Protonation and Partitioning

    Very often drug-like molecules are weak acids or bases with multiple low-energy ionization states. The reliable prediction of these states is essential during pharmaceutical research or the characterization of various organic and inorganic chemical processes. These functions provide a robust toolkit to predict protonation related molecular properties.

    Major microspecies

    The Major microspecies Plugin calculates the dominant protonation state of a molecule at a specified pH.

    For more information regarding this plugin, see Major Microspecies Plugin.


    Returns the number of microspecies.

    Isoelectric Point

    The isoelectric point (pI) is the pH at which a molecule carries no net electrical charge. The Isoelectric Point Plugin calculation considers all macro ionization states of an ionizable molecule across the pH range. The net charge at a given pH is calculated from the weighted sum of the macro distribution.

    Proteins have minimal solubility at their isoelectric point. The mobility of a molecule is minimal at pI and so it is an important parameter for electroanalytical separation techniques.

    For more information regarding this plugin, see Isoelectric Point Plugin.


    Returns the isoelectric point value.



    Returns the octanol/water partition coefficient, which is used in Quantitative structure-activity relationship (QSAR) analysis and rational drug design as a measure of molecular hydrophobicity. The calculation method is based on the publication of Viswanadhan et al. The logP value of a molecule is composed of the increment values of its atoms. Though logP is generally calculated for the neutral molecule forms only, this function can handle ionic species as well, owing to the improved algorithm.

    For more information, see logP Plugin.