You will want to check all your synthesis and purification procedures. 1) you have to ensure that all reactants are fully dissolved before initiating the reaction, also ensure that you have activated the carboxylic group fully before introducing it to the amine group, you can do this by reacting the EDC with the molecule whose carboxylic group will be reacting for an hour at least before introducing it to the fully dissolved second reactant. 2) you are likely to loose products depending on your purification techniques, I will suggest you try using dialysis for purification with a molecular cut off that allows for good separation. you can check. Article Synthesis and Characterization of Fatty Acid Grafted Chitosa...