pKa

Most molecules contain some specific functional groups likely to lose or gain proton(s) under specific circumstances. Each equilibrium between the protonated and deprotonated forms of the molecule can be described with a constant value called pKa. The pKa Plugin calculates the pKa values of the molecule based on its partial charge distribution.

Options

Mode
micro, macro: micro and macro acidic dissociation constants.
Acid/base prefix
  • static: submitted ionic forms are converted to their neutral forms (adding or removing protons) and their pKa is calculated.
  • dynamic: the pKa of ionic forms are calculated, not their conjugated acids or bases.
Min basic pKa
Widens the calculation range because weak bases will have lower pKa values than the default -2.
Max acidic pKa
Widens the calculation range because weak acids will have higher pKa values than the default 16.
Temperature
Setting the temperature in Kelvin.
Correction library
  • Use correction library: check this box to use a file with experimental data for the calculation.
Consider tautomerization
Checking this option, the most feasible tautomer and resonance structures are considered as subject of the pKa calculation.
Structure column
The structure column.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains pKa.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.4

A zipped version of the software site can be downloaded here.

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v240300
On NodePit since: 2024-12-06
Last update: 2024-12-21
Tags: Streamable
KNIME versions: v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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