DynaFit Scripting Manual

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Molar response coefficients

DynaFit internally defines (bio)chemical reaction rates as the change in molar concentrations per unit of time (e.g., seconds, minutes, hours) in which the experimental data are expressed. However, the observed reaction rates are always expressed in instrument units (e.g., absorbance, fluorescence, or radioactivity) per unit of time.

For this reason, the computation of observed reaction velocities requires that at least one molecular species (reactant, product, or catalyst) has nonzero molar response coefficient. In other words the section [response] must always contain at least one chemical species that is ``visible'' by the given instrumental technique. DynaFit then computes the observed reaction rate as

$${\rm observed~rate} = {\rm molar~response} \times \frac{\rm concentration~change}{\rm ~unit~of~ time} \quad .$$

Example 1

Compute the reaction rates in mOD-per-minute^8.1for the following reaction mechanism. The only spectroscopically visible species is the product P, with $\epsilon_{\rm P}$ = 5,670 absorbance units / mol / centimeter at the given wavelength. The rate constants are expressed in reciprocal seconds, and substrate concentrations in the data file MILLIOD-VS-[S].TXT are micromolar.

[mechanism]
   E + S <===> ES  :  k1  k-1
   ES ---> E + P   :  k3
[responses]
   P = 0.0945 ; = 1,000 x 5,670 / 1,000,000 / 60
[velocity]
   data MILLIOD-VS-[S].TXT

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Petr Kuzmic | Jul 12 2005