Water chemistry hydrogen bonding

Paschek, D., R. Day, and A. E. Garcia. 2011. Influence of water-protein hydrogen bonding on the stability of Tip-cage miniprotein. A comparison between the l iP3P and TIP4P-Ew water models. Physical Chemistry Chemical Physics. 13, 19840. 

Chaplin MF. Water s hydrogen bond strength. In Ruth M, Lynden-BeU, Simon Conway M, Barrow JD, Finney JL, Harper CL Jr, eds. In Water of Life Counterfactiud Chemistry and Fine-Tuning in Biochemistry. Boca Raton, FL CRC Press 2010 69-86. 

A carboxylic acid can be represented as R — CO2 H. Many different carboxylic acids participate in organic chemistry and biochemishy. Although carboxylic acids react in many different ways, breaking the C—OH bond is the only reaction that is important in polymer formation. A carboxylic acid is highly polar and can give up H to form a carboxylate anion, R — CO2. The carboxyl group (— CO2 H) also forms hydrogen bonds readily. These properties enhance the solubility of carboxylic acids in water, a particularly important property for biochemical macromolecules. 

Another marked physical difference between sulphides and sulphoxides (or sulphones) is that sulphoxides (and lower alkyl sulphones) are hygroscopic and dissolve quite readily in water or protic solvents such as alcohols, and even more so lower alkyl or alkyl aryl sulphoxides are almost freely miscible with water. This can be accounted for by the formation of the strong hydrogen bond between the S—O bond in the sulphoxides and water molecules. Moreover, lower alkyl sulphoxides and sulphones such as dimethyl sulphoxide (DMSO) or sulpholene can dissolve a number of metallic salts, especially those of alkali and alkaline earth metals, and hence these compounds have been widely utilized as versatile and convenient solvents in modern organic chemistry (Table 3). 

The log octanol-water partition coefficient (log Pq/w) probably is the most frequently used physicochemical parameter in medicinal chemistry [101 104]. Octanol, with a polar head and a flexible, nonpolar tail, has hydrogen-bonding capabilities and amphilicity similar to... 

An understanding of the surface chemistry of silica is required to interpret its chromatographic properties. The silica surface consists of a network of silanol groups, some of which may. be hydrogen bonded to water, and siloxane groups, as shown in Figure 4.2. A fully hydroxylat silica surface contains about 8... 

Let us now look at the chemistry of the reaction of water and hydrogen with the active sites. When water reacts with the active site, it seems quite clear that this should be viewed as heterolytic fission of an OH bond with the proton adding to the oxide ion and the hydroxide ion adding to the zinc ion. This is shown schematically below ... 

Another case is where the chemistry is known, but the spectroscopy is unknown, because the pure material is not available. Protein, for example, cannot be extracted from wheat (or at least not and still remain protein), so the spectrum of pure protein as it exists in wheat is unknown. Even simpler molecules are subject to this effect we can measure the spectrum of pure water easily enough, for example, but that is not the same spectrum as water has when it is present as an intimate mixture in a natural product -the changes in the hydrogen bonding completely change the nature of the spectrum. 

Fig. 2. Perspective view of the V(OH2)6 (OH2)i2 ion exhibiting D2 symmetry. The dashed lines represent the hydrogen bonds within the cyclic water trimers in the second coordination sphere. Reproduced from Ref. (3) by permission of the Royal Society of Chemistry.

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