stability of the π-π stacking interactions in the ben||substituted-coronene and hfben||substituted-coronene complexes was studied using the computational quantum chemistry methods (where ben and hfben are benzene and hexaflourobenzene, || denotes π-π stacking interaction, substituted-coronene is coronene molecule which substituted with four x groups, and x= nh2, ch3, oh, h, f, cf3, cn and no). ...

A brief overview of proton and electron transfer history is given, and various features influencing enzymatic catalysis are discussed. Examples of generic behavior are considered, together with questions that can be addressed for both experimental and computational results. Examples of high and low pre-exponential factors A of the intrinsic rate constant kH ranging from B10 17 s 1 to B10 s 1 an...

Introduction: Microdosimetry is a fundamental method that studies the nature of energy transfer in micron volumes in the particular biological cells. In a biological target, the amount of ionization does not indicate the magnitude of biological radiation-induced damage. However, the severity of biological harm depends strongly on the amount of the linear energy transfer along t...

The electron transfer between the two quinones Q(A) and Q(B) in the bacterial photosynthetic reaction center (bRC) is coupled to a conformational rearrangement. Recently, the X-ray structures of the dark-adapted and light-exposed bRC from Rhodobacter sphaeroides were solved, and the conformational changes were characterized structurally. We computed the reaction free energy for the electron tra...

Molecular oxygen acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the reduction of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochemical gradi...

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of th...

We propose a network-based method for determining basins and barriers of complex free energy surfaces (e.g., the protein folding landscape) from the time series of a single intramolecular distance. First, a network of transitions is constructed by clustering the points of the time series according to the short-time distribution of the signal. The transition network, which reflects the short-tim...

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model...

The structures of the configuration space of the six-vertex models with various boundaries and boundary conditions are investigated, and it is derived that the free energies depend on the boundary conditions, and that they are classified by the fractal structures. The ”n-equivalences” of the boundary conditions are defined with a property that the models with nequivalent boundary conditions res...