In: Chemistry
Why is pH so important in the preparation of an N-Dinitrophenyl Derivative of a Dipeptide? I would like to understand why we need to make sure that pH is around 9 upon mixture of a dipeptide solution with NaHCO3 and dinitrofluorobenzene? And also why we need to ensure that pH drops to 2 before adding ether to our prepared dipeptide? Thank you.
In peptide synthesis, pH is plays a vital role as the concentration of protons or hydroxyl ions in the medium dictate the precise ionic form of the amino acids to be formed into a peptide and if the ionic form is not in the proper charge-distribution, pepitization does not occur. For N-dinitrophenyl peptides, during preparation, highly alakaline conditions are maintained in order to ensure that the amine group form the N-terminal amino acid is not protonated at any point, as that would lead to deprotection of the amine group, resulting in destabilization of the peptide chain formed, resulting in that amino acid falling off. Moreover, a highly acidic medium retards the formation of the amide linkage between two amino acids in a peptide. After formation, for the same reasons mentioned, an acidic pH is maintained, as now, the peptization process is complete and the N-terminal has to be deprotected now and that occurs only under strongly acidic conditions. Top of all, maintaining such a low pH will also ensure that the C-terminal amino acid's carobxylic acid group which will also be deprotected after peptization, does not be in its anionic form, as carboxylate. Because, if it exists like that, which happens in basic medium, a salt of the cation of the base and anion of the peptide will form, leaving the peptide in the aqueous layer itself thus preventing the peptide's extraction through ether.