Select the options. These will allow you to turn on C as an acid, select N as an acid or base and select the temperature.
When you press the Select Atom button you will be presented with the molecule to be used for the calculation. The system will present the SMILES string you entered with the ionizable sites in red. Clicking one of the red atoms will select this atom as the ionizable site and circle it in yellow. Now pressing the Calculate button will calculate the gas pKa.
The system will first calculate the pKa in water and perform several Henry's constant (gas/liquid transfer energy) calculations and perform a thermodynamic loop calculation to generate the value of the gas pKa.
Click here to watch a tutorial video.