Normally delocalized internal coordinates are generated automatically from the input Cartesian coordinates. This is accomplished by first determining the atomic connectivity list (i.e., which atoms are formally bonded) and then constructing a set of individual primitive internal coordinates comprising all bond stretches, all planar bends and all proper torsions that can be generated based on the atomic connectivity. The delocalized internal are in turn constructed from this set of primitives.
The atomic connectivity depends simply on distance and there are default bond lengths between all pairs of atoms in the code. In order for delocalized internals to be generated successfully, all atoms in the molecule must be formally bonded so as to form a closed system. In molecular complexes with long, weak bonds or in certain transition states where parts of the molecule are rearranging or dissociating, distances between atoms may be too great for the atoms to be regarded as formally bonded, and the standard atomic connectivity will separate the system into two or more distinct parts. In this event, the generation of delocalized internal coordinates will fail. Additional atomic connectivity can be included for the system to overcome this difficulty.
CONNECT defines the beginning of the additional connectivity section and ENDCONNECT the end. The format of the CONNECT section is:
CONNECT atom list_length list ENDCONNECT
| atom | Atom for which additional connectivity is being defined. |
|---|---|
| list_length | Number of atoms in the list of bonded atoms. |
| list | List of up to 8 atoms considered as being bonded to the given atom. |