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Author: Subject: How to get rid of iron
mick
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[*] posted on 14-2-2005 at 15:10
How to get rid of iron


I have been doing a bit of research on the side at work, part-time. Everthing was OK, run through all the reactions and the yields have been good or better. Get to near the end and the one reaction is sensitve to iron at catalytic levels. The stuff I have made (0.5g) is a waste of space because it is contaminated with iron and stuff.
I have just washed the filter aid (cellite) and all the the sand that I used for packing on columns with HCl and the colour says that there is iron there. The compound is a sugar attached to a purine, I have not worked out how to post a formula yet.
The stuff is insoluble in organics, slighty soluble in alcohols with heat.
Soluble in hot water and crystalizes out with a brown layer (the problem).
The stuff is soluble in conc ammonia.
I can not think of a way to get rid of the iron short of using H2S.
I have tried a strong acid ion exchange resin and the compound is only washed off under the conditions that washes everything else
off.
If anyone has an idea, much appreciated
mick
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tom haggen
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[*] posted on 14-2-2005 at 15:41


Well if the iron is bonded at a molecular level then I couldn't say. But if it's simply a composition maybe you could rig some kind of magnetic filtration device.

EDIT: I guess iron would be an ionic bond and not a molecular one. But you get the picture.

[Edited on 15-2-2005 by tom haggen]




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[*] posted on 14-2-2005 at 16:32


I'm assuming you mean ionic Iron. The ions aren't ferromagnetic, so that won't help. What you want is (cat)ion exchange resin, loaded with something that won't bother you (H+, Na+). Of course, separation would be lousy if the iron is strongly bound by whatever is in your solution. You could try adding something to chelate it more strongly. Or you could try reducing it to the metal with, say, zinc.

BTW: Sand? As in the stuff dunes are made of? Isn't that too coarse for chromatography? Or are you doing something else with it? You probably already know Iron is a common contaminant of silica sand.
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[*] posted on 14-2-2005 at 17:34


So you are using a sugar attached to a purine? Is it one of the building blocks of DNA, a nucleoside?
In any case- I suggest you wash your mix with EDTA, it should complex the iron. See if it still crystallises out in a 'brown layer' if EDTA is present.
Alternatively, iron chromate is quite insoluble, so it might help to add some sodium chromate to precipitate the iron before attempting crystallisation.

So you judge the presence of iron by colour? Now, I am sorry, but it isn't necessarily iron. High heat may cause the same colour, or polymerisation, or whatever. Did you do a specific test for iron ions?? I believe there are some involving prussiates.
I'd bet it's not iron that's causing the problem. It's unlikely that an ion exchange column co-elutes the 'brown stuff' together with your nucleoside.

Apart from that, if you really want decent advice, it might be useful to give some more detailed information on what exactly you made, and how you made it....




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[*] posted on 15-2-2005 at 15:18


I would avoid adding chromates to something sensitive as DNA...



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[*] posted on 15-2-2005 at 15:59


Sensitive? I thought we evolved from it.:o



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mick
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[*] posted on 16-2-2005 at 10:49


Thanks for the info.
I assume the iron is ionic and I assume that iron is the main problem.
I think a strong chelating agent has got to be worth a try, never had much to do with them. I am a straight forward synthetic organic chemist from history. The techniques in bioorganic chemistry are a bit new to me. I will have a look to see if you can get solid supported chelating agents which would be the easiest but there is plenty of EDTA around.

I know from a past large scale prep of a thiol amino HCl that celite filter aid contains iron since it was catalizing the oxidation to the disulphide and the stuff turned green when it picked up water. Changed to some filter aid called solkaflock (I think that was what it was called) which was low in iron and every thing was OK (except for one batch that was returned and we found a works spanner in one of the keg!!!!). Measured the iron (as the thiocyanate I think) quite accurately using an old (now very old) colourmetric
instrument made out of matt black painted wood.

I have washed the filter and sand that I am using with 5M HCL, the wash HCl was very greenish.

I use the sand for the flash silica chromatography. Rather than very expensive , easily broken commercial columns. Using a standard parrallel sided separating funnel, put a plug a glass wool inside above the tap, add sand to fill the tappered bit, add 5-6" depth of the right grade of silica, tap to pack the silica, added some sand on top, add solvent and pump through with a fish tank pump to degas the column. If the sample is pre-absorbed onto silica I add some sand on top so when adding solvent the sample layer is not disturbed (the separating always seems to be better with dry packing rather than slurry packing).

The reaction I am having a problem with is trying make the dimethoxytrityl protected nucleoside analogue. The starting material gave a very clean NMR spectrum (d6-DMSO), no organic crap, I thought it would be straight forward. First reaction I saw a hint of it (shows up orange with vanallin reagent on TLC) but lost it on work up. Tried it again and nothing. Tried a few other conditions and nothing. When you only have 0.3g to play with I tend to be careful. Then I found out the reaction is sensitive to catalytic amounts of iron (and other metallic ions I assume). This is the only reason I can think of for the complete failure or the reaction

The work has been to develop a practical synthetic route to a family of A, C, G, T and others of deoxyribose nucleotide analogoues . The idea is that these could form strongly bound, site specific triplexes with the DNA double helix. The stuff in the lit. suggests triplex forming oligonucleotide have potential as anti HIV, viral, cancerous tumour (a long way off?). Tagetting RNA is at clinical stages, targetting the specific bit of DNA responsible for the RNA that causes problems might be better, I do not know. Interesting. Recently similar stuff is being suggested for molecular computers, over my head.

The work is part off my part-time PhD. I have run out off time extentions and the powers that be have terminated my registration. However I have appealed and the termination has been suspended until the appeal is heard (weeks not a month). The plan is to submit the thesis with the appeal and get a bit of time for corrections to tidy thing up.

A ref to the stuff
SYNLETT (2): 335-337 FEB 2 2004

Hope thats enough info

mick

And then the last F******, B******, F******, etc, etc, etc, reactions do not play the game.

I still like thinking that I am a qualified and competant chemist
I dream on.

mick

[Edited on 16-2-2005 by mick]
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[*] posted on 16-2-2005 at 13:29


Quote:

Sensitive? I thought we evolved from it.


Maybe, but it's still quite a sensitive molecule from a chemical point of view. Hexavalent chromium is carcinogenic, which means it probably interacts with DNA...




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[*] posted on 16-2-2005 at 14:00


I'm probably missing something here because I'm tired but what would happen if you dissolved the stuff in water (or at least, wet alcohol) and added sodium bicarbonate?
Would the iron drop out as the hydroxide, and would the product survive at pH8?
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[*] posted on 3-3-2005 at 14:10


Sodium oxalate could precipate iron. But I dont know if it will fuck up the rest of the reactions, and how it could be removed.,



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