Water bridges

Fig. 6. Force profile obtained from a one nanosecond simulation of streptavidin-biotin rupture showing a series of subsequent force peaks most of these can be related to the rupture of individual microscopic interactions such as hydrogen bonds (bold dashed lines indicate their time of rupture) or water bridges (thin dashed lines).

Fig. 7. Snapshots of rupture taken (A) at the start of the simulation (zcant = 0), (li) at ZcB.nl = 2.8 A, (C) at Zcnm = 4.1 A, (D) at Zcnm = 7.1 A, and (E) at Zcant = 10.5 A. The biotin molecule is drawn as a ball-and-stick model within the binding )ocket (lines). The bold dashed lines show hydrogen bonds, the dotted lines show selected water bridges.

G lv nic Corrosion. Galvanic corrosion is an electrochemical process with four fundamental requirements (/) an anode (magnesium), 2) a cathode (steel, brass, or graphite component), (J) direct anode to cathode electrical contact, and (4) an electrolyte bridge at the anode and cathode interface, eg, salt water bridging the adjacent surfaces of steel and magnesium components. If any one of these is lacking, the process does not occur (133,134). 

The proton transfer in these clusters via the water bridge was found to be about three times as fast as a nonassisted transfer, underscoring the importance of the solvent for the reaction mechanism [98IJQ855]. In addition to the relative stabilities of the cytosine tautomers, the structures and properties of some cytosine derivatives have been investigated, mainly those of 5-hydroxycytosine 111 and 5,6-dihydroxycytosine 112 (Scheme 73) [99JST1, 99JST49]. 

Fig. 30. — Packing arrangement of 4-fold antiparallel double helices of potassium hyaluronate (32). (a) Stereo view of a unit cell approximately normal to the line of separation of the two helices. The two chains in each duplex, drawn in open and filled bonds for distinction, are linked by not only direct hydrogen bonds, but also water bridges. Inter double-helix hydrogen bonds are mediated between hydroxymethyl and iV-acetyl groups. Potassium ions (crossed circles) at special positions have only a passive role in the association of hyaluronate chains.

Reynolds and Lumry have discussed the role of water in this exchange and have suggested, for both steps, a mechanism involving water bridges. 

In deuterated solvent the rate of exchange was found to be lower than in aqueous media the ratio k H20) k D20) was found to be dependent on the acid concentration. Sullivan et al. have suggested a hydrogen atom transfer process and a water bridging process... 

Z = 8 D, = 1.84 R = 0.059 for 2,587 intensities. In the asymmetrical unit, there are two molecules that have similar conformations. The glycosyl dispositions are anti (45.8°, 40.9°) in both molecules. The D-ribosyl conformation is 2Tj (157.6°, 32.1°) in one molecule, and 2T3 (165.1°, 31.9°) in the other. The exocyclic, C-4 -C-5 bond torsion-angles are gauche+ (51.9°, 53.9°) in both molecules, and the C-5 -0-5 bond torsion-angles are trans (172.5°, 176.6°). The two UDP molecules form a dimer coordinated by three K+ ions. There is no metal-ion or water bridge between the pyrophosphate chain and the uracil base of the same molecule. The three K+ ions are coordinated by oxygen atoms of... 

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...

Figure 7-4. Excess coordination number plots for (a) MEP (three-water-bridge) [27] and (b) PMF (H64 in ) [14] simulations for the proton transfer in CAII. Note that the MEP calculation follows a very concerted mechanism while PMF simulation follows a step-wise proton hole mechanism...

X=S or Se. The X=S compound remains HS-HS at all temperatures with weak coupling (/=-4 cm-1) and the X=Se compound shows a broad half-SCO, to the HS-LS state, between 200-100 K, with no hysteresis. Interestingly, attempts to crystallize these compounds led to loss of bipyrimidine and formation of water-bridged chain species [Fe(pypz)2(NCS)2](iU-OH2) n, from which the H-bonded water-bridged dimers described in 2.4.2.4 were developed. 

Adsorption of nonionic compounds on subsurface solid phases is subject to a series of mechanisms such as protonation, water bridging, cation bridging, ligand exchange, hydrogen bonding, and van der Waals interactions. Hasset and Banwart (1989) consider that the sorption of nonpolar organics by soils is due to enthalpy-related and entropy-related adsorption forces. 

Concentrated particle suspensions may also show a yield point which must be exceeded before flow will occur. This may result from interaction between irregularly shaped particles, or the presence of water bridges at the interface between particles which effectively bind them together. Physical and chemical attractive forces between suspended particles can also promote flocculation and development of particle network structures, which can be broken down by an applied shear stress [2]. 

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