Carbodiimide side reaction

Fig. 42. Carbodiimide side reaction on primary and protected amino functions...

Poly (ethylene oxide) macromonomers72 761 are made in a similar way, as the alkoxide end group is reactive enough towards benzylic halides. With methacryloyl chloride, side reactions are involved. It is better to first protonate the PEO, and then to have it react with methacryloyl chloride in the presence of some triethyl amine. One can also react co-hydroxy polyethylene oxide) with methacryloyl imidazole, or with methacrylic acid in the presence of dicyclohexyl carbodiimide (DCCf)77). 

Like the carbodiimide method, the mixed anhydride method results in an amide complex (Table 5, Figure 17). The acid-containing hapten is dissolved in a dry, inert, dipolar, aprotic solvent such as p-dioxane, and isobutyl chloroformate is added with an amine catalyst. The activated mixed anhydride is chemically stable and can be isolated and characterized. The aqueous protein solution is added to the activated acid and the pH is maintained at around 8.5. A low temperature (around 10 °C) is necessary during the reaction to minimize side reactions. 

The symmetrical anhydride is less reactive and consequently more selective in its reactions than the O-acylisourea. Although the latter can acylate both N- and O-nucleophiles, the symmetrical anhydride will only acylate V-nuclcophilcs. This means that the hydroxyl groups of the side chains of serine, threonine, and tyrosine that have not been deprotonated are not acceptors of the acyl group of the symmetrical anhydride. An additional feature of this approach to carbodiimide-mediated reactions is that it avoids a possible side reaction between the carbodiimide and the iV-nucleophilc, which gives a trisubstituted guanidine [(C6HuN)2C=N-CHR5CO-... 

Additives increase efficiency in carbodiimide-mediated reactions by preventing intermediates from undergoing side reactions and by transforming them into activated esters that become the precursors of the peptide products. A-hydroxysuccinimide and 4-hydroxy-3-oxo-3,4-dihydrobenzotriazine are the best nucleophiles or acceptors of activated species. They trap oxazolones before they have time to isomerize. The popularity of HONSu as an additive has diminished considerably during the... 

FIGURE 2.27 More on additives. In a carbodiimide-mediated reaction between acid 1 and amine 2, addition of HOObt can lead to the side reaction of aminolysis at the carbonyl of the activating moiety of ester 3, generating addition product 4. Addition of HOBt to a mixed-anhydride reaction containing unconsumed chloroformate generates mixed carbonate 5, leading to production of urethane 6. 

A carbodiimide is added to the two reacting species. The urea generated from dicyclohexylcarbodiimide is insoluble and voluminous, so it is often replaced by diisopropylcarbodiimide, which generates a soluble urea. The soluble carbodiimide ethyl-(3-dimethylaminopropyl)-carbodiimide hydrochloride (see Section 1.16) is suitable but expensive. Efficiency of coupling is greater in dichloromethane than in dimethylformamide. There is also the option of adding 1-hydroxybenzotriazole to minimize the side reactions of A-acylurca (see Section 2.12), cyano (see Section 6.15), and aspartimide (see Section 6.13) formation. 

Amine-reactive biotinylation reagents contain functional groups off biotin s valeric acid side chain that are able to form covalent bonds with primary amines in proteins and other molecules. Two basic types are commonly available NHS esters and car-boxylates. NHS esters spontaneously react with amines to form amide linkages (Chapter 2, Section 1.4). Carboxylate-containing biotin compounds can be coupled to amines via a carbodiimide-mediated reaction using EDC (Chapter 3, Section 1.1). 

The reaction of 42 with 43 was attempted with dicyciohexylcarbodiimide (DCC) or water-soluble carbodiimide in solvent systems. All these reactions seemed to be unsuccessful because of the low solubility and low reactivity of 43. Among the methods of activation of a carboxy group, only the activated ester method of p-nitrophenyl ester was successful. In the acid chloride method a side reaction with the amino group of adenine was reported56. ... 

O-acylisourea species 22 are generated easily by reacting car-bodiimides with a mixture of the desired carboxyUc acid and amine. Then, they undergo aminolysis readily to form the amide and the urea by-product (48). Often, formation of unreactive IV-acylurea 23 by acetyl transfer and racemization are observed (see Fig. 7). This side reaction can be minimized substantially by reacting the acid with the carbodiimides at 0°C before adding the amine or by using DMAP or HOBt 24 as adjuvants (49). 

Active esters are chirally stable under the usual conditions of coupling in peptide synthesis, but with the single exception of piperidino esters they may undergo isomerization if left in the presence of tertiary amines. In addition to their role as shelf-stable reagents, active esters are postulated as intermediates in carbodiimide-mediated reactions where a substituted hydroxylanoine is added in order to suppress the side reaction of epimerization in the... 

The reaction in Scheme 3 for HOR = HODhbt is accompanied by a side reaction giving rise to the formation of oxobenzotriazinyl 2-azidobenzoate 50 (Scheme 10). ] The 2-azido-benzoate originates from reaction of HODhbt (48) with addition product 49 formed by reaction of the carbodiimide with 48. It is detectable by HPLC and by the azide absorbance at 2120 cm" in the IR spectrum. It is an acylating agent and thus causes chain termination if left as a contaminant of the ester. The side reaction is completely eliminated by allowing a 5-minute activation time before addition of the hydroxy compound.0 5 l... 

The advent of numerous new coupling reagents and the drawbacks discussed below have substantially decreased the popularity of mixed anhydrides for peptide synthesis in the laboratory. The mixed anhydride method is, therefore, a frequently overlooked technique which is an effective tool for peptide synthesis. This procedure has been comprehensively reviewed and, as stated by Meienhofer, the mixed anhydride method, when carried out under well-defined reaction conditions, is considerably less afflicted with undesired side reactions than, for example, the azide or carbodiimide procedures. 

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