Excitation energies of the bacteriochlorophyll (BChl) chromophores embedded in the photosynthetic light-harvesting complex of the purple bacterium Thermochromatium tepidum are computed using the time-dependent density functional theory based upon the fragmental molecular orbital (FMO-TDDFT) method. The results are correlated with the empirically based estimates of the Q(y) absorption maximum, as well as with the observed large red shift induced by the binding of calcium.

Ab initio approaches of quantum chemistry, including the fragment molecular orbital (FMO) method, as well as the multiconfigurational quasidegenerate perturbation theory (XMCQDPT2) and time-dependent density functional theory (TD DFT) were applied to compute optical spectra of a polyene dye molecule on the surface of titanium dioxide.

Based on molecular dynamics simulations of nanocars with fullerene wheels on the surface of an Au (110) gold crystal, estimates of diffusion coefficients are reported.

We describe a new implementation of the molecular dynamics method aimed at simulation of the properties of biomolecular systems in which chemical reactions are possible. The quantum mechanical/molecular mechanical method based on the effective fragment potential theory is used for calculating the energies and forces along trajectories. Due to specific features of the effective fragment theory, the behavior of the molecular mechanical subsystem is described by rigid body dynamics. The method has been applied to simulation of proton transfer along the chain of water molecules inside the gramicidin channel.