Molecular dynamics biological transfer models

The problem of linking atomic scale descriptions to continuum descriptions is also a nontrivial one. We will emphasize here that the problem cannot be solved by heroic extensions of the size of molecular dynamics simulations to millions of particles and that this is actually unnecessary. Here we will describe the use of atomic scale calculations for fixing boundary conditions for continuum descriptions in the context of the modeling of static structure (capacitance) and outer shell electron transfer. Though we believe that more can be done with these approaches, several kinds of electrochemical problems—for example, those associated with corrosion phenomena and both inorganic and biological polymers—will require approaches that take into account further intermediate mesoscopic scales. There is less progress to report here, and our discussion will be brief. 

The key new aspect of our investigation is two-fold first, we base all model parameters on molecular dynamics simulations second, the spin-boson model allows one to account for a very large number of vibrations quantum mechanically. We have demonstrated that the spin-boson model is well suited to describe the coupling between protein motion and electron transfer in biological redox systems. The model, through the spectral function can be matched to correlation functions of the redox energy... 

The several theoretical and/or simulation methods developed for modelling the solvation phenomena can be applied to the treatment of solvent effects on chemical reactivity. A variety of systems - ranging from small molecules to very large ones, such as biomolecules [236-238], biological membranes [239] and polymers [240] -and problems - mechanism of organic reactions [25, 79, 223, 241-247], chemical reactions in supercritical fluids [216, 248-250], ultrafast spectroscopy [251-255], electrochemical processes [256, 257], proton transfer [74, 75, 231], electron transfer [76, 77, 104, 258-261], charge transfer reactions and complexes [262-264], molecular and ionic spectra and excited states [24, 265-268], solvent-induced polarizability [221, 269], reaction dynamics [28, 78, 270-276], isomerization [110, 277-279], tautomeric equilibrium [280-282], conformational changes [283], dissociation reactions [199, 200, 227], stability [284] - have been treated by these techniques. Some of these... 

To understand the fundamental photochemical processes in biologically relevant molecular systems, prototype molecules like phenol or indole - the chromophores of the amino acids tyrosine respective trypthophan - embedded in clusters of ammonia or water molecules are an important object of research. Numerous studies have been performed concerning the dynamics of photoinduced processes in phenol-ammonia or phenol-water clusters (see e. g. [1,2]). As a main result a hydrogen transfer reaction has been clearly indicated in phenol(NH3)n clusters [2], whereas for phenol(H20)n complexes no signature for such a reaction has been found. According to a general theoretical model [3] a similar behavior is expected for the indole molecule surrounded by ammonia or water clusters. As the primary step an internal conversion from the initially excited nn state to a dark 7ta state is predicted which may be followed by the H-transfer process on the 7ia potential energy surface. 

The next two chapters are devoted to ultrafast radiationless transitions. In Chapter 5, the generalized linear response theory is used to treat the non-equilibrium dynamics of molecular systems. This method, based on the density matrix method, can also be used to calculate the transient spectroscopic signals that are often monitored experimentally. As an application of the method, the authors present the study of the interfadal photo-induced electron transfer in dye-sensitized solar cell as observed by transient absorption spectroscopy. Chapter 6 uses the density matrix method to discuss important processes that occur in the bacterial photosynthetic reaction center, which has congested electronic structure within 200-1500cm 1 and weak interactions between these electronic states. Therefore, this biological system is an ideal system to examine theoretical models (memory effect, coherence effect, vibrational relaxation, etc.) and techniques (generalized linear response theory, Forster-Dexter theory, Marcus theory, internal conversion theory, etc.) for treating ultrafast radiationless transition phenomena. 

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