[gspsaku]

So we received a homework assignment and there are a few questions I am not sure about. Here they are:

1. So we are given the Melphalan and we are supposed to draw the structure in an aqueous buffer at a pH of 2.0. What does that look like? We certainly did not cover this in class and it's not in our Biochem book. Any suggestions or help would be much appreciated. Is it as simple as protonating the two amine groups and the carboxylic acid?

2. We are given amoxicillin which has a phenol, an amine, two amides, a sulfide, and a carboxylic acid group. Which of these functional groups are acidic and which are basic? (I recall our professor mentioning that acidic and basic functional groups are only noted as such if they are ionizable and I don't believe we can ionize an amide, correct?)

[Babcock_Hall]

According to our Forum Rules (red link near the top of the page), we cannot help you until you show us your attempt or give your thoughts.  You could start by finding the pK_a values.  You are correct that amides do not ionize under typical conditions.

[gspsaku]

According to our Forum Rules (red link near the top of the page), we cannot help you until you show us your attempt or give your thoughts.  You could start by finding the pK_a values.  You are correct that amides do not ionize under typical conditions.

You must be a fellow Badger, I assume?

1. So with Melphalan, we have two different amine groups which have a pKa of roughly 10.5ish (protonated). Since the pH is 2.0, it's in an acidic medium and the pH is less than the pKa of the amine groups therefore the amine groups get protonated. The carboxylic acid has a pKa of around 4 therefore the pH is less than the pKa so the H stays on. Is this correct?

2. I believe alcohols, phenols, and the amide in amoxicillin will not ionize therefore what we have left is an amine group, a carboxylic acid, and a sulfide, all of which will ionize. The amine is basic, the carboxylic acid is acidic and the sulfide is acidic. Is this correct?

[Babcock_Hall]

Yes, I was a graduate student in biochemistry.  The ice cream was great!

1.  The pK_a values of the carboxylate groups of amino acids is depressed, relative to simple carboxylic acids (roughly between 1.9 and 2.4--See the table in Nelson and Cox's textbook).  This makes for a modest amount of ambiguity in this problem (I would probably assume a pK_a of 2 and go from there, just for the sake of simplicity).  I agree with respect to the two amino groups. 
2.  The pK_a of phenol is about 10.  Can you show what proton on a sulfide will dissociate?