Red and blue representation of pKa values

This manual explains the difference between the representations of coloured pK_a values:

• Static red & blue representation of pKa values

• Dynamic red & blue representation of pKa values

Static red & blue representation of pKa values

The static (default) red & blue colour annotation is related to the ionization steps shown in the figure below.

Fig. 1 Static red & blue colouring schema

The static red & blue coloring schema does not depend on the ionic form of a molecule submitted to the pKa calculation. The next three species have the same pKa values and the same colour.

Fig. 2 Calculated pK_a of the deprotonated, neutral and the protonated forms of ammonia in the static red & blue colouring schema

Dynamic red & blue representation of pKa values

The dynamic (non-default setting) red & blue colouring schema depends on the submitted molecule.

Fig. 3 Dynamic red & blue colouring schema

The result of the previous ammonia example with the non-default p K _a calculation:

Fig. 4 Calculated pKa of deprotonated, neutral, and the protonated forms of ammonia according to the dynamic red & blue colouring schema

Differences between the static and the dynamic red & blue colouring schema are summarized in the following table.

	static	dynamic
Subject of calculation	neutral state of the submitted molecule	the submitted molecule
Blue color assigned to	the acid dissociation constant between the neutral base and its conjugated acid	the acid dissociation constant between the submitted base and its conjugated acid
Red color assigned to	the acid dissociation constant between the neutral acid and its conjugated base	the acid dissociation constant between the submitted acid and its conjugated base
setting in the Options panel

Tab. 1 Differences between the static and dynamic red & blue colouring schema