Sidechains, ionizable

Molecular modeling of PT at dense arrays of protogenic surface groups (SGs) demands ab initio quantum mechanical calculations. The starting point for the development of a viable model of surface proton conduction in PEM is the self-organized PEM morphology at the mesoscopic scale. Eigure 2.30a illustrates the random array of hydrated and ionized sidechains that are anchored to the surface of ionomer bundles. 

The 20 natural amino acids differ from each other by the nature of their sidechains. Differences involve overall size, hydrophobic or hydrophilic character and, perhaps most importantly, ionization state. While the sidechains are normally written in terms of neutral structures, some may also exist in either protonated or deprotonated forms depending on pH. 

The presence of mycosamine or perosamine confers a basic character on the polyene molecule. Many of the polyene antibiotics, e.g. nystatin, amphotericin B and candicidin are amphoteric, possessing an equal number of basic (hexo-samine or aromatic sidechain) and acidic (carboxyl) groups. Other polyenes, e.g. filipin and fungichromin, possess no ionizable groups at all, i.e. they are nonpolar. 

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