Water solvation function

In this report we analyze the binding of hydrated Cu(ll) in pores of diameter in the range 0.7 to 5.8 nm, based on ESR spectra measured at X-band (9 GHz) and S-band (2.4 GHz), in the temperature range 77 K to 300 K. It will be shown that the results obtained in this study can best be rationalized in terms of cation solvation by water whose properties vary gradually, as a function of the distance from the polymer network. No evidence was observed for the presence of measurable amounts of bulk water in pores of diameter in the range studied. Some preliminary results have already been reported" 5. 

First results from our fluorescence upconversion experiments are shown in Fig. 2, which displays the solvation-functions of C343 in bulk water and adsorbed on ZrC>2 nanoparticles. The response in bulk water confirms the previously reported results of bimodal dynamics [8] and a corresponding behaviour can be found for the dye bound to Z1O2, indicating that similar processes are involved. The results from biexponential fits to the solvation function S(t) of C343 in pure water and at the ZrCh-water interface are listed in Table 1. In both cases we find a fast decay time of about 100 fs and a slower decay of about 750 fs. We can see that the individual decay times stay similar and only the relative contributions change, resulting in an overall somewhat faster solvation for adsorbed dyes. 

Free energies of solvation in water calculated with the use ofthe SM2/AM1 method were incorporated as independent variables in a predictive model of the structure-function relationship of polyamine transport inhibitors, which affect the maintenance ofthe intracellular polyamine concentrations necessary for cell growth and proliferation [89]. 

We recently developed a systematic method that uses the intrinsic tryptophan residue (Trp or W) as a local optical probe [49, 50]. Using site-directed mutagenesis, tryptophan can be mutated into different positions one at a time to scan protein surfaces. With femtosecond temporal and single-residue spatial resolution, the fluorescence Stokes shift of the local excited Trp can be followed in real time, and thus, the location, dynamics, and functional roles of protein-water interactions can be studied directly. With MD simulations, the solvation by water and protein (residues) is differentiated carefully to determine the hydration dynamics. Here, we focus our own work and review our recent systematic studies on hydration dynamics and protein-water fluctuations in a series of biological systems using the powerful intrinsic tryptophan as a local optical probe, and thus reveal the dynamic role of hydrating water molecules around proteins, which is a longstanding unresolved problem and a topic central to protein science. 

A series of 16 molecules, which include different monofunctional compounds, were chosen to determine the enthalpy of solvation in water. Besides four hydrocarbons (hexane, heptane, octane and cyclohexane) and water, the series of molecules include alcohols (2-methylpropan-2-ol, 1-butanol and 2-butanol), ethers (diethylether, tetrahydrofuran and tetrahydropyran), amines (propylamine, butylamine, diethy-lamine and dibutylamine) and piperidine. This choice allows us to examine the differences between different functional groups, as well as the influence of the molecular size on the enthalpic contributions for a given series of monofunctional compounds. Free energies of hydration as well as the corresponding enthalpies taken from the data compiled by Cabani and coworkers [26] are shown in Table 4-1. 

In other studies, precipitation of the dihydrate would cranplicate matters and particularly, would give a maximum rate as a function of N which varies according to the solubility of that species in different media, as oteerved. We wish to note here that the interpretation of initiation prcq>osed by Kucera and cdUaborators, based tm direct initiation and solvation by water molecules is untenable. In fact, Dainton et showed irrevocably that the rde of water is cocatdytic (chemical), by proving that when DjO replaces H2O deuterium is found in the polymer and the rate of initiation is lower (kinetic isotope effect). 

An even more striking comparison can be made between the wild-type signal peptide s conformation when adsorbed to the monolayer and its conformation in aqueous solution. In both of these environments, the peptide should be solvated by water, but its conformations are very different. The peptide is 100% )3 structure when adsorbed to the mono-layer, while it is 80% random in aqueous buffer. Thus, it appears that contact with the lipid surface induces substantial amounts of secondary structure in a molecule that takes on little structure in an aqueous environment. This finding implies that the initial binding of a signal sequence to a membrane may induce a particular structure, which may be important to the mechanism of signal-sequence function. 

Fig. 6.2 (a) Instantaneous normal modes in room temperature water as obtained from molecular dynamics simulations. The negative frequency axis is used to show the density of imaginary frequencies. (b) The solvation response function (see Chapter 15) for electron solvation in water, calculated from direct classical MD simulations (full line), from the instantaneous normal mode representation of water (dash-dotted line), and from a similar instantaneous normal mode representation in which the imaginary frequency modes were excluded (dashed line). The inset in Fig. 6.2 shows the short time behavior of the same data. (From C.-Y. Yang, K. F. Wong, M. S. Skaf, and P. J. Rossky, J. Chem. Phys. 114, 3598 (2001).)... 

Fig. 15.4 The experimental solvation function for water using sodium salt of coumarin-343 as a probe. The line marked expt. is the experimental solvation fimction S(t) obtained from the shift in the fluorescence spectrum. The line marked q is a simulation result based on the linear response ftinction C(t). The line Marked 5 is the linear response function for a neutral atomic solute with Lennard Jones parameters of the oxygen atom. (From R. Jimenez, G. R. Fleming, P. V. Kumar, and M. Maroncelli, Nature 369, 471 (1994).)...

Fig. 2 Solvation function of coumarin 343 dye in water and adsorbed on Zr02...

Specifically adsorbed ions " are those which directly contact the electrode surface. As indicated in Figure 1, specifically adsorbed ions are considered to be desolvated, and they displace solvent molecules adjacent to the electrode surface. Iodide, which is weakly solvated by water, is a good example of an ion which tends to specifically adsorb on electrode surfaces. The nature of specific adsorption is a function of both electrostatic and chemical interactions between the electrode and the ion. Specific adsorption can significantly alter the interfacial potential profiles as well as the kinetics of interfacial reactions. The thin solution layer closest to the electrode surface which contains specifically adsorbed ions as well as solvent molecules is often called the inner layer or the Helmholtz layer. The inner Helmholtz plane (IHP) is considered to pass through the centers of specifically adsorbed ions (see Figure 1). 

Although a DNA molecule is heavily solvated by water (and ions), a detailed study of the role of water in various biological functions of DNA has yet to be carried out. However, some progress has recently been made towards understanding the role of water in the intercalation of anti-tumor dmgs (such as daunomycin, actinomycin, and cisplatin see Figure 7.4) into DNA. This is an important problem from a medical point of view and at the same time the microscopic aspects turned out to be quite interesting. 

Inert gas solutes show large values of heat capacity of solvation in water compared with normal solvents. This quantity reflects the sharp slope of AH as a function of temperature. Clearly, this trend is a result of the breakdown of the HBs (or the structure ) in real water as well as in the 1-D model. 

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