Reaction Step Editor Dialog
When you create or edit a reaction step using a Compartment Editor Dialog or a single reactor scheme window, you use this dialog to enter data. You may
- enter the reaction equation in conventional chemical notation
- select the format for the rate constant and enter its numeric values
- select and edit the form of the rate law for this step
- scroll through the list of reaction steps for a compartment
The dialog looks like this:
Entering the Reaction Equation
Individual reaction equations are entered much as
a chemist would write them on a piece of paper.
The generalized format for a non-reversible reaction equation is:
where x, y, z, w, and v are stoichiometric coefficients, and A, B, C, D and E are mnemonics that you choose for the various reactant and product species.
You must separate coefficients from their species mnemonic by a blank space. If the stoichiometric coefficient is missing then it is taken to have a value of 1. Also note that the right arrow is typed in as "=>" using the characters "equals" "greater than".
The format for a reversible reaction equation is:
while the format for an electrochemical reaction equation is:
All symbol conventions are the same as for a non-reversible reaction. The double arrow is used to indicate that the reaction can proceed in either direction. The double arrow is typed is as "<=>" or "less than" "equals" "greater than".
The "=>" and "<=>" symbols must be separated by a blank space from nearby species mnemonics and stoichiometric coefficients.
You should follow these guidelines when using mnemonics:
- You may use any mnemonic which is composed of up to 32 characters. They do not need to be conventional chemical symbols. The only requirements are that the first character must be alphabetic, and the symbols "<", ">", and "=" are not permitted. In species mnemonics, Kinetiscope is not case-sensitive, i.e. it treats upper and lower case characters identically.
- Mnemonics must be used in a consistent manner throughout the entire reaction scheme. A species mnemonic refers to the same species even if used in a different compartment or step.
- You may use up to eight reactant species mnemonics and eight product species mnemonics in each reaction step.
A species mnemonics may be used only once on each side of a reaction equation. For example,
A + A <=> B
should be entered as
2 A <=> B.
A reaction equation like
A + B <=> A + C
where a species appears on both sides is allowed.
- The common chemical symbol for the electron "e-" has special meaning in Kinetiscope and is used solely when specifying an electrochemical reaction step. Do not use this symbol for another purpose.
When using this dialog, you can click on the Guidelines... hyperlink just above the Equation data entry field to view a quick summary of these as a tool tip. Move the mouse cursor away from the hyperlink to dismiss the tool tip.
Meaningful calculations can be performed even if the chemical identity of various species is unknown. Moreover, unique information can be gained in a reaction simulation if pseudo-species are used to track some of the system characteristics. Examples of this are illustrated in the example simulations.
The size of a simulation (i.e. number of reaction steps and number of chemical species) is limited by the memory available in the computer, since the array space necessary for a particular simulation is reserved when the reaction scheme is defined.
Since the simulator selects events randomly, the order in which the reaction steps are entered is immaterial.
- Click the mouse in the Equation data entry field.
- Type in the reaction equation.
Kinetiscope has an auto-completion feature whose purpose is to reduce typing errors when entering reaction equations. As you type a reaction equation, Kinetiscope will pop up a list of species mnemonics already used in the reaction scheme which start with the characters you have typed. You may select one of those mnemonics by scrolling through the list and pressing the Enter key, or by left-clicking that entry with the mouse. If you are typing a new mnemonic, just continue typing the new name; it will be added to the pop-up list after you have entered the complete reaction equation.
If you do not want the auto-completion feature to be active you may turn it off from the Application Options Dialog.
Entering the Rate Constants
Beneath the reaction equation data entry field is a drop-down list box where you select the format of the rate constant for the current reaction step. The data entry fields are labeled according to the rate constant format that you choose. If the reaction is non-reversible, only one set of parameters must be entered. If it is reversible, two sets are to be entered. The units of the rate constants were chosen by you when the reaction scheme was created.
Four different formats are available in Kinetiscope:
- Here the rate constant is specified as a single value in the reaction scheme's selected units. The Kinetiscope default setting is the temperature-independent form.
Temperature-dependent rate constants are entered in Arrhenius form. The
general Arrhenius form is:
k = A Tm e-Ea/RT (1)
where A is the pre-exponential A factor, m is the temperature exponent, Ea is the activation energy, R is the gas constant and T is the absolute temperature. You may wish to use Arrhenius parameters even if the temperature is to be held constant in order to make calculations at different temperatures faster to set up.
Voltage-dependent rate constants are intended to be used only with electrochemical
reaction steps, which contain the special reserved mnemonic for the electron "e-" as
a reactant or a product. Electrochemical reaction steps must be written as reversible, using
the "<=>" symbol. Kinetiscope accepts only one-electron electrochemical reactions, that is,
the stoichiometric coefficient of the electron is always one. The generalized format for an
electrochemical reaction step (in this example a reduction) is
Ox + e- <=> Rd
Where Ox and Rd represent the oxidized and reduced forms, respectively, of the electroactive species.
The rate constants are entered in Butler-Volmer form. The general equation is:
k = k0 eαnF(E-E0)/RT (2)
where k0 is the standard rate constant, α is the transfer coefficient, n is the number of electrons, F is the Faraday constant, E is the applied potential, E0 is the formal potential, and R and T are defined as above. For the reverse reaction the transfer coefficient term α is replaced by (1-α).
The voltage-dependent rate constant option is only available for three-dimensional reaction schemes.
- External stimulus-dependent
In numerous situations some external factor, such as the opening and closing
of a shutter or the operation of a pump, influences the kinetic behavior of
a reacting system. Examples include chemical reactions initiated by pulse photolysis,
the periodic introduction of an additional dosage of a drug to a biological system, and the
effect of variation in sunlight throughout a day on the chemistry of photochemical smog.
Kinetiscope provides a means to incorporate such kinetic behavior into a reaction scheme by employing
a rate constant that is proportional to a user-defined, programmable
The general equation is:
k = k' Se (3)
where Se is the value of the programmed external stimulus at a given instant in elapsed time, and k' is the proportionality coefficient that relates the rate constant k to external stimulus.
The stimulus-dependent rate constant option is not available for single reactor reaction schemes.
- Using the drop-down list in the Rate Constants area, select the form of the rate constant from the available options.
- Using the mouse and keyboard, type the new values for the rate constant parameters into the data entry fields.
Entering the Rate Law
Kinetiscope uses the numerical value of the rate of each step in the mechanism to determine its instantaneous probability. The general form of a rate law R for the reaction step
n A + m B → products
|R = k [A]n [B]m||(3)|
where k is the rate constant, multiplied by reactant concentrations raised to an order equal to the stoichiometry in the reaction step.
The rate law for each reaction step may be specified in one of two ways. Usually, it corresponds to the reaction step as written, and is derived by the simulator from the stoichiometry of the reaction step. Kinetiscope also allows you to supply special kinetics data for situations where the stoichiometric rate law and the actual rate law may differ.
If the rate law is known to depend on species which are not part of the stoichiometry, the step should be rewritten to include those species as both reactants and products. In this way, they appear in the sample rate law but are not actually consumed in the reaction step.
- Using the drop-down list in the Rate Laws area at the bottom of the dialog, select User-defined rate law
Click the (Edit rate law) push button
This opens the Rate Law Editor Dialog:
- On the table of the Rate Law Editor Dialog, double-click the value of the exponent you wish to change
- Type the new value, and press the Enter key.
- Verify that the modified rate law shown at the top of the Rate Law Editor Dialog is correct.
OKpush button on the Rate Law Editor Dialog when finished.
Scrolling through a Reaction List
If more than one step has been entered in a compartment, or in a single reactor reaction scheme, you may move through the list of reaction steps by clicking on the two arrow buttons at the top left corner of the dialog.