User`s guide

3. Running Jobs
Coordinate Scan (Pro)
A Coordinate Scan calculation steps an internal coordinate (bond length, bond angle, or dihedral
angle) and computes the energy at each point. The remaining coordinates can be all optimized
(relaxed scan), all fixed (rigid scan), or a combination of both.
The Z-Matrix Editor is used to define the coordinate to be scanned (S), and whether the remaining
coordinates should be optimized (O) or fixed (F).
The resulting energy values can be visualized or exported in spreadsheet format.
IRC Calculation
An IRC (Intrinsic Reaction Coordinate) Calculation changes the molecular geometry by
moving along a normal vibrational mode coordinate, in either the forward or reverse direction.
IRC calculations are useful for checking transition state calculations, in order to verify that the
reaction coordinate vibrational motion leads to reactants in one direction and products in the other
direction.
Saddle Calculation
A Saddle Calculation is a useful way to locate a transition state. Two geometries on opposite
sides of the transition state are specified, and the saddle calculation merges the structures together
while moving up in energy toward the transition state. The job number of a previously calculated
second geometry is specified on the Advanced Options page.
It is essential that both molecular geometries have the same atomic numbering in a saddle
calculation. Thus, to generate a second geometry on the other side of the transition state, one must
start with New Job Using This Geometry and then edit bond lengths and angles appropriately,
taking care not to add or delete atoms which would automatically renumber the atoms.
The result of a saddle calculation should be a geometry that is close to the transition state
connecting the two initial geometries. However, a transition state optimization calculation must
still be carried out on the result to locate the actual transition state, and the resulting transition state
should be verified as discussed above.
Molecular Orbitals (Pro)
A Molecular Orbitals calculation computes the molecular orbitals of the current molecule. From
the molecular orbitals, the electron density, electrostatic potential, and frontier orbital densities can
be computed. These can all be visualized using the MOViewer helper application, which must
first be installed on the client computer.
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