[peptideismylife]

Hey,

I want to purify my porduct, Boc-Lys(N3)-OH. I want to do it by Column chromatography using Silica, but I am afraid about a possible deprotection of the Boc group due to this protecting group is not stable in acidic conditions (and silica is quiet acid...)

What do u think about it?

[Honclbrif]

If you're worried about your substrate's stability on silica gel, there's an easy test you can do:

Make up a square TLC plate, draw a baseline along two adjacent sides, spot your compound at the intersection, run the plate as you normally would, turn the plate 90°, and run it again. If your compound is stable it should fall on the angle bisecting the two sides you ran it up. If you find the spot significantly deviating from the diagonal, then it is probably degrading on the silica.

_{Do we get 2nd author on this paper?}

[Zainb]

The Boc group is very stable on silica gel,,, IBoc removed only on strong acidity conditions.

[discodermolide]

Mr or Ms Peptideismylife,
Judging from your questions and lack of response to answers to your questions, in particular mine,  I don't think you are cut out for organic chemistry, or at least peptide chemistry.
Why not look for something easier to do?

[Honclbrif]

Lighten up, Disco. I intended my comment to be a little good natured ribbing but I do realize such things do not translate well via the intertubes. I suspect Peptide is moving in from another branch of Science and is unfamiliar with synthesis or is a founding student of a group without any guidance from experienced members.

I was in the latter situation. You don't realize how valuable institutional memory is until you need to function without its benefit. The first few years were spent just figuring out how to get stupid day to day stuff working which is a little tough when you don't have someone around to tell you retrospectively obvious things like "drying ether with sodium sulfate doesn't work", or "HEPES gels will not work in TRIS-glycine buffer", or that one particular reference is gold and another is garbage that looks sparkly in the right light. I spent a hell of a lot of time cornering profs, post docs, and senior students in halls, offices, elevators, and buses to pick their brains about a lot of stuff, spent a lot of time reading various chemistry blogs, and going on marathon lit. sessions.

So cut him/her some slack; the point of being a student is to learn. Who here can claim they have ever learned without making a few stupid mistakes or asking a few stupid questions? My only criticism is that you must think about all of this stuff (the steps in your scheme) before you ever start mixing chemicals together. Seat-of-the-pants chemistry is a fast road to failures which cost a lot of time and money, accidents, or both.

[Yoker]

I've seen Boc groups fall off on silica columns and also on SCX cartridges. Honclbrif's advice is probably the best you can take to see if your compound will degrade. If the Boc group does come off, then theoretically you should be able to strip the deprotected stuff off the column as well (provided it's soluble in your mobile phase) and then put the Boc group back on with Boc-anhydride and DMAP. It adds an extra step but if you need the Boc group on then it's a must.

[OC pro]

In >90%+ cases Boc group will easily survive silica gel chromatography.

[discodermolide]

Lighten up, Disco. I intended my comment to be a little good natured ribbing but I do realize such things do not translate well via the intertubes. I suspect Peptide is moving in from another branch of Science and is unfamiliar with synthesis or is a founding student of a group without any guidance from experienced members.

I was in the latter situation. You don't realize how valuable institutional memory is until you need to function without its benefit. The first few years were spent just figuring out how to get stupid day to day stuff working which is a little tough when you don't have someone around to tell you retrospectively obvious things like "drying ether with sodium sulfate doesn't work", or "HEPES gels will not work in TRIS-glycine buffer", or that one particular reference is gold and another is garbage that looks sparkly in the right light. I spent a hell of a lot of time cornering profs, post docs, and senior students in halls, offices, elevators, and buses to pick their brains about a lot of stuff, spent a lot of time reading various chemistry blogs, and going on marathon lit. sessions.

So cut him/her some slack; the point of being a student is to learn. Who here can claim they have ever learned without making a few stupid mistakes or asking a few stupid questions? My only criticism is that you must think about all of this stuff (the steps in your scheme) before you ever start mixing chemicals together. Seat-of-the-pants chemistry is a fast road to failures which cost a lot of time and money, accidents, or both.

That may well be the case, but for example he/she has asked the DMSO question several times now.
He/she asked a question about azide group polarity http://www.chemicalforums.com/index.php?topic=49772.0
Which I answered as well as asking for clarification, no response. Is that the way to learn?
I don't think questions are stupid and would never say or think that. However an intelligent discussion is required to learn and if this person does not have the manners to reply how do they expect to learn?

[peptideismylife]

Thanks Honcibrif,

In fact this is something that I was thinking to do. I mean, what u mean, is a 2D TLC. The main product as well as the side products have to be in the diagonal...otherwise it means that my product is damaging in the silica. But the time that my sample would be in the column is not the same as in the TLC...

Anyway I will check it by 2D TLC and probably I will run a column with a small amount to see what happens. I found a protocol in which they are using HPLC preparative to purify but we don't have it....

Discodermolide, so sorry if I couldn't bring anything that makes this discussions more interesting...and my apologies for my poor background in organic chemistry...I hope I could improve in the future and show u my best....

Thanks to all....

[discodermolide]

Thanks Honcibrif,

In fact this is something that I was thinking to do. I mean, what u mean, is a 2D TLC. The main product as well as the side products have to be in the diagonal...otherwise it means that my product is damaging in the silica. But the time that my sample would be in the column is not the same as in the TLC...

Anyway I will check it by 2D TLC and probably I will run a column with a small amount to see what happens. I found a protocol in which they are using HPLC preparative to purify but we don't have it....

Discodermolide, so sorry if I couldn't bring anything that makes this discussions more interesting...and my apologies for my poor background in organic chemistry...I hope I could improve in the future and show u my best....

Thanks to all....

It's not a question of being interesting, we all learn from the discussions posted here, however, a monologue is not a discussion. For example you still did not respond to the polarity question of the azide group.

[fledarmus]

Thanks Honcibrif,

In fact this is something that I was thinking to do. I mean, what u mean, is a 2D TLC. The main product as well as the side products have to be in the diagonal...otherwise it means that my product is damaging in the silica. But the time that my sample would be in the column is not the same as in the TLC...

Time in contact with silica is something you control on a 2D TLC. You can leave the plate for as long as you want between the first and second development. If you are worried about whether solvent might be important, put the TLC plate on a glass plate and cover it with a watch glass so it doesn't evaporate. For me, it's never been an issue - if I haven't seen any decomposition letting the plate sit for 15 minutes or so between developments, I don't see decomposition on the column.

[peptideismylife]

Hey people,

Finally I run the column and I got my product. Afterthat I run a LCMS to see how pure was my product...and also a proton NMR. By LC/MS I could see one more peak that even before the column....and by NMR I could see also side products (but also tBu is there). Definitely something happens in the silica. It seems that the Boc group is quiet stable in the silica....but I am also afraid about a possible interaction between the carboxylic group of the amino acid and the silica groups. I am going to repeat the synthesis in order to get better yield....maybe doing HPLC preparative for purification...or also adding triethylamine in the column to avoid the Boc deprotection...

Data:

Boc-Lys(N3)-OH
Column: Ethyl acetate 4 / Toluene 1