Intramolecular interactions water

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

The special interaction terms are necessary to describe intramolecular interactions between different parts of the molecule that cannot be accounted for when considering the transfer of the isolated parts. Obviously, this type of approach has a big advantage in that it allows one to estimate a partition constant based solely on the compound s structure. Good results can be anticipated particularly in those cases where the partition constant of a structurally closely related compound is known, and thus only the contributions of the parts that are different between the two compounds have to be added and/or subtracted, respectively. The most advanced and most widely used method that is based on this concept is the structural group contribution method for estimating octanol-water partition constants. We will discuss this method in Chapter 7. 

Tetraalkylammonium fluoride (R4N 1 F ) is well known as being highly receptive to protic compounds such as hydrogen halides and water, affording non-stoichiometric hydrogen-bonded adducts, R N F (HY) , in non-polar solvents. This property reasonably accounts for the hygroscopic nature of ammonium fluorides. However, under strictly anhydrous conditions, intramolecular interactions are predominant and result in self-destruction of the tetraalkylammonium cation via Hoffman elimination to furnish tetraalkylammonium bifluoride, trialkylamine, and olefin (Scheme 9.12) [22]. Consequently, the resulting tetraalkylammonium bifluoride,... 

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