Reaction Profile Viewer Panel

Display a diagram of the energies of the reactants, transition states, intermediates, and products of a reaction, showing its progress through the various stages. The energies at each stage are derived from the energies of specified Maestro project entries.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Materials → Quantum Mechanics → Tools → Reaction Profile Viewer
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Reaction Network → Reaction Profile Viewer
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Quantum ESPRESSO → Reaction Profile Viewer
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → Reaction Profile Viewer

The following licenses are required to use this panel: MS Maestro

  • Using
  • Features
  • Additional Resources

Using the Reaction Profile Viewer Panel

In this panel, you can plot an energy diagram of a multistep reaction, that shows the energy changes through the course of the reaction. Each step of the reaction can involve one or more structures, which can be participants or spectators at any given stage. The procedure involves importing the structures at each step and setting the stoichiometry. Structures that enter a reaction at a later stage should be included from the beginning as spectators, to ensure that the relative energies are correctly calculated. Similarly, reaction products that do not participate in later stages should be kept throughout, to ensure correct energetics.

To set up a reaction profile to view:

  1. Choose the energy property to plot.

    Note that the first reaction step is already in the table, ready to be defined.

  2. Select the structures for this step of the reaction, in the Entry List or the Project Table.

    These could be the separated reactants, or a pre-reactive complex, for example. Include any structures that are spectators at this step but participate in later (or earlier) stages: this allows the energetics of the reaction to be correctly calculated.

  3. Click Import in the step row.

    The structures are added below, each in a separate row. The energy in the step row is calculated as the sum of the energies in the structure rows, multiplied by the multipliers.

  4. Set any multipliers for the number of instances of a structure in the reaction step, to specify the stoichiometry of the reaction.

    For example, if there are two molecules of a reactant in the equation for the reaction, the multiplier would be 2. The energy in the structure row and the step row is updated to reflect the new stoichiometry.

  5. Change the title of the step, if desired.

  6. Click Add to add a new step, and repeat steps 2-5 for the new step. Repeat for as many steps as there are in the reaction.

  7. Choose the reaction energy units.

  8. Click Plot to display the reaction profile.

If you import an incorrect structure into a step:

  1. Select the correct structure in the Project Table or Entry List.

  2. Click Import for the step to add the structure to the step.

  3. Select the incorrect structure row in the step.

  4. Click Delete to remove it from the step.

If the structures are in a single entry for each point along the reaction path, you can select the entries and import them into separate steps with the Import to New Steps button.

Reaction Profile Viewer Panel Features

Energy options and menus

Select an option for the product whose energies will be plotted, and choose the energy property. The property must exist in the entries that are imported from the Project Table.

  • Jaguar—plot energies from Jaguar (small molecule DFT) calculations, using the chosen energy property. The properties include total QM energies as well as free energy, internal energy, and enthalpy.

  • Quantum ESPRESSO—plot energies from Quantum ESPRESSO (periodic DFT) calculations, using the chosen energy property.

Reaction table

Specify the structures that correspond to each step in a reaction (reactant, transition state, intermediate, product). Each step can involve more than one structure, e.g. when there are multiple reactants, or structures that are spectators for some steps before being used in a particular step.

The table consists of two kinds of rows: (1) rows for the reaction steps, which contain information and controls for the step as a whole, and (2) rows for the structures in each reaction step, which contain information for the individual structures within a reaction step. The table is populated by adding step rows or importing structures (entries) from the project. You can select multiple rows to delete from the table. The columns of the table, which contain the information, are:

Title

Title of the step or structure.

  • For steps, the title is editable, and is used to label the steps in the plot. By default, the first is titled Reactant, and new ones are titled Product.
  • For structures, the title is the entry title of the structure, and is noneditable.
Multiplier

Coefficient in the equation for the reaction of the structure in the row. Specifying the multiplier defines the stoichiometry of the reaction, allowing you to ensure mass balance. The multiplier can be a fraction. For example, in the reaction CH4 + 2O2 → CO2 + 2H2O, the multiplier is 1 for CH4 and CO2, and 2 for O2 and H2O.

You can also specify a coefficient for an entire step. Setting the coefficient for a step to zero removes the step from the diagram.
Energy (au)
  • For structures, total energy of the structure weighted by the multiplier.
  • For steps, sum of total energies of the structures in the step, weighted by their multipliers.

The column contains None if the energy property is not available for a structure, and is colored red. If any structure in a step has None for the energy property, the step energy is also given as None, and the step is not included in the plot.

Formula

Empirical formula of the structure represented by a row, determined from the elemental composition of the structure and any multipliers. For a step row, the formula is the sum of the formulas over all the structures for the step. In the reaction example above, the formula for the row for O2 would be O4 as it includes the multiplier in the equation. The formula for the reactants and for the products would be CH4O4. This column can be used to check the reaction stoichiometry: the text is colored red if the reactant and product stoichiometries are different.
Import Button (Selected Entries) to import the selected entries in the Project Table into a step. Only present in step rows.

 

Add New Step button

Add a step to the table. The added step is empty, and you can import the structures using the Selected Entries button in the Import column.

Import to New Steps button

Import each of the entries that are selected in the Project Table to a new step. This is appropriate for reactions in which the structure at each step is contained in a single entry—for example, for NEB calculations from Quantum ESPRESSO (see Nudged Elastic Band Calculations Panel).

Delete button

Delete the selected step (including its structures) or structure in the table.

Export button

Export the contents of the table in CSV format, with headers. Opens a file selector so you can name and save the file.

Reaction energy units option menu

Choose the energy units to use when displaying the reaction energy in the plot.

Plot button

Update the plot with the current structures and options.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

Shows a diagram of reaction energy as a function of reaction progress through the stages. The energies are shown relative to the first stage in the reaction, whose energy is given as zero in the plot. Each stage is represented as a horizontal, thick black line, with the energy above and the label of the stage below it. These lines are connected by gray lines that visually indicate the energy changes between stages.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

Related Topics