The model will have a Reactions in section for each phase where reactions occur. By default, there is a Reactions in Solution section. For a biphasic system, you might have a Reactions in Organic and a Reactions in Aqueous section. The phases are named and defined in the Process Scheme section, and the names of the Reactions in sections come from the phase names, which can be edited by the user.

You will see below that it is easy to add reaction lines in this section.  Please adopt the following best practices in order to develop successful and chemically realistic models:

• Ensure individual reaction lines are balanced in terms of both mass and charge; icons appear on screen to indicate when a reaction is not balanced.
• Because reactions in nature most commonly occur when two molecules meet, ensure that maximum two reactants appear to the left of the reaction arrow; when this is not possible, break your reaction line into two or more lines, with intermediate products. This best practice will lead to reactions that are first or second order unless you override the reaction orders as an advanced option.
• The only exception that we recommend is for catalytic systems, where in some cases it is valid to have the catalyst present as a third component on the left of the reaction arrow. In these cases, remember also to include the catalyst on the right hand side of the reaction arrow so that it is not consumed as the reaction proceeds.
• When your reaction scheme contains many lines, the number of parameters to fit may become large.  Consider whether your data are likely to contain enough information to reliably estimate/ fit all of these parameters:
  • Reaction lines in your scheme may be set as 'fixed' if you believe that you know their kinetic parameters and do not wish to fit them to data; this is common for fast reactions. Examples include equilibrium reactions, such as those involving dissociation and pH changes, or catalyst adsorption steps.
  • Reaction lines may also be set as 'dependent' if you want their kinetics to be linked with those of another reaction line, for example if you have identical reactive sites on multiple species involved in a reaction.
  • Both of these measures help capture your chemical knowledge in the model and reduce the number of parameters that need to be fitted to your data.  To activate either of these options, click the '=' sign that appears when you hover your mouse pointer over the reaction name and right-click.
• See the reaction schemes shown below for some examples of using these best practices.

Below is the catalytic cycle for the Heck reaction where each step is labeled with a reaction number:

This can be written into Reactions in Solution as follows. Note that the Na cation and NaBr has been omitted for clarity:

Using the Heck Reaction model as an example, the input of a second order reaction is shown below:

You will see that once the reaction is entered and the Enter button is pressed, the reactants 4-bromobenzaldehyde and Pd_cat will be in the Reactants column and the product for the elementary reaction, Int_1, will be in the products column. When the reaction is created, you will see a slider bar in the forward rate column. This is used to increase/decrease the reaction rate. If you want to input your own value, click on the  icon on the right-hand side and this will show the kinetics parameters.

There are two ways to do this:

1. You can type in a reaction separating the reactants and products with an equals (=) sign.

2. You can type in a forward reaction, and click in the reaction arrow to make it reversible. Clicking on the arrow again will make the reaction irreversible again.

Both cases are shown below using the Heck reaction model:

If you would prefer to type in the pKa value rather than the equilibrium constant as it is more accessible (for example, the pKa of Acetic acid is 4.75). There is a dropdown menu located to the left of the equilibrium constant value. Clicking on this will bring you to a dropdown menu that contains pKa and pKb. Select pKa from this menu. Then type in the pKa value instead of the equilibrium constant.

If you want to find out if a reaction is mass balanced, go to the Bal column. If it is checked, then it is balanced. Similarly, if you want to check if the reaction is charge balance go to the [+/-] column if this is checked, it is charge balanced.

If either of these are not balanced you will see one of the following icons , the former means that the products side is lighter, and the latter is that the reactants side is lighter.