Molecular dynamics transferability issues

The main shortcoming of the molecular dynamics approach discussed in the previous section is that it ignores the fact that an electron transfer at the solution/metal interface occurs between an ion in a well-defined electronic state and a continuum of electronic states in the metal. For example, depending on the ion s orbital energy, the reorganization free energy and the overpotential, the electron could be transferred from, or to, any level around the Fermi level of the metal. Therefore, a sum over all these possibilities must be performed. Analytical theories of electron transfer at the solution/metal interface recognized this issue very early on, and the reader is referred to many excellent expositions on this sub-... 

Studies[71-73] of the free energy curves for electron transfer at liquid/liquid interfaces have been concerned with several issues. First, to what degree is the linear response assumption which leads to parabolic free energy curves accurate Second, what qualitatively new features does the interface region introduce into the solvent free energy curves Finaly, how do continuum electrostatic models for the free energy curves compare with the molecular dynamics results Here we consider the first two points. For a recent study of continuum models see reference [73]. 

These mechanistic issues have been studied via several different theoretical approaches. Cummins et al. assessed the energetically most likely substrate and enzyme protonation sites and pathways by performing QM/MM calculations [llj. In addition to explaining control of the likely protonation site by a structurally conserved water molecule that hydrogen bonds to both the carboxyl of Asp-27 and the 04 of the pterin, their results support a mechanism in which Asp-27 is protonated first, followed by direct protonation of the keto form of the pterin at the N 5 position for H2F reduction. Analysis of the hydrogen-bonding distances between water molecules and the N5 position in classical molecular dynamics simulations has been used to postulate a mechanism in which the hydride transfer occurs before... 

In Section I we briefly discuss the relationship between the theoretical parameters and experimental observables in these experiments in terms of the spectroscopy of electrons in liquids. Experimental techniques are considered in more detail in Section II, while the data from electron solvation in pure liquids are reviewed in Section III in the context of the molecular dynamics of the host liquid. Section IV presents current results on electron trapping in very dilute polar systems and leads to speculation on mechanisms of electron localization. In Section V the first direct observations of a photoselective, laser-induced electron-transfer process are presented, following which we summarize as yet unresolved issues and speculate on future directions in the laser spectroscopy of electron-relaxation processes. 

The energetic stabilization of a proton in a membrane provided by a proton wire raises a question about the likelihood of the spontaneous formation of such wires. This issue was addressed in separate calculations in which the free energy of a chain of water molecules spanning the bilayer was estimated at approximately 25 kcal/mol [14]. In unconstrained molecular dynamics simulations it was further found that transmembrane water chains are very transient, with lifetimes of only a few picoseconds. These lifetimes are much shorter that the time required for the water reorientation in the chain needed to transfer another pro-... 

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