Chromatography Forum

Hey!

I have some doubts. I am working with peptides and I have different functionals groups to be protonated. I am carrying out a MS detection and I would like to know which functional group is proner to be protonated.

alkyl-NH2 (secondary amine)

alkyl-OH.

or R-NH-R (primary amine). In fact i have to say that this primary amine corresponds to the peptide bond. (NH-C=O).

I would say that its proner to be protonated alkyl-NH2....but Im not sure...

If somebody could help me...

Thanks in advance.

Problemeste


This sort of info should be available in a first or second year level university organic chemistry book.

If you look around on line, you can find a table of pK b values (b shold be subsript).

An amide bond is not the same as an amine.

Your "secondary" amine is actually primary, an amide is not an amine, as pointed out.

nooooo, be careful, be careful! Chemistry in spray chambers (and even more so, in those parts of a mass spec that are under vacuum) is not identical to chemistry in simple solution. To take a simple example, in aqueous solution, primary amines are more basic than secondary, but this is because the cation of a primary amine is greatly stabilised by hydrogen bonding to the water. In the gas phase, secondary or tertiary amines may be more basic than primary amines if the groups around the N are electron-donating (e.g. alkyl groups). Interpret text-books with care. They are biased towards synthetic chemistry in solution. (And interpret my posting with even more care; I have little formal training in chemistry, and that a long time ago).

lmh, for the last ~40 years I have considered and partially experienced secondary amines to be more basic than primary in solution, unless you have certain substitution. Also, I always considered gas phase reactions much simpler than wet (solution) chemistry.

OK, sorry, I exaggerated and over-stated things! The point I was trying to make was that ammonia has a pKa of 9.25, relative to Me-NH2 at 10.64, i.e. addition of Me makes it more basic by 1.4 units. Dimethyl-NH has a pKa of 10.77, so the extra substitution has much, much less effect than it "should", a mere 0.13 units. A further substitution to trimethyl-N gives pKa 9.8, less basic than any but NH3, the effect I had in mind when I wrote my misguided reply.
The point was, though, that the solvent is very influential on acidity and basicity, and it's not clear to me that spray-chamber conditions are all that similar to those where pKa values are typically measured. I'd agree that gas-phase ought to be a lot simpler, but I'm no chemist, and never ventured out of aqueous solution. Thanks for setting me right (as usual; I learn a lot here).