher plants and its interaction with previously proposed excitation quencher in the form of the lutein molecule Lut 1. The resulting description is valid over a broad range of timescales relevant for single molecule spectroscopy, i.e. from ps to minutes. Validity of these equations is demonstrated by comparing simulations of ensemble and single-molecule spectra of monomeric LHCII with experiments. Using a conformational change of the LHCII protein as a switching mechanism, the intensity and spectral time traces of individual LHCII complexes are simulated, and the experimental statistical distributions are reproduced. Based on our model, it is shown that with reasonable assumptions about its interaction with chlorophylls, Lut 1 can act as an efficient fluorescence quencher in LHCII.