I want to bond the triethyl citrate to the amine DNA (Aptamer), like this article (A case study on the myth of emission from aliphatic amides). We tried for bond the triethyl citrate to the amine in methanolic condition at RT but we failed. Also, can I convert citric acid to aconitic acid and then aconitate acid to trimethyl aconitate and then trimethyl aconitate to amid band?! like this article (A case study on the myth of emission from aliphatic amides)?!
Apparently, triethyl citrate or their derivatives in amidation process, produce cyclic products.
Anyone have any suggestion and simple method for our purpose (Like attached file)?!
Several issues:
1) The direct conversion of an ester to an amide is a difficult one, often requiring high heat, strong base, and/or nucleophilic activating agent like DBU so i am not surprised your attempt to condense triethyl citrate with NH2-aptamer failed at room temperature.
2) You have unprotected hydroxyl group which could react as nucleophile if you were to try to condense citric acid with NH2 aptamer.
my suggestion is this: take triethyl citrate and protect your hydroxyl grpup (silyl protecting group or benzyl protecting group). Then look for method that is specific for conversion of ester to amide (I know one out there that uses DBU). The method will probably require high heat. If the method works, get your product and remove hydroxyl protecting group.
If that does not work then try this: take triethyl citrate and protect the hydroxyl. Use saponification to go from ester to carboxylic acid. Then use a peptide coupling agent like HATU to couple citric acid with NH2-aptamer. Then deprotect hydroxyl.
the mentioned conversion carried out in basic environment with heating.
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