To set formal charge:

• Read in a chemical spreadsheet File/Open SDF
• Chemistry/Set Formal Charges
• Enter the name of the chemical spreadsheet (table).
• Choose the option to either make Charge, Make Neutral, Auto using ICM pKa Model or NN Assisted pKa Model Equilibrium.
• Select the groups you want to charge or neutralize.
• The charges will automatically be added to your table.

About the Methods

Auto using ICM pKa Model The method for pKa prediction is unpublished/proprietary. It is a machine learning (PLS) model based on contributions of various molecular graph fragments to atomic pKa, trained on a carefully curated set of experimental pKa values.

NN Assisted pKa Model Equilibrium This is a new neural network model has been introduced for pKa prediction based on a chemical graph convolutional architecture with enhanced propagation through conjugated systems. The model captures long-range electronic effects, improving the treatment of resonance-stabilized functional groups and delocalized charge distributions. Training was performed using MolSoft’s in-house, diverse, manually curated pKa dataset.