Firefly and PC GAMESS-related discussion club

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Thomas H.
thomas.hochrein@web.de

I want to scale the y-axis (IR activity) for a better direct comparison with experimental values (e. g. absorbance or absorption coefficient in 1/cm).

I guess the unit for the Firefly IR intensities of the output file is km/mol (in comparison to Gaussian etc.). This is more or less the integrated absorptivity. I know the definition (integral of the molar absorption coefficient under a absorbing band), but it’s difficult to get the values in units like 1/cm or 1/(mol*cm).

But how can I get from the frequencies and the IR activities a spectrum like experimental absorption spectra? E. g. in Gabedit (or Avogadro, Molekel) I can choose a peak width for Gaussian or Lorentz fits. But in no of these pre-processing programs the y-scale is defined/named.

If I chose a special peak width for fitting (e. g. in Gabedit) and then I chose a second peak width (e. g. the half width or ten times widen etc.) I get more or less the same maximum peak intensity of the fit, which disagrees with the definition of the integrated absorptivity (wider peak -> higher max. value; smaller peak -> higher max. value in case of the same peak area/integral).

I searched for relevant papers, but I did not found anything useful. I know, that the IR activity values are not literally, however it would be very useful to get a feeling for the magnitude. So I have the following questions:

a) How can I transform the Firefly output values to a spectra like experimental results (and transform the scale from km/mol to 1/cm or 1/(cm*mol), respectively)?
b) Are there standard/useful guidelines, how the value for the width (Gaussian or Lorentz fit) have to be chosen?

Thanks for any remarks,

Thomas