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The Chemical Bond


Chemical Thermodynamics and the Equilibrium State


Acids and Bases

Organic Acids and Bases

Here is an interesting fact, a step beyond MCAT prerequisite knowledge, maybe, but representative of the kind of subject matter you will often see in MCAT passages. Secondary amines are more basic than both tertiary and primary amines. Why is that? How could that be?

Two separate substituent effects are involved, which operate in different directions. Alkyl groups increase basicity by stabilizing the ammonium cation by donating electrons inductively. (In the gas phase, this is the only pertinent substituent effect, so tertiary amines are the more basic in the gaseous phase). In aqueous solution, the increased alkyl substitution decreases the ability of the ammonium cation to form hydrogen bonds with water molecules. In other words, tertiary ammonium cations are less able to disperse positive charge through solvation than secondary amines.

In summary, while secondary ammonium cations aren't as inductively stabilized as tertiary ammonium cations, the difference is more than made for up by the solvation of the secondary ammonium cation by water molecules.

Acids and Bases

Organic Acids and Bases

Organic Acids and Bases


If the pH of the surrounding solution environment is below the pKa of a functional group the predominate form will be the acidic form of the group. The Henderson-Hasselbalch equation serves as good conceptual shorthand for this relationship.

The acidic form of an amine group is the ammonium cation, so if the pH is below the pKa of the amine, it will be in the ammonium form.

Lysine and arginine are the amino acids with amine side chains. Because the typical pKa of a lysine side chain is 10.0 and that of an arginine side chain is 12.0, if a protein has a high percentage of lysine or arginine, at neutral pH, the protein will be positively charged. This is a favorite concept for the MCAT.

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