By Lorenz Gubler, Günther G. Scherer (auth.), Günther G. Scherer (eds.)
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In order to accomplish the transition from chemical architectures at microscopic scale to the formation of structural conformations at mesoscopic and macroscopic scales, relevant concepts of polymer physics [54, 55, 66] have to be fused with those of the physics of random heterogeneous media . Upon the transition from primary polymer architectures to secondary structural units at the mesoscopic scale interactions of solvent–solvent, solvent–polymer, polymer–polymer types are renormalized into effective interactions between sidechains and aqueous domains, as indicated in Fig.
The precise proton distribution is, however, not known, as well as the precise structure of the pore space. Mean ﬁeld theory of proton distribution in “sample” pores  suggests a smooth radial distribution with a ﬁnite proton population in the center of the pore, where they would move very much like in bulk water. Simulation results show strong pinning of protons to immobile negative charges on the pore walls if they are considered point-like and static (see also Fig. 7 below). The localization of protons is, however, much weaker for distributed and ﬂuctuating counter charges or models of real sidechains .
Eventually, the motion along the proton coordinate proceeds almost barrierless. The only quantum effect present here is the resonance splitting of the adiabatic potential energy surfaces caused by hy- 30 M. Eikerling et al. dron tunneling in the double well potential spanned by reaction coordinate. These features are seen in the kinetic isotope effect, as discussed in detail in Sects. 4 of . How will this process be modiﬁed when water is conﬁned by the membrane interior? This can be parameterized  or simulated [83, 84, 109] for a given picture of the membrane interior particularly its structural units that comprise the bottleneck for the proton transport.