The coord and connect Sections of the Jaguar Input File

For some geometry or transition-state optimizations, you might want to specify that the optimizer use particular internal coordinates. For example, if you study a bond-forming reaction, you can require Jaguar to use the bond in question as an internal coordinate even when the bond distance is very long. You also might want to generate your own list of internal coordinates for cases that involve multiple separate (unbonded) fragments.

It is often useful to specify internal coordinates for pairs of atoms that are on separate sections of a large floppy molecule, but are close to being in van der Waals contact. Otherwise, small changes in a torsional coordinate far away from these atoms can then lead to steep changes in the energy. Adding explicit coordinates for these non-bonded contacts makes it possible for the optimization algorithm to control their approach more effectively.

For transition state searches, where bonds are being broken and formed, it is important to specify the atoms involved as being bonded, because the broken bonds might be outside the normal range for bonding, and not be included when internal coordinates are generated.

To control the internal coordinates used in an optimization, you should first make sure that Jaguar is going to generate internal coordinates for the job. Optimization jobs generate and use redundant internal coordinates unless you have set the keyword intopt in the gen section of your input file. (See Geometry Optimization and Transition-State Keywords in the Jaguar Input File for more details.)

To require particular bonds or angles to be included in the internal coordinates used for an optimization, use a coord section. Each line of a coord section should contain a list of atoms used to specify a bond, bond angle, or torsional angle coordinate to be included among the internal coordinates generated by Jaguar.

To specify atoms that are considered to be bonded, use a connect section. This section is used by the coordinate generator to generate internal coordinates The bonds in the connect section are used to generate angles and torsions involving those bonds.