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Topic: Fmoc deprotection! piperidine, DBU...having an azide at the side chain...  (Read 18738 times)

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Offline peptideismylife

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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...)

what about using DBU (non nucleophilic base)...?

Offline peptideismylife

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I mean, using piperidine as a deprotecting group I am afraid to have a nucleophilic attack of piperidine to azido group...

Offline Åke

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Hi Mr. Peptide,

I wouldn't worry about the azido group as the conditions you intend to employ are comparatively mild. It isn't uncommon to hydrolyse Evans-type oxazolidinone auxiliary using LiOH in presence of an alkylazide.1,2 The azido group remains stable under these relatively forcing conditions.

1. Evans, D. A. and Britton, T. C. J. Am. Chem. Soc. 1987, 109, 6881–6883
2. Evans, D. A.; Ellman, J. A.; Dorow, R. L. Tetrahedron Lett. 1987, 28, 1123–1126

Offline peptideismylife

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Hi Ake,

I had a look to the papers that u attached. But in my case I am afraid with possible side reactions with piperidine (remember that piperidine is a nucleophilic base) and DBU...

I did the deprotection with these mild conditions, 10% piperidine in DMF and 2 % DBU in DMF and I couldnt see my mass by LC/MS...so I guess that side reactions happen during the deprotection.

Offline Åke

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Hi,

There are plenty of substances where both an amino and an azido group are present in the same molecule1, if your hypothesis was true then amino azides couldn't exist or would rapidly decompose but evidently they do exist and are stable. I have no experience with Fmoc chemistry but there is at least one study which details the use of DBU for removal of the Fmoc protecting group.2 More precisely, DBU cleaves off the Fmoc group and an alkyl thiol acts as a dibenzofulvene scavenger.

1. Carboni, B.; Benalil, A.; Vaultier, M. Aliphatic amino azides as key building blocks for efficient polyamine syntheses. J. Org. Chem. 1993, 58, 3736– 3741 http://pubs.acs.org/doi/abs/10.1021/jo00066a028
2. Sheppeck, J. E.; Kar, H.; Hong, H. A convenient and scaleable procedure for removing the Fmoc group in solution.  Tetrahedron Lett. 2000, 41, 5329−5333 http://www.sciencedirect.com/science/article/pii/S0040403900008534

Offline discodermolide

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Hi Ake,

I had a look to the papers that u attached. But in my case I am afraid with possible side reactions with piperidine (remember that piperidine is a nucleophilic base) and DBU...

I did the deprotection with these mild conditions, 10% piperidine in DMF and 2 % DBU in DMF and I couldnt see my mass by LC/MS...so I guess that side reactions happen during the deprotection.


I doubt you will see your  mass in the MS as the azide group is labile under the conditions. The instrument may require fine tuning to see the required mass.
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Offline peptideismylife

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discodermolide: I can see the mass of my peptide having the azido group.

Ake: The point is that the azido group is at the side chain of the last amino acid. I run the deproteciton of Fmoc group and I saw others peaks which make me thing in side reactions, due to only just a minor peak correspond to my peptide (in case of DBU).

In the case of deprotection with piperdine I didnt saw my product...for that reason I think that something happens with piperidine, which is a nucleophilic base and has to have an influence...

Offline Dan

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I have to agree with Åke - I really doubt the azide will be a problem. I worked with alkyl azides regularly during my Ph. D., where I employed azide as a protected amine eventually revealed at the end of the synthesis - I have taken alkyl azides through up to ~15 linear steps. They were stable under a variety of basic conditions - including heating at 100oC in neat benzylamine for 24 h, which was probably the most harsh nucleophilic basic conditions I had to expose an azide to. I also prepared a few compounds bearing 1-amino-2-azido motifs and never had any issues with stability.

You have to be very cautious about putting too much faith in MS, some products simply will not fly well and fragment easily leading to false negatives. How complicated is the peptide, could you analyse it easily be NMR?
« Last Edit: June 21, 2011, 05:56:43 AM by Dan »
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Offline discodermolide

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discodermolide: I can see the mass of my peptide having the azido group.


Well peptidismylife, I know people must learn about chemistry, especially something as complicated as peptides! But you don't have the required scientific approach, in my opinion. All you do is post here, before you try the chemistry, at least that is the impression you give.
Why not do the experiments, analyze the results and what you don't understand ask here. Also I would recommend that you do the required literature work before experimenting, most of this chemistry has been known for many years.
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Offline peptideismylife

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discodermolide: thanks for your advice. I have done it and I got my peptide (check it by LC/MS). It looks that there are other side reactions but could happen due to Im cleaving of the resin and I guess that also I got untruncated peptide and other side reactions. I just wondering about known side reactions, and yes I check it in the literature and I didnt find anything related with the Fmoc deprotection and azides. But as I said, thanks for your help as well as your advices.




Offline discodermolide

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discodermolide: thanks for your advice. I have done it and I got my peptide (check it by LC/MS). It looks that there are other side reactions but could happen due to Im cleaving of the resin and I guess that also I got untruncated peptide and other side reactions. I just wondering about known side reactions, and yes I check it in the literature and I didnt find anything related with the Fmoc deprotection and azides. But as I said, thanks for your help as well as your advices.

A resin, first I read about a resin, I thought you were doing solution phase!


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Offline Åke

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To appreciate how stable an aliphatic azide can be, please check out the recent total synthesis of Pactamycin.1 Yes, the alkyl azide is taken throughout a 20 step linear sequence :o

1. Hanessian, S.; Vakiti, R.; Dorich, S.; Banerjee, S.; Lecomte, F.; DelValle, J.; Zhang, J.; Deschênes-Simard, B. Total Synthesis of Pactamycin. Angew. Chem., Int. Ed. 2011, 50, 3497-3500 http://onlinelibrary.wiley.com/doi/10.1002/anie.201008079/abstract

Offline peptideismylife

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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...

Offline peptideismylife

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any idea?

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