Re: Structurally, why are some acids stronger than others?

The most commonly used definition of an acid is a substance that can lose a proton (H⁺ ion):

HA <===> H⁺ + A^-

Thus, anything that makes A^- (the anion) a more stable chemical species will favor the right hand side of the equilibrium, and make HA a stronger acid.

There are two primary ways to help stabilize a negative charge:

1. The inductive effects of strongly electronegative atoms (O, N, F, Cl) or groups (e.g. NO₂), and
2. resonance effects such as the COO^- group. This matter is taken up in more depth in most organic chemistry textbooks-- check your library!

In your question, trifluoroacetic acid is a much stronger acid than acetic acid because the extremely electronegative fluorine atoms stabilize the negative charge on the trifluoroacetate anion relative to the acetate anion:

CF₃COOH <===> H⁺ + CF₃COO^-
K_a = 5.9 x 10^-1

CH₃COOH <===> H⁺ + CH₃COO^-
K_a = 1.75 x 10^-5

This discussion has ignored the effect of the solvent (usually water), polyprotic acids (capable of giving up more than one H⁺), and the conjugate acid of a base (e.g. NH₄⁺). You can find out more about these topics in your textbook.