What protecting group can I use if I want to protect the secondary amine functional group in aminoethylpiperazine over the tertiary and primary amine functionalities in the molecule.
The primary amine will probably be more reactive than the secondary amine. You could protect the primary amine, for example with phthaloyl, then protect the secondary amine, and then remove the phthaloyl group (see Greene's Protective Groups).
However, it would probably be easier to start with 1-BOC-piperazine.
Practically trifluoroacetyl protection would first go on a secondary amine and is as easy to de-protect as the Boc-protection. NaOH-MeOH would take 15-30 mins.
One can also form imine with e.g. benzaldehyde on the primary amine, protect the secondary, and then hydrolyze the imine to regenerate the -NH2.
CF3COOEt is selective reagent to protect primary amine in presence of secondary amine . One from many examples : http://www.sciencedirect.com/science/article/pii/004040399500630U - in CH3CN/H2O ; THF is also suitable solvent
Boc-protection of piperazine ring in aminoethylpiperazine with 92% yield in two-stage process (via benzaldehyde as suggested by Jacek Martynov): http://www.tandfonline.com/doi/abs/10.1080/00397919208019091
Best protecting group that is selective for a secondary amine functionality Trimethyl silyl chloride
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