Working with Reactions and Stoichiometry

You can add a reaction and its stoichiometry to your experiment. You can only define a reaction in Reaction Scheme and Stoichiometry panes in an experiment created using the Synthetic Chemistry experiment type.

This task shows you how to:

See Also
Experiment Page
Reactions and Stoichiometry

Draw a Reaction Scheme

You can use the Pipette Sketcher to draw a reaction scheme for your experiment.

  1. In the Reaction Scheme pane of your experiment, click Draw a New Reaction.
  2. Draw the reactants, products, and other components of the reaction in the Pipette Sketcher.
  3. Click Submit.

The Reaction Scheme pane displays your reaction and the Stoichiometry pane lists each of the reaction components. The first reactant is automatically defined as the limiting reagent. The number of equivalents of each component uses the defined stoichiometric coefficient ratios in the reaction scheme. The purity of each component is initially defined as 100%.

Add a Reaction Scheme from a File

You can load a reaction from an existing standard chemical file (such as .skc, .mol, .rxn, .cdx, .sdf, .rdf, .inchi).

With the Reaction Scheme pane of your experiment visible, do one of the following:
  • Click Browse for a chemistry file, and then select your chemistry file containing a reaction. Click Open.
  • Drag your chemistry file containing a reaction from a file browser into the Reaction Scheme pane.
  • If you already have a reaction, click Import from chemistry file below the reaction scheme to replace the existing reaction with the contents of a chemistry file containing a reaction. Click Confirm.

The Reaction Scheme pane displays your reaction and the Stoichiometry pane lists each of the reaction components. For a new reaction, the first reactant is automatically defined as the limiting reagent. The number of equivalents of each component uses the defined stoichiometric coefficient ratios in the reaction scheme. The purity of each component is initially defined as 100%.

Edit a Reaction Scheme

You can use the Pipette Sketcher to make changes to the reaction scheme.

  1. Below the reaction scheme, click to open the reaction in the Pipette Sketcher.
  2. Edit the reaction scheme as required.
  3. Click Submit.
  4. Click Confirm.
  5. Optional: If you made significant changes to any reaction participants, click Confirm for the listed updates.

The Reaction Scheme pane displays your updated reaction and the Stoichiometry pane lists updates for each of the reaction components.

Add Reaction Components

You can add reaction components directly to the stoichiometry list without having to draw them in the reaction scheme.

  1. Above the Stoichiometry pane table, click .
  2. In the new row of the stoichiometry table, enter the name of the reaction component you want to add and press Enter.

    Tip: If the name of the reaction component is not recognized as a chemical substance, no structure displays but you can continue to edit the other properties of the reaction component.

The reaction component appears in the Stoichiometry pane table with its structure and formula included and other properties calculated. For more information, see Automatic Calculations. Initially, the new component is defined as a reagent. The Reaction Scheme updates with the reaction component added.

Remove Reaction Components

You can remove reaction components that you do not require.

  1. In the Stoichiometry pane table, select the rows for the components you want to remove.

    Tips:
    • You can press CTRL and click multiple rows.
    • You can select in the first column for each of the rows.
    • Select in the header row to select all rows.

    The selected components to remove display with a blue background to the row and in the first column.
  2. Click Remove Materials.

The Stoichiometry pane and the Reaction Scheme pane update with the selected reaction components removed and any calculated properties update accordingly.

Edit Stoichiometry Information

You can define the properties of each reaction component in the Stoichiometry pane.

  1. For a row in the Stoichiometry table, click in the cell for the property you want to edit.

    You cannot edit all properties of reaction components. When you select a row and place the cursor over it, the editable cells display with a blue triangle in the upper-left corner.

  2. Enter the value for the property that you require.

    Each property has defined default units. You can enter different units as required. Scientific Notebook supports all standard units and conversions. If you enter an inconsistent unit, indicates a problem and you can view a list of valid units in a tooltip.

    Tip: The column header tooltips provide a longer description of the property.
    Note: You cannot specify both purity and concentration. If one of these properties is defined and you add the other, a warning message displays.
    Warning: If you enter an invalid unit and move out of a cell, the previous value remains, even if it was empty.

  3. Choose the role of the reaction component.

    Reactants and products display either side of the reaction arrow in the Reaction Scheme. Reagents, solvents, and catalysts display above and below the reaction arrow.

The Stoichiometry pane table updates with your new value and updates any calculated properties as required. For more information, see Automatic Calculations.

Configure the Stoichiometry Display

You can configure the display of the table in the Stoichiometry pane.

  1. Right-click the header row of the table in the Stoichiometry pane to configure the table. You can:
    • Pin column
    • Size Column to Fit
    • Size All Columns to Fit
  2. Select Custom Views... to configure a personalized preferred view of the table.
    1. Do one of the following:

      • Click to create a new custom view.
      • Select the existing custom view you want to configure or apply.

    2. Click Update from current view to load the column widths, pinning, and sorting from the table.
    3. Customize the settings for the view, including:

      • Select the columns you want to include in the custom view.
      • Specify widths for columns as required.
      • Choose whether to pin columns to the left or right of the table, or not at all.
      • Choose a column by which to sort the rows and whether to sort ascending or descending.
      • Select the density of the display.

    4. Click Reset to Default to discard any customizations.
    5. Click Save or Save and Apply.
    The Stoichiometry pane table updates with the display settings selected.