WebMO Help - Adjust Tool

Invoking the Adjust Tool

The WebMO Editor has an adjust tool for defining the precise conformation of atoms in a molecule. It is also used to adjust atomic charge, atomic hybridization, bond order, and chirality.

The adjust tool can also be used to manipulate a selection of atoms relative to the rest of the molecule.

The adjust tool is invoked with Tools:Adjust or on the toolbar with .


Adjust Tool Menu

Use the toolbar to invoke the adjust tool with . Select 2, 3, or 4 atoms. Then use , , or to adjust the bond length, bond angle, or dihedral angle.

Adjusting Geometry

Molecular geometry can be defined by bond length, bond angle, and dihedral angle, which are specified by selecting 2, 3, or 4 atoms, respectively.

Selecting atoms:

Changing geometry:

When changing a bond angle, all bond lengths remain unchanged. When changing a dihedral angle, all bond lengths and angles remain unchanged.

When 2, 3, 4 atoms are selected, the current bond length, bond angle, or dihedral angle is displayed in the status line. Lengths are in Angstroms, and angles are in degrees.

The order in which atoms are selected is extremely important when defining geometry. The first atom selected is the one that moves.


Adjust Tool and Bond Angle Dialog Box

Adjusting Atomic Charge, Atomic Hybridization, Bond Order

Set atomic charge:

Set atomic hybridization:

Set bond order:

Set atomic charges before cleaning-up because they factor into the available valence. Also, the sum of all atomic charges determines the molecular charge used in subsequent calculations.


Adjust Tool and Hybridization Menu

Adjusting Chirality

Chiral centers are atoms with four different substituents. WebMO can display the chiral label (R,S) and change the chirality of a chiral center.

Display chirality: Selecting a chiral atom will display is chirality on the status line. Choosing File:Preferences... and then on the Display tab choosing Labels:Stereochemistry will display the chirality of chiral centers on the atoms. Note that the molecule geometry must be cleaned up in order for the stereochemistry to be displayed or updated.

Invert chirality: Select a chiral atom and choose Adjust:Invert Chiral Center.


(2R)-2-Chloropropanoic Acid

(2S)-2-Chloropropanoic Acid