[runcyclexcski]

Hi all,

I am a biochemist with minimal organic chemistry capabilities: I only do click-, maleimide- and NHS-based coupling of peptides, DNA and proteins in aqueous solutions. I do have access to an HPLC. May I ask if there is a straightforward method to make 5-functionalized 1-chloro-pentane (or 6-functionalized 1-chlorohexane). By "functionalized" I mean groups that could then be coupled to standard building blocks in biochemist-friendly conditions (no gloveboxes, refluxes, etc). Examples of functionalized chloro-pentane/hexane could be:

Cl-(CH2)5-NH2 (couples via NHS)
Cl-(CH2)5-COOH (EDC)
Cl-(CH2)5-N3 (click)
Cl-(CH2)5-C|||CH (alkyne) (click)
Cl-(CH2)5-SH (couples via mal)
Cl-(CH2)5-NHS (couples via NH2)
Cl-(CH2)5-mal (couples via HS)

Sigma ssells Cl-(CH2)5-I -- are Cl and I reactive differently? Also, I found Cl-(CH2)5-OH, not sure what I can do with it

Cheers!

[Dan]

Sigma ssells Cl-(CH2)5-I -- are Cl and I reactive differently? Also, I found Cl-(CH2)5-OH, not sure what I can do with it

Note: I have highlighted key search terms for you in bold.

Yes, iodide is a much more reactive leaving group than chloride. New groups can be introduced by S_N2 displacement of iodide with a nucleophile (e.g. azide displacement, alkyne alkylation). Note though, that iodide is a good nucleophile and there is a possibility that the iodide released could react with the alkyl chloride (Finkelstein reaction). The alcohol may be a better option in parctice; it can be converted into a good leaving group (a sulfonate leaving group e.g. tosylate, mesylate or triflate) and engaged in S_N2 reactions.

Amines are available through azide reduction, maleimide synthesis is usually performed by condensation of amines with maleic anhydride.

Carboxylic acids are available through alcohol oxidation, and can be converted to NHS esters via their acid chlorides

You will need a suitably equipped chemistry lab to do these experiments, but they are straightforward.

Finally, I would leave the thiol unless you absolutely must prepare it (stench). The only thing worse than working with thiols is an inexperienced chemist next door working with thiols!

[Alwin Kristen]

Finally, I would leave the thiol unless you absolutely must prepare it (stench). The only thing worse than working with thiols is an inexperienced chemist next door working with thiols!

Because of the smell, right? Rotten eggs, garlic... uh, my favorites.

[runcyclexcski]

Hey-hey, thanks a lot for the responses! Regarding the azide displacement... this is good b.c. I could then use click chemistry. I guess I could do it in DMSO? I like azide, b.c. it's not as water labile as say NHS or Mal.

Wouldn't Cl also get displaced as well(by the azide), or would I have to play with the conditions to favour Cl over I? I guess, even if both Cl and I got replaced by N3, I do not care, the double-species won'be reactive for what I want.

Another thing is how to get rid of thefree  azide after the reaction is over... extraction with an organic solvent? I could use an HPLC, but would prefer some simple washing approaches. I remember I once coupled azide to polysryene beads... that was a blast to wash, as PS is not water-soluble.

BTW, as a biochemist I do not care about the stink of SH, we use bme and dtt everyday, and there is stuff with much, much, worse smell... thiophenol and cadaverine come to mind.

[runcyclexcski]

Further to my note on azides: this book lists remarkably simple conditions of converting halo-alkanes into azido-aklanes (water at room temp... sign me up!). I can get 1-iodo-6-chloroxane from Sigma. The only question is how easy it is to selectively modify I over Cl. Purification seems easy, too. And... I should be able to follow the progress of the reaction with something simple like a TLC plate, right?

Science of Synthesis: Houben-Weyl Methods of Molecular Transformations

[Dan]

I can get 1-iodo-6-chloroxane from Sigma. The only question is how easy it is to selectively modify I over Cl.

The rate of substitution of iodide is much faster than chloride. You can cool down the reaction to improve selectivity if necessary, but I doubt you will need to. Using 1 molar equivalent of azide (no excess) will limit formation of 1,6-diazidohexane, but again I would expect this to be minimal unless the reaction is heated (but it would be catalysed by the potential Finkelstein side reaction I mentioned earlier). Another option is to use an even better leaving group than iodide, like triflate (which you could form from 6-chlorohexan-1-ol, but is generally done at cryogenic temperatures, not sure if that would be an issue for you). This (or other sulfonates) is something to consider in the event of Finkelstein side reactions.

Another option is diphenylphosphoryl azide, which directly converts alcohols to azides.

Purification seems easy, too. And... I should be able to follow the progress of the reaction with something simple like a TLC plate, right?

Yes, generally you can just wash out the salts with an organic/aqueous extraction and often further purification is not necessary (depending on the next step).

Do be careful with sodium azide, it can be very dangerous. Never add acid.

Re: thiols, DTT is not very volatile and while it certainly smells bad, 6-chlorohexane-1-thiol will probably have a much higher vapour pressure and smell even worse (stronger). You'll probably also have to use NaSH to make it, meaning considerable potential for release of The Hot Breath of Satan H₂S.

[runcyclexcski]

Thank you, Dan! Excellent point on adding a molar equivalent of the N3 to avoid the Cl reacting... doh! I think I will stick with the azide approach then... the reagents are affordable, and I can take the N3 directly to the next step: will couple with an alkyne-dye, which will give me my desired product -- a fluorescently labeled chloro-hexane. I may have to add a PEG linker though, as the whole contraption is getting quite greasy. So I may couple an alkyne-PEG-amine linker first (available... pricey though), and couple the dye to the amine via NHS.

I am not very concerned about N3 explosions, as amount involved are minimal. I have a jar of NaN3... and will use 100 mg at the most.

H2S... we used to do pranks in middle school where we would mix photo-fixer (Na2S2O5?) with H2O2-soaked tablets in matchboxes and slide these into a classroom under the door. H2S would come out in all its glory in about 5 seconds, giving us enough time to retreat.

[Babcock_Hall]

Carboxylic acids (and some esters) with terminal -CH₂Br (I like to think of them as ω-Bromocarboxylic acids) are available commercially in a number of lengths.  They are useful, because the bromine can be displaced by a nucleophile.  We often trade out the bromine for iodine (which can be done at room temperature), because iodine is more easily displaced than bromine, which is more easily displaced than chlorine in nucleophilic substitutions, as Dan said.