Defining Charge Transitions

Each macro-pK_a transition (observed in experiment) is associated with a transition between two neighboring charges (C to C-1) in the Macro-pKa workflow. There are two ways you can define the transitions to consider in the calculation: 1). specifying relative charges or 2). specifying a pK_a range.

In the output file (<jobname>.out), the macro-pK_a associated with a transition C to C-1 is reported as Macro-pKa (C to C-1). For example,

Macro-pKa (2 to 1) = 1.692
Macro-pKa (1 to 0) = 7.889
Macro-pKa (0 to -1) = 11.073

Define macro-pK_a transitions by relative charge

You can define macro-pK_a transitions by specifying the relative charges of the transitions that you would like to consider. For example, if a molecule has a total charge of 2, and you would like to calculate the macro-pK_a transitions of total charges 5 to 4, 4 to 3, 3 to 2, and 2 to 1, the maximum and minimum of relative charges associated with these transitions is 3 and -1. If any specified transitions involve unphysical protonations/deprotonations, that transition is not considered.

Define macro-pK_a transitions by pK_a range

To define macro-pK_a by pK_a range, a minimum and maximum pK_a needs to be specified. By default, the minimum pK_a is 2.0 and the maximum pK_a is 12.0.

For a given molecule with total charge C, the following steps are taken to determine the macro-pK_a transitions:

1. Tautomers are generated with charges C, C+1, and C-1

2. The macro-pK_a corresponding to the C+1 to C and C to C-1 transitions are computed using the Macro-pKa workflow

3. Two scenarios are possible for the macro-pK_a corresponding to the C+1 to C transition

   • If the macro-pK_a (C+1 to C) falls below the minimum pK_a, additional tautomers with increasing charges are not generated, and the macro-pK_a of transitions involving charges beyond C+1 are not considered

   • If the macro-pK_a (C+1 to C) is above the minimum pK_a, tautomers with charge C+2 are generated, and the macro-pK_a corresponding to the C+2 to C+1 transition is calculated. This newly computed macro-pK_a is compared to the minimum pK_a. The process of generating tautomers with increasing charges and calculating the macro-pK_a of the associated transition continues until the macro-pK_a falls below the minimum pK_a or until further protonation is not possible

4. Two scenarios are possible for the macro-pK_a corresponding to the C to C-1 transition

   • If the macro-pK_a (C to C-1) is above the maximum pK_a, additional tautomers with decreasing charges are not generated, and the macro-pK_a of transitions involving charges below C-1 are not considered

   • If the macro-pK_a (C to C-1) is below the maximum pK_a, tautomers with charge C-2 are generated, and the macro-pK_a corresponding to the C-1 to C-2 transition is calculated. This newly computed macro-pK_a is compared to the maximum pK_a. The process of generating tautomers with decreasing charges and calculating the macro-pK_a of the associated transition continues until the macro-pK_a falls above the maximum pK_a or until further deprotonation is not possible

Note that the minimum pK_a and maximum pK_a values define the limits at which the generation of the tautomers must stop, but they are not necessarily the boundaries of the lowest and highest predicted pKa values. The output file includes all the macro-pK_a computed in the process.