Specifying Fragment Placement Behavior

The small triangle above the Current Fragment area of the GaussView control window can be clicked to reveal some advanced options for specify how new fragments are joined to an existing molecular structure. The Mode popup allows you to select the Default 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 in Figure 44, sets restrictions for how fragments may be added to a structure. The After panel (see Figure 45) specifies how the structure is treated after a fragment is added.

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

• The target atom is the one selected with a mouse click.

• The hot atom is the atom in the new fragment that takes the place of the existing target atom when the two pieces are joined.

• A terminal atom is any atom bonded to only one atom.

• A terminal valence atom is a hydrogen atom or an open valence bonded to only one atom.

• A join-bond is a bond between the hot atom atom and any terminal atom. These are bonds that can be eliminated in the process of connecting the fragment to the target atom. When a fragment is joined to the target atom, there must be one join bond in the fragment for each corresponding bond to the target atom.

Figure 44. 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.

These are the items in the Fragment Placement Before panel

• Target and Fragment Join-Bond Types Must Match: The selected join-bonds in the fragment must match the bond types of the target atom. Enabling this item will prevent many placements.

• Fragment Join-Bonds Can Be Any Terminal Bonds: Normally, only hydrogen or open valences are taken as join-bonds. When this option is on, any terminal atoms are also candidates for join-bonds. For example, the oxygen atom in formaldehyde could be used as a join-bond for ethylene because the bond type matches (double bond).

• Create Fragment Join-Bonds If Necessary: This option will allow most fragments to be attached to any target. If the fragment does not have enough join-bonds for a given target selection, additional valences will be added to satisfy the requirement. Again, the join-bonds are deleted when fragment and target are joined as well as the target atom (on by default).

• Terminal Atoms Define Join-Bonds: This option makes it easier to choose terminal atoms as hot atoms. Since most terminal atoms have no join-bonds, the option will use the one bond as the join-bond. However, the bond will not be deleted. This is useful when you have a central atom with more than one terminal bond, and you want to explicitly choose which terminal bond will be used to do the joining.

• Bond to Target Atom Instead of Deleting It. This option allows you to bond the fragment to target atom itself, deleting only the join-bonds.

• Delete Any Terminal Atoms Bonded to Target Atom: Remove extra terminal bonds.

• Automatically Select Hot Atom: This item is designed for use with biological fragments (which is its default setting). It causes GaussView to determine the hot atom dynamically. This makes it easier to build AA residues, etc., by producing a sensible backbone as you add residues.

Figure 45. Structure Options After a Fragment Addition
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

• Use Fragment Join-Bond Type For New Bond: Normally, the bond connecting the fragment to the target bond type is determined by the original target bond. If this option is on, the fragment's bond type is used instead. This option is useful when the Match Bond Types option is off.

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.

• Delete Terminal Valence Atoms to Satisfy Valency: Allows terminal valence atoms to be deleted to reduce overloaded valency at the target atom site

• Delete Terminal Atoms to Satisfy Valency: Allows for any terminal atom to be deleted to reduce overloaded valency.

• Add Hydrogens to Satisfy Valency: Automatically adds hydrogen atoms 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 Atom, and Apply Clean to Whole Structure.