Tautomers

Tautomers are organic compounds that are interconvertible by tautomerization. Tautomerization results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and an adjacent double bond. Usually the catalysts of these reactions are acids or bases. In solution there is an equilibrium state between the tautomeric forms. Some types of tautomers: ketone-enol, amid-imidic acid, lactam-lactim, enamine-imine tautomeric forms. The Tautomer Generation Plugin is able to calculate tautomers based on many user-defined options.

Options

Calculation

Dominant tautomer distribution: calculates the distribution of different tautomer forms present at the given pH.
Canonicalization: calculates a unique tautomer form for the input structure by default.
Major tautomer: gives the first structure from the dominant tautomer distribution.
All tautomers: combinatorially generates all possible tautomers. If any deuterium or tritium is involved in the tautomerization, isotopes are not removed; rational tautomer generation mode can be activated.

Max. number of structures

Maximize the number of structures to display.

Consider pH effect

Takes into account the protonation states at given pH. Applicable for Major tautomer and Dominant tautomer distribution calculations.

Normal tautomer generation

This scope narrows down the possible tautomerization paths and results in chemically more relevant tautomer forms according to our model. This is the strict scope in our model.

Set max. allowed length of the tautomerization path

Sets the number of bonds (a path) which are considered by displacing a double bond.

Protect aromaticity

If checked (default), the aromaticity is kept.

Protect charge

If checked (default), charges of atoms are kept during calculation.

Exclude antiaromatic compounds

If checked (default), any tautomer structure having an antiaromatic ring system will be discarded.

Protect double bond stereo

If checked, all double bonds with stereo information remain intact. If unchecked (default), tautomer regions will lose the double bond stereo information, any other stereo information in the molecule is kept intact.

Protect all tetrahedral stereo centers

If checked, stereocenters are not included in the tautomerization. If unchecked (default), tautomer regions will lose the tetrahedral stereo information, any other stereo information in the molecule is kept intact.

Protect labeled tetrahedral stereo centers only

If checked, stereocenters labeled with chiral flag or MDL Enhanced Stereo Represenation flags will not be included in tautomerization, other stereocenters will.

Protect ester groups

If checked, ester groups are not taking part in tautomerization.

Ring-chain tautomerization is allowed

This option can be activated when "All tautomers" function is selected; if checked, tautomer generation will take into account the possibility of ring closure.

Structure column

The structure column.

Input Ports

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

Output Ports

: Output table that contains tautomer structure.

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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: 2024-04-18

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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