DynaFit Scripting Manual

  Index

Chemical notation

Writing reaction mechanisms in the script file closely follows the usual chemical notation. The only difference is that rate constants are not placed above and below the arrows, but instead are written on the same line as the reaction step to which they belong. For example, the Michaelis-Menten mechanism

$$\begin{array}{rcl} {\rm E} + {\rm S} & {\begin{array}{c}... ...\ \phantom{x} \end{array}} & {\rm E} + {\rm P} \end{array}$$

can be written with each mechanism step on a single line as

$$\begin{array}{rclll} & \phantom{i_{M_{M}}} & & \quad \qua... ...+ {\rm P} & \quad \quad k _{r } & \phantom{x} \end{array}$$

which is represented in DynaFit by the following text:

[mechanism]         
   E + S <==> ES      :   k    ks
      ES  --> E + P   :   kr

Notational flexibility

DynaFit allows a significant degree of notational flexibility. The Michaelis-Menten reaction mechanism can be written equivalently as

[mechanism]         
   E + A ----> E.A     : k+1      
   E.A   ----> E + A   : k-1      
   E.A   ----> E + P   : k+2

or even in a condensed form as

[mechanism] | E + A -> EA : k1 | EA <=> E + P : k2 k3

where the vertical bar represents a line break.

Formal rules

The plus sign in writing reactions must be surrounded by one or more blank spaces (E + S, not E+S).

Each elementary step in the reaction mechanism must written on a separate line, unless a particular step denotes a reversible reaction (thus, in fact, it represents two different elementary reactions). In the reversible case, the forward and reverse steps can be written either on separate lines using two single-sided arrows, or on the same line using one double-sided arrow. Thus,

     E + I <===> EI    :     k1    k2

is equivalent to

     E + I ---> EI     :     k1
     EI ---> E + I     :     k2

Single-sided arrows can point to either directions. Thus,

     E + I ---> EI     :     k1

is equivalent to

     EI <--- E + I     :     k1

Each elementary step is followed by a colon (:) followed by the name of one or two associated rate constants. An irreversible reaction step must be followed always by a single rate constant. If the step is reversible, the colon separator is followed by two rate constants. The first rate constant always refers to the left-to-right (forward) step, and the second rate constant refers to the right-to-left (reverse) step.

Oligomerization equilibria deserve a special mention here. In a DynaFit script file we are not allowed to use numerical stoichiometric coefficients, so that a dimerization equilibrium must be written as

     A + A <===> A2    :    k1    k2

while the alternate notation using stoichiometric coefficients

     2 A <===> A2      :    k1    k2 ; NOT ALLOWED

is not allowed.

Equilibrium constants

Equilibrium constants proper

In the analysis of equilibrium binding data we encounter a special case, where the double sided arrow is followed by a single equilibrium constant, followed by the keyword equil. For example, while in the above example k1 was a label representing an association rate constant for the forward reaction step, here Ka is a name of the equilibrium constant for the reaction:

     E + I <===> EI    :     Ka    equil

It is important to remember that the equilibrium constant always refers to the reaction proceeding from left to right. In other words, in the above example Ka is the association equilibrium constant, with the dimension ${\rm M}^{-1}$ (liter per mole). If we insisted that an equilibrium be defined as a dissociation constant, with the dimension M (moles per liter), then the reaction step above would have to be written as a dissociation (reading from left to right):

     EI <===> E + I    :     Kd    equil

Dissociation constants

It is possible to override the left-to-right convention and designate certain equilibrium constants specifically as dissociation constants. In this case the name of the equilibrium constant is followed by the keyword dissociation, which can be abbreviated as diss or dissoc. In the following examples, both Kii and Kis are dissociation equilibrium constants although the left-to-right convention shows the reaction steps ass association equilibria.

      E + I <===>  EI     :   Kis    dissoc
      ES + I <===> ESI    :   Kii    dissoc

Association constants

In certain applications (e.g., analytical chemistry) it is common to describe chemical equilibria in terms of association constants, rather then dissociation constants. In this case we can override the conventional left-to-right notation by using the keyword association, which can be abbreviated as assoc. In the following examples, the dimension of the equilibrium constants K1 and K2 is ${\rm M}^{-1}$ and ${\rm M}^{-2}$ respectively, because they are treated as association constants.

      ABC <==> AB + C   :   K1  assoc
      AB <==> A + B     :   K2  assoc

Total association constant can also be specified in this manner. For example, the total association constant of the complex ABCD below is written as

      ABCD <==> A + B + C + D  :   K(tot) assoc

which has precisely the same meaning as the text below:

      A + B + C + D <==> ABCD  :   K(tot) assoc

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Petr Kuzmic | Jul 12 2005