Step 1. Input compounds
The pKa calculation uses the following equation,
HA ----> A- + H+ Ka = [A-][H+]/[HA] pKa = -log Ka
. Therefore, it requires the user to provide both the deprotonated (A-) and the protonated (HA) forms of the compound.The user has two options to input the structure of the molecule,
a) Draw it with the plugin from PubChem. While drawing, the plugin will generate a SMILES code for your structure. Once finished, just paste the SMILES code to the frame on the right. Remember to draw the point charge(s) explicitly, if your compound is cation/anion/zwitterion!)b) Upload your own coordinates for the structure. Structures in xyz, pdb, sdf, and mol2 are supported.
NOTE: The SMILES code is a simplified version of chemical notation, and it does not handle proton well. If protons are important in your structure, you'd better upload your own coordinates in xyz format.
