Figure 14. Deleting a Dangling Bond (Open Valence)
The Delete Atom button may be used to remove atoms and dangling bonds. An example of the latter is shown at the top of the molecule.
The Add Valence button attaches additional valences (shown as hydrogen atoms) to the center clicked with the mouse. The new valences will be placed as far as possible from the other atoms attached to the center.
Similarly, the Delete Atom button removes atoms and open valences. When used, the function will eliminate the selected atom and all single valences (hydrogens) attached to it. It may also be used to remove a dangling bond by clicking on the bond stick (see Figure 14).
Figure 14. Deleting a Dangling Bond (Open Valence)
The Delete Atom button may be used to remove atoms and dangling bonds. An
example of the latter is shown at the top of the molecule.
The Clean button and Edit=>Clean menu item both adjust the geometry of the molecule, based on a defined set of rules, to more closely match chemical intuition. The results are only approximations and are not intended to be perfect. Geometries may require adjustment for non-classical cases such as transition states.
The GaussView clean function may be customized via the Clean Controls preferences panel.
The Rebond button and Edit=>Rebond menu path both initiate a rebonding process in which GaussView reidentifies bonded atoms, based on a distance algorithm. Note that Gaussian does not use the bond information of the screen for calculations. This information is presented only to make it convenient for you to visualize the chemistry of the molecule.
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