Protonation and Partitioning in JChem for Excel

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.

JCMicrospeciesCount

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.

JCIsoelectricPoint

Returns the isoelectric point value.

Partitioning

JClogP

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.

JClogD

Returns the octanol-water distribution coefficient of the compound at any pH value. Compounds having ionizable groups exist in solution as a mixture of different ionic forms.
The ionization of those groups and so the ratio of the ionic forms depend on the pH. Since logP describes the hydrophobicity of one form only, the apparent logP value can be different.

For more information, see logD Plugin.

pKa

Most molecules contain some specific functional groups likely to lose or gain a proton under specific circumstances. Each ionization equilibrium between the protonated or deprotonated forms of the molecule can be described with a constant value called pKa. The pKa function calculates the pKa values of all proton gaining or losing atoms based on the partial charge distribution.

There is no upper limit for the number of ionizable atoms in the molecule and so the pKa function can also be used for proteins.

For more information regarding this plugin, see pKa Plugin.

JCAcidicpKa

Returns the acidic pKa value for the specified strength index.

JCBasicpKa

Returns the basic pKa value for the specified strength index.

JCAcidicpKaLargeModel

Returns the acidic pKa value for the specified strength index using a large model, which is optimized for structures having a large number of ionizable atoms. If the number of the ionizable atoms is smaller or equals to 8 it is advised to use the simple JCAcidicpKa function.

For more information, see A method for calculating the pKa values of small and large molecules , J. Szegezdi, and F. Csizmadia, American Chemical Society Spring Meeting, March 25-29th, 2007.

JCBasicpKaLargeModel

Returns the basic pKa value for the specified strength index using a large model, which is optimized for structures having a large number of ionizable atoms. If the number of the ionizable atoms is smaller or equals to 8 it is advised to use the simple JCBasicpKa function.

For more information, see A method for calculating the pKa values of small and large molecules , J. Szegezdi, and F. Csizmadia, American Chemical Society Spring Meeting, March 25-29th, 2007.