Atom Menu

This menu contains all atom-related properties, for example, charge, atom radicals, maps, and many more.

Menu item

Icon

Description

Stereo > R/S > Off

N/A

Removes the absolute stereo configuration from a chiral atom along with the marking wedge bond.

Stereo > R/S > R

N/A

Sets the absolute stereo configuration on a chiral atom to R, marking it with wedge bond.

Stereo > R/S > S

N/A

Sets the absolute stereo configuration on a chiral atom to S, marking it with wedge bond.

Stereo > Reaction > Off

N/A

Sets the stereo configuration of the atom not to be considered during the reaction.

Stereo > Reaction > Inversion

N/A

Sets the stereo configuration of the atom to be inverted during the reaction.

Stereo > Reaction > Retention

N/A

Sets the stereo configuration of the atom to be retained during the reaction.

Stereo > Enhanced

N/A

See Stereochemistry for details.

Charge

N/A

Allows you to change the charge of an atom between [-128, 128]. The number of implicit hydrogens will be adjusted if possible to accommodate the new charge. Valence errors will be highlighted in red.

Valence

N/A

Allows you to change the valence of an atom between [0, 8].

Radical > Off

N/A

Removes the radical designation from an atom.

Radical > Monovalent

N/A

Sets Monovalent radical center.

Radical > Divalent

N/A

Sets Divalent radical center.

Radical > Divalent Singlet

N/A

Sets Divalent radical center with singlet electronic configuration.

Radical > Divalent Triplet

N/A

Sets Divalent radical center with triplet electronic configuration.

Radical > Trivalent

N/A

Sets Trivalent radical center.

Radical > Trivalent Doublet

N/A

Sets Trivalent radical center with doublet electronic configuration.

Radical > Trivalent Quartet

N/A

Sets Trivalent radical center with quartet electronic configuration.

Isotope

N/A

Sets or changes the isotope number of the selected element, or resets the default atom (no isotope) when it is set to Off.

Map

N/A

Sets map labels/identifiers on the selected atoms that do not change while altering the molecule. They are useful when dealing with reactions, and can be saved in SMILES and MDL formats.

R-group

N/A

Changes the selected atom to an R-group label. R-groups symbolize alternative substituents.

R-group Attachment

N/A

The selected atom becomes the attachment point for the substituent.

R-group Attachment Order

N/A

Changes the order (numbering) of the attachment points.

Link Node

N/A

Specifies query structures containing rings or chains of variable size.

Periodic Table

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Shows Periodic Table and query/atom property drawing window.

Edit Properties

N/A

Specifies the property of an atom.

Add S-group attachment

N/A

Creates an attachment point on the selected atom of an S-group.

Remove S-group attachment

N/A

Removes the highest-numbered attachment point from an atom of an S-group.

Label Editor

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Format the atom label and replaces/overwrites any atom/atom label in a structure with a (formatted) abbreviation group, list/not list, R group, alias, or pseudo atom. For more information, see Atom Label Editor.