May 17 2024 Feedback.
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
 Chemical Spreadsheets
 Chemical Search
 2D Interaction
 Convert to 3D
 Find Bioisostere
 Calculate Properties
 Standardize Table
 Align/Color by 2D Scaffold
 Formal Charges
 Torsion Analysis
 Enumerate Formal Charge States
 Protonation vs pH
  List Species at pH
 Build Prediction Model
 Generate 3D Conformers
 Generate Tautomers
 Generate Stereoisomers
 Ligand Energetics
 Cluster Set
 PCA Analysis
 Visualize Chemical Space
 Compare Two Sets
 Merge Two Sets
 Select Duplicates
 Combinatorial Chemistry
 SAR Analysis
 Chemical Superposition
 APF Tools
Learn and Predict
Virtual Screening
Molecular Dynamics
3D Ligand Editor
Tables and Plots
Local Databases
PrevICM User's Guide
10.18 Protonation States vs pH

[ Concentration | Charge | List Species at pH ]

You can perform the following analysis of Protonation states vs pH using MolSoft's pKa Model:

  • Plot Concentration vs pH
  • Plot Charge vs pH
  • List Species at pH

To do this:

  • Read in a sd file or sketch the molecule of interest.
  • Right click on the chemical and choose Chemistry/Protonation states vs pH
  • Click on the tab for the analysis you want to undertake.

Concentration is percentage of that protonation form at certain pH. You may have mixture of of different species/states at some pH (e.g: 40% + 60%)

10.18.1 Plot Concentration vs pH

You will see a plot of Specie Fraction vs pH and the table will contain the specie fraction for pH The plot and table is fully interactive so you can click on either the plot or row and it will make a selection. You can also unselect and remove from the plot using the toggle button in the 'sel' column.

10.18.2 Plot Charge vs pH

You will see a plot of Charge vs pH and the table will contain the pH and the charge. There is an option to display the isoelectric point.

10.18.3 List Species at pH

A table will be displayed with the Specie and concentration.

Enumerate Formal Charge States

Copyright© 1989-2020, Molsoft,LLC - All Rights Reserved.
This document contains proprietary and confidential information of Molsoft, LLC.
The content of this document may not be disclosed to third parties, copied or duplicated in any form,
in whole or in part, without the prior written permission from Molsoft, LLC.