 |
|
|
|
|
Tautomers are organic compounds that are interconvertible by tautomerization. Tautomerization reaction results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond. Commonly, the catalysts of these reactions are acids or bases. In solution a chemical equilibrium of the tautomers will be reached. Some types of tautomers: ketone-enol, amid-imidic acid, lactam-lactim, enamine-imine.
All tautomers of a compound can be determined with the help of the Tautomerization plugin. Following options can be adjusted in the Tautomers Options panel:
 |
Max. number of structures: maximize the number of structures to display.
Take canonical form: display the canonical structure of the molecule.
Show dominant tautomer distribution: display the percentage of different tautomers present at the given pH.
Decimal places: setting the number of decimal places with which the tautomer distirbution values are given.
Set max. allowed length of the tautomerization path: Path length: sets the number of bonds which are considered by displacing a double bond.
Consider pH effect: takes into account the protonation states at given pH.
Protect aromaticity: if checked (default), the aromaticity will be maintained.
Protect charge: defined charged atoms maintain their charge during calculation.
Exclude antiaromatic compounds: any tautomer structure having an antiaromatic ring system will be discarded.
Single fragment mode: if checked (default), the results are displayed in separate windows, if unchecked, the calculation handles unlinked molecules together and results are in the same window..
For example, the next structures (on the left) are the calculated tautomers of pyrimidine-2,4-diol. The tautomers shown on the result window below were generated taking into consideration the pH effect, and the dominant tautomer distribution is shown for each tautomer. The plugin is also able to generate the canonical tautomeric form (the generated canonical tautomer of pyrimidine-2,4-diol can be seen on the right).
 |
 |
The Resonance plugin generates all resonance structures of a molecule. The major contributors of the resonance structures can be calculated separately. Following options can be adjusted in the Resonance Options panel:
 |
Max. number of structure: maximize the number of structures to display (decrease calculation time).
Take canonical form: display the canonical structure of the molecule.
Take major contributors: select the most relevant structures.
Single fragment mode : if checked (default), the results are displayed in separate windows, if unchecked, the calculation handles unlinked molecules together and results are in the same window.
For example the two structures below, on the left are the major resonance contributors of diazomethane, while the structure on the right is the canonical form:
 |
 |
The Stereoisomer plugin produces all possible stereoisomers of a given compound. The plugin handles both tetrahedral and double bond stereo centers.
 |
Generate
only the R/S isomers are generated.
Generate all stereoisomers: all isomers are generated
Generate maximum: only the given number of structures are generated.
Filter invalid 3D structures: sterically restricted isomers are discarded.
Display in 3D: results are displayed in a 3D viewer.
Results are displayed in a 2D viewer by default:
 |
To replace your drawn molecule in the sketcher with any of the isomers shown, click on the structure then press "Select" at the bottom of the cells (the result window will be closed).
If "Filter invalid 3D structures" option is switched on in the Stereoisomers Options panel, the stereoisomers can also be displayed in 3D.
 |