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 p K a 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