A simple theoretical model of exciton dynamics was proposed to interpret the fast excitation energy-transfer process in the type I homodimeric reaction center of Heliobacterium modesticaldum (hRC); this structure was recently identified and shown to resemble that of the plant/cyanobacterial photosystem I (PSI) reaction center. The exciton state model, which mainly relies on the geometries of 54 bacteriochlorophyll (BChl) g, 4 BChl-g′, and 2 chlorophyll (Chl) a on hRC and assumes constant site energy values for the pigments, reproduced the absorption spectrum of hRC rather well. The model also enabled numerical analysis of the exciton dynamics on hRC, which can be compared with the decay-associated spectra obtained by the laser spectroscopy experiments. The model indicates that the stronger transition–dipole moment on BChl-g contributes to the faster energy transfer due to the higher coherency of the delocalized exciton states on hRC compared to that on PSI that arranges Chl-a at almost homologous locations.

The hydration structure around nanometer-size hydrophobic solutes is studied with molecular dynamics simulation by taking aqueous solutions of C60 and C60H60 as examples. In the hydration shell around a single C60 or C60H60, dipoles of simulated water molecules tend to be aligned to form the vortexlike coherent pattern which lasts for 100 ps, while individual water molecules stay within the hydration shell for about 10 ps. This structural pattern organized by fluctuating and diffusively moving molecules should be called a "fluctuating cage". In the narrow region between a pair of C60 molecules or a pair of C60H60 molecules, water density strongly fluctuates and is correlated to the mean force between solutes. The fluctuating caging and drying between solutes affect the hydrophobic interaction and dynamical behaviors of solutes.

Developing the quantum transition rate theory of Prezhdo and Rossky (J. Chem. Phys. 1997, 107, 5863), we produced a new non-Condon theory of the rate of electron transfer (ET) which happens through a protein medium with conformational fluctuation. The new theory is expressed by a convolution form of the power spectrum for the autocorrelation function of the electronic tunneling matrix element T(DA)(t) with quantum correction and the ordinary Franck-Condon factor. The new theory satisfies the detailed balance condition for the forward and backward ET rates. The ET rate formula is divided into two terms of elastic and inelastic tunneling mechanisms on the mathematical basis. The present theory is applied to the ET from Bph(-) to Q(A) in the reaction center of Rhodobacter sphaeroides. Numerical calculations of T(DA)(t) were made by a combined method of molecular dynamics simulations and quantum chemistry calculations. We showed that the normalized autocorrelation function of T(DA)(t) is almost expressed by exponential forms. The calculated energy gap law of the ET rate is nearly Marcus' parabola in most of the normal region and around the maximum region, but it does not decay substantially in the inverted region, which is called the anomalous inverted region. We also showed that the energy gap law at the high uphill energy gap in the normal region is elevated considerably from the Marcus' parabola, which is called the anomalous normal region. Those anomalous energy gap laws are due to the inelastic tunneling mechanism which works actively at the energy gap far from zero. We presented an empirical formula for easily calculating the non-Condon ET rate, which is usable by many researchers. We provided experimental evidence for the anomalous inverted region which was basically reproduced by the present theory. The present theory was extensively compared with the previous non-Condon theories.

Theory of excitation transfer in the intermediate coupling case is proposed. This theory is appropriate to such molecular systems where the interaction between donor and acceptor is considerably strong so that the excitation transfer takes place before the thermal equilibrium is attained in the excited intermediate state of the donor but is not so strong as the exciton mechanism holds true. The expected remarkable properties of the intermediate coupling excitation transfer are that there exists a concurrent process of the superexchange mechanism and the sequential mechanism in the same way as the electron transfer reaction. We have proposed a new method of evaluating the degree of sequentiality which bases on much physical background, namely counting the fraction of density flow passing through the intermediate state.

Electron tunneling routes for the electron transfer from the bacteriopheophytin anion to the primary quinone in the bacterial photosynthetic reaction center of Rhodobactor sphaeroides are investigated by a combined method of molecular dynamics simulations for the protein conformation fluctuation and quantum chemical calculations for the electronic states of the donor, acceptor, and protein medium. The analysis of the tunneling route is made by mapping interatomic electron tunneling currents for each protein conformation. We found that there are two dominant routes mainly passing through Trp(M252) (Trp route) or mainly passing through Met(M218) (Met route). Actual electron tunneling pathways alternate between the two routes, depending on the protein conformation which varies with time. When either the Trp route or the Met route dominates, the electron tunneling matrix element /T(DA)/ becomes large. When both the Trp route and the Met route dominate, /T(DA)/ becomes very small due to the destructive interference of the electron tunneling currents between the two routes. We found that a linear relationship exists between the value of /T(DA)/ and the inverse of the degree of destructive interference Q for a wide range of values (ca. 3-10(3) for Q). A similar relationship was also found previously for electron transfer in ruthenium-modified azurins, suggesting that this relationship holds true in general. From these results, we are led to the conclusion that /T(DA)/ cannot exceed a maximum value at Q = 1, even if much variation of /T(DA)/ happens due to the fluctuation of protein conformation. We also conclude that the property of the electron transfer alternates between constructive and destructive interference, due to the fluctuation of protein conformation. It is impossible to keep a system in either constructive or destructive interference because thermal fluctuation of protein conformation takes place.