Charge transfer potentials parameterization

In contrast, for cases where the protein is more rigid, the standard continuum approach can give excellent results. A striking example is the case of photosystems and redox proteins, where a low reorganization is needed to maintain fast charge-transfer kinetics. For these systems, carefully parameterized continumm models can give an accurate picture of redox potentials and their coupling to acid/base reactions [126-128],... 

The final part is devoted to a survey of molecular properties of special interest to the medicinal chemist. The Theory of Atoms in Molecules by R. F.W. Bader et al., presented in Chapter 7, enables the quantitative use of chemical concepts, for example those of the functional group in organic chemistry or molecular similarity in medicinal chemistry, for prediction and understanding of chemical processes. This contribution also discusses possible applications of the theory to QSAR. Another important property that can be derived by use of QC calculations is the molecular electrostatic potential. J.S. Murray and P. Politzer describe the use of this property for description of noncovalent interactions between ligand and receptor, and the design of new compounds with specific features (Chapter 8). In Chapter 9, H.D. and M. Holtje describe the use of QC methods to parameterize force-field parameters, and applications to a pharmacophore search of enzyme inhibitors. The authors also show the use of QC methods for investigation of charge-transfer complexes. 

Although a valence-type force field of the type illustrated by Eq. [1] is most suitable for modeling molecular systems, the electronegativity equalization approach to treating polarization can be coupled equally well to other types of potentials. Streitz and Mintmire used an EE-based model in conjunction with an embedded atom method (EAM) potential to treat polarization effects in bulk metals and oxides. The resulting ES + EAM model has been parameterized for aluminum and titanium oxides, and has been used to study both charge-transfer effects and reactivity at interfaces. 

Nevertheless, these methods are mostly applied with fixed charges (even if these are chosen in a sophisticated way) and with pairwise additivity approximation as well as with the neglect of nuclear quantum effects. Suggestions for polarizable models appeared in literature mainly for water [23], The quality of potential parameterization varies from system to system and from quantity to quantity, raising the question of transferability. Spontaneous events like reactions cannot appear in simulations unless the event is included in the parameterization. Despite these problems, it is possible to reproduce important quantities as structural, thermodynamic and transport properties with traditional MD (MC) mainly due to the condition of the nanosecond time scale and the large system size in which the simulation takes place [24],... 

Most nonpolarizable water models are actually fragile in this regard they are not transferable to temperatures or densities far from where they were parameterized.190 Because of the emphasis on transferability, polarizable models are typically held to a higher standard and are expected to reproduce monomer and dimer properties for which nonpolarizable liquid-state models are known to fail. Consequently, several of the early attempts at polarizable models were in fact less successful at ambient conditions than the benchmark nonpolarizable models, SPC191 (simple point charge) and TIP4P192 (transferable interaction potential, 4 points). Nonetheless, there is now a large collection of models that reproduce many properties of both the gas phase... 

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