Reaction Grid Plot
A Reaction Grid Plot dialog is used to show the energy (Heat of Formation) plotted versus two of the Z-Matrix internal coordinates (the "reaction coordinates") for a series of molecules in a molecule group. This dialog is accessible if the parent view window's current molecule was loaded from an Ampac result file generated from an Ampac "Reaction Grid" calculation, and if the molecule has not been modified.
The Reaction Grid Plot dialog for the active view window is opened and / or activated by selecting "Reaction Grid..." from the Results Menu of the main window or the context popup menu of the active view window.
While this dialog is open the current molecule in the parent view window is read-only, i.e., it cannot be modified, though it can be deleted from the molecule group. When a molecule is deleted from a group, its corresponding point on the plot is simply removed.
The general features and usage of the Reaction Grid Plot dialog can be found in 3D Result Plots. That section includes detailed information on manipulating the plots. The pictures below and their corresponding captions demonstrate by example what a Reaction Grid Plot is and how to generate and use one. The example examines the relaxed potential energy surface as a function of the two dihedral angles linking the phenyl groups in a triphenyl derivative.
Figure 1. A view window for a triphenyl derivative, built from fragments with the Builder. The molecule has been setup for an Ampac Reaction Grid calculation, as shown in Figures 2 and 3, and then saved to the Ampac input file "triben_pna.dat".
Figure 2. The Atom List Editor for the view window shown in Figure 1. Note that the optimization flags for atoms 12 and 22 are set to "Rxn". All other optimization flags for the molecule's Z-Matrix coordinates are set to "Yes". The table in the Atom List Editor is sorted according to the "Opt 3" column.
Figure 3. The Job Type panel in the Ampac Calculation Setup dialog for the molecule in Figure 1. The Job Type is set to do a Reaction Grid calculation in which the Z-Matrix dihedral angle coordinate between atoms 12, 11, 3 and 2 is the first "reaction coordinate" and the dihedral angle coordinate between atoms 22, 11, 6 and 1 is the second reaction coordinate. Both reaction coordinates are set to vary 90 degrees on each side of their current value. The reaction grid will have 121 points, each point being a relaxed geometry (all coordinates optimized except the reaction coordinates) for a different pair of values of the reaction coordinates.
Figure 4. A view window for the molecule group loaded from the Ampac result file "triben_pna.vis", which was generated by submitting the corresponding input file referred to in Figures 1-3 to Ampac.
Figure 5. The Reaction Grid Plot for the view window shown in Figure 4, showing the Heat of Formation (HOF) versus the two reaction coordinates (RC1 and RC2). Note that the current node in the plot has a small green sphere and corresponds to the current molecule in the view window, as shown in Figure 4. The other nodes have a small white sphere. In general, when a node in the plot is selected, the corresponding molecule in the view window becomes the current molecule. Likewise, if the current molecule in the view window is switched using its Molecule Number toolbar, then the corresponding point in the Reaction Grid Plot becomes the current point.
Figure 6. The view window shown in Figure 4, but with the current molecule set to 25 instead of 1. The current molecule was selected by selecting a node which is approximate minimum point in the Reaction Grid Plot, as shown in Figure 7.
Figure 7. The Reaction Grid Plot corresponding to Figure 6. The (3,3) node has been selected and it appears to approximate a minimum energy structure. This structure can be subjected to further refinement calculations (e.g., a TRUSTE optimization) to try and locate the nearby minimum more precisely.
Figure 8. The view window shown in Figure 4, but with the current molecule set to 61 instead of 1. The current molecule was selected by selecting an approximate transition state node in the Reaction Grid Plot, as shown in Figure 9.
Figure 9. The Reaction Grid Plot corresponding to Figure 6. The (3,3) node has been selected and it appears to approximate a transition state structure. This structure can be subjected to further refinement calculations (e.g., a TRUSTG optimization) to try and locate the nearby transition state more precisely.