Water chains

Drukker, K., Hammes-Schiffer, S. An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions Initial application to protonated water chains. J. Chem. Phys. 107 (1997) 363-374. 

Siegbahn, P. E. M., 1996b, Two, Three, and Four Water Chain Models for the Nucelophilic Addition Step in the Wacker Process , J. Phys. Chem., 100, 14672. 

Pomes, R. Roux, B., Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel, Biophys. J. 2002, 82, 2304-2316... 

Cheruzel, L.E., Pometum, M.S., Cecil, M.R., Mashuta, M.S., Wittebort, R.J. and Buchanan, R.M. (2003) Structures and solid-state dynamics of onedimensional water chains stabilized by imidazole channels. Angewandte... 

The best physical properties are obtained with polyethylene adipate as the backbone. After the manufacture of the prepolymer with the polyethylene adipate and NDI, the polyurethane was completed with the addition of BDO. The use of diamines gave too fast a reaction for successful processing. Water and glycols also were used for cross-linking. Glycols do not give the C02 gas the water chain extension does. 

Literature reports applications for disinfecting medical equipment, oculars (Shimmura et al. 2000), fuel cells, vegetables (Izumi 1999) and green house substrates (internet presentation 2005), pipes and containers in breweries (Gutknecht et al. 1981) or in other fields of food industry (Hemlem and Tsai 2000 Tsai et al. 2002), ship waste waters, etc. Applications outside the drinking water area are mentioned here because many waters are environmentally important and connected with the drinking water chain (Fig. 7.1). Thus, the problem is much more relevant than may at first be expected. 

In fact, transient assembly of H-bonded water files is probably common in enzyme function. In carbonic anhydrase, for example, the rate-limiting step is proton transfer from the active-site Zn2+-OH2 complex to the surface, via a transient, H-bonded water network that conducts H+. Analysis of the relationship between rates and free energies (p K differences) by standard Marcus theory shows that the major contribution to the observed activation barrier is in the work term for assembling the water chain (Ren et al., 1995). 

Figure 10 shows the proposed ubiquinol oxidation and electron bifurcation mechanism at Qp site. (A) In the absence of the ubiquinone, the side chain of Glu-271 is connected to the solvent in the mitochondrial intermembrane space via a water chain. (B) As a reduced ubiquinol molecule binds to the site, the side chain of Glu-271 flips to form a hydrogen bond to the bound ubiquinone. (C) Now, the ISP, which is moving around the intermediate position by thermal motion is trapped at the b" position by a hydrogen bond to the bound ubiquinone. (D,E) Coupled to deprotonation, the first electron transfer occurs. Since the Rieske FeS cluster has a much higher redox potential (ca. +300 mV) than heme bl (ca. 0 mV), the first electron is favorably transferred to ISP. This yields ubisemiquinone, (F,G). After ubisemiquinone formation, the hydrogen bond to the His-161 of ISP is destabilized. The ISP moves to the c position, where the electron is transferred from the Rieske FeS cluster to heme c. Now unstable ubisemiquinone is left in the Qp pocket. The redox potential of the deprotonated ubisemiquinone is assumed to be several hundred millivolts. Now the electron transfer to the heme bl is a downhill reaction. (H) Coupled to the second electron transfer, the second proton is transferred to Glu-271 and subsequently to the mitochondrial intermembrane space. The fully oxidized ubiquinone is released to the membrane. 

Interactions of the same water molecules with RNA nucleotides (via H-bonding) and metal ions (via inner-sphere coordination) could stabilize specific metal ion-nucleic acid complexes (e.g. in Mg + -tRNA chelates) and also create the possibility for direct proton transfer through a water chain that could play a role in ribozyme-metal ion catalysis and in the mechanism of metal-dependent nucleases and polymerases. Similar types of H-bonds between different nucleotide residues have been found in tRNA tertiary structures, where they provide additional stabilization of tertiary interactions. 

Suhai, S., Cooperative effects in hydrogen bonding Fourth-order many-body perturbation theory studies of water oligomers and of an infinite water chain as a model for ice, J. Chem. Phys. 101,9766-9782 (1994). 

Ojamae, L., and Hermansson, K., Ab initio study of cooperativity in water chains Binding energies and anhartnonic frequencies, J. Phys. Chem. 98, 4271 282 (1994). 

Water is present in protein cavities as individual molecules, water chains, and clusters. Indeed, tightly bound waters can be resolved in X-ray crystallography experiments. Water molecules in larger cavities, especially those with a hydrophobic surface, are mobile and less readily resolved. In some proteins, such as the cytochrome b(f complex or cytochrome c oxidase, bound water molecules tend to form water chains. These water molecules provide hydrogen-bonded relays for proton transfer, and they may mediate donor-to-acceptor electronic coupling (2-6). 

It is possible that the water chain interacts with the Rieske 2Fe-2S protein when the latter approaches the hydrophobic... 

Sainz G, CarreU CJ, Ponamarev MV, Soriano GM, Cramer WA, Smith JL. Interruption of the internal water chain of cytochrome f impairs photosynthetic function. Biochemistry 2000 39 9164-9173. 

M.P. Fulscher and E. L. Mehler, Analysis of nonadditivity effects and estimation of many-body effects in linear water chains, Int. J. Quantum. Chem., 29 (1986) 627-638. 

Fig. 9. Image of the water chain extending from the Qa-binding site across the H-subunit to the cytopiasm in the Rb. sphaeroides reaction center. Symbols for water molecules and the L-, M- and H-subunit polypeptide chains are shown in the figure itself. Figure adapted from Ermler, Fritzsch, Buchanan and Michel (1994) Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution cofactors and protein-cofactor interactions. Structure 2 933. The same figure in color is shown in Color plate 2.

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