Solid-phase synthesis side products

The vast majority of linker systems used in solid phase synthesis undergo product cleavage by acidolysis (for some recent reviews see references [1, 2]). The reason for this preference is partly because most linkers were originally designed for use in peptide synthesis, where the use of acid-cleavable linkers and side-chain protecting groups are favored, but is also due to the ease with which the properties of such linkers can be fine-tuned to suit particular applications. 

Then N-Boc-O-benzylserine is coupled to the free amino group with DCC. This concludes one cycle (N° -deprotection, neutralization, coupling) in solid-phase synthesis. All three steps can be driven to very high total yields (< 99.5%) since excesses of Boc-amino acids and DCC (about fourfold) in CHjClj can be used and since side-reactions which lead to soluble products do not lower the yield of condensation product. One side-reaction in DCC-promoted condensations leads to N-acylated ureas. These products will remain in solution and not reaa with the polymer-bound amine. At the end of the reaction time, the polymer is filtered off and washed. The times consumed for 99% completion of condensation vary from 5 min for small amino acids to several hours for a bulky amino acid, e.g. Boc-Ile, with other bulky amino acids on a resin. A new cycle can begin without any workup problems (R.B. Merrifield, 1969 B.W. Erickson, 1976 M. Bodanszky, 1976). 

During the first decade when solid-phase synthesis was executed using Fmoc/tBu chemistry, the first Fmoc-amino acid was anchored to the support by reaction of the symmetrical anhydride with the hydroxymethylphenyl group of the linker or support. Because this is an esterification reaction that does not occur readily, 4-dimethylaminopyridine was employed as catalyst. The basic catalyst caused up to 6% enantiomerization of the activated residue (see Section 4.19). Diminution of the amount of catalyst to one-tenth of an equivalent (Figure 5.21, A) reduced the isomerization substantially but did not suppress it completely. As a consequence, the products synthesized during that decade were usually contaminated with a small amount of the epimer. In addition, the basic catalyst was responsible for a second side reaction namely, the premature removal of Fmoc protector, which led to loading of some dimer of the first residue. Nothing could be done about the situation,... 

The major side reaction associated with the use of mixed anhydrides is aminolysis at the carbonyl of the carbonate moiety (Figure 7.4, path B). The product is a urethane that resembles the desired protected peptide in properties, except that the amino-terminal substituent is not cleaved by the usual deprotecting reagents. Hence, its removal from the target product is not straightforward. The problem is serious when the residues activated are hindered (Val, lie, MeXaa), where the amounts can be as high as 10%. Other residues generate much less, but the reaction cannot be avoided completely, with the possible exception of activated proline (see Section 7.22). This is one reason why mixed anhydrides are not employed for solid-phase synthesis. 

ATR FT-IR spectroscopy has also been employed to monitor the solid-phase synthesis of substituted benzopyranoisoxazoles [180]. Finally, Huber et al. [181] have also reported that this technique is particularly suitable for the characterization of supported molecules in combinatorial chemistry, as well as for the identification of side products and for Photoacoustic (PA) FT-IR. 

The 9-fluorenylmethoxycarbonyl group, developed by Carpino and co-workers in 1972 [257], has become one of the most widely used protective groups for aliphatic or aromatic amines in solid-phase synthesis. For solid-phase peptide synthesis in particular, this protective group plays an important role [258] (Section 16.1). The Fmoc group is not well suited for liquid-phase synthesis because non-volatile side products are formed during deprotection. 

In solid-phase synthesis intermediates and products are bound to a solid support via a covalent linker. The linker must allow selective removal of the final product from the support, but must be stable under the reaction conditions throughout the synthesis. The advantage of a solid-phase approach is that reagents can be used in large excess to drive reactions to completion and most side products are just washed off from the solid support. However, the solid-phase implies steric constraints onto the reactions performed. The choice of method depends on the synthetic problem it is often not obvious and usually results from a reaction optimization study. 

Polymer-supported technologies have been widely used in peptide and protein chemistry. Especially in automated solid-phase synthesis, there is a need to separate products from side products deficient in one or several units. In particular, the (n-1) products are notoriously difficult to separate from the end products. As fluorous... 

UNCAs are able to dimerize in the presence of some bases to yield pyrrolidine-2,4-diones, therefore the solvent and the base have to be chosen with care since, if the acylation step is slow, the risk of dimerization increases. This problem is not very important in solid-phase synthesis as the formed pyrrolidine-2,4-diones can be easily eliminated by the washing steps, but the concentration of reactive UNCAs can be drastically reduced by this phenomenon. No pyrrolidine-2,4-diones are formed when NMM is used as a base in di-chloromethane, DMF, and THF as solvents, while DIPEA in dichloromethane and DMF can yield this side-product. 

To overcome the problems associated with these reaction conditions, Backes et al. developed an alkanesulfonamide safety-catch linker for solid-phase s)rnthesis [34]. In this method, acylation of a sulfonamide support affords a support-bound iV-acylsulfonamide that is able to withstand the basic and strongly nucleophilic reaction conditions required for Fmoc-based SPPS. On completion of the solid-phase synthesis sequence, iodoacetonitrile treatment yields iV-cyanomethyl derivatives that can be cleaved under mild nucleophilic reaction conditions to afford the target compounds. Coupling conditions of alkanesulfonamide resin with Boc- and Fmoc-amino acids were developed to minimize the racemization. Using this method, a short synthesis sequence, followed by iodoacetonitrile activation and nucleophilic displacement is able to form dipeptide products from a number of support-bound amino acids incorporating diverse side-chain functionalities. 

Solution-phase combinatorial chemistry so far has played a considerably lesser role than its solid-phase counterpart. This is probably due to the main problem of solution-phase combinatorial synthesis, i.e., to obtain pure products. In solid-phase synthesis, components such as auxiliary reagents and unreacted starting materials can be easily separated from the desired products by simple washing procedures since both reside in different phases. In solution-phase synthesis, all components occur in the same phase so that purification becomes a much more demanding task. With respect to side products derived from the resin-bound reaction component, the purification problems are, however, the same in both solution- and solid-phase synthesis. 

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