Molecular reasons

In these examples, we apply atomic and molecular reasoning to predict trends in the absolute entropies. We verily that our predictions make sense by consulting tabies of quantitative S ° vaiues. 

The same molecular reasoning shows that a buffer solution can absorb added hydronium ions. Consider what happens when some hydronium ions are added to the acetic acid-acetate buffer solution described in Example. The hydronium ion is a strong acid, and the acetate anion is a weak base, so proton transfer from CH3 CO2 to H3 goes essentially to completion ... 

To test whether we could accurately calculate the fold-difference of ADA inhibitory potency between purine riboside (8) and analogues of purine riboside, we selected 8-azapurine riboside (9) for our studies. Compound 9 was reported to be a 400-fold more potent ADA inhibitor relative to 8 despite differing from 8 only by the replacement of C8 with a nitrogen (Figure 8).19 The molecular reason for this enhancement in potency was not determined, but could be due either to enhanced hydration or enhanced ADA binding affinity of the hydrated species or both. To determine the reason,... 

Tjeerdsma, B.F., Boonstra, M., Pizzi, A., Tekely, P. and Militz, H. (1998b). Characterisation of thermally treated wood molecular reasons for wood performance improvement. Holz als Roh- und Werkstojf, 56(3), 149-153. 

The substitutions that reversed the amide bond, the derivatives of graduate student Mona A. Mahran s (the MM) series were all weaker allosteric effectors. We spent the next few years sorting out the molecular reason for the behavior of this class of molecules. 

The mode of substitutions of the molecules may trigger effects on monocots and dicots. Thus, 5-chloro-6-methoxy-2-benzoxazolinone was fovmd to be especially toxic to the monocots Avena sativa, Phleum pratense L., Digitaria sanguinalis (L.) Scop., and Lolium multiflorum Lam. [99]. The dicots Amaranthus caudatus L., Lepidium sativum, and Lactuca sativa were less affected. The molecular reasons for the switch in sensitivity were, however, not discussed. 

But what makes this special class of protein soluble As we shall see, the answer is not fully known. However, some indications as to the molecular reasons for the solubility were recently revealed (Wang and Ben-Naim 1996, 1997). 

We shall leave this problem for a while. We next discuss some aspects of the solvation Gibbs energy of protein, and at the end of this section present some tentative conclusions regarding the molecular reasons for the solubility of proteins. 

Hydration and steric-protmsion forces are repulsive forces that have been found to be present at rather short separations between hydrophilic siufaces such as surfactant head-groups. At least two molecular reasons for these forces have... 

The chapter, however, does not give extensive references to the experimental determination of the polysaccharide shape and size in different solvents, but rather it attempts to focus on the molecular reasons of these perturbations. A digression is also made to include the electrostatic charges in polyelectrolytic polysaccharides, because of their diffusion and use and because of interesting variations occurring in these systems. Thus, provided that all the interactions are taken into account, the calculation of the energetic state of each conformation provides the quantitative definition of the chain dimensions. 

Finally, it should be noted that the molecular reason underlying the negative temperature dependence of the volume is the same as in real liquid water, namely the unique correlation between binding energy and local density. The principle for this particular model is depicted in Fig. 2.7. 

In all of these models, the hydrogen bonds, or the structure of liquid water, were traditionally emphasized as the main molecular reasons for the anomalous behavior exhibited by liquid water. However, underlying this relatively ill-defined concept of structure (which was much later defined in statistical mechanical terms see Sec. 2.7) lies a more fundamental principle which can be defined in molecular terms, and which does not explicitly mention the concept of structure yet is responsible for the unusual properties of liquid water. This principle was first formulated in terms of generalized molecular distribution functions in 1973. It states that there exists a range of temperatures and pressures at which the water-water interactions produce a unique correlation between high local density and a weak binding energy. Clearly, this principle does not mention structure. As will be demonstrated in this section, it is this principle, not the structure per se, which is responsible for the unique properties of water as well as of aqueous solutions. ... 

In the next section, we shall follow the molecular reason for this behavior. As we have learned in Sec. 2.4, by studying simple mixture models, the outstanding behavior of liquid water is due to structural changes (in the sense discussed in Sec. 2.4) that are induced by changing either the temperature or the pressure (or the added solute in Chapter 3). 

Once again we note that the success of this model in reproducing some of the properties of liquid water does not teach us anything new about the molecular reasons for these properties nor does it tell us anything about the reality of the potential function used in these calculations. It does show, however, that implementation of the principle is essential for the manifestation of water-like behavior. 

As we shall see below in this model, the addition of a solute will always lead to an increase in the mole fraction of the L component. This is, of course, unrealistic for high concentrations of the solutes. We shall therefore examine only the limit of very dilute solutions of s in w. In this particular model, the molecular reason for such a stabilization effect is quite obvious. Since we allow s to occupy only interstitial sites, the addition of s to the system causes a decrease in the available number of holes ... 

In Sec. 2.5, we introduced two 1-D models for water. The two models are almost equivalent in their capacity to unveil the molecular reasons for the outstanding properties of liquid water. Extending the application of these two models for aqueous solutions shows that while the primitive model fails to show large negative anomalous entropy and enthalpy of solvation of inert solutes, the primitive cluster succeeds. The reason is that the entropy and enthalpy of solvation of a solute in water are due to the capability of the solute to induce structural changes in the solute. In the TD primitive model, one could not achieve that effect, not because of any deficiency of the model but because of the assumption of nearest-neighbor interactions only. 

As in the one-dimensional model, a great deal of insight into the molecular reasons for the outstanding properties of water has been achieved by this relatively simple model. In my opinion, the overwhelming success of this BN2D model is mainly due to the fact that the principle was a built-in feature of the model. The interested reader is referred to an extensive review by Dill et al. (2005). 

To summarize this section and the whole chapter, we can pause to reflect on the merits of the various models suggested for water in 1-D, 2-D, and 3-D. In my opinion, the molecular reasons underlying the anomalous thermodynamics of solvation of inert solutes in water are now well understood. This situation has been arrived at mainly by studying simple molecular models of water. Further refinements of the models will certainly add more detail but no new insights into the molecular origins of the outstanding properties of aqueous solutions of inert solutes. 

Elkoshi and Ben-Naim (1979) attempted to study the problem of the H(pO interaction within this model, hoping that the fact that the principle is a built-in feature of Bell s model would be helpful in clarifying the molecular reasons for the phenomenon of the H(pO interaction. At that time it was not known whether or not the HtpO interaction was a result of the principle. As we noted in Sec. 3.9, the hydrophobic interaction is nothing but the difference in solvation Gibbs energies. Therefore, since the solvation Gibbs energy is not a result of the principle, we can also expect that the H(f)0 interaction will not depend on the principle. 

The field of aqueous solutions has become so huge that it is impossible to review the whole field in a single book. Therefore, I have selected only a few topics, giving preference to those that have contributed the most to our understanding of the molecular reasons underlying the outstanding properties of liquid water and its solutions. 

It should be noted that the molecular reasons for the large positive values of Gbb Xa 1 are similar to the large positive values of Gaa - a 0. In the case of Gbb at Xa 1, we have B diluted in A. The stronger the BB interaction is, the larger the positive affinities between two B particles are. 

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