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PrevICM User's Guide
7.16 Enumerate Formal Charge States

To enumerate formal charge states.

  • Read in a chemical spreadsheet File/Open SDF
  • Choose Chemistry/Enumerate Formal Charge States
  • Enter the name of the chemical spreadsheet (Molecular Table)
  • Choose the pH at which you wish to evaluate the charge
  • Choose a window value.
  • Click OK and a new table "_charge" will be displayed with the enumerated charge states.

About the Method

For basic charges the logic is following:

  • atoms with pKa > pH+window is always charged
  • atoms with pKa inside the range [ pH-window : pH+window ] will be enumerated as charged and uncharged.

For example if you have two centers with pKa within the range then four states will be generated ( [0,0] [+1,0] [0,+1] [+1,+1] )

For acids it is similar.

The method for pKa prediction is unpublished/proprietary.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.

Formal Charges

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