Specifying Fragment Placement Behavior

i_fragplace.tif
The small triangle above the Current Fragment area of the GaussView control window can be clicked to reveal some advanced options to specify how new fragments are joined to an existing molecular structure. The Mode popup allows you to select the settings (in which case, all fields are disabled), to specify Custom settings, or to restore the previously-used (Old) non-default settings (also nonmodifiable). You must select Custom in order to make changes to these items. The values for these three groups of settings can be specified in the Building Preferences.

There are two panels in this area. The Before panel, pictured below, sets restrictions for how fragments may be added to a structure. The After panel (the third image) specifies how the structure is treated after a fragment is added.

Here are some preliminary definitions necessary for understanding the options in these panels:

These are the items in the Fragment Placement Before panel:

bld_before.tif
Fragment Placement Restrictions

The items in this window set restrictions on the circumstances in which fragments may be joined to an existing structure. This window shows the default values.

bld_after.tif
Structure Options After a Fragment Placement

The options in this panel allow you to select actions for GaussView to perform automatically after a fragment is added to a molecular structure. The settings in this example are the defaults.

These are the items in the After panel:

The next three items activate electron bookkeeping at the target atom site. Note, however, that non-terminal atoms are not affected. Also, GaussView does not reduce or elevate the bond type to satisfy valency requirements.

The remaining options enable automatic cleaning operations, and they are self-explanatory: Optimize Dihedral Angle About New Bond, Apply “Clean” Around Hot Atoms, and Apply “Clean” to Whole Structure.