Water Structure and Protonation State

Figure 7-2. Properties of CAII active site in the COHH state (zinc-bound hydroxide and protonated His 64). (a) Superposition of a few key residues from two stochastic boundary SCC-DFTB/MM simulations with the X-ray structure [87] (colored based on atom-types) the two sets of simulations did not have any cut-off for the electrostatic interactions between SCC-DFTB and MM atoms but used different treatments for the electrostatic interactions among MM atoms group-based extended electrostatics (in yellow) and atom-based force-shift cut-off (in green). Extended electrostatics simulations sampled configurations with the protonated His 64 too close to the zinc moiety while force-shift simulations consistently sampled the out configuration of His 64 in multiple trajectories, (b) Statistics for productive water-bridges (only from two and four shown here) between the zinc bound water and His 64 with different electrostatics protocols...

First, micelles have very loose, mobile, structures and there are considerable entropy costs in a concerted reaction. These costs are much less serious in enzymic systems where conformation at the active site is tailor-made to fit the transition state. Secondly, the sites of micellar reactions are very wet and omnipresent water molecules are available to transfer protons. 

The structure of this interface determines fhe sfabilify of PEMs, the state of water, the strength of interactions in the polymer/water/ion system, the vibration modes of side chains, and the mobilities of wafer molecules and protons. The charged polymer side chains contribute elastic ("entropic") and electrostatic terms to the free energy. This complicated inferfacial region thereby largely contributes to differences in performance of membranes wifh different chemical architectures. Indeed, the picture of a "polyelectro-lyfe brush" could be more insighttul than the picture of a well-separated hydrophobic or hydrophilic domain structure in order to rationalize such differences. ... 

The first step of the reaction path involves the addition of H2O2 to the Fe " resting state to form an iron-oxo derivative known as Compound I, which is formally two oxidation equivalents above the Fe state (Fig. 2). The well studied Compound I contains a Fe" = 0 structure and a n cation radical. In the second step. Compound I is reduced to Compound II with a Fe =0 structure. The reduction of the n cation radical by a phenol or enol is accompanied by an electron transfer to Compound I and a proton transfer to a distal basic group (B), probably His 42 (Fig. 3, step 1). The native state is regenerated on one-electron reduction of Compound II by a phenol or an enol. In this process, electron and proton transfers occur to the ferryl group with simultaneous reduction of Fe" to Fe (Fig. 3, steps 2-3) and formation of water as the leaving group (Fig. 3, step 4). 

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