The experimental observation of long-lived quantum coherences in the Fenna-Matthews-Olson (FMO) light-harvesting complex at low temperatures has challenged general intuition in the field of complex molecular systems and provoked considerable theoretical effort in search for explanations. Here we report on room-temperature calculations of the excited-state dynamics in FMO using a combination of molecular dynamics simulations and electronic structure calculations. Thus we obtain trajectories for the Hamiltonian of this system which contains time-dependent vertical excitation energies of the individual bacteriochlorophyll molecules and their mutual electronic couplings. The distribution of energies and couplings are analyzed together with possible spatial correlations. It is found that in contrast to frequent assumptions the site energy distribution is non-Gaussian. In a subsequent step, averaged wave packet dynamics is used to determine the exciton dynamics in the system. Finally, with the time-dependent Hamiltonian linear and two-dimensional spectra are determined. The thus obtained linear absorption lineshape agrees well with experimental observation and is largely determined by the non-Gaussian site energy distribution. The two-dimensional spectra are in line with what one would expect by extrapolation of the experimental observations at lower temperatures and indicate almost total loss of long-lived coherences.

In many physical, chemical, and biological systems energy and charge transfer processes are of utmost importance. To determine the influence of the environment on these transport processes, equilibrium molecular dynamics simulations become more and more popular. From these simulations, one usually determines the thermal fluctuations of certain energy gaps, which are then either used to perform ensemble-averaged wave packet simulations, also called Ehrenfest dynamics, or to employ a density matrix approach via spectral densities. These two approaches are analyzed through energy gap fluctuations that are generated to correspond to a predetermined spectral density. Subsequently, density matrix and wave packet simulations are compared through population dynamics and absorption spectra for different parameter regimes. Furthermore, a previously proposed approach to enforce the correct long-time behavior in the wave packet simulations is probed and an improvement is proposed.

The photosynthetic light-harvesting system II (LH2) of Rhodospirillum molischianum is investigated using a timedependent combination of molecular dynamics simulations and semiempirical ZINDO/S electronic structure calculations. The classical simulations are performed on the available crystal structure of the LH2 complex. Snapshots of the atomic fluctuations along this 12 ps long trajectory serve as input for the calculation of the excitation energies of the individual bacteriochlorophylls embedded in the LH2 complex. Furthermore, the couplings between the bacteriochlorophylls are computed using the method of transition charges from electrostatic potentials and for comparison also using the point-dipole approximation. With these quantities the excitonic energies of the complete system as well as the linear absorption spectra are calculated and compared to experimental findings.

By using a combination of an initial pump pulse and a degenerate four-wave mixing (DFWM) process, we show that an interrogation of the vibrational dynamics occurring in high-lying electronic states of molecules is possible. As a test case, the technique is applied to iodine in experiment and in simulation. The initial pump pulse is used to populate the B ( 3 + u ) state of molecular iodine in the gas phase. By using an internal time delay in the subsequent DFWM process, which is resonant with the transition between the B state and a higher lying ion-pair state, the vibrational dynamics of the B state as well as of the ion-pair state could be observed. From the possible ion-pair states, the states of even symmetry are investigated, which are accessible by a one-photon transition from the B state. By a proper choice of the wavelengths used for the pump and DFWM beams, the dynamics of ion-pair states belonging to two different tiers are monitored. Very good agreement between experimental and theoretical results is observed in most of the studied wavelength combinations.

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