Side chain-transfer

Only a few important representatives of the non-proteinogenic amino acids are mentioned here. The basic amino acid ornithine is an analogue of lysine with a shortened side chain. Transfer of a carbamoyl residue to ornithine yields citrulline. Both of these amino acids are intermediates in the urea cycle (see p.l82). Dopa (an acronym of 3,4-dihydroxy-phenylalanine) is synthesized by hydroxyla-tion of tyrosine. It is an intermediate in the biosynthesis of catecholamines (see p.352) and of melanin. It is in clinical use in the treatment of Parkinson s disease. Selenocys-teine, a cysteine analogue, occurs as a component of a few proteins—e.g., in the enzyme glutathione peroxidase (see p.284). 

ATP is the most common donor of phosphoryl groups. The terminal (y) phosphoryl group of ATP is transferred to a specific amino acid. In eukaryotes, the acceptor is always one of the three containing a hydroxyl group inils side chain. Transfers to serine and threonine residues are handled by one class of protein kinases and to tyrosine residues by another. Tyrosine kinases, which are unique to multicellular organisms, play pivotal roles in growth regulation, and mutations in these enzymes are commonly observed in cancer cells. 

The kinetic chain length should be related to the number-average degree of polymerization. The degree of complexity of this relation will depend on the existence or otherwise of side (chain-transfer) reactions. We now consider first the case where there are no chain-transfer reactions. By definition... 

It is worth noting that significant side reactions may occur with prolonged reaction time furthermore, it is possible to generate branched structures due to side chain transfer. Transesterification during the polymerization of cyclic aliphatic esters is known to cause the scission of the backbone chain and the formation of different stmctures. Differing from tetravalent carbon atoms in aliphatic cyclic esters and polyesters, the phos-phoms atom is pentavalent, and, therefore, the side chain transfer reaction may be more complicated. As illustrated in eqn [5]... 

We can descnbe the major elements of fatty acid biosynthesis by considering the for mation of butanoic acid from two molecules of acetyl coenzyme A The machinery responsible for accomplishing this conversion is a complex of enzymes known as fatty acid synthetase Certain portions of this complex referred to as acyl carrier protein (ACP), bear a side chain that is structurally similar to coenzyme A An important early step m fatty acid biosynthesis is the transfer of the acetyl group from a molecule of acetyl coenzyme A to the sulfhydryl group of acyl carrier protein... 

Only trace amounts of side-chain chlorinated products are formed with suitably active catalysts. It is usually desirable to remove reactive chlorides prior to fractionation in order to niinimi2e the risk of equipment corrosion. The separation of o- and -chlorotoluenes by fractionation requires a high efficiency, isomer-separation column. The small amount of y -chlorotoluene formed in the chlorination cannot be separated by fractionation and remains in the -isomer fraction. The toluene feed should be essentially free of paraffinic impurities that may produce high boiling residues that foul heat-transfer surfaces. Trace water contamination has no effect on product composition. Steel can be used as constmction material for catalyst systems containing iron. However, glass-lined equipment is usually preferred and must be used with other catalyst systems. 

Reactions of the Side Chain. Benzyl chloride is hydrolyzed slowly by boiling water and more rapidly at elevated temperature and pressure in the presence of alkaHes (11). Reaction with aqueous sodium cyanide, preferably in the presence of a quaternary ammonium chloride, produces phenylacetonitrile [140-29-4] in high yield (12). The presence of a lower molecular-weight alcohol gives faster rates and higher yields. In the presence of suitable catalysts benzyl chloride reacts with carbon monoxide to produce phenylacetic acid [103-82-2] (13—15). With different catalyst systems in the presence of calcium hydroxide, double carbonylation to phenylpymvic acid [156-06-9] occurs (16). Benzyl esters are formed by heating benzyl chloride with the sodium salts of acids benzyl ethers by reaction with sodium alkoxides. The ease of ether formation is improved by the use of phase-transfer catalysts (17) (see Catalysis, phase-thansfer). 

Another example of the analogy between pyrazole and chlorine is provided by the alkaline cleavage of l-(2,4-dinitrophenyl)pyrazoles. As occurs with l-chloro-2,4-dinitrobenzene, the phenyl substituent bond is broken with concomitant formation of 2,4-dinitrophenol and chlorine or pyrazole anions, respectively (66AHC(6)347). Heterocyclization of iV-arylpyrazoles involving a nitrene has already been discussed (Section 4.04.2.1.8(i)). Another example, related to the Pschorr reaction, is the photochemical cyclization of (515) to (516) (80CJC1880). An unusual transfer of chlorine to the side-chain of a pyrazole derivative was observed when the amine (517 X = H, Y = NH2) was diazotized in hydrochloric acid and subsequently treated with copper powder (72TL3637). The product (517 X = Cl, Y = H) was isolated. 

The calculation of E] and X from computational methods is the focus here. Generally, the energetics of these quantities are separated into contributions from the inner and outer shells. For transfer between small molecules, the inner shell generally is defined as the entire solutes A and D, and the outer shell is generally defined as only the solvent. However, in a more practical approach for proteins, the inner shell is defined as only the redox site, which consists of the metal plus its ligands no further than atoms of the side chains that are directly coordinated to the metal, and the outer shell is defined as the rest of the protein plus the surrounding solvent. Thus... 

The side chains of the 20 different amino acids listed in Panel 1.1 (pp. 6-7) have very different chemical properties and are utilized for a wide variety of biological functions. However, their chemical versatility is not unlimited, and for some functions metal atoms are more suitable and more efficient. Electron-transfer reactions are an important example. Fortunately the side chains of histidine, cysteine, aspartic acid, and glutamic acid are excellent metal ligands, and a fairly large number of proteins have recruited metal atoms as intrinsic parts of their structures among the frequently used metals are iron, zinc, magnesium, and calcium. Several metallo proteins are discussed in detail in later chapters and it suffices here to mention briefly a few examples of iron and zinc proteins. 

Figure 1.9 Examples of functionally important intrinsic metal atoms in proteins, (a) The di-iron center of the enzyme ribonucleotide reductase. Two iron atoms form a redox center that produces a free radical in a nearby tyrosine side chain. The iron atoms are bridged by a glutamic acid residue and a negatively charged oxygen atom called a p-oxo bridge. The coordination of the iron atoms is completed by histidine, aspartic acid, and glutamic acid side chains as well as water molecules, (b) The catalytically active zinc atom in the enzyme alcohol dehydrogenase. The zinc atom is coordinated to the protein by one histidine and two cysteine side chains. During catalysis zinc binds an alcohol molecule in a suitable position for hydride transfer to the coenzyme moiety, a nicotinamide, [(a) Adapted from P. Nordlund et al., Nature 345 593-598, 1990.)...

The catalytic triad consists of the side chains of Asp, His, and Ser close to each other. The Ser residue is reactive and forms a covalent bond with the substrate, thereby providing a specific pathway for the reaction. His has a dual role first, it accepts a proton from Ser to facilitate formation of the covalent bond and, second, it stabilizes the negatively charged transition state. The proton is subsequently transferred to the N atom of the leaving group. Mutations of either of these two residues decrease the catalytic rate by a factor of 10 because they abolish the specific reaction pathway. Asp, by stabilizing the positive charge of His, contributes a rate enhancement of 10. ... 

In addition, subsequent chain transfer reactions may occur on side chains and the larger the resulting polymer, the more likely will it be to be attacked. These features tend to cause a wide molecular weight distribution for these materials and it is sometimes difficult to check whether an effect is due inherently to a wide molecular weight distribution or simply due to long chain branching. 

Polyalkylene oxides (PAO) are prone to chain transfer. This tendency was used by Union Carbide to graft acrylate side chains via UV exposure of a PAO/acrylic monomer(carbamyloxy alkyl acrylate)/photoinitiator blend [58]. The final product was a water-sensitive PSA. 

Both of these structures are open-chained compounds corresponding to crown ethers in function if not exactly in structure (see Chap. 7). They have repeating ethyleneoxy side-chains generally terminated in a methyl group. Montanari and co-workers introduced the polypodes 22 as phase transfer catalysts . These compounds were based on the triazine nucleus as illustrated below. The first octopus molecule (23) was prepared by Vogtle and Weber and is shown below. The implication of the name is that the compound is multiarmed and not specifically that it has eight such side-chains. Related molecules have recently been prepared by Hyatt and the name octopus adopted. For further information on this group of compounds and for examples of structures, refer to the discussion and tables in Chap. 7. 

Two-step 1,4 cycloaddition of enamines, such as was observed with methyl vinyl ketone, is not possible with acrylate or maleate esters. This is due to the fact that, following the initial simple substitution, no side-chain carbanion is available for nueleophilic attack on the a carbon of the iminium ion. Likewise two-step 1,3 eycloaddition, such as that found when alicyclic enamines were treated with acrolein, is impossible with acrylate or maleate esters because transfer of the amine moiety from the original enamine to the side chain to form a new enamine just prior to the final cyclization step is not possible. That is, the reaction between a seeondary amine and an ester does not produce an enamine. 

In general, the activation energies for both cationic and anionic polymerization are small. For this reason, low-temperature conditions are normally used to reduce side reactions. Low temperatures also minimize chain transfer reactions. These reactions produce low-molecular weight polymers by disproportionation of the propagating polymer ... 

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