Transfer Step Editor Dialog
- select the type of transfer step
- select the species that is transferred
- select the format for the rate constant and enter its numeric values
- scroll through the entire list of transfer steps defined for the transfer path that contains these transfer steps
The Transfer Step Editor Dialog looks like this:
The schematic diagram at the top of the dialog depicts the two compartments and the directionality of the transfer step.
Types of Transfer Steps
A number of different types of transfer steps may be specified; these differ mainly in the form of the rate law. Some are specific to compartmental reaction schemes and the others specific to three-dimensional reaction schemes.
The types specific to compartmental reaction schemes are:
- Constant Flow
- means that a material flows from a source compartment to a target compartment at a rate that is independent of the concentration of the transferred species. This flow continues so long as the species is present in the source compartment. This flow is a zero order rate process.
- Proportional Flow
- means that a material flows from a source compartment to a target compartment at a rate that is directly proportional to the concentration of the transferred species. This flow is therefore a first order rate process.
- Gradient Diffusion
- is classic gradient-driven (or Fickian) diffusion, where the transport rate depends on the difference in concentration between two compartments and the distance between their centers.
- Exchange Diffusion
- is a variant of gradient-driven diffusion. Here the transport rate again depends on the difference in concentration between two compartments and the distance between their centers, but in this case, if a species moves from one compartment to another, a second species (the Exchanged Species) moves in the opposite direction in direct proportion to the first.
- Electron Transfer
- indicates that an electron can be transferred across the interface of an electrode (the first compartment) with another medium (the second compartment). No rate law is associated with electron transfer. Defining a step of this type indicates to Kinetiscope that the surface area of this interface is to be used in the calculation of any electrochemical rates in the second compartment.
- Using the left mouse button, click on the Transfer Type drop-down list box and select the type.
- Click on the Transferred Species list box and choose the species.
- If you selected Exchange diffusion in Step 1, choose the name of the exchanged species from the Exchanged Species list box;
- Choose the direction of transfer from the Direction list box.
- 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 or D = 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.
- 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
- 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 in the data entry fields.
Entering the Rate Constants
Beneath the schematic diagram is a drop-down list box where you select the format of the rate constant for the current transfer step. Data entry fields appear below the list, labeled according to the rate constant format that you choose.
If the transfer step is non-reversible, only one set of parameters must be entered. If it is reversible, two sets are entered. The units of the rate constants are those you chose when the reaction file was created.
Three different rate constant formats are available in Kinetiscope:
Scrolling through a Transfer Step List
If more than one step has been entered in the transfer path, you may move through the list of transfer steps using the two arrow push buttons at the top left corner of the dialog.