Fmoc deprotection with piperidine having azide at the N-terminus

[Valine_Leucine]

Hey people,

 

I want to run a Fmoc deprotection of my peptide. The point is that I have an azide group in the side chain of the last aminoacid that I attached. Usually I run it with 20% piperidine in DMF but I am afraid about a possible reaction between the azido group and the free amino group after deprotection. I mean, which influence could have piperidine after the Fmoc deprotection in a possible reaction between azide and amino group (piperidine is a nucleophilic base...)

 

Thanks in advance...

[hypervalent_iodine]

You should be fine and I would not expect it to react to any extent with the azide. The easiest way to find out is of course to do a small scale reaction and figure out what you have at the end. Alternatively, you could do a reaction search with scifinder and see what other people use with similar reactions (though that's something you should have already done).

 

If I'm not mistaken, this is another thread of yours: http://www.chemicalf...p?topic=49569.0

 

In response to this comment:

 

Sorry to re-open the topic.

I did several test to check how the Fmoc deprotection take place...using piperidine (10 % and 20%) and also non-nucleophilic base DBU (2 %)....when I analyze by LC/MS I detect a new peak with the same intensity of the main product. It seems that is a side reaction....It has a m/z of 58 units more than than the product and also another mass of 56 units less than the product.

 

m/z of the product = 813

m/z of side produts = 757 and 871

 

So definitely its seems that some side products are formed during the depreoction....as I said, the amino acid at the N-temrinus is azido lysine having the azide in the side chain...I doubt if piperidine could produce an intramolecular reaction between azide and the free amino group...or if the piperidine react with the azide forming a side product. Even that all the suggestions that I did don't give any mass related with the side products....

 

Anyone of u have any idea...about what is happening....

 

I am going to try with other non nucleophilic bases and also with other reaction times...

 

 

Go look at your NMR and/or go and get a low res mass spec. I don't trust some LC-MS's as far as I can throw them, depending on who else is using (read: breaking) the machine.

 

Additionally, without knowing the structure of your compound and the reaction conditions you are using to couple your amino acids and strip the finished peptide from the resin, it is impossible for anyone here or on chemical forums to give an opinion on what might have happened.

Edited July 27, 2011 by hypervalent_iodine