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.

    images/download/attachments/1806726/redblue1.png

    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.

    images/download/attachments/1806726/redblue2.png

    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.

    images/download/attachments/1806726/redblue4.png

    Fig. 3 Dynamic red & blue colouring schema

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

    images/download/attachments/1806726/redblue6.png

    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 images/download/attachments/1806726/redblue7.png images/download/attachments/1806726/redblue8.png

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