I understand that the imidazole ring in histidine is aromatic. I also realize that it retains its aromaticity when protonated. I am wondering why this is not mentioned at all in basic text books such as Lehninger? Also, across the web there are a number of places claiming that histidine isn't aromatic in all cases. Another reason I am a little confused is, if protonation doesn't alter the aromatic nature, then why is histidine such a weak base?
This is one of my favorite charts demonstrating the complexity of amino acid properties:
Histidine is probably the most complicated amino acid in this regard (just compare how many circles it falls into). But don't undersell cysteine and methionine: those sulfurs exhibit some surprising behavior, especially when coordinated properly. Cysteine, of course, forms disulfide bonds, with methionine occasionally functioning as a methyltransferase.
Biochemistry textbooks make some oversimplifications because presenting the full messiness of these classifications is pretty confusing. Lehninger is the worst about this, especially when presenting math. Voet and Voet is probably the most reliable about presenting this complexity. I still think Lehninger is a better teaching textbook overall (I was first taught biochemistry from the 3rd edition), but I also recall spending a week being confused about a topic before someone pointed me at V and V and I realized Lehninger was oversimplified to the point of being wrong, in that case.
I am wondering why it is not mentioned at all in basic text books such as Lehninger?
Books are not flawless.
Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base?
Pyrroles have a weak basicity because of delocalization of the electron lone pair of nitrogen. It is the lone pair of nitrogen, in amines, which gives it basicity (Check Lewis bases and acids) .
In imidazole, the other nitrogen (N-2) has a free lone pair and does contribute to its basicity. As you pointed out before, imidazolium is a stable moiety and imidazole is a much stronger base than pyridine, although it is a weaker
(pKb ≃ 7) base than lysine
(pKb ≃ 10.5) and arginine
(pKb ≃ 12.48).
Imines are generally weaker bases than amines because the
sp2 hybridization of the former gives them a more
s-like character; this causes the lone pair to be held more tightly to the nucleus thereby reducing the basicity. Also, the C-N(2)-C angle is constrained (small) because of the planar ring. This again leads to a more
The strong basicity of arginine is because of the guanidium group.
The imidazole ring in histidine is indeed aromatic. But "aromatic amino acid" does not usually mean "amino acid with an aromatic ring". Rather, it indicates one or more particular chemical properties, such as high absorption at 280nm, or, better, its metabolic pathway.
Histidine as a stand-alone amino acid is a weak base, but this is mainly due to the amino group and acid group that every amino acid has. The imidazole ring itself has a neutral pKa.