logD

Compounds having ionizable groups exist in solution as a mixture of different ionic forms. The ionization of those groups, thus the ratio of the ionic forms depends on the pH. Since loP describes the hydrophobicity of one form only, the apparent logP value can be different. The logD represents the octanol-water coefficient of compounds at a given pH value.

Options

Method
  • Consensus: this method uses a consensus model built on the ChemAxon and Klopman et al. models and the PhysProp database.
  • ChemAxon: this method is based on ChemAxon's own logP model, which is based on the VG method (derived from Viswanadhan et al.).
  • User defined: if a training set of structures and corresponding experimental logP values is available, it can be used as a database for logP calculations.
LogP training ID
If the User defined method is selected, this dropdown list becomes active. All created training sets are listed here. Choose the one you want to apply for the calculation.
Electrolyte concentration
  • Cl- concentration: can be set between 0.1 and 0.25 mol/L.
  • Na+/ K+ concentration: can be set between 0.1 and 0.25 mol/L.
Use pKa correction library
A custom pKa training library for the compounds may be used. First, create a training set for your compunds, which then will appear in the dropdown list. If the option is checked, this list becomes active.
Consider tautomerization/resonance
In case of tautomer structures, all dominant tautomers at the given pH are taken into account during the logD calculation.
Reference pH value
The logD at the given reference pH value are calculated.
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 logD.

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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:

v5.2

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v240101
On NodePit since: 2023-12-06
Last update: 2024-04-19
Tags: Streamable
KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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