Reaction Path Plot

A Reaction Path Plot dialog is used to show the energy (Heat of Formation) plotted versus one of the Z-Matrix internal coordinates (the "reaction coordinate") 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 Path" calculation, and if the molecule has not been modified.

The Reaction Path Plot dialog for the active view window is opened and / or activated by selecting "Reaction Path..." 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 Path Plot dialog can be found in Result Plots and Spectra.  That section includes detailed information on manipulating the plots, such as showing / hiding, zooming, printing, and changing units.  A specific example of a reaction path plot is given below.

Example

The pictures below and their corresponding captions demonstrate by example what a Reaction Path Plot is and how to generate and use one.  The objective of the example is to investigate a possible reaction pathway going from (1,4) difluoro cis-butadiene to (1,2) trans-difluoro cyclobutene.

Figure 1.   A view window for (1,4) difluoro cis-butadiene, optimized with Ampac using AM1.  The molecule has been setup for an Ampac Reaction Path calculation, as shown in Figures 2 and 3, and then saved to the Ampac input file "difluorocisbut_rxn.dat".

 

Figure 2.  The Atom List Editor for the view window shown in Figure 1.  Note that the Z-matrix entries for atom 8 are defined so that the atom is connected to atom 5 by a Z-Matrix bond coordinate.  Also, note that the optimization flag for this coordinate ("Opt 1")  has been set to "Rxn".  All other optimization flags for the molecule's Z-Matrix coordinates are set to "Yes".

 

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 Path calculation in which the Z-Matrix bond coordinate between atoms 8 and 5 is the "reaction coordinate".  This reaction coordinate is set to vary from its current value of 2.97766 Angstroms to a final value of 1.27766 Angstroms.  The reaction path will have 18 points, each point being a relaxed geometry (all coordinates optimized except the reaction coordinate) for a different value of the reaction coordinate.

 

Figure 4.  A view window for the molecule group loaded from the Ampac result file "difluorocisbut_rxn.vis", which was generated by submitting the corresponding input file referred to in Figures 1-3 to Ampac.

 

Figure 5.  The primary Reaction Path Plot for the view window shown in Figure 4, showing the Heat of Formation versus the reaction coordinate.  Other available plots are shown in Figures 10 and 13.  Note that the current point in the plot has a red circle around and corresponds to the current molecule in the view window, the starting molecule, as shown in Figure 4.  In general, when a point 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 Path Plot becomes the current point.

 

Figure 6.  The view window shown in Figure 4, but with the current molecule set to 10 instead of 1.  The current molecule was selected by selecting the approximate transition state point in the Reaction Path Plot, as shown in Figure 7.

 

Figure 7.  The Reaction Path Plot corresponding to Figure 6.  The tenth point along the reaction path (right-to-left) has been selected and it appears to approximate a transition state.  This molecule can be subjected to further refinement calculations (e.g., a TRUSTG optimization) to try and locate the nearby transition state more precisely.

 

Figure 8.  The view window shown in Figure 4, but with the current molecule set to 15 instead of 1.  The current molecule is (1,2) trans-difluoro cyclobutene, which was selected by selecting the approximate local minimum near 1.6 Angstroms in the Reaction Path Plot, as shown in Figure 9.

 

Figure 9.  The Reaction Path Plot corresponding to Figure 8.  The 15th point along the reaction path (right-to-left) has been selected and appears to approximate a local minimum.  This structure can be subjected to further calculations (e.g., a TRUSTE optimization) to try and locate the nearby minimum more precisely.

 

Figure 10.  The other two main Reaction Path Plots, showing the "reaction gradient" along the reaction path (top) and the "gradient norm" along the reaction path (bottom).  The approximate transition state point, molecule 10, is currently selected.  The reaction gradient is the derivative of the energy with respect to the reaction coordinate.  The top plot shows that the reaction gradient between points 9 and 10 passes through zero so molecule 10 is indeed a good candidate for a refined transition state search.  The gradient norm is the normalized sum of the magnitudes of the energy derivatives with respect to all of the other Z-Matrix coordinates.  It is very small for all points since all of the other Z-Matrix coordinates were set to be optimized during the "Reaction Path" calculation.

 

Figure 11.  A "Plots" menu of a Reaction Path Plot dialog.  Each available plot in the dialog can be shown or hidden by checking or unchecking the corresponding item in the menu.  The "Show All Plots..." menu item is self-explanatory.  The "Internal Coordinate Plot..." menu item can be used create additional plots of arbitrary internal coordinates versus the reaction coordinate, as shown in Figures 12 and 13.

 

Figure 12.  The dialog used to setup a new internal coordinate plot.  Any bond, angle or dihedral internal coordinate can be requested, not just Z-Matrix coordinates.  In this example, a plot of the bond internal coordinate between atoms 5 and 6 versus the reaction coordinate will be shown if the Ok button is selected.  See Figure 13.

 

Figure 13.  A plot of the bond length between atoms 5 and 6 versus the reaction coordinate values for the "Reaction Path" molecule group.

 

Figure 14.  A context popup menu for any plot in the Reaction Path Plot dialog.  On most systems the menu can be shown by right-clicking on a plot.  "Show All Plots" and "Hide Other Plots" are self-explanatory.  "Zoom Out" will show the default unzoomed plot. See Figure 15 for how to "Zoom" a plot.  "Print" will print all of the visible plots to the specified printer.  "Save Data" will save the numerical values corresponding to the plot points to a specified text file.  Export will save an SVG (Scalable Vector Graphics) image of the plot to a specified file.

 

Figure 15.  The bottom plot is a "zoomed" version of the top plot, to increase the scale of the part of the plot around the interesting points 10 and 15.  Any rectangular region of a plot can be zoomed in on by dragging the mouse in the plot with the left button down, to outline the desired region.  The green rectangle in the the top plot shows the outline of the area about to be zoomed in on.  To unzoom, select "Unzoom" from the plots context popup menu.  See Figure 14 for how to "Unzoom" a plot.