Red and blue representation of pKa values

This manual explains the difference between the representations of coloured 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.

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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.

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Fig. 2 Calculated pKa 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.

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Fig. 3 Dynamic red & blue colouring schema

The result of the previous ammonia example with the non-default pKa calculation:

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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

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