Response to "a fast and simple method to calculate protonation states in proteins"

A strong acid is a compound that dissociates completely in an aqueous solution and produces a concentration of hydronium ions equal to the initial concentration of acid. For example, 0.20 M hydrobromic acid will dissociate completely in water and produces 0.20 M of hydronium ions and 0.20 M of bromide ions.

Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:

The ionization-constant expression for a solution of a weak acid can be written as:

A polyprotic acid contains more than one ionizable hydrogen and undergoes a stepwise ionization process. If the acid dissociation constants of the ionizable protons differ sufficiently from each other, then the titration curve for such polyprotic acid generates a distinct equivalence point for each of its ionizable hydrogens. Therefore, titration of a diprotic acid results in the formation of two equivalence points, whereas the titration of a triprotic acid results in the formation of three...

Polyprotic acids of the type H2M constitute two ionizable protons. As a result, on titration with a base, they exhibit two equivalence points in the titration curve. During titration, the species H2M, HM−, and M2− will be present in the solution at different points. The fractions of H2M, HM−, and M2− present at the various instances of the titration are denoted by α0, α1, and α2, respectively.
A graph with the alpha values is plotted against the volume of base added during titration. Here, a...

Titration of a polyprotic acid, which contains multiple ionizable protons, involves distinct dissociation steps, each with its own dissociation constant (Ka). Each successive Ka is weaker than the previous one. In the titration of a polyprotic acid like sulfurous acid with a strong base such as sodium hydroxide, the base first neutralizes the initial ionizable proton, forming an intermediate species (e.g., hydrogen sulfite ions). This step's titration curve resembles that of a weak monoprotic...