DynaFit Scripting Manual

  Index

Specific molar responses

The program's primary function is to fit experimental data obtained on a (bio)chemical system, either by following the reaction time-course, by measuring the initial reaction velocity, or by measuring the composition at equilibrium. In either case, it is important to realize that the chemical reacting system is always observed by using a certain physical instrument. For example, the chemical system might be observed by using

• fluorescence spectroscopy;
• UV/VIS absorption spectroscopy;
• IR spectroscopy;
• NMR spectroscopy;
• HPLC peak area integration;
• optical densitometry (gel shift assays);
• radiochemical methods;
• conductivity;
• polarimetry;
• mass spectrometry;
• other instrumental methods.

The main point is that concentrations are never measured directly. Instead, we always indirectly observe a certain physical signal (e.g., absorbance or peak area). Importantly, the program always assumes that the measured physical signal is related to the concentrations of reactants by a linear relationship.

Specific molar response coefficients can be assigned globally (pertaining to all datasets) or locally (pertaining to individual datasets). Global instrumental responses are gathered in the section of the script file denoted as [responses]. Local instrumental responses are listed after each file name either of the following sections: [progress] for the analysis of reaction progress curves, [velocities] for the analysis of initial reaction velocities, or [equilibria] for the analysis of equilibrium composition.

Any number of molar response coefficients can be considered as optimized (adjustable) parameters by appending a question mark after the numerical value. This applies both to the global response coefficients and to the local response coefficients.

Species the molar response coefficients of which are zero need not be listed in the script file. If a species is not mentioned in the [response] section (or after the response keyword for local response coefficients) it is assumed that its molar response coefficient is zero.

As was mentioned before in section 2.5, nominal values of molar responses depend on the concentration scale of the experiment. The same concentration unit (e.g., mM, $\mu$M, or nM) must be used for the following quantities:

• concentrations of reactants;
• specific molar responses;
• bimolecular association rate constants;
• equilibrium constants.

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Petr Kuzmic | Jul 12 2005