[kelloggs93]

Hi! I'm a organic chemistry PhD student and I'm a new member of this forum
I'm writing because I have problems with a reaction. Normally, I do a lot of coupling reactions but this time I have a thiol terminal group that maybe causes troubles. I've never worked with thiols.
So, I did a coupling reaction between a cyclopeptides with a free primary amine and the mercaptopropionic acid. The condition of the reaction are:

-1 equivalent of amine
-1.2 equivalent of acid
-2 equivalent of Collidinen
-2 equivalent of DIPEA
-1.2 equivalent of HATU
-1.2 equivalent of HOAt
Solvent: DMFdry/DCM dry 1/3

The starter cyclopeptides that I'm using is a TFA salt.
Normally, I put amine, HATU, HOAt, DIPEA, Collidinen in a flask with DMFdry and DCMdry and then I put the flask in the ice for 15 min. I also degased the solvent and put the reaction under Ar. After this I add the acid and after I make the reaction goes to rt.

When I see the starting materials disappear on TLC, I do 3 extraction in EtOAc and then I dry the organic phase with MgSO4.
At the end of this process, normally I purify on reverse phase the crude, and and sometimes at the NMR I see the product that I want, but the yield is 5-10% and I don't know why.
Could maybe the thiols be trapped in the MgSO4? Do you have suggestions for this reaction?
Thanks to everyone!

Kelly

[Babcock_Hall]

While we wait for a synthesis expert, I can offer a few thoughts.  One is that the thiol group itself can be a useful method of detection and sometimes of quantitation.  One can use Ellman's reagent (DTNB) for both, assuming that the product is sufficiently water soluble.  The TNB anion has a molar absorptivity of 14,150.  You mentioned that your starting material is a TFA salt.  How many equivalents of TFA are present in the salt?  Are you sure that mercaptopropionic acid does not cyclize under your conditions?

[pgk]

1). Given the selectivity of thiols with bivalent metal cations, it is better to use anhydrous Na2SO4 as a drying agent in extractions, instead of anhydrous MgSO4 when working with thiol derivatives, though this might not have happened.
2). HATU side products of peptides that contain thiol groups, are reported in the literature. If this has happened, your peptide might be water soluble and might have passed in the aqueous phase during extraction. So, it is better to adjust the pH to slightly acidic before extracting.

Unveiling and tackling guanidinium peptide coupling reagent side reactions towards the development of peptide-drug conjugates, RSC Advances, (2017), 7, 50519-50526
http://pubs.rsc.org/en/content/articlehtml/2017/RA/C7RA06655D

[TheUnassuming]

I would guess the thiol is causing problems.  Its been a while, but I'm relatively sure a free thiol will be kinetically favored to do the coupling, but the amine is thermodynamically favored.   It could also be an issue with water solubility, which for me has been an issue when working with peptide or peptide like scaffolds.

For the thiol issue: when you TLC, are you seeing multiple new products or only one?  If you are seeing multiple, you might let it stir for longer and see if one or more of the spots disappears over time (what should be the thioester if its forming which should slowly convert to the amide if there is still free amine around).  The other option is to just use the thiol protected starting material.

For possible aqueous solubility: after doing your extraction, do any of the product spots stay in the aqueous layer?