Carboxylic acids hydrogen-bonding effects

While this notion may conjure up visions of plastic materials it is important to remember that proteins and nucleic acids are also polymers. Many proteins form globular structures and, indeed, may interlock to encapsulate a large volume of space as exemplified by the coatings of capsid viruses. In a prebiotic world, polypeptides could have formed in aqueous solution through the sequential reaction of amino acids. The individual amino acids hydrogen bond donor and acceptor groups, amines, carbonyls and carboxylic acids, would all have helped to keep the molecules in solution. Once a polypeptide had formed, however, many of these would be unavailable as they became incorporated in the hydrogen bond network that formed the secondary and tertiary structure. This would result in a more hydrophobic surface for the protein capsule which would make an effective cell. 

On an industrial scale, the traditional method for cleavage of carbon-carbon double bonds is ozonolysis, used for the manufacture of azelaic acid and nonanoic acids from oleic acid, and of butane tetracarboxylic acid from tetrahydrophthalic anhydride. The process is effectively a quantitative and mild process.178 However, it is capital and energy intensive. The intermediate ozonide is worked up either reductively or oxidatively to produce the aldehyde, ketone or carboxylic acid. Hydrogen peroxide is the common oxidizing agent used in the second step.179-181 Oxygen can also be used either alone182 or in combination with zeolites.183 Reviews on ozonolysis are available and the reader is directed to reference 184 for further information. 

Additional effects can be classified as statistical considerations (e.g., the effect of an additional carboxylic acid group on the pKa of a carboxylic acid), tautomeric, solvation, polarizability, and internal hydrogen bonding effects. Clark, J. Perrin, D, D. Q. Rev. Chem. Soc. 1964, 18, 295. 

It may be argued that the effective concentration of carboxylate ion at the protein surface due to a glutamic acid side chain is also very high if it is held close to a tyrosyl residue. However, as already stated, it becomes difficult to distinguish such a situation from a tyrosyl-carboxylate ion hydrogen bond. 

With aromatic acids the presence of the aromatic ring absorptions in the 1600—1500 cm region complicates the spectrum a good deal, but nevertheless j3-phenylalanine, tyrosine and similar products appear to be essentially normal [13, 17]. Anthranilic acid, on the other hand, shows normal carboxyl and amine absorptions shghtly modified by the internal hydrogen bond, and so does not behave as a typical amino-acid. The absence of the zwitterion form in this case may be associated with the hydrogen bond effect. 

The use of NO and sulphur tetrafluoride (SF4) gas treatments allows more precise identification and quantification of hydroxyl (OH) and hydroperoxy (OOH) groups (as nitrites and nitrates, respectively, after NO reaction) and carboxylic acids (after SF4 treatment to produce acid fluorides) (cf. section 10.17.1.5) and ketones (after removal of the overlapping acid absorptions and hydrogen-bonding effects with —OH groups by SF4 reactions) [362]. The NO reaction products are particularly informative because of their intense absorptions (up to 4-7 times stronger than those of the original OH species) and because primary, secondary and tertiary products have different IR absorptions [362]. 

Solvent Effects on the Rate of Substitution by the S 2 Mechanism Polar solvents are required m typical bimolecular substitutions because ionic substances such as the sodium and potassium salts cited earlier m Table 8 1 are not sufficiently soluble m nonpolar solvents to give a high enough concentration of the nucleophile to allow the reaction to occur at a rapid rate Other than the requirement that the solvent be polar enough to dis solve ionic compounds however the effect of solvent polarity on the rate of 8 2 reactions IS small What is most important is whether or not the polar solvent is protic or aprotic Water (HOH) alcohols (ROH) and carboxylic acids (RCO2H) are classified as polar protic solvents they all have OH groups that allow them to form hydrogen bonds... 

Maleic and fiimaric acids have physical properties that differ due to the cis and trans configurations about the double bond. Aqueous dissociation constants and solubiUties of the two acids show variations attributable to geometric isomer effects. X-ray diffraction results for maleic acid (16) reveal an intramolecular hydrogen bond that accounts for both the ease of removal of the first carboxyl proton and the smaller dissociation constant for maleic acid compared to fumaric acid. Maleic acid isomerizes to fumaric acid with a derived heat of isomerization of —22.7 kJ/mol (—5.43 kcal/mol) (10). The activation energy for the conversion of maleic to fumaric acid is 66.1 kJ/mol (15.8 kcal/mol) (24). 

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